Podcasts about Ribosome

Transcript with time code:  https://cuttingedgehealth.com/wp-content/uploads/2025/02/Transcript-47-Dr-Venki-Ramakrishnan.pdf   In this episode, Jane interviews Nobel Prize winner Venki Ramakrishnan, a molecular biologist who offers a balanced perspective on the anti-aging field.   Ramakrishnan discusses various promising areas of anti-aging research, including caloric restriction drugs like rapamycin, senolytics to target senescent cells, and stem cell therapies. He emphasizes the importance of clinical trials and cautions against rushing into unproven treatments. The conversation covers lifestyle factors that can promote healthy aging, such as regular exercise, proper nutrition, and maintaining social connections.   Ramakrishnan shares personal insights, including his father's experience of maintaining an active lifestyle until age 99. He also touches on his own career journey and winning the Nobel Prize. Throughout the interview, he stresses the need for a scientific approach to anti-aging research while acknowledging the urgency felt by many to combat aging. The podcast provides a thoughtful exploration of the current state of anti-aging science, balancing excitement for potential breakthroughs with the need for rigorous scientific validation.   *****   Venki Ramakrishnan shared the 2009 Nobel Prize in Chemistry for uncovering the structure of the ribosome. A National Academy of Sciences member, Venki runs his research group at the MRC Laboratory of Molecular Biology in Cambridge, England. From 2015 to 2020, he served as president of the Royal Society, one of the world's oldest scientific organizations. He is the author of the frank scientific memoir Gene Machine: The Race to Decipher the Secrets of the Ribosome and Amazon bestselling book Why We Die: The New Science of Aging and the Quest for Immortality.   *****   Cutting Edge Health podcast website: https://cuttingedgehealth.com/   Cutting Edge Health Social and YouTube:   YouTube channel: youtube.com/@cuttingedgehealthpodcast   Instagram - https://instagram.com/cuttingedgehealthpodcast   Facebook - https://www.facebook.com/Cutting-Edge-Health-Podcast-with-Jane-Rogers-101036902255756   Please note that the information provided in this show is not medical advice, nor should it be taken or applied as a replacement for medical advice. The Cutting Edge Health podcast, its employees, guests and affiliates assume no liability for the application of the information discussed.   Special thanks to Alan and Maria on the Cutting Edge Health team!    

المصادر The Catalyst: RNA and the Quest to Unlock Life's Deepest Secrets By Cech, Thomas R. https://www.researchgate.net/figure/Human-cornea-structure-and-composition-A-Human-cornea-anatomy-B-The-human-cornea_fig1_379012868 https://www.genome.gov/genetics-glossary/Messenger-RNA-mRNA https://www.genome.gov/genetics-glossary/Transfer-RNA-tRNA https://www.genome.gov/genetics-glossary/Ribosome https://en.wikipedia.org/wiki/Ribozyme https://en.wikipedia.org/wiki/List_of_RNAs https://www.salk.edu/news-release/modeling-the-origins-of-life-new-evidence-for-an-rna-world/ https://www.thoughtco.com/dna-versus-rna-608191 https://math.mit.edu/classes/18.417/index.html https://www.genome.gov/genetics-glossary/Nucleolus https://www.sciencefacts.net/rna-polymerase.html https://www.vedantu.com/biology/start-codons-in-dna-and-rna https://www.slideshare.net/slideshow/structure-and-function-of-messenger-rna-mrna/56603656 https://www.genome.gov/genetics-glossary/Intron https://rsscience.com/ribosomes/ https://earth.callutheran.edu/Academic_Programs/Departments/BioDev/omm/jsmolnew/trna/trna.html https://www.nist.gov/image/rnagraphics-introv2-01png https://en.wikipedia.org/wiki/Hammerhead_ribozyme

Before the 1990s, small bits of RNA were considered junk by most, but the 1993 discovery of microRNA (miRNAs) began to reveal that bits of only 19-24 nucleotides of RNA can have an important gene regulation function in cells. Since their discovery, there has been a flurry of work to catalog known miRNAs and understand their functions, which include being tied to specific disease states such as leukemia. According to our guest, Dr. Guy Novotny, Molecular Biologist at Herlev Hospital in Copenhagen, it's now relatively easy to identify a miRNAs and follow their expression, but to figure out what they're actually doing is a real challenge. We hear how he and his team have recently adopted digital PCR, and the benefits that come with it, to study microRNAs and figure out what proteins they're regulating the expression of. This includes basic research, where Guy is “adding to the big pile of data that's existing out there,” and he also does clinical research that has a closer connection to specific disease states and subject outcomes. As always, you'll get to learn about his career journey and learn that there's really not much that cake cannot fix.Visit the Absolute Gene-ius page to learn more about the guests, the hosts, and the Applied Biosystems QuantStudio Absolute Q Digital PCR System. 

In this episode, Xavier Bonilla has a dialogue with Venki Ramakrishnan about his discovering and mapping the ribosome structure. They discuss his background in coming from India to study physics and then biology, layout of ribosome, DNA, RNA, mRNA, and proteins, what we have learned about the ribosome over the past 50+ years, x-ray crystallography, and his trip to the LMB. They also discuss his experience of seeing atomic subunits of ribosomes for the first time, winning the Nobel Prize, and the future of ribosome research. Venki Ramakrishnan is a biologist and group leader of the Medical Research Center (MRC) Laboratory of Molecular Biology and is a fellow of Trinity College, Cambridge. He was President of the Royal Society from 2015 to 2020. He was awarded the Nobel Prize in Chemistry in 2009 for his work on the sequence of the ribosome structure. He is also a member of the Order of Merit since 2012. He is the author of, Gene Machine: The Race to Decipher the Secrets of the Ribosome. Get full access to Converging Dialogues at convergingdialogues.substack.com/subscribe

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Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.10.548420v1?rss=1 Authors: Machado, J. P., Almeida, V., Zuardi, A. W., Hallak, J. E., Crippa, J. A., Schwambach Vieira, A. Abstract: Background: Cannabidiol (CBD), one of the main cannabinoids present in the female flowers of Cannabis sativa, has been a therapeutic alternative for a plurality of disorders. Previous investigation has already provided insights into the CBD molecular mechanism, however, there is no transcriptome data for CBD effects on hippocampal subfields. Here, we explore the transcriptomic changes in dorsal and ventral CA1 of adult mice hippocampus after 100 mg/kg of CBD administration (i.p.) for one or seven consecutive days. Methods: C57BL/6JUnib mice were divided into 4 groups treated with either vehicle or CBD for 1 or 7 days. The collected brains were sectioned and the hippocampal subregions were laser microdissected for RNA-Seq analysis. Data alignment, quantification and analysis were conducted with the STAR Aligner/DESeq2/clusterProfiler R-package pipeline. Results: We found changes in gene expression in CA1 neurons after single and multiple CBD administrations. Furthermore, the enrichment analysis of differentially expressed genes following 7 days of CBD administration indicates a widespread decrease in the expression levels of electron transport chain and ribosome biogenesis transcripts, while chromatin modifications and synapse organization transcripts were increased. Conclusion: This dataset provides a significant contribution toward advancing our comprehension of the mechanisms responsible for CBD effects on hippocampal neurons. The findings suggest that CBD prompts a significant reduction in energy metabolism genes and the protein translation machinery in CA1 neurons. 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/2023.05.03.539259v1?rss=1 Authors: Garadi Suresh, H., Bonneil, E., Albert, B., Dominique, C., Costanzo, M., Pons, C., Masinas, M. P. D., Shuteriqi, E., Shore, D., Henras, A. K., Thibault, P., Boone, C., Andrews, B. J. Abstract: Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with Ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs), Ubp2 and Ubp14, and E3 ligases, Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the Ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the Intranuclear Quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with Ribosomopathies. 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/2023.04.06.535853v1?rss=1 Authors: Danan, C. H., Naughton, K. E., Hayer, K. E., Vellapan, S., McMillan, E. A., Zhou, Y., Matsuda, R., Nettleford, S. K., Katada, K., Parham, L. R., Ma, X., Chowdhury, A., Wilkins, B. J., Shah, P., Weitzman, M. D., Hamilton, K. E. Abstract: The METTL3-METTL14 methyltransferase complex adds N6-methyladenosine (m6A) to mRNA with profound impacts on cell fate. Studies delete METTL3 or METTL14 interchangeably to define the role of m6A in target tissues despite a lack of data confirming that these deletions are equivalent. Intestinal epithelial METTL14 deletion triggers stem cell death in the colon with no overt phenotype in the small intestine. The effect of METTL3 deletion in the same tissues remains unknown. We report that intestinal epithelial METTL3 deletion caused unexpected severe defects in the small intestine, including crypt and villus atrophy associated with cellular senescence and death in the crypt transit amplifying zone. Ribosome profiling and m6A-sequencing demonstrated downregulated translation of hundreds of unique methylated transcripts, including genes essential to growth factor signal transduction, such as Kras. Our study suggests that METTL3 is essential for small intestinal homeostasis via enhanced translation of growth factor signaling in crypt transit amplifying cells. 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/2023.03.23.533914v1?rss=1 Authors: Fedry, J., Silva, J., Vanevic, M., Fronik, S., Mechulam, Y., Schmitt, E., des Georges, A., Faller, W., Förster, F. Abstract: Aberrantly slow mRNA translation leads to ribosome stalling and subsequent collision with the trailing neighbor. Ribosome collisions have recently been shown to act as stress sensors in the cell, with the ability to trigger stress responses balancing survival and apoptotic cell-fate decisions depending on the stress level. However, we lack a molecular understanding of the reorganization of translation processes over time in mammalian cells exposed to an unresolved collision stress. Here we visualize the effect of a persistent collision stress on translation using in situ cryo electron tomography. We observe that low dose anisomycin collision stress leads to the stabilization of Z-site bound tRNA on elongating 80S ribosomes, as well as to the accumulation of an off-pathway 80S complex possibly resulting from collision splitting events. We visualize collided disomes in situ, occurring on compressed polysomes and revealing a stabilized geometry involving the Z-tRNA and L1 stalk on the stalled ribosome, and eEF2 bound to its collided rotated-2 neighbor. In addition, non-functional post-splitting 60S complexes accumulate in the stressed cells, indicating a limiting Ribosome associated Quality Control clearing rate. Finally, we observe the apparition of tRNA-bound aberrant 40S complexes shifting with the stress timepoint, suggesting a succession of different initiation inhibition mechanisms over time. Altogether, our work visualizes the changes of translation complexes under persistent collision stress in mammalian cells, indicating how perturbations in initiation, elongation and quality control processes contribute to an overall reduced protein synthesis. 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/2023.03.15.532818v1?rss=1 Authors: Hendrix, E., Andrijes, R., Boora, U., Kaur, A., Bundred, J. R., Zayer, A., Heilig, R., Westrip, C. A. E., Fletcher, S. F., Eaton, C. D., Kennedy, T. J., Piasecka, S., Fischer, R., Smerdon, S. J., Coleman, M. L. Abstract: Jumonji-C (JmjC) ribosomal protein hydroxylases are an ancient class of oxygen- and Fe(II)-dependent oxygenases that spawned the wider JmjC family and Histone Lysine Demethylases (KDMs) in eukaryotes. Myc-induced Antigen (MINA) has been implicated in ribosome biogenesis and was assigned as a nucleolar-localized JmjC histidyl hydroxylase of the large ribosomal subunit protein RPL27A, consistent with reports that it supports cell growth and viability in a variety of tumor cell types. Reported roles in diverse aspects of disease biology may be consistent with additional MINA functions, although the molecular mechanisms involved remain unclear. Here, we describe an extra-nucleolar interaction of MINA with the Hinge domain of the membrane-associated guanylate kinase, MPP6. We show that MINA promotes the expression and membrane localization of MPP6 and that the MINA-MPP6 pathway is required for epithelial tight junction integrity and barrier function. The function of MINA in this novel pathway is suppressed by ribosomal RNA transcription and the nucleolar MINA interactome, which sequesters MINA in the nucleoli of growing cells. Our work sheds light on how quiescent cells lose adhesion as they switch to proliferate states associated with increased ribosome biogenesis. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

https://psychiatry.dev/wp-content/uploads/speaker/post-12271.mp3?cb=1678965803.mp3 Playback speed: 0.8x 1x 1.3x 1.6x 2x Download: Dysregulation of ribosome-associated quality control elicits cognitive disorders via overaccumulation of TTC3 – PubMed Ryo Endo et al. PNAS. 2023. Ribosome-associated qualityFull EntryDysregulation of ribosome-associated quality control elicits cognitive disorders via overaccumulation of TTC3 – PubMed

