Heredity In The Epigenetic Era: Are We Facing A Politics Of Reproductive Obligations?, 2016 University of Windsor
Heredity In The Epigenetic Era: Are We Facing A Politics Of Reproductive Obligations?, Michael J. Crawford
Biological Sciences Publications
Recent research in the emerging field of epigenetics has implications with the potential to re-ignite acrimony in the discourse of reproductive rights, medical ethics, and the role of the state in our homes and in our lives. For scientists, epigenetics has profoundly realigned our understanding of heredity: epigenetics provides a mechanism through which the environmental challenges met in one generation can be inscribed and transmitted to future offspring. Although both genetic parents have the potential to transmit heritable epigenetic changes to their offspring, mothers have a particularly potent effect because nutrition in the uterine environment can exert a supplemental effect ...
A Platform For Fast Detection Of Let-7 Micro Rna Using Polyaniline Fluorescence And Image Analysis Techniques, 2015 University of Southern Mississippi
A Platform For Fast Detection Of Let-7 Micro Rna Using Polyaniline Fluorescence And Image Analysis Techniques, Partha P. Sengupta
The project describes a new strategy for transducing hybridization events through modulating intrinsic properties of the electroconductive polymer polyaniline (PANI). When DNA based probes electrostatically interact with PANI, its fluorescence properties are increased, a phenomenon that can be enhanced by UV irradiation. Hybridization of target nucleic acids results in dissociation of probes causing PANI fluorescence to return to basal levels. By monitoring restoration of base PANI fluorescence as little as 10-11 M (10 pM) of target oligonucleotides could be detected within 15 minutes of hybridization. Detection of complementary oligos was specific, with introduction of a single mismatch failing to ...
Meta-Analysis Of Genome-Wide Association Studies With Correlated Individuals: Application To The Hispanic Community Health Study/Study Of Latinos (Hchs/Sol), Tamar Sofer, John R. Shaffer, Misa Graff, Qibin Qi, Adrienne M. Stilp, Stephanie M. Gogarten, Kari E. North, Carmen R. Isasi, Cathy C. Laurie, Adam A. Szpiro
UW Biostatistics Working Paper Series
Investigators often meta-analyze multiple genome-wide association studies (GWASs) to increase the power to detect associations of single nucleotide polymorphisms (SNPs) with a trait. Meta-analysis is also performed within a single cohort that is stratified by, e.g., sex or ancestry group. Having correlated individuals among the strata may complicate meta-analyses, limit power, and inflate Type 1 error. For example, in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), sources of correlation include genetic relatedness, shared household, and shared community. We propose a novel mixed-effect model for meta-analysis, “MetaCor", which accounts for correlation between stratum-specific effect estimates. Simulations show ...
Evidence Of Field-Evolved Resistance To Bifenthrin In Western Corn Rootworm (Diabrotica Virgifera Virgifera Leconte) Populations In Western Nebraska And Kansas, Adriano E. Pereira, Haichuan Wang, Sarah N. Zukoff, Lance Meinke, B. Wade French, Blair Siegfried
Faculty Publications: Department of Entomology
Pyrethroid insecticides have been used to control larvae or adults of the western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, a key pest of field corn in the United States. In response to reports of reduced efficacy of pyrethroids in WCR management programs in southwestern areas of Nebraska and Kansas the present research was designed to establish a baseline of susceptibility to the pyrethroid insecticide, bifenthrin, using susceptible laboratory populations and to compare this baseline with susceptibility of field populations. Concentration-response bioassays were performed to estimate the baseline susceptibility. From the baseline data, a diagnostic concentration (LC99) was determined and ...
Playing God, 2015 Dordt College
Playing God, Jeff Ploegstra
Faculty Work: Comprehensive List
"Technically speaking, animals and plants that we have selectively bred are genetically modified organisms (GMOs)."
Posting about the benefits and dangers of genetic modification from In All Things - an online hub committed to the claim that the life, death, and resurrection of Jesus Christ has implications for the entire world.
Origins Of An Unmarked Georgia Cemetery Using Ancient Dna Analysis, 2015 University of Oklahoma, Norman Campus
Origins Of An Unmarked Georgia Cemetery Using Ancient Dna Analysis, Andrew T. Ozga, Raúl Y. Tito, Brian M. Kemp, Hugh Matternes, Alexandra Obregon-Tito, Leslie Neal, Cecil M. Lewis, Jr.
Human Biology Open Access Pre-Prints
Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we utilize ancient DNA extraction methods to investigate the origins of Avondale Burial Place through the use of well-preserved skeletal fragments from 20 individuals ...
