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Diverse Sequences Within Tlr Elements Target Programmed Dna Elimination In Tetrahymena Thermophila, Jeffrey D. Wuitschick, Kathleen M. Karrer

Biological Sciences Faculty Research and Publications

Tlr elements are a novel family of ~30 putative mobile genetic elements that are confined to the germ line micronuclear genome in Tetrahymena thermophila. Thousands of diverse germ line-limited sequences, including the Tlr elements, are specifically eliminated from the differentiating somatic macronucleus. Macronucleusretained sequences flanking deleted regions are known to contain cis-acting signals that delineate elimination boundaries. It is unclear whether sequences within deleted DNA also play a regulatory role in the elimination process. In the current study, an in vivo DNA rearrangement assay was used to identify internal sequences required in cis for the elimination of Tlr elements. Multiple, …

Cloning And Sequencing Of Glucosyltransferase (Gt) Genes From Grapefruit (Citrus Paradisi) Seedlings, Searching For 7-O-Gt., Mebrahtu Berhane Sibhatu

Electronic Theses and Dissertations

Flavonoids play crucial roles in plant life cycles and in human welfare. Grapefruit plants produce several glycosylated flavonoids and the glycosylation reactions are catalyzed by UDP-glucose: glucosyltransferases (GTs). Our objective was to use the SMART RACE RT-PCR strategy to obtain cDNA sequences of putative grapefruit flavonoid GTs. Gene specific primers were designed from the plant secondary product glucosyltransferase (PSPG) box and used to amplify 5’GT clones. Clone-specific primers were designed from 5’clones to amplify 3’ GT clones. We obtained 5 5’ clones and 1 3’ clone as candidate GTs. We used 3 of these clones to predict 2 compiled GT …

Aerial Detection Of Waste Disposal Sites Near Donna Reservoir In South Texas., C. F. Webster, James H. Everitt, D. E. Escobar, M. R. Davis

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Aerial color-infrared (CIR) photography was used to detect and catalog unauthorized solid waste disposal sites around Donna Reservoir in the Lower Rio Grande Valley (LRGV) of southern Texas. Qualitative visual evaluation of the positive transparencies showed 25 possible disposal sites randomly scattered throughout the study area, located in sites ranging from bare soil to grass and mixed brush/woods. These sites were transposed onto a computer-generated area map for ground survey confirmation and use by organizations planning to clean-up the sites. Ground-truthing was used to identify waste contents at each site and to estimate waste volumes and areas covered. Unauthorized solid …

Overproduction And Analysis Of Eukaryotic Multiprotein Complexes In Escherichia Coli Using A Dual-Vector Strategy, Jeff Finkelstein, Edwin Antony, Manju M. Hingorani, Michael O’Donnell

Biological Sciences Faculty Research and Publications

Biochemical studies of eukaryotic proteins are often constrained by low availability of these typically large, multicomponent protein complexes in pure form. Escherichia coli is a commonly used host for large-scale protein production; however, its utility for eukaryotic protein production is limited because of problems associated with transcription, translation, and proper folding of proteins. Here we describe the development and testing of pLANT, a vector that addresses many of these problems simultaneously. The pLANT vector contains a T7 promoter-controlled expression unit, a p15A origin of replication, and genes for rare transfer RNAs and kanamycin resistance. Thus, the pLANT vector can be …

Molecular Pharmacology Of Somatostatin Receptors, Fredric C. Mazza

Seton Hall University Dissertations and Theses (ETDs)

Somatostatin (somatotropin release inhibitory factor, SRIF), inhibits animal cell secretion and proliferation. SRIF is transcribed from a single gene as a 1 t 6 amino acid that in precursor is cleaved a cell specific manner into two distinct peptides, SRIF-14 and SRIF-28. Each binds with high affinity to all five known SRIF-receptor subtypes (sst, - ssts) and several of these receptor subtypes are endogenously expressed in the AtT-20 cell, a murine pituitary corticotroph. SRIF receptors belong to the G protein-coupled family of integral membrane receptors. Within the SRIF receptor family, it has been shown that the sst, receptor subtype exists …

Heavy Metal Contamination Of Mangrove Sediments And The Associated Biota In Dar Es Salaam, Tanzania, Sd Mremi, Jf Machiwa

