Role of mucin 2 gene for growth in Anas platyrhynchos: a novel report.

Introduction: The mucin gene is expressed in the mucous membrane of the inner layer of the internal organs. Intestinalmucin 2 (MUC2), amajor gel-formingmucin, represents a primary barrier component of mucus layers. Materials and methods: This is the first report on the role of mucin genes in growth traits in animals. In this study, we randomly studied Bengal ducks (Anas platyrhynchos) reared from day old to 10 weeks of age under an organized farm and studied the growth parameters as well as body weight and average daily body weight gain. Result and discussion: We characterized the mucin gene for Bengal ducks and observed glycosylation and EGF1 (EGF-like domain signature) as important domains for growth traits in ducks. We observed a better expression profile for the mucin gene in high-growing ducks in comparison to that of low-growing ducks with real-time PCR. Hence, the mucin gene may be employed as a marker for growth traits.

A sequence space search engine for computational protein design to modulate molecular functionality.

De-novo protein design explores the untapped sequence space that is otherwise less discovered during the evolutionary process. This necessitates an efficient sequence space search engine for effective convergence in computational protein design. We propose a greedy simulated annealing-based Monte-Carlo parallel search algorithm for better sequence-structure compatibility probing in protein design. The guidance provided by the evolutionary profile, the greedy approach, and the cooling schedule adopted in the Monte Carlo simulation ensures sufficient exploration and exploitation of the search space leading to faster convergence. On evaluating the proposed algorithm, we find that a dataset of 76 target scaffolds report an average root-mean-square-deviation (RMSD) of 1.07 Å and an average TM-Score of 0.93 with the modeled designed protein sequences. High sequence recapitulation of 48.7% (59.4%) observed in the design sequences for all (hydrophobic) solvent-inaccessible residues again establish the goodness of the proposed algorithm. A high (93.4%) intra-group recapitulation of hydrophobic residues in the solvent-inaccessible region indicates that the proposed protein design algorithm preserves the core residues in the protein and provides alternative residue combinations in the solvent-accessible regions of the target protein. Furthermore, a COFACTOR-based protein functional analysis shows that the design sequences exhibit altered molecular functionality and introduce new molecular functions compared to the target scaffolds.Communicated by Ramaswamy H. Sarma.

Modularity-based parallel protein design algorithm with an implementation using shared memory programming.

Given a target protein structure, the prime objective of protein design is to find amino acid sequences that will fold/acquire to the given three-dimensional structure. The protein design problem belongs to the non-deterministic polynomial-time-hard class as sequence search space increases exponentially with protein length. To ensure better search space exploration and faster convergence, we propose a protein modularity-based parallel protein design algorithm. The modular architecture of the protein structure is exploited by considering an intermediate structural organization between secondary structure and domain defined as protein unit (PU). Here, we have incorporated a divide-and-conquer approach where a protein is split into PUs and each PU region is explored in a parallel fashion. It has been further analyzed that our shared memory implementation of modularity-based parallel sequence search leads to better search space exploration compared to the case of traditional full protein design. Sequence-based analysis on design sequences depicts an average of 39.7% sequence similarity on the benchmark data set. Structure-based comparison of the modeled structures of the design protein with the target structure exhibited an average root-mean-square deviation of 1.17 Å and an average template modeling score of 0.89. The selected modeled structures of the design protein sequences are validated using 100 ns molecular dynamics simulations where 80% of the proteins have shown better or similar stability to the respective target proteins. Our study informs that our modularity-based protein design algorithm can be extended to protein interaction design as well.

RIGI, TLR7, and TLR3 Genes Were Predicted to Have Immune Response Against Avian Influenza in Indigenous Ducks.

