Biology Commons^™

Reversing Sodium Differentials Between The Hemolymph And Hindgut Speeds Chill Coma Recovery But Reduces Survival In The Fall Field Cricket, Gryllus Pennsylvanicus, Jacqueline E. Lebenzon, Lauren E. Des Marteaux, Brent J. Sinclair

Biology Publications

Chill-susceptible insects enter the reversible state of chill coma at their critical thermal minimum (CT_min­). During chill coma, movement of Na⁺ and water from the hemolymph to the gut lumen disrupt ion and water balance. Recovery from cold exposure requires re-establishment of this balance, and failure to do so results in chilling injury or death. We hypothesized that the passive leak of Na⁺ and consequently water during cold exposure is driven by the [Na⁺] differential between the gut and hemolymph. To determine the extent to which this [Na⁺] differential affects cold …

Dissection Of Anoplophora Glabripennis (Coleoptera: Cerambycidae) Larval Tissues For Physiological And Molecular Studies, Alex S. Torson, Lauren E. Des Marteaux, Susan Bowman, Meng Lei Zhang, Kevin Ong, Daniel Doucet, Brent J Sinclair, Amanda D. Roe

Biology Publications

Many biological processes are partitioned among organs and tissues, necessitating tissue-specific or organ-specific analysis (particularly for comparative -omics studies). Standardised techniques for tissue identification and dissection are therefore imperative for comparing among studies. Here we describe dissection protocols for isolating six key tissues/organs from larvae of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae): the supraoesophageal ganglion, posterior midgut, hindgut, Malpighian tubules, fat body, and thoracic muscle. We also describe how to extract haemolymph and preserve whole larvae for measurements such as protein, lipid, and carbohydrate content. We include dissection protocols for both fresh-killed and previously frozen specimens. Although …

Isolation And Characterization Of Pectobacterium Phage Vb_Patm_Cb7: New Insights Into The Genus Certrevirus, Colin Buttimer, Caoimhe Lynch, Hanne Hendrix, Horst Neve, Jean Paul Noben, Rob Lavigne, Aidan Coffey

Department of Biological Sciences Publications

To date, Certrevirus is one of two genera of bacteriophage (phage), with phages infecting Pectobacterium atrosepticum, an economically important phytopathogen that causes potato blackleg and soft rot disease. This study provides a detailed description of Pectobacterium phage CB7 (vB_PatM_CB7), which specifically infects P. atrosepticum. Host range, morphology, latent period, burst size and stability at different conditions of temperature and pH were examined. Analysis of its genome (142.8 kbp) shows that the phage forms a new species of Certrevirus, sharing sequence similarity with other members, highlighting conservation within the genus. Conserved elements include a putative early promoter like that of the …

Antimicrobial Resistance Determinants Circulating Among Thermophilic Campylobacter Isolates Recovered From Broilers In Ireland Over A One-Year Period, Caoimhe T. Lynch, Helen Lynch, Sarah Burke, Kayleigh Hawkins, Colin Buttimer, Conor Mc Carthy, John Egan, Paul Whyte, Declan Bolton, Aidan Coffey, Brigid Lucey

Department of Biological Sciences Publications

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Campylobacteriosis is the leading cause of human bacterial gastroenteritis, very often associated with poultry consumption. Thermophilic Campylobacter (Campylobacter jejuni and Campylobacter coli) isolates (n = 158) recovered from broiler neck skin and caecal contents in Ireland over a one-year period, resistant to at least one of three clinically relevant antimicrobial classes, were screened for resistance determinants. All ciprofloxacin-resistant isolates (n = 99) harboured the C257T nucleotide mutation (conferring the Thr-86-Ile substitution) in conjunction with other synonymous and nonsynonymous mutations, which may have epidemiological value. The A2075G nucleotide mutation and amino acid …

Book Review: Nature’S Giants: The Biology And Evolution Of The World’S Largest Lifeforms., William Gearty

School of Biological Sciences: Faculty Publications

We as humans have always been in awe of big things, whether they are in space, the oceans, or the fossil record. Ruxton uses this inspiration as the entry point to explore the biology (and even physics) and evolu- tion of large animals in Nature’s Giants, covering nu- merous great lifeforms spanning from giant whales to enormous sauropods. Although readers may ini- tially be drawn in by the size of these creatures, as the author writes in the introduction, “size matters,” and the weight of these animals brings with it many other fascinating implications that he goes into with moderate …

