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Articles 1 - 14 of 14
Full-Text Articles in Entire DC Network
Genetic Diversity And Economic Development: Assessing The Key Findings In Ashraf And Galor (2013), Raymond Caraher, Michael Ash
Genetic Diversity And Economic Development: Assessing The Key Findings In Ashraf And Galor (2013), Raymond Caraher, Michael Ash
Economics Department Working Paper Series
We replicate Ashraf and Galor (2013) and find that its conclusions concerning the association between human genetic diversity and economic development depend substantially on coding errors and sample selection. We correct the coding errors and add or update data on genetic diversity and population density from high-quality sources. We find little support for the hypothesis that variation in genetic diversity among subpopulations has a systematic relationship with economic development.
Metastatic Tumor Evolution In Diuse Gastric Cancer And Cancer Organoid Modeling Implicate Tgfbr2 As A Potential Driver, Patrick Flaherty
Metastatic Tumor Evolution In Diuse Gastric Cancer And Cancer Organoid Modeling Implicate Tgfbr2 As A Potential Driver, Patrick Flaherty
Mathematics and Statistics Department Faculty Publication Series
Background: Gastric cancer is the second-leading cause of global cancer deaths, with metastatic disease representing the primary cause of mortality. To identify candidate drivers involved in oncogenesis and tumor evolution, we conduct an extensive genome sequencing analysis of metastatic progression in a diffuse gastric cancer. This involves a comparison between a primary tumor from a hereditary diffuse gastric cancer syndrome proband and its recurrence as an ovarian metastasis. Results: Both the primary tumor and ovarian metastasis have common biallelic loss-of-function of both the CDH1 and TP53 tumor suppressors, indicating a common genetic origin. While the primary tumor exhibits amplification of …
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 …
Ultrasensitive Detection Of Rare Mutations Using Next-Generation Targeted Resequencing, Patrick Flaherty, Georges Natsoulis, Omkar Muralidharan, Mark Winters, Jason Buenrostro, John Bell, Sheldon Brown, Mark Holodniy, Nancy Zhang, Hanlee P. Ji
Ultrasensitive Detection Of Rare Mutations Using Next-Generation Targeted Resequencing, Patrick Flaherty, Georges Natsoulis, Omkar Muralidharan, Mark Winters, Jason Buenrostro, John Bell, Sheldon Brown, Mark Holodniy, Nancy Zhang, Hanlee P. Ji
Mathematics and Statistics Department Faculty Publication Series
With next-generation DNA sequencing technologies, one can interrogate a specific genomic region of interest at very high depth of coverage and identify less prevalent, rare mutations in heterogeneous clinical samples. However, the mutation detection levels are limited by the error rate of the sequencing technology as well as by the availability of variant-calling algorithms with high statistical power and low false positive rates. We demonstrate that we can robustly detect mutations at 0.1% fractional representation. This represents accurate detection of one mutant per every 1000 wild-type alleles. To achieve this sensitive level of mutation detection, we integrate a high accuracy …
Dopamine Controls Locomotion By Modulating The Activity Of The Cholinergic Motor Neurons In C. Elegans, Andrew T. Allen
Dopamine Controls Locomotion By Modulating The Activity Of The Cholinergic Motor Neurons In C. Elegans, Andrew T. Allen
Masters Theses 1911 - February 2014
Dopamine is an important neurotransmitter in the brain, where it plays a regulatory role in the coordination of movement and cognition by acting through two classes of G protein-coupled receptors to modulate synaptic activity. In addition, it has been shown these two receptor classes can exhibit synergistic or antagonistic effects on neurotransmission. However, while the pharmacology of the mammalian dopamine receptors have been characterized in some detail, less is known about the molecular pathways that act downstream of the receptors. As in mammals, the soil nematode Caenorhabditis elegans uses two classes of dopamine receptors to control neural activity and thus …
Identification Of Pmt, Tr1, And H6h Gene Polymorphism And Tropane Alkaloid Chemotypes In Hyoscyamus Niger L. (Black Henbane), Lawrence Kramer
Identification Of Pmt, Tr1, And H6h Gene Polymorphism And Tropane Alkaloid Chemotypes In Hyoscyamus Niger L. (Black Henbane), Lawrence Kramer
Masters Theses 1911 - February 2014
No abstract provided.
