Dr Roghaiyeh (Rugi) Safari’s Post

🔬🧫🧬  The application of omics techniques in analysing the microbiome within clinical trials has become a cornerstone in biomedical research. 👩⚕️ Genomics, transcriptomics, andmetabolomics, collectively provide an intricate understanding of microbial communities and their functional roles in health and disease. 🧬 By employing NGS and complementary advanced bioinformatics tools, we decipher the composition, dynamics, and functional potential of the microbiome, enabling diagnostic, therapeutic targets as well as novel LPB selection. 👨🔬 We present recent advances in omics technologies and how we can exploit microbiome data to gain holistic understanding of the microbiome-host interplay, informing clinical decision-making and advancing our knowledge of interplay between host and microbiome. 🎤 To find out more, meet Eline S. Klaassens from BaseClear at the 17th IPC2024 in Prague, 18-21 June 2024 and Hit the bell 🔔🔔🔔 to stay tuned on to International Scientific Conference on #Probiotics, #Prebiotics, #Gut #Microbiota and #Health - IPC2024 and get updated on probiotic, prebiotic #science and #microbiota #research.

Australian Genomics’ DNA dialogue seminar series returns this Thursday 29 February at 9am (AEDT). DNA dialogue features an exciting lineup of international speakers across a wide range of health genomic disciplines. Seminars are held live via zoom and registration is open to anyone working in, or impacted by, medical genomics. This month’s seminar “Mexican biobank advances population and medical genomics of diverse ancestries” features Associate Professor Mashaal Sohail from the National Autonomous University of Mexico. The Mexican Biobank project genotyped 6,057 individuals from 898 rural and urban localities across all 32 states in Mexico at a resolution of 1.8 million genome-wide markers with linked complex trait and disease information creating a valuable nationwide genotype–phenotype database. This study provides insights into the genetic histories of individuals in Mexico and dissects their complex trait architectures, both crucial for making precision and preventive medicine initiatives accessible worldwide. Find out more and register here: https://lnkd.in/gMEcKN9S Tiffany Boughtwood #AusGenomics #DNAdialogue #SeminarSeries #genomics #biobank #biobanking #mexico

### Disordered Proteins: A New Frontier in Biology Proteins are the workhorses of biology, each traditionally understood to have a specific three-dimensional shape critical for its function. However, this view is challenged by intrinsically disordered proteins (IDPs), which, despite lacking a stable structure, play crucial roles in biological processes. Remarkably, these shape-shifting proteins make up about one-third of all proteins. In a groundbreaking study published in Nature (https://lnkd.in/dDtr7qie), researchers from the University of Copenhagen's Department of Biology have provided insights into the behavior of nearly all 28,000 disordered proteins in the human body. This research marks a significant leap in our understanding of these enigmatic proteins. IDPs and intrinsically disordered regions (IDRs) are ubiquitous across all life forms, driving key biological functions and being implicated in numerous diseases. Unlike their structured counterparts, IDRs defy the conventional sequence-structure-function paradigm, forming diverse, transient structures. This characteristic has made it challenging to study them comprehensively. Advancements in protein science have allowed the prediction of folded protein structures at a proteome scale, yet knowledge about IDRs has lagged due to their poorly conserved sequences and limited experimental characterization. To address this, the researchers developed a sophisticated molecular model to generate conformational ensembles of IDRs, predicting their structures based on their sequences. By simulating nearly all IDRs in the human proteome, the study reveals how chain compaction correlates with cellular function and localization. The team utilized a machine-learning model trained on simulation data to demonstrate the conservation of these conformational properties across different species. This approach not only confirms findings from individual protein studies but also links conformational ensembles with cellular roles, sequence features, evolutionary conservation, and disease associations at a proteome-wide scale. The creation of a freely accessible database of these conformational properties is expected to spur further experimental investigations and generate new hypotheses about the biological roles and evolutionary pathways of IDRs. #Proteins #Biology #Research #AI #BigData #Bioinformatics #ProteinScience #IntrinsicallyDisorderedProteins #IDPs #NatureResearch #UniversityOfCopenhagen #ScientificBreakthrough

