Large-Scale microRNA Expression Profiling Identifies Putative Retinal miRNA-mRNA Signaling Pathways Underlying Form-Deprivation Myopia in Mice

Development of myopia is associated with large-scale changes in ocular tissue gene expression. Although differential expression of coding genes underlying development of myopia has been a subject of intense investigation, the role of non-coding genes such as microRNAs in the development of myopia is largely unknown. In this study, we explored myopia-associated miRNA expression profiles in the retina and sclera of C57Bl/6J mice with experimentally induced myopia using microarray technology.

type: 
Journal Paper
journal: 
PLoS One. 2016 Sep 13; 11(9):e0162541. doi: 10.1371/journal.pone.0162541
Url: 
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162541
Impact Factor: 
3.1
Date of acceptance: 
2016-08-24

A Reversible Association between Smc Coiled Coils is Regulated by Lysine acetylation and Is Required for Cohesin Association with the DNA

Cohesin is a ring-shaped protein complex that is capable of embracing DNA. Most of the ring circumference is comprised of the anti-parallel intramolecular coiled coils of the Smc1 and Smc3 proteins, which connect globular head and hinge domains. Smc coiled coil arms contain multiple acetylated and ubiquitylated lysines. To investigate the role of these modifications, we substituted lysines for arginines to mimic the unmodified state and uncovered genetic interaction between the Smc arms.

type: 
Journal Paper
journal: 
Molecular Cell, Volume 63, Issue 6, p1044–1054, 15 September 2016, doi: 10.1016/j.molcel.2016.08.008
pubmed: 
27618487
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27618487
Impact Factor: 
13.958
Date of acceptance: 
2016-08-05

Impairing Cohesin Smc1/3 Head Engagement Compensates for the Lack of Eco1 Function

The cohesin ring, which is composed of the Smc1, Smc3, and Scc1 subunits, topologically embraces two sister chromatids from S phase until anaphase to ensure their precise segregation to the daughter cells. The opening of the ring is required for its loading on the chromosomes and unloading by the action of Wpl1 protein. Both loading and unloading are dependent on ATP hydrolysis by the Smc1 and Smc3 “head” domains, which engage to form two composite ATPase sites.

type: 
Journal Paper
journal: 
Structure, 2016, doi: 10.1016/j.str.2016.09.001
pubmed: 
27692962
Url: 
http://www.cell.com/structure/abstract/S0969-2126(16)30265-9
Impact Factor: 
5.237
Date of acceptance: 
2016-08-05

Dynamic convergent evolution drives the passage adaptation across 48 years’ history of H3N2 influenza evolution

Influenza viruses are often propagated in a diverse set of culturing media and additional substitutions known as passage adaptation can cause extra evolution in the target strain, leading to ineffective vaccines. Using 25,482 H3N2 HA1 sequences curated from Global Initiative on Sharing All Influenza Data and National Center for Biotechnology Information databases, we found that passage adaptation is a very dynamic process that changes over time and evolves in a seesaw like pattern.

type: 
Journal Paper
journal: 
Molecular Biology and Evolution, 2016 Sep 7, doi: 10.1093/molbev/msw190
pubmed: 
27604224
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/?term=27604224
Impact Factor: 
13.6
Date of acceptance: 
2016-08-30

Action Recognition in Still Images With Minimum Annotation Efforts

We focus on the problem of still image-based human action recognition, which essentially involves making prediction by analyzing human poses and their interaction with objects in the scene. Besides image-level action labels (e.g., riding, phoning), during both training and testing stages, existing works usually require additional input of human bounding boxes to facilitate the characterization of the underlying human–object interactions. We argue that this additional input requirement might severely discourage potential applications and is not very necessary.

type: 
Journal Paper
journal: 
IEEE Transactions on Image Processing, Vol. 25, Issue 11, Nov 2016, Pg 5479-5490, doi: 10.1109/TIP.2016.2605305
Url: 
http://ieeexplore.ieee.org/document/7558119/
Impact Factor: 
3.735

SWORD—a highly efficient protein database search

MOTIVATION:Protein database search is one of the fundamental problems in bioinformatics. For decades, it has been explored and solved using different exact and heuristic approaches. However, exponential growth of data in recent years has brought significant challenges in improving already existing algorithms. BLAST has been the most successful tool for protein database search, but is also becoming a bottleneck in many applications. Due to that, many different approaches have been developed to complement or replace it.

type: 
Journal Paper
journal: 
Bioinformatics, Vol. 32, Issue 17, Sept 1, Pg i680-i684, doi: 10.1093/bioinformatics/btw445
pubmed: 
27587689
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27587689?dopt=Abstract
Impact Factor: 
5.766

Weibel-Palade body size modulates the adhesive activity of its von Willebrand Factor cargo in cultured endothelial cells

Changes in the size of cellular organelles are often linked to modifications in their function. Endothelial cells store von Willebrand Factor (vWF), a glycoprotein essential to haemostasis in Weibel-Palade bodies (WPBs), cigar-shaped secretory granules that are generated in a wide range of sizes. We recently showed that forcing changes in the size of WPBs modifies the activity of this cargo. We now find that endothelial cells treated with statins produce shorter WPBs and that the vWF they release at exocytosis displays a reduced capability to recruit platelets to the endothelial cell surface.

type: 
Journal Paper
journal: 
Scientific Reports 6, Article no. 32473 (2016), doi:10.1038/srep32473
Url: 
http://www.nature.com/articles/srep32473
Impact Factor: 
5.228
Date of acceptance: 
2016-08-09

Molecular and biochemical characterization of the NS1 protein of non-cultured influenza B virus strains circulating in Singapore

In this study we compared the NS1 protein of Influenza B/Lee/40 and several non-cultured Influenza B virus clinical strains detected in Singapore. In B/Lee/40 virus-infected cells and in cells expressing the recombinant B/Lee/40 NS1 protein a full-length 35 kDa NS1 protein and a 23 kDa NS1 protein species (p23) were detected.

type: 
Journal Paper
journal: 
Microbial Genomics 2016 Aug; 2(8): e000082, doi: 10.1099/mgen.0.000082
pubmed: 
28348873
Url: 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320597/#!po=73.5294
Date of acceptance: 
2017-08-02

Edlib: AC/C++ library for fast, exact sequence alignment using edit distance

We present Edlib, an open-source C/C++ library for exact pairwise sequence alignment using edit distance. We compare Edlib to other libraries and show that it is the fastest while not lacking in functionality, and can also easily handle very large sequences. Being easy to use, flexible, fast and low on memory usage, we expect it to be a cornerstone for many future bioinformatics tools. Source code, installation instructions and test data are freely available for download at https://github.com/Martinsos/edlib, implemented in C/C++ and supported on Linux, MS Windows, and Mac OS.

type: 
Journal Paper
journal: 
bioRxiv, 23 Aug 2016, doi: http://dx.doi.org/10.1101/070649
Url: 
http://biorxiv.org/content/early/2016/08/23/070649
Date of acceptance: 
2016-12-06

Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design

Protein flexibility poses a major challenge in binding site identification. Several computational pocket detection methods that utilize small-molecule probes in molecular dynamics (MD) simulations have been developed to address this issue. Although they have proven hugely successful at reproducing experimental structural data, their ability to predict new binding sites that are yet to be identified and characterized has not been demonstrated.

type: 
Journal Paper
journal: 
Journal of Physical Chemistry, 2016, 7, Pg 3452-3457, doi: 10.1021/acs.jpclett.6b01525
pubmed: 
27532490
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/27532490
Impact Factor: 
8.539
Date of acceptance: 
2016-08-17
Syndicate content