Biology Commons^™

The Lineage-Specific Evolution Of Aquaporin Gene Clusters Facilitated Tetrapod Terrestrial Adaptation, Roderick Nigel Finn, François Chauvigné, Jón Baldur Hlidberg, Christopher P. Cutler, Joan Cerdà

Department of Biology Faculty Publications

A major physiological barrier for aquatic organisms adapting to terrestrial life is dessication in the aerial environment. This barrier was nevertheless overcome by the Devonian ancestors of extant Tetrapoda, but the origin of specific molecular mechanisms that solved this water problem remains largely unknown. Here we show that an ancient aquaporin gene cluster evolved specifically in the sarcopterygian lineage, and subsequently diverged into paralogous forms of AQP2, -5, or -6 to mediate water conservation in extant Tetrapoda. To determine the origin of these apomorphic genomic traits, we combined aquaporin sequencing from jawless and jawed vertebrates with broad taxon assembly of …

An Active Role For The Ribosome In Determining The Fate Of Oxidized Mrna, Carrie L. Simms, Benjamin H. Hudson, John W. Mosior, Ali S. Rangwala, Hani S. Zaher

Biology Faculty Publications & Presentations

Chemical damage to RNA affects its functional properties and thus may pose a significant hurdle to the translational apparatus; however, the effects of damaged mRNA on the speed and accuracy of the decoding process and their interplay with quality-control processes are not known. Here, we systematically explore the effects of oxidative damage on the decoding process using a well-defined bacterial in vitro translation system. We find that the oxidative lesion 8-oxoguanosine (8-oxoG) reduces the rate of peptide-bond formation by more than three orders of magnitude independent of its position within the codon. Interestingly, 8-oxoG had little effect on the fidelity …

Ribosomes Left In The Dust: Diverse Strategies For Peptide-Mediated Translation Stalling, Benjamin H. Hudson, Hani S. Zaher

Biology Faculty Publications & Presentations

In two recent papers, Arenz et al. (2014a) and Bischoff et al. (2014) provide structural insights into drug-induced, peptide-mediated stalling of the ribosome.

Characterization Of Juvenile Hormone Biosynthetic Enzymes In The Mosquito, Aedes Aegypti, Pratik Nyati

FIU Electronic Theses and Dissertations

The juvenile hormones (JHs) are sesquiterpenoid compounds that play a central role in insect reproduction, development and behavior. They are synthesized and secreted by a pair of small endocrine glands, the corpora allata (CA), which are intimately connected to the brain. The enzymes involved in the biosynthesis of JH are attractive targets for the control of mosquito populations. This dissertation is a comprehensive functional study of five Aedes aegypti CA enzymes, HMG-CoA synthase (AaHMGS), mevalonate kinase (AaMK), phosphomevalonate kinase (AaPMK), farnesyl diphosphate synthase (AaFPPS) and farnesyl pyrophosphate phosphatase (AaFPPase).

The …

Cross-Disciplinary Sciences At Gettysburg College: Second Annual Poster Presentation, X-Sig

Student Publications

This booklet includes Biology student presentations by: Taylor Bury, Abigail Dworkin-Brodsky, Mary Pearce, Jasper Leavitt, Morgan Panzer, Ellen Petley, Kalli Qutub, Taylor Randell, Samantha Eck, Lana McDowell, Jenn Soroka, Celina Harris, Natalie Tanke, Alexandra Turano, and Caroline Garliss.

This booklet includes Biochemistry & Molecular Biology student presentations by: Matthew Dunworth, Andrew Sydenstricker, Brianne Tomko, Albert Vill, Warren Campbell, David Van Doren, Kevin Mrugalski, Stacey Heaver, Alecia Achimovich, and Katherine Boas.

This booklet includes Chemistry student presentations by: Kristen Baker, Laura Lee, Kathryn Fodale, Daniel Ruff, Michael Counihan, Ida DiMucci, Joshua Sgroi, Celina Harris, and Natalie Tanke.

