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2018

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Articles 331 - 360 of 616

Full-Text Articles in Genetics and Genomics

Diversity, Structure And Sources Of Bacterial Communities In Earthworm Cocoons., Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez Apr 2018

Diversity, Structure And Sources Of Bacterial Communities In Earthworm Cocoons., Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez

Computational Biology Institute

Animals start interactions with the bacteria that will constitute their microbiomes at embryonic stage. After mating, earthworms produce cocoons externally which will be colonized with bacteria from their parents and the environment. Due to the key role bacterial symbionts play on earthworm fitness, it is important to study bacterial colonization during cocoon formation. Here we describe the cocoon microbiome of the earthworms Eisenia andrei and E. fetida, which included 275 and 176 bacterial species, respectively. They were dominated by three vertically-transmitted symbionts, Microbacteriaceae, Verminephrobacter and Ca. Nephrothrix, which accounted for 88% and 66% of the sequences respectively. Verminephrobacter and Ca. …


Transcriptomics To Develop Biochemical Network Models In Cyanobacteria, Bridget E. Hegarty, Jordan Peccia, Ratanachat Racharaks Apr 2018

Transcriptomics To Develop Biochemical Network Models In Cyanobacteria, Bridget E. Hegarty, Jordan Peccia, Ratanachat Racharaks

Yale Day of Data

Through targeted genetic manipulations guided by network modeling, we will create a flexible, cyanobacteria-based platform for the production of biofuel-precursors and valuable chemical products. To build gene-metabolite predictive models, we have characterized Synecococcus elongatus sp. UTEX 2973’s (henceforth, UTEX 2973) gene expression and metabolite production under a number of environmental conditions.


Author Correction: A Population-Specific Reference Panel Empowers Genetic Studies Of Anabaptist Populations., Liping Hou, Rachel L Kember, Jared C Roach, Jeffrey R O'Connell, David W Craig, Maja Bucan, William K Scott, Margaret Pericak-Vance, Jonathan L Haines, Michael H Crawford, Alan R Shuldiner, Francis J Mcmahon Apr 2018

Author Correction: A Population-Specific Reference Panel Empowers Genetic Studies Of Anabaptist Populations., Liping Hou, Rachel L Kember, Jared C Roach, Jeffrey R O'Connell, David W Craig, Maja Bucan, William K Scott, Margaret Pericak-Vance, Jonathan L Haines, Michael H Crawford, Alan R Shuldiner, Francis J Mcmahon

Articles, Abstracts, and Reports

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.


Asas-Ssr Triennnial Reproduction Symposium: Looking Back And Moving Forward—How Reproductive Physiology Has Evolved: Fetal Origins Of Impaired Muscle Growth And Metabolic Dysfunction: Lessons From The Heat-Stressed Pregnant Ewe, Dustin T. Yates, Jessica Lynn Petersen, Ty B. Schmidt, Caitlin N. Cadaret, Taylor L. Barnes, Robert J. Posont, Kristin A. Beede Apr 2018

Asas-Ssr Triennnial Reproduction Symposium: Looking Back And Moving Forward—How Reproductive Physiology Has Evolved: Fetal Origins Of Impaired Muscle Growth And Metabolic Dysfunction: Lessons From The Heat-Stressed Pregnant Ewe, Dustin T. Yates, Jessica Lynn Petersen, Ty B. Schmidt, Caitlin N. Cadaret, Taylor L. Barnes, Robert J. Posont, Kristin A. Beede

Department of Animal Science: Faculty Publications

Intrauterine growth restriction (IUGR) is the second leading cause of perinatal mortality and predisposes offspring to metabolic disorders at all stages of life. Muscle-centric fetal adaptations reduce growth and yield metabolic parsimony, beneficial for IUGR fetal survival but detrimental to metabolic health after birth. Epidemiological studies have reported that IUGRborn children experience greater prevalence of insulin resistance and obesity, which progresses to diabetes, hypertension, and other metabolic disorders in adulthood that reduce quality of life. Similar adaptive programming in livestock results in decreased birth weights, reduced and inefficient growth, decreased carcass merit, and substantially greater mortality rates prior to maturation. …


