Genetics and Genomics Commons^™

Anomalous Constitutive Src Kinase Activity Promotes B Lymphoma Survival And Growth, Jiyuan Ke, R. Lakshman Chelvarajan, Vishal Sindhava, Darrell A. Robertson, Lazaros Lekakis, C. Darrell Jennings, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Background: Previously we have shown that B cell receptor (BCR) expression and B cell receptor signaling pathways are important for the basal growth of B lymphoma cells. In particular we have shown that the activation of Syk, a non-src family protein tyrosine kinase and the mitogen activated protein kinases (MAPK), ERK and JNK that mediate BCR signals are required for the constitutive growth of B lymphoma cells. Since src family protein tyrosine kinases (SFKs) like Lyn are known to be needed for the phosphorylation of BCR co-receptors, Ig-alpha and Ig-beta, we hypothesized that one or more SFKs will be constitutively …

Rearrangement Of The Rna Polymerase Subunit H And The Lower Jaw In Archaeal Elongation Complexes, Sebastian Grünberg, Christoph Reich, Mirijam E. Zeller, Michael S. Bartlett, Michael Thomm

Biology Faculty Publications and Presentations

The lower jaws of archaeal RNA polymerase and eukaryotic RNA polymerase II include orthologous subunits H and Rpb5, respectively. The tertiary structure of H is very similar to the structure of the C-terminal domain of Rpb5, and both subunits are proximal to downstream DNA in pre-initiation complexes. Analyses of reconstituted euryarchaeal polymerase lacking subunit H revealed that H is important for open complex formation and initial transcription. Eukaryotic Rpb5 rescues activity of the ΔH enzyme indicating a strong conservation of function for this subunit from archaea to eukaryotes. Photochemical cross-linking in elongation complexes revealed a striking structural rearrangement of RNA …

Mir319a Targeting Of Tcp4 Is Critical For Petal Growth And Development In Arabidopsis, Anwesha Nag, Stacey King, Thomas Jack

Dartmouth Scholarship

In a genetic screen in a drnl-2 background, we isolated a loss-of-function allele in miR319a (miR319a¹²⁹). Previously, miR319a has been postulated to play a role in leaf development based on the dramatic curled-leaf phenotype of plants that ectopically express miR319a (jaw-D). miR319a¹²⁹ mutants exhibit defects in petal and stamen development; petals are narrow and short, and stamens exhibit defects in anther development. The miR319a¹²⁹ loss-of-function allele contains a single-base change in the middle of the encoded miRNA, which reduces the ability of miR319a to recognize targets. Analysis of the expression patterns of the …

Genetic Structure Of Yonahlossee Salamander Populations., Joshua Andrew Rudd

Electronic Theses and Dissertations

Plethodon yonahlossee is the largest eastern Plethodontid salamander. It has been classified as a species of greatest conservation need by the Tennessee Wildlife Resources Agency (TWRA). Found only in mountainous areas along the borders of Tennessee, North Carolina, and Virginia, populations of the yonahlossee are considered to be rare and local throughout their range. Genetic differentiation among populations of any species is usually attributable to long-standing, extrinsic barriers to gene flow. Because of their disjunct population structure and some observed morphological variation, genetic differentiation among yonahlossee populations is expected. A genetic structure study of yonahlossee was conducted to identify any …

Transcription Analysis Of The Chlorovirus Paramecium Bursaria Chlorella Virus-1, Giane M. Yanai

School of Biological Sciences: Dissertations, Theses, and Student Research

Paramecium bursaria chlorella virus (PBCV-1), a member of the family Phycodnaviridae, is a large dsDNA, plaque-forming virus that infects the unicellular green alga Chlorella NC64A. The 331 kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To follow global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDS) was constructed. Competitive hybridization experiments were conducted employing cDNAs from poly A-containing RNAs obtained from cells at seven time points after virus infection. The results led to the following conclusions: i) the PBCV-1 replication cycle is temporally programmed and regulated; ii) 360 …

