Podcasts about plasmids

Welcome to The Nonlinear Library, where we use Text-to-Speech software to convert the best writing from the Rationalist and EA communities into audio. This is: Multiplex Gene Editing: Where Are We Now?, published by sarahconstantin on July 16, 2024 on LessWrong. We're starting to get working gene therapies for single-mutation genetic disorders, and genetically modified cell therapies for attacking cancer. Some of them use CRISPR-based gene editing, a new technology (that earned Jennifer Doudna and Emmanuelle Charpentier the 2020 Nobel Prize) to "cut" and "paste" a cell's DNA. But so far, the FDA-approved therapies can only edit one gene at a time. What if we want to edit more genes? Why is that hard, and how close are we to getting there? How CRISPR Works CRISPR is based on a DNA-cutting enzyme (the Cas9 nuclease), a synthetic guide RNA (gRNA), and another bit of RNA (tracrRNA) that's complementary to the gRNA. Researchers can design whatever guide RNA sequence they want; the gRNA will stick to the complementary part of the target DNA, the tracrRNA will complex with it, and the nuclease will make a cut there. So, that's the "cut" part - the "paste" comes from a template DNA sequence, again of the researchers' choice, which is included along with the CRISPR components. Usually all these sequences of nucleic acids are packaged in a circular plasmid, which is transfected into cells with nanoparticles or (non-disease-causing) viruses. So, why can't you make a CRISPR plasmid with arbitrary many genes to edit? There are a couple reasons: 1. Plasmids can't be too big or they won't fit inside the virus or the lipid nanoparticle. Lipid nanoparticles have about a 20,000 base-pair limit; adeno-associated viruses (AAV), the most common type of virus used in gene delivery, has a smaller payload, more like 4700 base pairs. 1. This places a very strict restriction on how many complete gene sequences that can be inserted - some genes are millions of base pairs long, and the average gene is thousands! 2. but if you're just making a very short edit to each gene, like a point mutation, or if you're deleting or inactivating the gene, payload limits aren't much of a factor. 2. DNA damage is bad for cells in high doses, particularly when it involves double-strand breaks. This also places limits on how many simultaneous edits you can do. 3. A guide RNA won't necessarily only bind to a single desired spot on the whole genome; it can also bind elsewhere, producing so-called "off-target" edits. If each guide RNA produces x off-target edits, then naively you'd expect 10 guide RNAs to produce 10x off-target edits…and at some point that'll reach an unacceptable risk of side effects from randomly screwing up the genome. 4. An edit won't necessarily work every time, on every strand of DNA in every cell. (The rate of successful edits is known as the efficiency). The more edits you try to make, the lower the efficiency will be for getting all edits simultaneously; if each edit is 50% efficient, then two edits will be 25% efficient or (more likely) even less. None of these issues make it fundamentally impossible to edit multiple genes with CRISPR and associated methods, but they do mean that the more (and bigger) edits you try to make, the greater the chance of failure or unacceptable side effects. How Base and Prime Editors Work Base editors are an alternative to CRISPR that don't involve any DNA cutting; instead, they use a CRISPR-style guide RNA to bind to a target sequence, and then convert a single base pair chemically - they turn a C/G base pair to an A/T, or vice versa. Without any double-strand breaks, base editors are less toxic to cells and less prone to off-target effects. The downside is that you can only use base editors to make single-point mutations; they're no good for large insertions or deletions. Prime editors, similarly, don't introduce double-strand breaks; instead, they include an enzyme ("nickase") that produces a single-strand "nick"...

Link to original articleWelcome to The Nonlinear Library, where we use Text-to-Speech software to convert the best writing from the Rationalist and EA communities into audio. This is: Multiplex Gene Editing: Where Are We Now?, published by sarahconstantin on July 16, 2024 on LessWrong. We're starting to get working gene therapies for single-mutation genetic disorders, and genetically modified cell therapies for attacking cancer. Some of them use CRISPR-based gene editing, a new technology (that earned Jennifer Doudna and Emmanuelle Charpentier the 2020 Nobel Prize) to "cut" and "paste" a cell's DNA. But so far, the FDA-approved therapies can only edit one gene at a time. What if we want to edit more genes? Why is that hard, and how close are we to getting there? How CRISPR Works CRISPR is based on a DNA-cutting enzyme (the Cas9 nuclease), a synthetic guide RNA (gRNA), and another bit of RNA (tracrRNA) that's complementary to the gRNA. Researchers can design whatever guide RNA sequence they want; the gRNA will stick to the complementary part of the target DNA, the tracrRNA will complex with it, and the nuclease will make a cut there. So, that's the "cut" part - the "paste" comes from a template DNA sequence, again of the researchers' choice, which is included along with the CRISPR components. Usually all these sequences of nucleic acids are packaged in a circular plasmid, which is transfected into cells with nanoparticles or (non-disease-causing) viruses. So, why can't you make a CRISPR plasmid with arbitrary many genes to edit? There are a couple reasons: 1. Plasmids can't be too big or they won't fit inside the virus or the lipid nanoparticle. Lipid nanoparticles have about a 20,000 base-pair limit; adeno-associated viruses (AAV), the most common type of virus used in gene delivery, has a smaller payload, more like 4700 base pairs. 1. This places a very strict restriction on how many complete gene sequences that can be inserted - some genes are millions of base pairs long, and the average gene is thousands! 2. but if you're just making a very short edit to each gene, like a point mutation, or if you're deleting or inactivating the gene, payload limits aren't much of a factor. 2. DNA damage is bad for cells in high doses, particularly when it involves double-strand breaks. This also places limits on how many simultaneous edits you can do. 3. A guide RNA won't necessarily only bind to a single desired spot on the whole genome; it can also bind elsewhere, producing so-called "off-target" edits. If each guide RNA produces x off-target edits, then naively you'd expect 10 guide RNAs to produce 10x off-target edits…and at some point that'll reach an unacceptable risk of side effects from randomly screwing up the genome. 4. An edit won't necessarily work every time, on every strand of DNA in every cell. (The rate of successful edits is known as the efficiency). The more edits you try to make, the lower the efficiency will be for getting all edits simultaneously; if each edit is 50% efficient, then two edits will be 25% efficient or (more likely) even less. None of these issues make it fundamentally impossible to edit multiple genes with CRISPR and associated methods, but they do mean that the more (and bigger) edits you try to make, the greater the chance of failure or unacceptable side effects. How Base and Prime Editors Work Base editors are an alternative to CRISPR that don't involve any DNA cutting; instead, they use a CRISPR-style guide RNA to bind to a target sequence, and then convert a single base pair chemically - they turn a C/G base pair to an A/T, or vice versa. Without any double-strand breaks, base editors are less toxic to cells and less prone to off-target effects. The downside is that you can only use base editors to make single-point mutations; they're no good for large insertions or deletions. Prime editors, similarly, don't introduce double-strand breaks; instead, they include an enzyme ("nickase") that produces a single-strand "nick"...

