Digital Commons Network^™

Biologically Enhanced Cathode Design For Improved Capacity And Cycle Life For Lithium-Oxygen Batteries, Dahyun Oh, Jifa Qi, Yi-Chun Lu, Yong Zhang, Yang Shao-Horn, Angela Belcher

Faculty Publications

Lithium-oxygen batteries have a great potential to enhance the gravimetric energy density of fully packaged batteries by two to three times that of lithium ion cells. Recent studies have focused on finding stable electrolytes to address poor cycling capability and improve practical limitations of current lithium-oxygen batteries. In this study, the catalyst electrode, where discharge products are deposited and decomposed, was investigated as it has a critical role in the operation of rechargeable lithium-oxygen batteries. Here we report the electrode design principle to improve specific capacity and cycling performance of lithium-oxygen batteries by utilizing high-efficiency nanocatalysts assembled by M13 virus …

Sedimentary Constraints On The Duration Of The Marinoan Oxygen-17 Depletion (Mosd) Event, Bryan A. Killingsworth, Justin A. Hayles, Chuanming Zhou, Huiming Bao

Faculty Publications

The ∼635 Ma Marinoan glaciation is marked by dramatic Earth system perturbations. Deposition of nonmass-dependently 17Odepleted sulfate (SO42) in worldwide postglacial sediments is, thus far, unique to this glaciation. It is proposed that an extremely high-pCO2 atmosphere can result in highly 17O-depleted atmospheric O2, or the Marinoan Oxygen-17 Depletion (MOSD) event. This anomalous 17O signal was imparted to sulfate of oxidative weathering origin. However, 17O-depleted sulfate occurs in limited sedimentary intervals, suggesting that Earth surface conditions conducive to the MOSD had a finite duration. An MOSD duration can, therefore, provide much needed constraint on modeling Earth system responses at that …

Sedimentary Constraints On The Duration Of The Marinoan Oxygen-17 Depletion (Mosd) Event, Bryan A. Killingsworth, Justin A. Hayles, Chuanming Zhou, Huiming Bao

Faculty Publications

The ∼635 Ma Marinoan glaciation is marked by dramatic Earth system perturbations. Deposition of nonmass-dependently 17Odepleted sulfate (SO42) in worldwide postglacial sediments is, thus far, unique to this glaciation. It is proposed that an extremely high-pCO2 atmosphere can result in highly 17O-depleted atmospheric O2, or the Marinoan Oxygen-17 Depletion (MOSD) event. This anomalous 17O signal was imparted to sulfate of oxidative weathering origin. However, 17O-depleted sulfate occurs in limited sedimentary intervals, suggesting that Earth surface conditions conducive to the MOSD had a finite duration. An MOSD duration can, therefore, provide much needed constraint on modeling Earth system responses at that …

Streptomyces Coelicolor Encodes A Urate-Responsive Transcriptional Regulator With Homology To Pecs From Plant Pathogens, Hao Huang, Brian J. Mackel, Anne Grove

Faculty Publications

Many transcriptional regulators control gene activity by responding to specific ligands. Members of the multiple-antibiotic resistance regulator (MarR) family of transcriptional regulators feature prominently in this regard, and they frequently function as repressors in the absence of their cognate ligands. Plant pathogens such as Dickeya dadantii encode a MarR homolog named PecS that controls expression of a gene encoding the efflux pump PecM in addition to other virulence genes. We report here that the soil bacterium Streptomyces coelicolor also encodes a PecS homolog (SCO2647) that regulates a pecM gene (SCO2646). S. coelicolor PecS, which exists as a homodimer, binds the …

Antiviral Rna Silencing Initiated In The Absence Of Rde-4, A Double-Stranded Rna Binding Protein, In Caenorhabditis Elegans, Xunyang Guo, Rui Zhang, Jeffrey Wang, Rui Lu

Faculty Publications

Small interfering RNAs (siRNAs) processed from double-stranded RNA (dsRNA) of virus origins mediate potent antiviral defense through a process referred to as RNA interference (RNAi) or RNA silencing in diverse organisms. In the simple invertebrate Caenorhabditis elegans, the RNAi process is initiated by a single Dicer, which partners with the dsRNA binding protein RDE-4 to process dsRNA into viral siRNAs (viRNAs). Notably, in C. elegans this RNA-directed viral immunity (RDVI) also requires a number of worm-specific genes for its full antiviral potential. One such gene is rsd-2 (RNAi spreading defective 2), which was implicated in RDVI in our previous studies. …