Avian influenza is a disease with every possibility to evolve as a human-to-human pandemic arising out of frequent mutations and genetic reassortment or recombination of avian influenza (AI) virus. The greatest concern is that till date, no satisfactory medicine or vaccines are available, leading to massive culling of poultry birds, causing huge economic loss and ban on export of chicken products, which emphasizes the need to develop an alternative strategy for control of AI. In the current study, we attempt to explore the molecular mechanism of innate immune potential of ducks against avian influenza. In the present study, we have characterized immune response molecules such as duck TLR3, TLR7, and RIGI that are predicted to have potent antiviral activities against the identified strain of avian influenza through in silico studies (molecular docking) followed by experimental validation with differential mRNA expression analysis. Future exploitation may include immunomodulation with the recombinant protein, and transgenic or gene-edited chicken resistant to bird flu.

Ovine CD14- an Immune Response Gene Has a Role Against Gastrointestinal Nematode Haemonchus contortus-A Novel Report.

CD14 (also known as the monocyte differentiation antigen) is an important immune response gene known to be primarily responsible for innate immunity against bacterial pathogens, and as a pattern recognition receptor (PRR), binds with LPS (endotoxin), lipoproteins, and lipotechoic acid of bacteria. So far very limited work has been conducted in parasitic immunology. In the current study, we reported the role of CD14 in parasitic immunology in livestock species (sheep) for the first time. Ovine CD14 is characterized as a horse-shoe shaped bent solenoid with a hydrophobic amino-terminal pocket for CD14 along with domains. High mutation frequency was observed, out of total 41 mutations identified, 23 mutations were observed to be thermodynamically unstable and 11 mutations were deleterious in nature, causing major functional alteration of important domains of CD14, an indication of variations in individual susceptibility for sheep against Haemonchus contortus infestations. In silico studies with molecular docking reveal a role of immune response against Haemonchus contortus in sheep, which is later confirmed with experimental evidence through differential mRNA expression analysis for sheep, which revealed better expression of CD14 in Haemonchus contortus infected sheep compared to that of non-infected sheep. We confirmed the above findings with supportive evidence through haematological and biochemical analyses. Phylogenetic analysis was conducted to assess the evolutionary relationship with respect to humans and it was observed that sheep may well be used as model organisms due to better genetic closeness compared to that of mice.

A computational framework for modeling functional protein-protein interactions.

Protein interactions and their assemblies assist in understanding the cellular mechanisms through the knowledge of interactome. Despite recent advances, a vast number of interacting protein complexes is not annotated by three-dimensional structures. Therefore, a computational framework is a suitable alternative to fill the large gap between identified interactions and the interactions with known structures. In this work, we develop an automated computational framework for modeling functionally related protein-complex structures utilizing GO-based semantic similarity technique and co-evolutionary information of the interaction sites. The framework can consider protein sequence and structure information as input and employ both rigid-body docking and template-based modeling exploiting the existing structural templates and sequence homology information from the PDB. Our framework combines geometric as well as physicochemical features for re-ranking the docking decoys. The proposed framework has an 83% success rate when tested on a benchmark dataset while considering Top1 models for template-based modeling and Top10 models for the docking pipeline. We believe that our computational framework can be used for any pair of proteins with higher confidence to identify the functional protein-protein interactions.

RIG-I Has a Role in Immunity Against Haemonchus contortus, a Gastrointestinal Parasite in Ovis aries: A Novel Report.

Retinoic acid inducible gene I (RIG-I) is associated to the DExD/H box RNA helicases. It is a pattern recognition receptor (PRR), playing a crucial role in the system and is a germ line encoded host sensor to perceive pathogen-associated molecular patterns (PAMPs). So far, reports are available for the role of RIG-I in antiviral immunity. This is the first report in which we have documented the role of RIG-I in parasitic immunity. Haemonchus contortus is a deadly parasite affecting the sheep industry, which has a tremendous economic importance, and the parasite is reported to be prevalent in the hot and humid agroclimatic region. We characterize the RIG-I gene in sheep (Ovis aries) and identify the important domains or binding sites with Haemonchus contortus through in silico studies. Differential mRNA expression analysis reveals upregulation of the RIG-I gene in the abomasum of infected sheep compared with that of healthy sheep, further confirming the findings. Thus, it is evident that, in infected sheep, expression of RIG-I is triggered for binding to more pathogens (Haemonchus contortus). Genetically similar studies with humans and other livestock species were conducted to reveal that sheep may be efficiently using a model organism for studying the role of RIG-I in antiparasitic immunity in humans.

