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Articles 1 - 30 of 547
Full-Text Articles in Life Sciences
Special Muscles, Annamaria C. Scaccia
Special Muscles, Annamaria C. Scaccia
Capstones
Special Muscles is a documentary that explores living with Duchenne muscular dystrophy, a fatal degenerative disease that weakens the muscles at an aggressive rate. The film will give an uncensored look at how one family copes with inevitability of the disease and their journey chasing a promising experimental cure.
Special Muscles follows 7-year-old Pietro Scarso and his family as they face the challenges, complications and promise of treating Pietro’s progressive muscle disorder. The film travels from New York to Los Angeles to Philadelphia to document the Scarso family’s race against time as Pietro undergoes a 96-week clinical trial for Eteplirsen, …
Effects Of Melatonin On Heartbeat And Possible Identification Of A Melatonin Receptor In Drosophila Melanogaster, Tricia L. Vankirk
Effects Of Melatonin On Heartbeat And Possible Identification Of A Melatonin Receptor In Drosophila Melanogaster, Tricia L. Vankirk
Electronic Theses and Dissertations
Chapter 1 of this manuscript is a literature review that serves as an introduction to the entire dissertation. Chapter 2 examines the effects of the melatonin injection on heart rate and rhythmicity in Drosophila melanogaster Canton-S (wild-type) pupae and pupae bearing a variety of heart mutations. Chapter 3 investigates further the possible mechanisms of melatonin’s ability to increase heart rhythmicity without significantly affecting heart rate. A melatonin antagonist, luzindole; a high-affinity melatonin agonist, 2-iodomelatonin and RNAi techniques are used to identify a possible melatonin receptor in Drosophila melanogaster.
An appendix contains a previously published manuscript detailing experiments performed at the …
Phylogenetic Investigation Of Enteric Bovine Coronavirus In Ireland Reveals Partitioning Between European And Global Strains, Lynda Gunn, P. J. Collins, M. J. O'Connell, Helen O'Shea
Phylogenetic Investigation Of Enteric Bovine Coronavirus In Ireland Reveals Partitioning Between European And Global Strains, Lynda Gunn, P. J. Collins, M. J. O'Connell, Helen O'Shea
Department of Biological Sciences Publications
Background
Bovine coronavirus is a primary cause of neonatal calf diarrhea worldwide, and is also associated with acute diarrhea in adult cattle during the winter season. There are no reports on molecular characterization of bovine coronavirus in Ireland, and little data exists apart from serological studies.
Findings
In this study, 11 neonatal (mean age 9 days) calf BCoV strains from the south of Ireland were collected over a one year period and characterized using molecular methods. The spike gene which encodes a protein involved in viral entry, infectivity and immune response shows the most variability amongst the isolates and was …
Alternative Use Of Dna Binding Domains By The Neurospora White Collar Complex Dictates Circadian Regulation And Light Responses, Bin Wang, Xiaoying Zhou, Jennifer J. Loros, Jay C. Dunlap
Alternative Use Of Dna Binding Domains By The Neurospora White Collar Complex Dictates Circadian Regulation And Light Responses, Bin Wang, Xiaoying Zhou, Jennifer J. Loros, Jay C. Dunlap
Dartmouth Scholarship
In the Neurospora circadian system, the White Collar complex (WCC) of WC-1 and WC-2 drives transcription of the circadian pacemaker gene frequency (frq), whose gene product, FRQ, as a part of the FRQ-FRH complex (FFC), inhibits its own expression. The WCC is also the principal Neurospora photoreceptor; WCC-mediated light induction of frq resets the clock, and all acute light induction is triggered by WCC binding to promoters of light-induced genes. However, not all acutely light-induced genes are also clock regulated, and conversely, not all clock-regulated direct targets of WCC are light induced; the structural determinants governing the shift …
