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Haplotype Variety Analysis Of Human Populations: An Application To Hapmap Data, Michelle Creek, Cyril Rakovski 2014 Chapman University

Haplotype Variety Analysis Of Human Populations: An Application To Hapmap Data, Michelle Creek, Cyril Rakovski

e-Research: A Journal of Undergraduate Work

We undertake a study to investigate the haplotype variety of distinct human populations. We use a natural measure of haplotype variety, the total number of haplotypes (TNH) present that reflects the number of haplotypes with nonzero frequencies estimated from the data at hand for each selection of multiple loci. For the analysis of real human populations, we use the haplotype data of the Denver Chinese, Tuscan Italians, Luhya Kenyans, and Gujarati Indians from release III of the HapMap database. Moreover, we show that the TNH statistic is biased in small sample data scenarios such as the HapMap and implement a ...


On The Ranking Of The Disease Susceptibility Locus In Family-Based Candidate Gene Studies: A Simulation-Based Analysis, Lisa A. Brown, Cyril Rakovski 2014 Chapman University

On The Ranking Of The Disease Susceptibility Locus In Family-Based Candidate Gene Studies: A Simulation-Based Analysis, Lisa A. Brown, Cyril Rakovski

e-Research: A Journal of Undergraduate Work

The ranking of the p-value of the true causal single nucleotide polymorphism in the ordered list of individual SNP p-values is an important factor for achieving success in the ultimate objective of association studies - identifying deleterious genetic variants. Thus, we undertake a study to assess the implications of complex, multimarker correlation structure, sample size and disease models on the ranking of the causal SNP. We carry out an extensive family-based candidate gene simulation study to analyze the position of the disease susceptibility locus in the complete list of individual SNP p-values ordered according to their statistical significance. We simulate data ...


Nsf Bets Big On David Angelini, Gerry Boyle 2014 Colby College

Nsf Bets Big On David Angelini, Gerry Boyle

Colby Magazine

Something has been bugging Colby geneticist David Angelini.

How, Angelini wonders, can a single species (in this case the soapberry bug) produce two distinctly different forms, one with long wings and one with short, that are not linked to sex? What is the genetic mechanism that causes the wings to develop differently?

"Why does it not overshoot the long form? he asked. "Why doesn't it undershoot the short form? Why doesn't it end up somewhere in the middle? That's an open question."

And a question that the National Science Foundation wants him to answer.


Did Pre-Clovis People Inhabit The Paisley Caves (And Why Does It Matter)?, Stuart J. Fiedel 2014 Wayne State University

Did Pre-Clovis People Inhabit The Paisley Caves (And Why Does It Matter)?, Stuart J. Fiedel

Human Biology Open Access Pre-Prints

The date and processes of initial human colonization of the Americas are crucial issues for the understanding of human biological and cultural development. For example, Soares et al. (2009) cited the American archaeological record to validate their proposed revision of the human mitochondrial molecular clock. Their suggested mutation rate puts the date of rapid expansion of Native American clades at around 13,500–15,000 cal BP. Similarly, Poznik et al. (2013) have used the “high-confidence archaeological dating” of the initial peopling of the Americas to calibrate the rates of both Y-chromosome and mtDNA mutation and thereby to reconcile the ...


Comparing Partial Least Square Approaches In Gene-Or Region-Based Association Study For Multiple Quantitative Phenotypes, Zhongshang Yuan, Xiaoshuai Zhang, Fangyu Li, Jinghua Zhao, Fuzhong Xue 2014 Wayne State University

Comparing Partial Least Square Approaches In Gene-Or Region-Based Association Study For Multiple Quantitative Phenotypes, Zhongshang Yuan, Xiaoshuai Zhang, Fangyu Li, Jinghua Zhao, Fuzhong Xue

Human Biology Open Access Pre-Prints

On thinking quantitatively of complex diseases, there are at least three statistical strategies for association study: single SNP on single trait, gene-or region (with multiple SNPs) on single trait and on multiple traits. The third of which is the most general in dissecting the genetic mechanism underlying complex diseases underpinning multiple quantitative traits. Gene-or region association methods based on partial least square (PLS) approaches have been shown to have apparent power advantage. However, few attempts are developed for multiple quantitative phenotypes or traits underlying a condition or disease, and the performance of various PLS approaches used in association study for ...


