Genetics and Genomics Commons^™

Chemical Synthesis Of Sensitive Dna, Komal Chillar

Dissertations, Master's Theses and Master's Reports

Over the past decades, researchers have tried various chemical methods to synthesize modified oligodeoxynucleotides (ODNs, i.e. short segments of DNAs). Traditional ODN synthesis methods require strong basic, and nucleophilic conditions for the deprotection and cleavage of the ODN from the solid support. However, the sensitive ODNs containing labile functionalities are vulnerable to such harsh conditions. Sensitive ODNs have a wide range of applications in research and pharmaceuticals. To synthesize sensitive ODNs, researchers devised different strategies but no practical methods have been developed. To overcome these challenges, we developed alkyl Dim alkyl Dmoc technology. This innovative technology uses weakly basic and …

Role Of Cdx4 And Sp5l In Zebrafish Development, Wesley Tsai

Honors Theses

The Caudal Type Homeobox transcription factors cdx are a family of genes found in vertebrates that regulates body regionalization and anterior-posterior patterning. They are also responsible for regulating axial elongation, but the mechanisms behind this behavior are not known. Previous studies in mouse embryonic stem cells have shown that the cdx genes are necessary for upregulating the gene sp5 which may be linked to axial elongation. Sp5 is a zinc-finger transcription factor belonging to the specificity protein (sp) family. Our group has used in-situ hybridization experiments on zebrafish embryos to show that sp5-like (sp5l) is transcribed within tailbud tissues that …

Understanding The Genetics Of Schizophrenia, Matthew Toohey

Thinking Matters Symposium

Schizophrenia has been considered heritable for a long time, but only with the advent of new technologies such as whole-genome sequencing and genome-wide association studies can we begin to identify specific molecular causes of schizophrenia. This poster will review some of the genetic variants that research groups have associated with schizophrenia. Current research has indicated that schizophrenia is a polygenic disease and has been linked to many genes. Some of these common risk variants are in protein coding sections of the DNA. These proteins are often linked to neurological development or immune system function. Other variants that have been associated …

The Genetic Links Between Archaic And Modern Humans, Maria J. Orellana Rosales

Thinking Matters Symposium

Our modern physiology is the mixture of many archaic humans that once roamed our planet. The evidence of these archaic humans is still present in our DNA. This poster reviews how our understanding of ancient human genetics has drastically changed due to advances in molecular genetics. Neanderthal and Denisovan remains have been sequenced for nuclear and mitochondrial DNA. Neanderthal and Denisovan genetic ancestry have been identified by genomic studies in modern human populations across Eurasia and Pacific Island regions. Studies have shown a gene flow of 4±1% from Neanderthals to present-day Eurasians. Whereas, Papuan and Melanesian individuals share 4±0.7% more …

The Psychosocial Effects Of Unexpected Findings On Direct To Consumer Genetic Testing, Emily Wiseman

KGI Theses and Dissertations

Direct to Consumer (DTC) genetic testing has grown in popularity since its inception in 2010. Consumers can now order DTC tests giving them more information on their ancestry, health and ethnicity than ever before. With more information and more consumers taking the tests, this has allowed for the opportunity of unexpected findings to be generated from the tests. Previous studies have shown that consumers can learn about a health risk they were previously unaware of, and this can impact the health management and surveillance practices of consumers receiving them. Additionally, studies have shown that ethnicity results can impact consumers’ previously …

American Population Study Of Pigmentation Based Genotype Interpretation For Phenotypic Determination Of Hair And Eye Color Using Hirisplex, Emma Leigh Combs

Graduate Theses, Dissertations, and Problem Reports

Currently the largest limitation with DNA evidence is that a comparison to a known source sample is required for any interpretation with the current methods. Simply put, if an unknown sample from a crime scene is collected and results in a profile, but there is no suspect or match from CODIS to compare it to, the profile is essentially useless and no information can be gained from it. Research has been performed within the area of forensic DNA phenotyping as a potential tool to aid in taking steps forward to use genotypic information as an investigative tool. Populations studies have …

