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Bioinformatics Tools and Software in Clinical Research
Published in Rishabha Malviya, Pramod Kumar Sharma, Sonali Sundram, Rajesh Kumar Dhanaraj, Balamurugan Balusamy, Bioinformatics Tools and Big Data Analytics for Patient Care, 2023
Deepika Bairagee, Nitu Singh, Neelam Jain, Urvashi Sharma
“ProtParam” is a computational device that calculates a variety of physiochemical parameters found inside a required protein. The gene models are identified using series positioning utilizing Gene Manufacturing Using Multiple Sources of Evidence (JIGSAW). In comparison to existing identification algorithms like Ensembl and UCSC’s well-known Gene track, it is expected to generate significantly higher accuracy. Single nucleotide polymorphisms (SNPs) will be utilized to identify the genetic disorders that are being studied. ORF stands for open-frame reading which is used for a variety of BI analysis, graphical viewing, and data management. The prokaryotic cost promoter (PPPT) is used to upstream the conventional promoter sequence. Virtual Footprint is a tool for studying the bacterial zone [35].
Nanobiosensors
Published in Vinod Kumar Khanna, Nanosensors, 2021
Xiao et al. (2003) reconstituted an apo-flavoenzyme, apo-glucose oxidase, on a 1.4-nm gold nanocrystal functionalized with the cofactor flavin adenine dinucleotide (FAD), a substance that must be associated with an enzyme for it to function. A flavoenzyme is an enzyme that possesses a flavin nucleotide as coenzyme; an apo-enzyme is the protein component of an enzyme, to which the coenzyme attaches to form an active enzyme. The electron transfer turnover rate of the reconstituted bioelectrocatalyst was ~5000 second−1. The AuNP acted as an electron relay or “electrical nanoplug” for the alignment of the enzyme on the conductive support and for the electrical cabling of its redox active center. Figure 9.3 shows the procedure of assembling the AuNP-reconstituted GOx electrode. For this purpose, AuNP (1.4-nm), with a single N-hydroxysuccinimide (NHS)-functionalization was reacted with N-6-(2-aminoethyl)-FAD (1) to yield the FAD-functionalized AuNP. FAD (1) is the structural gene for flavin adenine dinucleotide synthetase of a species of yeast called Saccharomyces cerevisiae. FAD1 gene has 1 transcript (RNA copy) and 305 orthologues (homologous gene sequenes); it is a member of 1 Ensembl protein family. Steps in the assembly of AuNP-reconstituted GOx electrode. (Xiao, Y., et al., Science, 299, 1877, 2003.)
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Published in Michael Hehenberger, Zhi Xia, Huanming Yang, Our Animal Connection, 2020
Michael Hehenberger, Zhi Xia, Huanming Yang
As a model biological system, the zebrafish genome has attracted the interest of several leading research institutions. The Sanger Institute146 (UK) started zebrafish genome sequencing in 2001, and the full genome sequence of the Tübingen147reference strain is available at the NIH National Center for Biotechnology Information (NCBI)’s Zebrafish Genome Page. The zebrafish reference genome sequence is annotated as part of the Ensembl project, and is maintained by NCBI’s Genome Reference Consortium.148 In 2009, the Institute of Genomics and Integrative Biology in Delhi, India, announced the sequencing of the genome of a wild zebrafish strain, containing an estimated 1.7 billion base pairs.149 Comparative analysis with the zebrafish reference genome revealed a significant number of insertion deletion variations. Finally, the zebrafish reference genome sequence of 1.4 GB and over 26,000 protein coding genes was published in 2013.150
Spawning time in adult polar cod (Boreogadus saida) altered by crude oil exposure, independent of food availability
Published in Journal of Toxicology and Environmental Health, Part A, 2023
Leah C. Strople, Ireen Vieweg, Fekadu Yadetie, Derrick Kwame Odei, Anders Thorsen, Odd André Karlsen, Anders Goksøyr, Lisbet Sørensen, Antonio Sarno, Bjørn Henrik Hansen, Marianne Frantzen, Øyvind J. Hansen, Velmurugu Puvanendran, Jasmine Nahrgang
Five high-feed control and five high-feed-oil-exposed female tRNA samples from day 47 were sent for RNA sequencing (RNA-seq) by Novogene (Novogene – Genome sequencing). All female RNA samples from the high-food treatment at the day 47 sampling time-point were analyzed using Agilent 2100 Bioanalyzer. Samples with an RNA intergrity value (RIN) value above seven were chosen for RNA-seq. If more than five samples had a sufficient RIN value, the samples with the highest values were selected first. The RNA-seq data were analyzed as described by Yadetie et al. (2018) using the recently developed RASflow pipeline (Zhang and Jonassen 2020) and the Atlantic cod reference genome (Ensembl, https://www.ensembl.org/index.html). False discovery rate (FDR) < 0.05 and fold change 2.00 (for up-regulated) or 0.5 (for downregulated) were considered differentially expressed. Mapping polar cod genes to the Atlantic cod orthologs facilitated the extraction of human (Homo sapiens) and zebrafish (Danio rerio) orthologs from the Ensembl database for pathway analysis as described before (Yadetie et al. 2018). Pathway and network analysis were conducted using the Cytoscape network visualization and analysis tools with Cluego application (Bindea et al. 2009; Shannon et al. 2003).