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.07.531644v1?rss=1 Authors: Yang, L., Yi, L., Yang, J., Zhang, R., Xie, Z., Wang, H. Abstract: The significance of A-to-I RNA editing in neurological development is widely recognized, however, its influence on retina development remains to be thoroughly understood. In this study, we aimed to characterize the temporal landscape of A-to-I editing in mouse retina development using total RNA-seq and Ribosome profiling, with a specific emphasis on its effect on gene translation. Our findings revealed that the editing underwent plastic changes and distinct editing contents facilitated stage-specific functions. Further analysis showed a dynamic interplay between A-to-I editing and alternative splicing, with A-to-I editing having a significant impact on splicing efficiency and increasing the quantity of splicing events. A-to-I editing held the potential of enhancing the translatome's diversity, but this came at the expense of reduced translational efficiency. When coupled with splicing, it could produce a coordinated regulatory effect on translatome dynamics. Overall, our study presents a temporally resolved atlas of A-to-I editing, connecting its dynamic changes with the regulatory impact on splicing and translation. 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/2022.12.28.522136v1?rss=1 Authors: Costa, D. S., Kenny-Ganzert, I. W., Chi, Q., Park, K., Kelley, L. C., Garde, A., Matus, D. Q., Park, J., Yogev, S., Goldstein, B., Gibney, T. V., Pani, A. M., Sherwood, D. R. Abstract: Cell invasion through basement membrane (BM) barriers is important in development, immune function, and cancer progression. As invasion through BM is often stochastic, capturing gene expression profiles of cells actively transmigrating BM in vivo remains elusive. Using the stereotyped timing of C. elegans anchor cell (AC) invasion, we generated an AC transcriptome during BM breaching. Through a focused RNAi screen of transcriptionally enriched genes, we identified new invasion regulators, including TCTP (Translationally Controlled Tumor Protein). We also discovered gene enrichment of ribosomal proteins. AC-specific RNAi, endogenous ribosome labeling, and ribosome biogenesis analysis revealed a burst of ribosome production occurs shortly after AC specification, which drives the translation of proteins mediating BM removal. Ribosomes also strongly localize to the ACs endoplasmic reticulum (ER) and the endomembrane system expands prior to invasion. We show that AC invasion is sensitive to ER stress, indicating a heightened requirement for translation of ER trafficked proteins. These studies reveal key roles for ribosome biogenesis and endomembrane expansion in cell invasion through BM and establish the AC transcriptome as a resource to identify mechanisms underlying BM transmigration. 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/2022.12.05.519155v1?rss=1 Authors: Wang, L., Xu, Y., Yun, S., Yuan, Q., Satpute-Krishnan, P., Ye, Y. Abstract: Translocon clogging at the endoplasmic reticulum (ER) as a result of translation stalling triggers ribosome UFMylation, activating a Translocation-Associated Quality Control (TAQC) mechanism that degrades clogged substrates. How cells sense ribosome UFMylation to initiate TAQC is unclear. Here we use a genome-wide CRISPR/Cas9 screen to identify an uncharacterized membrane protein named SAYSD1 that facilitates TAQC. SAYSD1 associates with the Sec61 translocon, and also recognizes both ribosome and UFM1 directly, engaging a stalled nascent chain to ensure its transport via the TRAPP complex to lysosomes for degradation. Like UFM1 deficiency, SAYSD1 depletion causes the accumulation of translocation-stalled proteins at the ER and triggers ER stress. Importantly, disrupting UFM1- and SAYSD1-dependent TAQC in Drosophila leads to intracellular accumulation of translocation-stalled collagens, defective collagen deposition, abnormal basement membranes, and reduced stress tolerance. Together, our data support a model that SAYSD1 acts as a UFM1 sensor that collaborates with ribosome UFMylation at the site of clogged translocon, safeguarding ER homeostasis during animal development. 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/2022.11.30.518484v1?rss=1 Authors: Koppers, M., Ozkan, N., Nguyen, H. H., Jurriens, D., McCaughey, J., Stucchi, R., Altelaar, M., Kapitein, L. C., Hoogenraad, C. C., Farias, G. G. Abstract: Local mRNA translation in axons is critical for the spatial and temporal regulation of the axonal proteome. A wide variety of mRNAs are localized and translated in axons, however how protein synthesis is regulated at specific subcellular sites in axons remains unclear. Here, we establish that the axonal endoplasmic reticulum (ER) supports axonal translation. Axonal ER tubule disruption impairs local translation and ribosome distribution. Using nanoscale resolution imaging, we find that ribosomes make frequent contacts with ER tubules in the axon in a translation-dependent manner and are influenced by specific extrinsic cues. We identify P180/RRBP1 as an axonally distributed ribosome receptor that regulates local translation in an mRNA-dependent manner. Our results establish an important role for the axonal ER in localizing mRNA translation and in dynamically regulating the axonal proteome in response to neuronal stimuli. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

On this ID the Future, philosopher of biology Paul Nelson further explores AlphaFold 2, a cutting edge computer program from Google's DeepMind designed to rapidly suss out important secrets in the realm of proteins, indispensable molecular biological workhorses that come in thousands of different shapes and sizes. Nelson enthuses about AlphaFold 2 but also explains why he is convinced that AlphaFold's creators have hit a series of immovable obstacles. The watchword here—orphans. Tune in to learn what these mischievous orphan proteins are about, and what they suggest for AlphaFold, evolution, and intelligent design. Source

Today's ID the Future spotlights AlphaFold, an artificial intelligence program in the news for its impressive breakthroughs at predicting a protein's 3D structure from its amino acid sequence. Philosopher of Biology Paul Nelson walks listeners through the importance of this “amazing breakthrough,” as he describes it in a recent Evolution News article; but don't uncork the champagne bottles just yet. The reason, according to Nelson, is that while proteins, protein sequences, and protein folding promise to reveal much that is still mysterious in molecular biology, we now know that biological information involves far more than just an organism's proteome—that is, far more than the full suite of proteins expressed by an organism. Nelson uses analogies to manmade machines and cognates Read More › Source

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.11.09.515899v1?rss=1 Authors: Shamsuzzaman, M., Rahman, N., Gregory, B., Bommakanti, A., Zengel, J. M., Bruno, V., Lindahl, L. Abstract: Many mutations in genes for ribosomal proteins and assembly factors cause cell stress and altered cell fate resulting in congenital diseases, collectively called ribosomopathies. Even though all such mutations depress the cell's protein synthesis capacity, they generate many different phenotypes, suggesting that the diseases are not due simply to insufficient protein synthesis capacity. To learn more, we have investigated how the global transcriptome in Saccharomyces cerevisiae responds to reduced protein synthesis generated in two different ways: abolishing the assembly of new ribosomes or inhibiting ribosomal function. Our results show that the mechanism by which protein synthesis is obstructed affects the ribosomal protein transcriptome differentially: ribosomal protein mRNA abundance increases during the abolition of ribosome formation but decreases during the inhibition of ribosome function. Interestingly, the ratio between mRNAs from some, but not all, paralogous genes encoding slightly different versions of a given r-protein change differently during the two types of stress, suggesting that specific ribosomal protein paralogues may contribute to the stress response. Unexpectedly, the abundance of transcripts for ribosome assembly factors and translation factors remains relatively unaffected by the stresses. On the other hand, the state of the translation apparatus does affect cell physiology: mRNA levels for some other proteins not directly related to the translation apparatus also change differentially, though not coordinately with the r-protein genes, in response to the stresses. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

ORN Dr. Tom Cowan show notes 10/31/22 What responses has Dr. Cowan received regarding his stance on viruses? What is needed to prove something exists? They say there's not enough virus in a person to measure, even in someone who is said to have died from it. Supposed isolation of a virus by giving antibiotics and starving the cell sample. Separating the snot from the person and putting it in a culture. Culture cells die, supposedly proving the virus exists. List of structures or functions said to exist in human biology that haven't been proven to exist or proven to not exist. They are actually artifacts of the way we find thing in cells. Ribosome supposedly makes protein and means the rib of the body. They are mocking you. DNA in nucleus makes RNA, which supposedly goes to ribosome and makes protein. How can RNA escape from the nucleus yet nothing can get into the nucleus? Mitochondria supposedly located in endoplasmic reticulum. But the cristae lines look like cracks formed from freezing. Can't be receptors in membranes. How does water make structure out of impulse? Wedding ring image created in water in petri dish laid on top of a wedding invitation. What is falling down? Water creates a London Bridge image. Antenna on top of Taj Mahal dome structure, and other historical buildings, conveying information to water. Thoughts or conceptions become actions which have consequences. What was the cause of death of a HIV scientist dying after 4 COVID jabs? His belief that the jabs would help him. Can't treat anyone for an illness as long as their brain work is delusional. Dr. Cowan doesn't want to change the system. Instead, commit to finding reality. The world will give you clues and help you. Trust senses, verify reality with others, then do science and validate every step. Keep looking to see if evidence is congruent with belief. Guides or angels will help you in your quest for discovering reality. How come all these smart people think something else? How smart are they really? Are they committed to not looking at the evidence? No such thing as right or wrong. No objective reality – it's only what I say that determines right or wrong. That is the path of nothing is real, of nihilism. There is an ultimate reality. We don't create reality, it is given in the world. We do create beliefs though. Creating reality is where we went wrong. Real food comes from nature. Eating fake or human engineered food is what makes people sick. Is more meat and less carbs a species appropriate diet? There are no successful human cultures that only ate animal foods. They ate what was growing In abundance in their area. You can't live without killing things. Overly sentimental to think otherwise. Parasites come in and eat the impurities in us. Stop poisoning yourself and the parasites go away. They recycle your dead and dying tissue. Parasites eat poisons. What to do for someone that's had the jab? Use it as a lesson in you've got to see the world differently. It's a spiritual awakening. DrTomCowan.com.

In sociology and psychology, mass hysteria is a phenomenon that transmits collective illusions of threats, whether real or imaginary, through a population and society as a result of rumors and fear. In medicine, the term is used to describe the spontaneous manifestation—or production of chemicals in the body—of the same or similar hysterical physical symptoms by more than one person.  Are we allowing our love for scaring ourselves and anxiety to force changes in the way we think? Dr. Fred Clary, founder of Functional Analysis Chiropractic Technique and lifting/life coach/ gym-chalk covered philosopher asks who is controlling your thinking. 

