Digital Commons Network^™

Optimizing Rna Extraction From Fungal-Algal Tissues For Transcriptomic Gene Expression Analysis, Michael J. Hohl

Honors Theses

Extracting high-quality RNA is critical for downstream applications such a qRT-PCR and RNA-Seq based transcriptomics. Single-stranded RNA is readily susceptible to degradation by environmental RNases, necessitating rapid and sterile homogenization techniques; freezing at -80°C, lysis buffer addition, and short bursts of beadbeating have been shown to increase yields and quality of extracted RNA. Utilizing fungal-algal tissues from the model symbiosis between the filamentous fungi Aspergillus nidulans and the green alga Chlamydomonas reinhardtii, three different commercial homogenizers and six RNA extractions kits were assessed and an optimized extraction protocol for total RNA from fungal-algal tissues was determined. Using the protocol designed …

Intrinsic And Extrinsic Regulation Of Pineal Melatonin Rhythms, Ye Li

Theses and Dissertations--Biology

Circadian rhythm is a biological rhythm with period of about 24 hours. Circadian rhythm is universal in phyla from bacteria to mammals and exists in different level from gene expression to behavior. Circadian system consists of three components: 1) a self-sustained oscillator; 2) an input pathway which can alter the phase of the oscillator; and 3) an output such as gene expression, enzyme activity, hormone production, heart rate, body temperature or locomotor activities. The way the oscillator regulates its outputs is complicated, in that on one hand usually the oscillator is not the only factor affecting the outputs, and on …

Pyroglutamylated Amyloid Beta Peptides Enhance Non-Fibrillogenic Aggregation Of The Unmodified Peptide, Gregory Goldblatt

Electronic Theses and Dissertations

Alzheimer's disease (AD) is accompanied by abnormal extracellular deposition of amyloid b (Ab) peptide. This has led to the amyloid cascade hypothesis, causatively relating Ab with AD. While Ab deposits assume a fibrillar cross-b structure, prefibrillar oligomers of Ab have been identified as the main cytotoxic agents in AD. Pyroglutamylated amyloid beta (AbpE) peptides are N-terminally truncated and pyroglutamylated (at Glu3 or Glu11) Ab molecules that display enhanced cytotoxicity and represent up to 50% of total Ab in AD brains. AbpE significantly enhances the toxicity of unmodified Ab by an unknown mechanism. Although in situ Ab populations are heterogeneous, the …

Moss In The Classroom: A Tiny But Mighty Tool For Teaching Biology, Erin E. Shortlidge, James R. Hashimoto

Biology Faculty Publications and Presentations

Here we present a mechanism to infuse ecology into the classroom using a broadly adaptable system. We developed a novel moss-based project that introduces research-based experiences for middle school students, and can be modified for integration into K-16 classrooms. The project is ecologically relevant, facilliating opportunities for students to experience intimate interactions with ecosystem subtleties by asking their own questions. We describe and suggest how students can develop, build, test, and assess microcosm experiments of their own design, learning the process of science by “doing science.” Details on project execution, representative examples of distinctive research-question-based projects are presented. We aim …

Impact Of Sleep And Circadian Disruption On Energy Balance And Diabetes: A Summary Of Workshop Discussions, Deanna M. Arble, Joseph Bass, Cecilia Diniz Behn, Matthew P. Butler, Etienne Challet, Charles Czeisler, Christopher M. Depner, Joel Elmquist, Paul Franken, Michael A. Grandner, Erin C. Hanlon, Alex C. Keene, Michael J. Joyner, Ilia Karatsoreos, Philip A. Kern, Samuel Klein, Christopher J. Morris, Allan I. Pack, Satchidananda Panda, Louis J. Ptacek, Naresh M. Punjabi, Paolo Sessone-Corsi, Frank A. Scheer, Richa Saxena, Elizabeth R. Seaquest, Matthew S. Thimgan, Eve Van Cauter, Kenneth P. Wright

Biological Sciences Faculty Research and Publications

A workshop was held at the National Institute for Diabetes and Digestive and Kidney Diseases with a focus on the impact of sleep and circadian disruption on energy balance and diabetes. The workshop identified a number of key principles for research in this area and a number of specific opportunities. Studies in this area would be facilitated by active collaboration between investigators in sleep/circadian research and investigators in metabolism/diabetes. There is a need to translate the elegant findings from basic research into improving the metabolic health of the American public. There is also a need for investigators studying the impact …

