Biology Commons^™

Genetic Origins Of Lactase Persistence And The Spread Of Pastoralism In Africa, Michael Campbell

Department of Biology Faculty Publications

In humans, the ability to digest lactose, the sugar in milk, declines after weaning because of decreasing levels of the enzyme lactase-phlorizin hydrolase, encoded by LCT. However, some individuals maintain high enzyme amounts and are able to digest lactose into adulthood (i.e., they have the lactase-persistence [LP] trait). It is thought that selection has played a major role in maintaining this genetically determined phenotypic trait in different human populations that practice pastoralism. To identify variants associated with the LP trait and to study its evolutionary history in Africa, we sequenced MCM6 introns 9 and 13 and ∼2 kb of the …

A 54 Year-Old Man With Progressive Vision And Hearing Loss, A. A. Gru, G. Kolar, N. D. Wagner-Johnston, R. Schmidt, N. R. Yaseen

Biological Sciences Faculty Research & Creative Works

No abstract provided.

Strad Pseudokinases Regulate Axogenesis And Lkb1 Stability, Biliana O. Veleva-Rotse, James L. Smart, Annette F. Baas, Benjamin Edmonds, Zi-Ming Zhao, Allyson Brown, Lillian R. Klug, Kelly Hansen, Gabrielle Rielly, Alexandria P. Gardner, Krishnaveni Subbiah, Eric A. Gaucher, Hans Clevers, Anthony P. Barnes

Faculty Publications - Department of Biological & Molecular Science

No abstract provided.

Using Crossword Puzzles To Enhance Students' Learning Of Technical Biological Terms, William D. Stansfield

Biological Sciences

No abstract provided.

Darwin’S Diagram Of Divergence Of Taxa As A Causal Model For The Origin Of Species, Juan Luis Bouzat

Biological Sciences Faculty Publications

On the basis that Darwin's theory of evolution encompasses two logically independent processes (common descent and natural selection), the only figure in On the Origin of Species (the Diagram of Divergence of Taxa) is often interpreted as illustrative of only one of these processes: the branching patterns representing common ancestry. Here, I argue that Darwin's Diagram of Divergence of Taxa represents a broad conceptual model of Darwin's theory, illustrating the causal efficacy of natural selection in producing well-defined varieties and ultimately species. The Tree Diagram encompasses the idea that natural selection explains common descent and the origin of organic diversity, …

Ua66 Ogden College Of Science & Engineering Newsletter, Cheryl Stevens, Dean

Ogden College of Science & Engineering Publications

No abstract provided.

Cluster M Mycobacteriophages Bongo, Pegleg, And Rey With Unusually Large Repertoires Of Trna Isotopes, Welkin H. Pope, Kirk R. Anders, Madison Baird, Charles A. Bowman, Michelle M. Boyle, Gregory W. Broussard, Tiffany Chow, Kari L. Clase, Shannon Cooper, Kathleen A. Cornely, Randall J. Dejong, Veronique A. Delesalle, Lisa Deng, David Dunbar, Nicholas P. Edgington, Christina M. Ferreira, Kathleen Weston Hafer, Grant A. Hartzog, J. Robert Hatherill, Lee E. Hughes, Khristina Ipapo, Gregory P. Krukonis, Christopher G. Meier, Denise L. Monti, Matthew R. Olm, Shallee T. Page, Craig L. Peebles, Claire A. Rinehart, Michael R. Rubin, Daniel A. Russell, Erin R. Sanders, Morgan Schoer, Christopher D. Shaffer, James Wherley, Edwin Vazquez, Han Yuan, Daiyuan Zhang, Steven G. Cresawn, Deborah Jacobs-Sera, Roger W. Hendrix, Graham F. Hatfull

Biology Faculty Publications

Genomic analysis of a large set of phages infecting the common hostMycobacterium smegmatis mc²155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average …

Review Of "Once We All Had Gills: Growing Up Evolutionist In An Evolving World" By R. A. Raff, Scott F. Gilbert

Biology Faculty Works

No abstract provided.

Cal Poly Library Of Pyroprints: Quality Control Analysis And Web Development, Chase Ricketts

Computer Science and Software Engineering

No abstract provided.

