WormBase 2024: status and transitioning to Alliance infrastructure.

WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable.

Bone Cement Waste in Total Knee Arthroplasty: A Preliminary Study of Scope and Cost.

Background: Medical waste is both costly and detrimental to the environment, and operating room waste represents a substantial portion of this. To the authors' knowledge, bone cement waste in total knee arthroplasty (TKA) has not previously been studied. The vast majority of TKA are cemented, and the volume of TKA is forecast to increase.

Evidence of glucosinolates translocation from inflorescences to stems during postharvest storage of broccoli.

Broccoli is a vegetable appreciated by consumers for its nutritional properties, particularly for its high glucosinolate (GLS) content. However, broccoli shows a high rate of senescence during postharvest and the GLS content in inflorescences decreases sharply. Usually, postharvest studies on broccoli focus on inflorescences, ignoring the other tissues harvested such as the stems and main stalk.

Ensembl 2023.

Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years.

Accelerated variant curation from scientific literature using biomedical text mining.

Biological databases collect and standardize data through biocuration. Even though major model organism databases have adopted some automation of curation methods, a large portion of biocuration is still performed manually. To speed up the extraction of the genomic positions of variants, we have developed a hybrid approach that combines regular expressions, Named Entity Recognition based on BERT (Bidirectional Encoder Representations from Transformers) and bag-of-words to extract variant genomic locations from papers for WormBase.

The Common Bean Gene Encodes Flavonoid 3'5' Hydroxylase: A Major Mutational Target for Flavonoid Diversity in Angiosperms.

The classic (violet, purple) gene of common bean () functions in a complex genetic network that controls seed coat and flower color and flavonoid content. was cloned to understand its role in the network and the evolution of its orthologs in the Viridiplantae. mapped genetically to a narrow interval on chromosome Pv06.

WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans.

WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans.

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.

Ensembl 2022.

Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation.

The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data.

The COVID-19 pandemic has seen unprecedented use of SARS-CoV-2 genome sequencing for epidemiological tracking and identification of emerging variants. Understanding the potential impact of these variants on the infectivity of the virus and the efficacy of emerging therapeutics and vaccines has become a cornerstone of the fight against the disease. To support the maximal use of genomic information for SARS-CoV-2 research, we launched the Ensembl COVID-19 browser; the first virus to be encompassed within the Ensembl platform.

Right-sided heart failure is also associated with transverse tubule remodeling in the left ventricle.

Right-sided heart failure is a common consequence of pulmonary arterial hypertension. Overloading the right ventricle results in right ventricular hypertrophy, which progresses to failure in a process characterized by impaired Ca dynamics and force production that is linked with transverse (t)-tubule remodeling. This also unloads the left ventricle, which consequently atrophies.

SARS-CoV-2 RT-PCR test results across symptomatic COVID-19 cases in Auckland, New Zealand, February-June 2020.

During the first wave of COVID-19 transmission in New Zealand, a review of RT-PCR testing in all symptomatic cases reported in the Auckland Region found 74% of test results to have been positive. Detection rate was superior for nasopharyngeal swabs than for oropharyngeal samples, and highest one week after symptom onset. Certain symptom presentations may associate with these cases returning negative results, with dyspnoea reported by a greater proportion of cases who tested negative.

Proteomic Polyphenism in Color Morphotypes of , Insect Vector of Citrus Greening Disease.

is a vector of " Liberibacter asiaticus (Las), associated with citrus greening disease. . exhibit at least two color morphotypes, blue and non-blue, the latter including gray and yellow morphs.

GENCODE 2021.

The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs.

Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm.

Haemonchus contortus is a globally distributed and economically important gastrointestinal pathogen of small ruminants and has become a key nematode model for studying anthelmintic resistance and other parasite-specific traits among a wider group of parasites including major human pathogens. Here, we report using PacBio long-read and OpGen and 10X Genomics long-molecule methods to generate a highly contiguous 283.4 Mbp chromosome-scale genome assembly including a resolved sex chromosome for the MHco3(ISE).

Ensembl 2021.

The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species.

Development on Citrus medica infected with 'Candidatus Liberibacter asiaticus' has sex-specific and -nonspecific impacts on adult Diaphorina citri and its endosymbionts.

Huanglongbing (HLB) is a deadly, incurable citrus disease putatively caused by the unculturable bacterium, 'Candidatus Liberibacter asiaticus' (CLas), and transmitted by Diaphorina citri. Prior studies suggest D. citri transmits CLas in a circulative and propagative manner; however, the precise interactions necessary for CLas transmission remain unknown, and the impact of insect sex on D.

Comparative Proteomics of Root Apex and Root Elongation Zones Provides Insights into Molecular Mechanisms for Drought Stress and Recovery Adjustment in Switchgrass.

Switchgrass plants were grown in a Sandwich tube system to induce gradual drought stress by withholding watering. After 29 days, the leaf photosynthetic rate decreased significantly, compared to the control plants which were watered regularly. The drought-treated plants recovered to the same leaf water content after three days of re-watering.

Siderophores from the Entomopathogenic Fungus .

We report NMR- and MS-based structural characterizations of siderophores and related compounds from (Balsamo-Crivelli) Vuillemin, including ten new chemical entities (-, -, -, and ) and five known compounds, (, , , , and ). The siderophore mixture from ARSEF strain #2680 included two compounds in which -mevalonyl--hydroxyornithine replaces both () or one () of the -anhydromevalonyl--hydroxyornithine units of dimerumic acid (). Mevalonolactone () was present as a degradation product of and .

Longitudinal Transcriptomic, Proteomic, and Metabolomic Analyses of (L.) Osbeck Graft-Inoculated with " Liberibacter asiaticus".

" Liberibacter asiaticus" (Las) is the bacterium associated with the citrus disease Huanglongbing (HLB). Current Las detection methods are unreliable during presymptomatic infection, and understanding Las pathogenicity to help develop new detection techniques is challenging because Las has yet to be isolated in pure culture. To understand how Las affects citrus metabolism and whether infected plants produce systemic signals that can be used to develop improved detection techniques, leaves from Washington Navel orange ( (L.

Ensembl 2020.

The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation and comparative genomics across the vertebrate subphylum and key model organisms.

WormBase: a modern Model Organism Information Resource.

WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture.