Immunoinformatics Approach to Design T-cell Epitope-Based Vaccine Against Hendra Virus

Screening of HLA class II epitope-based peptides as potential vaccine candidates is one of the most rational approach for vaccine development against Hendra virus (HeV) infection, for which currently there is no successful vaccine in practice. In this study, screening of epitopes from HeV proteins viz matrix, glycoprotein, nucleocapsid, fusion, C protein, V protein, W protein and polymerase, followed by highest binding affinity & molecular dynamic simulation of selected T-cell epitopes with their corresponding HLA class II alleles has been done. The server ProPred facilitates the binding prediction of HLA class II allele specific epitopes from the antigenic protein sequences of HeV. PEPstrMOD server was used for PDB structure modeling of the screened epitopes and MODELLER was used for HLA alleles modeling. We docked the selected T-cell epitopes with their corresponding HLA allele structures using the AutoDock 4.2 tool. Further the selected docked complex structures were optimized by NAnoscale Molecular Dynamics program (NAMD) at 5 ps, with the CHARMM-22 force field parameter incorporated in Visual Molecular Dynamics (VMD 1.9.2) and complex structure stability was evaluated by calculating RMSD values. Epitopes IRIFVPATN (Nucleocapsid), MRNLLSQSL (Nucleocapsid), VRRAGKYYS (Matrix) and VRLKCLLCG (Fusion) proteins have shown considerable binding with DRB1*0806, DRB1*1304, DRB1*0701 and DRB1*0301 HLA class II allele respectively. Toxicity, antigenicity and population coverage of epitopes IRIFVPATN, MRNLLSQSL, VRRAGKYYS and VRLKCLLCG were analyzed by Toxin Pred, Vexijen and IEDB tool, respectively. The potential T-cell epitopes can be utilized in designing comprehensive epitope-based vaccines and diagnostic kits against Hendra virus after further in-vivo studies.

     

The Role of Resting State Networks in Focal Neocortical Seizures

Objective

The role of resting state functional networks in epilepsy is incompletely understood. While some pathologic diagnoses have been shown to have maintained but altered resting state connectivity, others have implicated resting state connectivity in disease progression. However little is known about how these resting state networks influence the behavior of a focal neocortical seizure.

Methods

Using data taken from invasively monitored patients with intractable focal neocortical epilepsy, we evaluated network connectivity (as determined by oscillatory covariance of the slow cortical potential (<0.5 Hz)) as it relates to neocortical seizure foci both in the interictal and ictal states.

Results

Similar to what has been shown in the past for sleep and anesthesia, electophysiologic resting state networks that are defined by this slow cortical potential covariance maintain their topographic correlation structure throughout an ictal event. Moreover, in the context of focal epilepsy in which the seizure has a specific site of onset, seizure propagation is not chaotic or random. Rather, the seizure (reflected by an elevation of high frequency power) preferentially propagates along the network that contains the seizure onset zone.

Significance

Taken together, these findings further undergird the fundamental role of resting state networks, provide novel insights into the network-influenced behavior of seizures, and potentially identify additional targets for surgical disconnection including informing the location for the completion of multiple subpial transections (MSPTs).     

Germline soma communication mediated by gap junction proteins regulates epithelial morphogenesis

Gap junction (GJ) proteins, the primary constituents of GJ channels, are conserved determinants of patterning. Canonically, a GJ channel, made up of two hemi-channels contributed by the neighboring cells, facilitates transport of metabolites/ions. Here we demonstrate the involvement of GJ proteins during cuboidal to squamous epithelial transition displayed by the anterior follicle cells (AFCs) from Drosophila ovaries. Somatically derived AFCs stretch and flatten when the adjacent germline cells start increasing in size. GJ proteins, Innexin2 (Inx2) and Innexin4 (Inx4), functioning in the AFCs and germline respectively, promote the shape transformation by modulating calcium levels in the AFCs. Our observations suggest that alterations in calcium flux potentiate STAT activity to influence actomyosin-based cytoskeleton, possibly resulting in disassembly of adherens junctions. Our data have uncovered sequential molecular events underlying the cuboidal to squamous shape transition and offer unique insight into how GJ proteins expressed in the neighboring cells contribute to morphogenetic processes.     

Homogeneous screening assay for human tankyrase

Tankyrase, a member of human PARP protein superfamily, catalyzes a covalent post-translational modification of substrate proteins. This modification, poly(ADP-ribos)ylation, leads to changes in protein interactions and modifies downstream signaling events. Tankyrase 1 is a potential drug target due to its functions in telomere homeostasis and in Wnt signaling. We describe here optimization and application of an activity-based homogenous assay for tankyrase inhibitors in a high-throughput screening format. The method measures the consumption of substrate by the chemical conversion of the remaining NAD(+) into a stable fluorescent condensation product. Conditions were optimized to measure the enzymatic auto-modification of a recombinant catalytic fragment of tankyrase 1. The fluorescence assay is inexpensive, operationally easy and performs well according to the statistical analysis (Z'= 0.7). A validatory screen with a natural product library confirmed suitability of the assay for finding new tankyrase inhibitors. Flavone was the most potent (IC(50)=325 nM) hit from the natural compounds. A flavone derivative, apigenin, and isopropyl gallate showed potency on the micromolar range, but displayed over 30-fold selectivity for tankyrase over the studied isoenzymes PARP1 and PARP2. The assay is robust and will be useful for screening new tankyrase inhibitors.     

