Biology Commons^™

Estimating Changing Marshland Habitat And Conservation Potential For Diamondback Terrapins (Malaclemys Terrapin) In New Jersey Under Climate Change, Jacqueline Ganter, Zachary Christman

School of Earth & Environment Departmental Research

The diamondback terrapin (Malaclemys terrapin), a brackish water turtle species native to the eastern United States, is under “special concern” in the state of New Jersey, due to decreasing habitat from development and changing climatic conditions. Diamondback terrapins reside in saline marshes and coastal wetlands and nest in sandy substrate, primarily beaches and dunes, in June and July. New Jersey is vulnerable to sea level rise, leaving diamondback terrapin habitats and nesting areas at risk of inundation under future climate scenarios, and, as the most densely populated state, subject to continual development pressures on potentially conservable land. Changing sea levels …

Refining The Use Of Stable Isotope Analysis In Detecting Wildlife Laundering, Kevin Guilfoyle

Electronic Theses and Dissertations, 2020-2023

The international wildlife trade has caused significant declines in wild populations. Captive breeding can reduce the pressure on wild populations caused by overcollection, but if not properly monitored, wildlife laundering can lead to further population declines. Improving the forensic ability to detect wildlife laundering will assist in monitoring the wildlife trade and enforcing regulations, thereby aiding recovery of wild populations. Stable isotope analysis has grown in importance as a forensic tool, but improvements are needed. Here, stable isotope analysis (δ13C) on eggshells of captive bred and wild sourced island apple snails (Pomacea maculata) distinguished between the two; eggshells of captive …

Evaluation Of Plaster Creek Stewards: Results And Recommendations From Surveys, Interviews, And Education Event Feedback Forms, Laura Luchies, Jax Heil, Taylor E. Hartson

Watershed Reports

No abstract provided.

Dormant Propagules In Demographic Studies: A Recurrent Bias And Potential Solutions, Federico Borghesi

Graduate Thesis and Dissertation 2023-2024

In the face of unprecedented anthropogenic change, we increasingly turn to emergent technologies and extensive data sets for solutions that complement much needed systemic changes in our societies. These technological solutions, however, must be approached with care. We must recognize and address biases in the way data has been accumulated. In demographic studies, dormant life stages, such as seed banks, and other cryptic factors have often been neglected. The potential consequences of these omissions have been extensively described in the literature. In the first chapter, I analyze patterns of seed bank omissions in demographic models, finding unjustified omissions are widespread …

Deep Learning-Based Technique For The Perception Of The Cervical Cancer, Aya Haraz, Hossam El-Din Moustafa, Abeer Twakol Khaleel, Ahmed H. Eltanboly

Mansoura Engineering Journal

In third-world countries, cervical cancer is the most prevalent and leading cause of death. It is affected by a variety of factors, including smoking, poor nutritional status, immunological inadequacy, and prolonged use of contraception. The Pap smear test, which is intended to prevent cervical cancer, finds preneoplastic changes in cervical epithelial cells. This study framework classified cervical cancer cells from Pap smears into five specified cell types using machine learning-based classification algorithms. The SIPaKMeD database is used in this investigation. This public dataset, which was manually cropped from 966 cluster cell images taken from Pap smear slides, has 4045 isolated …

Evolutionary History And Adaptation To Salinity In American Alligators, John Konvalina

Electronic Theses and Dissertations, 2020-2023

Stressful environments can commonly be found at the edge of a species range and may be a driver for adaption in suboptimal environments. Furthermore, the edge of a species' range can expand and contract over time, resulting in multiple independent invasions of the same stressful habitat. Elucidating population genetic structure and demographic history can aid in determining the which geologic factors impact range distributions and when climatic changes occurred driving genetic patterns observed in contemporary populations. Moreover, populations at the edge of the species range may adapt to the stressful environments that occur at the range edge and exhibit genetic …

Homogeneity Test On Error Rates From Ordinal Scores And Application To Forensic Science, Ngoc Ty Nguyen

