Digital Commons Network^™

The Sortee Guidelines For Data And Code Quality Control In Ecology And Evolutionary Biology, Joel L. Pick, Bethany J. Allen, Benedicte Bachelot, Kevin R. Bairos-Novak, Jack A. Brand, Barbara Class, Tad Dallas, Pietro B. D'Amelio, Erola Fenollosa, Esteban Fernández-Juricic, Dylan G. Gomes, Matthew J. Grainger, Thomas Guillemaud, John Christian, Ruby Krasnow, Malgorzata Lagisz, Sebastian Lequime, Daniel S. Maynard, Shinichi Nakagawa, Rose E. O'Dea, Et. Al.

Faculty Publications

Open data and code are crucial to increasing transparency and reproducibility, and in building trust in scientific research. However, despite an increasing number of journals in ecology and evolutionary biology mandating for data and code to be archived alongside published articles, the amount and quality of archived data and code, and subsequent reproducibility of results, has remained worryingly low. As a result, a handful of journals have recruited dedicated data editors, whose role is to help authors increase the overall quality of archived data and code. There is, however, a general lack of consensus around what a data editor should …

Early Preclinical Studies Of Ergosterol Peroxide And Biological Evaluation Of Its Derivatives, Taotao Ling, Luz V. Arroyo-Cruz, William R. Smither, Emily K. Seighman, Michelle M. Martínez-Montemayor, Fatima Rivas

Faculty Publications

Ganoderma lucidum is a medicinal mushroom that produces various pharmacological compounds, including triterpenoids. A major bioactive component of G. lucidum is ergosterol peroxide (EP), which is attributed to its anticancer effects. The current study focuses on the in vitro ADME (absorption, distribution, metabolism, and elimination), in vivo efficacy and toxicity of EP, and the synthesis of new EP derivatives to improve aqueous solubility. It was found that EP is metabolically stable in liver microsomes and plasma. In vivo studies showed that EP inhibits tumor growth in murine cancer models, and it is well tolerated by mice. The maximum tolerated dose …

Boron Neutron Capture Therapy Of Cancer: Where Do We Stand Now?, Rolf F. Barth, Gong Wu, Maria Da Graca H. Vicente, John C. Grecula, Nilendu Gupta

Faculty Publications

No abstract provided.

Theory And Tools: The Future Of Technology-Based Learning (Slides), Andrew S. Gibbons Iii

Faculty Publications

We are entering a narrow passage that will see great instability in learning technology, instruction, and distance education. My purpose is to talk about two changes that I believe will redirect the entire future of technology-based education.

Theory And Tools: The Future Of Technology-Based Learning (Script), Andrew S. Gibbons Iii

Faculty Publications

We are entering a narrow passage that will see great instability in learning technology, instruction, and distance education. My purpose is to talk about two changes that I believe will redirect the entire future of technology-based education.

Teaching Difficult Topics: Reflections From The Undergraduate Music Classroom, Olivia R. Lucas, Laura Moore Pruett

Faculty Publications

Teaching Difficult Topics provides a series of on-the-ground reflections from college music instructors working in a wide variety of institutional settings about their approaches to inclusive, supportive pedagogy in the music classroom. Although some imagine the music classroom to be an apolitical space, instructors find themselves increasingly in need of resources for incorporating issues of race and ethnicity, gender and sexuality, and historical trauma into their classrooms in ways that support student learning and safeguard their classroom communities. The teaching reflections in Teaching Difficult Topics examine difficult themes that fall into three primary categories: subjects that instructors sense to be …

Recent Advances In Chemistry And Antioxidant/Anticancer Biology Of Monoterpene And Meroterpenoid Natural Product, Benedict J. Barras, Taotao Ling, Fatima Rivas

