Physical Sciences and Mathematics Commons^™

Seasonal Origins Of Soil Water Used By Trees, Scott T. Allen, James W. Kirchner, Sabine Braun, Rolf T. W. Siegwolf, Gregory R. Goldsmith

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Rain recharges soil water storages and either percolates downward into aquifers and streams or is returned to the atmosphere through evapotranspiration. Although it is commonly assumed that summer rainfall recharges plant-available water during the growing season, the seasonal origins of water used by plants have not been systematically explored. We characterize the seasonal origins of waters in soils and trees by comparing their midsummer isotopic signatures (δ2H) to seasonal isotopic cycles in precipitation, using a new seasonal origin index. Across 182 Swiss forest sites, xylem water isotopic signatures show that summer rain was not the predominant water source …

Allosteric Mechanism Of The Circadian Protein Vivid Resolved Through Markov State Model And Machine Learning Analysis, Hongyu Zhou, Zheng Dong, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an …

Student-Faculty Collaborative Research Grant Report, Megan Bestwick

Post-Grant Reports

Mitochondria are essential organelles in most eukaryotic cells because of their role in metabolism and the production of ATP by the oxidative phosphorylation (OXPHOS) pathway, as well as other key cellular processes. Metal cofactors, such as copper (Cu) and iron (Fe), are incorporated into OXPHOS protein complexes of yeast located within the inner membrane of the mitochondria. Misincorporation or modulation of these available metals in mitochondrial enzymes leads to the production of reactive oxygen species (ROS). ROS are reactive molecules containing oxygen such as peroxides, superoxide, and hydroxyl radicals. Yeast are a good model for studying aging and the effect …

Seed Germination Responses To Seasonal Temperature And Drought Stress Are Species‐Specific But Not Related To Seed Size In A Desert Steppe: Implications For Effect Of Climate Change On Community Structure, Fengyan Yi, Zhaoren Wang, Carol C. Baskin, Jerry M. Baskin, Ruhan Ye, Hailian Sun, Yuanyuan Zhang, Xuehua Ye, Guofang Liu, Xuejun Yang, Zhenying Huang

Biology Faculty Publications

Investigating how seed germination of multiple species in an ecosystem responds to environmental conditions is crucial for understanding the mechanisms for community structure and biodiversity maintenance. However, knowledge of seed germination response of species to environmental conditions is still scarce at the community level. We hypothesized that responses of seed germination to environmental conditions differ among species at the community level, and that germination response is not correlated with seed size. To test this hypothesis, we determined the response of seed germination of 20 common species in the Siziwang Desert Steppe, China, to seasonal temperature regimes (representing April, May, June, …

Creative Citizen Science Illuminates Complex Ecological Responses To Climate Change, Abraham J. Miller-Rushing, Amanda S. Gallinat, Richard B. Primack

Biology Faculty Publications

Climate change is causing the timing of key behaviors (i.e., phenology) to shift differently across trophic levels and among some interacting organisms (e.g., plants and pollinators, predators and prey), suggesting that interactions among species are being disrupted (1, 2). Studying the phenology of interactions, however, is difficult, which has limited researchers’ ability to zero in on changes in specific interactions or on the consequences of mismatches. In PNAS, Hassall et al. (3) use a combination of citizen science techniques to investigate the effects of climate change on dozens of specific interactions. They focus on a Batesian mimicry complex involving stinging …

2019 Patterns Around Us Handout, Benjamin Davidovitch, Narayanan Menon, Wayne Kermenski, Jennifer Welborn

Patterns Around Us

This is a FREE two-day program designed for Middle and High School General Science, Biology, Physics, Technology/Engineering teachers. It is funded by the National Science Foundation.Space is limited, so apply soon! Some limited funding is available for overnight stay.

“Science may be described as the attempt to give good accounts of the patterns in nature. The result of scientific investigation is an understanding of natural processes.... Overall, the key criterion of science is that it provides a clear, rational, and succinct account of a pattern in nature....” Massachusetts State Frameworks for Science and Technology.

