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科技前緣💉 腸道菌的「隱形針筒」：揭開共生菌調節免疫的分子真相📝 摘要 (Summary)
長期以來，科學界認為只有沙門氏菌或志賀氏菌等「致病菌」，才會利用像針筒般的 「第三型分泌系統」（T3SS） 來攻擊人體細胞。然而，2026 年 1 月發表於 《Nature Microbiology》 的研究徹底顛覆了這個觀點。
由 Helmholtz Munich 領導的國際團隊發現，健康腸道中竟有高達 80% 的假單胞菌門（Pseudomonadota）菌株也擁有完整的 T3SS 系統。這些共生菌會主動向宿主細胞注入「效應蛋白」，精準調節 NF-κB 訊號與細胞激素分泌。這項發現不僅重新定義了腸道共生關係，更為克隆氏症等發炎性腸道疾病提供了關鍵的分子因果證據。
📌 關鍵重點 (Keypoints)
🚀 顛覆傳統觀念：研究證實 T3SS 蛋白質注入系統並非致病菌專利。健康腸道中的大腸桿菌等共生菌，同樣具備這種「主動通訊」能力，與人體進行分子層級的對話。
📊 高普及率的「分子針筒」：在健康人的腸道內，約 80% 的常見共生菌株都配備了這種能穿透細胞膜的針筒結構，顯示這套系統在演化上具有維持共生平衡的重要功能。
🗺️ HuMMI 圖譜：人菌對話地圖：科學家繪製了包含超過 1,000 種蛋白質交互作用的圖譜，首次記錄了細菌蛋白如何精準「對接」人體的免疫路徑，特別是控制發炎反應的樞紐。
🔬 與克隆氏症（Crohn’s disease）的因果連結：研究發現克隆氏症患者腸道中，這類帶有「針筒蛋白」基因的菌株比例顯著增加，這可能是誘發慢性腸道發炎、讓免疫系統失控的關鍵因子。
🤖 機器學習預測新蛋白：透過 AI 模型，研究團隊預測出 3,002 種全新的效應蛋白。這些蛋白的結構與致病菌截然不同，證實了它們是為了「共生調節」而演化出來的特殊工具。
💡 專家觀點：不再只是路人甲
過去我們以為腸道菌只是透過產出廢料（代謝產物）來影響我們，但這項研究告訴我們，它們其實是主動的「駭客」。它們攜帶著特製的隨身碟（效應蛋白），直接插入我們免疫系統的終端機（人體細胞）。當這些「駭客行為」是為了維護系統穩定時，我們就是健康的；一旦特定的干預蛋白過多，就可能導致像克隆氏症這樣的免疫系統大混亂。
📚 參考文獻 (References)
核心研究論文：
Nature Microbiology: "Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation." (2026-01-26, Veronika Young, et al. DOI: 10.1038/s41564-025-02241-y)
專業新聞報導：
Phys.org: "How gut bacteria control immune responses." (2026-01-26, Helmholtz Association)
Helmholtz Munich Newsroom: "More Than Just Gut Cohabitants: How Gut Bacteria Control Immune Responses." (2026-01-23)
數據開放資源：
Zenodo: HuMMI Data and Scripts. (DOI: 10.5281/zenodo.16883544)
💬 聲明稿 (Disclaimer)
本頻道所有內容均為個人觀點與分析，不代表我現任或曾任職公司的立場。所有資訊均來自公開管道，不涉及任何內部或機密資訊。 (Disclaimer: The views and opinions expressed on this channel are my own and do not represent those of my employer. All information is based on publicly available sources.)
🏷️ 標籤 (Hashtags)
#科技前緣 #腸道健康 #免疫系統 #克隆氏症 #微生物學 #NatureMicrobiology #T3SS #分子生物學 #NFκB #生物科技 #健康科學 #Podcast
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2026-01-2717 min
The InteractomeEpisode 39: Hurricane SeasonNote: This episode was recorded on September 17, 2025.
When you think of meteorology, you probably think of someone giving a weather forecast on TV. But predicting the weather requires a whole team of scientists, from those who run simulations in labs to researchers on boats, and even a few who fly planes into storms to get measurements up close. In this episode, we invite Colorado State University graduate student Delián Colón-Burgos to teach us all about forecasting hurricanes. She guides us through the field of hurricane meteorology, from what a hurricane is to how scientists are up...
2025-10-3159 min
Paper Talk147-Predicting the Human Protein-Protein InteractomeThis research article from David Baker team details a novel approach for systematic and accurate prediction of protein-protein interactions (PPIs) in the human proteome. The core innovation lies in the development of omicMSAs, which are deeply enriched multiple sequence alignments derived from petabytes of untapped eukaryotic genomic data to enhance coevolutionary signals, and RoseTTAFold2-PPI (RF2-PPI), a rapid deep learning network. This new network was trained on an extensive dataset, including novel domain-domain interactions (DDIs) distilled from over 200 million predicted protein structures, making it much more efficient and accurate for high-throughput screening than previous methods like AlphaFold2. Using...
2025-10-1921 min
Base by Base137: Rethinking RNA-binding proteins: Riboregulation challenges prevailing views️ Episode 137: Rethinking RNA-binding proteins: Riboregulation challenges prevailing views
In this episode of PaperCast Base by Base, we explore how a sweeping expansion of the RNA-binding proteome has reframed long‑held assumptions about RNA–protein interactions, spotlighting ‘non‑canonical’ RBPs and the emerging concept of riboregulation—RNA directly regulating protein function.
