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Data Figure 3 In "Insights From The Application Of Genetics On Pocillopora-Symbiodinium Associations In The Eastern Tropical Pacific.", Jorge Pinzon

Biology Datasets - Archive

Supporting data for the chapter entitled: "Insights from the application of genetics on Pocillopora-Symbiodinium associations in the eastern tropical Pacific."

As one of the most widely distributed and most studied scleractinian genera in the world, Pocillopora encompasses an important group of corals. In the eastern tropical Pacific, Pocillopora species thrive and are the major reef-building scleractinian taxon, even though conditions are considered suboptimal for coral growth and reef development. Early observations on reproduction and species distributions appear to be complicated by high phenotypic diversity and often inaccurate species identifications. New genetic-based evidence reorganizes species classifications within Pocillopora by delimiting boundaries …

Temperature Dependent Transcription Initiation In Archaea: Interplay Between Transcription Factor B And Promoter Sequence, Ming-Hsiao Wu

Dissertations and Theses

In Pyrococcus furiosus (Pfu), a hyperthermophile archaeon, two transcription factor Bs, TFB1 and TFB2 are encoded in the genomic DNA. TFB1 is the primary TFB in Pfu, and is homologous to transcription factor IIB (TFIIB) in eukaryotes. TFB2 is proposed to be a secondary TFB that is compared to TFB1, TFB2 lacks the conserved B-finger / B-reader / B-linker regions which assist RNA polymerase in transcription start site selection and promoter opening functions respectively. P. furiosus, like all Archaea, encodes a single transcription factor E (TFE), that is homologous to the N-terminus of transcription factor II …

Male-Male Clasping May Be Part Of An Alternative Reproductive Tactic In Xenopus Laevis, Heather J. Rhodes, Rachel J. Stevenson, Courtney L. Ego

Faculty Publications

No abstract provided.

Genomic Classification Of The Ras Network Identifies A Personalized Treatment Strategy For Lung Cancer, Nader N. El-Chaar, Stephen R. Piccolo, Kenneth M. Boucher, Adam L. Cohen, Jeffrey T. Chang, Philip J. Moos, Andrea H. Bild

Faculty Publications

Better approaches are needed to evaluate a single patient's drug response at the genomic level. Targeted therapy for signaling pathways in cancer has met limited success in part due to the exceedingly interwoven nature of the pathways. In particular, the highly complex RAS network has been challenging to target. Effectively targeting the pathway requires development of techniques that measure global network activity to account for pathway complexity. For this purpose, we used a gene-expression-based biomarker for RAS network activity in non-small cell lung cancer (NSCLC) cells, and screened for drugs whose efficacy was significantly highly correlated to RAS network activity. …

Bioactivities Of Compounds From Elephantopus Scaber, An Ethnomedicinal Plant From Southwest China, Jianjun Wang, Ping Li, Basosai Li, Zhiyong Guo, Edward J. Kennelly, Chunlin Long

Publications and Research

Elephantopus scaber is an ethnomedicinal plant used by the Zhuang people in Southwest China to treat headaches, colds, diarrhea, hepatitis, and bronchitis. A new δ-truxinate derivative, ethyl, methyl 3,4,3′,4′-tetrahydroxy-δ-truxinate (1), was isolated from the ethyl acetate extract of the entire plant, along with 4 known compounds. The antioxidant activity of these 5 compounds was determined by ABTS radical scavenging assay. Compound 1 was also tested for its cytotoxicity effect against HepG2 by MTT assay (IC50 = 60 μM), and its potential anti-inflammatory, antibiotic, and antitumor bioactivities were predicted using target fishing method software.

Joint Phenotypes, Evolutionary Conflict And The Fundamental Theorem Of Natural Selection, David C. Queller

Biology Faculty Research

Multiple organisms can sometimes affect a common phenotype. For example, the portion of a leaf eaten by an insect is a joint phenotype of the plant and insect and the amount of food obtained by an offspring can be a joint trait with its mother. Here, I describe the evolution of joint phenotypes in quantitative genetic terms. A joint phenotype for multiple species evolves as the sum of additive genetic variances in each species, weighted by the selection on each species. Selective conflict between the interactants occurs when selection takes opposite signs on the joint phenotype. The mean fitness of …

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 …

Identification And Characterization Of Microbial Contaminants And Associated Bacterial Viruses In Bioethanol Production Facilities To Suggest A Potential Alternative To Antibiotic Treatment, Charles Austin Coomer

