Digital Commons Network^™

All-Atomic Molecular Dynamic Studies Of Human And Drosophila Cdk8: Insights Into Their Kinase Domains, The Lxxll Motifs, And Drug Binding Site, Wu Xu, Xiao-Jun Xie, Ali K. Faust, Mengmeng Liu, Xiao Li, Feng Chen, Ashlin A. Naquin, Avery C. Walton, Peter W. Kishbaugh, Jun-Yuan Ji

Faculty Publications

Cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC) play conserved roles in modulating RNA polymerase II (Pol II)-dependent gene expression. To understand the structure and function relations of CDK8, we analyzed the structures of human and Drosophila CDK8 proteins using molecular dynamics simulations, combined with functional analyses in Drosophila. Specifically, we evaluated the structural differences between hCDK8 and dCDK8 to predict the effects of the LXXLL motif mutation (AQKAA), the P154L mutations, and drug binding on local structures of the CDK8 proteins. First, we have observed that both the LXXLL motif and the kinase activity of CDK8 …

Dietary Methionine Restriction Signals To The Brain Through Fibroblast Growth Factor 21 To Regulate Energy Balance And Remodeling Of Adipose Tissue, Laura A. Forney, Han Fang, Landon C. Sims, Kirsten P. Stone, Leighann Y. Vincik, Alicia M. Vick, Amanda N. Gibson, David H. Burk, Thomas W. Gettys

Faculty Publications

© 2020 The Obesity Society. Objective: Restricting dietary methionine to 0.17% in mice increases energy expenditure (EE), reduces fat deposition, and improves metabolic health by increasing hepatic fibroblast growth factor 21 (FGF21). The goal of this study was to compare each of these responses in mice with the coreceptor for FGF21 deleted in either adipose tissue or the brain. Methods: Methionine-restriction (MR) diets were fed to age-matched cohorts of mice with the coreceptor for FGF21 deleted in either adipose tissue or the brain. The physiological and transcriptional responses to MR were compared in the respective cohorts. Results: Tissue-specific deletion of …

African American Emerging Adult Perspectives On Unintended Pregnancy And Meeting Their Needs With Mobile Technology: Mixed Methods Qualitative Study, Lucy Annang Ingram, Crystal Stafford, Quentin Mccollum, Mckenzie Isreal

Faculty Publications

Background: In the United States, a disproportionate number of unintended pregnancies occur among African Americans, particularly those in their later teenage years and early 20s. Mobile technology is becoming more ubiquitous as a method for health promotion; however, relatively little research has been done with this population to determine their perspectives about unintended pregnancy, the potential of successfully using mobile technology to prevent unintended pregnancy, and the content of such programs.

Objective: The purpose of this study was to obtain the perspectives of African American emerging adults about unintended pregnancy and the use of mobile technology to reduce unintended pregnancy …

The Case For Re-Examining Glycosylation Inhibitors, Mimetics, Primers And Glycosylation Decoys As Antivirals And Anti-Inflammatories In Covid19, Roger A. Laine

Faculty Publications

No abstract provided.

Montana Native Entomopathogenic Nematode Species Against Limonius Californicus (Coleoptera: Elateridae), Ramandeep Kaur Sandhi, David Shapiro-Ilan, Gadi V.P. Reddy

Faculty Publications

Wireworms are destructive soil inhabiting polyphagous pests in the Pacific Northwest and Intermountain region of the United States. Continuously increasing wireworm populations and damage in small grain crops such as spring wheat in Northern Great Plains has become a challenge for growers. Due to unavailability of effective control measures, alternative methods, including biological control agents such as entomopathogenic nematodes (EPNs) are needed. Native/indigenous EPN species are expected to have better potential than exotic species to control the local insect pests. Two Montana native EPN species (Steinernema feltiae and Heterorhabditis bacteriophora) were tested against, Limonius californicus (Coleoptera: Elateridae) in laboratory and …