Stand Density And Age Affect Tree-Level Structural And Functional Characteristics Of Young, Postfire Lodgepole Pine In Yellowstone National Park, Paige E. Copenhaver-Parry, Daniel B. Tinker

Faculty Publications - Department of Biological & Molecular Science

More frequent fire activity associated with climate warming is expected to increase the extent of young forest stands in fire-prone landscapes, yet growth rates and biomass allocation patterns in young forests that regenerated naturally following stand-replacing fire have not been well studied. We assessed the structural and functional characteristics of young, postfire lodgepole pine (Pinus contorta var. latifolia) trees across the Yellowstone subalpine plateaus to understand the influence of postfire stand density and age on tree-level aboveground biomass (AB), component biomass (bole, branch, foliage), partitioning to components, tree-level aboveground net primary productivity (ANPP) and leaf area (LA). Sixty …

What Kind Of Seed Dormancy Might Palms Have?, Jerry M. Baskin, Carol C. Baskin

Biology Faculty Publications

Palm diaspores are reported to have various kinds of dormancy. However, (1) the embryo is underdeveloped; (2) the endocarp is water permeable; and (3) the diaspores take a long time to germinate. Thus, we conclude that the diaspores of the majority of palm species have morphophysiological dormancy (MPD). The ones that do not have MPD are morphologically dormant.

Structural And Functional Analyses Of A Glutaminyl Cyclase From Ixodes Scapularis Reveal Metal-Independent Catalysis And Inhibitor Binding, Kai-Fa Huang, Hui-Ling Hsu, Shahid Karim, Andrew H.-J. Wang

Faculty Publications

Glutaminyl cyclases (QCs) from mammals and Drosophila are zinc-dependent enzymes that catalyze N-terminal pyroglutamate formation of numerous proteins and peptides. These enzymes have been found to be critical for the oviposition and embryogenesis of ticks, implying that they are possible physiological targets for tick control. Here, 1.10–1.15 Å resolution structures of a metal-independent QC from the black-legged tick Ixodes scapularis (Is-QC) are reported. The structures exhibit the typical scaffold of mammalian QCs but have two extra disulfide bridges that stabilize the central β-­sheet, resulting in an increased thermal stability. Is-QC contains ∼0.5 stoichiometric zinc ions, which could …

Hp1a: A Structural Chromosomal Protein Regulating Transcription, Joel Eissenberg, Sarah C.R. Elgin

Biology Faculty Research

Heterochromatin protein 1 (HP1a in Drosophila) is a conserved eukaryotic chromosomal protein that is prominently associated with pericentric heterochromatin and mediates the concomitant gene silencing. Mechanistic studies implicate HP1 family proteins as 'hub proteins,' able to interact with a variety of chromosomal proteins through the chromo-shadow domain (CSD), as well as to recognize key histone modification sites [primarily histone H3 di/trimethyl Lys9 (H3K9me2/3)] through the chromodomain (CD). Consequently, HP1 has many important roles in chromatin architecture and impacts both gene expression and gene silencing, utilizing a variety of mechanisms. Clearly, HP1 function is altered by context, and potentially by post-translational …

Apolipoprotein E Pathology In Vascular Dementia, Troy T. Rohn, Ryan J. Day, Colin B. Sheffield, Alexander J. Rajic, Wayne W. Poon

Biology Faculty Publications and Presentations

Vascular dementia (VaD) is the second most common form of dementia and is currently defined as a cerebral vessel vascular disease leading to ischemic episodes. Apolipoprotein E (apoE) gene polymorphism has been proposed as a risk factor for VaD, however, to date there are few documented post-mortem studies on apoE pathology in the VaD brain. To investigate a potential role for the apoE protein, we analyzed seven confirmed cases of VaD by immunohistochemistry utilizing an antibody that specifically detects the amino-terminal fragment of apoE. Application of this antibody, termed N-terminal, apoE cleavage fragment (nApoECF) revealed consistent labeling within neurofibrillary tangles …

