The variation in promoter sequences of the Akt3 gene between cow and buffalo revealed different responses against mastitis

Background Serine/threonine kinase 3 (AKT3) is a protein-coding gene that is associated with several cattle immune diseases including different tumors and cancers. The objective of this study was to investigate the differences in structures and functions of AKT3 of cow and buffalo cattle. Methods The sequence differences of gene-coding sequence (CDS) and core promoter region of AKT3 in cow and buffalo were analyzed by using bioinformatics tools and PCR sequencing. Also, the functional analysis of promoter regulating gene expression by RT-PCR was performed using 500 Holstein cows and buffalos. And, evaluation of AKT3 inflammatory response to the lipopolysaccharide (LPS)-induced mastitis was performed between both species. Results The results revealed the variation in 6 exons out of 13 exons of the two species of CDS. Also, 4 different regions in 3-kb promoters of the AKT3 gene were significantly different between cow and buffalo species, in which cow’s AKT3 promoter sequence region was started from − 371 to − 1247, while in buffalo, the sequence was started from − 371 to − 969 of the promoter crucial region. Thus, the promoter was overexpressed in cows compared to buffaloes. As a result, significant differences (P < 0.05) between the two species in the AKT3 gene expression level related to the LPS stimulation in their mammary epithelial cell line. Conclusions This study emphasized the great importance of the structural differences of AKT3 between the animal species on their different responses against immune diseases like mastitis.

Endophytic Fungal Diversity of Aerides crispa, an Epiphytic Orchid

Aerides crispa is an epiphytic plant that belongs to Orchidaceae family. Re-quirement of special habitat makes epiphytic orchids different from other plants. Day by day favourable conditions for these plants are decreasing. Here we have isolated six endophytic fungi from a single orchid. Isolated fungal cultures were molecularly characterized using ITS sequence region comparison with known fungi from NCBI data base and submitted to Gen-Bank. Homology of the fungi were confirmed by similarity matrix generation and phylogenetic tree construction. Thus, the endophytic fungi obtained were Cladosprium cladosporioides, Nigrospora sphaerica, Colletotricum gloe-osporioides, Fusarium circinatum, F.equiseti, Cl.cladosporioides. From the research study, it is revealed that genotypic characterization is a better method for identification of fungi than traditional methods, since same fungi were identified from different parts and also different species from same part of the same plant shows the interesting part of biodiversity. Richness of fungi in A crispaspeaks a lot about the importance of conservation of or-chids, endophytes and thereby biodiversity. The study describes endophytic fungi from an epiphytic orchid Acrispa to its sequence level identification.

Incidence of CarassiusAuratus Gibelio Gill Hemorrhagic Disease Caused by CyHV-2 Infection Can Be Reduced by Vaccination with Polyhedra Incorporating Antigens

Encapsulation of antigens within protein microcrystals (polyhedra) is a promising approach for the stable delivery of vaccines. In this study, a vaccine was encapsulated into polyhedra against cyprinid herpesvirus II (CyHV-2). CyHV-2 typically infects gibel carp, Carassius auratus gibelio, causing gill hemorrhagic disease. The vaccine was constructed using a codon-optimized sequence, D4ORF, comprising the ORF72 (region 1–186 nt), ORF66 (region 993–1197 nt), ORF81 (region 603–783 nt), and ORF82 (region 85–186 nt) genes of CyHV-2. The H1-D4ORF and D4ORF-VP3 sequences were, respectively, obtained by fusing the H1-helix sequence (region 1–90 nt) ofBombyx mori cypovirus(BmCPV) polyhedrin to the 5′ terminal end of D4ORF and by fusing a partial sequence (1–279 nt) of the BmCPV VP3 gene to the 3′ terminal end of D4ORF. Furthermore, BmNPV-H1-D4ORF-polh and BmNPV-D4ORF-VP3-polh recombinant B. mori nucleopolyhedroviruses (BmNPVs), belonging to the family Baculoviridae, and co-expressing BmCPV polyhedrin and H1-D4ORF or D4ORF-VP3, were constructed. H1-D4ORF and D4ORF-VP3 fusion proteins were confirmed to be encapsulated into recombinant cytoplasmic polyhedra by Western blotting. Degradation of vaccine proteins was assessed by SDS-PAGE, and the results showed that the encapsulated vaccine proteins in polyhedra could be protected from degradation. Furthermore, when gibel carp were vaccinated with the purified polyhedra from BmNPV-H1-D4ORF-polh and BmNPV-D4ORF-VP3-polh via injection, the antibody titers in the serum of the vaccinated fish reached 1:6400–1:12,800 at 3 weeks post-vaccination. Therelative percentage of survival of immunized gibel carp reached 64.71% and 58.82%, respectively, following challenge with CyHV-2. These results suggest that incorporating vaccine protein into BmCPV polyhedra may be a novel approach for developing aquaculture microencapsulated vaccines.

Digital maturity of territories during digital transformation

The formation of a full-fledged digital national economy integrated into a single world order is today’s trend. Under a single technological human habitat, it is necessary to understand territories as separate systemic mechanisms of the state, lined up in a logical sequence region-city-municipality city-municipality of each element’s region position to the previous and subsequent ones. That is consideration of the socio-economic development of the system from the standpoint of the agglomeration effect. Based on the above, the article considered various approaches to identifying a territory from the point of view of digital maturity in the global digital transformation process. The existing methods for assessing the digital maturity of Russian regions are considered, groups of metrics for such an assessment are given, and a critical assessment of existing methods is given to develop new ones or improve old ones. The rationale for this is the ability to track digital transformation dynamics through the digital maturity of territories.