Study Highlights:The authors synthesize discovery platforms that tripled the number of candidate RBPs, including UV crosslinking–based interactome capture (RIC/eRIC), silica‑based workflows (TRAPP/2C), and organic‑phase methods (OOPS/XRNAX), together with mass spectrometry to map RNA‑binding regions across the proteome. T...
2025-09-1525 min
Base by Base️ 99: NXT2: A Testis-Specific RNA Export Factor Essential for Spermatogenesis️ Episode 99: NXT2: A Testis-Specific RNA Export Factor Essential for Spermatogenesis In this episode of PaperCast Base by Base, we explore how the testis-enriched paralog NXT2 orchestrates nucleocytoplasmic mRNA export in human germ cells and its critical role in male infertility. Study Highlights:Proteomic analyses of human testicular tissue uncovered a specialized interactome of NXT2 that associates with nuclear export factors NXF1, NXF2, and NXF3 as well as nuclear pore components. Domain deletion and co-immunoprecipitation studies demonstrated that NXT2 binds testis-specific NXF paralogs via its NTF2-like domain. Genetic screening of large cohorts of in...
2025-08-0714 min
The InteractomeEpisode 38: Process EngineeringHave you ever wondered how new medications go from being a research project to being safely used in hospitals and clinics around the world? In this episode of the Interactome, host Sam talks about their work on technical challenges in the field of process development. From the different types of therapeutic molecules to how horseshoe crabs keep patients safe, this episode covers many of the steps on the path between a potential medication working in a petri dish to saving lives.
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
I...
2025-07-141h 21
The InteractomeEpisode 37: EpigeneticsThe age old nature vs. nurture question is complicated, especially when genetics are involved. On this episode, we dive into the concept of “epigenetics,” which translates to “above the genome.” Joe, Sam and Natalie cover how your environment can play a role in how your genes are expressed, how you can have different kinds of cells from the same DNA, and … jello? You’ll walk away with an understanding of why your DNA is a lot more like a cook book than you think.
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinter...
2025-06-0956 min
The InteractomeEpisode 36: Noninvasive NeuroengineeringThe human brain is arguably the most complex organ in the body - and its hard to do experiments on it in a lab setting without invasive tools like electrodes and injections in the brain itself. But what if we had less invasive tools for understanding the brain in the lab? Join Sarah and Joe as they talk with Schuyler, an MD-PhD candidate, about the wild world of non-invasive neuroengineering... and Dungeons & Dragons!
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
M...
2025-04-281h 04
The Science PawdcastEpisode 12 Season 7: Autism Rates, Dire Wolves, and Puppy TrainingSend us a textThis week we look to deunk myths about rising autism rates and explain the genetic and environmental factors at play, while exploring the resurrection of dire wolves through genetic engineering and how puppy cognition predicts adult dog behavior.• CDC data shows autism diagnoses increased from 1 in 150 children in 2000 to 1 in 31 in 2022• Approximately 80% of autism cases stem from inherited genetic variations with 200+ genes linked to early brain development• Better screening, diagnosis, and awareness accounts for much of the increase in autism rates• Scientists have genetically engineered puppies with dire wolf tra...
2025-04-2429 min
The InteractomeEpisode 35: Space RoboticsWhen you think of health care, space probably doesn’t come to mind! But the emerging field of space robotics can provide groundbreaking insights to the world of medicine!
This episode, Texas A&M robotics engineer Emily Wilkinson sits down with Natalie and Sarah to discuss her career journey, current research, and her NASA internship (where she met Sarah!).
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
Mastodon: @interactome@universeodon.com
Texas A&M RAD Lab: https://rad.engr...
2025-03-241h 14
Yale Journal of Biology and MedicineYJBM Science News Episode 29Does mRNA play a role in cell migration? Can we use therapeutic vaccines to treat cancers like kidney cancer? Join co-hosts Majo and Roxanna in this week’s installment of YJBM Science News as they discuss the most recent Yale-affiliated biomedical and biological research that answers these questions and more!
Papers featured in this episode:
“Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment” – http://dx.doi.org/10.1016/j.cell.2025.01.007
https://news.yale.edu/2025/02/06/study-sheds-light-genetic-changes-shaped-human-brain-evolution
“A neoantigen vaccine generates antitumour immunity in renal cell carcinoma” – https://doi.org/10.1038/s41586-024-08507-5...
2025-02-2717 min
YaleUniversityYJBM Science News Episode 29Does mRNA play a role in cell migration? Can we use therapeutic vaccines to treat cancers like kidney cancer? Join co-hosts Majo and Roxanna in this week’s installment of YJBM Science News as they discuss the most recent Yale-affiliated biomedical and biological research that answers these questions and more!
Papers featured in this episode:
“Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment” - http://dx.doi.org/10.1016/j.cell.2025.01.007
https://news.yale.edu/2025/02/06/study-sheds-light-genetic-changes-shaped-human-brain-evolution
“A neoantigen vaccine generates antitumour immunity in renal cell carcinoma” - https://doi.org/10.1038/s41586-024-08507-5
https://medicine.yale.edu/n...
2025-02-2617 min
The InteractomeEpisode 34: Understanding Urban PlanningWhether it's the city, the suburbs, or somewhere else, have you ever stopped to think about why place where you live is designed the way that it is? That's thanks to urban planners, of which our guest this episode - Angela Lei - is! Join Angela, Sam, and Sarah as they discuss what urban planners and engineers do in terms of zoning, considerations made for pedestrians, and a little bit of history around Boston's Chinatown.
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_m...