Mahurin Honors College Capstone Experience/Thesis Projects

In recent years, bioethanol has received worldwide interest as a bioenergy source. This interest has stimulated the production of substantial quantities of ethanol annually. However, the inability to produce bioethanol under sterile conditions plagues the industry, resulting in frequent microbial contamination. Bacterial contamination is one of the more challenging problems facing the bioethanol industry because contaminants drastically lower ethanol yield. Conventional methods of antibiotic application to eradicate bacterial contaminants are expensive and prohibitive. A more sustainable approach to control bacterial contamination of industrial ethanol fermentation systems is to use bacteriophages (phage). The goal of this research was to create a …

The Reaction Of Platinum Triamine Complex With Different Dna And Protein Complexes, Morgan Gruner

Mahurin Honors College Capstone Experience/Thesis Projects

The platinum compound Cl [Chloro[N,N-diethyldiethylenetriamine] Platinum(II) Chloride] was synthesized and reacted with N-acetylmethionine (N-AcMet) and guanosine 5’-monophosphate (5’-GMP). Previous experiments show that N-AcMet reacts kinetically faster with the central platinum atom and that 5’-GMP bonds slower yet stronger. When Cl was reacted with N-AcMet the N-AcMet displaced the chloride ion as expected. When Cl was reacted with 5’-GMP the 5’-GMP binds to the chloride ion and the reaction is finished. Yet, when 5’-GMP was added in the solution already containing N-AcMet, the N-AcMet was not displaced as predicted. Through ­¹­H NMR Spectroscopy and Mass Spectrometry we observed that …

Correlation Of Environmental Risks With The Prevalence Of Essential Hypertension And Chronic Cardiac Disease In Kasigau, Kenya, Addie Dodson

Mahurin Honors College Capstone Experience/Thesis Projects

Cardiovascular disease (CVD) is a chronic non-communicable disease (NCD) that is the leading cause of death across the world. In developing nations, like Kenya, the prevalence of NCDs like CVD are on the rise. Hypertension is the major risk factor for CVD and can be influenced by various environmental risk factors, like physical inactivity, unhealthy diets, tobacco use, and alcohol use. Though these are known factors that can affect blood pressure in developed nations, research over the prevalence of essential hypertension (EH) in developing countries is low. In an area in southeast Kenya known as Kasigau, there is a high …

Examining Human Perception Of Elephants And Large Trees For Insights Into Conservation Of An African Savanna Ecosystem, Adam Edge

Mahurin Honors College Capstone Experience/Thesis Projects

In savanna ecosystems, African elephants (Loxodonta africana) and large trees such as marula (Sclerocarya birreaand) and knobthorn (Acacia nigrescens) have ecological and human value; however, elephants have a large impact on favored trees, motivating the need for ecological conservation strategies. This study examined the perceptions of tourists and residents towards elephants, large trees, and other relevant factors for management purposes. In the Associated Private Nature Reserves, South Africa, a survey was distributed to tourists and residents to determine perceptions of elephants of different age classes, group sizes and sex, and toward savanna habitat impacted …

Allelic Variability In The Cyp11b2 C344t Single Nucleotide Polymorphism From A Cohort Of East Africans, Spencer Wright

Mahurin Honors College Capstone Experience/Thesis Projects

Non-communicable disease (NCD), in particular cardiovascular disease, is a significant problem in developing countries. Essential hypertensions (EH) is a leading risk factor for vascular disease and while managing EH in developing countries is considered a high global priority, few studies exist from third world populations. From a cohort of Kenyans living in the Kasigau region, we have investigated the allele frequency of a single nucleotide polymorphism (SNP) previously reported to correlate with salt-sensitive EH. The SNP being investigated is aldosterone synthase CYP11B2 C344T (rs1799998), a polymorphism in the renin-angiotensin system (RAS). The C344T polymorphism is located in the promoter region …

The Isolation And Characterization Of Tirotheta9, A Novel A4 Mycobacterium Phage, Sarah Schrader