Dr Ardis's Site: https://theDrArdisShow.com USE Code BBARDISLIVE for a discount.Dr. Ardis' Healing for the AGES link below. Code BB10 gets you $50 OFF!https://my.energetichealthinstitute.org/healing-for-the-ages/go/checkout-healing-for-the-ages/? Use Code BB10GET COMMERCIAL FREE PODCASTS and Exclusive Content: Become a Patron. https://Patreon.com/DisguisetheLimitsPriestcraft: Beyond Babylon is getting Great Feedback! 8.5x11 Paperback, Hardcover, & Kindle: https://www.amazon.com/dp/B0CNGX53L7/Barnes & Noble: Priestcraft: Beyond Babylon 426 pages, and ebook: https://www.barnesandnoble.com/w/book/1144402176KOBO: https://www.kobo.com/us/en/ebook/priestcraft-beyond-babylonAdd to the Kristos Family Apocalypse Fund: https://GiveSendGo.com/BaalBustersDR MONZO Products: https://drmonzo.kartra.com/page/shopDR MONZO ATB BOOK: https://drmonzo.kartra.com/page/ATBBookUSE CODE: BaalBusters15 for 15% OFF Dr. MONZO's store itemsGet Healthy with DR PETER GLIDDEN, ND https://leavebigpharmabehind.com/?via=pgndhealthGet KRATOM HERE: https://klaritykratom.com/?ref=BaalBustersSubmit Questions: https://buymeacoffee.com/BaalBusters or just Call-in!Have you tired TRY BLUE? https://tryblue.refr.cc/baalbusters for 17% Off!SHIRTS & MERCH https://my-store-c960b1.creator-spring.com/THIS CHANNEL IS INDEPENDENT and has no sponsors but YOUJOIN Locals by Clicking the JOIN Button Beneath the video.AWESOME Hot Sauce: https://SemperFryLLC.com Use Code at site for 11% Off qualified purchasesBa'al Busters channel: https://rumble.com/c/BaalBustersTwitter: https://twitter.com/DisguiseLimitsInstagram: https://www.instagram.com/baalbusters/Telegram: https://t.me/BaalBustersStudiosJoshWhoTV channel: https://BaalBuster.JoshWhoTV.comSpotify: https://open.spotify.com/show/3N7fqqG6MX84vKbANtxrWS

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Welcome to November! In this episode, we bring you the work of Álvaro San Millán, group leader at the National Center for Biotechnology in Spain, where he researches the role of plasmids in antibiotic resistance. In this interview, among other things, we talk about how understanding plasmid biology can lead to new ways of tackling resistance, and learn about his impressions of being a young group leader and setting up a multidisciplinary team. In the news section, we are being very “communicative” this month, first covering a recent study looking at 6 different terms used in AMR communications in terms of being able to evoque risk and being remembered, and a paper published by CE4AMR, where they share their insights on what to include while co-creating solutions with communities, and why. We hope you have a great time with us! Check relevant links in the show notes at http://www.uac.uu.se/the-amr-studio/episode53 . Follow our updates on twitter on http://www.twitter.com/uac_uu with #theAMRstudio hashtag! Theme music by Henrik Niss: http://www.tinyurl.com/henriknissspotify.

Looking 4 Healing Radio with Dr. Bryan Ardis, Nichola Burnett, Dr. Jana Schmidt, and Dr. Henry Ealy – In the latest episode we unpack the EPA's controversial stance on Berkey Water Filters and debunk myths surrounding Colloidal Silver. Delving deeper, we share our experiences with nature's healing power and offer insights on osteoporosis. Plus, don't miss our discussion on bioweapons and everyday health queries. Join the conversation!

Looking 4 Healing Radio with Dr. Bryan Ardis, Nichola Burnett, Dr. Jana Schmidt, and Dr. Henry Ealy – In the latest episode we unpack the EPA's controversial stance on Berkey Water Filters and debunk myths surrounding Colloidal Silver. Delving deeper, we share our experiences with nature's healing power and offer insights on osteoporosis. Plus, don't miss our discussion on bioweapons and everyday health queries. Join the conversation!

Looking 4 Healing Radio with Dr. Bryan Ardis, Nichola Burnett, Dr. Jana Schmidt, and Dr. Henry Ealy – In this episode of Looking 4 Healing Radio, natural medicine experts Nichola Burnett, Dr. Jana Schmidt, Dr. Bryan Ardis & Dr. Henry Ealy take on more important questions regarding things that impact us all out there as we lead up to the Healing for the A.G.E.S. The topics are bioweapons… Plasmids, Venoms, CRISPR, and so...