Formation Of A Salsolinol-Like Compound, The Neurotoxin, 1-Acetyl-6,7-Dihydroxy-1,2,3,4-Tetrahydroisoquinoline, In A Cellular Model Of Hyperglycemia And A Rat Model Of Diabetes, De-Wei Song, Nian Xin, Bing-Jie Xie, Yu-Juan Li, Ling-Yan Meng, Hong-Mei Li, Michael Schläppi, Yu-Lin Deng

Biological Sciences Faculty Research and Publications

There are statistical data indicating that diabetes is a risk factor for Parkinson's disease (PD). Methylglyoxal (MG), a biologically reactive byproduct of glucose metabolism, the levels of which have been shown to be increase in diabetes, reacts with dopamine to form 1-acetyl-6,7-dihydroxy-1,2,3,4-tetrahydroisoquinoline (ADTIQ); this formation may provide further insight into the connection between PD and diabetes. In this study, we investigated the role of ADTIQ in these two diseases to determine in an aim to enhance our understanding of the link between PD and diabetes. To this end, a cell model of hyperglycemia and a rat model of diabetes were …

Snowshoe Hares Display Limited Phenotypic Plasticity To Mismatch In Seasonal Camouflage, Marketa Zimova, L. Scott Mills, Paul M. Lukacs, Michael S. Mitchell

Ecosystem and Conservation Sciences Faculty Publications

As duration of snow cover decreases owing to climate change, species undergoing seasonal colour moults can become colour mismatched with their background. The immediate adaptive solution to this mismatch is phenotypic plasticity, either in phenology of seasonal colour moults or in behaviours that reduce mismatch or its consequences. We observed nearly 200 snowshoe hares across a wide range of snow conditions and two study sites in Montana, USA, and found minimal plasticity in response to mismatch between coat colour and background. We found that moult phenology varied between study sites, likely due to differences in photoperiod and climate, but was …

Life Line March 2014, Otterbein Biology And Earth Science Department

Life Line - The Biology Department Newsletter

Dr. Svitana - In Remembrance of Kyle Miller - Remembering Alima Kasongo - Sustainable Aquarium - Dr. Vasiloff Gives Concert - Student Research in Panama - The Aviary

Shelter-Building Behavior And Natural History Of Two Pyralid Caterpillars Feeding On Piper Stipulaceum, Mariana Abarca, Karina Boege, Alejandro Zaldívar-Riverón

Biological Sciences: Faculty Publications

Shelter-building behavior by caterpillars provides a mechanism of defense against predators, microenvironment enhancement, and in some cases nutritional benefits. This study provides a detailed description of the life cycle and shelter-building process of caterpillars, and identifies constraints and factors influencing this adaptive behavior in Lepidomys n. sp. near proclea Druce (Pyralidae: Chrysauginae), a tropical dry forest pyralid. Five macroscopic larval instars were detected during the life cycle, and activities performed during shelter-building were categorized and timed. Caterpillar predators were identified, and 20% of all collected larvae died due to attack by parasitoid wasps. Shelter-building behavior was found to be constrained …

Assessing High School Biology Academic Achievement By Comparing Traditional Versus Virtual Dissection Of Rat Specimens, Arthur L. Jamison Jr.

Graduate Student Dissertations, Theses, Capstones, and Portfolios

American's lagging student performance on standardized assessments in critical subject areas such as science has in-part led to numerous educational reforms including No Child Left Behind and Race to the Top, resulting in an increased focus on student achievement. International and national government officials note the direct correlation between the value of science and driving the economic prosperity of a nation adding increased pressure to improve science scores in the United States. Local districts and schools struggle with how to improve student achievement in order to meet the requirements of state and federal educational reforms.

The purpose of this mixed-methods …

Chip-Seq And Rna-Seq Reveal An Amrz-Mediated Mechanism For Cyclic Di-Gmp Synthesis And Biofilm Development By Pseudomonas Aeruginosa, Christopher J. Jones, David Newsom, Benjamin Kelly, Yasuhiko Irie, Laura K. Jennings, Binjie Xu, Dominique H. Limoli, Joe J. Harrison, Matthew R. Parsek, Peter White, Daniel J. Wozniak

