Biology Commons^™

Global Climate Change: Changing Weather Patterns, Janna Jann '20, Sabrina Meng '20

UN Sustainable Development Goals Infographics

You can take action to combat global climate change! Here are some starting points:

• Use heating only when necessary
• Reduce energy consumption
• Reduce, Reuse, Recycle!
• Use resources wisely!

Agricultural Practices Destroying The Environment, Ayan Mallik '20, Ethan Talreja '20

UN Sustainable Development Goals Infographics

• 50% of the world's habitable land has been converted for farming (Farming: Habitat Conversion, 2017)
• Indonesia rain forests have been cleared for the construction of palm oil plantations
• This threatens the habitats of endangered species such as the Asian elephant

Effects Of Agriculture, Riley Brutto '20, Maddy Chow '20

UN Sustainable Development Goals Infographics

Due to a lack of education among their population, many Brazilians turn to agriculture as a way to provide for themselves and their families. Additionally, low labor costs draw in large commercial companies that establish business in these developing worlds. However, to obtain farmland in the first place, deforestation has become a common practice, where thousands of miles of lush jungles are cleared away for agricultural practices. According to NASA imaging, 224,000 square miles of rainforest have been cleared in the Amazon. If left unchecked, the drastic consequences could harm not only the countries practicing deforestation, but the entire earth.

Coastal Erosion And Flooding, Arohi Singh '20, Neha Maddali '20

UN Sustainable Development Goals Infographics

The effects of human activities on our coasts.

Waste Management, Rachel Moreno '20, Alana Depaz '20

UN Sustainable Development Goals Infographics

"Human society sustains itself by transforming nature into garbage."

~Mason Cooley

Solution & Effects Of Agricultural Practices, Ryan Talusan '20, Caitlyn Castillo '20

UN Sustainable Development Goals Infographics

A potential solution of vertical farming

• PROFITABLE
• SCALABLE
• YEAR-ROUND

Urbanization In India: An Obituary, Meghana Karan '20, Shruti Shakthivel '20

UN Sustainable Development Goals Infographics

India is urbanizing very rapidly due to the movement of people from rural areas to urban cities for better opportunities. India does not have the resources or money to back this rapid urbanization of the population in general. This urbanization has created many environmental problems with air and water pollution.

Effects Of Elevated Co2, Increased Nitrogen Deposition, And Plant Diversity On Aboveground Litter And Root Decomposition, Xiaoan Zuo, Johannes Knops

School of Biological Sciences: Faculty Publications

Global change-induced litter decomposition strongly affects the carbon (C) and nitrogen (N) dynamics in grassland ecosystems. However, few studies show the interactive effects of global change factors on litter and root decomposition. We conducted a four-year grassland field experiment to examine the quality and decomposition of litter and root in a three-factorial experiment with elevated CO₂, increased N deposition, and plant species richness. We found that elevated CO₂ decreased the litter N content and root lignin content. N addition increased the root N content and decreased the litter lignin content. Increasing plant richness decreased the N and …

Agrochemicals Increase Risk Of Human Schistosomiasis By Supporting Higher Densities Of Intermediate Hosts, Neal T. Halstead, Christopher M. Hoover, Arathi Arakala, David J. Civitello, Guilio A. De Leo, Manoj Gambhir, Steve A. Johnson, Nicolas Jouanard, Kristin A. Loerns, Karena Nguyen, Jason R. Rohr

Integrative Biology Faculty and Staff Publications

Schistosomiasis is a snail-borne parasitic disease that ranks among the most important water-based diseases of humans in developing countries. Increased prevalence and spread of human schistosomiasis to non-endemic areas has been consistently linked with water resource management related to agricultural expansion. However, the role of agrochemical pollution in human schistosome transmission remains unexplored, despite strong evidence of agrochemicals increasing snail-borne diseases of wildlife and a projected 2- to 5-fold increase in global agrochemical use by 2050. Using a field mesocosm experiment, we show that environmentally relevant concentrations of fertilizer, a herbicide, and an insecticide, individually and as mixtures, increase densities …

Simian Virus 40 Large T Antigen As A Model To Test The Efficacy Of Flouroquinolones Against Viral Helicases, Sammer Siddiqui, Muhammad F. Anwar, Sadaf Naeem, Syed Hani Abidi, Shamshad Zarina, Syed Ali