There are many examples in biology of the incredible fine-tuning of life. On this episode of Mind Matters, you’ll learn about fine-tuning, population genetics, and probability as Robert J. Marks speaks with Ola Hössjer and Daniel Díaz. Show Notes 00:47 | Introducing Dr. Daniel Díaz 01:00 | Introducing Dr. Ola Hössjer 01:14 | Fine-tuning in biology 07:15 | A cellular… Source

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.20.346684v1?rss=1 Authors: Joiret, M., Rapino, F., Close, P., Geris, L. Abstract: The impact of the ribosome exit tunnel electrostatics on the protein elongation rate or on the forces acting upon the nascent polypeptide chain are currently not fully elucidated. In the past, researchers have measured the electrostatic potential inside the ribosome polypeptide exit tunnel at a limited number of spatial points, at least in prokaryotes. Here, we present a basic electrostatic model of the exit tunnel of the ribosome, providing a quantitative physical description of the tunnel interaction with the nascent proteins at all centro-axial points inside the tunnel. We show how the tunnel geometry causes a positive potential difference between the tunnel exit and entry points which impedes positively charged amino acid residues from progressing through the tunnel, affecting the elongation rate in a range of minus 40% to plus 85% when compared to the average elongation rate. The time spent by the ribosome to decode the genetic encrypted message is constrained accordingly. We quantitatively derived, at single residue resolution, the axial forces acting on the nascent peptide from its particular sequence embedded in the tunnel. The model sheds light on how the experimental data point measurements of the potential are linked to the local structural chemistry of the inner wall and the shape and size of the tunnel. The model consistently connects experimental observations coming from different fields in molecular biology, structural and physical chemistry, biomechanics, synthetic and multi-omics biology. Our model should be a valuable tool to gain insight into protein synthesis dynamics, translational control and into the role of the ribosome's mechanochemistry in the co-translational protein folding. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.12.336511v1?rss=1 Authors: Waudby, C. A., Burridge, C., Christodoulou, J. Abstract: NMR measurements of cross-correlated nuclear spin relaxation provide powerful probes of polypeptide dynamics and rotational diffusion, free from contributions due to chemical exchange or interactions with external spins. Here, we report on the development of a sensitivity-optimized pulse sequence for the measurement of cross-correlated relaxation in methyl spin systems by analysis of the differential relaxation of transitions within the 13C multiplet. We describe the application of optimal design theory to implement a real-time 'on-the-fly' adaptive sampling scheme that maximizes the accuracy of the measured rate constants. The increase in sensitivity obtained using this approach enables, for the first time, quantitative measurements of rotational diffusion within folded states of translationally-arrested ribosome-nascent chain complexes of the FLN5 filamin domain, and can be used to place strong limits on interactions between the domain and the ribosome surface. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.29.318998v1?rss=1 Authors: Huang, H., Karbstein, K. Abstract: Ribosomes are among the largest folded RNAs, whose function depends on their structure. Nonetheless, in vitro studies indicate a propensity of rRNAs to misfold. We use a combination of DMS-MaPseq, structural analyses, biochemical experiments, and yeast genetics to dissect the final RNA folding steps of the small ribosomal subunit head. Our data demonstrate how a succession of assembly factors prevent the early folding of an RNA loop, thereby allowing an adjacent helical junction to fold first. Deletion of the assembly factors to allow the loop to fold first traps a misfolded junction, demonstrating how assembly factors modulate the folding pathway to enable challenging motifs to fold independent of their interaction partners and guide folding to the native structure. Analysis of ribosome intermediate structures indicates that this role for assembly factors is ubiquitous and suggests that helical junctions present significant obstacles to folding. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.03.281675v1?rss=1 Authors: Terrey, M., Adamson, S. I., Gibson, A. L., Deng, T., Ishimura, R., Chuang, J. H., Ackerman, S. L. Abstract: Ribosome-associated quality control pathways respond to defects in translational elongation to recycle arrested ribosomes and degrade aberrant polypeptides and mRNAs. Loss of an individual tRNA gene leads to ribosomal pausing that is resolved by the translational GTPase GTPBP2, and in its absence causes neuron death. Here we show that loss of the homologous protein GTPBP1 during tRNA deficiency in the mouse brain also leads to codon-specific ribosome pausing and neurodegeneration, suggesting that these non-redundant translational GTPases function in the same pathway to mitigate ribosome pausing. Ribosome stalling in the mutant brain led to activation of the integrated stress response (ISR) mediated by GCN2 and decreased mTORC1 signaling. However, in contrast to the ISR, which enhanced neuron survival, reduced mTORC1 signaling increased neuronal death. Our data demonstrate that GTPBP1 functions as an important quality control mechanism during translation elongation and suggest that translational signaling pathways intricately interact to regulate neuronal homeostasis during defective translation elongation. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.03.282277v1?rss=1 Authors: Barthelson, K., Pederson, S. M., Newman, M., Lardelli, M. Abstract: The early cellular stresses which eventually lead to Alzheimer's disease (AD) remain poorly understood because we cannot access living, asymptomatic human AD brains for detailed molecular analyses. Sortilin-related receptor 1 (SORL1) encodes a multi-domain receptor protein genetically associated with both rare, early-onset familial AD (EOfAD) and common, sporadic late-onset AD (LOAD). SORL1 has been shown to play a role in the trafficking of the amyloid {beta} A4 precursor protein (APP) which is cleaved proteolytically to form one of the pathological hallmarks of AD, amyloid {beta} (A{beta}) peptide. However, the other functions of SORL1 are less well understood. Here, we employed a reverse genetics approach to characterise the effect of an EOfAD mutation in SORL1 using zebrafish as a model organism. We performed targeted mutagenesis to generate an EOfAD-like mutation in the zebrafish orthologue of SORL1, and performed RNA-sequencing on mRNA isolated from a family of fish either heterozygous for the EOfAD-like mutation or their wild type siblings and identified subtle effects on the expression of genes which likely indicate changes in mitochondrial and ribosomal function. These changes appear to be independent of changes to expression of APP-related proteins in zebrafish, and mitochondrial content. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.03.281279v1?rss=1 Authors: Crowe-McAuliffe, C., Takada, H., Murina, V., Polte, C., Kasvandik, S., Tenson, T., Ignatova, Z., Atkinson, G. C., Wilson, D. N., Hauryliuk, V. N. Abstract: In all branches of life, stalled translation intermediates are recognized and processed by ribosome-associated quality-control (RQC) pathways. RQC begins with splitting of stalled ribosomes, leaving an unfinished polypeptide still attached to the large subunit. Ancient and conserved NEMF family RQC proteins target these incomplete proteins for degradation by the addition of C-terminal tails. How such tailing can occur without the regular suite of translational components is, however, unclear. Using ex vivo single-particle cryo-EM, we show that C-terminal tailing in Bacillus subtilis is mediated by NEMF protein RqcH in concert with YabO, a protein homologous to, yet distinct from, Hsp15. Our structures reveal how these factors mediate tRNA movement across the ribosomal 50S subunit to synthesize polypeptides in the absence of mRNA or the small subunit. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.30.274597v1?rss=1 Authors: Loveland, A. B., Svidritskiy, E., Susorov, D., Lee, S., Park, A., Demo, G., Gao, F.-B., Korostelev, A. A. Abstract: Toxic dipeptide repeat (DPR) proteins are produced from expanded G4C2 hexanucleotide repeats in the C9ORF72 gene, which cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Two DPR proteins, poly-PR and poly-GR, repress cellular translation but the molecular mechanism remains unknown. Here we show that poly-PR and poly-GR of [≥] 20 repeats inhibit the ribosome's peptidyl-transferase activity at nanomolar concentrations, comparable to specific translation inhibitors. High-resolution cryo-EM structures reveal that poly-PR and poly-GR block the polypeptide tunnel of the ribosome, extending into the peptidyl-transferase center. Consistent with these findings, the macrolide erythromycin, which binds in the tunnel, competes with the DPR proteins and restores peptidyl-transferase activity. Our results demonstrate that strong and specific binding of poly-PR and poly-GR in the ribosomal tunnel blocks translation, revealing the structural basis of their toxicity in C9ORF72-ALS/FTD. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.26.268680v1?rss=1 Authors: Kostinski, S., Reuveni, S. Abstract: Eukarya and Bacteria are the most evolutionarily distant domains of life, which is reflected by differences in their cellular structure and physiology. For example, Eukarya feature membrane-bound organelles such as nuclei and mitochondria, whereas Bacteria have none. The greater complexity of Eukarya renders them difficult to study from both an experimental and theoretical perspective. However, encouraged by a recent experimental result showing that budding yeast (a unicellular eukaryote) obeys the same proportionality between ribosomal proteome fractions and cellular growth rates as Bacteria, we derive a set of relations describing eukaryotic growth from first principles of ribosome biogenesis. We recover the observed ribosomal protein proportionality, and then continue to obtain two growth-laws for the number of RNA polymerases synthesizing ribosomal RNA per ribosome in the cell. These growth-laws, in turn, reveal two invariants of eukaryotic growth, i.e. quantities predicted to be conserved by Eukarya regardless of growth conditions. The invariants, which are the first of their kind for Eukarya, clarify the coordination of transcription and translation kinetics as required by ribosome biogenesis, and link these kinetic parameters to cellular physiology. We demonstrate application of the relations to the yeast S. cerevisiae and find the predictions to be in good agreement with currently available data. We then outline methods to quantitatively deduce several unknown kinetic and physiological parameters. The analysis is not specific to S. cerevisiae and can be extended to other lower (unicellular) Eukarya when data become available. The relations may also have relevance to certain cancer cells which, like bacteria and yeast, exhibit rapid cell proliferation and ribosome biogenesis. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.20.259770v1?rss=1 Authors: Lapointe, C. P., Grosely, R., Johnson, A. G., Wang, J., Fernandez, I. S., Puglisi, J. D. Abstract: SARS-CoV-2 recently emerged as a human pathogen and is the causative agent of the COVID-19 pandemic. A molecular framework of how the virus manipulates host cellular machinery to facilitate infection remains unclear. Here, we focus on SARS-CoV-2 NSP1, which is proposed to be a virulence factor that inhibits protein synthesis by directly binding the human ribosome. Using extract-based and reconstitution experiments, we demonstrate that NSP1 inhibits translation initiation on model human and SARS-CoV-2 mRNAs. NSP1 also specifically binds to the small (40S) ribosomal subunit, which is required for translation inhibition. Using single-molecule fluorescence assays to monitor NSP1-40S subunit binding in real time, we demonstrate that eukaryotic translation initiation factors (eIFs) modulate the interaction: NSP1 rapidly and stably associates with most ribosomal pre-initiation complexes in the absence of mRNA, with particular enhancement and inhibition by eIF1 and eIF3j, respectively. Using model mRNAs and an inter-ribosomal-subunit FRET signal, we elucidate that NSP1 competes with RNA segments downstream of the start codon to bind the 40S subunit and that the protein is unable to associate rapidly with 80S ribosomes assembled on an mRNA. Collectively, our findings support a model where NSP1 associates with the open head conformation of the 40S subunit to inhibit an early step of translation, by preventing accommodation of mRNA within the entry channel. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.16.250183v1?rss=1 Authors: Szaflarski, W., Sowinski, M., Lesniczak, M., Ojha, S., Aulas, A., Dave, D., Malla, S., Anderson, P., Ivanov, P., Lyons, S. M. Abstract: Production of ribosomes is an energy-intensive process owing to the intricacy of these massive macromolecular machines. Each human ribosome contains 80 ribosomal proteins and four non-coding RNAs. Accurate assembly requires precise regulation of protein and RNA subunits. In response to stress, the integrated stress response (ISR) rapidly inhibits global translation. How rRNA is coordinately regulated with the rapid inhibition of ribosomal protein synthesis is not known. Here we show that stress specifically inhibits the first step of rRNA processing. Unprocessed rRNA is stored within the nucleolus, and, when stress resolves, it re-enters the ribosome biogenesis pathway. Retention of unprocessed rRNA within the nucleolus aids in the maintenance of this organelle. This response is independent of the ISR or inhibition of cellular translation but represents an independent stress-response pathway that we term Ribosome Biogenesis Stress Response (RiBiSR). Failure to coordinately regulate ribosomal protein translation and rRNA production results in nucleolar fragmentation. Our study unveils a novel stress response pathway that aims at conserving energy, preserving the nucleolus, and prevents further stress by regulation of rRNA processing. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.07.236406v1?rss=1 Authors: Raveendran, M., Leach, A. R., Hopes, T. S., Aspden, J., Actis, P. Abstract: Nanopores hold great potential for the analysis of complex biological molecules at the single entity level. One particularly interesting macromolecular machine is the ribosome, responsible for translating mRNA into proteins. In this study, we use a solid-state nanopore to fingerprint 80S ribosomes and polysomes from a human neuronal cell line and, Drosophila melanogaster cultured cells and ovaries. Specifically, we show that the peak amplitude and dwell time characteristics of 80S ribosomes are distinct from polysomes and can be used to discriminate ribosomes from polysomes in mixed samples. Moreover, we are able to distinguish large polysomes, containing more than 7 ribosomes, from those containing 2-3 ribosomes, and demonstrate a correlation between polysome size and peak amplitude. This study highlights the application of solid-state nanopores as a rapid analytical tool for the detection and characterization of ribosomal complexes. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.20.212019v1?rss=1 Authors: Puentes-Mestril, C., Delorme, J., Wang, L., Donnelly, M., Popke, D., Jiang, S., Aton, S. Abstract: Sleep and sleep loss are thought to impact synaptic plasticity, and recent studies have shown that sleep and sleep deprivation (SD) differentially affect gene transcription and protein translation in the mammalian forebrain. However, much less is known regarding how sleep and SD affect these processes in different microcircuit elements within the hippocampus and neocortex - for example, in inhibitory vs. excitatory neurons. Here we use translating ribosome affinity purification (TRAP) and in situ hybridization to characterize the effects of sleep vs. SD on abundance of ribosome-associated transcripts in Camk2a-expressing (Camk2a+) pyramidal neurons and parvalbumin-expressing (PV+) interneurons in mouse hippocampus and neocortex. We find that while both Camk2a+ neurons and PV+ interneurons in neocortex show concurrent SD-driven increases in ribosome-associated transcripts for activity-regulated effectors of plasticity and transcriptional regulation, these transcripts are minimally affected by SD in hippocampus. Similarly we find that while SD alters several ribosome-associated transcripts involved in cellular timekeeping in neocortical Camk2a+ and PV+ neurons, effects on circadian clock transcripts in hippocampus are minimal, and restricted to Camk2a+ neurons. Taken together, our results indicate that SD effects on transcripts destined for translation are both cell type- and brain region-specific, and that these effects are substantially more pronounced in the neocortex than the hippocampus. We conclude that SD-driven alterations in the strength of synapses, excitatory-inhibitory balance, and cellular timekeeping are likely more heterogeneous than previously appreciated. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.01.182360v1?rss=1 Authors: Lehmkuhl, E. M., Loganathan, S., Alsop, E., Blythe, A. D., Kovalik, T., Barrameda, D., Kueth, C., Eck, R. J., Siddegowda, B. B., Joardar, A., Mortimore, N. P., Bowser, R., Van Keuren-Jensen, K., Zarnescu, D. C. Abstract: Amyotrophic lateral sclerosis (ALS) is a genetically heterogeneous neurodegenerative disease in which 97% of patients exhibit cytoplasmic aggregates containing the RNA binding protein TDP-43. Using a combination of RNA immunoprecipitations and tagged ribosome affinity purifications in Drosophila models of TDP-43 proteinopathy, we identified several TDP-43 dependent translational alterations including the glypican Dally like protein (Dlp), a wingless (wg/wnt) signaling component. Here we show that dlp mRNA is enriched in TDP-43 protein complexes and depleted from ribosomes in the context of TDP-43 proteinopathy. We also show that dlp mRNA is insolubilized and Dlp protein is significantly depleted from neuromuscular synapses while steady state transcript levels remain unchanged, consistent with mRNA sequestration and translation inhibition. Furthermore, we find that Dlp accumulates in cytoplasmic puncta in the Drosophila ventral cord, supporting the possibility of added axonal transport deficits, a well-established ALS phenotype. Notably, overexpression of dlp in Drosophila motor neurons is sufficient to mitigate TDP-43 dependent neurodegenerative phenotypes indicating that dlp is a physiologically relevant target of TDP-43. Finally, we show that similar to Dlp in the Drosophila ventral cord, the human ortholog GPC6 forms puncta-like structures in ALS patient spinal cords, further supporting a role for Dlp/GPC6 in TDP-43 induced neurodegeneration. Copy rights belong to original authors. Visit the link for more info

