Biology Commons^™

Photosynthetic Activity Under Low Light, Danijela Lonco

Williams Honors College, Honors Research Projects

Are bacteria capable of undergoing oxygenic photosynthesis under low-light conditions inside of caves? Inside of an Australian cave, Chlorophyll f was recently discovered. This chlorophyll pigment was found to demonstrate the capability for photosynthesis, suggesting that Chlorophyll f extends the spectrum of usable light needed for oxygenic photosynthesis (Lars, 2015). Due to the findings in this study, a team went to Carlsbad Caverns to see if there were any bacteria capable of undergoing oxygenic photosynthesis under low light.

Western Snowy Plover Nest Survival In Humboldt County, California, Katelyn M. Raby

Cal Poly Humboldt theses and projects

Productivity measures, such as nest survival, are often used to indirectly assess habitat quality and guide targeted management practices for the conservation of threatened and endangered species. The coastal population of the Western Snowy Plover (Charadrius nivosus nivosus) is listed as threatened due to three limiting factors: human disturbance, loss and degradation of habitat as a result of invasive plants, and increasing predator populations. I examined the relative influence of these three limiting factors on nest survival, using data from 2004 to 2017 at eight sites in Humboldt County, California. I assigned nests (n = 610) to three …

Release From Intraspecific Competition Promotes Dominance Of A Non-Native Invader, Robert Warren

Biology Faculty Datasets

Species can coexist through equalizing (similar fitness abilities) and stabilizing (unique niche requirements) mechanisms – assuming that intraspecific competition imposes more limitation than interspecific competition. Non-native species often de-stabilize coexistence, suggesting that they bring either a fitness advantage or a distinct niche requirement. We tested whether greater fitness or unique niche requirements best explained a successful North American invasion by the European Myrmica rubra ant. North American invaded-range M. rubra aggressively sting and occur in enormous numbers (suggesting a fitness advantage), yet our study site has a history of anthropogenic disturbance that might favor M. rubra (suggesting a unique niche). …

Evaluation Of The Phylogenetic Relationships Of The Marine Rivulariaceae., Jose Alberto Martinez Yerena

Masters Theses

Historically, the Rivulariaceae family has grouped all heteropolar, tapered and heterocitous Cyanobacteria, however recent description of multiple cyanobacterial populations with this morphotype using 16S rRNA phylogenies have reported that the populations with this morphotype are polyphyletic, and many new and old tapered and heteropolar genera (Cyanomargarita, Gloeothrichia, Rohoaltiella, etc.) have been classified and reclassified to different families than the Rivulariaceae. This is also the case of the main genera of the family (Rivularia and Calothrix), which have been repeatedly reported as polyphyletic, and whose separation to different families has been called for. In this project I carried out the evaluation …

A Novel Quantitative Real-Time Pcr Diagnostic Assay For Seal Heartworm (Acanthocheilonema Spirocauda) Provides Evidence For Possible Infection In The Grey Seal (Halichoerus Grypus), Caroline D. Keroack, Kalani M. Williams, M. K. Fessler, Kaela E. Deangelis, Eirini Tsekitsidou, Jillian M. Tozloski, Steven A. Williams

Biological Sciences: Faculty Publications

The distinct evolutionary pressures faced by Pinnipeds have likely resulted in strong coevolutionary ties to their parasites (Leidenberger et al., 2007). This study focuses on the phocid seal filarial heartworm speciesAcanthocheilonema spirocauda. A. spirocauda is known to infect a variety of phocid seals, but does not appear to be restricted to a single host species (Measures et al., 1997; Leidenberger et al., 2007; Lehnert et al., 2015). However, to date, seal heartworm has never been reported in grey seals (Halichoerus grypus) (Measures et al., 1997; Leidenberger et al., 2007; Lehnert et al., 2015). The proposed vector for seal heartworm is …

The Role Of Climate In The Dynamics Of Annual Plants In A Chihuahuan Desert Ecosystem, Danielle Ignace, Nancy Huntly, Peter Chesson

Biological Sciences: Faculty Publications

Question: What is the role of temporal climate fluctuations in the dynamics of desert winter annual plants in the Portal Bajada, and in the sustained irruption of the non-native annual plant species, Erodium cicutarium?

Field site: Portal Bajada, San Simon Valley, Arizona, USA. Methods: We counted plants at flowering over a 21-year period on twelve permanent plots and related these numbers to weather data collected at an on-site weather station, supplemented by observations from the National Climate Data Center. Specific summary climate variables considered most relevant to annual plant biology were developed as candidate predictors of plant response variables.

