Specialized subunit within a cell that has a specific function
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2 episodes with organelle
2 episodes with organelle
11 episodes with organelle
2 episodes with organelle
2 episodes with organelle
2 episodes with organelle
D'Songwriterin Hannah Grevis - Bünennumm Hannah Ida - huet ee Brudder beim Film: de Lukas Grevis. Zesummeschaffen, dat wier deenen zwee virun e puer Joer ni an de Sënn komm. Bis d'Hannah hir Experienz vum Danzen am Club an eng lëfteger, Organelle-baséiert Indie-Pop-Nummer verwandelt huet, an de Brudder net méi anescht konnt, wéi Deel vu "Galaxies" ze ginn. De Marc Clement war op de Videdréi.
(0:00) The Besties welcome Tim Dillon! (6:56) Nvidia H20 export controls, the China workaround, plausible deniability by chipmakers selling to China-linked entities (28:45) Trump vs. Harvard: Why the White House is threatening to take Harvard's tax-exempt status away (57:04) Hollywood's DEI facade, thoughts on AI, and more (1:18:06) Celebrity Jeopardy update: Friedberg is heading to the finals! (1:26:44) Science Corner: Mitochondrial Therapy Follow Tim: https://x.com/TimJDillon Check out Tim's new special: https://www.netflix.com/title/81992010 Follow the besties: https://x.com/chamath https://x.com/Jason https://x.com/DavidSacks https://x.com/friedberg Follow on X: https://x.com/theallinpod Follow on Instagram: https://www.instagram.com/theallinpod Follow on TikTok: https://www.tiktok.com/@theallinpod Follow on LinkedIn: https://www.linkedin.com/company/allinpod Intro Music Credit: https://rb.gy/tppkzl https://x.com/yung_spielburg Intro Video Credit: https://x.com/TheZachEffect Referenced in the show: https://www.youtube.com/watch?v=wUzmVo2dZNs https://www.wsj.com/livecoverage/stock-market-trump-tariffs-trade-war-04-15-25/card/nvidia-records-5-5-billion-charge-on-new-h20-export-restrictions-LXjxlqr2m80QIrfJxnYZ https://www.wsj.com/economy/trade/trump-chip-exports-nvidia-h20-china-amd-d2c4c866 https://www.reuters.com/technology/exclusive-nvidia-offers-new-advanced-chip-china-that-meets-us-export-controls-2022-11-08 https://abachy.com/news/nvidia-unveil-new-ai-chips-chinese-market-after-us-bans-a800-and-h800 https://www.moomoo.com/community/feed/compared-to-the-h100-how-is-the-performance-of-the-111725151846805 https://www.reuters.com/technology/tsmc-could-face-1-billion-or-more-fine-us-probe-sources-say-2025-04-08 https://www.bis.gov https://www.cnbc.com/2025/04/15/us-is-unable-to-replace-rare-earths-supply-from-china-warns-csis-.html https://www.bloomberg.com/news/articles/2025-03-31/trump-administration-to-review-billions-in-grants-to-harvard https://www.harvard.edu/research-funding/wp-content/uploads/sites/16/2025/04/Letter-Sent-to-Harvard-2025-04-11.pdf https://www.harvard.edu/president/news/2025/the-promise-of-american-higher-education https://apnews.com/article/harvard-trump-administration-federal-cuts-antisemitism-0a1fb70a2c1055bda7c4c5a5c476e18d https://www.cnn.com/2025/04/16/politics/irs-harvard-tax-exempt-status/index.html https://www.boston.com/news/local-news/2024/09/05/harvard-comes-in-dead-last-in-nationwide-free-speech-rankings https://en.wikipedia.org/wiki/Bob_Jones_University_v._United_States https://en.wikipedia.org/wiki/Students_for_Fair_Admissions_v._Harvard https://www.thecrimson.com/article/2022/7/13/faculty-survey-political-leaning https://www.reuters.com/world/europe/ukraines-parliament-extends-martial-law-until-august-2025-04-16 https://www.nature.com/articles/s41586-023-06537-z https://www.nature.com/articles/d41586-025-00848-z https://www.researchgate.net/publication/389907980_Organelle-tuning_condition_robustly_fabricates_energetic_mitochondria_for_cartilage_regeneration/fulltext/67d8575e478c5a3feda50563/Organelle-tuning-condition-robustly-fabricates-energetic-mitochondria-for-cartilage-regeneration.pdf https://www.foxnews.com/media/george-clooney-calls-breaking-biden-2024-his-civic-duty-says-democrats-werent-telling-truth
In this episode of Tiny Show and Tell Us, we cover the recent discovery of a new (relatively speaking, more like 100 million year old) organelle called a nitroplast that could revolutionize agriculture. Then we embark on a highly entertaining journey of 1930s chemistry poetry, sometimes written by inebriated chemists, and track down a rare and stunning Chemical Map of North America. Check out the map in this YouTube short and this Instagram post. We need your stories — they're what make these episodes possible! Write in to tinymatters@acs.org *or fill out this form* with your favorite science fact or science news story you found captivating for a chance to be featured in a future episode!
Join Fazale “Fuz” Rana and Hugh Ross as they discuss new discoveries taking place at the frontiers of science that have theological and philosophical implications, including the reality of God's existence. A New Organelle? A team of life scientists has claimed to discover a new organelle (called a nitroplast) that fixes nitrogen. It looks like this organelle evolved from an endosymbiont that assumed permanent residence in a eukaryotic cell. If so, this discovery provides support for the endosymbiont hypothesis, challenging the notion that a Creator is responsible for life's origin and design. In this episode, biochemist Fuz Rana describes this work and its significance to life's history, and offers a critical assessment of the study's conclusion. Atmospheric Oxygenation An international team of 17 scientists has proposed that a dramatic weakening of Earth's magnetic field caused an oxygen level jump 575 million years ago. They showed that a much weaker magnetic field would cause solar particles to split apart water molecules in Earth's atmosphere into hydrogen and oxygen. The hydrogen would escape to interplanetary space, leaving the oxygen to accumulate in Earth's atmosphere. They demonstrated that that the magnetic field decline is sufficient to explain most of the rapid oxygen rise (from 2% to 8%) that occurred at the time of the Avalon explosion, which marked the first appearance of macroscopic animals. In this episode, Hugh Ross explains that the transition of Earth's core from being 100% liquid to where a solid inner core begins to form would explain the dramatic weakening of Earth's magnetic field—and the minimum oxygen level needed for complex life—that occurred 0.6 million years ago. Links & Resources: Nitrogen-Fixing Organelle in a Marine Alga Mitochondrial Protein Import Advances the Case for Creation Near-Collapse of the Geomagnetic Field May Have Contributed to Atmospheric Oxygenation and Animal Radiation in the Ediacaran Period Designed to the Core, 183–197
]Researchers are testing HIV drugs and monoclonal antibodies against long-lasting COVID-19, and what it takes to turn a symbiotic friend into an organelle First up on the show this week, clinical trials of new and old treatments for Long Covid. Producer Meagan Cantwell is joined by Staff Writer Jennifer Couzin-Frankel and some of her sources to discuss the difficulties of studying and treating this debilitating disease. People in this segment: · Michael Peluso · Sara Cherry · Shelley Hayden Next: Move over mitochondria, a new organelle called the nitroplast is here. Host Sarah Crespi talks with Tyler Coale, a postdoctoral scholar in the University of California, Santa Cruz's Ocean Sciences Department, about what exactly makes an organelle an organelle and why it would be nice to have inhouse nitrogen fixing in your cells. This week's episode was produced with help from Podigy. About the Science Podcast Authors: Sarah Crespi; Meagan Cantwell; Jennifer Couzin-Frankel Episode page: https://www.science.org/doi/10.1126/science.zof5fvk Learn more about your ad choices. Visit megaphone.fm/adchoices
]Researchers are testing HIV drugs and monoclonal antibodies against long-lasting COVID-19, and what it takes to turn a symbiotic friend into an organelle First up on the show this week, clinical trials of new and old treatments for Long Covid. Producer Meagan Cantwell is joined by Staff Writer Jennifer Couzin-Frankel and some of her sources to discuss the difficulties of studying and treating this debilitating disease. People in this segment: · Michael Peluso · Sara Cherry · Shelley Hayden Next: Move over mitochondria, a new organelle called the nitroplast is here. Host Sarah Crespi talks with Tyler Coale, a postdoctoral scholar in the University of California, Santa Cruz's Ocean Sciences Department, about what exactly makes an organelle an organelle and why it would be nice to have inhouse nitrogen fixing in your cells. This week's episode was produced with help from Podigy. About the Science Podcast Authors: Sarah Crespi; Meagan Cantwell; Jennifer Couzin-Frankel Episode page: https://www.science.org/doi/10.1126/science.zof5fvk Learn more about your ad choices. Visit megaphone.fm/adchoices
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.08.03.551853v1?rss=1 Authors: Chen, J., Yue, F., Kim, K. H., Zhu, P., Qiu, J., Tao, W. A., Kuang, S. Abstract: Mitochondria are not only essential for energy production in eukaryocytes but also a key regulator of intracellular signaling. Here, we report an unappreciated role of mitochondria in regulating cytosolic protein translation in skeletal muscle cells (myofibers). We show that the expression of mitochondrial protein FAM210A (Family With Sequence Similarity 210 Member A) is positively associated with muscle mass in mice and humans. Muscle-specific Myl1Cre-driven Fam210a knockout (Fam210aMKO) in mice reduces mitochondrial density and function, leading to progressive muscle atrophy and premature death. Metabolomic and biochemical analyses reveal that Fam210aMKO reverses the oxidative TCA cycle towards the reductive direction, resulting in acetyl-CoA accumulation and hyperacetylation of cytosolic proteins. Specifically, hyperacetylation of several ribosomal proteins leads to disassembly of ribosomes and translational defects. Transplantation of Fam210aMKO mitochondria into wildtype myoblasts is sufficient to elevate protein acetylation in recipient cells. These findings reveal a novel crosstalk between the mitochondrion and ribosome mediated by FAM210A. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.10.548452v1?rss=1 Authors: Schmied, C., Ebner, M., Samso, P. F., Haucke, V., Lehmann, M. Abstract: Eukaryotic cells are highly compartmentalized by a variety of organelles that carry out specific cellular processes. The position of these organelles within the cell is elaborately regulated and vital for their function. For instance, the position of lysosomes relative to the nucleus controls their degradative capacity and is altered in pathophysiological conditions. The molecular components orchestrating the precise localization of organelles remain incompletely understood. A confounding factor in these studies is the fact that organelle positioning is surprisingly non-trivial to address. E.g., perturbations that affect the localization of organelles often lead to secondary phenotypes such as changes in cell or organelle size. These phenotypes could potentially mask effects or lead to the identification of false positive hits. To uncover and test potential molecular components at scale, accurate and easy to use analysis tools are required that allow robust measurements of organelle positioning. Here, we present an analysis workflow for the faithful, robust, and quantitative analysis of organelle positioning phenotypes. Our workflow consists of an easy to use Fiji plugin and an R Shiny App. These tools enable users without background in image or data analysis to (1) segment single cells and nuclei and to detect organelles, (2) to measure cell size and the distance between detected organelles and the nucleus, (3) to measure intensities in the organelle channel plus one additional channel, and (4) to plot the results in informative graphs. Using simulated data and immunofluorescent images of cells in which the function of known factors for lysosome positioning has been perturbed, we show that the workflow is robust against common problems for the accurate assessment of organelle positioning such as changes of cell shape and size, organelle size and background. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
This episode begins with the newest PSO, no.212, which was recorded in the traditional manner on my porch but with a twist. After spending some time in Mark Menjivar's studio talking about field recordings, bird calls, archives, innumerable sound gadgets, and exciting new projects, Mark lent me a curious piece of sound hardware crafted by Brooklyn-based electronic savants Critter & Guitari, the Organelle M. Thanks, Mark! You can use the Organelle to make beats, as a synthesizer, or to process sound, which is what I did. For this week's piece, I routed the audio recorded on the porch through the Organelle and cycled through the approximately 200 delay patterns (I only used around 5) to create some cool textures to augment my improvised melody. The cars and the air conditioner sounded amazing too. Listen for Mark's PSO collaboration from June of last year, no.142 Cicada Song, which is included in this week's streams (podcast and on YouTube), The piece combined a field recording Mark made on July 17, 2018, outside the Walls Unit in Huntsville, TX, with music recorded from my porch in Austin. Mark's recording captured a clarion call by Gloria Rubac protesting the imminent execution of Chris Young. In both our recordings, you can hear the song of summer cicadas in the background, which creates a shared space for reflection and meditation on the deep implications of our criminal justice system.In addition to Mark's piece, another highlight from the stream is a collaboration with my longtime friend Shannon Spurgeon. PSO no. 113 Princess Moonstep was released in September of 2020. Shannon sent me a tune featuring a sample from the Dukes of Hazard in tribute to his dad, who had recently passed away. The title, Princess Moonstep, is taken from a racehorse his dad owned, which won a bunch of races at Evangeline Downs in Lafayette, Louisiana. Shannon provided the piano, the samples, and the percussion. I brought in some slide guitar.Also featured is PSO no. 81 Science Fairport Convention, made in the aftermath of many an egg splatter sacrificed in the name of science and in service of my daughter's Covid science fair project of January 2020Here is a list of all the recordings included in this week's episode.no. 212 Quilted Daze and Delays, July 5, 2023 no. 142 Cicada Song with Mark Menjivar, June 3, 2021 no. 81 Science Fairport Convention, January 20, 2020no. 68 Sprinkler Shadow, September 19, 2021 no. 113 Princess Moonstep with Shannon Spurgeon, September 30, 2020 no. 175 Eye of the Song Storm, May 17, 2022Porch Swing Orchestra is an art project that pairs music recorded outside with photographs made on-site. Performed and recorded at home and away, solo and with others – birds, guitars, and trucks conspire to form a chance-operated orchestra of delight.The Podcast and YouTube streams include the most current PSO piece along with randomly selected pieces from the past. Get full access to Porch Swing Orchestra at porchswingorchestra.substack.com/subscribe
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.26.538448v1?rss=1 Authors: Chen, R., Qiu, K., Han, G., Kundu, B. K., Ding, G., Sun, Y., Diao, J. Abstract: Detecting cell viability is crucial in research involving the precancerous discovery of abnormal cells, the evaluation of treatments, and drug toxicity testing. Although conventional methods afford cumulative results regarding cell viability based on a great number of cells, they do not permit investigating cell viability at the single-cell level. In response, we rationally designed and synthesized a fluorescent probe, PCV-1, to visualize cell viability under the super-resolution technology of structured illumination microscopy. Given its sensitivity to mitochondrial membrane potential and affinity to DNA, PCV-1's ability to stain mitochondria and nucleoli was observed in live and dead cells, respectively. During cell injury induced by drug treatment, PCV-1's migration from mitochondria to the nucleolus was dynamically visualized at the single-cell level. By extension, harnessing PCV-1's excellent photostability and signal-to-noise ratio and by comparing the fluorescence intensity of the two organelles, mitochondria and nucleoli, we developed a powerful analytical assay named organelle ratiometric probing (ORP) that we applied to quantitatively analyze and efficiently assess the viability of individual cells, thereby enabling deeper insights into the potential mechanisms of cell death. In ORP analysis with PCV-1, we identified 0.3 as the cutoff point for assessing whether adding a given drug will cause apparent cytotoxicity, which greatly expands the probe's applicability. To the best of our knowledge, PCV-1 is the first probe to allow visualizing cell death and cell injury under super-resolution imaging, and our proposed analytical assay using it paves the way for quantifying cell viability at the single-cell level. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.23.538008v1?rss=1 Authors: Wang, T. S., Coppens, I., Brady, N. R., Hamacher-Brady, A. Abstract: Damaged mitochondria can be subject to lysosomal degradation via mitophagy. However, whole-organelle degradation exhibits relatively slow kinetics and thus its impact may be limited in response to acute, fast-acting cellular stress. We previously reported that in Parkin-deficient cells endolysosomes directly target mitochondria when subjected to bioenergetic stress. Here, using high-resolution live cell imaging we reveal a striking level of dynamic targeting of Rab5+ early endosomes to stressed mitochondria, culminating in a switch-like accumulation in the entire mitochondrial population, independently of canonical autophagy. This process of rapid, largescale Rab5+ vesicle trafficking to mitochondria coincides with, and is mediated by, XIAP E3 ligase activated mitochondrial ubiquitylation and results in ultrastructural changes to, and degradation of, intra-mitochondrial components. Mitochondria-targeting vesicles include early endosomal subpopulations marked by Rab5 effector APPL1 and ubiquitin-binding endocytic adaptors OPTN, TAX1BP1 and Tollip, and Rab7-positive late endosomes/lysosomes. In Parkin expressing cells, XIAP- and Parkin-dependent mitochondrial targeting and resulting processing modes are competitively regulated. Together, our data suggest that XIAP-mediated targeting of endolysosomes to mitochondria functions as a stress-responsive, sub-organelle level mitochondrial processing mode that is distinct from, and competitive to, Parkin-mediated mitophagy. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.31.535026v1?rss=1 Authors: Deolal, P., Ramalingam, K., Das, B., Mishra, K. Abstract: When yeast cells are exposed to nutrient-limiting conditions, they undergo transcriptional and translational reprogramming that results in the remodeling of metabolite utilization and organelle architecture. Organelle membranes and contacts also undergo structural and functional alterations. In the budding yeast Saccharomyces cerevisiae, regulated expression of Uip4 is shown to be a critical effector of nuclear shape and function, particularly during the stationary phase. In this work, we demonstrate that the absence of UIP4 affects the morphology of multiple other organelles including mitochondria, endoplasmic reticulum, vacuole and the distribution of lipid droplets. The results show that modulating carbon source, nitrogen availability and cellular energy state impact Uip4 expression. This expression of Uip4 is controlled by the transcription factor Msn2, downstream of Sch9 signaling pathway. Cells lacking Uip4 have poor survival in the stationary phase of the growth cycle. These cellular changes are concomitant with dysregulation of the global lipidome profile and aberrant organelle interaction. We propose that the dynamic and regulated expression of Uip4 is required to maintain lipid homeostasis and organelle architecture which is ultimately required to survive in nutrient-limiting conditions such as stationary phase. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.19.533383v1?rss=1 Authors: Chaiamarit, T., Verhelle, A., Chassefeyre, R., Shukla, N., Weiser Novak, S., Andrade, L. R., Manor, U., Encalada, S. E. Abstract: Dystrophic axons comprising misfolded mutant prion protein (PrP) aggregates are a characteristic pathological feature in the prionopathies. These aggregates form inside endolysosomes -called endoggresomes-, within swellings that line up the length of axons of degenerating neurons. The pathways impaired by endoggresomes that result in failed axonal and consequently neuronal health, remain undefined. Here, we dissect the local subcellular impairments that occur within individual mutant PrP endoggresome swelling sites in axons. Quantitative high-resolution light and electron microscopy revealed the selective impairment of the acetylated vs tyrosinated microtubule cytoskeleton, while micro-domain image analysis of live organelle dynamics within swelling sites revealed deficits uniquely to the MT-based active transport system that translocates mitochondria and endosomes toward the synapse. Cytoskeletal and defective transport results in the retention of mitochondria, endosomes, and molecular motors at swelling sites, enhancing mitochondria-Rab7 late endosome contacts that induce mitochondrial fission via the activity of Rab7, and render mitochondria dysfunctional. Our findings point to mutant Pr Pendoggresome swelling sites as selective hubs of cytoskeletal deficits and organelle retention that drive the remodeling of organelles along axons. We propose that the dysfunction imparted locally within these axonal micro-domains spreads throughout the axon over time, leading to axonal dysfunction in prionopathies. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.19.533351v1?rss=1 Authors: Houngue, R., Sangare, L. O., Alayi, T. D., Dieng, A., Bitard-Feildel, T., Boulogne, C., Slomianny, C., Atindehou, C. M., Fanou, L. A., Hathout, Y., Saeij, J. P., Callebaut, I., Tomavo, S. Abstract: Apicomplexan parasites have specialized secretory organelles called rhoptries, micronemes, and dense granules that are essential for host infection. Here, we show that TgREMIND, a Toxoplasma gondii protein containing a membrane phospholipid interacting domain, is required for the biogenesis of rhoptries and dense granules. TgREMIND contains a Fes/CIP4 homology-Bin/Amphiphysin/Rvs (F-BAR) domain at the N-terminus, known to promote cell membrane bending, and a novel uncharacterized domain that we named REMIND for regulator of membrane interacting domain at the C-terminus. TgREMIND binds to PIP2 lipid species and both F-BAR and REMIND domains are necessary to ensure proper biological activities in vitro and in cellulo. Conditional depletion of TgREMIND results in the absence of dense granules and abnormal transparent rhoptries, leading to a severe inhibition of parasite motility, host invasion, and dissemination. Thus, our study demonstrates that TgREMIND is essential for the proper functioning of key secretory organelles required for successful infection by Toxoplasma. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.03.531038v1?rss=1 Authors: Bao, X., Jia, H., Zhang, X., Zhao, Y., Li, X., Lin, P., Ma, C., Wang, P., Song, C.-P., Zhu, X. Abstract: The cytosol-facing outer membrane (OM) of organelles communicates with other cellular compartments to exchange proteins, metabolites and signaling molecules. Cellular surveillance systems also target OM-resident proteins to control organellar homeostasis and ensure cell survival under stress. Using traditional approaches to discover OM proteins and identify their dynamically interacting partners remains challenging. In this study, we developed an OM proximity labeling (OMPL) system using biotin ligase-mediated proximity biotinylation to map the proximity proteome of the OMs of mitochondria, chloroplasts, and peroxisomes in living Arabidopsis (Arabidopsis thaliana) cells. We demonstrate the power of this system with the discovery of cytosolic factors and OM receptor candidates involved in local protein translation and translocation, membrane contact sites, and organelle quality control. This system also performed admirably for the rapid isolation of intact mitochondria and peroxisomes. Our data support the notion that TOM20-3 is a candidate for both a mitochondrial and a chloroplast receptor, and that PEX11D is a candidate for a peroxisome receptor for the coupling of protein translation and import. OMPL-generated OM proximity proteomes are valuable sources of candidates for functional validation and suggest directions for further investigation of important questions in cell biology. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Lexman Artificial interviews Diana Walsh Pasulka, a paediatrician and necessitarian philosopher. They discuss the relative merits of lameness and necessitarianism, the necessity of pediatric care, and the use of photozincography to study organelles.