This booklet include Health …

A Distinct Tethering Step Is Vital For Vacuole Membrane Fusion, Michael Zick, William T. Wickner

Dartmouth Scholarship

Past experiments with reconstituted proteoliposomes, employing assays that infer membrane fusion from fluorescent lipid dequenching, have suggested that vacuolar SNAREs alone suffice to catalyze membrane fusion in vitro. While we could replicate these results, we detected very little fusion with the more rigorous assay of lumenal compartment mixing. Exploring the discrepancies between lipid-dequenching and content-mixing assays, we surprisingly found that the disposition of the fluorescent lipids with respect to SNAREs had a striking effect. Without other proteins, the association of SNAREs in trans causes lipid dequenching that cannot be ascribed to fusion or hemifusion. Tethering of the SNARE-bearing proteoliposomes was …

Acute Effects Of Tio2 Nanomaterials On The Viability And Taxonomic Composition Of Aquatic Bacterial Communities Assessed Via High-Throughput Screening And Next Generation Sequencing, Binh Chu, Tiezheng Tong, Jean-François Gaillard, Kimberley A. Gray, John J. Kelly

Biology: Faculty Publications and Other Works

The nanotechnology industry is growing rapidly, leading to concerns about the potential ecological consequences of the release of engineered nanomaterials (ENMs) to the environment. One challenge of assessing the ecological risks of ENMs is the incredible diversity of ENMs currently available and the rapid pace at which new ENMs are being developed. High-throughput screening (HTS) is a popular approach to assessing ENM cytotoxicity that offers the opportunity to rapidly test in parallel a wide range of ENMs at multiple concentrations. However, current HTS approaches generally test one cell type at a time, which limits their ability to predict responses of …

Xrf Analyses Of Prehanford Orchards, Komal Rana

STAR Program Research Presentations

Subsequent to 1943, the use of Lead Arsenic was banned from the Orchards standing on the Hanford site. This use of Lead Arsenate pesticide was popular among the orchard owners and was dispersed over the site in a myriad of ways. The presence of the traces of lead and arsenic are found today, more than half a century later. Using a portable X-ray florescence analyzer (XRF), the values of lead and arsenic are evaluated while determining the efficiency of the equipment itself. Samples from different decision sites were collected, with lead arsenic values in the low, high and medium range …

Metagenomic Identification Of A Novel Salt Tolerance Gene From The Human Gut Microbiome Which Encodes A Membrane Protein With Homology To A Brp/Blh-Family Beta-Carotene 15,15'-Monooxygenase, Eamonn P. Culligan, Roy D. Sleator, Julian R. Marchesi, Colin Hill

Department of Biological Sciences Publications

The human gut microbiome consists of at least 3 million non-redundant genes, 150 times that of the core human genome. Herein, we report the identification and characterisation of a novel stress tolerance gene from the human gut metagenome. The locus, assigned brpA, encodes a membrane protein with homology to a brp/blh-family β-carotene monooxygenase. Cloning and heterologous expression of brpA in Escherichia coli confers a significant salt tolerance phenotype. Furthermore, when cultured in the presence of exogenous β-carotene, cell pellets adopt a red/orange pigmentation indicating the incorporation of carotenoids in the cell membrane.

[Accepted Article Manuscript Version (Postprint)] Auxin Input Pathway Disruptions Are Mitigated By Changes In Auxin Biosynthetic Gene Expression In Arabidopsis, Gretchen Spiess, Amanda Hausman, Peng Yu, Jerry Cohen, Rebekah Rampey, Bethany Zolman

Biology Department Faculty Works

Auxin is a phytohormone involved in cell elongation and division. Levels of indole-3-acetic acid (IAA), the primary auxin, are tightly regulated through biosynthesis, degradation, sequestration, and transport. IAA is sequestered in reversible processes by adding amino acids, polyol or simple alcohols, or sugars, forming IAA conjugates, or through a two-carbon elongation forming indole-3-butyric acid. These sequestered forms of IAA alter hormone activity. To gain a better understanding of how auxin homeostasis is maintained, we have generated Arabidopsis (Arabidopsis thaliana) mutants that combine disruptions in the pathways, converting IAA conjugates and indole-3-butyric acid to free IAA. These mutants show phenotypes indicative …

Anthropogenic Litter In Urban Freshwater Ecosystems: Distribution And Microbial Interactions, Timothy Hoellein, Miguel Rojas, Adam Pink, Joseph Gasior, John J. Kelly

