Biology Commons^™

Comparative Analysis Of Hepatic And Pulmonary Immune Mediators During Postnatal Development, Michelle Mack

Seton Hall University Dissertations and Theses (ETDs)

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Multilocus And Parametric Analyses Of The Evolutionary History Of The Amazonian Peacock Cichlids, The Genus Cichla (Teleostei: Cichlidae), Stuart Clayton Willis

School of Biological Sciences: Dissertations, Theses, and Student Research

Accurate knowledge of species boundaries and species phylogeny are fundamental to testing hypotheses of recent evolutionary processes, but the estimation of these partitions is challenging due both to inherent confusion about what is being estimated as well as the data available to estimate them. Using multilocus data from mtDNA, microsatellites, and nuclear locus sequences of over 1100 individuals, we delimited eight separately evolving species of Cichla rather than the 15 described. Among species we found evidence of rare but widespread introgressive hybridization, while within these species we observed evidence of long-term gene exchange and constrained evolutionary trajectories. In most cases …

Color Polymorphism Of Sand Crabs, Lepidopa Benedicti (Decapoda: Anomura: Albuneidae), Unnam Nasir, Zen Faulkes

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

Sand crabs (Lepidopa benedicti) are highly specialized digging animals that spend the vast majority of their adult life submerged in fine sand. The carapace color of L. benedicti varies from gray to white. Given that the environment in which they live is uniform and dark, most of the functional scenarios to explain color variation seem unlikely to apply. Carapace color has a bimodal distribution, indicating that it is better characterized as a polymorphism than simply as normal variation. Gray crabs are larger and more common than white ones. Crabs mostly swim ventral-side up, which suggests that countershading does …

Protection Against Divergent Influenza H1n1 Virus By A Centralized Influenza Hemagglutinin, Eric A. Weaver, Adam M. Rubrum, Richard J. Webby, Michael A. Barry

School of Biological Sciences: Faculty Publications

Influenza poses a persistent worldwide threat to the human population. As evidenced by the 2009 H1N1 pandemic, current vaccine technologies are unable to respond rapidly to this constantly diverging pathogen. We tested the utility of adenovirus (Ad) vaccines expressing centralized consensus influenza antigens. Ad vaccines were produced within 2 months and protected against influenza in mice within 3 days of vaccination. Ad vaccines were able to protect at doses as low as 107 virus particles/kg indicating that approximately 1,000 human doses could be rapidly generated from standard Ad preparations. To generate broadly cross-reactive immune responses, centralized consensus antigens were constructed …

Increased Population Sampling Confirms Low Genetic Divergence Among Pteropus (Chiroptera: Pteropodidae) Fruit Bats Of Madagascar And Other Western Indian Ocean Islands, Lauren M. Chan, Steven M. Goodman, Michael D. Nowak, David W. Weisrock, Anne D. Yoder

Biology Faculty Publications

Fruit bats of the genus Pteropus occur throughout the Austral-Asian region west to islands off the eastern coast of Africa. Recent phylogenetic analyses of Pteropus from the western Indian Ocean found low sequence divergence and poor phylogenetic resolution among several morphologically defined species. We reexamine the phylogenetic relationships of these taxa by using multiple individuals per species. In addition, we estimate population genetic structure in two well-sampled taxa occurring on Madagascar and the Comoro Islands (P. rufus and P. seychellensis comorensis). Despite finding a similar pattern of low sequence divergence among species, increased sampling provides insight into the phylogeographic history …

Characterization Of Promoter Specific Effects Displayed By Beta-Catenin And Fkbp52 In The Regulation Of Ar, Karen Olivares^, Marc B. Cox*, Cheryl Storer

COURI Symposium Abstracts, Spring 2011

One of the most interesting topics in steroid hormone research is examining the influence of regulators of the steroid hormone signaling pathways. By identifying and understanding the relationship between these regulators on events of transcriptional regulation, receptor localization, and degradation events, we can target these regulators to enhance or decrease their influence on the steroid hormone receptors’ activities within the cell. Increased transcription by the Androgen Receptor has been implicated in several prostate cancer studies. Two proteins in particular, FKBP52 and β-Catenin, are of interest to our group, to examine for potential interaction in signaling cascades promoting prostate cancer.  β-Catenin’s …

Automated Upscaling Of River Networks For Macroscale Hydrological Modeling, Huan Wu, John S. Kimball, Nate Mantua, Jack Arthur Stanford

