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The Human Salivary Proteome Wiki: A Community-Driven Research Platform.
Saliva has become an attractive body fluid for on-site, remote, and real-time monitoring of oral and systemic health. At the same time, the scientific community needs a saliva-centered information platform that keeps pace with the rapid accumulation of new data and knowledge by annotating, refining, and updating the salivary proteome catalog. We developed the Human Salivary Proteome (HSP) Wiki as a public data platform for researching and retrieving custom-curated data and knowledge on the...
New wiki on salivary proteins may transform diagnostic testing and personalized medicine
A diagram that shows the interconnectedness of the thousands of salivary proteins originating from blood plasma, parotid glands, and submandibular and sublingual glands. The diagram is one of many tools available to researchers and clinicians through the Human Salivary Proteome Wiki. By Marcene Robinson BUFFALO, N.Y. – To improve the development of new saliva-based diagnostic tests and personalized medicine, the National Institute of Dental and Craniofacial Research (NIDCR) has...
Forensic Microbiome Database: A Tool for Forensic Geolocation Meta-Analysis Using Publicly Available 16S rRNA Microbiome Sequencing.
The human microbiome has been proposed as a tool to investigate different forensic questions, including for the identification of multiple personal information. However, the fragmented state of the publicly available data has retarded the development of analysis techniques and, therefore, the implementation of microbiomes as a forensic tool. To address this, we introduce the forensic microbiome database (FMD), which is a collection of 16S rRNA data and associated metadata generated from...
Influenza A Viruses in Whistling Ducks (Subfamily Dendrocygninae).
As compared to other Anseriformes, data related to influenza A virus (IAV) detection and isolation, and IAV antibody detection in whistling ducks ( spp. and ; subfamily Dendrocygninae) are limited. To better evaluate the potential role of whistling ducks in the epidemiology of IAV, we (1) conducted surveillance for IAV from black-bellied whistling ducks (BBWD, ) sampled in coastal Louisiana, USA, during February 2018 and 2019, and (2) reviewed the published literature and Influenza Resource...
Epidemiology and Sequence-Based Evolutionary Analysis of Circulating Non-Polio Enteroviruses.
Enteroviruses (EVs) are positive-sense RNA viruses, with over 50,000 nucleotide sequences publicly available. While most human infections are typically associated with mild respiratory symptoms, several different EV types have also been associated with severe human disease, especially acute flaccid paralysis (AFP), particularly with endemic members of the EV-B species and two pandemic types-EV-A71 and EV-D68-that appear to be responsible for recent widespread outbreaks. Here we review the...
Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants.
There remains a significant proportion of deaths due to pneumococcal pneumonia in infants from low- and middle-income countries despite the marginal global declines recorded in the past decade. Monitoring changes in pneumococcal carriage is key to understanding vaccination-induced shifts in the ecology of carriage, patterns of antimicrobial resistance, and impact on health. We longitudinally investigated pneumococcal carriage dynamics in PCV-13 vaccinated infants by collecting nasopharyngeal...
A simple method to generate PCR-RFLP typing profiles from DNA sequences in Toxoplasma gondii.
Multilocus polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) has been widely used to genotype microorganisms. Accumulation of data generated by this method has helped to reveal genetic diversity, population structure and transmission of many microbial pathogens. Advances in DNA sequencing technologies have made it possible to identify microorganisms by multilocus sequencing typing (MLST) or whole genome sequence typing (WGST) to reach high resolution of...
METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies-Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses.
We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include ingestion of complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, and metagenome assembled genomes), prediction of the least common ancestor (LCA) for a peptide shared...
A comparative metagenomic study reveals microbial diversity and their role in the biogeochemical cycling of Pangong lake.
The environment of a high altitude brackish water lake presents an unprecedented reservoir for the microbial community with adaptability towards surviving stressful conditions. Pangong lake is a high altitude brackish water lake of the Himalayas situated in the eastern part of Ladakh (Indian Tibet), at the height of 4250 m above the sea level. Shotgun metagenomics sequencing of Pangong Lake sediments was performed to examine the taxonomic diversity and functional adaptations of the resident...
Saliva Proteome Database
Saliva is an important body fluid biofluid that helps in mastication, protection of oral and esophageal tissues, as well as provide immune functions against pathogens. Saliva has also systemic functions as it provides mucosal immunity and production of antibodies and antimicrobial proteins. Because of these functions, saliva has long been investigated known for its biological potential and as a diagnostic medium for both oral and systemic diseases. Compared to blood and other body fluids,...