Biology: Faculty Publications and Other Works

Accumulation of anthropogenic litter (i.e. garbage; AL) and its ecosystem effects in marine environments are well documented. Rivers receive AL from terrestrial habitats and represent a major source of AL to marine environments, but AL is rarely studied within freshwater ecosystems. Our objectives were to 1) quantify AL density in urban freshwaters, 2) compare AL abundance among freshwater, terrestrial, and marine ecosystems, and 3) characterize the activity and composition of AL biofilms in freshwater habitats. We quantified AL from the Chicago River and Chicago's Lake Michigan shoreline, and found that AL abundance in Chicago freshwater ecosystems was comparable to previously …

Deriving High-Resolution Protein Backbone Structure Propensities From All Crystal Data Using The Information Maximization Device, Armando D. Solis

Publications and Research

The most informative probability distribution functions (PDFs) describing the Ramachandran phi-psi dihedral angle pair, a fundamental descriptor of backbone conformation of protein molecules, are derived from high-resolution X-ray crystal structures using an information-theoretic approach. The Information Maximization Device (IMD) is established, based on fundamental information-theoretic concepts, and then applied specifically to derive highly resolved phi-psi maps for all 20 single amino acid and all 8000 triplet sequences at an optimal resolution determined by the volume of current data. The paper shows that utilizing the latent information contained in all viable high-resolution crystal structures found in the Protein Data Bank (PDB), …

Biological Surveys Of Selected Lower Grand River Streams: Ionia, Kent, Muskegon, And Ottawa Counties, Michigan, August-September 2014, Michigan Department Of Environmental Quality Water Resources Division

Faculty and Professional Research

The biologic integrity and physical habitat conditions of the lower Grand River (Hydrologic Unit Code (HUC) 04050006) and selected tributaries were surveyed during August and September 2014 by staff of the Surface Water Assessment Section (SWAS), Water Resources Division (WRD). The objectives of this study were to: 1. Evaluate the attainment status of the other indigenous aquatic life and wildlife (OIALW) designated use. 2. Identify and investigate effects of nonpoint sources (NPS) of pollution. 3. Satisfy monitoring requests submitted by internal and external customers.

Abundance And Diversity Of Ammonia-Oxidizing Archaea And Bacteria In Sediments Of Trophic End Members Of The Laurentian Great Lakes, Erie And Superior, Annette Bollmann, George S. Bullerjahn, Robert Michael Mckay

Great Lakes Institute for Environmental Research Publications

Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyro-sequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy …

Spatial Variability In Iron Nutritional Status Of Large Diatoms In The Sea Of Okhotsk With Special Reference To The Amur River Discharge, K. Suzuki, A. Hattori-Saito, Y. Sekiguchi, J. Nishioka, M. Shigemitsu, T. Isada, H. Liu, R. M.L. Mckay

Great Lakes Institute for Environmental Research Publications

The Sea of Okhotsk is known as one of the most biologically productive regions among the world's oceans, and its productivity is supported in part by the discharge of iron (Fe)-rich water from the Amur River. However, little is known about the effect of riverine-derived Fe input on the physiology of the large diatoms which often flourish in surface waters of the productive continental shelf region. We conducted diatom-specific immunochemical ferredoxin (Fd) and flavodoxin (Fld) assays in order to investigate the spatial variability of Fe nutritional status in the microplankton-sized (20-200 1/4m; hereafter micro-sized) diatoms. The Fd index, defined as …

The Mechanism Of Small Rna Biogenesis, Degradation, And Function In Arabidopsis, Meng Xie

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

Eukaryotic small RNAs play important roles in many biological processes through sequence-specific RNA silencing. In plants, there are mainly two small RNAs triggering gene silencing: microRNAs (miRNAs) and small interfering RNAs (siRNAs). The biogenesis and precise regulation of small RNA abundance are crucial for plant growth, development, genomic stability, and the resistance to both abiotic and biotic stresses. In this study, we used Arabidopsis thaliana, the model plant, to study the mechanism of RNA-directed DNA methylation (RdDM), in which siRNAs can trigger DNA methylation and gene silencing. In addition, we investigated the mechanism of miRNA biogenesis and degradation. For …