Effect Of Mutation Of Cvn7 Conservon Genes Sco6796 And Sco6798 Of Streptomyces Coelicolor., Caroline Fulmer Apr 2018

Effect Of Mutation Of Cvn7 Conservon Genes Sco6796 And Sco6798 Of Streptomyces Coelicolor., Caroline Fulmer

Undergraduate Distinction Papers

Abstract

Streptomyces coelicolor is a gram-positive Actinobacterium. It is a filamentous soil organism that performs complex multicellular development. Its physiological and morphological differentiation produces active secondary metabolite antibiotics that have pharmaceutical applications. Studies of S. coelicolor show that cyclic di-GMP proteins regulate physiological and morphological development. S. coelicolor has 13 copies of an operon that are collectively named “conservon” because they are highly conserved. The operons are named cvn1-13 and genes in each operon are denoted cvnA-D. RNA-Seq data of a cyclic di-GMP phosphodiesterase double mutant showed differential expression between wild type and many of the operons in the …


Identifying Rmda Protein Interactions In Streptomyces Using A Bacterial Two-Hybrid System, Rachel Nguyen Apr 2018

Identifying Rmda Protein Interactions In Streptomyces Using A Bacterial Two-Hybrid System, Rachel Nguyen

Undergraduate Distinction Papers

Streptomyces is a genus of the phylum actinobacteria most commonly found as soil bacteria and used as a major source of antibiotics. RmdA and RmdB are phosphodiesterases that break down the ubiquitous second messenger cyclic-di-GMP which determines colony morphology and development of Streptomyces. The objective of this research is to identify whether RmdA will have interactions with itself using the Bacterial Adenylate Cyclase Two-Hybrid (BACTH) System. Each gene was fused into one of two BACTH vectors that encode a different domain of a single protein (T18 and T25) and then cotransformed into the BACTH indicator strain. The transformants were …


The Identification And Characterization Of A Putative Chromosome Segregation Gene In Streptomyces Coelicolor, Sean Kirk Apr 2018

The Identification And Characterization Of A Putative Chromosome Segregation Gene In Streptomyces Coelicolor, Sean Kirk

Undergraduate Distinction Papers

Streptomyces coelicolor is a soil bacterium that is a model for bacterial development. It is a filamentous, sporulating bacterium known to produce many medically utilized antibiotics. The goal of this research was to examine several developmental mutants and characterize novel genes of interest. Previously generated random transposon insertion mutants were analyzed using visual and microscopic phenotyping. Mutants of interest were further pursued and each transposon disruption site was identified by Inverse PCR and DNA sequencing. One of the novel genes is suspected to be involved in DNA segregation and codes for a putative membrane protein. Staining with propidium iodide was …


Threshold-Dependent Repression Of Spl Gene Expression By Mir156/Mir157 Controls Vegetative Phase Change In Arabidopsis Thaliana, Jia He, Mingli Xu, Matthew R. Willmann, Kevin Mccormick, Tieqiang Hu, Li Yang, Colby G. Starker, Daniel F. Voytas, Blake C. Meyers, R. Scott Poethig Apr 2018

Threshold-Dependent Repression Of Spl Gene Expression By Mir156/Mir157 Controls Vegetative Phase Change In Arabidopsis Thaliana, Jia He, Mingli Xu, Matthew R. Willmann, Kevin Mccormick, Tieqiang Hu, Li Yang, Colby G. Starker, Daniel F. Voytas, Blake C. Meyers, R. Scott Poethig

Faculty Publications

Vegetative phase change is regulated by a decrease in the abundance of the miRNAs, miR156 and miR157, and the resulting increase in the expression of their targets, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. To determine how miR156/miR157 specify the quantitative and qualitative changes in leaf morphology that occur during vegetative phase change, we measured their abundance in successive leaves and characterized the phenotype of mutations in different MIR156 and MIR157 genes. miR156/miR157 decline rapidly between leaf 1&2 and leaf 3 and decrease more slowly after this point. The amount of miR156/miR157 in leaves 1&2 greatly exceeds the …


Metabolic And Inflammatory Biomarkers Are Associated With Epigenetic Aging Acceleration Estimates In The Goldn Study, Marguerite R. Irvin, Stella Aslibekyan, Anh Do, Degui Zhi, Bertha Hidalgo, Steven A. Claas, Vinodh Srinivasasainagendra, Steve Horvath, Hemant K. Tiwari, Devin M. Absher, Donna K. Arnett Apr 2018