Mahurin Honors College Capstone Experience/Thesis Projects

Bacteriophages are the most abundant biological entities on earth, yet relatively few have been characterized. In this project, a novel bacteriophage was isolated from the environment, characterized, and compared with others in the databases. Mycobacterium smegmatis, a harmless soil bacterium, served as the host and facilitated the enrichment and recovery of mycobacteriophages. A single phage type was purified to homogeneity and named TiroTheta9 (TT9). Electron microscopy revealed that the phage particles have icosahedral heads 58 ± 2 nm in diameter and tails 174 ± 5 nm in length. The TT9 genomic DNA was purified and sequenced using 454 pyrosequencing …

Characterization Of A Mutant Bacteriophage That Overcomes An Antitermination Defect In E. Coli Rna, Kimberly Baugh

Mahurin Honors College Capstone Experience/Thesis Projects

Mutations in the highly conserved zinc-binding domain of the β’ subunit of E.coli RNA polymerase prevent the growth of phage that use a unique RNA-based mechanism of transcription antitermination. Here, we describe the isolation and characterization of a mutant phage that overcomes this block. The genome of the mutant only differs from the parental phage by 2 nucleotides. Close inspection of the sequences surrounding the mutation suggested that a new promoter had been created. This was confirmed by cloning the potential promoter sequences into a promoter probe expression vector. We hypothesize that the new promoter permits the expression of phage …

Use Of Coastal Islands By Seabirds: A Tool To Guide Future Marine Protected Areas In California, Dana A. Page

Master's Projects and Capstones

Seabird breeding colonies on islands off the coast of California offer a unique tool to help guide marine spatial planning. The life histories of seabirds can be used to develop locations of ecological importance along the coast of California. Tracking methodologies and habitat modeling related to seabird habitat utilization can be used to inform management approaches which can aid in the expansion of marine protected areas (MPAs). Protecting ocean habitats will help mitigate impacts of climate change and ensure the ecosystem services provided by marine environments. Areas within the Monterey Bay National Marine Sanctuary were analyzed to locate candidate MPA …

Neural Circuitry Underlying The Central Hypertensive Action Of Nesfatin-1: Melanocortins, Corticotropin-Releasing Hormone, And Oxytocin, Gina L.C. Yosten, Willis K. Samson

Biological Sciences Faculty Research & Creative Works

Nesfatin-1 is produced in the periphery and in the brain where it has been demonstrated to regulate appetite, stress hormone secretion, and cardiovascular function. The anorexigenic action of central nesfatin-1 requires recruitment of neurons producing the melanocortins and centrally projecting oxytocin (OT) and corticotropin-releasing hormone (CRH) neurons. We previously have shown that two components of this pathway, the central melanocortin and oxytocin systems, contribute to the hypertensive action of nesfatin-1 as well. We hypothesized that the cardiovascular effect of nesfatin-1 also was dependent on activation of neurons expressing CRH receptors, and that the order of activation of the melanocortin-CRH-oxytocin circuit …

Projected Future Distributions Of Vectors Of Trypanosoma Cruzi In North America Under Climate Change Scenarios, Miroslava Garza, Teresa Patricia Feria-Arroyo, Edgar A. Casillas, Victor Sanchez-Cordero, Chissa-Louise Rivaldi, Sahotra Sarkar

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

Background

Chagas disease kills approximately 45 thousand people annually and affects 10 million people in Latin America and the southern United States. The parasite that causes the disease, Trypanosoma cruzi, can be transmitted by insects of the family Reduviidae, subfamily Triatominae. Any study that attempts to evaluate risk for Chagas disease must focus on the ecology and biogeography of these vectors. Expected distributional shifts of vector species due to climate change are likely to alter spatial patterns of risk of Chagas disease, presumably through northward expansion of high risk areas in North America.

Methodology/Principal Findings

We forecast the future …

Use Of Cholera Toxin B As A Vaccine Adjuvant Activates Antigen Presenting Cells And Stimulates Production Of Pro-Inflammatory Cytokines, Heather C. Romlein

Seton Hall University Dissertations and Theses (ETDs)

Francisella tularensis is an intracellular pathogen that has been classified as a category “A” bioterrorism agent by the Centers For Disease Control. To date, there is no approved vaccine to provide protection against this pathogen. Previous in vivo studies with mice have shown that a mucosally targeted vaccine preparation of inactivated F. tularensis (iFt) adjuvanted with Cholera toxin “B” (CTB), successfully granted full protection against a less virulent strain (FT LVS) of the bacterium and provided partial protection against a more virulent strain (SchuS4). However, the mechanisms of this protection are not fully understood. In this …