Environmentally Clean Access To Antarctic Subglacial Aquatic Environments, Alexander B. Michaud, Trista (Vick-Majors, Amanda M. Achberger, Mark L. Skidmore, Brent C. Christner, Martyn Tranter, John C. Priscu

Faculty Publications

Subglacial Antarctic aquatic environments are important targets for scientific exploration due to the unique ecosystems they support and their sediments containing palaeoenvironmental records. Directly accessing these environments while preventing forward contamination and demonstrating that it has not been introduced is logistically challenging. The Whillans Ice Stream Subglacial Access Research Drilling (WISSARD) project designed, tested and implemented a microbiologically and chemically clean method of hot-water drilling that was subsequently used to access subglacial aquatic environments. We report microbiological and biogeochemical data collected from the drilling system and underlying water columns during sub-ice explorations beneath the McMurdo and Ross ice shelves and …

Reducing Host Dna Contamination In 16s Rrna Gene Surveys Of Anthozoan Microbiomes Using Pna Clamps, Alicia M. Reigel, Sarah M. Owens, Michael E. Hellberg

Faculty Publications

Efforts to study the microbial communities associated with corals can be limited by inefficiencies in the sequencing process due to high levels of host amplification by universal bacterial 16S rRNA gene primers. Here, we develop an inexpensive peptide nucleic acid (PNA) clamp that binds to a target sequence of host DNA during PCR and blocks amplification. We then test the ability of this PNA clamp to mitigate host contamination and increase overall microbial sequence coverage on samples from three coral species: the gorgoniansEunicea flexuosaandGorgonia ventalina,and the scleractinianPorites panamensis. The 20-bp PNA clamp was designed using DNA fromE. flexuosa. Adding the …

Assessment Of Surface Hydrological Connectivity In An Ungauged Multi-Lake System With A Combined Approach Using Geostatistics And Spaceborne Sar Observations, Yueqing Chen, Lili Wu, Guangxin Zhang, Y. Jun Xu, Zhiqiang Tan, Sijia Qiao

Faculty Publications

Connectivity metrics for surface water are important for predicting floods and droughts, and improving water management for human use and ecological integrity at the landscape scale. The integrated use of synthetic aperture radar (SAR) observations and geostatistics approach can be useful for developing and quantifying these metrics and their changes, including geostatistical connectivity function (GCF), maximum distance of connection (MDC), surface water extent (SWE), and connection frequency. In this study, we conducted a geostatistical analysis based on 52 wet and dry binary state (i.e., water and non-water) rasters derived from Sentinel-1 A/B GRD products acquired from 2015 to 2019 for …

International Reverse Transfer Students: A Critical Analysis Based On Field, Habitus, And Social And Cultural Capital, Yu “April” Chen, Ran Li, Linda Serra Hagedorn

Faculty Publications

Objective: International reverse transfer students are international students who begin their postsecondary journey at a four-year institution but subsequently transfer to a community college. In this qualitative study, we examine the lived experiences of international reverse transfers to understand the reasons for reverse-transfer and to understand the students’ learning experiences. Methods: Using a phenomenological approach, we recruited 10 international reverse transfer students attending one four-year university or one of the two community colleges. We conducted individual interviews with all participants and analyzed transcript data through Bourdieu’s sociological theory of field, habitus, and social and cultural capital. Results: We identified three …

Gis Tool To Predict Photosynthetically Active Radiation In A Dry Valley, Dimitri Acosta, Peter T. Doran, Madeline Myers

Faculty Publications

© Antarctic Science Ltd 2020 Understanding primary productivity is a core research area of the National Science Foundation's Long-Term Ecological Research Network. This study presents the development of the GIS-based Topographic Solar Photosynthetically Active Radiation (T-sPAR) toolbox for Taylor Valley. It maps surface photosynthetically active radiation using four meteorological stations with ∼20 years of data. T-sPAR estimates were validated with ground-truth data collected at Taylor Valley's major lakes during the 2014-15 and 2015-16 field seasons. The average daily error ranges from 0.13 mol photons m-2 day-1 (0.6%) at Lake Fryxell to 3.8 mol photons m-2 day-1 (5.8%) at Lake Hoare. …

