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The Pollution Of River Ibër With Heavy Metals From Landfill Of Kelmend, Innovative Research Publications IRP India, Rafet Zeqiri, Izet Zeqiri, Sadija Nikshiq -Kadriu, Mehush Aliu 2015 Innovative Research Publications

The Pollution Of River Ibër With Heavy Metals From Landfill Of Kelmend, Innovative Research Publications Irp India, Rafet Zeqiri, Izet Zeqiri, Sadija Nikshiq -Kadriu, Mehush Aliu

Innovative Research Publications IRP India

In this paper treated the degree of water pollution that emerges from mining and mixed with industrial wastes and as such in the form of pulp thrown in landfills. From the landfill through drainage and water flows in the river Ibër, penetrate the different pollutants that affect in water quality of this river. The degree of contamination of the river Ibër is monitored at several points, on which it is made water sampling of landfill and where we have reached the conclusion on the possibilities of prevention of water pollution of the river Ibër


Introduction To Gene Enrichment Analysis Tools, Rolando Garcia-Milian 2015 Yale University

Introduction To Gene Enrichment Analysis Tools, Rolando Garcia-Milian

Rolando Garcia-Milian

Bioinformatics enrichment tools play an important role in identifying, annotating, and functionally analyzing large list of genes generated by high-throughput technologies (e.g. microarrary, RNA-seq, ChIP-chip). This workshop will provide an overview of the principle, type of enrichments, and the infrastructure of enrichment tools. By using concrete examples, it will also introduce some of the most popular tools for gene enrichment analysis such as DAVID, GSEA, and WebGestalt.


Quentin Welch Papers, Brantley Palmer 2015 Keene State College

Quentin Welch Papers, Brantley Palmer

Finding Guides

A collection of the work of Quentin Welch who worked in Malaysia from late 1970-August, 1973 on genetic variants among the people there. Included are photographs, notebooks, dermatological prints, and blood slides.


Childhood-Onset Schizophrenia Case With 2.2 Mb Deletion At Chromosome 3p12.2-P12.1 And Two Large Chromosomal Abnormalities At 16q22.3-Q24.3 And Xq23-Q28, Danielle Rudd, Michael Axelsen, Eric A. Epping, Nancy Andreasen, Thomas Wassink 2015 University of Iowa

Childhood-Onset Schizophrenia Case With 2.2 Mb Deletion At Chromosome 3p12.2-P12.1 And Two Large Chromosomal Abnormalities At 16q22.3-Q24.3 And Xq23-Q28, Danielle Rudd, Michael Axelsen, Eric A. Epping, Nancy Andreasen, Thomas Wassink

Genetics Publications

Childhood-onset schizophrenia is rare, comprising 1% of known schizophrenia cases. Here, we report a patient with childhood-onset schizophrenia who has three large chromosomal abnormalities: an inherited 2.2 Mb deletion of chromosome 3p12.2–p12.1, a de novo 16.7 Mb duplication of 16q22.3–24.3, and a de novo 43 Mb deletion of Xq23–q28.


Loss Of Vascular Endothelial Growth Factor A (Vegfa) Isoforms In Granulosa Cells Using Pdmrt-1-Cre Or Amhr2-Cre Reduces Fertility By Arresting Follicular Development And By Reducing Litter Size In Female Mice, Kevin M. Sargent, Ningxia Lu, Debra T. Clopton, William E. Pohlmeier, Vanessa Brauer, Napoleone Ferrara, David W. Silversides, Andrea S. Cupp 2015 University of Nebraska-Lincoln

Loss Of Vascular Endothelial Growth Factor A (Vegfa) Isoforms In Granulosa Cells Using Pdmrt-1-Cre Or Amhr2-Cre Reduces Fertility By Arresting Follicular Development And By Reducing Litter Size In Female Mice, Kevin M. Sargent, Ningxia Lu, Debra T. Clopton, William E. Pohlmeier, Vanessa Brauer, Napoleone Ferrara, David W. Silversides, Andrea S. Cupp

Faculty Papers and Publications in Animal Science

Because VEGFA has been implicated in follicle development, the objective of this study was to determine the effects of granulosa- and germ cell-specific VEGFA loss on ovarian morphogenesis, function, and female fertility. pDmrt1-Cre mice were mated to floxed VEGFA mice to develop granulosa-/germ cell-specific knockouts (pDmrt1-Cre;Vegfa-/-). The time from mating to first parturition was increased when pDmrt1-Cre;Vegfa-/- females were mated to control males (P = 0.0008) and tended to be longer for heterozygous females (P < 0.07). Litter size was reduced for pDmrt1-Cre;Vegfa-/- females (P < 0.007). The time between the first and second parturitions was also increased for heterozygous females (P < 0.04) and tended to be increased for pDmrt1-Cre;Vegfa-/- females (P < 0.07). pDmrt1-Cre;Vegfa-/- females had smaller ovaries (P < 0.04), reduced plasma estradiol (P < 0.007), fewer developing follicles (P < 0.008) and tended to have fewer corpora lutea (P < 0.08). Expression of Igf1r was reduced ...