Faculty Publications

Monoterpenes and meroterpenes are two large classes of isoprene-based molecules produced by terrestrial plants and unicellular organisms as diverse secondary metabolites. The global rising incidence of cancer has led to a renewed interest in natural products. These monoterpenes and meroterpenes represent a novel source of molecular scaffolds that can serve as medicinal chemistry platforms for the development of potential preclinical leads. Furthermore, some of these natural products are either abundant, or their synthetic strategies are scalable as it will be indicated here, facilitating their derivatization to expand their scope in drug discovery. This review is a collection of representative updates …

Discovery Of Novel Bioactive Tanshinones And Carnosol Analogues Against Breast Cancer, Miguel A. González-Cardenete, Natalia González-Zapata, Lucinda Boyd, Fatima Rivas

Faculty Publications

The abietane diterpenoids ferruginol (1), tanshinone IIA (3), and carnosol (4) are well-known for their interesting pharmacological properties, including antitumor, similar to other natural and semisynthetic abietanes. In this study, a pair of semisynthetic C18-functionalized analogues of 3 and 4 were prepared from the commercially available (+)-dehydroabietylamine or readily obtained methyl dehydroabietate. Semisynthetic ferruginol (1) and some selected analogues, together with the synthesized analogues, were tested in vitro for the inhibition of proliferation in four breast cancer cell lines, SUM149, MDA-MB231, T47D, and MCF07. As a result, several tested abietane analogues decreased cell proliferation and enhanced cell death, with IC50 …

Dynamic Modeling Of Aba-Dependent Expression Of The Arabidopsis Rd29a Gene, Ruth Ndathe, Renee Dale, Naohiro Kato

Faculty Publications

The abscisic acid (ABA) signaling pathway is the key defense mechanism against drought stress in plants. In the pathway, signal transduction among four core proteins, pyrabactin resistance (PYR), protein phosphatase 2C (PP2C), sucrose-non-fermenting-1-related protein kinase 2 (SnRK2), and ABRE binding factor (ABF) leads to altered gene expression kinetics that is driven by an ABA-responsive element (ABRE). A most recent and comprehensive study provided data suggesting that ABA alters the expression kinetics in over 6,500 genes through the ABF-ABRE associations in Arabidopsis. Of these genes, termed ABA gene regulatory network (GRN), over 50% contain a single ABRE within 4 kb of …

Completing Single-Cell Dna Methylome Profiles Via Transfer Learning Together With Kl-Divergence, Sanjeeva Dodlapati, Zongliang Jiang, Jiangwen Sun

Faculty Publications

The high level of sparsity in methylome profiles obtained using whole-genome bisulfite sequencing in the case of low biological material amount limits its value in the study of systems in which large samples are difficult to assemble, such as mammalian preimplantation embryonic development. The recently developed computational methods for addressing the sparsity by imputing missing have their limits when the required minimum data coverage or profiles of the same tissue in other modalities are not available. In this study, we explored the use of transfer learning together with Kullback-Leibler (KL) divergence to train predictive models for completing methylome profiles with …

Natural Products Inhibitors Of Monoamine Oxidases—Potential New Drug Leads For Neuroprotection, Neurological Disorders, And Neuroblastoma, Narayan D. Chaurasiya, Francisco León Ph.D., Ilias Muhammad, Babu L. Tekwani

Faculty Publications

Monoamine oxidase inhibitors (MAOIs) are an important class of drugs prescribed for treatment of depression and other neurological disorders. Evidence has suggested that patients with atypical depression preferentially respond to natural product MAOIs. This review presents a comprehensive survey of the natural products, predominantly from plant sources, as potential new MAOI drug leads. The psychoactive properties of several traditionally used plants and herbal formulations were attributed to their MAOI constituents. MAO inhibitory constituents may also be responsible for neuroprotective effects of natural products. Different classes of MAOIs were identified from the natural product sources with non-selective as well as selective …

Pocket2drug: An Encoder-Decoder Deep Neural Network For The Target-Based Drug Design, W T. Shi, M Singha, G Srivastava, L M. Pu, W T. Shi, M Brylinski