Biological Sciences Faculty Publications

We developed a hierarchical dominant river tracing (DRT) algorithm for automated extraction and spatial upscaling of basin flow directions and river networks using fine-scale hydrography inputs (e. g., flow direction, river networks, and flow accumulation). In contrast with previous upscaling methods, the DRT algorithm utilizes information on global and local drainage patterns from baseline fine-scale hydrography to determine upscaled flow directions and other critical variables including upscaled basin area, basin shape, and river lengths. The DRT algorithm preserves the original baseline hierarchical drainage structure by tracing each entire flow path from headwater to river mouth at fine scale while prioritizing …

Nuclear Scaffold Attachment Sites Within Encode Regions Associate With Actively Transcribed Genes, Christopher M. Taylor, Mignon A. Keaton, Ryan M. Layer, Anindya Dutta

Computer Science Faculty Publications

The human genome must be packaged and organized in a functional manner
for the regulation of DNA replication and transcription. The nuclear
scaffold/matrix, consisting of structural and functional nuclear
proteins, remains after extraction of nuclei and anchors loops of DNA.
In the search for cis-elements functioning as chromatin domain
boundaries, we identified 453 nuclear scaffold attachment sites
purified by lithium-3,5-iodosalicylate extraction of HeLa nuclei across
30 Mb of the human genome studied by the ENCODE pilot project. The
scaffold attachment sites mapped predominately near expressed genes and
localized near transcription start sites and the ends of genes but not
to …

Reduced Activity Of Multiple Endocrine Disrupting Compounds: 17Β-Estradiol And Bisphenol A With A Chemi-Luminescent Assay, Anna C. Ortiz^, Roberto J. De La Torre-Roche, Marc B. Cox, Wen-Yee Lee*

COURI Symposium Abstracts, Spring 2011

The concern about the impacts of endocrine disrupting compounds (EDCs) in the environment has increased recently with their high occurrence in surface waters and sex changes in various aquatic organisms. EDCs include ubiquitously used pharmaceuticals and personal care products, such as soap, detergents, contraceptives, and other medicines, which are released constantly into the environment, in waste water treatment plant effluent. Though toxicological effects of these individual, EDCs have been studied, knowledge on how these chemicals interact together in the environment is very limited. The objective of this project is to study the multi-residue effect of EDCs using a chemi-luminescent yeast …

Across Bacterial Phyla, Distantly-Related Genomes With Similar Genomic Gc Content Have Similar Patterns Of Amino Acid Usage, John Lightfield, Noah R. Fram, Bert Ely

Faculty Publications

The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both Gram negative and Gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria. We found that similar patterns of codon usage and protein amino acid content have evolved independently in all eight groups of bacteria. …

Comprehensive Identification Of Protein Substrates Of The Dot/Icm Type Iv Transporter Of Legionella Pneumophila., Wenhan Zhu, Simran Banga, Yunhao Tan, Cheng Zheng, Robert E. Stephenson, Jonathan Gately, Zhao-Qing Luo

Department of Biological Sciences Faculty Publications

A large number of proteins transferred by the Legionella pneumophila Dot/Icm system have been identified by various strategies. With no exceptions, these strategies are based on one or more characteristics associated with the tested proteins. Given the high level of diversity exhibited by the identified proteins, it is possible that some substrates have been missed in these screenings. In this study, we took a systematic method to survey the L. pneumophilagenome by testing hypothetical orfs larger than 300 base pairs for Dot/Icm-dependent translocation. 798 of the 832 analyzed orfs were successfully fused to the carboxyl end of β-lactamase. The …

Traversing Swanton Road, 4th Ed., James A. West

Academic, Government & Associated Organizational Research Resources

Situated at the northwest end of Santa Cruz County and occupying circa 30 square miles of sharply contrasted terrain, the Scott Creek Watershed concentrates within its geomorphological boundaries, at least 10-12% of California's flora, both native and introduced. Paradoxically, the use/abuse that the watershed has sustained over the past 140+ years, has not necessarily diminished the biodiversity and perhaps parallels the naturally disruptive but biologically energizing processes (fire, flooding, landslides and erosion), which have also been historically documented for the area for +60 years. This is an early edition of an extensive document by James A. West. Please visit the …

Prevalence And Lineage Diversity Of Avian Haemosporidians From Three Distinct Cerrado Habitats In Brazil, Nayara Belo, Renato Pinheiro, Elivânia Reis, Robert Ricklefs, Érika Braga

Biology Department Faculty Works

No abstract provided.

