Digital Commons Network^™

Genome-Wide Detection Of Novel Regulatory Rnas In E. Coli, Rahul Raghavan, Eduardo Groisman, Howard Ochman

Biology Faculty Publications and Presentations

The intergenic regions in bacterial genomes can contain regulatory leader sequences and small RNAs (sRNAs), which both serve to modulate gene expression. Computational analyses have predicted the presence of hundreds of these noncoding regulatory RNAs in Escherichia coli; however, only about 80 have been experimentally validated. By applying a deep-sequencing approach, we detected and quantified the vast majority of the previously validated regulatory elements and identified 10 new sRNAs and nine new regulatory leader sequences in the intergenic regions of E. coli. Half of the newly discovered sRNAs displayed enhanced stability in the presence of the RNA-binding protein …

Optimized Production Of Lignin Peroxidase, Manganese Peroxidase And Laccase In Submerged Cultures Of Trametes Trogii Using Various Growth Media Compositions, F. Patrick, G. Mtui, A. M. Mshandete, A. Kivaisi

Tanzania Journal of Science

A white-rot fungus, Trametes trogii, was isolated from coastal Tanzania and screened for crude lignolytic enzymes production using Rhemazol Brilliant blue R (RBBR) dye, 2,2-azino-bis (3-ethylbenzthiazoline)-6-sulfonate (ABTS) and guaiacol in a semi-solid medium. Lignin peroxidase (LiP), manganese peroxidase (MnP) and Laccase (Lac) were detected by pyrogallol and !- napthol solutions, respectively on the guaiacol supplemented solid media. The effect of temperature, pH, carbon, nitrogen, Cu2+, 2,5-xylidine, ferulic acid, varatryl alcohol and Mn2+ in submerged culture fermentations were investigated for maximum enzymes production. After 7 days of incubation, 72-100% oxidation of RBBR, ABTS and guaiacol was observed. With optimized culture conditions, …

Phylogenetic Relationships Of The Metazoan Parasites Of The Clariid Fishes Of Lake Victoria Inferred From Partial 18s Rdna Sequences, C. J. Mwita, G. Nkwengulila

Tanzania Journal of Science

Phylogenetic relationships among twenty two metazoan parasites recovered from seven species of clariid fish from Lake Victoria were analysed using partial 18S rDNA sequences. The 18S rDNA gene was amplified by polymerase chain reaction, directly sequenced, aligned and phylogenies inferred using maximum parsimony. Heuristic bootstrap MP searches yielded one most parsimonious tree (CI = 61%, HI = 39%), which showed that clariid parasites are monophyletic at higher taxonomic levels (Cestodea, Nematodea, Digenea and Crustacea). However the position of two trematodes (Allocredium mazoensis and Clinostomum sp.) and a nematode (Contracaecum sp.) were not stable. Despite the present findings, the study utilised …

Urban Dietary Heavy Metal Intake From Protein Foods And Vegetables In Dar Es Salaam, F. N. Ngassapa, O. C. Othman, E. Elisante

Tanzania Journal of Science

Contamination of food and food products by heavy metals has made dietary intake as one of the major routes of these harmful elements to human beings. The human dietary intake of heavy metals cadmium, copper, lead and zinc from protein-foods (beans, meat, fish, milk) and green vegetables consumed daily from restaurants and street food-vendor kiosks in Dar es Salaam were determined using the Total Diet Study (TDS) method. The cooked food was bought from the restaurants and street food-vendors at several city locations (i.e. Buguruni, Manzese, Mwenge, Temeke and Ubungo) over several months and analyzed. Heavy metal concentrations were determined …

Geomorphological Potential Of Coelacanth Habitat Across Mozambique-Tanzania Border, N. Nyandwi

