Biology Commons^™

The Intervening Sequence Of Coxiella Burnetii: Characterization And Evolution, Indu Warrier, Mathias C. Walter, Dimitrios Frangoulidis, Rahul Raghavan, Linda D. Hicks, Michael F. Minnick

Biology Faculty Publications and Presentations

The intervening sequence (IVS) of Coxiella burnetii, the agent of Q fever, is a 428-nt selfish genetic element located in helix 45 of the precursor 23S rRNA. The IVS element, in turn, contains an ORF that encodes a hypothetical ribosomal S23 protein (S23p). Although S23p can be synthesized in vitro in the presence of an engineered E. coli promoter and ribosome binding site, results suggest that the protein is not synthesized in vivo. In spite of a high degree of IVS conservation among different strains of C. burnetii, the region immediately upstream of the S23p start codon …

Incomplete Denitrification In Thermus Species, Chrisabelle Mefferd

UNLV Theses, Dissertations, Professional Papers, and Capstones

Members the bacterial genus Thermus have been shown to be incomplete denitrifiers, terminating with nitrite or nitrous oxide (N2O). However, the ability to carry out denitrification and the evolution of nitrogen oxide reductase genes in Thermus remains poorly understood. This study tests the hypothesis that incomplete denitrification is common in Thermus and seeks to uncover patterns in the evolution of denitrification pathways in Thermus. Denitrification capacity was determined in a collection of 25 strains representing ten species of Thermus and phylogenetic analysis was performed to determine whether denitrification genes evolved horizontally in Thermus. No strains in this study reduced nitrate …

Tlr3 Signaling In Human Bdca-3 Dendritic Cells Results In The Formation Of Several Ilt3 And Ilt4 Populations, Nicholas J. Colletti

Seton Hall University Dissertations and Theses (ETDs)

Dendritic cells (DCs) represent a population of innate immune cells that are highly efficient at promoting immune responses. DCs are capable of presenting antigens to both CD4 and CD8 T cells. DC presentation and interaction with T cells can result in either immune stimulation or tolerance. This study intends to phenotype a rare subset of DCs found in the human blood and is distinguishable by the expression of various surface markers including: lineage markers (Lin), HLADR, CD1c, and CD141 or BDCA-3. Stimulating BDCA-3 DCs with Poly I:C, a toll-like receptor (TLR) 3 agonist, resulted in the up-regulation of various canonical …

The Role Of Mfd In Stationary-Phase Oxidative Damage Repair In Bacillus Subtilis, Katelyn E. Porter

UNLV Theses, Dissertations, Professional Papers, and Capstones

Since the 1950’s it has been shown that bacterial cells accumulate mutations even in non- dividing conditions, but how this type of mutation occurs is still highly debated. In Bacillus subtilis, Mfd, a precursor of the nucleotide excision repair (NER) system, mediates the formation of mutations in stationary-phase or non-replicating cells. In growing cells, Mfd recruits repair when RNA polymerase is stalled during transcription; it then recruits proteins from NER to repair damage. Here, we examine the hypothesis that Mfd mediates the formation of mutations by interacting with cellular components that repair reactive oxygen species (ROS), a natural byproduct of …

The Effect Of Manganese (Mn) On Cell Proliferation And Migration In The Michigan Cancer Foundation-7 (Mcf-7) Human Breast Cancer Cell Line In Vitro, Justin Lloyd Wendel

Theses and Dissertations

Manganese (Mn) is a common environmental element necessary for mammalian physiological processes. However, dietary excess or deficiency can lead to detrimental health effects. Therefore, I investigated the effect Mn has on breast cancer progression in vitro. Utilizing MCF-7 breast cancer cells an MTT assay was performed to identify proliferative potential. After 5 days, results showed 100 nM manganese chloride (MnCl2) had a significant (p<0.01) increase in cell number over control. Using a scratch wound-healing assay, 100 nM MnCl2 was found to increase cellular motility as well as induce a possible change in morphology and cytoskeletal organization. Given Mn was shown to localize in the mitochondrial, we investigated Mn-induced ROS expression. 500 nM Mn significantly decreased (p<0.05) ROS levels. Collectively, I provide evidence that Mn may potentially drive less aggressive cancer cells towards a more invasive phenotype.