2-Acylamido Analogues Of N-Acetylglucosamine Prime Formation Of Chitin Oligosaccharides By Yeast Chitin Synthase 2, Jacob Gyore, Archana Parameswar, Carleigh Hebbard, Younghoon Oh, Erfei Bi, Alexei Demchenko, Neil Price, Peter Orlean

Chemistry & Biochemistry Faculty Works

Chitin, a homopolymer of β1,4-linked N-acetylglucosamine (GlcNAc) residues, is a key component of the cell walls of fungi and the exoskeletons of arthropods. Chitin synthases transfer GlcNAc from UDP-GlcNAc to preexisting chitin chains in reactions that are typically stimulated by free GlcNAc. The effect of GlcNAc was probed by using a yeast strain expressing a single chitin synthase, Chs2, by examining formation of chitin oligosaccharides (COs) and insoluble chitin, and by replacing GlcNAc with 2-acylamido analogues of GlcNAc. Synthesis of COs was strongly dependent on inclusion of GlcNAc in chitin synthase incubations, and N,N′-diacetylchitobiose (GlcNAc2) was the major reaction product. …

Defining The Sites Of Interaction Of The Fancd2, Fance, And Fancl Proteins, Joseph Mcclanaghan

Senior Honors Projects

Fanconi anemia (FA) is a rare genetic disease characterized by congenital defects, bone marrow failure and increased cancer susceptibility. FA is caused by mutations in any one of 16 genes. These genes encode for proteins that function in the FA-BRCA pathway to repair damaged DNA. Because of its important r­­­ole in DNA repair, this pathway is considered a major cellular tumor suppressor pathway, i.e. is critical for the prevention of cancer. Underscoring this fact, several of the FA genes - including BRCA2, BRIP1, PALB2, and RAD51C - are bona fide breast and ovarian cancer susceptibility genes.

My …

Antimicrobial And Antiinsectan Phenolic Metabolites Of Dalea Searlsiae, Gil Belofsky, Mario Aronica, Eric Foss, Jane Diamond, Felipe Santana, Jacob Darley, Patrick F. Dowd, Christina M. Coleman, Daneel Ferreira

All Faculty Scholarship for the College of the Sciences

Continued interest in the chemistry of Dalea spp. led to investigation of Dalea searlsiae, a plant native to areas of the western United States. Methanol extractions of D. searlsiae roots and subsequent chromatographic fractionation afforded the new prenylated and geranylated flavanones malheurans A–D (1–4) and known flavanones (5 and 6). Known rotenoids (7 and 8) and isoflavones (9 and 10) were isolated from aerial portions. Structure determination of pure compounds was accomplished primarily by extensive 1D- and 2D-NMR spectroscopy. The absolute configurations of compounds 1–5, 7 …

The Last Frontier: Catch Records Of White Sharks (Carcharodon Carcharias) In The Northwest Pacific Ocean, Heather M. Christianson, Victor Lin, Sho Tanaka, Anatoly Velikanov, Henry F. Mollet, Sabine T. Wintner, Sonja V. Fordham, Aaron T. Fisk, Nigel E. Hussey

Great Lakes Institute for Environmental Research Publications

White sharks are highly migratory apex predators, globally distributed in temperate, sub-tropical, and tropical waters. Knowledge of white shark biology and ecology has increased recently based on research at known aggregation sites in the Indian, Atlantic, and Northeast Pacific Oceans; however, few data are available for the Northwest Pacific Ocean. This study provides a meta-analysis of 240 observations of white sharks from the Northwest Pacific Ocean between 1951 and 2012. Records comprise reports of bycatch in commercial fisheries, media accounts, personal communications, and documentation of shark-human interactions from Russia (n = 8), Republic of Korea (22), Japan (129), China (32), …

Carbon Source-Dependent Alteration Of Puf3p Activity Mediates Rapid Changes In The Stabilities Of Mrnas Involved In Mitochondrial Function, Melanie Miller, Joseph Russo, Anthony Fischer, Florencia Leban, Wendy Olivas