- Wer bekam den Ig-Nobelpreis für eine Geburtszentrifuge? - Was sind eigentlich Mikronationen? - Wie kann der Alterungsprozess durch einen Pilz verlangsamt werden?
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.12.09.519571v1?rss=1 Authors: Haukedal, H., Corsi, G. I., Gadekar, V. P., Doncheva, N. T., Kedia, S., de Haan, N., Chandrasekaran, A., Jensen, P., Schionning, P., Vallin, S., Marlet, F. R., Poon, A., Pires, C., Agha, F. K., Wandall, H. H., Cirera, S., Simonsen, A. H., Nielsen, T. T., Nielsen, J. E., Hyttel, P., Muddashetty, R., Aldana, B. I., Gorodkin, J., Nair, D., Meyer, M., Larsen, M. R., Freude, K. Abstract: Alzheimers disease (AD) is the most common cause of dementia, with no current cure. Consequently, alternative approaches focusing on early pathological events in specific neuronal populations, besides targeting the well-studied Amyloid beta (A{beta}) accumulations and Tau tangles, are needed. In this study, we have investigated disease phenotypes specific to glutamatergic forebrain neurons and mapped the timeline of their occurrence, by implementing familial and sporadic human induced pluripotent stem cell models as well as the 5xFAD mouse model. We recapitulated characteristic late AD disease phenotypes, such as increased A{beta} secretion and Tau hyperphosphorylation, as well as previously well documented mitochondrial and synaptic deficits. Intriguingly, we identified Golgi fragmentation as one of the earliest AD phenotypes, indicating potential impairments in protein processing and post-translational modifications. Computational analysis of RNA sequencing data revealed differentially expressed genes involved in glycosylation and glycan patterns, whilst total glycan profiling revealed minor glycosylation differences. This indicates general robustness of glycosylation besides the observed fragmented morphology. Importantly, we identified that genetic variants in Sortilin-related receptor 1 (SORL1) associated with AD could aggravate the Golgi fragmentation and subsequent glycosylation changes. In summary, we identified Golgi fragmentation as one of the earliest disease phenotypes in AD neurons in various in vivo and in vitro complementary disease models, which can be exacerbated via additional risk variants in SORL1. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/519571v1_ufig1.gif" ALT="Figure 1" greater than View larger version (39K): org.highwire.dtl.DTLVardef@cf9375org.highwire.dtl.DTLVardef@1d9f206org.highwire.dtl.DTLVardef@1a0731forg.highwire.dtl.DTLVardef@e60457_HPS_FORMAT_FIGEXP M_FIG C_FIG Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.11.30.518502v1?rss=1 Authors: Needs, H. I., Henley, J., Collinson, I. Abstract: Protein import into mitochondria is an intricate and highly conserved process essential for organellar biogenesis, and maintenance of its structure and function. Defects in the import apparatus impact the assembly of the respiratory chain and ATP synthase complexes required for oxidative phosphorylation, compromising the ready supply of ATP to the cell. The consequences of reduced bioenergetic function are particularly severe for cells with high energetic demands such as neurons. However, relatively little is known about howdefectiveimportcontributestoneurodegeneration, or how neurotoxic proteins characteristic ofneurodegenerative diseases impact mitochondrial import efficiency. Here, we used HeLa cells to investigate how expressing high levels of Tau variants affect mitochondrial import activity, morphology, and function. We found that the variant associated with neurodegeneration (TauP301L) colocalises with mitochondria. TauP301L, but not wildtype Tau, interacts with TOM40, the protein-channel component of the outer membrane protein import complex. Interestingly, TauP301L expression had no discernible effect on overall mitochondrial import function, despite associating with TOM40 and altering mitochondrial morphology, suggesting that a rescue mechanism is at play. This rescue could be explained by the appearance of microtubule and actin containing tunnelling nanotubes (TNTs), used to recruit healthy mitochondria from neighbouring cells and/or dispose of mitochondria with aggregated Tau. Furthermore, in primary neuronal cultures TauP301L induces morphological changes that resemble a neurodegeneration like phenotype, and this is mirrored in cells where the import sites are blocked artificially. These results reveal an intriguing link between the production of aggregation prone protein variants, such as Tau, and the mitochondrial protein import machinery relevant to neurodegenerative disease. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.11.09.515818v1?rss=1 Authors: Laan, S. N. J., Dirven, R., Eikenboom, J., Bierings, R., Symphony consortium Abstract: One of the most used and versatile methods to study number, dimensions, content and localization of secretory organelles is confocal microscopy analysis. However, considerable heterogeneity exists in the number, size and shape of secretory organelles that can be present in the cell. One thus needs to analyze large numbers of organelles for valid quantification. Properly evaluating these parameters requires an automated, unbiased method to process and quantitatively analyze microscopy data. Here, we describe two pipelines, run by CellProfiler software, called OrganelleProfiler and OrganelleContentProfiler. These pipelines were used on confocal images of endothelial colony forming cells (ECFC) which contain unique secretory organelles called Weibel-Palade bodies. Results show that the pipelines can quantify the cell count and size, and the organelle count, size, shape, relation to cells and nuclei, and distance to these objects. Furthermore, the pipeline is able to quantify secondary signals located in or on the organelle or in the cytoplasm. Cell profiler measurements were checked for validity using Fiji. To conclude, these pipelines provide a powerful, high-processing quantitative tool for analysis of cell and organelle characteristics. These pipelines are freely available and easily editable for use on different cell types or organelles. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.11.03.514994v1?rss=1 Authors: Simon, C., Asaro, A., Feng, S., Riezman, H. Abstract: Phosphatidylethanolamine metabolism plays essential roles in eukaryotic cells but has not been completely resolved due to its complexity. This is because lipid species, unlike proteins or nucleic acids, cannot be easily manipulated at the single molecule level or controlled with subcellular resolution, two of the key factors toward understanding their functions. Here, we use the organelle-targeting photoactivation method to study PE metabolism in living cells with a high spatiotemporal resolution. Containing predefined PE structures, we designed probes which can be selectively introduced to the ER or mitochondria to compare their metabolic products according to their subcellular localization. We combined photo-uncaging method with dual stable isotopic labeling to track PE metabolism in living cells by mass spectrometry analysis. Our results reveal that both mitochondrial- and ER-released PE participate in phospholipid remodeling, and that PE methylation can be detectable only under particular conditions. Thus, our method provides a framework to study phospholipid metabolism at subcellular resolution. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC
Don't Miss These ThoughtsPaola on Instagram HEREWork virtually with Paolo HEREDon't Miss These ThoughtsWho is Paola Xhuli?What is a cell and how does it relate to our body as a whole?What are mitochondria and what are their roles in cells?How does gut dysbiosis and mitochondrial dysfunction build off of one another?What are the main factors leading to mitochondrial damage?What are some changes we can make in order to prevent mitochondrial damage?What are some signs of cellular dysfunction?What tests can be done to test for cellular dysfunction?How does food play into cellular health?What are some of the best foods to support our mitochondria?What are some lifestyle habits that can boost cellular health?What does Paola incorporate in her daily life for her own mitochondrial health?How can EMFs affect our cells?Cells are known as the smallest living units in our body.They are the foundation for our entire body as they clump together to form each of our organ systems.Healthy cells build healthy tissues, which build healthy organs, which build healthy organs systems, which makes an all around healthy you! Cells → Tissues → Organs → Organ systems → Body!One aspect of cells that Paola draws special attention to is the mitochondria. Organelle responsible for cellular energyProvides 90% of our body's energyMore mitochondria= more energyHealthy mitochondria= more energyGut dysbiosis directly connected to mitochondrial dysfunctionMitochondrial dysfunction correlated with chronic conditions such as IBS or IBDCellular DysfunctionCellular dysfunction can be the root cause of virtually any symptom. “If you are having symptoms, there are cells that are dysfunctional”Paola Xhuli If cells are damaged, then there will be damage to the organ as well- which can show up in any place in the body.The body's cells are the first place that health issues start.There are some factors to be aware of that can easily cause this cellular damage.Free radicalsmolecules found in the body that are missing electrons and take it from other moleculesoften damage proteinradicals can be produced by mitochondria but also when exposed to environmental toxinsInfectionsstealth infections in particularpathogens such as parasites, yeast, fungi, bacteria, virusesDysregulated immune systemimmune system can either overreact or under-reactresults in autoimmune disorders or insufficient immune responseEnvironmental pollutionsmold, mycotoxins, heavy metals, organic pollutantsharmful toxins can interfere with cellular healthAs you can see the risk for cellular damage is high, as many of us are exposed to these issues on a regular basis.However Paola emphasizes several steps you can take to minimize damage:Reduce exposureremove mold sourceswitching to more organic producefiltering your water → HUGE exposureReducing inflammation through connection with naturegrounding reduces inflammationIncluding a more nutritious diet limits free radicalsMinimize stressTRAUMA CAN BE STORED IN THE BODY!Cellular detoxificationusing binders with the help of a qualified practitionerInflammationOne of the most common causes of cellular dysfunction Paola mentions is chronic inflammation.Many people struggling with digestive concerns face the battle of almost constant inflammation.This occurs due to an overactive immune system, that sends out an immune response to cells even when there is no immediate cause to.This can result in damage of healthy body cells and eventually tissue.Here are some common inflammatory diseases:diabetesheart diseaseallergiesautoimmune disordersAll of these can result in an increase of inflammation and long lasting damage.To combat some of this inflammation you can follow an anti-inflammatory diet with anti-inflammatory foods, which minimizes food that is known to increase immune responses.This encourages you to eat foods such as olive oil and good fats, tomatoes, and berries. It minimizes processed foods and fried foods that is proven to cause a flare-up of inflammation.Another great choice is just switching to a mediterranean diet. This diet is proven to be anti-inflammatory by minimizing salt intake and increasing fatty acids, polyphenols, vitamins, and minerals. The emphasis on good fats such as olive oil is extremely helpful for minimizing inflammation.Sources: HERE and HEREEating for Cellular HealthPaola mentions several food choices that can help support healthy cells or a “cellular healing diet.” Notice how this closely aligns with an anti-inflammatory diet. Lots of overlap!Nutrient dense dietchoosing foods that contain many different nutrientswhole grains, diverse fruits and vegetablesWhole foodsemphasis on unprocessed foods, as close to nature as possiblecombination of plant and animal productsanimal nutrients are easier for our body to absorbplants contain probiotics and fiber that we needEating enoughmaking sure to support your cells with adequate fuelSome of her favorite nutrient dense foods are animal products; grass-fed meat and organ meats, raw dairy, starchy vegetables, fermented foods, fruit, dark chocolate, and green tea.Each of these foods is supportive of cellular maintenance as well as gut health.Other foods that have cellular healing benefits are:leafy greens (high vitamin C, folate, magnesium)eggs (protein for cellular support)wild-caught salmon (protein and vitamins)nuts (healthy fats)chicken and turkey (amino acids)cruciferous vegetables (antioxidants- help prevent oxidative stress)Some easy way to incorporate these foods into your diet are adding a serving of almond milk to your coffee or tea, adding some spinach to your smoothie, or having a boiled egg as a snack.Also for a yummy way to eat cruciferous vegetables such as your Brussels sprouts – try air frying them or cooking them in olive oil.As a rough rule of thumb, most nutritionally dense foods will fall into the category of optimal cellular nutrition. Feed your cells, friends!SourceSupplementing for Optimal Cellular HealthPaola mentions 3 supplements to help obtain essential nutrients for optimal health:Spore-based probiotic (A Gutsy Girl's choice probiotic is the Just Thrive Probiotic HERE — use code AGUTSYGIRL at checkout to save 15%)Magnesium – because we don't get enough + soil has been depleted of this nutrient (A Gutsy Girl has her own magnesium supplement which you can get HERE)Beef liver – for those who just cannot seem to tolerate the whole beef liver food (A Gutsy Girl loves the Desiccated Liver Capsules from Perfect Supplements HERE – use code GUTSY10 at checkout to save 10%)GET THE A GUTSY GIRL MAGNESIUM HERELifestyle Habits for the Body's Cells!There are also small changes you can implement into your daily life to support optimal mitochondria functioning. fasting- intermittent fastingsun exposure- especially during sunrise and sunset (red light)cold exposure- increases mitochondrial activityregular exercise- any form of exercise, improves function and structureSome other tidbits Paola recommends is to prioritize time outdoors, minimize time on electronics, and optimize sleep.All of these small changes can help bump up your cells, which helps support a healthy gut!Electronics in particular have a negative effect on our cells, with more and more research coming out on it.These EMF waves have been found to affect our cells on a cellular level.Paola recommends to unplug your Wifi when possible, turn your phone on airplane mode, and stay away from electronics as much as physically possible to protect your cells.Cells and the GutCellular health and gut function are directly related.Since cells make up the tissue found in our GI tract, they are essential to the function of our digestive system.By ensuring that our cells are in good health, we can help create the foundation for our gut healing journey.Here are some simple things you can do to make sure you are on the right path:Check your diet- try to remove inflammatory foods such as processed grains and man-made fatsIncorporate more fresh fruits and veggiesBe intentional about spending time in the sunMake sleep a priority!!!!TestsWhile Paola does say that any symptom leads her to believe in some sort of cellular dysfunction, she also recommends a couple of tests to check for internal markers.Organic Acid Testurine test that checks for nutritional adequacy and has many markers of mitochondrial activityHeavy metal and mycotoxin exposuretoxins can cause cellular damageGI Mapcan help further find internal markers of dysfunctionThese help look at the human body from a microscopic scale, which could give you a good starting place for your healing journey.Some of the most common symptoms are low energy levels and brain fog.Chronic fatigue syndrome is another strong indication of cellular dysfunction.More from A Gutsy GirlWant to learn even more about the gut and ways to heal it?Learn all the secrets via my signature book, A Gutsy Girl's Bible: a 21-day approach to healing the gut. Grab your copy on Amazon HERE. Welcome to A Gutsy Girl PodcastHang out on InstagramBFF's on YouTubeFree resource: The Master Gutsy SpreadsheetRated-G Email ClubWrap UpTime to wrap this up. As always, a huge goal for this show is to connect with even more people. Feel free to send an email to our team at podcast@agutsygirl.com. We want to hear questions, comments, show ideas, etc.Did you enjoy this episode? Please drop a comment below or leave a review on Apple Podcasts.Bio: Paola XhuliPaola is a Functional Nutritionist and Detox Specialist that specializes in stimulating the body's natural self-healing and self-regulating mechanisms to tackle health issues and symptoms.Her main research focus areas are mitochondrial health, gut health, parasites, drainage & detox, and hormonal imbalances.If you liked this episode, you might also enjoy:Micronutrients and the GutViome Gut Microbiome Test Reviews {2022}Best Place to Buy Grass Fed Beef {Online in 2022}Xox,SKH Connect with A Gutsy GirlThrough the websiteOn InstagramVia LinkedIn
Don't Miss These ThoughtsPaola on Instagram HEREWork virtually with Paolo HEREDon't Miss These ThoughtsWho is Paola Xhuli?What is a cell and how does it relate to our body as a whole?What are mitochondria and what are their roles in cells?How does gut dysbiosis and mitochondrial dysfunction build off of one another?What are the main factors leading to mitochondrial damage?What are some changes we can make in order to prevent mitochondrial damage?What are some signs of cellular dysfunction?What tests can be done to test for cellular dysfunction?How does food play into cellular health?What are some of the best foods to support our mitochondria?What are some lifestyle habits that can boost cellular health?What does Paola incorporate in her daily life for her own mitochondrial health?How can EMFs affect our cells?Cells are known as the smallest living units in our body.They are the foundation for our entire body as they clump together to form each of our organ systems.Healthy cells build healthy tissues, which build healthy organs, which build healthy organs systems, which makes an all around healthy you! Cells → Tissues → Organs → Organ systems → Body!One aspect of cells that Paola draws special attention to is the mitochondria. Organelle responsible for cellular energyProvides 90% of our body's energyMore mitochondria= more energyHealthy mitochondria= more energyGut dysbiosis directly connected to mitochondrial dysfunctionMitochondrial dysfunction correlated with chronic conditions such as IBS or IBDCellular DysfunctionCellular dysfunction can be the root cause of virtually any symptom. “If you are having symptoms, there are cells that are dysfunctional”Paola XhuliIf cells are damaged, then there will be damage to the organ as well- which can show up in any place in the body.The body's cells are the first place that health issues start.There are some factors to be aware of that can easily cause this cellular damage.Free radicalsmolecules found in the body that are missing electrons and take it from other moleculesoften damage proteinradicals can be produced by mitochondria but also when exposed to environmental toxinsInfectionsstealth infections in particularpathogens such as parasites, yeast, fungi, bacteria, virusesDysregulated immune systemimmune system can either overreact or under-reactresults in autoimmune disorders or insufficient immune responseEnvironmental pollutionsmold, mycotoxins, heavy metals, organic pollutantsharmful toxins can interfere with cellular healthAs you can see the risk for cellular damage is high, as many of us are exposed to these issues on a regular basis.However Paola emphasizes several steps you can take to minimize damage:Reduce exposureremove mold sourceswitching to more organic producefiltering your water → HUGE exposureReducing inflammation through connection with naturegrounding reduces inflammationIncluding a more nutritious diet limits free radicalsMinimize stressTRAUMA CAN BE STORED IN THE BODY!Cellular detoxificationusing binders with the help of a qualified practitionerInflammationOne