Manganese-Reducing Bacterial Communities From A Hypersaline Estuary In South Texas Under Conditions Of Changing Salinity, Omar R. Elizondo, Rebecca Vasquez Villarreal, Sonia Y. Del Rio, Kristine L. Lowe

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

Manganese reducing bacteria were quantified and enriched from sediments at two sites (ABC and LMT050) in the Laguna Madre of South Texas. Bacteria were tested for Mn(IV) reduction under different salinities. Denaturing gradient gel electrophoresis (DGGE) was used to profile bacterial communities from Mn(IV) saline enrichments. Results showed that the density of manganese reducing bacteria at ABC was 30X greater than LMT050. The ABC bacteria were able to reduce Mn(IV) at similar rates at different salinities; however, at LMT050, Mn(IV) reduction rates decreased at higher salinities. Three population genotypes were observed by DGGE. All were present and similarly abundant in …

Experimental Assessment Of Floating Seagrass Wrack As Potential Habitat For Benthic Organisms, Joseph R. Mcginnis

Theses, Dissertations and Culminating Projects

During the summer, seagrass blades are frequently released into the water column as a method to reduce respiration demands of the plant and through physical disruption of the bed (e.g., crab foraging, boat propellers). This wrack has the potential to serve as both food and habitat for organisms dislodged or actively moving within the system. The purpose of this research was to determine how benthic organisms may use floating wrack as a food resource and shelter. Three experimental floating wrack bag treatments were assembled containing using artificial Zoster a marina (i.e., poly-ribbon), Z. marina blades, and a wrack bag control …

Coevolution Of Cyanogenic Bamboos And Bamboo Lemurs On Madagascar, Daniel J. Ballhorn, Fanny Patrika Rakotoarivelo, Stefanie Kautz

Biology Faculty Publications and Presentations

Feeding strategies of specialist herbivores often originate from the coevolutionary arms race of plant defenses and counter-adaptations of herbivores. The interaction between bamboo lemurs and cyanogenic bamboos on Madagascar represents a unique system to study diffuse coevolutionary processes between mammalian herbivores and plant defenses. Bamboo lemurs have different degrees of dietary specialization while bamboos show different levels of chemical defense. In this study, we found variation in cyanogenic potential (HCNp) and nutritive characteristics among five sympatric bamboo species in the Ranomafana area, southeastern Madagascar. The HCNp ranged from 209±72 μmol cyanide* g^-1 dwt in Cathariostachys madagascariensis to no cyanide …

Naturally Occurring Mellein-Type 3,4-Dihydroisocoumarins And Related Lactones: Synthetic Approaches - A Review, Stephen Jm Mdachi

Tanzania Journal of Science

Mellein and its derivatives are the most common 3,4-dihydroisocoumarins and are known to exhibit an array of biological activities such as antibacterial, antifungal, antimalarial, antiallergic, antitumor, anti-inflammatory, antiulcer, pheromonal, plant growth-promoting and antileukemic activities. Other mellein derivatives are recognized phytotoxins, neurotoxins, hepatotoxins, nephrotoxins and teratogens. Consequently, considerable efforts have been directed at studying these natural products. While most of the reported studies have focused on the isolation, characterization and bioassay studies of melleins, a number of synthetic studies have also been reported. This paper focuses on synthetic approaches towards these biologically active and, thus, potentially useful natural products. The aim …

Identification Of Tanzanian Saprophytic Edible Mushrooms By Amplification And Sequencing Of Its/Lsu Regions Of Ribosomal Rna Operon, Ibrahim Juma, Anthony Manoni Mshandete, Donatha Damiani Tibuhwa, Amelia Kajumulo Kivaisi