Department of Biological & Biomedical Sciences

Simian virus 40 large T-antigen (SV40 LT-Ag) is a 708 amino acid nuclear phosphoprotein. Among many functions of LT-Ag is its ability to perform as an ATPase-helicase, catalyzing the unwinding of viral genome during replication. The LT-Ag has been employed in the studies of helicase structure and function, and has served as a model helicase for the screening of antiviral drugs that target viral helicase. In this study, using in vitro enzyme assays and in silico computer modeling, we screened a batch of 18 fluoroquinolones to assess their potential as antivirals by virtue of their inhibition of the LT-Ag helicase. …

Complete Genome Sequences Of 44 Arthrobacter Phages, Karen K. Klyczek, Deborah Jacobs-Sera, Tamarah L. Adair, Sandra D. Adams, Sarah L. Ball, Robert C. Benjamin, J. Alfred Bonilla, Caroline A. Breitenberger, Charles J. Daniels, Bobby L. Gaffney, Melinda Harrison, Lee E. Hughes, Rodney A. King, Gregory P. Krukonis, A. Javier Lopez, Kirsten Monsen-Collar, Marie C. Pizzorno, Claire A. Rinehart, Amanda K. Staples, Emily L. Stowe, Rebecca A. Garlena, Daniel A. Russell, Steven G. Cresawn, Welkin H. Pope, Graham F. Hatfull

Department of Biology Faculty Scholarship and Creative Works

We report here the complete genome sequences of 44 phages infecting Arthrobacter sp. strain ATCC 21022. These phages have double-stranded DNA genomes with sizes ranging from 15,680 to 70,707 bp and G+C contents from 45.1% to 68.5%. All three tail types (belonging to the families Siphoviridae, Myoviridae, and Podoviridae) are represented.

Evolution Of Enzymes With New Specificity By High-Throughput Screening Using Dmpr-Based Genetic Circuits And Multiple Flow Cytometry Rounds, Kil Koang Kwon, Dae-Hee Lee, Su Jin Kim, Su-Lim Choi, Eugene Rha, Soo-Jin Yeom, Bindu Subhadra, Jinhyuk Lee, Ki Jin Jeong, Seung-Goo Lee

Faculty Publications - Biological Sciences

Genetic circuit-based biosensors are useful in detecting target metabolites or in vivo enzymes using transcription factors (Tx) as a molecular switch to express reporter signals, such as cellular fluorescence and antibiotic resistance. Herein, a phenol-detecting Tx (DmpR) was employed as a critical tool for enzyme engineering, specifically for the rapid analysis of numerous mutants with multiple mutations at the active site of tryptophan-indole lyase (TIL, EC 4.1.99.1). Cellular fluorescence was monitored cell-by-cell using flow cytometry to detect the creation of phenolic compounds by a new tyrosine-phenol-lyase (TPL, EC 4.1.99.2). In the TIL scaffold, target amino acids near the indole ring …

Beyond The Matrix: The Many Non-Ecm Ligands For Integrins, Bryce Lafoya, Jordan A. Munroe, Alison Miyamoto, Michael A. Detweiler, Jacob J. Crow, Tana Gazdik, Allan R. Albig

Biology Faculty Publications and Presentations

The traditional view of integrins portrays these highly conserved cell surface receptors as mediators of cellular attachment to the extracellular matrix (ECM), and to a lesser degree, as coordinators of leukocyte adhesion to the endothelium. These canonical activities are indispensable; however, there is also a wide variety of integrin functions mediated by non-ECM ligands that transcend the traditional roles of integrins. Some of these unorthodox roles involve cell-cell interactions and are engaged to support immune functions such as leukocyte transmigration, recognition of opsonization factors, and stimulation of neutrophil extracellular traps. Other cell-cell interactions mediated by integrins include hematopoietic stem cell …

Pleiotropic And Novel Phenotypes In The Drosophila Gut Caused By Mutation Of Drop-Dead, Sean Conway, Christine Lynn Sansone, Anika Benske, Kaitlin Kentala, Johan Billen, Jozef Vanden Broeck, Edward M. Blumenthal

Biological Sciences Faculty Research and Publications

Normal gut function is vital for animal survival, and deviations from such function can contribute to malnutrition, inflammation, increased susceptibility to pathogens, diabetes, neurodegenerative diseases, and cancer. In the fruit fly Drosophila melanogaster, mutation of the gene drop-dead (drd) results in defective gut function, as measured by enlargement of the crop and reduced food movement through the gut, and drd mutation also causes the unrelated phenotypes of neurodegeneration, early adult lethality and female sterility. In the current work, adult drd mutant flies are also shown to lack the peritrophic matrix (PM), an extracellular barrier that lines the lumen of the …