2025-02-181h 14
The InteractomeEpisode 33: Spectacular Space MedicineWhat do doctors and astronauts have in common? Turns out, it’s more than you might think! On this episode, Sarah and Maia are joined by Shawna Pandya, MD. Shawna is a physician, astronaut and scientist. Tune in to hear her talk about navigating health care in the most extreme environments, and how she helps patients survive and thrive!
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
Mastodon: @interactome@universeodon.com
Credits:
Audio/Video Editi...
2025-01-2146 min
Epigenetics PodcastR-Loop Biology in Health and Disease (Natalia Gromak)In this episode of the Epigenetics Podcast, we talked with Natalia Gromak from the University of Oxford about her work on R-Loop biology in health and disease.
In this interview Dr. Gromak delves into her significant research on transcription and RNA biology, particularly focusing on the molecular mechanisms involved at transcriptional pause sites. She describes her early work in understanding transcription termination and how her team investigated the role of specific RNA and DNA structures, including R-loops, that could influence polymerase progression. This exploration into R-loops—complexes formed by RNA and DNA interactions—was a key turning poin...
2024-12-0529 min
The InteractomeEpisode 32: How to Parent Your AIAI doesn’t typically make people think of parenting, but when you listen to this episode you’ll be shocked by the similarities! Cole Smith walks us through how to train AI, how it differs from machine learning, and why building an AI system can feel a lot like raising a child.
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
Mastodon: @interactome@universeodon.com
Credits:
Audio/Video Editing: Sam Pickell
Artwork: Maia Reyes
Transcript: Margaret Downs
I...
2024-12-021h 06
The InteractomeEpisode 31: Perceiving the Big PictureEffectively communicating scientific concepts and discoveries is one of the hardest, and most important, ways of bridging gaps between scientists and the general public. But as all things in science, this is easier said than done.
On this episode, Joe, Sam and Natalie chat with New York Times science journalist and bestselling author Jim Robbins. He discusses his approach to writing about untold stories of the natural world, new research, and more.
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
2024-09-031h 04
The InteractomeEpisode 30: Diet on the BrainOn this episode of the Interactome, special guest Rasa Valiauga joins Natalie and Sarah to discuss the link that our diet has with our brains. Topics include what foods are considered highly glycemic and what that can mean for our bodies, how diabetes links to our diet, and discussing how to trim the fat from sensationalized diet advice and find the facts.
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
Mastodon: @interactome@universeodon.com
Credits:
Audio/Video Editing: S...
2024-05-2849 min
The InteractomeEpisode 29: Demystifying the MicrobiomeYou’ve probably heard of the microbiome, but there’s much more to it than just gut health. Tune in to hear from Bridget O’Connor, career microbiologist, for a discussion on the microbiome, how microbiologists study organisms they can’t see, and more!
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
Mastodon: @interactome@universeodon.com
Credits:
Audio/Video Editing: Sam Pickell
Artwork: Maia Reyes
Transcript: Margaret Downs
Intro/Outro Music: Geovane Bruno - Dancing...
2024-04-2955 min
The InteractomeEpisode 28: Bird Biology BonanzaThis week, the Interactome team is joined by Dr. Alex Champagne, Associate Professor of Biology at University of Southern Indiana! The team talks all things bird physiology — the age old question of flight evolution, interesting anatomical structures, and Dr. Champagne’s current work (which just got published, by the way)!
After listening to the episode, read about how skin lipids in desert bats suggest wing and tail membranes are important to evaporation cooling! https://www.sciencedirect.com/science/article/abs/pii/S1095643324000473
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https...
2024-03-181h 09
The InteractomeEpisode 27: Neural NetworksYou've probably heard of AI powered neural networks, but are you familiar with biological neural networks? Join Sam, Natalie, and returning guest Youngmin as they compare, contrast, and generally discuss both types of networks. Can a single neuron "think"? And how do neural networks "learn"? We cover these questions and more on this episode of the interactome.
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
Mastodon: @interactome@universeodon.com
Youngmin's channel: https://www.youtube.com/c/ADHDMathematician
Credits:
2024-01-291h 02
The InteractomeEpisode 26: Wheying In on ProteinsWe all know that protein is something in our food, but what else do proteins do? For our final episode of our 3-part series on the Central Dogma, we discuss (one of) the final products of DNA and RNA: proteins! We cover everything from where proteins come from to some of their roles as molecular machines. Along the way, we touch on topics such as how eating protein helps you make muscles to "the protein fold that kills." Correction: X-ray crystallography shoots high-energy photons (x-rays), not electrons, at crystals to obtain their structure. Sam was probably too excited thinking...
2024-01-011h 03
The InteractomeEpisode 25: It’s RNA’s World, And We’re Just Living In ItWelcome to our part 2 of the central dogma of biology series! In this episode, Maia, Joe and Natalie talk all things RNA. Tune in to learn about the molecular structure differences between RNA and DNA, mRNA vaccines, and to hear some polarizing biological theories!
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
Mastodon: @interactome@universeodon.com
Credits:
Audio/Video Editing: Sam Pickell
Artwork: Maia Reyes
Transcript: Margaret Downs
Intro/Outro Music: Geovane Bruno - Dancing I...
2023-11-201h 01
The InteractomeEpisode 24: Phishing and SmishingWhat’s spookier than identity theft, scams and fraud? In the digital age, cybersecurity is more important than ever. Yet, there are many misconceptions about the field and what it entails. October is cybersecurity month, and to celebrate Sam, Joe and Natalie spoke with SecOp analyst Virginia Gresham. The crew talked about about her role, the importance of protecting your information, and more. Give it a listen, guarantee you’ll learn something new!
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
Mastod...
