Animal Gene最新文献

The cis-regulatory modules are non-coding DNA regions responsible for controlling gene transcription and being involved in the anatomical and embryonic development of animal species. This study aimed to perform a prediction analysis of cis-regulatory modules in spliced genes associated, commonly, with ribeye area (REA) and intramuscular fat (IF) of Nelore cattle. For this, JuncBASE v.0.9 (Junction-Based Analysis of Splicing Events) software was used to identify and classify exon-centered alternative splicing events in the group of animals selected for REA and IF. The prediction of transcription factors and cis-regulatory modules was performed for the genes found using iRegulon v.1.3. The prediction analysis exhibited 45 cis-regulatory modules, of which module 11 had the highest number (N = 9) of binding sites shared commonly by 11 spliced genes and five transcription factors from the MEF2 family. These modules could potentially regulate spliced exons and, thus, contribute to the production of isoforms, which may be involved in essential pathways and biological processes involved in the evaluated animals muscular development and lipid metabolism.

Egg production is the most important commercial attribute of layer hens since it has a direct impact on the efficiency of the poultry industry. This research aimed to study the age at first egg (AFE), egg number (EN), egg quality, and some plasma hormones within the period from the start of laying eggs until day 90 of production in three strains of laying hens (Lohman Brown (LB), Golden Sabahia (GS)) and White Leghorn (WL) as the reference breed for egg production. In addition, a time series expression profile of growth differentiation factor 9 (GDF9) gene was investigated to get a better understanding of the genetic basis of egg production. The LB laying hens recorded the highest improved estimates of egg production and egg quality traits. Further, GDF9 was highly expressed in LB tissues (magnum and isthmus) compared to WL except in the uterus. These results suggest that there is a direct relationship between number of eggs produced, quality of eggs and the expression level of the GDF9 gene in the LB strains. Besides, the LB strain is superior with candidate productive traits, therefore they can be used as proven ancestors to improve laying hens.

Insulin-like Growth Factor 2 (IGF2) plays important roles in stimulating cell proliferation, differentiation and migration culminating its effects as a modulator of juvenile growth in animals. Although the gene that codes for IGF2 (IGF2) has been investigated as a candidate gene in several livestock species, there is no information on polymorphisms in IGF2 in guinea fowls (gIGF2), an important indigenous poultry species from West Africa. Therefore, this study sought to identify the Single Nucleotide Polymorphisms (SNPs) in three populations of indigenous guinea fowls in northern Ghana. Target genomic regions in gIGF2 were amplified and sequenced from 84 indigenous guinea fowls from Upper East Region (n = 17), former Northern Region (n = 22) and Upper West Region (n = 45) of Ghana together with domesticated French variety (n = 3). The sequences were aligned with the reference genomic sequence (domesticated French variety) of chromosome 6 (GenBank accession no., NC_034414.1) to identify SNPs. Statistical associations among the genotypes arising from the SNPs and juvenile growth traits were estimated using linear models. Two novel SNPs were identified in gIGF2 among the indigenous guinea fowls. An insertion of a Guanine (G) within a poly G motif of the intron following the third exon at the 13,955,730 bp location was identified in the majority (84.5%) of indigenous guinea fowls, while the wild type allele was observed in the minority of indigenous guinea fowls and in the domesticated French variety sampled. Also, a biallelic transition arising from the substitution of G by Adenine (A) at position 13,956,496 bp (13,956,496 G > A) located on the fourth exon, which codes for most of the extension peptide of prepro IGF2, was observed in the minority (11.9%) of indigenous guinea fowls. No significant associations among the genotypes arising from the two SNPs, with body weights and weekly growth rates, were identified.

In order to study the mechanism of early and late neuropathic pain, Ribonucleic acid sequencing (RNA-seq) technique was used to analyze the dorsal root ganglion (DRG) transcriptome of rat induced by spinal nerve ligation (SNL). It was found that most of the reactions leading to neuropathic pain at dorsal root ganglion, such as pro-inflammatory response and immunity, occurred in the early phase.378 genes are up-regulated and 42 genes are down-regulated in the early phase, while in the late phase, there are 27 up-regulated genes and 23 down-regulated genes. Four new pain related genes are found: Cd8a, Bub1b, Ccna2 and Cdk1. From the analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene Ontology (GO) functions enriched by differentially expressed genes (DEGs), dorsal root ganglion should carry out immunities, pro-inflammations and related compensatory regulation in response to peripheral nerve injury in the early phase. The late phase is characterized by maintaining long-term or chronic inflammation.

Antimicrobial peptides (AMPs) are considered a promising therapeutic strategy because of their high potential for fighting against antibiotic-resistant pathogens. Scorpion venom is a rich resource of AMPs because of their biodiversity. Accordingly, we aimed to employ a bioinformatics-based approach to search for new putative AMPs from available omics datasets. The amino acid sequence of the peptide Ctriporin was used as query for a blast search in the UniProt and NCBI databases, resulting in the identification of 14 homologous peptides from scorpion venom. To predict antimicrobial activity, all sequences were analyzed using various machine learning-based algorithms on the Collection of Anti-Microbial Peptides (CAMP_R3) database. Furthermore, the online tools Antifp, AVPpred, and iACP were used to predict the antifungal, antiviral, and anticancer activity, respectively. The physicochemical properties were also evaluated by online tools and compared with Antimicrobial Peptide Database Calculator and Predictor (APD3). Finally, the three-dimensional structure modeling of the peptides Ctriporin, Ctri10036, Ctri9610, and Ctri10033 was performed using I-TASSER and PEP-FOLD 3.5. Our in silico analysis led to the identification of three new peptides with potential antimicrobial properties from the venom of the scorpion Chaerilus tricostatus, which can be suitable candidates for further experimental validation studies.