Distorted Drug Patents, Erika Lietzan

Faculty Publications

Drug patents are distorted. Unlike most other inventors, drug inventors must complete years of testing to the government’s specifications and seek government approval to commercialize their inventions. All the while, the patent term runs. When a drug inventor finally launches a medicine that embodies the invention, only a fraction of the patent life remains. And yet, conventional wisdom holds — and empirical studies show — that patent life is essential to innovation in the pharmaceutical industry, perhaps more so than any other inventive industry. Congress tried to do something about this in 1984, authorizing the Patent and Trademark Office to …

Measuring The Resilience Of Criminogenic Ecosystems To Global Disruption: A Case-Study Of Covid-19 In China, Hervé Borrion, Justin Kurland, Nick Tilley, Peng Chen

Faculty Publications

Copyright: © 2020 Borrion et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This paper uses resilience as a lens through which to analyse disasters and other major threats to patterns of criminal behaviour. A set of indicators and mathematical models are introduced that aim to quantitatively describe changes in crime levels in comparison to what could otherwise be expected, and what might be expected by way of adaptation and subsequent resumption of …

Oil-Producing Metabolons Containing Dgat1 Use Separate Substrate Pools From Those Containing Dgat2 Or Pdat, Anushobha Regmi, Jay Shockey, Hari Kiran Kotapati, Philip D. Bates

Faculty Publications

© 2020 American Society of Plant Biologists. All rights reserved. Seed triacylglycerol (TAG) biosynthesis involves a metabolic network containing multiple different diacylglycerol (DAG) and acyl donor substrate pools. This network of pathways overlaps with those for essential membrane lipid synthesis and utilizes multiple different classes of TAG biosynthetic enzymes. Acyl flux through this network ultimately dictates the final oil fatty acid composition. Most strategies to alter seed oil composition involve the overexpression of lipid biosynthetic enzymes, but how these enzymes are assembled into metabolons and which substrate pools are used by each is still not well understood. To understand the …

Covid-19 And The Black Death: Nutrition, Frailty, Inequity, And Mortality, Katherine D. Van Schaik, Sharon Dewitte

Faculty Publications

Introduction: COVID-19 has challenged governments, healthcare systems, and individuals, drawing attention to the limits of modern technology and the extent of social inequity. Such challenges have directed attention to historical epidemics as repositories of data that could contribute to effective public health strategies and prognostic modeling. In light of the well-established correlation between frailty and mortality from COVID-19, this paper investigates the relationship between frailty, inequity, and mortality in the setting of the Black Death of 1346 – 1353, in order to identify trends over time in populations at the greatest risk of mortality during pandemics.

Methods: A comparative review …

Effects Of Germline And Somatic Events In Candidate Brca-Like Genes On Breast-Tumor Signatures, Weston R. Bodily, Brian H. Shirts, Tom Walsh, Suleyman Gulsuner, Mary-Claire King, Alyssa Parker, Moom Roosan, Stephen R. Piccolo

Faculty Publications

Mutations in BRCA1 and BRCA2 cause deficiencies in homologous recombination repair (HR), resulting in repair of DNA double-strand breaks by the alternative non-homologous end-joining pathway, which is more error prone. HR deficiency of breast tumors is important because it is associated with better responses to platinum salt therapies and PARP inhibitors. Among other consequences of HR deficiency are characteristic somatic-mutation signatures and gene-expression patterns. The term “BRCA-like” (or “BRCAness”) describes tumors that harbor an HR defect but have no detectable germline mutation in BRCA1 or BRCA2. A better understanding of the genes and molecular events associated with tumors being …

177Lu-Labeled Eu-Doped Mesoporous Sio2Nanoparticles As A Theranostic Radiopharmaceutical For Colorectal Cancer, Rodrigo Da Silva Viana, Luciana Amaral De Mescana Costa, Ashlyn C. Harmon, Manoel Adrião Gomes Filho, Eduardo H.L. Falcão, Maria G.H. Vicente, Severino A. Junior, J. Michael Mathis

