Computer Simulations First Step Toward Designing New, More Efficient Amine Chemical Scrubbers

A proof-of-concept molecular modeling study from North Carolina State University analyzes the efficiency of amine solutions in capturing carbon dioxide. This series of new computer models is the first step toward the design of cheaper, more efficient amine chemicals for capturing carbon dioxide – and reducing harmful CO2 emissions – in industrial installations…

 

The rest of this article can be found here

Adverse drug reactions triggered by the common HLA-B*57:01 variant: a molecular docking study

New computer models from North Carolina State University show how a variant of a common protein involved in human immune response binds to the antiviral drug abacavir, causing a severe reaction known as the abacavir hypersensitivity syndrome (AHS). The work has implications for Personalized Medicine by predicting adverse reactions caused by existing drugs and future drug candidates in sub-populations of patients.
Full article can be found here

The Proximity Principle: Bioinformatics is a science melting pot, bringing together many disciplines to answer big questions about our health.

Recently the BRC was featured on both the College of Sciences website and the main NC State University website for the groundbreaking work being done through the Bioinformatics cluster.

The Bioinformatics cluster is part of NC State’s groundbreaking Chancellor’s Faculty Excellence Program, which aims to put faculty together, both physically and intellectually, to combine ideas and experience in ways that solve big problems. Faculty clusters and interdisciplinary work have become hot topics in higher education around the world, but this “new” interdisciplinary approach has actually permeated science for centuries.  NC State’s program, focusing on assembling groups of faculty with complementary areas of expertise to study interdisciplinary research challenges, was one of the first major initiatives Chancellor Randy Woodson announced after coming to the university in 2010.

To read the article in its entirety, please visit the College of Sciences website here: https://sciences.ncsu.edu/news/the-proximity-principle

Variation in the glucose transporter gene SLC2A2 is associated with glycemic response to metformin.

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Drs. Daniel Rotroff and Alison Motsinger-Reif, in collaboration with the international Metformin Genetics (MetGen) Consortium, have uncovered new genetic evidence of how the benefits of the world’s most commonly used Type 2 diabetes drug, Metformin, may vary between individuals. Metformin is the first-line antidiabetic drug and has over 100 million users worldwide, yet its mechanism of action remains unclear. The study conducted a genome-wide association study (GWAS) that identified a genetic variant in the gene encoding the glucose transporter GLUT2, a protein that plays an important role in transporting glucose inside the body. They showed that those people who carried this variant had reduced levels of GLUT2 in the liver and other tissues resulting in a defect in how the body handles glucose. Metformin acted to specifically reverse this deficiency resulting in a better response to metformin in people carrying this gene variant. This is the largest precision medicine study on an anti-diabetic drug performed to date, and represents an exciting step towards personalized therapy for Type 2 diabetes.

 

The entire publication can be viewed here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5007158/

Bioinformatics Student Ranked in the Nvidia ACS COMP award 2016

Please help us in congratulating Jeremy Ash (Bioinformatics, Ph.D.)who recently won second place in the competitive Nvidia ACS COMP poster contest.  His work is relevant for the development of extremely predictive QSAR models needed for lead optimization, which is of great interest to pharmaceutical companies for modeling technology. Congratulations, Jeremy!!

 

ASH_ERK2_MDdescriptors Jeremy Ash

2016 Summer Short Courses

When: Wednesday 6/1/16 – Friday 6/17/16
Location: North Carolina State University
Talley Student Union
2610 Cates Ave.Raleigh, NC 27606
Talley Student Union
Lodging Options:

Doubletree by Hilton-Raleigh Brownstone
1707 Hillsborough St,

Raleigh, NC 27605
(919) 828-0811

Aloft Raleigh
2100 Hillsborough St.Raleigh, NC 27607
(919) 828-9900

 


Introduction To Linux (Dr. Galen Collier) – Wed., June 8th
This one-day short course offers a brief introduction to command-line operations using the Linux operating system. The primary objective is to provide you with beginner-level familiarity accessing and using a Linux system for common research computing tasks.