The Varieties Of Individual Engagement (Vie) Scales: Confirmatory Factor Analyses Across Two Samples And Contexts, Jayme L. Renfro, Lisa M. Pytlikzillig, Myiah J. Hutchens, Peter Muhlberger, Shiyuan Wang, Rabecca Harris

Faculty Publications

The field of public engagement, participation and deliberation is fraught with conflicting results that are difficult to interpret due to the very different methods and measures used. Theory advancement and consistent operationalization and assessment of key public deliberation and engagement variables will benefit considerably from standardized measures of constructs and the ability to compare across studies. In this article, drawing from social and educational psychology, we describe the theoretical bases for scales assessing eight varieties of participant engagement that may be experienced during participation activities: Active learning, conscientious, uninterested, creative, open-minded, closed-minded, angry, and social engagement. We describe our development …

Tunable Cytotoxicity Of Rhodamine 6g Via Anion Variations, Paul K.S. Magut, Susmita Das, Vivian E. Fernand, Jack Losso, Karen Mcdonough, Brittni M. Naylor, Sita Aggarwal, Isiah M. Warner

Faculty Publications

Chemotherapeutic agents with low toxicity to normal tissues are a major goal in cancer research. In this regard, the therapeutic activities of cationic dyes, such as rhodamine 6G, toward cancer cells have been studied for decades with observed toxicities toward normal and cancer cells. Herein, we report rhodamine 6G-based organic salts with varying counteranions that are stable under physiological conditions, display excellent fluorescence photostability, and more importantly have tunable chemotherapeutic properties. Our in vitro studies indicate that the hydrophobic compounds of this series allow production of nanoparticles which are nontoxic to normal cells and toxic to cancer cells. Furthermore, the …

Mammalian Cells Preferentially Internalize Hydrogel Nanodiscs Over Nanorods And Use Shape-Specific Uptake Mechanisms, Rachit Agarwal, Vikramjit Singh, Patrick Jurney, Li Shi, S. Sreenivasan, Krishnendu Roy

Faculty Publications

Size, surface charge, and material compositions are known to influence cell uptake of nanoparticles. However, the effect of particle geometry, i.e., the interplay between nanoscale shape and size, is less understood. Here we show that when shape is decoupled from volume, charge, and material composition, under typical in vitro conditions, mammalian epithelial and immune cells preferentially internalize disc-shaped, negatively charged hydrophilic nanoparticles of high aspect ratios compared with nanorods and lower aspect-ratio nanodiscs. Endothelial cells also prefer nanodiscs, however those of intermediate aspect ratio. Interestingly, unlike nanospheres, larger-sized hydrogel nanodiscs and nanorods are internalized more efficiently than their smallest counterparts. …

A Clamped Dual-Ridged Waveguide Measurement System For The Broadband, Nondestructive Characterization Of Sheet Materials, Milo W. Hyde Iv, Michael J. Havrilla

Faculty Publications

A novel two-port probe which uses dual-ridged waveguides for the nondestructive, broadband characterization of sheet materials is presented. The new probe is shown to possess approximately 2 to 3 times the bandwidth of traditional coaxial and rectangular/circular waveguide probe systems while maintaining the structural robustness characteristic of rectangular/circular waveguide probe systems. The theoretical development of the probe is presented, namely, by applying Love’s equivalence theorem and enforcing the continuity of transverse fields at the dual-ridged waveguide apertures, a system of coupled magnetic field integral equations is derived. The system of coupled magnetic field integral equations is solved using the method …

Conformational Response To Solvent Interaction And Temperature Of A Protein (Histone H3.1) By A Multi-Grained Monte Carlo Simulation, Ras B. Pandey, Barry L. Farmer

Faculty Publications

Interaction with the solvent plays a critical role in modulating the structure and dynamics of a protein. Because of the heterogeneity of the interaction strength, it is difficult to identify multi-scale structural response. Using a coarse-grained Monte Carlo approach, we study the structure and dynamics of a protein (H3.1) in effective solvent media. The structural response is examined as a function of the solvent-residue interaction strength (based on hydropathy index) in a range of temperatures (spanning low to high) involving a knowledge-based (Miyazawa-Jernigan(MJ)) residue-residue interaction. The protein relaxes rapidly from an initial random configuration into a quasi-static structure at low …