Faculty Publications

Computational modeling is an essential component of modern drug discovery. One of its most important applications is to select promising drug candidates for pharmacologically relevant target proteins. Because of continuing advances in structural biology, putative binding sites for small organic molecules are being discovered in numerous proteins linked to various diseases. These valuable data offer new opportunities to build efficient computational models predicting binding molecules for target sites through the application of data mining and machine learning. In particular, deep neural networks are powerful techniques capable of learning from complex data in order to make informed drug binding predictions. In …

A Southwestern United States Pilot Investigation Of Triatomine–Mite Prevalence, Kyndall C. Dye-Braumuller, Hanna Waltz, Mary K. Lynn, Stephen A. Klotz, Justin O. Schmidt, Alvaro Romero, Marvin Stanley Rodriguez Aquino, Jose Ricardo Palacios Valladares, Pamela Michelle Cornejo Rivas, Melissa Nolan Ph.D., Mph

Faculty Publications

An estimated 70 million persons in the Western Hemisphere are living at risk for Chagas disease, a parasitic infection transmitted to humans by over 156 different competent triatomine insect vector species. Prior Pan American Health Organization insecticide campaigns throughout Latin America in the 1990s and 2000s demonstrated that domestic insecticide spraying had temporary effects, which resulted in the re-establishment of triatomine species within a few years. Serendipitously, our team found ectoparasitic mites parasitizing triatomines collected from the field in multiple locations in the southwestern United States, where human–triatomine interaction was high but human parasite infection remains low. Upon further investigation …

Heteroacene-Based Amphiphile As A Molecular Scaffold For Bioimaging Probes, Tharindu A. Ranathunge, Mahesh Loku Yaddehige, Jordan H. Varma, Cameron Smith, Jay Nguyen, Iyanuoluwani Owolabi, Wojciech Kolodziejczyk, Nathan I. Hammer, Glake Hill, Alex Flynt, Davita L. Watkins

Faculty Publications

The challenges faced with current fluorescence imaging agents have motivated us to study two nanostructures based on a hydrophobic dye, 6H-pyrrolo[3,2-b:4,5-b’]bis [1,4]benzothiazine (TRPZ). TRPZ is a heteroacene with a rigid, pi-conjugated structure, multiple reactive sites, and unique spectroscopic properties. Here we coupled TRPZ to a tert-butyl carbamate (BOC) protected 2,2-bis(hydroxymethyl)propanoic acid (bisMPA) dendron via azide-alkyne Huisgen cycloaddition. Deprotection of the protected amine groups on the dendron afforded a cationic terminated amphiphile, TRPZ-bisMPA. TRPZ-bisMPA was nanoprecipitated into water to obtain nanoparticles (NPs) with a hydrodynamic radius that was TRPZ-PG was encapsulated in pluronic-F127 (Mw …

Citations Versus Expert Opinions: Citation Analysis Of Featured Reviews Of The American Mathematical Society, Lawrence Smolinsky, Daniel S. Sage, Aaron J. Lercher, Aaron Cao

Faculty Publications

Peer review and citation metrics are two means of gauging the value of scientific research, but the lack of publicly available peer review data makes the comparison of these methods difficult. Mathematics can serve as a useful laboratory for considering these questions because as an exact science, there is a narrow range of reasons for citations. In mathematics, virtually all published articles are post-publication reviewed by mathematicians in Mathematical Reviews (MathSciNet) and so the data set was essentially the Web of Science mathematics publications from 1993 to 2004. For a decade, especially important articles were singled out in Mathematical Reviews …

Transepithelial Anti-Neuroblastoma Response To Kale Among Four Vegetable Juices Using In Vitro Model Co-Culture System, John Piletz, Yuhan Mao, Debarshi Roy, Bilal Qizilbash, Eurielle Nkamssi, Enleyona Weir, Jessica Graham, Mary Emmanuel, Suwaira Iqbal, Kellie Brue, Bidisha Roy Sengupta