Elimination Of Chromosomal Island Spycim1 From Streptococcus Pyogenes Strain Sf370 Reverses The Mutator Phenotype And Alters Global Transcription, Christina Hendrickson, Chad W. Euler, Scott V. Nguyen, Maliha Rahman, Kimberly A. Mccullor, Catherine J. King, Vincent A. Fischetti, W. Michael Mcshan
Elimination Of Chromosomal Island Spycim1 From Streptococcus Pyogenes Strain Sf370 Reverses The Mutator Phenotype And Alters Global Transcription, Christina Hendrickson, Chad W. Euler, Scott V. Nguyen, Maliha Rahman, Kimberly A. Mccullor, Catherine J. King, Vincent A. Fischetti, W. Michael Mcshan
Publications and Research
Streptococcus pyogenes chromosomal island M1 (SpyCIM1) integrates by site-specific recombination into the 5’ end of DNA mismatch repair (MMR) gene mutL in strain SF370SmR, blocking transcription of it and the downstream operon genes. During exponential growth, SpyCIM1 excises from the chromosome and replicates as an episome, restoring mutL transcription. This process is reversed in stationary phase with SpyCIM1 re-integrating into mutL, returning the cells to a mutator phenotype. Here we show that elimination of SpyCIM1 relieves this mutator phenotype. The downstream MMR operon genes, multidrug efflux pump lmrP, Holliday junction resolution helicase ruvA, and DNA base excision …
Period-1 Encodes An Atp-Dependent Rna Helicase That Influences Nutritional Compensation Of The Neurospora Circadian Clock, Jillian M. Emerson, Bradley M. Bartholomai, Carol S. Ringelberg, Scott E. Baker, Jennifer Loros, Jay Dunlap
Period-1 Encodes An Atp-Dependent Rna Helicase That Influences Nutritional Compensation Of The Neurospora Circadian Clock, Jillian M. Emerson, Bradley M. Bartholomai, Carol S. Ringelberg, Scott E. Baker, Jennifer Loros, Jay Dunlap
Dartmouth Scholarship
Mutants in the period-1 (prd-1) gene, characterized by a recessive allele, display a reduced growth rate and period lengthening of the developmental cycle controlled by the circadian clock. We refined the genetic location of prd-1 and used whole genome sequencing to find the mutation defining it, confirming the identity of prd-1 by rescuing the mutant circadian phenotype via transformation. PRD-1 is an RNA helicase whose orthologs, DDX5 [DEAD (Asp-Glu-Ala-Asp) Box Helicase 5] and DDX17 in humans and DBP2 (Dead Box Protein 2) in yeast, are implicated in various processes, including transcriptional regulation, elongation, and termination, ribosome biogenesis, and mRNA decay. …
Rna Sequencing Analysis Of The Msl2msl3, Crl, And Ggps1 Mutants Indicates That Diverse Sources Of Plastid Dysfunction Do Not Alter Leaf Morphology Through A Common Signaling Pathway, Darron R. Luesse, Margaret E. Wilson, Elizabeth S. Haswell
Rna Sequencing Analysis Of The Msl2msl3, Crl, And Ggps1 Mutants Indicates That Diverse Sources Of Plastid Dysfunction Do Not Alter Leaf Morphology Through A Common Signaling Pathway, Darron R. Luesse, Margaret E. Wilson, Elizabeth S. Haswell
Biology Faculty Publications & Presentations
Determining whether individual genes function in the same or in different pathways is an important aspect of genetic analysis. As an alternative to the construction of higher-order mutants, we used contemporary expression profiling methods to perform pathway analysis on several Arabidopsis thaliana mutants, including the mscS-like (msl)2msl3 double mutant. MSL2 and MSL3 are implicated in plastid ion homeostasis, and msl2msl3 double mutants exhibit leaves with a lobed periphery, a rumpled surface, and disturbed mesophyll cell organization. Similar developmental phenotypes are also observed in other mutants with defects in a range of other chloroplast or mitochondrial functions, including …