X-Inactivation And Epigenetics, Serena Weston

Thinking Matters Symposium Archive

To prevent abnormal development caused by expressing both X chromosomes, female mammals inactivate one of their X chromosomes using an epigenetic process called dosage compensation. This literature review examines how X chromosome inactivation (XCI) occurs during the formation and development of an embryo. This condensation of DNA is marked by histone tail modifications, DNA methylation, and the arrival of structural proteins resulting in extraordinarily stable heterochromatin. X-inactivation is regulated in cis by the X-inactivation center (Xic) that contains the Xist gene and its antisense gene, Tsix. On one X chromosome, Xist RNA is expressed and coats the center of the …

N-Terminal Domain Of Human Uracil Dna Glycosylase (Hung2) Promotes Targeting To Uracil Sites Adjacent To Ssdna-Dsdna Junctions, Brian P Weiser, Gaddiel Rodriguez, Philip A Cole, James T Stivers

Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship

The N-terminal domain (NTD) of nuclear human uracil DNA glycosylase (hUNG2) assists in targeting hUNG2 to replication forks through specific interactions with replication protein A (RPA). Here, we explored hUNG2 activity in the presence and absence of RPA using substrates with ssDNA-dsDNA junctions that mimic structural features of the replication fork and transcriptional R-loops. We find that when RPA is tightly bound to the ssDNA overhang of junction DNA substrates, base excision by hUNG2 is strongly biased toward uracils located 21 bp or less from the ssDNA-dsDNA junction. In the absence of RPA, hUNG2 still showed an 8-fold excision bias …

Deciphering Mechanisms Governing The Development Of The Rod Epigenome, Philip Andrew Ruzycki

Arts & Sciences Electronic Theses and Dissertations

Precisely coordinated expression of distinct sets of genes is essential for cellular development and function, especially in complex multicellular organisms. This regulation is achieved by the action of transcription factors (TF), proteins that bind specific genomic locations and alter the activity state and packaging of the DNA to promote or repress gene expression. However, while tremendous effort has defined networks of transcription factors that work together to drive specific phenotypes, little is known about their differential activity at the hundreds or thousands of sites where they bind. There are also many questions regarding the basic principles of the packaging of …

Dna Sequences Of Mitochondrial Cytochrome C Oxidase I (Coi) Genes From Deep Sea Fishes Collected During Deepend Cruise Dp05 From 2017-05-01 To 2017-05-11, Kimberly A. Finnegan, Andrea Bernard, M. Weber, Ron Eytan, Mahmood S. Shivji

DEEPEND Datasets

Deep sea fishes were collected in the northern Gulf of Mexico during DEEPEND cruise DP05 from May 1 to 11, 2017. This dataset contains Genbank accession numbers of DNA sequences of the mitochondrial Cytochrome c oxidase I (COI) gene from fish species collected.

The Technologies Of Race: Big Data, Privacy And The New Racial Bioethics, Christian Sundquist

Articles

Advancements in genetic technology have resurrected long discarded conceptualizations of “race” as a biological reality. The rise of modern biological race thinking – as evidenced in health disparity research, personal genomics, DNA criminal forensics, and bio-databanking - not only is scientifically unsound but portends the future normalization of racial inequality. This Article articulates a constitutional theory of shared humanity, rooted in the substantive due process doctrine and Ninth Amendment, to counter the socio-legal acceptance of modern genetic racial differentiation. It argues that state actions that rely on biological racial distinctions undermine the essential personhood of individuals subjected to such taxonomies, …

Dna Sequences Of The Mitochondrial Cytochrome C Oxidase I (Coi) Genes From Deep Sea Fishes. Cruises Dp01 And Dp02 From May 2015 - August 2015, Andrea Bernard, Max Weber, Kimberly A. Finnegan, Mahmood S. Shivji, Ron Eytan

DEEPEND Datasets

The deep sea ecosystem is believed to contain the highest biomass of fish in the oceans. However, the taxonomic diversity in this ecosystem is incompletely described and likely to be vastly underestimated. DNA sequence data (barcodes) have become a key tool to discover hidden biodiversity. We generated mitochondrial DNA barcode datasets based on the Cytochrome c oxidase I (COI) gene from deep sea fishes. These data were analyzed using phylogenetic and statistical methods to reveal cryptic species and make taxonomic linkages between adult fishes and their early life stages. These datasets were generated from fishes collected in the Northern Gulf …