2023-10-2353 min
The InteractomeEpisode 23: Investigative MindsetContent Warning: this episode discusses dead bodies, violent crime, and international conflict
On this show, we talk a lot about modeling the scientific mindset, but scientists aren’t the only professionals asking tough questions. This week, we’re joined by a retired FBI agent who tells us all about how to ask the right questions and solve problems at hand. Oh, and there’s a surprise connection between our guest and a host, so make sure to tune in!
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
Instagr...
2023-09-1854 min
The InteractomeEpisode 22: Lightning McDNA (Genetics)In this episode, Joe, Maia, and Natalie talk about genetics. They start with the basics, and then delve into how we get our DNA and how it can change over many many years. You're bound to learn something new with this episode of the interactome!
Links:
Our Website: https://interactomemedia.wixsite.com/website
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
Mastodon: @interactome@universeodon.com
Credits:
Audio/Video Editing: Sam Pickell
Artwork: Maia Reyes
Transcript: Margaret Downs
Intro/Outro Music: Geovane Bruno - D...
2023-08-2447 min
The InteractomeEpisode 21: Gateway to GISWhen we think of science, we often think of data being collected in test tubes and laboratories, but lots of data actually exists in the context of mountains, roads, neighborhoods and countries. Join Joe, Sarah and Natalie and special guest Rylee Wrenner as they discuss Geographic Information Science (GIS), which allows researchers to understand the kinds of data that are best visualized on a map. Along the way, they discuss how to make useful models, the centuries-old origins of GIS in epidemiology, and somehow manage to relate GIS to cheese. Join us to learn about GIS and witness our...
2023-07-1744 min
The InteractomeEpisode 20: Mighty MitochondriaYou might have heard the phrase "the mitochondria is the powerhouse of the cell" back in high school biology class, but what does that mean? Join Joe, Sam, and Maia as they explore everyone's favorite part of the cell. We had some fun with this, so join us as we explain what exactly the mitochondria is, how it works, and what happens if it breaks. Along the way, we'll talk about electron hot potato, grand theft organelle, at least one deadly poison, and, yes, find out that Joe has more than one brain cell.
Links:
Our...
2023-06-1958 min
The InteractomeEpisode 19: Food ScienceThis episode of the interactome is all about food science! Join Christina Allingham, A.K.A @biteofnewengland, as she talks about her experience in the food industry. Natalie, Sam, and Maia host as they ask Christina how she got into the industry, what food science is all about, and how her job has evolved over the course of covid.
Links:
Christina's Blog: https://www.instagram.com/biteofnewengland/
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
Mastodon: @interactome@universeodon.com
Credits:
Audio/Video Editing: Sam Pickell
2023-05-1554 min
Circulation on the RunCirculation April 18, 2023 Issue This week, please join authors Marc Sabatine and Prakriti Gaba, as well as Associate Editor Amit Khera, as they discuss the article "Association Between Achieved Low-Density Lipoprotein Cholesterol Levels and Long-Term Cardiovascular and Safety Outcomes: An Analysis of FOURIER-OLE." Dr Greg Hundley: Welcome listeners, to this April 18th issue of Circulation on the Run and I am Dr. Greg Hundley, Associate Editor, Director of the Pauley Heart Center at VCU Health in Richmond, Virginia. Dr Peder Myhre: And I'm Dr. Peder Myhre, Social Media Editor from Akershus University Hospital and University...
2023-04-1722 min
The InteractomeEpisode 18: Science Stories Part 3It's time for more science stories! This time Sam has too many snails, Natalie is impacted by woodpeckers, and Joe discusses mentorship.
Links:
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
Mastodon: @interactome@universeodon.com
Credits:
Audio/Video Editing: Sam Pickell
Artwork: Maia Reyes
Intro/Outro Music: Geovane Bruno - Dancing In The Future
Timestamps:
0:00 Intro
3:38 Sam's story: Too Many Snails
14:42 Joe's nuclear hermit crab
22:14 Natalie's story: 1000 G-Force Woodpeckers
34:48 Joe's Story: The Importance of Mentorships
51:53 Outro
2023-04-1753 min
Science Research WeeklyEpisode 13: Crazy Ants, Crazier VirusesGet ready for chimeric crazy ants, viruses abounding in protists and infants alike, solar system generation in R, an awesome Python list, and a couple of nifty niche funding opportunities. Science On.
References:
Obligate chimerism in male yellow crazy ants
Large-scale invasion of unicellular eukaryotic genomes by integrating DNA viruses
Expanding known viral diversity in the healthy infant gut
Make “Solar System” Plots With {ggsolar}
Awesome Python
Microsoft PowerToys
NOSI: Assembling the Addiction Organelle Interactome
NIAID: Mechanisms of Neurotropic Virus-mediated Disease
R-packages:
fakir: Generate Fake Datasets for Prototyping and...
2023-04-1405 min
The InteractomeEpisode 17: What the Heck is Mass Spec?On this episode of the Interactome, join Joe, Natalie, Sarah, and special guest Margaret as they discover what the heck mass spectrometry actually is. From generating ideas for experiments to protein identification and avenues for treatment in diseases like cancer, mass spec is truly a powerful tool. And with cutting-edge technologies to further its versatility across many science disciplines, this is an episode you don't want to miss!
Links:
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
Mastodon: @interactome@universeodon.com
Credits:
Audio/Video Editing: Sam Pickell
2023-03-2052 min
The InteractomeMinisode 1: Pi DayIn our inaugural minisode, Sam, Natalie, and Pickle have a conversation with mathematician Youngmin Park to celebrate Pi day! Youngmin and the team cover everything from what Pi actually is, to being drowned because of math, to the math behind biological rhythms, and even 4th dimensional spaghetti!
