genomics – My WordPress Site

Energetics associated with the occupancy of the K1 site and the position of the M2 ion. (A) Free energy surface of the concerted motions of Prp11 Lys10 and M2, with the initial PDB conformation marked by a yellow star. (B–D) Representative structures of three metastable states from metadynamics simulations. State 1 (B) represents a PDB-like arrangement where Lys10 (slate blue sticks) remains at the K1 site, and M2 (yellow sphere) is properly positioned at the U6 snRNA triple-helix (yellow cartoon). State 2 (C): Lys10 leaves the K1 site, allowing a K+ ion to occupy it and stabilize M2 in place. State 3 (D): M2 directly coordinates G52, losing its catalytic position and partially occupying the K1 site. -- PNAS

Astropharmacy / Biotechnology, Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Nanotechnology & SynBio

Computational Chemistry And Supercomputers To Help Understand The Mechanisms Of Life

by Keith CowingApril 13, 2026April 13, 2026

A new study from the Italian Institute of Technology (IIT), in collaboration with Uppsala University (Sweden) and AstraZeneca, shows how computational chemistry and supercomputers can help scientists better understand the fundamental mechanisms of life, specifically those of human cells.

Evidence for ribozyme mass extinction. (A) Abundance distribution across all ten known small self-cleaving ribozyme families, showing the hammerhead's 91% dominance, a pattern characteristic of disaster taxa following mass extinction events. (B) Circular phylogeny of 80,548 unique hammerhead sequences colored by host taxonomic group. The star-like topology is consistent with post-bottleneck radiation, and the interspersion of distantly related host phyla around the tree reflects repeated independent colonization events rather than co-speciation, consistent with horizontal transfer of a single dominant survivor lineage. (C) Null distribution tests for Tajima's D (left) and Fu's Fs (right), each based on 10,000 coalescent replicates (n = 200, S = 40). Blue and orange histograms show the null distributions under neutral expectations; red dashed lines indicate the observed values (D = +2.28, upper-tail p = 0.013; Fs = −618.0, p < 0.0001). Observed D falls in the extreme upper tail (98.7% of null replicates below observed), indicating deep hierarchical structure; observed Fs falls far below any null replicate, indicating massive haplotype excess. The discordance between positive D and extremely negative Fs is diagnostic of ancient divergence preserved through a bottleneck followed by rapid within-lineage expansion. Full-sample values (n = 5,036) are D = +3.79, Fs = −690.8. -- biorxiv.org

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life

A Ribozyme Mass Extinction At The RNA-cellular Boundary And Its Potential Imprint On The Genetic Code

by Keith CowingApril 13, 2026April 13, 2026

Community composition and functional profiles of 152 samples. a, The relative abundance of archaea and bacteria in 152 samples. b, The proportion of all archaea in all samples. Bars in different colors represented different classes of archaea. c, The proportion of all bacteria in all samples. Bars in different colors represented different phyla of bacteria. d, the relative abundance of KEGG standard categories (level B) in all samples. e-f, Principal coordinate analysis (PCoA) of all RMAGs, archaea, bacteria, and KOs in different sites based on Bray–Curtis distances. -- biorxiv.org

Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biophysics, Biosignatures & Paleobiology, Extremeophiles and Extreme Environments, Genomics, Proteomics, Bioinformatics, Habitable Zones, Lava / magma ocean / Volcanic Worlds, Microbiology & Virology, Sample Return

The Recovery Of 12,789 Genomes Revealed The Diversity, Function, And Microbial Interactions Of The Geothermal Spring Microbiome

by Keith CowingApril 12, 2026April 13, 2026

Structural features of Nerearchaeum marumarumayae cell -- Current Biology

Biosignatures & Paleobiology, Extremeophiles and Extreme Environments, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life, Sample Return

From Asgard to Earth: Tiny Discoveries Hold Clues To Life’s Greatest Leap

by Keith CowingApril 10, 2026April 10, 2026

Heatmap analysis of bacterial community composition across cave samples at phylum (A) and class (B) levels. A Euclidean dendrogram visualizes the hierarchical clustering of both samples and taxa. -- Microorganisms via PubMed

Analog Studies, Biosignatures & Paleobiology, Caves, Craters, Mountains & Lava Tubes, Exploration Gear & Tech, Extremeophiles and Extreme Environments, Genomics, Proteomics, Bioinformatics, Habitable Zones, Microbiology & Virology, Sample Return