Statistical …

Amphibians And Reptiles Of The State Of San Luis Potosi, Mexico, With Comparisons With Adjoining States, J. A. Lemos-Espinal, Geoffrey R. Smith, G. A. Woolrich-Pina

Faculty Publications

No abstract provided.

Amphibians And Reptiles Of The State Of Durango, Mexico, With Comparisons With Adjoining States, J. A. Lemos-Espinal, Geoffrey R. Smith, H. Gadsden-Esparza, R. Valdez-Lares, G. A. Woolrich-Pina

Faculty Publications

No abstract provided.

Dna Extraction And Microsatellite Amplification Of Daphnia Pulicaria Resting Eggs: Analysis Of Allele Frequencies Through Time, Anna Ries

Departmental Honors Projects

A paleoecological approach allows for the study of genetic change in populations over longer periods of time than would be possible if one were sampling populations from year to year. Daphnia and other cladoceran zooplankton are amenable to this type of study because they produce diapausing embryos (ephippial eggs) when they sexually reproduce, and these resting eggs can remain viable for decades to centuries in lake sediments. This study uses paleoecological methods as well as a new methodology for ephippial DNA extraction and amplification to assay for genetic variation in ephippial eggs obtained from sediments of varying ages from Square …

Chlorate And Other Oxychlorine Contaminants Within The Dairy Supply Chain, William P. Mccarthy, Tom F. O'Callaghan, Martin Danaher, David Gleeson, Christine O'Connor, Mark A. Fenelon, John Tobin

Articles

The presence of chlorate in milk and dairy products can arise from the use of chlorinated water and chlorinated detergents for cleaning and sanitation of process equipment at both farm and food processor level. Chlorate and other oxychlorine species have been associated with inhibition of iodine uptake in humans and the formation of methemoglobin, with infants and young children being a high‐risk demographic. This comprehensive review of chlorate and chlorine derivatives in dairy, highlights areas of concern relative to the origin and/or introduction of chlorate within the dairy supply chain. This review also discusses the associated health concerns, regulations, and …

Characterizing Borrelia Burgdorferi In Virginia : Lyme Disease Prevalence As A Matter Of Bacterial Genetic Variation, Hannah Cornman

Honors Theses

yme Disease (LD) incidence and spatial distribution has grown dramatically in the past 20 years. In Virginia, the growth has been especially drastic, primarily in the Western part of the state. This research project investigates how genetic variability of the Lyme Disease causing bacteria, Borrelia burgdorferi, might be contributing to this increase in LD incidence in western Virginia. To do this, B. burgdorferi samples were isolated from ticks found across the state and were characterized by multilocus sequence typing (MLST). Phylogenetic and minimum spanning tree analyses were also performed. It was hypothesized that the increasing number of Lyme disease infections …

Parasites Of The Spotted Sucker, Minytrema Melanops (Cypriniformes: Catostomidae) From Arkansas And Oklahoma, Chris T. Mcallister, Donald G. Cloutman, Anindo Choudhury, Tomas Scholz, Stanley E. Trauth, Thomas J. Fayton, Henry W. Robison

Journal of the Arkansas Academy of Science

During October 2015, March and April 2016 and again between March and April 2017, 15 Spotted Sucker (Minytrema melanops) were collected from sites in the Ouachita (n = 5), Red (n = 1), and St. Francis (n = 5) river drainages, Arkansas, and the Arkansas River drainage, Oklahoma (n = 4), and examined for protozoan and metazoan parasites. Found were Calyptospora sp., Myxobolus sp., Pseudomurraytrema alabarrum, Biacetabulum banghami, Penarchigetes oklensis, and Acanthocephalus sp. New host and distributional records are documented for these parasites.

The Role Of Environmental Filtering In Structuring Appalachian Tree Communities: Topographic Influences On Functional Diversity Are Mediated Through Soil Characteristics, Julia I. Chapman, Ryan W. Mcewan

Biology Faculty Publications

Identifying the drivers of community assembly has long been a central goal in ecology, and the development of functional diversity indices has provided a new way of detecting the influence of environmental gradients on biotic communities. For an old-growth Appalachian forest, we used path analysis to understand how patterns of tree functional diversity relate to topography and soil gradients and to determine whether topographic effects are mediated through soil chemistry. All of our path models supported the idea of environmental filtering: stressful areas (high elevation, low soil moisture, low soil nutrients) were occupied by communities of low functional diversity, which …