Mechanisms Of Adaptation In The Newly Invasive Species Brachypodium Sylvaticum (Hudson) Beauv., Gina Lola Marchini
Mechanisms Of Adaptation In The Newly Invasive Species Brachypodium Sylvaticum (Hudson) Beauv., Gina Lola Marchini
Dissertations and Theses
It is common knowledge that invasive species cause worldwide ecological and economic damage, and are nearly impossible to eradicate. However, upon introduction to a novel environment, alien species should be the underdogs: They are present in small numbers, possess low genetic diversity, and have not adapted to the climate and competitors present in the new habitat. So, how are alien species able to invade an environment occupied by native species that have already adapted to the local environment? To discover some answers to this apparent paradox I conducted four ecological genetic studies that utilized the invasive species Brachypodium sylvaticum (Hudson) …
Rnai-Mediated Control Of Aflatoxins In Peanut: Method To Analyze Mycotoxin Production And Transgene Expression In The Peanut/Aspergillus Pathosystem, Renee S. Arias, Phat M. Dang, Victor S. Sobolev
Rnai-Mediated Control Of Aflatoxins In Peanut: Method To Analyze Mycotoxin Production And Transgene Expression In The Peanut/Aspergillus Pathosystem, Renee S. Arias, Phat M. Dang, Victor S. Sobolev
United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications
The Food and Agriculture Organization of the United Nations estimates that 25% of the food crops in the world are contaminated with aflatoxins. That represents 100 million tons of food being destroyed or diverted to non-human consumption each year. Aflatoxins are powerful carcinogens normally accumulated by the fungi Aspergillus flavus and A. parasiticus in cereals, nuts, root crops and other agricultural products. Silencing of five aflatoxin-synthesis genes by RNA interference (RNAi) in peanut plants was used to control aflatoxin accumulation following inoculation with A. flavus. Previously, no method existed to analyze the effectiveness of RNAi in individual peanut transgenic events, …
Epacs: Epigenetic Regulators That Affect Cell Survival In Cancer., Catherine Murari
Epacs: Epigenetic Regulators That Affect Cell Survival In Cancer., Catherine Murari
Theses & Dissertations
Cyclic adenosine monophosphate (cAMP) is a second messenger responsive to many external stimuli, playing an important role in cellular gene expression, metabolism, migration, differentiation, hypertrophy, apoptosis and secretion. All of these cellular functions are important in many diseases including cancer. Most of its effects were initially attributed to the classical protein kinase A (PKA) protein, but cellular functions such as proliferation and migration were found to be PKA independent and dependent on the newly discovered exchange proteins directly activated by cAMP (EPACs). EPACs are single polypeptides that primarily function as guanine exchange factors (GEFs) for Rap proteins that allow the …
Finding Function In The Unknown, Kelly Boyd, Emma Highland, Amanda Misch, Amber Hu, Sushma Reddy, Catherine Putonti
Finding Function In The Unknown, Kelly Boyd, Emma Highland, Amanda Misch, Amber Hu, Sushma Reddy, Catherine Putonti
Bioinformatics Faculty Publications
Through high-throughput RNA sequencing (RNAseq), transcriptomes for a single cell, tissue, or organism(s) can be ascertained at a high resolution. While a number of bioinformatic tools have been developed for transcriptome analyses, significant challenges exist for studies of non-model organisms. Without a reference sequence available, raw reads must first be assembled de novo followed by the tedious task of BLAST searches and data mining for functional information. We have created a pipeline, PyRanger, to automate this process. The pipeline includes functionality to assess a single transcriptome and also facilitate comparative transcriptomic studies.
