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Patil A.,University at Albany | Patil A.,RNA Institute | Towns W.,University at Albany | Towns W.,RNA Institute | And 4 more authors.
Database | Year: 2012

A codon consists of three nucleotides and functions during translation to dictate the insertion of a specific amino acid in a growing peptide or, in the case of stop codons, to specify the completion of protein synthesis. There are 64 possible single codons and there are 4096 double, 262 144 triple, 16 777 216 quadruple and 1 073 741 824 quintuple codon combinations available for use by specific genes and genomes. In order to evaluate the use of specific single, double, triple, quadruple and quintuple codon combinations in genes and gene networks, we have developed a codon counting tool and employed it to analyze 5780 Saccharomyces cerevisiae genes. We have also developed visualization approaches, including codon painting, combination and bar graphs, and have used them to identify distinct codon usage patterns in specific genes and groups of genes. Using our developed Gene-Specific Codon Counting Database, we have identified extreme codon runs in specific genes. We have also demonstrated that specific codon combinations or usage patterns are over-represented in genes whose corresponding proteins belong to ribosome or translation-associated biological processes. Our resulting database provides a mineable list of multi-codon data and can be used to identify unique sequence runs and codon usage patterns in individual and functionally linked groups of genes. © The Author(s) 2012.

Xu D.,Albany State University | Xu D.,RNA Institute | Chatakonda V.-K.,Albany State University | Chatakonda V.-K.,RNA Institute | And 6 more authors.
Nucleic Acid Therapeutics | Year: 2014

Estrogen receptor α (ERα) is a well-validated drug target for a majority of breast cancers. But the target sites on this receptor are far from exhaustively defined. Almost all ER antagonists in clinical use function by binding to the ligand-binding pocket to occlude agonist access. Resistance to this type of drugs may develop over time, not caused by the change of ERα itself, but by changes in ER associated proteins. This observation is fueling the development of reagents that downregulate ER activity through novel binding sites. However, it is challenging to find general ER antagonists that act independently from other known ER ligands. In this report, we describe the utility of RNA aptamers in the search for new drug target sites on ERα. We have identified three high affinity aptamers and characterized one of them in detail. This aptamer interacted with ERα in a way not affected by the presence or absence of either the steroidal ligands or the estrogen response DNA elements, and effectively inhibited ER-mediated transcriptional activation in a breast cancer cell line. Serving as a novel drug lead, it may also be used to guide the rational chemical synthesis of small molecule drugs or to perform screens of small molecule libraries for those that are able to displace the aptamer from its binding site. © 2014 Mary Ann Liebert, Inc.

News Article | February 16, 2017
Site: phys.org

Yigit, an assistant chemistry professor at the University at Albany, has developed a new, cost-effective technique that can rapidly detect Ebola and other deadly illnesses. It would allow more people to be diagnosed and treated in a shorter time period. His technique first identifies disease biomarkers that are found in human urine. Then, by using a gold nanoprobe sensor, the research team, led by UAlbany graduate students Mustafa Balcioglu and Muhit Rana, visually-detect if the associated biomarkers are present in a person's urine sample and can diagnose within minutes. The sample changes color from purple to red if infected. To confirm the detection, Yigit's team measures the amount light absorbed by the infected sample at a given wavelength – also known as absorbance spectroscopy. "Our goal is to assemble a small kit that can be used for rapid disease screening," said Yigit, also a member of The RNA Institute. "The current detection methods for Ebola, and other diseases, are costly, time-consuming and require sophisticated equipment. We are working to make real-time diagnosis a reality. This will narrow the population who need to be tested through conventional methods." In total, 25 urine samples spiked with four Ebola-associated biomarkers were tested by Yigit's team. The technique provided accurate results in 24 samples, including each of the four subtypes of Ebola that infect humans. The researchers needed just one fifth of 1 milliliter of a sample to identify if it was infected. Full results were published last month in Advanced Healthcare Materials. Yigit said the Ebola results serve as only a model for the potential of his methodology. Previously, his team published findings in Chemical Communications on identifying biomarkers from breast cancer cells. They also released a second paper last month in Chemical Science on visual detection of mercury in different environmental and biological sources (urine, water, and soil). The lab is currently testing for Zika virus detection. "We are not biologists or classical biochemists. We are materials scientists developing methodologies for biomedical and environmental challenges by looking at them from a different angle," Yigit said. "Our approach can be implemented in any scenario where the associated biomarkers and their recognition elements are identified. It has a broad application spectrum." Yigit's research is supported by internal funding from UAlbany start-up funds. He was also the recipient of the University's Presidential Initiatives Fund for Research and Scholarship, the SUNY Health Network of Excellence Award and the SUNY Network of Excellence Award in Materials and Advanced Manufacturing. "The funding I've received from the University has enabled me to work independently and obtain everything I need for my research to be successful," Yigit said. "I am thankful to be surrounded by incredibly supportive faculty and hard-working student research assistants." More information: Mustafa Balcioglu et al. Virus Biomarkers: Rapid Visual Screening and Programmable Subtype Classification of Ebola Virus Biomarkers (Adv. Healthcare Mater. 2/2017), Advanced Healthcare Materials (2017). DOI: 10.1002/adhm.201770007

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