Metabolic And Inflammatory Biomarkers Are Associated With Epigenetic Aging Acceleration Estimates In The Goldn Study, Marguerite R. Irvin, Stella Aslibekyan, Anh Do, Degui Zhi, Bertha Hidalgo, Steven A. Claas, Vinodh Srinivasasainagendra, Steve Horvath, Hemant K. Tiwari, Devin M. Absher, Donna K. Arnett

Epidemiology and Environmental Health Faculty Publications

Background: Recently, epigenetic age acceleration-or older epigenetic age in comparison to chronological age-has been robustly associated with mortality and various morbidities. However, accelerated epigenetic aging has not been widely investigated in relation to inflammatory or metabolic markers, including postprandial lipids.

Methods: We estimated measures of epigenetic age acceleration in 830 Caucasian participants from the Genetics Of Lipid Lowering Drugs and diet Network (GOLDN) considering two epigenetic age calculations based on differing sets of 5′-Cytosine-phosphate-guanine-3′ genomic site, derived from the Horvath and Hannum DNA methylation age calculators, respectively. GOLDN participants underwent a standardized high-fat meal challenge after fasting for at least …


Efficient Reduced Bias Genetic Algorithm For Generic Community Detection Objectives, Aditya Karnam Gururaj Rao Apr 2018

Efficient Reduced Bias Genetic Algorithm For Generic Community Detection Objectives, Aditya Karnam Gururaj Rao

Theses

The problem of community structure identification has been an extensively investigated area for biology, physics, social sciences, and computer science in recent years for studying the properties of networks representing complex relationships. Most traditional methods, such as K-means and hierarchical clustering, are based on the assumption that communities have spherical configurations. Lately, Genetic Algorithms (GA) are being utilized for efficient community detection without imposing sphericity. GAs are machine learning methods which mimic natural selection and scale with the complexity of the network. However, traditional GA approaches employ a representation method that dramatically increases the solution space to be searched by …


The Ecology And Feeding Behavior Of Mosquitoes In The Galapagos Islands, Samoa S. Asigau Apr 2018

The Ecology And Feeding Behavior Of Mosquitoes In The Galapagos Islands, Samoa S. Asigau

Dissertations

Mosquitoes remain important vectors in transmitting wildlife diseases. This dissertation aims to understand the role that mosquitoes play in transmitting wildlife diseases such as avian malaria, a protozoan parasite belonging to the genus Plasmodium. Using data from wild-caught mosquitoes captured in multiple years and across multiple islands on the Galapagos Archipelago, we describe distributional patterns of mosquitoes, their range limits and assess whether there exists a disease-free refuge as occurs in Hawaii. We show that altitudinal ranges for disease transmission of avian malaria may not be bounded by a stable disease-free refuge, since mosquitoes are found at all elevations, …


Restoration Of Phage Growth On A Non-Permissive Host By Bypassing Transcription Termination Signals, Millicent Ronkainen Apr 2018

Restoration Of Phage Growth On A Non-Permissive Host By Bypassing Transcription Termination Signals, Millicent Ronkainen

Mahurin Honors College Capstone Experience/Thesis Projects

RNA polymerase is the central enzyme in all gene expression. The rpoCY75N mutation in the zinc-binding domain of the β’ subunit of E. coli RNA polymerase blocks a unique RNA-based mechanism of transcription antitermination utilized by bacteriophage HK022 and its relatives. Here, we describe the characterization of mutant phage, orc0368, which overcomes the rpoCY75N mutation. The orc0368 genome varies from the wild type phage genome by 4 single base pair mutations. Three of these mutations were not characterized because they occur in intergenic regions but the fourth was chosen for study because of its location between a series …


Changes In Myoblast Responsiveness To Tnfα And Il-6 Contribute To Decreased Skeletal Muscle Mass In Intrauterine Growth Restricted Fetal Sheep, Robert J. Posont, Kristin A. Beede, Sean W. Limesand, Dustin T. Yates Apr 2018