Looking 4 Healing Radio with Dr. Bryan Ardis, Nichola Burnett, Dr. Jana Schmidt, and Dr. Henry Ealy – In this episode of Looking 4 Healing Radio, natural medicine experts Nichola Burnett, Dr. Jana Schmidt, Dr. Bryan Ardis & Dr. Henry Ealy take on more important questions regarding things that impact us all out there as we lead up to the Healing for the A.G.E.S. The topics are bioweapons… Plasmids, Venoms, CRISPR, and so...

Looking 4 Healing Radio with Dr. Bryan Ardis, Nichola Burnett, Dr. Jana Schmidt, and Dr. Henry Ealy – Listen in as Dr. Ardis shares this paper from 2003 that openly talks about acceptor plasmids and donor plasmids and their ability to infect mammalian cells to kill the host. And later in the show, Dr. H gives a preview into his research surrounding the...

Looking 4 Healing Radio with Dr. Bryan Ardis, Nichola Burnett, Dr. Jana Schmidt, and Dr. Henry Ealy – Listen in as Dr. Ardis shares this paper from 2003 that openly talks about acceptor plasmids and donor plasmids and their ability to infect mammalian cells to kill the host. And later in the show, Dr. H gives a preview into his research surrounding the...

Looking 4 Healing Radio with Dr. Henry Ealy – In this episode of Looking 4 Healing Radio, Dr. H is joined by Monique Bilodeau-Nestmann, who works with Dr. H and leads the research on Plasmid Curing Compounds for his research team. As you learned several weeks ago, Plasmids have the capability of delivering genetic bioweapons into human cells and especially into bacteria like E. coli. Understanding that this is the primary...

In this episode of Microbe Talk, David Walker Sunderhaulf chats with Clare about his paper "Removal of AMR plasmids using a mobile, broad host-range CRISPR-Cas9 delivery tool" published in Microbiology. If you'd like to read David's paper, you can find it here https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.001334. You can also follow him on twitter @davvi36. Music: Time Technology by Comma-Media from Pixabay

Looking 4 Healing Radio with Dr. Henry Ealy – In this episode of Looking 4 Healing Radio, Dr. H is joined by special guest and Gene Editing Expert Mike Donio. Listen in as Dr. H takes you on a history lesson that begins at the end of World War II with Operation Paperclip and ends at the beginning of the COVID Plandemic. If it walks like a Nazi and talks like a Nazi…it's a Nazi. The hell and horror all of us have been...

This Episode is all about Plasmids, what they do, how much they cost and where to get them. You can follow us on Twitter at @ALorecast, where we give updates on next episodes. You can also email us at rapturebioshockpod@gmail.com, we want to hear what you think about the podcast, any request that you have, or any suggestions. --- This episode is sponsored by · Anchor: The easiest way to make a podcast. https://anchor.fm/app Support this podcast: https://anchor.fm/william-presser/support

An Introduction to Genetic Engineering, Chapters 4-5. Plasmids, restriction enzymes, gene manipulation techniques, mode of action, type II restriction enzymes, DNA modifying enzymes, selecting viable hosts and vectors. --- Support this podcast: https://anchor.fm/osuz504-tech/support

Uncover the history of molecular therapeutics, the staggering current applications and developments of these therapeutics and what their future could hold, in this episode of Talking Techniques. To explore the field of molecular therapeutics and provide an insight into their production, is Aaron Clauson, Product Manager at Zymo research. First, we cover the ins and outs of targeting the therapies and how to select the correct type of molecular therapeutic to begin developing a drug for a specific disease, before looking at some of the setbacks and safety errors that have occurred during the development of molecular therapeutics and how researchers have learned from these tragic events. Aaron also highlights the vital role of plasmids in almost all molecular therapeutic development, detailing the importance of keeping plasmid solutions and transfections free of endotoxins, revealing key solutions for avoiding these contaminants. Listen today to get all you need to know about molecular therapeutics, from their inception to their most exciting examples and how we can better communicate their benefits to the public in order to avoid mistrust and confusion - as has occurred during the COVID-19 pandemic. Contents:What counts as a molecular therapeutic? 01:45-02:40Well known molecular therapeutics 02:40-05:00What can molecular therapeutics achieve that synthetic chemicals can't? 05:00-05:55Targeting molecular therapeutics and picking the right type of therapeutic 05:55-08:25Selecting the appropriate molecular therapeutic 08:35-11:00Setbacks and safety concerns in gene therapies 11:00-15:45Preventing off-target effects in gene therapies 15:45-17:35Challenges in the development of molecular therapeutics 17:35-19:05 Plasmids in molecular therapeutic development 19:05-23:55 Avoiding endotoxins: 23:55-27:45What fields do you find most exciting? 27:45-28:50Better communication of gene therapies to the public 28:50-32:00 “security agencies detecting molecular therapeutics” 29:10Improving molecular therapeutic development: 32:00-37:10

