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Posts by Arkadiy Garber

Applications are officially OPEN for the 2027 Gordon Research Conference on Multidrug Efflux Systems.

📅 When: March 21–26, 2027
📍 Where: Ventura, California
🔗 Apply here: www.grc.org/multi-drug-e...

#GRC #MultidrugEfflux

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Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis. Published in The ISME journal

Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.

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Temperature-dependent molecular evolution of dissolved black carbon and its interaction mechanism with dissimilatory iron reduction. Published in Bioresource technology

Temperature-dependent molecular evolution of dissolved black carbon and its interaction mechanism with dissimilatory iron reduction.

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Advancing specialized biofoundries via automated adaptive laboratory evolution. Published in Current opinion in biotechnology

Advancing specialized biofoundries via automated adaptive laboratory evolution.

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Comparative transcriptomics of closely related Geobacter sulfurreducens strains uncovers strain-level variations in extracellular electron transfer www.frontiersin.org/journals/mic... #jcampubs

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Beyond metabolic dormancy: metabolic rewiring in bacterial persistence - Nature Communications Bacterial persister cells exhibit a transient state of antibiotic tolerance and are commonly assumed to be metabolically ‘dormant’. In this Perspective, Orman et al. re-examine common assumptions and ...

Beyond metabolic dormancy: metabolic rewiring in bacterial persistence www.nature.com/articles/s41... #jcampubs

5 days ago 4 1 0 0
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EvolvingSTEM Brings Lab Experiments Straight Into the Classroom — Hot Metal Campus Based out of Bridgeside Point II in Hot Metal Campus, EvolvingSTEM is a science outreach program that brings evolution and microbiology research directly into classrooms across the Pittsburgh region. ...

Great article about EvolvingSTEM & Dr. Abigail Matela's leadership to infuse dozens of schools w/ authentic microbiology research experiences that demonstrate evolution in real time.

We've engaged more than 11,000 students over 11 years! 😅 🧪 🧫
www.hotmetalcampus.com/news-researc...

6 days ago 14 5 0 0
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Histone diversity in the archaeal domain of life - Nature Communications Archaea encode histone-like proteins that differ from eukaryotic sequences and among lineages. Here, the authors perform computational analyses to reveal five histone clusters in Archaea, which class ...

Histone diversity in the archaeal domain of life www.nature.com/articles/s41... #jcampubs

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Neuronal APOE4-induced early hippocampal network hyperexcitability in Alzheimer’s disease pathogenesis - Nature Aging Young, cognitively normal APOE4 mice display hippocampal network hyperactivity that predicts later memory decline. This phenotype is driven by neuronal APOE4 expression, which causes hyperexcitability of hippocampal neurons and can be reversed by targeting Nell2.

A study in Nature Aging shows that the strongest Alzheimer’s Disease risk gene, APOE4, can make certain brain cells in young mice hyperactive, which can predict later memory decline. The study also implicates Nell2 protein as a contributor to APOE4-driven dysfunction. #Alzsky 🧬🧪

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Bacterial endosymbionts initiate morphogenesis of symbiotic organs at specific locations in auchenorrhynchan insects of Hemiptera. Published in Insect science

Bacterial endosymbionts initiate morphogenesis of symbiotic organs at specific locations in auchenorrhynchan insects of Hemiptera.

6 days ago 0 1 1 0
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Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery - Nature Communications Benchmarking metagenomic binning tools with simulated and real datasets reveals factors affecting genome recovery and provides practical guidelines for improving metagenome assembled genome reconstruc...

Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery www.nature.com/articles/s41... #jcampubs

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DefensePredictor: A machine learning model to discover prokaryotic immune systems Antiphage defense systems protect bacteria from viral infection and have inspired important biotechnologies such as CRISPR-Cas9 while also revealing the evolutionary roots of eukaryotic innate immunit...

DefensePredictor: A machine learning model to discover prokaryotic immune systems
#microbiology #prokaryotes #CRISPR #MicroSky
@science.org
www.science.org/doi/10.1126/...

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No problem, good luck catching mitos!

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Breathing both ways: simultaneous aerobic–anaerobic respiration in microbes
www.sciencedirect.com/science/arti...

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The documentation is pretty detailed, I think. So you should be good if you reference that. Only thing I can add is to suggest playing around with the --disentangle-time-limit flag. Set it to super high so that get organelle doesn't give up on the graph due to time (unless you're in a hurry).

1 week ago 1 0 1 0
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GitHub - Kinggerm/GetOrganelle: Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS) Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS) - Kinggerm/GetOrganelle

I personally prefer GetOrganelle: github.com/kinggerm/get....

mtGrasp is another one I've heard good things about: github.com/BirolLab/mtG...