Molecular characterization of Bu-1 and TLR2 gene in Haringhata Black chicken.

Haringhata Black is the only registered indigenous poultry genetic resource of West Bengal till date. Molecular characterization of HB revealed that Bu-1 to be highly glycoylated transmembrane protein unlike mammalian Bu-1, whereas TLR2 of HB chicken was observed to be rich in Leucine rich repeat. HB chicken was observed to be genetically close to chicken of Japan, while distant to chicken breed of UK and Chicago. Avian species wise evolution study indicates genetic closeness of HB chicken with turkey. Differential mRNA expression profile for the immune response genes (TLR2, TLR4 and Bu1 gene) were studied for HB chicken with respect to other chicken breed and poultry birds, which reveals that HB chicken were better in terms of B cell mediated immunity and hence better response to vaccination. Hence HB chicken is one of the best poultry genetic resources to be reared under backyard system where biosecurity measures are almost lacking.

Mutation in Cytochrome B gene causes debility and adverse effects on health of sheep.

Cytochrome B is the mitochondrial protein, which functions as part of the electron transport chain and is the main subunit of transmembrane cytochrome bc1 and b6f complexes affecting energy metabolism through oxidative phosphorylation. The present study was conducted to study the effect of mutation of Cytochrome B gene on the health condition of sheep, which the first report of association of mitochondrial gene with disease traits in livestock species. Non-synonymous substitutions (F33 L and D171N) and Indel mutations were observed for Cytochrome B gene, leading to a truncated protein, where anemia, malfunctioning of most of the vital organs as liver, kidney and mineral status was observed and debility with exercise intolerance and cardiomyopathy in extreme cases were depicted. These findings were confirmed by bioinformatics analysis, haematological and biochemical data analysis, and other phenotypical physiological data pertaining to different vital organs. The molecular mechanism of cytochrome B mutation was that the mutant variant interferes with the site of heme binding (iron containing) domain and calcium binding essential for electron transport chain. Mutation at amino acid site 33 is located within transmembrane helix A, a hydrophobic environment at the Qi site and close to heme binding domain, and mutation effects these domain and diseases occur. Thermodynamic stability was also observed to decrease in mutant variant. Sheep Cytochrome B being genetically more similar to the human, it may be used as a model for studying human diseases related to cytochrome B defects. Future prospect of the study includes the therapeutic application of recombinant protein, gene therapy and marker-assisted selection of disease-resistant livestock.

Ebolavirus interferon antagonists-protein interaction perspectives to combat pathogenesis.

Zaire ebolavirus, one of the most pathogenic species of Ebolavirus, is a significant threat to the human community being both highly infectious and lethal. The viral proteins (VPs), specifically VP24 and VP35, antagonize the interferon (IFN) proteins accountable for human immune response. Several efforts have been made to design vaccines and therapeutics drugs. However, the success is not encouraging because of limited knowledge about the binding site information of the VPs. Such limitations stem largely from the highly infectious nature of the virus that requires specialized personnel and biosafety laboratories. As an alternative, computational techniques have also been adopted to improve the success rate of drug discovery. This article elaborates on the interactions between viral and human IFN proteins that lead to IFN antagonism. A computational framework is proposed after evaluating existing computational studies. This protein interaction and protein design-based computational framework identified critical interacting residues of the VP (VP24) responsible for the formation of a stable complex with the human KPNA5 (karyopherin alpha proteins 5). The mutations of those critical residues, as demonstrated in this article, affected the overall stability of the complex because of a sharp decrease in both the number of hydrogen bonds and possible charge-charge interactions. Therefore, we proposed that the framework could be an effective alternative to experimental work for destabilizing interactions between the VPs and human proteins responsible for IFN induction and response.