Tanzania Journal of Science

In this study, ten wild saprophytic edible mushrooms samples, collected from Tanzania natural forests and planted trees, and their two domesticated forms were characterized by in-vitro/in-vivo amplification and sequencing of ITS/LSU regions. Mushroom genomic DNA was extracted by ZR Fungal/Bacterial DNA MniPrep Kit. ITS and LSU regions were amplified using ITS-4/ITS-5 and LR16/LROR primers, respectively and sequenced. The amplicons with messy sequences were cloned. For analyzing recombinant E. coli DH5α cells, colony PCR and sequencing were done using M13-F/M13-R primers. The studied mushrooms were identified as Amylosporus sp. IJ-2014, Polyporales sp., Polyporus tenuiculus, Pleurotus cystidiosus, Laetiporus sp. IJ-2014, Lentinus sajor-caju, …

Spread Of Tylodelphys Mashonense (Digenea: Diplostomidae) By Grey Heron Ardea Cinerea And Great White Egret A. Alba In Lake Victoria, Tanzania, Fred D. Chibwana, Gamba Nkwengulila

Tanzania Journal of Science

Despite the fact that Tylodelphys mashonense, parasites of the cranial cavity of the catfish Clarias gariepinus, are ubiquitous in freshwater systems, little is known on their spread. As such, we examined a total of 152 piscivorous birds, belonging to 6 species; 43 great cormorant Phalacrocorax carbo, 33 grey heron Ardea cinerea, 26 hamerkop Scopus umbretta, 22 great white egret Ardea alba, 15 marabou stork Leptoptilos crumeniferus and 13 pied kingfisher Ceryle rudis foraging in the Lake Victoria. Out of the six bird species only A. cinerea and A. alba were found infected by T. mashonense with prevalence of 42.4% and …

Variation Of Small Mammal Populations Across Different Habitat Types In The Serengeti Ecosystem, Flora J Magige

Tanzania Journal of Science

This study investigated the abundance and diversity of small mammals in cultivated land (unprotected area) and wooded grassland in the Serengeti National Park (protected area) in the Serengeti ecosystem. Small mammal populations were sampled through capture-mark-recapture trapping techniques in March-April 2010. A total of 896 trap nights covering wet season, 9 species of rodents and 1 species of soricomorphs (shrew family) were captured. Overall, Multimammate rat Mastomys natalensis (Smith) was by far the most abundant rodent in cultivated land (28%) while inside the park, shrew Crocidura sp., was high in numbers (8%). A significantly higher abundance (trap success) of small …

Ligninolytic Enzymes Of The Fungus Isolated From Soil Contaminated With Cow Dung, Rose J. Masalu

Tanzania Journal of Science

Lignin is the complex polymer and very few microorganisms are able to degrade it. The study aimed at isolating lignin degrading fungi from soil contaminated with cow dung using ligninolytic screening media. The study was able to isolate one ligninolytic fungus by using lignin media. The strain was screened for  production of ligninolytic enzymes  using Rhemazol Brilliant blue R (RBBR) dye, 2,2-azino-bis (3- ethylbenzthiazoline)-6-sulfonate (ABTS) and guaiacol in a semi-solid medium. The isolate decolourized RBBR dye, ABTS and guaiacol in a semi solid media. The strain was further tested for lignin peroxidase (LiP), manganese peroxidase (MnP) and laccase (Lac) enzymatic …

Functional Diversity Of Small And Large Trees Along Secondary Succession In A Tropical Dry Forest, Lucía Sanaphre-Villanueva, Juan Manuel Dupuy, José Luis Andrade, Casandra Reyes-García, Horacio Paz, Paula C. Jackson

Faculty Articles

Functional Diversity is considered an important driver of community assembly in environmental and successional gradients. To understand tree assembly processes in a semideciduous tropical forest, we analyzed the variation of Functional Richness (FRic), Functional Divergence (FDiv), and Functional Evenness (FEve) of small vs. large trees in relation to fallow age after slash-and-burn agriculture and topographical position (flat sites vs. hills). FRic of small trees was lower than null model predicted values across the successional gradient, and decreased unexpectedly in older successional ages. FRic of large trees was higher than null model predictions early in succession and lower in late-successional stands …

Thirty Years Of Compositional Change In An Old-Growth Temperate Forest: The Role Of Topographic Gradients In Oak-Maple Dynamics, Julia I. Chapman, Ryan W. Mcewan