Angiostatin Like Peptides In Milk: Potential Development For Dairy Products Capable Of Cancer Prevention, Erin Stefanutti

Master's Theses

For the past 40 years, antiangiogenic approaches have been of major interest in the development of methods to cure and prevent cancer. Angiogenesis, the development of blood vessels from pre-existing vascularization, is essential for cancer growth and spread of metastasis through the delivery of nutrients and oxygen essential to sustain the metabolic activity of these malignant cells. Blocking access to blood will cause cancerous cells to assume a dormant state creating inactive micro-tumors innocuous to the host. Angiostatin, the internal fragment of the fibrinolytic zymogen plasminogen, has shown great potential in reducing cancer size and number of metastatic colonies in …

Unionid Mussels From Nearshore Zones Of Lake Erie, Todd D. Crail, Robert A. Krebs, David T. Zanatta

Biological, Geological, and Environmental Faculty Publications

Concern exists that the introduction of dreissenid mussels following long-term effects of pollution may have completely eliminated native mussel species from Lake Erie. Natural seiche events were used to facilitate surveys for live unionids on five occasions in the western basin of Lake Erie and Sandusky Bay between 2007 and 2009, and beach and estuary surveys were conducted at numerous additional sites between 2004 and 2009. Sixteen unionid species were found living in or near Lake Erie, including six sites in the nearshore zone of the lake. Each community consisted of live individuals from two to eight species, and evidence …

Regional Scale Monitoring Of Methane Production By Dairy Farm Ungulates; A Proposal To The National Science Foundation (Nsf) And The National Ecological Observatory Network (Neon, Inc.), Lindsey Anne Peterson

Biological Sciences

No abstract provided.

Patatin-Related Phospholipase Pplaiiiβ-Induced Changes In Lipid Metabolism Alter Cellulose Content And Cell Elongation In Arabidopsis, Xuemin Wang, Maoyin Li, Sung Chul Bahn, Liang Guo, William Musgrave, Howard Berg, Ruth Welti

Biology Department Faculty Works

The release of fatty acids from membrane lipids has been implicated in various plant processes, and the patatin-related phospholipases (pPLAs) constitute a major enzyme family that catalyzes fatty acid release. The Arabidopsis thaliana pPLA family has 10 members that are classified into three groups. Group 3 pPLAIII has four members but lacks the canonical lipase/esterase consensus catalytic sequences, and their enzymatic activity and cellular functions have not been delineated. Here, we show that pPLAIIIβ hydrolyzes phospholipids and galactolipids and additionally has acyl-CoA thioesterase activity. Alterations of pPLAIIIβ result in changes in lipid levels and composition. pPLAIIIβ-KO plants have longer leaves, …

The Composition, Stability, And Kinship Of Reproductive Coalitions In A Lekking Bird, Thomas Ryder, John Blake, Patricia Parker, Bette Loiselle

Biology Department Faculty Works

Male vertebrates often form reproductive coalitions to gain access to or defend females. One striking example occurs in the wire-tailed manakin (Pipra filicauda; Aves: Pipridae), where pairs of males form coalitions to display for females on leks. Here, we use data from a long-term study of the wire-tailed manakin to quantify the composition and stability of display coalitions, to examine how coalitions influence behavioral variation, and to determine if males gain indirect genetic benefits from coalition membership. Our data show that coalitions were most often formed between males of different status and that the presence of coalition partners increased a …

The Forgotten Stage Of Forest Succession: Early-Successional Ecosystems On Forest Sites, Mark E. Swanson, Jerry F. Franklin, Robert L. Beschta, Charles M. Crisafulli, Dominick A. Dellasala, Richard L. Hutto, David B. Lindenmaver, Frederick J. Swanson

Biological Sciences Faculty Publications

Early-successional forest ecosystems that develop after stand-replacing or partial disturbances are diverse in species, processes, and structure. Post-disturbance ecosystems are also often rich in biological legacies, including surviving organisms and organically derived structures, such as woody debris. These legacies and post-disturbance plant communities provide resources that attract and sustain high species diversity, including numerous early-successional obligates, such as certain woodpeckers and arthropods. Early succession is the only period when tree canopies do not dominate the forest site, and so this stage can be characterized by high productivity of plant species (including herbs and shrubs), complex food webs, large nutrient fluxes, …