Identification and characterisation of the Volvox carteri Moco carrier protein

The molybdenum cofactor (Moco) is a redox active prosthetic group found in the active site of Moco-dependent enzymes (Mo-enzymes). As Moco and its intermediates are highly sensitive towards oxidative damage, these are believed to be permanently protein bound during synthesis and upon maturation. As a major component of the plant Moco transfer and storage system, proteins have been identified that are capable of Moco binding and release but do not possess Moco-dependent enzymatic activities. The first protein found to possess these properties was the Moco carrier protein (MCP) from the green alga Chlamydomonas reinhardtii. Here, we describe the identification and biochemical characterisation of the Volvox carteri (V. carteri) MCP and, for the first time, employ a comparative analysis to elucidate the principles behind MCP Moco binding. Doing so identified a sequence region of low homology amongst the existing MCPs, which we showed to be essential for Moco binding to V. carteri MCP.

Deciphering Oxidative Stress Responsive Microrna (Mirna) in Hilsa (Tenualosa ilisha) and Rohu (Labeo rohita)

microRNAs (miRNAs) and their target gene expression under oxidative stress play a crucial role in cellular antioxidant regulation. Information on oxidative stress responsive miRNA and their target genes of the fishes of Bangladesh is not reported yet. This study was performed to profile oxidative stress-responsive miRNAs by computational and experimental methods in economically important fish of Bangladesh. Using in silico approach, we could not trace any miRNA of fish of Bangladesh as none has been reported yet in existing databases. We, therefore enlist here the miRNAs that are expressed under different stress conditions in fish applying an extensive literature review. From the list, we selected 10 potential oxidative stressresponsive miRNAs followed by predicting their target genes using miRNA target prediction software (TargetScan Fish). This study decoded the mature sequences of oxidative stress-responsive miRNA (miR-21) in Hilsa (Tenualosa ilisha) and Rohu (Labeo rohita) through specific miRNA primer-based cDNA fragment sequencing. Next, we identified an oxidative stress responsive gene, programmed cell death 4b (pdcd4b) in hilsa genome and showed that the hilsa miR-21 binds within coding sequence region of the predicted hilsa pdcd4b. This study is pioneer in decoding oxidative stress responsive miRNA in fish of Bangladesh using an experimental and bioinformatics approach.

Reference transcriptome data in silkworm Bombyx mori

The silkworm Bombyx mori has long been used in the silk industry and utilized in studies of physiology, genetics, molecular biology, and pathology. We recently reported high quality reference genome data for B. mori. In the present study, we constructed a reference transcriptome data set using the reference genome data and RNA-seq data of 10 tissues from P50T strain larvae. Reference transcriptome data contained 51,926 transcripts, with 39,619 having one or more coding sequence region. The abundance of each transcript in the 10 tissues as well as 5 tissues from other strain larvae was estimated, and hierarchical clustering was performed. The results obtained showed that data on abundance were highly reproducible and there here is a little difference of transcriptome abundance between the two strain larvae. New isoforms of silk-related genes were searched for in the reference transcriptomes, and the longest isoform of sericin-1 possessing a long exon was identified. We also extracted transcripts that were strongly expressed in one or more parts of the silk glands. An enrichment analysis performed using the functional annotation data of the transcripts provided novel insights into the functions of the silk gland parts. Therefore, the reference transcriptome data set obtained has extended B. mori genomic and transcriptomic insights and may contribute to advances in entomologic and vertebrate research, including that on humans.

Expressional artifact caused by a co-injection marker rol-6 in C. elegans

ABSTRACTIn transgenic research, selection markers have greatly facilitated the generation of transgenic animals. A prerequisite for a suitable selection marker to be used along with a test gene of interest is that the marker should not affect the phenotype of interest in transformed animals. One of the most common selection markers used in C. elegans transgenic approaches is the rol-6 co-injection marker, which induces a behavioral roller phenotype due to a cuticle defect but is not known to have other side effects. However, we found that the rol-6 co-injection marker can cause expression of GFP in the test sequence in a male-specific interneuron called CP09. We found that the rol-6 gene sequence included in the marker plasmid is responsible for this unwanted expression. Accordingly, the use of the rol-6 co-injection marker is not recommended when researchers intend to examine precise expression or perform functional studies especially targeting male C. elegans neurons. The rol-6 sequence region we identified can be used to drive a specific expression in CP09 neuron for future research.

Epitranscriptomic mechanisms of N6-methyladenosine methylation regulating mammalian hypertension development by determined spontaneously hypertensive rats pericytes

Aim: Pericytes maintain homeostatic functions in the blood–brain barrier. N6-methyladenosine (m6A) is critical for various biological processes, but the role of mRNA m6A methylation in hypertension has not been fully elucidated. Methods: The m6A methylation levels of Wistar Kyoto rat pericytes and spontaneously hypertensive rat pericytes were detected via m6A high-throughput sequencing. Results: The m6A methylations were more enriched in the coding sequence region, 3′UTR and 5′UTR of mRNAs, with the m6A motifs being relatively conserved across the different conditions investigated. The average m6A abundance of spontaneously hypertensive rat pericytes exhibited global reductions in the pericytes. Conclusion: This study revealed the m6A landscapes and identified an epitranscriptomic mechanism during the development of mammalian hypertension.