Learn about the RLR gene editing tool; Victorian-era emoji; and why “night shift” screen settings don't help you sleep. RLR is a new gene editing tool that's safer and more useful than CRISPR by Cameron Duke Move over CRISPR, the retrons are coming. (2021). EurekAlert! https://www.eurekalert.org/pub_releases/2021-04/wifb-moc042921.php  Schubert, M. G., Goodman, D. B., Wannier, T. M., Kaur, D., Farzadfard, F., Lu, T. K., Shipman, S. L., & Church, G. M. (2021). High-throughput functional variant screens via in vivo production of single-stranded DNA. Proceedings of the National Academy of Sciences, 118(18), e2018181118. https://doi.org/10.1073/pnas.2018181118  Swingle, B., Markel, E., & Cartinhour, S. (2010). Oligonucleotide recombination: A hidden treasure. Bioengineered Bugs, 1(4), 265–268. https://doi.org/10.4161/bbug.1.4.12098  Irving, M. (2021, May 4). Harvard gene-editing tool “sneaks” DNA into cells without making cuts. New Atlas. https://newatlas.com/biology/retron-library-recombineering-gene-editing-crispr/  ‌Are Retrons the Next CRISPR? | Cell And Molecular Biology. (2021). Labroots. https://www.labroots.com/trending/cell-and-molecular-biology/20347/retrons-crispr  Flowers Were Emoji For Victorians by Anna Todd Romie Stott. (2016, August 15). How Flower-Obsessed Victorians Encoded Messages in Bouquets. Atlas Obscura; Atlas Obscura. https://www.atlasobscura.com/articles/how-flowerobsessed-victorians-encoded-messages-in-bouquets  The meaning of flowers, Floriography, language of flowers, advice hints and tips from All Florists.co.uk. Allflorists.co.uk. http://www.allflorists.co.uk/advice_flowerMeanings.asp  "Night shift" screen settings don't really help you sleep by Kelsey Donk Is night shift really helping you sleep better? (2021). EurekAlert! https://www.eurekalert.org/pub_releases/2021-04/byu-ins042621.php Duraccio, K. M., Zaugg, K. K., Blackburn, R. C., & Jensen, C. D. (2021). Does iPhone night shift mitigate negative effects of smartphone use on sleep outcomes in emerging adults? Sleep Health. https://doi.org/10.1016/j.sleh.2021.03.005  Follow Curiosity Daily on your favorite podcast app to learn something new every day withCody Gough andAshley Hamer — for free!  See omnystudio.com/listener for privacy information.

https://medicienterprises.com/2020/12/04/show-499/

The gang returns to the city of Rapture and find it's a lot less stable than they remember it. (BioShock 2)

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.01.361691v1?rss=1 Authors: Yu, M. K., Fogarty, E. C., Eren, A. M. Abstract: Plasmids play a critical role in rapid bacterial adaptation by encoding accessory functions that may increase the host's fitness. However, the diversity and ecology of plasmids is poorly understood due to computational and experimental challenges in plasmid identification. Here, we report the Plasmid Classification System (PCS), a machine learning classifier that recognizes plasmid sequences based on gene functions. To train PCS, we performed a large-scale discovery and comparison of gene functions in a reference set of >16,000 plasmids and >14,000 chromosomes. PCS accurately recognizes a diverse range of plasmid subtypes, and it outperforms the previous state-of-the-art approach based on k-mer decomposition of sequences. Armed with this model, we conducted, to our knowledge, the largest search for naturally occurring human gut plasmids in 406 publicly available metagenomes representing 5 countries. This search yielded 6,257 high-confidence predicted plasmids, of which 576 had evidence of a circular conformation based on pair-end mapping. These predicted plasmids were found to be highly prevalent across the metagenomes compared to the reference set of known plasmids, suggesting there is extensive and uncharacterized plasmid diversity in the human gut microbiome. Copy rights belong to original authors. Visit the link for more info

https://medicienterprises.com/2020/09/18/show-487/

クモについて詳しいゲストを迎え、フリーハンドで丸と直線を描くトレーニング、メールで進むかまいたちの夜、自作PC、論文管理の難しさ、趣味としてのポッドキャスト、コーディング環境とWet/Dryのデータ管理について話しました。Show notes Readable Lab NotebookのTipsを集めたいので、ご協力いただける方はtwitterにつぶやいていただくか(我々が検索可能な形であればうれしいです)、お便りコーナーから連絡いただけると助かります。そのうちまた紹介したいと思います。 幻影旅団 HUNTER×HUNTER (Amazon) フリーハンドで丸と直線を書く…デザイナーの山中俊治さんによると、 「今でもスケッチを描く前には、初心に返って、一枚の紙を楕円で埋めつくすことから始めます」 とのことです。 手塚治虫 (Wikipedia) かまいたちの夜ニワンゴ版…JavaとPHPで実装されていた ニワンゴトップページ…Internet Archive (2009年)。懐かしい。ちなみにこの頃、ニコニコ動画は Youtube の上にコメントを表示するサービスでした。 Linux Ubuntu AMD Ryzen 7 3700X NVIDIA Tesla V100 32GB GTX 1070 Ti…このあたりがお値段も手頃で良い。 CUDA AWS 光るメモリ…どうだ明るくなったろう。 光るキーボード…明るい！ LG 27 inch UltraFine 5K Display Apple Pro Display XDR MacBookProの車輪 MacBookProの脚 液浸冷却 サーバを丸ごと液体に浸して冷やす「液浸冷却システム」【FUJITSU JOURNAL】…解説があります。ドッキリに使えそう。 MOD PIT 02: The end results (水冷式)…見てると欲しくなりますよね。 EK’s ultimate CPU water block…格好いい。 TSUBAME フロリナート Zotero…論文のPDF管理ソフトのうちの一つ。Nakamuraさんが使っている。 Mendeley GoodNotes…iPadで手書きメモ Blue Microphones Yeti USBマイク Anchor Stand.fm click…Python用のコマンドラインツールを便利に作れるライブラリ jupyter notebook Docker elm…JavaScriptにコンパイルできる関数型プログラミング言語の一つ。 リーダブルコード (Amazon) Plasmids 101: How to Name Your Plasmid in 3 Easy Steps…Addgeneにもドンピシャのブログがありました。ぜひ参考に。 地球平面協会のウェブサイト…地球平面説は、ガリレオの時代の話が有名ですが、これは現代の話。 ビハインド・ザ・カーブ ー地球平面説ー (Netflix)…地球は平面だと信じる人達を追ったドキュメンタリー。見終わるとモヤッとした気分になります。Nakamuraさん紹介でsohもおすすめ。 殺人鬼との対話：テッド・バンディの場合 (Netflix)…多分これのことを言っていたんだと思うNetflix はこの手のサイコパス物が充実していて、他にはピザ配達人爆死事件の番組もおすすめ 殺人犯の視聴率 (Netflix)…マナウスで大人気のテレビ番組司会者、ウォレス・ソウザ。彼とクルーは報道番組「カナル・リブレ」を通じて、犯罪撲滅のため日々戦っていた。しかしある日…… ハイパー ハードボイルド グルメリポート…ヤバいところに行っヤバイ人と飯を食う番組。ディレクターの上出遼平さんのインタビューも面白い。書籍が出たそうです。 Editorial notes 光るPCはロマンだと思ってます (nakamura) 昼飯作っていて最初らへんの収録に乗り遅れました (soh) 次作るキーボードはめっちゃ光らせるって決めてる(coela) readable lab notebook ほしいなぁ(tadasu)