of the most common causes of cellular dysfunction Paola mentions is chronic inflammation.Many people struggling with digestive concerns face the battle of almost constant inflammation.This occurs due to an overactive immune system, that sends out an immune response to cells even when there is no immediate cause to.This can result in damage of healthy body cells and eventually tissue.Here are some common inflammatory diseases:diabetesheart diseaseallergiesautoimmune disordersAll of these can result in an increase of inflammation and long lasting damage.To combat some of this inflammation you can follow an anti-inflammatory diet with anti-inflammatory foods, which minimizes food that is known to increase immune responses.This encourages you to eat foods such as olive oil and good fats, tomatoes, and berries. It minimizes processed foods and fried foods that is proven to cause a flare-up of inflammation.Another great choice is just switching to a mediterranean diet. This diet is proven to be anti-inflammatory by minimizing salt intake and increasing fatty acids, polyphenols, vitamins, and minerals. The emphasis on good fats such as olive oil is extremely helpful for minimizing inflammation.Sources: HERE and HEREEating for Cellular HealthPaola mentions several food choices that can help support healthy cells or a “cellular healing diet.” Notice how this closely aligns with an anti-inflammatory diet. Lots of overlap!Nutrient dense dietchoosing foods that contain many different nutrientswhole grains, diverse fruits and vegetablesWhole foodsemphasis on unprocessed foods, as close to nature as possiblecombination of plant and animal productsanimal nutrients are easier for our body to absorbplants contain probiotics and fiber that we needEating enoughmaking sure to support your cells with adequate fuelSome of her favorite nutrient dense foods are animal products; grass-fed meat and organ meats, raw dairy, starchy vegetables, fermented foods, fruit, dark chocolate, and green tea.Each of these foods is supportive of cellular maintenance as well as gut health.Other foods that have cellular healing benefits are:leafy greens (high vitamin C, folate, magnesium)eggs (protein for cellular support)wild-caught salmon (protein and vitamins)nuts (healthy fats)chicken and turkey (amino acids)cruciferous vegetables (antioxidants- help prevent oxidative stress)Some easy way to incorporate these foods into your diet are adding a serving of almond milk to your coffee or tea, adding some spinach to your smoothie, or having a boiled egg as a snack.Also for a yummy way to eat cruciferous vegetables such as your Brussels sprouts – try air frying them or cooking them in olive oil.As a rough rule of thumb, most nutritionally dense foods will fall into the category of optimal cellular nutrition. Feed your cells, friends!SourceSupplementing for Optimal Cellular HealthPaola mentions 3 supplements to help obtain essential nutrients for optimal health:Spore-based probiotic (A Gutsy Girl's choice probiotic is the Just Thrive Probiotic HERE — use code AGUTSYGIRL at checkout to save 15%)Magnesium – because we don't get enough + soil has been depleted of this nutrient (A Gutsy Girl has her own magnesium supplement which you can get HERE)Beef liver – for those who just cannot seem to tolerate the whole beef liver food (A Gutsy Girl loves the Desiccated Liver Capsules from Perfect Supplements HERE – use code GUTSY10 at checkout to save 10%)GET THE A GUTSY GIRL MAGNESIUM HERELifestyle Habits for the Body's Cells!There are also small changes you can implement into your daily life to support optimal mitochondria functioning. fasting- intermittent fastingsun exposure- especially during sunrise and sunset (red light)cold exposure- increases mitochondrial activityregular exercise- any form of exercise, improves function and structureSome other tidbits Paola recommends is to prioritize time outdoors, minimize time on electronics, and optimize sleep.All of these small changes can help bump up your cells, which helps support a healthy gut!Electronics in particular have a negative effect on our cells, with more and more research coming out on it.These EMF waves have been found to affect our cells on a cellular level.Paola recommends to unplug your Wifi when possible, turn your phone on airplane mode, and stay away from electronics as much as physically possible to protect your cells.Cells and the GutCellular health and gut function are directly related.Since cells make up the tissue found in our GI tract, they are essential to the function of our digestive system.By ensuring that our cells are in good health, we can help create the foundation for our gut healing journey.Here are some simple things you can do to make sure you are on the right path:Check your diet- try to remove inflammatory foods such as processed grains and man-made fatsIncorporate more fresh fruits and veggiesBe intentional about spending time in the sunMake sleep a priority!!!!TestsWhile Paola does say that any symptom leads her to believe in some sort of cellular dysfunction, she also recommends a couple of tests to check for internal markers.Organic Acid Testurine test that checks for nutritional adequacy and has many markers of mitochondrial activityHeavy metal and mycotoxin exposuretoxins can cause cellular damageGI Mapcan help further find internal markers of dysfunctionThese help look at the human body from a microscopic scale, which could give you a good starting place for your healing journey.Some of the most common symptoms are low energy levels and brain fog.Chronic fatigue syndrome is another strong indication of cellular dysfunction.More from A Gutsy GirlWant to learn even more about the gut and ways to heal it?Learn all the secrets via my signature book, A Gutsy Girl's Bible: a 21-day approach to healing the gut. Grab your copy on Amazon HERE. Welcome to A Gutsy Girl PodcastHang out on InstagramBFF's on YouTubeFree resource: The Master Gutsy SpreadsheetRated-G Email ClubWrap UpTime to wrap this up. As always, a huge goal for this show is to connect with even more people. Feel free to send an email to our team at podcast@agutsygirl.com. We want to hear questions, comments, show ideas, etc.Did you enjoy this episode? Please drop a comment below or leave a review on Apple Podcasts.Bio: Paola XhuliPaola is a Functional Nutritionist and Detox Specialist that specializes in stimulating the body's natural self-healing and self-regulating mechanisms to tackle health issues and symptoms.Her main research focus areas are mitochondrial health, gut health, parasites, drainage & detox, and hormonal imbalances.If you liked this episode, you might also enjoy:Micronutrients and the GutViome Gut Microbiome Test Reviews {2022}Best Place to Buy Grass Fed Beef {Online in 2022}Xox,SKH
Say it with us: mitochondria are the powerhouse of the cell. On this episode, Neil deGrasse Tyson and co-hosts Chuck Nice and Gary O'Reilly discover the original horse power, equine physiology, and the science behind the Kentucky Derby. NOTE: StarTalk+ Patrons can watch or listen to this entire episode commercial-free here: https://www.startalkradio.net/show/horsepower-with-dr-sarah-white-springer/Thanks to our Patrons Cosmic Scapegoat, Tom Kearns, Valeri Williams, Zeki Majed, Ethan Fink, Mariano Quiroga, John Marc Roberson, Fredrik Östervald, Crimson, and Colt for supporting us this week.Photo Credit: Bill Brine, CC BY 2.0, via Wikimedia Commons
Der 2020 Nobelpreis für Chemie ging an Emmanuelle Charpentier und Jennifer Doudna für "die Entwicklung einer Methode der Genomeditierung“. Ihre Arbeit hat die Werkzeuge, die einem Forscher in den Biowissenschaften zur Verfügung stehen, signifikant erweitert. Deswegen will ich mir die Zeit nehmen, um ein bißchen darüber zu reden, was an dieser Arbeit so besonders ist. Damit das auch klappt, muss man erst mit ein paar Folgen einsteigen, die den Kontext bieten. Diese erste Episode geht über die Struktur der DNS. Willst du einen Kommentar zu dieser Episode oder zu diesem Podcast abgeben, dann gibt es zwei Möglichkeiten. Entweder schreibe mir auf Twitter unter @alltagschemie oder schicke mir einfach altmodisch eine email auf chem.podcast@gmail.com. Quellen · https://www.nobelprize.org/prizes/chemistry/2020/summary/ · https://en.wikipedia.org/wiki/Human_genome · https://en.wikipedia.org/wiki/Genome · https://en.wikipedia.org/wiki/DNA · https://en.wikipedia.org/wiki/List_of_Nobel_laureates · https://en.wikipedia.org/wiki/Chromosome · https://en.wikipedia.org/wiki/Organelle · https://en.wikipedia.org/wiki/Mitochondrion · https://en.wikipedia.org/wiki/Cell_nucleus · https://en.wikipedia.org/wiki/Nucleoid
The 2020 Nobel Prize in Chemistry went to Emmanuelle Charpentier and Jennifer Doudna for "for the development of a method for genome editing”. Their work has markedly added to the toolbox available to researchers in the life sciences and in my humble opinion, it is worth talking about. To understand why this work is so important, we will need to have some introductory episodes first and this here is part number I, where we will discuss the structure of DNA. I can now be reached on twitter under @ChemistryinEve1 , if you have feedback that you would like to share. Alternatively, you can send an email to chem.podcast@gmail.com . Sources · https://www.nobelprize.org/prizes/chemistry/2020/summary/ · https://en.wikipedia.org/wiki/Human_genome · https://en.wikipedia.org/wiki/Genome · https://en.wikipedia.org/wiki/DNA · https://en.wikipedia.org/wiki/List_of_Nobel_laureates · https://en.wikipedia.org/wiki/Chromosome · https://en.wikipedia.org/wiki/Organelle · https://en.wikipedia.org/wiki/Mitochondrion · https://en.wikipedia.org/wiki/Cell_nucleus · https://en.wikipedia.org/wiki/Nucleoid
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.02.279398v1?rss=1 Authors: Kamal, M. A., Janes, J. A., Li, L., Thibaudau, F., Smith, A.-S., Sengupta, K. Abstract: The interactions between different intra-cellular organelles, including the endoplasmic reticulum, have recently been in focus thanks to the tremendous progress in imaging them using cryogenic transmission electron microscopy. However, they are still difficult to study in cellulo, and reconstituting these systems has been a standing challenge. Here we achieve this task using a giant unilamellar vesicle (GUV) and supported lipid bilayer (SLB) system. The tethers, which may reside in the cytosol when unbound, are mimicked by single (or double) stranded DNA sequences of two different lengths with ends that are self-sticky, and with terminal cholesterol moieties which insert into GUV or SLB membranes. The DNA-tethers, bound by their sticky-end, can exist in two possible states - either with both cholesterols in the same membrane or each cholesterol in a different membrane, the latter conformation leading to adhesion. Exchange of tether-molecules between the membranes occurs through the aqueous phase. By developing theoretical arguments that are supported in our experiments, we show that this possibility of exchange and the relative difference in the projected area between the two states drives the adhesion due to collective entropic considerations, rather than the usually considered enthalpy of binding. The establishment of this fundamentally different interaction between two membranes suggests that in physiological conditions, the regulation of contact formation inside cells may be very different from the case of the much studied ligand-receptor pairing on the external cell membrane. Copy rights belong to original authors. Visit the link for more info
Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.31.276428v1?rss=1 Authors: Bauer, D., Ishikawa, H., Wemmer, K., Marshall, W. F. Abstract: Stochastic variations (noise) in gene expression have been extensively characterized, but the ramifications of this gene-level variation for cellular structure and function remain unclear. To what extent are cellular structures subject to noise? We show that flagellar length in Chlamydomonas exhibits significant variation that results from a combination of intrinsic fluctuations within the flagella and extrinsic cell to cell variation. We analyzed a series of candidate genes affecting flagella and found that flagellar length variation is increased in mutations which increase the average flagellar length, an effect that can be explained using a theoretical model for flagellar length regulation. Cells with greater differences in their flagellar lengths show impaired swimming but improved gliding motility, raising the possibility that cells have evolved mechanisms to tune intrinsic noise in length. Taken together our results show that biological noise exists at the level of subcellular structures, with a corresponding effect on cell function. Copy rights belong to original authors. Visit the link for more info
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A brief preview of the upcoming full episode 53, featuring upcoming topics that include tips for amplifying learning in the A&P course, updates regarding the role of exosomes in the spread of cancer and how heart shape relates to human activity. There's more... some word dissections and Kevin's recommendation for The A&P Professor Book Club. If you cannot see or activate the audio player click here. Questions & Feedback: 1-833-LION-DEN (1-833-546-6336) Follow The A&P Professor on Twitter, Facebook, Blogger, Nuzzel, Tumblr, or Instagram! Topics 1 minute Strategies to amplify learning in the A&P course The role of exosomes in the spread of cancer How heart shape relates to type of activity Word Dissections 8.5 minutes Metastasis Extracellular vesicle (EV) Exosome Oncosome Transcytosis Book Club 3.5 minutes Prime Mover: A Natural History of Muscle by Steve Vogel amzn.to/30jcKcm Special opportunity Contribute YOUR book recommendation for A&P teachers! First five submitted and used will be in a drawing for a Kindle Fire HD 10 tablet amzn.to/2WwLZvb Any contribution used will receive a $25 gift certificate The best contribution is one that you have recorded in your own voice (or in a voicemail at 1-833-LION-DEN) Check out The A&P Professor Book Club If the hyperlinks here are not active, go to TAPPradio.org to find the episode page. More details at the episode page. Transcript available at the script page. Listen to any episode on your Alexa device. Need help accessing resources locked behind a paywall? Check out this advice from Episode 32 to get what you need! https://youtu.be/JU_l76JGwVw?t=440 Sponsors Transcript and captions for this episode are supported by the American Association for Anatomy. anatomy.org The Human Anatomy & Physiology Society also provides marketing support for this podcast. theAPprofessor.org/haps Distribution of this episode is supported by NYCC's online graduate program in Human Anatomy & Physiology Instruction (HAPI) nycc.edu/hapi Clicking on sponsor links helps let them know you appreciate their support of this podcast! Referrals also help defray podcasting expenses. Amazon TextExpander Snagit & Camtasia The A&P Professor Logo Items Follow The A&P Professor on Twitter, Facebook, Blogger, Nuzzel, Tumblr, or Instagram! The A&P Professor® and Lion Den® are registered trademarks of Lion Den Inc. (Kevin Patton)
Eukaryotic cells have many different membrane-bound organelles with distinct functions and characteristic shapes. How does this happen? Dr. Tom Rapoport explains the important role of protein sorting in determining organelle shape and function.
Many of us are used to seeing cartoons of cells with organelles shown as static, isolated structures.
Eukaryotic cells have many different membrane-bound organelles with distinct functions and characteristic shapes. How does this happen? Dr. Tom Rapoport explains the important role of protein sorting in determining organelle shape and function.
Many of us are used to seeing cartoons of cells with organelles shown as static, isolated structures.
At the Institute of Molecular Biology at Johannes Gutenberg University of Mainz, Christopher Reinkemeier is a Ph.D. student who's involved with a project that's providing breakthrough evidence of the ability of synthetic organelles to carry out complex tasks in living cells. How complex? One of the most complex and important processes that cells carry out: translation or the synthesis of proteins. In the body, translation involves hundreds of organic molecules, but the synthetic organelle Reinkemeier has helped to develop requires just five components, which, once in a living cell, recruit all of the other necessary components of translation. Reinkemeier provides an in-depth discussion about the science behind what they've created, and the significance of the fact that it's capable of modifying one messenger RNA (mRNA) for the production of one, specifically modified protein. Tune in for all the details.
Tobias Hertlein ist als Musikvermittler für die Elbphilharmonie Hamburg tätig, ist Gast bei renommierten Ensembles und Orchestern und spielte bereits bei zahlreichen STAGE Musicals. Er liebt Experimente mit elektronischen Musikinstrumenten – und ist außerdem ein wahnsinnig sympathischer Zeitgenosse. Wir sprechen über Kreativität, Zeitmanagement, Offenheit für Neues und die Zukunft. Und hier noch die in der Folge versprochenen Links zu den angesprochenen Themen: Das Buch "RETTET DAS SPIEL - Weil Leben mehr als Funktionieren ist" von Gerald Hüther: https://amzn.to/2NHOhGG Die ORGANELLE, ein Musikcomputer vom Hersteller Critter & Guitari: https://www.critterandguitari.com/organelle Die App BINAURAL BEATS im App Store und Google Play Store: https://itunes.apple.com/de/app/binaural-beats/id597146594?mt=8 https://play.google.com/store/apps/details?id=com.ihunda.android.binauralbeat&hl=de
Daniel and Vincent solve the case of the Woman With Anal Area Discomfort, and discuss the multiple functions of a clathrin adapter protein in formation of rhoptry and microneme secretory organelles of Toxoplasma gondii. Hosts: Vincent Racaniello and Daniel Griffin Become a patron of TWiP. Links for this episode: Journal of Microbiology and Biology Education SciComm Issue (link) TWiP 19: Enterobius vermicularis, the pinworm Multiple roles of Toxoplasma gondii clathrin adaptor AP1 protein (PLoS Path) Image credit Letters read on TWiP 133 Case Study for TWiP 133 Seen while working in remote mountain makeshift mobile clinic in Dominican Republic, on Haitian border. Traveled 3 h by pickup truck, remote mountain town, womens centers. Set up makeshift mobile clinic in this center. Mother concerned about 6 yo girl, failure to thrive compared with sister, protuberant belly, frequent abdominal discomfort, going on over 1 year. No surgeries, no meds, first time ever seeing medical person. Mother and sister are family. Three children in family. Father does timber work. Very impoverished region, living in dirt floor home, drinking untreated water from local stream, go to bathroom outside, could be contamination. Diet: carbohydrate, plantains, rice, beans. On exam: lungs clear, heart fine, belly protuberant, liver and spleen not enlarged, some edema. Mother said noticed long motile worm in girls feces. Firm belly, not painful to her. Send your case diagnosis, questions and comments to twip@microbe.tv Music by Ronald Jenkees
Welcome to the conversation. It is April 20th 2016, and this is our 44th podcast. Today will be a discussion led by Dr. Sergio Muñoz-Gómez on "The specialization of the proto-mitochondrion as the respiratory organelle of eukaryotes." The show is about 60 minutes long.
Hosts: Vincent Racaniello, Michael Schmidt, Elio Schaechter and Michele Swanson. Vincent, Elio, Michael, and Michele consider whether our eating behavior is manipulated by gastrointestinal microbiota, and an aphid gene of bacterial origin whose gene product encodes a protein that is transported to an obligate endosymbiont. Subscribe to TWiM (free) on iTunes, via RSS feed, by email or listen on your mobile device with the Microbeworld app. Links for this episode National Biosafety Stewardship month Aphid gene of bacterial origin (Curr Biol) Eroding symbiont/organelle distinction (Curr Biol) Is our eating manipulated by our microbiota? (Bioessays) Road to microbial endocrinology (STC) Microbial endocrinology (STC) Letters read on TWiM 86 Send your microbiology questions and comments (email or mp3 file) to twim@twiv.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twim.