Are Immune Modulating Single Nucleotide Polymorphisms Associated With Necrotizing Enterocolitis?, Ashanti L Franklin, Mariam Said, Clint D Cappiello, Heather Gordish-Dressman, Zohreh Tatari-Calderone, Stanislav Vukmanovic, Khodayar Rais-Bahrami, Naomi L C Luban, Joseph M Devaney, Anthony D Sandler
Are Immune Modulating Single Nucleotide Polymorphisms Associated With Necrotizing Enterocolitis?, Ashanti L Franklin, Mariam Said, Clint D Cappiello, Heather Gordish-Dressman, Zohreh Tatari-Calderone, Stanislav Vukmanovic, Khodayar Rais-Bahrami, Naomi L C Luban, Joseph M Devaney, Anthony D Sandler
Genomics and Precision Medicine Faculty Publications
Necrotizing enterocolitis (NEC) is a devastating gastrointestinal emergency. The purpose of this study is to determine if functional single nucleotide polymorphisms (SNPs) in immune-modulating genes pre-dispose infants to NEC. After Institutional Review Board approval and parental consent, buccal swabs were collected for DNA extraction. TaqMan allelic discrimination assays and BglII endonuclease digestion were used to genotype specific inflammatory cytokines and TRIM21. Statistical analysis was completed using logistic regression. 184 neonates were analyzed in the study. Caucasian neonates with IL-6 (rs1800795) were over 6 times more likely to have NEC (p = 0.013; OR = 6.61, 95% CI 1.48-29.39), and over …
Differential Expression Of Cyb5a In Chinese And European Pig Breeds Due To Genetic Variations In The Promoter Region..Pdf, Ying Bai, Jibin Zhang, Y Xue, Yl Peng, Gang Chen, Meiying Fang
Differential Expression Of Cyb5a In Chinese And European Pig Breeds Due To Genetic Variations In The Promoter Region..Pdf, Ying Bai, Jibin Zhang, Y Xue, Yl Peng, Gang Chen, Meiying Fang
Jibin Zhang
Leveraging Global Gene Expression Patterns To Predict Expression Of Unmeasured Genes, James Rudd, René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene S. Greene, Jennifer A. Doherty
Leveraging Global Gene Expression Patterns To Predict Expression Of Unmeasured Genes, James Rudd, René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene S. Greene, Jennifer A. Doherty
Dartmouth Scholarship
BackgroundLarge collections of paraffin-embedded tissue represent a rich resource to test hypotheses based on gene expression patterns; however, measurement of genome-wide expression is cost-prohibitive on a large scale. Using the known expression correlation structure within a given disease type (in this case, high grade serous ovarian cancer; HGSC), we sought to identify reduced sets of directly measured (DM) genes which could accurately predict the expression of a maximized number of unmeasured genes.
Language And Literacy Development In Individuals With Velo‐Cardio‐Facial Syndrome, Kevin Antshel, Eileen Marrinan, Wendy Kates, Wanda Fremont, Robert Shprintzen
Language And Literacy Development In Individuals With Velo‐Cardio‐Facial Syndrome, Kevin Antshel, Eileen Marrinan, Wendy Kates, Wanda Fremont, Robert Shprintzen
Robert J. Shprintzen
Velo-cardio-facial syndrome (VCFS) is a genetic disorder caused by a microdeletion of chromosome 22q11.2. Although there is some variability, VCFS is associated with a characteristic physical, behavioral, and cognitive phenotype. This review article focuses on aspects of language and literacy development in VCFS, describing what is known and offering avenues for future research. The most consistently reported language and literacy findings in the VCFS population include reading, spelling, phonological processing, and auditory verbal rote memory abilities as areas of relative strength. Receptive language abilities are noted to be relatively stronger than expressive language abilities in individuals with VCFS. Speech disorders …
Atlas-Based White Matter Analysis In Individuals With Velo-Cardio-Facial Syndrome (22q11.2 Deletion Syndrome) And Unaffected Siblings, Petya Radoeva, Ioana Coman, Kevin Antshel, Wanda Fremont, Christopher Mccarthy, Ashwini Kotkar, Dongliang Wang, Robert Shprintzen, Wendy Kates