Questioning The “Melting Pot”: Analysis Of Alu Inserts In Three Population Samples From Uruguay, Pedro C. Hidalgo, Patricia Mut, Elizabeth Ackermann, Gonzalo Figueiro, Monica Sans 2014 Wayne State University

Questioning The “Melting Pot”: Analysis Of Alu Inserts In Three Population Samples From Uruguay, Pedro C. Hidalgo, Patricia Mut, Elizabeth Ackermann, Gonzalo Figueiro, Monica Sans

Human Biology Open Access Pre-Prints

The way that immigrants integrate to recipient societies has been discussed for decades, mainly from the perspective of the social sciences. Uruguay, as other American countries, received different waves of European immigrants, although the details of the process of assimilation, when occurred, are unclear. In this paper, we use genetic markers to understand the process experienced by the Basques, one of the major migration waves that populated Uruguay, and its relation to other immigrants as well as to Native American and African descendants. For this purpose, we analyze the allele frequencies of ten ALU loci (A25, ACE, APOA1, B65, F13B ...


Mitochondrial Dna Variability Among Six South-American Amerindian Villages From The Pano Linguistic Group, Celso T. Mendes-Junior, Aguinaldo L. Simoes 2014 Wayne State University

Mitochondrial Dna Variability Among Six South-American Amerindian Villages From The Pano Linguistic Group, Celso T. Mendes-Junior, Aguinaldo L. Simoes

Human Biology Open Access Pre-Prints

Although scattered throughout a large geographic area, the members of the Pano linguistic group present strong ethnic, linguistic and cultural homogeneity, a feature that causes them to be considered as components of a same “Pano” tribe. Nevertheless, the genetic homogeneity between Pano villages has not been examined before. To study the genetic structure of the Pano linguistic group, four major Native American mitochondrial DNA (mtDNA) founder haplogroups were analyzed in 77 Amerindians from six villages of four Pano tribes (Katukina, Kaxináwa, Marúbo, and Yaminawa) located in the Brazilian Amazon. The central position of these tribes in the continent makes them ...


Phylogeography Of E1b1b1b-M81 Haplogroup And Analysis Of Its Subclades In Morocco, Ahmed Reguig, Nourdin Harich, Abdelhamid Barakat, Hassan Rouba 2014 Wayne State University

Phylogeography Of E1b1b1b-M81 Haplogroup And Analysis Of Its Subclades In Morocco, Ahmed Reguig, Nourdin Harich, Abdelhamid Barakat, Hassan Rouba

Human Biology Open Access Pre-Prints

In this work, we have analyzed a total of 295 unrelated Berber-speaking men from the northern, center and southern of Morocco, in order to characterize frequency of E1b1b1b-M81 haplogroup and to refine the phylogeny of its subclades: E1b1b1b1-M107, E1b1b1b2-M183 and E1b1b1b2a-M165. For this purpose, we have typed four biallelic polymorphisms: M81, M107, M183 and M165. As results, a large majority of the Berber-speaking male lineages belong to the Y chromosomal E1b1b1b-M81 haplogroup. The frequency ranged from 79.1 to 98.5% in all localities sampled. Then, the E1b1b1b2-M183 was the most dominant subclade in our samples, which ranged from 65 ...


Human Paternal Lineages, Languages And Environment In The Caucasus, David Tarkhnishvili, Alexander Gavashelishvili, Marine Murtskhvaladze, Mariam Gabelaia, Gigi Tevzadze 2014 Wayne State University

Human Paternal Lineages, Languages And Environment In The Caucasus, David Tarkhnishvili, Alexander Gavashelishvili, Marine Murtskhvaladze, Mariam Gabelaia, Gigi Tevzadze

Human Biology Open Access Pre-Prints

Publications that describe the human Y-DNA haplogroup composition in different ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus – a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. 224 men that identified themselves as ethnic Georgian were genotyped for Y-chromosome 23 STR markers and assigned to their geographic places of origin. The genotyped data were supplemented with the published data on the haplogroup composition and location ...