Links:
Twitter: https://twitter.com/theinteractome
Instagram: https://www.instagram.com/interactome_media/
Mastodon: @interactome@universeodon.com
Youngmin's channel: https://www.youtube.com/c/ADHDMathematician
Audio/Video Editing: Sam Pickell
Artwork: Maia Reyes
Intro/Outro Music: Geovane Bruno - Dancing In The F...
2023-03-1426 min
The InteractomeEpisode 16: Science Stories Part 2On this edition of Interactome Science Stories, it's Lauren, Joe and Pickle's turns to talk about what in the world of science has impacted them! From islands in the sky, to the story of Emily Whitehead, to the importance of learning from your mistakes, we hope to inspire and entertain with these short stories. So gather 'round and settle in as we take you through some of our favorite science stories.
Audio/Video Editing: Sam Pickell
Artwork: Maia Reyes
Intro/Outro Music: Geovane Bruno - Dancing In The Future
Ti...
2023-02-2149 min
The InteractomeEpisode 15: All About AstrophysicsOn this episode of the Interactome, we speak with astrophysicist Kenneth Lin about space, physics, astronomy, and more! How does one study space from a lab? And how does the James Webb telescope produce such beautiful pictures of space? Join Joe, Natalie, Sarah, and Kenneth as they talk all about astrophysics.
Note: Kenneth informed us that a teaspoon of neutron star material does not in fact have the same mass as the earth. A more accurate statement is that a teaspoon of material from a neutron star weighs as much as Mount Everest, or that a sphere...
2023-01-171h 15
Stem Cell Channel (Video)One Niche to Rule Them All: Stem Cell-Lymphatic Interactome in Regeneration and Cancer with Shiri Gur-Cohen - Sanford Stem Cell Symposium 2022Shiri Gur-Cohen, Ph.D., UC San Diego, explains how her lab studies how epithelial stem cells communicate with their vascular microenvironment to advance regeneration and combat metastatic diseases.
Series: "Stem Cell Channel" [Education] [Show ID: 38409]
2022-12-2624 minStem Cell Channel (Audio)One Niche to Rule Them All: Stem Cell-Lymphatic Interactome in Regeneration and Cancer with Shiri Gur-Cohen - Sanford Stem Cell Symposium 2022Shiri Gur-Cohen, Ph.D., UC San Diego, explains how her lab studies how epithelial stem cells communicate with their vascular microenvironment to advance regeneration and combat metastatic diseases.
Series: "Stem Cell Channel" [Education] [Show ID: 38409]
2022-12-2624 min
The InteractomeEpisode 14: Flu FactsHave you ever wondered about the yearly flu vaccine? What goes into it, how it changes year to year, how the vaccine has evolved alongside the flu itself? Join special guest Erin Deans, along with Natalie, Sam, and Maia as they discuss the flu and the flu vaccine. This episode is bound to teach you something new that you may not have already known about the flu!
Timestamps:
0:00 Intro
1:13 Introducing Erin
2:57 Erin's background
6:38 How viruses get into cells
9:49 What is the flu?
14:39 Where the flu comes from
16:40 Why there is...
2022-12-1958 min
The InteractomeEpisode 13: An Introduction to Lab ConstructionArchitect Ewan Ellis joins Joe, Maia and Sam to discuss how research labs are built. We cover everything from the planning process to the plumbing, and along the way talk about the challenges and triumphs of building all kinds of research facilities. If you work in a lab, or have only just driven past one, this is an episode that you won't want to miss!
Content warning: Contains mentions of animal research and accidental research animal death.
Timestamps:
0:00 Intro
4:54 Introducing Ewan
10:50 What does Ewan do
13:24 What would you need t...
2022-11-211h 01
The InteractomeEpisode 12: Science StoriesThis episode of the Interactome features Sam, Sarah, and Natalie as they each tell a science story that resonates with them. Each member brings their own unique spin on what a science story is to them, as they discuss topics ranging from famous photos to clarinets. Join us for some thought provoking and entertaining discussion as we tell our stories, and be sure to share your science story with us on social media or in the comments after the episode!
0:00 - Intro
0:44 - Meeting this episode's members
3:00 - Sam's Story: Radithor
17:37 - Radium Girls
2022-10-181h 06
The InteractomeEpisode 11: Guide to Grad SchoolWelcome back to another episode of the Interactome. In this episode, Joe, Lauren, Maia, and Pickle discuss the process of applying to grad school. We focus on grad school as it applies to the sciences, from a Master's degree to an MD PhD. If you have ever thought "is grad school right for me?" or have been curious about what it's like to be a grad student, this is the episode for you!
Chapters:
0:00 - Intro
0:49 - Meeting our new member: Pickle
5:15 - Lauren's start to her PhD program
7:38 - Maia's experience mid-way...
2022-09-261h 09
PubReadingPubReading [183] - From structure to function: Route to understanding lncRNA mechanism - J. Graf and M. KretzRNAs have emerged as a major target for diagnostics and therapeutics approaches. Regulatory nonprotein-coding RNAs (ncRNAs) in particular display remarkable ver- satility. They can fold into complex structures and interact with proteins, DNA, and other RNAs, thus modulating activity, localization, or interactome of multi-protein complexes. Thus, ncRNAs confer regulatory plasticity and represent a new layer of reg- ulatory control. Interestingly, long noncoding RNAs (lncRNAs) tend to acquire complex secondary and tertiary structures and their function—in many cases—is dependent on structural conservation rather than primary sequence conservation. Whereas for many proteins, structure and its associated function are closely con...
