naturepoker<p>Our poster abstract for <a href="https://genomic.social/tags/ASMicrobe2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ASMicrobe2025</span></a> is up! First bit of info from our warehouse lab led Haloarchaea study project. Session EEB-P-302 - EEB02 Saturday Microbial Evolution. Please feel free to come say hi 👋</p><p><a href="https://genomic.social/tags/microbiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>microbiology</span></a> <a href="https://genomic.social/tags/archaea" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>archaea</span></a> <a href="https://genomic.social/tags/sequencing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sequencing</span></a> <a href="https://genomic.social/tags/methylation" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>methylation</span></a> </p><p><a href="https://www.abstractsonline.com/pp8/#!/20974/presentation/3670" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">abstractsonline.com/pp8/#!/209</span><span class="invisible">74/presentation/3670</span></a></p>
#sequencing
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@firefoxx66 People who are interested in that, might also be interested in:
* the GenomeTrakr Network https://www.fda.gov/food/whole-genome-sequencing-wgs-program/genometrakr-network
* GCpathogen (potentially) https://nmdc.cn/gcpathogen/ ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10767814/ )
Open Sourcing databases with a sharp focus like that are essential for good research. Especially if there is a good interoperability and thus data exchange which seems to be the case with pathoplexus.
U.S. Food and Drug Administration · GenomeTrakr NetworkThe GenomeTrakr network is the first distributed network of laboratories to utilize whole genome sequencing for pathogen identification.
Well, have decided to try my hand at creating music with #sequencing after rekindling my interest in #electronicmusic - bearing in mind the last time I used a sequencer it was an #Alesis MMT8 - and it was new!
This time it will all be #inthebox though. Cubase includes a simple but handy sequencer called Step Designer and I've installed the free VST plugin called #Stochas which has more advanced capabilities like 'probability' attribute per note and more... I may be 'asking the audience'.. soon!
#Virome #Sequencing Identifies #H5N1 Avian #Influenza in #Wastewater from Nine #Cities. MedRxIV, https://www.medrxiv.org/content/10.1101/2024.05.10.24307179v1
19 of 23 monitored sites had at least one detection event, and H5N1 serotype became dominant over seasonal influenza over time. A variant analysis suggests avian or #bovine origin but other potential sources, especially humans, could not be excluded.
medRxiv · Virome Sequencing Identifies H5N1 Avian Influenza in Wastewater from Nine Cities.Avian influenza (serotype H5N1) is a highly pathogenic virus that emerged in domestic waterfowl in 1996. Over the past decade, zoonotic transmission to mammals, including humans, has been reported. Although human to human transmission is rare, infection has been fatal in nearly half of patients who have contracted the virus in past outbreaks. The increasing presence of the virus in domesticated animals raises substantial concerns that viral adaptation to immunologically naive humans may result in the next flu pandemic. Wastewater-based epidemiology (WBE) to track viruses was historically used to track polio and has recently been implemented for SARS-CoV2 monitoring during the COVID-19 pandemic. Here, using an agnostic, hybrid-capture sequencing approach, we report the detection of H5N1 in wastewater in nine Texas cities, with a total catchment area population in the millions, over a two-month period from March 4th to April 25th, 2024. Sequencing reads uniquely aligning to H5N1 covered all eight genome segments, with best alignments to clade 2.3.4.4b. Notably, 19 of 23 monitored sites had at least one detection event, and the H5N1 serotype became dominant over seasonal influenza over time. A variant analysis suggests avian or bovine origin but other potential sources, especially humans, could not be excluded. We report the value of wastewater sequencing to track avian influenza.
### Competing Interest Statement
The authors have declared no competing interest.
### Funding Statement
This work was supported by S.B. 1780, 87th Legislature, 2021 Reg. Sess. (Texas 2021) (E.B., A.W.M., and J.F.P.), NIH/NIAID (Grant number U19 AI44297) (A.W.M.), Baylor College of Medicine Melnick Seed (A.W.M) and Alkek Foundation Seed (J.F.P.), and Pandemic Threat Technology Center (P.A.P.).
### Author Declarations
I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.
Yes
I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.
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I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).
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I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.
Yes
All data produced are available online at https://zenodo.org/doi/10.5281/zenodo.11175923 and NCBI SRA BioProject: PRJNA966185
#genomics #bioinformatics #hivemind #sequencing
Anyone have an idea for databases of human tRNA-derived fragment? There was a 2015 publication for tRFdb. The site is still there and doesn't work.
I'd rather not have to pull all the tRNAs and trim them myself into the most common tDR portions.
Cross-posting
I need to align high-coverage (1000+) long-amplicon nanopore reads (in fastq format) onto the human genome and call SNPs and indels.
I'm looking for software recommendations for the alignment and variant calling steps.
I tried mapping with minimap2 and calling the SNPs with longshot. I am visualizing in IGV.
Please share!
#nanopore #genomics #genetics #sequencing #variants #bioinformatics
I modified the in-house HMW genome extraction protocol for the fourth annual sequencing of our Halobacterium mutant. Looking promising so far! #microbiology #halobacteria #archaea #sequencing
With only the pawprints, researchers study elusive bobcat https://phys.org/news/2024-01-pawprints-elusive-bobcat.html
A novel eDNA approach for rare species monitoring: Application of long-read shotgun #sequencing to #Lynx rufus soil pawprints https://www.sciencedirect.com/science/article/abs/pii/S0006320723004160 by Samantha Koda et al.
"#DNA recovered from #bobcat #pawprints can be used to determine the #animals' ancestral background and even identify their unique #microbial community. All from the errant DNA left behind long after the #animal has left the area."
Using #DNAsequencing to show how marine worms adapt to #DeepSea conditions https://phys.org/news/2023-10-dna-sequencing-marine-worms-deep-sea.html
Third-Generation #Sequencing Reveals the Adaptive Role of the #Epigenome in Three Deep-Sea #Polychaetes: Maeva Perez et al. https://academic.oup.com/mbe/article/40/8/msad172/7231443
"#epigenetic regulation by #DNAmethylation could be an adaptive mechanism that counteracts the effects of hydrostatic pressure at the bottom of the #ocean"
Profiling of Urinary #RNA biomarkers in patients with chronic kidney disease using #Nanopore #sequencing.
With @MorganMacKenz12 (Twitter handle), @MRoumelioti (Twitter handle) Darren Schmidt and yours truly from #Nephrology at @unmhsc (Twitter handle) @UNM_CTSC (Twitter handle)
#protein #sequencing on #nanopore moves faster than I expected: here they used standard (R9.4) flowcell with custom motor protein (ClpX unfoldase) to characterise full-length peptides at single-molecule resolution https://www.biorxiv.org/content/10.1101/2023.10.19.563182v1
Looking for a tool that can simulate 
short NGS reads from real long (ONT, PacBio) read data. Any suggestions and comments on your experience? 
#Bioinformatics #NGS #Sequencing
Using #DNAsequencing to show how marine #worms adapt to deep-sea conditions https://phys.org/news/2023-10-dna-sequencing-marine-worms-deep-sea.html
Third-Generation #Sequencing Reveals the Adaptive Role of the #Epigenome in Three #DeepSea #Polychaetes: Maeva Perez et al. https://academic.oup.com/mbe/article/40/8/msad172/7231443
"#Methylation is an #epigenetic process that chemically modifies some of DNA bases. It plays a role in environmental acclimatization, making organisms living in habitats where conditions are unpredictable more resilient to environmental changes"
Environmental DNA reveals the genetic diversity and population structure of an invasive species in the Laurentian Great Lakes