Faculty Publications

Juicing vegetables is thought to be an anticancer treatment. Support exists for a rank order of anticancer greens (kale > dandelion > lettuce > spinach) based on degrees of bioavailability of different phytochemicals, also offset by some noxious molecules (i.e., calcium-oxalate). We developed a new in vitro transepithelial anti-neuroblastoma model system. The juices were diluted as predicted once in the small intestine. They were applied to apical Caco-2Bbe1 cells atop dividing SH-SY5Y neuroblastoma cells, and changes in transepithelial electrical resistance (TEER) and cell growth were considered with juice spectroscopies. Studied first in monoculture, kale and dandelion were the most cytostatic juices on SH-SY5Ys, …

Photoreceptor Phosphodiesterase (Pde6): Activation And Inactivation Mechanisms During Visual Transduction In Rods And Cones, Rick H. Cote

Faculty Publications

Rod and cone photoreceptors of the vertebrate retina utilize cGMP as the primary

intracellular messenger for the visual signaling pathway that converts a light stimulus into an electrical response. cGMP metabolism in the signal-transducing photoreceptor outer segment reflects the balance of cGMP synthesis (catalyzed by guanylyl cyclase) and degradation (catalyzed by the photoreceptor phosphodiesterase, PDE6). Upon light stimulation, rapid activation of PDE6 by the heterotrimeric G-protein (transducin) triggers a dramatic drop in cGMP levels that lead to cell hyperpolarization. Following cessation of the light stimulus, the lifetime of activated PDE6 is also precisely regulated by additional processes. This review summarizes …

The Promise Of A Multi-Disciplinary, Mixed-Methods Approach To Inform Insect Pest Management: Evidence From Wyoming Alfalfa, Randa Jabbour, Shiri Noy

Faculty Publications

No abstract provided.

Expression, Purification, And Glycosylation Of Epidermal Growth Factor-Like Repeat 27 From Mouse Notch1, Justin A. Grennell, Kendra D. Jenkins, Huimin Zhong, Amid Paudyal, Kelvin B. Luther, Robert S. Haltiwanger, Megan A. Macnaughtan

Faculty Publications

© 2020 Elsevier Inc. Notch receptors have large extracellular domains containing up to 36 tandem epidermal growth factor-like (EGF) repeats, which facilitate cell signaling by binding ligands on neighboring cells. Notch receptors play major roles in a variety of developmental processes by controlling cell fate decisions. Each EGF repeat consists of about 40 amino acids with 3 conserved disulfide bonds. Many of the EGF repeats are modified by O-linked fucose glycans, and more than half have calcium-binding sites, but the sequences of the EGF repeats vary giving distinct roles to each repeat. EGF repeat 27 (EGF27) from mouse NOTCH1 is …

Bionoinet: Ligand-Binding Site Classification With Off-The-Shelf Deep Neural Network, Wentao Shi, Jeffrey M. Lemoine, Abd El Monsif A. Shawky, Manali Singha, Limeng Pu, Shuangyan Yang, J. Ramanujam, Michal Brylinski

Faculty Publications

© The 2020 Author(s). Published by Oxford University Press. All rights reserved. Motivation: Fast and accurate classification of ligand-binding sites in proteins with respect to the class of binding molecules is invaluable not only to the automatic functional annotation of large datasets of protein structures but also to projects in protein evolution, protein engineering and drug development. Deep learning techniques, which have already been successfully applied to address challenging problems across various fields, are inherently suitable to classify ligand-binding pockets. Our goal is to demonstrate that off-the-shelf deep learning models can be employed with minimum development effort to recognize nucleotide-and …

Listeria Monocytogenes Response To Anaerobic Environments, Brandy N. Roberts, Damayanti Chakravarty, J.C. Gardner Iii, Steven C. Ricke, Janet R. Donaldson