Changes In Myoblast Responsiveness To Tnfα And Il-6 Contribute To Decreased Skeletal Muscle Mass In Intrauterine Growth Restricted Fetal Sheep, Robert J. Posont, Kristin A. Beede, Sean W. Limesand, Dustin T. Yates

Department of Animal Science: Faculty Publications

Intrauterine growth restriction (IUGR) is a leading cause of perinatal morbidity and mortality (Alisi et al., 2011). Skeletal muscle growth is disproportionately reduced in IUGR fetuses and offspring (Padoan et al. 2004; Yates et al. 2014). These individuals present with reduced muscle mass and increased risk for metabolic disorders at all stages of life (Godfrey and Barker, 2000; Yates et al. 2016.). Muscle growth requires proliferation, differentiation, and fusion of myoblasts (muscle stem cells) to form muscle fibers early in gestation and to increase myonuclear content of existing fibers during late gestation and after birth (Yates et al., 2014). These …


Impaired Muscle Stem Cell Function In Cows With High Concentrations Of Androstenedione In Their Follicular Fluid, Taylor L. Barnes, Kiristen A. Beede, Elena M. Merrick, Caitlin N. Cadaret, Andrea S. Cupp, Dustin T. Yates Apr 2018

Impaired Muscle Stem Cell Function In Cows With High Concentrations Of Androstenedione In Their Follicular Fluid, Taylor L. Barnes, Kiristen A. Beede, Elena M. Merrick, Caitlin N. Cadaret, Andrea S. Cupp, Dustin T. Yates

Department of Animal Science: Faculty Publications

It is unclear whether androstenedione (A4) increases muscle mass and strength similar to testosterone or whether it produces primarily catabolic effects on muscle-like estrogen (Rasmussen et al., 2000). Summers et al. (2014) observed two populations of cows that exhibit either high (>40 ng/mL; High A4) or low (<20 ng/mL; Low A4) concentrations of A4 within the fluid of the dominant follicle just prior to ovulation. High A4 cows had decreased reproductive rates and shorter times before falling out of the herd, but those that did produce calves weaned them ~10-kg heavier than their low A4 counterparts (Summers et al., 2014). It appears that the difference in weights is due to faster growing and more efficient skeletal muscle. High A4 cows share many characteristics with women suffering from polycystic ovary syndrome (PCOS), whose high levels of circulating androgens are associated with changes in body composition (Kirchengast and Huber, 2001).


Generating And Repairing Genetically Programmed Dna Breaks During Immunoglobulin Class Switch Recombination, Laura Nicolas, Montserrat Cols, Jee Eun Choi, Jayanta Chaudhuri Apr 2018

Generating And Repairing Genetically Programmed Dna Breaks During Immunoglobulin Class Switch Recombination, Laura Nicolas, Montserrat Cols, Jee Eun Choi, Jayanta Chaudhuri

Publications and Research

Adaptive immune responses require the generation of a diverse repertoire of immunoglobulins (Igs) that can recognize and neutralize a seemingly infinite number of antigens. V(D)J recombination creates the primary Ig repertoire, which subsequently is modified by somatic hypermutation (SHM) and class switch recombination (CSR). SHM promotes Ig affinity maturation whereas CSR alters the effector function of the Ig. Both SHM and CSR require activation-induced cytidine deaminase (AID) to produce dU:dG mismatches in the Ig locus that are transformed into untemplated mutations in variable coding segments during SHM or DNA double-strand breaks (DSBs) in switch regions during CSR. Within the Ig …


Testing Viability Of Oligonucleotide Primers On Microsatellite Markers Amplified By Polymerase Chain Reaction On Dermacentor Variabilis Samples From The Bulloch County Region Of Georgia, Usa, Danielle Souza Apr 2018

Testing Viability Of Oligonucleotide Primers On Microsatellite Markers Amplified By Polymerase Chain Reaction On Dermacentor Variabilis Samples From The Bulloch County Region Of Georgia, Usa, Danielle Souza

Honors College Theses

Dermacentor variabilis, more commonly known as the wood tick, or the American dog tick, can be found all over North America. D. variabilis is a common tick in Bulloch county, Georgia, USA, and little is known about the population structure of this population of the species. Microsatellite markers are able to locate sections of the genome and can aid in estimating relatedness among individuals in a population. Six different oligonucleotide primer pairs were published for D. variabilis, however, published and non-published works indicated that not all of those primer pairs were working equally well for PCR. This study is …