Prospective Study Of The Feasibility Of Point-Of-Care Testing Strategy For Carbapenem-Resistant Organism Detection, Rahul Pannala, Bruce Baldwin, Vijay Aluru, Thomas E. Grys, Jordan Holmes, Laurence J. Miller, M. Edwyn Harrison, Cuong C. Nguyen, Fred C. Tenover, David Persing, Douglas O. Faigel

Biology Faculty Publications

Background/aims: In an investigator-initiated, prospective study, we evaluated the feasibility of a five-gene sequence point-of-care (POC) testing strategy (Xpert CARBA-R Assay, Cepheid Inc., Sunnyvale, CA, USA), compared to reference laboratory PCR (48 – 72 hours turnaround time, two gene sequences), in patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) and in a hospital outbreak investigation.

Methods: After informed consent, patients undergoing ERCP (September 2015 – April 2016, n = 191) at Mayo Clinic and potential hospital contacts (n = 9) of an index carbapenem-resistant organism (CRO)-positive inpatient were included. Two rectal swabs, one each for reference and POC assays were obtained. The …

Range Expansion And The Origin Of Usa300 North American Epidemic Methicillin-Resistant Staphylococcus Aureus, Lavanya Challagundla, Isabella A. Tickler, Xavier Didelot, David C. Coleman, Anna C. Shore, Geoffrey W. Coombs, Daniel O. Sordelli, Eric L. Brown, Robert Skov, Anders Rhod Larsen, Jinnethe Reyes, Iraida E. Robledo, Guillermo J. Vazquez, Paul Rivera, Paul D. Fey, Kurt Stevenson, Shu-Hua Wang, Barry N. Kreiswirth, Jose R. Mediavilla, Cesar A. Arias, Paul J. Planet, Rathel L. Nolan, Fred C. Tenover, Richard V. Goering, D. Ashley Robinson

Biology Faculty Publications

The USA300 North American epidemic (USA300-NAE) clone of methicillin-resistant Staphylococcus aureus has caused a wave of severe skin and soft tissue infections in the United States since it emerged in the early 2000s, but its geographic origin is obscure. Here we use the population genomic signatures expected from the serial founder effects of a geographic range expansion to infer the origin of USA300-NAE and identify polymorphisms associated with its spread. Genome sequences from 357 isolates from 22 U.S. states and territories and seven other countries are compared. We observe two significant signatures of range expansion, including decreases in genetic diversity …

Parrots And Palms: Analyzing Data To Determine Best Management Strategies And Sustainable Harvest Levels, James P. Gibbs, J. Michelle Cawthorn, Adriana Bravo, Ana L. Porzecanski

Biology: Faculty Publications

This exercise¹ presents a scenario and raw data on a realistic conflict between parrot conservation and palm tree harvest. It requires that students analyze data very comparable to what would be gathered in the field, to: 1) construct a life tables for the palm and parrot, 2) extract vital statistics about both the palm and parrot population from the life tables, 3) estimate maximum sustainable yield for both species, and 4) make a decision about the sustainability of harvest intensity. It illustrates the importance of data analysis skills for conservation.

Forelimb Position Affects Facultative Bipedal Locomotion In Lizards, Chase T. Kinsey, Lance D. Mcbrayer

Biology: Faculty Publications

Recent work indicates that bipedal posture in lizards is advantageous during obstacle negotiation. However, little is known about how bipedalism occurs beyond a lizard's acceleratory threshold. Furthermore, no study to date has examined the effects of forelimb position on the body center of mass (BCoM) in the context of bipedalism. This study quantified the frequency of bipedalism when sprinting with versus without an obstacle at 0.8 m from the start of a sprint. Forelimb positions were quantified during bipedal running at the start of a sprint and when crossing an obstacle. Two species with contrasting body forms (and thus different …

Cold Tolerance, Diapause And Winter Survival Of The Brown Marmorated Stink Bug (Halyomorpha Halys), Naomi Sibayan

All Master's Theses

The brown marmorated stink bug, Halyomorpha halys, is native to eastern Asia and is an invasive pest in the United States. Limited research has been done regarding the factors influencing this species’ winter survival within invaded northern regions. Cold tolerance has been previously evaluated in the eastern United States, bot nut within western populations. Winter diapause. Along with any potential links between diapause and cold tolerance remain unstudied. I examined characteristics of cold tolerance, diapause and overwintering sites to evaluate the factors contributing to the winter survival and, ultimately, persistence of this pest within central Washington. This study measured seasonal …

Modeling The Psychiatric Aspects Of Polycystic Ovary Syndrome And Induced Stress, Danielle Peecher

