A5106316146- Genomics and Phylogenetic Studies
- Protist diversity and phylogeny
- Parasite Biology and Host Interactions
- Insect symbiosis and bacterial influences
- Parasitic Diseases Research and Treatment
- RNA and protein synthesis mechanisms
- Tardigrade Biology and Ecology
- RNA modifications and cancer
- Nematode management and characterization studies
- Genetics, Aging, and Longevity in Model Organisms
- Biocrusts and Microbial Ecology
- Parasites and Host Interactions
- CRISPR and Genetic Engineering
- Hepatitis C virus research
- Parasitic Infections and Diagnostics
- Fungal Infections and Studies
- Trypanosoma species research and implications
- Plant Diversity and Evolution
- Chromosomal and Genetic Variations
- Invertebrate Immune Response Mechanisms
- Insect-Plant Interactions and Control
- Bacteriophages and microbial interactions
- Neutrophil, Myeloperoxidase and Oxidative Mechanisms
- Biochemical and Structural Characterization
- Phytoplasmas and Hemiptera pathogens
National Institutes of Health
2014-2025
National Institute of Allergy and Infectious Diseases
2014-2025
University of Edinburgh
1999-2020
Wellcome Sanger Institute
2008-2014
European Bioinformatics Institute
2014
Howard Hughes Medical Institute
2008-2010
Hospital for Sick Children
2009
Centre for Immunity, Infection and Evolution
2007
J. Craig Venter Institute
2007
Imperial College London
2007
The Rfam database (available at http://rfam.xfam.org) is a collection of non-coding RNA families represented by manually curated sequence alignments, consensus secondary structures and annotation gathered from corresponding Wikipedia, taxonomy ontology resources. In this article, we detail updates improvements to the data website for 12.0 release. We describe upgrade our search pipeline use Infernal 1.1 demonstrate its improved homology detection ability comparison with previous version. new...
Rfam is a collection of RNA sequence families, represented by multiple alignments and covariance models (CMs). The primary aim to annotate new members known families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs. A minority very broad taxonomic range (e.g. tRNA rRNA) provide the majority annotations, whilst snoRNAs miRNAs) have limited number annotations. Recent improvements website, methodologies data used are discussed. freely...
The Rfam database (available via the website at http://rfam.sanger.ac.uk and through our mirror http://rfam.janelia.org) is a collection of non-coding RNA families, primarily RNAs with conserved secondary structure, including both genes mRNA cis-regulatory elements. Each family represented by multiple sequence alignment, predicted structure covariance model. Here we discuss updates to in latest release, 11.0, introduction genome-based alignments for large Biomart as well other user interface...
Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions people in the developing world. We have sequenced approximately 90 megabase (Mb) genome human filarial parasite Brugia malayi predict 11,500 protein coding genes 71 Mb robustly assembled sequence. Comparative analysis with free-living, model nematode Caenorhabditis elegans revealed that, despite these having maintained little conservation local synteny during 350 million years evolution, they...
The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss pros cons using online encyclopedia, Wikipedia, a source community-derived annotation. We addition groupings related RNA families into clans new developments website. is available on Web at http://rfam.sanger.ac.uk.
Generating expressed sequence tags is a simple, cheap, and efficient way to sample the genome of target organism. An tag (EST) single-pass derived from single complementary DNA (cDNA) clone, serves identify gene which it derives. We present set tested laboratory protocols for setting up performing an EST analysis any chosen species. These medium-throughput do not require dedicated genomics equipment, such as robots, focus on use microtiter plates multichannels. Using these protocols,...
Background. Chronic granulomatous disease (CGD) is due to defective nicotinamide adenine dinucleotide phosphate oxidase activity and characterized by recurrent infections with a limited spectrum of bacteria fungi as well inflammatory complications. To understand the impact common severe in CGD, we examined records 268 patients followed at single center over 4 decades. Methods. All had confirmed diagnoses genotype was determined where possible. Medical were excerpted into standard format....
Ecdysozoa is the recently recognized clade of molting animals that comprises vast majority extant animal species and most important invertebrate model organisms—the fruit fly nematode worm. Evolutionary relationships within ecdysozoans remain, however, unresolved, impairing correct interpretation comparative genomic studies. In particular, affinities three Panarthropoda phyla (Arthropoda, Onychophora, Tardigrada) position Myriapoda Arthropoda (Mandibulata vs. Myriochelata hypothesis) are...
A molecular survey technique was used to investigate the diversity of terrestrial tardigrades from three sites within Scotland. Ribosomal small subunit sequence classify specimens into operational taxonomic units (MOTU). Most MOTU were identified generic level using digital voucher photography. Thirty–two defined, a surprising abundance given that documented British fauna is 68 species. Some tardigrade shared between two rural collection sites, but no found in both urban and which conflicts...
Hookworms are gut-dwelling, blood-feeding nematodes that infect hundreds of millions people, particularly in the tropics. As part a program aiming to define novel drug targets and vaccine candidates for human parasitic nematodes, genes expressed adults hookworm Necator americanus were surveyed by sequence tag approach. In total 161 new identified. For majority these, function could be assigned homology. The dataset includes proteases, protease inhibitors, lipid binding protein, C-type...
The Apicomplexa are a group of phylogenetically related parasitic protists that include Plasmodium , Cryptosporidium and Toxoplasma . Together they major global burden on human health economics. To meet this challenge, several international consortia have generated vast amounts sequence data for many these parasites. Here, we exploit to perform systematic analysis protein family domain incidence across the phylum. A total 87,736 sequences were collected from 15 apicomplexan species. These...
To advance and facilitate molecular studies of Brugia malayi, one the causative agents human lymphatic filariasis, an expressed sequence tag (EST)-based gene discovery programme has been carried out. Over 22 000 ESTs have produced deposited in public databases by a consortium laboratories from endemic non-endemic countries. The analysed using custom informatic tools to reveal patterns individual expression that may point potential targets for future research on anti-filarial drugs vaccines....
Parasitism is a highly successful mode of life and one that requires suites gene adaptations to permit survival within potentially hostile host. Among such the secretion proteins capable modifying or manipulating host environment. Nippostrongylus brasiliensis well-studied model nematode parasite rodents, which secretes products known modulate immunity.Taking genomic approach characterize potential secreted products, we analyzed expressed sequence tag (EST) sequences for putative...
Abstract Refractory disseminated coccidioidomycosis (DCM) is a severe disease with limited treatment options. This report reviews our own and prior published experiences using adjunctive interferon-γ therapy in refractory DCM, showing overall favorable responses patients without Signal Transducer Activator of Transcription 1 gain-of-function mutations.
ABSTRACT We used an expressed sequence tag approach to analyze genes by the infective larvae of rodent filarial parasite Litomosoides sigmodontis . One hundred fifty two new were identified, including several proposed as vaccine candidates in studies with human parasites. Our findings have important implications for use L. a model infection.