Biology Commons^™

Mechanosensing Of Shear By Pseudomonas Aeruginosa Leads To Increased Levels Of The Cyclic-Di-Gmp Signal Initiating Biofilm Development, Christopher A. Rodesney, Brian Roman, Numa Dhamani, Benjamin J. Cooley, Ahmed Touhami, Vernita D. Gordon

Physics & Astronomy Faculty Publications

Biofilms are communities of sessile microbes that are phenotypically distinct from their genetically identical, free-swimming counterparts. Biofilms initiate when bacteria attach to a solid surface. Attachment triggers intracellular signaling to change gene expression from the planktonic to the biofilm phenotype. For Pseudomonas aeruginosa, it has long been known that intracellular levels of the signal cyclic-di-GMP increase upon surface adhesion and that this is required to begin biofilm development. However, what cue is sensed to notify bacteria that they are attached to the surface has not been known. Here, we show that mechanical shear acts as a cue for surface adhesion …

Examination Of Human Impacts On The Biodiversity And Ecology Of Lichen And Moss Communities, Hannah Marie Prather

Dissertations and Theses

Globally, more than half of the world's population is living in urban areas and it is well accepted that human activities (e.g. climate warming, pollution, landscape homogenization) pose a multitude of threats to ecosystems. Largely, human-related impacts on biodiversity will hold consequences for larger ecological processes and research looking into human impacts on sensitive epiphytic lichen and moss communities is an emerging area of research. While seemingly small, lichen and moss communities exist on nearly every terrestrial ecosystem on Earth and contribute to whole-system processes (e.g. hydrology, mineral cycling, food web energetics) worldwide. To further examine human impacts on epiphytic …

Temporal Dynamics Of Fish And Macroinvertebrate Assemblages On Military Land In Western Louisiana, Janey Dudley

Biology Theses

Headwater streams are known to have an impact on higher order river systems downstream; therefore, it is important to monitor their water quality. The United States Army is mandated to ensure their training activities do not have a negative impact on freshwater biotic communities and the overall water chemistry. The goals of this study include: (1) to quantify the long-term effects of military land management practices on headwater stream biodiversity in western Louisiana using biological indices and (2) to measure changes in fish and macroinvertebrate assemblages over time using multivariate techniques. Because the natural disturbance regime in these streams is …

Spokony Is A Hands-On Researcher, Teacher Of Genetics., Aldemaro Romero Jr.

Publications and Research

“When I was very little, my parents always took

us to the American Museum of Natural History,

the Bronx Zoo, and then even just watching on TV

we would pick the shows that were about science.”

That is how Dr. Rebecca Spokony traces back her

interest in science.

A native of Brooklyn Heights, New York City,

she remembers how when her mother was an

undergraduate, she worked on fruit flies. “Even

though she did not go on to work on science after

she graduated from college, it still was important

to her, and she shared that with me, and I …

Exploring The Impact Of Olfaction On Short-Term And Long-Term Maternal Recognition In Peromyscus Californicus, Mariah F. Conley

Honors Projects

Previous studies have established a connection between social behavior and olfaction, in that as anosmia causes a decrease in perception of social cues, social behavior itself decreases. Studies investigating maternal behavior specifically have focused on foster care, in which the behaviors formed during parturition are conserved and displayed with unrelated pups. The combination of long-term retention of maternal behavior, maternal recognition, and olfaction has yet to be explored. In this study, I induced anosmia in Peromyscus californicus, a monogamous, biparental species, and analyzed their behavior with their own pups and with foreign pups in the days after birth, as well …

Trypanosoma Brucei Rap1 Maintains Telomere And Subtelomere Integrity By Suppressing Terra And Telomeric Rna: Dna Hybrids, Vishal Nanavaty, Ranjodh Sandhu, Sanaa E. Jehi, Unnati M. Pandya, Bibo Li

