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Genotyping-by-sequencing (GBS) is a powerful approach for studying the genetic diversity of legume species. By using restriction enzymes or other methods to generate a reduced representation of the genome for sequencing, GBS can provide genome-wide single nucleotide polymorphisms (SNP) for diversity analysis at high throughput and low cost. Here we describe a novel double-digest restriction site-associated DNA sequencing (ddRAD-seq) approach. We also describe the downstream bioinformatic analysis of the sequencing data, including alignment to a reference genome, de novo assembly, SNP calling, phylogenetic analysis, and structure analysis.
This article was published in the following journal.
Name: Methods in molecular biology (Clifton, N.J.)
is a recently recognized human enteropathogen that is closely related to . In many Gram-negative bacteria, including , O-antigen variation has long been used for the serotyping of strains. In , while ...
Globally, crustaceans represent one of the most taxonomically diverse and economically important invertebrate group. Notwithstanding, the diversity within this group is poorly known because most crust...
The partitioning of β-diversity is a recurrent practice in biogeographic and ecological studies that can provide key insights for land management, such as identification of biodiversity hot-spots. In...
Chiroptera form the second largest order of mammals and compromise >1200 species, of which only 51 species are abundant in Europe. As bats are important hosts involved in the emergence and spread of z...
Accurate identification of fungi occurring on agrofood products is the key aspect of any prevention and pest management program, offering valuable information in leading crop health and food safety. F...
DIGEST I Pilot study is a feasibility study for evaluating the safety and efficacy of DCBs.
Not all infectious agents have the same epidemic potential, and this can vary widely within the same species. Rapid determination of this potential is essential to optimize control of infe...
Physicians know that their patients can react differently to the same medical treatment: for some of them, the drug will prove inefficient, whereas for others it might provoke side-effects...
The present study aims to evaluate the efficacy of Arom Digest Slim in facilitating weight reduction along with a series of minimal nutritional interventions.
The human oral cavity is a diverse habitat that contains approximately 700 prokaryotic species. The oral microbiome is comprised of 44% named species, 12% isolates representing unnamed spe...
Systematic identification of a population's needs or the assessment of individuals to determine the proper level of services needed.
The phenomenon of immense variability characteristic of ANTIBODIES. It enables the IMMUNE SYSTEM to react specifically against the essentially unlimited kinds of ANTIGENS it encounters. Antibody diversity is accounted for by three main theories: (1) the Germ Line Theory, which holds that each antibody-producing cell has genes coding for all possible antibody specificities, but expresses only the one stimulated by antigen; (2) the Somatic Mutation Theory, which holds that antibody-producing cells contain only a few genes, which produce antibody diversity by mutation; and (3) the Gene Rearrangement Theory, which holds that antibody diversity is generated by the rearrangement of IMMUNOGLOBULIN VARIABLE REGION gene segments during the differentiation of the ANTIBODY-PRODUCING CELLS.
Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms).
Evaluation procedures that focus on both the outcome or status (OUTCOMES ASSESSMENT) of the patient at the end of an episode of care - presence of symptoms, level of activity, and mortality; and the process (ASSESSMENT, PROCESS) - what is done for the patient diagnostically and therapeutically.
Activities and programs intended to assure or improve the quality of care in either a defined medical setting or a program. The concept includes the assessment or evaluation of the quality of care; identification of problems or shortcomings in the delivery of care; designing activities to overcome these deficiencies; and follow-up monitoring to ensure effectiveness of corrective steps.
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...
Restriction enzymes are DNA-cutting enzymes, also referred to as restriction endonucleases. When sequencing DNA, it is first necessary to cut it into smaller fragments using DNA-digesting enzymes which cleave the DNA molecule at a few precisely-located...