The TWiM team reveals how ribosome modification resuscitates bacterial persister cells, and explain how a phage tail fiber protein exploits rotation of flagella to move towards the cell membrane. Become a patron of TWiM. Links for this episode: Ribosome modification resuscitates persister cells (Environ Micro) Flagellotrophic phage targets host with tail fiber (Mol Micro) Hydrodynamics of phage migration along flagella (Phys Rev Fluids) Music used on TWiM is composed and performed by Ronald Jenkees and used with permission. Send your microbiology questions and comments to twim@microbe.tv  

  Dr. Carolyn Lam: Welcome to Circulation on the Run, your weekly podcast summary and backstage pass to the journal and its editors. We're your cohosts. I'm Dr. Carolyn Lam, Associate Editor from the National Heart Center, and Duke National University of Singapore. Dr. Greg Hundley: And I'm Greg Hundley, associate editor from the Poly Heart Center at VCU health in Richmond, Virginia. Dr. Carolyn Lam: Greg, I'm so excited about the feature paper this week. You know it deals with machine learning. It's such a hot topic now, and this one particularly deals with machine learning and the prediction of the likelihood of an acute myocardial infarction. So everyone's going to want to listen to it. Let's discuss a couple of papers and get to it, shall we? Dr. Greg Hundley: Absolutely Carolyn, would you like to go first? Dr. Carolyn Lam: I sure would. So my first pick is the first study to investigate the overall importance of translational regulatory networks in myocardial fibrosis. This is the study from doctors Rackham and Cook from Duke NUS Medical School here in Singapore. Dr. Carolyn Lam: What they did is they generated nucleotide resolution translatome data during transforming growth factor beta one, or TGF beta one-driven cellular transition of human cardiac fibroblasts to myofibroblasts. So this technique identified the dynamic changes of RNA transcription and translation at several time points during the fibrotic response, revealing transient and early responder genes. Dr. Carolyn Lam: Now, very remarkably about one third of all the changes in gene expression in activated fibroblasts was subject to translational regulation and dynamic variation in the ribosome occupancy, affected protein abundance independent of RNA levels. Ribosome occupancy in the hearts of patients with dilated cardiomyopathy suggest that the same post-transcriptional regulatory network, which was underlying cardiac fibrosis. Now key network hubs included RNA binding proteins such as PUM2 and QKI that worked in concert to regulate the translation of target transcripts in the human disease hearts. Dr. Carolyn Lam: Furthermore, the authors showed that silencing of both PUM2 and QKI inhibited the transition of fibroblasts towards profibrotic myofibroblast in response to TGF beta one. Dr. Greg Hundley: You know, Carolyn, this whole aspect of fibroblasts and how they turn on and turn off, become myofibroblasts, such a hot topic in heart failure. What are the clinical implications of this work? Dr. Carolyn Lam: Yes, I agree. Well, threefold. First, these authors identified previously unappreciated genes under translational control, which could be novel candidates for disease biology and therapeutic targets. Dr. Carolyn Lam: Number two, they found that critical fibrosis factors impacted cellular phenotypes at a protein level only, and hence these cannot be appreciated using single cell, or bulk RNA sequencing approaches. So that was significant. Finally, RNA binding proteins was shown to be central to the fibrotic response and represent unexplored gene expression regulators, and of course potential diagnostic or therapeutic targets. Dr. Greg Hundley: Very nice Carolyn. Well, my next paper is also from the world of basic science, and it comes from Dr. Joseph Hill. Have we ever heard of him? Well of course, he's our Editor in Chief. He's going to discuss, he and his team investigated Polycycstin-1. Well, what is Polycycstin-1? It's a trans membrane protein, originally identified in autosomal dominant polycystic kidney disease, where it regulates the calcium permeate cation channel polycystin-2. So autosomal dominant, polycystic kidney disease patients develop renal failure, hypertension, left ventricular hypertrophy, atrial fibrillation and other cardiovascular disorders. These individuals harbor PC1 loss of function mutations in their cardiomyocytes, but the functional consequences of this are relatively unknown. Dr. Greg Hundley: Now PC1 is ubiquitously expressed in its experimental ablation in cardiomyocyte specific knockout mice reduces contractile function, and in this paper the authors set out to determine the pathophysiologic role of PC1 in these cardiomyocytes. Dr. Carolyn Lam: Huh--very interesting. I liked the way you laid that out. So what did they find? Dr. Greg Hundley: What the investigators identified is that PC1 ablation reduced action potential duration in cardiomyocytes. They decreased calcium transients and therefore myocyte contractility. PC1 deficient cardiomyocytes manifested a reduction in sarcoplasmic reticulum calcium stores due to reduced action potential duration and circa activity, an increase in outward potassium currents decreased action potential durations in cardiomyocytes lacking PC1. PC1 coimmunoprecipitated with a potassium 4.3 channel and modeled PC1 C terminal structure suggested the existence of two docking sites for PC1 within the end terminus of K4.3. Supporting a physical interaction between the cells. Finally, a naturally occurring human mutant PC1 manifested no suppressive effects on this potassium channel activity. Thus, Carolyn, Dr Hill and colleagues' results help uncover a role for PC1 in regulating multiple potassium channels, governing membrane repolarization and alterations in circa that reduce cardiomyocyte contractility. Dr. Carolyn Lam: Oh wow. What a bonanza of really interesting papers in this week. Now my next pick is a secondary analysis of the reveal trial. It hinges on the hypothesis that was generated from prior trials that the clinical response to cholesterol ester transfer protein or CETP inhibitor therapy may differ by ADCY9 genotype. So in the current study, authors Dr. Hopewell and colleagues from Nuffield Department of Population Health, University of Oxford examine the impact of ADCY9 genotype on the response to the CETP inhibitor Anacetrapib within the reveal trial. Dr. Greg Hundley: Tell me, I've forgotten a little bit, but can you remind me a little about what was the reveal trial? Dr. Carolyn Lam: Yes, of course. So the randomized placebo controlled reveal trial actually demonstrated the clinical efficacy of the CETP inhibitor Anacetrapib among more than 30,000 patients with preexisting atherosclerotic vascular disease. Now, in the current study, among more than 19,000 genotyped individuals with European ancestry, 13% had a first major vascular event during four years median follow up. The proportional reductions in the risk of major vascular events did not differ significantly by ADCY9 genotype. Furthermore, the authors showed that there were no associations between the ADCY9 genotype and the proportional reductions in the separate components of major vascular events, or any meaningful differences in lipid response to Anacetrapib. Dr. Carolyn Lam: So in conclusion, the reveal trial being the single largest study to date to evaluate the ADCY9 pharmacogenetic interaction provided no support for the hypothesis that ADCY9 genotype is materially relevant to the clinical effects of the CETP inhibitor Anacetrapib. The ongoing dal-GenE study, however, will provide direct evidence as to whether there's any specific pharmacogenetic interaction with dalcetrapib. Dr. Greg Hundley: Oh, very good. So we've got some results coming from dal-GenE. Dr. Carolyn Lam: Mm. Dr. Greg Hundley: Well, Carolyn, my last selection relates to a paper regarding the incidence of atrial fibrillation among those that exercise, and I mean really exercise. Dr. Carolyn Lam: Ooh. Dr. Greg Hundley: So the paper comes from Dr Nicholas Svedberg from Uppsala University, and studies have revealed a higher incidence of atrial fibrillation among well trained athletes. The authors in this study aim to investigate associations of endurance training with the incidents of atrial fibrillation and stroke, and to establish potential sex differences of such associations in this cohort of endurance trained athletes. They studied all Swedish skiers, so 208,654 that completed one or more races of the 30 to 90 kilometer cross country skiing event called the Vasaloppet from 1989 through 2011, and they had a matched sample of 527,448 non-skiers, and all of the individuals were followed until their first event of either atrial fibrillation or stroke. Dr. Carolyn Lam: Wow. What an interesting and what a big study. So tell us, what are the results and especially were there any sex differences? Dr. Greg Hundley: Well, interesting that you ask about those sex and gender differences. So female skiers had a lower incidence of atrial fibrillation than female non-skiers, independent of their finishing time and the number of races, whereas male skiers had a similar incidence to that of non-skiers. Second, skiers with the highest number of races or fastest finishing times had the highest incidents of the AFib, but skiers of either sex had a lower incidence of stroke than non-skiers independent of the number of races and finishing time. Third, skiers with atrial fibrillation had a higher incidence of stroke than skiers and non-skiers without atrial fibrillation. That's true for both men and women. We would think that. Finally after one had been diagnosed with atrial fibrillation, skiers with atrial fibrillation had a lower incidence of stroke and a lower mortality compared to non-skiers with atrial fibrillation. Dr. Carolyn Lam: Very interesting. Could you sum it up for us? What's the take home? Dr. Greg Hundley: Couple things. One, female endurance athletes appear to be less susceptible to atrial fibrillation than male endurance athletes. Second, both male and female endurance athletes have a lower risk of stroke independent of their fitness level. Third, after the diagnosis of atrial fibrillation, participants in a long distance skiing event with atrial fibrillation had a 27% lower risk of stroke and a 43% lower risk of dying compared to individuals from the general population with the diagnosis of atrial fibrillation. Dr. Greg Hundley: So there's some clinical implications. Although very well trained men have a higher incidence of atrial fibrillation than less trained men, the incidence is on par with that of the general population and not related to a higher incidence of stroke at that group level. This indicates that exercise has very beneficial effects on other risk factors for stroke. Then lastly, atrial fibrillation in well trained individuals should be treated according to our other usual guidelines for the population at whole. Dr. Carolyn Lam: Wow. What a fantastic study to end our little coffee chat on, but it's time to move on to our feature discussion. Dr. Carolyn Lam: Today's feature discussion touches on super-hot topics. First of all, the perennially interesting and hot topic of the prediction of acute myocardial infarction, or should I say the more precise predictions that we can do these days. The second part of the hot topic is machine learning. Oh my goodness. This is creeping into cardiovascular medicine like never before. So I'm so glad to welcome to this discussion corresponding author of the featured paper Professor Nicholas Mills from the University of Edinburgh, as well as our Associate Editor Doctor Deborah Diercks from UT Southwestern. So welcome