19 research outputs found
Genetic aberration analysis in thai colorectal adenoma and early-stage adenocarcinoma patients by whole-exome sequencing
Colorectal adenomas are precursor lesions of colorectal adenocarcinoma. The transition from adenoma to carcinoma in patients with colorectal cancer (CRC) has been associated with an accumulation of genetic aberrations. However, criteria that can screen adenoma progression to adenocarcinoma are still lacking. This present study is the first attempt to identify genetic aberrations, such as the somatic mutations, copy number variations (CNVs), and high-frequency mutated genes, found in Thai patients. In this study, we identified the genomic abnormality of two sample groups. In the first group, five cases matched normal-colorectal adenoma-colorectal adenocarcinoma. In the second group, six cases matched normal-colorectal adenomas. For both groups, whole-exome sequencing was performed. We compared the genetic aberration of the two sample groups. In both normal tissues compared with colorectal adenoma and colorectal adenocarcinoma analyses, somatic mutations were observed in the tumor suppressor gene APC (Adenomatous polyposis coli) in eight out of ten patients. In the group of normal tissue comparison with colorectal adenoma tissue, somatic mutations were also detected in Catenin Beta 1 (CTNNB1), Family With Sequence Similarity 123B (FAM123B), F-Box And WD Repeat Domain Containing 7 (FBXW7), Sex-Determining Region Y-Box 9 (SOX9), Low-Density Lipoprotein Receptor-Related Protein 5 (LRP5), Frizzled Class Receptor 10 (FZD10), and AT-Rich Interaction Domain 1A (ARID1A) genes, which are involved in the Wingless-related integration site (Wnt) signaling pathway. In the normal tissue comparison with colorectal adenocarcinoma tissue, Kirsten retrovirus-associated DNA sequences (KRAS), Tumor Protein 53 (TP53), and Ataxia-Telangiectasia Mutated (ATM) genes are found in the receptor tyrosine kinase-RAS (RTK–RAS) signaling pathway and p53 signaling pathway, respectively. These results suggest that APC and TP53 may act as a potential screening marker for colorectal adenoma and early-stage CRC. This preliminary study may help identify patients with adenoma and early-stage CRC and may aid in establishing prevention and surveillance strategies to reduce the incidence of CRC
Genomics of alkaliphiles
Alkalinicity presents a challenge for life due to a “reversed” proton gradient that is unfavourable to many bioenergetic processes across the membranes of microorganisms. Despite this, many bacteria, archaea, and eukaryotes, collectively termed alkaliphiles, are adapted to life in alkaline ecosystems and are of great scientific and biotechnological interest due to their niche specialization and ability to produce highly stable enzymes. Advances in next-generation sequencing technologies have propelled not only the genomic characterization of many alkaliphilic microorganisms that have been isolated from nature alkaline sources but also our understanding of the functional relationships between different taxa in microbial communities living in these ecosystems. In this review, we discuss the genetics and molecular biology of alkaliphiles from an “omics” point of view, focusing on how metagenomics and transcriptomics have contributed to our understanding of these extremophiles.https://link.springer.com/bookseries/10hj2021BiochemistryGeneticsMicrobiology and Plant Patholog
Promoter analysis of Mucor rouxii delta9-desaturase: its implication for transcriptional regulation in Saccharomyces cerevisiae.
Mucor rouxii Δ9-desaturase gene is transcriptionally regulated during cell growth and by low temperature
Unsaturated fatty acids are essential lipid components
of Mucor rouxii. g-Linolenic acid (GLA) is synthesized
via the desaturase enzymes: D9-desaturase
catalyzes mono-unsaturated fatty acids that are utilized
as substrate for GLA biosynthesis. We cloned and
characterized a M. rouxii gene highly homologous to
D9-desaturase genes. This sequence encodes for a protein
of 452 amino acids and contains two introns of 60
and 61 nucleotides. D9-desaturase of M. rouxii is expressed
during cell growth when cells are subjected to
temperature shifts. At 30°C, the mRNA level of late log
phase is about 6.4-fold higher than that of early log
phase. A shift from 30 to 15°C induced transcription of
D9-desaturase gene in both early and late log phases.
However, the pattern of increased transcription by
cold induction varied depending on growth conditions:
transcription of late log phase is higher than
that of early log phase. These results indicate that cell
growth and low temperature influence the expression
of D9-desaturase gene and fatty acid composition of M.
rouxii
SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1
Probing the mechanism of a cyanobacterial \u3949 fatty acid desaturase from Spirulina platensis C1 (Arthrospira sp. PCC 9438)
The initial and rate determining step in the mechanism of fatty acid desaturases has been proposed to be breakage of one of the C\ue5f8H bonds at the site of the incipient double bond. This has been investigated and supported for a number of eukaryotic fatty acid desaturases through the use of kinetic isotope effect experiments with deuterated substrates. In order to probe the reaction catalyzed by the cyanobacterial \u3949 desaturase and compare it to the eukaryotic desaturases, the desC gene of Spirulina platensis, strain C1 (Arthrospira sp. PCC 9438) was expressed in a desaturase mutant of baker's yeast. Kinetic isotope effects were performed by culturing yeast transformants with deuterated thia-substituted stearic acids. A large kinetic isotope effect was found for the 9 position, in qualitative agreement with results from eukaryotic desaturases.NRC publication: Ye