Human Diversity In Jordan: Polymorphic Alu Insertions In General Jordanian And Bedouin Groups, Daniela Zanetti, May Sadiq, Robert Carreras-Torres, Omar Khabour, Almuthanna Alkaraki, Esther Esteban, Marc Via, Pedro Moral 2014 Wayne State University

Human Diversity In Jordan: Polymorphic Alu Insertions In General Jordanian And Bedouin Groups, Daniela Zanetti, May Sadiq, Robert Carreras-Torres, Omar Khabour, Almuthanna Alkaraki, Esther Esteban, Marc Via, Pedro Moral

Human Biology Open Access Pre-Prints

Jordan, located in the Levant region, is a crucial area to investigate human migration between Africa and Eurasia. Even thought, the genetic history of Jordanians is far to be clarified including the origin of the Bedouins today resident in Jordan. Here, we provide new genetic data on autosomal independent markers in two Jordanian population samples (Bedouins and general population) in order to approach the genetic diversity inside this country and to give new information about the genetic position of these populations in the frame of the Mediterranean and Middle East area. The analyzed markers are 18 Alu polymorphic insertions characterized ...


Comparison Of Sequence Alignment Algorithms, Tejas Gandhi 2014 Minnesota State University, Mankato

Comparison Of Sequence Alignment Algorithms, Tejas Gandhi

Journal of Undergraduate Research at Minnesota State University, Mankato

The fact that biological sequences can be represented as strings belonging to a finite alphabet (A, C, G, and T for DNA) plays an important role in connecting biology to computer science. String representation allows researchers to apply various string comparison techniques available in computer science. As a result, various applications have been developed that facilitate the task of sequence alignment. The problem of finding sequence alignments consists of finding the best match between two biological sequences. A best match can infer an evolutionary relationship and functional similarity. However, there is a lack of research on how reliable and efficient ...


A New Species Of Small-Eared Shrew (Mammalia, Eulipotyphla, Cryptotis) From The Lacandona Rain Forest, Mexico, Lázaro Guevara, Victor Sánchez-Cordero, Livia León-Paniagua, Neal Woodman 2014 SelectedWorks

A New Species Of Small-Eared Shrew (Mammalia, Eulipotyphla, Cryptotis) From The Lacandona Rain Forest, Mexico, Lázaro Guevara, Victor Sánchez-Cordero, Livia León-Paniagua, Neal Woodman

Neal Woodman

The diversity and distribution of mammals in the American tropics remain incompletely known. We describe a new species of small-eared shrew (Soricidae, Cryptotis) from the Lacandona rain forest, Chiapas, southern Mexico. The new species is distinguished from other species of Cryptotis on the basis of a unique combination of pelage coloration, size, dental, cranial, postcranial, and external characters, and genetic distances. It appears most closely related to species in the Cryptotis nigrescens species group, which occurs from southern Mexico to montane regions of Colombia. This discovery is particularly remarkable because the new species is from a lowelevation habitat (approximately 90 ...


Two Spotted Spider Mite (Tetranychus Urticae) Selection To Arabidopsis Thaliana, Huzefa Ratlamwala 2014 Western University

Two Spotted Spider Mite (Tetranychus Urticae) Selection To Arabidopsis Thaliana, Huzefa Ratlamwala

University of Western Ontario - Electronic Thesis and Dissertation Repository

Spider mite feeding on A. thaliana induces the production of indole glucosinolates (IGs), plant secondary metabolites that negatively affect mite performance. In this study I conducted selection experiments on A. thaliana with varying levels of IGs, to determine if mites could adapt to IGs and other defense compounds. After 12 months, mites reared on host with IGs performed significantly better on A. thaliana than mites maintained on beans. However, an adaptation cost was detected between selected mite lines and their ancestral host. The qRT-PCR data on different mite lines revealed that the detoxification genes previously identified may only be involved ...