Assessment Of Pathways For The Introduction And Spread Of Mycobacterium Bovis In The United States, Katie Portacci, Jason Lombard, Lauren Abrahamsen, Eric Bush, Charles Fossler, Robert Harris, Kamina Johnson, Ryan S. Miller, Dianna Mitchell, Randy Pritchard, Steven Sweeney, Todd Weaver

Zoonotics and Wildlife Disease: Publications

Bovine tuberculosis (TB) was responsible for more losses among U.S. farm animals in the early 20th century than all other infectious diseases combined. The Cooperative State-Federal Tuberculosis Eradication Program (established in 1917 and administered by APHIS, State animal health agencies, and U.S. livestock producers) has nearly eradicated bovine TB from the nation’s livestock population. However, despite the many accomplishments of the program, bovine TB remains a serious and costly disease of livestock in the United States. In 1992, VS conducted an assessment to identify pathways for the introduction and spread of bovine TB, in order to develop the most effective …

New World Origins Of Southwest Pacific Gesneriaceae: Multiple Movements Across And Within The South Pacific, Vincent L. Woo, Minde M. Funke, James F. Smith, Peter J. Lockhart, Philip J. Garnock-Jones

Biology Faculty Publications and Presentations

Coronanthereae is a tribe of ~20 species with a suite of unique morphological characters and a disjunct geographic distribution in the Southern Hemisphere. Three species are found in southern South America and the remainder in the southwest Pacific. It has been suggested, because of this distribution and disjunction, that Coronanthereae represents a relictual Gondwanan group from which the two major lineages in the family, the Old World Cyrtandroideae and the New World Gesnerioideae, originated. We tested this hypothesis by using phylogenetic analyses of nuclear and chloroplast DNA sequences, ancestral-area reconstruction, and molecular dating. The tribe is placed within the mostly …

Amid The Vipers: Establishing Malware's Position Within The Information Ecosystem, Shawn Louis Everett Robertson

Computer Science and Software Engineering

The paper consists of a detailed examination of malware broken down into three main sections.

1. Introduction: Malware in the World Today. Begins with a definition of terms, examination of the types of malware, research into historical pieces of malicious code, a detailed analysis of the attackers, why malware is so prevalent, and why it is so hard to defend against. This section finishes with a comparison of reasons to create and not to create malware.
2. Background: "Good" Pieces of Malware. Examination of what makes malware effective. Analysis of the existing CVSS standard and proposal of the alternative VIPERS classification system. …

Blood-Brain Barrier Impairment In An Animal Model Of Mps Iii B, Svitlana N. Garbuzova-Davis, Michael Louis, Edward M. Haller, Hiranya M. Derasari, Ashley E. Rawls, Paul R. Sanberg

Integrative Biology Faculty and Staff Publications

Background: Sanfilippo syndrome type B (MPS III B) is caused by a deficiency of α-N-acetylglucosaminidase enzyme, leading to accumulation of heparan sulfate within lysosomes and eventual progressive cerebral and systemic multiple organ abnormalities. However, little is known about the competence of the blood-brain barrier (BBB) in MPS III B. BBB dysfunction in this devastating disorder could contribute to neuropathological disease manifestations.

Methodology/Principal Findings: In the present study, we investigated structural (electron microscope) and functional (vascular leakage) integrity of the BBB in a mouse model of MPS III B at different stages of disease, focusing on brain structures known to experience …

Comparative Biology Of Sympatric Red Diamond And Southern Pacific Rattlesnakes In Southern California, Eric Allen Dugan

Loma Linda University Electronic Theses, Dissertations & Projects

I compared the biology of two sympatric rattlesnakes within the context of resource use and niche partitioning. Using radio-telemetry and mark-recapture involving passive integrated transponders (PIT) tags, I studied Red Diamond (Crotalus ruber) and Southern Pacific (C. oreganus helleri) Rattlesnakes in Chino Hills State Park, California, from March 2003 through March 2010. The first of three studies compared the two species in terms of home range size, movements, and mating phenology. Crotalus o. helleri occupied larger home ranges than C. ruber, and exhibited 1.9–2.8-fold greater movement distances (depending on year) than C. ruber. Mating phenology also varied, with C. ruber …

