Polyploidy occurrences

Polyploidy occurs when two complete genomes from each of two parents, potentially of differing species, merge to form an offspring with four total copies of that/those genome/genomes. Polyploid is common in flowering plants and seems to give rise to important evolutionary innovations. However, it is unstable, and descendants of polyploid founders rapidly lose many of their duplicate genes. Previous analyses have argued that the losses tend to favor one of the parental genomes: however, methodological concerns have led to some doubt on this point.  By modeling the resolution of these three polyploidy events across 21 genomes (10 plants and 11 yeasts), we confirm the existence of this bias in loss patterns and present new data to suggest that one source of the bias is selection to maintain function in co-adapted complexes from the alternative parental genomes.

Researchers Find Vitamin D Receptor is Target for Disruption by Environmental Chemicals

New research from North Carolina State University sheds light on the ways in which environmental chemicals can affect vitamin D receptors (VDR). The work shows that compounds identified as possible VDR disruptors in the Tox21 database interact with VDR in vitro and supports the efficacy of high throughput screening programs to identify compounds of interest.

“Most people think of vitamin D as only a vitamin, but in the body vitamin D is converted to a hormone, so VDR is part of the endocrine system which regulates hormonal function,” says Seth Kullman, professor of biological sciences at NC State. “If something – an endocrine disrupting chemical, for example – interferes with the hormone’s function at different times of development or aging, it could drastically alter physiology of a number of important systems.”

Researchers Find Vitamin D Receptor is Target for Disruption by Environmental Chemicals

New research from North Carolina State University sheds light on the ways in which environmental chemicals can affect vitamin D receptors (VDR). The work shows that compounds identified as possible VDR disruptors in the Tox21 database interact with VDR in vitro and supports the efficacy of high throughput screening programs to identify compounds of interest.

“Most people think of vitamin D as only a vitamin, but in the body vitamin D is converted to a hormone, so VDR is part of the endocrine system which regulates hormonal function,” says Seth Kullman, professor of biological sciences at NC State. “If something – an endocrine disrupting chemical, for example – interferes with the hormone’s function at different times of development or aging, it could drastically alter physiology of a number of important systems.”

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Researchers Find Vitamin D Receptor is Target for Disruption by Environmental Chemicals

Statistician Wright Named Goodnight Innovation Distinguished Professor

Congratulation to the BRC’s very own, Fred Wright, professor in the Departments of Statistics and Biological Sciences and director of the Bioinformatics Research Center, for being named as a Goodnight Innovation Distinguished Professor. The professorship was made possible by a gift from longtime NC State supporters Jim and Ann Goodnight.

“Fred Wright is a key leader in interdisciplinary research in our college and across NC State,” said Chris McGahan, dean of the College of Sciences. “Gifts from generous donors like the Goodnights allow us to support and amplify his incredible work.”

Wright is an internationally known biostatistician who joined the NC State faculty in 2013. His wide-ranging research interests include genomic bioinformatics, toxicogenomics and the statistical principles underlying high-dimensional data analysis.

Wright has been principal investigator on numerous grants, with activities ranging from development of new methods of gene mapping to expression-quantitative trait mapping for multiple tissues. He was also principal investigator of an EPA-funded STAR Center to apply genomics principles to long-standing problems in toxicology. He is a key investigator in the International Cystic Fibrosis Genetic Modifier Consortium, which seeks to unravel the unexpected complexities of this disease, and in the GTEx Consortium, which seeks to assess genetic regulation in multiple human tissues.

Wright has been awarded over $15 million in research grants over the course of his career. He has authored or coauthored more than 150 scientific publications and delivered more than 80 invited presentations. He is a fellow of the American Statistical Association and of Delta Omega, the public health honor society.

Jim Goodnight is CEO and a co-founder of SAS, the world’s largest privately held software company. SAS emerged from NC State’s Department of Statistics when Goodnight was on its faculty in the 1970s. Ann Goodnight, a 1968 College of Humanities and Social Sciences graduate, is the senior director of community relations at SAS. She is a member of the NC State Board of Trustees and the Friday Institute National Advisory Board. The Goodnights are generous supporters of the College of Sciences and the university, establishing several professorships and the Goodnight Scholars Program and serving as co-chairs of the Think and Do the Extraordinary Campaign for NC State.

ChemMaps Lets Researchers Navigate the Chemical Universe

Researchers from North Carolina State University have created a new online service – ChemMaps – that allows users to interactively navigate the chemical space of over 8,000 drugs and 47,000 environmental compounds in 3D and real time. ChemMaps is designed to be a central resource for students and researchers who want to easily visualize and study complicated sets of chemical structures. The first release of the free-to-use website is available at www.chemmaps.com.

 

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Designing the Next Generation of Hair Dyes

Designing the Next Generation of Hair Dyes

North Carolina State University researchers have created the largest publicly available chemical database of hair dye substances as a resource for developing a new generation of hair color products that are safer for consumers, stylists and the environment.

