Comparison Of Sequence Alignment Algorithms,
2014
Minnesota State University, Mankato
Comparison Of Sequence Alignment Algorithms, Tejas Gandhi
Journal of Undergraduate Research at Minnesota State University, Mankato
The fact that biological sequences can be represented as strings belonging to a finite alphabet (A, C, G, and T for DNA) plays an important role in connecting biology to computer science. String representation allows researchers to apply various string comparison techniques available in computer science. As a result, various applications have been developed that facilitate the task of sequence alignment. The problem of finding sequence alignments consists of finding the best match between two biological sequences. A best match can infer an evolutionary relationship and functional similarity. However, there is a lack of research on how reliable and efficient …
Characterizations Of Proteins Interacting With The Alpha Subunit Of Actin Capping Protein,
2014
Minnesota State University, Mankato
Characterizations Of Proteins Interacting With The Alpha Subunit Of Actin Capping Protein, Angelique Ducharme, Charity Zabel
Journal of Undergraduate Research at Minnesota State University, Mankato
Actin, a filamentous component of all cells, contributes to cell shape, cell motility and force transmission. Actin assembly and dynamics are regulated by a diverse array of regulatory proteins, including actin capping protein (CP). CP is a heterodimeric protein composed of two subunits, alpha (a) and beta (ß). Three isoforms of each subunit exist in eukaryotes. The ß isoforms have been shown to have distinct functions in vivo. The functions of the specific a isoforms have yet to be determined. Overall, the amino acid sequence of the a isoforms are highly conserved, sharing approximately 90% sequence identity. The region of …
Sma-Causing Missense Mutations In Survival Motor Neuron (Smn) Display A Wide Range Of Phenotypes When Modeled In Drosophila,
2014
University of North Carolina at Chapel Hill
Sma-Causing Missense Mutations In Survival Motor Neuron (Smn) Display A Wide Range Of Phenotypes When Modeled In Drosophila, Kavita Praveen, Ying Wen, Kelsey M. Gray, John J. Noto, Akash R. Patlolla, Gregory D. Van Duyne, A. Gregory Matera
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Mutations in the human survival motor neuron 1 (SMN) gene are the primary cause of spinal muscular atrophy (SMA), a devastating neuromuscular disorder. SMN protein has a well-characterized role in the biogenesis of small nuclear ribonucleoproteins (snRNPs), core components of the spliceosome. Additional tissue-specific and global functions have been ascribed to SMN; however, their relevance to SMA pathology is poorly understood and controversial. Using Drosophila as a model system, we created an allelic series of twelve Smn missense mutations, originally identified in human SMA patients. We show that animals expressing these SMA-causing mutations display a broad range of …
Identification Of Snps In The Coding Region Of Human Mtdna,
2014
Minnesota State University, Mankato
Identification Of Snps In The Coding Region Of Human Mtdna, Cassidy Punt, Elizabeth Smalley
Journal of Undergraduate Research at Minnesota State University, Mankato
Two novel single nucleotide polymorphisms (SNPs) were discovered within the coding region of the NADH dehydrogenase subunit 2 gene of mitochondrial DNA (mtDNA). mtDNA is of particular importance in forensic analysis as well as in the study of the origin and dispersal of humans. Two segments of the coding region of human mtDNA, as well as the hyper-variable region 2 (HV 2) were selected and sequenced in order to determine if any previously unknown SNPs were present in our test subjects. Target regions were designed to include known SNPs; appropriate primers were developed using the OLIGO 6 Primer Analysis Software. …
Biofilm Formation By Escherichia Coli Csga And Fima Mutants,
2014
Minnesota State University, Mankato
Biofilm Formation By Escherichia Coli Csga And Fima Mutants, Nicole Snyder, Sean Willaert
Journal of Undergraduate Research at Minnesota State University, Mankato
Biofilms are a structured community of bacterial cells enclosed in a self-produced polymeric matrix and adherent to an inert or living surface. These structures and the organisms that cause them can pose a very serious problem if they colonize on medical devices. This is because biofilms have the ability to communicate within the colony and with other organisms that might attach to the surface, acting like a community working together. Biofilms allow the organism to be resistant to harsh and unfavorable conditions allowing them to survive longer and spread. Several genes in Escherichia coli (E. coli) have been associated …
Regulation Of Mor By Different Abiotic Stresses In Arabidopsis Thaliana,
2014
Purdue University
Regulation Of Mor By Different Abiotic Stresses In Arabidopsis Thaliana, Luke Stepan, Rucha Karve, Anjali Iyer-Pascuzzi
The Summer Undergraduate Research Fellowship (SURF) Symposium