2022-09-2144 min
Listen In - Bitesize Bio Webinar AudiosUsing FIT probes and Super-Resolution MicroscopyAll mRNA molecules recruit specific proteins to form ribonucleoprotein complexes (mRNPs). Composition and localization of many mRNPs change dynamically from translation to decay. Microscopic techniques with high spatial and temporal resolution are invaluable for studying mRNP biogenesis.We have developed new tools based on fluorogenic forced intercalation (FIT) probes for RNA detection, quantification and interference in biological samples. The probes contain a thiazole orange (TO) dye introduced at a position normally occupied by a nucleobase. Upon binding to target nucleic acids, the TO dye increases its quantum yield and brightness substantially (greater than10 fold). These probes detect...
2022-08-3154 min
Beyond Biotech - the podcast from LabiotechBeyond Biotech podcast 11: Ilya Pharma, IRB Barcelona, Krystal Biotech, Phase Genomics2:15 Labiotech.eu news5:12 Phase Genomics16:44 IRB Barcelona29:37 Ilya Pharma43:00 Krystal Biotech53:54 JLLOur guests are Ilya Pharma CEO and co-founder Evelina Vågesjö and chief financial officer Oskar Lund; Miguel Martín-Álvarez, postdoctoral fellow in the cancer science unit at IRB Barcelona; Hubert Chen, head of clinical development at Krystal Biotech; and Ivan Liachko, CEO of Phase Genomics.We also have a new weekly addition, as JLL will be joining us with a look at financial news. This week, we’re joined by Robert Coughlin, JLL managing directo...
2022-08-2658 min
The InteractomeEpisode 10: Fisheries InteractionMarine scientist Jess Veo joins Sarah, Maia and Sam to discuss fishing, conservation, and the seafood industry in New England. We talk about sustainability in the seafood industry, how marine mammals interact with fisheries, and how scientists can work together with people who work on fishing boats to keep animals like whales and seals safe. Join us to learn about lobster fishing, hear some anecdotes about clam bakes and fishing TV shows (and at least one Oscar-winning movie), and much, much more.
2022-08-221h 02
The InteractomeEpisode 9: Forecasting Fire ActivityOn this episode of The Interactome, meet Ronnie Abolafia-Rosenzweig, PhD, a scientist whose research helps predict fires! Join Natalie and Lauren as we talk about the western fire season, machine learning, Ronnie's predictions for the 2022 season, and more!
2022-07-1841 min
The InteractomeEpisode 8: A Source of Course!This month, join Sam, Sarah, Natalie, and Joe as we share stories and tips on research and sources. From PubMed and preprints to anecdotes of validating sources and Dairy Law, this episode is one you don't want to miss!
Got a research story to share or want to join the conversation? Visit us at interactomemedia.org and on our socials! We look forward to hearing from you.
2022-06-2043 min
OncotargetTrending With Impact: Dual Requirement in Stem Cell Leukemia/LymphomaListen to a blog summary of a trending research paper published by Oncotarget, entitled, "Proteomic analysis reveals dual requirement for Grb2 and PLCγ1 interactions for BCR-FGFR1-Driven 8p11 cell proliferation."
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Chromosomes are found in the nucleus of cells and consist of proteins and tightly coiled strands of DNA. During cell division, chromosomal translocations can occur while the chromosomes are being copied. This type of mutation can mean that an entire chromosome has moved to another location, or that a chromosome has broken, usually into two pieces, and moved to another site. Some translocations are harmless, but others can lead to a...
2022-05-1807 min
The InteractomeEpisode 7: The Science of Stem CellsWhat exactly are stem cells, and why are they special? And why are there ethical controversies behind them? Join Maia, Lauren, and Sarah as they discuss the science, medical applications, and bioethics of stem cells.
Editor’s note
CRISPR-Cas9 genetic editing of hematopoietic stem cells (HSCs) to cure the sickle cell anemia mutation is still in early clinical trials - there is no concrete news about long term effects the patients are experiencing. Other stem-cell based strategies (such as approaches to turn on fetal hemoglobin and HSC transplants from healthy donors) have been succ...
2022-05-1650 min
The InteractomeEpisode 6: Swab Story (with Dr. Ramy Arnaout, MD, DPhil)Join us and special guest Dr. Ramy Arnaout, MD, DPhil on a discussion of how he led his team to resolve a nationwide COVID swab shortage within three weeks through 3D printing and effective cooperation. Quite possibly the coolest episode we've ever done, it's a conversation with takeaways you don't want to miss!
Dr. Arnaout's reflection in the Journal of Clinical Microbiology
02:12 Introducing Dr. Arnaout
06:25 Swab crisis basics, team formation, influences from prior studies of cooperation
25:36 Team size and roles, effective utilization of resources, swab design and 3D...
2022-04-181h 00
Neurology® PodcastGenetic Testing for White Matter DisordersDr. Justin Abbatemarco talks with Dr. Aurora Pujol about diagnosing genetic white matter disorders by singleton whole-exome and whole-genome sequencing using interactome-driven prioritization. Read the full article in Neurology.
2022-04-0718 min
The InteractomeEpisode 5: Six Stumped ScientistsWelcome back to the Interactome, trivia-style! This month, our hosts take on a new challenge - with trivia questions outside their domain. Join us and play along. Can you beat us? Answer: Most likely. Which team will claim victory?
Disclaimer: At one point in the episode, we mention working with hazardous materials. Everyone mentioned is a trained professional working in a laboratory with proper accreditation. We do not condone the use of these materials outside these circumstances. In other words, please do not try this at home!