Faculty Publications

Copyright © 2020 American Chemical Society. Colorectal cancer is one of the most significant types of cancer, ranking second in the world's mortality cases. As colorectal cancer is often diagnosed at a late stage of disease progression, effective treatments are necessary. Therefore, radiotherapy has become a fundamental approach in the treatment of colorectal cancer, especially those based on the use of 177Lu. A potential approach to meet this challenge is the use of nanotechnology through the development of radionuclide-based nanomaterials. In this work, we investigated a SiO2-derived class of nanomaterials formed by the insertion of the coordination complex, based on …

Engineering And Application Of A Biosensor With Focused Ligand Specificity, Dennis Della Corte, Hugo L. Van Beek, Falk Syberg, Marcus Schallmey, Felix Tobola, Kai U. Cormann, Christine Schlicker, Philipp T. Baumann, Karin Krumbach, Sascha Sokolowsky, Connor J. Morris, Alexander Grünberger

Faculty Publications

Cell factories converting bio-based precursors to chemicals present an attractive avenue to a sustainable economy, yet screening of genetically diverse strain libraries to identify the best-performing whole-cell biocatalysts is a low-throughput endeavor. For this reason, transcriptional biosensors attract attention as they allow the screening of vast libraries when used in combination with fluorescence-activated cell sorting (FACS). However, broad ligand specificity of transcriptional regulators (TRs) often prohibits the development of such ultra-high-throughput screens. Here, we solve the structure of the TR LysG of Corynebacterium glutamicum, which detects all three basic amino acids. Based on this information, we follow a semi-rational engineering …

Real-Time Time-Dependent Electronic Structure Theory, Xiaosong Li, Niranjan Govind, Christine Isborn, A. Eugene Deprince, Kenneth Lopata

Faculty Publications

Copyright © 2020 American Chemical Society. Real-time electronic structure methods provide an unprecedented view of electron dynamics and ultrafast spectroscopy on the atto- and femtosecond time scale with vast potential to yield new insights into the electronic behavior of molecules and materials. In this Review, we discuss the fundamental theory underlying various real-time electronic structure methods as well as advantages and disadvantages of each. We give an overview of the numerical techniques that are widely used for real-time propagation of the quantum electron dynamics with an emphasis on Gaussian basis set methods. We also showcase many of the chemical applications …

Low Aflatoxin Levels In Aspergillus Flavus-Resistant Maize Are Correlated With Increased Corn Earworm Damage And Enhanced Seed Fumonisin, Subbaiah Chalivendra, Fangneng Huang, Mark Busman, W. Paul Williams, Jong Hyun Ham

Faculty Publications

Preharvest mycotoxin contamination of field-grown crops is influenced not only by the host genotype, but also by inoculum load, insect pressure and their confounding interactions with seasonal weather. In two different field trials, we observed a preference in the natural infestation of corn earworm (CEW; Helicoverpa zea Boddie) to specific maize (Zea mays L.) genotypes and investigated this observation. The field trials involved four maize lines with contrasting levels of resistance to Aspergillus flavus. The resistant lines had 7 to 14-fold greater infested ears than the susceptible lines. Seed aflatoxin B1 (AF) levels, in mock- and A. flavus-inoculated ears were …

Targeted Engagement Of The Action Selection Network During Task-Oriented Arm Training After Stroke, Jill Campbell Stewart Pt,Phd, Kaci Handlery, Jessica F. Baird, Erika L. Blanck, Geetanjali Pathak, Stacy L. Fritz

Faculty Publications

Action selection (AS), or selection of an action from a set of alternatives, is an important movement preparation process that engages a frontal-parietal network. The addition of AS demands to arm training after stroke could be used to engage this motor planning process and the neural network that supports it. The purpose of this case series is to describe the feasibility and outcomes associated with task-oriented arm training aimed at engaging the AS behavioral process and the related neural network in three individuals with chronic stroke. Three participants with mild to moderate motor deficits completed 13 to 15 sessions of …