Biology Faculty Publications

Ecological communities are structured in response to spatial and temporal variation of numerous factors, including edaphic conditions, biotic interactions, climatic patterns and disturbance regimes. Widespread anthropogenic factors such as timber harvesting can create long-lasting impacts, obscuring the relationship between community structure and environmental conditions. Minimally impacted systems such as old-growth forests can serve as a useful ecological baseline for predicting long-term compositional shifts. We utilized decadal tree species sampling data (1979–2010) divided into three strata (understory, midstory, overstory) to examine temporal changes in relative abundances and spatial distributions of dominant taxa, as well as overall shifts in community composition, in …

Odorant Receptors Can Mediate Axonal Identity And Gene Choice Via Campindependent Mechanisms, Kiavash Movahedi, Xavier Grosmaitre, Paul Feinstein

Publications and Research

Odorant receptors (ORs) control several aspects of cell fate in olfactory sensory neurons (OSNs), including singular gene choice and axonal identity. The mechanisms of OR-induced axon guidance have been suggested to principally rely on G-protein signalling. Here, we report that for a subset of OSNs, deleting G proteins or altering their levels of signalling does not affect axonal identity. Signalling-deficient ORs or surrogate receptors that are unable to couple to Gs/Golf still provide axons with distinct identities and the anterior–posterior targeting of axons does not correlate with the levels of cAMP produced by genetic modifications. In addition, we refine the …

The Effects Of Δ9-Tetrahydrocannabinol (Thc) On Development And Hyperekplexia In Embryonic Zebrafish Model, Olivia Christine Mistretta

Master of Science in Integrative Biology Theses

Marijuana is one of the most commonly used illicit drugs around the world. It has gained attention as an alternative medicine to many different disorders. Though initially investigated in modern medicine for its analgesic and antiemetic properties, cannabis has been recently found to benefit numerous neurological disorders. Though there are over 100 different cannabinoids produced by the cannabis plant, Δ⁹ – tetrahydrocannabinol (THC) has been shown to the most efficacious phytocannabinoid in neurological disorders. THC has been shown in numerous previous studies to be effective at treating spasticity caused by multiple sclerosis and spinal cord injury, as well as …

Chemical Similarity And Local Community Assembly In The Species Rich Tropical Genus Piper, Robert Marquis, Diego Salazar, M. Jaramillo

Biology Department Faculty Works

Community ecologists have strived to find mechanisms that mediate the assembly of natural communities. Recent evidence suggests that natural enemies could play an important role in the assembly of hyper‐diverse tropical plant systems. Classic ecological theory predicts that in order for coexistence to occur, species differences must be maximized across biologically important niche dimensions. For plant–herbivore interactions, it has been recently suggested that, within a particular community, plant species that maximize the difference in chemical defense profiles compared to neighboring taxa will have a relative competitive advantage. Here we tested the hypothesis that plant chemical diversity can affect local community …

Mousensor: A Versatile Genetic Platform To Create Super Sniffer Mice For Studying Human Odor Coding, Charlotte D'Hulst, Raena B. Mina, Zachary Gershon, Sophie Jamet, Antonio Cerullo, Delia Tomoiaga, Li Bai, Leonardo Belluscio, Matthew E. Rogers, Yevgeniy Sirotin, Paul Feinstein

Publications and Research

Typically, 0.1% of the total number of olfactory sensory neurons (OSNs) in the main olfactory epithelium express the same odorant receptor (OR) in a singular fashion and their axons coalesce into homotypic glomeruli in the olfactory bulb. Here, we have dramatically increased the total number of OSNs expressing specific cloned OR coding sequences by multimerizing a 21-bp sequence encompassing the predicted homeodomain binding site sequence, TAATGA, known to be essential in OR gene choice. Singular gene choice is maintained in these ‘‘MouSensors.’’ In vivo synaptopHluorin imaging of odor-induced responses by known M71 ligands shows functional glomerular activation in an M71 …

Opn-A Induces Muscle Inflammation By Increasing Recruitment And Activation Of Pro-Inflammatory Macrophages., Gina M Many, Yasuyuki Yokosaki, Kitipong Uaesoontrachoon, Peter P Nghiem, Luca Bello, Sherry Dadgar, Ying Yin, Jesse M Damsker, Heather B Cohen, Joe N Kornegay, Marcas M Bamman, David M Mosser, Kanneboyina Nagaraju, Eric P Hoffman

