Biology Commons^™

Protein Trap Lines Of Drosophila To Demonstrate Spatio-Temporal Localization Of Proteins In An Undergraduate Lab, Oorvashi Roy Puli, Amit Singh

Biology Faculty Publications

The objective of this teaching note is to generate a laboratory exercise, which allows students to get a hands-on experience of a cell biology technique. The short duration of the laboratory classes is the biggest challenge with the development of a cell biology lab for an undergraduate curriculum. Therefore, it is necessary to design a laboratory exercise that enables the students to carry out cell biological assays in the desired time. This laboratory exercise focuses on tracking protein expression levels along a spatial (space) and temporal (time) axis in developing Drosophila melanogaster organ primordium. Here we use the protein trap …

Quantitative Comparison Of Cis-Regulatory Element (Cre) Activities In Transgenic Drosophila Melanogaster, William A. Rogers, Thomas M. Williams

Biology Faculty Publications

Gene expression patterns are specified by cis-regulatory element (CRE) sequences, which are also called enhancers or cis-regulatory modules. A typical CRE possesses an arrangement of binding sites for several transcription factor proteins that confer a regulatory logic specifying when, where, and at what level the regulated gene(s) is expressed. The full set of CREs within an animal genome encodes the organism′s program for development¹, and empirical as well as theoretical studies indicate that mutations in CREs played a prominent role in morphological evolution^2-4. Moreover, human genome wide association studies indicate that genetic variation in CREs …

Molecular Systematics Of The Middle American Genus Hypopachus (Anura: Microhylidae), Eli Greenbaum, Eric N. Smith, Rafael O. De Sá

Biology Faculty Publications

We present the first phylogenetic study on the widespread Middle American microhylid frog genus Hypopachus. Partial sequences of mitochondrial (12S and 16S ribosomal RNA) and nuclear (rhodopsin) genes (1275 bp total) were analyzed from 43 samples of Hypopachus, three currently recognized species of Gastrophryne, and seven arthroleptid, brevicipitid and microhylid outgroup taxa. Maximum parsimony (PAUP), maximum likelihood (RAxML) and Bayesian inference (MrBayes) optimality criteria were used for phylogenetic analyses, and BEAST was used to estimate divergence dates of major clades. Population-level analyses were conducted with the programs NETWORK and Arlequin. Results confirm the placement of Hypopachus …

Heart And Ventilatory Measures In Crayfish During Copulation, Richard M. Cooper, Heidi Schapker Finucane, Megan Adami, Robin L. Cooper

Biology Faculty Publications

Monitoring heart rate (HR) and ventilatory rate (VR) during defined sensory stimuli and during aggressive and submissive social interactions has provided additional information of a crayfish's physiological state which is not achieved by behavioral observations. In this study, the HR and VR of crayfish were monitored before, during and after the act of copulation in both heterosexual partners. The female crayfish abruptly reduces HR and VR during copulation but the male maintains HR and VR. After separation from copulation the female HR and VR are elevated, potentially paying back the O₂ debt. The tight relationship with HR and VR …

Laboratory Diagnosis Of Clostridium Difficile Infection: Can Molecular Amplification Methods Move Us Out Of Uncertainty?, Fred C. Tenover, Ellen Jo Baron, Lance R. Peterson, David Persing

Biology Faculty Publications

The laboratory diagnosis of Clostridium difficile infection (CDI) continues to be challenging. Recent guidelines from professional societies in the United States note that enzyme immunoassays for toxins A and B do not have adequate sensitivity to be used alone for detecting CDI, yet the optimal method for diagnosing this infection remains unclear. Nucleic acid amplification tests (NAATs) that target chromosomal toxin genes (usually the toxin B gene, tcdB) show high sensitivity and specificity, provide rapid results, and are amenable to both batch and on-demand testing, but these tests were not universally recommended for routine use in the recent guidelines. …

Linking Fruit Traits To Variation In Predispersal Vertebrate Seed Predation, Insect Seed Predation, And Pathogen Attack, Noelle G. Beckman, Helene C. Muller-Landau

Biology Faculty Publications

The importance of vertebrates, invertebrates, and pathogens for plant communities has long been recognized, but their absolute and relative importance in early recruitment of multiple coexisting tropical plant species has not been quantified. Further, little is known about the relationship of fruit traits to seed mortality due to natural enemies in tropical plants. To investigate the influences of vertebrates, invertebrates, and pathogens on reproduction of seven canopy plant species varying in fruit traits, we quantified reductions in fruit development and seed germination due to vertebrates, invertebrates, and fungal pathogens through experimental removal of these enemies using canopy exclosures, insecticide, and …

