In silico structural and functional modelling of Antifreeze protein (AFP) sequences of Ocean pout (Zoarces americanus, Bloch & Schneider 1801)

Antifreeze proteins (AFPs) are known to polypeptide components formed by certain plants, animals, fungi and bacteria which support to survive in sub-zero temperature. Current study highlighted the seven different antifreeze proteins of fish Ocean pout (Zoarces americanus), in which protein (amino acids sequence) were collected from National Centre for Biotechnology Information and finely characterized using several in silico tools. Such biocomputational techniques applied to figure out the physicochemical, functional and conformational characteristics of targeted AFPs. Multiple physicochemical properties such as Isoelectric Point, Extinction Coefficient and Instability Index, Aliphatic Index, Grand Average Hydropathy were calculated and analysed by ExPASy-ProtParam prediction web server. EMBOSS: pepwheel online tool was used to represent the protein sequences in a helical form. The primary structure analysis shows that most of the AFPs are hydrophobic in nature due to the high content of non-polar residues. The secondary structure of these proteins was calculated using SOPMA tool. SOSUI server and CYS_REC program also run for ideal prediction of transmembrane helices and disulfide bridges of experimental proteins respectively. The modelling of 3D structures of seven desired AFPs were executed by the homology modelling programmes; SWISS MODEL and ProSA web server. UCSF Chimera, Antheprot 3D, PyMOL and RAMPAGE were used to visualize and analysis of the structural variation of the predicted protein model. MEGA7.0.9 software used to know the phylogenetic relationship among these AFPs. These models offered excellent and reliable baseline information for functional characterization of the experimentally derived protein domain composition by using the advanced tools and techniques of Computational Biology.     

Rotaviral nonstructural protein 4 triggers dynamin‐related protein 1‐dependent mitochondrial fragmentation during infection

Dynamic equilibrium between mitochondrial fission and mitochondrial fusion serves as an important quality control system within cells ensuring cellular vitality and homeostasis. Viruses often target mitochondrial dynamics as a part of their obligatory cellular reprogramming. The present study was undertaken to assess the status and regulation of mitochondrial dynamics during rotavirus infection. Distinct fragmentation of mitochondrial syncytia was observed during late hours of RV (SA11, Wa, A5‐13) infection. RV nonstructural protein 4 (NSP4) was identified as the viral trigger for disrupted mitochondrial morphology. Severance of mitochondrial interconnections was found to be a dynamin‐related protein 1 (Drp1)‐dependent process resulting synergistically from augmented mitochondrial fission and attenuated mitochondrial fusion. Cyclin‐dependent kinase 1 was subsequently identified as the cellular kinase responsible for fission‐active Ser616 phosphorylation of Drp1. In addition to its positive role in mitochondrial fission, Drp1 also resulted in mitochondrial translocation of E3‐ubiquitin ligase Parkin leading to degradation of mitochondrial fusion protein Mitofusin 1. Interestingly, RV‐NSP4 was found to interact with and be involved in recruiting fission‐active pool of Serine 616 phosphoDrp1 (Ser616 pDrp1) to mitochondria independent of accessory adaptors Mitochondrial fission factor and Fission protein 1 (Fis1). Inhibition of either Drp1 or Ser616 pDrp1 resulted in significant decrease in RV‐NSP4‐induced intrinsic apoptotic pathway. Overall, this study underscores an efficient strategy utilised by RV to couple apoptosis to mitochondrial fission facilitating dissemination of viral progeny.     

Breast Cancer Stem Cell Therapeutics,Multiple Strategies Versus Using Engineered Mesenchymal Stem Cells With Notch Inhibitory Properties: Possibilities and Perspectives

Relapse cases of cancers are more vigorous and difficult to control due to the preponderance of cancer stem cells (CSCs). Such CSCs that had been otherwise dormant during the first incidence of cancer gradually appear as radiochemoresistant cancer cells. Hence, cancer therapeutics aimed at CSCs would be an effective strategy for mitigating the cancers during relapse. Alternatively, CSC therapy can also be proposed as an adjuvant therapy, along‐with the conventional therapies. As regenerative stem cells (RSCs) are known for their trophic effects, anti‐tumorogenicity, and better migration toward an injury site, this review aims to address the use of adult stem cells such as dental pulp derived; cord blood derived pure populations of regenerative stem cells for targeting CSCs. Indeed, pro‐tumorogenicity of RSCs is of concern and hence has also been dealt with in relation to breast CSC therapeutics. Furthermore, as notch signaling pathways are upregulated in breast cancers, and anti‐notch antibody based and sh‐RNA based therapies are already in the market, this review focuses the possibilities of engineering RSCs to express notch inhibitory proteins for breast CSC therapeutics. Also, we have drawn a comparison among various possibilities of breast CSC therapeutics, about, notch1 inhibition. J. Cell. Biochem. 119: 141–149, 2018. © 2017 Wiley Periodicals, Inc.     