The Genesis Of Sars-Cov-2 Virus And The Origin Of The Covid-19 Pandemic, Alan L. Gillen

Faculty Publications and Presentations

The current outbreak of the 2019 novel coronavirus (SARS-CoV-2, fig. 1), causing a respiratory-tract illness, first started in Wuhan, China, and has been escalating worldwide. The official disease name became known as COVID-19 in mid-spring 2020. It shares some characteristics of the SARS virus of 2002–3. Early on, with many cases in Wuhan, China, it was reported that the outbreak had some association with animal markets, which indicated that there was animal-to-person transmission. Like SARS-CoV-1, the suspected animal source of the virus is bats. We have not seen this virus before, and our bodies were not ready for this, nor …

Quantifying The Relative Importance Of Variation In Predation And The Environment For Species Coexistence, Lauren G. Shoemaker, Allison K. Barner, Leonora S. Bittleston, Ashley I. Teufel

Biology Faculty Publications and Presentations

Coexistence and food web theory are two cornerstones of the long‐standing effort to understand how species coexist. Although competition and predation are known to act simultaneously in communities, theory and empirical study of these processes continue to be developed largely independently. Here, we integrate modern coexistence theory and food web theory to simultaneously quantify the relative importance of predation and environmental fluctuations for species coexistence. We first examine coexistence in a theoretical, multitrophic model, adding complexity to the food web using machine learning approaches. We then apply our framework to a stochastic model of the rocky intertidal food web, partitioning …

First International External Quality Assessment Scheme Of Nucleic Acid Amplification Tests For The Detection Of Schistosoma And Soil-Transmitted Helminths, Including Strongyloides: A Pilot Study, Piet Cools, Lisette Van Lieshout, Rob Koelewijn, David Addiss, Sitara S.R. Ajjampur, Mio Ayana, Richard S. Bradbury, Jason L. Cantera, Daniel Dana, Kerstin Fischer, Rubina Imtiaz, Joyce Kabagenyi, James Lok, James Mccarthy, Rojelio Mejia, Zeleke Mekonnen, Sammy M. Njenga, Nurulhasanah Othman, Hongguang Shao, Rebecca Traub, Marjan Van Esbroeck, Jozef Vercruysse, Johnny Vlaminck, Steven A. Williams, Jaco J. Verweij, Jaap J. Van Hellemond, Bruno Levecke

Biological Sciences: Faculty Publications

Background Nucleic acid amplification tests (NAATs) are increasingly being used as diagnostic tools for soil-transmitted helminths (STHs; Ascaris lumbricoides, Trichuris trichiura, Necator ameri-canus, Ancylostoma duodenale and A. ceylanicum), Strongyloides stercoralis and Schisto-soma in human stool. Currently, there is a large diversity of NAATs being applied, but an external quality assessment scheme (EQAS) for these diagnostics is lacking. An EQAS involves a blinded process where test results reported by a laboratory are compared to those reported by reference or expert laboratories, allowing for an objective assessment of the diagnostic performance of a laboratory. In the current study, we piloted an international …

Dynamical Behavior Of A Malaria Relapse Model With Insecticide Treated Nets (Itns) As Protection Measure, Reuben I. Gweryina, Anande R. Kimbir

Applications and Applied Mathematics: An International Journal (AAM)

Malaria is a tropical disease which is mainly spread by plasmodium falciparum which has been the principal enemy to the existence of mankind till date. In this paper a version of a malaria model incorporating the use of treated mosquito nets as a disease control strategy is proposed and then transformed into proportions, so as to assess the global impact of ITNs on the prevalence of malaria. Constructing a Lyapunov function using matrix-theoretic approach, a malaria-free equilibrium state is obtained, which is globally asymptotically stable if the control reproduction number, 𝑅_𝑚<1. This means that malaria can be controlled or eradicated under such a threshold quantity, 𝑅𝑚. On the other hand, a malaria-persistence equilibrium state exists which is globally stable when 𝑅_𝑚>1, using geometric theoretic method with Lozoskii …

