Agalactia is a disease affecting small ruminants which is caused by a mycoplasma agalactiae. P40 protein is the most important surface antigen in mycoplasma agalactiae bacteria that can be used to design recombinant vaccine. The objective of present study was obtain the bioinformatic characteristics of p40 antigen. A wide range of on-line prediction softwares were used to predict B and T-cells epitopes, secondary and tertiary structure and antigenicity. Applied bioinformatic approaches used in this study was validated by comparing results with four different experimental epitope predictions. Bioinformatic analysis, identified B-cell epitopes located at amino acid residues 24-40, 98-114, 218-240, 251-265 and 333-350, and T-cell epitopes at amino acids 5-25, 86-105, 198-215, 143-153, 214-223 and 337-345. All final predicted B and T-cell epitopes had antigenic ability except 5-25, 98-144, 141-157, 199-215 and 333-350 residuals. Finally, bioinformatic analysis showed that these regions had proper epitopes characteristics and may be useful for developing recombinant vaccines.. Running title: Bioinformatic tools and epitopes prediction.

Chitinase has many applications amongst which is its chitinolytic activity towards environmental clean up and converting the chitin into its building blocks. In a world with fast growing population and limited natural resources, the enzyme technology can be helpful to a lot of industries, helping to overcome to the future problems. For this reason, a near fulllength endochitinase gene from Serratia marcescens B4A, was isolated from shrimp farming pond waste water and cloned in Escherichia coli. Subsequent to the deposition of sequence information in GenBank, further bioinformatic analyses were performed.

Brucellosis, caused by the genus Brucella bacterium, is a well-known infection among domestic animals. Considering the serious economic and medical consequences of this infection, various preventive efforts have been made through using recombinant vaccines, based on outer membrane protein (OMP) antigens of Brucella species. The objective of the present study was to clone, analyze the sequence, and predict the epitopes of Omp31 gene as a major B. melitensis antigen. The full-length open reading frame (ORF) for this gene was amplified by specific primers and cloned into the pTZ57R/T vector. The gene sequence of B. melitensis Rev 1 strain was submitted to NCBI database. The results of phylogenetic analysis showed that Omp31 is almost similar in different Brucella species. Online prediction software programs were also used to predict B- and T-cell epitopes, secondary and tertiary structures, antigenicity, and enzymatic degradation sites. The bioinformatic tools in the current study were confirmed by the results of three different experimental epitope prediction studies. Bioinformatic analysis identified one T-cell and three B-cell epitopes for Omp31 antigen. Finally, based on the antigenicity and proteosome recognition sites, common B- and T-cell epitopes were predicted for Omp31 (amino acids 191-204). Bioinformatic analysis showed that these regions had proper epitope characterization and could be useful for recombinant vaccine development.

The SRY gene (SRY) provides instructions for making a transcription factor called the sex-determining region Y protein. The sex-determining region Y protein causes a fetus to develop as a male. In this study, SRY of 15 spices included of human, chimpanzee, dog, pig, rat, cattle, buffalo, goat, sheep, horse, zebra, frog, urial, dolphin and killer whale were used for determine of bioinformatic differences.
Nucleotide sequences of SRY were retrieved from the NCBI databank. Bioinformatic analysis of SRY is done by CLC Main Workbench version 5.5 and ClustalW (http:/www.ebi.ac.uk/clustalw/) and MEGA6 softwares.
The multiple sequence alignment results indicated that SRY protein sequences from Orcinus orca (killer whale) and Tursiopsaduncus (dolphin) have least genetic distance of 0.33 in these 15 species and are 99.67% identical at the amino acid level. Homosapiens and Pantroglodytes (chimpanzee) have the next lowest genetic distance of 1.35 and are 98.65% identical at the amino acid level.
These findings indicate that the SRY proteins are conserved in the 15 species, and their evolutionary relationships are similar.