Arash Komeili cell biologist, Assc. Prof. plant and microbial biology UC Berkeley. His research uses bacterial magnetosomes as a model system to study the molecular mechanisms governing the biogenesis and maintenance of bacterial organelles. Part 2.TranscriptSpeaker 1: Spectrum's next Speaker 2: [inaudible] [inaudible]. Speaker 1: [00:00:30] Welcome to spectrum the science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Hello and good afternoon. My name is Renee Rao. I'll be hosting today's show. Today we present part two of our interview with a Rosh Kamali. Dr [inaudible] is a cell biologist and associate [00:01:00] professor of plant and microbial biology at UC Berkeley. Previously on spectrum, he discussed his work with magneto tactic bacteria. Here's Dr Camilia explaining why these bacteria so interesting. Speaker 4: We work with a specific type of bacteria. They're called magneto is tactic bacteria and these are organisms that are quite widespread. You can find them in most aquatic environments by almost any sort of classification. You can really group them together if you [00:01:30] take their shape or if you look at even the genes they have, you can't really group them into one specific group as opposed to many other bacteria that you can do that, but unites them together as a group is that they're able to orient in magnetic fields. And some along magnetic fields Speaker 3: today. In part two of his interview, Dr [inaudible] explains how these discoveries might be applied and discusses the scientific outreach he does in our community. Here is Brad swift interviewing a Kamali, Speaker 4: [00:02:00] so how is it that you're trying to leverage what you're learning about the magnetic zone? You're trying to apply it in any way. Are you still really in the pure research mode? I think we're starting to move out or at least branch out to try to do some applications as well. This has been a really, one of the areas of research that's been the most active, or at least the most thought about for Magna [inaudible] bacteria for the last 40 years or so of that people have been working on it. You have two [00:02:30] features of the magnesiums that immediately can be thought of as being very useful for applications, but one is that they're making something that's nanometers size. Very small is magnetic and it has very, very irregular dimensions, quite free of impurities. So you can make magnetic particles in the lab and people have gotten very good at it actually, but it's often very hard to control some of their features. Speaker 4: Maybe contaminants can kind of bind my net [00:03:00] particles pretty easily. And then on top of that you have to sort of use certain types of chemical conditions that are not so favorable. Maybe the Ph has to be a little bit high or chemicals that you don't want to use. And that's one of the reasons why the bacteria are so great. Right? Then as I said, they make an Organelle in this case to magnetism. So then within this tiny 50 nanometers sphere, they can just make what is otherwise a toxic condition inside of that and make this magnetic particle. But the cells are [00:03:30] growing in relatively harmless growth media at 30 degrees centigrade. So you can make magnetic particles under what are not toxic conditions because the bacteria are taking care of that inside of the cell. So that's one of the reasons people have been really fascinated by them. Speaker 4: So how can we take these sort of perfect crystals out of these bacteria and apply them to something else? The other aspect of it that's really important to recognize is that it's not just that the bacteria are randomly making magnetic particles. [00:04:00] They actually have a whole set of genes that they're used to build a magnetism and build the magnetic particle. So the ability to make a magnetic crystal is in coated in jeans, so you can not only extract the magnets out of these bacteria to use it for applications. Maybe you can extract the genes and put them into another organism and now give that other organism the capability to make magnetic nanoparticles. They're [00:04:30] magnetic properties, mixed them, really useful for many different kinds of applications. One of them, they can be potentially contrast agents for magnetic resonance imaging or MRI. When you get an MRI, does a lot of structures that are easily seen, but a lot of things are sort of invisible to the MRI and if you had a little magnetic particle in that region, you'd be able to see it better. One idea is can we put the genes as we learn more about them, can we sort of gather [00:05:00] up a minimum set of genes that are sort of sufficient to make a magnetism and a magnetic particle and then just put those into some other cell types and then see if that's enough to make a magnetic particle and that settle and they can we track it by MRI or something so that that's actually the focus of a grant that we recently got with a few other groups on campus. As a large collaborative grant, Speaker 4: how will you start to [00:05:30] prove that concept? I think we're taking many parallel approaches for it. You know, both to show the utility or the different ways that you would have to image them. One group is working on essentially technologies for imaging, magnetic nanoparticles and animals, and then we are sort of at the very other end of the spectrum and the collaboration, we're trying to say, we think we have a set of genes that are sufficient. This process, let's start taking baby steps [00:06:00] and move them to other types of cells, whether they're bacteria or other cells. And see if we can produce magnetic particles in those cells. Are other collaborators they're focusing more on, well, if we know these genes, can we start transferring them to mammalian cells and then in animal studies we could track cells using magnetic resonance imaging. Each group has focusing on a different aspect of the project. Speaker 4: Some of the other applications are really fascinating too. There's one where [00:06:30] particles hold their magnetic properties very stably and if you give a very strong magnetic field then you can kind of flip the dipole moment of the crystal. You can do this back and forth, keeps switching it, and if the pulse is switching faster than the dipole man can flip on the magnetic protocol. The difference in energies essentially released as heat. We can in that way heat the particle. There's a lot of anticancer treatments to try to essentially have the particles adhere to [00:07:00] a tumor and then heat the particles using this method. Just have the heat of the particles, kill the cells locally. There's been quite a few papers on it and some of these types of studies are in clinical trials to see how effective that could be for different kinds of tumors. Speaker 4: Yeah. Bacteria seems to get used that way. More and more to go into a tumor and linger just on the tumor and continue to just be very local in terms of very specific. And that's, you know, [00:07:30] local drug delivery or local attacking of tumor cells would be something that's very, this bacteria have this great access that other organisms don't have. If you can localize them and direct them. And that's sort of some, there's some other work which I think is also really interesting is to thinking about the magna detected bacteria as a vehicle for delivering drugs. You know, one of the things you can imagine is that you could guide them with a magnetic fields so you can have them guided to some [00:08:00] areas in the body by an external magnetic field. And there's definitely some people who are working on that. Can they move the bacteria through vasculature to a certain area because they can swim along magnetic field. Speaker 4: So if you want to localize it somewhere, you would have to instigate that field there. Yeah, exactly. To direct it. Right. The stuff I was telling you about with the heat treatment, I think all of that is trying to, right now at least because there's not much known about how to target the bacteria, they work with kinds of tumors that are accessible [00:08:30] so that you could inject the particles into the tumor directly directly to the tumor as opposed to try to do a systemic thing. Yeah, exactly. But you can imagine that maybe one benefit of the is is that they are surrounded by biological membrane and you can have proteins on them and people have done this pretty, you can display specific proteins on the surface of magnesiums, so then you could customize your, I need a zone to have affinity for certain types of proteins [00:09:00] or certain types of cells. Some proof of concept of that has been done for sure. Speaker 5: Mm MM. Speaker 3: Our guest on spectrum today, is it rush Molly, I cell biologist and associate professor at UC Berkeley. In the next segment. Dr Camelli speaks more about some of his collaborative. This is k a l x Berkeley. [00:09:30] [inaudible]. Speaker 4: The work you're doing with a sequencing is a lot of it. Trying to catalog everything. Keep track of what's, what sort of explain the sequencing side of what you're doing. The sequencing side, we are fortunate that the organism that we work with is in pure culture. Our lab rat essentially has been already sequenced by someone else. When we sequence, [00:10:00] it's more to make sure if we're going to put some gene fusion into the bacteria or that what we have is correct. Our sequencing is relatively limited. We are trying to branch out more and say nowadays technologies for sequencing the whole genome are much more accessible, affordable, certain types of genetics that we do where we try to delete genes or randomly mutate them. Then we can just start identify what's changed by going back and just sequencing the whole [00:10:30] genome or the bacteria. We are doing a little bit of that. Speaker 4: We do it on campus very accessible and affordable, but it's really something that was unthinkable even five, six years ago that you could do this on a large scale, do it affordably. And it could be a pretty routine tool in research. Sorry, I mean it's a really exciting, actually you're not gonna necessarily have to be restricted to these lab rats that do represent some of the general features of the process you're interested [00:11:00] in, but not the diversity of fitness necessarily. And so you can say, instead of studying just one organism, maybe I can study many other ones. There's still a lot that I can do with my model system in the law that I can't do with some of these other unconventional organisms, but they're at least visible to me. Their genes are visible to me and I don't have to isolate them away from everybody else to get an understanding of [00:11:30] what their genetic makeup is and where they are. Speaker 4: And for things like microbiome studies is revolutionize the whole field. They were, they were always just looking at such a small sliver of what they could isolate. Yeah. And now you can look at everything, you know, they can do lots of really interesting experiments like what's on your fingers, what's on your, you know, how's your right hand different from your left hand and microbial content. Yeah. You know, so that's really interesting. Yeah, it gets very refined. Is synthetic [00:12:00] biology involved in what you're doing in some way? Yeah, definitely. So what I was telling you about the applications, you know, essentially, I mean synthetic biology, I guess there's different ways of defining it. For me, you have inspiration from some biological system and now you're trying to extrapolate that and put it in a new context to do something new or something different than it normally does. Speaker 4: Though. What I was telling you about this, this project that we have on campus or does not support [00:12:30] it by the Keck foundation to put the magnetism genes into other organisms, but that's essentially synthetic biology. So yeah, we are really relying on that and trying to see if we're going to move these genes, how are they going to be more, how can we customize them so that they work better in the new organisms they go to? Can we add on things to them or take things away and doing this using synthetic biology essentially that it would fall under the category of synthetic biology. Sort started like mixing and matching genes and in [00:13:00] new contexts that you wouldn't have naturally. And what sort of safety protocols do you have to abide by in your research? For? For our research, we are working with something that's non-pathogenic that's quite harmless. Speaker 4: We follow the, the university has pretty strict guidelines for even for nonpathogenic organisms. Anytime you're working with recombinant DNA, even those things I was telling you where we are making a fluorescent protein fusion, we really [00:13:30] have to be careful about how we get rid of things and you know, don't just dump it down the drain. Safety-Wise. We don't really use anything harmful in the lab. I think maybe you're getting more into like what do you do with the hybrid organisms somehow and there we have to be, you know, we're always careful about how we dispose of materials. Eat cultures are always killed by bleach or heating before we dispose of it. You know, often people [00:14:00] say imagination runs wild with them. Right. You know? Yeah. And a lot of that has to do with fiction. Yeah. Books and movies and things. But I think it's important to sort of sort of what prompts me to ask. Speaker 4: And I think a lot of times maybe scientists think about that too late, you know, so, so maybe it may not be the first thing you say. That'd be the first thing you think about. And then it may also, it may not be in your training expertise or whatever to even know what would be dangerous. So I, I, [00:14:30] is that something that the university is helping with in the sense of certainly providing those kinds of resources to you so you don't have to be expert, right? We don't. Yeah, exactly. How can you be, and also you know, we have to comply with not just handling of biological organisms, but just how the lab functions. We have not only have to comply with university rules, but we have federal rules for worker safety, city rules that are different. So we have five or six different sort of safety protocols that we have to [00:15:00] abide by and we do get inspections once a year and I know people who work with animals, they have even more extensive things. I'd have to go through a whole separate set of protocols to just the sort of ethical treatment of the animals approved by independent boards and things like that. And the funding agencies have a lot of rules, so they give us money, but they expect us to follow certain types of rules. Speaker 2: [inaudible] [00:15:30] you're listening to spectrum on k a Alex Berkeley. Our guest is a Raj Chameleon. In the next segment he speaks about his work on outreach to the broader public [inaudible] [inaudible] [inaudible] Speaker 4: I noticed you've got a Twitter account. I do, yeah. And is that sort of part [00:16:00] of an outreach effort on your part to get the community involved or people interested in what you're doing? How do you view outreach going forward for your projects? Yeah, so the Twitter thing is you'd asked me that outreach are fun and I think it's both. It's not anonymous. You can be social, my name, you can find it. We have one for the lab also, which not very active at all by mine. A lot of people that I follow are other scientists. I think it is not known so well that there are many scientists on Twitter and there's great outreach [00:16:30] because often is a great way to share new findings and research or things that are exciting to people or having a discussion within the community, but this all accessible. Speaker 4: None of it is anonymous, so you can really see that. It's also fun obviously. For example, I encourage people to look out there. There's a lot of great science writers who take research findings and they in science blogs turn it into very accessible stories to understand the latest developments in research for [00:17:00] outreach. We try to do a lot of things. Members of my lab go out to, there's different events where scientists can interact with the community. I've done a few microbiology experiments with my son's classroom and you know, kindergarten, first, second grade. For me it's been really eye opening to do that because you see you all, sometimes you think what you're doing is so inaccessible on out there. But when you go and just talk to people you see that they can get really excited about, especially kids, [00:17:30] kids can get really excited about micro was, which is kind of funny because it's not something they can see and they really only heard about bad germs. Speaker 4: They've only heard about things that can hurt them and it's just great to go out there and talk about things that are good germs and on their bodies and everything. So we do a little experiment where we take the little auger played, which has the growth for the bacteria. They put their little fingerprints on it or they can see over the course of few days, bacteria grow on there. They washed her hands and they can see that that changes whether they can grow, [00:18:00] and I do the exact same experiment. I teach undergraduate microbiology lab here. You know, the questions that the undergrads ask are almost exactly the same questions that the third graders ask. So it's great to see that they have the insight and the excitement to learn about science. It just has to be, I think, encouraged and followed up more as they go through schooling. Speaker 4: I think another reason for us to go and do outreaches to just sort of, I get more excited about my work when I go and talk to other people and see that it's not so out there [00:18:30] and the university provides a lot of chances for us to do outreach to it. I mean, just recently we had cal day. There was lots of science on campus. Other blogs that you follow because you'd want to mention some colleagues at Berkeley have blogs, but I think people are more active through Twitter than they are through blogs. The scientific American blogs in general are pretty good. You mentioned the Keck Foundation that's brought together this collaboration that you're going to try to do the applied research on. Are there other collaborations [00:19:00] that you're trying to pursue? Yeah. You know our work, we rely on a lot of collaborations mainly because the bacteria do this really amazing thing of building these magnetic particles and we're always just like the example I told you about with the more high resolution electron microscopy where we were able to see something that we hadn't seen before. Speaker 4: There was a lot of people who were interested in imaging magnetic particles. They're developing instruments all the time that you would be able to look at these things in new ways and [00:19:30] we can't build the same instruments, but it ends up being a really great interaction all the time to find these groups that are developing technologies for imaging bacteria or imaging particles and then see how what we've learned can be applied to their technologies. One great collaboration we've had recently is with the walls worth group at Harvard and they have these, essentially there is a way you can treat diamonds so that there's certain defects on the surface of the diamonds and then you can detect magnetic [00:20:00] fields close to the surface of the diamond can actually essentially image these bacteria that we've worked with sitting on the surface of these diamonds because of their magnetic properties. Speaker 4: It's been great for us because working with them, hopefully we're able to fine tune some aspects of their technique to then study the magnetic particles and the magnetic chains in a different way than we had been so far and learn new things. Basically at any given point we might have seven or eight active collaboration's going on. [00:20:30] A lot of it on our part is not that difficult. We just provide a sample of the bacteria and then they work on it and if it goes somewhere then we go and get more involved in the collaboration. You start iterating with them. Yeah, exactly. This Keck collaboration was out of a brainstorming session. Went from there and we have another collaboration. Also synthetic biology that was just funded by the office of naval research and that's between two or three groups that are in different universities. We had always just talked here and there to each other and all of a sudden we realized that we could do something [00:21:00] together. Speaker 4: And that's how that came about. It's a huge part of science I think is even more now with funding situation and you have to really look for more creative ways of doing your science and your sense is that the funding environment is dwindling. Is that good? Yeah. Yeah. I think it was already bad and the sequester just sort of pushed it down even further. For example, you look at NIH, the amount of money is that increasing, which means it's not keeping up with inflation. So your purchasing power is much less and then all of [00:21:30] a sudden the sequester takes out a few percentages off of what was getting funded to you. So I think both the success rates for getting a grant and the amount of money that you get from that grant are lower. Even if you're lucky enough to be able to get the grant. What you could do with the money is less than before. Obviously, you know, I'm biased, but I don't think it's that great. You're essentially sacrificing the next generation of scientists, limiting [00:22:00] it, limiting it big time. Speaker 4: Was there anything that you wanted to mention? One thing I was going to say is that we've talked a lot about these bacteria, but obviously the visual is the easiest way to really appreciate what they do. And we have a, on my lab website, we have a page of videos where you can see how these bacteria migrate along magnetic fields and you can see images of them and you can see the structures within the solid with the magnesium. So clinic. So, so people go to [inaudible] [00:22:30] lab.org they can actually see videos of the bacteria. Great. Yeah, that'd be good. Yeah. Arash Kamali. Thanks very much for being on spectrum. Thank you so much. This was a lot of fun. Speaker 2: [inaudible]. You can follow Rajkot Maley on Twitter at micro magnet or you can watch them. Fantastic [00:23:00] sell videos on his website Oh Maley, that is k o n e I l I e lab.org and now a few of the science and technology events happening locally over the next few weeks and Rick chronicity joins me in presenting the calendarSpeaker 3: this Monday. The California Academy of Sciences will host a talk by Dr. John Jenkins, [00:23:30] senior research scientist at the Seti Institute. Dr. Jenkins will speak about NASA search for other habitable planets. In 2009 NASA launched the space cough known as Kepler into orbit in order to survey our own region of the Milky Way. Kepler's has been looking for planets that are similar in size and distance from a son to our owners. In those four years. The probe has collected data on over 190,000 stars and confirmed over 130 new planets. Dr. Jenkins [00:24:00] will discuss the exciting you dated that capital has provided as well as a few of the technical and scientific challenges that went into building a vessel at Kepler. He will also give a brief overview of tests. NASA's next mission to detect earth's closest cousins. This event will be held Monday, July 15th at 7:30 PM in the planetarium of the California Academy of Sciences. Go to cal academy.org to reserve a ticket in advance. Speaker 6: The theme for July is adult science, happy hour science, [00:24:30] neat. His brains, brains, grains, everything you've always wanted to know about your brain and more. There'll be talks in demos on memory, truth and tricks, neurobiology, human brains, a sheep brain dissection and illusions. Science neat takes place at the El Rio bar. Three one five eight mission street in San Francisco and mission for those 21 and over is $4 this month's [00:25:00] science need is on Tuesday, July 16th with doors at six and then talks at six 30 Speaker 3: every Sunday. This month the UC Berkeley Botanical Gardens will be hosting special be explained explainer lectures about the importance of wild bees in the care and maintenance of all gardens and especially in the native California Habitat. The botanical garden also features and amazing collection of plants from nearly every continent. Although there is a focus on plants that thrive in our Mediterranean climate. [00:25:30] The Asian, Californian and South American collections are currently blooming. The garden will be open from 9:00 AM to 5:00 PM most days. Although bee explainer tours are only offered from 11 to one 30 on Sundays, admission is $10 for adults and $8 for students. Speaker 6: On Saturday, July 20th at 11:00 AM Dr Steve Croft. We'll give the free public science at cal lecture on snacking gorgeous and cannibalizing the [00:26:00] feeding habits of black holes. Learn about the latest telescopes and how they are giving more information about how black holes grow and merge. Steve Leads the science at cal lecture series and as an assistant project astronomer working on large radio surveys and transient and variable astronomical sources. He helps commission the Allen Telescope Array for science operations and develop data analysis pipelines. He is an expert in the use of data at [00:26:30] a wide range of wavelengths from many different telescopes. The talk is@dwinellehallroomonefortyfivevisitscienceatcaldotberkeley.edu for more information and now Speaker 3: spectrum brings you some of our favorite stories in science and technology news. Rick Kaneski joins me again for the news science news summarized an article published on July 3rd in the proceedings of the royal society a about how surface [00:27:00] tension can lead to upstream contamination. Sebastian BN. Connie observed this when watching the preparation of Argentinian Montay t when hot water was poured from a pot into a container of leaves below some of the tea leaves float upward against the force of gravity and upstream of the water flow being Kinney and his colleagues from the University of Havana and from Rutgers showed through both experiments and simulations. [00:27:30] The particles can flow upstream several meters and up central meter high waterfalls because the downstream flow of clean water creates a gradient. What the container of t or other particles lowering the surface tension of the water, the particles are thus pulled into the clean water which has a greater surface tension. Speaker 3: The team also demonstrated that these results could have practical applications such as through the discharge of a standard pipette in other lab work [00:28:00] or in the simulated release of waste into larger scale channels. Indiana University scientist have transformed mouse embryonic stem cells into key structures of the inner ear. The discovery provides new insight into the sensory Oregon's developmental process and sets the stage for laboratory models of disease, drug discovery, and potential treatments for hearing loss and balance disorders. A research team led by ear. He has Chino Phd and Russi Holton. A professor [00:28:30] at the school of Medicine reported that by using a three dimensional cell culture method, they were able to Koch stem cells to develop into inner ear sensory epithelia containing hair cells, supporting cells and neurons that collectively detect sound had movement and gravity. The researchers reported online Wednesday in the journal Nature, Karl Kohler, the papers first author and a graduate student at the medical school said the three dimensional culture allows the cells to self [00:29:00] organize into complex tissues using mechanical cues that are found during embryonic development. Additional research is needed to determine how exactly inner ear cells involved in auditory sensing might develop as well as how these processes can be applied to develop human inner ear cells. Speaker 7: [inaudible] music heard during the shows witness produced by Alex. Thanks to Rick krones for contributing [00:29:30] to our news and calendar section and to Rene Rao for editing systems. Thank you for listening to spectrum. If you have comments about [inaudible] about Speaker 3: the show, please send them to us via email Speaker 1: or email address is spectrum. Doug k a l x@yahoo.com join us in two weeks at the same time. Hosted on Acast. See acast.com/privacy for more information.