Tanzania Journal of Science

The coelacanth is a new fish in Tanzania. It was first discovered in September 2003 after it was spotted by a tourist in a fish market. It was caught by fishermen in the deep waters off Songo Mnara Island offshore of Kilwa Masoko Town in Southern Tanzania. The find potentially added southern Tanzania to the list of known coelacanth areas of the southern Western Indian Ocean Region. Observed current conditions indicate that the waters are swept by strong (2 m/sec) northward flowing current. This suggests that there must exist hideouts for the fish, such as caves in canyons and overhangs. …

Spatial Distribution Of Calcium-Gated Chloride Channels In Olfactory Cilia, Donald A. French, Dorjsuren Badamdorj, Steven J. Kleene

Mathematical Sciences Faculty Research

Background

In vertebrate olfactory receptor neurons, sensory cilia transduce odor stimuli into changes in neuronal membrane potential. The voltage changes are primarily caused by the sequential openings of two types of channel: a cyclic-nucleotide-gated (CNG) cationic channel and a calcium-gated chloride channel. In frog, the cilia are 25 to 200 µm in length, so the spatial distributions of the channels may be an important determinant of odor sensitivity.

Principal Findings

To determine the spatial distribution of the chloride channels, we recorded from single cilia as calcium was allowed to diffuse down the length of the cilium and activate the channels. …

Global Patterns And Predictions Of Seafloor Biomass Using Random Forests, Chih-Lin Wei, Gilbert T. Rowe, Elva Escobar-Briones, Antje Boetius, Thomas Soltwedel, M. Julian Caley, Yousria Soliman, Falk Huettmann, Fangyuan Qu, Zishan Yu, C. Roland Pitcher, Richard L. Haedrich, Mary K. Wicksten, Michael A. Rex, Jeffrey G. Baguley, Jyotsna Sharma, Roberto Danovaro, Ian R. Macdonald, Clifton C. Nunnally, Jody W. Deming, Paul Montagna, Mélanie Lévesque, Jan Marcin Weslawski, Maria Wlodarska-Kowalczuk, Baban S. Ingole, Brian J. Bett, David S. M. Billett, Andrew Yool, Bodil A. Bluhm, Katrin Iken, Bhavani E. Narayanaswamy

Biology Faculty Publication Series

A comprehensive seafloor biomass and abundance database has been constructed from 24 oceanographic institutions worldwide within the Census of Marine Life (CoML) field projects. The machine-learning algorithm, Random Forests, was employed to model and predict seafloor standing stocks from surface primary production, water-column integrated and export particulate organic matter (POM), seafloor relief, and bottom water properties. The predictive models explain 63% to 88% of stock variance among the major size groups. Individual and composite maps of predicted global seafloor biomass and abundance are generated for bacteria, meiofauna, macrofauna, and megafauna (invertebrates and fishes). Patterns of benthic standing stocks were positive …

Biphasic Targeting And Cleavage Furrow Ingression Directed By The Tail Of A Myosin Ii, X. Fang, J. Y. Luo, R. Nishihama, C. Wloka, C. Dravis, M. Travaglia, M. Iwase, Elizabeth Ann Vallen, E. Bi

Biology Faculty Works

Cytokinesis in animal and fungal cells utilizes a contractile actomyosin ring (AMR). However, how myosin II is targeted to the division site and promotes AMR assembly, and how the AMR coordinates with membrane trafficking during cytokinesis, remains poorly understood. Here we show that Myo1 is a two-headed myosin II in Saccharomyces cerevisiae, and that Myo1 localizes to the division site via two distinct targeting signals in its tail that act sequentially during the cell cycle. Before cytokinesis, Myo1 localization depends on the septin-binding protein Bni5. During cytokinesis, Myo1 localization depends on the IQGAP Iqg1. We also show that the Myo1 …

Complexity Through Recombination: From Chemistry To Biology, Niles Lehman, Carolina Diaz Arenas, Wesley A. White, Francis J. Schmidt

