BOL: Related items

Naegleria fowleri: brain eating amoebae

Neel — Thu, 10 Oct 2019 22:12:03 -0500

Naegleria fowleri is a free living, universally distributed amoeba, which is mostly found in natural, stagnant, warm water bodies such as ponds, lakes, etc. It is also reported to be present even in indoor water bodies, such as swimming pools within a temperature range of 40–45°C.

N. fowleri infects the central nervous system of human body by entering through the nose during swimming and outdoor baths in natural stagnant water bodies, leading to meningoencephalitis. It is a condition of inflammation of cerebral tissues and membranes of the brain and is mostly fatal in nature. Casualties due to N. fowleri infections are reported all across the globe including a few in India but only seven survivors in the entire world have been reported till 2015.

You can find two genome assembly at

https://www.ncbi.nlm.nih.gov/assembly/?term=naegleria%20fowleri

More at https://www.ncbi.nlm.nih.gov/search/all/?term=naegleria+fowleri

HS3D: Homo Sapiens Splice Sites Dataset

Jit — Fri, 12 Jun 2020 12:33:17 -0500

HS3D (Homo Sapiens Splice Sites Dataset) is a data set of Homo Sapiens Exon, Intron and Splice regions extracted from GenBank Rel.123. The aim of this data set is to give standardized material to train and to assess the prediction accuracy of computational approaches for gene identification and characterization. From the complete GenBank (Primate Sequences Division) Rel.123 (162,557 entries), entries of Human Nuclear DNA including Complete CDS and more than one Exon have been selected, and 4523 exons and 3802 introns have been extracted from these entries. Details about extracted exons and introns are reported (Locus, number, Start and End position in the entry, sequence, length, G+C content, presence of not AGCT data (nucleotide scan check)). Statistics are also reported (overall nucleotides, average G+C content, nucleotide scan check results, number of not GT starting / AG ending introns, minimum / maximum / average length, length standard deviation) . 3799+3799 donor and acceptor sites, as windows of 140 nucleotides around each splice site have been extracted. After discarding sequences not including canonical GT–AG junctions (65+74), including insufficient data (not enough material for a 140 nucleotide window) (686+589), including not AGCT bases (29+30), and redundant (218+226) there are 2796+ 2880 windows.

1. P.Pollastro, S.Rampone (2002). HS3D, a Dataset of Homo Sapiens Splice Regions, and its Extraction Procedure from a Major Public Database , International Journal of Modern Physics C, 13(8), 1105-1117. (please cite this paper)

2. P.Pollastro, S.Rampone (2003). HS3D: Homo Sapiens Splice Site Data Set , Nucleic Acids Research, 2003 Annual Database Issue.

Address of the bookmark: http://www.sci.unisannio.it/docenti/rampone/

HiBC: Human Intestinal Bacteria Collection

BioStar — Wed, 07 May 2025 05:49:19 -0500

The human gut is home to trillions of microorganisms, forming one of the most complex and dynamic microbial ecosystems known to science. The Human Intestinal Bacteria Collection (HiBC) is a pioneering initiative aimed at cataloging, preserving, and studying the diverse bacterial species that inhabit the human gastrointestinal tract. This curated collection serves as a critical resource for researchers working on microbiome-related health, disease, and therapeutics.

What is HiBC?

The Human Intestinal Bacteria Collection (HiBC) is a comprehensive, high-quality reference repository of bacterial isolates derived from human fecal samples. It focuses on anaerobic and facultative anaerobic bacteria that play pivotal roles in digestion, immune modulation, vitamin synthesis, and pathogen resistance. The collection includes both culturable strains and genomic data from unculturable taxa, bridging the gap between culture-dependent and -independent microbiome studies.

Why is HiBC Important?

Understanding Microbiome-Host Interactions
HiBC enables deeper insight into the functions of specific bacterial taxa in the gut. With well-characterized isolates, researchers can conduct mechanistic studies to explore how certain bacteria influence metabolism, inflammation, or mental health.
Precision Probiotics and Therapeutics
By providing access to native human gut microbes, HiBC supports the development of next-generation probiotics, live biotherapeutic products (LBPs), and fecal microbiota transplantation (FMT) alternatives.
Standardization and Reproducibility
With standardized cultivation and genomic protocols, HiBC ensures consistency across microbiome research studies, improving reproducibility and comparability of findings.
Antimicrobial Resistance (AMR) Surveillance
HiBC includes metadata on antibiotic resistance genes (ARGs), helping track the spread of AMR in commensal gut bacteria and understanding its implications for human health.

