Animal Gene最新文献

The genome of Mycobacterium orygis encodes 3767 proteins that includes 442 functionally uncharacterized proteins, known as hypothetical proteins (HPs). These functionally unknown proteins may play significant biological role in bacterium's survivability, virulence etc., hence functional annotation of these HPs with bioinformatics techniques might shed light on these aspects. So, the present study aimed to assign functions to those HPs in M. orygis genome. With the help of an extensive in silico workflow involving several bioinformatic tools, physicochemical characteristics, protein-protein interaction, sub-cellular localization, functional classification, and antigenicity of the HPs were analyzed. Out of 4039 genes and 3767 encoded proteins, 422 were annotated as “hypothetical protein, unknown function” in NCBI database. Out of 422 HPs, the FASTA sequences of 400 proteins, available in the NCBI database, were extracted. Preliminarily 400 proteins were screened for presence of conserved domain by different bioinformatic tools and 32 shortlisted proteins were further analyzed. The analysis revealed that these proteins may be involved in enzymatic, toxin-antitoxin system, cellular and other processes. Virulence and antigenicity of the complete set of HPs were also predicted. Based on antigenicity scores and sub-cellular localization, four proteins were selected for secondary and tertiary structure modelling. Molecular docking and MD-simulation of four proteins with TLR1 showed stable binding. B-cell and T-cell epitopes were identified for two proteins (QOY47331.1 and QOY49361.1) with highest antigenicity scores. The result of the present study may facilitate better understanding of virulence, pathogenesis and therapeutic target. The information about the structures of the HPs with highest antigenicity score could aid in structure-based inhibitor design and devising novel diagnostic assays.

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by aberrant lipid metabolism and mitochondrial dysfunction, features related to mitochondria-associated ER membranes (MAM). ApoE is recognized as the major AD risk factor. Human ApoE has three isoforms including Apoε2, Apoε3 and Apoε4. It has revealed that ε4 allele carriers are at higher risk of developing AD than ε3 allele carriers. Given that Apoε4 is a major AD risk factor and that MAM dysfunction in lipid metabolism may affect mitochondrial function, we assessed the expression pattern of cardiolipin synthetase (CLS) and glycerol-3-phosphate acyltransferase 2 (MINO) genes in Drosophila model of AD. To the best of our knowledge, this is the first study to investigate the effect of ApoE isoforms on mitochondrial function in Drosophila model of AD. RNA extraction was performed using glazt2a.gal4.UAS.hapoe transgenic flies harboring Apoε isoforms. Following cDNA synthesis, mRNA expression levels of target (CLS and MINO) and housekeeping (eEF1α) genes were measured by qRT-PCR. Our results did not show a significant decrease in CLS and MINO expression level in Apoɛ3 and Apoɛ4 groups as compared to the control. Although this reduction was not statistically significant, the decreasing trend indicates a kind of disruption in lipid biosynthesis and may directly affect mitochondrial function. Though the impact of Apoɛ4 on AD pathogenesis has been elucidated, the exact mechanism through which Apoɛ4 mediates AD progression is still unknown. Investigating the biology of ApoE isoforms using both human and AD animal models is recommended.

Heat stress is a prominent factor responsible for losses economically in poultry meat industry due to adverse effects on the general performance of broiler chickens. In this study, we evaluated the effects of probiotic (Saccharomyces cerevisiae) and ascorbic acid on oxidative gene damage biomarker, heat shock protein 70 (HSP70) and interleukin 10 (IL-10) in broiler chickens exposed to heat stress under natural conditions. Fifty-six broiler chickens served as the subjects, they were divided into 4 groups of 14 as follows: group I (control), group II (probiotic S. cerevisiae at 1 g/kg of feed), group III (ascorbic acid at 200 mg/kg of feed) and group IV (probiotic + ascorbic acid at 1 g/kg and 200 mg/kg of feed, respectively). The treatments were administered via feed for 35 days (D1 to D35). Enzyme-linked immunosorbent assay (ELISA) and one step real time reverse transcription polymerase chain reaction (RT-PCR) was utilised to study the effects of heat stress on the expression levels of 8-hydroxy-2′-deoxyguanosine (8-OHdG), HSP70 and IL-10 respectively, in broiler chickens raised during the hot summer season. The level of 8-OHdG gene was significantly lower in the probiotic administered group. The expression level of HSP70 was lowest in the ascorbic acid group while, IL-10 level of expression was highest in the probiotic + ascorbic acid group. The administered antioxidants were efficient in exhibiting anti-stress effects at the level of gene expression. We conclude that probiotic, ascorbic acid and probiotic + ascorbic acid reduced oxidative gene damage, affected the expression of HSP70 and increased the level of IL-10 gene respectively, in broiler chickens exposed to heat stress.

