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

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
pubmed: 
28692701
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28692701
Impact Factor: 
2.8
Date of acceptance: 
2017-07-20

AlloSigMA: Allosteric Signalling and Mutation Analysis server

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
Url: 
https://doi.org/10.1093/bioinformatics/btx430
Impact Factor: 
7.307
Date of acceptance: 
2017-07-29

Semi-automated quantitative Drosophila wings measurements

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
pubmed: 
28659123
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28659123
Impact Factor: 
2.435
Date of acceptance: 
2017-06-09

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

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
pubmed: 
28648612
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28648612
Impact Factor: 
5.618

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

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
Url: 
https://www.nature.com/articles/s41598-017-02756-3
Impact Factor: 
4.259
Date of acceptance: 
2017-04-18

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

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
Url: 
https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx389
Impact Factor: 
7.307
Date of acceptance: 
2017-06-11

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

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
Url: 
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178381
Impact Factor: 
2.8
Date of acceptance: 
2017-05-11

Systems-based approach to examine the cytokine responses in primary mouse lung macrophages infected with low pathogenic avian Influenza virus circulating in South East Asia

BACKGROUND:
Influenza A virus (IAV) is a major public health concern, being responsible for the death of approximately half a million people each year. Zoonotic transmissions of the virus from swine and avian origin have occurred in the past, and can potentially lead to the emgergence of new IAV stains in future pandemics. Pulmonary macrophages have been implicated in disease severity in the lower airway, and understanding the host response of macrophages infected with avian influenza viruses should provide new therapeutic strategies.

RESULTS:

type: 
Journal Paper
journal: 
BMC Genomics. 2017 May 30;18(1):420. doi: 10.1186/s12864-017-3803-6
pubmed: 
28558796
Url: 
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3803-6
Impact Factor: 
3.867
Date of acceptance: 
2017-05-05

A novel community driven software for functional enrichment analysis of extracellular vesicles data

Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture “what the community needs in a tool”. Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes.

type: 
Journal Paper
journal: 
Journal of Extracellular Vesicles 2017, Vol. 6, 2017, Issue 1, doi: 10.1080/20013078.2017.1321455
Url: 
http://www.tandfonline.com/doi/abs/10.1080/20013078.2017.1321455
Impact Factor: 
4.259

Role of N-glycosylation in EGFR ectodomain ligand binding

The epidermal growth factor receptor (EGFR) is a tyrosine kinase protein, overexpressed in several cancers. The extracellular domain of EGFR is known to be heavily glycosylated. Growth factor (mostly epidermal growth factor or EGF) binding activates EGFR. This occurs by inducing the transition from the autoinhibited tethered conformation to an extended conformation of the monomeric form of EGFR and by stabilizing the flexible preformed dimer.

type: 
Journal Paper
journal: 
Proteins: Structure, Function, and Bioinformatics, Vol. 85, Issue 8, Aug 2017, Pg. 1529-1549, doi: 10.1002/prot.25314
pubmed: 
28486782
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28486782
Impact Factor: 
2.289
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