both, and Nick, if I could start with you, tell us about MI Cubed. Prof Nicholas Mills: First thing to say, it was a major international collaboration, involved researchers from over nine different countries and we got together to develop and test an innovative algorithm that estimates for individual patients the probability when they attend the emergency department with acute chest pain that they may or may not have had a myocardial infarction. Prof Nicholas Mills: Machine learning is a really new area in cardiovascular medicine as you say. Our algorithm called MI Cubed uses a fairly simple algorithm which is a decision tree. It takes into consideration really important patient factors such as age, sex, troponin concentration at presentation, and troponin concentration on subsequent testing, and the change in troponin in between those two tests in order to estimate or calculate the probability of the diagnosis. One of the really interesting aspects of this is it's not just an algorithm for research, it's a clinical decision support tool as well. So what we've done is taken the output from that algorithm and translated it into something that is meaningful for clinicians. We've kept it quite simple. It gives an output between zero and a hundred, which is directly proportional to the likelihood of the patient having a myocardial infarct. We also provide estimated diagnostic metrics. So sensitivities and specificities that relate to that individual patient. It's really going to change the way we think about the interpretation of cardiac troponin in clinical practice. Dr. Carolyn Lam: Indeed, and first audience please, please look up the beautiful figures of this paper. I think it summarizes it all. The algorithm shows you what MI Cubed is and then compares it to the ESC three hour algorithm, one hour algorithm. Then I love the last figure, where you actually show us that very important component that you just said. As a clinical support tool, how it's going to work. So we actually have pictures of your cell phone and showing you the pictures that you're going to get from it. So super cool. Beautiful paper. Dr. Carolyn Lam: Now I just have so much to talk about, first the machine learning bit, always sexy sounding, but a bit scary for clinicians. So I really like the fact that you broke it down to actually say what components go in so that people aren't afraid of this black box. We don't know what's going on. Is there like a set time between samples, or how does this work? Do you need to have it within a certain timing? How does that fall in? Is it a particular type of troponin, what are some of the specs of the model that a practicing clinician needs to know? Prof Nicholas Mills: Well, in order to answer that question, I might explain to you the rationale for developing it. So when you're assessing a patient in the emergency department, we all recognize in our daily practice that patients differ. So interpreting troponin has been challenging. One threshold for all may not be the right way to approach this really important clinical diagnosis. Troponin concentrations differ in men and women. They differ by age, and as a surrogate of the presence of comorbidities. They differ depending on the timing of when you take that sample and when you repeat that measurement, and that has introduced some complexity. So many interesting pathways have been developed for guidelines which try and apply fixed thresholds and fixed time points, and it's pretty tough to deliver in the real world setting of a super busy emergency department. So the premise for developing this algorithm was we wanted something that was really flexible, that recognized that patients are different, they're not all the same. Prof Nicholas Mills: That's why we went for a machine learned approach rather than a more conventional statistical model. So you asked about the specification. You can do your two troponin tests whenever you like. So I had across the 11,000 patients huge variation in the timing of samples, but that is okay for MI Cubed. If you repeat the test within an hour, two hours, three hours, six hours, it still provides the same diagnostic performance. I think that's really important. Prof Nicholas Mills: You also mentioned specification about the assay. This algorithm has been developed using a particular high sensitivity cardiac troponin assay developed by Abbott Diagnostics. It will be effective for other high sensitive troponin assays, but it's unlikely to be as effective using a contemporary assay. So if your hospital uses a contemporary or conventional cardiac troponin assay, this might not be the right algorithm for you. Dr. Carolyn Lam: Great. Thank you for breaking down the issue so beautifully and practically. It really makes me think, oh my goodness, this paper's just far more than about MI. Because you know, natriuretic peptides, you could say the same thing. A prediction of heart failure is the same thing, you know? So the whole approach is novel. Deb, could you please share your thoughts and perspectives on where this is going perhaps? Dr. Deborah Diercks: I think this study is terrific because I think it does, as Dr. Mills stated, reflect reality. We don't draw measures at zero, exactly at zero, and exactly at one and exactly at three, especially in a busy emergency department. So I think it provides flexibility to the physician and provider in using it to be able to interpret values in a world that doesn't fit complete structure like the guidelines are written out. What I find really interesting about this study, and I'd love to hear more about, is how you decided the thresholds of where low risk and high risk were cut at. It mentions by consensus, and I guess I would have loved to have been a fly on the wall to hear how those discussions went, and would love to hear more from you Dr. Mills about that. Prof Nicholas Mills: Fascinating discussions amongst all the investigators on this project as to how we would define that. The first point I would make though is we designed the algorithm to provide a continuous output, a continuous measure of risk. So your MI Cubed score is between zero and a hundred. You don't have to apply a threshold, but we are used to in clinical practice having processes that support our triage of patients, and identifying people as low risk and high risk. Therefore we felt upfront that we should evaluate specific low risk and high risk thresholds. Prof Nicholas Mills: So low-risk, we were completely unanimous on how to define that, and it was based on some really nice work done by emergency physicians in New Zealand. Martin Fan, who's the first author on this paper, surveyed many emergency physicians and asked about their acceptance of risk. They came up with the concept that an algorithm to be considered safe in emergency medicine would be acceptable if the sensitivity was greater than 99% or the negative predictive value was greater than 99.5%. Prof Nicholas Mills: So we agreed up front that we would hold our low risk thresholds to those bars. Those metrics. Where there was less agreement was how you defined high risk. That didn't surprise me hugely. The positive predictive value of troponin is one of the most controversial topics around. Most cardiologists [crosstalk 00:20:52] of troponin has been difficult for them in clinical practice because with the improvements in sensitivity we are seeing lower specificity and lower causative link to value. If I put it into context, just measuring troponin and using the 99 percentile in consecutive patients gives you a positive predictive value of around about 45 to 50% in most healthcare systems for the diagnosis of type one myocardial infarction. Therein lies the problem. So one in every two patients has an abnormal troponin result but doesn't have the condition that we have evidence based treatments for, and whom cardiologists who are often quite simplistic in their approach to the assessment of these patients know how to manage. Prof Nicholas Mills: Every second patient we don't know how to manage, and therefore we wanted an algorithm that would help us identify those patients who can go through our often guideline-based pathways and treatment pathways for acute coronary syndromes more effectively. We eventually agreed that a positive predictive value of 75% would be ideal. So three out of every four patients would have the diagnosis that we knew how to manage and treat. That was our target. We got pretty close to it in our test set. I think the actual positive predictive value at the threshold of around an MI Cubed value of 50 was 72%, so pretty effective. Certainly a lot better than relying on a kind of binary threshold such as the 99 percentile to identify high risk patients. Dr. Deborah Diercks.: Thanks for that great answer. My next question is how do you think MI Cubed is going to integrate, or will it even replace the need for other risk stratification tools that we often use the emergency departments such as TIMI or the heart score? Prof Nicholas Mills: Fabulous question. In this analysis, we haven't specifically compared the performance of MI Cubed with TIMI or heart, so my answer is going to be a little speculative. You can forgive me hopefully. Both those scores were developed prior to the widespread use of high sensitive cardiac troponin tests. I think what we've learned since the introduction of high sensitive cardiac troponin is that we're using this test as a risk stratification tool, and a lot of the power of the MI Cubed algorithm comes from the way that it identifies extremely low risk patients with very low and unchanging cardiac troponin concentrations way below the diagnostic threshold. Prof Nicholas Mills: TIMI and heart simply consider troponin as a binary test, a positive or negative test, and do not take advantage of the real power of the test to restratify patients. All the evidence to date that has compared TIMI and heart with pathways that use high sensitive troponin in this way, both to restratify and diagnose patients show that these risk tools add very little in terms of safety, but do make pathways more conservative. So they identify fewer patients that are lower risk and permit discharge of those patients. Prof Nicholas Mills: So my concern about using an algorithm like MI Cubed with an existing tool like heart is that it will undermine much of the effectiveness of this tool which identifies around about two thirds of patients as low risk. If you were to combine that with a heart score, you would reduce the effectiveness. I don't think you get a gain in performance, but further research is required to do a head to head comparison with these sorts of traditional restratification tools. Dr. Carolyn Lam: I'm so grateful for this discussion, both Nick and Deb. In fact, I was about to ask what are the next steps and I think Nick you just articulated it. Deb, I want to leave the final words to you. Do you have anything else to add? Dr. Deborah Diercks: I think this study represents a real change in how we can practice medicine, where we can actually take our biomarkers that actually have really strong value and utilize them in a manner that is pragmatic. It can actually introduce and take full advantage of them, and so I think this is a great opportunity for us to rethink our usual approach, which frankly, especially for troponin has really been very binary and very static. Thank you so much Dr Mills for the innovation and the willingness to look into this area. Dr. Carolyn Lam: Thank you so much. This paper is like a sneak peak into the future of what we'll be practicing medicine like. Well, audience, you heard it right here on Circulation on the Run. Don't forget to tune in again next week. This program is copyright American Heart Association 2019.

