Structural modeling and gene expression analysis of phosvitinless vitellogenin (vgc) in the Indian freshwater murrel, Channa punctatus (Bloch, 1793).

Vitellogenin (Vg) is a female-specific egg-yolk precursor protein, synthesized in the liver of fish in response to estrogens. In the present study, complete gene of phosvitinless vitellogenin (vgc) was sequenced, its 3D structure was predicted and validated by web-based softwares. The complete nucleotide sequence of vgc was 4126 bp which encodes for 1272 amino acids and showed the presence of three conserved domains viz. LPD_N, DUF1943 and DUF1944. The retrieved amino acid sequence of VgC protein was subjected to in silico analysis for understanding the structural and functional properties of protein. mRNA levels of multiple vg genes have also been quantified during annual reproductive cycle employing qPCR. A correlation has been observed between seasonal changes in gonadosomatic index with estradiol levels and hepatic expression of three types of vg genes (vga, vgb, vgc) during ovarian cycle of murrel. During preparatory phase, when photoperiod and temperature are low; low titre of E2 in blood induces expression of vgc gene. A rapid increase in the levels of E2 favours induction of vgb and vga genes in liver of murrel during early pre-spawning phase when photoperiod is long and temperature is high in nature. These results suggest that among three vitellogenin proteins, VgC is synthesized earlier than VgA and VgB during oogenesis.

A compact and efficient AES-32GF for encryption in small IoT devices.

The phenomenal growth of resource constrained devices in IoT set ups has motivated the researchers to develop solutions for securing information flow. In this paper, we present a compact and efficient field programmable gate array (FPGA) implementation of AES with 32-bit data-path named, AES-32GF. The implementation is carried out on different Xilinx FPGAs. In FPGAs, utilization of slices and look up tables (LUTs) reflect on the compactness of the design. Numerical results show that lesser resources are required with smaller data path in comparison with the original standard. With the help of data path compression and Galois field implementation of the s-box resource consumption is minimized. S-box is the most resource consuming component in the AES structure. In our implementation, Artix-7 series FPGA for the same. It results in significant resource savings. In comparison to unrolled AES-128 architecture, it achieves 87 % resource savings. With 595 slices and 2.004 Gbps throughput, AES-32GF cipher achieves an efficiency of 3.37 Mbps/slice. It outperforms other designs in terms of efficiency. •A compact and efficient FPGA implementation of AES with 32-bit data-path has been proposed.•The proposed design utilizes data path compression and Galois field implementation of the s-box to minimize resource consumption.•With 595 slices and 2.004 Gbps throughput, AES-32GF cipher achieves an efficiency of 3.37 Mbps/slice.

The potential role of the KFG and KITLG proteins in preventing granulosa cell apoptosis in Bubalus bubalis.

BACKGROUND: The dynamics of mammalian follicular development and atresia is an intricate process involving the cell-cell communication mediated by secreted ovarian factors. These interactions are critical for oocyte development and regulation of follicular atresia which in part are mediated by keratinocyte growth factor (KGF) and kit ligand (KITLG), but their roles in the regulation of apoptosis in buffalo granulosa cells have not yet been defined. During mammalian follicular development, granulosa cell apoptosis triggers the atresia so ~ 1% follicles reach the ovulation stage. In the present study, we used buffalo granulosa cells to examine the effects of KGF and KITLG in apoptosis regulation and investigated potential mechanism on Fas-FasL and Bcl-2 signaling pathways. RESULT: Isolated buffalo granulosa cells were cultured with KGF and KITLG proteins using different doses (0, 10, 20, and 50 ng/ml) independently or in combination. Expression analysis for both anti-apoptotic (Bcl-2, Bcl-xL, and cFLIP) and pro-apoptotic (Bax, Fas, and FasL) genes at transcriptional levels were carried out by real-time PCR. Upon treatments, expression levels of anti-apoptotic genes were significantly upregulated in a dose-dependent manner, showing an upregulation at 50 ng/ml (independently), and at 10 ng/ml in combination. Additionally, upregulation of growth-promoting factors, bFGF, and α-Inhibin was also observed. CONCLUSIONS: Our findings suggest the potential roles of KGF and KITLG in determining granulosa cell growth and regulating apoptosis.

Molecular phylogeny, structure modeling and in silico screening of putative inhibitors of aerolysin of Aeromonas hydrophila EUS112.