Individual-Level Variation And Higher-Level Interpretations Of Space Use In Wide-Ranging Species: An Albatross Case Study Of Sampling Effects, Sarah Gutowsky, Marty Leonard, Melinda Conners, Scott A. Shaffer, Ian Jonsen

Faculty Publications, Biological Sciences

Marine ecologists and managers need to know the spatial extent of at-sea areas most frequented by the groups of wildlife they study or manage. Defining group-specific ranges and distributions (i.e., space use at the level of species, population, age-class, etc.) can help to identify the source or severity of common or distinct threats among different at-risk groups. In biologging studies, this is accomplished by estimating the space use of a group based on a sample of tracked individuals. A major assumption of these studies is consistency in individual movements among members of a group. The implications of scaling up individual-level …

Acetyl Coa Carboxylase Inactivation And Meiotic Maturation In Mouse Oocytes, Deepa S. Valsangkar, Stephen M. Downs

Biological Sciences Faculty Research and Publications

In mouse oocytes, meiotic induction by pharmacological activation of PRKA (adenosine monophosphate-activated protein kinase; formerly known as AMPK) or by hormones depends on stimulation of fatty acid oxidation (FAO). PRKA stimulates FAO by phosphorylating and inactivating acetyl CoA carboxylase (ACAC; formerly ACC), leading to decreased malonyl CoA levels and augmenting fatty-acid transport into mitochondria. We investigated a role for ACAC inactivation in meiotic resumption by testing the effect of two ACAC inhibitors, CP-640186 and Soraphen A, on mouse oocytes maintained in meiotic arrest in vitro. These inhibitors significantly stimulated the resumption of meiosis in arrested cumulus cell-enclosed oocytes, denuded oocytes, …

Paenibacillus Larvae Spore Germination And American Foulbrood Disease Development In Honey Bee Larvae, Israel Alvarado

UNLV Theses, Dissertations, Professional Papers, and Capstones

Honey bee (Apis mellifera) pollination plays an important role in meeting our agricultural needs, yet we are incapable of completely preventing a decline in bee health, partially due to bacterial diseases. American Foulbrood (AFB), a bacterial disease of honey bee larvae, is particularly troublesome because the infectious agent is the bacterial spore of Paenibacillus larvae. Bacterial spores are resistant to extreme temperatures, unaffected by antibiotics, withstand exposure to disinfectants, and can remain dormant for years until they can revert back to vegetative cells.

Our research investigated P. larvae spore germination at the functional and pathogen-host level. We have found that …

Mesquite (Prosopis Juliflora): Livestock Grazing, Its Toxicity And Management, Kainaat William, Laila Jafri

Journal of Bioresource Management

Prospis juliflora is an invasive tree native to Northern South America, Central America, and the Caribbean. It has been used as a folk remedy for catarrh, cold, diarrhea, dysentery, excrescences, flu, hoarseness, inflammation, measles, sore throat, and in the healing of wounds. Its antibacterial, antioxidant, antifungal, antitumor, and anthelminitic activities are also reported and it contain phytochemicals such as flavonols, alkaloids, tannins, ellagic acid, glycosides, steroids, and various phenolic compounds. It is reported to be used as feed for cattle worldwide. Low intake of this plant doesn’t affect the health of cattle but excessive intake is harmful and can cause …

Bears In Pakistan: Distribution, Population Biology And Human Conflicts, Fakhar -I- Abbas, Zahid Iqbal Bhatti, Jibran Haider, Afsar Mian

Journal of Bioresource Management

We conducted questionnaire based interviews (n = 1873) of respondents coming from 258 localities about bear tracts in northern parts of Pakistan in 2012-2014 to study Himalyan brown (U. arctos isalbellinus) and Himalayan black (U. t. laniger) bears. Brown bears were more frequent in northern latitudes (northern Chitral, Ghizer, Gilgit and Skardu), while black bears were widely distributed in southern latitudes (Battagram). Both brown and black bears are present in central latitudes (Astor, Diamir, Kohistan and Mansehra). We identified 34 populations of brown bears; a large population in the Deosai Plateau and small to very small …

The Roles Of Mist1 And Rab26 In Zymogenic (Chief) Cell Differentiation And Subcellular Organization, Ramon Jin

Arts & Sciences Graduate Student Theses and Dissertations

Little is known about how differentiating cells reorganize their cellular structure to perform specialized physiological functions. Specifically, exocrine cells like pancreatic acinar and zymogenic chief cells have a highly developed secretory architecture that is rapidly established upon differentiation. What is known in these cells is that the evolutionarily conserved transcription factor MIST1 is required for final maturation. We hypothesized that MIST1 directly regulates specific subcellular components that facilitate functional maturation of secretory cells.We show that MIST1 binds to conserved CATATG E-boxes to activate transcription of 6 genes, including the small GTPases RAB26 and RAB3D. We next demonstrate that RAB26 and …

Biological Sciences Newsletter - May 2015, Department Of Biological Sciences, East Tennessee State University

Biological Sciences Newsletters

No abstract provided.