Novel Telomere-Anchored Pcr Approach For Studying Sexual Stage Telomeres In Aspergillus Nidulans, Nengding Wang, Saajidha Rizvydeen, Mithaq Vahedi, Daysi M. Vargas Gonzalez, Amanda L. Allred, Dustin Wayne Perry, Peter M. Mirabito, Karen E. Kirk

Biology Faculty Publications

Telomere length varies between germline and somatic cells of the same organism, leading to the hypothesis that telomeres are lengthened during meiosis. However, little is known about the meiotic telomere length in many organisms. In the filamentous fungus Aspergillus nidulans, the telomere lengths in hyphae and asexual spores are invariant. No study using existing techniques has determined the telomere length of the sexual ascospores due to the relatively low abundance of pure meiotic cells in A. nidulans and the small quantity of DNA present. To address this, we developed a simple and sensitive PCR strategy to measure the telomere length …

Fox Squirrel Response To Bark Calls, Michael Ryan Keller

Undergraduate Honors Thesis Collection

Sciurus niger (fox squirrel) produces a characteristic bark call that has long been assumed to serve as an alarm call. However, to date, no definitive research has been conducted to support these assumptions. Over the course of six months, I executed an audio playback study with free-living fox squirrels in central Indiana. When a squirrel came into view, its behavior was video recorded during a 30 second playing of either an S. niger bark call or a cardinal (Cardinalis cardinals) control call. The subjects were also filmed thirty seconds prior to and immediately following the call. Each squirrel's behavior was …

Investigation Of Fshr-L Protein Function In Regulating Synaptic Transmission At The Neuromuscular Junction In C. Elegans, Julie Christine Kolnik

Undergraduate Honors Thesis Collection

euronal communication (synaptic transmission) is critical for nervous system function. This communication occurs at specialized junctions called synapses where chemical neurotransmitters signal from presynaptic to postsynaptic cells. Additional signaling via neuropeptide activated G protein-coupled receptors (GPCRs) fine-tunes synaptic communication. GPCRs are a large family of transmembrane receptor proteins that bind extracellular neurotransmitters and neuropeptides to activate intracellular signaling pathways. My project investigated the function of FSHR-l, a GPCR and potential neuropeptide receptor, in regulating synaptic transmission at the neuromuscular junction (NMJ) in Caenorhabditis elegans roundworms, which share conservation of nervous system structure and function with humans. Worms lacking the fshr-I …

The Passive Perching Mechanism In Passeriformes Birds, Deena Ahmed Elsahy

Undergraduate Honors Thesis Collection

Passeriformes, or perching birds and songbirds, are an order of birds that includes crows, jays, starlings, wrens, cardinals, finches and many other species. It has been suggested that these birds are able to passively perch due to a tendon locking mechanism. This mechanism allows them to rest for hours in trees without falling. When the bird's foot is placed on a perch, the weight of the bird causes the tendons to pull, thus closing the toes around the perch. However, there is currently much debate about whether the mechanism is entirely passive. Recent studies argue that the mechanism must be …

Quantification Of Salicylic Acid And Analysis Of Defense-Related Genes In The Moss Physcomitrella Patens, Ryan Jospeh Eller

Undergraduate Honors Thesis Collection

The moss Physcomitrella patens is an invaluable non-vascular plant specimen to study genetic interactions because its entire genome is sequenced. Therefore, any gene studies conducted in more evolved vascular plants can be transferred to this specimen fairly easily by utilizing comparative genomic techniques made possible through the National Center for Biotechnology Information (NCBI). The questions that were asked in this thesis revolved around the Systemic Acquired Resistance, or the basic mechanism that allows plants to protect themselves against biotic and abiotic stressors. Two main approaches were used to analyze this complex system. First, an analytical chemistry technique was used to …

The Effects Of Jasmonic Acid And Chemicals In The Ja Pathway On The Defense Systems And Gene Expression In Moss, Physcomitrella Patens And Amblystegium Serpens, Allison Shanks

Undergraduate Honors Thesis Collection

Systemic acquired resistance (SAR) is a defense system used by plants that results in increased resistance to future pathogen infection following an initial pathogen exposure. SAR in vascular plants has been well documented; however, a similar defense system has only recently been documented in non-vascular plants. It is believed that chemicals in the jasmonic acid (JA) pathway are able to activate the SAR response in vascular plants. The non-vascular plant, Amb/ystegium serpens, will be used as a model to test if SAR is triggered by JA and two other molecules in the JA pathway, 12-oxo-phytodieonic acid, and methyl jasmonate. To …