Chemistry Faculty Publications and Presentations

Recombination is a common event in nature, with examples in physics, chemistry, and biology. This process is characterized by the spontaneous reorganization of structural units to form new entities. Upon reorganization, the complexity of the overall system can change. In particular the components of the system can now experience a new response to externally applied selection criteria, such that the evolutionary trajectory of the system is altered. In this work we explore the link between chemical and biological forms of recombination. We estimate how the net system complexity changes, through analysis of RNA-RNA recombination and by mathematical modeling. Our results …

Role For Sumoylation In Systemic Inflammation And Immune Homeostasis In Drosophila Larvae, Indira Paddibhatla, Mark J. Lee, Marta E. Kalamarz, Roberto Ferrarese, Shubha Govind

Publications and Research

To counter systemic risk of infection by parasitic wasps, Drosophila larvae activate humoral immunity in the fat body and mount a robust cellular response resulting in encapsulation of the wasp egg. Innate immune reactions are tightly regulated and are resolved within hours. To understand the mechanisms underlying activation and resolution of the egg encapsulation response and examine if failure of the latter develops into systemic inflammatory disease, we correlated parasitic wasp-induced changes in the Drosophila larva with systemic chronic conditions in sumoylation-deficient mutants. We have previously reported that loss of either Cactus, the Drosophila (IkB) protein or Ubc9, the SUMO-conjugating …

Sensitivity And Exposure Of Brook Trout (Salvelinus Fontinalis) Habitat To Climate Change, Bradly Allen Trumbo

Masters Theses, 2010-2019

Predicting coldwater fisheries distributions under various climate scenarios is of interest to many fisheries managers and researchers. Larger scale models have been useful in highlighting the potential large scale threat. However, the error associated with these models makes predictions of the persistence of individual cold water fisheries problematic. Most of this error is associated with predicted air and water temperatures which typically are simple elevation and location (latitude/longitude) models with simple caveats such as 1°C increase in air temperature equals 0.8°C increase in water temperatures. I directly measured paired air and water temperatures in watersheds containing reproducing populations of brook …

A Profile Of Rural Southern Appalachian Hiv Patients: Vamc Versus Com., Lauren Brooks

Undergraduate Honors Theses

Although the AIDS epidemic in America began approximately three decades ago, much remains to be learned about the epidemiology of human immunodeficiency virus (HIV) infections in rural America. This study compared profiles of HIV patients at the James H. Quillen Veterans Affairs Medical Center (VAMC) in Mountain Home, TN to those seen at a university-based community HIV care clinic (COM) in Johnson City, TN.

Phylogenetics, Morpohology, And Genomic Evolution In Physarieae (Brassicaceae), Sara Fuentes-Soriano

Dissertations

The mustard family (Brassicaceae) is economically important but the evolution of its morphology is not well understood. I investigate the evolution of morphological and genomic characters and calculate ancestral trait values in the Brassicaceae within a phylogenetic context using the tribe Physarieae as a model system. Physarieae are a unique and diverse group of American mustards characterized by multi-aperturate pollen. Phylogenetic analyses of DNA sequences (chloroplast ndhF and nuclear ITS and LUMINIDEPENDENS) were used to test the monophyly and explore evolutionary relationships of Physarieae. The phylogenetic inferences were used to identify morphological traits to delimit the tribe, to interpret the …

Development Of A Methodology To Attain High Levels Of Storage Proteins In Cassava Tuberized Roots And Its Implications, Mohammad Abhary

Dissertations

Cassava (Manihot esculenta Crantz.) is a member of the Euphorbiaceae family, cultivated in the tropics and subtropical areas as a staple food crop for more than 700 million people around the world. The starchy storage roots of cassava are rich in calories and deficient in all other nutrients, cassava meals has the lowest of all sources of dietary protein. Severe protein deficiencies and malnutrition problems are common among those who rely on cassava as their daily meal. Although cassava is ranked the fifth most important crop in the world, the research on this crop is very limited. Among the limited …