Zebrafish (Danio rerio) stands as a valuable model organism for delving into molecular mechanisms, notably detoxification. MicroRNAs (miRNAs), small non-coding RNA molecules, serve as post-transcriptional regulators of gene expression, potentially shaping the complex network of genes engaged in detoxification pathways. This study employs bioinformatic analysis, utilizing Target Scan and DIANA databases, to explore the potential of miRNAs in modulating the expression of detoxification-associated genes in zebrafish. By meticulously scrutinizing miRNA and mRNA datasets in zebrafish, we pinpoint candidate miRNAs predicted to target established detoxification genes. Leveraging bioinformatic algorithms, we dissect the plausible interactions between these miRNAs and their target detoxification genes, which include pgp, gpx1a, gpx3, aldh3b1, gstm3, cyp3c1, gstp1, gpx1b, cyp17a1, sod1, sod2, gsto2, gstz1, akr7a3, gsr, ahr1b, cat, ahr2, and abcb4. Moreover, we assess the conservation of miRNA-target interactions across species and scrutinize potential miRNA binding sites within the 3' untranslated regions (UTRs) of target mRNAs. Our findings unveil the intricate regulatory interplay between miRNAs and genes involved in detoxification in zebrafish, providing a cornerstone for future experimental validations. This study significantly contributes to our evolving understanding of miRNA-mediated gene regulation within the context of detoxification pathways in zebrafish

Mismatch repair (MMR) proteins play important roles in maintaining genome stability in all the organisms. UvrD helicase is a component of MMR complex and plays an essential role in the DNA repair by providing the unwinding function. In the current manuscript we presented a bioinformatic analysis of UvrD helicase from two plant species (Arabidopsis and rice). The Arabidopsis thaliana and Oryza sativa UvrD had 1149 (129 kDa) and 1165 amino-acids (130 kDa) proteins, respectively. These proteins were larger than the E. coli UvrD because they contained a longer N-terminal extension and linker sequences. This research showed UvrD in both plants contained ATP-binding site. The existence of the N terminal ATP-binding site and conserved motifs in both plants suggest that the N terminal and C terminal sequences can show ATPase and a 3' to 5' DNA helicase activity similar to the E. coli UvrD. To gain some insight into the structure of UvrD using bioinformatic analysis softwares, three- dimentional structure of this enzyme was predicted in two different plant species. Molecular graphic images and structural analysis of the best models were produced using the UCSF Chimera package. The results demonstrated that there were not obvious differences in three- dimentional structure of AtUvrd and OsUvrd and during the evolutionary changes they have preserved their major domains and biochemical characteristics like ATPase and DNA helicase activity.

Phenylketonuria (PKU) is the most prevalent inborn error of amino acid metabolism in the world and its incidence rate is increasing in Iran. The aim of the present study was to assess the efficiency of HRM technique as a fast and suitable method in identifying common mutations of phenylalanine hydroxylase gene including IVS10-11G>A and P281L in order to improve the early detection of the disease to prevent the occurrence of it.
In this case-control study, 20 DNA samples including one sample with IVS10-11G>A mutation , one sample with P281L mutation and 18 control samples were extracted from peripheral blood collected in Medical Genetic Center of Isfahan and were genotyped with HRM technique. To validate the mutations, the mutant samples were genotyped using sequencing. Bioinformatic analyses were used for determining structural and functional effects of P281L mutation on the of PAH protein.
FINDINGS: HRM analysis identified IVS10-11G>A and P281L mutations with a sensitivity and specificity of 100% and the mutant and normal samples differentiated well in normalized and difference plots. Bioinformatic analyses demonstrated instability and pathological effects of PAH protein containing P281L mutation.
HRM is a simple and fast technique detecting the two IVS10-11G>A and P281L mutations with 100% sensitivity and specificity.