The climate is changing and as a consequence the environment is becoming hotter and drier. How different plants will react to these changes is unknown. Identification of genes involved in stress tolerance can help predict plant-environment interactions and lead to stress tolerant plants. The MOR gene (Modulator Of Root ROS, ROS = Reactive Oxygen Species) in the model plant Arabidopsis thaliana encodes a transcription factor that may regulate stress responses, as mor mutants are drought tolerant. We hypothesized that MOR expression changes in response to different abiotic stress stimuli. We tested MOR expression in response to salt (NaCl), abscisic acid …
Development Of Transgenic North American White Ash (Fraxinus Americana) Expressing A Bacillus Thuringiensis Protein For Management Of The Emerald Ash Borer,
2014
Purdue University
Development Of Transgenic North American White Ash (Fraxinus Americana) Expressing A Bacillus Thuringiensis Protein For Management Of The Emerald Ash Borer, Eric A. Dean, Paula M. Pijut Phd., Micah E. Stevens
The Summer Undergraduate Research Fellowship (SURF) Symposium
White ash (WA), Fraxinus americana, is an integral part of the hardwood forest ecosystem. Economically, WA provides wood for important products such as baseball bats, tool handles, and hardwood flooring. Ecologically WA provides cover and mast to support wildlife. The emerald ash borer (EAB) is a significant threat to all ash species because of a lack of native resistance in North American ash trees, its rapid spread, and the ineffectiveness and expense of control measures. EAB is a non-native beetle that consumes tree vascular tissue while in the larval stage. The development of an Agrobacterium-mediated transformation protocol may …
Gene-Environment Interactions In Human Health: Case Studies And Strategies For Developing New Paradigms And Research Methodologies,
2014
Howard University
Gene-Environment Interactions In Human Health: Case Studies And Strategies For Developing New Paradigms And Research Methodologies, Fatimah Linda Collier Jackson
Department of Biology Faculty Publications
THE SYNERGISTIC EFFECTS OF GENES AND THE ENVIRONMENT ON HEALTH ARE EXPLORED IN THREE CASE STUDIES: adult lactase persistence, autism spectrum disorders, and the metabolic syndrome, providing examples of the interactive complexities underlying these phenotypes. Since the phenotypes are the initial targets of evolutionary processes, understanding the specific environmental contexts of the genetic, epigenetic, and environmental changes associated with these phenotypes is essential in predicting their health implications. Robust databases must be developed on the local scale to deconstruct both the population substructure and the unique components of the environment that stimulate geographically specific changes in gene expression patterns. To …
Multiplex Ssr-Pcr Analysis Of Genetic Diversity And Redundancy In The Philippine Rice (Oryza Sativa L.) Germplasm Collection,
2014
Ateneo de Manila University
Multiplex Ssr-Pcr Analysis Of Genetic Diversity And Redundancy In The Philippine Rice (Oryza Sativa L.) Germplasm Collection, Jamaica L. Delos Reyes, Vivian A. Panes, Dindo A. Tabanao, Gabriel O. Romero
Biology Faculty Publications
Rice germplasm conservation is vital to ensuring the availability of a rich gene pool for future varietal improvement programs. However, with limited resources for gene banking, there is a need to identify and prioritize unique accessions in the PhilRice gene bank for maximum resource utilization. A robust and unequivocal way to identify duplicates is through multiplex SSR-PCR DNA fingerprinting. The present study established the optimal concentrations and reaction conditions for the successful amplification of PCR products using a multiplex panel composed of rice simple sequence repeat (SSR) markers, namely RM312, RM316, RM514 and RM171. The panel was then used to …
Genetic Predictors Of Metabolic Side Effects Of Diuretic Therapy,
2014
The University of Texas Graduate School of Biomedical Sciences at Houston
Genetic Predictors Of Metabolic Side Effects Of Diuretic Therapy, Jorge L. Del Aguila
Dissertations and Theses (Open Access)
Thiazide diuretics are a recommended first-line monotherapy for hypertension (i.e.SBP>140 mmHg or DBP>90 mmHg). Even so, diuretics are associated with adverse metabolic side effects, such as hyperlipidemia, hyperglycemia and hypokalemia which increase the risk of developing type II diabetes. This thesis used three analytical strategies to identify and quantify genetic factors that contribute to the development of adverse metabolic effects due to thiazide diuretic treatment. I performed a genome-wide association study (GWAS) and meta-analysis of the change in fasting plasma glucose and triglycerides in response to HCTZ from two different clinical trials: the Pharmacogenomic Evaluation of Antihypertensive Responses …
Utilizing Haplotypes For Sensitive Snp Array-Based Discovery Of Somatic Chromosomal Mutations,
2014
The University of Texas Graduate School of Biomedical Sciences at Houston