🔬 A New Discovery in Human Microbiome: 'Obelisks' - Tiny RNA Structures with Big Implications 🌐 Researchers have uncovered a groundbreaking addition to the human microbiome: RNA structures, named 'Obelisks', that are even tinier than viruses and inhabit the bacteria in our guts and mouths. This remarkable finding, detailed in a preprint on bioRxiv & medRxiv by researchers at Stanford University, introduces a new dimension to our understanding of the microbiome. 🧬 What Are Obelisks? Obelisks are flattened circles of RNA, folded into rod-like structures, and distinct from known viroids or viruses. They encode unique sequences, termed 'Oblins', which are novel to science and play a crucial role in information transfer to cells. 🌍 Global Presence Extensive research has found Obelisks in stool samples from individuals across every continent, indicating their widespread presence in human microbiomes. 6.6% of gut microbiome and 53 % of oral microbiome samples contained Obelisks! 🧐 The Big Picture This discovery could offer insights into the origin of life, as some scientists speculate that such simple, self-replicating structures might be precursors to all life on Earth. The study marks a significant milestone, revealing that these elements are not just sporadic but affect a considerable portion of the population…the question is why? Understanding their role in the microbiome could be crucial in comprehending the delicate balance of our body's internal ecosystem. 🔎 Further Research The mechanism of Obelisks' interaction with host cells, their role in the microbial community, and potential health implications remain areas for future exploration. 🔗https://lnkd.in/e9Biazr9 #microbiomeresearch # microbiome #rnastructures #rna #obelisks #research #healthsciences #injoy

🌟 𝐄𝐱𝐜𝐢𝐭𝐢𝐧𝐠 𝐆𝐞𝐧𝐨𝐦𝐢𝐜 𝐁𝐫𝐞𝐚𝐤𝐭𝐡𝐫𝐨𝐮𝐠𝐡: 𝐓𝐡𝐞 𝐅𝐢𝐫𝐬𝐭 𝐇𝐮𝐦𝐚𝐧 𝐏𝐚𝐧𝐠𝐞𝐧𝐨𝐦𝐞!🌟 I am thrilled to share a groundbreaking milestone in the field of genomics - the creation of the first human " 𝐏𝐚𝐧𝐠𝐞𝐧𝐨𝐦𝐞! This monumental project, spearheaded by a consortium of international scientists, aims to catalog genetic diversity across different populations, significantly enhancing our understanding of the genetic basis of diseases and traits. 𝐊𝐞𝐲 𝐇𝐢𝐠𝐡𝐥𝐢𝐠𝐡𝐭𝐬 𝐨𝐟 𝐭𝐡𝐞 𝐏𝐚𝐧𝐠𝐞𝐧𝐨𝐦𝐞 𝐏𝐫𝐨𝐣𝐞𝐜𝐭: 🔍 𝐂𝐨𝐦𝐩𝐫𝐞𝐡𝐞𝐧𝐬𝐢𝐯𝐞 𝐆𝐞𝐧𝐞𝐭𝐢𝐜 𝐃𝐢𝐯𝐞𝐫𝐬𝐢𝐭𝐲: Unlike previous efforts that focused primarily on individuals of European descent, the pangenome project includes diverse populations, ensuring a more accurate and inclusive representation of human genetic variation. 💡 𝐄𝐧𝐡𝐚𝐧𝐜𝐞𝐝 𝐔𝐧𝐝𝐞𝐫𝐬𝐭𝐚𝐧𝐝𝐢𝐧𝐠 𝐨𝐟 𝐇𝐮𝐦𝐚𝐧 𝐆𝐞𝐧𝐞𝐭𝐢𝐜𝐬: By capturing the full range of genetic variation, the pangenome provides a more complete reference for studying human genetics, aiding researchers in identifying genetic factors associated with diseases and traits across different ethnic groups. 🔬 𝐈𝐦𝐩𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧𝐬 𝐟𝐨𝐫 𝐏𝐞𝐫𝐬𝐨𝐧𝐚𝐥𝐢𝐳𝐞𝐝 𝐌𝐞𝐝𝐢𝐜𝐢𝐧𝐞: The insights gained from the pangenome project will be instrumental in developing targeted therapies and personalized treatments, improving healthcare outcomes for individuals worldwide. 🌐 𝐂𝐨𝐥𝐥𝐚𝐛𝐨𝐫𝐚𝐭𝐢𝐯𝐞 𝐄𝐟𝐟𝐨𝐫𝐭:This project is a testament to the power of international collaboration, bringing together leading scientists and researchers from various institutions to achieve a common goal of advancing human health. The 𝐏𝐚𝐧𝐠𝐞𝐧𝐨𝐦𝐞 project represents a giant leap forward in our quest to understand human biology and develop targeted therapies for various genetic conditions. It promises to revolutionize medical research and patient care, making healthcare more precise and inclusive. 📚 **Read more about this groundbreaking project here**: [Nature](https://lnkd.in/g87EDaEQ) Let's celebrate this incredible achievement and the bright future it promises for medical research and patient care! #Genomics #Pangenome #GeneticDiversity #MedicalResearch #HealthcareInnovation #PersonalizedMedicine #Biotechnology #Science #Research