Phylogeny, Systematics And Biogeography Of Short-Tailed Opossums (Didelphidae: Monodelphis), Silvia E. Pavan

Dissertations, Theses, and Capstone Projects

Short-tailed opossums (genus Monodelphis) comprise the most species-rich genus of New World marsupials, with 25 currently recognized species. Monodelphis comprise small, terrestrial species collectively widespread in South America, which makes the group potentially informative about biogeographic processes that have shaped the continental fauna. The genus exhibits striking variation in several phenotypic characters, notably pelage coloration, behavior, and reproductive strategies. This diversity is unique among Neotropical marsupials, and makes the group particularly interesting to investigate the evolution and the adaptive significance of phenotypic trait variation. Despite this potential, missing knowledge on phylogeny and basic taxonomy precludes broader studies on evolution …

Using Hadoop To Identify False Positives In Bacterial Strain Typing From Dna Fingerprints, Colin C. Adams

Computer Science and Software Engineering

Pyroprinting is a novel technique used by the Department of Biological Sciences to obtain “fingerprints” from the DNA of E. coli isolates in order to categorize them into strains. To determine the number of false positives that occur in the pyroprinting process, isolates with the same pyroprints needed to be sequenced to see if their underlying alleles match. If they do match, this shows they are indeed the same strain and are a true positive. If the alleles don’t match, they are different strains and are a false positive. To do this 100 isolates with nucleotide identifiers were sequenced. Over …

Characterization Of The Marine Sponge Amphimedon Compressa Microbiome Across A Spatial Gradient, Renee Michelle Potens

HCNSO Student Theses and Dissertations

Diverse and ecologically important microbial communities (microbiomes) are symbiotic within marine sponges. In this study, the microbiome of Amphimedon compressa from three sample locations (Broward and Dade Counties, Southeast Florida, USA and the Southern Caribbean, Bocas del Toro, Panama) is characterized using 16S rRNA Illumina sequencing. The predominant taxa are Proteobacteria and Cyanobacteria, as expected for Low Microbial Abundance sponges, accounting for over 53% of the total microbiome community. The numbers of Operational Taxonomic Units (OTUs) decrease from Broward County (2,900) to Dade County (2,300) and then Bocas del Toro (1,200). The correlates to a decreasing north-south gradient of …

Beyond Dna: Epigenetics And Proteomics In Forensic Science, Diane F. Eilerts

Themis: Research Journal of Justice Studies and Forensic Science

The use of genetic evidence in criminal cases is well established and has improved the public opinion and credibility of forensic science. However, several shortcomings associated with current genetic profiling techniques exist. Scientific research aimed at increasing the overall knowledge and understanding of biological factors will lead to the development of methods capable of improving the discriminating power of DNA evidence, overcoming limitations associated with DNA evidence, or complementing current methods of DNA profiling. Increased research in the fields of epigenetics and proteomics are particularly promising and relevant to forensic science. Research suggests that epigenetic biomarkers can be used to …

Molecular Analysis Confirming The Introduction Of Nile Crocodiles, Crocodylus Niloticus Laurenti 1768 (Crocodylidae), In Southern Florida, With An Assessment Of Potential For Establishment, Spread, And Impacts., Michael R. Rochford, Kenneth L. Krysko, Frank J. Mazzotti, Matthew W. Shirley, Mark W. Parry, Joseph A. Wasilewski, Jeffrey S. Beauchamp, Christpher R. Gillette, Edward F. Metzger Iii, Michiko A. Squires, Louis A. Somma

Papers in Herpetology

The state of Florida, USA, has more introduced herpetofauna than any other governmental region on Earth. Four species of nonnative crocodilians have been introduced to Florida (all since 1960), one of which is established. Between 2000–2014 we field-collected three nonnative crocodilians in Miami-Dade County, Florida, and one in Hendry County, Florida. We used DNA barcoding and molecular phylogenetics to determine species identification and native range origin. Also, we described diet, movement, and growth for one crocodile. Our molecular analyses illustrated that two of the crocodiles we collected are most closely related to Nile Crocodiles (Crocodylus niloticus) from South Africa, suggesting …

Dna Sequencing Activity, Sarah O'Leary-Driscoll

Sequencing & Genome Mining

This activity is meant to introduce students to basic DNA sequencing techniques. Using a hands-on approach helps them understand the fundamentals of what is happening in the lab, and the questions that accompany the activity can lead to more in depth discussions about sequencing, and the development of the next generation sequencing techniques.