Mongolians In The Genetic Landscape Of Central Asia: Exploring The Genetic Relations Among Mongolians And Other World Populations, Jane E. Brissenden, Judith R. Kidd, Baigalmaa Evsanaa, Ariunaa Togtokh, Andrew J. Pakstis, Françoise Friedlaender, Kenneth K. Kidd, Janet M. Roscoe
Human Biology Open Access Pre-Prints
Genetic data on North Central Asian populations are underrepresented in the literature, especially autosomal markers. In the present study we use 812 single nucleotide polymorphisms that are distributed across all the human autosomes and that have been extensively studied at Yale to examine the affinities of two recently collected, samples of populations: rural and cosmopolitan Mongolians from Ulaanbaatar and nomadic, Turkic-speaking Tsaatan from Mongolia near the Siberian border. We compare these two populations to one another and to a global set of populations and discuss their relationships to New World populations. Specifically, we analyze data on 521 autosomal loci (single ...
Evolution And Otitis Media: A Review, And A Model To Explain High Prevalence In Indigenous Populations, 2015 UCL Ear Institute, Royal National Throat Nose and Ear Hospital, London
Evolution And Otitis Media: A Review, And A Model To Explain High Prevalence In Indigenous Populations, Mahmood F. Bhutta
Human Biology Open Access Pre-Prints
Inflammation of the middle ear (otitis media) comprises a group of disorders that are highly prevalent in childhood, and indeed are amongst the most common disorders of childhood. Otitis media is also heritable, and has effects on fecundity. This means that otitis media is subject to evolution, yet the evolutionary selection forces that may determine susceptibility to otitis media have never been adequately explored.
Here I undertake a critical analysis of evolutionary forces that may determine susceptibility to middle ear inflammation. These forces include those determining function of the middle ear, those affecting host immunity, and those affecting colonization by ...
Novel Pathways Revealed In Bursa Of Fabricius Transcriptome In Response To Extraintestinal Pathogenic Escherichia Coli (Expec) Infection, Hongyan Sun, Peng Liu, Lisa K. Nolan, Susan J. Lamont
Animal Science Publications
Extraintestinal pathogenic Escherichia coli (ExPEC) has major negative impacts on human and animal health. Recent research suggests food-borne links between human and animal ExPEC diseases with particular concern for poultry contaminated with avian pathogenic E. coli (APEC), the avian ExPEC. APEC is also a very important animal pathogen, causing colibacillosis, one of the world’s most widespread bacterial diseases of poultry. Previous studies showed marked atrophy and lymphocytes depletion in the bursa during APEC infection. Thus, a more comprehensive understanding of the avian bursa response to APEC infection will facilitate genetic selection for disease resistance. Four-week-old commercial male broiler chickens ...
Odorant Receptor-Based Discovery Of Natural Repellents Of Human Lice, 2015 University of California-Davis
Odorant Receptor-Based Discovery Of Natural Repellents Of Human Lice, Julien Pelletier, Pingxi Xu, Kyong-Sup Yoon, John M. Clark, Walter S. Leal
SIUE Faculty Research, Scholarship, and Creative Activity
The body louse, Pediculus humanus humanus, is an obligate blood-feeding ectoparasite and an important insect vector that mediates the transmission of diseases to humans. The analysis of the body louse genome revealed a drastic reduction of the chemosensory gene repertoires when compared to other insects, suggesting specific olfactory adaptations to host specialization and permanent parasitic lifestyle. Here, we present for the first time functional evidence for the role of odorant receptors (ORs) in this insect, with the objective to gain insight into the chemical ecology of this vector. We identified seven putative full-length ORs, in addition to the odorant receptor ...
Bacteriophages Isolated From Lake Michigan Demonstrate Broad Host-Range Across Several Bacterial Phyla, 2015 Loyola University Chicago
Bacteriophages Isolated From Lake Michigan Demonstrate Broad Host-Range Across Several Bacterial Phyla, Kema Malki, Alex Kula, Katherine Bruder, Emily Sible, Thomas Hatzopoulos, Stephanie Steidel, Siobhan C. Watkins, Catherine Putonti
Biology: Faculty Publications and Other Works
The study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics of bacteriophages cannot be examined by sequencing alone, further highlighting the necessity for isolation and examination of phages from environmental samples. While much of our current knowledge base has been generated by the study of marine phages, freshwater viruses are understudied in comparison. Our group has previously conducted metagenomics-based studies samples collected from Lake Michigan - the data presented in this study relate to four phages that were extracted from the same samples.