Loss-Of-Function Of Constitutive Expresser Of Pathogenesis Related Genes5 Affects Potassium Homeostasis In Arabidopsis Thaliana, Monica Borghi, Ana Rus, David E. Salt

Biology Faculty Publications

Here, we demonstrate that the reduction in leaf K+ observed in a mutant previously identified in an ionomic screen of fast neutron mutagenized Arabidopsis thaliana is caused by a loss-of-function allele of CPR5, which we name cpr5-3. This observation establishes low leaf K+ as a new phenotype for loss-of-function alleles of CPR5. We investigate the factors affecting this low leaf K+ in cpr5 using double mutants defective in salicylic acid (SA) and jasmonic acid (JA) signalling, and by gene expression analysis of various channels and transporters. Reciprocal grafting between cpr5 and Col-0 was used to determine the relative importance of …

Activation Of Jnk Signaling Mediates Amyloid-Ss- Dependent Cell Death, Meghana Tare, Rohan Modi, Jaison Nainaparampil, Oorvashi Roy Puli, Shimpi Bedi, Pedro Fernandez-Funez, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Background: Alzheimer's disease (AD) is an age related progressive neurodegenerative disorder. One of the reasons for Alzheimer's neuropathology is the generation of large aggregates of Aß42 that are toxic in nature and induce oxidative stress, aberrant signaling and many other cellular alterations that trigger neuronal cell death. However, the exact mechanisms leading to cell death are not clearly understood.

Methodology/Principal Findings: We employed a Drosophila eye model of AD to study how Aß42 causes cell death. Misexpression of higher levels of Aß42 in the differentiating photoreceptors of fly retina rapidly induced aberrant cellular phenotypes and cell death. We found that …

No Evidence Of Association Between Hiv-1 And Malaria In Populations With Low Hiv-1 Prevalence, Diego F. Cuadros, Adam J. Branscum, Gisela García-Ramos

Biology Faculty Publications

BACKGROUND: The geographic overlap between HIV-1 and malaria has generated much interest in their potential interactions. A variety of studies have evidenced a complex HIV-malaria interaction within individuals and populations that may have dramatic effects, but the causes and implications of this co-infection at the population level are still unclear. In a previous publication, we showed that the prevalence of malaria caused by the parasite Plasmodium falciparum is associated with HIV infection in eastern sub-Saharan Africa. To complement our knowledge of the HIV-malaria co-infection, the objective of this work was to assess the relationship between malaria and HIV prevalence in …

Effect Of Variable Transmission Rate On The Dynamics Of Hiv In Sub-Saharan Africa, Diego F. Cuadros, Phillip H. Crowley, Ben Augustine, Sarah L. Stewart, Gisela García-Ramos

Biology Faculty Publications

BACKGROUND: The cause of the high HIV prevalence in sub-Saharan Africa is incompletely understood, with heterosexual penile-vaginal transmission proposed as the main mechanism. Heterosexual HIV transmission has been estimated to have a very low probability; but effects of cofactors that vary in space and time may substantially alter this pattern.

METHODS: To test the effect of individual variation in the HIV infectiousness generated by co-infection, we developed and analyzed a mathematical sexual network model that simulates the behavioral components of a population from Malawi, as well as the dynamics of HIV and the co-infection effect caused by other infectious diseases, …

Disseminated Neoplasia And Clam Populations In A Canadian National Park-Kouchibouguac National Park., S. Anne Boettger, M J. Abgrall, N Taraska, L Leblanc, E Tremblay

Biology Faculty Publications

No abstract provided.

Disseminated Neoplasia In Mya Arenaria Linked To Chronic Heavy Metal Pollution., S. Anne Boettger, N G. Taraska, J Joseph, C W. Walker

Biology Faculty Publications

No abstract provided.

The Cellular Model Of Eastern Oyster (Grassostrea Virginica) Shell Formation, Andrew S. Mount, Neeraj V. Gohad, Karolyn Hansen, Mary Beth Johnstone, Douglas C. Hansen

Biology Faculty Publications

No abstract provided.