Nsf Bets Big On David Angelini, Gerry Boyle

Colby Magazine

Something has been bugging Colby geneticist David Angelini.

How, Angelini wonders, can a single species (in this case the soapberry bug) produce two distinctly different forms, one with long wings and one with short, that are not linked to sex? What is the genetic mechanism that causes the wings to develop differently?

"Why does it not overshoot the long form? he asked. "Why doesn't it undershoot the short form? Why doesn't it end up somewhere in the middle? That's an open question."

And a question that the National Science Foundation wants him to answer.

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, 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 …

Population And Demographic Structure Of Ixodes Scapularis Say In The Eastern United States., Joyce M. Sakamoto, Jerome Goddard, Jason L. Rasgon

College of Agriculture & Life Sciences Publications and Scholarship

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, …

Quantitative Field Testing Heterodera Glycines From Metagenomic Dna Samples Isolated Directly From Soil Under Agronomic Production., Yan Li, Gary W. Lawrence, Shien Lu, Clarissa Balbalian, Vincent P. Klink

College of Agriculture & Life Sciences Publications and Scholarship

A quantitative PCR procedure targeting the Heterodera glycines ortholog of the Caenorhabditis elegans uncoordinated-78 gene was developed. The procedure estimated the quantity of H. glycines from metagenomic DNA samples isolated directly from field soil under agronomic production. The estimation of H. glycines quantity was determined in soil samples having other soil dwelling plant parasitic nematodes including Hoplolaimus, predatory nematodes including Mononchus, free-living nematodes and biomass. The methodology provides a framework for molecular diagnostics of nematodes from metagenomic DNA isolated directly from field soil.

Electrotransfer Of Single-Stranded Or Double-Stranded Dna Induces Complete Regression Of Palpable B16.F10 Mouse Melanomas, Loree Heller, Vesba Todorovic, Maja Cemazar

Bioelectrics Publications

Enhanced tumor delivery of plasmid DNA with electric pulses in vivo has been confirmed in many preclinical models. Intratumor electrotransfer of plasmids encoding therapeutic molecules has reached Phase II clinical trials. In multiple preclinical studies, a reduction in tumor growth, increased survival or complete tumor regression have been observed in control groups in which vector or backbone plasmid DNA electrotransfer was performed. This study explores factors that could produce this antitumor effect. The specific electrotransfer pulse protocol employed significantly potentiated the regression. Tumor regression was observed after delivery of single-stranded or double-stranded DNA with or without CpG motifs in both …

An Intergenic Region Shared By At4g35985 And At4g35987 In Arabidopsis Thaliana Is A Tissue Specific And Stress Inducible Bidirectional Promoter Analyzed In Transgenic Arabidopsis And Tobacco Plants, Joydeep Banerjee, Dipak K. Sahoo, Nrisingha Dey, Robert Houtz, Indu B. Maiti

Kentucky Tobacco Research and Development Center Faculty Publications

On chromosome 4 in the Arabidopsis genome, two neighboring genes (calmodulin methyl transferase At4g35987 and senescence associated gene At4g35985) are located in a head-to-head divergent orientation sharing a putative bidirectional promoter. This 1258 bp intergenic region contains a number of environmental stress responsive and tissue specific cis-regulatory elements. Transcript analysis of At4g35985 and At4g35987 genes by quantitative real time PCR showed tissue specific and stress inducible expression profiles. We tested the bidirectional promoter-function of the intergenic region shared by the divergent genes At4g35985 and At4g35987 using two reporter genes (GFP and GUS) in both orientations in transient tobacco protoplast and …