Arash Komeili cell biologist, Assc. Prof. plant and microbial biology UC Berkeley. His research uses bacterial magnetosomes as a model system to study the molecular mechanisms governing the biogenesis and maintenance of bacterial organelles. Part 2.TranscriptSpeaker 1: Spectrum's next Speaker 2: [inaudible] [inaudible]. Speaker 1: [00:00:30] Welcome to spectrum the science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Hello and good afternoon. My name is Renee Rao. I'll be hosting today's show. Today we present part two of our interview with a Rosh Kamali. Dr [inaudible] is a cell biologist and associate [00:01:00] professor of plant and microbial biology at UC Berkeley. Previously on spectrum, he discussed his work with magneto tactic bacteria. Here's Dr Camilia explaining why these bacteria so interesting. Speaker 4: We work with a specific type of bacteria. They're called magneto is tactic bacteria and these are organisms that are quite widespread. You can find them in most aquatic environments by almost any sort of classification. You can really group them together if you [00:01:30] take their shape or if you look at even the genes they have, you can't really group them into one specific group as opposed to many other bacteria that you can do that, but unites them together as a group is that they're able to orient in magnetic fields. And some along magnetic fields Speaker 3: today. In part two of his interview, Dr [inaudible] explains how these discoveries might be applied and discusses the scientific outreach he does in our community. Here is Brad swift interviewing a Kamali, Speaker 4: [00:02:00] so how is it that you're trying to leverage what you're learning about the magnetic zone? You're trying to apply it in any way. Are you still really in the pure research mode? I think we're starting to move out or at least branch out to try to do some applications as well. This has been a really, one of the areas of research that's been the most active, or at least the most thought about for Magna [inaudible] bacteria for the last 40 years or so of that people have been working on it. You have two [00:02:30] features of the magnesiums that immediately can be thought of as being very useful for applications, but one is that they're making something that's nanometers size. Very small is magnetic and it has very, very irregular dimensions, quite free of impurities. So you can make magnetic particles in the lab and people have gotten very good at it actually, but it's often very hard to control some of their features. Speaker 4: Maybe contaminants can kind of bind my net [00:03:00] particles pretty easily. And then on top of that you have to sort of use certain types of chemical conditions that are not so favorable. Maybe the Ph has to be a little bit high or chemicals that you don't want to use. And that's one of the reasons why the bacteria are so great. Right? Then as I said, they make an Organelle in this case to magnetism. So then within this tiny 50 nanometers sphere, they can just make what is otherwise a toxic condition inside of that and make this magnetic particle. But the cells are [00:03:30] growing in relatively harmless growth media at 30 degrees centigrade. So you can make magnetic particles under what are not toxic conditions because the bacteria are taking care of that inside of the cell. So that's one of the reasons people have been really fascinated by them. Speaker 4: So how can we take these sort of perfect crystals out of these bacteria and apply them to something else? The other aspect of it that's really important to recognize is that it's not just that the bacteria are randomly making magnetic particles. [00:04:00] They actually have a whole set of genes that they're used to build a magnetism and build the magnetic particle. So the ability to make a magnetic crystal is in coated in jeans, so you can not only extract the magnets out of these bacteria to use it for applications. Maybe you can extract the genes and put them into another organism and now give that other organism the capability to make magnetic nanoparticles. They're [00:04:30] magnetic properties, mixed them, really useful for many different kinds of applications. One of them, they can be potentially contrast agents for magnetic resonance imaging or MRI. When you get an MRI, does a lot of structures that are easily seen, but a lot of things are sort of invisible to the MRI and if you had a little magnetic particle in that region, you'd be able to see it better. One idea is can we put the genes as we learn more about them, can we sort of gather [00:05:00] up a minimum set of genes that are sort of sufficient to make a magnetism and a magnetic particle and then just put those into some other cell types and then see if that's enough to make a magnetic particle and that settle and they can we track it by MRI or something so that that's actually the focus of a grant that we recently got with a few other groups on campus. As a large collaborative grant, Speaker 4: how will you start to [00:05:30] prove that concept? I think we're taking many parallel approaches for it. You know, both to show the utility or the different ways that you would have to image them. One group is working on essentially technologies for imaging, magnetic nanoparticles and animals, and then we are sort of at the very other end of the spectrum and the collaboration, we're trying to say, we think we have a set of genes that are sufficient. This process, let's start taking baby steps [00:06:00] and move them to other types of cells, whether they're bacteria or other cells. And see if we can produce magnetic particles in those cells. Are other collaborators they're focusing more on, well, if we know these genes, can we start transferring them to mammalian cells and then in animal studies we could track cells using magnetic resonance imaging. Each group has focusing on a different aspect of the project. Speaker 4: Some of the other applications are really fascinating too. There's one where [00:06:30] particles hold their magnetic properties very stably and if you give a very strong magnetic field then you can kind of flip the dipole moment of the crystal. You can do this back and forth, keeps switching it, and if the pulse is switching faster than the dipole man can flip on the magnetic protocol. The difference in energies essentially released as heat. We can in that way heat the particle. There's a lot of anticancer treatments to try to essentially have the particles adhere to [00:07:00] a tumor and then heat the particles using this method. Just have the heat of the particles, kill the cells locally. There's been quite a few papers on it and some of these types of studies are in clinical trials to see how effective that could be for different kinds of tumors. Speaker 4: Yeah. Bacteria seems to get used that way. More and more to go into a tumor and linger just on the tumor and continue to just be very local in terms of very specific. And that's, you know, [00:07:30] local drug delivery or local attacking of tumor cells would be something that's very, this bacteria have this great access that other organisms don't have. If you can localize them and direct them. And that's sort of some, there's some other work which I think is also really interesting is to thinking about the magna detected bacteria as a vehicle for delivering drugs. You know, one of the things you can imagine is that you could guide them with a magnetic fields so you can have them guided to some [00:08:00] areas in the body by an external magnetic field. And there's definitely some people who are working on that. Can they move the bacteria through vasculature to a certain area because they can swim along magnetic field. Speaker 4: So if you want to localize it somewhere, you would have to instigate that field there. Yeah, exactly. To direct it. Right. The stuff I was telling you about with the heat treatment, I think all of that is trying to, right now at least because there's not much known about how to target the bacteria, they work with kinds of tumors that are accessible [00:08:30] so that you could inject the particles into the tumor directly directly to the tumor as opposed to try to do a systemic thing. Yeah, exactly. But you can imagine that maybe one benefit of the is is that they are surrounded by biological membrane and you can have proteins on them and people have done this pretty, you can display specific proteins on the surface of magnesiums, so then you could customize your, I need a zone to have affinity for certain types of proteins [00:09:00] or certain types of cells. Some proof of concept of that has been done for sure. Speaker 5: Mm MM. Speaker 3: Our guest on spectrum today, is it rush Molly, I cell biologist and associate professor at UC Berkeley. In the next segment. Dr Camelli speaks more about some of his collaborative. This is k a l x Berkeley. [00:09:30] [inaudible]. Speaker 4: The work you're doing with a sequencing is a lot of it. Trying to catalog everything. Keep track of what's, what sort of explain the sequencing side of what you're doing. The sequencing side, we are fortunate that the organism that we work with is in pure culture. Our lab rat essentially has been already sequenced by someone else. When we sequence, [00:10:00] it's more to make sure if we're going to put some gene fusion into the bacteria or that what we have is correct. Our sequencing is relatively limited. We are trying to branch out more and say nowadays technologies for sequencing the whole genome are much more accessible, affordable, certain types of genetics that we do where we try to delete genes or randomly mutate them. Then we can just start identify what's changed by going back and just sequencing the whole [00:10:30] genome or the bacteria. We are doing a little bit of that. Speaker 4: We do it on campus very accessible and affordable, but it's really something that was unthinkable even five, six years ago that you could do this on a large scale, do it affordably. And it could be a pretty routine tool in research. Sorry, I mean it's a really exciting, actually you're not gonna necessarily have to be restricted to these lab rats that do represent some of the general features of the process you're interested [00:11:00] in, but not the diversity of fitness necessarily. And so you can say, instead of studying just one organism, maybe I can study many other ones. There's still a lot that I can do with my model system in the law that I can't do with some of these other unconventional organisms, but they're at least visible to me. Their genes are visible to me and I don't have to isolate them away from everybody else to get an understanding of [00:11:30] what their genetic makeup is and where they are. Speaker 4: And for things like microbiome studies is revolutionize the whole field. They were, they were always just looking at such a small sliver of what they could isolate. Yeah. And now you can look at everything, you know, they can do lots of really interesting experiments like what's on your fingers, what's on your, you know, how's your right hand different from your left hand and microbial content. Yeah. You know, so that's really interesting. Yeah, it gets very refined. Is synthetic [00:12:00] biology involved in what you're doing in some way? Yeah, definitely. So what I was telling you about the applications, you know, essentially, I mean synthetic biology, I guess there's different ways of defining it. For me, you have inspiration from some biological system and now you're trying to extrapolate that and put it in a new context to do something new or something different than it normally does. Speaker 4: Though. What I was telling you about this, this project that we have on campus or does not support [00:12:30] it by the Keck foundation to put the magnetism genes into other organisms, but that's essentially synthetic biology. So yeah, we are really relying on that and trying to see if we're going to move these genes, how are they going to be more, how can we customize them so that they work better in the new organisms they go to? Can we add on things to them or take things away and doing this using synthetic biology essentially that it would fall under the category of synthetic biology. Sort started like mixing and matching genes and in [00:13:00] new contexts that you wouldn't have naturally. And what sort of safety protocols do you have to abide by in your research? For? For our research, we are working with something that's non-pathogenic that's quite harmless. Speaker 4: We follow the, the university has pretty strict guidelines for even for nonpathogenic organisms. Anytime you're working with recombinant DNA, even those things I was telling you where we are making a fluorescent protein fusion, we really [00:13:30] have to be careful about how we get rid of things and you know, don't just dump it down the drain. Safety-Wise. We don't really use anything harmful in the lab. I think maybe you're getting more into like what do you do with the hybrid organisms somehow and there we have to be, you know, we're always careful about how we dispose of materials. Eat cultures are always killed by bleach or heating before we dispose of it. You know, often people [00:14:00] say imagination runs wild with them. Right. You know? Yeah. And a lot of that has to do with fiction. Yeah. Books and movies and things. But I think it's important to sort of sort of what prompts me to ask. Speaker 4: And I think a lot of times maybe scientists think about that too late, you know, so, so maybe it may not be the first thing you say. That'd be the first thing you think about. And then it may also, it may not be in your training expertise or whatever to even know what would be dangerous. So I, I, [00:14:30] is that something that the university is helping with in the sense of certainly providing those kinds of resources to you so you don't have to be expert, right? We don't. Yeah, exactly. How can you be, and also you know, we have to comply with not just handling of biological organisms, but just how the lab functions. We have not only have to comply with university rules, but we have federal rules for worker safety, city rules that are different. So we have five or six different sort of safety protocols that we have to [00:15:00] abide by and we do get inspections once a year and I know people who work with animals, they have even more extensive things. I'd have to go through a whole separate set of protocols to just the sort of ethical treatment of the animals approved by independent boards and things like that. And the funding agencies have a lot of rules, so they give us money, but they expect us to follow certain types of rules. Speaker 2: [inaudible] [00:15:30] you're listening to spectrum on k a Alex Berkeley. Our guest is a Raj Chameleon. In the next segment he speaks about his work on outreach to the broader public [inaudible] [inaudible] [inaudible] Speaker 4: I noticed you've got a Twitter account. I do, yeah. And is that sort of part [00:16:00] of an outreach effort on your part to get the community involved or people interested in what you're doing? How do you view outreach going forward for your projects? Yeah, so the Twitter thing is you'd asked me that outreach are fun and I think it's both. It's not anonymous. You can be social, my name, you can find it. We have one for the lab also, which not very active at all by mine. A lot of people that I follow are other scientists. I think it is not known so well that there are many scientists on Twitter and there's great outreach [00:16:30] because often is a great way to share new findings and research or things that are exciting to people or having a discussion within the community, but this all accessible. Speaker 4: None of it is anonymous, so you can really see that. It's also fun obviously. For example, I encourage people to look out there. There's a lot of great science writers who take research findings and they in science blogs turn it into very accessible stories to understand the latest developments in research for [00:17:00] outreach. We try to do a lot of things. Members of my lab go out to, there's different events where scientists can interact with the community. I've done a few microbiology experiments with my son's classroom and you know, kindergarten, first, second grade. For me it's been really eye opening to do that because you see you all, sometimes you think what you're doing is so inaccessible on out there. But when you go and just talk to people you see that they can get really excited about, especially kids, [00:17:30] kids can get really excited about micro was, which is kind of funny because it's not something they can see and they really only heard about bad germs. Speaker 4: They've only heard about things that can hurt them and it's just great to go out there and talk about things that are good germs and on their bodies and everything. So we do a little experiment where we take the little auger played, which has the growth for the bacteria. They put their little fingerprints on it or they can see over the course of few days, bacteria grow on there. They washed her hands and they can see that that changes whether they can grow, [00:18:00] and I do the exact same experiment. I teach undergraduate microbiology lab here. You know, the questions that the undergrads ask are almost exactly the same questions that the third graders ask. So it's great to see that they have the insight and the excitement to learn about science. It just has to be, I think, encouraged and followed up more as they go through schooling. Speaker 4: I think another reason for us to go and do outreaches to just sort of, I get more excited about my work when I go and talk to other people and see that it's not so out there [00:18:30] and the university provides a lot of chances for us to do outreach to it. I mean, just recently we had cal day. There was lots of science on campus. Other blogs that you follow because you'd want to mention some colleagues at Berkeley have blogs, but I think people are more active through Twitter than they are through blogs. The scientific American blogs in general are pretty good. You mentioned the Keck Foundation that's brought together this collaboration that you're going to try to do the applied research on. Are there other collaborations [00:19:00] that you're trying to pursue? Yeah. You know our work, we rely on a lot of collaborations mainly because the bacteria do this really amazing thing of building these magnetic particles and we're always just like the example I told you about with the more high resolution electron microscopy where we were able to see something that we hadn't seen before. Speaker 4: There was a lot of people who were interested in imaging magnetic particles. They're developing instruments all the time that you would be able to look at these things in new ways and [00:19:30] we can't build the same instruments, but it ends up being a really great interaction all the time to find these groups that are developing technologies for imaging bacteria or imaging particles and then see how what we've learned can be applied to their technologies. One great collaboration we've had recently is with the walls worth group at Harvard and they have these, essentially there is a way you can treat diamonds so that there's certain defects on the surface of the diamonds and then you can detect magnetic [00:20:00] fields close to the surface of the diamond can actually essentially image these bacteria that we've worked with sitting on the surface of these diamonds because of their magnetic properties. Speaker 4: It's been great for us because working with them, hopefully we're able to fine tune some aspects of their technique to then study the magnetic particles and the magnetic chains in a different way than we had been so far and learn new things. Basically at any given point we might have seven or eight active collaboration's going on. [00:20:30] A lot of it on our part is not that difficult. We just provide a sample of the bacteria and then they work on it and if it goes somewhere then we go and get more involved in the collaboration. You start iterating with them. Yeah, exactly. This Keck collaboration was out of a brainstorming session. Went from there and we have another collaboration. Also synthetic biology that was just funded by the office of naval research and that's between two or three groups that are in different universities. We had always just talked here and there to each other and all of a sudden we realized that we could do something [00:21:00] together. Speaker 4: And that's how that came about. It's a huge part of science I think is even more now with funding situation and you have to really look for more creative ways of doing your science and your sense is that the funding environment is dwindling. Is that good? Yeah. Yeah. I think it was already bad and the sequester just sort of pushed it down even further. For example, you look at NIH, the amount of money is that increasing, which means it's not keeping up with inflation. So your purchasing power is much less and then all of [00:21:30] a sudden the sequester takes out a few percentages off of what was getting funded to you. So I think both the success rates for getting a grant and the amount of money that you get from that grant are lower. Even if you're lucky enough to be able to get the grant. What you could do with the money is less than before. Obviously, you know, I'm biased, but I don't think it's that great. You're essentially sacrificing the next generation of scientists, limiting [00:22:00] it, limiting it big time. Speaker 4: Was there anything that you wanted to mention? One thing I was going to say is that we've talked a lot about these bacteria, but obviously the visual is the easiest way to really appreciate what they do. And we have a, on my lab website, we have a page of videos where you can see how these bacteria migrate along magnetic fields and you can see images of them and you can see the structures within the solid with the magnesium. So clinic. So, so people go to [inaudible] [00:22:30] lab.org they can actually see videos of the bacteria. Great. Yeah, that'd be good. Yeah. Arash Kamali. Thanks very much for being on spectrum. Thank you so much. This was a lot of fun. Speaker 2: [inaudible]. You can follow Rajkot Maley on Twitter at micro magnet or you can watch them. Fantastic [00:23:00] sell videos on his website Oh Maley, that is k o n e I l I e lab.org and now a few of the science and technology events happening locally over the next few weeks and Rick chronicity joins me in presenting the calendarSpeaker 3: this Monday. The California Academy of Sciences will host a talk by Dr. John Jenkins, [00:23:30] senior research scientist at the Seti Institute. Dr. Jenkins will speak about NASA search for other habitable planets. In 2009 NASA launched the space cough known as Kepler into orbit in order to survey our own region of the Milky Way. Kepler's has been looking for planets that are similar in size and distance from a son to our owners. In those four years. The probe has collected data on over 190,000 stars and confirmed over 130 new planets. Dr. Jenkins [00:24:00] will discuss the exciting you dated that capital has provided as well as a few of the technical and scientific challenges that went into building a vessel at Kepler. He will also give a brief overview of tests. NASA's next mission to detect earth's closest cousins. This event will be held Monday, July 15th at 7:30 PM in the planetarium of the California Academy of Sciences. Go to cal academy.org to reserve a ticket in advance. Speaker 6: The theme for July is adult science, happy hour science, [00:24:30] neat. His brains, brains, grains, everything you've always wanted to know about your brain and more. There'll be talks in demos on memory, truth and tricks, neurobiology, human brains, a sheep brain dissection and illusions. Science neat takes place at the El Rio bar. Three one five eight mission street in San Francisco and mission for those 21 and over is $4 this month's [00:25:00] science need is on Tuesday, July 16th with doors at six and then talks at six 30 Speaker 3: every Sunday. This month the UC Berkeley Botanical Gardens will be hosting special be explained explainer lectures about the importance of wild bees in the care and maintenance of all gardens and especially in the native California Habitat. The botanical garden also features and amazing collection of plants from nearly every continent. Although there is a focus on plants that thrive in our Mediterranean climate. [00:25:30] The Asian, Californian and South American collections are currently blooming. The garden will be open from 9:00 AM to 5:00 PM most days. Although bee explainer tours are only offered from 11 to one 30 on Sundays, admission is $10 for adults and $8 for students. Speaker 6: On Saturday, July 20th at 11:00 AM Dr Steve Croft. We'll give the free public science at cal lecture on snacking gorgeous and cannibalizing the [00:26:00] feeding habits of black holes. Learn about the latest telescopes and how they are giving more information about how black holes grow and merge. Steve Leads the science at cal lecture series and as an assistant project astronomer working on large radio surveys and transient and variable astronomical sources. He helps commission the Allen Telescope Array for science operations and develop data analysis pipelines. He is an expert in the use of data at [00:26:30] a wide range of wavelengths from many different telescopes. The talk is@dwinellehallroomonefortyfivevisitscienceatcaldotberkeley.edu for more information and now Speaker 3: spectrum brings you some of our favorite stories in science and technology news. Rick Kaneski joins me again for the news science news summarized an article published on July 3rd in the proceedings of the royal society a about how surface [00:27:00] tension can lead to upstream contamination. Sebastian BN. Connie observed this when watching the preparation of Argentinian Montay t when hot water was poured from a pot into a container of leaves below some of the tea leaves float upward against the force of gravity and upstream of the water flow being Kinney and his colleagues from the University of Havana and from Rutgers showed through both experiments and simulations. [00:27:30] The particles can flow upstream several meters and up central meter high waterfalls because the downstream flow of clean water creates a gradient. What the container of t or other particles lowering the surface tension of the water, the particles are thus pulled into the clean water which has a greater surface tension. Speaker 3: The team also demonstrated that these results could have practical applications such as through the discharge of a standard pipette in other lab work [00:28:00] or in the simulated release of waste into larger scale channels. Indiana University scientist have transformed mouse embryonic stem cells into key structures of the inner ear. The discovery provides new insight into the sensory Oregon's developmental process and sets the stage for laboratory models of disease, drug discovery, and potential treatments for hearing loss and balance disorders. A research team led by ear. He has Chino Phd and Russi Holton. A professor [00:28:30] at the school of Medicine reported that by using a three dimensional cell culture method, they were able to Koch stem cells to develop into inner ear sensory epithelia containing hair cells, supporting cells and neurons that collectively detect sound had movement and gravity. The researchers reported online Wednesday in the journal Nature, Karl Kohler, the papers first author and a graduate student at the medical school said the three dimensional culture allows the cells to self [00:29:00] organize into complex tissues using mechanical cues that are found during embryonic development. Additional research is needed to determine how exactly inner ear cells involved in auditory sensing might develop as well as how these processes can be applied to develop human inner ear cells. Speaker 7: [inaudible] music heard during the shows witness produced by Alex. Thanks to Rick krones for contributing [00:29:30] to our news and calendar section and to Rene Rao for editing systems. Thank you for listening to spectrum. If you have comments about [inaudible] about Speaker 3: the show, please send them to us via email Speaker 1: or email address is spectrum. Doug k a l x@yahoo.com join us in two weeks at the same time. See acast.com/privacy for privacy and opt-out information.