Graduate Thesis and Dissertation 2023-2024

The Receiver Operating Characteristic (ROC) curve is used to measure the classification accuracy of tests that yield ordinal or continuous scores. Ordinal scores are common in medical imaging studies and, more recently, in black-box studies on forensic identification accuracy (Phillips et al., 2018). To assess the accuracy of radiologists in medical imaging studies or the accuracy of forensic examiners in biometric studies, one needs to estimate the ROC curves from the ordinal scores and account for the covariates related to the radiologists or forensic examiners. In this thesis, we propose a homogeneity test to compare the performance of raters. We …

An Integrative Salt Marsh Conceptual Framework For Global Comparisons, Erik S. Yando, Scott F. Jones, W. Ryan James, Denise D. Colombano, Diana I. Montemayor, Stefanie Nolte, Jacqueline L. Raw, Shelby L. Ziegler, Luzhen Chen, Daniele Daffonchio, Marco Fusi, Kerrylee Rogers, Liudmila Sergienko

Biological Sciences Faculty Publications

Salt marshes occur globally across climatic and coastal settings, providing key linkages between terrestrial and marine ecosystems. However, salt marsh science lacks a unifying conceptual framework; consequently, historically well-studied locations have been used as normative benchmarks. To allow for more effective comparisons across the diversity of salt marshes, we developed an integrative salt marsh conceptual framework. We review ecosystem-relevant drivers from global to local spatial scales, integrate these multi-scale settings into a framework, and provide guidance on applying the framework using specific variables on 11 global examples. Overall, this framework allows for appropriate comparison of study sites by accounting for …

Eye Lens Β-Crystallins Are Predicted By Native Ion Mobility-Mass Spectrometry And Computations To Form Compact Higher-Ordered Heterooligomers, Amber D. Rolland, Takumi Takata, Micah T. Donor, Kirsten J. Lampi, James S. Prell

Faculty Publications - Department of Biological & Molecular Science

Eye lens crystallin proteins maintain the refractive properties of the lens but are not replaced after denucleation. Rolland et al. use native ion mobility-mass spectrometry, kinetics experiments, and computations to reveal that b-crystallins form heterodimers. These likely assemble into compact heterooligomers that enable the very high protein concentrations found in lens tissue.

Edna Metabarcoding Of Avocado Flowers: ‘Hass’ It Got Potential To Survey Arthropods In Food Production Systems?, Joshua H. Kestel, Philip W. Bateman, David L. Field, Nicole E. White, Rose Lines, Paul Nevill

Research outputs 2022 to 2026

In the face of global biodiversity declines, surveys of beneficial and antagonistic arthropod diversity as well as the ecological services that they provide are increasingly important in both natural and agro-ecosystems. Conventional survey methods used to monitor these communities often require extensive taxonomic expertise and are time-intensive, potentially limiting their application in industries such as agriculture, where arthropods often play a critical role in productivity (e.g. pollinators, pests and predators). Environmental DNA (eDNA) metabarcoding of a novel substrate, crop flowers, may offer an accurate and high throughput alternative to aid in the detection of these managed and unmanaged taxa. Here, …

Island Meltdown: Demise Of The Abrolhos Painted Button-Quail Turnix Varius Scintillans In The Face Of Multiple Threats, Ryan Carter

Theses: Doctorates and Masters

Island avifauna suffer high rates of extinction and decline. The major threats to island birds centre around the ecological impacts of invasive predators, competitors, and grazers. The Abrolhos Painted Button-quail (Turnix varius scintillans) is a subspecies that has been determined to be the 5th most likely taxon to become extinct in Australia. T. v. scintillans historically inhabited three islands in the Houtman Abrolhos archipelago off the mid-west coast of Australia. This study aimed to 1) confirm the status of T. v. scintillans on North Island and determine the main causes of decline, 2) model habitat variables with detections from camera …

Ecological Niche Comparison Among Closely Related Tree Species Of Lauraceae Using Climatic And Edaphic Data, Laura J. Giraldo-Kalil, Gonzalo E. Pinilla Buitrago, Andrés Lira-Noriega, Francisco Lorea-Hernández, Juan Núñez-Farfán

Publications and Research

ABSTRACT:

Edaphic specialization is considered to promote ecological differentiation among closely related species of Damburneya (Lauraceae) occurring in sympatry. However, little is known about the effects of soil and other key environmental factors like climate on the ecological niche and distribution of these tree species. Here, we assessed the role of climate and soil on niche divergence and potential distribution of four Damburneya species whose distributions span Central America and Mexico. We performed ecological niche modeling with MaxEnt using three sets of environmental data: climatic-only, edaphic-only, and a combination of both, to characterize species niches and suitable distribution areas. Niche …