Identification Of Eurycea Using Cytochrome B, Karis A. Myers

Senior Honors Theses

Genomic sequencing is a powerful tool that has many applications for research, one of which is in the field of taxonomy and the identification of species. This thesis discusses the mitochondrial gene cytochrome b and its utility in population genetics and identification of larval amphibians. The development of the Polymerase Chain Reaction and primers are an integral part of the modern DNA sequencing process. The Polymerase Chain Reaction is used to amplify a target DNA sequence, and the protocol for this procedure must be optimized for the specific sequence of target DNA. Primers must also be designed and modified for …

Vitisnet: ‘‘Omics’’ Integration Through Grapevine Molecular Networks, Jerome Grimplet, Grant R. Cramer, Julie A. Dickerson, Kathy Mathiason, John Van Hemert, Anne Y. Fennell Dr

Agronomy, Horticulture and Plant Science Faculty Publications

Background: Genomic data release for the grapevine has increased exponentially in the last five years. The Vitis vinifera genome has been sequenced and Vitis EST, transcriptomic, proteomic, and metabolomic tools and data sets continue to be developed. The next critical challenge is to provide biological meaning to this tremendous amount of data by annotating genes and integrating them within their biological context. We have developed and validated a system of Grapevine Molecular Networks (VitisNet). Methodology/Principal Findings: The sequences from the Vitis vinifera (cv. Pinot Noir PN40024) genome sequencing project and ESTs from the Vitis genus have been paired and the …

The Lyme Disease Spirochete, Borrelia Burgdorferi, In Tick Species Collected From Raccoons (Procyon Lotor) And Opossums (Didelphis Virginiana) Trapped In The Warren And Barren Counties Of South Central Kentucky, Kristina Tackett

Masters Theses & Specialist Projects

The incidence of tick-borne zoonoses such as Ehrlichiosis, Rocky Mountain Spotted Fever, and Lyme disease has steadily increased in the southeastern United States in recent years. According to the Centers for Disease Control and Prevention (CDC), the southeastern states accounted for 1,200 of the 27,000 total cases of Lyme disease reported in the U.S. in 2007. Although Ixodes scapularis is the most commonly recognized vector for the Lyme disease spirochete Borrelia burgdorferi, Dermacentor variabilis (a common vector for Rocky Mountain Spotted Fever) also has been shown to be a viable host for this pathogen. The purpose of the present …

Selecting, Marketing And Rebuilding A Herd Of Genetically Superior Animals, Katherine Rector

Dairy Science

No abstract provided.

Cloning Of "Animal Cryptochrome" Cdna From The Model Organism Chlamydomonas Reinhardtii For Functional Analysis Of Its Protein Product, Shobha Lavanya Silparasetty

Masters Theses & Specialist Projects

reinhardtii, a unicellular green alga, is a model organism to study the circadian clock. Cryptochromes are the blue light photoreceptors that entrain the clock in some organisms. The CPH1 protein of C. reinhardtii resembles the cryptochromes of the plant model Arabidopsis, but whether CPH1 entrains the circadian clock in C. reinhardtii is not yet known. Recent reports have suggested the existence of one more cryptochrome in C. reinhardtii, which resembles the cryptochromes of animals. However, the amino acid sequence of this protein shows even higher sequence similarity with the 6-4 DNA photolyase of Arabidopsis. DNA photolyases …

Dna, Red Tide And The Sea: A New Exhibit At Mystic Aquarium & Ife, Margaret (Peg) A. Van_Patten

Wrack Lines

DNA, Red Tide and the Sea is a new exhibit at Mystic Aquarium & IFE. It was developed by UConn Marine Sciences Professor Senjie Lin, and Mystic Aquarium. Children can extract DNA from fruit and learn about genetic codes and red tides in the ocean.