Participants will explore the processes of …

Memory Formation In Matter, Joseph Paulsen, Nathan C. Keim, Zorana Zeravcic, Srikanth Sastry, Sidney R. Nagel

Physics - All Scholarship

Memory formation in matter is a theme of broad intellectual relevance; it sits at the interdisciplinary crossroads of physics, biology, chemistry, and computer science. Memory connotes the ability to encode, access, and erase signatures of past history in the state of a system. Once the system has completely relaxed to thermal equilibrium, it is no longer able to recall aspects of its evolution. The memory of initial conditions or previous training protocols will be lost. Thus many forms of memory are intrinsically tied to far-from-equilibrium behavior and to transient response to a perturbation. This general behavior arises in diverse contexts …

Urban Aerobiological Risk Mapping Of Ornamental Trees Using A New Index Based On Lidar And Kriging: A Case Study Of Plane Trees, Raúl Pecero-Casimiro, Santiago Fernández-Rodríguez, Rafael Tormo-Molina, Alejandro Monroy-Colín, Inmaculada Silva-Palacios, Juan Pedro Cortés-Pérez, Ángela Gonzalo-Garijo, J. M. Maya-Manzano

Articles

Ornamental trees bring benefits for human health, including reducing urban pollution. However, some species, such as plane trees (Platanus sp.), produce allergenic pollen. Consequently, urban maps are a valuable tool for allergic patients and allergists, but they often fail to include variables that contribute to the “building downwash effect”, such as the width and shape of streets and the height of buildings. Other factors that directly influence pollen dispersion (slopes and other geographical features) also have not traditionally been discussed. The LiDAR (Laser Imaging Detection and Ranging) technique enables one to consider these variables with high accuracy. This work proposes …

Betting & Hierarchy In Paleontology, Leonard Finkelman

Faculty Publications

In his Rock, Bone, and Ruin: An Optimist’s Guide to the Historical Sciences, Adrian Currie argues that historical scientists should be optimistic about success in reconstructing the past on the basis of future research. This optimism follows in part from examples of success in paleontology. I argue that paleontologists’ success in these cases is underwritten by the hierarchical nature of biological information: extinct organisms have extant analogues at various levels of taxonomic, ecological, and physiological hierarchies, and paleontologists are adept at exploiting analogies within one informational hierarchy to infer information in another. On this account, fossils serve the role …

Crossed Tracks: Mesolimulus, Archaeopteryx, And The Nature Of Fossils, Leonard Finkelman

Faculty Publications

Organisms leave a variety of traces in the fossil record. Among these traces, vertebrate and invertebrate paleontologists conventionally recognize a distinction between the remains of an organism’s phenotype (body fossils) and the remains of an organism’s life activities (trace fossils). The same convention recognizes body fossils as biological structures and trace fossils as geological objects. This convention explains some curious practices in the classification, as with the distinction between taxa for trace fossils and for tracemakers. I consider the distinction between “parallel taxonomies,” or parataxonomies, which privileges some kinds of fossil taxa as “natural” and others as “artificial.” The motivations …

Frequent Prescribed Fires Can Reduce Risk Of Tick-Borne Diseases, Elizabeth R. Gleim

Environmental Studies / Environmental Science Faculty Scholarship

Recently, a two-year study found that long-term prescribed fire significantly reduced tick abundance at sites with varying burn regimes (burned surrounded by burned areas [BB], burned surrounded by unburned areas [BUB], and unburned surrounded by burned areas [UBB]). In the current study, these ticks were tested for pathogens to more directly investigate the impacts of long-term prescribed burning on human disease risk. A total of 5,103 ticks (4,607 Amblyomma americanum, 76 Amblyomma maculatum, 383 Ixodes scapularis, two Ixodes brunneus, and 35 Dermacentor variabilis) were tested for Borrelia spp., Rickettsia spp., Ehrlichia spp., and Anaplasma phagocytophilum. Long-term prescribed fire did not …

Ua84 Sigma Chi, Wku Archives

WKU Archives Collection Inventories

Records created by and about the WKU chapter of Sigma Xi.