How Akron Affects The Water Quality Of The Cuyahoga River, Allyson Darst

Williams Honors College, Honors Research Projects

The purpose of this study was to analyze whether the city of Akron had negative effects on the Cuyahoga river, and determine if the Cuyahoga River was naturally able to remediate these effects downstream. The pollutants measured in this study include hardness, bromine, residual chlorine, iron, copper, lead, nitrate, nitrite, ammonium chloride, total chlorine, fluoride, carbonate, pH, total alkalinity and cyanuric acid. This study was done using water testing strips (JNW Direct) to test the water at four different locations along the Cuyahoga River downstream (North) of Akron. This study found that the city of Akron does have a negative …

College Of Natural Sciences 2022 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

This is the 2022 issue of the annual College of Natural Sciences year-end publication.

Contents:
[Page] 2 Dean's message
[Page] 3 Department highlights
[Page] 4 Overview of Bold & Blue Campaign
[Page] 5 Dr. Edward Hogan recognition & endowment
[Page] 6 Career milestones
[Page] 7 Student travel and research
[Page] 8 $11 million COBRE grant
[Page] 9 Professional Science Masters & Research highlights
[Page]10 Outreach highlights throughout the state
[Page] 11 2022 events recap – join us in 2023!
[Page] 12 Updates on our VR initiative
[Page] 14 Overview of awards and recognitions from 2022

Effects Of Velocity And Substrate Size On The Formation Of Zebra Mussel Druses, Ian Mott

Journal of Earth and Life Science

Zebra Mussels Dreissena polymorpha are an invasive bivalve species that are highly successful at dominating new environments. These invaders have been known to colonize substrate so thoroughly that all they have to attach to are members of their own species. When large mats of interconnected mussels completely cover a riverbed, it can have a drastic effect on the surrounding environment. This study serves to create a better understanding of the hydrologic parameters needed for Zebra Mussels to create these ecosystem-transforming colonies known as druses. Data was collected on a small stretch of the Upper Mississippi River in Northern Minnesota, previously …

Analysis Of ‘Touch’ Dna Recovered From Metal Substrates: An Investigation Into Cfdna-Metal Interactions And The Efficacy Of Different Collection Techniques On Dna Yield, Jessica E. Thornton

Graduate Theses, Dissertations, and Problem Reports (ETD)

While several improvements have been made in recent years to optimize the recovery of ‘touch’ DNA, relatively little research has been conducted to understand the relationship between ‘touch’ DNA and the binding affinity of that DNA to metal surfaces, specifically those with a significant copper presence. Furthermore, characterization of cell-free DNA (cfDNA) and its contribution to ‘touch’ samples and those cfDNA-metal interactions from objects commonly identified at crime scenes (cartridge casings, knives, doorknobs) have been lacking. Research has identified the tendency of copper ions to intercalate with DNA helices, resulting in sample degradation among other damaging conformational changes; however, while …

Room-Temperature Crystallography Reveals Altered Binding Of Small-Molecule Fragments To Ptp1b, Tamar Skaist Mehlman, Justin T. Biel, Syeda Maryam Azeem, Elliot R. Nelson, Sakib Hossain, Louise Dunnett, Neil G. Paterson, Alice Douangamath, Romain Talon, Danny Axford, Helen Orins, Frank Von Delft, Daniel A. Keedy

Advanced Science Research Center

Much of our current understanding of how small-molecule ligands interact with proteins stems from X-ray crystal structures determined at cryogenic (cryo) temperature. For proteins alone, room-temperature (RT) crystallography can reveal previously hidden, biologically relevant alternate conformations. However, less is understood about how RT crystallography may impact the conformational landscapes of protein-ligand complexes. Previously, we showed that small-molecule fragments cluster in putative allosteric sites using a cryo crystallographic screen of the therapeutic target PTP1B (Keedy et al., 2018). Here, we have performed two RT crystallographic screens of PTP1B using many of the same fragments, representing the largest RT crystallographic screens of …