"Targeting Cell Cycle Proteins In Breast Cancer Cells With Sirna By Using Lipid-Substituted Polyethylenimines" Data Files, Manoj Parmar, Hamidreza Montazeri Aliabadi, Parvin Mahdipoor, Cezary Kucharski, Robert Maranchuk, Judith C. Hugh, Hasan Uludag 2015 Chapman University

"Targeting Cell Cycle Proteins In Breast Cancer Cells With Sirna By Using Lipid-Substituted Polyethylenimines" Data Files, Manoj Parmar, Hamidreza Montazeri Aliabadi, Parvin Mahdipoor, Cezary Kucharski, Robert Maranchuk, Judith C. Hugh, Hasan Uludag

Pharmacy Faculty Data Sets

The cell cycle proteins are key regulators of cell cycle progression whose de-regulation is one of the causes of breast cancer. RNA interference (RNAi) is an endogenous mechanism to regulate gene expression and it could serve as the basis of regulating aberrant proteins including cell cycle proteins. Since the delivery of small interfering RNA (siRNA) is a main barrier for implementation of RNAi therapy, we explored the potential of a non-viral delivery system, 2.0 kDa polyethylenimines substituted with linoleic acid and caprylic acid, for this purpose. Using a library of siRNAs against cell cycle proteins, we identified cell division ...


Targeting Cell Cycle Proteins In Breast Cancer Cells With Sirna By Using Lipid-Substituted Polyethylenimines, Manoj Parmar, Hamidreza Montazeri Aliabadi, Parvin Mahdipoor, Cezary Kucharski, Robert Maranchuk, Judith C. Hugh, Hasan Uludag 2015 Chapman University

Targeting Cell Cycle Proteins In Breast Cancer Cells With Sirna By Using Lipid-Substituted Polyethylenimines, Manoj Parmar, Hamidreza Montazeri Aliabadi, Parvin Mahdipoor, Cezary Kucharski, Robert Maranchuk, Judith C. Hugh, Hasan Uludag

Pharmacy Faculty Articles and Research

The cell cycle proteins are key regulators of cell cycle progression whose de-regulation is one of the causes of breast cancer. RNA interference (RNAi) is an endogenous mechanism to regulate gene expression and it could serve as the basis of regulating aberrant proteins including cell cycle proteins. Since the delivery of small interfering RNA (siRNA) is a main barrier for implementation of RNAi therapy, we explored the potential of a non-viral delivery system, 2.0 kDa polyethylenimines substituted with linoleic acid and caprylic acid, for this purpose. Using a library of siRNAs against cell cycle proteins, we identified cell division ...


Estimation Of Breed-Specific Heterosis Effects For Birth, Weaning, And Yearling Weight In Cattle, Lauren N. Schiermiester, R. M. Thallman, Larry Kuehn, Stephen D. Kachman, Matthew L. Spangler 2015 University of Nebraska-Lincoln

Estimation Of Breed-Specific Heterosis Effects For Birth, Weaning, And Yearling Weight In Cattle, Lauren N. Schiermiester, R. M. Thallman, Larry Kuehn, Stephen D. Kachman, Matthew L. Spangler

Faculty Papers and Publications in Animal Science

Heterosis, assumed proportional to expected breed heterozygosity, was calculated for 6834 individuals with birth, weaning and yearling weight records from Cycle VII and advanced generations of the U.S. Meat Animal Research Center (USMARC) Germplasm Evaluation (GPE) project. Breeds represented in these data included: Angus, Hereford, Red Angus, Charolais, Gelbvieh, Simmental, Limousin and Composite MARC III. Heterosis was further estimated by proportions of British × British (B × B), British × Continental (B × C) and Continental × Continental (C × C) crosses and by breed-specific combinations. Model 1 fitted fixed covariates for heterosis within biological types while Model 2 fitted random breed-specific combinations nested within ...


