Arkadiy Garber
@theironark
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Bioinformatics, microbiology, evolution, astrobiology, symbiosis, mealybugs, iron cycling @ASUBiodesign PapersAloud: https://t.co/Hmaq24T3UI
Joined February 2017
Have you ever worked with samples containing DNA from prokaryotes and eukaryotes (e.g. host and microbe)? If so, I recently wrote a software program that can separate out bacterial/archaeal sequences from eukaryotic ones:
bmcgenomics.biomedcentral.com
Background Shotgun sequencing of cultured microbial isolates/individual eukaryotes (whole-genome sequencing) and microbial communities (metagenomics) has become commonplace in biology. Very often,...
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Is that right?? If so, every month, she makes twice what a typically grad student might receive in a year’s worth of stipend.
This Whitehead Institute for Biomedical Research is a nonprofit. It turns out the Director makes 1M+ , the VP 500K+, and the Secretary 400K+. https://t.co/osGgzvQ8RG
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It is not just the mother’s mitochondria anymore. For decades, we have believed that mitochondrial traits are passed only through the maternal line because mitochondria come from the egg as they occupy too much space to be carried by spermatozoids. This new study shows that
cell.com
Yin et al. show that paternal exercise improves offspring endurance capacity and metabolic health via sperm microRNAs that reprogram gene expression in early embryos, revealing how exercise benefits...
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HERE IS THE MERRILL REESE CALL OF THE GAME WINNING BLOCK GOOSEBUMPS
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Breaking Bad has an alternate ending on DVD where Bryan Cranston wakes up as Hal from Malcolm in the Middle — revealing the entire series was just a nightmare.
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Plasmodium falciparum is the protozoan parasite behind the most severe form of malaria, transmitted by Anopheles mosquitoes. If you want to see where P. falciparum sits in the tree of life, you can now do so easily with our microbial omics web app: https://t.co/1M6zEatvxP in
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🦠 BII CME Annual Symposium 2025 - Mechanisms of Cellular Evolution 🔗 https://t.co/B9U3YDzeZ8 🗓️ Nov. 5-8 2025 📍 Arizona State University 📄 Abstract submission deadline (posters and short-talks): October 1, 2025 (11:59pm Arizona time) #evolution #cell #biology
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Our new preprint! #Bartonellaceae bacteria, known as mammalian #pathogens, also colonizes #planthoppers. The planthopper #symbionts typically resemble related ant symbionts in their nutritional functions, but show a much greater breadth of #genome sizes and functions. 1/2
Contrasting genomic trajectories of Bartonellaceae symbionts of planthoppers https://t.co/ATyDmWIh7R
#biorxiv_ecology
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A genome is not a one-dimensional object. It is dynamic and quickly-changing, not only in TIME but also in SPACE. A new paper, published in Nature, reports the 3D structure of the E. coli genome. The whole thing was mapped with a resolution of 10 base pairs; enough to clearly
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In a single E. coli, about 25 percent of all proteins use metals (like zinc, iron, copper, magnesium, etc) to do their chemistries. And yet, incredibly, fewer than ONE FREE METAL ION is present per cell on average. There are, in other words, basically no loose metal ions
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Siderophores produced by marine microorganisms
link.springer.com
Antonie van Leeuwenhoek - Siderophores are iron-chelating, low-molecular-weight compounds secreted by microorganisms in iron-deficient environments that enhance iron uptake. When compared to the...
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Isolation and characterization of a bacterium affiliated with the hitherto uncultured candidate phylum WOR-3 from a deep-sea hydrothermal fluid
journals.asm.org
Genome analysis from various environments has revealed the overall diversity of microorganisms. However, there are many lineages for which culture representatives do not yet exist, and the characte...
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Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria | mSphere
journals.asm.org
We hypothesized that the unique environment of seaweeds in coastal oceans shapes bacterial genomes and promotes a symbiotic lifestyle. We compared the genomes of bacteria isolated from seaweed with...
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Enhancing genome recovery across metagenomic samples using MAGmax
biorxiv.org
Summary The number of metagenome-assembled genomes (MAGs) is rapidly increasing with the growing scale of metagenomic studies, driving fast progress in microbiome research. Sample-wise assembly has...
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A genomic catalog of Earth's bacterial and archaeal symbionts
biorxiv.org
Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth, yet remains underexplored due to culturing challenges. This study employed machine learning (ML) to...
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The impact of background selection in mutation-selection-drift balance models of complex trait evolution https://t.co/IdDzx5OIAq
#biorxiv_evobio
biorxiv.org
Over the past three decades, theoretical population genetic models and empirical analyses have elaborated on how the elimination of deleterious variants reduces variation at linked neutral sites....
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Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes
biorxiv.org
Background Soil ecosystems have long been recognized as hotspots of microbial diversity, but most estimates of their complexity remain speculative, relying on limited data and extrapolation from...
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The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes | bioRxiv
biorxiv.org
Viruses are among the most abundant and genetically diverse entities on Earth, yet the functions and evolutionary origins of most viral proteins remain poorly understood. Their rapid evolution often...
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Virus-mediated recycling of chemoautotrophic biomass | bioRxiv
biorxiv.org
Aquatic environments absorb ∼2.5 gigatonnes of atmospheric carbon each year[1][1], more than the carbon stored in the atmosphere, soils, and all biomass combined. Primary producers transform this...
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Widespread and Abundant CRISPR-Cas Systems in the Deep Ocean https://t.co/S8ODGGu5C3
#biorxiv_micrbio
biorxiv.org
CRISPR-Cas systems have revolutionized modern biology. Most CRISPR-Cas systems in use for biotechnological applications derive from cultivated bacteria, but evidence suggests that environmental...
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