2022-03-2147 min
The InteractomeEpisode 4: You Can Go Far with PCRWelcome back to episode - or as we call them, node - 4 of the Interactome Podcast. This week, we’ll be discussing a lab technique you might have heard of by now: PCR. Join us as we talk about what PCR is, how it works, and the many different things PCR can be used for.
2022-02-2241 min
The InteractomeEpisode 3: It’s All in the NameThis episode, we discuss where scientific names come from. We’ll be discussing some of the wackiest names in the scientific community along with their origin stories!
2022-01-1742 min
The InteractomeEpisode 2: A Conversation About Cancer (Part 2)Welcome back to part two of node two of the Interactome Podcast! This week, we’ll be discussing the many facets of cancer: This second part covers what it's like to study cancer in a lab as well as some personal anecdotes from our very own researchers! We had so much to say that we split it into two parts. Enjoy!
2021-12-1430 min
The InteractomeEpisode 2: A Conversation About Cancer (Part 1)Welcome back to episode - or as we call them, node - 2 of the Interactome Podcast! This week, we’ll be discussing the many facets of cancer: the causes as well as some personal anecdotes from our very own researchers! We had so much to say that we split it into two parts. Enjoy!
2021-11-0228 min
The InteractomeEpisode 1: We Are Swiss CheeseWelcome to The Interactome! In this inaugural episode, Join Lauren, Joe, Sam, and Maia as they discuss Interactome Media's philosophy and cool science history, ethics, and more! Get to know the hosts and learn why "we are all Swiss cheese."
2021-11-0235 min
Authentic BiochemistryThe Aging Immune Response and Cellular Differentiation are characterized by Apoptosis vs. Necroptosis Mechanisms. DJGPhD. 20.9.21.Authentic Biochemistry Productions.A general audio lecture involving a molecular interactome mediating the innate immune response and the control over T and B lymphocyte memory cells resulting in long term potentiation of autoimmune disease during aging.
2021-09-2030 min
Digital Pathology Podcast21: Introduction to multiplex for tissue image analysis (part 1) w/ Regan Baird, VisiopharmSend us a textThis episode is brought to you by Visiopharm.After experimenting with multidimensional, multimarker, and multicolor single-cell imaging modalities during his postdoc at Beth Israel Deaconess Medical Center in Boston, looking at 2D images of tissue stained just with hematoxylin and eosin (H&E) seemed to him a bit simplistic…and then he was tasked with doing tissue image analysis (IA). When relying just on H&E, IA can be a very challenging task. So, to both simplify it and extract more information from the tissue, multiplex staining can be implemented. I...
2021-04-2709 min
Weeding the GemsMarcel Bach-Pages describes the plant RNA Interactome Capture MethodMarcel Bach-Pages works with Gail Preston at the University of Oxford and we discuss a new protocol to identify the RNA-Binding Proteome from Arabidopsis leaves. This community-focused work includes full instructions for use of the protocol and they provide an accessible list of proteins that they have identified. This research is published in Biomolecules and[...]
The post Marcel Bach-Pages describes the plant RNA Interactome Capture Method appeared first on Weeding the Gems.
2020-07-2211 minGARNet UK Plant Science RoundupMarcel Bach-Pages describes the plant RNA Interactome Capture MethodMarcel Bach-Pages works with Gail Preston at the University of Oxford and we discuss a new protocol to identify the RNA-Binding Proteome from Arabidopsis leaves. This community-focused work includes full instructions for use of the protocol and they provide an accessible list of proteins that they have identified. This research is published in Biomolecules and[...]
The post Marcel Bach-Pages describes the plant RNA Interactome Capture Method appeared first on Weeding the Gems.
2020-07-2200 minEpigenetics PodcastIdentification of Functional Elements in the Genome (Bing Ren)In this episode of the Epigenetics Podcast, we caught up with Bing Ren, Ph.D., from the University of California, San Diego and the Ludwig Institute for Cancer Research to talk about his work on identifying functional elements of the genome and higher order genome structure.
Dr. Ren’s lab invented an approach using chromatin immunoprecipitation-based methods for the identification of transcription factor binding sites and chromatin modification status genome-wide. His group was a major part of the ENCODE Project and the demonstration of this being an effective method for genome-wide mapping of cis-elements, has made...
2020-05-0743 min
The FEBS Journal PodcastReview article - Yang YangRaf-interactome in tuning the complexity and diversity of Raf function
2015-01-0907 min
Fakultät für Chemie und Pharmazie - Digitale Hochschulschriften der LMU - Teil 05/06GroEL/ES modulates the mechanism and accelerates the rate of TIM-barrel domain foldingThe interactome of GroEL/ES has been characterized extensively in several studies and substrates of the chaperonin have been classified (Kerner et al., 2005; Fijiwara et al., 2010). However, the question of what makes some proteins GroEL-dependent and how exactly the chaperonin system promotes their folding remained unresolved. Moreover, it has been unclear how the chaperonin acts on its substrates and whether the protein folding pathway is modified inside the cage as compared to free solution. The aim of this study, therefore, was to characterise and compare the spontaneous and chaperonin-assisted refolding pathway of an obligate substrate of GroEL/ES, in order...