Biological, Geological, and Environmental Faculty Publications

Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, VSG, thereby evading the host's immune response. VSGs are monoallelically expressed from subtelomeric expression sites (ESs), and VSG switching exploits subtelomere plasticity. However, subtelomere integrity is essential for T. brucei viability. The telomeric transcript, TERRA, was detected in T. brucei previously. We now show that the active ES-adjacent telomere is transcribed. We find that TbRAP1, a telomere protein essential for VSG silencing, suppresses VSG gene conversionmediated switching. Importantly, TbRAP1 depletion increases the TERRA level, which appears to result from longer read-through into the telomere downstream of the …

A Genetic Signature Of The Evolution Of Loss Of Flight In The Galapagos Cormorant, Patricia Parker, Alejandro Burga, Weiguang Wang, Eyal Ben-David, Paul Wolf, Andrew Ramey, Claudio Verdugo, Karen Lyons, Leonid Kruglyak

Biology Department Faculty Works

We have a limited understanding of the genetic and molecular basis of evolutionary changes in the size and proportion of limbs. We studied wing and pectoral skeleton reduction leading to flightlessness in the Galapagos cormorant (Phalacrocorax harrisi). We sequenced and de novo assembled the genomes of four cormorant species and applied a predictive and comparative genomics approach to find candidate variants that may have contributed to the evolution of flightlessness. These analyses and cross-species experiments in Caenorhabditis elegans and in chondrogenic cell lines implicated variants in genes necessary for transcriptional regulation and function of the primary cilium. Cilia are essential …

Exploring The Biogeography Of South American Rainforest Understory Birds Using Morphological Variation In The Wedge-Billed Woodcreeper ( Glyphorynchus Spirurus ), Gregory Tito

Theses and Dissertations

Tropical rainforests in the Amazon Basin show an extraordinarily high degree of biodiversity, the reasons for which are poorly understood. A number of biogeographical models have been proposed to account for the variation present within and among species, including birds. This study tests the predictive ability of six major historical vicariant biogeographical models (Andean uplift, marine incursion, Amazonian lake, river barrier, refuge, and river refuge) using a large data set of morphological characters in the Wedge-billed Woodcreeper (Glyphorynchus spirurus), a small understory songbird found mostly in terra firme tropical rain forest. It also characterizes variation in key morphological characters and …

Newman, Eric A., Alfonso Araque, Janet M. Dubinsky, Larry W. Swanson, Lyndel Saunders King, And Eric Himmel. The Beautiful Brain: The Drawings Of Santiago Ramón Y Cajal. New York: Abrams, 2017. 207 Pp. $40.00 Hardcover (Isbn: 9781419722271)., Aldemaro Romero Jr.

Publications and Research

Santiago Ramón y Cajal is one of the scientific giants of the twentieth century. By all accounts he was the founder of neuroscience. But these two phrases fall short of understanding not only his impact on science but also his unique talents.

Investigating Species Boundaries And Taxonomy In The California Pincushion Plants, Theresa Saunders, Leigh Johnson

Journal of Undergraduate Research

Species in the genus Navarretia are annual wildflowers found almost exclusively in California. The Navarretia atractyloides group consists of just two species, N. atractyloides and N. hamata, that are more similar to each other morphologically than to any other Navarretia species. The most recent taxonomic investigation of these two species distinguishes between them based on bract shape, stamen attachment to the corolla, and whether the style is included and anthers included to slightly exserted from the corolla tube versus style exserted and anthers long exserted (Day, 1993). However, we have noticed that some specimens that seem to be …

The Recycling Gtpase, Rab-10, Regulates Autophagy Flux In Caenorhabditis Elegans, Nicholas J. Palmisano