Faculty Publications

Listeria monocytogenes is a Gram-positive facultative anaerobic bacterium that is responsible for the disease, listeriosis. It is particularly lethal in pregnant women, the fetus, the elderly and the immunocompromised. The pathogen survives and replicates over a wide range of temperatures (4 to 42 °C), pH, salt and oxygen concentrations. Because it can withstand various environments, L. monocytogenes is a major concern in food processing industries, especially in dairy products and ready-to-eat fruits, vegetables and deli meats. The environment in which the pathogen is exposed can influence the expression of virulence genes. For instance, studies have shown that variations in oxygen …

A Deda Family Membrane Protein Is Required For Burkholderia Thailandensis Colistin Resistance, Pradip R. Panta, Sujeet Kumar, Caroline F. Stafford, Caitlin E. Billiot, Martin V. Douglass, Carmen M. Herrera, M. Stephen Trent, William T. Doerrler

Faculty Publications

© Copyright © 2019 Panta, Kumar, Stafford, Billiot, Douglass, Herrera, Trent and Doerrler. Colistin is a “last resort” antibiotic for treatment of infections caused by some multidrug resistant Gram-negative bacterial pathogens. Resistance to colistin varies between bacterial species. Some Gram-negative bacteria such as Burkholderia spp. are intrinsically resistant to very high levels of colistin with minimal inhibitory concentrations (MIC) often above 0.5 mg/ml. We have previously shown DedA family proteins YqjA and YghB are conserved membrane transporters required for alkaline tolerance and resistance to several classes of dyes and antibiotics in Escherichia coli. Here, we show that a DedA family …

Age And Growth Of Hardhead Catfish And Gafftopsail Catfish In Coastal Louisiana, Usa, Shane Flinn, Stephen Midway

Faculty Publications

The Hardhead Catfish Ariopsis felis and Gafftopsail Catfish Bagre marinus are marine catfishes that have low recreational and commercial landings in U.S. waters, although they are among the most abundant species in coastal waters of the Gulf of Mexico. Few biological studies exist on marine catfishes, with most studies focusing on their unique reproductive biology. This study evaluated weight-length relationships for Gafftopsail Catfish (n = 264) and Hardhead Catfish (n = 823) sampled from across coastal Louisiana, USA, during 2016-2018; subsamples (93 and 266, respectively) were aged using lapilli for age and growth analyses. Hardhead Catfish showed a small but …

A Gradient Of Pollination Specialization In Three Species Of Bolivian Centropogon, Laura P. Lagomarsino, Nathan Muchhala

Faculty Publications

© 2019 Botanical Society of America Premise: Closely related plant species with overlapping ranges often experience competition for pollination services. Such competition can select for divergence in floral traits that attract pollinators or determine pollen placement. While most species in Centropogon (Campanulaceae: Lobelioideae) have flowers that suggest adaptation to bat or hummingbird pollination, actual pollinators are rarely documented, and a few species have a mix of traits from both pollination syndromes. We studied the pollination biology of a “mixed-syndrome” species and its co-occurring congeners to examine the relationship between floral traits and visitation patterns for Centropogon. Methods: Fieldwork at two …

Bed Bugs (Cimex Lectularius L.) Exhibit Limited Ability To Develop Heat Resistance, Aaron R. Ashbrook, Michael E. Scharf, Gary W. Bennett, Ameya D. Gondhalekar

Faculty Publications

The global population growth of the bed bug, Cimex lectularius (L.), is attributed to their cryptic behavior, diverse insecticide resistance mechanisms, and lack of public awareness. Bed bug control can be challenging and typically requires chemical and non-chemical treatments. One common non-chemical method for bed bug management is thermal remediation. However, in certain instances, bed bugs are known to survive heat treatments. Bed bugs may be present after a heat treatment due to (i) abiotic factors associated with the inability to achieve lethal temperatures in harborage areas for a sufficient time period, (ii) re-infestation from insects that escaped to cooler …