Genome Sequence And Phenotypic Characterization Of Caulobacter Segnis, Sagar Patel

Senior Theses

Caulobacter segnis is a unique species of Caulobacter in that it is slow growing, found in soil samples, and has other phenotypic differences from the freshwater Caulobacter that it is most closely related to. Initially deemed Mycoplana segnis, it was reclassified after a 16s rRNA analysis and found to be most closely related to the Caulobacter NA1000 branch. Because the annotated sequence available in GenBank contained a large number of pseudogenes (126), we compared the original sequencing data to the GenBank sequence and determined that many of the pseudogenes were due to sequence errors in the Genbank sequence. Consequently, …

A Thermal Window For Yawning In Humans: Yawning As A Brain Cooling Mechanism, Jorg J. M. Massen, Kim Dusch, Omar T. Eldakar, Andrew C. Gallup

Biology Faculty Articles

The thermoregulatory theory of yawning posits that yawns function to cool the brain in part due to counter-current heat exchange with the deep inhalation of ambient air. Consequently, yawning should be constrained to an optimal thermal zone or range of temperature, i.e., a thermal window, in which we should expect a lower frequency at extreme temperatures. Previous research shows that yawn frequency diminishes as ambient temperatures rise and approach body temperature, but a lower bound to the thermal window has not been demonstrated. To test this, a total of 120 pedestrians were sampled for susceptibly to self-reported yawn contagion during …

The Role Of Lipocalin 2 In Early Stage Colon Cancer Metastasis To The Liver, Fides Elamparo

Senior Theses

Metastasis, frequently from the colon to the liver, is the major cause of death with colorectal cancer, reducing the five-year survival to less than 6%. Metastasis occurs due to productive collaborations between tumor cells and host-derived cells in the tumor microenvironment, where a pre-metastatic niche is created to prime for cancer cell invasion into the target organ. In a highly metastatic colorectal cancer cell line implanted into the cecum of Balb/c mice, microarray analysis showed lipocalin 2 (Lcn2) is one of the most highly expressed proteins in the liver of tumor-bearing mice prior to metastasis.

When RT-PCR was performed, greater …

Determining A Correlation Between Individual Differences In Eye Movements And Working Memory, Mackenzie Sunday

Senior Theses

This study determined if a relationship exists between individual differences in eye movements and working memory measures. The eye movement system can provide insight into processes that occur in the mind as well as a better understanding of the relationship between quantifiable aspects of eye movements and the more abstract inner workings of the mind. Recently, consistent and reliable individual differences have been found in individuals’ eye movement behaviors. For example, individuals with longer fixation durations for one visual task have longer fixations across all other visual tasks. The eye movements of participants were collected during four different viewing tasks …

Exploration Of Genomic Determinants For Host Range In Phages Of Pathogenic And Non-Pathogenic Mycobacteria, Anisa Christine Tracy

Masters Theses, 2010-2019

The genus Mycobacterium is diverse, ranging from slow-growing human pathogens such as M. tuberculosis to fast-growing saprophytes such as M. smegmatis. M. ulcerans is the causative agent of the neglected disease known as Buruli ulcer, an emerging pathogen first described in Buruli County, Uganda. Antibiotic resistance among Mycobacterial pathogens is growing at an alarming rate and is creating an urgent need for novel diagnostic and therapeutic approaches. Elucidating the details of virus/host interactions among the mycobacteria and their phages thus has the potential to affect how we think about the role of these bacteria in both clinical and environmental settings. …

Effects Of Fine Sediment On Juvenile Brook Trout Habitat Use And Social Interactions, Kyle Snow

Masters Theses, 2010-2019

Streambed sedimentation is a persistent cause of impairment to the ecological condition of streams. The objectives of this study were to investigate 1) the effects of sedimentation and temperature on the use of streambed cover as a velocity refuge by juvenile brook trout in simulated winter flood conditions and 2) the effects of sedimentation, temperature, and time of day on cover use and social interactions of brook trout cohorts in low flow summer water conditions. Using artificial stream channels, experiments were conducted with wild juvenile brook trout collected from the North Fork Tye River, Nelson County, VA. Brook trout did …