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cAMRah: a scalable and portable workflow for harmonized antimicrobial resistance gene prediction from bacterial genomes.
cAMRah is a curated workflow designed to predict antimicrobial resistance (AMR) genes in microbial genomes, either in the cloud or on any personal computer running Docker containers. Numerous AMR gene-finding packages exist, each utilizing different algorithms and prediction methods. cAMRah adopts a consensus-based approach to AMR prediction, recognizing that no single tool can identify all AMR genes. It integrates and runs six AMR-finder tools and databases (with plans for future expansion),...
Salivary Proteome Role in Infection and Immunity.
This chapter is a comprehensive overview of the role of the salivary proteome in infection and immunity. It emphasizes saliva's multifaceted nature, highlighting its composition, functions, and origin from major and minor salivary glands. The dynamic nature of the salivary proteome is explored, emphasizing its complexity and the challenges in its analysis due to factors like high dynamic range and proteolytic activity. We underscore saliva's significance in oral and systemic health, detailing...
An undescribed species within the Gymnodinium sensu stricto group found responsible for an exceptional bloom in the Southern Ocean.
Naked dinoflagellates are a regular component of the Antarctic phytoplankton but remain poorly studied. In December 2016, the first massive bloom (9.5 × 10 cells · L) of small (~15 μm) naked dinoflagellates was recorded in the western Antarctic Peninsula. To identify these organisms, we performed Illumina next-generation sequencing analysis on field samples to obtain genetic information (SSU rDNA 18SV9 and 16SV4-V5). In addition, we performed polymerase chain reaction (PCR)...
BV-BRC Zoonosis or Reverse Zoonosis Example.
This bioinformatics workflow utilizes the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) to investigate a potential zoonotic or reverse zoonotic transmission event on a North Carolina swine farm in 2022 (Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C, Davis JJ, Dempsey DM, Dickerman A, Dietrich EM, Kenyon RW, Kuscuoglu M, Lefkowitz EJ, Lu J, Machi D, Macken C, Mao C, Niewiadomska A, Nguyen M, Olsen GJ, Overbeek JC, Parrello B, Parrello V, Porter JS, Pusch GD, Shukla M, Singh I,...
3rd Minimal Cell Workshop
View complete playlist for the workshop on YouTube. Day 1 — September 15, 2023 Time PDT Video Title Presenter Organization PI 5:00 - 5:20 Welcome and introduction John Glass (jglass@jcvi.org) JCVI John Glass 5:20 - 5:35 Building the in silico minimal cell: Achievements and a rallying call for experimental data ...
Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing.
The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic...
Meta-Analysis of the Expansion in the Field of Structural Biology of ABC Transporters.
ABC transporters are molecular machines which power the solute transport using ATP hydrolysis. The structural biology of ABC transporters has been exploding for the last few years, and this study explores timelines and trends for various attributes such as structural tools, resolution, fold, sources, and group leaders. This study also evidences the significance of mammalian expression systems, advancements in structural biology tools, and the developing interest of group leaders across the...
Flexible B<sub>12</sub> ecophysiology of <i>Phaeocystis antarctica</i> due to a fusion B<sub>12</sub>-independent methionine synthase with widespread homologues.
Coastal Antarctic marine ecosystems are significant in carbon cycling because of their intense seasonal phytoplankton blooms. Southern Ocean algae are primarily limited by light and iron (Fe) and can be co-limited by cobalamin (vitamin B). Micronutrient limitation controls productivity and shapes the composition of blooms which are typically dominated by either diatoms or the haptophyte . However, the vitamin requirements and ecophysiology of the keystone species remain poorly characterized....
Novel proteins from proteomic analysis of the trunk disease fungus <i>Lasiodiplodia theobromae</i> (Botryosphaeriaceae).
Many basic science questions remain regarding protein functions in the pathogen: host interaction, especially in the trunk disease fungi family, the Botryosphaeriaceae, which are a global problem for economically important plants, especially fruiting trees. Proteomics is a highly useful technology for studying protein expression and for discovering novel proteins in unsequenced and poorly annotated organisms. Current fungal proteomics approaches involve 2D SDS-PAGE and extensive, complex,...
Data from proteome analysis of <i>Lasiodiplodia theobromae</i> (Botryosphaeriaceae).
Trunk disease fungi are a global problem affecting many economically important fruiting trees. The Botryosphaeriaceae are a family of trunk disease fungi that require detailed biochemical characterization in order to gain insight into their pathogenicity. The application of a modified Folch extraction to protein extraction from the Botryosphaeriaceae generated an unprecedented data set of protein identifications from fragmentation analysis and peptide sequencing of its proteome. This article...