Biology Department Faculty Works

The Puf family of RNA-binding proteins regulates gene expression primarily by interacting with the 3′ untranslated region (3′ UTR) of targeted mRNAs and inhibiting translation and/or stimulating decay. Physical association and computational analyses of yeast Puf3p identified >150 potential mRNA targets involved in mitochondrial function. However, only COX17 has been established as a target of Puf3p-mediated deadenylation and decapping. We have identified 10 new targets that are rapidly degraded in a Puf3p-dependent manner. We also observed changes in Puf3p activity in response to environmental conditions. Puf3p promotes rapid degradation of mRNA targets in the fermentable carbon source dextrose. However, Puf3p-mediated …

Do Omnivorous Shrimp Influence Mayfly Nymphs In A Tropical Island Stream?, Nicholas A. Macías, Jose Checo Colón-Gaud, Jonathan W. Duggins, Alonso Ramírez

Department of Biology Faculty Publications

Interspecific interactions can play an important role in determining habitat selection and resource use between competing species. We examined interactions between an omnivorous shrimp and a grazing mayfly, two co-dominant taxa found in Puerto Rican headwater streams, to assess how predator presence may influence mayfly resource use and instantaneous growth in a tropical rainforest ecosystem. We conducted a series of behavioral and growth experiments to determine the effects of the freshwater shrimp, Xiphocaris elongata, on the growth rate and resource selection of mayfly nymphs in the family Leptophlebiidae. For resource choice assessments, we conducted a series of five day laboratory …

Novel Insights Into The Mechanisms Of Regulation Of Tyrosine Kinase Receptors By Ras Interference 1, Adriana Galvis

FIU Electronic Theses and Dissertations

Receptor-tyrosine kinases (RTKs) are membrane bound receptors characterized by their intrinsic kinase activity. RTK activities play an essential role in several human diseases, including cancer, diabetes and neurodegenerative diseases. RTK activities have been regulated by the expression or silencing of several genes as well as by the utilization of small molecules.

Ras Interference 1 (Rin1) is a multifunctional protein that becomes associated with activated RTKs upon ligand stimulation. Rin1 plays a key role in receptor internalization and in signal transduction via activation of Rab5 and association with active form of Ras. This study has two main objectives: (1) It determines …

Structural Insights Into The Interaction Between A Potent Anti-Inflammatory Protein, Viral Cc Chemokine Inhibitor (Vcci), And The Human Cc Chemokine, Eotaxin-1, Nai-Wei Kuo, Yong-Guang Gao, Megan Schill, Nancy Isern, Cynthia Dupureur, Patricia Liwang

Chemistry & Biochemistry Faculty Works

Chemokines play important roles in the immune system, not only recruiting leukocytes to the site of infection and inflammation but also guiding cell homing and cell development. The soluble poxvirus-encoded protein viral CC chemokine inhibitor (vCCI), a CC chemokine inhibitor, can bind to human CC chemokines tightly to impair the host immune defense. This protein has no known homologs in eukaryotes and may represent a potent method to stop inflammation. Previously, our structure of the vCCI·MIP-1β (macrophage inflammatory protein-1β) complex indicated that vCCI uses negatively charged residues in β-sheet II to interact with positively charged residues in the MIP-1β N …

Septin Assemblies Form By Diffusion-Driven Annealing On Membranes, Andrew A. Bridges, Huaiying Zhang, Shalin B. Mehta, Patricia Occhipinti, Tomomi Tani, Amy S. Gladfelter

Dartmouth Scholarship

Septins assemble into filaments and higher-order structures that act as scaffolds for diverse cell functions including cytokinesis, cell polarity, and membrane remodeling. Despite their conserved role in cell organization, little is known about how septin filaments elongate and are knitted together into higher-order assemblies. Using fluorescence correlation spectroscopy, we determined that cytosolic septins are in small complexes, suggesting that septin filaments are not formed in the cytosol. When the plasma membrane of live cells is monitored by total internal reflection fluorescence microscopy, we see that septin complexes of variable size diffuse in two dimensions. Diffusing septin complexes collide and make …