The consumer market has significantly increased in the search for nutritional and probiotic formulated products. In the present study, probiotic characterization parameters have been evaluated for the bacteria isolated from fermented millet porridge or ragi koozh and jalebi batter. Initially, 30 colonies were randomly picked and screened for lactic acid production. Lactic acid-producing 13 isolates showing gram-positive cell wall, non-spore-forming capacity and catalase-negative strains were subjected to probiotic characterization. Among 13 isolates, 2 isolates S9 and S13 exhibited good tolerance towards in-vitro characterization parameters such as acid and bile tolerance, adhesion to hydrocarbons, autoaggregation, co-aggregation, antibacterial activity, and safety measures. The potential probiotic strains S9 and S13 were identified by molecular methods, and evolutionary imprints and submitted to GenBank as Weisella cibaria and Enterococcus lactis. Results showed the efficacy of probiotic characteristics of isolates S9 and S13 which can be used for the formulation of probiotic products.

The incidence of Extended Spectrum β-Lactamases (ESBL) in Escherichia coli has generated trepidations because dissemination of ESBL genes constitutes risk to public health. The current study aims to determine antibiotic susceptibility and carriage of ESBL bla_SHV, bla_TEM and bla_CTX-M by E. coli isolated from apparently healthy dogs in Ibadan conurbation, Nigeria.

Freshly passed fecal samples (n = 60) were collected from dogs into sterile sample bottles and processed to isolate E. coli following standard methods. Isolated E. coli were confirmed through Polymerase Chain Reaction (PCR) by means of uidA and tested against 10 antibiotics via Kirby-Bauer disc diffusion technique. Escherichia coli showing phenotypic ESBL production were selected for ESBL bla_SHV, bla_TEM bla_CTX-M genotyping using multiplex PCR.

Of the 31 E. coli isolates confirmed, 10 (32.3%), 9 (29.0%) and 7 (22.6%) were resistant to ampicillin, tetracycline and trimethoprim/sulfamethoxazole, respectively while 8 (25.8%) were multidrug resistant (MDR). Escherichia coli isolates (n = 2/8) that were MDR harboured at least one of bla_SHV, bla_TEM and bla_CTX-M genes while another isolate (n = 1) simultaneously possessed the three ESBL genes. Apparently healthy dogs are likely reservoirs of ESBL- E. coli that can spread to pet owners through close contact with their companion animals.

North East (NE) India, referred as Biodiversity Hot Spot, is the natural habitat of a large variety of ornamental fishes. Among all the ornamental fishes available in NE India, Loaches are of great importance in the ornamental fish trade. In this study, 38 specimens from ten loaches species of North-eastern India are characterized using three mitochondrial genes i.e. cytochrome c oxidase subunit I (COI), 16S rRNA and cytochrome b (Cyt b). The average genetic distance values for all the three mitochondrial genes have increased gradually when moving up from species to genus to family levels. Among the genes, Cyt b gene showed relatively higher genetic distance values than mitochondrial 16S rRNA and COI genes. Some of the specimens of Botia and Lepidocephalichthys showed higher intraspecific genetic distance values compared to other specimens under analysis.

Defensins are an important class of AMPs, rich in cysteine with antibacterial, antifungal and antiviral functions. The present study identified and functionally characterised a β-defensin gene from Grey mullet, Mugil cephalus, termed as Mc-Def. A 192 base pair complementary DNA with an open reading frame encoding 63 amino acids comprising 20 amino acid signal and 43 amino acid mature peptide region was obtained. Mc-Def has a net charge of 3.9 and a molecular weight of 7.27 kDa with an isoelectric point of 8.88. It possessed six cysteines forming 3 disulphide bonds between C¹–C⁵, C²–C⁴ and C³–C⁶. Three dimensional structure identified a short N-terminal α helix followed by β sheet strands stabilized by disulfide bonds. The mRNA structure was predicted by Biomodel server with significant MEF score. Multiple sequence alignment and phylogeny revealed the sequence similarity of Mc-Def with fish β-defensin 2 type of AMPs. Molecular diversity and evolution of β-defensin provided immunity to host system against various infections. In silico analysis identified its potential as antibacterial, antifungal, anticancer, antioxidant and non-hemolytic peptide activity. These intriguing results firmly suggest that the Mc-Def can be used as a potent drug molecule in fish health management.

Environmental changes due to the domestication of wild population in hatchery conditions often lead to morphogenetic alterations in fish. Therefore, this study aimed to determine the genetic purity, demographic history, and population structure of Labeo rohita collected from three hatcheries in Bangladesh using a geometric morphometric approach in conjunction with mtDNA cyt b gene sequences and microsatellite markers. The geometric morphometric analysis revealed significant variation in centroid size (body size) among the different populations of L. rohita. However, MANCOVA and subsequent ANCOVA models showed no significant variation in body shape (relative wraps, RW_s) among those populations. Both DNA-based techniques amplified all genotypes and revealed a high degree of genetic diversity across all populations. Clustering analyses based on the Neighbour-Joining (NJ) phylogenetic approach found that the hatchery populations have indisputably diverged from the wild populations. The study of haplotype networks, neutrality testing, and mismatch distributions revealed a complex population expansion pattern involving genetic introgression resulting from human translocation. This tendency is exacerbated further by anthropogenic factors, resulting in the loss of various alleles from hatchery populations. The unevenness of pair-wise F_ST and the hierarchical analysis of molecular variance of population structure showed a distinct variation between wild and hatchery populations. This genetic loss occurs due to improper domestication processes of the hatchery populations. Ignorance of appropriate hatchery procedures may lead to adverse selection by using poor seed leading to stock deterioration in the hatchery population. This study could help to establish appropriate breeding strategies and provide essential information for the genetic improvement program of L. rohita.