All Master's Theses

Polycystic ovary syndrome (PCOS) is an endocrine disorder in women that is characterized by excess testosterone and is associated with increased risk of infertility. Women with PCOS also show higher rates of depression and anxiety. Modeling PCOS in mice via administration of dihydrotestosterone (DHT) results in physiological alterations that are consistent with the physiological symptoms of PCOS in women. While some studies have investigated behavioral changes in PCOS mouse models, findings have varied. Thus, the current research examined whether a PCOS model with an additional stress factor resulted in behavioral changes. To create a stress condition, subjects were implanted with …

Single And Pair Housed Chacma Baboons’ (Papio Ursinus) Response To Caregivers’ Use Of Species-Specific Behavior, Josefine Holm

All Master's Theses

Most captive primates suffer from stereotypical or abnormal behavior which can be reduced by implementing enrichment protocols. There is, however, often spatial or economic limitations to facilities’ enrichment programs, and implementing the most beneficial and cost-effective enrichment is therefore crucial to ensure the best welfare for captive primates. Social enrichment has been designated as the most effective type of enrichment, but often captive primates cannot be housed in social groups. Through this study, I wanted to determine if species-specific behavioral interactions between human caregivers and captive chacma baboons (Papio ursinus)would alter the baboons’ behaviors, and if these interactions could …

Draft Genome Sequence Of Streptomyces Sp. Strain Jv178, A Producer Of Clifednamide-Type Polycyclic Tetramate Macrolactams, Yunci Qi, John M. D’Alessandro, Joshua A.V Blodgett

Biology Faculty Research

Here, we report the draft genome sequence of Streptomyces sp. JV178, a strain originating from Connecticut (USA) garden soil. This strain produces the polycyclic tetramate macrolactam compounds clifednamides A and B. The draft genome contains 10.65 Mb, 9,045 predicted protein coding sequences, and several natural product biosynthetic loci.

Colonization Of And Adaptation To Tidal Marshes In The Savannah Sparrow (Passerculus Sandwichensis), Phred M. Benham

Graduate Student Theses, Dissertations, & Professional Papers

Intraspecific patterns of geographic variation reflect a dynamic history of colonization and divergence in response to spatially varying selective pressures. Analysis of this phenotypic variation has long stimulated biological thought, yet many outstanding questions remain regarding the ecological and evolutionary mechanisms driving patterns of geographic variation. In my dissertation, I collected data on demographic history, physiological traits contributing to salinity tolerance, and acclimation responses to different salinities to elucidate the mechanisms shaping colonization and adaptive divergence in tidal marsh populations of Savannah Sparrows (Passerculus sandwichensis). Specifically, I addressed two main questions related to adaptive divergence in this species: (1) how …

Lack Of Delayed-Type Hypersensitivity In Striped Bass (Morone Saxatilis), Jessica Shannon Miller

Biological Sciences Theses & Dissertations

Mycobacteriosis is a fatal disease in fishes caused by acid-fast bacteria in the genus Mycobacterium. This disease impacts aquaculture, aquariums, and wild fishes. Unfortunately, there are currently no non-lethal diagnostic tests for mycobacterial infection in fishes. Type IV delayed type hypersensitivity (DTH) responses in vivo and in vitro are currently used for the non-lethal detection of mycobacterial infections in humans and in animals; however, there is little information available on DTH responses in fishes. In this work, we examine in vivo DTH response in Striped Bass (Morone saxatilis), an important U.S. Eastern seaboard fish species, experimentally …

Role Of Nest Site Microclimate And Food Availability In Chick Development And Reproductive Success In Black-Legged Kittiwakes (Rissa Tridactyla), Lindsay Mae Lacey

Honors Theses

Seabirds are marine top predators, and as such are often studied as bioindicators of climate shifts (Oswald and Arnold 2012). Though many studies have analyzed the effect of macroclimatic variation on marine prey species availability and thus seabirds, few have analyzed effects of microclimate - fine spatial patterns of climate (Mantua and Hare 2002; Hatch 2013; Kim and Monaghan 2005a). I tested the hypothesis that localized temperature and humidity at nest sites interact with food availability to alter black-legged kittiwake (Rissa tridactyla) nest site quality, chick body condition during growth and development, and reproductive parameters including Julian lay …

Treatment Outcomes Of Mohs Surgery Vs. Imiquimod In Basal Cell Carcinoma, Mir Saleem, Julianna Robinson