Distinguishing The Neches River Rose Mallow, Hibiscus Dasycalyx, From Its Congeners Using Dna Sequence Data And Niche Modeling Methods, Melody P. Sain

Biology Theses

The accurate identification of species that are in need of protection is one of the most essential challenges of conservation biology (Lovich and Gibbons, 1997). When deciding if a species needs conservation protection, there are two main scientific concerns that must be addressed: (1) determining if the taxonomic standing of the target species is upheld (i.e., if it is a real, rare species) and (2) deciding where the target species occurs or is likely to occur. In this study we used an integrative approach combining ecological niche modeling and molecular genetics to understand the taxonomy of a federally threatened Hibiscus …

Identification Of A New Fatty Acid Catabolic Pathway During Heterotrophic Growth In Chlamydomonas Reinhardtii, Clayton Mccuiston

Honors Capstones

No abstract provided.

Engaging Students In Current Topics: Ecosystem Disruption, Sarah O'Leary-Driscoll

Faculty Publications & Research

One of the most compelling aspects of studying biology is that it has immediate relevance to the world around us. It is the study of life, which can give us amazing insight into how we as organisms work as well as our place in Earth’s ecosystem. This second point is especially crucial for our students to understand, as the Earth is in many ways in a state of ecological crisis. Ecosystems across the globe are changing, often as the result of human influence, and an understanding of the causes and effects of these changes is essential for our students, especially …

Effects Of Long-Term Exposure Of Female Rats To Low Levels Of Lead: Ovary And Uterus Histological Architecture Changes, Eugenia Dumitrescu, Viorica Chiurciu, Florin Muselin, Roxana Popescu, Diana Brezovan, Romeo Teodor Cristina

Turkish Journal of Biology

The aim of the current study was to evaluate lead accumulation in the ovaries, fallopian tubes, and uterus and to take note of any consequent histo-architectural changes. The experiment involved a 12-month chronic exposure of 28 Wistar female rats at sexual maturity (221 ± 0.88 g/individual) to lead acetate in drinking water. The rats were divided into 4 groups based on the level of lead exposure: E1 at 0.050 mg L^{-1}, E2 at 0.100 mg L^{-1}, E3 at 0.150 mg L^{-1} , and a control group that received tap water. Lead level evaluation was performed by atomic absorption spectrometry at …

A Novel Method For Studying Gene Regulatory Elements In Vivo Reveals Essential Roles For Intron Splicing In Neurofilament Gene Expression, Chen Wang

Legacy Theses & Dissertations (2009 - 2024)

Axon outgrowth requires coordinated expression of critical cytoskeletal genes in response to extracellular cues. The spatial and temporal expression of these genes is regulated transcriptionally and posttranscriptionally. Such regulation is largely mediated through the activity of cis-regulatory elements within the cytoskeletal DNAs and RNAs, which recruit specific sets of trans-factors such as DNA- and RNA-binding proteins, as well as microRNAs. To identify the functionally active cis-elements, characterize their dynamically changing sets of trans-factors, and investigate the association between the two sets of regulators in the context of an intact developing nervous system, one needs to combine appropriate in vivo strategies …

Cytokine Dynamics, Diagnosis And Treatment Of Neuroinflammation In Chronic Constriction Injury Rat Model, Kiran Vasudeva

Electronic Theses and Dissertations

Chronic neuropathic pain is a serious, worldwide health problem leading to life-long treatment and the possibility of significant disability. In this study, neuropathic pain was modeled using the chronic constriction injury (CCI) in rats. The CCI rats exhibited hypersensitivity (typical neuropathic pain symptom) to mechanical stimulation of the affected paw 11 days post-surgery, at a time when sham surgery animals did not. It is known that immune cells play a role in the development of neuropathic pain and to further explore the relationship between neuropathic pain and immune cells, we hypothesized that the infiltration of immune cells into the affected …