Atlas-Based White Matter Analysis In Individuals With Velo-Cardio-Facial Syndrome (22q11.2 Deletion Syndrome) And Unaffected Siblings, Petya Radoeva, Ioana Coman, Kevin Antshel, Wanda Fremont, Christopher Mccarthy, Ashwini Kotkar, Dongliang Wang, Robert Shprintzen, Wendy Kates
Robert J. Shprintzen
Background: Velo-cardio-facial syndrome (VCFS, MIM#192430, 22q11.2 Deletion Syndrome) is a genetic disorder caused by a deletion of about 40 genes at the q11.2 band of one copy of chromosome 22. Individuals with VCFS present with deficits in cognition and social functioning, high risk of psychiatric disorders, volumetric reductions in gray and white matter (WM) and some alterations of the WM microstructure. The goal of the current study was to characterize the WM microstructural differences in individuals with VCFS and unaffected siblings, and the correlation of WM microstructure with neuropsychological performance. We hypothesized that individuals with VCFS would have decreased indices …
Velo-Cardio-Facial Syndrome, Doron Gothelf, Amos Frisch, Elena Michaelovsky, Abraham Weizman, Robert Shprintzen
Velo-Cardio-Facial Syndrome, Doron Gothelf, Amos Frisch, Elena Michaelovsky, Abraham Weizman, Robert Shprintzen
Robert J. Shprintzen
Velocardiofacial syndrome (VCFS), also known as DiGeorge, conotruncal anomaly face, and Cayler syndromes, is caused by a microdeletion in the long arm of Chromosome 22. We review the history of the syndrome from the first clinical reports almost half a century ago to the current intriguing molecular findings associating genes from the microdeletion region and the physical and neuropsychiatric phenotype of the syndrome. Velocardiofacial syndrome has a wide spectrum of more than 200 physical manifestations including palate and cardiac anomalies. Yet, the most challenging manifestations of VCFS are the learning disabilities and neuropsychiatric disorders. As VCFS is relatively common and …
Genomic Disorders On Chromosome 22, Shihui Yu, William Graf, Robert Shprintzen
Genomic Disorders On Chromosome 22, Shihui Yu, William Graf, Robert Shprintzen
Robert J. Shprintzen
Purpose of review: Chromosome 22, the first human chromosome to be completely sequenced, is prone to genomic alterations. Copy-number variants (CNVs) are common because of an enrichment of low-copy repeat sequences that precipitate a high frequency of nonallelic homologous misalignments and unequal recombination during meiosis. Among these is one of the most common multiple anomaly syndromes in humans and the most common microdeletion syndrome, velocardiofacial syndrome (VCFS), also known as 22q11.2 deletion syndrome and DiGeorge syndrome. This review will focus on the recent literature dealing with both the molecular and clinical aspects of chromosome 22 genomic variations. Although the literature …
Identifying Gene-Gene Interactions That Are Highly Associated With Body Mass Index Using Quantitative Multifactor Dimensionality Reduction (Qmdr), Rishika De, Shefali S. Verma, Fotios Drenos, Emily R. Holzinger
Identifying Gene-Gene Interactions That Are Highly Associated With Body Mass Index Using Quantitative Multifactor Dimensionality Reduction (Qmdr), Rishika De, Shefali S. Verma, Fotios Drenos, Emily R. Holzinger
Dartmouth Scholarship
Despite heritability estimates of 40–70% for obesity, less than 2% of its variation is explained by Body Mass Index (BMI) associated loci that have been identified so far. Epistasis, or gene-gene interactions are a plausible source to explain portions of the missing heritability of BMI. Using genotypic data from 18,686 individuals across five study cohorts – ARIC, CARDIA, FHS, CHS, MESA – we filtered SNPs (Single Nucleotide Polymorphisms) using two parallel approaches. SNPs were filtered either on the strength of their main effects of association with BMI, or on the number of knowledge sources supporting a specific SNP-SNP interaction in …