Discovery Of A Reproducing Wild Population Of The Swamp Eel Amphipnous Cuchia (Hamilton, 1822) In North America., F. Jordan, L. G. Nico, Kristal Alissa Huggins, Peter J. Martinat, D. A. Martinez, V. L. Rodrigues

Faculty and Staff Publications

We report discovery of an established population of the Asian swamp eel Amphipnous cuchia (Hamilton, 1822) in Bayou St. John, an urban waterway in New Orleans, Louisiana, USA. This fish, commonly referred to as cuchia (kuchia), is a member of the family Synbranchidae and is native to southern and southeastern Asia. Recently-used synonyms include Monopterus cuchia and Ophichthys cuchia. We collected both adult and young-of-year cuchia from dense mats of littoral vegetation at several locations in Bayou St. John. Presence of multiple age and size classes is the first documented evidence of reproduction of this species outside of its native …

Mathematical Modeling For Studying The Sustainability Of Plants Subject To The Stress Of Two Distinct Herbivores, B. Chen-Charpentier, M. C.A. Leite, O. Gaoue, F. B. Agusto

Applications and Applied Mathematics: An International Journal (AAM)

Viability of plants, especially endangered species, are usually affected by multiple stressors, including insects, herbivores, environmental factors and other plant species. We present new mathematical models, based on systems of ordinary differential equations, of two distinct herbivore species feeding (two stressors) on the same plant species. The new feature is the explicit functional form modeling the simultaneous feedback interactions (synergistic or additive or antagonistic) between the three species in the ecosystem. The goal is to investigate whether the coexistence of the plant and both herbivore species is possible (a sustainable system) and under which conditions sustainability is feasible. Our theoretical …

Viral Dynamics Of Delayed Ctl-Inclusive Hiv-1 Infection Model With Both Virus-To-Cell And Cell-To-Cell Transmissions, M. L. Mann Manyombe, J. Mbang, L. Nkague Nkamba, D. F. Nkoa Onana

Applications and Applied Mathematics: An International Journal (AAM)

We consider a mathematical model that describes a viral infection of HIV-1 with both virus-tocell and cell-to-cell transmission, CTL response immune and four distributed delays, describing intracellular delays and immune response delay. One of the main features of the model is that it includes a constant production rate of CTLs export from thymus, and an immune response delay. We derive the basic reproduction number and show that if the basic reproduction number is less than one, then the infection free equilibrium is globally asymptotically stable; whereas, if the basic reproduction number is greater than one, then there exist a chronic …

The Impact Of Nonlinear Harvesting On A Ratio-Dependent Holling-Tanner Predator-Prey System And Optimum Harvesting, Manoj Kumar Singh, B. S. Bhadauria

Applications and Applied Mathematics: An International Journal (AAM)

In this paper, a Holling-Tanner predator-prey model with ratio-dependent functional response and non-linear prey harvesting is analyzed. The mathematical analysis of the model includes existence, uniqueness and boundedness of positive solutions. It also includes the permanence, local stability and bifurcation analysis of the model. The ratio-dependent model always has complex dynamics in the vicinity of the origin; the dynamical behaviors of the system in the vicinity of the origin have been studied by means of blow up transformation. The parametric conditions under which bionomic equilibrium point exist have been derived. Further, an optimal harvesting policy has been discussed by using …

Mathematical Modeling Of Nonlinear Blood Glucose-Insulin Dynamics With Beta Cells Effect, Gabriela Urbina, Daniel N. Riahi, Dambaru Bhatta

Applications and Applied Mathematics: An International Journal (AAM)

We consider mathematical modeling of blood glucose-insulin regulatory system with the additional effect of the secreted insulin by the pancreatic beta cells and in the presence of an external energy input to such system. Such modeling system is investigated to determine the time-dependent nonlinear dynamics that take place by the quantities, which represent the glucose and insulin concentrations in the blood, insulin action as well as in the absence or presence of secreted insulin due to the pancreatic beta cells. Using both analytical and numerical procedures, we determine such quantities versus time for both diabetes patients and normal human and …