No Mow May Lawns Have Higher Pollinator Richness And Abundances: An Engaged Community Provides Floral Resources For Pollinators, Relena R. Ribbons, Israel Del Toro

Faculty Publications

No Mow May is a community science initiative popularized in recent years that encourages property owners to limit their lawn mowing practices during the month of May. The goal of No Mow May is to provide early season foraging resources for pollinators that emerge in the spring, especially in urban landscapes when few floral resources are available. We worked with the city council of Appleton, Wisconsin, USA. to allow No Mow May to take place in May 2020. Four hundred and thirty-five property owners registered for No Mow May in Appleton. We measured floral and bee richness and abundance in …

Stoichiometrically Coupled Carbon And Nitrogen Cycling In The Microbial-Mineral Carbon Stabilization Model Version 1.0 (Mimics-Cn V1.0), Emily Kyker-Snowman, William R. Wieder, Serita D. Frey, A. Stuart Grandy

Faculty Publications

Explicit consideration of microbial physiology in soil biogeochemical models that represent coupled carbon–nitrogen dynamics presents opportunities to deepen understanding of ecosystem responses to environmental change. The MIcrobial-MIneral Carbon Stabilization (MIMICS) model explicitly represents microbial physiology and physicochemical stabilization of soil carbon (C) on regional and global scales. Here we present a new version of MIMICS with coupled C and nitrogen (N) cycling through litter, microbial, and soil organic matter (SOM) pools. The model was parameterized and validated against C and N data from the Long-Term Inter-site Decomposition Experiment Team (LIDET; six litter types, 10 years of observations, and 13 sites …

Stories To Tell, Meredith Jones Gray, Wanda Lovice Cantrell, Donald Bedney, Elynda Bedney, Michael Nixon, Harvey Burnett, Desmond Murray

Faculty Publications

No abstract provided.

Insomnia Is Associated With Frequency Of Suicidal Ideation Independent Of Depression: A Replication And Extension Of Findings From The National Health And Nutrition Examination Survey, Zach Simmons, Lance D. Erickson, Dawson Hedges, Daniel Kay

Faculty Publications

Objective: Insomnia is associated with suicidality, although the mechanisms of this association are unclear. This study sought to replicate previous findings showing that insomnia symptoms but not sleep duration are associated with frequency of suicidal ideation in adults. We further investigated whether depression or sleep duration moderates the association between insomnia symptoms and frequency of suicidal ideation.

Materials and Methods: We used the 2005–2006 cycle of the National Health and Nutrition Examination Survey to replicate previously reported findings from the 2007–2008 cycle. We used ordered logistic regression to determine whether insomnia symptoms were associated with frequency of suicidal ideation independently …

Effect Of Oxidation Level On The Interfacial Water At The Graphene Oxide-Water Interface: From Spectroscopic Signatures To Hydrogen-Bonding Environment, Rolf David, Aashish Tuladhar, Le Zhang, Christopher Arges, Revati Kumar

Faculty Publications

Copyright © 2020 American Chemical Society. The interfacial region of the graphene oxide (GO)-water system is nonhomogenous due to the presence of two distinct domains: an oxygen-rich surface and a graphene-like region. The experimental vibrational sum-frequency generation (vSFG) spectra are distinctly different for the fully oxidized GO-water interface as compared to the reduced GO-water case. Computational investigations using ab initio molecular dynamics were performed to determine the molecular origins of the different spectroscopic features. The simulations were first validated by comparing the simulated vSFG spectra to those from the experiment, and the contributions to the spectra from different hydrogen bonding …

Phosphoregulation Of The Cytokinetic Protein Fic1 Contributes To Fission Yeast Growth Polarity Establishment, K. Adam Bohnert, Anthony M. Rossi, Quan Wen Jin, Jun Song Chen, Kathleen L. Gould