Seasonal Changes In Microbial Community Structure And Activity Imply Winter Production Is Linked To Summer Hypoxia In A Large Lake, Steven W. Wilhelm, Gary R. Lecleir, George S. Bullerjahn, Robert M. Mckay, Matthew A. Saxton, Michael R. Twiss, Richard A. Bourbonniere

Great Lakes Institute for Environmental Research Publications

Carbon and nutrient cycles in large temperate lakes such as Lake Erie are primarily driven by phototrophic and heterotrophic microorganisms, although our understanding of these is often constrained to late spring through summer due to logistical constraints. During periods of > 90% ice cover in February of 2008, 2009, and 2010, we collected samples from an icebreaker for an examination of bacterial production as well as microbial community structure. In comparison with summer months (August 2002 and 2010), we tested hypotheses concerning seasonal changes in microbial community diversity and production. Bacterial production estimates were c. 2 orders of magnitude higher (volume …

Trans Fatty Acids – A Risk Factor For Cardiovascular Disease, Mohammad Perwaiz Iqbal

Department of Biological & Biomedical Sciences

Trans fatty acids (TFA) are produced either by hydrogenation of unsaturated oils or by biohydrogenation in the stomach of ruminant animals. Vanaspati ghee and margarine have high contents of TFA. A number of studies have shown an association of TFA consumption and increased risk of cardiovascular disease (CVD). This increased risk is because TFA increase the ratio of LDL cholesterol to HDL cholesterol. Food and Agriculture Organization of the United Nations and World Health Organization have come up with the recommendation that the contents of TFA in human dietary fat should be reduced to less than 4%. There is high …

Ecdysis Triggering Hormone And Its Role In Juvenile Hormone Synthesis In The Yellow-Fever Mosquito, Aedes Aegypti, Maria Areiza

FIU Electronic Theses and Dissertations

Ecdysis triggering hormone (ETH) is a neuropeptide known for its role in the orchestration of ecdysis. However, its role in the regulation of Juvenile Hormone (JH) synthesis is unknown. In Aedes aegypti, JH is synthesized by the corpora allata (CA) and titers are tightly regulated by allatoregulatory factors. In this study I describe the effect of ETH on JH synthesis during the late pupal stage and in the adult female after blood feeding. Analysis of ETH receptor (ETHRs) expression showed that ETHRs are present in both the CA and the corpora cardiaca (CC), a neurohemal organ. The data suggest …

Disassembly Of Actin Structures By Nanosecond Pulsed Electric Field Is A Downstream Effect Of Cell Swelling, Andrei G. Pakhomov, Shu Xiao, Olga N. Pakhomova, Iurii Semenov, Marjorie A. Kuipers, Bennett L. Ibey

Bioelectrics Publications

Disruption of the actin cytoskeleton structures was reported as one of the characteristic effects of nanosecond-duration pulsed electric field (nsPEF) in both mammalian and plant cells. We utilized CHO cells that expressed the monomeric fluorescent protein (mApple) tagged to actin to test if nsPEF modifies the cell actin directly or as a consequence of cell membrane permeabilization. A train of four 600-ns pulses at 19.2 kV/cm (2 Hz) caused immediate cell membrane poration manifested by YO-PRO-1 dye uptake, gradual cell rounding and swelling. Concurrently, bright actin features were replaced by dimmer and uniform fluorescence of diffuse actin. To block the …

Bipolar Nanosecond Electric Pulses Are Less Efficient At Electropermeabilization And Killing Cells Than Monopolar Pulses, Bennett L. Ibey, Olga N. Pakhomova, Caleb C. Roth, Shu Xiao, Karl Schoenbach, Andrei G. Pakhomov

Bioelectrics Publications

Multiple studies have shown that bipolar (BP) electric pulses in the microsecond range are more effective at permeabilizing cells while maintaining similar cell survival rates as compared to monopolar (MP) pulse equivalents. In this paper, we investigated whether the same advantage existed for BP nanosecond-pulsed electric fields (nsPEF) as compared to MP nsPEF. To study permeabilization effectiveness, MP or BP pulses were delivered to single Chinese hamster ovary (CHO) cells and the response of three dyes, Calcium Green-1, propidium iodide (PI), and FM1-43, was measured by confocal microscopy. Results show that BP pulses were less effective at increasing intracellular calcium …