Background

Antimicrobial peptides (AMPs) are small peptides that form the first line of defence in all living organisms. In addition to conventional AMPs, there exist molecules that are often not regarded as part of the innate defences, but possess antimicrobial activity. Histone H2A-derived peptides are a group of unconventional AMPs that represent very ancient defence factors, re-used in new ways during evolution. The present study attempts to compare histone H2A-derived AMPs from four commercially important teleost fishes inhabiting various habitats, viz. Asian sea bass (Lates calcarifer), tank goby (Glossogobius giuris), grey mullet (Mugil cephalus), and Malabar trevally (Carangoides malabaricus).

Methods and results

RT-PCR amplification of the mRNAs extracted from these fishes yielded H2A-derived AMP genes with slight differences in the nucleotide sequences, nevertheless with similar translated amino acid sequences. The amino acid sequence was found to possess marked similarity at the N-terminal region and showed antimicrobial motif sequence characteristic of histone H2A-derived AMPs. Phylogenetic analysis showed an evolutionary relationship with invertebrate ones suggesting a common ancestral origin for the vertebrate and invertebrate histone H2A. The secondary structure of histone H2A-derived AMP showed the presence of α-helices and intermittent coils having a proline hinge connecting the N- and C-terminus. The peptide was also predicted to be a cell-penetrating one.

Conclusion

In silico structural and functional characterization of histone H2A-derived AMP revealed its potential antibacterial property and point towards the possibility of being an efficient AMP with the potential of being made use of in therapeutics.

Antimicrobial peptides (AMPs) derived from histone precursors form a significant class of therapeutic molecules. The study explores the comprehensive molecular characterization of core histone H2A-derived antimicrobial peptide, Etroplusin from Pearl spot, Etroplus suratensis. Etroplusin exhibited characteristic features of AMP such as net +11 charge and amphipathic alpha-helical structure. Multiple sequence alignment showed the homologous nature of etroplusin with previously reported H2A peptides. Phylogenetic analysis revealed that etroplusin is similar to Carassius auratus H2A-derived peptide and comes under the fish H2A peptide clade. Structure modelling with bioinformatics tools predicted alpha-helical structure and random coils with a proline hinge. The functional characterization of etroplusin revealed its antibacterial, antifungal, and anticancer activities. Significant upregulation of etroplusin was observed in the systemic tissues of E. suratensis on a challenge with the bacterial fish pathogen, Streptococcus agalactiae. The present study will shed light on fish innate immune responses and the importance of etroplusin, the H2A-derived peptide as a defense molecule.

Background

Betanin is an antioxidant and anti-inflammatory compound that has attracted the attention of researchers in a variety of diseases in recent years. Therefore, In the present study the effect of pretreatment of betanin nanoparticles (NB) in cerebral ischemia rats was investigated.

Methods

Oral administration of NB started five days before bilateral common carotid artery occlusion (BCCAO) induction and continued for three days thereafter in rats. The neurological disorder scores (NDS), brain swelling and edema were evaluated. After preparing brain homogenate, the intensity of oxidative stress, the activities of antioxidant enzymes, GSH content, the activities of mitochondrial enzymes SDH, MDH and LDH were studied. Also, the expressions of IL-1β, IL-6, TNF-α cytokines were measured. The expression levels of NF-ĸB and pSTAT3 genes and proteins and ERK and TFEB proteins were also studied.

Results

NB showed strong anti-inflammatory and antioxidant effects in cerebral I/R rats and improved mitochondrial and antioxidant enzymes activities. Decreases in NDS, swelling and edema of the brain were also observed in the cerebral I/R rats receiving NB. Also, administration of NB decreased the expressions of inflammatory cytokines and upregulated the expressions of NF-KB and pSTAT3 genes and proteins and overexpressed ERK and TEFB proteins.

Conclusion

NB has neuroprotective effects in cerebral I/R condition due to its antioxidant and anti-inflammation properties, which can be considered as a suitable treatment option in stroke conditions.