The Roles Of Elevated Bcl-2 In Ovarian Cancer, Nicole Shree Anderson

USF Tampa Graduate Theses and Dissertations

Ovarian cancer (OC) is the second most common gynecologic cancer; however it is responsible for the most gynecologic cancer-related deaths. Apoptosis evasion is an important mechanism in OC tumorigenesis, and the prototypic anti-apoptotic protein, B-cell lymphoma 2 (Bcl-2), is often overexpressed in OC tumors. Gaining a better understanding of the mechanism(s) behind Bcl-2 overexpression and potential extra-anti-apoptotic functions of Bcl-2 could elucidate the importance of elevated Bcl-2 in OC. In the current study, I show through immunohistochemical analysis of normal, benign, and OC tissue sections, that both epithelial and stromal Bcl-2 expression decreases with OC progression. However, the number of …

Distribution And Molecular Analysis Of Avian Malaria Vectors On Four Central Virginia Prothonotary Warbler (Protonotaria Citrea) Breeding Sites, Catherine Wallace

Theses and Dissertations

Avian malaria is a devastating disease that has decimated numerous bird species. This study sought to identify the vectors of avian malaria at four central Virginia Prothonotary warbler breeding sites. Twenty one thousand mosquitoes were collected and Culex salinarius, Cx. erraticus, and Cx. pipiens/restuans were found to be the dominant species at these sites. Geographic factors, such as crop land and forest type, were determined to be potential indicators for species abundance variation between sites. Of the mosquitoes collected, ninety one (0.4%) were identified as blood fed. The blood fed mosquitoes were found to have fed on avian, mammalian, amphibian, …

Adaptive Divergence In The Thyroid Hormone Signaling Pathway In The Stickleback Radiation, Jun Kitano, Sean C. Lema, J. Adam Luckenbach, Seiichi Mori, Yui Kawagishi, Makoto Kusakabe, Penny Swanson, Catherine L. Peichel

Biological Sciences

During adaptive radiations, animals colonize diverse environments, which requires adaptation in multiple phenotypic traits. Because hormones mediate the dynamic regulation of suites of phenotypic traits, evolutionary changes in hormonal signaling pathways might contribute to adaptation to new environments. Here we report changes in the thyroid hormone signaling pathway in stream-resident ecotypes of threespine stickleback fish (Gasterosteus aculeatus), which have repeatedly evolved from ancestral marine ecotypes. Stream-resident fish exhibit a lower plasma concentration of thyroid hormone and a lower metabolic rate, which is likely adaptive for permanent residency in small streams. The thyroid-stimulating hormone-β2 (TSHβ …

Type Ii Protein Arginine Methyltransferase 5 (Prmt5) Is Required For Circadian Pperiod Determination In Arabidopsis Thaliana, Sunghyun Hong, Hae-Ryoung Song, Kerry Lutz, Randall A. Kerstetter, Todd P. Michael, C. Robertson Mcclung

Dartmouth Scholarship

Posttranslational modification is an important element in circadian clock function from cyanobacteria through plants and mammals. For example, a number of key clock components are phosphorylated and thereby marked for subsequent ubiquitination and degradation. Through forward genetic analysis we demonstrate that protein arginine methyltransferase 5 (PRMT5; At4g31120) is a critical determinant of circadian period in Arabidopsis. PRMT5 is coregulated with a set of 1,253 genes that shows alterations in phase of expression in response to entrainment to thermocycles versus photocycles in constant temperature. PRMT5 encodes a type II protein arginine methyltransferase that catalyzes the symmetric dimethylation of arginine residues (Rsme2). …

Campylobacter Ureolyticus: An Emerging Gastrointestinal Pathogen?, Susan Bullman, Daniel Corcoran, James O'Leary, Brigid Lucey, Deirdre Byrne, Roy D. Sleator

Department of Biological Sciences Publications

A total of 7194 faecal samples collected over a 1-year period from patients presenting with diarrhoea were screened for Campylobacter spp. using EntericBios, a multiplex-PCR system. Of 349 Campylobacter-positive samples, 23.8% were shown to be Campylobacter ureolyticus, using a combination of 16S rRNA gene analysis and highly specific primers targeting the HSP60 gene of this organism. This is, to the best of our knowledge, the first report of C. ureolyticus in the faeces of patients presenting with gastroenteritis and may suggest a role for this organism as an emerging enteric pathogen.