Start your day geek with LRMornings. LRM‘s daily morning show with Kyle and Jammer (or Christine) (or Brian). Join them as they discuss all things geek with a little news just for fun. In today's episode, Kyle and Brian discuss the Bioshock franchise. Its past games, how it could be adapted to the big or small screen, and what the next game should be. The Malone family needs help: gf.me/u/xpukwy Question of the day: What do you want from a fourth Bioshock game? Please like, share, and subscribe!

Dive in and learn about the roll that ethics and philosophy can have within AMR with Dr. Christian Munthe (currently part of the Centre for Antibiotic Resistance Research -CARe-) in this month's episode of The AMR Studio. With his background in practical philosophy, Dr. Munthe works with translating thoughts into actions when it comes to the various dilemmas that AMR poses regularly. In the news section, we cover a recent study looking into how contextual factors shape distinct ethical challenges in different parts of the world; and an article showing how antibiotic persistence can be linked to plasmid transfer. Check relevant links and material at www.uac.uu.se/the-amr-studio/episode12/. Follow our updates on twitter on www.twitter.com/uac_uu with #theAMRstudio hashtag! Theme music by Henrik Niss: www.tinyurl.com/henriknissspotify.

We take a stroll through Rapture and see what Andrew Ryan has built. Developer: Irrational Games | Publisher: 2K Games  | Release Date:  August 21, 2007 Mike, Jacob and Moe share stories about the great year 2007 was for games, how they came to Bioshock, and whether the twist holds up in the current day and age. Join our Discord server! Go to LeftBehindGame.Club and scroll down to the Discord section of the homepage! If you love the show, please consider a review on iTunes. It helps a lot. Players: Michael Ruffolo (@ruffolom), Jacob McCourt (@JacobMcCourt), and Moe Murtadi (@mmurtadi) Website: LeftBehindGame.Club | Twitter: @LeftBehindClub | Instagram: @LeftBehindGameClub Show Notes (spoilers): 2:00 What did we know about Bioshock coming into this? 4:30 Bioshock was like going to Disney world 5:10 2007 was a great year for games 7:25 Expectations were high and it broke Mike's heart playing it again 8:15 Do the game mechanics age well? 8:40 "The Citizen Kane of Games" and Roger Ebert 10:10 How did we play it? PC, console, original and remaster 11:58 What is Bioshock and how does it start? 13:15 Morality system and consequences (or lack thereof) 13:50 Who is Andrew Ryan? 15:30 Splicers and Atlas 16:30 What does the game look like? Answer: dark and creepy 19:10 Rapture feels like a character 20:00 This game still looks good, and looked great back in the day 20:45 What are Plasmids? 22:00 What is Adam and Eve and where did it come from? Sea slugs and superhumans 23:15 "Little Sisters are Demons" 24:00 Big Daddies are like momma bears and just as tough 26:00 How did you take down Big Daddies? 28:00 Incinerate and Shock 28:50 Plasmids and the wrench 30:15 Jacob feels the gameplay is dated 32:30 KOTOR is the best game ever made and Mike's co-hosts are trollish dickheads :) 33:30 The AI is really good 34:20 What are your favourite parts of the game? 38:30 Jacob and Mike geek out over Fort Frolic and Sander Cohen 41:30 What did you do with the Little Sisters? Jacob McCourt is a bad man 45:00 Tennenbaum and the different endings 48:30 Bioshock and the illusion of choice 51:00 Frustrated with a second playthrough 52:00 The bad PS3 port made Mike happy 53:20 Jacob felt it drags on and doesn't end well 54:00 What we felt about the ending 55:00 Randian Objectivism and the politics of the game 59:00 Simple impressions on the sequels, Bioshock 2 and Bioshock Infinite 1:01:00 LBGC connection to Bioshock 2 1:03:00 What's next for Ken Levine? 1:04:30 Sharing our final thoughts and takeaways 1:05:20 Mike almost got a regrettable Bioshock tattoo

Welcome to a new episode of The AMR Studio! This time, we have the interview we did with Dr. Coll De Lima Hutchison from the London School of Hygiene and Tropical Medicine. We chatted with him about his work in anthropology, and got a good insight into the importance of cultural and historical backgrounds when trying to change behaviours. In our news section we bring to you the latest research on the presence of antibiotic resistance genes in the environment, and the transmission of plasmids between bacteria. Check relevant links and material at www.uac.uu.se/the-amr-studio/episode4/. Follow our updates on twitter on www.twitter.com/uac_uu with #theAMRstudio hashtag! Theme music by Henrik Niss: www.tinyurl.com/henriknissspotify.