Four phages were extracted from Lake Michigan on ...
A Survey Of Big Data Research, 2015 University of Massachusetts Medical School
A Survey Of Big Data Research, Hua (Julia) Fang, Zhaoyang Zhang, Chanpaul Jin Wang, Mahmoud Daneshmand, Chonggang Wang, Honggang Wang
Quantitative Health Sciences Publications and Presentations
Big data create values for business and research, but pose significant challenges in terms of networking, storage, management, analytics, and ethics. Multidisciplinary collaborations from engineers, computer scientists, statisticians, and social scientists are needed to tackle, discover, and understand big data. This survey presents an overview of big data initiatives, technologies, and research in industries and academia, and discusses challenges and potential solutions.
Reactive Oxygen Species-Mediated Neurodegeneration Is Independent Of The Ryanodine Receptor In Caenorhabditis Elegans, 2015 Coastal Carolina University
Reactive Oxygen Species-Mediated Neurodegeneration Is Independent Of The Ryanodine Receptor In Caenorhabditis Elegans, Lyndsay E.A. Young, Daniel C. Williams
Journal of the South Carolina Academy of Science
Despite the significant impacts on human health caused by neurodegeneration, our understanding of the degeneration process is incomplete. The nematode Caenorhabditis elegans is emerging as a genetic model organism well suited for identification of conserved cellular mechanisms and molecular pathways of neurodegeneration. Studies in the worm have identified factors that contribute to neurodegeneration, including excitotoxicity and stress due to reactive oxygen species (ROS). Disruption of the gene unc-68, which encodes the ryanodine receptor, abolishes excitotoxic cell death, indicating a role for calcium (Ca2+) signaling in neurodegeneration. We tested the requirement for unc-68 in ROS-mediated neurodegeneration using the genetically encoded ...
Ordinal Probit Wavelet-Based Functional Models For Eqtl Analysis, 2015 Bucknell University
Ordinal Probit Wavelet-Based Functional Models For Eqtl Analysis, Mark J. Meyer, Jeffrey S. Morris, Craig P. Hersh, Jarrett D. Morrow, Christoph Lange, Brent A. Coull
Mark J Meyer
Current methods for conducting expression Quantitative Trait Loci (eQTL) analysis are limited in scope to a pairwise association testing between a single nucleotide polymorphism (SNPs) and expression probe set in a region around a gene of interest, thus ignoring the inherent between-SNP correlation. To determine association, p-values are then typically adjusted using Plug-in False Discovery Rate. As many SNPs are interrogated in the region and multiple probe-sets taken, the current approach requires the fitting of a large number of models. We propose to remedy this by introducing a flexible function-on-scalar regression that models the genome as a functional outcome. The ...
Genome-Wide Dna Methylome Variation In Two Genetically Distinct Chicken Lines Using Methylc-Seq, 2015 China Agricultural University
Genome-Wide Dna Methylome Variation In Two Genetically Distinct Chicken Lines Using Methylc-Seq, Jinxiu Li, Rujiao Li, Ying Wang, Xiaoxiang Hu, Yiqiang Zhao, Li Li, Chungang Feng, Xiaorong Gu, Fang Liang, Susan J. Lamont, Songnian Hu, Huaijun Zhou, Ning Li
Animal Science Publications
DNA cytosine methylation is an important epigenetic modification that has significant effects on a variety of biological processes in animals. Avian species hold a crucial position in evolutionary history. In this study, we used whole-genome bisulfite sequencing (MethylC-seq) to generate single base methylation profiles of lungs in two genetically distinct and highly inbred chicken lines (Fayoumi and Leghorn) that differ in genetic resistance to multiple pathogens, and we explored the potential regulatory role of DNA methylation associated with immune response differences between the two chicken lines. The MethylC-seq was used to generate single base DNA methylation profiles of Fayoumi and ...
Whole-Genome Sequencing Of Kshv From Zambian Kaposi’S Sarcoma Biopsies Reveals Unique Viral Diversity, 2015 University of Nebraska-Lincoln
Whole-Genome Sequencing Of Kshv From Zambian Kaposi’S Sarcoma Biopsies Reveals Unique Viral Diversity, Landon N. Olp, Adrien Jeanniard, Clemence Marimo, John T. West, Charles Wood
Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent for Kaposi’s sarcoma (KS). Both KSHV and KS are endemic in sub-Saharan Africa where approximately 84% of global KS cases occur. Nevertheless, whole-genome sequencing of KSHV has only been completed using isolates from Western countries—where KS is not endemic. The lack of whole-genome KSHV sequence data from the most clinically important geographical region, sub-Saharan Africa, represents an important gap as it remains unclear whether genomic diversity has a role on KSHV pathogenesis. We hypothesized that distinct KSHV genotypes might be present in sub-Saharan Africa compared to Western countries. Using ...