A Genome-Wide Association Study Of Red-Blood Cell Fatty Acids And Ratios Incorporating Dietary Covariates: Framingham Heart Study Offspring Cohort, Anya Kalsbeek, Jenna Veenstra, Jason Westra, Craig Disselkoen, Kristin Koch, Katelyn A. Mckenzie, Jacob O'Bott, Jason Vander Woude, Karen Fischer, Greg C. Shearer, William S. Harris, Nathan L. Tintle Apr 2018

A Genome-Wide Association Study Of Red-Blood Cell Fatty Acids And Ratios Incorporating Dietary Covariates: Framingham Heart Study Offspring Cohort, Anya Kalsbeek, Jenna Veenstra, Jason Westra, Craig Disselkoen, Kristin Koch, Katelyn A. Mckenzie, Jacob O'Bott, Jason Vander Woude, Karen Fischer, Greg C. Shearer, William S. Harris, Nathan L. Tintle

Faculty Work Comprehensive List

Recent analyses have suggested a strong heritable component to circulating fatty acid (FA) levels; however, only a limited number of genes have been identified which associate with FA levels. In order to expand upon a previous genome wide association study done on participants in the Framingham Heart Study Offspring Cohort and FA levels, we used data from 2,400 of these individuals for whom red blood cell FA profiles, dietary information and genotypes are available, and then conducted a genome-wide evaluation of potential genetic variants associated with 22 FAs and 15 FA ratios, after adjusting for relevant dietary covariates. Our analysis …


Marker Of Proliferation Ki-67 Expression Is Associated With Transforming Growth Factor Beta 1 And Can Predict The Prognosis Of Patients With Hepatic B Virus-Related Hepatocellular Carcinoma, Chengkun Yang, Hao Su, Xiwen Liao, Chuangye Han, Tingdong Yu, Guangzhi Zhu, Xiangkun Wang, Cheryl Ann Winkler, Stephen J. O’Brien, Tao Peng Apr 2018

Marker Of Proliferation Ki-67 Expression Is Associated With Transforming Growth Factor Beta 1 And Can Predict The Prognosis Of Patients With Hepatic B Virus-Related Hepatocellular Carcinoma, Chengkun Yang, Hao Su, Xiwen Liao, Chuangye Han, Tingdong Yu, Guangzhi Zhu, Xiangkun Wang, Cheryl Ann Winkler, Stephen J. O’Brien, Tao Peng

Biology Faculty Articles

Hepatocellular carcinoma (HCC) is the most frequent malignancy of the liver. Transforming growth factor beta 1 (TGFB1) and marker of proliferation Ki-67 (MKI67) regulate cell proliferation, differentiation, and growth. The association between MKI67 and TGFB1 expression and its clinical implications in HCC remain unknown. Methods: Public databases were used to analyze TGFB1 and MKI67 expression in different pathologic grades/stages and tissue types of HCC. The association between MKI67 and TGFB1 expression was explored using pathway analysis and in a HepG2 cell line treated with TGFB1. Survival analysis was performed to evaluate the prognostic value of TGFB1 and MKI67 expression in …


Epigenome-Wide Association Study Of Metabolic Syndrome In African-American Adults, Tomi Akinyemiju, Anh N. Do, Amit Patki, Stella Aslibekyan, Degui Zhi, Bertha Hidalgo, Hemant K. Tiwari, Devin Absher, Xin Geng, Donna K. Arnett, Marguerite R. Irvin Apr 2018

Epigenome-Wide Association Study Of Metabolic Syndrome In African-American Adults, Tomi Akinyemiju, Anh N. Do, Amit Patki, Stella Aslibekyan, Degui Zhi, Bertha Hidalgo, Hemant K. Tiwari, Devin Absher, Xin Geng, Donna K. Arnett, Marguerite R. Irvin

Epidemiology and Environmental Health Faculty Publications

Background: The high prevalence of obesity among US adults has resulted in significant increases in associated metabolic disorders such as diabetes, dyslipidemia, and high blood pressure. Together, these disorders constitute metabolic syndrome, a clinically defined condition highly prevalent among African-Americans. Identifying epigenetic alterations associated with metabolic syndrome may provide additional information regarding etiology beyond current evidence from genome-wide association studies.