Dave Rasko uses comparative bacterial genomics to find DNA sequences that influence virulence or antibiotic resistance. Dave talks about his studies of E. coli, Acinetobacter baumanii, and B. anthracis, and the state of bacterial genomics past, present, and future. Host: Julie Wolf Subscribe (free) on iPhone, Android, RSS, or by email. You can also listen on your mobile device with the ASM Podcast app. Julie's biggest takeaways: Genome sequencing speed has significantly increased: The first bacterial genome sequenced, Haemophilus influenzae, took about 10 years to complete. The first organism with two sequenced genomes was Helicobacter pylori, published in 1999, and the first organism with three published genomes was Escherichia coli. Rasko’s initial project at TIGR to sequence 11 E. coli genomes took about 2 years. Today, Rasko’s lab can sequence 500 genomes in about five days.   In E. coli, up to half of the genome can differ between two strains. The core genome is the collection of genes that will be shared among all isolates of a particular species. Core gene conservation varies among species and is important to consider in analyses for one’s species of interest.   Working on the Amerithrax investigation was unlike many other scientific inquiries for many reasons, including that the Federal Bureau of Investigation only gave the scientists involved the information pieces necessary to conduct their studies. Rasko and collaborators sequenced the genomes of spores within the samples, and found that the morphology of the colonies that grew were associated with genetic differences between the spores within the sample, linking phenotype and genotype.   While comparative genomics can provide a lot of information, there are some phenomena that will always require further study. For example, Rasko is researching isolates of A. baumanii and Klebiella pneumoniae that quickly develop drug resistance when grown in sub-inhibitory drug concentrations. The genomic sequences of resistant or susceptible strains show no difference in DNA sequence, suggesting the phenotype is due to transcriptional changes. Featured Quotes (in order of appearance) “Genomics is fun in that we can hypothesize all day long, every day. It’s really the start of a lot of very very hard work figuring out why.” “There’s a lot of DNA pieces that we don’t fully understand how they moved, where they moved, where they came from. In some cases, there’s evidence to say where they came from; in terms of G-C content and coding biases, we can make some assumptions, but in the grand scheme of things, we have no idea where they’re coming from! In some cases, we’ll see them dominant throughout a lineage, and in some cases we’ll see them in sporadic isolates around the entire phylogenetic tree. . .We all thought genomics was going to solve so many problems, and it’s really just made it more difficult!” “Plasmids tend to be mobile and exchangeable, and the pieces tend to be - I tend to think of them as legos, in the fact that you can put a plasmid together in a bunch of different ways.” “I think a lot of conventional PCR fails and people assume that it’s because it’s negative, and not necessarily that it fails because of diversity.” “Many microbiologists think of that colony on a plate as a clone. I force the people in my group to think about it a little differently, because it’s really what I like to call ‘genome space’. They’re not all the same; bacteria are constantly evolving. There’s changes all the time, some of them are positive, some of the are negative, the negative ones get lost, the positive ones unusually become dominant - and then there’s lots of neutral changes that just kind of hang out.” “Genomes really normalized everything. Before that, there were certain labs that could clone and there were certain labs that could sequence, and it was a little bit restrictive to the elite labs who had those resources. Now with the genome sequences out there, everyone was starting from the same place.” “You really have to understand your organism to make the bioinformatics work.” Links for this episode Rasko lab at the University of Maryland FBI summary of Amerithrax investigation 2011 PNAS report on B. anthracis comparative genomics Bugs N the ‘hood HOM Tidbit: Stanley Falkow gives both video history and written history of plasmid biology Save on Microbe 2018, use code: asmpod Send your stories about our guests and/or your comments to jwolf@asmusa.org.

The final round of Bioinformatics Contest 2018 was held on February 24-25th, and the qualification round took place two weeks earlier. I invited the organizers of the contest, Alexey Sergushichev and Ekaterina Vyahhi, to discuss the problems and find out what it was like to organize the contest. Timestamps for the problems: Qualification round 0:41:38 Problem 1. Synthesis of ATP 0:48:46 Problem 2. Restriction Sites 1:06:42 Problem 3. Tandem Repeats Final round 1:14:00 Problem 1. Recombination of Plasmids 1:25:30 Problem 2. Species Recovering 1:28:39 Problem 3. Haplotype Phasing 1:36:34 Problem 4. Cluster the Reads 1:40:25 Problem 5. Cattle Breeding Links: The contest problems on Stepik The final scoreboard Bioinformatics Institute

RJ tokes all things GMO's , Plasmids and Cannabis

Vi firar vår wrap-up av Ludosonans första säsong med storfrämmen från schnitzlarnas hemland då Sebastian dyker upp och medverkar rent fysiskt hemma i studion. Vi snackar fest, testar drinkar och spelar sociala argumentationsspel. Tillsammans med en skvätt kulturkoallition, en nypa spoilerfria recensioner (läs: åsikter) samt en runda E-tankar blir det en sjudundrande säsongsavslutning. Häng med i dimman, det här är Ludosonans.   INNEHÅLL 00:00:43 - Introduktion och avsnittets tema, PARTY 00:48:40 - Recension av Tanooki Tonic och våra egna drinknamn 01:09:40 - Metagame, första omgången 01:39:30 - Recension av Jack Ryan's Plasmids och Sebastian hittar på nya drinknamn 02:06:43 - Fienden, ROBOT och tv-spelstidningarnas framtid 02:19:10 - Vi kollar in den officiella Pac-Man skämtboken, Pac-Mania 02:23:48 - Vad vi spelat under sommaren 02:55:05 - Metagame, andra omgången 03:11:35 - Kontaktinformation och avslut MUSIKSPELLISTA College & Electric Youth - A Real Hero (GM's 16-Bit Cover) [Filmen Drive] (00:45:47) Musicalman - Snake's Revenge [Metal Gear] (01:36:06) Evil Horde - El Lagarto [The Adventures of Bayou Billy] (02:02:10) LÄNKAR I AVSNITT GTA San Andreas-reklam: Logger Beer Guitar Hero-ungen The Drunken Moogle Metagame Sveriges första kulturella tidskrift om tv-spel - Fienden Giantbomb testar Djungelvrål och Turkisk Peber i sin podcast Geocachen "GC1BE91 - International Space Station" av Ultima-skaparen Richard "Lord British" Garriott DRINKAR I AVSNITTET Tanooki Tonic 1 del Kahlua 1 del Baileys Irish Creme 1 del Cognac eller annan brandy Kyl ned ingredienserna och fördela jämt lager för lager i ett högt glas. Kahlua först, sen Baileys och sist brandyn. Servera, drick och flyg iväg! Jack Ryan’s Plasmids (Bioshock shots) 1 del triple sec 2 delar blå curaçao (för färgens skull) 2 delar Sourz Sour Apple eller annan sur äppellikör Blanda ingredienserna i en flaska. Om man inte vill ha en hel flaska så fungerar receptet lika bra till enkla shottar. Metroid Cocktail ½ shot Bacardi Apple ½ shot kokosnötsrom ½ glas kiwi-/jordgubbsjuice eller liknande (grön i färgen) Mindre än ½ glas Sprite 3 jordgubbar Skaka rommen och kiwi-/jordgubbsjuicen och häll över i ett lowball-glas. Tillsätt Sprite för smakens och kolsyrans skull. Garnera med tre jordubbar i triangulär formation. Om så önskas, använd iskanonen frys ned alkoholen innan drinken blandas.