A Bio-Based Pro-Antimicrobial Polymer Network Via Degradable Acetal Linkages, Douglas V. Amato, Dahlia N. Amato, Logan T. Blancett, Olga V. Mavrodi, William B. Martin, Sarah N. Swilley, Michael J. Sandoz, Glenmore Shearer, Dmitri V. Mavrodi, Derek Patton

Faculty Publications

The synthesis of a fully degradable, bio-based, sustained release, pro-antimicrobial polymer network comprised of degradable acetals (PANDA) is reported. The active antimicrobial agent – p-anisaldehyde (pA) (an extract from star anise) – was converted into a UV curable acetal containing pro-antimicrobial monomer and subsequently photopolymerized into a homogenous thiol-ene network. Under neutral to acidic conditions (pH < 8), the PANDAs undergo surface erosion and exhibit sustained release of pA over 38 days. The release of pA from PANDAs was shown to be effective against both bacterial and fungal pathogens. From a combination of confocal microscopy and transmission electron microscopy, we observed that the released pA disrupts the cell membrane. Additionally, we demonstrated that PANDAs have minimal cytotoxicity towards both epithelial cells and macrophages. Although a model platform, these results point to promising pathways for the design of fully degradable sustained-release antimicrobial systems with potential applications in agriculture, pharmaceuticals, cosmetics, household/personal care, and food industries.

Condition-Dependence Of Blue Plumage Coverage In Indigo Buntings Passerina Cyanea, Spencer B. Hudson, Travis E. Wilcoxen

Biology Faculty Publications

Nuptial plumage colouration is seemingly favoured by females of avian species with regards to sexual selection. This particular secondary sexual characteristic has been previously shown to be a condition-dependent signal of individual quality among passerines with pigment-based colouration (i.e. yellows and reds). In contrast, relationships between structural plumage colouration (i.e. blues) and aspects of both physical quality and physiological function have been understudied. Using free-living Indigo Buntings (Passerina cyanea) as a study species, we compared the percentage of blue feather coverage to body condition, innate immune responses, antioxidant capacity, stress physiology, reproductive physiology, and …

Eight-Legged Encounters—Arachnids, Volunteers, And Art Help To Bridge The Gap Between Informal And Formal Science Learning, Eileen Hebets, Melissa Welch-Lazoritz, Pawl Tisdale, Patricia Wonch Hill

Eileen Hebets Publications

Increased integration and synergy between formal and informal learning environments is proposed to provide multiple benefits to science learners. In an effort to better bridge these two learning contexts, we developed an educational model that employs the charismatic nature of arachnids to engage the public of all ages in science learning; learning that aligns with the Next Generation Science Standards (NGSS Disciplinary Core Ideas associated with Biodiversity and Evolution). We created, implemented, and evaluated a family-focused, interactive science event—Eight-Legged Encounters (ELE)—which encompasses more than twenty modular activities. Volunteers facilitated participant involvement at each activity station and original …

Draft Genome Sequence Of A Novel Thermofilum Sp. Strain From A New Zealand Hot Spring Enrichment Culture, Anna-Louise Reysenbach, John A. Donaho, Todd M. Hinsch, John F. Kelley, Kathleen Kouba, Mircea Podar, Matthew B. Stott

Biology Faculty Publications and Presentations

A draft genome of a new Thermofilum sp. strain was obtained from an enrichment culture metagenome. Like its relatives, Thermofilum sp. strain NZ13 is adapted to organic-rich thermal environments and has to depend on other organisms and the environment for some key amino acids, purines, and cofactors.

Replication Rapidly Recovers And Continues In The Presence Of Hydroxyurea In Escherichia Coli, Samvel A. Nazaretyan, Neda Savic, Michael Sadek, Brandy J. Hackert, Justin Courcelle, Charmain T. Courcelle

Biology Faculty Publications and Presentations

In both prokaryotes and eukaryotes, hydroxyurea is suggested to inhibit DNA replication by inactivating ribonucleotide reductase and depleting deoxyribonucleoside triphosphate pools. In this study, we show that the inhibition of replication in Escherichia coli is transient even at concentrations of 0.1 M hydroxyurea and that replication rapidly recovers and continues in its presence. The recovery of replication does not require the alternative ribonucleotide reductases, NrdEF and NrdDG, or translesion DNA polymerases, Pol II, Pol IV, or Pol V. Ribonucleotides are incorporated at higher frequencies during replication in the presence of hydroxyurea. However, these do not contribute significantly to the observed …