Key Features of HiBC

Culturable Bacteria Repository: A living collection of anaerobic and facultative strains isolated from healthy and diseased individuals worldwide.
Metadata-rich Entries: Each isolate is annotated with host details (age, health status, diet), geographical origin, phenotypic traits, and antibiotic susceptibility profiles.
Whole Genome Sequencing (WGS): High-quality genome assemblies for most strains to support functional and comparative genomics.
Interactive Database Access: User-friendly search and filtering options for strain selection based on taxonomy, function, or clinical relevance.
Cross-linking with Other Databases: Integration with NCBI, GOLD, and Human Microbiome Project (HMP) data for broader context and validation.

Applications of HiBC

Microbiome-based diagnostics and biomarker discovery
Host-microbe interaction studies in gnotobiotic mouse models
Gut microbiome modulation through diet, drugs, or engineered bacteria
Longitudinal studies of gut flora across age, geography, and lifestyle
Environmental and evolutionary microbiology of human-associated bacteria

Accessing HiBC

Researchers and interested parties can explore the HiBC database through its official website: https://www.hibc.rwth-aachen.de/. The platform offers comprehensive information on bacterial isolates, including taxonomy, cultivation conditions, and genomic data, facilitating advanced research in human gut microbiome studies.

Final Thoughts

The HiBC is a cornerstone resource in the rapidly evolving field of microbiome research. As science moves toward personalized medicine and microbial therapeutics, having a reliable and diverse collection of human gut bacteria is not just useful — it's essential. Whether you're a microbiologist, clinician, computational biologist, or biotechnologist, HiBC offers tools to accelerate discovery and innovation in gut microbiome science.

Carefully opt for human reference genome

biogeek — Tue, 18 Feb 2020 07:43:32 -0600

Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome.

if you map reads to GRCh38 or hg38, use the following:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

There are several other versions of GRCh37/GRCh38. What’s wrong with them? Here are a collection of potential issues:

More at http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

Address of the bookmark: http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

SeqMule: Automated human exome/genome variants detection

BioStar — Tue, 18 Feb 2020 03:22:54 -0600

SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file.

Address of the bookmark: https://doc-openbio.readthedocs.io/projects/seqmule/en/latest/

PhD student / Bio-informatician in computational protein modeling

Sun, 23 Feb 2020 03:46:46 -0600

PhD student / Bio-informatician in computational protein modeling
Job Profile
You will perform research on drug/protein interaction analysis in the context of lung cancer, using computational protein modeling. You will implement existing models predicting drug efficacy, related to EGFR-driven cancer. You will translate these models to novel oncogenes, including ROS1. You will validate these models against experimental data from a parallel project, with the final goal of deployment of your methods into clinical decision making. Your work will be embedded in an international network consisting of both academic partners and ROS1-NSCLC patient organizations.

Requirements

You are (or soon will be) a master in bio-informatics. You have strong ICT skills and you are eager to fully submerge into the world of protein modeling. You have good experience with Linux and one or more programming languages as well as knowledge of tertiary structure analysis. Candidates with a Master degree in one of the life sciences (Biomedical sciences, Biochemistry, Bio-engineering, Biostatistics, …), with relevant interest and extended experience in this field are also welcome. A general background cancer biology and genetics is needed. You are willing and eligible to apply for a personal PhD fellowship with the Flemish FWO (FWO.be). Therefore, it is required that you hold a master degree from a European university, and have not obtained your master diploma more than three years ago (see FWO website for detailed conditions). Proficiency in English, and good communication skills, both oral and written, are required. You are highly motivated, and you like to work in an interactive research team. You are willing to work on a 4-year PhD project starting beginning of 2020.

What we offer

We offer a one year position, as a PhD student, which can be extended up to 4 year upon positive evaluation, even if a personal fellowship application is not successful. Wages are according to the standard Flemish bursary levels for PhD students.

Interested?
For additional information please contact dr. Geert Vandeweyer. To apply, send a copy of your CV including details of your relevant skills and a motivation letter by e-mail to dr. Geert Vandeweyer (geert.vandeweyer@uantwerpen.be) before March 15, 2020.

Source:https://academicpositions.be/ad/university-of-antwerp/2020/phd-student-bio-informatician-in-computational-protein-modeling/141252?utm_source=jooble&utm_medium=cpc&utm_campaign=jooble

World of Omics

Rahul Agarwal — Tue, 16 Jul 2013 17:11:48 -0500

How many variants of "omics" techniques presently in use ?

Should you get sequenced? Not all bad genes predict disease

Rahul Agarwal — Thu, 29 Aug 2013 15:10:53 -0500

“What we really don’t know yet is whether the predictive aspects of the genome are going to turn out to be beneficial or potentially harmful”

“As we roll out genomic medicine we are fighting against this society-wide misconception that having the bad gene means you’re going to get the disease. That’s only true in a very few cases.”

Source:Today Health

Address of the bookmark: http://www.today.com/health/should-you-get-sequenced-not-all-bad-genes-predict-disease-8C11017154