Genomic analysis

Starch metabolism is known to be an important pathway in the growth and development of plants. This study was conducted to investigate the genome-wide identification and structural analysis of genes encoding uridine diphosphate glucose pyrophosphorylase (UGPase), a key enzyme in starch synthesis in cassava, and to analyze the expression profiles of these genes based on publicly available RNA-seq data.

6p vibecca 01-10-2024 0 0   Download

The objective of this study was to analyze the features of FtsZ proteins in the Bacillus and Lactococcus genus groups. By exploring the available genomes, we identified and characterized FtsZ proteins in 19 Bacillus and 22 Lactococcus species.

12p vibecca 01-10-2024 2 2   Download

Microsatellite (MS) is a genetic marker widely used in the studies of pedigree, individual identification, gene mapping, and genetic diversity within and between populations. The genetic diversity of the indigenous Ven dog breed, along with two imported dog breeds, the Berger and Poodle dogs raised in Vietnam, was analyzed based on seven microsatellite markers.

8p viling 27-09-2024 6 2   Download

In the present study, out of 22 Streptomyces strains, Streptomyces parvulus VCCM 22513 produced the highest chitinase activity. Time courses of incubation revealed that the maximum chitinase (0.91 ± 0.04 U/mL) of this strain was observed after 96 hours in the yeast extract salts medium supplemented with 10.0 g/L colloidal chitin.

10p dianmotminh02 03-05-2024 13 1   Download

Alternative polyadenylation (APA) affects most mammalian genes. The genome-wide investigation of APA has been hampered by an inability to reliably profile it using conventional RNA-seq. We describe ‘Quantification of APA’ (QAPA), a method that infers APA from conventional RNA-seq data.

18p vimichaelfaraday 25-03-2022 17 1   Download

Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this process at single-cell resolution remain elusive.

20p vimichaelfaraday 25-03-2022 20 1   Download

Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method that addresses these challenges, and enables streamlined analysis across multiple conditions taking into account biological variability.

11p vimichaelfaraday 25-03-2022 20 1   Download

Compared to RNA-sequencing transcript differential analysis, gene-level differential expression analysis is more robust and experimentally actionable. However, the use of gene counts for statistical analysis can mask transcript-level dynamics. We demonstrate that ‘analysis first, aggregation second,’ where the p values derived from transcript analysis are aggregated to obtain gene-level results, increase sensitivity and accuracy.

11p vimichaelfaraday 25-03-2022 13 3   Download

Single-cell analysis is a powerful tool for dissecting the cellular composition within a tissue or organ. However, it remains difficult to detect rare and common cell types at the same time. Here, we present a new computational method, GiniClust2, to overcome this challenge.

13p vimichaelfaraday 25-03-2022 12 1   Download

S100A2, a member of the S100 protein family, is abnormally expressed and plays a vital role in multiple cancers. However, little is known about the clinical significance of S100A2 in endometrial carcinoma. Methods: Clinicopathological data were obtained from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Gene Expression Omnibus (GEO), and Clinical Proteomic Tumor Analysis Consortium (CPTAC).

11p vielonmusk 21-01-2022 24 0   Download

Circulating cell-free DNA (cfDNA) in the plasma of cancer patients contains cell-free tumour DNA (ctDNA) derived from tumour cells and it has been widely recognized as a non-invasive source of tumour DNA for diagnosis and prognosis of cancer.

13p vielonmusk 21-01-2022 20 0   Download

Polyhydroxyalkanoate (PHA) is stored as an important carbon and energy source in bacterial cells. For biomedical applications, gram-positive bacteria can be better sources of PHAs, since they lack outer membrane lipopolysaccharide. Although gram-positive Streptomyces coelicolor A3(2) has been indicated as a high potential PHA producer, phaC gene that encodes the key enzyme PHA synthase in the metabolic pathway is not determined in its genome.

12p thiencuuchu 27-11-2021 18 2   Download

Research purpose: Determine the composition, structure of mitochondrial genome, compare the difference in sequence, identify specific genetic characteristics of the six indigenous pig breeds, thereby contributing to the database to identification and conservation.

27p extraenglish 24-05-2021 22 4   Download

Collecting complete data of mitochondrial genome of 6 indigenous pig breeds in Vietnam (I, Mong Cai, Muong Lay, Huong, Muong Khuong and Ha Lang pigs) and deposited on the Genebank; determine the composition, structure of mitochondrial genome, compare the difference in sequence, identify specific genetic characteristics of the six indigenous pig breeds, thereby contributing to the database to identification and conservation.

27p capheviahe26 25-01-2021 14 4   Download

The basic helix-loop-helix transcription factors play important roles in diverse cellular and molecular processes. Comparative functional genomics can provide powerful approaches to draw inferences about gene function and evolution among species.

21p vishikamaru2711 29-04-2020 15 3   Download

Photosynthesis is able to convert solar energy into chemical energy in the form of biomass, but the efficiency of photosynthetic solar energy conversion is low. Chlorophyll fluorescence measurements are rapid, nondestructive, and can provide a wealth of information about the efficiencies of the photosynthetic light reaction processes.

19p vishikamaru2711 29-04-2020 13 1   Download

The glycogen synthase kinase 3/shaggy kinase (GSK3) is a serine/threonine kinase with important roles in animals. Although GSK3 genes have been studied for more than 30 years, plant GSK genes have been studied only since the last decade.

21p vishikamaru2711 29-04-2020 18 0   Download

CRISPR/Cas9 technology is one of the most powerful and useful tools for genome editing in various living organisms. In higher plants, the system has been widely exploited not only for basic research, such as gene functional analysis, but also for applied research such as crop breeding.

9p vishikamaru2711 29-04-2020 12 0   Download

The auxin response factor (ARF) gene family is involved in plant development and hormone regulation. Although the ARF gene family has been studied in some plant species, its structural features, molecular evolution, and expression profiling in Brachypodium distachyon L. are still not clear.

15p vishikamaru2711 29-04-2020 31 2   Download

Abiotic stress severely influences plant growth and development. MYB transcription factors (TFs), which compose one of the largest TF families, play an important role in abiotic stress responses.

18p vishikamaru2711 29-04-2020 13 1   Download