New Classification Of The Dictyostelids, Sanea Sheikh, Mats Thulin, James C. Cavender, Ricardo Escalante, Shin-Ichi Kawakami, Carlos Lado, John C. Landolt, Vidyanand Nanjundiah, David C. Queller, Joan E. Strassmann, Frederick W. Spiegel, Steven L. Stephenson, Eduardo M. Vadell, Sandra L. Baldauf

Biology Faculty Research

Traditional morphology-based taxonomy of dictyostelids is rejected by molecular phylogeny. A new classification is presented based on monophyletic entities with consistent and strong molecular phylogenetic support and that are, as far as possible, morphologically recognizable. All newly named clades are diagnosed with small subunit ribosomal RNA (18S rRNA) sequence signatures plus morphological synapomorphies where possible. The two major molecular clades are given the rank of order, as Acytosteliales ord. nov. and Dictyosteliales. The two major clades within each of these orders are recognized and given the rank of family as, respectively, Acytosteliaceae and Cavenderiaceae fam. nov. in Acytosteliales, and Dictyosteliaceae …

Insights Into The Cyclooxygenase Pathway In A Progressive Rat Model Of Parkinson’S Disease Induced By Prostaglandin J2: Protection With Ibuprofen, Chuhyon Corwin

Dissertations, Theses, and Capstone Projects

Parkinson’s disease (PD) is a neurodegenerative disease with aging as a major risk factor. Its defining symptoms are motor deficits that are primarily associated with dopaminergic neuronal loss in the substantia nigra pars compacta (SNpc) in the midbrain. Post-mortem PD brains exhibit abnormal intraneuronal inclusions of α-synuclein and ubiquitinated protein aggregates known as Lewy bodies, a hallmark of PD pathology.

Currently, there is no validated biomarker for PD. Especially the early stage of PD is difficult to detect as the pathology develops progressively. While symptom-managing treatments are available, there is no neuroprotective treatment as of yet, mainly due to the …

Anti-Proliferative Effects Of Garcinia Fruits In Breast Cancer Cells, Harini Anandhi Senthilkumar

Dissertations, Theses, and Capstone Projects

Breast cancer continues to be the second leading cause of death in women, even with the recent advances in research that has led to an improved understanding of molecular pathways and targets. Increasing mortality due to recurrence and lack of targeted drugs, especially in aggressive breast cancer subtypes such as triple negative breast cancer, has gained attention from the research community. With nearly 50% of the commonly used cancer drugs being sourced from plants, bioactive small molecules derived from a natural origin have immense potential as therapeutics. This study focuses on the anti-proliferative activities of benzophenones isolated from the edible …

Analysis Of Motility In Multicellular Chlamydomonas Reinhardtii Evolved Under Predation, Margrethe Boyd, Frank Rosenzweig, Matthew D. Herron

Biological Sciences Faculty Publications

The advent of multicellularity was a watershed event in the history of life, yet the transition from unicellularity to multicellularity is not well understood. Multicellularity opens up opportunities for innovations in intercellular communication, cooperation, and specialization, which can provide selective advantages under certain ecological conditions. The unicellular alga Chlamydomonas reinhardtii has never had a multicellular ancestor yet it is closely related to the volvocine algae, a clade containing taxa that range from simple unicells to large, specialized multicellular colonies. Simple multicellular structures have been observed to evolve in C. reinhardtii in response to predation or to settling rate-based selection. Structures …

Rewired Rnai-Mediated Genome Surveillance In House Dust Mites, Mosharrof H. Mondal, Pavel Klimov, Alex S. Flynt

Faculty Publications

House dust mites are common pests with an unusual evolutionary history, being descendants of a parasitic ancestor. Transition to parasitism is frequently accompanied by genome rearrangements, possibly to accommodate the genetic change needed to access new ecology. Transposable element (TE) activity is a source of genomic instability that can trigger large-scale genomic alterations. Eukaryotes have multiple transposon control mechanisms, one of which is RNA interference (RNAi). Investigation of the dust mite genome failed to identify a major RNAi pathway: the Piwi-associated RNA (piRNA) pathway, which has been replaced by a novel small-interfering RNA (siRNA)-like pathway. Co-opting of piRNA function by …