Methods: Data on metabolic syndrome and DNA methylation was assessed on 614 African-Americans from the Hypertension Genetic Epidemiology Network (HyperGEN) study. Metabolic syndrome was defined using the joint harmonized criteria, and DNA methylation was assessed using the Illumina HumanMethylation450K Bead …


Performance And Carcass Characteristics Of Steers Fed With Two Levels Of Metabolizable Energy Intake During Summer And Winter Season, R A. Arias, J P. Keim, M Gandarillas, A Velasquez, C Alvarado-Gilis, T L. Mader Apr 2018

Performance And Carcass Characteristics Of Steers Fed With Two Levels Of Metabolizable Energy Intake During Summer And Winter Season, R A. Arias, J P. Keim, M Gandarillas, A Velasquez, C Alvarado-Gilis, T L. Mader

Department of Animal Science: Faculty Publications

Climate change is producing an increase on extreme weather events around the world such as flooding, drought and extreme ambient temperatures impacting animal production and animal welfare. At present, there is a lack of studies addressing the effects of climatic conditions associated with energy intake in finishing cattle in South American feed yards. Therefore, two experiments were conducted to assess the effects of environmental variables and level of metabolizable energy intake above maintenance requirements (MEI) on performance and carcass quality of steers. In each experiment (winter and summer), steers were fed with 1.85 or 2.72 times of their requirements of …


Skeletal, Cardiac, And Respiratory Muscle Function And Histopathology In The P448lneo- Mouse Model Of Fkrp-Deficient Muscular Dystrophy., Qing Yu, Melissa Morales, Ning Li, Alexander G Fritz, Ren Ruobing, Anthony Blaeser, Ershia Francois, Qi-Long Lu, Kanneboyina Nagaraju, Christopher F Spurney Apr 2018

Skeletal, Cardiac, And Respiratory Muscle Function And Histopathology In The P448lneo- Mouse Model Of Fkrp-Deficient Muscular Dystrophy., Qing Yu, Melissa Morales, Ning Li, Alexander G Fritz, Ren Ruobing, Anthony Blaeser, Ershia Francois, Qi-Long Lu, Kanneboyina Nagaraju, Christopher F Spurney

Genomics and Precision Medicine Faculty Publications

BACKGROUND: Fukutin-related protein (FKRP) mutations are the most common cause of dystroglycanopathies known to cause both limb girdle and congenital muscular dystrophy. The P448Lneo- mouse model has a knock-in mutation in the FKRP gene and develops skeletal, respiratory, and cardiac muscle disease.

METHODS: We studied the natural history of the P448Lneo- mouse model over 9 months and the effects of twice weekly treadmill running. Forelimb and hindlimb grip strength (Columbus Instruments) and overall activity (Omnitech Electronics) assessed skeletal muscle function. Echocardiography was performed using VisualSonics Vevo 770 (FujiFilm VisualSonics). Plethysmography was performed using whole body system (ADInstruments). Histological evaluations included …


Rapid Regeneration Offsets Losses From Warming-Induced Tree Mortality In An Aspen-Dominated Broad-Leaved Forest In Northern China, Pengwu Zhao, Chongyang Xu, Mei Zhou, Bo Zhang, Peng Ge, Nan Zeng, Hongyan Liu Apr 2018

Rapid Regeneration Offsets Losses From Warming-Induced Tree Mortality In An Aspen-Dominated Broad-Leaved Forest In Northern China, Pengwu Zhao, Chongyang Xu, Mei Zhou, Bo Zhang, Peng Ge, Nan Zeng, Hongyan Liu

Aspen Bibliography

Worldwide tree mortality as induced by climate change presents a challenge to forest managers. To successfully manage vulnerable forests requires the capacity of regeneration to compensate for losses from tree mortality. We observed rapid regeneration and the growth release of young trees after warming-induced mortality in a David aspen-dominated (Populus davidiana) broad-leaved forest in Inner Mongolia, China, as based on individual tree measurements taken in 2012 and 2015 from a 6-ha permanent plot. Warming and drought stress killed large trees 10–15 m tall with a total number of 2881 trees during 2011–2012, and also thinned the upper crowns. …


