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Full-Text Articles in Biomedical Engineering and Bioengineering
Atypical Glycolysis In Clostridium Thermocellum, Jilai Zhou, Daniel G. Olson, D. Aaron Argyros, Yu Deng, Walter M. Van Gulik, Johannes P. Van Dijken, Lee R. Lynd
Atypical Glycolysis In Clostridium Thermocellum, Jilai Zhou, Daniel G. Olson, D. Aaron Argyros, Yu Deng, Walter M. Van Gulik, Johannes P. Van Dijken, Lee R. Lynd
Dartmouth Scholarship
Cofactor specificities of glycolytic enzymes in Clostridium thermocellum were studied with cellobiose-grown cells from batch cultures. Intracellular glucose was phosphorylated by glucokinase using GTP rather than ATP. Although phosphofructokinase typically uses ATP as a phosphoryl donor, we found only pyrophosphate (PPi)-linked activity. Phosphoglycerate kinase used both GDP and ADP as phosphoryl acceptors. In agreement with the absence of a pyruvate kinase sequence in the C. thermocellum genome, no activity of this enzyme could be detected. Also, the annotated pyruvate phosphate dikinase (ppdk) is not crucial for the generation of pyruvate from phosphoenolpyruvate (PEP), as deletion of the ppdk gene did …
Systematic Genomic Identification Of Colorectal Cancer Genes Delineating Advanced From Early Clinical Stage, Hojoon Lee, Patrick Flaherty, Hanlee P. Ji
Systematic Genomic Identification Of Colorectal Cancer Genes Delineating Advanced From Early Clinical Stage, Hojoon Lee, Patrick Flaherty, Hanlee P. Ji
Mathematics and Statistics Department Faculty Publication Series
Background: Colorectal cancer is the third leading cause of cancer deaths in the United States. The initial assessment of colorectal cancer involves clinical staging that takes into account the extent of primary tumor invasion, determining the number of lymph nodes with metastatic cancer and the identification of metastatic sites in other organs. Advanced clinical stage indicates metastatic cancer, either in regional lymph nodes or in distant organs. While the genomic and genetic basis of colorectal cancer has been elucidated to some degree, less is known about the identity of specific cancer genes that are associated with advanced clinical stage and …
Rvd: A Command-Line Program For Ultrasensitive Rare Single Nucleotide Variant Detection Using Targeted Next-Generation Dna Resequencing, Anna Cushing, Patrick Flaherty, Erik Hopmans, John M. Bell, Hanlee P. Ji
Rvd: A Command-Line Program For Ultrasensitive Rare Single Nucleotide Variant Detection Using Targeted Next-Generation Dna Resequencing, Anna Cushing, Patrick Flaherty, Erik Hopmans, John M. Bell, Hanlee P. Ji
Mathematics and Statistics Department Faculty Publication Series
Background: Rare single nucleotide variants play an important role in genetic diversity and heterogeneity of specific human disease. For example, an individual clinical sample can harbor rare mutations at minor frequencies. Genetic diversity within an individual clinical sample is oftentimes reflected in rare mutations. Therefore, detecting rare variants prior to treatment may prove to be a useful predictor for therapeutic response. Current rare variant detection algorithms using next generation DNA sequencing are limited by inherent sequencing error rate and platform availability. Findings: Here we describe an optimized implementation of a rare variant detection algorithm called RVD for use in targeted …