Utilizing Haplotypes For Sensitive Snp Array-Based Discovery Of Somatic Chromosomal Mutations, Selina M. Vattathil
Dissertations and Theses (Open Access)
Somatic copy-number (CN) gains and losses and copy-neutral loss of heterozygosity (CNLOH) frequently occur in tumors and play a major role in the progression of disease by altering gene dosage and unmasking deleterious recessive variants. Characterizing these mutations in an individual tumor sample is therefore critical for research on the relationship of specific mutations to disease outcome and for clinical decision-making based on mutations with known impact. A pervasive hindrance to sensitive detection of these mutations is genetic heterogeneity and high levels of contaminating normal cells in tumor samples, which limit the fraction of cells carrying informative mutations. The method …
Construction Of 3d Biomimetic Tissue Niches For Directing Pancreatic Lineage Differentiation Of Human Embryonic Stem Cells,
2014
University of Arkansas, Fayetteville
Construction Of 3d Biomimetic Tissue Niches For Directing Pancreatic Lineage Differentiation Of Human Embryonic Stem Cells, Weiwei Wang
Graduate Theses and Dissertations
The potential of human embryonic stem cells (hESCs) to differentiate into insulin producing beta cells offers great hope for cell-based therapy for diabetes treatment. However, in vitro pancreatic differentiation of hESCs remains challenging. In the past decade, most protocols for differentiating pancreatic cells have been focused on the use of signaling molecule cocktails on 2D substrates. Studies on embryonic development biology strongly suggest that extracellular matrix (ECM) plays a critical role on hESCs behavior. In this work, we first established a 3D collagen scaffold culture system for hESCs differentiating into definitive endoderm (DE), which is the first and most important …
Population And Demographic Structure Of Ixodes Scapularis Say In The Eastern United States.,
2014
Mississippi State University
Population And Demographic Structure Of Ixodes Scapularis Say In The Eastern United States., Joyce M. Sakamoto, Jerome Goddard, Jason L. Rasgon
CALS Publications
INTRODUCTION: The most significant vector of tick-borne pathogens in the United States is Ixodes scapularis Say (the blacklegged tick). Previous studies have identified significant genetic, behavioral and morphological differences between northern vs. southern populations of this tick. Because tick-borne pathogens are dependent on their vectors for transmission, a baseline understanding of the vector population structure is crucial to determining the risks and epidemiology of pathogen transmission. METHODS: We investigated population genetic variation of I. scapularis populations in the eastern United States using a multilocus approach. We sequenced and analyzed the mitochondrial COI and 16S genes and three nuclear genes (serpin2, …
Key Residues Of Human Cytoplasmic Protein Tyrosine Phosphatase-A And -B For Substrate Binding And Specificity,
2014
Purdue University
Key Residues Of Human Cytoplasmic Protein Tyrosine Phosphatase-A And -B For Substrate Binding And Specificity, Byunghyun Park
Open Access Theses
Reversible tyrosine phosphorylation plays an important role in signaling pathways that are essential for regulating cellular growth, differentiation and metabolism. Moreover, several human diseases such as diabetes, obesity and cancers are associated with the deregulation of protein tyrosine phosphatases (PTPs). Several studies provide evidence that PTPs not only contribute to cellular differentiation, but over-expression of these molecules also leads to transformation of non-transfomed cells as well. Based on these results, designing specific PTP inhibitors may ultimately function as potential therapeutic agents to treat various diseases including cancer, diabetes, and autoimmune diseases. EphA2 is a receptor tyrosine kinase which is hypo-phosphorylated …
A Classification And Characterization Of Two-Locus, Pure, Strict, Epistatic Models For Simulation And Detection,
2014
Dartmouth College
A Classification And Characterization Of Two-Locus, Pure, Strict, Epistatic Models For Simulation And Detection, Ryan J. Urbanowicz, Ambrose L. S. Granizo-Mackenzie, Jeff Kiralis, Jason H Moore
Dartmouth Scholarship
BackgroundThe statistical genetics phenomenon of epistasis is widely acknowledged to confound disease etiology. In order to evaluate strategies for detecting these complex multi-locus disease associations, simulation studies are required. The development of the GAMETES software for the generation of complex genetic models, has provided the means to randomly generate an architecturally diverse population of epistatic models that are both pure and strict, i.e. all n loci, but no fewer, are predictive of phenotype. Previous theoretical work characterizing complex genetic models has yet to examine pure, strict, epistasis which should be the most challenging to detect. This study addresses three goals: …