Genetic Variability In Hydrastis Canadensis L. Using Rapd Analysis, Kerry Kelley
Genetic Variability In Hydrastis Canadensis L. Using Rapd Analysis, Kerry Kelley
Masters Theses 1911 - February 2014
ABSTRACT GENETIC VARIABILITY IN HYDRASTIS CANADENSIS L. USING RAPD ANALYSIS FEBRUARY 2009 KERRY J. KELLEY, B.A. MOUNT HOLYOKE COLLEGE M.A. UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Lyle Craker Hydrastis canadensis L. (goldenseal) is an endangered perennial wildflower species native to eastern North America. In this study, several populations of goldenseal, (both cultivated and wild type) were analyzed for genetic variability. The samples were collected from plant populations in North Carolina, Ohio, Pennsylvania and West Virginia and preserved using silica gel during collection. Random amplified polymorphic DNA (RAPD) analysis technique was used to generate DNA profiles from individual plants and …
Hunters Of The Ice Age: The Biology Of Upper Paleolithic People, Brigitte M. Holt, Vincenzo Formicola
Hunters Of The Ice Age: The Biology Of Upper Paleolithic People, Brigitte M. Holt, Vincenzo Formicola
Anthropology Department Faculty Publication Series
The Upper Paleolithic represents both the phase during which anatomically modern humans appeared and the climax of hunter–gatherer cultures. Demographic expansion into new areas that took place during this period and the diffusion of burial practices resulted in an unprecedented number of well-preserved human remains. This skeletal record, dovetailed with archeological, environmental, and chronological contexts, allows testing of hypotheses regarding biological processes at the population level. In this article, we review key studies about the biology of Upper Paleolithic populations based primarily on European samples, but integrating information from other areas of the Old World whenever possible. Data about cranial …
Genome-Wide Requirements For Resistance To Functionally Distinct Dna-Damaging Agents, Patrick Flaherty
Genome-Wide Requirements For Resistance To Functionally Distinct Dna-Damaging Agents, Patrick Flaherty
Mathematics and Statistics Department Faculty Publication Series
The mechanistic and therapeutic differences in the cellular response to DNA-damaging compounds are not completely understood, despite intense study. To expand our knowledge of DNA damage, we assayed the effects of 12 closely related DNA-damaging agents on the complete pool of ;4,700 barcoded homozygous deletion strains of Saccharomyces cerevisiae. In our protocol, deletion strains are pooled together and grown competitively in the presence of compound. Relative strain sensitivity is determined by hybridization of PCR-amplified barcodes to an oligonucleotide array carrying the barcode complements. These screens identified genes in well-characterized DNAdamage-response pathways as well as genes whose role in the DNA-damage …
A Latent Variable Model For Chemogenomic Profiling, Patrick Flaherty
A Latent Variable Model For Chemogenomic Profiling, Patrick Flaherty
Mathematics and Statistics Department Faculty Publication Series
Motivation: In haploinsufficiency profiling data, pleiotropic genes are often misclassified by clustering algorithms that impose the constraint that a gene or experiment belong to only one cluster. We have developed a general probabilistic model that clusters genes and experiments without requiring that a given gene or drug only appear in one cluster. The model also incorporates the functional annotation of known genes to guide the clustering procedure. Results: We applied our model to the clustering of 79 chemogenomic experiments in yeast. Known pleiotropic genes PDR5 and MAL11 are more accurately represented by the model than by a clustering procedure that …
Chemogenomic Profiling: Identifying The Functional Interactions Of Small Molecules In Yeast, Patrick Flaherty
Chemogenomic Profiling: Identifying The Functional Interactions Of Small Molecules In Yeast, Patrick Flaherty
Mathematics and Statistics Department Faculty Publication Series
We demonstrate the efficacy of a genome-wide protocol in yeast that allows the identification of those gene products that functionally interact with small molecules and result in the inhibition of cellular proliferation. Here we present results from screening 10 diverse compounds in 80 genome-wide experiments against the complete collection of heterozygous yeast deletion strains. These compounds include anticancer and antifungal agents, statins, alverine citrate, and dyclonine. In several cases, we identified previously known interactions; furthermore, in each case, our analysis revealed novel cellular interactions, even when the relationship between a compound and its cellular target had been well established. In …
Functional Profiling Of The Saccharomyces Cerevisiae Genome, Patrick Flaherty
Functional Profiling Of The Saccharomyces Cerevisiae Genome, Patrick Flaherty
Mathematics and Statistics Department Faculty Publication Series
Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth …
A Study Of Rhode Island Red Feather Pigmentation, Fred P. Jeffrey
A Study Of Rhode Island Red Feather Pigmentation, Fred P. Jeffrey
Masters Theses 1911 - February 2014
No abstract provided.