Biology Faculty Publications

The transcription factor AmrZ regulates genes important for P. aeruginosa virulence, including type IV pili, extracellular polysaccharides, and the flagellum; however, the global effect of AmrZ on gene expression remains unknown, and therefore, AmrZ may directly regulate many additional genes that are crucial for infection. Compared to the wild type strain, a ΔamrZ mutant exhibits a rugose colony phenotype, which is commonly observed in variants that accumulate the intracellular second messenger cyclic diguanylate (c-di-GMP). Cyclic di-GMP is produced by diguanylate cyclases (DGC) and degraded by phosphodiesterases (PDE). We hypothesized that AmrZ limits the intracellular accumulation of c-di-GMP through transcriptional repression …

The Effects Of Substituting True Protein With Non-Protein Nitrogen In Holstein Dairy Heifers Precision-Fed Different Forage To Concentrate Ratios, Noe Alberto Gomez

Animal Science

Understanding the efficiency and digestibility of dietary nutrients in dairy heifers is essential for minimizing costs and environmental impacts of the dairy industry. The objective of this study was to interpret the effects of manipulating rumen-degradable protein (RDP) in a precision feeding system. Eight Holstein ruminally cannulated heifers (14.6 ± 0.1 mo of age, and 386 ± 9.1 kg of weight) were randomly assigned to 2 forage levels: HC (25% forage) and LC (75% forage) and to a degradable protein sequence [0% degradable protein from urea U, 100% casein C (no urea treatment U0); 33% U, 67% C …

Levels Of Altruism, Martin Zwick, Jeffrey Alan Fletcher

Complex Systems Faculty Publications and Presentations

The phenomenon of altruism extends from the biological realm to the human socio-cultural realm. This paper sketches a coherent outline of multiple types of altruism of progressively increasing scope that span these two realms and are grounded in an ever-expanding sense of"self." Discussion of this framework notes difficulties associated with altruisms at different levels. It links scientific ideas about the evolution of cooperation and about hierarchical order to perennial philosophical and religious concerns. It offers a conceptual background for inquiry into societal challenges that call for altruistic behavior, especially the challenge of environmental and social sustainability.

Kif11 Dependent Cell Cycle Progression In Radial Glial Cells Is Required For Proper Neurogenesis In The Zebrafish Neural Tube, Kimberly Johnson, Chelsea Moriarty, Nessy Tania, Alissa Ortman, Kristina Dipietrantonio, Brittany Edens, Jean Eisenman, Deborah Ok, Sarah Krikorian, Jessica Barragan, Christophe Golé, Michael J.F. Barresi

Mathematics Sciences: Faculty Publications

Radial glia serve as the resident neural stem cells in the embryonic vertebrate nervous system, and their proliferation must be tightly regulated to generate the correct number of neuronal and glial cell progeny in the neural tube. During a forward genetic screen, we recently identified a zebrafish mutant in the kif11 loci that displayed a significant increase in radial glial cell bodies at the ventricular zone of the spinal cord. Kif11, also known as Eg5, is a kinesin-related, plus-end directed motor protein responsible for stabilizing and separating the bipolar mitotic spindle. We show here that Gfap+ radial glial cells express …

A Study Of Biliverdin, Serum Albumin And Hemoglobin In The Scincid Lizard, Prasinohaema, Oliver Sinquefield

Honors Capstones

No abstract provided.

Environmental Correlates Of Assemblages Of Fishes In The Tilostoc River Of Central Mexico, Juan Manuel Rivas-González, Felipe De Jesús Rodríguez-Romero, María De Lourdes Ruiz-Gómez, Diego Alfonso Viveros-Guardado, Christopher M. Taylor

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

Ordination, correlation, and regression analyses were used to identify trophic and taxonomic distributional patterns of fishes in the Tilostoc River (located west of Valle de Bravo Lake in the Middle Balsas Basin, central Mexico) and associations of these patterns with environmental variables. Nonmetric multidimensional scaling analysis indicated that trophic and taxonomic assemblages corresponded similarly to measured environmental gradients, especially elevation and velocity of currents. We also compared the trophic structure of assemblages of fishes of the Tilostoc River to that of Terreros Creek, a temperate system of similar size and species richness but with a taxonomically different group of species. …

Bulk Elastic Moduli And Solute Potentials In Leaves Of Freshwater, Coastal, And Marine Hydrophytes. Are Marine Plants More Rigid?, Brant W. Touchette, Sarah E. Marcus, Emily C. Adams