Faculty Publications

© 2020. Published by The Company of Biologists Ltd. Cellular polarization underlies many facets of cell behavior, including cell growth. The rod-shaped fission yeast Schizosaccharomyces pombe is a well-established, genetically tractable system for studying growth polarity regulation. S. pombe cells elongate at their two cell tips in a cell cycle-controlled manner, transitioning from monopolar to bipolar growth in interphase when new ends established by the most recent cell division begin to extend. We previously identified cytokinesis as a critical regulator of new end growth and demonstrated that Fic1, a cytokinetic factor, is required for normal polarized growth at new ends. …

Effect Of Oxidation Level On The Interfacial Water At The Graphene Oxide-Water Interface: From Spectroscopic Signatures To Hydrogen-Bonding Environment, Rolf David, Aashish Tuladhar, Le Zhang, Christopher Arges, Revati Kumar

Faculty Publications

The interfacial region of the graphene oxide (GO)-water system is nonhomogenous due to the presence of two distinct domains: an oxygen-rich surface and a graphene-like region. The experimental vibrational sum-frequency generation (vSFG) spectra are distinctly different for the fully oxidized GO-water interface as compared to the reduced GO-water case. Computational investigations using ab initio molecular dynamics were performed to determine the molecular origins of the different spectroscopic features. The simulations were first validated by comparing the simulated vSFG spectra to those from the experiment, and the contributions to the spectra from different hydrogen bonding environments and interfacial water orientations were …

Consequences Of Plume Encounter On Larval Fish Growth And Condition In The Gulf Of Mexico, Kelia E. Axler, Su Sponaugle, Frank Hernandez, Carla Culpepper, Robert K. Cowen

Faculty Publications

© Inter-Research 2020. Freshwater input into nearshore continental shelf waters from coastal river-estuarine plumes can greatly alter the physical and trophic environments experienced by fish larvae. However, the biological consequences of plume encounter on larval fish survival remain equivocal, largely due to the extreme variability of these systems but also because traditional sampling techniques alone are too coarse to effectively characterize the dynamic biophysical environment at spatiotemporal scales relevant to individual larvae. Using a multidimensional approach, we simultaneously collected in situ imagery and net samples of larval fishes and zooplankton from the Mobile Bay plume (Alabama, USA) and ambient continental …

Magma Reservoir Formation And Evolution At A Slow-Spreading Center (Atlantis Bank, Southwest Indian Ridge), Marine Boulanger, Lydéric France, Jeremy R.L. Deans, Carlotta Ferrando, C. Johan Lissenberg, Anette Von Der Handt

Faculty Publications

© Copyright © 2020 Boulanger, France, Deans, Ferrando, Lissenberg and von der Handt. Several ODP-IODP expeditions drilled oceanic core complexes interpreted as exhumed portions of lower crust close to the ridge axis, and provide the community with invaluable sampling opportunity for further constraining magmatic processes involved in the formation of the slow-spreading lower oceanic crust. ODP Hole 735B presents the most primitive lithologies sampled at Atlantis Bank oceanic core complex (Southwest Indian Ridge) in a ∼250 m thick section that was previously interpreted as a single crustal intrusion. We combined detailed structural and petrographic constraints with whole rock and in …

Zika Virus Infection Causes Widespread Damage To The Inner Ear, Kathleen T. Yee, Biswas Neupane, Fengwei Bai, Douglas E. Vetter

Faculty Publications

Zika virus (ZIKV) has been recently recognized as a causative agent of newborn microcephaly, as well as other neurological consequences. A less well recognized comorbidity of prenatal ZIKV infection is hearing loss, but cases of hearing impairment following adult ZIKV infection have also been recognized. Diminished hearing following prenatal ZIKV infection in a mouse model has been reported, but no cellular consequences were observed. We examined the effects of ZIKV infection on inner ear cellular integrity and expression levels of various proteins important for cochlear function in type I interferon receptor null (Ifnar1^−/−) mice following infection at …