Avian Developmental Endocrinology: The Effects And Role Of Yolk Hormones, Sibling Dynamics, And Life-History, Corinne Patricia Kozlowski

Dissertations

Inter-specific variation of the endocrine system is an underlying component for variation in avian life-history. Females deposit hormones into the yolks of their eggs, and embryonic exposure affects nestling phenotype. Hormones are also produced endogenously by developing nestlings, further influencing their behavior and physiology. This dissertation examines the role of the endocrine system in development by focusing on several different avian taxa. Yolk hormone concentrations often vary across the laying order and may mediate hatching asynchrony. These patterns were characterized in two species that lay asynchronously hatching clutches: Eastern screech owls (Megascops asio) and cockatiels (Nymphicus hollandicus). The patterns described …

Gene Flow And Dispersal Of The Flatworm, Polycelis Coronata: A Multiscale Analysis, Jeffrey N. Moore

Theses and Dissertations

We determined genetic variance and gene flow across multiple scales (reaches, headwater segments, and catchments) to examine the dispersal ability of the flatworm Polycelis coronata along the Wasatch Mountains of Utah. Multiple models predict patterns of genetic differentiation in stream invertebrates based on dispersal traits and the spatial connectivity of the habitat. The stream hierarchy model predicts genetic differentiation to be low and gene flow to be high between reaches nested in segments, moderate among segments within catchments, and differentiation to be highest and gene flow lowest among catchments, whereas the headwater model predicts the greatest differentiation between headwater segments. …

The Burden Of Motherhood: The Effect Of Reproductive Load On Female Lizard Locomotor, Foraging, And Social Behavior, Michele A. Johnson, J. L. Caton, R. E. Cohen, J. R. Vandecar, J. Wade

Biology Faculty Research

The costs of reproduction, involving demands associated with both current and future reproductive efforts, may place a substantial burden on females. However, animals may minimize these costs by modifying their behavior across the reproductive cycle. We examined the effects of reproductive load on three types of behavior (locomotion, foraging, and social displays) in green anole lizards (Anolis carolinensis) by comparing egg, follicle, and oviduct mass and volume with field observational data. We found that female locomotor and social display behaviors decreased as reproductive load increased, suggesting behavioral modification in these traits, but we detected no relationship between foraging and …

Flowering Locus C Influences The Timing Of Shoot Maturation In Arabidopsis Thaliana, Laurie Mentzer, Tarah Yee, Tina Y. Wang, Edward Himelblau

Biological Sciences

No abstract provided.

Cloning Of A Chlamydomonas Reinhardtii Marker Into A Rna Interference Construct To Test Whether The Photoreceptor Chlamyrhodopsin Is Involved In Circadian Clock Resetting, Shravya Reddy Maddi

Masters Theses & Specialist Projects

Chlamydomonas reinhardtii, a unicellular eukaryotic green alga, serves as a model organism to study the circadian clock in plants and animals. Rhodopsins are blue/green-light photoreceptors also found in C. reinhardtii. Chlamyrhodopsin (COP), the most abundant eyespot protein, was reported to have no role in the phototactic and photophobic responses in C. reinhardtii. Its function is yet unknown.
In the present study, we hypothesized that the function of COP is to mediate entrainment of the circadian clock by light. In order to test this hypothesis, a C. reinhardtii selection marker conferring resistance to the antibiotic paromomycin was cloned …