Identification Of Snps In The Coding Region Of Human Mtdna, Cassidy Punt, Elizabeth Smalley 2014 Minnesota State University, Mankato

Identification Of Snps In The Coding Region Of Human Mtdna, Cassidy Punt, Elizabeth Smalley

Journal of Undergraduate Research at Minnesota State University, Mankato

Two novel single nucleotide polymorphisms (SNPs) were discovered within the coding region of the NADH dehydrogenase subunit 2 gene of mitochondrial DNA (mtDNA). mtDNA is of particular importance in forensic analysis as well as in the study of the origin and dispersal of humans. Two segments of the coding region of human mtDNA, as well as the hyper-variable region 2 (HV 2) were selected and sequenced in order to determine if any previously unknown SNPs were present in our test subjects. Target regions were designed to include known SNPs; appropriate primers were developed using the OLIGO 6 Primer Analysis Software ...


Biofilm Formation By Escherichia Coli Csga And Fima Mutants, Nicole Snyder, Sean Willaert 2014 Minnesota State University, Mankato

Biofilm Formation By Escherichia Coli Csga And Fima Mutants, Nicole Snyder, Sean Willaert

Journal of Undergraduate Research at Minnesota State University, Mankato

Biofilms are a structured community of bacterial cells enclosed in a self-produced polymeric matrix and adherent to an inert or living surface. These structures and the organisms that cause them can pose a very serious problem if they colonize on medical devices. This is because biofilms have the ability to communicate within the colony and with other organisms that might attach to the surface, acting like a community working together. Biofilms allow the organism to be resistant to harsh and unfavorable conditions allowing them to survive longer and spread. Several genes in Escherichia coli (E. coli) have been associated with ...


Rna Interference As A Tool For The Functional Analysis Of Genes In The Colorado Potato Beetle, Leptinotarsa Decemlineata (Say), Ashley Danielle Yates 2014 University of Nebraska - Lincoln

Rna Interference As A Tool For The Functional Analysis Of Genes In The Colorado Potato Beetle, Leptinotarsa Decemlineata (Say), Ashley Danielle Yates

Dissertations and Student Research in Entomology

RNA interference (RNAi) is a naturally occurring phenomenon in eukaryotes in which a double-stranded RNA (dsRNA) suppresses the expression of a target gene. RNAi has markedly changed the way in which functional genetics studies are performed, especially in non-model organisms. In insects, the efficacy of RNAi is influenced by several factors, including the species and the methods of dsRNAs delivery.

The Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say), is a pest of the plant family Solanaceae. RNAi in the CPB is of interest for potential use in insect management and as a tool to study the interaction with host plants ...


The Evolution Of Genomic Imprinting: Theories, Predictions And Empirical Tests, M M. Patten, L Ross, J P. Curley, David C. Queller, R Bonduriansky, J B. Wolf 2014 Washington University in St. Louis

The Evolution Of Genomic Imprinting: Theories, Predictions And Empirical Tests, M M. Patten, L Ross, J P. Curley, David C. Queller, R Bonduriansky, J B. Wolf

Biology Faculty Publications

The epigenetic phenomenon of genomic imprinting has motivated the development of numerous theories for its evolutionary origins and genomic distribution. In this review, we examine the three theories that have best withstood theoretical and empirical scrutiny. These are: Haig and colleagues’ kinship theory; Day and Bonduriansky’s sexual antagonism theory; and Wolf and Hager’s maternal–offspring coadaptation theory. These theories have fundamentally different perspectives on the adaptive significance of imprinting. The kinship theory views imprinting as a mechanism to change gene dosage, with imprinting evolving because of the differential effect that gene dosage has on the fitness of matrilineal ...


