Victor Braham Goldman
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PROVIDER: S-EPMC1124466 | biostudies-literature | 2002 Oct
REPOSITORIES: biostudies-literature
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Project description:MotivationBacterial and archaeal viruses are crucial for global biogeochemical cycles and might well be game-changing therapeutic agents in the fight against multi-resistant pathogens. Nevertheless, it is still unclear how to best use genome sequence data for a fast, universal and accurate taxonomic classification of such viruses.ResultsWe here present a novel in silico framework for phylogeny and classification of prokaryotic viruses, in line with the principles of phylogenetic systematics, and using a large reference dataset of officially classified viruses. The resulting trees revealed a high agreement with the classification. Except for low resolution at the family level, the majority of taxa was well supported as monophyletic. Clusters obtained with distance thresholds chosen for maximizing taxonomic agreement appeared phylogenetically reasonable, too. Analysis of an expanded dataset, containing >4000 genomes from public databases, revealed a large number of novel species, genera, subfamilies and families.Availability and implementationThe selected methods are available as the easy-to-use web service 'VICTOR' at https://victor.dsmz.de.Contactjan.meier-kolthoff@dsmz.de.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC5860169 | biostudies-literature
Project description:Victor McKusick's many contributions to medicine are legendary, but his magnum opus is Mendelian Inheritance in Man (MIM), his catalog of Mendelian phenotypes and their associated genes. The catalog, originally published in 1966 in book form, became available on the internet as Online Mendelian Inheritance in Man (OMIM®) in 1987. The first of 12 editions of MIM included 1486 entries; this number has increased to over 25,000 entries in OMIM as of April 2021, which demonstrates the growth of knowledge about Mendelian phenotypes and their genes through the years. OMIM now has over 20,000 unique users a day, including users from every country in the world. Many of the early decisions made by McKusick, such as to maintain MIM data in a computer-readable format, to separate phenotype entries from those for genes, and to give phenotypes and genes MIM numbers, have proved essential to the long-term utility and flexibility of his catalog. Based on his extensive knowledge of genetics and vision of its future in the field of medicine, he developed a framework for the capture and summary of information from the published literature on phenotypes and their associated genes; this catalog continues to serve as an indispensable resource to the genetics community.
| S-EPMC8596664 | biostudies-literature
Project description:BackgroundLight transmission aggregometry (LTA) can be performed with microtiter plates (96-well LTA). When conducting LTA, an agonist is added to platelet-rich plasma and the sample is shaken for minutes after which absorbance readings are done. Platelet aggregation is detected as decrease in absorbance. However, the classical method is cumbersome and therefore microtiter plates can be used for concomitant testing of multiple samples. Furthermore, it would be convenient to prepare the plate in advance of platelet aggregation testing. Aim: The aim of the present study was to establish a simplified 96-well LTA protocol, where plates were pre-coated with agonists and stored at -80 C until use.ResultsWe developed and validated a protocol for 96-well LTA using a Victor X5 plate reader and pre-coated microtiter plates. The minimum requirement of platelet-rich plasma was 45 ?L per sample and the sample platelet count should not be below 100 x109/L. Optimal absorbance reading was 595 nm wavelengths. Platelet aggregation results were higher at 37°C than at room temperature. Platelet adherence to wells after stimulation was observed; it was not avoided by pre-coating of the wells with gelatin. A range of up to 7 concentrations for each agonist (collagen, arachidonic acid, adenosine diphosphate, thrombin receptor-activating peptide and protease-activated receptor-4) was tested concomitantly. A transient rise in platelet aggregation was observed after 2 minutes of shaking in some samples with low agonist concentration, and platelet aggregation was optimal after 10 minutes of shaking for samples with high agonist concentration. Plates could be stored at -80°C for 15 days without significant change in the platelet aggregation results.ConclusionThe 96-well LTA is suitable for platelet aggregation testing and a range of agonist concentrations can be concomitantly tested.
| S-EPMC5638243 | biostudies-literature
Project description:The true crabs (Brachyura) including Calappidea are one of the most diverse groups of Decapod crustaceans However, despite their great diversity and commercial importance, phylogenetic and classification relationships within Calappidea are still complicated and controversial. In this study, we report the first complete mitochondrial genome of Matuta victos. The mitogenome has 17,782 base pairs (70.1% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and two ribosomal RNAs), plus a putative control region. This study will provide useful molecular resources for clarifying evolutionary and phylogenetic confusion within Calappidea.
| S-EPMC7832593 | biostudies-literature