Temperature Compensation Of Auxin Dependent Developmental Patterning, Nicholas J. Kaplinsky

Biology Faculty Works

The establishment of localized auxin gradients plays a central role in developmental patterning in plants. Auxin levels and responses have been shown to increase with temperature although developmental patterning is not affected. This suggests the existence of a homeostatic mechanism that ensures that patterning occurs normally over a range of temperatures. We recently described the cloning and characterization of BOBBER1 (BOB1), an Arabidopsis gene which encodes a small heat shock protein. BOB1 is required for the establishment of auxin gradients and for normal developmental patterning. BOB1 is also required for organismal thermotolerance and localizes to heat shock granules at elevated …

Cloned Meat, Voluntary Food Labeling, And Organic Oreos, Donna M. Byrne

The University of New Hampshire Law Review

[Excerpt] “In December 2006, the Food and Drug Administration (FDA) announced that it had reviewed all the available evidence and was poised to approve meat and milk from cloned animals and their progeny. I remember telling one of my colleagues, a patent law professor, who should be as comfortable with technology as anyone, about this development, and his response was, “Yuck. I’m not eating it!” To which of course I replied, “Humph. You won’t know the difference.” Meat or milk from a clone or its descendant is virtually identical to meat or milk from a non-clone, said the FDA, as …

Pot1 Proteins In Green Algae And Land Plants: Dna-Binding Properties And Evidence Of Co-Evolution With Telomeric Dna, Eugene V. Shakirov, Xiangyu Song, Jessica A. Joseph, Dorothy E. Shippen

Biological Sciences Faculty Research

Telomeric DNA terminates with a single-stranded 3′ G-overhang that in vertebrates and fission yeast is bound by POT1 (Protection Of Telomeres). However, no in vitro telomeric DNA binding is associated with Arabidopsis POT1 paralogs. To further investigate POT1–DNA interaction in plants, we cloned POT1 genes from 11 plant species representing major branches of plant kingdom. Telomeric DNA binding was associated with POT1 proteins from the green alga Ostreococcus lucimarinus and two flowering plants, maize and Asparagus. Site-directed mutagenesis revealed that several residues critical for telomeric DNA recognition in vertebrates are functionally conserved in plant POT1 proteins. However, the plant proteins …

Apolipoprotein E But Not B Is Required For The Formation Of Infectious Hepatitis C Virus Particles, Jieyun Jiang, Guangxiang Luo

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Our previous studies have found that hepatitis C virus (HCV) particles are enriched in apolipoprotein E (apoE) and that apoE is required for HCV infectivity and production. Studies by others, however, suggested that both microsomal transfer protein (MTP) and apoB are important for HCV production. To define the roles of apoB and apoE in the HCV life cycle, we developed a single-cycle HCV growth assay to determine the correlation of HCV assembly with apoB and apoE expression, as well as the influence of MTP inhibitors on the formation of HCV particles. The small interfering RNA (siRNA)-mediated knockdown of apoE expression …

Drosophila Adult Eye Model To Teach Scanning Electron Microscopy In An Undergraduate Cell Biology Laboratory, Meghana Tare, Oorvashi Roy Puli, Sarah M. Oros, Amit Singh

Biology Faculty Publications

We have devised an undergraduate laboratory exercise to study tissue morphology using fruit fly, Drosophila melanogaster, as the model organism. Drosophila can be reared in a cost effective manner in a short period of time. This experiment was a part of the undergraduate curriculum of the cell biology laboratory course aimed to demonstrate the use of scanning electron microscopy (SEM) technique to study the morphology of adult eye of Drosophila. The adult eye of Drosophila is a compound eye, which comprises of 800 unit eyes, and serves as an excellent model for SEM studies. We used flies that …