An Efficient And Sensitive Method For Preparing Cdna Libraries From Scarce Biological Samples, Catherine H. Sterling, Isana Veksler-Lublinsky, Victor R. Ambros 2015 University of Massachusetts Medical School Worcester

An Efficient And Sensitive Method For Preparing Cdna Libraries From Scarce Biological Samples, Catherine H. Sterling, Isana Veksler-Lublinsky, Victor R. Ambros

Program in Molecular Medicine Publications and Presentations

The preparation and high-throughput sequencing of cDNA libraries from samples of small RNA is a powerful tool to quantify known small RNAs (such as microRNAs) and to discover novel RNA species. Interest in identifying the small RNA repertoire present in tissues and in biofluids has grown substantially with the findings that small RNAs can serve as indicators of biological conditions and disease states. Here we describe a novel and straightforward method to clone cDNA libraries from small quantities of input RNA. This method permits the generation of cDNA libraries from sub-picogram quantities of RNA robustly, efficiently and reproducibly. We demonstrate ...


Year-End Report On Rac Project Entitled "Propagating Aspen Clones: Survival In The 21st Century", Ralph Baierlein 2015 Utah State University

Year-End Report On Rac Project Entitled "Propagating Aspen Clones: Survival In The 21st Century", Ralph Baierlein

Aspen Bibliography

No abstract provided.


The Molecular Evolution Of Non-Coding Dna And Population Ecology Of The Spiny Softshell Turtle (Apalone Spinifera) In Lake Champlain, Lucas Edward Bernacki 2015 University of Vermont

The Molecular Evolution Of Non-Coding Dna And Population Ecology Of The Spiny Softshell Turtle (Apalone Spinifera) In Lake Champlain, Lucas Edward Bernacki

Graduate College Dissertations and Theses

ABSTRACT

Spiny softshell turtles (Apalone spinifera) occur at the northwest limit of their range in Lake Champlain. This species, although widespread across North America, is listed as threatened in Vermont due to habitat destruction and disturbances of anthropogenic origin. The population of spiny softshell turtles in Lake Champlain is isolated from other North American populations and is considered as an independent management unit. Efforts to obtain information on the biology of spiny softshell turtles in Lake Champlain precede 1936 with conservation measures being initiated in 1987.

Methods of studying spiny softshell turtles in Lake Champlain have included direct observation, mark-recapture ...


"The Genetic Ancestry Of African Americans, Latinos, And European Americans Across The United States" Data Files, Katarzyna Bryc, Eric Y. Durand, J. Michael Macpherson, David Reich, Joanna Mountain 2015 Harvard University

"The Genetic Ancestry Of African Americans, Latinos, And European Americans Across The United States" Data Files, Katarzyna Bryc, Eric Y. Durand, J. Michael Macpherson, David Reich, Joanna Mountain

Biology, Chemistry, Earth, and Environmental Sciences Faculty Data Sets

Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans (brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry ...


Novel Computational Methods For Transcript Reconstruction And Quantification Using Rna-Seq Data, Yan Huang 2015 University of Kentucky

Novel Computational Methods For Transcript Reconstruction And Quantification Using Rna-Seq Data, Yan Huang

Theses and Dissertations--Computer Science

The advent of RNA-seq technologies provides an unprecedented opportunity to precisely profile the mRNA transcriptome of a specific cell population. It helps reveal the characteristics of the cell under the particular condition such as a disease. It is now possible to discover mRNA transcripts not cataloged in existing database, in addition to assessing the identities and quantities of the known transcripts in a given sample or cell. However, the sequence reads obtained from an RNA-seq experiment is only a short fragment of the original transcript. How to recapitulate the mRNA transcriptome from short RNA-seq reads remains a challenging problem. We ...


The Genetic Ancestry Of African Americans, Latinos, And European Americans Across The United States, Katarzyna Bryc, Eric Y. Durand, J. Michael Macpherson, David Reich, Joanna Mountain 2015 Harvard University

The Genetic Ancestry Of African Americans, Latinos, And European Americans Across The United States, Katarzyna Bryc, Eric Y. Durand, J. Michael Macpherson, David Reich, Joanna Mountain

Biology, Chemistry, Earth, and Environmental Sciences Faculty Articles and Research

Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans (brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry ...


Fatty Acid Snp Interaction Analysis In Angus Sired Beef Cattle, Luke M. Kramer, James E. Koltes, Eric R. Fritz-Waters, Mary Sue Mayes, Alysta Markey, Mahdi Saatchi, Nathan T. Weeks, James M. Reecy 2015 Iowa State University

Fatty Acid Snp Interaction Analysis In Angus Sired Beef Cattle, Luke M. Kramer, James E. Koltes, Eric R. Fritz-Waters, Mary Sue Mayes, Alysta Markey, Mahdi Saatchi, Nathan T. Weeks, James M. Reecy

Animal Industry Report

The triacylglyceride (TAG) fatty acid content in meat from Angus-sired cattle was analyzed for non-additive genetic effects. A total of 11,482 significant DNA marker interactions (false discovery rate [FDR] < 0.05) were detected across thirty-seven different TAG fatty acids. Interactions were not evenly distributed amongst all fatty acids analyzed, and types of interactions (additive-by-additive, additive-by-dominance, and dominance-by-dominance) varied within each individual fatty acid. These results indicate that it may be possible to account for additional genetic variance amongst TAG fatty acids over and above individual markers.


