Gene fragmentation

Efficient presentation of mutant peptide fragments by the human leukocyte antigen class I (HLA-I) genes is necessary for immune-mediated killing of cancer cells. According to recent reports, patient HLA-I genotypes can impact the efficacy of cancer immunotherapy, and the somatic loss of HLA-I heterozygosity has been established as a factor in immune evasion.

12p vicwell 29-02-2024 3 1   Download

This study aimed to develop a method using DNA barcode fragments to identify the hybrid Eucalyptus UP99 and UP95. The total genomic DNA was extracted from leaf samples of UP99 and UP95 and was used to amplify the DNA barcodes (matK, rbcL, trnH-psbA, ITS and ITS2) by PCR.

11p vikissinger 21-12-2023 6 1   Download

Part 1 book "Environmental microbiology - Methods and protocols" includes content: Methods for isolation and cultivation of filamentous fungi, rapid extraction of PCR-competent DNA from recalcitrant environmental samples, quantitative PCR for detection of mRNA and gDNA in environmental isolates, analysis of community dynamics in environmental samples using denaturing gradient gel electrophoresis, terminal restriction fragment length polymorphism (T-RFLP) profiling of bacterial 16S rRNA genes,... and other contents.

134p oursky10 04-12-2023 4 2   Download

Metabolic reprogramming is one of hallmarks of cancer progression and is of great importance for the tumor microenvironment (TME). As an abundant metabolite, lactate has been found to play a critical role in cancer development and immunosuppression of TME. However, the potential role of lactate metabolism-related genes in endometrial cancer (EC) remains obscure.

17p visharma 20-10-2023 3 2   Download

The new species is clearly distinguished from its congener Weygoldtia davidovi (Fage, 1946) by having more articles in the tibia and tarsus of leg I. A fragment of the cytochrome c oxidase subunit I (COI) gene is also provided for the new species. The K2P genetic distance of the COI between the new species and W. davidovi is 20%, and phylogenetic analysis also supported the new species.

10p vicaptainmarvel 21-04-2023 4 2   Download

Rosaceae is a family containing many economically important fruit and ornamental species. Although fluorescence in situ hybridization (FISH)-based physical mapping of plant genomes is a valuable tool for map-based cloning, comparative genomics and evolutionary studies, no studies using high resolution physical mapping have been performed in this family.

10p vinarcissa 21-03-2023 2 1   Download

Transfer ribonucleic acids (tRNAs) serve not only as amino acid carriers during translation but also as a template for the biogenesis of short fragments that can regulate gene expression. Despite recent progress in the function of tRNA-derived fragments (tRFs), their intracellular localization, protein partners, and role in regulating translation are not well understood. We used synthetic tRFs to investigate their localization and function in Drosophila S2 cells.

11p lyhuyenthu 31-01-2023 8 2   Download

Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure.

12p vihagrid 30-01-2023 7 3   Download

Constraints in migratory capabilities, such as the disruption of gene flow and genetic connectivity caused by habitat fragmentation, are known to affect genetic diversity and the long-term persistence of populations. Although negative population trends due to ongoing forest loss are widespread, the consequence of habitat fragmentation on genetic diversity, gene flow and genetic structure has rarely been investigated in Bornean small mammals.

13p vihagrid 30-01-2023 8 3   Download

Kurniwan et al. (2010) specified the distribution of F. cancrivora to the south of the Isthmus of Kra and a large area in the North of the Isthmus of Kra, including Vietnam, is the distribution range of F. moodiei, but the samples analyzed in that study did not include samples collected from Vietnam. Based on the results of morphological and genetic analyses on two mitochondrial gene fragments (16S and Cytb) of populations of Fejervarya moodiei and F. cacrivora, this study confirmed that the Northern Crab-eating Frog F. moodiei distributed in Vietnam.

11p vikoenigsegg 26-09-2022 21 3   Download

Gut microbes significantly contribute to nutrient digestion and absorption, intestinal health and immunity, and are essential for the survival and environmental adaptation of wild animals. However, there are few studies on the gut microbiota of captive and wild North China leopard (Panthera pardus japonensis).

11p vigandhi 23-02-2022 13 1   Download

Most gene prediction methods detect coding sequences from transcriptome assemblies in the absence of closely related reference genomes. Such methods are of limited application due to high transcript fragmentation and extensive assembly errors, which may lead to redundant or false coding sequence predictions.

12p vialfrednobel 29-01-2022 13 0   Download

Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information.

7p viaristotle 29-01-2022 13 0   Download

We investigated the effect of endoplasmic reticulum (ER) protein 29 (ERp29) on thyroglobulin (Tg) secretion and its negative regulation by microRNAs (miRNAs). ERp29 overexpression promoted Tg secretion from thyrocytes of PCCL3 cells via activation of ER stress sensors, including activation of transcription factor 6 fragmentation, XBP1 mRNA splicing by inositol-requiring enzyme 1, and phosphorylation of eukaryotic initiation factor 2 alpha as downstream actions of RNA-dependent protein kinase-like ER kinase.

6p dolomite36 30-12-2021 10 0   Download

In this study, the DNA fragment encoding for the C-terminus domain of the AopB from Aeromonas hydrophila AH-1 was cloned into pET-M expression vector and expressed in Escherichia coli BL21 (DE3) host cells. The recombinant AopB-C-terminus domain was successfully purified using immobilized nickel affinity chromatography as a soluble form. Crosslinking analysis among AopB-C-terminus molecules in solution showed that this domain existed as a mixture of tetramer, trimer, dimer, and monomer forms.

6p guitaracoustic02 08-12-2021 18 3   Download

Soybean homeobox gene GmSBH1 has previously been proven to be involved in response to high temperature and humidity (HTH) stress. To investigate its expression patterns and active cis-elements, a 2040-bp 5’-upstream genomic DNA fragment of GmSBH1, named GmSBH1P, was isolated by PCR walking and characterized. Sequence analysis revealed that the fragment contains a series of cis-acting elements related to stress responses.

13p tudichquannguyet 29-11-2021 9 1   Download

The early phases of Diaporthe helianthi pathogenesis on sunflower are characterized by the production of phytotoxins that may play a role in host colonisation. In previous studies, phytotoxins of a polyketidic nature were isolated and purified from culture filtrates of virulent strains of D. helianthi isolated from sunflower. A highly aggressive isolate (7/96) from France contained a gene fragment of a putative nonaketide synthase (lovB) which was conserved in a virulent D. helianthi population.

13p vilarryellison 29-10-2021 11 1   Download

Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions.

15p vibeauty 23-10-2021 11 0   Download

Obtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene regions. Genomes are widely transcribed, generating messenger and non-coding RNAs. These widespread transcripts can be used to scaffold genomes and complete transcribed regions.

13p vibeauty 23-10-2021 9 0   Download

Pasteurella multocida (P. multocida) is a widespread opportunistic pathogen that infects human and various animals. Genomic Islands (GIs) are one of the most important mobile components that quickly help bacteria acquire large fragments of foreign genes. However, the effects of GIs on P. multocida are unknown in the evolution of bacterial populations.

11p vigiselle2711 30-08-2021 10 1   Download