Tanzania Journal of Science

Mangrove wetlands are efficient in trapping pollutants that may have detrimental effects on mangrove dependent food chains. Mangrove ecosystems that are within urban areas are likely to suffer more from chemical pollution than those in rural areas. Heavy metals in mangrove plant parts, sediments and crabs from mbweni, msimbazi and mtoni mangrove ecosystems in Dar es salaam were analysed using an atomic absorption spectrophotometer, in order to assess the impact of heavy metal pollution on mangrove biota. Sediment samples from msimbazi and mtoni mangrove areas which are located within the city, had higher levels of pb, zn and cu than …

Effects Of Chromium Uptake On The Growth Characteristics Of Eichhornia Crassipes (Mart.) Solms, Zk Rulangaranga, Al Mugasha

Tanzania Journal of Science

The uptake of chromium from fresh water by Eichhornia crassipes was studied under greenhouse conditions where the species was raised in culture solutions containing varying concentrations of chromium (VI) ions. There were positive correlations between the concentration of chromium in the culture media and the amounts of the metal accumulated in the tissues of E. crassipes at any given time. Furthermore, the total accumulated chromium in the tissues of E crassipes increased with increase in the duration for which the plant was exposed to the nutrient solutions containing chromium ions. Most of the absorbed chromium was accumulated in the roots …

The Galapagos Giant Tortoise (Geochelone Elephantopus) And The Spread Of Invasive Plants, Anne D. Schultz

Biology ETDs

Island ecosystems are commonly thought to be more vulnerable to the effects of invasive species than mainland systems. In recent decades, the number of exotic plants known to be present in the Galapagos archipelago has increased exponentially. Several of these plants are aggressive invaders that pose a threat to the biodiversity of the islands. Two of these plant species, Passiflora edulis Sims and Psidium guajava L. were introduced to Santa Cruz Island during the 20th century. Both pose a threat to the floristic diversity of the National Park land on Santa Cruz Island.

This paper explores the role played by …

Functional And Comparative Genomic Analyses Of An Operon Involved In Fructooligosaccharide Utilization By Lactobacillus Acidophilus, Rodolphe Barrangou, Eric Altermann, Robert Hutkins, Raul J. Cano, Todd Klaenhammer

Biological Sciences

Lactobacillus acidophilus is a probiotic organism that displays the ability to use prebiotic compounds such as fructooligosaccharides (FOS), which stimulate the growth of beneficial commensals in the gastrointestinal tract. However, little is known about the mechanisms and genes involved in FOS utilization by Lactobacillus species. Analysis of the L. acidophilus NCFM genome revealed an msm locus composed of a transcriptional regulator of the LacI family, a four-component ATP-binding cassette (ABC) transport system, a fructosidase, and a sucrose phosphorylase. Transcriptional analysis of this operon demonstrated that gene expression was induced by sucrose and FOS but not by glucose or fructose, …

Effect Of Phosphorus Amendments On Present Day Plankton Communities In Pelagic Lake Erie, Steven W. Wilhelm, Jennifer M. Debruyn, Osnat Gillor, Michael R. Twiss, Kasey Livingston, Richard A. Bourbonniere, Lisa D. Pickell, Charles G. Trick, Amanda L. Dean, Robert Michael Mckay

Biological Sciences Faculty Publications

To address questions regarding the potential impact of elevated total phosphorus (TP) inputs (due to relaxed regulations of TP loading), a series of TP enrichment experiments were conducted at pelagic stations in the 3 hydrologically distinct basins of Lake Erie. Results of nutrient assimilation measurements and assays for nutrient bioavailability suggest that the chemical speciation, and not concentration, of nitrogenous compounds may influence phytoplankton community structure; this in turn may lead to the selective proliferation of cyanobacteria in the eastern basin of the lake. Assays with cyanobacterial bioluminescent reporter systems for P and N availability as well as N-tot:P-tot assimilation …

Decoupling Between Bacteria And The Surf-Zone Diatom Asterionellopsis Glacialis At Cassino Beach, Brazil, Paulo C. Abreu, Leonardo R. Rorig, Virginia Garcia, Clarisse Odebrecht, Bopaiah Biddanda

Peer-reviewed scientific publications

The surf-zone diatom Asterionellopsis glacialis (Castracane) Round attains extremely high abundances (up to 109 cells l–1) and chl a concentrations (up to 1.5 mg chl a l–1), forming darkbrown patches in Cassino Beach, southern Brazil. Several lines of evidence from this study indicate a decoupling between A. glacialis and heterotrophic bacteria. For instance, despite the high abundance of diatoms, associated high levels of chl a and rates of dissolved organic carbon (DOC) production by A. glacialis, bacterial abundance at Cassino Beach was extremely low (0.03 to 0.7 × 106 cells ml–1) compared to the nearby estuarine waters, adjacent coastal waters …