2014-12-1000 minFakultät für Chemie und Pharmazie - Digitale Hochschulschriften der LMU - Teil 05/06A human interactome
2014-09-1900 minFakultät für Mathematik, Informatik und Statistik - Digitale Hochschulschriften der LMU - Teil 01/02Finding correlations and independences in omics dataBiological studies across all omics fields generate vast amounts of data. To understand these complex data, biologically motivated data mining techniques are indispensable. Evaluation of the high-throughput measurements usually relies on the identification of underlying signals as well as shared or outstanding characteristics. Therein, methods have been developed to recover source signals of present datasets, reveal objects which are more similar to each other than to other objects as well as to detect observations which are in contrast to the background dataset. Biological problems got individually addressed by using solutions from computer science according to their needs. The study of...
2012-01-3100 minFakultät für Chemie und Pharmazie - Digitale Hochschulschriften der LMU - Teil 04/06DnaK Functions as a Central Hub in the E. coli Chaperone NetworkUpon emerging from the ribosomal exit tunnel, folding of the polypeptide chain is necessary to form the fully functional protein. In E. coli, correct and efficient protein folding is mainly secured by an organized and complex chaperone system which includes two main principles: The first principle consists of the nascent binding chaperones including trigger factor (TF) and the DnaK/DnaJ system, while the second principle is represented by the downstream GroEL/ES chaperonin system. The identification of ~250 natural GroEL substrates demonstrated that GroEL/ES specifically folds a small group of proteins with complex domain topologies (Kerner et al., 2005) which include...
2011-12-1200 min
Medizin - Open Access LMU - Teil 18/22The SARS-coronavirus-host interactomeCoronaviruses (CoVs) are important human and animal pathogens that induce fatal respiratory, gastrointestinal and neurological disease. The outbreak of the severe acute respiratory syndrome (SARS) in 2002/2003 has demonstrated human vulnerability to (Coronavirus) CoV epidemics. Neither vaccines nor therapeutics are available against human and animal CoVs. Knowledge of host cell proteins that take part in pivotal virus-host interactions could define broad-spectrum antiviral targets. In this study, we used a systems biology approach employing a genome-wide yeast-two hybrid interaction screen to identify immunopilins (PPIA, PPIB, PPIH, PPIG, FKBP1A, FKBP1B) as interaction partners of the CoV non-structural protein 1 (Nsp1). These molecules...
2011-10-0100 minMedizin - Open Access LMU - Teil 17/22A potential role for intragenic miRNAs on their hosts' interactomeBackground: miRNAs are small, non-coding RNA molecules that mainly act as negative regulators of target gene messages. Due to their regulatory functions, they have lately been implicated in several diseases, including malignancies. Roughly half of known miRNA genes are located within previously annotated protein-coding regions ("intragenic miRNAs"). Although a role of intragenic miRNAs as negative feedback regulators has been speculated, to the best of our knowledge there have been no conclusive large-scale studies investigating the relationship between intragenic miRNAs and host genes and their pathways. Results: miRNA-containing host genes were three times longer, contained more introns and had longer 5...
2010-01-0100 min
PROTEOMICS podcastPROTEOMICS podcast, August 2008Toward cancer biomarker discovery using the Glycomics Approach, Quantitative membrane proteomics of small cell lung cancer resistance mechanisms, Identification of protein interactome in pancreatic cancer: A Yeast Two-Hybrid Approach, A peptide-based 2D LC platform for quantitative analysis of the disease proteome
2008-07-3128 minMedizinische Fakultät - Digitale Hochschulschriften der LMU - Teil 07/19Proteomics of Acute Myeloid Leukemia:Acute Myeloid Leukemia (AML) is characterized by specific cytogenetic aberrations that are strong determinants of prognostic outcome and therapeutic response. Because the pathological outcome of AML patients with cytogentic abnormalities differs considerably we hypothesized that their proteome may also differ specifically in their expression pattern, protein interaction pathways and posttranslational modifications. We performed this study using 42 AML patients diagnosed for various cytogenetic abnormalities based on two-dimensional gel electrophoresis and MALDI TOF Tandem MS (MS/MS) analysis. We could identify significant differences in the proteome and posttranslational modifications of peptides, later confirmed by other methods, between cytogenetic groups. The interactome analysis...
2007-06-1200 min
Futures in Biotech (Audio)Dr. Marc Vidal, Part 2
Dr. Vidal is working on the next stage in big biotech. Now that we've mapped the human genome it's time to map the interactome, the human protein-protein interaction network. In this episode we talk about the network of interactions, and how closely it mimics other networks, including social networks.
Hosts: Marc Pelletier and Leo Laporte
Guest: Marc Vidal, Ph.D.
Thanks to CacheFly for providing the bandwidth for this podcast.
2006-08-171h 09Futures in Biotech (Audio)Dr. Marc Vidal, Part 1
Dr. Vidal is working on the next stage in big biotech. Now that we've mapped the human genome it's time to map the interactome, the human protein-protein interaction network. In this episode he gives us the groundwork for understanding his work. Next week, in part two, Dr. Vidal explains how the network of protein interactions resembles human social networks.
Hosts: Marc Pelletier and Leo Laporte
Guest: Marc Vidal, Ph.D.
Thanks to CacheFly for providing the bandwidth for this podcast.
2006-08-1154 minMedizin - Open Access LMU - Teil 14/22Inferring topology from clustering coefficients in protein-protein interaction networksBackground: Although protein-protein interaction networks determined with high-throughput methods are incomplete, they are commonly used to infer the topology of the complete interactome. These partial networks often show a scale-free behavior with only a few proteins having many and the majority having only a few connections. Recently, the possibility was suggested that this scale-free nature may not actually reflect the topology of the complete interactome but could also be due to the error proneness and incompleteness of large-scale experiments. Results: In this paper, we investigate the effect of limited sampling on average clustering coefficients and how this can help to...
2006-01-0100 min