Rates And Patterns Of Evolution In A Duplicated Genome In The Family Catostomidae [Poster], Megann Michelle Schmidt, Zachary Sperstad, Peter Berendzen Apr 2018

Rates And Patterns Of Evolution In A Duplicated Genome In The Family Catostomidae [Poster], Megann Michelle Schmidt, Zachary Sperstad, Peter Berendzen

Research in the Capitol

Whole genome duplication (WGD) is a process in which the entire genome of an organism is duplicated, making redundant genes which are subject to unique evolutionary forces. Various modes of selection create different genetic fates such as retention of ancestral function, development of new function, or loss of function. Because of these differing fates, WGD is hypothesized to be a major driving force behind diversification. In this project, DNA sequences from fish species in the family Catostomidae were examined to observe patterns of evolution following a known WGD. Gene trees were generated for 179 loci to determine the amount of …


Characterization Of Sex-Based Dna Methylation Signatures In The Airways During Early Life., Cesar L Nino, Geovanny F Perez, Natalia Isaza, Maria J Gutierrez, Jose L Gomez, Gustavo Nino Apr 2018

Characterization Of Sex-Based Dna Methylation Signatures In The Airways During Early Life., Cesar L Nino, Geovanny F Perez, Natalia Isaza, Maria J Gutierrez, Jose L Gomez, Gustavo Nino

Pediatrics Faculty Publications

Human respiratory conditions are largely influenced by the individual's sex resulting in overall higher risk for males. Sex-based respiratory differences are present at birth suggesting a strong genetic component. Our objective was to characterize early life sex-based genomic signatures determined by variable X-chromosome methylation in the airways. We compared male versus female genome-wide DNA methylation in nasal airway samples from newborns and infants aged 1-6 months (N = 12). We analyzed methylation signals across CpG sites mapped to each X-linked gene using an unsupervised classifier (principal components) followed by an internal evaluation and an exhaustive cross-validation. Results were validated in …


Characterizing The Role Of Cp1 In Drosophila Melanogaster: Its Effects On Basement Membrane Degradation And Signaling, Dane Alan Flinchum Apr 2018

Characterizing The Role Of Cp1 In Drosophila Melanogaster: Its Effects On Basement Membrane Degradation And Signaling, Dane Alan Flinchum

Masters Theses & Specialist Projects

CP1 is a well-conserved cathepsin L-like protease essential for proper growth and development in Drosophila melanogaster. Previous research has demonstrated that CP1 has the ability to break down the extracellular matrix. Using the UAS-GAL4 system, immunohistochemistry, and antibody-staining, this research attempts to characterize the role of CP1 and its effects on basement membrane degradation and signaling. These effects include actions at the cellular level and on a known signaling pathway. The genes involved in this pathway are known to be required for proper development of the wing disc into the adult wing. We have demonstrated the collagenase activity of CP1 …


Transcriptomic Response To Immune Challenge In Zebra Finch (Taeniopygia Guttata) Using Rna-Seq, Cassandra Scalf Apr 2018

Transcriptomic Response To Immune Challenge In Zebra Finch (Taeniopygia Guttata) Using Rna-Seq, Cassandra Scalf

Masters Theses & Specialist Projects

Despite the convergence of rapid technological advances in genomics and the maturing field of ecoimmunology, our understanding of the genes that regulate immunity in wild populations is still nascent. Previous work to assess immune function has relied upon relatively crude measures of immunocompetence. However, with next-generation RNA-sequencing, it is now possible to create a profile of gene expression in response to an immune challenge. In this study, captive zebra finch (Taeniopygia guttata; adult males) were challenged with bacterial lipopolysaccharide (2 mg/Kg BW; dissolved in 0.9% saline) or vehicle (0.9% saline) to stimulate the immune system. Two hours after injection, birds …


Glucocorticoids Modulate Gastrointestinal Microbiome In A Wild Bird., José C Noguera, Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez, Alberto Velando Apr 2018

Glucocorticoids Modulate Gastrointestinal Microbiome In A Wild Bird., José C Noguera, Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez, Alberto Velando