Chromatin Interaction Analysis Reveals Changes In Small Chromosome And Telomere Clustering Between Epithelial And Breast Cancer Cells, 2015 University of Massachusetts Medical School
Chromatin Interaction Analysis Reveals Changes In Small Chromosome And Telomere Clustering Between Epithelial And Breast Cancer Cells, Ahmet Rasim Barutcu, Bryan R. Lajoie, Rachel Patton Mccord, Coralee E. Tye, Deli Hong, Terri L. Messier, Gillian Browne, Andre J. Van Wijnen, Jane B. Lian, Janet L. Stein, Job Dekker, Anthony N. Imbalzano, Gary S. Stein
Program in Systems Biology Publications and Presentations
BACKGROUND: Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, changes in higher-order chromatin organization during tumorigenesis have not been fully explored. To probe the differences in higher-order chromatin structure between mammary epithelial and breast cancer cells, we performed Hi-C analysis on MCF-10A mammary epithelial and MCF-7 breast cancer cell lines.
RESULTS: Our studies reveal that the small, gene-rich chromosomes chr16 through chr22 in the MCF-7 breast cancer genome display decreased interaction frequency with each other compared to the inter-chromosomal interaction frequency ...
K-Mer Analysis On Developmental And Housekeeping Enhancer Peaks, 2015 Yale University
K-Mer Analysis On Developmental And Housekeeping Enhancer Peaks, Yunsi Yang, Anurag Sethi, Mark Gerstein
Yale Day of Data
The regulation of gene expression involves interaction between transcriptional enhancers and core promoters. However, the separation between developmental and housekeeping gene regulation remains unknown. Here, we present a method to detect if different core promoters exhibit specificity to certain enhancers within massively parallel assays for enhancer detection. We use k-mers of various length (3-8bp) as sequence features and compare k-mer frequencies between developmental and housekeeping enhancers. This method shows promoter specificity of enhancers in D. melanogaster.
Caenorhabditis Elegans Alg-1 Antimorphic Mutations Uncover Functions For Argonaute In Microrna Guide Strand Selection And Passenger Strand Disposal, 2015 University of Massachusetts Medical School
Caenorhabditis Elegans Alg-1 Antimorphic Mutations Uncover Functions For Argonaute In Microrna Guide Strand Selection And Passenger Strand Disposal, Anna Y. Zinovyeva, Isana Veksler-Lublinsky, Ajay A. Vashisht, James A. Wohlschlegel, Victor R. Ambros
Program in Molecular Medicine Publications and Presentations
MicroRNAs are regulators of gene expression whose functions are critical for normal development and physiology. We have previously characterized mutations in a Caenorhabditis elegans microRNA-specific Argonaute ALG-1 (Argonaute-like gene) that are antimorphic [alg-1(anti)]. alg-1(anti) mutants have dramatically stronger microRNA-related phenotypes than animals with a complete loss of ALG-1. ALG-1(anti) miRISC (microRNA induced silencing complex) fails to undergo a functional transition from microRNA processing to target repression. To better understand this transition, we characterized the small RNA and protein populations associated with ALG-1(anti) complexes in vivo. We extensively characterized proteins associated with wild-type and mutant ALG-1 and ...
Play As The Foundation Of Human Intelligence: The Illuminating Role Of Human Brain Evolution And Development And Implications For Education And Child Development., 2015 University of California, Los Angeles
Play As The Foundation Of Human Intelligence: The Illuminating Role Of Human Brain Evolution And Development And Implications For Education And Child Development., Aaron P. Blaisdell
Journal of Evolution and Health
Children love to play. Why do they find such a frivolous activity so pleasurable and desirable? Perhaps it is not frivolous, but instead is an adaptation designed to guide proper cognitive development in human children. To understand why, I marshal evidence from different fields to build a case for play as a central behavioral mechanism of human brain and cognitive development. I start with a discussion of human evolution, focusing on the evolution of human physiology, tool-use, the human brain, and life-history strategy, and development, and how these are all connected as an adaptive suite. The anthropological and developmental evidence ...