Dissertations, Theses, and Capstone Projects

Autophagy and endocytosis are two cellular pathways that are vital to cell growth and homeostasis. Autophagy is a dynamic and catabolic process involving the formation of a double-membrane vesicle called the autophagosome, which engulfs long-lived proteins and damaged organelles. Endocytosis involves the uptake of extracellular material into the cell through the formation of intracellular vesicles termed endosomes. Although both endocytosis and autophagy are interconnected processes, the extent to which endocytic proteins and/or compartments contribute to autophagy, and how these endocytic components do so, is still unknown. To improve our understanding of the connections that exist between autophagy and endocytosis, we …

The P53 Independent Functions Of Estrogen-Activated Mdm2 In Cell Signaling And Mammary Architecture, Nandini Kundu

Dissertations, Theses, and Capstone Projects

Estrogen receptor positive (ER+) breast cancers often have MDM2 overexpression indicating a critical role for MDM2 in breast cancer tumorigenesis. The cancer genome atlas (TCGA) found that increased MDM2 expression is one of the four pathways that correlate with all breast cancer subtypes. MDM2 is mainly known as the negative regulator of wild type p53. However, aggressive breast cancers often have MDM2 overexpression and mutant p53 (mtp53). We previously reported that MDM2 provides an estrogen-mediated proliferative advantage to MCF-7 breast cancer cells (ER+, MDM2 overexpression, wild type p53), independent of wild type p53 in both 2D and 3D culture conditions. …

Body Size Regulation Via Bmp Signaling In Caenorhabditis Elegans, Uday Madaan

Dissertations, Theses, and Capstone Projects

The body size of an organism can be a crucial determinant of access to nutrition, reproductive success and overall survival in the wild. However, how body size of an individual is determined is incompletely understood. Body size is a complex trait determined by multiple pathways and genes, making it difficult to understand the role of individual genes and pathways in determining overall size. In Caenorhabditis elegans, a homolog of Bone Morphogenetic Proteins (BMP) is a major regulator of body size; functional loss of DBL-1 leads to a small body size. Due to a drastic change in body size in dbl-1 …

An Efficient Pipeline For Assaying Whole-Genome Plastid Variation For Population Genetics And Phylogeography, Brendan F. Kohrn

Dissertations and Theses

Tracking seed dispersal using traditional, direct measurement approaches is difficult and generally underestimates dispersal distances. Variation in chloroplast haplotypes (cpDNA) offers a way to trace past seed dispersal and to make inferences about factors contributing to present patterns of dispersal. Although cpDNA generally has low levels of intraspecific variation, this can be overcome by assaying the whole chloroplast genome. Whole-genome sequencing is more expensive, but resources can be conserved by pooling samples. Unfortunately, haplotype associations among SNPs are lost in pooled samples and treating SNP frequencies as independent estimates of variation provides biased estimates of genetic distance. I have developed …

In Vivo Effects Of Long-Term Cigarette Smoke Exposure On Mammary Tissue In Mice, Shannon Kispert, Susan Crawford, Grant Kolar, Jane Mchowat

Biological Sciences Faculty Research & Creative Works

Cigarette smoking is the leading cause of preventable death worldwide and has been linked to the development and progression of cancer. Many cohort studies have described the link between patients with breast cancer and those with long-term smoking history. Despite the claim of correlation, the mechanism by which cigarette smoke alters normal breast epithelial cells and stroma and contributes to tumor cell growth remains undefined. To investigate whether cigarette smoke promotes ductal epithelial cell hyperplasia by stimulating stromal endothelial cell proliferation, we exposed mice to cigarette smoke for 6 months. We observed epithelial proliferation, increased fibrosis, increased vascularity, and mast …

In Vivo Effects Of Long-Term Cigarette Smoke Exposure On Mammary Tissue In Mice, Shannon Kispert, Susan Crawford, Grant Kolar, Jane Mchowat

Biological Sciences Faculty Research & Creative Works

Cigarette smoking is the leading cause of preventable death worldwide and has been linked to the development and progression of cancer. Many cohort studies have described the link between patients with breast cancer and those with long-term smoking history. Despite the claim of correlation, the mechanism by which cigarette smoke alters normal breast epithelial cells and stroma and contributes to tumor cell growth remains undefined. To investigate whether cigarette smoke promotes ductal epithelial cell hyperplasia by stimulating stromal endothelial cell proliferation, we exposed mice to cigarette smoke for 6 months. We observed epithelial proliferation, increased fibrosis, increased vascularity, and mast …