Survival, Breeding Frequency, And Migratory Orientation In The Jefferson Salamander, Ambystoma Jeffersonianum, Stephen P. De Lisle, Kristine L. Grayson

Biology Faculty Publications

Accurate estimates of demographic parameters, such as survival and breeding frequency, are necessary for the conservation and management of animal populations. Additionally, life-history data are required for gaining an empirical understanding of the ecology of natural populations. We monitored a population of Jefferson Salamanders (Ambystoma jeffersonianum) breeding in a permanent mountain-top pond at the southern limit of this species’ geographic range in Virginia over four years. We used closed multistate mark-recapture models with Pollock's robust design to estimate the demographic parameters of this population. Additionally, we used point-of-capture data to compare the orientation of migrations into and out …

Mechanical Test Methods For Assessing Porcine Carotid And Uterine Artery Burst Pressure Following Ex Vivo Ultrasonic Ligature Seal And Transection, Carissa M. Krane, Margaret Pinnell, Courtney Gardner, Mercedes Thompson, James Coleman, Robert Wilkens

Biology Faculty Publications

A test method was developed to identify those variables important for assessing the performance of ultrasonic surgical devices in ex vivo ligature sealing of porcine carotid and uterine arteries. Ruggedness testing using a small sample size in pilot experiments was conducted using a newly developed test method in an effort to assess the usefulness of this methodology and to identify test variables that might warrant further testing. The development of this test method included the use of a custom-designed prototypic tension device for load-controlled ex vivo vessel stretching during saline perfusion and subsequent seal and transection of porcine arteries with …

Cooperative And Antagonistic Contributions Of Two Heterochromatin Proteins To Transcriptional Regulation Of The Drosophila Sex Determination Decision, Hui Li, Janel Rodriguez, Youngdong Yoo, Momin Mohammed Shareef, Ramakrishna Badugu, Jamila I. Horabin, Rebecca Kellum

Biology Faculty Publications

Eukaryotic nuclei contain regions of differentially staining chromatin (heterochromatin), which remain condensed throughout the cell cycle and are largely transcriptionally silent. RNAi knockdown of the highly conserved heterochromatin protein HP1 in Drosophila was previously shown to preferentially reduce male viability. Here we report a similar phenotype for the telomeric partner of HP1, HOAP, and roles for both proteins in regulating the Drosophila sex determination pathway. Specifically, these proteins regulate the critical decision in this pathway, firing of the establishment promoter of the masterswitch gene, Sex-lethal (Sxl). Female-specific activation of this promoter, Sxl(Pe), is essential to females, as it provides SXL …

Yeast Bax Inhibitor, Bxi1p, Is An Er-Localized Protein That Links The Unfolded Protein Response And Programmed Cell Death In Saccharomyces Cerevisiae, Nicanor Austriaco, James Cebulski, Joshua Malouin, Nathan Pinches, Vincent Cascio

Biology Faculty Publications

Bax inhibitor-1 (BI-1) is an anti-apoptotic gene whose expression is upregulated in a wide range of human cancers. Studies in both mammalian and plant cells suggest that the BI-1 protein resides in the endoplasmic reticulum and is involved in the unfolded protein response (UPR) that is triggered by ER stress. It is thought to act via a mechanism involving altered calcium dynamics. In this paper, we provide evidence that the Saccharomyces cerevisiae protein encoded by the open reading frame, YNL305C, is a bona fide homolog for BI-1. First, we confirm that yeast cells from two different strain backgrounds lacking YNL305C, …

Life History Benefits Of Residency In A Partially Migrating Pond-Breeding Amphibian, Kristine L. Grayson, Larissa L. Bailey, Henry M. Wilbur

Biology Faculty Publications

Species with partial migration, where a portion of a population migrates and the other remains residential, provide the opportunity to evaluate conditions for migration and test mechanisms influencing migratory decisions. We conducted a five-year study of two populations of red-spotted newts (Notophthalmus viridescens), composed of individuals that either remain as residents in the breeding pond over the winter or migrate to the terrestrial habitat. We used multistate mark-recapture methods to (1) test for differences in survival probability between migrants and residents, (2) determine if migrants breed every year or skip opportunities for reproduction, and (3) estimate the frequency …

Ecosystem Management Of The Missouri River From Gavins Point Dam To Ponca State Park, Nebraska, Robert S. Nebel