Cup Is Essential For Oskar Mrna Translational Repression During Early Drosophila Oogenesis, Livia V. Bayer, Samantha Milano, Stephen K. Formel, Harpreet Kaur, Rishi Ravichandran, Juan A. Cambeiro, Lizaveta Slinko, Irina E. Catrina, Diana P. Bratu

Publications and Research

Study of the timing and location for mRNA translation across model systems has begun to shed light on molecular events fundamental to such processes as intercellular communication, morphogenesis, and body pattern formation. In D. melanogaster, the posterior mRNA determinant, oskar, is transcribed maternally but translated only when properly localized at the oocyte’s posterior cortex. Two effector proteins, Bruno1 and Cup, mediate steps of oskar mRNA regulation. The current model in the field identifies Bruno1 as necessary for Cup’s recruitment to oskar mRNA and indispensable for oskar’s translational repression. We now report that this Bruno1-Cup interaction leads …

Quantity Of Questing Black-Legged Ticks And Associated Micro-Scale Environmental Data Collected From Four Suburban Parks Near New York City, Shipeng Sun, Chong Di, Li Li, Brian Sulkow, Weigang Qiu

Publications and Research

During 2017 and 2018, we collected the quantity of questing black-legged ticks (Ixodes scapularis), also known as deer ticks, in 124 sampling sites of 5m by 5m in four state parks—Caumsett State Historic Park, Connetquot River State Park, Rockefeller State Park, and Fire Island National Seashore—around New York City. The black-legged tick is the primary vector for the spirochete Borrelia burgdorferi, the pathogen of Lyme disease, in Northeastern United States. Using the flagging method, we collected and counted the numbers of adult and nymphal black-legged ticks at each site. Along with these quantities, we also recorded the …

Land Systems, Soils And Vegetation Of The Southern Goldfields And Great Western Woodlands Of Western Australia - Volume 2, Peter-Jon A. Waddell, Paul Galloway

Technical Bulletins

This technical bulletin defines and maps the land resources of the southern Goldfields region of Western Australia (WA). The southern Goldfields region, as featured in this bulletin, covers 151,753 km². The western and eastern borders are variable because they align with various cadastral boundaries. The western survey border, which in part follows the WA State Barrier Fence, demarcates cleared agricultural land from the intact, western extent of the Great Western Woodlands. The eastern border abuts the westernmost Nullarbor pastoral lease boundaries, except for the north-easternmost and south-easternmost edges which continue into Crown land. Major towns are Coolgardie, Kalgoorlie …

Competition And Herbivory Influence The Survival, Growth, And Physiology Of Native Tree Seedlings In The Kentucky Inner Bluegrass Savanna-Woodland, James D. Shaffer

Theses and Dissertations--Biology

Terrestrial plant communities are shaped by competition for resources, herbivory, and abiotic processes. Savanna systems represent a dynamic coexistence of contrasting life forms (grasses and trees) shaped by competition and disturbance. The Kentucky Inner Bluegrass Savanna-Woodland (KIBSW) is described as an open woodland of shade intolerant species; however, climatic, and edaphic conditions can support closed-canopy forest. After European pioneer settlement (c1750-1800), over 99% of “savanna-woodlands” have been lost. KIBSW remnants are experiencing a recruitment failure, leading to a dominance shift in tree communities. I researched how tree-grass competition and mammalian herbivory influence KIBSW regeneration and maintenance. The KIBSW does not …

The Coral Bleaching Automated Stress System (Cbass): A Low-Cost, Portable System For Standardized Empirical Assessments Of Coral Thermal Limits, Nicholas R. Evensen, Katherine E. Parker, Thomas A. Oliver, Stephen R. Palumbi, Cheryl A. Logan, James S. Ryan, Courtney N. Klepac, Gabriela Perna, Mark E. Warner, Christian R. Voolstra, Daniel J. Barshis

Biological Sciences Faculty Publications

Ocean warming is increasingly affecting marine ecosystems across the globe. Reef-building corals are particularly affected by warming, with mass bleaching events increasing in frequency and leading to widespread coral mortality. Yet, some corals can resist or recover from bleaching better than others. Such variability in thermal resilience could be critical to reef persistence; however, the scientific community lacks standardized diagnostic approaches to rapidly and comparatively assess coral thermal vulnerability prior to bleaching events. We present the Coral Bleaching Automated Stress System (CBASS) as a low-cost, open-source, field-portable experimental system for rapid empirical assessment of coral thermal thresholds using standardized temperature …