The online Hair Dye Substance Database contains detailed information about the structure and properties of 313 substances in current and past commercial hair dyes. Using computer-based classification – what’s known as cheminformatics – researchers grouped the dyes into clusters with similar structures and properties. The results revealed some surprises and promising new avenues for research.

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Building 3-D models of molecules with RealityConvert

Denis Fourches wants to make the search for new drugs faster and less expensive. So he uses powerful computers to help model interactions between chemical compounds and biological targets to predict the compound’s effectiveness, thus narrowing the field of potential drug candidates for testing and saving researchers time and money.

Now he has a new tool in his arsenal – a computer program that will allow anyone to rapidly create three-dimensional models of molecules for 3-D printing as well as augmented and virtual reality applications, making it easier to study these complex biomolecular structures.

“Large and complex biomolecules like proteins make it difficult for researchers and students to accurately visualize their structure or how they might interact with a given compound,” says Fourches, assistant professor of chemistry at NC State. “But if we can easily build an accurate 3-D model of the protein into a virtual reality or augmented reality environment, we can enable a much better perception of the geometrical and structural characteristics of that molecule.”

RealityConvert is a software tool that converts molecular objects – such as proteins and drugs – to high quality 3-D models. It generates 3-D molecular and biomolecular models in standard file formats that are compatible with the vast majority of augmented and virtual reality programs as well as 3-D printing tools. The conversion is fast and the program is specifically geared toward generating models for various chemicals and small proteins. Fourches is already utilizing the program with his undergraduate organic chemistry students. RealityConvert is open access and freely available to the public.

“The ultimate goal of RealityConvert is to facilitate and boost the development of augmented reality and virtual reality content for bioinformatics and cheminformatics applications,” Fourches says. “These technologies allow for stunning and immersive experiences, offering untapped opportunities for both research and education purposes.”

The latest version of the program is available on Fourches’ GitHub platform and on its website.

Funding for RealityConvert was provided by the NC State Chancellor’s Faculty Excellence Program.

The above article and video can be found here: Building 3-D models of molecules with RealityConvert

ACS CINF awards for Bioinformatics students

Two students in Denis Fourches’ Cheminformatics lab recently received highly competitive ACS CINF awards at the American Chemical Society ACS National Meeting in Washington,DC.

Phyo Phyo Kyaw Zin presented her most recent work on the development of the PKS enumerator, a software to generate large libraries of macrocycles with user-defined constrains (she showcased a dataset of 10 million compounds). This work is done in close collaboration with Dr. Gavin Williams (Chemistry, NCSU) and has applications for the virtual screening of new bioactive macrolides for the development of new antimicrobials and agrochemicals.

Jeremy Ash presented his work on the first study using cheminformatics for the analysis and modeling of metabolomics data. The technique allows for a better identification of individual and groups of small molecule metabolites that can discriminate cancer patients versus healthy individuals. This is relevant for the development of disease biomarkers and precision medicine.

RealityConvert: A tool for preparing 3D models of biochemical structures for augmented and virtual reality

RealityConvert: A tool for preparing 3D models of biochemical structures for augmented and virtual reality

The Fourches group has developed the RealityConvert software tool and associated website, which allow users to easily convert molecular objects to high quality 3D models directly compatible for AR and VR applications. The ultimate goal of RealityConvert is to facilitate and boost the development of AR and VR contents for bioinformatics and cheminformatics applications.

RealityConvert: A tool for preparing 3D models of biochemical structures for augmented and virtual reality

 

Bioinformatics Student Receives Fellowship from the Triangle Center of Evolutionary Medicine

       

Jeremy Ash (Bioinformatics, Ph.D. student) recently received a fellowship for Fall 2017 from the Triangle Center of Evolutionary Medicine (TriCEM).   His proposed project is an extension of his recently accepted publication in the Journal of Chemical Information and Modeling on the use of molecular dynamics extracted chemical descriptors to characterize and model a series of ERK2 inhibitors.  The extension will focus on the evolution of resistance to chemotherapy drugs in mitogen activated protein kinases:

Kinase inhibitors represent the new generation of highly promising bioactive molecules for combating various types of cancer. With compounds already on the market and even more currently in clinical trials, the research community is on the path to developing a large collection of kinase-mediating drugs and chemical probes. However, drug resistance is the “Achilles heel” of kinases inhibitors. As members of signaling pathways that are critical to an array of cellular processes, kinase inhibition gives rise to strong selection pressure for drug resistance conferring mutations in patients. In this project, we focus on studying the ERK1 and ERK2 kinase, especially the dynamic interactions small molecule inhibitors undergo within the ERK binding site. To do so, we will rely on our novel modeling approach that integrates several state-of-the-art cheminformatics methods (molecular docking, molecular dynamics, and machine learning). We posit this analysis will deepen the understanding of why certain inhibitors interact differently with these two isoforms. This will help identify residues where the selection pressure driving drug resistance is different, and inform chemists of strategies to design new ERK inhibitors with greater efficacy. At last, our analysis of ERK-ligand dynamic interactions that confer specificity to ERK1, ERK2, or both will aide in the development of new chemical probes capable of more selective inhibition.

The TriCEM website: http://tricem.dreamhosters.com/