Human Diversity In Jordan: Polymorphic Alu Insertions In General Jordanian And Bedouin Groups,
2014
Department of Animal Biology-Anthropology, University of Barcelona, Barcelona, Spain
Human Diversity In Jordan: Polymorphic Alu Insertions In General Jordanian And Bedouin Groups, Daniela Zanetti, May Sadiq, Robert Carreras-Torres, Omar Khabour, Almuthanna Alkaraki, Esther Esteban, Marc Via, Pedro Moral
Human Biology Open Access Pre-Prints
Jordan, located in the Levant region, is a crucial area to investigate human migration between Africa and Eurasia. Even thought, the genetic history of Jordanians is far to be clarified including the origin of the Bedouins today resident in Jordan. Here, we provide new genetic data on autosomal independent markers in two Jordanian population samples (Bedouins and general population) in order to approach the genetic diversity inside this country and to give new information about the genetic position of these populations in the frame of the Mediterranean and Middle East area. The analyzed markers are 18 Alu polymorphic insertions characterized …
Human Paternal Lineages, Languages And Environment In The Caucasus,
2014
1Center of Biodiversity Studies, Institute of Ecology, Ilia State University, Tbilisi, Georgia
Human Paternal Lineages, Languages And Environment In The Caucasus, David Tarkhnishvili, Alexander Gavashelishvili, Marine Murtskhvaladze, Mariam Gabelaia, Gigi Tevzadze
Human Biology Open Access Pre-Prints
Publications that describe the human Y-DNA haplogroup composition in different ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus – a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. 224 men that identified themselves as ethnic Georgian were genotyped for Y-chromosome 23 STR markers and assigned to their geographic places of origin. The genotyped data were supplemented with the published data on the haplogroup composition and …
Phylogeography Of E1b1b1b-M81 Haplogroup And Analysis Of Its Subclades In Morocco,
2014
Laboratoire de Génétique Moléculaire Humaine, Département de Recherche Scientifique, Institut Pasteur du Maroc
Phylogeography Of E1b1b1b-M81 Haplogroup And Analysis Of Its Subclades In Morocco, Ahmed Reguig, Nourdin Harich, Abdelhamid Barakat, Hassan Rouba
Human Biology Open Access Pre-Prints
In this work, we have analyzed a total of 295 unrelated Berber-speaking men from the northern, center and southern of Morocco, in order to characterize frequency of E1b1b1b-M81 haplogroup and to refine the phylogeny of its subclades: E1b1b1b1-M107, E1b1b1b2-M183 and E1b1b1b2a-M165. For this purpose, we have typed four biallelic polymorphisms: M81, M107, M183 and M165. As results, a large majority of the Berber-speaking male lineages belong to the Y chromosomal E1b1b1b-M81 haplogroup. The frequency ranged from 79.1 to 98.5% in all localities sampled. Then, the E1b1b1b2-M183 was the most dominant subclade in our samples, which ranged from 65.1% to 83.1%. …
Mitochondrial Dna Variability Among Six South-American Amerindian Villages From The Pano Linguistic Group,
2014
Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Brazil
Mitochondrial Dna Variability Among Six South-American Amerindian Villages From The Pano Linguistic Group, Celso T. Mendes-Junior, Aguinaldo L. Simoes
Human Biology Open Access Pre-Prints
Although scattered throughout a large geographic area, the members of the Pano linguistic group present strong ethnic, linguistic and cultural homogeneity, a feature that causes them to be considered as components of a same “Pano” tribe. Nevertheless, the genetic homogeneity between Pano villages has not been examined before. To study the genetic structure of the Pano linguistic group, four major Native American mitochondrial DNA (mtDNA) founder haplogroups were analyzed in 77 Amerindians from six villages of four Pano tribes (Katukina, Kaxináwa, Marúbo, and Yaminawa) located in the Brazilian Amazon. The central position of these tribes in the continent makes them …
Questioning The “Melting Pot”: Analysis Of Alu Inserts In Three Population Samples From Uruguay,
2014
Departamento de Antropología Biológica. Facultad de Humanidades y Ciencias de la Educación. Universidad de la República, Uruguay
Questioning The “Melting Pot”: Analysis Of Alu Inserts In Three Population Samples From Uruguay, Pedro C. Hidalgo, Patricia Mut, Elizabeth Ackermann, Gonzalo Figueiro, Monica Sans
Human Biology Open Access Pre-Prints
The way that immigrants integrate to recipient societies has been discussed for decades, mainly from the perspective of the social sciences. Uruguay, as other American countries, received different waves of European immigrants, although the details of the process of assimilation, when occurred, are unclear. In this paper, we use genetic markers to understand the process experienced by the Basques, one of the major migration waves that populated Uruguay, and its relation to other immigrants as well as to Native American and African descendants. For this purpose, we analyze the allele frequencies of ten ALU loci (A25, ACE, APOA1, B65, F13B, …