Genomics and Precision Medicine Faculty Publications

New Findings

• What is the central question of this study? What is the functional relevance of OPN isoform expression in muscle pathology?
• What is the main finding and its importance? The full‐length human OPN‐a isoform is the most pro‐inflammatory isoform in the muscle microenvironment, acting on macrophages and myoblasts in an RGD‐integrin‐dependent manner. OPN‐a upregulates expression of tenascin‐C (TNC), a known Toll‐like receptor 4 (TLR4) agonist. Blocking TLR4 signalling inhibits the pro‐inflammatory effects of OPN‐a, suggesting that a potential mechanism of OPN action is by promoting TNC–TLR4 signalling.

Although osteopontin (OPN) is an important mediator of muscle remodelling in health …

Breast Cancer Cell Proliferation Upon Exposure To Endocrine Disrupting Chemicals, Annie Kopera

Biology Summer Fellows

Endocrine Disrupting Chemicals (EDCs) can cause adverse health effects by tampering with the body’s endocrine system, which controls growth, development, and overall homeostasis. Bisphenols are a group of chemicals that are structurally similar; some are known endocrine disrupters. Bisphenol A (BPA) is a common chemical found in thermoplastics and epoxy resins, and can be found in products such as hard-plastic water bottles, the inside lining of food cans, medical equipment, dental sealants, and thermal receipt paper. The release of studies detailing the estrogenic activity of BPA prompted both scientists and consumers to campaign for a BPA-free movement. Producers looking for …

Mutation Selection On The Metabolic Pathway And The Effects On Protein Co-Evolution And The Rate Limiting Steps On The Tree Of Life, Katherine S. Porter

Mathematics Summer Fellows

Metabolic pathways are made of a series of reactions by enzymes at different speeds. These pathways include the rate limiting step, which is the slowest step that determines the rate of the overall reaction. To date, one study has examined the pathway of glycolysis and found no evidence of evolutionary stability of its rate limiting step. In addition, phylogenetic evidence has shown evolution in the pathway over time including gene duplication and positive selection within the pathway. This evidence suggests that there is coevolutionary selection on glycolysis. The evidence from this previous study is simulation-based. The Michaelis-Menten kinetics that describe …

Ciliate Codon Translator Program Manual, Quentin D. Altemose

Mathematics Summer Fellows

Understanding the evolutionary history of organisms allows us to better comprehend selective pressures and their effects on larger populations. In our study, we focused on analyzing the DNA of ciliate groups, which are single celled protozoans characterized by the presence of cilia on their outer membrane. We utilized the DNA of the organisms to analyze the changes in population genotype over time. We tested existing evolutionary models (designed to represent natural genetic variation over time in populations) against our data to identify the model with the best fit and likelihood. From the DNA and the evolutionary model with the highest …

Effects Of Shoreline Dynamics On Saltmarsh Vegetation, Shailesh Sharma, Joshua Goff, Ryan M. Moody, Ashley Mcdonald, Dorothy Byron, Kenneth L. Heck Jr., Sean Powers, Carl Ferraro, Just Cebrian

University Faculty and Staff Publications

We evaluated the impact of shoreline dynamics on fringing vegetation density at mid- and low-marsh elevations at a high-energy site in the northern Gulf of Mexico. Particularly, we selected eight unprotected shoreline stretches (75 m each) at a historically eroding site and measured their inter-annual lateral movement rate using the DSAS method for three consecutive years. We observed high inter-annual variability of shoreline movement within the selected stretches. Specifically, shorelines retrograded (eroded) in year 1 and year 3, whereas, in year 2, shorelines advanced seaward. Despite shoreline advancement in year 2, an overall net erosion was recorded during the survey …

The Effects Of Estrogen (E2), Bisphenol A (Bpa), Bisphenol S (Bps), And Bisphenol F (Bpf) On The Proliferation Of Mcf-7 Cells, Colleen Leahy