Arash Komeili cell biologist, Assc. Prof. plant and microbial biology UC Berkeley. His research uses bacterial magnetosomes as a model system to study the molecular mechanisms governing the biogenesis and maintenance of bacterial organelles. Part1TranscriptSpeaker 1: Spectrum's next. Speaker 2: Okay. Speaker 3: [inaudible] [inaudible]. Speaker 1: [00:00:30] Welcome to spectrum the science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews, featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 4: Hi, and good afternoon. My name is Brad Swift. I'm the host of today's show. We are doing another two part interview on spectrum. Our guest is Arash Kamali, [00:01:00] a cell biologist and associate professor of plant and microbial biology at cal Berkeley. His research uses bacterial magneta zones as a model system to study the molecular mechanisms governing the biogenesis and maintenance of bacterial organelles. Today. In part one, Arash walks us through what he is researching and how he was drawn to it in part two, which will air in two weeks. [00:01:30] He explains how these discoveries might be applied and he discusses the scientific outreach he does. Here's part one, a rush. Camelli. Welcome to spectrum. Thank you. I wanted to lay the groundwork a little bit. You're studying bacteria and why did you choose bacteria and not some other micro organism to study? One Speaker 5: practical motivation was that they're easier to study. They're easier to grow in [00:02:00] the lab. You can have large numbers of them. If you're interested in a specific process, you have the opportunity to go deep and try to really understand maybe all the different components that are involved in that process, but it wasn't necessarily a deliberate choice is just as I worked with them it became more and more fascinating and then I wanted to pursue it further. Speaker 4: And then the focus of your research on the bacteria, can you explain that? Speaker 5: Yeah, so we work with [00:02:30] a specific type of bacteria. They're called magnate as hectic bacteria and these are organisms that are quite widespread. You can find them in most aquatic environments by almost any sort of classification. You can really group them together if you take their shape or if you look at even the genes they have, the general genes they have, you can really group them into one specific group as opposed to many other bacteria that you can do that. But Unites Together as a group [00:03:00] is that they're, they're able to orient in magnetic fields and some along magnetic fields. This behavior was discovered quite by accident a couple of times independently. Somebody was looking under a microscope and they noticed that there were bacteria were swimming all in the same direction and they couldn't figure out why. They thought maybe the light from the window was attracting them or some other type of stimuli and they tried everything and they couldn't really figure out why the bacteria were swimming in one direction except they noticed that [00:03:30] regardless of where they were in the lab, they were always swimming in the same geographic direction and so they thought, well, the only thing we can think of that would attract them to the same position is the magnetic field, and they were able to show that sure enough, if you bring a magnet next to the microscope, you can change the swimming direction. Speaker 5: This type of behavior is mediated by a very special structure that the bacteria build inside of their cell, and this was sort of [00:04:00] what attracted me to it. Can you differentiate them? The UK erotic? Yeah. Then the bacterial, can you differentiate those two for us so that we kind of get a sense of is there, they're easy, different differentiate, you know the generally speaking you out excels, enclose their genetic material in an organelle called the nucleus. They're generally much bigger. They have a lot more genetic information associated with them and they have a ton of different kinds of organelles that perform [00:04:30] functions. All these Organelles to fall the proteins to break them down. They have organelles for generating energy, but all those little specific features, you know, you can find some bacterium that has organelles or you can find some bacterial solid that's really huge. Or you can find some bacteria so that encloses its DNA and an organelle. Speaker 5: It's just that you had accels have all of them together. Many of the living organisms that you encounter everyday because you can see them [00:05:00] very easily. Are you carry out, almost all of them are plants and fungi and animals. They're all made up of you. Charismatic cells. It's just that there's this whole unseen world of bacteria and what function does that capability serve, that magnetic functions that it can be realized that yet in many places on earth, the magnetic field will act as a guide through these changes in oxygen levels, sort of like a straight line through these. These [00:05:30] bacteria are stuck in these sort of magnetic field highways. It's thought to be a simpler method for finding the appropriate oxygen levels and simpler in this case means that they have to swim less as swimming takes energy. So the advantage is that they use less energy, get to the same place, that bacteria and that doesn't have the same capabilities relatively speaking, as a simple explanation, it's actually, because it is so simple, the model, you can kind of replicate [00:06:00] it in the lab a little bit. Speaker 5: If you set up a little tube that has the oxygen grading and then the bacteria will go to a certain place and you can actually see that they're sort of a band of bacteria at what they consider for them to be appropriate oxygen levels. And then if you inject some oxygen at the other end of the tube, the bacteria will swim away from this oxygen gradient. Now, if you give them a magnetic field that they can swim along, they can move away from this advancing oxygen threat much more quickly than [00:06:30] bacteria that can't navigate along magnetic fields. So that's sort of a proof of concept a little bit in the lab. There's a lot of reasons why it also doesn't make sense. For example, some of these bacteria make so many of these magnetic structures that we haven't talked about yet, but they make so many of these particles way more than they would ever need to orient in the magnetic field. Speaker 5: So it seems excessive. There are other bacteria that live in places on earth where there is not really this kind of a magnetic field guide. And in those environments there's [00:07:00] plenty of other bacteria that don't have these magneto tactic capabilities and they still can find that specific oxygen zone very easily. So in some ways I think it is an open question but there isn't really enough yet to refute the kind of the generally accepted model on the movement part of it. You were mentioning that they use magnetic field to move backwards and forwards. Only explain the limiting factor. Yeah, that's [00:07:30] an important point actually because it's not that they use the magnetic field for sensing in a way. It's not that they are getting pulled or pushed by the magnetic field. They are sort of passively aligned and the magnetic field sort of like if you have two bar magnets and if one of them is perpendicular to the other one and you bring the other one closer, I'll just move until they're parallel to each other. Speaker 5: This is the same thing. The bacteria have essentially a bar magnet and inside of the cell and so the alignment to the magnetic field [00:08:00] is passive that you can kill the bacteria and they'll still align with the magnetic field. The swimming takes advantage of structures and and machines that are found in all bacteria essentially. So they have flagella that they can use to swim back and forth as you mentioned. And they have a whole bunch of other different kinds of systems for sensing the amount of oxygen or other materials that they're interested in to figure out, should I keep swimming or should I stop swimming? And [00:08:30] as I mentioned earlier, the bacteria are quite diverse. So when you look at different magnatech active bacteria, the types of flagella they have are also different from each other. So it's not one universal mechanism for the swimming, it's just the idea that that the swimming is limited by these magnetic field lines. Speaker 6: [inaudible] [inaudible]. Speaker 5: Our guest today on spectrum is [inaudible] Chameleon, a cell biologist Speaker 7: and associate professor at cal Berkeley. In our next segment, [00:09:00] Arash talks about what attracted him to study the magnetism and why it remains in some bacteria and not others. This is k a l x Berkeley. So Speaker 5: let's talk about the magnetic zone, right? This is sort of my fascination. I was a graduate student at UCF and I studied cell biology. I use the yeast, which are not bacteria but in many ways they are kind of like bacteria. They're much simpler to study than maybe other do care attic [00:09:30] organisms and we have genetics available and so I was very fascinated by east, but I was studying a problem with XL organization and communication within the cell and yeast. We were taught sort of as students in cell biology at the time, that cell organization and having compartments in the cell organelles basically that do different functions was very unique feature of you carry attic cells and there's one of the things I've defined them. I received my phd to do a postdoctoral fellowship. I happen to be [00:10:00] in interviewing at cal tech and professor Mel Simon there he was talking about all kinds of bacteria that he was interested in and he said there's these bacteria that have organelles and I just, it kind of blew my mind because we were told explicitly that that's not true and in many textbooks, even today it still says that bacteria don't have organelles. Speaker 5: I learned more about men and I learned that these magnatech to bacteria that we've been talking about so far, you can actually build a structure inside of the cell, out of their cell membrane and within [00:10:30] this membrane compartment, it's essentially a little factory for making magnetic particles so they can build crystals of mineral called magnetite, which is just an iron oxide. Every three or four and some organisms make a different kind of magnetic minerals called Greg [inaudible], which is an iron sulfur mineral, but these are perfect little crystals, about 50 nanometers in diameter, and they make a chain of these magnesiums, so these membrane enclosed magnetic particles. [00:11:00] This chain is sort of on one side of the cell and it allows the bacteria to orient and magnetic fields because each of those crystals has this magnetic dipole moment in the same direction and all those little dipole moments interact with each other to make a little bar magnet, a little compass needle essentially that forces the bacterium to Orient in the magnetic field. Speaker 5: When I heard about this, I realized that this is just incredibly fascinating. Nobody really knew how it was that the membrane compartment forum [00:11:30] or even if it formed first and the mineral formed inside of it. There wasn't much or anything known about the proteins that were involved in building the compartment and then making the magnetic particle. It just seemed like something that needed to be studied and it was fascinating to me and I've been working on it for 1213 years now. Have we covered what the of the magnetic is that idea behind the function of the magnetism, which is the [00:12:00] structures of the cells build to allow them to align with a magnetic field. We think that function is to simplify the search for low oxygen environments. That's the main model in our field and I think there are definitely some groups that are actively working on understanding that aspect of the behavior better. Speaker 5: How it is that the bacteria can find a certain oxygen concentration. These bacteria in particular, what are the mechanics of them swimming along [00:12:30] the magnetic field and the, is there some other explanation for why they do this? For example, if they are changing orientations into magnetic field, can they sense the strain that the magnetic field is putting onto the cell? Can that be sensed somehow and then used for some work down the line and there are groups that are actively pursuing those kinds of ideas. You were mentioning that this is a particular kind of bacteria that has this capability, right, and others don't. Right. Yet both seem to be equally [00:13:00] effective and populating the water areas that you're studying. No apparent advantage. Disadvantage, so winning in Canada? Yeah, I mean it's a lot of the Darwinian, you could say as long as it's not severely disadvantageous, then maybe they wouldn't be a push for it to be lost. Speaker 5: What is kind of intriguing a little bit is there's examples of magna detective bacteria in many different groups, phylogenetic groups, so many different types of species that will be, let's [00:13:30] say bacterium that normally just lives free in the ocean and then I'll have a relative that's very similar to it, but it's also a magnet, a tactic. In recent years, people have studied this a little bit more and we know now what are the specific set of genes that allow bacteria to become magnetic tactic. So you can look at those genes specifically and say, how is it that bacteria that are otherwise so different from each other can all perform the same function? And if you know the genes that build the structures that allow them to orient [00:14:00] the magnetic fields, you can look at how different those genes are from each other or has similar they are. Speaker 5: And normally with a lot of these types of behaviors in bacteria, there's something called horizontal gene transfer that explains how it is that otherwise similar bacteria can have different functionalities. For example, you can think of that as bacteria being cars and everybody has sort of the same standard set of know features on the car. But you can add on different features if you want to. So you can upgrade and have other kinds of features like leather [00:14:30] seats or regular seats. And so the two cars that have different kinds of seats are very similar to each other. It's just one that got the leather seats. And so these partly are thought to occur by bacteria exchanging genes with each other. Somebody who wasn't magna tactic maybe got these jeans from another organism, but when people look at the genes that make these mag Nita zones, these magnetic structures inside of the cell, what you see is that they appear to be very, very ancient. Speaker 5: So it doesn't seem like there was a lot of recent [00:15:00] exchange of genes between these various groups of bacteria to make them magna tactic. And it almost seems to map to the ancestral divergence of all of these bacteria from each other. One big idea is that the last common ancestor of all these organisms was mag new tactic and that many, many other bacteria have sort of lost this capability over what would be almost 2 billion years of evolution for these bacteria. And then some have retained it. [00:15:30] Those of that have retained it is it's still serving an advantage for them, or is it just sort of Vista GL and they have it and they're sort of stuck in magnetic fields and they have to deal with it? No, but nobody really knows. Actually. The other option is that there was a period of horizontal gene transfer, but it was a very long time ago so that the signature is sort of lost from, again, a couple of billion years of evolution or divergence from each other, but it really looks like whenever this process happened, it was quite anxious. Speaker 3: [00:16:00] You are listening to spectrum on KALX Berkeley. Our guest is Arash [inaudible]. In the next segment, rush talks about organelles in bacterial cells. Speaker 5: [00:16:30] Explain what the Organelle is, so there's a lot of functions within the cell that need to be enclosed in a compartment for various reasons. You can have a biochemical reaction that's not very efficient, but if you put it in within a compartment and concentrates, all of the components that carry that reaction, it can be carried out more efficiently. The other thing is that for some reactions to to happen, you need a chemical environment that's different than the rest of the cellular environment. You can't convert [00:17:00] the whole environment of the cell to that one condition. So by compartmentalizing it you able to carry it out and often the products of these reactions can be toxic to the rest of the cell. And so by componentizing again you can keep the toxic conditions away from the rest of the, so these are the different reasons why you care how to excels. Speaker 5: Like the cells in our body have organelles that do different things like how proteins fold or modify proteins break him down and in bacterial cells it [00:17:30] was thought that they're so simple and so small that they don't really have a need for compartments. Although for many years people have had examples of bacteria that do form compartments. You carrot axles are big and Organelles are really easy to see where the light microscope so you can easily see that the cell has compartments within it. Whereas a lot of bacteria are well studied, are quite simple, they don't have much visible structure within them. And that's maybe even further the bias that there is some divide and this [00:18:00] allowed you carry out access to become more complex, quote unquote, and then it just doesn't exist in bacteria. How is it that they then were revealed? I think they'd been revealed for a long time. Speaker 5: You know, for example, there's electron microscope images from 40 years ago or more where you see for example, photosynthetic bacteria, these are bacteria that can do photosynthesis. They have extensive membrane structures inside of the cell that how's the proteins that harvest light and carry [00:18:30] out photosynthesis and they're, it seems like the idea for having an Organelle is that you just increased it area that you can use for photosynthesis sorta like you just have more solar panels if you just keep spreading the solar panels. Right. So that in this way, by just sort of making wraps of membranes inside of the cell, you just increased the amount of space that you can harvest light. So those were known for a long time and I think it just wasn't a problem that was studied from the perspective of cell biology and cell [00:19:00] organization that much. That's sort of a different angle that people are bringing to it now with many different bacterial organelles. Speaker 5: And part of the reason why it's important to think of it that way is that of course what the products of the bike chemistry inside of the Organelles is fascinating and really important to understand. But to build the organ out itself is also a difficult thing. So for example, you have to bend and remodel the cell membrane [00:19:30] to create, whether it's a sphere or it's wraps of membrane, and that is not a energetically favorable thing to do. It's not easy. So in your cataract cells, we know that there are specific proteins and protein machines. Then their only job is really to bend and remodeled the membrane cause it's not going to happen by itself very easily. And with all of these different structures that are now better recognized in bacteria, we really have no idea how it is that they performed the same function. Is [00:20:00] it using the same types of proteins as what we know in your care at excels or are they using different kinds of proteins? Speaker 5: That was sort of a very basic question to ask. How similar or different is it than how you carry? Like some makes an Oregon own fester was one of the first inspirations for us to study this process in magnatech the bacteria. And what sort of tools are you using to parse this information? In our field we use various tools and it's turned out to be incredibly beneficial [00:20:30] because different approaches have sort of converged on the same answer. So my basic focus was to use genetics as a tool. And the idea here was if we go in and randomly mutate or delete genes in these bacteria and then see which of these random mutations results in a loss of the magnetic phenotype and prevents the cell from making the magnetism Organelles, then maybe we know [00:21:00] those genes that are potentially involved. And so that was sort of what I perfected during my postdoctoral fellowship. Speaker 5: And that was my main approach to study the problem. And then on top of that, the other approach has been really helpful for us. And this is again something we've worked on is once we know some of the candidate proteins to be able to study them, their localization in the cell and they're dynamics, we modify the protein. So that they're linked to fluorescent proteins. So then we can, uh, use for us in this microscopy to follow them within the cell. [00:21:30] Other people, their approach was to say, well, these structures are magnetic. If we break open the cell, we can use a magnet and try to separate the magnesiums from the rest of the cell material. And then if we have the purified magnesiums, we can look to see what kinds of proteins are associated with them and sort of guilt by association. If there is a protein there, it should do something or maybe it does something. Speaker 5: That was the other approach. And the final approach that's been really helpful, [00:22:00] particularly because Magno take it back to your, our diverse, as we talked about earlier, is to take representatives that are really distantly related to each other and sequence their genomes. So get the sequence of their DNA and see what are the things