PNAS’ Post

Microbial Mysteries: Meet the 'Obelisks' in Our Microbiome! 🦠 The scientific world just got a surprise visit from the 'Obelisks' - a novel class of viroid-like elements residing in the human gut and oral environment What are Obelisks? Unveiled in human gut metatranscriptomic data, these 'Obelisks' boast a ∼1kb genome, predicted rod-like structures, and open reading frames coding for a fresh protein superfamily. They form a distinct phylogenetic group with no resemblance to known biological agents. Continental Drift: A staggering 29,959 Obelisks identified globally, spanning all seven continents and diverse ecological niches. These RNA enigmas seem to have made themselves comfortable worldwide. 🌎 Persistent Puzzles: Obelisks show site-specific compositions and can persist in individuals for over 300 days, showcasing their resilience in the ever-changing microbial landscape. Molecular Surprises: Some Obelisks even code for hammerhead type-III self-cleaving ribozymes, adding another layer to their molecular complexity. 🧬✨ Preprint Alert: It's worth noting that this ground-breaking work was posted on the bioRxiv preprint server on 21st January and is yet to undergo peer review. Nonetheless, the findings are both relevant and fascinating, opening doors to new realms of microbial exploration. 🔍📚 💬 Join the Discussion: The microbiome continues to surprise us with 'Obelisks.' What implications might these mysterious RNA elements have on human health and microbial dynamics? 🔬Future Frontiers: Streptococcus sanguinis harbours a specific Obelisk RNA population, opening doors for experiments that might uncover more about their replication and impact on bacteria. The journey into the microbial unknown continues! 📖 Read the Full Article: https://lnkd.in/dJSg6_Yf #MicrobiomeMysteries #RNAElements #ScientificDiscovery #MicrobialEcology #Obelisks #ResearchFrontiers

Genetic algorithms aim to solve optimization and modeling tasks by iterating, variation and combining target parameters with the help of mechanisms similar to biological evolution. https://lnkd.in/exHhXTby

🧫 Enhancing Microbial Community Engineering with CRISPR 🧫 Researchers are forging ahead with innovative techniques to genetically engineer microbial communities, yet the scarcity of sophisticated tools limits progress. We must shift our focus to developing strategies for precisely targeting organisms within these complex ecosystems. The critical role of DNA as the blueprint for microbial community functions. To alter these functions, we need to manipulate this blueprint directly. CRISPR technology emerges as the key, allowing precise and efficient genomic alterations. With CRISPR expanding our genetic toolkit, we edge closer to not only understanding but also reshaping microbial interactions and their broader ecological impact. Credit: The Scientist #MicrobiomeEngineering #GeneticToolbox #CRISPR #ScientificInnovation

A fundamental question in evolution is how new genes evolved? Recently, there is a growing opinion that the resulting proteins from newly formed genes are often intrinsically disordered (idp). These are questions, though fundamental are important because they define the continuity, health and disease of any living organism including humans.  In this out of the press, we addressed some of these important evolutionary questions of evolution of new genes. https://lnkd.in/dP8ECFpn

Scientists at Berkeley Lab, Los Alamos National Laboratory and the Joint Genome Institute are working to catalog microbiomes using Oak Ridge National Laboratory's Frontier #supercomputer. The ExaBiome team has spent years developing and optimizing codes for assembling genomes from microbial samples. These applications harness #exascale’s speeds to reconstruct, classify and compare collected genome sequences and to understand the relationship and function of genes within microbial species. 🌿 https://bit.ly/3zARYZg

My new publication is in the plant evolution and genomics field.

Exciting news from our team! We've just released our latest research on plant evolution and adaptation to terrestrial environments, shedding light on the fascinating journey of plants transitioning from aquatic to land habitats. Our comparative approach explored stress dynamics across 600 million years of plant evolution, uncovering crucial genetic pathways and regulatory networks. Our findings provide fresh insights into the molecular foundations of plant adaptation to environmental challenges. Our research revealed conserved hub genes and signaling components that played a key role in ancient plant stress responses. Dive into the details of our comparative co-expression network analysis and Granger causal inference to explore the evolutionary assembly of plant signaling cascades. Curious to learn more or discuss potential collaborations? Reach out to explore connections between our study and your interests. And don't forget to check out our Streptotime Shiny App for interactive exploration of our results! Many thanks to the whole study team including Darienko Tatyana, Janine F., Stefan Rensing, Iker Irisarri, Ivo Feussner, and Jan de Vries. bioRxiv: https://lnkd.in/eBR7ncxD Streptotime Shiny App: https://lnkd.in/ewA937-7 #PlantEvolution #TerrestrialAdaptation #GeneticPathways #EvolutionaryBiology #GeneRegulation #StressResponses #Collaboration #ResearchDiscovery

Can a single RNA molecule be considered "living"? It certainly stretches any classic definitions of life, but I've always been a fan of the odd cases of biology. A recent study published as a preprint in bioRxiv describes a new minimalist life form that consists of single circular RNA genomes with only about 1,000 basepairs and 2 genes. These show up in a variety of microbiome communities and appear to have bacterial hosts that handle replication of the genome much like viruses. Without any protein coat or other cell-like structures Obelisks are pushing the boundaries of what it takes to be considered living. But even so these genomes show sequence conservation across several types living in a range of microbial communities. Read more of my thoughts on Obelisks here: https://lnkd.in/eU8eknE4

Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences https://lnkd.in/e6XHidb8

What was the name of the first bacteriophage which genome was sequenced? Prior to the development of the electron microscope, the size of an object, such as a virus, was estimated by filtration through membranes of various pore sizes. By this criterion, the bacterial virus (bacteriophage) fX174, first described in 1935 (1), and its close relative S13 (2) were classified as much smaller than the T phages that were under investigation in the early days of molecular biology. Moreover, the fact that their genetic material is DNA made these two viruses attractive candidates as front runners in the race to unravel the molecular basis of heredity. The contributions began with the initial characterization of the fX174 DNA as being single stranded, as reported in the first issue of the Journal of Molecular Biology (3). The culmination came when fX174 was the first organism to have its genome subjected completely to DNA sequencing (4), which offered the first direct documentation of the existence of overlapping genes in nature. Youtube video: https://lnkd.in/dsAZQyf8 #nikolaysgeneticslessons