Internesting Diving Behavior And Population Structure Of Hawksbill Sea Turtles (Eretmochelys Imbricata) On St. Croix, Usvi, Jacob E. Hill 2014 Indiana University – Purdue University Fort Wayne

Internesting Diving Behavior And Population Structure Of Hawksbill Sea Turtles (Eretmochelys Imbricata) On St. Croix, Usvi, Jacob E. Hill

Master's Theses

Hawksbill sea turtles (Eretmochelys imbricata) are distributed circumtropically and populations in many locations have been severely depleted. Developing management plans for this species is hindered by major gaps in knowledge concerning habitat use, behavior, and population structure. This study addresses these knowledge gaps for hawksbill sea turtles nesting at Sandy Point National Wildlife Refuge, St. Croix, US Virgin Islands. Specifically, I will focus on research priorities identified by the US Fish and Wildlife Service in the Recovery Plan for Hawksbill Sea Turtles in the US Caribbean Sea.

The first chapter addresses Recovery Plan Objective 111: Identify Important Nesting Beaches. Three ...


Quantitative Proteomic Analysis Reveals Posttranslational Responses To Aneuploidy In Yeast, Noah Dephoure, Sunyoung Hwang, Ciara O'Sullivan, Stacie E. Dodgson, Steven P. Gygi, Angelika Amon, Eduardo M. Torres 2014 University of Massachusetts Medical School

Quantitative Proteomic Analysis Reveals Posttranslational Responses To Aneuploidy In Yeast, Noah Dephoure, Sunyoung Hwang, Ciara O'Sullivan, Stacie E. Dodgson, Steven P. Gygi, Angelika Amon, Eduardo M. Torres

Program in Gene Function and Expression Publications and Presentations

Aneuploidy causes severe developmental defects and is a near universal feature of tumor cells. Despite its profound effects, the cellular processes affected by aneuploidy are not well characterized. Here, we examined the consequences of aneuploidy on the proteome of aneuploid budding yeast strains. We show that although protein levels largely scale with gene copy number, subunits of multi-protein complexes are notable exceptions. Posttranslational mechanisms attenuate their expression when their encoding genes are in excess. Our proteomic analyses further revealed a novel aneuploidy-associated protein expression signature characteristic of altered metabolism and redox homeostasis. Indeed aneuploid cells harbor increased levels of reactive ...


Synergistic Tumor Suppression By Combined Inhibition Of Telomerase And Cdkn1a, Romi Gupta, Yuying Dong, Peter D. Solomon, Hiromi I. Wettersten, Christopher J. Cheng, JIn-Na Min, Jeremy Henson, Shaillay Kumar Dogra, Sung H. Hwang, Bruce D. Hammock, Lihua Julie Zhu, Roger R. Reddel, W. Mark Saltzman, Robert H. Weiss, Sandy Chang, Michael R. Green, Narendra Wajapeyee 2014 University of Massachusetts Medical School

Synergistic Tumor Suppression By Combined Inhibition Of Telomerase And Cdkn1a, Romi Gupta, Yuying Dong, Peter D. Solomon, Hiromi I. Wettersten, Christopher J. Cheng, Jin-Na Min, Jeremy Henson, Shaillay Kumar Dogra, Sung H. Hwang, Bruce D. Hammock, Lihua Julie Zhu, Roger R. Reddel, W. Mark Saltzman, Robert H. Weiss, Sandy Chang, Michael R. Green, Narendra Wajapeyee

Program in Gene Function and Expression Publications and Presentations

Tumor suppressor p53 plays an important role in mediating growth inhibition upon telomere dysfunction. Here, we show that loss of the p53 target gene cyclin-dependent kinase inhibitor 1A (CDKN1A, also known as p21WAF1/CIP1) increases apoptosis induction following telomerase inhibition in a variety of cancer cell lines and mouse xenografts. This effect is highly specific to p21, as loss of other checkpoint proteins and CDK inhibitors did not affect apoptosis. In telomerase, inhibited cell loss of p21 leads to E2F1- and p53-mediated transcriptional activation of p53-upregulated modulator of apoptosis, resulting in increased apoptosis. Combined genetic or pharmacological inhibition of telomerase ...


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