Compressed Property Suffix Trees, Wing Kai Hon, Manish Patil, Rahul Shah, Sharma V. Thankachan

Faculty Publications

Property matching is a biologically motivated problem where the task is to find those occurrences of an online pattern P in a string text T (of size n), such that the matched text part satisfies some conceptual property. The property of a string is a set π of (possibly overlapping) intervals {( s1,f1),(s2,f2),.} corresponding to the part of text and an occurrence of a pattern P=T[i,.,(i+|P|-1)] is a valid output only if T[i,.,(i+|P|-1)] is completely contained in at least one interval (sj,fj)â̂̂π. The indexing version of this problem was introduced by A. Amir (2008), where the text is preprocessed in …

Zebrafish Cytosolic Carboxypeptidases 1 And 5 Are Essential For Embryonic Development, Peter J. Lyons, Matthew R. Sapio, Lloyd D. Fricker

Faculty Publications

The cytosolic carboxypeptidases (CCPs) are a subfamily of metalloenzymes within the larger M14 family of carboxypeptidases that have been implicated in the post-translational modification of tubulin. It has been suggested that at least four of the six mammalian CCPs function as tubulin deglutamylases. However, it is not yet clear whether these enzymes play redundant or unique roles within the cell. To address this question, genes encoding CCPs were identified in the zebrafish genome. Analysis by quantitative polymerase chain reaction indicated that CCP1, CCP2, CCP5, and CCP6 mRNAs were detectable between 2 h and 8 days postfertilization with highest levels 5–8 …

Day-Night Differences In Neural Activation In Histaminergic And Serotonergic Areas With Putative Projections To The Cerebrospinal Fluid In A Diurnal Brain, Alexandra Castillo-Ruiz, Andrew J. Gall, Laura Smale, Antonio A. Nunez

Faculty Publications

In nocturnal rodents, brain areas that promote wakefulness have a circadian pattern of neural activation that mirrors the sleep/wake cycle, with more neural activation during the active phase than during the rest phase. To investigate whether differences in temporal patterns of neural activity in wake-promoting regions contribute to differences in daily patterns of wakefulness between nocturnal and diurnal species, we assessed Fos expression patterns in the tuberomammillary (TMM), supramammillary (SUM), and raphe nuclei of male grass rats maintained in a 12:12 h light-dark cycle. Day-night profiles of Fos expression were observed in the ventral and dorsal TMM, in the SUM, …

Is Dna A Good Model Polymer?, Douglas R. Tree, Abhiram Muralidhar, Patrick S. Doyle, Kevin D. Dorfman

Faculty Publications

The details surrounding the crossover from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy, and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the pruned-enriched Rosenbluth method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike …

Sensitivity-Enhanced Solid-State Nmr Detection Of Expansin's Target In Plant Cell Walls, Tuo Wang, Yong Bum Park, Marc A. Caporini, Melanie Rosay, Linghao Zhong, Daniel J. Cosgrove, Mei Hong

Faculty Publications

Structure determination of protein binding to noncrystalline macromolecular assemblies such as plant cell walls (CWs) poses a significant structural biology challenge. CWs are loosened during growth by expansin proteins, which weaken the noncovalent network formed by cellulose, hemicellulose, and pectins, but the CW target of expansins has remained elusive because of the minute amount of the protein required for activity and the complex nature of the CW. Using solid-state NMR spectroscopy, combined with sensitivity-enhancing dynamic nuclear polarization (DNP) and differential isotopic labeling of expansin and polysaccharides, we have now determined the functional binding target of expansin in the Arabidopsis thaliana …

Variation In One Residue Associated With The Metal Ion-Dependent Adhesion Site Regulates Αiibβ3 Integrin Ligand Binding Affinity, Joel Raborn, Ting Fu, Xue Wu, Zhilong Xiu, Guohui Li, Bing Hao Luo

Faculty Publications

The Asp of the RGD motif of the ligand coordinates with the β I domain metal ion dependent adhesion site (MIDAS) divalent cation, emphasizing the importance of the MIDAS in ligand binding. There appears to be two distinct groups of integrins that differ in their ligand binding affinity and adhesion ability. These differences may be due to a specific residue associated with the MIDAS, particularly the β3 residue Ala252 and corresponding Ala in the β1 integrin compared to the analogous Asp residue in the β2 and β7 integrins. Interestingly, mutations in the adjacent to MIDAS (ADMIDAS) of integrins α4β7 and …

