scholarly journals PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences

2008 ◽  
Vol 8 (1) ◽  
pp. 185 ◽  
Author(s):  
Jiqiang Yao ◽  
Hong Lin ◽  
Allen Van Deynze ◽  
Harshavardhan Doddapaneni ◽  
Martha Francis ◽  
...  
Keyword(s):  
Genomic Sequences ◽  
Whole Genome ◽  
Web Tool ◽  
Genome Selection ◽  
Allele Specific ◽  
Selection Of

scholarly journals Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 847
Author(s):  
Kyungmin Park ◽  
Seung-Ho Lee ◽  
Jongwoo Kim ◽  
Jingyeong Lee ◽  
Geum-Young Lee ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Republic Of Korea ◽  
Hantaan Virus ◽  
Genomic Sequences ◽  
Whole Genome ◽  
Nanopore Sequencing ◽  
Apodemus Agrarius ◽  
Copy Numbers ◽  
Nanopore Sequencer

Whole-genome sequencing of infectious agents enables the identification and characterization of emerging viruses. The MinION device is a portable sequencer that allows real-time sequencing in fields or hospitals. Hantaan orthohantavirus (Hantaan virus, HTNV), harbored by Apodemus agrarius, causes hemorrhagic fever with renal syndrome (HFRS) and poses a critical public health threat worldwide. In this study, we aimed to evaluate the feasibility of using nanopore sequencing for whole-genome sequencing of HTNV from samples having different viral copy numbers. Amplicon-based next-generation sequencing was performed in A. agrarius lung tissues collected from the Republic of Korea. Genomic sequences of HTNV were analyzed based on the viral RNA copy numbers. Amplicon-based nanopore sequencing provided nearly full-length genomic sequences of HTNV and showed sufficient read depth for phylogenetic analysis after 8 h of sequencing. The average identity of the HTNV genome sequences for the nanopore sequencer compared to those of generated from Illumina MiSeq revealed 99.8% (L and M segments) and 99.7% (S segment) identities, respectively. This study highlights the potential of the portable nanopore sequencer for rapid generation of accurate genomic sequences of HTNV for quicker decision making in point-of-care testing of HFRS patients during a hantavirus outbreak.

scholarly journals Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guilherme B. Neumann ◽  
Paula Korkuć ◽  
Danny Arends ◽  
Manuel J. Wolf ◽  
Katharina May ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Studies ◽  
Bos Indicus ◽  
Diversity Management ◽  
Whole Genome Sequencing Data ◽  
General Interest ◽  
Whole Genome ◽  
Sequencing Data ◽  
Snp Chip ◽  
Selection Of

Abstract Background German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN’s genetic diversity and to provide avenues for genetic improvement. Results Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%. Conclusion The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.

scholarly journals A Novel Test System for Genotyping rs43703016 Single-nucleotide Substitutions in the Bovine CSN3 Gene

2019 ◽  
pp. 1-5
Author(s):  
Svetlana Kovalchuk ◽  
Arina Tagmazyan ◽  
Eugene Klimov
Keyword(s):  
Nucleotide Substitution ◽  
Milk Proteins ◽  
Test System ◽  
Nucleotide Polymorphisms ◽  
Dna Testing ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Allele Specific ◽  
Selection Of

Aims: Caseins are among the main milk proteins that determine many of its properties. Bovine kappa-casein (CSN3) is associated with the qualitative composition of milk, as well as with the quality of cheese obtained from this milk. The rs43703016 single-nucleotide substitution (g.88532332A>C; Asp148Ala) in exon 4 of the bovine CSN3 gene plays an important role in the production of quality hard cheeses. Various methods for the DNA testing of this substitution have been developed in the last three decades. Emergent DNA technologies provide an opportunity to modernize methods of genotyping single-nucleotide polymorphisms. Results: We have developed and verified a method to differentiate A/C alleles of the rs43703016 substitution in the bovine CSN3 gene by real-time PCR using allele-specific fluorescent probes. Conclusion: Our new method allows fast genotyping of animals, and may be used for selection of cows carrying the CC genotype, which determines good cheese-making properties of milk.

Genomic sequences for fungi.

2021 ◽  
pp. 231-254
Author(s):  
Riccardo Baroncelli ◽  
Giovanni Cafà
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Fungal Genome ◽  
Basic Knowledge ◽  
Genomic Sequences ◽  
Whole Genome ◽  
Fungal Genomics

Abstract This chapter aims to give an overview of the basic knowledge, understanding and perspectives in fungal genomics. It is likely that fungal genome sequencing will soon become simpler and cheaper, and allow most research laboratories to undertake in-house, whole genome sequencing on a regular basis, as sequencers will be accessible to most laboratories. Nonetheless, most of the innovation in the next decade will be driven by theories in innovative perspectives and fields of investigation, rather than in novel technical approaches.

