scholarly journals Cellular thermal shift analysis for interrogation of CRISPR-assisted proteomic changes

BioTechniques ◽  
2020 ◽  
Vol 68 (4) ◽  
pp. 180-184 ◽  
Author(s):  
Nam-Gu Her ◽  
Ivan Babic ◽  
Venkata M Yenugonda ◽  
Santosh Kesari ◽  
Elmar Nurmemmedov
Keyword(s):  
Protein Complexes ◽  
Physiological State ◽  
Protein Coding ◽  
Coding Sequences ◽  
Missing Link ◽  
Disease States ◽  
Shift Analysis ◽  
Versatile Tool ◽  
Thermal Shift

CRISPR–Cas9 has proven to be a versatile tool for the discovery of essential genetic elements involved in various disease states. CRISPR-assisted dense mutagenesis focused on therapeutically challenging protein complexes allows us to systematically perturb protein-coding sequences in situ and correlate them with functional readouts. Such perturbations can mimic targeting by therapeutics and serve as a foundation for the discovery of highly specific modulators. However, translation of such genomics data has been challenging due to the missing link for proteomics under the physiological state of the cell. We present a method based on cellular thermal shift assays to easily interrogate proteomic shifts generated by CRISPR-assisted dense mutagenesis, as well as a case focused on NuRD epigenetic complex.

scholarly journals CRISPRO Identifies Functional Protein Coding Sequences Based on Genome Editing Dense Mutagenesis

2018 ◽  
Author(s):  
Vivien A. C. Schoonenberg ◽  
Mitchel A. Cole ◽  
Qiuming Yao ◽  
Claudio Macias-Treviño ◽  
Falak Sher ◽  
...  
Keyword(s):  
Machine Learning ◽  
Computational Pipeline ◽  
Functional Protein ◽  
Protein Coding ◽  
Coding Sequences ◽  
Guide Rna ◽  
Guide Rnas ◽  
Functional Scores ◽  
Parallel Evaluation

AbstractCRISPR/Cas9 pooled screening permits parallel evaluation of comprehensive guide RNA libraries to systematically perturb protein coding sequences in situ and correlate with functional readouts. For the analysis and visualization of the resulting datasets we have developed CRISPRO, a computational pipeline that maps functional scores associated with guide RNAs to genome, transcript, and protein coordinates and structure. No available tool has similar functionality. The ensuing genotype-phenotype linear and 3D maps raise hypotheses about structure-function relationships at discrete protein regions. Machine learning based on CRISPRO features improves prediction of guide RNA efficacy. The CRISPRO tool is freely available at gitlab.com/bauerlab/crispro.

Genome organisation in the murine sperm nucleus

Zygote ◽  
1995 ◽  
Vol 3 (2) ◽  
pp. 123-131 ◽  
Author(s):  
Carol Jennings ◽  
Don Powell
Keyword(s):  
Repetitive Dna ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sperm Nucleus ◽  
Genome Organisation ◽  
Telomeric Dna ◽  
Protein Coding ◽  
Coding Sequences ◽  
Restricted Domains

SummaryThe organisation of DNA sequences in the murine sperm nucleus was studied using in situ hybridisation of biotinylated DNA probes. The efficiency of this reaction was assessed using a dispersed repetitive DNA probe. Telomeric DNA was distributed around the nucleus. Centromeric and ribosomal DNA sequences occupied restricted domains in the sperm nucleus. DNA sequences for a transgene and a cluster of homeogenes occupied different, and rather less defined, domains. Together these results imply that both repetitive and protein-coding sequences are arranged in the nucleus in an ordered fashion.

scholarly journals The contribution of qualitative behavioural assessment to appraisal of livestock welfare

2016 ◽  
Vol 56 (10) ◽  
pp. 1569 ◽  
Author(s):  
Patricia A. Fleming ◽  
Taya Clarke ◽  
Sarah L. Wickham ◽  
Catherine A. Stockman ◽  
Anne L. Barnes ◽  
...  
Keyword(s):  
Animal Welfare ◽  
Assessment Tool ◽  
Physiological State ◽  
Welfare Assessment ◽  
Wide Range ◽  
Behavioural Assessment ◽  
Versatile Tool ◽  
Key Steps ◽  
Housing Options

Animal welfare is increasingly important for the Australian livestock industries, to maintain social licence to practice as well as ensuring market share overseas. Improvement of animal welfare in the livestock industries requires several important key steps. Paramount among these, objective measures are needed for welfare assessment that will enable comparison and contrast of welfare implications of husbandry procedures or housing options. Such measures need to be versatile (can be applied under a wide range of on- and off-farm situations), relevant (reveal aspects of the animal’s affective or physiological state that is relevant to their welfare), reliable (can be repeated with confidence in the results), relatively economic to apply, and they need to have broad acceptance by all stakeholders. Qualitative Behavioural Assessment (QBA) is an integrated measure that characterises behaviour as a dynamic, expressive body language. QBA is a versatile tool requiring little specialist equipment suiting application to in situ assessments that enables comparative, hypothesis-driven evaluation of various industry-relevant practices. QBA is being increasingly used as part of animal welfare assessments in Europe, and although most other welfare assessment methods record ‘problems’ (e.g. lameness, injury scores, and so on), QBA can capture positive aspects of animal welfare (e.g. positively engaged with their environment, playfulness). In this viewpoint, we review the outcomes of recent QBA studies and discuss the potential application of QBA, in combination with other methods, as a welfare assessment tool for the Australian livestock industries.