My contention is Obelisks developed by eating too much Ultra-processed food and meat ! Ultra-processed food isn't just bad for your health—it messes with your mind https://lnkd.in/gTvU_Xwj How food companies ‘sweetened the world’ – and increased the risk of disease https://lnkd.in/gBVVYP5P Why do so many people in industrialized Western societies have unhealthy microbiomes that lack diversity? https://lnkd.in/g_Pb4Pxk It’s been estimated that we lose at least 13 years by eating a typical U.S. diet. https://lnkd.in/g5FJx2Kh Benefits of a plant-based diet: What happens to your body when you stop eating meat? https://lnkd.in/gRKsJywj? Want to live longer? Influence your genes.  https://lnkd.in/gxyC9ASz Why the Mediterranean diet rules and much more https://lnkd.in/gjnbUDEV

𝐏𝐫𝐞𝐬𝐞𝐧𝐭𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐍𝐞𝐰 𝐑𝐞𝐬𝐞𝐚𝐫𝐜𝐡 𝐑𝐞𝐬𝐮𝐥𝐭𝐬 🗣️ DDEA Grant Recipient Virginia Díez has just presented her postdoc project 𝘝𝘢𝘳𝘪𝘢𝘯𝘵-𝘵𝘰-𝘧𝘶𝘯𝘤𝘵𝘪𝘰𝘯 𝘵𝘳𝘢𝘯𝘴𝘭𝘢𝘵𝘪𝘰𝘯 𝘰𝘧 𝘰𝘣𝘦𝘴𝘪𝘵𝘺-𝘢𝘴𝘴𝘰𝘤𝘪𝘢𝘵𝘦𝘥 𝘭𝘰𝘤𝘪 𝘵𝘩𝘳𝘰𝘶𝘨𝘩 𝘮𝘶𝘭𝘵𝘪-𝘰𝘮𝘪𝘤𝘴 𝘥𝘢𝘵𝘢 𝘪𝘯𝘵𝘦𝘨𝘳𝘢𝘵𝘪𝘰𝘯 at the Annual Variant to Function Symposium, organised by the Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at the Broad Institute of MIT and Harvard in Boston.   “𝘐𝘵 𝘸𝘢𝘴 𝘢 𝘱𝘭𝘦𝘢𝘴𝘶𝘳𝘦 𝘵𝘰 𝘣𝘦 𝘣𝘢𝘤𝘬 𝘵𝘰 𝘵𝘩𝘦 𝘉𝘳𝘰𝘢𝘥 𝘸𝘩𝘦𝘳𝘦 𝘐 𝘥𝘪𝘥 𝘢 3-𝘮𝘰𝘯𝘵𝘩 𝘳𝘦𝘴𝘦𝘢𝘳𝘤𝘩 𝘴𝘵𝘢𝘺 𝘭𝘢𝘴𝘵 𝘧𝘢𝘭𝘭 𝘵𝘰 𝘳𝘦𝘤𝘰𝘯𝘯𝘦𝘤𝘵 𝘸𝘪𝘵𝘩 𝘤𝘰𝘭𝘭𝘦𝘢𝘨𝘶𝘦𝘴, 𝘥𝘪𝘴𝘤𝘶𝘴𝘴 𝘷𝘢𝘳𝘪𝘢𝘯𝘵-𝘵𝘰-𝘧𝘶𝘯𝘤𝘵𝘪𝘰𝘯 𝘴𝘤𝘪𝘦𝘯𝘤𝘦 𝘢𝘯𝘥 𝘱𝘳𝘦𝘴𝘦𝘯𝘵 𝘯𝘦𝘸 𝘳𝘦𝘴𝘶𝘭𝘵𝘴 𝘰𝘧 𝘮𝘺 𝘱𝘰𝘴𝘵𝘥𝘰𝘤 𝘱𝘳𝘰𝘫𝘦𝘤𝘵” says Virginia Díez. Virginia Díez presented new genes discovered to be targeted by body mass index genetic variants. She also gave an update on tissue specificity of the genes, whose names are saved for an up-coming publication. 🤫 The postdoc project is being developed at the Novo Nordisk Foundation Center for Basic Metabolic Research and is funded by the Danish Diabetes and Endocrine Academy. Well done, Virginia! 👏🏽 We are looking forward to reading your publication. 𝐑𝐞𝐚𝐝 𝐦𝐨𝐫𝐞 𝐚𝐛𝐨𝐮𝐭 𝐕𝐢𝐫𝐠𝐢𝐧𝐢𝐚'𝐬 𝐫𝐞𝐬𝐞𝐚𝐫𝐜𝐡 𝐩𝐫𝐨𝐣𝐞𝐜𝐭 𝐡𝐞𝐫𝐞: https://lnkd.in/dPFZZx64 #DDEA #Researcher #Postdoc #Presentation