Evaluation Of The Bacterial Diversity In The World’s Deepest Cave—Veryovkina, Arabika Massif, Western Caucasus

by Keith CowingApril 10, 2026April 10, 2026

A) Subcluster of viral genomes within the family Microviridae. Network constructed using vConTACT3 and visualized in Cytoscape. Reference nodes are colored by genus (RefSeq and vConTACT3 predictions), while fumarole viruses are colored by sample site. Edges represent genesharing strength. The blue node (phiX174) forms a weakly resolved clade with fumarole viruses in the maximum-likelihood phylogeny based on major capsid protein amino acid sequences. B) Pairwise genome comparisons of RefSeq and fumarole Microviridae using local alignment (MMseqs2). The top row and left column indicate predicted genus assignments (vConTACT3) for fumarole and RefSeq viruses. The top-left quadrant shows RefSeq–RefSeq comparisons; the top-right shows fumarole–RefSeq comparisons (RefSeq colored by genus). The second row (genome source) is colored by fumarole sample site. The star denotes comparisons involving the phiX174 RefSeq genome. -- biorxiv.org

Analog Studies, Away Teams & Field Reports, Biophysics, Biosignatures & Paleobiology, Caves, Craters, Mountains & Lava Tubes, Extremeophiles and Extreme Environments, Lava / magma ocean / Volcanic Worlds, Microbiology & Virology, Sample Return

Hawaiian Geothermal Fumaroles Contain Diverse and Novel Viruses

by Keith CowingApril 9, 2026April 9, 2026

Correlations of Asgardarchaeota with other microbial lineages in DAN-LK4 microbial mats inferred by co-occurrence network analyses. a, Sankey plot showing positive correlations of Asgard archaeal orders based on normalized USCGs (RPKM) inferred by SparCC alongside their distribution across the redox gradient in the indigenous and mesocosm-maintained microbial mat. The size of boxes is proportional to the relative abundance of Asgard archaea (center) and the number of links with prokaryotic taxa (left) in co-occurrence networks. The relative abundance of the different asgardarchaeal orders is indicated by the thickness of links connecting with the different mat layers (right). -- biorxiv.org

Away Teams & Field Reports, Biosignatures & Paleobiology, Extremeophiles and Extreme Environments, Genomics, Proteomics, Bioinformatics, Habitable Zones, Microbiology & Virology, Origin & Evolution of Life, Sample Return

Redox distribution Of Asgard Archaea And Co-occurring Taxa In Microbial Mats From An Early Proterozoic Ecosystem Analog

by Keith CowingApril 9, 2026April 9, 2026

Graphical Abstract -- Cell

Astropharmacy / Biotechnology, Commercial & Private Sector, Genomics, Proteomics, Bioinformatics, Gravitational Biology, Radiation, Space Life Science, Space Physiology & Medicine, Space Stations

ASTROREPOMICS: A Curated Transcriptomic Database For Reproductive Biology In Space

by Keith CowingApril 8, 2026April 8, 2026

Astronaut Peggy Whitson At Work on the ISS — NASA

Microgravity, Space Life Science, Space Stations, SPACELINE Current Awareness List

NASA Spaceline Current Awareness List #1,194 3 April 2026 (Space Life Science Research Results)

by Keith CowingApril 7, 2026April 7, 2026

Relationship between total group age T and crown group age tcg across various diversification rates λ − µ, equation 4. The heatmap represents the crown group age for a given rate and total group age (isolines are presented for reference). The orange dot-dashed line is the minimum value for T to fit the observed eukaryotic-grade fossil record of the late Palaeoproterozoic (1780 Ma), the red-dashed isoline is the minimum age for tcg fitting the observed crown-eukaryote fossil record from the end of the Mesoproterozoic (1050 Ma), and the grey interval is the range of possible tcg require to obtain the living diversity for a given rate and total age. The isolines for late LECA (tcg = 1200) or generous late LECA (tcg = 1400 Ma) are the red-dotted lines. -- biorxiv.org

Biosignatures & Paleobiology, Fossils & Paleontology, Genomics, Proteomics, Bioinformatics, Habitable Zones, Microbiology & Virology, Origin & Evolution of Life, Sample Return

Clade Dynamics Support An Early Origin Of Crown Eukaryotes

by Keith CowingApril 7, 2026April 7, 2026