Introduction To R: Practical Bioinformatics (Dr. David Reif) – Thurs., June 9th
This one-day short course is an introduction to the R language for Bioinformatics applications. The main learning objective is to introduce practical coding skills that will allow you to perform basic Bioinformatics tasks and interact with popular tools/applications. These tasks include the creation, extraction, and manipulation of large data sets; the basics of graphics and visualization; and the automation of analysis using scripts. You will develop skills to perform these tasks in the context of practical application vignettes. Previous coding experience is not necessary.

Expression Analysis (Drs. Steffen Heber, Alison Motsinger-Reif, Fred Wright & Yi-Hui Zhou) – Mon., June 13th & Tues., June 14th
This two-day short course will cover basic concepts of gene expression, including analyses of microarrays and of transcriptomic sequencing.  The basic principles of differential expression testing, multiple hypotheses, and false discoveries will be covered.  Specific other topics include: the principles of pathway analysis and the utility of genomic annotation; alignment and calling of sequence-based methods, using tools such as tophat, cufflinks, and cuffdiff; and tools for RNA sequence analysis, including the negative binomial model, edgeR, DESeq. CAMERA-ROAST-Voom for pathway analysis.

BRC Hosts Spring B.I.G. talks

The Bioinformatics Research Center will be hosting weekly Industry and Government partners in informal talks aimed at partnership, collaboration, and the sharing of ideas. Each Monday at 11:30am, we will welcome a different partner to speak to our Graduate students, faculty and research staff. Talks last roughly 30 minutes, and are followed by pizza. Schedule is as follows:

BIG schedule

B.I.G. schedule

 

‘Development of Novel Therapeutics to Modulate Bacterial Biofilms’ Research Project to start in 2016

Drs. Pierce (Chemistry), Fourches (Chemistry, BRC), and Elfenbein (CVM) have received a grant from the Research and Innovation Funding (RISF) program. Their research project is entitled “Development of Novel Therapeutics to Modulate Bacterial Biofilms” and will be conducted in 2016.

Tanguay & Reif labs awarded new Systems Toxicology grant!

The Environmental Protection Agency (EPA) has awarded a 3-year grant to fund a collaboration between Oregon State University (Robert Tanguay, Jane La Du, Mike Simonich, Chris Sullivan) and North Carolina State University (David Reif) entitled “System Toxicological Approaches to Define Flame Retardant Adverse Outcome Pathways”.

From the EPA webpage:

A team of researchers from Oregon State University and North Carolina State University proposes to conduct the first comprehensive in vivo,structure-activity based toxicity studies of flame retardant chemicals (FRCs), including FRCs that EPA has phased out, FRCs that companies manufacture now, and FRCs that companies have proposed as replacements. (They) will test the hypothesis that the toxicity of FRCs will be highly dependent on their chemical structure.

Computer-aided design of carbon nanotubes with the desired bioactivity and safety profiles

Growing experimental evidences suggest the existence of direct relationships between the surface chemistry of nanomaterials and their biological effects. Herein, we have employed computational approaches to design a set of biologically active carbon nanotubes (CNTs) with controlled protein binding and cytotoxicity. Quantitative structure–activity relationship (QSAR) models were built and validated using a dataset of 83 surface-modified CNTs. A subset of a combinatorial virtual library of 240 000 ligands potentially attachable to CNTs was selected to include molecules that were within the chemical similarity threshold with respect to the modeling set compounds. QSAR models were then employed to virtually screen this subset and prioritize CNTs for chemical synthesis and biological evaluation. Ten putatively active and 10 putatively inactive CNTs decorated with the ligands prioritized by virtual screening for either protein-binding or cytotoxicity assay were synthesized and tested. We found that all 10 putatively inactive and 7 of 10 putatively active CNTs were confirmed in the protein-binding assay, whereas all 10 putatively inactive and 6 of 10 putatively active CNTs were confirmed in the cytotoxicity assay. This proof-of-concept study shows that computational models can be employed to guide the design of surface-modified nanomaterials with the desired biological and safety profiles.
Authors: Denis Fourches, Dongqiuye Pu, Liwen Li, Hongyu Zhou, Qingxin Mu, Gaoxing Su, Bing Yan & Alexander Tropsha
Link: http://www.tandfonline.com/doi/full/10.3109/17435390.2015.1073397#.VpAZ5lm8R64