P-Limitation Of Respiration In The Sargasso Sea And Uncoupling Of Bacteria From P-Regeneration In Size-Fractionation Experiments, Ingrid Obernosterer, Nobu Kawasaki, Ronald Benner

Faculty Publications

Community respiration rates were measured in unfiltered seawater collected in the upper 75 m of the water column along a transect in the Sargasso Sea and at the Bermuda Atlantic Time-series Study (BATS) station (31° 50’ 00 N; 64° 10’ 00 W) during a cruise in June and July 2001. Community respiration rates in the upper 75 m of the water column averaged 1.1 ± 0.4 μM O₂ d^-1 and exhibited significant spatial and temporal variability. Concurrent determination of the heterotrophic and autotrophic community revealed no relationship between community respiration and the abundance of any of the major …

Matgat: An Application That Generates Similarity/Identity Matrices Using Protein Or Dna Sequences, James Campanella, Ledion Bitincka, John Smalley

Department of Biology Faculty Scholarship and Creative Works

Background: The rapid increase in the amount of protein and DNA sequence information available has become almost overwhelming to researchers. So much information is now accessible that high-quality, functional gene analysis and categorization has become a major goal for many laboratories. To aid in this categorization, there is a need for non-commercial software that is able to both align sequences and also calculate pairwise levels of similarity/identity. Results: We have developed MatGAT (Matrix Global Alignment Tool), a simple, easy to use computer application that generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. Conclusions: The …

Variation Between Observed And True Terminal Restriction Fragment Length Is Dependent On True Trf Length And Purine Content, Christopher W. Kaplan, Christopher L. Kitts

Biological Sciences

Terminal Restriction Fragment (TRF) pattern analysis has become a widely used and informative tool for studying microbial communities. Variation between sequence-determined or true TRF length and observed TRF length (TRF drift) has been previously reported and can significantly affect identification of bacterial species using TRF lengths predicted from sequence databases. In this study TRF drift was determined for 21 bacterial species using an ABI 310 Genetic Analyzer. TRF drift was positively correlated with true TRF length and negatively correlated with TRF purine content. This implies that subtle differences in molecular weight, whether from purine content or dye label, can significantly …

Insect-Mediated Pollination In Slickspot Peppergrass, Lepidium Papilliferum L. (Brassicaceae), And Its Implications For Population Viability, Ian Robertson, Danielle Klemash

Biology Faculty Publications and Presentations

Field experiments on the pollination biology of slickspot peppergrass, Lepidium papilliferum L. (Brassicaceae), a rare species endemic to microsites in sagebrush-steppe habitat in southwestern Idaho, were conducted at 2 sites from May to July 2001. Site KB contained over 10,000 plants, whereas site WG contained less than 150 plants. Insect exclusion experiments revealed that seed production in L. papilliferum is dependent on insect-mediated pollination; median percent seed set dropped from 70% to 2% when insects were excluded from flowers. A total of 25 insect families from 5 orders visited L. papilliferum flowers: 24 families at KB and 11 families at …

On Temporal Variation And Conflicting Selection Pressures: A Test Of Theory Using Newts, Jason R. Rohr, Dale M. Madison, Aaron M. Sullivan

Faculty Publications - Department of Biological & Molecular Science

Most studies that examine conflicting selection pressures hold resources and risks constant, despite their ubiquitous fluctuation. Since little is known about the consequences of neglecting this variation, we examined the temporal response of male red-spotted newts, Notophthalmus viridescens, to conflicting female pheromones and damage-release alarm chemicals signaling predation. After a single exposure in both the laboratory and field, males were attracted to female odor and avoided conspecific alarm chemicals. Response to these combined cues depended on time after exposure, with males initially avoiding, and then being attracted to, the cue combination. This response shift was due to the resource and …

Mismatch Recognition-Coupled Stabilization Of Msh2-Msh6 In An Atp-Bound State At The Initiation Of Dna Repair, Edwin Antony, Manju M. Hingorani

Biological Sciences Faculty Research and Publications

Mismatch repair proteins correct errors in DNA via an ATP-driven process. In eukaryotes, the Msh2-Msh6 complex recognizes base pair mismatches and small insertion/deletions in DNA and initiates repair. Both Msh2 and Msh6 proteins contain Walker ATP-binding motifs that are necessary for repair activity. To understand how these proteins couple ATP binding and hydrolysis to DNA binding/mismatch recognition, the ATPase activity of Saccharomyces cerevisiae Msh2-Msh6 was examined under pre-steady-state conditions. Acid-quench experiments revealed that in the absence of DNA, Msh2-Msh6 hydrolyzes ATP rapidly (burst rate = 3 s^-1 at 20 °C) and then undergoes a slow step in the …

Developmental Toxicity Of Atrazine And Copper Sulfate Using The Frog Embryo Teratogenesis Assay-Xenopus (Fetax), Misty D. Hamilton

Morehead State Theses and Dissertations

A thesis presented to the faculty of the College of Science and Technology at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Science by Misty D. Hamilton on June 25, 2003.

