Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses

Published date : 18 Jul 2017

Objective To analyse the proportions of protein identity between Zika virus and dengue, Japanese encephalitis, yellow fever, West Nile and chikungunya viruses as well as polymorphism between different Zika virus strains.

type
Journal Paper
journal
Bulletin of the World Health Organization, 2017, Jul 1: 95(7): Pg 517-525i
Impact Factor
4.939

Molecular features of influenza A (H1N1) pdm09 prevalent in Mexico during winter seasons 2012-2014

Published date : 10 Jul 2017

Since the emergence of the pandemic H1N1pdm09 virus in Mexico and California, biannual increases in the number of cases have been detected in Mexico. As observed in previous seasons, pandemic A/H1N1 09 virus was detected in severe cases during the 2011-2012 winter season and finally, during the 2013-2014 winter season it became the most prevalent influenza virus. Molecular and phylogenetic analyses of the whole viral genome are necessary to determine the antigenic and pathogenic characteristics of influenza viruses that cause severe outcomes of the disease.

type
Journal Paper
journal
PLOs One, July 10, 2017, doi: 10.1371/journal.pone.0180419
Impact Factor
2.8

AlloSigMA: Allosteric Signalling and Mutation Analysis server

Published date : 06 Jul 2017

Motivation: Allostery is an omnipresent mechanism of the function modulation in proteins via either effector binding or mutations in the exosites. Despite the growing number of on-line servers and databases devoted to prediction/classification of allosteric sites and their characteristics, there is a lack of resources for an efficient and quick estimation of the causality and energetics of allosteric communication.

type
Journal Paper
journal
Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx430
Impact Factor
7.307

Semi-automated quantitative Drosophila wings measurements

Published date : 28 Jun 2017

BACKGROUND:
Drosophila melanogaster is an important organism used in many fields of biological research such as genetics and developmental biology. Drosophila wings have been widely used to study the genetics of development, morphometrics and evolution. Therefore there is much interest in quantifying wing structures of Drosophila. Advancement in technology has increased the ease in which images of Drosophila can be acquired. However such studies have been limited by the slow and tedious process of acquiring phenotypic data.

RESULTS:

type
Journal Paper
journal
BMC Bioinformatics 2017 Jun 28;18(1):319. doi: 10.1186/s12859-017-1720-y
Impact Factor
2.435

A Spring-Loaded Mechanism Governs the Clamp-like Dynamics of the Skp Chaperone

Published date : 22 Jun 2017

The trimeric periplasmic holdase chaperone Skp binds and stabilizes unfolded outer membrane proteins (OMPs) as part of bacterial OMP biogenesis. Skp binds client proteins in its central cavity, thereby reducing its backbone dynamics, but the molecular mechanisms that govern Skp dynamics and adaptation to differently sized clients remains unknown.

type
Journal Paper
journal
Structure, 2017 Jul 5;25(7):1079-1088.e3. doi: 10.1016/j.str.2017.05.018
Impact Factor
5.618

Gland segmentation in prostatehistopathological images

Published date : 21 Jun 2017

Glandular structural features are important for the tumor pathologist in the assessment of cancer malignancy of prostate tissue slides. The varying shapes and sizes of glands combined with the tedious manual observation task can result in inaccurate assessment. There are also discrepancies and low-level agreement among pathologists, especially in cases of Gleason pattern 3 and pattern 4 prostate adenocarcinoma. An automated gland segmentation system can highlight various glandular shapes and structures for further analysis by the pathologist.

type
Journal Paper
journal
Journal of Medical Imaging, 2017 Apr;4(2):027501, doi: 10.1117/1.JMI.4.2.027501

The role of apical contractility in determining cell morphology in multilayered epithelial sheets and tubes

Published date : 19 Jun 2017

A multilayered epithelium is made up of individual cells that are stratified in an orderly fashion, layer by layer. In such tissues, individual cells can adopt a wide range of shapes ranging from columnar to squamous. From histological images, we observe that, in flat epithelia such as the skin, the cells in the top layer are squamous while those in the middle and bottom layers are columnar, whereas in tubular epithelia, the cells in all layers are columnar.

type
Journal Paper
journal
Physical Biology, Vol. 14, No. 4, 2017, doi: 10.1088/1478-3975/aa7afc
Impact Factor
1.837

The role of Antibody Vκ Framework 3 region towards Antigen binding: Effects on recombinant production and Protein L binding

Published date : 19 Jun 2017

Antibody research has traditionally focused on heavy chains, often neglecting the important complementary role of light chains in antibody formation and secretion. In the light chain, the complementarity-determining region 3 (VL-CDR3) is specifically implicated in disease states. By modulating VL-CDR3 exposure on the scaffold through deletions in the framework region 3 (VL-FWR3), we further investigated the effects on secretion in recombinant production and antigen binding kinetics.

type
Journal Paper
journal
Scientific Reports 7, Article no: 3766 (2017), doi:10.1038/s41598-017-02756-3
Impact Factor
4.259

The interfacial character of antibody paratopes: analysis of antibody-antigen structures

Published date : 16 Jun 2017

In this study, computational methods are applied to investigate the general properties of antigen engaging residues of a paratope from a non-redundant dataset of 403 antibody-antigen complexes to dissect the contribution of hydrogen bonds, hydrophobic, van der Waals contacts and ionic interactions, as well as role of water molecules in the antigen-antibody interface. Consistent with previous reports using smaller datasets, we found that Tyr, Trp, Ser, Asn, Asp, Thr, Arg, Gly, His contribute substantially to the interactions between antibody and antigen.

type
Journal Paper
journal
Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx389
Impact Factor
7.307

Targeting YAP/TAZ-TEAD protein-protein interactions using fragment-based and computational modeling approaches

Published date : 01 Jun 2017

The Hippo signaling pathway, which is implicated in the regulation of organ size, has emerged as a potential target for the development of cancer therapeutics. YAP, TAZ (transcription co-activators) and TEAD (transcription factor) are the downstream transcriptional machinery and effectors of the pathway. Formation of the YAP/TAZ-TEAD complex leads to transcription of growth-promoting genes. Conversely, disrupting the interactions of the complex decreases cell proliferation. Herein, we screened a 1000-member fragment library using Thermal Shift Assay and identified a hit fragment.

type
Journal Paper
journal
PLoS One, 2017 Jun 1, doi: org/10.1371/journal.pone.0178381
Impact Factor
2.8