scholarly journals Draft Genome Sequence of Urease-Producing Pseudorhodobacter sp. Strain E13, Isolated from the Yellow Sea in Gunsan, South Korea

2019 ◽  
Vol 8 (23) ◽  
Author(s):  
Si Chul Kim ◽  
Hyo Jung Lee
Keyword(s):  
South Korea ◽  
Genome Sequence ◽  
Yellow Sea ◽  
Draft Genome ◽  
The Yellow Sea ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Gram Negative ◽  
Content Type

Here, we report the draft genome sequence of Pseudorhodobacter sp. strain E13, a Gram-negative, aerobic, nonflagellated, and rod-shaped bacterium which was isolated from the Yellow Sea in South Korea. The assembled genome sequence is 3,878,578 bp long with 3,646 protein-coding sequences in 159 contigs.

scholarly journals Evolutionary Patterns of Sex-Biased Genes in Three Species of Haplodiploid Insects

Insects ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 326
Author(s):  
Yu-Jun Wang ◽  
Hua-Ling Wang ◽  
Xiao-Wei Wang ◽  
Shu-Sheng Liu
Keyword(s):  
Gene Expression ◽  
Slow Rate ◽  
Species Complex ◽  
Evolutionary Patterns ◽  
Protein Coding ◽  
Coding Sequences ◽  
Species Comparisons ◽  
Differential Gene ◽  
Males And Females ◽  
And Behavior

Females and males often differ obviously in morphology and behavior, and the differences between sexes are the result of natural selection and/or sexual selection. To a great extent, the differences between the two sexes are the result of differential gene expression. In haplodiploid insects, this phenomenon is obvious, since males develop from unfertilized zygotes and females develop from fertilized zygotes. Whiteflies of the Bemisia tabaci species complex are typical haplodiploid insects, and some species of this complex are important pests of many crops worldwide. Here, we report the transcriptome profiles of males and females in three species of this whitefly complex. Between-species comparisons revealed that non-sex-biased genes display higher variation than male-biased or female-biased genes. Sex-biased genes evolve at a slow rate in protein coding sequences and gene expression and have a pattern of evolution that differs from those of social haplodiploid insects and diploid animals. Genes with high evolutionary rates are more related to non-sex-biased traits—such as nutrition, immune system, and detoxification—than to sex-biased traits, indicating that the evolution of protein coding sequences and gene expression has been mainly driven by non-sex-biased traits.

scholarly journals Draft Genome Sequences of 10 Clinical K2-Type Klebsiella pneumoniae Strains Isolated in Russia

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Nikolay V. Volozhantsev ◽  
Angelina A. Kislichkina ◽  
Anastasia I. Lev ◽  
Ekaterina V. Solovieva ◽  
Vera P. Myakinina ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Klebsiella Pneumoniae ◽  
Draft Genome ◽  
Capsular Type ◽  
Genome Sequences ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type ◽  
Neurosurgical Intensive Care ◽  
Neurosurgical Intensive Care Unit

We report here the genome sequences of 10 Klebsiella pneumoniae strains of capsular type K2 isolated in Russia from patients in an infectious clinical hospital and neurosurgical intensive care unit. The draft genome sizes range from 5.34 to 5.87 Mb and include 5,448 to 6,137 protein-coding sequences.

scholarly journals Genome Sequence of Rheinheimera salexigens sp. nov. Isolated from a Fishing Hook off O‘ahu, Hawai‘i

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Xuehua Wan ◽  
Shaobin Hou ◽  
Kazukuni Hayashi ◽  
James Anderson ◽  
Stuart P. Donachie
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Coding Regions ◽  
Roche 454

Rheinheimera salexigens KH87 T is an obligately halophilic gammaproteobacterium. The strain’s draft genome sequence, generated by the Roche 454 GS FLX+ platform, comprises two scaffolds of ~3.4 Mbp and ~3 kbp, with 3,030 protein-coding sequences and 58 tRNA coding regions. The G+C content is 42 mol%.

scholarly journals The influence of protein coding sequences on protein folding rates of all-β proteins

2011 ◽  
Vol 30 (Special Issue) ◽  
pp. 154-161 ◽  
Author(s):  
R. Li ◽  
H. Li
Keyword(s):  
Protein Folding ◽  
Protein Coding ◽  
Coding Sequences ◽  
Folding Rates
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