Aeromonas hydrophila, a Gram-negative bacterium, causes diseases in fish, resulting in excessive loss to the aquaculture industry. Aeromonas is a highly heterogeneous group of bacteria, and the heterogeneity of the genus is attributed to variation and diversity in the virulence factors and toxins among various Aeromonas strains. One of the major toxins aerolysin, secreted by the bacterium, causes hemorrhagic-septicemia and diarrhea and can serve as a drug target. Here, we describe characterization, molecular phylogeny, and homology modeling of the aerolysin of A. hydrophila strain EUS112 (AhEUS112) cloned in our lab. The encoded aerolysin is 485 amino acids long with an N-terminal signal sequence of 23 amino acids. Phylogenetic analysis of the aerolysin of AhEUS112 revealed that it belongs to a diverse group of toxins, showing maximum similarity with aerolysins of other Aeromonas strains followed by Vibrio toxin. The homology model of the mature aerolysin of AhEUS112 was generated using the crystal structure of a mutant aerolysin (PDB#3g4n) as the template, which showed that the encoded aerolysin exists as a channel protein. Validation of the generated model using bioinformatics tool confirmed it to be a good quality model that can be used for drug design. Molecular dock analysis revealed that drugs, aralia-saponin I, cyclamin, ardisiacrispin B, and aralia-saponin II bind to aerolysin with a higher affinity as compared to other drugs and at functionally important amino acids of aerolysin. Hence, these molecules can act as an effective therapeutics for inhibiting the aerolysin pore formation and curtail the severity of Aeromonas infection.Communicated by Ramaswamy H. Sarma.

Molecular docking analysis of P2X7 receptor with the beta toxin from Clostridium perfringens.

Clostridium perfringens beta-toxin (CPB) is linked to necrotic enteritis (over proliferation of bacteria) in several species showing cytotoxic effect on primary porcine endothelial and human precursor immune cells. P2X7 receptor on THP-1 cells is known to bind CPB. This is critical to understand the mechanism of pore formation for effective drug design. The structure of CPB and P2X7 receptor proteins were modeled using standard molecular modeling procedures (I-TASSER and Robetta server). This is followed by protein-protein docking (HADDOCK server) to study their molecular interaction. Interacting residues (19 residues from CPB and 21 residues from P2X7) were identified using the PISA server. Thus, we document the molecular docking analysis of P2X7 receptor with the beta toxin from Clostridium perfringens towards drug design and development of drugs to control necrotic enteritis.

Major Histocompatibility Complex Dmα/ß Genes and Their Expressional Diversity in Healthy and Diseased Water Buffalo Bubalus bubalis.

BACKGROUND/AIMS: The major histocompatibility complex (MHC) categorized into three (I, II and III) classes elicits the immunogenic response by presenting exogenous peptides to T cells. The MHC-II DM is composed of DMα and DMß, two polypeptide chains, both are encoded by separate MHC genes involved in antigen processing and presentation. Despite the acknowledged role of MHC complex in humans, the literature is silent on the organization and expression of these genes in water buffalo Bubalus bubalis, an agriculturally important animal species. METHODS: We deduced the full-length mRNA sequences of DMα and DMß genes, localized them onto the chromosome 2, assessed their copy number per haploid genome and studied tissue and disease specific expression. RESULTS: The Real Time PCR showed higher expression of both the genes and their seven interacting partners in spleen, gonads and spermatozoa. Significantly, upregulation of DMα and DMß genes and their interacting partners were detected in diseased group of buffaloes as compared to that in healthy ones. CONCLUSION: The upregulation of Bubalus bubalis (BuLA)-DMα and DMß genes and their interacting partners reflect their role in regulating immune responses towards the amelioration of diseases. Work on this line would enhance our understanding on the overall roles of MHC locus, allowing development of possible therapeutic treatment strategies.

Intermolecular Interactions Between DMα and DMß Proteins in BuLA-DM Complex of Water Buffalo Bubalus bubalis.

The major histocompatibility complex (MHC) with its three classes represents a cluster of tightly linked genes with defined immunological and non-immunological functions. The DM, a MHC class II molecule is formed by the non-covalent association of DMα and DMß chains. It binds with the processed peptide antigens and presents them to T lymphocytes, thereby triggering the immune responses. Startlingly, the expression pattern and structural organization of DMα and DMß proteins in buffalo remains undefined. We isolated and purified the DMα and DMß proteins from Bubalus bubalis using gel filtration chromatography. Employing western blotting and immunohistochemistry, highest expression of these proteins was observed in spleen and were later localized in the cytoplasm. We modelled 3D structures of the proteins and assessed the binding interface of BuLA-DM docked complex. In the process, we uncovered 9 DMα and 8 DMß specific residues participating in the formation of BuLA-DM complex. Our work demonstrated active participation of the critical amino acid residues engaged in the formation of BuLA-DM complex facilitating deeper understanding on the structure-function relationship of these proteins. J. Cell. Biochem. 118: 4254-4266, 2017. © 2017 Wiley Periodicals, Inc.

Cross Talk between KGF and KITLG Proteins Implicated with Ovarian Folliculogenesis in Buffalo Bubalus bubalis.

