A whole-genome bioinformatics approach to selection of antigens for systematic antibody generation

PROTEOMICS ◽  
2008 ◽  
Vol 8 (14) ◽  
pp. 2832-2839 ◽  
Author(s):  
Lisa Berglund ◽  
Erik Björling ◽  
Kalle Jonasson ◽  
Johan Rockberg ◽  
Linn Fagerberg ◽  
...  
Keyword(s):  
Whole Genome ◽  
Selection Of

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 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 Unbiasing in the Genome Analysis of Iconic Shark Species

2019 ◽  
Author(s):  
Kazuaki Yamaguchi ◽  
Shigehiro Kuraku
Keyword(s):  
Molecular Evolution ◽  
Genome Stability ◽  
White Shark ◽  
Shark Species ◽  
Whole Genome ◽  
Potential Bias ◽  
Short Article ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Selection Of

A previous study involving whole genome sequencing of the white shark suggested unique molecular evolution accounting for gigantism and the enhanced longevity of sharks including positive selection of dozens of protein-coding genes potentially involved in genome stability. We performed a reanalysis on some of the genes and identified serious flaws in their results. In this short article, we scrutinize one of the serious problems we identified, report other concerns, and point out a potential bias in analyzing iconic shark species in general.

Selection of Potential Pharmacological Targets in ALS Based on Whole- Genome Expression Profiling

2015 ◽  
Vol 22 (17) ◽  
pp. 2004-2021 ◽  
Author(s):  
Giovanna Morello ◽  
Francesca Conforti ◽  
Rosalba Parenti ◽  
Velia D’Agata ◽  
Sebastiano Cavallaro
Keyword(s):  
Expression Profiling ◽  
Whole Genome ◽  
Genome Expression ◽  
Pharmacological Targets ◽  
Whole Genome Expression ◽  
Selection Of

scholarly journals Selection of unique Escherichia coli clones by random amplified polymorphic DNA (RAPD): Evaluation by whole genome sequencing

2014 ◽  
Vol 103 ◽  
pp. 101-103 ◽  
Author(s):  
Karen L. Nielsen ◽  
Paul A. Godfrey ◽  
Marc Stegger ◽  
Paal S. Andersen ◽  
Michael Feldgarden ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Random Amplified Polymorphic Dna ◽  
Whole Genome ◽  
Selection Of

scholarly journals Genetic Architecture and Selection of Chinese Cattle Revealed by Whole Genome Resequencing

2017 ◽  
Vol 35 (3) ◽  
pp. 688-699 ◽  
Author(s):  
Chugang Mei ◽  
Hongcheng Wang ◽  
Qijun Liao ◽  
Lizhong Wang ◽  
Gong Cheng ◽  
...  
Keyword(s):  
Genetic Architecture ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Chinese Cattle ◽  
Whole Genome Resequencing ◽  
Selection Of

scholarly journals Genotyping Study of Salmonella 4,[5],12:i:- Monophasic Variant of Serovar Typhimurium and Characterization of the Second-Phase Flagellar Deletion by Whole Genome Sequencing

2020 ◽  
Vol 8 (12) ◽  
pp. 2049
Author(s):  
Ainhoa Arrieta-Gisasola ◽  
Aitor Atxaerandio-Landa ◽  
Victoria Garrido ◽  
María Jesús Grilló ◽  
Ilargi Martínez-Ballesteros ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enteritidis ◽  
Genomic Region ◽  
Second Phase ◽  
Whole Genome ◽  
Serovar Typhimurium ◽  
Selection Of

After Salmonella Enteritidis and S. Typhimurium, S. 4,[5],12:i:- is the most reported serovar in human clinical cases. During the past 20 years, many tools have been used for its typing and second-phase flagellar deletion characterization. Currently, whole genome sequencing (WGS) and different bioinformatic programs have shown the potential to be more accurate than earlier tools. To assess this potential, we analyzed by WGS and in silico typing a selection of 42 isolates of S. 4,[5],12:i:- and S. Typhimurium with different in vitro characteristics. Comparative analysis showed that SeqSero2 does not differentiate fljB-positive S. 4,[5],12:i:- strains from those of serovar Typhimurium. Our results proved that the strains selected for this work were non-clonal S. 4,[5],12:i:- strains circulating in Spain. Using WGS data, we identified 13 different deletion types of the second-phase flagellar genomic region. Most of the deletions were generated by IS26 insertions, showing orientation-dependent conserved deletion ends. In addition, we detected S. 4,[5],12:i:- strains of the American clonal line that would give rise to the Southern European clone in Spain. Our results suggest that new S. 4,[5],12:i:- strains are continuously emerging from different S. Typhimurium strains via different genetic events, at least in swine products.

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