Searching the Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
Zinc is an essential trace element that acts as a co-factor for many enzymes and transcription factors required for cellular growth and development. Altering intracellular zinc levels can produce dramatic effects ranging from cell proliferation to cell death. To avoid such fates, cells have evolved mechanisms to handle both an excess and a deficiency of zinc. Zinc homeostasis is largely maintained via zinc transporters, permeable channels, and other zinc-binding proteins. Variation in these proteins might affect their ability to interact with zinc, leading to either increased sensitivity or resistance to natural zinc fluctuations in the environment. We can leverage the power of the roundworm nematode Caenorhabditis elegans as a tractable metazoan model for quantitative genetics to identify genes that could underlie variation in responses to zinc. We found that the laboratory-adapted strain (N2) is resistant and a natural isolate from Hawaii (CB4856) is sensitive to micromolar amounts of exogenous zinc supplementation. Using a panel of recombinant inbred lines, we identified two large-effect quantitative trait loci (QTL) on the left arm of chromosome III and the center of chromosome V that are associated with zinc responses. We validated and refined both QTL using near-isogenic lines (NILs) and identified a naturally occurring deletion in sqst-5, a sequestosome-related gene, that is associated with resistance to high exogenous zinc. We found that this deletion is relatively common across strains within the species and that variation in sqst-5 is associated with zinc resistance. Our results offer a possible mechanism for how organisms can respond to naturally high levels of zinc in the environment and how zinc homeostasis varies among individuals.
Pubmed ID: 33175833
Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.
Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF.
View all literature mentionsOpen source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.
View all literature mentionsProvide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
View all literature mentionsA powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
View all literature mentionsThe Simons Foundation is a private foundation based in New York City, incorporated in 1994 by Jim and Marilyn Simons. The Simons Foundation''s mission is to advance the frontiers of research in mathematics and the basic sciences. We sponsor a range of programs that aim to promote a deeper understanding of our world. The primary focus of the foundation''s Mathematics & the Physical Sciences (MPS) program is on the theoretical sciences radiating from mathematics: in particular, the fields of mathematics, theoretical computer science and theoretical physics. Although we have supported basic research in mathematics and physics for years at institutions around the globe, the mode of our support entered an important new phase in fall 2009 with the introduction of grant opportunities with open application procedures. It is intended that this will become our primary mode of operation. In 2010, the MPS program issued its first requests for grant applications. These requests offered grants to establish post-doctoral fellowships, grants to promote collaboration between researchers, grants to create professorships that combine mathematics with other fields, and a grant to endow an institute for theoretical computer science. Other projects are under way, including the Africa Mathematics Project, intended to bolster mathematics scholarship on the African continent, and an oral history project: a series of interviews with renowned mathematicians and scientists which will be made available to the public for viewing. The Simons Foundation''s initial support of life sciences work has tended to focus on research that promotes synergy between biology and mathematics. Such projects have included quantitative biology programs at Cold Spring Harbor Laboratory, the Institut des Hautes ��tudes Scientifiques, the Institute for Advanced Study, and The Rockefeller University. The Life Sciences program is expected to expand in scope over the next two to three years. To date, the Simons Foundation''s single largest initiative has been in autism research. The Simons Foundation Autism Research Initiative (SFARI) program seeks to improve the diagnosis and treatment of autism spectrum disorders by funding, catalyzing, and driving innovative research of the greatest quality and relevance. In 2007, SFARI issued its first Request for Applications, its goal being to attract the best researchers to the field. In the years since, SFARI has given grants to 150 investigators in the United States and abroad. Additionally, to facilitate the field as a whole, SFARI has created the Simons Simplex Collection of extensive genetic and phenotypic data from almost 3,000 families with a child affected by autism. Although SFARI''s immediate priority is to benefit individuals challenged by autism spectrum disorders, the program''s research is expected to yield insights into the neural mechanisms of fundamental human capabilities, complementing the mission of the Simons Foundation to advance research in the basic sciences and mathematics.
View all literature mentionsSoftware for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes.
View all literature mentionsNational institute that reduces the burden of human illness and dysfunction from environmental causes by, defining how environmental exposures, genetic susceptibility, and age interact to affect an individual''s health. Its mission is to discover how the environment affects people in order to promote healthier lives. Achieving this mission depends on a set of core values that apply to all activities of the Institute: * Research excellence (innovation; discovery of new scientific knowledge and technology); * Management excellence; and * Community outreach, education, and involvement. At NIEHS and the National Toxicology Program, they engage in a special form of public service - producing scientific knowledge that promotes individual and public health. The Institute is uniquely positioned to help prevent disease and transform new scientific knowledge into improvements in human health. There are many opportunities before us to build and expand the contributions of the NIEHS: * Foster research on environmental triggers of disease; * Communicate advances in environmental health sciences to the public; * Foster training and development of emerging young environmental health scientists and practitioners; * Enhance translation of knowledge from research to disease prevention; and * Foster safety assessment research on chemicals and other environmental factors. The fulfillment of this mission requires the partnership and effort of everyone in the environmental health sciences communities.
View all literature mentionsMultiple sequence alignment method with reduced time and space complexity.Multiple sequence alignment with high accuracy and high throughput. Data analysis service for multiple sequence comparison by log- expectation.
View all literature mentionsAn independent federal agency created by Congress to promote the progress of science; to advance the national health, prosperity, and welfare; to secure the national defense They are the funding source for approximately 20 percent of all federally supported basic research conducted by America''s colleges and universities. In many fields such as mathematics, computer science and the social sciences, NSF is the major source of federal backing. NSF leadership has two major components: a director who oversees NSF staff and management responsible for program creation and administration, merit review, planning, budget and day-to-day operations; and a 24-member National Science Board (NSB) of eminent individuals that meets six times a year to establish the overall policies of the foundation.The director and all Board members serve six year terms. Each of them, as well as the NSF deputy director, is appointed by the President of the United States and confirmed by the U.S. Senate. At present, NSF has a total workforce of about 2,100 at its Arlington, Va., headquarters, including approximately 1,400 career employees, 200 scientists from research institutions on temporary duty, 450 contract workers and the staff of the NSB office and the Office of the Inspector General. NSF is the only federal agency whose mission includes support for all fields of fundamental science and engineering, except for medical sciences. They are tasked with keeping the United States at the leading edge of discovery in areas from astronomy to geology to zoology. So, in addition to funding research in the traditional academic areas, the agency also supports high-risk, high pay-off ideas, novel collaborations and numerous projects that may seem like science fiction today, but which the public will take for granted tomorrow. And in every case, they ensure that research is fully integrated with education so that today''s revolutionary work will also be training tomorrow''s top scientists and engineers NSF''s task of identifying and funding work at the frontiers of science and engineering is not a top-down process.
View all literature mentionsGene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool.
View all literature mentions