Peromyscus Boylii And Peromysus Californicus Differ In Physical Characteristic Measurements, Puja M. Kasondra

Biological Sciences

I provide a comparison of physical characteristics between Peromyscus boylii and Peromyscus californicus. All mice compared were captured in the dominant regions of the Los Padres National Forest during three different years – 2005, 2011, and 2014. The dominant regions of the Los Padres National Forest include Riparian, Woodlands, and Chaparral. All characteristics, ear (from notch), head and body, hind foot, tail, and weights, were compared between males of each species and then between females of each species. All data were analyzed in JMP 12. Out of all the characteristics, tail and weight had the greatest difference between the …

Linking Large Scale Ocean-Atmospheric Patterns With Recruitment In Kellet’S Whelk (Kelletia Kelletii), Katherine N. Rodriguez

Biological Sciences

Global warming influences the biogeography of many marine and terrestrial species. Understanding species range shifts is ecologically and socioeconomically important when guiding management decisions for ecosystems exposed to a rapidly changing climate. In this natural experiment, I follow Danielle Zacherl’s methods (Zacherl et al. 2003) to study the effects of large-scale ocean-atmospheric patterns on recruitment of a marine snail, Kellet’s whelk (Kelletia kelletii); these organisms recently expanded their range North past the geographic barrier of Point Conception to Monterey, CA, USA. I use shell length data collected at 32 subtidal rocky reef kelp forest sites in 2015 (before …

Fishing As Therapy: Impacts On Job Satisfaction And Implications For Fishery Management, Tarsila Seara, Richard Pollnac, John J. Poggie, Carlos Garcia-Quejano, Iris Monnereau, Victor Ruiz

Biology and Environmental Science Faculty Publications

"This study presents unique comparisons, across space and time, regarding aspects of fishers’ perception of their job satisfaction and well-being between two geographic areas where fishing constitutes integral part of the local economy and culture: the Northeast Region US and the Caribbean. Examining differences in aspects of job satisfaction and well-being in such highly different environments (both human and natural) will provide information for developing models to understand how different stressors (e.g. changes in the natural, socio-cultural, economic and managerial environments) affect those whose livelihoods depend directly on fishery resources. Models elucidating relationships between environmental and anthropogenic changes and the …

Growth Trade-Offs Accompany The Emergence Of Glycolytic Metabolism In Shewanella Oneidensis Mr-1, Lon Chubiz, Christopher Marx

Biology Department Faculty Works

Bacteria increase their metabolic capacity via the acquisition of genetic material or by the mutation of genes already present in the genome. Here, we explore the mechanisms and trade-offs involved when Shewanella oneidensis, a bacterium that typically consumes small organic and amino acids, rapidly evolves to expand its metabolic capacity to catabolize glucose after a short period of adaptation to a glucose-rich environment. Using whole-genome sequencing and genetic approaches, we discovered that deletions in a region including the transcriptional repressor (nagR) that regulates the expression of genes associated with catabolism of N-acetylglucosamine are the common basis for evolved glucose metabolism …

Insect Immunity Varies Idiosyncratically During Overwintering., Laura V Ferguson, Brent J Sinclair

Biology Publications

Overwintering insects face multiple stressors, including pathogen and parasite pressures that shift with seasons. However, we know little of how the insect immune system fluctuates with season, particularly in the overwintering period. To understand how immune activity changes across autumn, winter, and spring, we tracked immune activity of three temperate insects that overwinter as larvae: a weevil (Curculio sp., Coleoptera), gallfly (Eurosta solidaginis, Diptera), and larvae of the lepidopteran Pyrrharctia isabella. We measured baseline circulating hemocyte numbers, phenoloxidase activity, and humoral antimicrobial activity, as well as survival of fungal infection and melanization response at 12°C and 25°C to capture any …