Biotransformation of chlorpyrifos and bioremediation of contaminated soil

Five aerobic consortia capable of degrading chlorpyrifos as a sole carbon source in aqueous medium showed degradation in the range of 46–72% after 20 days. Pseudomonas fluorescence, Brucella melitensis, Bacillus subtilis, Bacillus cereus, Klebsiella species, Serratia marcescens and Pseudomonas aeroginosa, isolated from these consortium, showed 75–87% degradation of chlorpyrifos as compared to 18% in control after 20 days of incubation. Bioremediation of chlorpyrifos-contaminated soil with P. fluorescence, B. melitensis, B. subtilis and P. aeroginosa individually showed 89%, 87%, 85% and 92% degradation, respectively, as compared to 34% in control after 30 days. Population dynamics of the introduced isolates based on antibiotic resistance survival and REP-PCR indicated 60–70% survival based on antibiotic resistance, but only 35–45% of the inoculated population based on REP-PCR. During bioremediation studies, 3,5,6-trichloro-2-pyridinol (TCP) was detected as metabolite of chlorpyrifos degradation by P. aeroginosa after 20 days, which was utilized and disappeared after 30 days. Whole-cell studies also showed that P. aeroginosa gave TCP as the product of chlorpyrifos degradation, which was further metabolized to unknown polar metabolites.

Scientific relevance

Potential application in sites for effective in situ bioremediation of chlorpyrifos, a neurotoxic insecticide widely used in India.     

Missing Girls in India: Infanticide,Feticide and Made-to-Order Pregnancies? Insights from Hospital-Based Sex-Ratio-at-Birth over the Last Century

Background

There are 44 million missing women in India. Gender bias; neglect of girls, infanticides and feticides are responsible. The sex ratio at birth can be used to examine the influence of antenatal sex selection on the sex ratio.

Materials and Methods

Records from 321,991 deliveries at one hospital over 11 decades were utilized. The middle year in each decade was taken as representative of the decade. Data from 33,524 deliveries were then analyzed. Data for each decade was combined with that of previous decades and compared to the data of subsequent decades to look for any change in the trend. Sex ratio in the second children against sex of the first child was studied separately.

Results

The mean sex ratio for the 110 years examined was 910 girls to 1000 boys (95% CI; 891 to 930). The sex ratio dropped significantly from 935 (CI: 905 to 967) before 1979, to 892 (CI: 868 to 918) after 1980 (P = 0.04). The sex ratio in the second child was significantly lower if the first child was a girl [716 (CI: 672 to 762] (P<0.001). On the other hand, there was an excess of girls born to mothers whose first child was boy [1140 girls per 1000 boys (CI: 1072 to 1212 P<0.001)].

Conclusions

The sex ratio fell significantly after 1980 when ultra sound machines for antenatal sex determination became available. The sex ratio in second children if the first was a girl was even lower. Sex selective abortions after antenatal sex determination are thus implicated. However data on second children especially the excess of girls born to mothers who have a previous boy seen in the decade before the advent of antenatal ultra sound machines, suggests that other means of sex selection are also used.     

Calcium signaling induces a partial EMT

Epithelial plasticity, or epithelial‐to‐mesenchymal transition (EMT), is a well‐recognized form of cellular plasticity, which endows tumor cells with invasive properties and alters their sensitivity to various agents, thus representing a major challenge to cancer therapy. It is increasingly accepted that carcinoma cells exist along a continuum of hybrid epithelial–mesenchymal (E‐M) states and that cells exhibiting such partial EMT (P‐EMT) states have greater metastatic competence than those characterized by either extreme (E or M). We described recently a P‐EMT program operating in vivo by which carcinoma cells lose their epithelial state through post‐translational programs. Here, we investigate the underlying mechanisms and report that prolonged calcium signaling induces a P‐EMT characterized by the internalization of membrane‐associated E‐cadherin (ECAD) and other epithelial proteins as well as an increase in cellular migration and invasion. Signaling through Gαq‐associated G‐protein‐coupled receptors (GPCRs) recapitulates these effects, which operate through the downstream activation of calmodulin‐Camk2b signaling. These results implicate calcium signaling as a trigger for the acquisition of hybrid/partial epithelial–mesenchymal states in carcinoma cells.