Common Genetic Variation And The Control Of Hiv-1 In Humans, Jacques Fellay, Dongliang Ge, Kevin V. Shianna, Sara Colombo, Bruno Ledergerber, Elizabeth T. Cirulli, Thomas J. Urban, Kunlin Zhang, Curtis Gumbs, Jason P. Smith, Antonella Castagna, Alessandro Cozzi-Lepri, Andrea De Luca, Philippa Easterbrook, Huldrych F. Gunthard, Simon Mallal, Cristina Mussini, Judith Dalmau, Javier Martinez-Picado, Jose M. Miro, Niels Obel, Steven M. Wolinsky, Jeremy J. Martinson, Roger Detels, Joseph Margolick, Lisa Jacobson, Patrick Descombes, Stylianos E. Antonarakis, Jacques S. Beckmann, Stephen J. O'Brien, Norman L. Letvin, Andrew J. Mcmichael, Barton F. Haynes, Mary Carrington, Sheng Feng, Amalio Telenti, David B. Goldstein, Niaid Center For Hiv/Aids Vaccine Immunology (Chavi)

Biology Faculty Articles

To extend the understanding of host genetic determinants of HIV-1 control, we performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects. The study was powered to detect common genetic variants explaining down to 1.3% of the variability in viral load at set point. We provide overwhelming confirmation of three associations previously reported in a genome-wide study and show further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC). We also examined the polymorphisms reported in previous candidate gene studies and fail to support a role for any variant outside of …

Attempted Cloning Of A Wnt Gene From Botrylloides Violaceus, Manasa Chandra, James Tumulak

Biological Sciences

Botrylloides violaceus is a colonial ascidian with the ability to undergo sexual and asexual reproduction as well as regeneration. The canonical pathway starts with the extracellular protein Wnt and ends with β-catenin, a transcription factor, which also functions in cell adhesion. The Wnt signaling pathway is involved in embryogenesis and regeneration in a variety of other species. In our studies we attempt to isolate and sequence both a Wnt gene and from Botrylloides via degenerate primer design and PCR. Using bioinformatic methods we aligned sequences from other organisms, as the Botrylloides genome has not yet been sequenced. Using mouse, Ciona, …

Molecular Analysis Of Split Hand/Foot Malformation (Shfm) At The Shfm3 And Shfm5 Loci, Megan Chryst-Ladd

All Theses

Split hand/foot malformation (SHFM) is a congenital limb malformation observed in humans characterized by a reduction or loss of the central digits of the hands and/or feet. The condition affects one in every 8,500 to 25,000 births, accounting for 8-17% of all limb reduction defects. A tandem duplication of approximately 500 Kb has been determined to be the causative mutation at the SHFM3 locus. Patients that are heterozygous for this duplication have three copies of the genes BTRC, POLL, and DPCD as well as an extra copy of exons 6-9 of FBXW4. The SHFM3 critical region also contains the FGF8 …

Applications Of Variable Number Tandem Repeat Genotyping In The Validation Of An Animal Medical Model And Gene Flow Studies In Threatened Populations Of Reptiles, Candace D. Smith

Graduate Theses and Dissertations

We used variable number tandem repeats (VNTR) to validate the chicken as a human medical model for Pulmonary Arterial Hypertension. We identified seven regions on four chromosomes and interrogated for VNTR markers that significantly associate with Pulmonary Hypertension Syndrome/ascites. In those regions, we identified 7 candidate genes; AGTR1, ACE, p38MAPK, SST, 5HT2B, NET1, and CALM3 for further analysis as significantly contributing QTL for ascites/PHS. We also used variable number tandem repeats to measure gene flow and gather evidence for multiple paternity in a population of Timber rattlesnakes, Crotalus horridus. We were able to verify 1 VNTR that can be used …

Ceramide Kinase Regulates Phospholipase C And Phosphatidylinositol 4, 5, Bisphosphate In Phototransduction, Ujjaini Dasgupta, Takeshi Bamba, Salvatore Chiantia, Pusha Karim, Ahmad N. Abou Tayoun