Therapeutic potential of Lactobacillus ingluviei ADK10, a newly established probiotic organism against acetaminophen induced uremic rats

In the present study, Lactobacillus ingluviei ADK10 (Acc. No. JQ395039) from intestinal origin was tested for its probiotic characteristic as well as uremia ameliorating activity on acetaminophen induced uremic rats. The results revealed that L. ingluviei ADK10 was able to tolerate pH 3.0–9.0 and 0.5% bile salt along with good hydrophobicity (67%) and adherence index with Ht-29 cell line on 258/100 cells. It was susceptible to 20 antibiotics. The organism was able to degrade food ingredients, like starch and milk proteins. The strain showed significant growth inhibition of Escherichia coli, Bacillus subtilis, Staphylococcus aureus, Shigella dysentery, Pseudomonas aeruginosa, and Klebsiella pneumoniae (average diameter of 10 mm). The therapeutic potentiality of this probiotic bacterium was tested against acetaminophen induced uremic rats. It was found that supplementation of L. ingluviei ADK10 for 14 days with food reduced severe increase of uremic profiles, such as blood urea (85%), creatinine (68%) and uric acid (41%) in comparison to the uremic rats. Moreover, during the feeding of rats with probiotic strain at a dose of 1×10⁹ bacteria, reduction of enterobacteria in faeces was observed. Our studies indicated that L. ingluviei ADK10 could be used as a health-promoting probiotic along with antiuremic efficacy.     

Molecular Evolution of the HIV-1 Thai Epidemic between the Time of RV144 Immunogen Selection to the Execution of the Vaccine Efficacy Trial

The RV144 HIV-1 vaccine trial (Thailand, 2003 to 2009), using immunogens genetically matched to the regional epidemic, demonstrated the first evidence of efficacy for an HIV-1 vaccine. Here we studied the molecular evolution of the HIV-1 epidemic from the time of immunogen selection to the execution of the efficacy trial. We studied HIV-1 genetic diversity among 390 volunteers who were deferred from enrollment in RV144 due to preexisting HIV-1 infection using a multiregion hybridization assay, full-genome sequencing, and phylogenetic analyses. The subtype distribution was 91.7% CRF01_AE, 3.5% subtype B, 4.3% B/CRF01_AE recombinants, and 0.5% dual infections. CRF01_AE strains were 31% more diverse than the ones from the 1990s Thai epidemic. Sixty-nine percent of subtype B strains clustered with the cosmopolitan Western B strains. Ninety-three percent of B/CRF01_AE recombinants were unique; recombination breakpoint analysis showed that these strains were highly embedded within the larger network that integrates recombinants from East/Southeast Asia. Compared to Thai sequences from the early 1990s, the distance to the RV144 immunogens increased 52% to 68% for CRF01_AE Env immunogens and 12% to 29% for subtype B immunogens. Forty-three percent to 48% of CRF01_AE sequences differed from the sequence of the vaccine insert in Env variable region 2 positions 169 and 181, which were implicated in vaccine sieve effects in RV144. In conclusion, compared to the molecular picture at the early stages of vaccine development, our results show an overall increase in the genetic complexity of viruses in the Thai epidemic and in the distance to vaccine immunogens, which should be considered at the time of the analysis of the trial results.     

Quantitative analysis strengthens qualitative assessment: a case study of Devonian brachiopod species

Species recognition attributed to the brachiopod family Atrypidae is evaluated based on qualitative and quantified morphological characters. I identified two brachiopod species—Pseudoatrypa lineata and Pseudoatrypa devoniana—from a rich assemblage of brachiopods recovered from the middle Devonian Genshaw Formation of the Traverse Group. Qualitative examination suggested that the former had fine-medium-sized ribbing, a narrow hinge line, widened anterior, moderately steep mid-anterior fold, domal shaped dorsal valve, and an inflated ventral valve in contrast to the coarse ribbing, widened hinge line, narrow anterior, gentle mid-anterior fold, arched-shape dorsal valve, and flat ventral valve of the latter. The shell outline appears rounded for P. lineata and elongated for P. devoniana. Quantitative assessment of the morphological characters on the dorsal, ventral, anterior, and posterior regions of the valves of the two species using geometric morphometric and statistical analyses suggests that the morphologies of the two species are considerably different (P  $ \ll $  0.01). Thus, qualitative differences between the two atrypid species were further corroborated by quantitative results. This emphasizes the fact that these two species of Pseudoatrypa were indeed different from each other. This study highlights the necessity of incorporating quantified morphological characters to successfully investigate the taxonomic distinctness of fossil invertebrates to the species level.     

NMR Structures of a Nonapeptide from DNA Binding Domain of Human Polymerase-α Determined by Iterative Complete-Relaxation-Matrix Approach

Abstract

Nuclear magnetic resonance structures of a nonapeptide, ERFKCPCPT, selected from the DNA binding domain of human polymerase-a, were determined by complete relaxation matrix analysis of transverse NOE data. The structures exhibit a type III turn with residues KCPC, and the remaining residues exhibit non-ordered structures. The turn was confirmed by α, N (i,i+3) connectivity, a low temperature coefficient of NH chemical shift (?3.1 × 1O^?3) of the fourth residue, ³J_NHα coupling constants, and characteristic CD peaks at 228 and 200 nm. Furthermore, ø and ψ dihedral angles for the i + 1, and i + 2 residues of the tum are found to be?80 and?41 and?60 and?40 degrees. The first proline residue is trans- while the second exists in both eis- and trans- configurations, with trans- being more than 80% populated. The trans-configuration was established from C5α-P6α correlation and ø and ψ angles of the proline. The five-membered proline ring is in DOWN puckered (C-β-exo/C-γ-endo) conformation. The structure of the peptide reveals that the two cysteine thiols are?5 A° apart and appropriately positioned to covalently bind cis-diamminedichloroplatinum(II), a widely used anti-cancer drug.