Conservation Status Of The Recently Described Ecuadorian Amazon Parrot Amazona Lilacina, Rebecca Biddle, Ivette Solis Ponce, Paul Cun, Simon Tollington, Martin Jones, Stuart Marsden, Christian Devenish, Eric Horstman, Karl S. Berg, Mark Pilgrim

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

Amazona lilacina is a threatened species endemic to Ecuador, existing across a patchwork of mangroves, lowland coastal forests, agricultural and community owned land. The species was described in 2014 and listed as ‘Endangered’ on the IUCN Red List, however, full assessment of the population was lacking. Using a combination of field observations, roost surveys and community questionnaires, conducted over the last 20 years, we provide up-to-date information on the species’ Extent of Occurrence, estimate its global population size, and evaluate its level of threat. Our results suggest the species occurs across an area of 19,890 km2 in three distinct geographically …

A Network-Based Integrated Framework For Predicting Virus–Prokaryote Interactions, Weili Wang, Jie Ren, Kujin Tang, Emily Dart, Julio Cesar Ignacio-Espinoza, Jed A. Fuhrman, Jonathan Braun, Fengzhu Sun, Nathan A. Ahlgren

Biology

Metagenomic sequencing has greatly enhanced the discovery of viral genomic sequences; however, it remains challenging to identify the host(s) of these new viruses. We developed VirHostMatcher-Net, a flexible, network-based, Markov random field framework for predicting virus–prokaryote interactions using multiple, integrated features: CRISPR sequences and alignment-free similarity measures (s2∗ and WIsH). Evaluation of this method on a benchmark set of 1462 known virus–prokaryote pairs yielded host prediction accuracy of 59% and 86% at the genus and phylum levels, representing 16–27% and 6–10% improvement, respectively, over previous single-feature prediction approaches. We applied our host prediction tool to crAssphage, a human gut phage, …

Epithelial-Mesenchymal Status Predics Tumor Agressivenss, Chemoresistance And Invasiveness In High Grade Serous Ovarian Cancer, Linda Sanderman

Electronic Theses, Projects, and Dissertations

High Grade Serous Ovarian Cancer (HGSOC) is one of the deadliest gynecological diseases in the United States ranking fifth in cancer deaths among women. Approximately 22 thousand new cases are expected to occur in the year 2020, and unfortunately, it is estimated that 14 thousand women will succumb to the disease; the incidence to death ratio, 64%, remains high despite current research. Current treatment includes debulking surgery followed by combinatorial chemotherapeutics with platinum-based and taxol-based compounds. But despite aggressive surgery and standard-of-care chemotherapeutics, 80% of patients will experience a recurrence and only 15-30% of those with recurring disease will respond …

The Development Of An H1 Embryonic Stem Cell Line To Study The Role Of The Oncogenes Lmo1 And Mycn In Human Neuroblastoma Formation, Vincent Quiroz

Electronic Theses, Projects, and Dissertations

Neuroblastoma (NB) is an extracranial tumor that affects the nervous system and accounts for approximately 650 – 800 cases diagnosed per year in children under the age of 5 (www.cancer.org/cancer/neuroblastoma/about/key-statistics.html). NB occurs at a relatively rare rate of 10.2 per million children under 15 years old but accounts for 12-15% of pediatric cancer death because patients with high-risk NB (HRNB) have 5-year survival rates between 40-50%(Brodeur, 2003; Park et al. 2010). Developmental biology research has recognized neural crest cells (NCC) as the progenitor cells of NB, as tumors form in the trunk NC derived sympathetic nervous system (Dupin, 2013; Simões-Costa …

Elucidating The Role Of Apl-1, The C. Elegans Ortholog Of The Human Amyloid Precursor Protein, Adanna G. Alexander

Dissertations, Theses, and Capstone Projects

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, impacting approximately 6 million Americans. AD is the leading cause of dementia amongst the aged population. Post mortem analysis of the brains of AD patients shows high quantities of extracellular Aβ peptide deposits, which are derived from cleavage of the amyloid precursor protein (APP). Mutations in APP and proteins responsible for APP cleavage, PSENs, greatly increase the incidence of developing AD at an early age. Despite its strong correlation to the progression of AD, the role of APP remains unclear.