Dartmouth Scholarship

Phosphoinositide-specific phospholipase C (PLC) is a central effector for many biological responses regulated by G-protein-coupled receptors including Drosophila phototransduction where light sensitive channels are activated downstream of NORPA, a PLCbeta homolog. Here we show that the sphingolipid biosynthetic enzyme, ceramide kinase, is a novel regulator of PLC signaling and photoreceptor homeostasis. A mutation in ceramide kinase specifically leads to proteolysis of NORPA, consequent loss of PLC activity, and failure in light signal transduction. The mutant photoreceptors also undergo activity-dependent degeneration. Furthermore, we show that a significant increase in ceramide, resulting from lack of ceramide kinase, perturbs the membrane microenvironment of …

Detection Of Sub-Clinical Cwd Infection In Conventional Test-Negative Deer Long After Oral Exposure To Urine And Feces From Cwd+ Deer, Nicholas J. Haley, Candace K. Mathiason, Mark D. Zabel, Glenn C. Telling, Edward A Hoover

Microbiology, Immunology, and Molecular Genetics Faculty Publications

BACKGROUND: Chronic wasting disease (CWD) of cervids is a prion disease distinguished by high levels of transmissibility, wherein bodily fluids and excretions are thought to play an important role. Using cervid bioassay and established CWD detection methods, we have previously identified infectious prions in saliva and blood but not urine or feces of CWD+ donors. More recently, we identified very low concentrations of CWD prions in urine of deer by cervid PrP transgenic (Tg[CerPrP]) mouse bioassay and serial protein misfolding cyclic amplification (sPMCA). This finding led us to examine further our initial cervid bioassay experiments using sPMCA.

OBJECTIVES: We sought …

Investigation Of Van Gogh-Like 2 Mrna Regulation And Localisation In Response To Nociception In The Brain Of Adult Common Carp (Cyprinus Carpio), Siobhan C. Reilly, Anja Kipar, David J. Hughes, John P. Quinn, Andrew R. Cossins, Lynne U. Sneddon

Veterinary Science and Medicine Collection

The Van Gogh-like 2 (vangl2) gene is typically associated with planar cell polarity pathways, which is essential for correct orientation of epithelial cells during development. The encoded protein of this gene is a transmembrane protein and is highly conserved through evolution. Van Gogh-like 2 was selected for further study on the basis of consistent regulation after a nociceptive stimulus in adult common carp and rainbow trout in a microarray study. An in situ hybridisation was conducted in the brain of mature common carp (Cyprinus carpio), 1.5 and 3 h after a nociceptive stimulus comprising of an acetic acid injection to …

Quantifying And Resolving Multiple Vector Transformants In S. Cerevisiae Plasmid Libraries, Thomas C. Scanlon, Elizabeth C. Gray, Karl E. Griswold

Dartmouth Scholarship

In addition to providing the molecular machinery for transcription and translation, recombinant microbial expression hosts maintain the critical genotype-phenotype link that is essential for high throughput screening and recovery of proteins encoded by plasmid libraries. It is known that Escherichia coli cells can be simultaneously transformed with multiple unique plasmids and thusly complicate recombinant library screening experiments. As a result of their potential to yield misleading results, bacterial multiple vector transformants have been thoroughly characterized in previous model studies. In contrast to bacterial systems, there is little quantitative information available regarding multiple vector transformants in yeast. Saccharomyces cerevisiae is the …

Targeted Genomic Signature Profiling With Quasi-Alignment Statistics, Rao Mallik Kotamarti, Douglas W. Raiford, Michael Hahsler, Yuhang Wang, Monnie Mcgee, Maggie Dunham

COBRA Preprint Series

Genome databases continue to expand with no change in the basic format of sequence data. The prevalent use of the Classic alignment based search tools like BLAST have significantly pushed the limits of Genome Isolate research. The relatively new frontier of Metagenomic research deals with thousands of diverse genomes with newer demands beyond the current homologue search and analysis. Compressing sequence data into a complex form could facilitate a broader range of sequence analyses. To this end, this research explores reorganizing sequence data as complex Markov signatures also known as Extensible Markov Models. Markov models have found successful application in …