that they have in common with each other. Take two organisms that live in quite different environments and their lineages are quite different from each other, but they both can do this magnetic tactic behavior. And by doing that, people again found [00:22:30] some genes and so if you take the genes that we found by genetics, random mutations of the cell by isolating the magnesiums and cy counting their proteins, and then by doing the genome sequencing, it all converges on the same set of genes. Speaker 2: [inaudible] this concludes part one of our [00:23:00] interview. We'll be sure to catch part two Friday July 12th at noon. Spectrum shows are archived on iTunes university. Speaker 7: The link is tiny url.com/calex spectrum. Now a few of the science and technology events happening locally over the next two weeks. Speaker 5: Rick Karnofsky [00:23:30] joins me for the calendar on the 4th of July the exploratorium at pier 15 in San Francisco. He's hosting there after dark event for adults 18 and over from six to 10:00 PM the theme for the evening is boom, Speaker 4: learn the science of fireworks, the difference between implosions and explosions and what happens when hot water meets liquid nitrogen tickets are $15 and are available from www.exploratorium.edu [00:24:00] the Santa Clara County Parks has organized an early morning van ride adventure into the back country. To a large bat colony view the bat tornado and learn about the benefits of our local flying mammals. Meet at the park office. Bring a pad to sit on and dress in layers for changing temperatures. This will happen Saturday July six from 4:00 AM to 7:00 AM at Calero County Park [00:24:30] and Santa Clara. Reservations are required to make a reservation call area code (408) 268-3883 Saturday night July six there are two star parties. One is in San Carlos and the other is near Mount Hamilton. The San Carlos event is hosted by the San Mateo Astronomical Society and is held in Crestview Park San Carlos. If you would like to help [00:25:00] with setting up a telescope or would like to learn about telescopes come at sunset which will be 8:33 PM if you would just like to see the universe through a telescope come one or two hours after sunset. Speaker 4: The other event is being hosted by the Halls Valley Astronomical Group. Knowledgeable volunteers will provide you with a chance to look through a variety of telescopes and answer questions about the night. Sky Meet at the Joseph D. Grant ranch county park. [00:25:30] This event starts at 8:30 PM and lasted until 11:00 PM for more information. Call area code (408) 274-6121 July is skeptical hosted by the bay area. Skeptics is on exoplanet colonization down to earth planning. Join National Center for Science Education Staffer and Cal Alum, David Alvin Smith for a conversation [00:26:00] about the proposed strategies to reach other star systems which proposals might work and which certainly won't at the La Pena Lounge. Three one zero five Shattuck in Berkeley on Wednesday July 10th at 7:30 PM the event is free. For more information, visit [inaudible] skeptics.org the computer history museum presents Intel's Justin Ratiner in conversation with John Markoff. Justin Ratner is a corporate [00:26:30] vice president and the chief technology officer of Intel Corporation. He is also an Intel senior fellow and head of Intel labs where he directs Intel's global research efforts in processors, programming systems, security communications, and most recently user experience. Speaker 4: And interaction as part of Intel labs. Ratner is also responsible for funding academic research worldwide through its science and technology centers, [00:27:00] international research institutes and individual faculty awards. This event is happening on Wednesday, July 10th at 7:00 PM the Computer History Museum is located at 1401 north shoreline boulevard in mountain view, California. A feature of spectrum is to present news stories we find interesting. Rick Karnofsky and I present the News Katrin on months and others from the Eulich Research Center in Germany have published the results of their big brain [00:27:30] project. A three d high resolution map of a human brain. In the June 21st issue of science, the researchers cut a brain donated by a 65 year old woman into 7,404 sheets, stain them and image them on a flatbed scanner at a resolution of 20 micrometers. The data acquisition alone took a thousand hours and created a terabyte of data that was analyzed by seven super competing facilities in Canada. Speaker 4: Damn. Making the data [00:28:00] free and publicly available from modeling and simulation to UC Berkeley. Graduate students have managed to more accurately identify the point at which our earliest ancestors were invaded by bacteria that were precursors to organelles like Mitochondria and chloroplasts. Mitochondria are cellular powerhouses while chloroplasts allow plant cells to convert sunlight into glucose. These two complex organelles are thought to have begun as a result of a symbiotic relationship between single cell [00:28:30] eukaryotic organisms and bacterial cells. The graduate students, Nicholas Matzke and Patrick Schiff, examined genes within the organelles and larger cell and compared them using Bayesians statistics. Through this analysis, they were able to conclude that a protio bacterium invaded UCR writes about 1.2 billion years ago in line with earlier estimates and that asino bacterium which had already developed photosynthesis, invaded eukaryotes [00:29:00] 900 million years ago, much later than some estimates which are as high as 2 billion years ago. Speaker 2: Okay. Speaker 4: The music heard during the show was written and produced by Alex Simon. Speaker 3: Interview editing assistance by Renee round. Thank you for listening to spectrum. If you have comments about the show, please send them to us via [00:29:30] email or email address is spectrum dot [inaudible] dot com join us in two weeks. This same time. See acast.com/privacy for privacy and opt-out information.
Arash Komeili cell biologist, Assc. Prof. plant and microbial biology UC Berkeley. His research uses bacterial magnetosomes as a model system to study the molecular mechanisms governing the biogenesis and maintenance of bacterial organelles. Part1TranscriptSpeaker 1: Spectrum's next. Speaker 2: Okay. Speaker 3: [inaudible] [inaudible]. Speaker 1: [00:00:30] Welcome to spectrum the science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews, featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 4: Hi, and good afternoon. My name is Brad Swift. I'm the host of today's show. We are doing another two part interview on spectrum. Our guest is Arash Kamali, [00:01:00] a cell biologist and associate professor of plant and microbial biology at cal Berkeley. His research uses bacterial magneta zones as a model system to study the molecular mechanisms governing the biogenesis and maintenance of bacterial organelles. Today. In part one, Arash walks us through what he is researching and how he was drawn to it in part two, which will air in two weeks. [00:01:30] He explains how these discoveries might be applied and he discusses the scientific outreach he does. Here's part one, a rush. Camelli. Welcome to spectrum. Thank you. I wanted to lay the groundwork a little bit. You're studying bacteria and why did you choose bacteria and not some other micro organism to study? One Speaker 5: practical motivation was that they're easier to study. They're easier to grow in [00:02:00] the lab. You can have large numbers of them. If you're interested in a specific process, you have the opportunity to go deep and try to really understand maybe all the different components that are involved in that process, but it wasn't necessarily a deliberate choice is just as I worked with them it became more and more fascinating and then I wanted to pursue it further. Speaker 4: And then the focus of your research on the bacteria, can you explain that? Speaker 5: Yeah, so we work with [00:02:30] a specific type of bacteria. They're called magnate as hectic bacteria and these are organisms that are quite widespread. You can find them in most aquatic environments by almost any sort of classification. You can really group them together if you take their shape or if you look at even the genes they have, the general genes they have, you can really group them into one specific group as opposed to many other bacteria that you can do that. But Unites Together as a group [00:03:00] is that they're, they're able to orient in magnetic fields and some along magnetic fields. This behavior was discovered quite by accident a couple of times independently. Somebody was looking under a microscope and they noticed that there were bacteria were swimming all in the same direction and they couldn't figure out why. They thought maybe the light from the window was attracting them or some other type of stimuli and they tried everything and they couldn't really figure out why the bacteria were swimming in one direction except they noticed that [00:03:30] regardless of where they were in the lab, they were always swimming in the same geographic direction and so they thought, well, the only thing we can think of that would attract them to the same position is the magnetic field, and they were able to show that sure enough, if you bring a magnet next to the microscope, you can change the swimming direction. Speaker 5: This type of behavior is mediated by a very special structure that the bacteria build inside of their cell, and this was sort of [00:04:00] what attracted me to it. Can you differentiate them? The UK erotic? Yeah. Then the bacterial, can you differentiate those two for us so that we kind of get a sense of is there, they're easy, different differentiate, you know the generally speaking you out excels, enclose their genetic material in an organelle called the nucleus. They're generally much bigger. They have a lot more genetic information associated with them and they have a ton of different kinds of organelles that perform [00:04:30] functions. All these Organelles to fall the proteins to break them down. They have organelles for generating energy, but all those little specific features, you know, you can find some bacterium that has organelles or you can find some bacterial solid that's really huge. Or you can find some bacteria so that encloses its DNA and an organelle. Speaker 5: It's just that you had accels have all of them together. Many of the living organisms that you encounter everyday because you can see them [00:05:00] very easily. Are you carry out, almost all of them are plants and fungi and animals. They're all made up of you. Charismatic cells. It's just that there's this whole unseen world of bacteria and what function does that capability serve, that magnetic functions that it can be realized that yet in many places on earth, the magnetic field will act as a guide through these changes in oxygen levels, sort of like a straight line through these. These [00:05:30] bacteria are stuck in these sort of magnetic field highways. It's thought to be a simpler method for finding the appropriate oxygen levels and simpler in this case means that they have to swim less as swimming takes energy. So the advantage is that they use less energy, get to the same place, that bacteria and that doesn't have the same capabilities relatively speaking, as a simple explanation, it's actually, because it is so simple, the model, you can kind of replicate [00:06:00] it in the lab a little bit. Speaker 5: If you set up a little tube that has the oxygen grading and then the bacteria will go to a certain place and you can actually see that they're sort of a band of bacteria at what they consider for them to be appropriate oxygen levels. And then if you inject some oxygen at the other end of the tube, the bacteria will swim away from this oxygen gradient. Now, if you give them a magnetic field that they can swim along, they can move away from this advancing oxygen threat much more quickly than [00:06:30] bacteria that can't navigate along magnetic fields. So that's sort of a proof of concept a little bit in the lab. There's a lot of reasons why it also doesn't make sense. For example, some of these bacteria make so many of these magnetic structures that we haven't talked about yet, but they make so many of these particles way more than they would ever need to orient in the magnetic field. Speaker 5: So it seems excessive. There are other bacteria that live in places on earth where there is not really this kind of a magnetic field guide. And in those environments there's [00:07:00] plenty of other bacteria that don't have these magneto tactic capabilities and they still can find that specific oxygen zone very easily. So in some ways I think it is an open question but there isn't really enough yet to refute the kind of the generally accepted model on the movement part of it. You were mentioning that they use magnetic field to move backwards and forwards. Only explain the limiting factor. Yeah, that's [00:07:30] an important point actually because it's not that they use the magnetic field for sensing in a way. It's not that they are getting pulled or pushed by the magnetic field. They are sort of passively aligned and the magnetic field sort of like if you have two bar magnets and if one of them is perpendicular to the other one and you bring the other one closer, I'll just move until they're parallel to each other. Speaker 5: This is the same thing. The bacteria have essentially a bar magnet and inside of the cell and so the alignment to the magnetic field [00:08:00] is passive that you can kill the bacteria and they'll still align with the magnetic field. The swimming takes advantage of structures and and machines that are found in all bacteria essentially. So they have flagella that they can use to swim back and forth as you mentioned. And they have a whole bunch of other different kinds of systems for sensing the amount of oxygen or other materials that they're interested in to figure out, should I keep swimming or should I stop swimming? And [00:08:30] as I mentioned earlier, the bacteria are quite diverse. So when you look at different magnatech active bacteria, the types of flagella they have are also different from each other. So it's not one universal mechanism for the swimming, it's just the idea that that the swimming is limited by these magnetic field lines. Speaker 6: [inaudible] [inaudible]. Speaker 5: Our guest today on spectrum is [inaudible] Chameleon, a cell biologist Speaker 7: and associate professor at cal Berkeley. In our next segment, [00:09:00] Arash talks about what attracted him to study the magnetism and why it remains in some bacteria and not others. This is k a l x Berkeley. So Speaker 5: let's talk about the magnetic zone, right? This is sort of my fascination. I was a graduate student at UCF and I studied cell biology. I use the yeast, which are not bacteria but in many ways they are kind of like bacteria. They're much simpler to study than maybe other do care attic [00:09:30] organisms and we have genetics available and so I was very fascinated by east, but I was studying a problem with XL organization and communication within the cell and yeast. We were taught sort of as students in cell biology at the time, that cell organization and having compartments in the cell organelles basically that do different functions was very unique feature of you carry attic cells and there's one of the things I've defined them. I received my phd to do a postdoctoral fellowship. I happen to be [00:10:00] in interviewing at cal tech and professor Mel Simon there he was talking about all kinds of bacteria that he was interested in and he said there's these bacteria that have organelles and I just, it kind of blew my mind because we were told explicitly that that's not true and in many textbooks, even today it still says that bacteria don't have organelles. Speaker 5: I learned more about men and I learned that these magnatech to bacteria that we've been talking about so far, you can actually build a structure inside of the cell, out of their cell membrane and within [00:10:30] this membrane compartment, it's essentially a little factory for making magnetic particles so they can build crystals of mineral called magnetite, which is just an iron oxide. Every three or four and some organisms make a different kind of magnetic minerals called Greg [inaudible], which is an iron sulfur mineral, but these are perfect little crystals, about 50 nanometers in diameter, and they make a chain of these magnesiums, so these membrane enclosed magnetic particles. [00:11:00] This chain is sort of on one side of the cell and it allows the bacteria to orient and magnetic fields because each of those crystals has this magnetic dipole moment in the same direction and all those little dipole moments interact with each other to make a little bar magnet, a little compass needle essentially that forces the bacterium to Orient in the magnetic field. Speaker 5: When I heard about this, I realized that this is just incredibly fascinating. Nobody really knew how it was that the membrane compartment forum [00:11:30] or even if it formed first and the mineral formed inside of it. There wasn't much or anything known about the proteins that were involved in building the compartment and then making the magnetic particle. It just seemed like something that needed to be studied and it was fascinating to me and I've been working on it for 1213 years now. Have we covered what the of the magnetic is that idea behind the function of the magnetism, which is the [00:12:00] structures of the cells build to allow them to align with a magnetic field. We think that function is to simplify the search for low oxygen environments. That's the main model in our field and I think there are definitely some groups that are actively working on understanding that aspect of the behavior better. Speaker 5: How it is that the bacteria can find a certain oxygen concentration. These bacteria in particular, what are the mechanics of them swimming along [00:12:30] the magnetic field and the, is there some other explanation for why they do this? For example, if they are changing orientations into magnetic field, can they sense the strain that the magnetic field is putting onto the cell? Can that be sensed somehow and then used for some work down the line and there are groups that are actively pursuing those kinds of ideas. You were mentioning that this is a particular kind of bacteria that has this capability, right, and others don't. Right. Yet both seem to be equally [00:13:00] effective and populating the water areas that you're studying. No apparent advantage. Disadvantage, so winning in Canada? Yeah, I mean it's a lot of the Darwinian, you could say as long as it's not severely disadvantageous, then maybe they wouldn't be a push for it to be lost. Speaker 5: What is kind of intriguing a little bit is there's examples of magna detective bacteria in many different groups, phylogenetic groups, so many different types of species that will be, let's [00:13:30] say bacterium that normally just lives free in the ocean and then I'll have a relative that's very similar to it, but it's also a magnet, a tactic. In recent years, people have studied this a little bit more and we know now what are the specific set of genes that allow bacteria to become magnetic tactic. So you can look at those genes specifically and say, how is it that bacteria that are otherwise so different from each other can all perform the same function? And if you know the genes that build the structures that allow them to orient [00:14:00] the magnetic fields, you can look at how different those genes are from each other or has similar they are. Speaker 5: And normally with a lot of these types of behaviors in bacteria, there's something called horizontal gene transfer that explains how it is that otherwise similar bacteria can have different functionalities. For example, you can think of that as bacteria being cars and everybody has sort of the same standard set of know features on the car. But you can add on different features if you want to. So you can upgrade and have other kinds of features like leather [00:14:30] seats or regular seats. And so the two cars that have different kinds of seats are very similar to each other. It's just one that got the leather seats. And so these partly are thought to occur by bacteria exchanging genes with each other. Somebody who wasn't magna tactic maybe got these jeans from another organism, but when people look at the genes that make these mag Nita zones, these magnetic structures inside of the cell, what you see is that they appear to be very, very ancient. Speaker 5: So it doesn't seem like there was a lot of recent [00:15:00] exchange of genes between these various groups of bacteria to make them magna tactic. And it almost seems to map to the ancestral divergence of all of these bacteria from each other. One big idea is that the last common ancestor of all these organisms was mag new tactic and that many, many other bacteria have sort of lost this capability over what would be almost 2 billion years of evolution for these bacteria. And then some have retained it. [00:15:30] Those of that have retained it is it's still serving an advantage for them, or is it just sort of Vista GL and they have it and they're sort of stuck in magnetic fields and they have to deal with it? No, but nobody really knows. Actually. The other option is that there was a period of horizontal gene transfer, but it was a very long time ago so that the signature is sort of lost from, again, a couple of billion years of evolution or divergence from each other, but it really looks like whenever this process happened, it was quite anxious. Speaker 3: [00:16:00] You