Genome-Wide Association Study Of Birth And Weaning Weights In Brangus Beef Cattle, Ziqing Weng, Hailin Su, Jungjae Lee, Dorian J. Garrick 2015 Iowa State University

Genome-Wide Association Study Of Birth And Weaning Weights In Brangus Beef Cattle, Ziqing Weng, Hailin Su, Jungjae Lee, Dorian J. Garrick

Animal Industry Report

The objective of this study was to map quantitative trait loci (QTL) associated with birth weight and weaning weight in Brangus beef cattle. A total of 6 significant QTL over 4 chromosomes were identified. Two QTL were common to both traits. The genome-wide association study (GWAS) results could help us understand the biological process of growth in Brangus. Further analyses are needed to find and validate the casual mutations responsible for these QTL.


Gensim: Simulation Of Descendants From Sequenced Ancestors Data, Hao Cheng, Rohan L. Fernando, Dorian J. Garrick 2015 Iowa State University

Gensim: Simulation Of Descendants From Sequenced Ancestors Data, Hao Cheng, Rohan L. Fernando, Dorian J. Garrick

Animal Industry Report

High-density real or imputed SNP genotypes are now routinely used for genomic prediction and genome-wide association studies. This is extending to the use of actual or imputed next generation sequence data in these activities. Simulation studies are useful to mimic these complex scenarios and test different analytical methods. We have developed a software tool GenSim to simulate sequence data in descendants. In this software, a crossover position and origin simulation (CPOS) algorithm is implemented to efficiently drop down sequence data from founders in complex pedigrees. Parallel programming techniques are used to reduce computing time.


Characterization Of The F94l Double Muscling Mutation In Pure- And Crossbred Limousin Animals, Jungjae Lee, Hailin Su, Rohan L. Fernando, Dorian J. Garrick, Jeremy Taylor 2015 Iowa State University

Characterization Of The F94l Double Muscling Mutation In Pure- And Crossbred Limousin Animals, Jungjae Lee, Hailin Su, Rohan L. Fernando, Dorian J. Garrick, Jeremy Taylor

Animal Industry Report

The objective of this study was to investigate the nature of the effect of the F94L variant in the myostatin (MSTN) gene on economic traits in Limousin and Limousin-Angus crossbred animals in the context of genomic analyses using Illumina BovineSNP50 Bead chip genotypes.


Accuracy Of Genomic Predictions For Birth, Weaning And Yearling Weights In Us Simmental Beef Cattle, Hailin Su, Rohan L. Fernando, Dorian J. Garrick, Bruce Golden 2015 Iowa State University

Accuracy Of Genomic Predictions For Birth, Weaning And Yearling Weights In Us Simmental Beef Cattle, Hailin Su, Rohan L. Fernando, Dorian J. Garrick, Bruce Golden

Animal Industry Report

Direct genomic breeding values (DGV) based on actual or imputed GeneSeek Genomic Profiler HD (GGPHD) genotypes were obtained for birth, weaning and yearling weights using Bayesian regression on about 20,000 US Simmental pure- or cross-bred beef cattle. Accuracies of DGV were quantified using 4-fold cross validation. Accuracies expressed as genetic correlations between DGV and trait ranged from 0.61 to 0.65, and the regressions of phenotype on DGV ranged from 0.61 to 0.66. These results indicate good predictive ability of genomic prediction with GGPHD chips but DGV need to be adjusted for bias.


Rooster’S Genetic Response To Immune Stimulation, Melissa S. Herrmann, Michael G. Kaiser, Susan J. Lamont 2015 Iowa State University

Rooster’S Genetic Response To Immune Stimulation, Melissa S. Herrmann, Michael G. Kaiser, Susan J. Lamont

Animal Industry Report

Lipopolysaccharide (LPS), commonly used to mimic bacterial infection without using live bacteria, was injected into roosters from three genetically diverse lines and gene expression was measured at two time points post-injection. TLR4, MD-2, and MyD88 are three genes that are responsible for initiating the major immune pathway that responds to LPS. Results showed significant differences in gene expression at different times post-stimulation for both MyD88 and TLR4. The three chicken lines had different expression levels of TLR4 in response to LPS. This shows that there are genetic differences in this immune pathway. Further studies are needed, but it may be ...


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