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

Published date : 30 May 2017

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
Impact Factor
3.867

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

Published date : 26 May 2017

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
Impact Factor
4.259

Role of N-glycosylation in EGFR ectodomain ligand binding

Published date : 25 May 2017

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
Impact Factor
2.289

A Study of Nuclei Classification Methods in Histopathological Images

Published date : 21 May 2017

Cancer is a group of diseases involving abnormal cell growth with varying malignancy and extent across different patients. Cytological features like prominent nucleoli, nuclear enlargement, and hyperchromasia are important to the tumor pathologist in assessment of cancer malignancy from tissue biopsies. In a recent study, Yap et al. [21] proposed effective prominent nucleoli detectors in histopathological images and developed different feature generation methods.

type
Conference Paper/Poster
journal
Proceedings of the 5th KES International Conference on Innovation in Medicine and Healthcare (KES-InMed 2017)

Outbreak of Zika virus infection in Singapore: an epidemiological, entomological, virological, and clinical analysis

Published date : 17 May 2017

BACKGROUND:
An outbreak of Zika virus infection was detected in Singapore in August, 2016. We report the first comprehensive analysis of a national response to an outbreak of Zika virus infection in Asia.

METHODS:

type
Journal Paper
journal
The Lancet Infectious Diseases, Vol. 17, No. 8, pg 813-821, Aug 2017, doi: 10.1016/S1473-3099(17)30249-9
Impact Factor
19.864

Designing dual inhibitors of Mdm2/MdmX: Unexpected coupling of water with gatekeeper Y100/99

Published date : 17 May 2017

Mdm2 and MdmX share high structural similarity in their N-terminal domains, yet dual inhibitors are challenging to design due to differences in the conformations of the binding pockets, and notably of the proposed gatekeeper residue, Y100/99. Analysis of crystal structures and molecular dynamics (MD) simulations of complexes of Mdm2 and MdmX resulted in the identification of a water molecule with a long residence time that appears to be modulated by the conformation of Y100/99.

type
Journal Paper
Impact Factor
2.289

Modeling the Structure of Keratin 1 and 10 Terminal Domains and their Misassembly in Keratoderma

Published date : 16 May 2017

The terminal domains of suprabasal keratins of the skin epithelium are very resistant to evidence-based structural analysis because of their inherent flexibility and lack of predictable structure. We present a model for the structure and interactions of the head and tail domains of epidermal keratins 1 and 10, based on all-atom 3D simulations of keratin primary amino acid sequences, and tyrosine phosphorylation predictions, extracted from published databases.

type
Journal Paper
journal
Journal of Investigative Dermatology, 2017 May 16. pii: S0022-202X(17)31522-1. doi: 10.1016/j.jid.2017.03.038
Impact Factor
6.287

Hydration effects on the efficacy of the Epidermal growth factor receptor kinase inhibitor afatinib

Published date : 08 May 2017

Small molecules targeting the EGFR tyrosine kinase domain have been used with some success at treating patients with non-small cell lung cancer driven by activating mutations in the kinase domain. The initial class of inhibitors displaced ATP noncovalently but were rendered ineffective due to the development of resistance mutations in the kinase domain. These were overcome by the development of covalent inhibitors such as afatinib which also bind in the ATP pocket.

type
Journal Paper
journal
Scientific Reports 7, Article no: 1540 (2017), doi:10.1038/s41598-017-01491-z
Impact Factor
4.259

Aggregation of thrombin-derived C-terminal fragments as a previously undisclosed host defense mechanism

Published date : 04 May 2017

Effective control of endotoxins and bacteria is crucial for normal wound healing. During injury, the key enzyme thrombin is formed, leading to generation of fibrin. Here, we show that human neutrophil elastase cleaves thrombin, generating 11-kDa thrombin-derived C-terminal peptides (TCPs), which bind to and form amorphous amyloid-like aggregates with both bacterial lipopolysaccharide (LPS) and gram-negative bacteria.

type
Journal Paper
journal
Proceedings of the National Academy of Sciences (PNAS), May 4, 2017, doi: 10.1073/pnas.1619609114
Impact Factor
9.661

Progress in Molecular Dynamics Simulations of Bacterial Cell Envelopes

Published date : 03 May 2017

Bacteria are protected by complex molecular architectures known as the cell envelope. The cell envelope is composed of regions with distinct chemical compositions and physical properties, namely, membranes and a cell wall. To develop novel antibiotics to combat pathogenic bacteria, molecular level knowledge of the structure, dynamics, and interplay between the chemical components of the cell envelope that surrounds bacterial cells is imperative.

type
Journal Paper
journal
The Journal of Physical Chemistry Letters, 2017 Jun 1;8(11):2513-2518. doi: 10.1021/acs.jpclett.7b00473
Impact Factor
9.353