Hd2d Is A Regulator Of Abscisic Acid Responses In Arabidopsis, Joshua A. Farhi
Hd2d Is A Regulator Of Abscisic Acid Responses In Arabidopsis, Joshua A. Farhi
Electronic Thesis and Dissertation Repository
Histone deacetylases have important roles in development and stress response in plants. To further investigate their function, the HD2D gene, of the plant specific HD2 family, was studied. An hd2d-1 mutant and two HD2D overexpression lines were used in this study. Germination was delayed in hd2d-1 and HD2D overexpression seeds only in the presence of ABA. HD2D was found to positively regulate the expression of members of the ABA-response pathway (ABI1, ABI5, and RD29A) leading to increased resistance to drought and salinity treatments. Furthermore, HD2D expression delayed flowering by positively regulating FLC expression. Using bimolecular fluorescence complementation, the HD2D protein …
Genetic And Acute Cpeb1 Depletion Ameliorate Fragile X Pathophysiology, Tsuyoshi Udagawa, Natalie Farny, Mira Jakovcevski, Hanoch Kaphzan, Juan Alarcon, Shobha Anilkumar, Maria Ivshina, Jessica Hurt, Kentaro Nagaoka, Vijayalaxmi Nalavadi, Lori Lorenz, Gary Bassell, Schahram Akbarian, Sumantra Chattarji, Eric Klann, Joel Richter
Genetic And Acute Cpeb1 Depletion Ameliorate Fragile X Pathophysiology, Tsuyoshi Udagawa, Natalie Farny, Mira Jakovcevski, Hanoch Kaphzan, Juan Alarcon, Shobha Anilkumar, Maria Ivshina, Jessica Hurt, Kentaro Nagaoka, Vijayalaxmi Nalavadi, Lori Lorenz, Gary Bassell, Schahram Akbarian, Sumantra Chattarji, Eric Klann, Joel Richter
Natalie G. Farny
Fragile X syndrome (FXS), the most common cause of inherited mental retardation and autism, is caused by transcriptional silencing of FMR1, which encodes the translational repressor fragile X mental retardation protein (FMRP). FMRP and cytoplasmic polyadenylation element-binding protein (CPEB), an activator of translation, are present in neuronal dendrites, are predicted to bind many of the same mRNAs and may mediate a translational homeostasis that, when imbalanced, results in FXS. Consistent with this possibility, Fmr1(-/y); Cpeb1(-/-) double-knockout mice displayed amelioration of biochemical, morphological, electrophysiological and behavioral phenotypes associated with FXS. Acute depletion of CPEB1 in the hippocampus of adult Fmr1(-/y) mice …
Fgf2-Induced Effects On Transcriptome Associated With Regeneration Competence In Adult Human Fibroblasts, Olga Kashpur, David Lapointe, Sakthikumar Ambady, Elizabeth Ryder, Tanja Dominko
Fgf2-Induced Effects On Transcriptome Associated With Regeneration Competence In Adult Human Fibroblasts, Olga Kashpur, David Lapointe, Sakthikumar Ambady, Elizabeth Ryder, Tanja Dominko
Sakthikumar Ambady
BACKGROUND: Adult human fibroblasts grown in low oxygen and with FGF2 supplementation have the capacity to tip the healing outcome of skeletal muscle injury - by favoring regeneration response in vivo over scar formation. Here, we compare the transcriptomes of control adult human dermal fibroblasts and induced regeneration-competent (iRC) fibroblasts to identify transcriptional changes that may be related to their regeneration competence. RESULTS: We identified a unique gene-expression profile that characterizes FGF2-induced iRC fibroblast phenotype. Significantly differentially expressed genes due to FGF2 treatment were identified and analyzed to determine overrepresented Gene Ontology terms. Genes belonging to extracellular matrix components, adhesion …
Genomic Legacy Of The African Cheetah, Acinonyx Jubatus, Pavel Dobrynin, Shiping Liu, Gaik Tamazian, Zijun Xiong, Andrey A. Yurchenko, Ksenia Krasheninnikova, Sergey Kliver, A. Schmidt-Kunzel, Klaus-Peter Koepfli, Warren E. Johnson, Lukas F. K. Kuderna, Raquel Garcia-Perez, Marc De Manuel, Ricardo Godinez, Aleksey Komissarov, Alexey Makunin, Vladimir Brukhin, Weilin Qiu, Long Zhou, Fang Li, Jian Yi, Carlos A. Driscoll, Agostinho Antunes, T. K. Oleksyk, Eduardo Eizirik, Polina Perelman, Melody E. Roelke, David E. Wildt, Mark Diekhans, Tomas Marques-Bonet, Laurie Marker, Jong Bhak, Jun Wang, Guojie Zhang, Stephen J. O'Brien