Here we investigate the role of the Caenorhabditis elegans ortholog, APL-1. We …

Molecular Roles Of Small Inner Membrane Proteins In Escherichia Coli Cell Envelope Integrity, Aaron Mychack

Dissertations, Theses, and Capstone Projects

The biological membrane is an essential, defining feature of all cells. Biological membranes comprise phospholipid bilayers as well as a complement of proteins which are unique to a given organism. These proteins play a central role in dictating the biochemical state of the cell’s internal cytoplasm by controlling selective passage of solutes in and out of the cell, transducing signals in response to extracellular stimuli, and controlling the biogenesis of the bilayer itself which is critical towards barrier function. For most bacteria, the periphery of the cell is multi-layered, including both a biological membrane as well as a peptidoglycan cell …

Protein Phosphatase 2a Suppresses Spindle Elongation In Saccharomyces Cerevisiae, Shoily P. Khondker

Dissertations, Theses, and Capstone Projects

Eukaryotic cell division is an essential process that is carried out by the cell cycle, a tightly controlled process that has been extensively studied in the budding yeast Saccharomyces cerevisiae. The cell cycle is driven by Cyclin Dependent Kinase (Cdk1) activity. Protein phosphatase 2A-Cdc55 (PP2A^Cdc55) reverses Cdk1 phosphorylation events during late stages of the cell cycle to ensure the correct order of events. This thesis presents evidence that the anaphase inhibitor Pds1 is a PP2A^Cdc55 target. Pds1 binds to and inhibits separase (Esp1). Esp1 triggers sister chromatid segregation by cleaving the cohesin complex that holds the …

Evaluating Satellite-Based Sea Surface Temperatures, In Situ Observations, And Coral Symbioses In Southwestern Puerto Rico, Andrea Michelle Gomez

Dissertations, Theses, and Capstone Projects

I examined the effects of in situ and satellite-based sea surface temperatures (SST) on the seasonal coral-algae symbiotic relationship in La Parguera, Puerto Rico. Climate change-driven rising sea temperatures are endangering most of the world’s reefs, which are currently in decline. Satellite remote sensing datasets support global-scale characterization and monitoring of risks to reefs associated with increasing temperatures. Corals’ unique symbiotic relationship with unicellular algae in the family Symbiodiniaceae is largely responsible for helping corals cope with increasing ocean temperatures, and some corals are able to adjust their symbiont species in response to temperature disturbances. My research had two components …

Survey Of Human-Leopard (Panthera Pardus) Conflict In Ayubia National Park, Pakistan, Muhammad Nabeel Awan, Atif Yaqub, Muhammad Kamran

Journal of Bioresource Management

Wildlife populations are at a risk of extinction mainly because of human-wildlife conflict (HWC). The present study was designed to evaluate the ongoing HWC with special reference to Common Leopard (Panthera pardus) in Ayubia National park through field study as well as a literature-based approach. Questionnaire interview surveys were designed for wildlife officials working in the park and the locals who bear the cost for leopard conflict through livestock depredation and crop damage. The study showed that human-leopard conflict in the study area has been increasing. More than 60% of people considered livestock depredation as the major reason …

Impact Of Cover Crops On Insect Community Dynamics In Organic Farming, Lili Martinez, Pushpa Soti, Jasleen Kaur, Alexis Racelis, Rupesh R. Kariyat

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

Manipulating cover crops as an integrated pest management strategy has recently gained popularity in both traditional and organic agroecosystems. However, little information is available for producers to make informed decisions about cover crop selection, management, and their potential use as a pest management tool. To address this, we conducted a two-year, four-season field experiment on the potential of various cover crops during the summer seasons of both years, followed by monocultures of cash crops during winters. We hypothesized that the cover crop treatments would attract beneficial insects and repel damaging herbivores in a species-specific manner, and the insect community dynamics …

Exopolysaccharide From The Liquid Culture Of Ganoderma Lucidum As Feed Additive For Red Hybrid Tilapia (Oreochromis Sp.), Thiran Jaganath Puvanen

Student Works (2020-2029)