Molecular breeding for improving yield in wheat: recent advances and future perspectives.

2021 ◽  
pp. 197-212
Author(s):  
S. A. C. N. Perera ◽  
Saman Seneweera
Keyword(s):  
Genome Sequence ◽  
Genetic Improvement ◽  
Molecular Breeding ◽  
Wheat Breeding ◽  
Molecular Techniques ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Future Perspectives ◽  
Wheat Germplasm ◽  
Allele Specific

Abstract Out of the different objectives of wheat breeding, this chapter focuses on the direct increment of wheat yields via genetic improvement of the crop. The efficiency of modern molecular techniques, along with the availability of the whole-genome sequence of wheat, in mining wheat germplasm for allele-specific desirable traits is also discussed.

scholarly journals Simultaneous Infection with Enterobacteriaceae and Pseudomonas aeruginosa Harboring Multiple Carbapenemases in a Returning Traveler Colonized with Candida auris

2019 ◽  
Vol 64 (2) ◽  
Author(s):  
Ayesha Khan ◽  
William C. Shropshire ◽  
Blake Hanson ◽  
An Q. Dinh ◽  
Audrey Wanger ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Susceptibility Testing ◽  
Multidrug Resistant ◽  
Critically Ill Patient ◽  
Whole Genome ◽  
Candida Auris ◽  
Content Type ◽  
Simultaneous Infection ◽  
Polymicrobial Infections ◽  
Selection Of

ABSTRACT We report our clinical experience treating a critically ill patient with polymicrobial infections due to multidrug-resistant Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa in a 56-year-old woman who received health care in India and was also colonized by Candida auris. A precision medicine approach using whole-genome sequencing revealed a multiplicity of mobile elements associated with NDM-1, NDM-5, and OXA-181 and, supplemented with susceptibility testing, guided the selection of rational antimicrobial therapy.

scholarly journals On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

Database ◽  
2016 ◽  
Vol 2016 ◽  
Author(s):  
Hans Ienasescu ◽  
Kang Li ◽  
Robin Andersson ◽  
Morana Vitezic ◽  
Sarah Rennie ◽  
...  
Keyword(s):  
Human Body ◽  
Individual Cell ◽  
Cell Types ◽  
Large Datasets ◽  
Human Tissues ◽  
Web Tool ◽  
Expression Of Genes ◽  
Micro Rnas ◽  
Human Protein Atlas ◽  
Selection Of

Genomics consortia have produced large datasets profiling the expression of genes, micro-RNAs, enhancers and more across human tissues or cells. There is a need for intuitive tools to select subsets of such data that is the most relevant for specific studies. To this end, we present SlideBase, a web tool which offers a new way of selecting genes, promoters, enhancers and microRNAs that are preferentially expressed/used in a specified set of cells/tissues, based on the use of interactive sliders. With the help of sliders, SlideBase enables users to define custom expression thresholds for individual cell types/tissues, producing sets of genes, enhancers etc. which satisfy these constraints. Changes in slider settings result in simultaneous changes in the selected sets, updated in real time. SlideBase is linked to major databases from genomics consortia, including FANTOM, GTEx, The Human Protein Atlas and BioGPS. Database URL: http://slidebase.binf.ku.dk

Activity-Based Software Process Lines Tailoring

2014 ◽  
Vol 24 (09) ◽  
pp. 1357-1381 ◽  
Author(s):  
Wagner Gadêa Lorenz ◽  
Miguel Bauermann Brasil ◽  
Lisandra Manzoni Fontoura ◽  
Guilherme Vaz Pereira
Keyword(s):  
Systematic Approach ◽  
Selection Process ◽  
Software Process ◽  
Process Definition ◽  
Web Tool ◽  
Complex Time ◽  
Support Tool ◽  
Process Engineer ◽  
Process Elements ◽  
Selection Of

Software process definition requires choosing the process elements that appropriately fulfil the tailoring requirements, such as to prevent risks or to satisfy quality goals. The selection of appropriate process elements is usually done manually, making this process complex, time-consuming and error-prone. Our main objective is to define a systematic approach to tailor software process and a support tool to simplify and to support the tailoring process by improving the selection process of reusable process elements. We developed a systematic approach to tailor software process based on software process architectures and lines. This approach selects the process elements that appropriately match the tailoring requirements. A web tool was developed to support the use of the proposed approach. We concluded that the approach aids process engineer to make decisions for selecting a set of process elements suitable to the tailoring requirements and to the project context.

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