Biology Faculty Publications

•Authorized by a 1978 amendment to the National Parks and Recreation Act (PL 95- 625) which amended the Wild and Scenic Rivers Act of 1968 (PL 90-542)

• Corps is authorized to construct recreational development, bank stabilization, and other recreational river features as necessary to support the values for which the river was designated

• Life-of-project funding ceiling of $21 million; approximately $3.2 million spent to date

• The Corps and National Park Service signed a 1980 Cooperative Agreement outlining each agency's responsibilities

• The General Management Plan has recently been updated (1999) with an environmental emphasis

Design Of A Factorial Experiment With Randomization Restrictions To Assess Medical Device Performance On Vascular Tissue, Wiebke Diestelkamp, Carissa M. Krane, Margaret Pinnell

Biology Faculty Publications

Background: Energy-based surgical scalpels are designed to efficiently transect and seal blood vessels using thermal energy to promote protein denaturation and coagulation. Assessment and design improvement of ultrasonic scalpel performance relies on both in vivo and ex vivo testing. The objective of this work was to design and implement a robust, experimental test matrix with randomization restrictions and predictive statistical power, which allowed for identification of those experimental variables that may affect the quality of the seal obtained ex vivo.

Methods: The design of the experiment included three factors: temperature (two levels); the type of solution used to perfuse the …

Endo-Porter–Mediated Delivery Of Phosphorodiamidate Morpholino Oligos (Pmos) In Erythrocyte Suspension Cultures From Cope's Gray Treefrog Hyla Chrysoscelis, Venkateshwar Mutyam, Matthew V. Puccetti, James Frisbie, David L. Goldstein, Carissa M. Krane

Biology Faculty Publications

Cope's gray treefrog, Hyla chrysoscelis, is a freeze-tolerant anuran that accumulates cryoprotective glycerol during cold acclimation. H. chrysoscelis erythrocytes express the aquaglyceroporin HC-3, which facilitates transmembrane glycerol and water movement. Aquaglyceroporins have no pharmacological inhibitors, and no genetic knockout tools currently exist for H. chrysoscelis. A phosphorodiamidate morpholino oligo (PMO)–mediated expression knockdown approach was therefore pursued to provide a model for testing the role of HC-3. We describe a novel procedure optimized for specific, efficient knockdown of HC-3 expression in amphibian erythrocyte suspensions cultured at nonmammalian physiological temperatures using Endo-Porter. Our protocol includes three critical components: pre-incubation at 37°C, …

A Complement Receptor C5a Antagonist Regulates Epithelial To Mesenchymal Transition And Crystallin Expression After Lens Cataract Surgery In Mice, Rinako Suetsugu-Maki, Nobuyasu Maki, Timothy P. Fox, Kenta Nakamura, Richard Cowper.Solari, Craig R. Tomlinson, Hongchang Qu, John D. Lambris, Panagiotis A. Tsonis

Biology Faculty Publications

Purpose: To evaluate the effects of complement employing a mouse model for secondary cataract. Methods: The role of complement receptor C5a (CD88) was evaluated after cataract surgery in mice. An antagonist specific to C5a receptor was administered intraperitoneally to mice. Epithelial to mesenchymal transition (EMT) was evaluated by alpha-smooth muscle actin (α-SMA) staining and proliferation by bromodeoxyuridine (5-bromo-2'- deoxyuridine, BrdU) incorporation. Gene expression patterns was examined by microarray analysis and quantitative polymerase chain reaction (QPCR). Results: We found that administration of a C5aR antagonist in C57BL/6J mice decreases EMT, as evidenced by α-SMA expression, and cell proliferation. Gene expression by …

Structure/Function Assessment Of Synapses At Motor Nerve Terminals, Andrew Fredericks Moser Johnstone, Kert Viele, Robin L. Cooper

Biology Faculty Publications

The release of transmitter at neuromuscular junctions (NMJ) of the opener muscle in crayfish is quantal in nature. This NMJ offers the advantage of being able to record quantal events at specific visually identified release sites, thus allowing measurement of the physiological parameters of vesicle release and its response to be directly correlated with synaptic structure.