Dr. Venki Ramakrishnan, a molecular biologist, is president of the Royal Society in Great Britain, the same organization formerly headed by Sir Isaac Newton and Ernest Rutherford. He feels it is the duty and obligation of top scientists to explain, in understandable terms, their discoveries to the general population to extend understanding and knowledge. Dr. Ramakrishnan, in this Spectrum Podcast, explains ribosomes. They exist in every living cell to synthesize proteins. For his work in ribosomes, Dr. Ramakrishnan shared a Nobel Prize in Chemistry in 2009. In this podcast, he uses approachable metaphors to explain the functioning of these highly complex cell components. In recent years, Dr. Ramakrishnan has extended his work in ribosomes and has taken his discoveries to a higher level. He notes that malfunctioning ribosomes can be instrumental in causing certain diseases. However, harnessing and directing the functioning of ribosomes can bring about cures for some diseases and human maladies. For example, greater knowledge of ribosomes may lead to better antibiotics being developed against bacterial infections. Dr. Ramakrishnan also traces his career from his native India to getting a doctorate in physics from Ohio University. He then went on to have a postdoctoral position in biology with Dr. Peter Moore’s lab at Yale and he worked at several other American labs before transferring his talents to the Laboratory of Molecular Biology in Cambridge, England. Just recently, Dr. Ramakrishnan has released a book he authored titled: “Gene Machine: The Race to Decipher the Secrets of the Ribosome.” In the book, he talks about his discoveries and his path to uncover this critical component of living cells. In May, Dr. Ramakrishnan will receive an honorary doctorate from his alma mater Ohio University.

The Scholars of the Podcast reveal ribosomal proteins encoded in viral genomes, and a protein cell receptor for bat influenza viruses. Hosts: Vincent Racaniello, Dickson Despommier, Rich Condit, Kathy Spindler, and Brianne Barker Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode European Congress of Virology 2019 ASM Clinical Virology Symposium Intel ISEF judges needed Roald Dahl endorses measles vaccine Viruses encode ribosomal proteins (Nat Commun) Bat influenza virus receptor (Nature) Going to bat for flu research (TWiV 173) Letters read on TWiV 537 Timestamps by Jolene. Thanks! Weekly Science Picks Brianne - Yes, I'm a Scientist on Twitter. Stop Judging Me. Alan- Impact of vaccines, graphed in heat maps Dickson- Treehoppers Kathy- World watershed maps Rich-  Gene Machine by Venki Ramakrishnan Vincent - House hearing on measles outbreak (ASM comment) Listener Pick Jordan- Facebook may remove anti-vaccine recommendations Intro music is by Ronald Jenkees. Send your virology questions and comments to twiv@microbe.tv

The Scholars of the Podcast reveal ribosomal proteins encoded in viral genomes, and a protein cell receptor for bat influenza viruses. Hosts: Vincent Racaniello, Dickson Despommier, Rich Condit, Kathy Spindler, and Brianne Barker Subscribe (free): iTunes, Google Podcasts, RSS, email Become a patron of TWiV! Links for this episode European Congress of Virology 2019 ASM Clinical Virology Symposium Intel ISEF judges needed Roald Dahl endorses measles vaccine Viruses encode ribosomal proteins (Nat Commun) Bat influenza virus receptor (Nature) Going to bat for flu research (TWiV 173) Letters read on TWiV 537 Timestamps by Jolene. Thanks! Weekly Science Picks Brianne - Yes, I'm a Scientist on Twitter. Stop Judging Me. Alan- Impact of vaccines, graphed in heat maps Dickson- Treehoppers Kathy- World watershed maps Rich-  Gene Machine by Venki Ramakrishnan Vincent - House hearing on measles outbreak (ASM comment) Listener Pick Jordan- Facebook may remove anti-vaccine recommendations Intro music is by Ronald Jenkees. Send your virology questions and comments to twiv@microbe.tv

The 2019 Haldane Lecture was delivered by Sir Venki Ramakrishnan, President of the Royal Society, on February 7th at Wolfson College, Oxford. The lecture was introduced by College President Sir Tim Hitchens. The thousands of genes in our DNA are translated by ribosomes - ancient, enormous molecular machines that read the genetic code to make the thousands of proteins that carry out the functions of life. Although the ribosome was discovered in the 1950s, unravelling its million atom structure took over four decades. Venki Ramakrishnan will frame this in term of his career and show how science does not proceed in a series of logical steps but in fits and starts, with many characters and their egos, rivalries, competition and collaboration, blunders and dead ends. Sir Venki is a structural biologist who in 2009 received the Nobel Prize in Chemistry and was knighted in 2012. In 2015, he was elected as President of the Royal Society.

Venki Ramakrishnan in conversation with Priyamvada Natrajan. Nobel laureate Venki Ramakrishnan is a British-American structural biologist of Indian origin. He is also currently President of the Royal Society. His recent book, Gene Machine: The Race to Decipher the Secrets of the Ribosome is about the quest to understand the enormous ancient molecular machine, the ribosome, that decodes genetic information to build all life forms. But the book also is a frank description of what it was like for an outsider who found himself in a race to solve one of the most fundamental problems of biology. He will speak not only about the scientific voyage itself but also about the human side of science, including blunders, dead ends, changing careers, egos, competition and collaboration. The result is an insider look at how science actually works and what it felt like to be in the middle of it all. This episode is a live session from Day 2 of #ZEEJLF2019.

This time, we discuss and scrutinise Gene Machine: The Race to Decipher the Secrets of the Ribosome, by Venkatraman “Venki” Ramakrishnan. By the time Venki had earned a PhD in physics from Ohio University in the US, he had already made the unusual decision to change direction and focus full-force on uncovering the secrets of the ribosome, which eventually led to him co-winning the Nobel prize in 2009. Known as the mother of all molecules, you’ll find lots of information to help explain why the ribosome is so crucial in understanding DNA, as well as personal insights and tales of calamity on the way to the top.

For Real is sponsored this week by Book Riot Insiders, In the Name of the Children: An FBI Agent’s Relentless Pursuit of the Nation’s Worst Predators by Jeffrey Rinek from BenBella Books and Witness: Lessons from Elie Wiesel’s Classroom by Ariel Burger. FOLLOW UP Who Was series Holiday Gift Guide Episode! Email kim@riotnewmedia.com by November 20th if you need a nonfiction recommendation for a present, or want a book to put on your own gift list.   NEW BOOKS Gene Machine: The Race to Decipher the Secrets of the Ribosome by Venki Ramakrishnan Bringing Down the Colonel: A Sex Scandal of the Gilded Age, and the “Powerless” Woman Who Took on Washington by Patricia Miller Fed Up: Emotional Labor, Women, and the Way Forward by Gemma Hartley A Tale of Two Murders: Guilt, Innocence, and the Execution of Edith Thompson by Laura Thompson First Comes Marriage: My Not-So-Typical American Love Story by Huda Al-Marashi End of the Megafauna: The Fate of the World’s Hugest, Fiercest, and Strangest Animals by Ross D.E. MacPhee   Shout-Outs to: Dirty Tricks: Nixon, Watergate, and the CIA by Shane O’Sullivan Beyonce in Formation: Remixing Black Feminism by Omise’eke Natasha Tinsley Born to Be Posthumous: The Eccentric Life and Mysterious Genius of Edward Gorey by Mark Dery   WEEKLY THEME: Book Awards! Carnegie Award Shortlist: The Line Becomes a River: Dispatches from the Border by Francisco Cantu Longlist: High-Risers: Cabrini-Green and the Fate of American Public Housing by Ben Austen National Book Award Finalist: Heartland: A Memoir of Working Hard and Being Broke in the Richest Country on Earth by Sarah Smarsh Longlist: One Person, No Vote: How Voter Suppression is Destroying Our Democracy by Carol Anderson   SEGMENT THREE: Colonialism King Leopold’s Ghost: A Story of Greed, Terror, and Heroism in Colonial Africa by Adam Hochschild Bury My Heart at Wounded Knee: An Indian History of the American West by Dee Brown The Indian World of George Washington: The First President, the First Americans, and the Birth of the Nation by Colin G. Calloway (Oxford University Press) 1493: Uncovering the New World Columbus Created by Charles C. Mann   READING NOW Brothers of the Gun: A Memoir of the Syrian War by Marwan Hisham and Molly Crabapple Bullet Journal Method by Ryder Carroll I’d Rather Be Reading: The Delights and Dilemmas of the Reading Life by Anne Bogel   CONCLUSION Find us on Twitter @itsalicetime and @kimthedork.

The TWiVumvirate discuss the giant Tupanvirus, with the longest tail in the known virosphere, and dampened STING dependent interferon activation in bats. Hosts: Vincent Racaniello, Dickson Despommier, Alan Dove, Kathy Spindler, and Brianne Barker Become a patron of TWiV! Links for this episode ASM Microbe 2018 Tailed giant Tupanvirus (Nat Commun) Soda Lakes (Wikipedia) Dampened STING in bats (Cell Host Microbe) Image credit Letters read on TWiV 484 Weekly Science Picks Kathy - How to read a phylogenetic tree Brianne - No immune overload for vaccines Dickson - Flowchart of viral families Alan - Letters to a Pre-Scientist Vincent - True believers, entrepreneurs, and scammers in alternative medicine and Simply Put: Vaccines Save Lives Listener Picks Vinayaka - Code of Ethics for Young Scientists Matt - TWiV 443 Intro music is by Ronald Jenkees. Send your virology questions and comments to twiv@microbe.tv

Politics & Philosophy

Rich Condit joins Nels and Vincent to explain how a vaccinia virus protein customizes ribosomes to favor the translation of viral mRNAs with a stretch of A residues in the 5'-untranslated region. Hosts: Nels Elde and Vincent Racaniello   Become a patron of TWiEVO Rich Condit with Harry Noller (scroll down) Trans-Kingdom mimicry? (Nature) More on RACK1 (Nat Struct Mol Biol) Image credit Letters read on TWiEVO 21 This episode is brought to you by Blue Apron. Blue Apron is the #1 fresh ingredient and recipe delivery service in the country. See what’s on the menu this week and get your first 3 meals free with your first purchase – WITH FREE SHIPPING – by going to blueapron.com/twie. Science Picks Rich - Sniffing out significant “Pee values” Nels - Cuttlefish mimicking a hermit crab (evolutionary context) Vincent - Our first bioRxiv submission! Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

All information comes from an intelligent source. DNA in the first living cell contains extensive information. Therefore the information in the DNA of the first living cell came from an intelligent source whose intelligence and power are beyond anything ever discovered in the natural world. This video is based on teaching by Rob VandeWeghe

All information comes from an intelligent source. DNA in the first living cell contains extensive information. Therefore the information in the DNA of the first living cell came from an intelligent source whose intelligence and power are beyond anything ever discovered in the natural world. This video is based on teaching by Rob VandeWeghe

This week David has the pleasure of being joined by Dr. Vandre Casagrande Figuieredo, a post - doctoral researcher at the University of Kentucky, Lexington.   Dr. Figuieredo's main interests is in the role of ribosome biogenesis in muscle hypertrophy regulation. Vandre previously studied at the prestigious Karolinska institute, Sweden.   In this episode David and Vandre discuss:   Q1. What are ribosomes?    Q2. What is ribosome biogenesis and what role does it play in muscle hypertrophy?     Q3. From a practical perspective, is there anything we can do / should not do to maximise ribosome biogenesis following resistance training.     For full shownotes & links see: www.hpascience.com/episode28

Marat Yusupov, IGBMC-CERBM, Illkirch - France speaks on "Structure of bacteria and yeast ribosome". This seminar has been recorded by ICGEB Trieste

Alexander Mankin –called Shura --of the University of Illinois, Chicago, and Michael Jewett at Northwestern University talk with Jeff Fox about their recent success in joining the 30S and 50S bacterial ribosomal subunits into a single, functioning entity and the implications of that work in terms of making specialized proteins and for studying antibiotics that target the ribosome.  This story was featured in the October 2015 issue of Microbe magazine. Visit microbeworld.org/mmp for more.