Molecular interactions between mesenchymal-derived Keratinocyte growth factor (KGF) and Kit ligand (KITLG) are essential for follicular development. These factors are expressed by theca and granulosa cells. We determined full length coding sequence of buffalo KGF and KITLG proteins having 194 and 274 amino acids, respectively. The recombinant KGF and KITLG proteins were solubilized in 10 mM Tris, pH 7.5 and 50 mM Tris, pH 7.4 and purified using Ni-NTA column and GST affinity chromatography, respectively. The purity and molecular weight of His-KGF (~23 kDa) and GST-KITLG (~57 kDa) proteins were confirmed by SDS-PAGE and western blotting. The co-immunoprecipitation assay accompanied with computational analysis demonstrated the interaction between KGF and KITLG proteins. We deduced 3D structures of the candidate proteins and assessed their binding based on protein docking. In the process, KGF specific residues, Lys123, Glu135, Lys140, Lys155 and Trp156 and KITLG specific ones, Ser226, Phe233, Gly234, Ala235, Phe236, Trp238 and Lys239 involved in the formation of KGF-KITLG complex were detected. The hydrophobic interactions surrounding KGF-KITLG complex affirmed their binding affinity and stability to the interacting interface. Additionally, in-silico site directed mutagenesis enabled the assessment of changes that occurred in the binding energies of mutated KGF-KITLG protein complex. Our results demonstrate that in the presence of KITLG, KGF mimics its native binding mode suggesting all the KGF residues are specific to their binding complex. This study provides an insight on the critical amino acid residues participating in buffalo ovarian folliculogenesis.

Molecular docking uncovers TSPY binds more efficiently with eEF1A2 compared to eEF1A1.

Testis-specific protein, Y-encoded (TSPY) binds to eukaryotic translation elongation factor 1 alpha (eEF1A) at its SET/NAP domain that is essential for the elongation during protein synthesis implicated with normal spermatogenesis. The eEF1A exists in two forms, eEF1A1 (alpha 1) and eEF1A2 (alpha 2), encoded by separate loci. Despite critical interplay of the TSPY and eEF1A proteins, literature remained silent on the residues playing significant roles during such interactions. We deduced 3D structures of TSPY and eEF1A variants by comparative modeling (Modeller 9.13) and assessed protein-protein interactions employing HADDOCK docking. Pairwise alignment using EMBOSS Needle for eEF1A1 and eEF1A2 proteins revealed high degree (~92%) of homology. Efficient binding of TSPY with eEF1A2 as compared to eEF1A1 was observed, in spite of the occurrence of significant structural similarities between the two variants. We also detected strong interactions of domain III followed by domains II and I of both eEF1A variants with TSPY. In the process, seven interacting residues of TSPY's NAP domain namely, Asp 175, Glu 176, Asp 179, Tyr 183, Asp 240, Glu 244, and Tyr 246 common to both eEF1A variants were detected. Additionally, six lysine residues observed in eEF1A2 suggest their possible role in TSPY-eEF1A2 complex formation essential for germ cell development and spermatogenesis. Thus, more efficient binding of TSPY with eEF1A2 as compared to that of eEF1A1 established autonomous functioning of these two variants. Studies on mutated protein following similar approach would uncover the causative obstruction, between the interacting partners leading to deeper understanding on the structure-function relationship.

Differential expression of Homeobox C11 protein in water buffalo Bubalus bubalis and its putative 3D structure.

BACKGROUND: The Homeobox (Hox) family complex contains 39 genes, clustered into four groups (A-D) all expressing in sequential manner. The HOX proteins are transcriptional factors involved in regulation of pattern formation of the anterio-posterior body axis across the species. Most of the Hox family genes have been studied with respect to their organization and expression during the embryonic stages. However, expression pattern of Homeobox C11 (Hoxc11) gene in the 5' region, particularly in higher mammals remains largely unexplored. RESULTS: We cloned and expressed Homeobox C11 (Hoxc11) gene from water buffalo Bubalus bubalis. The recombinant HOXC11 protein expressed as inclusion bodies was solubilized in Tris buffer (10 mM, pH-6.5) and purified using Ni-NTA affinity column. The purity and molecular weight of HOXC11 protein (~33 kDa) were confirmed by SDS-PAGE and western blot analysis. Employing immunohistochemistry approach, we localized HOXC11 protein in the nuclei across the tissues of buffalo. Western blot analysis showed highest expression of HOXC11 protein in kidney and lung although its possible renal and respiratory roles are not yet established. Electrophoretic mobility shift assay (EMSA) demonstrated the specific binding of HOXC11 protein with the promoter element, CE-LPH1 of lactase-phlorizin hydrolase (LPH) gene showing reduced mobility of the protein-DNA complex, corroborating with earlier report on the possible role of this protein in intestinal functions. In silico analysis of HOXC11 showed predominance of α helices and presence of six conserved domains. We deduced the putative 3D structure of HOXC11 protein and fifteen possible DNA interacting residues within the homeodomain. CONCLUSIONS: Present study augments our understanding on the specific expression of HOXC11 protein in kidney and lung in water buffalo. The fifteen DNA interacting residues reported herein provide an opportunity to establish much broader structural and functional perspectives of HOXC11 protein in the context of genome analysis in general and animal biotechnology in particular.