Association of Genetic Polymorphisms of TERT with Telomere Length in Coke Oven Emissions-Exposed Workers
Published in International Journal of Environmental Health Research, 2022
Mengqing Yan, Shuai Cheng, Sihua Wang, Xiaoran Duan, Acquaye Reuben Mensah, Lei Li, Yuhong Zhang, Guoyu Li, Junfeng Zhao, Feifei Feng, Xiaoshan Zhou, Yongjun Wu, Yongli Yang, Wei Wang
This research adopts the principle of focusing on important functional SNP sites and supplemented by susceptible SNP sites, which is innovative and comprehensive in research. Mainly through: (1) Functional SNP: Find the research gene promoter 5’near gene),5’UTR, exon (missense, synonymous), functional SNP sites in the3’UTR region (MAF >.05, according to Hapmap or 1000 Genomes database). Next, search for SNP sites in the Splice region variant and Upstream gene variant regions of the gene in Ensembl (http://asia.ensembl.org/index.html/), and add them to the functional SNP sites. (2) Susceptible SNP: Search the research literature of candidate gene-related SNP loci in NCBI PubMed and Google Scholar databases, and screen out susceptible SNP loci. After screening, the sites with lower allele frequencies are eliminated according to the number of samples in the study.
GPR61 methylation in cord blood: a potential target of prenatal exposure to air pollutants
Published in International Journal of Environmental Health Research, 2022
Feifei Feng, Li Huang, Guoyu Zhou, Jia Wang, Ruiqin Zhang, Zhiyuan Li, Yawei Zhang, Yue Ba
We further assessed the methylation status of the GPR61 gene in 568 mother-infant pairs by quantitative methylation-specific PCR (QMS-PCR) (MX3000, STARTAGENE, USA). The promoter sequences of the GPR61 gene were searched using UCSC/Ensembl (http://genome.ucsc,edu/), and primer sequences were then designed using the methylation primer design software MethPrimer (http://www.urogene.org/cgi-bin/methprimer/methprimer.cgi). Two pairs of PCR primers of the GPR61 gene were used to conduct QMS-PCR (methylated specific primers: forward, 5ʹ-TGT GTT AGG TTA TTG GAG AGG TTAC-3ʹ; reverse, 5ʹ-CCC TAT TTT ATA AAT AAA AAA CCGAA-3ʹ; unmethylated specific primers: forward, 5ʹ-TTG TGT TAG GTT ATT GGA GAG GTTAT-3ʹ; reverse, 5ʹ-CCC TAT TTT ATA AAT AAA AAA CCAAA-3ʹ). QMS-PCR was carried out in a 15-μL reaction mixture using 7.5 μL of 2× Power SYBR Green PCR Master Mix, 2 μL of primer with a concentration of 1.25 μmol/L each and 60 ng of bisulfite-treated DNA template. The QMS-PCR conditions included denaturation at 95°C for 10 min, followed by 40 cycles of denaturation at 95°C for 15 s, annealing at 56°C for 30 s, and extension at 72°C for 30 s. The rate of DNA methylation was calculated using the reference method (Lu et al. 2007).