Fine Characterization Of Leafing Phenology In The Brazilian Atlantic Forest By Optical And Microwave Remote Sensing, James B. Bell

Dissertations and Theses

Tropical forests provide important ecosystem functions in the global biosphere, but they remain among the most poorly understood elements of land surface models, especially with regard to their seasonal dynamics. For instance, in seasonally dry forests, the pattern of the annual green-up in their canopies closely follows annual patterns of rainfall. The same, however, does not occur in wet forest canopies which are dominated by evergreen trees. In the latter, water is not scarce enough to limit leaf photosynthetic function. Canopy leafing phenology in these forests is therefore poorly characterized by optical remote sensing methods which are not sensitive to …

Potential Repercussions Of Offshore Wind Energy Development In The Northeast United States For The Atlantic Surfclam Survey And Population Assessment, Sarah Borsetti, Daphne M. Munroe, Andrew M. Scheld, Eric N. Powell, John M. Klinck, Eileen E. Hofmann

CCPO Publications

The Atlantic surfclam Spisula solidissima fishery, which spans the U.S. Northeast continental shelf, is among the most exposed to offshore wind energy development impacts because of the overlap of fishing grounds with wind energy lease areas, the hydraulic dredges used by the fishing vessels, and the location of vessel home ports relative to the fishing grounds. The Atlantic surfclam federal assessment survey is conducted using a commercial fishing vessel in locations that overlap with the offshore wind energy development. Once wind energy turbines, cables, and scour protection are installed, survey operations within wind energy lease areas may be curtailed or …

The Use Of A Habitat Quality Stress Index To Evaluate Stress As An Analog For Proximate Fitness In The American Crow Within A Matrix Of Landcover Characteristics To Assess Its Potential Contribution To Disease Etiologies, Theodore Lee Grabarz

Antioch University Dissertations & Theses

All organisms occur within spatial and temporal environments to maximize proximate fitness (health) and thus life history outcomes. Previous work has examined the temporal and behavioral aspects of proximate fitness on life history outcomes particularly regarding highly perturbed environments (i.e., climate and land use change, resource extraction, agricultural erosion, etc.). My work focuses on the less examined spatial aspect of these perturbed environments. More specifically, this dissertation examines habitat selection and quality as the basis for understanding stress response (negative and positive feedback mechanisms) to environmental stressors within the larger context of regional or gamma (ɣ) biodiversity. Through the lens …

Microscale Pollen Release And Dispersal Patterns In Flowering Grass Populations, Carl A. Frisk, Godfrey P. Apangu, Geoffrey M. Petch, Simon Creer, Mary Hanson, Beverley Adams-Groom, Carsten A. Skjøth

Research outputs 2022 to 2026

Characterizing pollen release and dispersion processes is fundamental for knowledge advancement in ecological, agricultural and public health disciplines. Understanding pollen dispersion from grass communities is especially relevant due to their high species-specific allergenicity and heterogeneously distributed source areas. Here, we aimed to address questions concerning fine level heterogeneity in grass pollen release and dispersion processes, with a focus on characterizing the taxonomic composition of airborne grass pollen over the grass flowering season using eDNA and molecular ecology methods. High resolution grass pollen concentrations were compared between three microscale sites ( < 300 m apart) in a rural area in Worcestershire, UK. The grass pollen was modelled with local meteorology in a MANOVA (Multivariate ANOVA) approach to investigate factors relevant to pollen release and dispersion. Simultaneously, airborne pollen was sequenced using Illumina MySeq for metabarcoding, analysed against a reference database with all UK grasses using the R packages DADA2 and phyloseq to calculate Shannon's Diversity Index ( -diversity). The flowering phenology of a local Festuca rubra population was observed. We found that grass pollen concentrations varied on a microscale level, likely attributed to local topography and the dispersion distance of pollen from flowering grasses in local source areas. Six genera (Agrostis, Alopecurus, Arrhenatherum, Holcus, Lolium and Poa) dominated the pollen season, comprising on average 77 % of the relative abundance of grass species reads. Temperature, solar radiation, relative humidity, turbulence and wind speeds were found to be relevant for grass pollen release and dispersion processes. An isolated flowering Festuca rubra population contributed almost 40 % of the relative pollen abundance adjacent to the nearby sampler, but only contributed 1 % to samplers situated 300 m away. This suggests that most emitted grass pollen has limited dispersion distance and our results show substantial variation in airborne grass species composition over short geographical scales.