are listening to spectrum on KALX Berkeley. Our guest is Arash [inaudible]. In the next segment, rush talks about organelles in bacterial cells. Speaker 5: [00:16:30] Explain what the Organelle is, so there's a lot of functions within the cell that need to be enclosed in a compartment for various reasons. You can have a biochemical reaction that's not very efficient, but if you put it in within a compartment and concentrates, all of the components that carry that reaction, it can be carried out more efficiently. The other thing is that for some reactions to to happen, you need a chemical environment that's different than the rest of the cellular environment. You can't convert [00:17:00] the whole environment of the cell to that one condition. So by compartmentalizing it you able to carry it out and often the products of these reactions can be toxic to the rest of the cell. And so by componentizing again you can keep the toxic conditions away from the rest of the, so these are the different reasons why you care how to excels. Speaker 5: Like the cells in our body have organelles that do different things like how proteins fold or modify proteins break him down and in bacterial cells it [00:17:30] was thought that they're so simple and so small that they don't really have a need for compartments. Although for many years people have had examples of bacteria that do form compartments. You carrot axles are big and Organelles are really easy to see where the light microscope so you can easily see that the cell has compartments within it. Whereas a lot of bacteria are well studied, are quite simple, they don't have much visible structure within them. And that's maybe even further the bias that there is some divide and this [00:18:00] allowed you carry out access to become more complex, quote unquote, and then it just doesn't exist in bacteria. How is it that they then were revealed? I think they'd been revealed for a long time. Speaker 5: You know, for example, there's electron microscope images from 40 years ago or more where you see for example, photosynthetic bacteria, these are bacteria that can do photosynthesis. They have extensive membrane structures inside of the cell that how's the proteins that harvest light and carry [00:18:30] out photosynthesis and they're, it seems like the idea for having an Organelle is that you just increased it area that you can use for photosynthesis sorta like you just have more solar panels if you just keep spreading the solar panels. Right. So that in this way, by just sort of making wraps of membranes inside of the cell, you just increased the amount of space that you can harvest light. So those were known for a long time and I think it just wasn't a problem that was studied from the perspective of cell biology and cell [00:19:00] organization that much. That's sort of a different angle that people are bringing to it now with many different bacterial organelles. Speaker 5: And part of the reason why it's important to think of it that way is that of course what the products of the bike chemistry inside of the Organelles is fascinating and really important to understand. But to build the organ out itself is also a difficult thing. So for example, you have to bend and remodel the cell membrane [00:19:30] to create, whether it's a sphere or it's wraps of membrane, and that is not a energetically favorable thing to do. It's not easy. So in your cataract cells, we know that there are specific proteins and protein machines. Then their only job is really to bend and remodeled the membrane cause it's not going to happen by itself very easily. And with all of these different structures that are now better recognized in bacteria, we really have no idea how it is that they performed the same function. Is [00:20:00] it using the same types of proteins as what we know in your care at excels or are they using different kinds of proteins? Speaker 5: That was sort of a very basic question to ask. How similar or different is it than how you carry? Like some makes an Oregon own fester was one of the first inspirations for us to study this process in magnatech the bacteria. And what sort of tools are you using to parse this information? In our field we use various tools and it's turned out to be incredibly beneficial [00:20:30] because different approaches have sort of converged on the same answer. So my basic focus was to use genetics as a tool. And the idea here was if we go in and randomly mutate or delete genes in these bacteria and then see which of these random mutations results in a loss of the magnetic phenotype and prevents the cell from making the magnetism Organelles, then maybe we know [00:21:00] those genes that are potentially involved. And so that was sort of what I perfected during my postdoctoral fellowship. Speaker 5: And that was my main approach to study the problem. And then on top of that, the other approach has been really helpful for us. And this is again something we've worked on is once we know some of the candidate proteins to be able to study them, their localization in the cell and they're dynamics, we modify the protein. So that they're linked to fluorescent proteins. So then we can, uh, use for us in this microscopy to follow them within the cell. [00:21:30] Other people, their approach was to say, well, these structures are magnetic. If we break open the cell, we can use a magnet and try to separate the magnesiums from the rest of the cell material. And then if we have the purified magnesiums, we can look to see what kinds of proteins are associated with them and sort of guilt by association. If there is a protein there, it should do something or maybe it does something. Speaker 5: That was the other approach. And the final approach that's been really helpful, [00:22:00] particularly because Magno take it back to your, our diverse, as we talked about earlier, is to take representatives that are really distantly related to each other and sequence their genomes. So get the sequence of their DNA and see what are the things that they have in common with each other. Take two organisms that live in quite different environments and their lineages are quite different from each other, but they both can do this magnetic tactic behavior. And by doing that, people again found [00:22:30] some genes and so if you take the genes that we found by genetics, random mutations of the cell by isolating the magnesiums and cy counting their proteins, and then by doing the genome sequencing, it all converges on the same set of genes. Speaker 2: [inaudible] this concludes part one of our [00:23:00] interview. We'll be sure to catch part two Friday July 12th at noon. Spectrum shows are archived on iTunes university. Speaker 7: The link is tiny url.com/calex spectrum. Now a few of the science and technology events happening locally over the next two weeks. Speaker 5: Rick Karnofsky [00:23:30] joins me for the calendar on the 4th of July the exploratorium at pier 15 in San Francisco. He's hosting there after dark event for adults 18 and over from six to 10:00 PM the theme for the evening is boom, Speaker 4: learn the science of fireworks, the difference between implosions and explosions and what happens when hot water meets liquid nitrogen tickets are $15 and are available from www.exploratorium.edu [00:24:00] the Santa Clara County Parks has organized an early morning van ride adventure into the back country. To a large bat colony view the bat tornado and learn about the benefits of our local flying mammals. Meet at the park office. Bring a pad to sit on and dress in layers for changing temperatures. This will happen Saturday July six from 4:00 AM to 7:00 AM at Calero County Park [00:24:30] and Santa Clara. Reservations are required to make a reservation call area code (408) 268-3883 Saturday night July six there are two star parties. One is in San Carlos and the other is near Mount Hamilton. The San Carlos event is hosted by the San Mateo Astronomical Society and is held in Crestview Park San Carlos. If you would like to help [00:25:00] with setting up a telescope or would like to learn about telescopes come at sunset which will be 8:33 PM if you would just like to see the universe through a telescope come one or two hours after sunset. Speaker 4: The other event is being hosted by the Halls Valley Astronomical Group. Knowledgeable volunteers will provide you with a chance to look through a variety of telescopes and answer questions about the night. Sky Meet at the Joseph D. Grant ranch county park. [00:25:30] This event starts at 8:30 PM and lasted until 11:00 PM for more information. Call area code (408) 274-6121 July is skeptical hosted by the bay area. Skeptics is on exoplanet colonization down to earth planning. Join National Center for Science Education Staffer and Cal Alum, David Alvin Smith for a conversation [00:26:00] about the proposed strategies to reach other star systems which proposals might work and which certainly won't at the La Pena Lounge. Three one zero five Shattuck in Berkeley on Wednesday July 10th at 7:30 PM the event is free. For more information, visit [inaudible] skeptics.org the computer history museum presents Intel's Justin Ratiner in conversation with John Markoff. Justin Ratner is a corporate [00:26:30] vice president and the chief technology officer of Intel Corporation. He is also an Intel senior fellow and head of Intel labs where he directs Intel's global research efforts in processors, programming systems, security communications, and most recently user experience. Speaker 4: And interaction as part of Intel labs. Ratner is also responsible for funding academic research worldwide through its science and technology centers, [00:27:00] international research institutes and individual faculty awards. This event is happening on Wednesday, July 10th at 7:00 PM the Computer History Museum is located at 1401 north shoreline boulevard in mountain view, California. A feature of spectrum is to present news stories we find interesting. Rick Karnofsky and I present the News Katrin on months and others from the Eulich Research Center in Germany have published the results of their big brain [00:27:30] project. A three d high resolution map of a human brain. In the June 21st issue of science, the researchers cut a brain donated by a 65 year old woman into 7,404 sheets, stain them and image them on a flatbed scanner at a resolution of 20 micrometers. The data acquisition alone took a thousand hours and created a terabyte of data that was analyzed by seven super competing facilities in Canada. Speaker 4: Damn. Making the data [00:28:00] free and publicly available from modeling and simulation to UC Berkeley. Graduate students have managed to more accurately identify the point at which our earliest ancestors were invaded by bacteria that were precursors to organelles like Mitochondria and chloroplasts. Mitochondria are cellular powerhouses while chloroplasts allow plant cells to convert sunlight into glucose. These two complex organelles are thought to have begun as a result of a symbiotic relationship between single cell [00:28:30] eukaryotic organisms and bacterial cells. The graduate students, Nicholas Matzke and Patrick Schiff, examined genes within the organelles and larger cell and compared them using Bayesians statistics. Through this analysis, they were able to conclude that a protio bacterium invaded UCR writes about 1.2 billion years ago in line with earlier estimates and that asino bacterium which had already developed photosynthesis, invaded eukaryotes [00:29:00] 900 million years ago, much later than some estimates which are as high as 2 billion years ago. Speaker 2: Okay. Speaker 4: The music heard during the show was written and produced by Alex Simon. Speaker 3: Interview editing assistance by Renee round. Thank you for listening to spectrum. If you have comments about the show, please send them to us via [00:29:30] email or email address is spectrum dot [inaudible] dot com join us in two weeks. This same time. Hosted on Acast. See acast.com/privacy for more information.
Fakultät für Biologie - Digitale Hochschulschriften der LMU - Teil 04/06
Fri, 27 Jul 2012 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/14668/ https://edoc.ub.uni-muenchen.de/14668/1/Zimmermann_Dennis.pdf Zimmermann, Dennis ddc:570, ddc:
In today's episode, it's all about the sweater love as I update you on my projects. And it is the Spring Equinox, when the world warms and prepares for the growing season...ShownotesHousekeeping:- Enter to win a project bag by Miso Crafty Knits, and one of three skeins of hand-dyed sock yarn. The Knitter's NeedlesOff the Needles:Arco Cowl:“Arco Cowl” by Sara Sprung.Yarn: Malabrigo “Rasta” super bulky, in “Arco Iris” colourway.Moonstone Sweater:“My favorite sweater” - basic top-down raglan formula pattern, by Amber Corcoran (Fancy Tiger Crafts). Yarn: Fleece Artist “Big Blue” BFL chunky, “Moonstone” colourway.Ripley Cardigan:“Favorite Cardigan” by Wendy Bernard, from the “Custom Knits” book.Yarn: The Sanguine Gryphon “QED” BFL worsted, in silver-gray “The Ripley Scrowle” My Chelsea Market Slouch:“Chelsea Market Hat” by Caryl Pierre (test knit)Yarn: The Sanguine Gryphon “QED” BFL worsted, in deep turquoise “Organelle”On the Needles: Fluffy Cardi:“Sedum” cardigan by Jane RichmondYarn: Bernat “Roving” - single ply bulky, 80% Acrylic, 20% Wool, in “Putty” gray colour.Doha Cardigan:“Calligraphy Cardigan” by Hannah FettigYarn: The Sanguine Gryphon “Traveller” DK (100% SW Merino), in “Doha”.Ben's Warthog:“Warthog” by Sarah Keen, from the “Knitted Wild Animals” book. Yarn: "Cascade 220", 100% Peruvian wool (not superwash), in colours “Rust” and “Cream”Music:David Baumgarten, "Your Spring Will Come Along"
Tanz Organelle Bio DJ and Producer : Electronic Tanz Organelle (aka Jay Brown) was a byproduct of the music scene in Manchester, England, in the early 1990s. The music that emerged from the Madchester scene, the mix of alternative, psychedelic rock and Acid house by artists such as New Order, The Stone Roses, Happy Mondays, 808 State, The Charlatans, A Guy Called Gerald and others. At that time, the Haçienda nightclub was a major catalyst for the scene and also for distilling the musical ethos in the fabric of Organelles DNA. With the submission of a C90 to DJ Nipper – a UK rave icon and one Sasha’s accredited inspirations, quickly brought Jay on board for his residency at the legendary Hacienda’s first ever Techno night, Hardware. Inspired by Jeff Mills and latterly Surgeon, Jays unfashionable approach to the Mancunian dance floor continually tore fac51’s roof off. Since then production has been the priority – Always looking forward but never on a wagon of trend, never fearing to address the foundations of his origin, combining a timbral sonic manipulation of past and present. Big room sounds come uncompromisingly architected with his remixes gaining fast support in the global techno community. BWLR-P007 Tanz Organelle, Melbourne, AU
Mitochondrien und Chloroplasten sind Zellkernbestandteile, die vor allem eines gemeinsam haben: ihre Entstehung. Sie stammen von Bakterien ab, die vor etwa zwei Milliarden Jahren von Wirtszellen aufgenommen wurden. An der LMU werden diese faszinierenden Zellorganellen in zwei Arbeitsgruppen erforscht. Professor Walter Neupert vom Adolf-Butenandt-Institut ist seit langem dominierend auf dem Gebiet der Mitochondrien, Professor Jürgen Soll vom Department Biologie I erhielt dieses Jahr den Leibniz-Preis für seine Arbeit an den Chloroplasten.
Background: Programmed cell death (PCD) is essential for development and homeostasis of multicellular organisms and can occur by caspase-dependent apoptosis or alternatively, by caspase-independent PCD (ciPCD). Bcl-2, a central regulator of apoptosis, localizes to both mitochondria and the endoplasmic reticulum (ER). Whereas a function of mitochondrial and ER-specific Bcl-2 in apoptosis has been established in multiple studies, corresponding data for ciPCD do not exist. Methods: We utilized Bcl-2 constructs specifically localizing to mitochondria (Bcl-2 ActA), the ER (Bcl-2 cb5), both (Bcl-2 WT) or the cytosol/nucleus (Bcl-2 Delta TM) and determined their protective effect on ceramide-mediated ciPCD in transiently and stably transfected Jurkat cells. Expression of the constructs was verified by immunoblots. Ceramide-mediated ciPCD was induced by treatment with human recombinant tumor necrosis factor and determined by flow cytometric measurement of propidium iodide uptake as well as by optical analysis of cell morphology. Results: Only wildtype Bcl-2 had the ability to efficiently protect from ceramide-mediated ciPCD, whereas expression of Bcl-2 solely at mitochondria, the ER, or the cytosol/nucleus did not prevent ceramide-mediated ciPCD. Conclusion: Our data suggest a combined requirement for both mitochondria and the ER in the induction and the signaling pathways of ciPCD mediated by ceramide.
Fakultät für Biologie - Digitale Hochschulschriften der LMU - Teil 03/06
Etioplasten sind hochspezialisierte pflanzliche Organelle der Plastidenfamilie, die während der Skotomorphogenese von Pflanzen gebildet werden. Die Morphologie der Etioplasten unterscheidet sich grundlegend von Chloroplasten, die während der Photomorphogenese gebildet werden. Durch Belichtung von Pflanzen, die im Dunkeln angezogen worden sind, kommt es zur Induktion der Transformation von Etioplasten zu Chloroplasten. Die unmittelbar vor Induktion des biologischen Systems bestehende Zusammensetzung der Proteine und Proteinkomplexe des Etioplasten ist allerdings bislang kaum untersucht worden. Im Rahmen dieser Arbeit erfolgten mehrere spezifische Analysen von plastidären Subproteomen. Ausgewählte Subproteome der inneren Membranen von Etioplasten der Gerste wurden im Vergleich zum Proteom der Thylakoidmembran von Chloroplasten analysiert. Durch die Kombination verschiedener gelelektrophoretischer Trennmethoden für Einzelproteine und Proteinkomplexe mit massenspektrometrischen Analysemethoden gelangen sensitivste Nachweise niedrig konzentrierter Untereinheiten von Membranproteinkomplexen. Darüber hinaus gelangen der Nachweis niedermolekularer membranintegraler Proteine und die spezifische Charakterisierung von Einzelproteinen. Im ersten Teil der Arbeit wurden die N-Termini von NADPH:Protochlorophyllid-Oxidoreduktase (POR) A und B durch ein LC-MS basiertes Verfahren bestimmt. Es erfolgte die Entwicklung einer Methode zur selektiven Isolation N-terminaler Peptide mittels Höchstdruckflüssigkeitschromatographie (UPLC). Dazu wurden zwei chemische Reaktionsschritte auf Protein- und Peptidebene durchgeführt, wodurch das N-terminale Peptid nach einem tryptischen Verdau ausschließlich acetyliert vorlag und interne Peptide durch eine weitere Modifikation mit 2,4,6-Trinitrobenzolsulfonsäure abgetrennt wurden. Dadurch konnte gezeigt werden, dass die N-Termini von PORA und PORB homolog zueinander sind und eine vergleichbare Erkennungssequenz für die prozessierende(n) Protease(n) vorliegt. Das Transitpeptid von PORA ist somit deutlich kürzer, als bislang vermutet, wodurch neue Rückschlüsse bezüglich einer möglichen Bindestelle von Protochlorophyllid gezogen werden konnten, da eine von Reinbothe et al. 2008 beschriebene Bindestelle nicht im Bereich des Transitpeptids, sondern in Bereich der maturen PORA liegt. Bei PORB konnten neben einem dominierenden N-terminalen Peptid zwei weitere um jeweils ein Alanin verkürzte N-terminale Peptide mit geringerer Signalintensität nachgewiesen werden. Dies deutet auf eine unpräzise N-terminale Prozessierung hin. Im zweiten Teil der Arbeit gelang die bislang umfassendste massenspektrometrische Charakterisierung des NAD(P)H-Dehydrogenase-Komplexes aus einer C3-Pflanze. In Etioplasten konnten sechs plastidär kodierte und mindestens fünf kernkodierte Untereinheiten des NDH-Komplexes identifiziert werden. Dies gelang durch die Isolation des Komplexes mittels nativer PAGE als 1. Dimension und die anschließende Aufkonzentrierung der Untereinheiten in einer SDS-PAGE als konzentrierende 2. Dimension. Dadurch konnte gezeigt werden, dass der NDH-Komplex bereits in Etioplasten neben dem membranintegralen Subkomplex aus mindestens zwei löslichen Subkomplexen aufgebaut ist. Aufgrund dieser umfangreichen Assemblierung ist eine physiologische Funktion wahrscheinlich und erste Versuche zur NAD(P)H-Dehydrogenase Aktivität lieferten Hinweise auf eine mögliche enzymatische Aktivität. Im dritten Teil der Arbeit gelang in Etioplasten erstmals der Nachweis aller bekannten membranintegralen, niedermolekularen Untereinheiten von Photosystem II, nicht aber von Photosystem I. Die Untereinheiten von PSI konnten ausschließlich in Chloroplasten nachgewiesen werden. Von PSII konnten 13 niedermolekulare Untereinheiten mit jeweils einer Transmembrandomäne nachgewiesen werden. Diese Untereinheiten konnten im Gegensatz zu Chloroplasten nicht in höhermolekularen Komplexen, sondern ausschließlich nahe der Lauffront einer BN-PAGE im Bereich der freien Proteine nachgewiesen werden. Der Nachweis von PsbN war ausschließlich in Etioplasten möglich. Aus diesen Ergebnissen wurde geschlossen, dass ausschließlich nicht-chlorophyllbindende Untereinheiten von PSII in Etioplasten akkumuliert werden und die Anreicherung von chlorophyllbindenden Untereinheiten von PSI und PSII von der Anwesenheit von Chlorophyll abhängt. Darüber hinaus konnten die vier niedermolekularen, membranintegralen Untereinheiten des Cytochrom b6f-Komplexes in Etioplasten und in Chloroplasten sowohl in der monomeren, als auch dimeren Assemblierungsstufe nachgewiesen werden. Ermöglicht wurden diese Nachweise durch eine neu entwickelte Methode zur Extraktion von Proteinen aus einem Polyacrylamid-Gel mit organischen Lösungsmitteln und der anschließenden massenspektrometrischen Charakterisierung mittels offline ESI-MS.
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