Biology Summer Fellows

Endocrine disrupting compounds (EDCs) are chemicals that disturb the endocrine system and exhibit adverse effects throughout the body. EDCs exert their effects by displaying hormone-like activity and can act as agonists or antagonists to normal hormonal function. Those EDCs that disturb the activity of estrogen are of particular interest. Estrogen, also known as 17β-estradiol, is a steroid hormone responsible for the development of the female sexual organs, secondary sexual characteristics, bone development and maintenance, and cardiovascular development. It has also been shown to play a role in the growth of certain breast cancers. Endocrine disrupting compounds that are structurally similar …

Model-Based Clustering With Certainty Estimation: Implication For Clade Assignment Of Influenza Viruses, Shunpu Zhang, Zhong Li, Kevin Beland, Guoquing Lu

Biology Faculty Publications

Background

Clustering is a common technique used by molecular biologists to group homologous sequences and study evolution. There remain issues such as how to cluster molecular sequences accurately and in particular how to evaluate the certainty of clustering results.

Results

We presented a model-based clustering method to analyze molecular sequences, described a subset bootstrap scheme to evaluate a certainty of the clusters, and showed an intuitive way using 3D visualization to examine clusters. We applied the above approach to analyze influenza viral hemagglutinin (HA) sequences. Nine clusters were estimated for high pathogenic H5N1 avian influenza, which agree with previous findings. …

System-Aware Smart Network Management For Nano-Enriched Water Quality Monitoring, Bassem Mokhtar, Mohamed Azab, Nader Shehata, Mohamed Rizk

Biology Faculty Publications

This paper presents a comprehensive water quality monitoring system that employs a smart network management, nano-enriched sensing framework, and intelligent and efficient data analysis and forwarding protocols for smart and system-aware decision making. The presented system comprises two main subsystems, a data sensing and forwarding subsystem (DSFS), and Operation Management Subsystem (OMS). The OMS operates based on real-time learned patterns and rules of system operations projected from the DSFS to manage the entire network of sensors. The main tasks of OMS are to enable real-time data visualization, managed system control, and secure system operation. The DSFS employs a Hybrid Intelligence …

Implicit Mental Processes Are An Improbable Basis For Personhood, Michael L. Woodruff

Animal Sentience

Rowlands argues that animals have implicit pre-reflective awareness and that this is adequate to create the unity of conscious thought required for personhood. For him pre-reflective awareness does not include intentionality and is probably an unconscious process. I suggest that his sense of implicit leads to significant difficulties for his argument and that including intentionality in the definition of a first-person perspective provides a stronger base for viewing animals as persons.

Dichotomous Key To Pea Aphid (Acyrthosiphon Pisum) Apterous Parthenogenic Instars, Bates College Department Of Biology, Daisy Diamond, Daniel Levitis

SCARAB Data Repository

We provide a dichotomous key, with photographs and illustrations, for distinguishing between instars of the pea aphid (Acyrthosiphon pisum) in the developmental pathway leading to the apterous parthenogenetic adult. Lengths of body, antenna and cauda are provided for a sample of each instar.

Comparisons Of The Socio-Behavioral Differences Between Chimpanzees (Pan Troglodytes) And Bonobos (Pan Paniscus), Investigating The Impact Of A Naturally Occurring Polymorphic Microsatellite Deletion In The 5’ Flanking Region Of Arginine Vasopressin Receptor 1a (Avpr1a) On Gene Expression And Sociality Within The Pan Genus, Robert E. Evans

Master of Science in Integrative Biology Theses

Among the great apes, chimpanzees are unique in having a polymorphic deletion of a ~350bp microsatellite containing region (DupB) in the 5’ flanking region of the arginine vasopressin receptor 1a (AVPR1a) gene. This results in three genotypes (DupB+/+, DupB+/- and DupB-/-) of AVPR1a in chimpanzees. Variations in the length of microsatellites 5’ of AVPR1a have been associated with social behaviors (pair-bonding, paternal care, degree of social interest) and differential levels of expression of AVPR1a in the brains of voles. The polymorphic DupB microsatellite in chimpanzees allows the investigation of microsatellite variation 5’ of AVPR1a in higher order primates. We hypothesized …