Ua66/6/1 Ogden College Of Science & Engineering Biology Administration, Wku Archives

WKU Archives Collection Inventories

Records created by and about the administration of the Biology Department.

Relationship Of Ndvi And Oak (Quercus)Pollen Including A Predictive Model In The Sw Mediterranean Region, Rocío González-Naharro, Elia Quirós, Santiago Fernández-Rodríguez, Inmaculada Silva-Palacios, J. M. Maya-Manzano, Rafael Tormo-Molina, Raúl Pecero-Casimiro, Alejandro Monroy-Colin, Ángela Gonzalo-Garijo

Articles

Techniques of remote sensing are being used to develop phenological studies. Our goal is to study the correlation among the Normalized Difference Vegetation Index (NDVI) related with oak trees included in three set data polygons (15, 25 and 50 km to aerobiological sampling point as NDVI-15, 25 and 50), and oak (Quercus) daily average pollen counts from 1994 to 2013. The study was developed in the SW Mediterranean region with continuous pollen recording within the mean pollen season of each studied year. These pollen concentrations were compared with NDVI values in the locations containing the vegetation under a study based …

One Fish, Two Fish, Red Fish, Whose Fish? Subjects: Life Science, Environmental Science, Marine / Ocean Science, Shelby White

Reports

This activity invites students to assume the role of various stakeholders in fisheries management and actively discuss the influence of economics, ecology and human interactions in decision-making.

Students will demonstrate their argument for/against a certain regulation by participating as a specific stakeholder (i.e. commercial fisher, recreational fisher, scientists/researcher, environmental group, management agency, and citizen). Students will recognize that stakeholders tend to advocate based on their individual needs, often making it difficult for proposed policies to satisfy the needs of all stakeholders and achieve sustainability goals.

Unclogging The Pipeline: Advancement To Full Professor In Academic Stem, Helga Van Miegroet, Christy Glass, Ronda R. Callister, Kimberly Sullivan

Ecology Center Publications

Purpose: Women remain underrepresented in academic STEM, especially at the highest ranks. While much attention has focused on early-career attrition, mid-career advancement is still largely understudied and undocumented. This paper analyzes gender differences in advancement to full professor within academic STEM at a mid-size public doctoral university in the western US, before and after the NSF-ADVANCE Program (2003-2007).

Methodology: Using faculty demographics and promotion data between 2008 and 2014, combined with faculty responses to two waves of a climate survey, the magnitude and longevity of the impact of ADVANCE on mid-career faculty advancement across gender is evaluated.

Findings: This study …

Phenogeneranker: A Tool For Gene Prioritization Using Complete Multiplex Heterogeneous Networks, Cagatay Dursun, Naoki Shimoyama, Mary Shimoyama, Michael Schläppi, Serdar Bozdag

Computer Science Faculty Research and Publications

Uncovering genotype-phenotype relationships is a fundamental challenge in genomics. Gene prioritization is an important step for this endeavor to make a short manageable list from a list of thousands of genes coming from high-throughput studies. Network propagation methods are promising and state of the art methods for gene prioritization based on the premise that functionally-related genes tend to be close to each other in the biological networks.

In this study, we present PhenoGeneRanker, an improved version of a recently developed network propagation method called Random Walk with Restart on Multiplex Heterogeneous Networks (RWR-MH). PhenoGeneRanker allows multi-layer gene and disease networks. …

Expedition Sediments: Mud's Journey Through The Watershed. Subjects: Earth Science / Environmental Science Grades: 9-12, Jessie Turner

Reports

Expedition Sediments is a game-in-a-lesson that allows students to explore the movement of sediments through watersheds by moving around the classroom. This lesson explores how grains of estuarine mud and sand move throughout estuaries and coastal regions, with a focus on processes surrounding a highly populated estuary such as the Chesapeake Bay. By the end of the lesson, students will be able to explain how sediments are transported through an estuary, graph sediment residence times in different locations, and compare the timescales of different sediment transport processes.