Genetic manipulation of crops is an issue of great current interest and controversy. This unit covers some of the basic science that underpins the debate and examines the hotly contested case study of the development of ‘Golden Rice’. By looking at the science 'behind the headlines' you will acquire a clearer idea of both what is possible in GM science and what may be desirable. This study unit is just one of many that can be found on LearningSpace, part of OpenLearn, a collection of open educational resources from The Open University. Published in ePub 2.0.1 format, some feature such as audio, video and linked PDF are not supported by all ePub readers.

Plasmid based gene therapy approaches often lack long term transgene expression in vivo due to silencing or loss of the vector. One way to overcome these limitations is to combine non-silenced promoters with strong viral enhancers. Here we combine cytomegalovirus (CMV) derived enhancer elements with the strong, human elongation factor 1 alpha (EF1a) promoter in a plasmid backbone devoid of potentially immunostimulating CpG sequences. The transgene expression of plasmids containing either the murine or human immediate early enhancer were monitored in vivo. The human CMV enhancer led to an enhanced and prolonged transgene signal compared to the murine enhancer. The elevated expression in the case of the human enhancer correlated with a higher plasmid copy number found in the liver two months after gene delivery. The transgene expression could be even further increased by using a new synthetic promoter, SCEP (shuffled CMV EF1 promoter) instead of the EF1 promoter, in combination with the human CMV enhancer. Secondly, to reach a tissue specific and high expression in liver carcinoma a plasmid with the AFP promoter was combined with the human CMV enhancer.

Trotz verbesserter Therapiemöglichkeiten ist die Prognose beim Fibrosarkom der Katze noch immer ungünstig. In der vorliegenden Arbeit sollte die Verträglichkeit eines neuen Therapieansatzes zur Behandlung des felinen Fibrosarkoms untersucht werden. Verwendet wurde ein nonviraler Gentransfer mittels Magnetofektion, um eine Transfektion mit dem felinen Zytokingen GM-CSF zu erreichen. Ziel der durchgeführten Phase-I-Studie war die Festlegung einer maximalen tolerierten Dosis. In die prospektive Dosis-Eskalations-Studie wurden Katzen, die definierte Einschlusskriterien erfüllten, aufgenommen. Die Steigerung der Dosis des Plasmids, das für feGM-CSF kodiert, erfolgte in vier festgelegten Schritten (50, 250, 750 und 1250 µg Plasmid). Jeweils vier Katzen wurden in eine Dosisgruppe aufgenommen. Die Plasmide wurden in wässriger Lösung in einem 1:1-Verhältnis mit magnetischen Nanopartikeln gemischt, die zur besseren Bindung an die DNA mit Polyethylenimin beschichtet waren. Die Plasmidlösung mit einem Volumen von 500 µl wurde intratumoral injiziert. Danach wurde durch Applikation eines Neodymium-Eisen-Bor-Magneten auf das Tumorgebiet ein Magnetfeld für die Dauer einer Stunde angelegt. Durch diese Magnetofektion wurde die Transfektion auf das Tumorgebiet beschränkt, sowie die Effektivität des Gentransfers verbessert. Das Behandlungsprotokoll umfasste zwei intratumorale Injektionen an den Tagen -14 und -7 sowie die großräumige en-bloc-Resektion des Fibrosarkoms an Tag 1. Eine Kontrollgruppe bestehend aus vier Katzen wurde ohne Zusatztherapie einer Operation unterzogen. Aus ethischen Gründen wurde dabei auf eine Verzögerung der chirurgischen Entfernung durch Placebo-Applikationen im Zeitraum von 14 Tagen verzichtet. Eine Untersuchung auf mögliche auftretende Toxizitäten erfolgte an den Tagen -7, 0, 14, 45, 90 und 180. Zwei weitere Untersuchungen an den Tagen 270 und 360 dienten zur Kontrolle auf Rezidiv- und Metastasenbildung. Aufgetretene klinische oder hämatologische Toxizitäten wurden anhand eines speziellen Nebenwirkungskatalogs (VCOG-CTCAE-Tabelle) erfasst und in Korrelation zur durchgeführten Therapie gestellt, um über eine Zuordnung als Nebenwirkung entscheiden zu können. Ein statistischer Vergleich erfolgte für die Parameter Körpergewicht, Leukozytenzahl und das Differentialblutbild zwischen Kontrollkatzen, behandelten Katzen und den Katzen der verschiedenen Dosisgruppen. Sieben weitere Katzen wurden mit derselben Gentherapie mit humanem GM-CSF behandelt, bei denen der Expressionsachweis von huGM-CSF mittels ELISA in den Zellkulturüberständen der angezüchteten Tumore gelang. In den ersten drei Dosisgruppen traten keine schwerwiegenden Nebenwirkungen auf. Da bei drei der vier Katzen der höchsten Dosis leichte Nebenwirkungen beobachtet wurden, wurden zwei weitere Katzen mit der höchsten Dosis behandelt. Dabei traten jedoch keine Toxizitäten auf, so dass die Dosis von 1250 µg für feGM-CSF kodierendes Plasmid als sichere, gut verträgliche Dosis für nachfolgende Phase-II-Studien festgelegt werden konnte. Auch die beobachteten Ergebnisse bezüglich Rezidivrate sind als sehr viel versprechend einzustufen.