[Accepted Article Manuscript Version (Postprint)] Pex5 Mutants That Differentially Disrupt Pts1 And Pts2 Peroxisomal Matrix Protein Import In Arabidopsis, Bibi Khan, Bethany Zolman

Biology Department Faculty Works

PEX5 and PEX7 are receptors required for the import of peroxisome-bound proteins containing one of two peroxisomal targeting signals (PTS1 or PTS2). To better understand the role of PEX5 in plant peroxisomal import, we characterized the Arabidopsis (Arabidopsis thaliana) pex5-10 mutant, which has a T-DNA insertion in exon 5 of the PEX5 gene. Sequencing results revealed that exon 5, along with the T-DNA, is removed in this mutant, resulting in a truncated pex5 protein. The pex5-10 mutant has germination defects and is completely dependent on exogenous Suc for early seedling establishment, based on poor utilization of seed-storage fatty acids. This …

What Brown Saw And You Can Too, Philip Pearle, Brian Collett, Kenneth Bart, David Bilderback, Dara Newman, D. Scott Samuels

Biological Sciences Faculty Publications

A discussion of Robert Brown’s original observations of particles ejected by pollen of the plant Clarkia pulchella undergoing what is now called Brownian motion is given. We consider the nature of those particles and how he misinterpreted the Airy disk of the smallest particles to be universal organic building blocks. Relevant qualitative and quantitative investigations with a modern microscope and with a “homemade” single lens microscope similar to Brown’s are presented.

Science As A Human Right: Esa And The Aaas Science And Human Rights Coalition, Clifford Duke, George Middendorf, Jessica Wyndham

Department of Biology Faculty Publications

No abstract provided.

The Status Of Dwarfed Populations Of Short-Horned Lizards (Phrynosoma Hernandesi) And Great Plains Toads (Anaxyrus Cognatus) In The San Luis Valley, Colorado, Megan E. Lahti

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The San Luis Valley is a large valley formation in Colorado surrounded on either side by mountain ranges exceeding 4,267 m. Within the Valley, two of the 14 amphibian and reptile species are dwarfed: the short-horned lizard (Phrynosoma hernandesi) and the Great Plains toad (Anaxyrus cognatus). Since its initial reporting in 1968 and confirmation in 1981, no research further investigating this dwarfism has been conducted. I collected morphological measurements to determine the extent and patterns of dwarfism of both species. I then investigated the genetics of both species using mitochondrial DNA to determine whether they are …

Flank Gland-Secreted Putative Chemosignals Pertaining To Photoperiod, Endocrine States, And Sociosexual Behavior In Golden Hamsters, Ying-Juan Liu, Da-Wei Wang, Lixing Sun, Jin-Hua Zhang, Jian-Xu Zhang

All Faculty Scholarship for the College of the Sciences

Behavioral studies have shown that flank glands are involved in chemical communication in golden hamsters Mesocricetus auratus but little chemical analysis has been conducted on volatiles arising from these glands. Using gas chromatography- mass spectrometry, we detected compounds from the flank glands of males, only eight of which were also produced in females. Based on these chemical data we performed a number of further experiments. By manipulating light we found that males exposed to short-photoperiods developed smaller flank glands than those exposed to long-photoperiods. Six flank gland volatiles reduced in relative abundance, which possibly coded for reproductive status of males …

The Gel Documentation System: A Cornerstone To The Implementation Of The Introduction To Biotechnology And Introduction To Bioinformatics Cross-Disciplinary Course Series (Final Report), Marcy Kelly, Gregory Lampard, Constance Knapp

Cornerstone 3 Reports : Interdisciplinary Informatics

Our original goal was to offer Pace undergraduate students opportunities to be introduced to both Biotechnology and Computer Science as it relates to Bioinformatics. We proposed a two course series, offered to both computer science and biology students that will increase both biological and computer science literacy of our students. The two courses are Introduction to Biotechnology (BIO 372) and Introduction to Bioinformatics.