Prediction Of Ice-Free Conditions For A Perennially Ice-Covered Antarctic Lake, M. K. Obryk, P. T. Doran, J. C. Priscu

Faculty Publications

©2019. American Geophysical Union. All Rights Reserved. Although perennially ice-covered Antarctic lakes have experienced variable ice thicknesses over the past several decades, future ice thickness trends and associated aquatic biological responses under projected global warming remain unknown. Heat stored in the water column in chemically stratified Antarctic lakes that have middepth temperature maxima can significantly influence the ice thickness trends via upward heat flux to the ice/water interface. We modeled the ice thickness of the west lobe of Lake Bonney, Antarctica, based on possible future climate scenarios utilizing a 1D thermodynamic model that accounts for surface radiative fluxes as well …

A Hydrodynamic Model For Galveston Bay And The Shelf In The Northern Gulf Of Mexico, J. Du, K. Park, J. Shen, Y.J. Zhang, X. Yu, F. Ye, Z. Wang, N.N. Rabalais

Faculty Publications

No abstract provided.

Toxoplasma Gondii Seropositivity And Substance Use In Us Adults, Bruce L. Brown, Andrew N. Berrett, Shawn D. Gale, Lance D. Erickson, Evan L. Thacker, Dawson W. Hedges

Faculty Publications

The intracellular parasite Toxoplasma gondii (Nicolle et Manceaux, 1908) infects humans resulting in acute toxoplasmosis, an infection that in immunocompetent people is typically mild but results in persistent latent toxoplasmosis. In that T. gondii appears to affect dopamine synthesis and because addicting drugs affect midbrain dopamine transmission, latent toxoplasmosis could influence substance use. Using both the third and continuous National Health and Nutrition Examination Surveys from the US Centers for Disease Control and Prevention, we used logistic regression to test for associations between T. gondii seropositivity and subject self-report of having ever used tobacco, alcohol, marijuana, cocaine, heroin, or methamphetamine. …

Comparative Analyses Of Zebrafish Anxiety-Like Behavior Using Conflict-Based Novelty Tests, Elana V. Kysil, Darya A. Meshalkina, Erin E. Frick, David J. Echevarria, Denis B. Rosemberg, Caio Maximino, Monica Gomes Lima, Murilo S. Abreu, Ana C. Giacomini, Leonardo J.G. Barcellos, Cai Song, Allan V. Kalueff

Faculty Publications

Modeling of stress and anxiety in adult zebrafish (Danio rerio) is increasingly utilized in neuroscience research and central nervous system (CNS) drug discovery. Representing the most commonly used zebrafish anxiety models, the novel tank test (NTT) focuses on zebrafish diving in response to potentially threatening stimuli, whereas the light-dark test (LDT) is based on fish scototaxis (innate preference for dark vs. bright areas). Here, we systematically evaluate the utility of these two tests, combining meta-analyses of published literature with comparative in vivo behavioral and whole-body endocrine (cortisol) testing. Overall, the NTT and LDT behaviors demonstrate a generally good cross-test correlation …

A New Species Of Shrew (Soricomorpha: Crocidura) From Java, Indonesia: Possible Character Displacement Despite Interspecific Gene Flow, Terrence C. Demos, Anang S. Achmadi, Heru Handika, Maharadatunkamsi, Kevin C. Rowe, Jacob A. Esselstyn

Faculty Publications

We describe a new species of shrew (Soricomorpha, Soricidae, Crocidura) from Mt. Gede, West Java, Indonesia. Relative to other Javan shrews, the new species is small with a relatively thick, dark brown, medium-length tail. The new species is known only from the type locality at 1,611 and 1,950 m elevation on Mt. Gede. It occurs syntopically with at least 3 other Crocidura species: C. orientalis, C. abscondita, and C. monticola. Phylogenetically, the new species is nested among sympatric and allopatric populations of C. monticola. Although topological inferences differ slightly between the mtDNA gene tree and multilocus species tree, the new …