Habitat Characteristics And Nesting Ecology Of Golden Eagles In Arizona, Michele J. Losee

Antioch University Dissertations & Theses

Golden Eagles (Aquila chrysaetos) have a broad range globally and in general are well-studied. However, Arizona’s Golden Eagle population remained essentially unstudied until 2011, when Arizona Game and Fish Department (AZGFD) began nest surveys for cliff nesting Golden Eagles throughout the state. As a result of this data collection, the natural history of Arizona’s Golden Eagles is finally revealing itself. This dissertation outlined a reliable description of their nesting phenology that provides a framework for timing surveys and a baseline to monitor the effects of climate change on Golden Eagles. The mean date for egg-laying was February 14 and pairs …

Modeling The Seasonal Cycle Of Iron And Carbon Fluxes In The Amundsen Sea Polynya, Antarctica, P. St-Laurent, P. L. Yager, R. M. Sherrell, H. Oliver, M. S. Dinniman, S. E. Stammerjohn

CCPO Publications

The Amundsen Sea Polynya (ASP) is distinguished by having the highest net primary production per unit area in the coastal Antarctic. Recent studies have related this high productivity to the presence of fast-melting ice shelves, but the mechanisms involved are not well understood. In this study we describe the first numerical model of the ASP to represent explicitly the ocean-ice interactions, nitrogen and iron cycles, and the coastal circulation at high resolution. The study focuses on the seasonal cycle of iron and carbon, and the results are broadly consistent with field observations collected during the summer of 2010–2011. The simulated …

Volume 11, Jacob Carney, Ryan White, Joseph Hyman, Jenny Raven, Megan Garrett, Ibrahim Kante, Summer Meinhard, Lauren Johnson, William "Editha" Dean Howells, Laura Gottschalk, Christopher Siefke, Pink Powell, Natasha Woodmancy, Katharine Colley, Abbey Mays, Charlotte Potts

Incite: The Journal of Undergraduate Scholarship

Table of Contents:

Introduction, Dr. Roger A. Byrne, Dean

From the Editor, Dr. Larissa "Kat" Tracy

From the Designers, Rachel English, Rachel Hanson

Synthesis of 3,5-substituted Parabens and their Antimicrobial Properties, Jacob Coarney, Ryan White

Chernobyl: Putting "Perestroika" and "Glasnot" to the Test, Joseph Hyman

Art by Jenny Raven

Watering Down Accessibility: The Issue with Public Access to Alaska's Federal Waterways, Meagan Garrett

Why Has the Democratic Republic of the Congo outsourced its Responsibility to Educate its Citizens? Ibrahim Kante

Art by Summer Meinhard

A Computational Study of Single Molecule Diodes, Lauren Johnson

Satire of …

Ua66/6/2 Ogden College Of Science & Engineering Biology Publications, Wku Archives

WKU Archives Collection Inventories

Publications created by and about Biology.

Metagenomic Sequencing Identifies Highly Diverse Assemblages Of Dinoflagellate Cysts In Sediments From Ships' Ballast Tanks, Lixia Shang, Zhangxi Hu, Yunyan Deng, Yuyang Liu, Xinyu Zhai, Zhaoyang Chai, Xiaohan Liu, Zifeng Zhan, Fred C. Dobbs, Ying Zhong Tang

OES Faculty Publications

Ships' ballast tanks have long been known as vectors for the introduction of organisms. We applied next-generation sequencing to detect dinoflagellates (mainly as cysts) in 32 ballast tank sediments collected during 2001-2003 from ships entering the Great Lakes or Chesapeake Bay and subsequently archived. Seventy-three dinoflagellates were fully identified to species level by this metagenomic approach and single-cell polymerase chain reaction (PCR)-based sequencing, including 19 toxic species, 36 harmful algal bloom (HAB) forming species, 22 previously unreported as producing cysts, and 55 reported from ballast tank sediments for the first time (including 13 freshwater species), plus 545 operational taxonomic units …