📢 Exciting News: Publication Announcement! I’m thrilled to announce the publication of an important new paper, "Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project," in Gut Microbes. I had the privilege of contributing to this international collaboration, which dives into the genetic complexity of Helicobacter pylori prophages, examining their role in bacterial evolution, adaptation, and pathogenicity. This work not only broadens our understanding of prophage biology but also paves the way for future research in microbial genomics and its clinical implications. For more details, check out the article here: DOI: https://lnkd.in/gqck3-p7 #Prophages #Research #HelicobacterPylori #GutMicrobes #ScienceInnovation #Collaboration National Hispanic Medical Association (NHMA)

🧬🎉 Reflecting on Milestones in Medical Science! 🎉🧬 In 2003, a monumental achievement was unlocked in medical science – the sequencing of the first human genome. Today, LinkOMed takes a moment to honor this incredible journey. 🌟 👁️🗨️ Quick Insights: 2003: A Year of Breakthrough Human Genome: Unlocked Secrets of Life Paving the Way for Medical Advances Why does this matter? The sequencing of the human genome was not just a scientific triumph; it marked the beginning of a new era in medicine and health. This breakthrough has led to remarkable advancements in understanding genetic diseases, personalized medicine, and much more. Let's discuss: How has this discovery impacted your field? Can you imagine the future of medicine in the next 20 years? #HumanGenome #MedicalScience #Genetics #Biotechnology #LinkOMed #HealthcareInnovation #PersonalizedMedicine #ScienceAdvancement #GenomeSequencing #MedicalBreakthrough

🎉 I am thrilled to share that our latest publication entitled "Systematic identification of structure-specific protein-protein interactions" has been published in the journal of Molecular Systems Biology by EMBO Press! Our research contributes to a better understanding of how distinct structural conformations of #proteins influence their protein-protein interactions and the subsequent effects on cellular functions and potential #disease progression. In this study, we employed limited proteolysis-mass spectrometry (LiP-MS) to explore interactions specific to different structural states of proteins, uncovering novel putative structure-specific #interactors. 🔬Key findings from our research include: 1. Validation of LiP-MS: We showcased the capability of LiP–MS in reliably detecting well-characterized protein-protein interactions, including antibody-target protein interactions, as well as interactions with membrane proteins. Moreover, LiP-MS allows for the identification of interaction interfaces, including epitopes. 2. Identification of structure-specific interactors: We applied the approach to study structure-specific interactors of the Parkinson’s disease hallmark protein alpha-synuclein. We identified known interactors of alpha-synuclein monomer and amyloid fibrils and provided a resource of novel putative structure-specific interactors. Additionally, we utilized our approach on the GDP- and GTP-bound forms of two Rab GTPases. 🙏 A sincere thank you to my supervisor at ETH Zürich, Paola Picotti, whose guidance was invaluable, and to all my co-authors for their hard work and dedication. This work could not have been possible without your insights and contributions. 🔗 Dina Schuster, Fabian Sesterhenn, Patrick Stalder, Walther Haenseler, Inigo Barrio-Hernanadez, Dhiman Ghosh, PhD, Basavraj Khanppnavar, PhD, Tetiana Serdiuk, Pedro Beltrao, Volodymyr Korkhov ➡ Check out our full article for a deeper dive into our findings 🙂 https://lnkd.in/eHjheJtp #Science #Research #Publication #Proteomics #SystemsBiology #MassSpectrometry