Multiple genome viewer (MGV): a new tool for visualization and comparison of multiple annotated genomes.

The assembled and annotated genomes for 16 inbred mouse strains (Lilue et al., Nat Genet 50:1574-1583, 2018) and two wild-derived strains (CAROLI/EiJ and PAHARI/EiJ) (Thybert et al., Genome Res 28:448-459, 2018) are valuable resources for mouse genetics and comparative genomics. We developed the multiple genome viewer (MGV; http://www.informatics.jax.org/mgv ) to support visualization, exploration, and comparison of genome annotations within and across these genomes. MGV displays chromosomal regions of user-selected genomes as horizontal tracks. Equivalent features across the genome tracks are highlighted using vertical \u27swim lane\u27 connectors. Navigation across the genomes is synchronized as a researcher uses the scroll and zoom functions. Researchers can generate custom sets of genes and other genome features to be displayed in MGV by entering genome coordinates, function, phenotype, disease, and/or pathway terms. MGV was developed to be genome agnostic and can be used to display homologous features across genomes of different organisms

Movements and spawning of white marlin (Tetrapturus albidus) and blue marlin (Makaira nigricans) off Punta Cana, Dominican Republic

With a focus on white marlin (Tetrapturus albidus), a concurrent electronic tagging and larval sampling effort was conducted in the vicinity of Mona Passage (off southeast Hispaniola), Dominican Republic, during April and May 2003. Objectives were 1) to characterize the horizontal and vertical movement of adults captured from the area by using pop-up satellite archival tags (PSATs); and 2) by means of larval sampling, to investigate whether fish were reproducing. Trolling from a sportfishing vessel yielded eight adult white marlin and one blue marlin (Makaira nigricans); PSAT tags were deployed on all but one of these individuals. The exception was a female white marlin that was unsuitable for tagging because of injury; the reproductive state of its ovaries was examined histologically. Seven of the PSATs reported data summaries for water depth, temperature, and light levels measured every minute for periods ranging from 28 to 40 days. Displacement of marlin from the location of release to the point of tag pop-up ranged from 3l.6 to 267.7 nautical miles (nmi) and a mean displacement was 3.4 nmi per day for white marlin. White and blue marlin mean daily displacements appeared constrained compared to the results of other marlin PSAT tagging studies. White marlin ovarian sections contained postovulatory follicles and final maturation-stage oocytes, which indicated recent and imminent spawning. Neuston tows (n=23) yielded 18 istiophorid larvae: eight were white marlin, four were blue marlin, and six could not be identified to species. We speculate that the constrained movement patterns of adults may be linked to reproductive activity for both marlin species, and, if true, these movement patterns may have several implications for management. Protection of the potentially important white marlin spawning ground near Mona Passage seems warranted, at least until further studies can be conducted on the temporal and spatial extent of reproduction and associated adult movement

Cancer Biology Data Curation at the Mouse Tumor Biology Database (MTB)

Many advances in the field of cancer biology have been made using mouse models of human cancer. The Mouse Tumor Biology (MTB, "http://tumor.informatics.jax.org":http://tumor.informatics.jax.org) database provides web-based access to data on spontaneous and induced tumors from genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice). These data include standardized tumor names and classifications, pathology reports and images, mouse genetics, genomic and cytogenetic changes occurring in the tumor, strain names, tumor frequency and latency, and literature citations.

Although primary source for the data represented in MTB is peer-reviewed scientific literature an increasing amount of data is derived from disparate sources. MTB includes annotated histopathology images and cytogenetic assay images for mouse tumors where these data are available from The Jackson Laboratory’s mouse colonies and from outside contributors. MTB encourages direct submission of mouse tumor data and images from the cancer research community and provides investigators with a web-accessible tool for image submission and annotation. 

Integrated searches of the data in MTB are facilitated by the use of several controlled vocabularies and by adherence to standard nomenclature. MTB also provides links to other related online resources such as the Mouse Genome Database, Mouse Phenome Database, the Biology of the Mammary Gland Web Site, Festing's Listing of Inbred Strains of Mice, the JAX® Mice Web Site, and the Mouse Models of Human Cancers Consortium's Mouse Repository. 

MTB provides access to data on mouse models of cancer via the internet and has been designed to facilitate the selection of experimental models for cancer research, the evaluation of mouse genetic models of human cancer, the review of patterns of mutations in specific cancers, and the identification of genes that are commonly mutated across a spectrum of cancers.

