Metabolomic Bioinformatic Analysis

2017 ◽  
pp. 341-352
Author(s):  
Allyson L. Dailey
Keyword(s):  
Bioinformatic Analysis

Bioinformatic Analysis on Jellyfish Hematoxin

2009 ◽  
Vol 7 (2) ◽  
pp. 145-149 ◽  
Author(s):  
Chun-Lei OUYANG ◽  
Jia-Dong GAO ◽  
Yu-Kun REN ◽  
Liang XIAO ◽  
Qian-Qian WANG ◽  
...  
Keyword(s):  
Bioinformatic Analysis

New Nucleotide Polymorphisms in the BTC1 gene of Sugar Beet

2020 ◽  
Vol 36 (6) ◽  
pp. 49-54
Author(s):  
A.A. Nalbandyan ◽  
T.P. Fedulova ◽  
I.V. Cherepukhina ◽  
T.I. Kryukova ◽  
N.R. Mikheeva ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Flowering Time ◽  
Molecular Genetic ◽  
Bioinformatic Analysis ◽  
Early Flowering ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Substitutions ◽  
Time Control ◽  
Flowering Time Control ◽  
Exon 10

The flowering time control gene of various sugar beet plants has been studied. The BTC1 gene is a regulator for the suppressor (flowering time 1) and inducer (flowering time 2) genes of this physiological process. The F9/R9 primer pair was used for polymerase chain reaction; these primers are specific to the BTC1 gene region containing exon 9, as well as intron and exon 10. For the first time, nucleotide substitutions in exon 10 of BTC1 gene were identified in bolting sensitive samples (HF1 and BF1), which led to a change in the amino acid composition of the coded polypeptide chain. Based on the results of bioinformatic analysis, it can be assumed that certain nucleotide polymorphisms in the BTC1 gene may determine with a high probability the predisposition of sugar beet genotypes to early flowering. The use of the Geneious Prime tool for the analysis of the BTC1 gene sequences may allow the culling of genotypes prone to early flowering at early stages of selection. sugar beet, flowering gene, BTC1, genetic polymorphism, PCR, molecular genetic markers, selection

Proteomic and Bioinformatic Analysis of Trypanosoma cruzi Chemotherapy and Potential Drug Targets: New Pieces for an Old Puzzle

2014 ◽  
Vol 15 (3) ◽  
pp. 255-271 ◽  
Author(s):  
Rubem Sadok Menna-Barreto ◽  
Kele Belloze ◽  
Jonas Perales ◽  
Floriano Silva-Jr
Keyword(s):  
Trypanosoma Cruzi ◽  
Drug Targets ◽  
Bioinformatic Analysis ◽  
Potential Drug ◽  
Potential Drug Targets

Aggregation prone regions in antibody sequences raised against Vibrio cholerae: A bioinformatic approach

2020 ◽  
Vol 15 ◽  
Author(s):  
Zakia Akter ◽  
Anamul Haque ◽  
Md. Sabir Hossain ◽  
Firoz Ahmed ◽  
Md Asiful Islam
Keyword(s):  
Vibrio Cholerae ◽  
Binding Sites ◽  
Bioinformatic Analysis ◽  
Antigen Binding ◽  
Short Term ◽  
Protein Database ◽  
The Stability ◽  
Bioinformatic Approach ◽  
Self Aggregation ◽  
Complementarity Determining Region

Background: Cholera, a diarrheal illness causes millions of deaths worldwide due to large outbreaks. Monoclonal antibody used as therapeutic purposes of cholera are prone to be unstable due to various factors including self-aggregation. Objectives: In this bioinformatic analysis, we identified the aggregation prone regions (APRs) of different immunogens of antibody sequences (i.e., CTB, ZnM-CTB, ZnP-CTB, TcpA-CT-CTB, ZnM-TcpA-CT-CTB, ZnP-TcpA-CT-CTB, ZnM-TcpA, ZnP-TcpA, TcpA-CT-TcpA, ZnM-TcpA-CT-TcpA, ZnP-TcpA-CT-TcpA, Ogawa, Inaba and ZnM-Inaba) raised against Vibrio cholerae. Methods: To determine APRs in antibody sequences that were generated after immunizing Vibrio cholerae immunogens on Mus musculus, a total of 94 sequences were downloaded as FASTA format from a protein database and the algorithms such as Tango, Waltz, PASTA 2.0, and AGGRESCAN were followed to analyze probable APRs in all of the sequences. Results: A remarkably high number of regions in the monoclonal antibodies were identified to be APRs which could explain a cause of instability/short term protection of anticholera vaccine. Conclusion: To increase the stability, it would be interesting to eliminate the APR residues from the therapeutic antibodies in a such way that the antigen binding sites or the complementarity determining region loops involved in antigen recognition are not disrupted.

scholarly journals Novel immune subtypes of lung adenocarcinoma identified through bioinformatic analysis

FEBS Open Bio ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1921-1933
Author(s):  
Fang‐lu Qin ◽  
Zhan‐yu Xu ◽  
Li‐qiang Yuan ◽  
Wen‐jie Chen ◽  
Jiang‐bo Wei ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Bioinformatic Analysis

scholarly journals Isolating an active and inactive CACTA transposon from lettuce color mutants and characterizing their family

2021 ◽  
Author(s):  
Csanad Gurdon ◽  
Alexander Kozik ◽  
Rong Tao ◽  
Alexander Poulev ◽  
Isabel Armas ◽  
...  
Keyword(s):  
Anthocyanin Biosynthesis ◽  
Mobile Element ◽  
Bioinformatic Analysis ◽  
Relative Expression Level ◽  
Gene Coding ◽  
Genes Encoding ◽  
Key Enzyme ◽  
Natural Derivative ◽  
Dark Green ◽  
Transposon Insertions

Abstract Dietary flavonoids play an important role in human nutrition and health. Flavonoid biosynthesis genes have recently been identified in lettuce (Lactuca sativa); however, few mutants have been characterized. We now report the causative mutations in Green Super Lettuce (GSL), a natural light green mutant derived from red cultivar NAR; and GSL-Dark Green (GSL-DG), an olive-green natural derivative of GSL. GSL harbors CACTA 1 (LsC1), a 3.9-kb active nonautonomous CACTA superfamily transposon inserted in the 5′ untranslated region of anthocyanidin synthase (ANS), a gene coding for a key enzyme in anthocyanin biosynthesis. Both terminal inverted repeats (TIRs) of this transposon were intact, enabling somatic excision of the mobile element, which led to the restoration of ANS expression and the accumulation of red anthocyanins in sectors on otherwise green leaves. GSL-DG harbors CACTA 2 (LsC2), a 1.1-kb truncated copy of LsC1 that lacks one of the TIRs, rendering the transposon inactive. RNA-sequencing and reverse transcription quantitative PCR of NAR, GSL, and GSL-DG indicated the relative expression level of ANS was strongly influenced by the transposon insertions. Analysis of flavonoid content indicated leaf cyanidin levels correlated positively with ANS expression. Bioinformatic analysis of the cv Salinas lettuce reference genome led to the discovery and characterization of an LsC1 transposon family with a putative transposon copy number greater than 1,700. Homologs of tnpA and tnpD, the genes encoding two proteins necessary for activation of transposition of CACTA elements, were also identified in the lettuce genome.

Sign in / Sign up

Export Citation Format

Share Document