Biological Sciences Faculty Publications

Bulk modulus of elasticity (ɛ), depicting the flexibility of plant tissues, is recognized as an important component in maintaining internal water balance. Elevated ɛ and comparatively low osmotic potential (Ψ_π) may work in concert to effectively maintain vital cellular water content. This concept, termed the ‘cell water conservation hypothesis’, may foster tolerance for lower soil-water potentials in plants while minimizing cell dehydration and shrinkage. Therefore, the accumulation of solutes in marine plants, causing decreases in Ψ_π, play an important role in plant–water relations and likely works with higher ɛ to achieve favourable cell …

Conservation Genetics Of Cyprinid Fishes In The Upper Nueces River Basin In Central Texas, Evan W. Carson, Ashley H. Hanna, Gary P. Garrett, Robert J. Edwards, John R. Gold

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

Sequences of the mitochondrial (mt) NADH dehydrogenase subunit 5 gene (ND5) were acquired to assess genetic diversity and female effective population size (Nef) of two forms of Cyprinella (C. lepida and C. sp. cf lepida) and two species of Dionda (D. serena and D. texensis) in headwaters of three rivers in the upper Nueces River basin in central Texas. As documented in prior studies, two divergent clades of haplotypes of mtDNA were found in both genera: one in the Frio and Sabinal rivers, representing C. lepida and D. serena; one in the …

The Genetic Drift Inventory: A Tool For Measuring What Advanced Undergraduates Have Mastered About Genetic Drift, Rebecca M. Price, Tessa C. Andrews, Teresa L. Mcelhinny, Louise S. Mead, Joel K. Abraham, Anna Thanukos, Kathryn E. Perez

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

Understanding genetic drift is crucial for a comprehensive understanding of biology, yet it is difficult to learn because it combines the conceptual challenges of both evolution and randomness. To help assess strategies for teaching genetic drift, we have developed and evaluated the Genetic Drift Inventory (GeDI), a concept inventory that measures upper-division students’ understanding of this concept. We used an iterative approach that included extensive interviews and field tests involving 1723 students across five different undergraduate campuses. The GeDI consists of 22 agree–disagree statements that assess four key concepts and six misconceptions. Student scores ranged from 4/22 to 22/22. Statements …

Environmental Correlates Of Assemblages Of Fishes In The Tilostoc River Of Central Mexico, Juan Manuel Rivas-González, Felipe De Jesús Rodríguez-Romero, María De Lourdes Ruiz-Gómez, Diego Alfonso Viveros-Guardado, Christopher M. Taylor

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

Ordination, correlation, and regression analyses were used to identify trophic and taxonomic distributional patterns of fishes in the Tilostoc River (located west of Valle de Bravo Lake in the Middle Balsas Basin, central Mexico) and associations of these patterns with environmental variables. Nonmetric multidimensional scaling analysis indicated that trophic and taxonomic assemblages corresponded similarly to measured environmental gradients, especially elevation and velocity of currents. We also compared the trophic structure of assemblages of fishes of the Tilostoc River to that of Terreros Creek, a temperate system of similar size and species richness but with a taxonomically different group of species. …

Transcriptome Analysis Of Listeria Monocytogenes Exposed To Biocide Stress Reveals A Multi-System Response Involving Cell Wall Synthesis, Sugar Uptake, And Motility, Aidan Casey, Edward M. Fox, Stephan Schmitz-Esser, Aidan Coffey, Olivia Mcauliffe, Kieran Jordan

Department of Biological Sciences Publications

Listeria monocytogenes is a virulent food-borne pathogen most often associated with the consumption of “ready-to-eat” foods. The organism is a common contaminant of food processing plants where it may persist for extended periods of time. A commonly used approach for the control of Listeria monocytogenes in the processing environment is the application of biocides such as quaternary ammonium compounds. In this study, the transcriptomic response of a persistent strain of L. monocytogenes (strain 6179) on exposure to a sub-lethal concentration of the quaternary ammonium compound benzethonium chloride (BZT) was assessed. Using RNA-Seq, gene expression levels were quantified by sequencing …