Genetic Indicators Of Drug Resistance In The Highly Repetitive Genome Of Trichomonas Vaginalis, Marina Bradic, Sally D. Warring, Grace E. Tooley, Paul Scheid, William E. Secor, Kirkwood M. Land, Po-Jung Huang, Ting-Wen Chen, Chi-Ching Lee, Petrus Tang, Steven A. Sullivan, Jane M. Carlton

College of the Pacific Faculty Articles

Trichomonas vaginalis, the most common nonviral sexually transmitted parasite, causes ∼283 million trichomoniasis infections annually and is associated with pregnancy complications and increased risk of HIV-1 acquisition. The antimicrobial drug metronidazole is used for treatment, but in a fraction of clinical cases, the parasites can become resistant to this drug. We undertook sequencing of multiple clinical isolates and lab derived lines to identify genetic markers and mechanisms of metronidazole resistance. Reduced representation genome sequencing of ∼100 T. vaginalis clinical isolates identified 3,923 SNP markers and presence of a bipartite population structure. Linkage disequilibrium was found to decay rapidly, suggesting genome-wide …

Analysis Of Copy Number Variation In The Abp Gene Regions Of Two House Mouse Subspecies Suggests Divergence During The Gene Family Expansions, Željka Pezer, Amanda G. Chung, Robert C. Karn, Christina M. Laukaitis

Scholarship and Professional Work - LAS

The Androgen-binding protein (Abp) gene region of the mouse genome contains 64 genes, some encoding pheromones that influence assortative mating between mice from different subspecies. Using CNVnator and quantitative PCR, we explored copy number variation in this gene family in natural populations of Mus musculus domesticus (Mmd) and Mus musculus musculus (Mmm), two subspecies of house mice that form a narrow hybrid zone in Central Europe. We found that copy number variation in the center of the Abp gene region is very common in wild Mmd, primarily representing the presence/absence of the final …

Animals And Their Epibiota As Net Autotrophs: Size Scaling Of Epibiotic Metabolism On Snail Shells, Nicole Lukens, Benjamin Kraemer, Vanessa Constant, Ellen J. Hamann, Ellinor Michel, Anne M. Socci, Yvonne Vadeboncoeur, Peter B. Mcintyre

Biological Sciences Faculty Publications

Animals are heterotrophic by definition, but species from many taxonomic groups are hosts to epibiota that may alter their net metabolism. We tested the degree to which snail-shell epibiota can generate net ecosystem productivity for snails and their epibiota (snail–epibiota ecosystems; SEEs) after accounting for snail respiration. We focused on 3 species from the Lavigeria snail assemblage in Africa’s Lake Tanganyika and quantified the scaling of SEE metabolism with shell size under light and dark conditions. The metabolism of snails and their epibiota shifted significantly across the size gradient. SEEs of large snails (>20 mm) were consistently autotrophic during …

Hematocrit Level On Blood Flow Through A Stenosed Artery With Permeable Wall: A Theoretical Study, A. Malek, A. Hoque

Applications and Applied Mathematics: An International Journal (AAM)

The paper deals with the hematocrit level on resistance of flow, wall shear stress in a stenosed artery of permeable wall. In the paper we have developed and solved some theoretical formulas based on stenosis and hematocrit effects. The results highlight that the resistance of flow increases for increasing of stenosis height where the hematocrit level (35%-45%) has significant effects. Moreover, the effects of slip parameter and Darcy number due to permeability of the wall on resistance of flow have been investigated. The effects of hematocrit level, slip parameter and Darcy number have been focused on wall shear stress of …

Two-Dimensional Model Of Nanoparticle Deposition In The Alveolar Ducts Of The Human Lung, Anju Saini, V. K. Katiyar, Pratibha Pratibha

