Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes

With the increasing accumulation of genomic sequence information of prokaryotes, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern within and across cyanobacterial species belonging to diverse taxonomic orders and habitats. We performed detailed comparative analysis of cyanobacterial genomes with respect to codon bias. Our analysis reflects that in cyanobacterial genomes, A- and/or T-ending codons were used predominantly in the genes whereas G- and/or C-ending codons were largely avoided.

type: 
Journal Paper
journal: 
Marine Genomics 2016 Oct 9, doi: 10.1016/j.margen.2016.10.00
pubmed: 
27733306
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27733306
Impact Factor: 
1.883
Date of acceptance: 
2016-10-03

Hydrocarbons are essential for optimal cell size, division and growth of cyanobacteria

Cyanobacteria are intricately organized, incorporating an array of internal thylakoid membranes, the site of photosynthesis, into cells no larger than other bacteria. They also synthesize C15-C19 alkanes and alkenes, which results in substantial production of hydrocarbons in the environment. All sequenced cyanobacteria encode hydrocarbon biosynthesis pathways, suggesting an important, undefined physiological role for these compounds. Here, we demonstrate that hydrocarbon-deficient mutants of Synechococcus sp. PCC 7002 and Synechocystis sp.

type: 
Journal Paper
journal: 
Plant Physiology Nov 2016, Vol. 172, No 3, Pg 1928-1940, doi:10.1104/pp.16.01205
pubmed: 
27707888
Url: 
http://www.plantphysiol.org/content/172/3/1928.long
Impact Factor: 
6.28
Date of acceptance: 
2016-10-05

Stapled peptide design: principles and roles of computation

Stapling is a key technique for stabilising peptides in an α-helical structure. The resultant stapled peptides are then able to compete efficiently for binding to protein targets involved in protein-protein interactions that are mediated by α-helices. Certain general design principles to optimise their binding and biological activity have emerged in recent years. This is accompanied by an increasing use of computational methods in stapled peptide design. In this article, we detail these design principles and review the contributions that computation has made to the field.

type: 
Journal Paper
journal: 
Drug Discovery Today, Vol. 21, Issue 10, October 2016, Pg 1642-1653, doi: 10.1016/j.drudis.2016.06.012
pubmed: 
27326912
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27326912
Date of acceptance: 
2016-06-13

Basic units of protein structure, folding, and function

Study of the hierarchy of domain structure with alternative sets of domains and analysis of discontinuous domains, consisting of remote segments of the polypeptide chain, raised a question about the minimal structural unit of the protein domain. The hypothesis on the decisive role of the polypeptide backbone in determining the elementary units of globular proteins have led to the discovery of closed loops.

type: 
Journal Paper
journal: 
Progress in Biophysics and Molecular Biology, 2016, Sep 30, doi: 10.1016/j.pbiomolbio.2016.09.009
pubmed: 
27697476
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27697476
Impact Factor: 
2.58

Basic units of protein structure, folding, and function.

Study of the hierarchy of domain structure with alternative sets of domains and analysis of discontinuous domains, consisting of remote segments of the polypeptide chain, raised a question about the minimal structural unit of the protein domain. The hypothesis on the decisive role of the polypeptide backbone in determining the elementary units of globular proteins have led to the discovery of closed loops.

type: 
Journal Paper
journal: 
Progress in Biophysics and Molecular Biology, 2016, Sep 30, doi: 10.1016/j.pbiomolbio.2016.09.009
pubmed: 
27697476
Url: 
http://www.sciencedirect.com/science/article/pii/S0079610716300864
Impact Factor: 
2.58

Functional characterization of p53 pathway components in the ancient metazoan Trichoplax adhaerens

The identification of genes encoding a p53 family member and an Mdm2 ortholog in the ancient placozoan Trichoplax adhaerens advocates for the evolutionary conservation of a pivotal stress-response pathway observed in all higher eukaryotes. Here, we recapitulate several key functionalities ascribed to this known interacting protein pair by analysis of the placozoan proteins (Tap53 and TaMdm2) using both in vitro and cellular assays.

type: 
Journal Paper
journal: 
Scientific Report 6, 33972, 2016, doi:10.1038/srep33972
pubmed: 
27678309
Url: 
http://www.nature.com/articles/srep33972
Date of acceptance: 
2016-09-06

South-east Asian Zika virus strain linked to cluster of cases in Singapore, August 2016

Zika virus (ZIKV) is an ongoing global public health emergency with 70 countries and territories reporting evidence of ZIKV transmission since 2015. On 27 August 2016, Singapore reported its first case of local ZIKV transmission and identified an ongoing cluster. Here, we report the genome sequences of ZIKV strains from two cases and find through phylogenetic analysis that these strains form an earlier branch distinct from the recent large outbreak in the Americas.

type: 
Journal Paper
journal: 
Eurosurveillance, Volume 21, Issue 38, 22 September 2016, DOI: http://dx.doi.org/10.2807/1560-7917.ES.2016.21.38.30347
Url: 
http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=22588
Impact Factor: 
5.8
Date of acceptance: 
2016-09-22

Comparative study of adipose-derived stem cells and bone marrow-derived stem cells in similar microenvironmental conditions

Mesenchymal stem cells (MSCs), which were first isolated from the bone marrow, are now being extracted from various other tissues in the body, including the adipose tissue. The current study presents systematic evidence of how the adipose tissue-derived stem cells (ASCs) and bone marrow-derived mesenchymal stem cells (Bm-MSCs) behave when cultured in specific pro-adipogenic microenvironments. The cells were first characterized and identified as MSCs in terms of their morphology, phenotypic expression, self-renewal capabilities and multi-lineage potential.

type: 
Journal Paper
journal: 
Experimental Cell Research, Vol. 348, Issue 2, 1 Nov 2016, Pg 155-164, doi: 10.1016/j.yexcr.2016.09.012
pubmed: 
27658569
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27658569
Impact Factor: 
3.378

Identification of a Lineage D Betacoronavirus in Cave Nectar Bats (Eonycteris spelaea) in Singapore and an Overview of Lineage D Reservoir Ecology in SE Asian Bats

Coronaviruses are a diverse group of viruses that infect mammals and birds. Bats are reservoirs for several different coronaviruses in the Alphacoronavirus and Betacoronavirus genera. They also appear to be the natural reservoir for the ancestral viruses that generated the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus outbreaks. Here, we detected coronavirus sequences in next-generation sequence data created from Eonycteris spelaea faeces and urine.

type: 
Journal Paper
journal: 
Transboundary and Emerging Diseases, 2016 Sep 16. doi: 10.1111/tbed.12568
pubmed: 
27637887
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/?term=27637887
Impact Factor: 
2.714

Topology independent comparison of RNA 3D structures using the CLICK algorithm

RNA molecules are attractive therapeutic targets because non-coding RNA molecules have increasingly been found to play key regulatory roles in the cell. Comparing and classifying RNA 3D structures yields unique insights into RNA evolution and function. With the rapid increase in the number of atomic-resolution RNA structures, it is crucial to have effective tools to classify RNA structures and to investigate them for structural similarities at different resolutions.

type: 
Journal Paper
journal: 
Nuclei Acids Research 2016, doi: 10.1093/nar/gkw819
pubmed: 
27634929
Url: 
http://nar.oxfordjournals.org/content/early/2016/09/14/nar.gkw819.abstract?keytype=ref&ijkey=WsEFoSR4nWzxvyH
Impact Factor: 
6.03
Date of acceptance: 
2016-09-14
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