North-eastern India has diverse Bos genus endemic animals which include Siri (Bos indicus), Yak (Bos grunniens) and Mithun (Bos frontalis). But very little is known about their origin and taxonomic position. Hence, a taxonomic revisit of the genesis needed to confirm their position in the family Bovidae. So, the present study focuses on molecular cataloguing through DNA barcoding and phylogenetic relationships. The generated CO1 sequences of Bos indicus, Bos grunniens, and Bos frontalis were analyzed through similarity search, Species delineation approach like K2P Distance, Neighbour-Joining tree and ML approaches to identify their taxonomic position with respect to global published data. The NJ tree revealed cohesive clustering of Bos indicus with the pre-existing sequences of zebu and taurine but distinct from other congeners. The collected specimen of Bos frontalis clustered distinctly from other congeners and failed to cluster with Bos gaurus, which nullifies the previous report of Bos frontalis as a domesticated form of Bos gaurus. Similarly, Bison bison clustered very closely with Bos grunniens as their nearest neighbour. This observation was confirmed by ML phylogeny. Our findings confirmed the Siri's species status as Bos indicus. Similarly, Bos frontalis is a different species within the genus Bos but not the domesticated form of Bos gaurus. The close clustering of Bos grunniens and Bison bison supported the previous reports, which suggest that the genus Bison should be regarded as a synonym of the genus Bos. Thus, the present study strongly recommends the revisiting of bovine taxonomy.

A genome-wide associations study (GWAS) of single nucleotide polymorphisms (SNP) with indicators of meat productivity in Russian Meat Merino was carried out. A new approach is based on the selection of animals for research considered with known productivity genes (MSTN, MYOD1, etc.). Animal genotyping was performed using Ovine Infinium HD BeadChip 600 K (Illumina, USA). As a result, 20 SNPs significantly associated with the body measurements and ultrasound parameters of the animals were identified. Around these SNPs, 14 candidate genes were discovered. Investigated parameters of phenotype can be associated with structural disorders in these genes. Most SNPs were located in the intergenic space, two polymorphisms were located in the Upstream and Downstream regions. One SNP was localized in the intron, two are in the exon of genes. Two substitutions were next to the long non-coding RNA and micro-RNA. The following candidate genes were annotated: ASB3, THADA, PRPS1L1, Ccdc130, MTHFS, RALGAPA1, MEIS1, AKIRIN1, GRXCR1, Lrig1, ANKS1B, CFI, KRAB, and SLCO2B1. These genes are involved in some metabolic processes of cell proliferation and differentiation, function of neurons and immune system. Further research should be oriented to study the structure of these genes and use discovered SNPs as new molecular markers in breeding.

The Indian crested porcupine (Hystrix indica) is a hystricomorph rodent species and has been suggested to be native to southern Asia and the Middle East. Complete mitochondrial genomes are available that can be used to identify and clarify the evolutionary history and phylogenetic relationships, but until now the mitochondrial genome of the crested porcupine was not available. The present study is the first report of the complete mitochondrial genome sequence of the H. indica, with a length of 16,811 bp (GenBank accession number: ON408241). The mitochondrial genome sequence encompassed 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one non-coding region (D-loop) in this study. The overall AT and GC contents of the mitochondrial genome of H. indica were 62.18% and 37.81% respectively. Ten protein-coding genes used ATG as the start codon except for ND-2 (ATC), ND3, and ND5 (ATA). Diverse patterns of stop codons were observed, such as TAG, TAA, AGA, and TA. Based on the phylogenic analysis, the 15 species included in the analysis were assembled into three main groups and were largely congruent with families of rodents, including Sciuridae species in the first group, Hystricidae species in the second group, and species of Castoridae, Dipodidae, Spalacidae, Cricetidae, and Muridae families in the third group. The complete mitochondrial genome of H. indica provides fundamental information for future research studies.

Probiotics are suitable substitutes to reduce the use of growth-promoting antibiotics and antibiotics used to treat livestock infections due to new international laws and consumers' expectations of livestock products. Although lactic acid bacteria, especially Lactobacillus, are safe strains (GRAS¹), a safety study of new probiotic strains is needed to evaluate their safety and pathogenicity parameters. Such investigations can reduce concerns about antibiotic resistance genes transfer and observe rare cases of infection caused by probiotic usage. In the previous project of Iran Animal Biotechnology Research Institute, several lactic acid species were isolated and identified from the gastrointestinal tract of different farm animals via phenotypic characteristics and 16S rRNA sequencing. These bacteria had probiotic properties and were assessed for acid resistance, antibiotic resistance, bile salts, and antimicrobial activity. In this study, the presence or absence of several genes, such as pathogenic genes, amine-producing genes, and genes associated with antibiotic resistance, were examined by PCR.² Furthermore, genes that lead to the emergence of antibiotic resistance through other mechanisms such as efflux pumps were also studied in the same way. These studies have led to the achievement of safe strains for the introduction to the large market of livestock, poultry, and aquatic probiotics.