Differences In Cottonwood Growth Between A Losing And A Gaining Reach Of An Alluvial Floodplain, Mary J. Harner, Jack Arthur Stanford

Biological Sciences Faculty Publications

Interstitial flow of river (hyporheic) water influences algal productivity, benthic assemblages, and locations of fish spawning. However, little is known of the effects of hyporheic flow on the growth of riparian vegetation. By increasing water availability and nutrient delivery, regional upwelling of hyporheic water may increase the growth of terrestrial vegetation. We tested and accepted the hypothesis that cottonwood trees (Populus trichocarpa) in a gaining reach of an alluvial floodplain grow faster than trees in a losing reach by comparing basal areas and ages on an expansive floodplain in western Montana (USA). Trees in the gaining reach had …

Life-History Variation In The Sagebrush Lizard (Sceloporus Graciosus): Phenotypic Plasticity Or Local Adaptation?, Michael W. Sears

Publications

We performed a laboratory common-environment study to determine the genetic and environmental sources of variation in growth rates of the sagebrush lizard (Sceloporus graciosus). Hatchling lizards were reared from gravid females collected from three study populations along an elevational gradient in southern Utah, USA. Hatchlings were fed ad libidum and were maintained on a 14:10 light:dark cycle, with temperatures at 33°C and 21°C during photophase and scotophase, respectively. Each hatchling was randomly assigned to either a water-supplementation treatment or a control group receiving no supplemental water. Once every five days, the water-supplemented lizards were administered orally a quantity …

Cellular Proliferation, Death And Histology In Gambusia Affinis Livers After Exposure To 2-Aminofluorene And Benzidine, Susan J. Lentz

Dissertations

A fundamental need exists for aquatic animals in the biomonitoring of aquatic ecosystems for environmental carcinogens. G. affinis, a small fish species, is selected for this study due to its hardiness, non-migratory nature, geographic diversity and ability to develop tumors. Molecular tools for cellular proliferation and death are examined for use with G. affinis. Additionally, these tools are used to investigate the early carcinogenic effects of 2-aminofluorene and benzidine, both individually and combined, on G. affinis livers.

Antibodies to proliferating cell nuclear antigen (PCNA), p53, cleaved caspase-3 and cleaved poly(ADP-ribose) polymerase (PARP) were examined for use in G. …

Life Cycle Of A Torrenticolous Hawaiian Chironomid (Telmatogeton Torrenticola): Stream Flow And Microhabitat Effects, M. Eric Benbow, Albert J. Burky, Carl M. Way

Biology Faculty Publications

In this study we documented the instar densities and life cycle of Telmatogeton torrenticola Terry (Chironomidae : Telmatogetoninae) from Kinihapai Stream, Maui, Hawaii. Greatest larval densities of this midge are found on substrates of high velocity, shallow flows of cascades, and splash zones of waterfalls, with lower densities in riffles. In the summer of 1994 we compared the effects of two microhabitats (termed optimal and suboptimal) on inter-instar density and relative abundance. In a second year (1995), we evaluated the effect of long-term reduced stream flow on these variables only in optimal microhabitats. A significant reduction in stream flow from …

Enhancer Trapping Reveals Widespread Circadian Clock Transcriptional Control In Arabidopsis, Todd P. Michael, C Robertson Mcclung

Dartmouth Scholarship

The circadian clock synchronizes the internal biology of an organism with the environment and has been shown to be widespread among organisms. Microarray experiments have shown that the circadian clock regulates mRNA abundance of about 10% of the transcriptome in plants, invertebrates, and mammals. In contrast, the circadian clock regulates the transcription of the virtually all cyanobacterial genes. To determine the extent to which the circadian clock controls transcription in Arabidopsis, we used in vivo enhancer trapping. We found that 36% of our enhancer trap lines display circadian-regulated transcription, which is much higher than estimates of circadian regulation based on …

On Water Bears, Frank A. Romano Iii

Research, Publications & Creative Work

Tardigrades, or “water bears” are microscopic invertebrates that require water in their environment and are found in freshwater, marine and terrestrial habitats. The morphology and phylogeny of this “little known phylum” is described as are ways the naturalist might collect water bears. Examples of species distributions in different locations in the southeastern USA are given.