Applications and Applied Mathematics: An International Journal (AAM)

In this paper a mathematical model for nanoparticle deposition in the alveolar ducts of the human lung airways is proposed. There were huge inconsistencies in deposition between ducts of a particular generation and inside every alveolated duct, signifying that limited particle concentrations can be much bigger than the mean acinar concentration. A large number of particles are unsuccessful to way out the structure during expiration. Finite difference method has been used to solve the unsteady nonlinear Navier–Stokes equations in cylindrical coordinate system governing flow assuming axial symmetry under laminar flow condition so that the problem efficiently turns into two-dimensional. An …

Bifurcation And Stability Of Prey-Predator Model With Beddington-Deangelis Functional Response, Moulipriya Sarkar, Tapasi Das, R. N. Mukherjee

Applications and Applied Mathematics: An International Journal (AAM)

In this paper we discuss the harvesting of the prey species making a fraction of them to be accessed by the predator while both the prey and predator are being subjected to Beddington-DeAngelis functional response. It is observed that a Hopf-bifurcation may occur around the interior equilibrium taking the environmental carrying capacity of the prey species as the parameter. Some numerical examples and the corresponding curves are studied using Maple to explain the results of the proposed model.

Molecular Assisted Identification Reveals Hidden Red Algae Diversity From The Burica Peninsula, Pacific Panama, David Wilson Freshwater, Jennifer N. Idol, Seth L. Parham, Cindy Fernández-García, Noemi León, Paul W. Gabrielson, Brian Wysor

Arts & Sciences Faculty Publications

The marine flora of Panama harbors a rich diversity of green, red and brown algae, and despite chronic understudy, it is reported as the second most diverse marine flora along the Pacific Central American coast, with 174 macroalgal species. Extensive new collections and molecular assisted identification (MAI) by an international team of researchers has revealed an even greater diversity for this country. Here, the intertidal and shallow subtidal marine flora of the remote Burica Peninsula is introduced. This area is characterized by an uplifted extensive intertidal flat composed of firm, sedimentary benthos known as mudrock, on which abundant algal communities …

Variation In Dna Methylation Is Not Consistently Reflected By Sociality In Hymenoptera, Karl M. Glastad, Samuel V. Arsenault, Kim L. Vertacnik, Scott M. Geib, Sasha Kay, Bryan N. Danforth, Sandra M. Rehan, Catherine R. Linnen, Sarah D. Kocher, Brendan G. Hunt

Biology Faculty Publications

Changes in gene regulation that underlie phenotypic evolution can be encoded directly in the DNA sequence or mediated by chromatin modifications such as DNA methylation. It has been hypothesized that the evolution of eusocial division of labor is associated with enhanced gene regulatory potential, which may include expansions in DNA methylation in the genomes of Hymenoptera (bees, ants, wasps, and sawflies). Recently, this hypothesis garnered support from analyses of a commonly used metric to estimate DNA methylation in silico, CpG content. Here, we test this hypothesis using direct, nucleotide-level measures of DNA methylation across nine species of Hymenoptera. In doing …

Asymmetric Dna Methylation Of Cpg Dyads Is A Feature Of Secondary Dmrs Associated With The Dlk1/Gtl2 Imprinting Cluster In Mouse, Megan Guntrum, Ekaterina Vlasova, Tamara L. Davis

Biology Faculty Research and Scholarship

Background: Differential DNA methylation plays a critical role in the regulation of imprinted genes. The differentially methylated state of the imprinting control region is inherited via the gametes at fertilization, and is stably maintained in somatic cells throughout development, influencing the expression of genes across the imprinting cluster. In contrast, DNA methylation patterns are more labile at secondary differentially methylated regions which are established at imprinted loci during post-implantation development. To investigate the nature of these more variably methylated secondary differentially methylated regions, we adopted a hairpin linker bisulfite mutagenesis approach to examine CpG dyad methylation at differentially methylated regions …