Evolution Of Repetitive Proteins: Spider Silks From Nephila Clavipes (Tetragnathidae) And Araneus Bicentenarius (Araneidae), Richard D. Beckwitt, Steven Arcidiacono, Robert Stote

Richard D Beckwitt

Spider silks are highly repetitive proteins, characterized by regions of polyalanine and glycine-rich repeating units. We have obtained two variants of the Spidroin 1 (NCF-1) silk gene sequence from Nephila clavipes. One sequence (1726 bp) was from a cloned cDNA, and the other (1951 bp) was from PCR of genomic DNA. When these sequences are compared with each other and the previously published Spidroin 1 sequence, there are differences due to sequence rearrangements, as well as single base substitutions. These variations are similar to those that have been reported from other highly repetitive genes, and probably represent the results …

Capture-Recapture Of White-Tailed Deer Using Dna Sampling From Fecal Pellet-Groups, Matthew James Goode

Masters Theses

Reliable density estimates of game and keystone species such as white-tailed deer (Odocoileus virginianus) are desirable to set proper management strategies and for evaluating those strategies over time. However, traditional methods for estimating white-tailed deer density have been inhibited by behavior, densely forested areas that can hamper observation (detection), and invalid techniques of estimating effective trapping area. We wanted to evaluate a noninvasive method of mark-recapture estimation using DNA extracted from fecal pellets as the individual marker and for gender determination, coupled with a spatial detection function to estimate density (Spatially Explicit Capture-Recapture, SECR). We collected pellet groups …

High Ethanol Titers From Cellulose By Using Metabolically Engineered Thermophilic, Anaerobic Microbes, D. Aaron Argyros, Shital A. Tripathi, Trisha F. Barrett, Stephen R. Rogers, Lawrence F. Feinberg, Daniel G. Olson, Justin M. Foden, Bethany B. Miller, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza

Dartmouth Scholarship

This work describes novel genetic tools for use in Clostridium thermocellum that allow creation of unmarked mutations while using a replicating plasmid. The strategy employed counter-selections developed from the native C. thermocellum hpt gene and the Thermoanaerobacterium saccharolyticum tdk gene and was used to delete the genes for both lactate dehydrogenase (Ldh) and phosphotransacetylase (Pta). The Δldh Δpta mutant was evolved for 2,000 h, resulting in a stable strain with 40:1 ethanol selectivity and a 4.2-fold increase in ethanol yield over the wild-type strain. Ethanol production from cellulose was investigated with an engineered coculture of organic acid-deficient engineered strains of …

Electrically Mediated Delivery Of Plasmid Dna To The Skin, Using A Multielectrode Array, Richard Heller, Yolmari Criz, Loree C. Heller, Richard A. Gilbert, Mark J. Jaroszeski

Bioelectrics Publications

The easy accessibility of skin makes it an excellent target for gene transfer protocols. To take full advantage of skin as a target for gene transfer, it is important to establish an efficient and reproducible delivery system. Electroporation is a strong candidate to meet this delivery criterion. Electroporation of the skin is a simple, direct, in vivo method to deliver genes for therapy. Previously, delivery to the skin was performed by means of applicators with relatively large distances between electrodes, resulting in significant muscle stimulation and pain. These applicators also had limitations in controlling the directionality of the applied field. …

Meiotic Dna Re-Replication And The Recombination Checkpoint, Nicole Ann Najor

Wayne State University Dissertations

Progression through meiosis occurs through a strict sequence of events, so that one round of DNA replication precedes programmed recombination and two nuclear divisions. Cyclin dependent kinase 1 (Cdk1) is required for meiosis, and any disruption in its activity leads to meiotic defects. The Cdk1 inhibitor, Sic1, regulates the G1-S transition in the mitotic cell cycle and the analogous transition in meiosis. We have employed a form of Sic1, Sic1deltaP^HA, that is mutated at multiple phosphorylation sites and resistant to degradation. Meiosis specific expression of Sic1deltaP^HA disrupts Cdk1 activity and leads to significant accumulation of over replicated …