Genomic Legacy Of The African Cheetah, Acinonyx Jubatus, Pavel Dobrynin, Shiping Liu, Gaik Tamazian, Zijun Xiong, Andrey A. Yurchenko, Ksenia Krasheninnikova, Sergey Kliver, A. Schmidt-Kunzel, Klaus-Peter Koepfli, Warren E. Johnson, Lukas F. K. Kuderna, Raquel Garcia-Perez, Marc De Manuel, Ricardo Godinez, Aleksey Komissarov, Alexey Makunin, Vladimir Brukhin, Weilin Qiu, Long Zhou, Fang Li, Jian Yi, Carlos A. Driscoll, Agostinho Antunes, T. K. Oleksyk, Eduardo Eizirik, Polina Perelman, Melody E. Roelke, David E. Wildt, Mark Diekhans, Tomas Marques-Bonet, Laurie Marker, Jong Bhak, Jun Wang, Guojie Zhang, Stephen J. O'Brien
Biology Faculty Articles
Background
Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations.
Results
Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one >100,000 years …
The Importance Of Physicochemical Characteristics And Nonlinear Classifiers In Determining Hiv-1 Protease Specificity, Timmy Manning, Paul Walsh
The Importance Of Physicochemical Characteristics And Nonlinear Classifiers In Determining Hiv-1 Protease Specificity, Timmy Manning, Paul Walsh
Department of Biological Sciences Publications
This paper reviews recent research relating to the application of bioinformatics approaches to determining HIV-1 protease specificity, outlines outstanding issues, and presents a new approach to addressing these issues. Leading machine learning theory for the problem currently suggests that the direct encoding of the physicochemical properties of the amino acid substrates is not required for optimal performance. A number of amino acid encoding approaches which incorporate potentially relevant physicochemical properties of the substrate are identified, and are evaluated using a nonlinear task decomposition based neuroevolution algorithm. The results are evaluated, and compared against a recent benchmark set on a nonlinear …
Genetic Parameters For Docility, Weaning Weight, Yearling Weight, And Intramuscular Fat Percentage In Hereford Cattle, J. A. Torres-Vázquez, Matthew L. Spangler
Genetic Parameters For Docility, Weaning Weight, Yearling Weight, And Intramuscular Fat Percentage In Hereford Cattle, J. A. Torres-Vázquez, Matthew L. Spangler
Department of Animal Science: Faculty Publications
Cattle behavior, including measures of docility, is important to beef cattle producers not only from a human safety perspective but also due to potential correlations to economically relevant traits. Field data from the American Hereford Association was used to estimate genetic parameters for chute score (CS; n = 25,037), weaning weight (WW; n = 24,908), yearling weight (YW; n = 23,978), and intramuscular fat percentage (IMF; n = 12,566). Single-trait and bivariate animal models were used to estimate heritabilities and genetic correlations. All models included fixed effects of sex and contemporary group, defined as herd–year–season, and direct genetic and residual …
Multipartite Graph Algorithms For The Analysis Of Heterogeneous Data, Charles Alexander Phillips
Multipartite Graph Algorithms For The Analysis Of Heterogeneous Data, Charles Alexander Phillips
Doctoral Dissertations
The explosive growth in the rate of data generation in recent years threatens to outpace the growth in computer power, motivating the need for new, scalable algorithms and big data analytic techniques. No field may be more emblematic of this data deluge than the life sciences, where technologies such as high-throughput mRNA arrays and next generation genome sequencing are routinely used to generate datasets of extreme scale. Data from experiments in genomics, transcriptomics, metabolomics and proteomics are continuously being added to existing repositories. A goal of exploratory analysis of such omics data is to illuminate the functions and relationships of …