The prognosis for cats with fibrosarcoma is still poor as the treatment options existing to date do not lead to satisfying results. After sole surgical removal of the tumor, up to 70 % of the cats develop local recurrences. Even with adjuvant radiation and/or chemotherapy, the recurrence rate can just be reduced to at most 40 %. In the present work an alternative treatment method in terms of neoadjuvant immunostimulatory gene therapy should be established. Via plasmids, three feline cytokine genes were transferred into the tumor. The plasmids coded for feIL-2, feIFN-γ and feGM-CSF. Using magnetofection, gene transfer should be optimized. The aim of this clinical dose escalation study was to define a well tolerated dose, which can be tested for its efficacy in a subsequent phase-II trial. Therefore the cats were examined at defined time points for treatment-related toxicity up to 180 days after surgery. Two more check-ups on day 270 and 360 after surgery were performed to elongate the observation period for local recurrences. Prerequisite for a cat’s admission to the study was the localization of the fibrosarcoma (primary tumor or recurrence) on the trunk. The tumor had to be excised in one setting without limb amputation. Affected cats were neither allowed to be pretreated with chemo-, radiation- or gene therapy nor with corticosteroids within the past six weeks. Further exclusion criteria were hints for metastases or other severe illnesses which reduce life expectancy to less than one year. Due to the potential teratogenic effect of the expressed cytokines, pregnancy had to be ruled out. Only cats with histopathologically confirmed fibrosarcoma continued the study after surgery. As this was a scientific study with a drug not registered yet, written informed consent from the owners was a prerequisite for the participation of each cat. Four treatment groups with defined dose escalation were prospectively fixed. The dose of the feline cytokines was 15, 50, 150 and 450 µg per plasmid in group I, II, III and IV. The initial dose (3 x 15 µg) was oriented to the total dose for small oral melanomas in dogs (400 µg) established by DOW et al. and is 1/10 of it. Plasmids as non-viral vectors were chosen for several reasons. Their handling is not liable to such strict regulations as the potentially more dangerous viral vectors. Their production is simple and affordable. They induce fewer side effects than viral vectors. Therefore plasmids are more suitable for application in veterinary clinical practice. Equal amounts of the plasmids were brought into 0.9 % saline. The positively charged magnetic nanoparticles were brought into solution with aqua for injections and were mixed with the plasmid formulation in a 1:1 ratio. This formulation had a total volume of 500 µl and was injected twice intratumorally in weekly intervals. Transfection was enhanced and targeted to the tumor area by the application of a neodymium-iron-boron magnet for the duration of 60 minutes. One week after the second application, wide en-bloc resection of the tumor was performed. Four cats were assigned to each treatment group. As questionable toxicity occured in group IV, four more cats were added to this group. A control group also consisting of four cats received surgery without neoadjuvant therapy. For ethical reasons, the application of empty plasmids was avoided so that in this group surgery could be performed without delay. Medical care of all the cats was carried out by the same team of internists, anesthetists and surgeons. Clinical and laboratory parameters were evaluated according to the VCOG-CTCAE system. All adverse events were registered, classified with severity grades and correlated to treatment. Plasma samples of all cats up to 14 days after surgery were examined for the existence of feGM-CSF and feIFN-γ with commercially available ELISA kits. Statistical analyses were performed comparing the treatment groups themselves as well as treatment groups and the control group regarding body weight, white blood cells and differential blood counts. Only one cat out of group IV showed adverse events during the neoadjuvant treatment period, which were classified as grade 3 and which were probably correlated to treatment (correlation grade 4). For this reason four more cats were treated with the highest dose. None of these cats showed side effects that could be correlate to treatment. The occurrence of early recurrences in four cats of group IV was outstanding, but of course, the expressiveness of this statement is low regarding the small group sizes. However it is known that biological drugs, especially IL-2, often do not have a linear dose-response profile. Therefore the optimal effective dose lies within a strictly defined area and is probably lower than the maximal tolerated dose. The highest applied dose which is 450 µg per plasmid was defined as a well tolerated dose. It can be safely tested for its efficacy in a subsequent phase-II trial. Because of the reflections mentioned above it would undoubtedly be convenient to test the third dose (150 µg per plasmid) in parallel for its effectiveness.

The immediate-early (IE) genes of murine cytomegalovirus (MCMV) are expressed in the absence of prior viral protein synthesis and regulate the transcription of MCMV early genes. The effect of MCMV IE genes on growth induction was studied. Different plasmids containing MCMV IE genes were microinjected into arrested NIH 3T3 mouse fibroblasts. Plasmids containing the ieI gene coding for the 89,000-Mr major IE protein pp89 were found to stimulate the expression of the c-fos protooncogene. Synthesis of pp89 and its transport to the nucleus appeared to be required for c-fos expression. DNA synthesis occurred in cells that were injected with MCMV IE genes and in neighboring cells that were not injected. The results suggest that the phosphoprotein pp89 stimulates cells to enter the cell cycle.