Biology Faculty Articles

Background: Basal Cell Carcinoma (BCC) is a type of skin cancer, and a growing number of cases are diagnosed each year. There are many treatment options available, however finding the best treatment that has the lowest recurrence rate and morbidity is a challenge. The treatment options vary from topical or systemic medications to special procedures to surgical interventions. Treatment’s effectiveness largely differs on the BCC sub-type and its individual features. Method: Data was collected from the charts of patients that were diagnosed with BCC. The selected patients were treated by either Mosh surgery or Imiquimod. Results: Majority …

Selective Serotonin Reuptake Inhibitor (Ssri) Efficiency, And Comparison To Alternative Antidepressant Treatments, Angela Camilli, Mir Saleem

Biology Faculty Articles

Depression is one of the most important causes of disability-adjusted life years. Currently, the majority of patients are treated with SSRIs. However, the effectiveness of SSRIs is questionable. Method: The purpose of this study was to determine the effectiveness of the pharmacotherapy treatment selective serotonin reuptake inhibitors (SSRIs) in patients diagnosed with major depression. This was achieved by comparison to other methods of antidepressant treatment such as, selective serotonin norepinephrine reuptake inhibitors (SNRIs), tricyclic antidepressants (TCAs), electroconvulsive therapy (ECT), and psychotherapy. Results: The majority of patients were taking SSRIs for treatment of depression alone or in combination with other antidepressant …

Hunter Harvest Effect On The Breeding Bird Population Of Northern Pintail Anas Acuta In North America, Matthew Wang

Journal of Earth and Life Science

Hunter harvest and the effects that it can have on population dynamics is a relationship used by wildlife professionals when making management decisions. Hunter harvest can be compensatory or additive on wildlife populations and instances where hunter harvest has been a key role in a population decline, and sometimes demise, is an occurrence studied in wildlife management. Waterfowl numbers in North America have increased 17% since 1960, but during that same time frame the Northern Pintail population has decreased 40%. Hunter harvest data has been recorded by the U.S. Fish and Wildlife Service since 1961, while they have simultaneously been …

Interactions Between Two Key Amphibian Defenses To Batrachochytrium Dendrobatidis In Panamanian Glass Frogs (Espadarana Prosoblepon), Andi Levorse

Honors Theses

Research on the amphibian pathogen Batrachochytrium dendrobatidis (Bd), the causative agent of the lethal disease chytridiomycosis, has advanced from assessments of pathogenicity and species susceptibility to more specialized questions concerning the complex interactions between the pathogen, species-specific immune responses, and the environment. Our work examines the potential for interactions between the two most important innate immune defenses of frogs against Bd: secretions of antimicrobial peptides and communities of commensal cutaneous bacteria. While both defenses have been studied individually, little data are available to examine interactions between these defenses. We conducted our study with field captured Panamanian glass frogs …

Tree Thinning And Fire Affect Ectomycorrhizal Fungal Communities And Enzyme Activities, Ann L. Rasmussen, J. Stephen Brewer, Colin R. Jackson, Jason D. Hoeksema

Faculty and Student Publications

Common ecological restoration treatments such as thinning trees and prescribed burning could result in changes to soil fungal communities and changes to the function of those communities. Ectomycorrhizal fungi are especially likely to be affected as they are symbionts on plant roots and exhibit host and niche preferences. Ectomycorrhizal fungi also produce extracellular enzymes that are important in soil nutrient cycling. We conducted a community survey of ectomycorrhizal fungi and assayed ectomycorrhizal root tip enzyme activity using substrate plugs in northern Mississippi upland oak–pine woodland plots differing in restoration history to explore the influence of woodland restoration on ectomycorrhizalfungal community …

Building Capacity For A Global Genome Editing Observatory: Institutional Design, Krishanu Saha, J. Benjamin Hurlbut, Sheila Jasanoff, Aziza Ahmed, Anthony Appiah, Elizabeth Bartholet, Francoise Baylis, Gaymon Bennett, George Church, I. Glenn Cohen, George Daley, Kevin Finneran, William Hurlbut, Rudolf Jaenisch, Laurence Lwoff, John Paul Kimes, Peter Mills, Jacob Moses, Buhm Soon Park, Erik Parens, Rachel Salzman, Abha Saxena, Hilton Simmet, Tania Simoncelli, O. Carter Snead, Kaushik Sunder Rajan, Robert D. Truog, Patricia Williams, Christiane Woopen

Journal Articles

A new infrastructure is urgently needed at the global level to facilitate exchange on key issues concerning genome editing. We advocate the establishment of a global observatory to serve as a center for international, interdisciplinary, and cosmopolitan reflection.