Feed additive plays a significant role in sustaining fish production. Exopolysaccharide (EPS) obtained from the fermented mycelium of Ganoderma lucidum produced by using submerged-liquid fermentation (SLF) was proposed as a feed additive in this study for red hybrid tilapia (Oreochromis sp.). Body composition, organosomatic indices, and haematological parameters were observed in fish fed with three different diets supplemented with EPS (1 g/kg, 2 g/kg, and 3 g/kg). Although higher concentration EPS feed was observed to produce minor effect on body composition and organosomatic indices, significant effect on both parameters was observed in fish fed with 1 g/kg diet. All diets …

Performance Of Mycelial Biomass From The Mushroom Ganoderma Lucidum As Feed Additive On Growth And Quality Of Red Hybrid Tilapia (Oreochromis Spp.), Yerima Grema

Student Works (2020-2029)

The present study describes the potentiality of dietary supplement of mycelial biomass of Ganoderma lucidum (MBGL) as functional feed additives formulated along with other feed ingredients at different inclusion levels (5g/kg diet, 10g/kg diet and 15g/kg diet). A hundred and twenty (120) red hybrid tilapia were used for this experiment in duplicates treatment. Fifteen fish were allocated to each tank with an average weight of 17.0g. A six (6) week feeding trial was conducted to evaluate the effect of GL biomass on red hybrid tilapia body composition, organosomatic index, as well as hematological indices. At the end of the feeding …

The Roles Of Inhibition In C. Elegans Locomotion, Lan Deng

Dissertations

Inhibition plays important roles in modulating neural activities at different levels from small synapses to brain regions, and different systems from sensory to motor. To achieve translocation, locomotor systems produce alternation of antagonist muscles, including axial posture and limb movement and alternation. In the nematode C. elegans, a cross-inhibition circuit, involving excitatory cholinergic and inhibitory GABAergic motoneurons, is believed to generate the dorsoventral alternation of body-wall muscles that supports backward undulatory locomotion. This dissertation challenges this prevalent hypothesis, delves into studying different roles of inhibition, and depicts the expression pattern and functional role of ionotropic GABAA receptor, UNC-49, in motoneurons …

Plant Evolution And Urbanization: Quantifying The Effects Of Natural Selection In Shaping Shepherd’S Purse (Capsella Bursa-Pastoris) Populations In New York City, Rebecca Panko

Dissertations

The aim of this study is to quantify the effects of natural selection in shaping Capsella bursa-pastoris populations along an urban-rural gradient in New York City.

A reciprocal transplant experiment with 168 lab-germinated C. bursa-pastoris seedlings from both urban and rural populations are grown in eight paired home and away sites distributed throughout the New York metropolitan area. Sites are visited approximately thirteen times to record plant fitness. There is evidence for local adaptation of urban populations: urban plants have longer reproductive durations and produce more seed pods in urban environments. These findings suggest that urban plants are better adapted …

Kcnq2 Localization In The Brainstem, Christina Valera

Honors Scholar Theses

KCNQ2 channels are potassium channels that serve to control neuronal excitability. Loss of function mutations in these channels are known to cause various forms of epilepsy. Recently, KCNQ2 R201C and R201H gain of function mutations have been shown to exhibit an exaggerated startle response and other unique phenotypes uncharacteristic of epilepsy. These phenotypes resemble hyperekplexia, a condition in which glycine neurotransmission in the spinal cord and brainstem is affected. While KCNQ2 has widespread localization throughout the brain, its presence in the brainstem remains unknown. We used immunostaining to determine the localization of KCNQ2 in the vagus nerve and hypoglossal nerve …

Morphometric Response Of Galaxias Maculatus (Jenyns) To Lake Colonization In Chile, Margaret Mercer, Peter C. Searle, Roberto Cifuentes, Evelyn Habit, Mark C. Belk

Faculty Publications

Body and head shape in fish responds to environmental factors such as water flow rate, food sources, and niche availability. However, the way in which fish respond to these environmental factors varies. In Central Chile, multiple river and lake systems along the coast provide an ideal study site to investigate these types of shape changes. We use geometric morphometrics to characterize shape differences in Galaxias maculatus (Jenyns) between river and lake populations. Lake fish converge on a shape with a more fusiform body, narrower head, and larger eyes, while river fish have a more robust body, rounder head, and smaller …