Yi Yang | Lightnews

Yi Yang @ohrp.bsky.social · Sep 4

Complete genome sequences of Acetobacterium wieringae strains Y and N, capable of conjugated diene biohydrogenation | Microbiology Resource Announcements journals.asm.org/doi/10.1128/...

Complete genome sequences of Acetobacterium wieringae strains Y and N, capable of conjugated diene biohydrogenation | Microbiology Resource Announcements

Acetobacterium wieringae is a strictly anaerobic bacterium in the order Eubacteriales (1). Here, A. wieringae strains Y and N, capable of metabolizing isoprene and 1,3-butadiene—pollutants linked to o...

journals.asm.org

Yi Yang @ohrp.bsky.social · Jul 22

Comparative Analysis of Phage Profiles in Environmental Samples: Metagenomic Sequencing Versus Culture-Based Isolation www.protocols.io/view/compara...

Comparative Analysis of Phage Profiles in Environmental Samples: Metagenomic Sequencing Versus Culture-Bas...

Culture-based isolation of bacteriophages from wastewater relies on a limited set of laboratory‐cultivable host strains, causing it to recover only a small fraction of the tru...

www.protocols.io

Yi Yang @ohrp.bsky.social · May 9

Complete genome sequence of Rhodococcus qingshengii strain R isolated from Antarctic soil | Microbiology Resource Announcements journals.asm.org/doi/full/10....

Complete genome sequence of Rhodococcus qingshengii strain R isolated from Antarctic soil | Microbiology Resource Announcements

Rhodococcus qingshengii strain R was isolated from a microcosm established with a sample of 5 g soil collected in 2010 from Beaufort Island in Antarctica (166° 58' 23.6" E, 76° 58' 23.6" S, depth 20.5...

journals.asm.org

Yi Yang @ohrp.bsky.social · Mar 15

Comparative proteogenomics reveals ecological and evolutionary insights into the organohalide-respiring Dehalobacter restrictus strain T | Applied and Environmental Microbiology journals.asm.org/doi/10.1128/...

Comparative proteogenomics reveals ecological and evolutionary insights into the organohalide-respiring Dehalobacter restrictus strain T | Applied and Environmental Microbiology

Organohalide-respiring bacteria (OHRB) are essential for breaking down harmful pollutants in the environment. This study investigates a newly discovered OHRB capable of degrading multiple contaminants...

journals.asm.org

Yi Yang @ohrp.bsky.social · Dec 26

“Candidatus Dehalogenimonas loeffleri” pubs.acs.org/doi/10.1021/...

Dehalogenimonas Strain W from Estuarine Sediments Dechlorinates 1,2-Dichloroethane under Elevated Salinity

Organohalide-respiring bacteria (OHRB) have been found in various environments and play an indispensable role in the biogeochemical cycling and detoxification of halogenated organic compounds (HOCs). Currently, few ORHB have been reported to perform reductive dechlorination under high salinity conditions, indicating a knowledge gap on the diversity of OHRB and the survival strategy of OHRB in saline environments (e.g., estuarine, marine). This study reports the characterization of an enrichment culture dominated by a new Dehalogenimonas population strain W derived from estuarine sediments, which demonstrates the capability to dechlorinate 1,2-dichloroethane (1,2-DCA) to ethene under elevated salinity (≥5.1% NaCl, w/v). Metagenomic and proteomic analyses revealed that the distinctive high-salinity dechlorination of strain W is primarily attributed to a putative reductive dehalogenase (RDase) DdeA, which shares >91.4% amino acid identity with the dihaloeliminating RDase DcpA from other Dehalogenimonas strains. Additionally, ectoine biosynthesis enzymes (EctABC) contribute to the strain’s salt tolerance. These findings underscore the potential of OHRB, particularly Dehalogenimonas, to detoxify HOCs in high-salinity environments, such as estuarine and marine ecosystems, by employing compatible solutes as an adaptive mechanism.

pubs.acs.org

All Earth 🌎 picture @allearthpic.bsky.social · Dec 26

The Pyramids of Giza, Egypt.

Animalcules @bacteriophile.bsky.social · Dec 25

www.nature.com/articles/s41...

Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater - npj Biofilms and Microbiomes

npj Biofilms and Microbiomes - Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater

www.nature.com

Katherine Caley @katherinecaley.bsky.social · Dec 17

🐍🌲 piqtree: IQ-TREE2 meets Python via cogent3! 🤝⚡️

The developers of IQ-TREE2 and cogent3 have joined forces to bring the power of IQ-TREE2 to Python users as piqtree.

piqtree exposes selected IQ-TREE2 capabilities within Python, using the cogent3 library as the interface...

piqtree: IQ-TREE2 meets Python via cogent3 · iqtree piqtree · Discussion #145

The developers of IQ-TREE2 and cogent3 have joined forces to bring the power of IQ-TREE2 to Python users as piqtree. piqtree exposes selected IQ-TREE2 capabilities within Python, using the cogent3 ...

github.com

Stephen Turner @stephenturner.us · Dec 17

SCARAP: scalable cross-species comparative genomics of prokaryotes https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae735/7921419 🧬🖥️🧪 https://github.com/swittouck/scarap

Ryan Wick @rrwick.bsky.social · Dec 17

New release of Canu - first one in over 3 years!
github.com/marbl/canu/r...

The notes say this will be the very last release. Many thanks to its devs Brian Walenz and @sergek.bsky.social. Canu may be a bit old and it's certainly not fast, but it makes good assemblies and so I still use it!

Release Canu v2.3 · marbl/canu

These are release notes for Canu version 2.3, which was released on December 17th, 2024. Canu is specialized for assembly of single-molecule sequences. Full documentation can be found at http://can...

github.com

SBGrid Consortium @sbgrid.bsky.social · Dec 16

New Title Alert: Boltz-1- an open-source model which predicts the 3D structure of proteins, rna, dna and small molecules; it handles modified residues, covalent ligands & glycans.

Learn more here: https://buff.ly/3ZAPowA

#SBGridSoftware #SBGrid

GitHub - jwohlwend/boltz: Official repository for the Boltz-1 biomolecular interaction model

Official repository for the Boltz-1 biomolecular interaction model - jwohlwend/boltz

buff.ly

Yi Yang @ohrp.bsky.social · Dec 16

Organohalide Respiration: Retrospective and Perspective through Bibliometrics www.frontiersin.org/journals/mic... #OHRB

Frontiers | Organohalide Respiration: Retrospective and Perspective through Bibliometrics

Organohalide-respiring bacteria (OHRB) play a pivotal role in the transformation of organohalogens in diverse environments. This bibliometric analysis provid...

www.frontiersin.org

Yi Yang @ohrp.bsky.social · Dec 16

CO-driven electron and carbon flux fuels synergistic microbial reductive dechlorination microbiomejournal.biomedcentral.com/articles/10....

CO-driven electron and carbon flux fuels synergistic microbial reductive dechlorination - Microbiome

Background Carbon monoxide (CO), hypothetically linked to prebiotic biosynthesis and possibly the origin of the life, emerges as a substantive growth substrate for numerous microorganisms. In anoxic e...

microbiomejournal.biomedcentral.com

Yi Yang @ohrp.bsky.social · Dec 16

Complete genome sequence of “Candidatus Dehalogenimonas loeffleri” strain W, a highly salt-tolerant chlorinated alkane-dechlorinating bacterium isolated from estuarine sediments journals.asm.org/doi/10.1128/...

Complete genome sequence of “Candidatus Dehalogenimonas loeffleri” strain W, a highly salt-tolerant chlorinated alkane-dechlorinating bacterium isolated from estuarine sediments | Microbiology Resourc...

Bioremediation of chlorinated contaminants in saline environments is challenging due to the inability of most organohalide-respiring bacteria (OHRB) to thrive under elevated salinity conditions (1–4),...

journals.asm.org

Typas Lab @typaslab.bsky.social · Dec 16

You want to learn about microbiology from a fantastic lineup of speakers on a beautiful Greek island? PhD students apply now for the @EMBO | @FEBSnews Lecture Course The New Microbiology!
Registration: 1 Apr 2025
Course: 03 – 11 Sep 2025 | Spetses, Greece
meetings.embo.org/event/25-new...

EMBL Events @events.embl.org · Dec 13

Hi Bluesky community! 👋

Are you looking forward to 2025 as much as we are? 👀

We just updated our 2025 Annual Poster to include even more events for you to join, so go and have a look!

➡️ s.embl.org/poster-bl

#EMBLEvents #molecularbiology #lifesciencetraining

The 2025 EMBL Annual Poster, listing all of the courses and conferences taking place in 2025 at EMBL

Light upyour news

Sign in to Lightnews

Sign up to start reading

Connect Bluesky

Connect with Bluesky

Light up
your news