Thu, 13 Aug 2015 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/18637/ https://edoc.ub.uni-muenchen.de/18637/1/Sohmen_Daniel.pdf Sohmen, Daniel ddc:540, ddc:500, Fakultät f

Hosts: Vincent Racaniello, Alan Dove, and Rich Condit Vincent, Alan and Rich explain how to make a functional ribosome with tethered subunits, and review the results of a phase III VSV-vectored Ebolavirus vaccine trial in Guinea.   Links for this episode Social media specialist position at ASM WHO dismisses Catholic church on vaccine safety U of T Dean resigns over anti-vaccine course (Tor Star) Vaccine Adverse Event Reporting System (VAERS) Countering anti-vaccination attitudes (PNAS) Designer ribosome (Nature) rVSV-EBOV preliminary report (NEJM) rVSV-EBOV phase III interim report (pdf, Lancet) World on verge of Ebolavirus vaccine (WHO) Ebolavirus vaccine in Africa (virology blog) Letters read on TWiV 349 11:55 This episode is sponsored by ASM GAP Weekly Science Picks Alan - Above and BeyondRich - DSCOVR (Dark moon side crossing Earth)Vincent - Stuxnet virus (Wired, YouTube) Listener Pick of the Week Konrad - Stated Clearly Send your virology questions and comments (email or mp3 file) to twiv@twiv.tv

The TWiM team reviews the microbiological safety of herbs in the United Kingdom, and how a peptide from the milkweek bug binds the ribosome and inhibits bacterial protein synthesis.   Links for this episode:   Microbes in whole-leaf herbs (J Appl Micro) Antimicrobial peptide blocks ribosome (Nat Struct Mol Biol) Bacterial protein synthesis (Micro Mol Biol Rev) Antimicrobial peptides (Nature) The battle for tryptophan (Front Cell Infect Micro) Image credit

To study the mechanisms of membrane protein insertion we established a protocol that allows isolation of in vivo assembled ribosome nascent chain complexes (RNCs) from E. coli in high yield and quality. To investigate the interaction of SecY with a translating ribosome, model membrane proteins of different length and topology were over-expressed and the respective RNCs were isolated under mild conditions to allow co-purification of the SecY complex. Analysis of the interaction of RNCs with SecY in vivo suggested that, as expected, a tight engagement of the ribosome and SecY is only established for nascent chains that are translocated co-translationally. We observed that SecY and the RNC do not form a stable complex at the moment of hydrophobic transmembrane segments inserting in the translocon. However, a stable engagement of the RNC with SecY was observed, when inserting a transmembrane segment with a type II topology into SecY followed by a hydrophilic loop of a certain length which allows the isolation of this complex. That suggested a dual binding mode of tight and loose coupling of SecY to the translating ribosome dependent on the nature of the nascent substrate. We present the first three dimensional structure of an in vivo assembled, tightly coupled polytopic RNC-SecYE complex at 7.2 Å solved by cryo-EM and single particle reconstruction. A molecular model based on the cryo-EM structure reveals that SecYE could be trapped in a post-insertion state, with the two substrate helices interacting with the periphery of SecY, while still translocating the hydrophilic loop. The lateral gate of SecY remains in a ‘pre-opened’ conformation during the translocation of the hydrophilic loop. The interaction sites of SecY with the ribosome were found as described. Remarkably, we could also reveal an interaction of helix 59 in the ribosome with nascent membrane protein via positively charged residues in the first cytoplasmic loop of the substrate. It is tempting to speculate that this interaction contributes to the positive inside rule. Though, we provided an unprecedented snapshot of an inserting polytopic membrane protein, the exact path of the nascent chain and the molecular mechanism of the actual insertion could not be solved so far. Expression of the E. coli tryptophanase (TnaA) operon is triggered by ribosome stalling during translation of the upstream TnaC leader peptide. Notably, this stalling is strictly dependent on the presence of tryptophan that acts in a hitherto unknown way. Here, we present a cryo-EM reconstruction of the stalled nascent TnaC leader peptide in the ribosomal exit tunnel. The structure of the TnaC-stalled ribosome was solved to an average resolution of 3.8 Å by cryo-EM and single particle analysis. It reveals the conformation of the silenced peptidyl-transferase center as well as the exact path of the stalled nascent peptide and its contacts in detail. Furthermore, we clearly resolve not a single but two free tryptophan molecules in the ribosomal exit tunnel. The nascent TnaC peptide chain together with distinct rRNA bases in the ribosomal exit tunnel creates two hydrophobic binding pockets for the tryptophan coordination. One tryptophan molecule is coordinated by V20 and I19 of TnaC and interacts with U2586 of the rRNA, the second tryptophan is bound between I19 and I15 in the area of A2058 and A2059 of the rRNA. Interestingly, the latter is also the binding platform for macrolide antibiotics. Engagement of L-Trp in these composite binding pockets leads to subtle conformational changes in residues of the ribosomal tunnel wall that are translated to the PTC eventually resulting in silencing by stabilizing the conformations of the conserved nucleotides A2602 and U2585. These conformations of the two nucleotides in the PTC are incompatible with the correct accommodation of the GGQ motive of release factor 2, thus inhibiting the peptide release.

Tue, 10 Mar 2015 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/18079/ https://edoc.ub.uni-muenchen.de/18079/1/Wickles_Stephan.pdf Wickles, Stephan ddc:540, ddc:500, Fakultät für Chemie und P

Marat Yusupov IGBMC, Illkirch - France speaks on "Crystal structure of bacterial and yeast ribosome - RNA Structure and Function 2014". This seminar has been recorded at ICTP Trieste by ICGEB Trieste

Wed, 20 Nov 2013 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/16307/ https://edoc.ub.uni-muenchen.de/16307/1/Anger_Andreas.pdf Anger, Andreas ddc:540, ddc:500, Fakultät für Chemie und Pharmazie

Hosts: Vincent Racaniello, Rich Condit, and Kathy Spindler Vincent, Rich and Kathy discuss mechanisms of protein synthesis and regulation in virus-infected cells. Links for this episode: Slides for this episode (pdf) T7 ribosomal binding sites (CSH Symp Quant Biol) Tinkering with translation (CSH Persp) Translation at nexus of infection and immunity (Cell Host Microbe) Viral subversion of protein synthesis machinery (Nat Rev Micr) Weekly Science Picks Kathy - Vaccine-preventable outbreaksRich -  To Catch a Virus by John Booss and Marilyn J. AugustVincent - This is Water by David Foster Wallace Listener Pick of the Week Jon - Confessions of a converted lecturer by Eric MazurPeter - FameLab Send your virology questions and comments (email or mp3 file) to twiv@twiv.tv

Tue, 20 Nov 2012 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/17955/ https://edoc.ub.uni-muenchen.de/17955/1/Deeng_Julian_Johannes.pdf Deeng, Julian Johannes ddc:540, ddc:500, Fakultät für

Thu, 29 Mar 2012 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/15636/ https://edoc.ub.uni-muenchen.de/15636/1/Doenhoefer_Alexandra.pdf Dönhöfer, Alexandra ddc:540, ddc:500, Fakultät für Chemie und Pharmazie

Thu, 8 Mar 2012 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/14203/ https://edoc.ub.uni-muenchen.de/14203/1/Franckenberg_Sibylle.pdf Franckenberg, Sibylle ddc:540, ddc:500, Fakultät für Chemie und Pharmazie

Albert E. Dahlberg, Brown University, Providence, RI - USA speaks on "How the ribosome finds the correct mRNA". This seminar has been recorded at ICTP Trieste by ICGEB Trieste

Albert E. Dahlberg, Brown University, Providence, RI - USA speaks on "Ribosome structure and function". This seminar has been recorded at ICTP Trieste by ICGEB Trieste

Protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. Although X-ray structures of bacterial ribosomes are available, high-resolution structures of eukaryotic 80S ribosomes are lacking. Using cryo-electron microscopy and single-particle reconstruction we have determined the structure of a translating plant (Triticum aestivum) 80S ribosome at 5.5 Å resolution. This map, together with a 6.1 Å map of a Saccharomyces cerevisiae 80S ribosome, has enabled us to model ~98 % of the rRNA and localize 74/80 (92.5 %) of the ribosomal proteins, encompassing 11 archaeal/eukaryote-specific small subunit proteins as well as the complete complement of the ribosomal proteins of the eukaryotic large subunit. Near-complete atomic models of the 80S ribosome provide insights into the structure, function and evolution of the eukaryotic translational apparatus.

Audio PodcastAired date: 4/27/2011 3:00:00 PM Eastern Time

Video PodcastAired date: 4/27/2011 3:00:00 PM Eastern Time

On episode #97 of the podcast This Week in Virology, Vincent visited Peter Sarnow and Bert Semler during a trip to California, and spoke with them about their work on internal ribosome entry, and the requirement for a cellular microRNA for hepatitis C virus replication.

In this study, cryo-electron microscopy (cryo-EM) and single particle reconstruction were used as a main technique to investigate the involvement of bacterial ribosomes in two crucial cellular processes: the regulation of gene expression and the biogenesis of membrane proteins. Whereas most nascent chains are thought to transit passively through the ribosomal exit tunnel during translation, a number of regulatory peptide sequences, such as TnaC and SecM, have been proposed to specifically interact with tunnel components, causing the ribosome to stall which in turn regulates the expression of downstream gene products. In the first part of this study, a 5.8 Å resolution cryo-EM reconstruction of an Escherichia coli 70S ribosome stalled during translation of the TnaC leader peptide could be determined. The high quality of the map allowed the visualization of the TnaC nascent chain within the exit tunnel of the ribosome, making contacts with ribosomal components at distinct sites. At the peptidyl transferase center (PTC), the universally conserved nucleotides A2602 and U2585 adopt conformations that are incompatible with co-habitation of the termination release factors. Moreover, a model could be proposed where interactions within the tunnel are relayed back to the PTC, leading to its inactivation. In addition, a foundation for the elucidation of the SecM-stalling mechanism could also be established. The membrane protein insertase YidC is the prokaryotic member of the conserved YidC/Oxa1/Alb3 protein family. It assists in the assembly and folding of membrane proteins in conjunction with the Sec translocase as well as on its own. E. coli YidC is a hexaspan protein with a large, non-conserved periplasmic domain between the first and second transmembrane (TM) segment. In contrast, YidC2 from the Gram-positive bacterium Streptococcus mutans contains five TM segments and an extended C-terminal region akin to the C-terminal ribosome binding domain of the mitochondrial YidC homolog Oxa1. In the second part of this study, programmed 70S ribosomes carrying the YidC-specific nascent chain MscL could be generated, and visualized in a preliminary low-resolution cryo-EM structure in complex with E. coli YidC. Furthermore, purified S. mutans YidC2 was reconstituted into proteoliposomes and the formation of a ribosome-YidC2-proteoliposome complex could be demonstrated. Thus, the foundations have been laid for the visualization of YidC2 in the membrane environment. Improvement of the preliminary RNC-YidC structure together with determination of an RNC-YidC2 complex are expected to provide insights into the molecular mechanism of YidC mediated membrane protein biogenesis.

Thu, 27 May 2010 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/12950/ https://edoc.ub.uni-muenchen.de/12950/1/Frauenfeld_Jens.pdf Frauenfeld, Jens ddc:540, ddc:500, Fakultät für Chemie und Pharmazie

Thu, 4 Feb 2010 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/12047/ https://edoc.ub.uni-muenchen.de/12047/1/Gartmann_Marco.pdf Gartmann, Marco ddc:540, ddc:500, Faku

The largest TWiV panel ever assembled takes on XMRV and chronic fatigue syndrome, 2009 chemistry Nobel prizes for ribosome structure, finding new poxvirus vaccine candidates, a brouhaha over leaked Canadian data on flu susceptibility, and transmission of H1N1 influenza to a pet ferret. Hosts: Vincent Racaniello, Dick Despommier, Alan Dove, Jason Rodriguez, and Rich Condit Links for this episode: XMRV and chronic fatigue syndrome XMRV not found in German prostate cancer 2009 Chemistry Nobel Prize for ribosome structure New poxvirus vaccines (e! Science and Virology articles - thanks Jim!) Seasonal flu shots and susceptibility to 2009 H1N1 (one, two, and three) Pet ferret gets H1N1 influenza from owner Weekly Science Picks Dick Nikon photomicroscopy contest winners at SciAm (Dick's article on vertical farming)Alan Make:Rich BBC's Planet Earth (DVD at Amazon)Jason The Collider, the Particle and a Theory About FateVincent An Epidemic of Fear and Misinformants at Wired Magazine

Dr. Thomas Steitz, Sterling Professor of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute Investigator, headed the team that mapped the ribosome's structure.