Cutin is a polymer that is constructed in plants by the condensation and oxidation of fatty acids and plays a key role in the protection of plants against pathogens. Cutinase is a hydrolase enzyme that breaks down the cutin. The purpose of this study was to extract cutin from red apples with oxalate buffer, cutinase enzyme activity assay in LB culture, and bioinformatic analysis. To attain these purposes the cutinase-producing strains that had previously been isolated were inoculated in culture medium containing cutin. After initial culture, the bacteria were cultured in LB medium and cutinase activity was measured using the p-Nitrophenyl butyrate. In order to execute bioinformatic analysis, the isolated sequences of six cutinase-producing bacteria were analyzed based on computational data bases and their phylogenetic trees were prepared. Then, the similarities in the sequences of a large number of cutinase-producing samples were analyzed by drawing the phylogenetic tree. The results showed the separation of cutinase-producing prokaryotes from cutinase-producing eukaryotes. Then, the sequence of 16S rDNA of these cutinase-producing samples as well as the samples we had prepared were evaluated and their phylogenetic relationships were determined. This analysis showed that the new sequence stood alongside the bacterial samples. Thus, our cutinases may be similar with these bacterial cutinases in structure and function.

In this study, in order to find the suitable tuber promoter, an experiment was conducted in Shahid Beheshti University in 2018. For this purpose, promoter sequences of different tuberous plants were searched at NCBI. Sequences were multiple-aligned and the target primers designed from conserved regions. PCR analysis confirmed the presence of the desired promoter in plants of sweet potato and taro. In order to further confirmation, bioinformatic analysis including identification of cis elements, transcription factors, their function, transcription factors with high and low expression were performed. Finally, the identified promoter was compared with patatin class 1 promoter in terms of cis elements and function. Results of bioinformatic analysis indicated that the promoter has specific and general cis elements. General cis elements that are present in most promoters and are involved in activation and regulation of promoters, cellular processes, developmental processes and tolerance to biological and non-biological stresses. Special cis elements of tuber are active in expression of storage protein and starch. Comparison between studied promoter and specific tuber promoter of patatin confirms activity of the studied promoter in the tuber. A tuber promoter can be used to express various proteins in tuber plants in the future.

Physical exercise has emerged as an effective therapy to mitigate cardiac remodelling in diabetic cardiomyopathy (DCM). The results of our previous studies revealed mammalian sterile 20-like kinase 1 (Mst1) is a key regulator of the progression of DCM. However, the precise molecular mechanism of physical exercise-induced cardiac protection and its association with Mst1 inhibition remain unclear. Wildtype and Mst1 transgenic mice were challenged with streptozotocin (STZ) to induce experimental diabetes and were divided into sedentary and exercise groups. The DCM phenotype was evaluated by echocardiography, Masson’s trichrome staining, TUNEL and immunoblotting analyses. The exercise-regulated miRNAs targeting Mst1 were predicted by bioinformatic analysis and later confirmed by RT-qPCR, immunoblotting, and dual-luciferase reporter assays. In addition, cultured neonatal mouse cardiomyocytes were subjected to simulate diabetes to elucidate the underlying mechanisms. Compared to the sedentary diabetic control, physical exercise inhibited Mst1 and alleviated cardiac remodelling in mice with DCM, as evidenced by decreases in the left ventricular end-systolic internal dimension (LVESD) and left ventricular end-diastolic internal dimension (LVEDD), increases in the left ventricular ejection fraction (LVEF) and left ventricular fractional shortening (LVFS), attenuation of collagen deposition, and the suppression of apoptosis. Bioinformatic analysis and apoptosis assessments revealed exercise exerted protective effects against DCM through miR-486a-5p release. Moreover, luciferase reporter assays confirmed miR-486a-5p directly suppressed the expression of Mst1, thereby inhibiting the apoptosis of cardiomyocytes subjected to high glucose treatment. Physical exercise inhibits cardiac remodelling in DCM, and the mechanism is associated with miR-486a-5p release-induced Mst1 inhibition.