MTB is supported by NCI grant CA089713

The Mouse Genome Database (MGD): from genes to mice—a community resource for mouse biology

The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics

The mouse genome database (MGD): new features facilitating a model system

The mouse genome database (MGD, ), the international community database for mouse, provides access to extensive integrated data on the genetics, genomics and biology of the laboratory mouse. The mouse is an excellent and unique animal surrogate for studying normal development and disease processes in humans. Thus, MGD's primary goals are to facilitate the use of mouse models for studying human disease and enable the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Core MGD data content includes gene characterization and functions, phenotype and disease model descriptions, DNA and protein sequence data, polymorphisms, gene mapping data and genome coordinates, and comparative gene data focused on mammals. Data are integrated from diverse sources, ranging from major resource centers to individual investigator laboratories and the scientific literature, using a combination of automated processes and expert human curation. MGD collaborates with the bioinformatics community on the development of data and semantic standards, and it incorporates key ontologies into the MGD annotation system, including the Gene Ontology (GO), the Mammalian Phenotype Ontology, and the Anatomical Dictionary for Mouse Development and the Adult Anatomy. MGD is the authoritative source for mouse nomenclature for genes, alleles, and mouse strains, and for GO annotations to mouse genes. MGD provides a unique platform for data mining and hypothesis generation where one can express complex queries simultaneously addressing phenotypic effects, biochemical function and process, sub-cellular location, expression, sequence, polymorphism and mapping data. Both web-based querying and computational access to data are provided. Recent improvements in MGD described here include the incorporation of single nucleotide polymorphism data and search tools, the addition of PIR gene superfamily classifications, phenotype data for NIH-acquired knockout mice, images for mouse phenotypic genotypes, new functional graph displays of GO annotations, and new orthology displays including sequence information and graphic displays

Support for the Slope Sea as a major spawning ground for Atlantic bluefin tuna: evidence from larval abundance, growth rates, and particle-tracking simulations

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hernandez, C. M., Richardson, D. E., Rypina, I. I., Chen, K., Marancik, K. E., Shulzitski, K., & Llopiz, J. K. Support for the Slope Sea as a major spawning ground for Atlantic bluefin tuna: evidence from larval abundance, growth rates, and particle-tracking simulations. Canadian Journal of Fisheries and Aquatic Sciences, 79(5), (2021): 814-824, https://doi.org/10.1139/cjfas-2020-0444.Atlantic bluefin tuna (Thunnus thynnus) are commercially and ecologically valuable, but management is complicated by their highly migratory lifestyle. Recent collections of bluefin tuna larvae in the Slope Sea off northeastern United States have opened questions about how this region contributes to population dynamics. We analyzed larvae collected in the Slope Sea and the Gulf of Mexico in 2016 to estimate larval abundance and growth rates and used a high-resolution regional ocean circulation model to estimate spawning locations and larval transport. We did not detect a regional difference in growth rates, but found that Slope Sea larvae were larger than Gulf of Mexico larvae prior to exogenous feeding. Slope Sea larvae generally backtracked to locations north of Cape Hatteras and would have been retained within the Slope Sea until the early juvenile stage. Overall, our results provide supporting evidence that the Slope Sea is a major spawning ground that is likely to be important for population dynamics. Further study of larvae and spawning adults in the region should be prioritized to support management decisions.Ship time was supported by NOAA, the Bureau of Ocean Energy Management, and the US Navy through interagency agreements for Atlantic Marine Assessment Program for Protected Species (AMAPPS). CMH and JKL received funding from the Woods Hole Oceanographic Institution’s Ocean Life Institute (#13080700) and Academic Programs Office. CMH was additionally supported by the Adelaide and Charles Link Foundation and the J. Seward Johnson Endowment in support of the Woods Hole Oceanographic Institution’s Marine Policy Center. IIR, KC, and JKL were supported by a US National Science Foundation (NSF) grant (OCE-1558806). JKL was additionally supported by the Lenfest Fund for Early Career Scientists and the Early Career Scientist Fund at Woods Hole Oceanographic Institution

