China 
Africa 
Explore chapters and articles related to this topic
Current Status and Future Prospects
Published in Stephen P. Slocombe, John R. Benemann, Microalgal Production, 2017
With the availability of inexpensive next-generation sequencing and ever-increasing improvements in computer algorithms for sequence assembly and annotation, we are witnessing a rapid rise in the number of algal genomes being sequenced (Tirichine and Bowler 2011). A quick Internet survey identifies nearly 30 complete microalgal genomes at the time of writing, although many more are known to be in progress or have not been made publicly available. For several of the model species such as C. reinhardtii and P. tricornutum, the genomic data continue to be refined and improved (Blaby et al. 2014) and are being complemented with extensive transcript, proteomic and metabolite data gathered under a range of physiological conditions. To make these big data accessible to researchers, online resources such as the Algal Functional Annotation Tool (pathways.mcdb.ucla.edu), DiatomCyc (www.diatomcyc.org), and the Nannochloropsis oceanica genome browser (benning-linux.bch.msu.edu) have been established. Importantly, the integration of the omics data, together with flux balance analysis, is allowing the development of dynamic models of algal cell biology (e.g., Boyle and Morgan 2009; Dal’Molin et al. 2011; Fabris et al. 2014). Such models serve to underpin and guide genetic engineering strategies and are catalyzing efforts to further develop and refine the transformation tools (Schmidt et al. 2010).
In Silico Approach to Cancer Therapy
Published in Anjana Pandey, Saumya Srivastava, Recent Advances in Cancer Diagnostics and Therapy, 2022
Anjana Pandey, Saumya Srivastava
The Reactome scheme is a curated resource of essential procedures and reactions in human biology (Vastrik et al., 2007; http://reactome.org). Other multiple databases cross-reference this database’s database, e.g., sequence databases available at NCBI, UniProt, Ensembl, the UCSC Genome Browser, KEGG, PubMed, and GO. It is a free online tool and its software is open source. The Reactome database consists of several cellular pathways (Joshi-Tope et al., 2005) with different signaling pathways associated with cancer.
Biochemical and transcriptional analyses of cadmium-induced mitochondrial dysfunction and oxidative stress in human osteoblasts
Published in Journal of Toxicology and Environmental Health, Part A, 2018
Cristina Monteiro, José Miguel P. Ferreira de Oliveira, Francisco Pinho, Verónica Bastos, Helena Oliveira, Francisco Peixoto, Conceição Santos
RNA extraction and qPCR-gene expression was analyzed. The forward and reverse primers for the selected genes were designed using Primer3 (Rozen and Skaletsky 2000) and are listed in Table 1. Primer specificity was confirmed using the In-Silico PCR UCSC Genome Browser (Kent et al. 2002). Cells (1.5 × 106) were plated in 100 mm dishes and treated with 50-µM Cd for 24 h. Then cells were washed in PBS pH 7.2, and 1-mL TRIzol® reagent (Life Technologies, Saint Louis, MO, USA) was added for cell lysis, and RNA extraction and preservation (Ferreira De Oliveira et al. 2014). cDNA synthesis was carried out after incubation of 2-μg total RNA with DNase I (Sigma-Aldrich, St. Louis, MO, USA). RNA was reverse-transcribed using the Omniscript RT Kit (Ref 205110, Qiagen, Hilden, Germany) and final qPCR reactions took place according to Ferreira De Oliveira et al. (2014). Gene expression relative to controls, and normalized with the GAPDH reference gene, was calculated (Pfaffl 2001).
Evidence of p-nitrophenol Biodegradation and Study of Genomic Attributes from a Newly Isolated Aquatic Bacterium Pseudomonas Asiatica Strain PNPG3
Published in Soil and Sediment Contamination: An International Journal, 2022
Sk Aftabul Alam, Pradipta Saha
PATRIC v- 3.6.12 (https://www.patricbrc.org/) platforms were used to confirm the existence of PNP degrading gene clusters/proteins within the genome of strain PNPG3. The complete sequence of the p-nitrophenol catabolic gene cluster from Pseudomonas putida strain DLL-E4 (FJ376608) and Pseudomonas strain WBC-3 (EF577044) were retrieved from the NCBI database (http://www.ncbi.nlm.nih.gov) in fasta alignment format. After that BLAST-N was performed by PATRIC against the selected genome of PNPG3. Annotated PNP degrading genes were visualized by J browse of Genome browser of Patric. Each of the deduced proteins was examined for sequence similarity with the protein sequences available at NCBI, GenBank database using BLAST_N and BLAST_P options available at NCBI.
Role of DNA methylation regulation of miR-130b expression in human lung cancer using bioinformatics analysis
Published in Journal of Toxicology and Environmental Health, Part A, 2019
Jin Wang, Xiao-Fan Yu, Nan OUYang, Qiulin Luo, Jian Tong, Tao Chen, Jianxiang Li
Based upon the UCSC genome browser, seven methylation probes were identified targeting the promoter region of miR-130b encoding genes (Supplementary Figure 1). As presented in Table 1, Pearson correlation analysis indicated that miR-130b expression exhibited a significant inverse correlation with four probe methylation values in both LUAD and LUSC, including cg2473781, cg1673244, cg4282607, and cg6974014.