Tue, 19 May 2009 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/10194/ https://edoc.ub.uni-muenchen.de/10194/2/Lakshmipathy_Sathish_Kumar.pdf Lakshmipathy, Sathish Kumar

Mon, 15 Dec 2008 12:00:00 +0100 https://edoc.ub.uni-muenchen.de/12563/ https://edoc.ub.uni-muenchen.de/12563/1/Malamoussi_Anastassia.pdf Malamoussi, Anastassia ddc:570, ddc:500, Fakultät für Biologi

The hallmark of embryonic stem (ES) cells is their ability for self-renewal (capability of unlimited cell division without the loss of pluripotency) as well as for differentiation into all cell types of the adult organism. One factor supposed to be involved in self-renewal is the rapid proliferation rate of ES cells, which is coupled to an unusual cell cycle distribution with the majority of cells in S-phase and a very short G1-phase. This is linked to the lack of a functional G1/S-phase checkpoint, which allows the cells to enter the S-phase almost directly after mitosis. Generally, cells have to closely coordinate growth and cell cycle progression during proliferation to prevent premature division. One important factor for cell growth is ribosome biogenesis. In mature cells, disruptions in ribosome biogenesis are directly linked to the cell cycle machinery by a p53-dependent activation of the G1/S-phase checkpoint, leading to an arrest of cells in G1-phase. During this work, the function of the proteins Pes1, Bop1 and WDR12, which were shown previously to be involved in ribosome biogenesis of mature cell lines, was investigated in mouse ES cells. Moreover, a putative crosstalk between ribosome biogenesis and proliferation of ES cells was assessed. A high expression of Pes1, Bop1 and WDR12 was observed in ES cells, which strongly decreased during in vitro differentiation. Localization of the proteins was predominantly nucleolar and the formation of a stable complex (PeBoW-complex), including all three proteins, was experimentally validated in mature mouse cells as well as in mouse ES cells. The function and stability of the proteins seems to be dependent on incorporation into the PeBOW-complex, as protein levels were interdependent on each other and no free, non-incorporated proteins were observed, except for WDR12. According to their nucleolar localization, depletion of Pes1 and Bop1 were shown to inhibit maturation of the 28S rRNA and thereby the large 60S ribosomal subunit. Further, impaired proliferation of ES cells was observed. Thus, the PeBoW-complex seems to be an essential factor for the rapid proliferation of ES cells and might therefore also be involved in self-renewal. However, first results suggest that the complex is not directly involved in the maintenance of pluripotency. No changes in the expression levels of pluripotency-genes like Nanog, KLF4 and Sox2 were observed. Moreover, alkaline phosphatase activity was equally detectable after depletion of Pes1 or Bop1 and no morphological changes within the ES cell colonies were observed. Impaired ribosome biogenesis is known to activate a p53-dependent checkpoint in mature cell lines, which leads to an arrest of cells in G1-phase. Treatment of mouse NIH3T3 cells with 5FU, a potent inhibitor of rRNA maturation, confirmed an activation of this checkpoint, leading to weak induction of the tumor suppressor p53, induction of the Cdk-inhibitor p21, an increase in active, hypo-phosphorylated Rb, and to accumulation of cells in the G1- and S-phase with an increase of cells in G1-phase. In contrast, ES cells showed strong induction of p53, but no induction of its target gene p21. The overall levels of Rb were strongly induced, but the ratio between inactive, hyper-phosphorylated Rb and active, hypo-phosphorylated Rb was not changed towards the active form. These results were observed upon 5FU treatment and upon depletion of Pes1 or Bop1. Hence, ribosomal stress does not lead to checkpoint activation via the p53-p21-Rb pathway in ES cells. Moreover, no robust accumulation of cells in G1-phase was observed. 5FU treated ES cells showed an accumulation of cells in S-phase instead. Whether this effect is regulated by the induced p53 needs further investigation. Overall, the results suggest that ES cells use different mechanisms as mature cells to coordinate their proliferation rate with ribosome biogenesis.

Protein translocation across the endoplasmic reticulum (ER) membrane is fundamental for protein sorting and secretion in all kingdoms. Translocation occurs through a protein-conducting channel in the ER membrane, which is formed by Sec61. Targeting of ribosome-nascent chain complexes (RNCs) to Sec61 is mediated by the signal recognition particle (SRP) and its cognate receptor (SR). However, Sec61 has a high affinity for nontranslating ribosomes and it is largely occupied in vivo. We addressed how RNC-SRP complexes can efficiently associate with the rER membrane, although most Sec61 seems to be occupied. We found that the spontaneous dissociation of ribosomes from the ER membrane is extremely slow. Surprisingly, membrane binding of RNC-SRP complexes does not require or cause the dissociation of prebound ribosomes. Instead, RNC-SRP complexes use a Sec61 population for translocation that cannot be bound by nontranslating ribosomes or RNCs alone. Complex formation between RNC-SRP and SR at the ER membrane facilitates the interaction between the RNC and the free Sec61. We have used biochemical and structural approaches to investigate why the free Sec61 fails to be bound by nontranslating ribosomes. Our data suggests that Sec61 is present in two interconvertible forms in the membrane, that are in an equilibrium with each other and provide high-affinity and low-affinity binding sites for ribosomes. The former are quickly occupied, while the latter remain free. The high-affinity binding sites are formed by tetrameric rings of Sec61, which provide several connections that each can break and reform, but together prevent the ribosome from detachment. In contrast, the low-affinity binding sites may correspond to lower oligomeric states of Sec61. Consistent with that, we could capture monomers or dimers of Sec61 bound to eukaryotic ribosomes by electron cryo-microscopy. A ribosome-bound Sec61 dimer was only observed in presence of a nascent chain, which could indicate that Sec61 oligomerization is induced by translocation of a nascent chain. We obtained similar results for bacterial ribosome-channel complexes. However, the low-affinity binding site seems to be more abundant in bacterial membranes, which indicates that the prokaryotic equilibrium between low- and high-affinity binding sites is adjusted differently from eukaryotes. 1 We propose a model, in which Sec61 exists in different oligomeric states in the ER membrane. Tetrameric Sec61 provides a high-affinity binding site for ribosomes and is readily occupied in vivo. Monomeric or dimeric Sec61 is accessible for targeting by the SRP pathway, which facilitates the interaction between RNC and free Sec61. After transfer of the nascent chain into the channel and dissociation of SR and SRP, more Sec61 molecules could be recruited to stabilize the interaction with the translating ribosome. A dynamic oligomerization equilibrium of Sec61 is thus the core of a mechanism that would guarantee efficient protein translocation in vivo.

Ribosome-associated Trigger factor (TF) is the first molecular chaperone to bind to nascent polypeptides in bacteria. The contribution of co-translational chaperone function is yet poorly understood. Using fluorescence spectroscopy to monitor, in real time, TF function and structural rearrangements, the present study investigates how TF interacts with ribosomes and translating polypeptides. Binding to the ribosome stabilizes an open, activated conformation of TF. Conformationally activated TF can stay associated with its nascent polypeptide substrate beyond ribosome departure. The occurence of hydrophobic motifs in the translating polypeptide correlates with the duration of TF-substrate interaction, leading to prolonged interaction with a high aggregation propensity. These findings can explain the contribution of TF in preventing protein misfolding and reveal an exquisitely regulated interaction cycle of TF with ribosome-nascent chain complexes.

The effect of the inclusion of EDTA and of heparin, in media used in the isolation of mitochondria, on the mitochindrial previous termribosomenext term has been investigated. 1. 1. Mitochondria isolated from previous termNeurospora crassanext term in the presence of EDTA contain only a single type of monomeric previous termribosome, viz. 73next term S. 2. 2. Mitochondria isolated in the presence of Mg2+ contain both 79-S and previous term73next term-S monomeric previous termribosomes.next term The heterogeneity of the previous termribosomesnext term was demonstrated by (a) ultracentrifugation on sucrose gradients, (b) electron microscopy, (c) immunoprecipitation with antibodies against mitochondrial previous term73next term-S and 79-S cytoplasmic previous termribosomes,next term (d) gel electrophoresis of high and low molecular weight RNAs. 3. 3. Inclusion of heparin in all media used for the isolation of mitochondria and previous termribosomesnext term resulted in (a) dissociation of previous term73next term-S mitochondrial previous termribosomesnext term into 50-S and 37-S subunits; (b) stabilization of 79-S cytoplasmic previous termribosomes;next term (c) in the case of mitochondria isolated in the presence of Mg2+ containing both previous term73next term-S and 79-S previous termribosomes,next term heparin causes the selective dissociation of the previous term73next term S monosome to yield previous termribosomesnext term containing only a single monomeric previous termribosomenext term type, viz. 79 S. 4. 4. It is concluded that (a) the 79-S previous termribosomesnext term present in mitochondria isolated in the presence of Mg2+ are contaminating cytoplasmic previous termribosomes,next term (b) the previous term73next term-S previous termribosomesnext term are the real functional mitochondrial previous termribosomes of Neurospora crassanext term.

Thu, 8 Jul 1971 12:00:00 +0100 http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-447N599-1K2&_user=616146&_coverDate=07%2F08%2F1971&_rdoc=9&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231971%23999849994%23268486%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docancho https://epub.ub.uni-muenchen.de/7181/1/Neupert_Walter_7181.pdf Neupert, Walter; Kleinow, W. ddc:610, Medizin

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.04.20.050815v1?rss=1 Authors: Jiang, H., Pederson, S. M., Newman, M., Dong, Y., Lardelli, M. Abstract: PRESENILIN 2 (PSEN2) is one of the genes mutated in early onset familial Alzheimer's disease (EOfAD). PSEN2 shares significant amino acid sequence identity with another EOfAD-related gene PRESENILIN 1 (PSEN1), and partial functional redundancy is seen between these two genes. However, the complete range of functions of PSEN1 and PSEN2 is not yet understood. In this study, we performed targeted mutagenesis of the zebrafish psen2 gene to generate a premature termination codon close downstream of the translation start with the intention of creating a null mutation. Homozygotes for this mutation, psen2S4Ter, are viable and fertile, and adults do not show any gross pigmentation defects, arguing against significant loss of {gamma}-secretase activity. Also, assessment of the numbers of Dorsal Longitudinal Ascending (DoLA) interneurons that are responsive to psen2 but not psen1 activity during embryogenesis did not reveal decreased psen2 function. Transcripts containing the S4Ter mutation show no evidence of destabilization by nonsense-mediated decay. Forced expression in zebrafish embryos of fusions of psen2S4Ter 5' mRNA sequences with sequence encoding enhanced green fluorescent protein (EGFP) indicated that the psen2S4Ter mutation permits utilization of cryptic, novel downstream translation start codons. These likely initiate translation of N-terminally truncated Psen2 proteins that obey the "reading frame preservation rule" of PRESENILIN EOfAD mutations. Transcriptome analysis of entire brains from a 6-month-old family of wild type, heterozygous and homozygous psen2S4Ter female siblings revealed profoundly dominant effects on gene expression likely indicating changes in ribosomal, mitochondrial, and anion transport functions. Copy rights belong to original authors. Visit the link for more info