Feeding dynamics of Northwest Atlantic small pelagic fishes

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Progress in Oceanography 165 (2018): 52-62, doi:10.1016/j.pocean.2018.04.014.Small pelagic fishes represent a critical link between zooplankton and large predators. Yet, the taxonomic resolution of the diets of these important fishes is often limited, especially in the Northwest Atlantic. We examined the diets, along with stable isotope signatures, of five dominant small pelagic species of the Northeast US continental shelf ecosystem (Atlantic mackerel Scomber scombrus, Atlantic herring Clupea harengus, alewife Alosa pseudoharengus, blueback herring Alosa aestivalis, and Atlantic butterfish Peprilus triacanthus). Diet analyses revealed strong seasonal differences in most species. Small pelagic fishes predominantly consumed Calanus copepods, small copepod genera (Pseudocalanus/Paracalanus/Clausocalanus), and Centropages copepods in the spring, with appendicularians also important by number for most species. Krill, primarily Meganyctiphanes norvegica, and hyperiid amphipods of the genera Hyperia and Parathemisto were common in the stomach contents of four of the five species in the fall, with hyperiids common in the stomach contents of butterfish in both seasons and krill common in the stomach contents of alewife in both seasons. Depth and region were also found to be sources of variability in the diets of Atlantic mackerel, Atlantic herring, and alewife (region but not depth) with krill being more often in the diet of alewife in more northerly locations, primarily the Gulf of Maine. Stable isotope data corroborate the seasonal differences in diet but overlap of isotopic niche space contrasts that of dietary overlap, highlighting the differences in the two methods. Overall, the seasonal variability and consumer-specific diets of small pelagic fishes are important for understanding how changes in the zooplankton community could influence higher trophic levels.Funding for this work was primarily through a US National Science Foundation (NSF) OCE-RIG grant (OCE 1325451) to JKL, with additional support from NOAA through the Cooperative Institute for the North Atlantic Region (CINAR) under Cooperative Agreement NA14OAR4320158 in the form a CINAR Fellow Award (JKL), an NSF Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE 1655686; JKL), a Hendrix College summer research award (ZRK), and an NSF REU-supported Woods Hole Oceanographic Institution Summer Student Fellowship (SLH)

Mouse Genome Database (MGD) 2019.

The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism genetic and genome resource for the laboratory mouse. MGD is the authoritative source for biological reference data sets related to mouse genes, gene functions, phenotypes, and mouse models of human disease. MGD is the primary outlet for official gene, allele and mouse strain nomenclature based on the guidelines set by the International Committee on Standardized Nomenclature for Mice. In this report we describe significant enhancements to MGD, including two new graphical user interfaces: (i) the Multi Genome Viewer for exploring the genomes of multiple mouse strains and (ii) the Phenotype-Gene Expression matrix which was developed in collaboration with the Gene Expression Database (GXD) and allows researchers to compare gene expression and phenotype annotations for mouse genes. Other recent improvements include enhanced efficiency of our literature curation processes and the incorporation of Transcriptional Start Site (TSS) annotations from RIKEN\u27s FANTOM 5 initiative

Mouse Genome Informatics (MGI): latest news from MGD and GXD.

The Mouse Genome Informatics (MGI) database system combines multiple expertly curated community data resources into a shared knowledge management ecosystem united by common metadata annotation standards. MGI\u27s mission is to facilitate the use of the mouse as an experimental model for understanding the genetic and genomic basis of human health and disease. MGI is the authoritative source for mouse gene, allele, and strain nomenclature and is the primary source of mouse phenotype annotations, functional annotations, developmental gene expression information, and annotations of mouse models with human diseases. MGI maintains mouse anatomy and phenotype ontologies and contributes to the development of the Gene Ontology and Disease Ontology and uses these ontologies as standard terminologies for annotation. The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are MGI\u27s two major knowledgebases. Here, we highlight some of the recent changes and enhancements to MGD and GXD that have been implemented in response to changing needs of the biomedical research community and to improve the efficiency of expert curation. MGI can be accessed freely at http://www.informatics.jax.org

Mouse Genome Database (MGD): Knowledgebase for mouse-human comparative biology.

The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism knowledgebase for the laboratory mouse, a widely used animal model for comparative studies of the genetic and genomic basis for human health and disease. MGD is the authoritative source for biological reference data related to mouse genes, gene functions, phenotypes and mouse models of human disease. MGD is the primary source for official gene, allele, and mouse strain nomenclature based on the guidelines set by the International Committee on Standardized Nomenclature for Mice. MGD\u27s biocuration scientists curate information from the biomedical literature and from large and small datasets contributed directly by investigators. In this report we describe significant enhancements to the content and interfaces at MGD, including (i) improvements in the Multi Genome Viewer for exploring the genomes of multiple mouse strains, (ii) inclusion of many more mouse strains and new mouse strain pages with extended query options and (iii) integration of extensive data about mouse strain variants. We also describe improvements to the efficiency of literature curation processes and the implementation of an information portal focused on mouse models and genes for the study of COVID-19