A High-Content Multiplexed Screening Platform For The Evaluation And Manipulation Of Force And Fatigue Of Adult Derived Skeletal Muscle Myotubes In Defined Serum-Free Medium, Christopher Mcaleer

Electronic Theses and Dissertations

The overall focus of this project has two parts: First, was to develop a protocol utilizing serum-free media formulations and defined plating and culture techniques to create functional in vitro myotubes derived from adult skeletal muscle satellite cells. The second was to manipulate the inherent muscle parameters such as force output and fatigue of these myotubes by employing exercise regimes or by small molecule application. The importance of serum-free medium use for in vitro cultures is becoming increasingly important in creating functional systems that can be validated for drug testing by the Food and Drug Administration (FDA). Also, the study …

Thermal Variation, Thermal Extremes And The Physiological Performance Of Individuals, W. Wesley Dowd, Felicia A. King, Mark W. Denny

Biology Faculty Works

In this review we consider how small-scale temporal and spatial variation in body temperature, and biochemical/physiological variation among individuals, affect the prediction of organisms’ performance in nature. For ‘normal’ body temperatures – benign temperatures near the species’ mean – thermal biology traditionally uses performance curves to describe how physiological capabilities vary with temperature. However, these curves, which are typically measured under static laboratory conditions, can yield incomplete or inaccurate predictions of how organisms respond to natural patterns of temperature variation. For example, scale transition theory predicts that, in a variable environment, peak average performance is lower and occurs at a …

A Comparison Of Two Low-Stakes Methods For Administering A Program-Level Biology Concept Assessment, Brian A. Couch, Jennifer K. Knight

School of Biological Sciences: Faculty Publications

Concept assessments are used commonly in undergraduate science courses to assess student learning and diagnose areas of student difficulty. While most concept assessments align with the content of individual courses or course topics, some concept assessments have been developed for use at the programmatic level to gauge student progress and achievement over a series of courses or an entire major. The broad scope of a program-level assessment, which exceeds the content of any single course, creates several test administration issues, including finding a suitable time for students to take the assessment and adequately incentivizing student participation. These logistical considerations must …

Cdna Cloning, Molecular Characterization, And Expression Analyses Of Two Novel Porcine Arrdc Genes-Arrdc1 And Arrdc, Hailong Huo, Pei Wang, Shuyan Wang, Yongwang Miao, Hongjiang Wei, Yongyun Zhang, Qiaoling Zhang, Fuquan Li, Lixian Liu, Rui Wang, Weizhen Li, Yue Zhao, Jinlong Huo, Heng Xiao

Turkish Journal of Biology

Arrestin-domain-containing proteins belong to the arrestin family, embers of which are important for regulating signal transduction within cells. In this study, two ARRDC genes (ARRDC1 and ARRDC5) of Diannan small-ear pigs were amplified by reverse transcription polymerase chain reaction and cloned for the first time (accession nos.: KF589202 and KF589203). The full-length coding sequence of ARRDC1 was 1284 nucleotides in length (molecular weight, 45.6 kDa; pI, 7.61) and encoded 427 amino acids. The ARRDC5CDS was 1014 nucleotides in length (molecular weight, 37.5 kDa; pI, 7.08) and encoded 337 amino acids. Sequence homology analysis revealed that the amino acid sequences of …

Effects Of Low Concentrations Of Carbon Nanotubes On Growth And Gas Exchange In Arabidopsis Thaliana, Rajeeva Voleti

Graduate Theses/Dissertations

The effect of pure single-walled carbon nanotubes (SWCNTs) on plant growth and gas exchange was investigated in Arabidopsis thaliana. To date there has been no research on the effects of SWCNTs on whole plant physiology. A. thaliana seeds were directly grown in growth medium containing SWCNTs concentrations of 24.93micrograms/ml and 53.55 micrograms/ml. control plants were grown in media containing distilled water. I determined growth by measuring dry mass of plants. I determined gas exchange by measuring photosynthetic rates, stomatal conductance, transpiration rates, and water use efficiency. I also examined the following physiological mechanisms that would limit plant growth: ATP and …

Daily Activity Budgets Reveal A Quasi-Flightless Stage During Non-Breeding In Hawaiian Albatrosses, Sarah Gutowsky, Lee Gutowsky, Ian Jonsen, Marty Leonard, Maura Naughton, Marc Romano, Scott A. Shaffer

Faculty Publications, Biological Sciences

Background Animals adjust activity budgets as competing demands for limited time and energy shift across life history phases. For far-ranging migrants and especially pelagic seabirds, activity during breeding and migration are generally well studied but the “overwinter” phase of non-breeding has received less attention. Yet this is a critical time for recovery from breeding, plumage replacement and gaining energy stores for return migration and the next breeding attempt. We aimed to identify patterns in daily activity budgets (i.e. time in flight, floating on the water’s surface and active foraging) and associated spatial distributions during overwinter for the laysan Phoebastria immutabilis …

Publication Trends In Model Organism Research, Michael Dietrich, Rachel Ankeny, Patrick Chen

Dartmouth Scholarship

In 1990, the National Institutes of Health (NIH) gave some organisms special status as designated model organisms. This article documents publication trends for these NIH-designated model organisms over the past 40 years. We find that being designated a model organism by the NIH does not guarantee an increasing publication trend. An analysis of model and nonmodel organisms included in GENETICS since 1960 does reveal a sharp decline in the number of publications using nonmodel organisms yet no decline in the overall species diversity. We suggest that organisms with successful publication records tend to share critical characteristics, such as being well …

Study The Quality Of Groundwater Of Al-Zoroup Area In Mahdah State, The Sultanate Of Oman, Fahad Khalifa Rashid Al-Shidi

Theses

The groundwater is the most important source of water in the Sultanate of Oman. Accordingly, the Oman Government has paid great attention commensurate with the importance of water resource in terms of their sources, quality, and ways to rationalize consumption to remain under the term of sustainability and validity of present and future generations. This study was conducted in Al Buraymi at Mahdah State in Al-Zoroub area targete a groundwater quality for 20 wells in private farms. The water samples were taken from these wells and subjected to analysis for microbial and geochemical aspects. For this analysis, the assorted devices …

Characterization Of Metal-Reducing Microorganisms In Walker Lake: A Terminal Saline Desert Lake, Memona Khan

Honors College Theses

Metal-reducing microorganisms are increasingly being recognized as an essential component of aquatic microbial ecosystems involved in decomposition of organic matter. Alkaliphilic microbial reduction from alkaline lakes is a little studied field and one particular ecosystem, Walker Lake, presents the opportunity to investigate alkaliphilic metal reducers in their native ecological setting. Walker lake is a terminal, saline, desert lake with pH 9.4, Walker Lake samples of surface and deep sediments and water column samples from 0, 10, 5, 15, 17.5, 19 m depths were cultured by serial dilution in synthetic Walker Lake medium and supplemented separately with Hydrous Ferric Oxide (HFO), …

Component Trees For The Exploration Of Macromolecular Structures In Biology, Lucas Oliveira

Dissertations, Theses, and Capstone Projects

Understanding the three-dimensional structure of a macromolecular complex is essential for understanding its function. A component tree is a topological and geometric image descriptor that captures information regarding the structure of an image based on the connected components determined by different grayness thresholds. This dissertation presents a novel interactive framework for visual exploration of component trees of the density maps of macromolecular complexes, with the purpose of improved understanding of their structure. The interactive exploration of component trees together with a robust simplification methodology provide new insights in the study of macromolecular structures. An underlying mathematical theory is introduced and …

Evaluating The Utility Of Natural History Collections In Research And For The Public, Bethany L. Abrahamson

Biology ETDs

Natural history collections (NHCs) are useful in many fields of study, but knowledge about how they are used in the modern day is poor. The first part of this study, focused on the collections data held by the Museum of Southwestern Biology (MSB), analyzes specimen-based publications, specimen loan records, and guestbook information to determine how NHCs have been used in scientific study over time. Using a novel methodology, I objectively sorted the publications into ten research subjects via particular phrases found in publication titles, places of publication, and keywords. I observed from this dataset the proportions of particular subjects for …

Branching Into Rnai: Synthesis, Characterization And Biology Of Branch And Hyperbranch Sirnas, Anthony Muriithi Maina

Seton Hall University Dissertations and Theses (ETDs)

The cancer epidemic continues to afflict millions of humans world-wide each year and despite a renewed hope with the development of new and improved forms of therapy, a cure for cancer remains an elusive goal. This is partly related to the rise of resilient forms of tumors that have evolved with resistance towards conventional chemotherapy and radiation treatments. Moreover, these non-specific therapeutic regimens are highly toxic, leading to severe immunosuppressive effects which poisons the body and compromises the road towards remission. In an effort to mitigate these limitations, cancer-targeting approaches are currently experiencing a renaissance in the translation of new …