Comprehensive Analysis Of The Chromatin Landscape In Drosophila Melanogaster, Peter Kharchenko, Artyom Alekseyenko, Yuri Schwartz, Aki Minoda, Nicole Riddle, Jason Ernst, Peter Sabo, Erica Larschan, Andrey Gorchakov, Tingting Gu, Daniela Linder-Basso, Annette Plachetka, Gregory Shanower, Michael Tolstorukov, Lovelace Luquette, Ruibin Xi, Youngsook Jung, Richard Park, Eric Bishop, Theresa Canfield, Richard Sandstrom, Robert Thurman, David Macalpine, John Stamatoyannopoulos, Manolis Kellis, Sarah C.R. Elgin, Mitzi Kuroda, Vincenzo Pirrotta, Gary Karpen, Peter Park

Biology Faculty Research

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory …

The Relationship Between 11-Ketotestosterone, Cortisol, And Testosterone And Condition Index For Poecilia Reticulata, Shelly Gupta, Brandy G. Kalbach

Biological Sciences

The guppy, Poecilia reticulata, is a common study organism for behavioral and other ecological experiments (Houde, 1997).  As far as we know, no previous data have been compiled regarding hormones and condition index of guppies.  In this experiment we examined the relationship between circulating levels of three hormones (testosterone, 11-ketotestosterone and cortisol) and condition index in males and also made comparisons among the hormone levels, for three guppy sites from the northern range of Trinidad – Aripo River, Marianne River and Small Crayfish River.  Hormone samples were obtained using non-invasive water borne techniques and quantified by our collaborator.  The condition …

Population Proteomics: Quantitative Variation Within And Among Populations In Cardiac Protein Expression, Bernard Rees

Biological Sciences Faculty Publications

Population analysis of gene expression is typically achieved by quantifying levels of mRNA; however, gene expression is also a function of protein translation and turnover. Therefore, a complete understanding of population variation in gene expression requires quantitative knowledge of protein expression within and among natural populations. We used two dimensional fluorescence difference gel electrophoresis (2D-DIGE) to quantitatively compare expression of heart ventricle proteins among 18 individuals in three populations of the teleost fish Fundulus. Among populations, expressions between orthologous proteins and mRNAs were generally positively correlated. Additionally, similar to the pattern of cardiac mRNA expression for the same populations, we …

Vocalization Behavior Of The Endangered Bahama Oriole (Icterus Northropi): Ontogenetic, Sexual, Temporal, Duetting Pair, And Geographic Variation, Valerie A. Lee

Loma Linda University Electronic Theses, Dissertations & Projects

Many birds communicate via a diverse set of vocalizations, but the contexts, roles, and structure of their varied songs and calls may change with age, differ between sexes, and vary temporally and geographically. In New World orioles, most tropical species exhibit the ancestral states of sexual monochromatism (both sexes have similar plumage) and monovocalism (both sexes sing and often duet together), whereas migratory temperate species tend toward dichromatism (males brightly colored and females drab) and divocalism (males sing almost exclusively). In this study, I examined the vocalizations of the Bahama Oriole, a non-migratory, monochromatic species, to learn where it fits …

A Synthesis Of Plant Invasion Effects On Biodiversity Across Spatial Scales, Kristin I. Powell, Jonathan M. Chase, Tiffany M. Knight

Biology Faculty Research

PREMISE OF THE STUDY:

Invasive plant species are typically thought to pose a large threat to native biodiversity, and local-scale studies typically confirm this view. However, plant invaders rarely cause regional extirpations or global extinctions, causing some to suggest that invasive species' influence on native biodiversity may not be so dire. We aim to synthesize the seemingly conflicting literature in plant invasion biology by evaluating the effects of invasive plant species across spatial scales.

METHODS:

We first conducted a meta-analysis on the effects of invasive plants on the species richness of invaded communities across a range of spatial extents. We …

New Implications On Genomic Adaptation Derived From The Helicobacter Pylori Genome Comparison, Edgar Eduardo Lara-Ramírez, Aldo Segura-Cabrera, Xianwu Guo, Gongxin Yu, Carlos Armando García-Pérez, Mario A. Rodríguez-Pérez

Biology Faculty Publications and Presentations

Background: Helicobacter pylori has a reduced genome and lives in a tough environment for long-term persistence. It evolved with its particular characteristics for biological adaptation. Because several H. pylori genome sequences are available, comparative analysis could help to better understand genomic adaptation of this particular bacterium.

Principal Findings: We analyzed nine H. pylori genomes with emphasis on microevolution from a different perspective. Inversion was an important factor to shape the genome structure. Illegitimate recombination not only led to genomic inversion but also inverted fragment duplication, both of which contributed to the creation of new genes and gene family, and further, …