Macrolichen Inventory Of The Horse Mountain Botanical Area, Six Rivers National Forest, California, Usa, Sarah Norvell Conway

Cal Poly Humboldt theses and projects

Macrolichen diversity and community composition was determined for an area of high botanical interest in the Coast Ranges of Northern California – the Horse Mountain Botanical Area (HMBA) in Six Rivers National Forest. The Coast Ranges have been suggested to have high epiphytic macrolichen diversity, yet detailed site-specific macrolichen surveys are lacking for the area. Here we present comprehensive data on macrolichens of the HMBA integrated with environmental metadata at the landscape level. Twenty 0.4 ha sampling plots were positioned across the varying habitats of the HMBA and macrolichens were intensively sampled from all substrata. Out of 888 total collections, …

The Coral Bleaching Automated Stress System (Cbass): A Low Cost, Portable System For Standardized Empirical Assessments Of Coral Thermal Limits, Nicolas R. Evensen, Katherine E. Parker, Thomas A. Oliver, Stephen R. Palumbi, Cheryl A. Logan, James S. Ryan, Courtney N. Klepac, Gabriela Perna, Mark E. Warner, Christian R. Voolstra, Daniel J. Barshis

Biological Sciences Faculty Publications

Ocean warming is increasingly affecting marine ecosystems across the globe. Reef-building corals are particularly affected by warming, with mass bleaching events increasing in frequency and leading to widespread coral mortality. Yet, some corals can resist or recover from bleaching better than others. Such variability in thermal resilience could be critical to reef persistence; however, the scientific community lacks standardized diagnostic approaches to rapidly and comparatively assess coral thermal vulnerability prior to bleaching events. We present the Coral Bleaching Automated Stress System (CBASS) as a low-cost, open-source, field-portable experimental system for rapid empirical assessment of coral thermal thresholds using standardized temperature …

Mechanical Devices For Census And Detection Of Off-Host Larval Ticks (Acari: Ixodidae), Donald B. Thomas, Holly D. Gaff, Brenda Leal-Galvan

Biological Sciences Faculty Publications

Standard off-host tick census techniques are generally inefficient for larval stages. Also, such techniques expose the investigator to environmental hazards including tick bites. Mechanical devices are an option which were tested under field conditions for proof of concept and in side-by-side comparison to the standard techniques. The tick-vac collected more ticks than the legging technique, but with lower frequency of positive detections. It may have utility for sampling small areas, such as weedy corrals suspected of harboring ticks. Different configurations of tick-bots, robotic vehicles with flags, depended on intensive operator control to avoid obstacles, limiting operation to line of sight. …

Blue Carbon Science, Management And Policy Across A Tropical Urban Landscape, Daniel A. Friess, Yasmine M. Gatt, Tze Kwan Fung, Jahson B. Alemu I, Natasha Bhatia, Rebecca Case, Siew Chin Chua, Danwei Huang, Valerie Kwan, Kiah Eng Lim, Yudhishthra Nathan, Yan Xiang Ow, Daniel Saavedra-Hortua, Taylor M. Sloey, Erik S. Yando, Hassan Ibrahim, Lian Pin Koh, Jun Yu Puah, Serena Lay-Ming Teo, Karenne Tun, Lynn Wei Wong, Siti Maryam Yaakub

Biological Sciences Faculty Publications

The ability of vegetated coastal ecosystems to sequester high rates of “blue” carbon over millennial time scales has attracted the interest of national and international policy makers as a tool for climate change mitigation. Whereas focus on blue carbon conservation has been mostly on threatened rural seascapes, there is scope to consider blue carbon dynamics along highly fragmented and developed urban coastlines. The tropical city state of Singapore is used as a case study of urban blue carbon knowledge generation, how blue carbon changes over time with urban development, and how such knowledge can be integrated into urban planning alongside …