Predators And Life Histories Shape Lestes Damselfly Assemblages Along A Freshwater Habitat Gradient, Robby Stoks, Mark A. Mcpeek

Dartmouth Scholarship

Survey data from New England showed that assemblages of Lestes damselflies are organized along the entire gradient of pond permanence and predator presence. One assemblage occupies vernal ponds lacking large dragonfly predators and fish; four are largely confined to temporary ponds that typically contain dragonfly predators; one dominates fishless permanent ponds and lakes where dragonflies are the top predators; and one dominates permanent ponds and lakes where fish are the top predators. We determined the role of life history and predation in maintaining this striking pattern by conducting a series of transplant experiments in the field and a laboratory experiment …

Is Hp1 An Rna Detector That Functions Both In Repression And Activation?, Rebecca Kellum

Biology Faculty Publications

Heterochromatin is defined as regions of compact chromatin that persist throughout the cell cycle (Heitz, 1928). The earliest cytological observations of heterochromatin were followed by ribonucleotide labeling experiments that showed it to be transcriptionally inert relative to the more typical euchromatic regions that decondense during interphase. Genetic studies of rearrangements that place euchromatic genes next to blocks of heterochromatin also pointed out the repressive nature of heterochromatin (Grigliatti, 1991; and references therein). The discovery of the heterochromatin-enriched protein heterochromatin protein 1 (HP1) by Elgin and co-workers in the mid-1980s suggested that the distinct cytological features of this chromatin may be …

Analysis Of Intermolecular Rna-Rna Recombination By Rubella Virus, Sandra Adams, Wen Pin Tzeng, Min Hsin Chen, Teryl K. Frey

Department of Biology Faculty Scholarship and Creative Works

To investigate whether rubella virus (RUB) undergoes intermolecular RNA-RNA recombination, cells were cotransfected with pairs of in vitro transcripts from genomic cDNA plasmid vectors engineered to contain nonoverlapping deletions: the replicative transcript maintained the 5′-proximal nonstructural (NS) ORF (which contained the replicase, making it RNA replication competent), had a deletion in the 3′-proximal structural protein (SP) ORF, and maintained the 3′ end of the genome, including the putative 3′ cis-acting elements (CSE), while the nonreplicative transcript consisted of the 3′ half of the genome including the SP-ORF and 3′ CSE. Cotransfection yielded plaque-forming virus that synthesized the standard genomic and …

Life History Of The Northern Madtom, Noturus Stigmosus (Siluriformes: Ictaluridae), In The Licking River, Kentucky, Jonathan F. Scheibly

Morehead State Theses and Dissertations

A thesis presented to the faculty of the College of Science and Technology at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Science by Jonathan F. Scheibly on May 9, 2003.

Host Defense Mechanisms In The Crayfish: The Effect Of Injection With Live Or Killed Bacteria., Kimberly R. Goins

Electronic Theses and Dissertations

An increase in attachment of SRBCs to Procambarus clarkii hemocytes has been shown after the crayfish were injected with a live or killed Pseudomonas strain RS2b. The increase in attachment occurred at 8 hours post injection and peaked at 24 hours for both experimental groups. The population of hemocytes with receptors for LPS and mannose also increased at 8 hours post injection and peaked at 24 hours for both experimental groups. At 96 hours post injection the number of receptor bearing hemocytes and hemocytes bound to SRBCs began to decrease to the level of the control for both groups. The …

Analysis Of The Effects Of Hypogeal And Epigeal Emergence On Seedling Competition In Legumes, Keith E. King

McCabe Thesis Collection

Seedling emergence is either hypogeal or epigeal. In hypogeal emergence the cotyledons remain below the soil surface during seedling development, while in epigeal emergence the cotyledons extend above the soil surface due to elongation of the hypocotyl. Here we examine the effect of seed size, and emergence type, on seedling growth. Six legumes with variation in seed size and either epigeal or hypogeal emergence were grown under dark and light conditions. A competition study was also conducted where a hypogeal and epigeal legume were grown in combination with wheat and ryegrass. Legumes expressing epigeal emergence were cowpea (Vigna unguiculata), mung …