Application Of Hidden Markov Model Based Methods For Gaining Insights Into Protein Domain Evolution And Function, Amit Anil Upadhyay
Application Of Hidden Markov Model Based Methods For Gaining Insights Into Protein Domain Evolution And Function, Amit Anil Upadhyay
Doctoral Dissertations
With the explosion in the amount of available sequence data, computational methods have become indispensable for studying proteins. Domains are the fundamental structural, functional and evolutionary units that make up proteins. Studying protein domains is an important part of understanding protein function and evolution. Hidden Markov Models (HMM) are one of the most successful methods that have been applied for protein sequence and structure analysis. In this study, HMM based methods were applied to study the evolution of sensory domains in microbial signal transduction systems as well as functional characterization and identification of cellulases in metagenomics datasets. Use of HMM …
Applications Of Evolutionary Bioinformatics In Basic And Biomedical Research, Ogun Adebali
Applications Of Evolutionary Bioinformatics In Basic And Biomedical Research, Ogun Adebali
Doctoral Dissertations
With the revolutionary progress in sequencing technologies, computational biology emerged as a game-changing field which is applied in understanding molecular events of life for not only complementary but also exploratory purposes. Bioinformatics resources and tools significantly help in data generation, organization and analysis. However, there is still a need for developing new approaches built based on a biologist’s point of view. In protein bioinformatics, there are several fundamental problems such as (i) determining protein function; (ii) identifying protein-protein interactions; (iii) predicting the effect of amino acid variants. Here, I present three chapters addressing these problems from an evolutionary perspective. Firstly, …
Preventing Thymus Involution In K5.Cyclin D1 Transgenic Mice Sustains The Naïve T Cell Compartment With Age, Michelle L. Bolner
Preventing Thymus Involution In K5.Cyclin D1 Transgenic Mice Sustains The Naïve T Cell Compartment With Age, Michelle L. Bolner
Dissertations & Theses (Open Access)
The thymus maintains T cell receptor (TCR) repertoire diversity through perpetual release of self-MHC restricted naive T cells. However, thymus involution during the aging process reduces naïve T cell output, leading to defective immune responsiveness to newly encountered antigens. We have found that early thymus involution precipitates the age-associated shift favoring memory T cell dominancy in young control mice. Furthermore, we have shown that age-related thymus involution is prevented in mice expressing a keratin 5 promoter-driven Cyclin D1 (K5.D1) transgene in thymic epithelial cells (TECs). Thymopoiesis occurs normally in K5.D1 transgenic thymi and sustains T cell output to prevent the …
Post Operative Fungal Endopthalmitis Due To Geotrichum Candidum, Thein Myint, Matthew J. Dykhuizen, Carolyn H. Mcdonald, Julie A. Ribes
Post Operative Fungal Endopthalmitis Due To Geotrichum Candidum, Thein Myint, Matthew J. Dykhuizen, Carolyn H. Mcdonald, Julie A. Ribes
Microbiology, Immunology, and Molecular Genetics Faculty Publications
Geotrichum species have been rarely reported as the cause of sepsis, disseminated infection in immunosuppressed patients. The patient we describe developed indolent endophthalmitis four months after her routine right eye cataract surgery. The intraoperative sample from right vitreous fluid grew Geotrichum candidum. The patient underwent vitrectomy, artificial lens explantation and intravitreal injection of amphotericin B followed by oral voriconazole. Despite these interventions, she underwent enucleation. This is the first published case of Geotrichum candidum endophthalmitis.