These experiments take advantage of areas between the varicosities on the nerve terminal that we define as "stems." Stems were chosen as the region to study because of their low synaptic output due to fewer synaptic sites. Through 3D reconstruction from hundreds of serial …

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 …

Membrane Potentials, Synaptic Responses, Neuronal Circuitry, Neuromodulation And Muscle Histology Using The Crayfish: Student Laboratory Exercises, Brittany Baierlein, Alison L. Thurow, Harold L. Atwood, Robin L. Cooper

Biology Faculty Publications

The purpose of this report is to help develop an understanding of the effects caused by ion gradients across a biological membrane. Two aspects that influence a cell's membrane potential and which we address in these experiments are: (1) Ion concentration of K⁺ on the outside of the membrane, and (2) the permeability of the membrane to specific ions. The crayfish abdominal extensor muscles are in groupings with some being tonic (slow) and others phasic (fast) in their biochemical and physiological phenotypes, as well as in their structure; the motor neurons that innervate these muscles are correspondingly different in …

Physiological Experimentation With The Crayfish Hindgut: A Student Laboratory Exercise, Ann S. Cooper, Bonnie Leksrisawat, Allison B. Gilberts, A. Joffre Mercier, Robin L. Cooper

Biology Faculty Publications

The purpose of the report is to describe dissection techniques for preparing the crayfish hindgut and to demonstrate how to make physiological recordings with a force transducer to monitor the strength of contraction. In addition, we demonstrate how to visually monitor peristaltic activity, which can be used as a bioassay for various peptides, biogenic amines and neurotransmitters. This preparation is amenable to student laboratories in physiology and for demonstrating pharmacological concepts to students. This preparation has been in use for over 100 years, and it still offers much as a model for investigating the generation and regulation of peristaltic rhythms …

Modeling Biological Membranes With Circuit Boards And Measuring Electrical Signals In Axons: Student Laboratory Exercises, Martha M. Robinson, Jonathan M. Martin, Harold L. Atwood, Robin L. Cooper

Biology Faculty Publications

This is a demonstration of how electrical models can be used to characterize biological membranes. This exercise also introduces biophysical terminology used in electrophysiology. The same equipment is used in the membrane model as on live preparations. Some properties of an isolated nerve cord are investigated: nerve action potentials, recruitment of neurons, and responsiveness of the nerve cord to environmental factors.

On The Use Of Log-Transformation Vs. Nonlinear Regression For Analyzing Biological Power-Laws, Xiao Xiao, Ethan P. White, M. B. Hooten, Susan L. Durham

Biology Faculty Publications

Power-law relationships are among the most well-studied functional relationships in biology. Recently the common practice of fitting power-laws using linear regression on log-transformed data (LR) has been criticized, calling into question the conclusions of hundreds of studies. It has been suggested that nonlinear regression (NLR) is preferable, but no rigorous comparison of these two methods has been conducted. Using Monte Carlo simulations we demonstrate that the error distribution determines which method performs better, with LR better characterizing data with multiplicative lognormal error and NLR better characterizing data with additive, homoscedastic, normal error. Analysis of 471 biological power-laws shows that both …

Species Compositionand Abundance Of Mammalian Communities, K. M. Thibault, S. R. Supp, M. Griffin, Ethan P. White, S.K. Morgan Ernest

Biology Faculty Publications

Ecologists have long sought to understand the mechanisms underlying the assembly and structure of communities. Such understanding is relevant to both basic science and conservation-related issues. The macroecological approach to this problem involves asking scientific questions using a large number of communities in order to elucidate generalities in pattern and process. Such analyses are typically conducted using a substantial amount of data from a particular taxonomic group across a diversity of systems. Large community databases are available for a number of taxa, but no publicly available database exists for mammals. Given the logistical challenges of collecting such data de novo, …

Variation, Systematics, And Relationships Of The Leptodactylus BolivianusComplex (Amphibia: Anura: Leptodactylidae), W. R. Heyer, Rafael O. De Sá

Biology Faculty Publications

A cluster of morphologically similar frogs of the genus Leptodactylus having a pair of distinct dorsolateral folds on the dorsum and well-developed lateral fringes on the toes has never been systematically evaluated by examining materials from throughout its geographic range. The species involved are herein referred to as members of the Leptodactylus bolivianus complex. There have been three names proposed for members of this complex: Leptodactylus bolivianus Boulenger, 1898; Leptodactylus insularum Barbour, 1906; and Leptodactylus romani Melin, 1941. The collective range for the L. bolivianus complex is from Costa Rica southward through Panama, extending across northern South America (east of …