Decreased Replication Origin Activity In Temporal Transition Regions, Zeqiang Guan, Christina M. Hughes, Settapong Kosiyatrakul, Paolo Norio, Ranjan Sen, Steven Fiering

Dartmouth Scholarship

In the mammalian genome, early- and late-replicating domains are often separated by temporal transition regions (TTRs) with novel properties and unknown functions. We identified a TTR in the mouse immunoglobulin heavy chain (Igh) locus, which contains replication origins that are silent in embryonic stem cells but activated during B cell development. To investigate which factors contribute to origin activation during B cell development, we systematically modified the genetic and epigenetic status of the endogenous Igh TTR and used a single-molecule approach to analyze DNA replication. Introduction of a transcription unit into the Igh TTR, activation of gene transcription, …

Genetic Relationship Between Longevity And Objectively Or Subjectively Assessed Performance Traits In Sheep Using Linear Censored Models, W. Mekkaway, Rainer Roehe, Ronald M. Lewis, M. H. Davies, L. Bünger, G. Simm, W. Haresign

Department of Animal Science: Faculty Publications

Genetic parameters of longevity in crossbred mule ewes, and genetic relationships among longevity, growth, body composition, and subjectively assessed traits on mule lambs and ewes have been estimated using Bayesian linear censored models. Additionally, the genetic associations between longevity and culling reasons were examined. Data comprised 1,797 observations of mule ewes for longevity, culling reasons, growth, body composition, mouth scores, and type traits. Longevity was defined as the time (in years) from 2 yr of age (the age at first lambing of most ewes) to culling or death. Censored data (i.e., observations for which only the lower bound of the …

Phylogeography Of The Frog Leptodactylus Validus (Amphibia: Anura): Patterns And Timing Of Colonization Events In The Lesser Antilles, Arley Camargo, W. Ronald Heyer, Rafael O. De Sá

Biology Faculty Publications

The frog Leptodactylus validus occurs in northern South America, Trinidad and Tobago, and the southern Lesser Antilles (Grenada and St. Vincent). Mitochondrial DNA sequences were used to perform a nested clade phylogeographic analysis (NCPA), to date colonization events, and to analyze colonization patterns using on a relaxed molecular clock and coalescent simulations. L. validus originated on the mainland and first colonized Trinidad with subsequent independent colonizations of Tobago and the Lesser Antilles from Trinidad. The NCPA suggests a historical vicariant event between populations in Trinidad and Tobago from those in the Lesser Antilles. The colonization of Trinidad occurred 1 million …

Genome 10k: A Proposal To Obtain Whole-Genome Sequence For 10000 Vertebrate Species, David Haussler, Stephen J. O'Brien, Oliver A. Ryder, F. Keith Barker, Michele Clamp, Andrew J. Crawford, Robert Hanner, Olivier Hanotte, Warren E. Johnson, Jimmy A. Mcguire, Webb Miller, Robert W. Murphy, William J. Murphy, Frederick H. Sheldon, Barry Sinervo, Byrappa Venkatesh, Edward O. Wiley, Fred W. Allendorf, George Amato, C. Scott Baker, Aaron Bauer, Albano Beja-Pereira, Eldredge Bermingham, Giacomo Bernardi, Cibele R. Bonvicino, Sydney Brenner, Terry Burke, Joel Cracraft, Mark Diekhans

Biology Faculty Articles

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16203 representative vertebrate species spanning evolutionary diversity across living …

Every Genome Sequence Needs A Good Map, Harris A. Lewin, Denis M. Larkin, J. U. Pontius, Stephen J. O'Brien

Biology Faculty Articles

No abstract provided.