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Welp, didn't realize transparent backgrounds became black when I posted the logo 😅
bsky.app/profile/jlst...

1 week ago 4 3 0 2
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Fig. 1.
Angular leaf spot (ALS) on common bean. A, ALS symptoms on common bean differential line G11796. B, Conidia of Pseudocercospora griseola. C, Fasciculate conidiophores. Scale bars: B = 25 µm and C = 150 µm.

Fig. 1. Angular leaf spot (ALS) on common bean. A, ALS symptoms on common bean differential line G11796. B, Conidia of Pseudocercospora griseola. C, Fasciculate conidiophores. Scale bars: B = 25 µm and C = 150 µm.

Unexpected Potential Bacterial Symbiosis Found in Fungus That Causes Angular Leaf Spot: www.apsnet.org/members/community/newsro...

Read the original article by Luz M. Serrato-Diaz et al. to learn more: https://doi.org/10.1094/PHYTO-09-24-0302-R

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Analysis of Bacterial Wilt Management Strategies From the Dynamic Perspective of Environmental Adaptation Approaches of Ralstonia solanacearum. Published in Environmental microbiology reports

Analysis of Bacterial Wilt Management Strategies From the Dynamic Perspective of Environmental Adaptation Approaches of Ralstonia solanacearum.

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Excited to see our work out in Science today! Using machine learning to identify prokaryotic immune systems www.science.org/doi/10.1126/...

2 weeks ago 94 36 5 0

Now out in AEM @asm.org! 🎉🧪

*High school student-isolated mutants 👉🏻 novel genetic causes of biofilm-associated adaptations
*We learn how diversity arises quickly and is maintained
*EvolvingSTEM enables scalable research in classrooms & promotes scientific literacy

journals.asm.org/eprint/FBU9M...

3 weeks ago 83 45 4 4
We are accepting RFPs!

We are looking to fund projects that will have a measurable impact in reducing indoor transmission of airborne pathogens. Projects that might be applicable:
- detection and screening systems
- deploying tools to improve IAQ
- ventilation and air quality standards
- indoor air infrastructure

PHAN logo

Terms and conditions apply. Please visit phan.global

We are accepting RFPs! We are looking to fund projects that will have a measurable impact in reducing indoor transmission of airborne pathogens. Projects that might be applicable: - detection and screening systems - deploying tools to improve IAQ - ventilation and air quality standards - indoor air infrastructure PHAN logo Terms and conditions apply. Please visit phan.global

March 31st is the last day to submit requests for proposals for projects with measurable results in reducing indoor airborne pathogens. Possible projects include breath-based multi-pathogen detection systems, HVAC compliance verification systems, and indoor air infrastructure deployment.

3 weeks ago 8 8 2 1
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The Impact of Adopting Whole Genome Sequencing for Tuberculosis Diagnosis in China: A Cost-Effectiveness Analysis

✅ Just Accepted
🔗 https://bit.ly/4m08xS9

3 weeks ago 1 2 1 1

Any immunologists looking for a 1yr staff scientist job in NC?

I’m not sure if I’m staying at UNC past 2027 but I’m feeling the weight of accumulating experimental backlog.

Ideally already in the area, experienced in T-cell assays like IFNg ELISpot, ICS, MHC multimer flow, &c

3 weeks ago 3 3 0 0

Have you assumed/learned that DNA damage repair (DDR) via the SOS pathway (LexA, RecA, etc.) is universal (in bacteria)? turns out it's more a maze than a 'pathway'...
#MicroSky

3 weeks ago 15 5 1 0
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SypC, a symbiont outer membrane vesicle protein, impacts the development of the squid–vibrio partnership | PNAS Bacterial outer membrane vesicles (OMVs) and the cargo they carry are increasingly recognized as a means of communication between microbial symbion...

#SymbioSky #MicroSky

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A history of symbiosis impacts the host evolutionary trajectory in experimentally evolved amoebas www.biorxiv.org/content/10.64898/2026.03...

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Congrats to Anish Pyne for winning the People’s Choice Award in tonight’s 3 Minute Thesis competition @cmu.edu 🥳🥳🥳 @cmuscience.bsky.social

3 weeks ago 5 1 0 0
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Comparative Physiology and Genomics of Thermincola and Carboxydocella Strains and Description of Two Novel Isolates Two novel thermophilic bacteria, Thermincola strain AZ34E and Carboxydocella strain AZ29I, were isolated from hydrothermal environments and shown to oxidise carbon monoxide via the water-gas shift re...

Comparative Physiology and Genomics of Thermincola and Carboxydocella Strains and Description of Two Novel Isolates enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs

4 weeks ago 2 2 0 1

Chlorophyll a degradation in Prokaryotes www.biorxiv.org/content/10.6... #jcampubs

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