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Full-Text Articles in Biomedical Engineering and Bioengineering

Systematic Genomic Identification Of Colorectal Cancer Genes Delineating Advanced From Early Clinical Stage, Patrick Flaherty Dec 2013

Systematic Genomic Identification Of Colorectal Cancer Genes Delineating Advanced From Early Clinical Stage, Patrick Flaherty

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 sitesin 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 metastasis ...


Systematic Genomic Identification Of Colorectal Cancer Genes Delineating Advanced From Early Clinical Stage, Patrick Flaherty Dec 2013

Systematic Genomic Identification Of Colorectal Cancer Genes Delineating Advanced From Early Clinical Stage, Patrick Flaherty

Patrick Flaherty

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 ...


Studying The Material Properties Of The Embryonic Chicken Heart, Kyra Burnett Jun 2013

Studying The Material Properties Of The Embryonic Chicken Heart, Kyra Burnett

Honors Theses

Congenital heart disease is the number one cause of birth defects in the United States, affecting approximately 40,000 newborns each year. Research has shown that serious structural defects of the heart can occur due to abnormal looping. Looping refers to the positional and morphological changes of the early embryo heart and is divided into different phases. Although progress has been made in identifying the genetic processes behind heart looping, the forces involved with the developmental process are still not fully understood. In this research, the chicken embryo heart was used as the experimental model and certain material properties were ...


Rvd: A Command-Line Program For Ultrasensitive Rare Single Nucleotide Variant Detection Using Targeted Next-Generation Dna Resequencing, Patrick Flaherty May 2013

Rvd: A Command-Line Program For Ultrasensitive Rare Single Nucleotide Variant Detection Using Targeted Next-Generation Dna Resequencing, Patrick Flaherty

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, detectingrare 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 gene ...


Rvd: A Command-Line Program For Ultrasensitive Rare Single Nucleotide Variant Detection Using Targeted Next-Generation Dna Resequencing, Patrick Flaherty May 2013

Rvd: A Command-Line Program For Ultrasensitive Rare Single Nucleotide Variant Detection Using Targeted Next-Generation Dna Resequencing, Patrick Flaherty

Patrick Flaherty

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 ...


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 Feb 2013

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

Open Dartmouth: Faculty Open Access 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 ...


The Molecular Genetics Learning Progressions: Revisions And Refinements Based On Empirical Testing In Three 10th Grade Classrooms, Amber Nicole Todd Jan 2013

The Molecular Genetics Learning Progressions: Revisions And Refinements Based On Empirical Testing In Three 10th Grade Classrooms, Amber Nicole Todd

Browse all Theses and Dissertations

In the past few decades, there has been a large push for increasing scientific literacy (AAAS, 1989; AAAS, 1993; Achieve, 2013; NRC, 1996; NRC, 2012), especially in areas that are rapidly advancing, like molecular genetics. Much research has been done on student understandings of molecular genetics and the consensus is that the concepts are difficult both to learn and teach (Fisher, 1992; Horwitz, 1996; Kindfield, 1992; Lewis & Kattmann, 2004; Marbach-Ad & Stavy, 2000; Stewart et al., 2005; Venville & Treagust, 1998; etc.). Two learning progressions in molecular genetics have been produced (Duncan et al., 2009; Roseman et al. 2006), but both progressions are hypothetical as neither have been ...