Lethal Effects Of Leaf Leachate From The Non-Native Invasive Shrub Amur Honeysuckle (Lonicera Maackii) On A Model Aquatic Organism (Hyalella Azteca), Eric B. Borth, Kevin W. Custer, Ryan W. Mcewan

Biology Faculty Publications

The invasive shrub Lonicera maackii (Amur honeysuckle) is a problematic species in the eastern United States and there is growing evidence that materials from this species have toxic effects on some organisms. We used a sequence of microcosm bioassays to assess the influence of L. maackii leaf leachate on the macroinvertebrate Hyalella azteca, which is a standard aquatic organism for toxicity assessment. In a laboratory setting, H. azteca were exposed to a leaf leachate dilution series (6.25%, 12.5%, 25%, 50%, 100%) in 48-h toxicity tests. This was repeated throughout the growing season to assess the potential for changes in …

Allenrolfea Wetland Genetics Data, Paul G. Wolf, Carol A. Rowe, Robert W. Lichvar

Browse all Datasets

The hydrophyte Allenrolfea occidentalis (S. Watson) Kuntze (iodine bush) is a halophytic shrub of the arid southwest that is listed as a facultative wetland (FACW) species on the National Wetland Plant List. This rating means the species is usually a hydrophyte but occasionally is found in uplands. We tested for genetic (ecotypic) differences between plants sampled from wetlands versus uplands. We used genotyping-by-sequencing (ddRAD-seq) to generate data from 133 plants from 30 locations representing both wetland and upland occurrences for over 1300 loci. Analyses indicated that the strongest signal is differences in geographic distribution: samples that are in close geographic …

Investigating Peroxiredoxins Impact On Amps, Noah Earland

SMU Journal of Undergraduate Research

The Orr-Radyuk lab is interested in understanding the link between aging and genetic influences controlling the cell’s redox state, as determined by enzymes involved in reducing and oxidizing (redox) reactions. They have observed that Drosophila normally exhibit a shift towards a pro-oxidizing cellular environment and spikes in AMP levels, independent of infections, when they reach old age. Additionally, peroxiredoxins (PRXs), a family of thiol-dependent peroxidases, have been shown to impact lifespan, and regulate the same pro-oxidizing shift seen in advanced age. Beyond their peroxidase functions, RXRs can also interact with signaling pathways related to immunity. Previous data showed that PRXs …

Ethics And Euthanasia, Nicole Marie Kasman

Biology: Student Scholarship & Creative Works

Illness is never easy to deal with and death is even harder whether it be for the patient, the patient's family, or the physician. Add into that, cases of sever and/or long-term suffering and people can begin wondering what there is to live for. Our animal companions have been able to escape pain via euthanasia for some time now but that same option is not generally available for their human counterparts. A suggested option for our terminally in is physician-assisted suicide. This has been met with a large amount of opposition, partly due to fear of promoting suicide, partly due …

Evaluating The Impact Of An Exotic Plant Invasion On Rodent Community Richness And Abundance, Trinity N. Smith, Eric M. Gese, Bryan M. Kluever

Wildland Resources Faculty Publications

Cheatgrass (Bromus tectorum), Russian thistle (Salsola kali), and tall tumblemustard (Sisymbrium altissimum) are nonnative plants widely distributed throughout the desert and shrubsteppe communities of the western United States. The impact of these invaders on plant community structure, form, and function has been well documented, but investigations determining the impacts of this cumulative invasion on terrestrial vertebrates have not been undertaken. Our objective was to assess community-level rodent responses to changes in plant community features, with an emphasis on dominance of invasive plant species. We sampled rodent and plant communities in the Great Basin Desert …

Experimental Evidence Of A Pathogen Invasion Threshold, Tad Dallas, Martin Krkošek, John M. Drake

Faculty Publications

Host density thresholds to pathogen invasion separate regions of parameter space corresponding to endemic and disease-free states. The host density threshold is a central concept in theoretical epidemiology and a common target of human and wildlife disease control programmes, but there is mixed evidence supporting the existence of thresholds, especially in wildlife populations or for pathogens with complex transmission modes (e.g. environmental transmission). Here, we demonstrate the existence of a host density threshold for an environmentally transmitted pathogen by combining an epidemiological model with a microcosm experiment. Experimental epidemics consisted of replicate populations of naive crustacean zooplankton (Daphnia dentifera …