Computational Biology Institute

It has recently been hypothesized that stress exposure (e.g. via glucocorticoid secretion) may dysregulate the bacterial gut microbiome, a crucial 'organ' in animal health. However, whether stress exposure (e.g. via glucocorticoid secretion) affects the bacterial gut microbiome of natural populations is unknown. We have experimentally altered the basal glucocorticoid level (corticosterone implants) in a wild avian species, the yellow-legged gull


The Association Of Polymorphism Rs3736228 Within The Lrp5 Gene With Bone Mineral Density In A Cohort Of Caucasian Young Adults, Mohamed J. H. Al-Amoodi, Whitney Jones, Danny Lee, Steven Mckenzie, Helen C. Miller, Zach Zeller, Seth Stubblefield, Susan Knoblach, Heather Gordish-Dressman, Dustin Hittel, Laura L. Tosi Apr 2018

The Association Of Polymorphism Rs3736228 Within The Lrp5 Gene With Bone Mineral Density In A Cohort Of Caucasian Young Adults, Mohamed J. H. Al-Amoodi, Whitney Jones, Danny Lee, Steven Mckenzie, Helen C. Miller, Zach Zeller, Seth Stubblefield, Susan Knoblach, Heather Gordish-Dressman, Dustin Hittel, Laura L. Tosi

GW Research Days 2016 - 2020

INTRODUCTION: Osteoporosis is a significant burden for our aging population. Developing a better understanding of the genetic underpinnings of poor bone quality may assist in the future development of prevention strategies. Correa-Rodriguez et al. have identified a group of single nucleotide polymorphisms (SNPs) that were associated with bone mineral density (BMD) in a population of Spanish Caucasians. In particular, they found that SNP rs3736228 in the low-density lipoprotein receptor related protein 5 (LRP5) gene had an influence on BMD. While the role of LRP5 in the Wnt canonical pathway has been fairly well characterized, its association with phenotypic BMD and …


Genetic Interactions Between Bob1 And Multiple 26s Proteasome Subunits Suggest A Role For Proteostasis In Regulating Arabidopsis Development, Elan W. Silverblatt-Buser , '12, Melissa A. Frick , '12, Christina Rabeler, Nicholas J. Kaplinsky Apr 2018

Genetic Interactions Between Bob1 And Multiple 26s Proteasome Subunits Suggest A Role For Proteostasis In Regulating Arabidopsis Development, Elan W. Silverblatt-Buser , '12, Melissa A. Frick , '12, Christina Rabeler, Nicholas J. Kaplinsky

Biology Faculty Works

Protein folding and degradation are both required for protein quality control, an essential cellular activity that underlies normal growth and development. We investigated how BOB1, an Arabidopsis thaliana small heat shock protein, maintains normal plant development. bob1 mutants exhibit organ polarity defects and have expanded domains of KNOX gene expression. Some of these phenotypes are ecotype specific suggesting that other genes function to modify them. Using a genetic approach we identified an interaction between BOB1 and FIL, a gene required for abaxial organ identity. We also performed an EMS enhancer screen using the bob1-3 allele to identify pathways that are …


Cross Talk Between Serum Kisspeptin-Leptin During Assisted Reproduction Techniques, Rehana Rehman, Zehra Jamil, Aqsa Khalid, Syeda Sadia Fatima Apr 2018

Cross Talk Between Serum Kisspeptin-Leptin During Assisted Reproduction Techniques, Rehana Rehman, Zehra Jamil, Aqsa Khalid, Syeda Sadia Fatima

Department of Biological & Biomedical Sciences

Background & Objective: Leptin facilitates onset of puberty by impact on hypothalamic Kisspeptin, gonadotropin releasing hormone, follicle stimulating and luteinizing hormone. The link of peripheral Leptin-Kisspeptin in regulating the ovarian and endometrial tissue in relation to adiposity is unknown. Therefore, we wanted to identify Kisspeptin-Leptin association with body mass index (BMI) and success of assisted reproductive treatments (ART) in infertile females.
Methods: A cross sectional study was carried from August 2014 till May 2016 after receiving ethical approval at Australian Concept Infertility Medical Centre, and Aga Khan University. The study group comprised of females with an age range …