The Effects Of Hematopoietic Growth Factors On Neurite Outgrowth, Ye Su, Lili Cui, Chunshu Piao, Bin Li, Li Ru Zhao

Faculty Publications

Stem cell factor (SCF) and granulocyte colony-stimulating factor (G-CSF) are initially discovered as the essential hematopoietic growth factors regulating bone marrow stem cell proliferation and differentiation, and SCF in combination with G-CSF (SCF+G-CSF) has synergistic effects on bone marrow stem cell mobilization. In this study we have determined the effect of SCF and G-CSF on neurite outgrowth in rat cortical neurons. Using molecular and cellular biology and live cell imaging approaches, we have revealed that receptors for SCF and G-CSF are expressed on the growth core of cortical neurons, and that SCF+G-CSF synergistically enhances neurite extension through PI3K/AKT and NFκB …

Ck1 Is Required For A Mitotic Checkpoint That Delays Cytokinesis, Alyssa E. Johnson, Jun Song Chen, Kathleen L. Gould

Faculty Publications

Failure to accurately partition genetic material during cell division causes aneuploidy and drives tumorigenesis [1]. Cell-cycle checkpoints safeguard cells from such catastrophes by impeding cell-cycle progression when mistakes arise. FHA-RING E3 ligases, including human RNF8 [2] and CHFR [3] and fission yeast Dma1 [4], relay checkpoint signals by binding phosphorylated proteins via their FHA domains and promoting ubiquitination of downstream targets [5]. Upon mitotic checkpoint activation, S. pombe Dma1 concentrates at spindle pole bodies (SPBs) in an FHA-dependent manner and ubiquitinates Sid4, a scaffold of Polo kinase, to suspend cytokinesis [6]. However, the kinase or kinases that phosphoprime Sid4 for …

Advances In The Redcat Software Package, Chris Schmidt, Stephanie J. Irausquin, Homayoun Valafar

Faculty Publications

Background

Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. The REDCAT software package was previously introduced for the analysis of molecular structures using RDC data. Here we report additional features that have been included in this software package in order to expand the scope of its analyses. We first discuss the features that enhance REDCATs user-friendly nature, such as the integration of a number of analyses into one single operation and enabling convenient examination of a structural ensemble …

Cell-Free Unnatural Amino Acid Incorporation With Alternative Energy Systems And Linear Expression Templates, Prashanta Shrestha, Mark Thomas Smith, Bradley Charles Bundy

Faculty Publications

Site-specific incorporation of unnatural amino acids (uAAs) during protein synthesis expands the proteomic code through the addition of unique residue chemistry. This field provides a unique tool to improve pharmacokinetics, cancer treatments, vaccine development, proteomics and protein engineering. The limited ability to predict the characteristics of proteins with uAA-incorporation creates a need for a low-cost system with the potential for rapid screening. Escherichia coli-based cell-free protein synthesis is a compelling platform for uAA incorporation due to the open and accessible nature of the reaction environment. However, typical cell-free systems can be expensive due to the high cost of energizing …

A Source Of Terrestrial Organic Carbon To Investigate The Browning Of Aquatic Ecosystems, Jay T. Lennon, Stephen K. Hamilton, Mario E. Muscarella, A. Stuart Grandy, Kyle Wickings, Stuart E. Jones

Faculty Publications

There is growing evidence that terrestrial ecosystems are exporting more dissolved organic carbon (DOC) to aquatic ecosystems than they did just a few decades ago. This “browning” phenomenon will alter the chemistry, physics, and biology of inland water bodies in complex and difficult-to-predict ways. Experiments provide an opportunity to elucidate how browning will affect the stability and functioning of aquatic ecosystems. However, it is challenging to obtain sources of DOC that can be used for manipulations at ecologically relevant scales. In this study, we evaluated a commercially available source of humic substances (“Super Hume”) as an analog for natural sources …

Performance Guarantees For C-Wmd Robot Missions, Shu Jiang, Ronald C. Arkin, Damian M. Lyons, Tsung-Ming Liu, Dagon Harrington

Faculty Publications

Robotics has been considered as one of the five key technology areas for defense against attacks with weapons of mass destruction (WMD). However, due to the mass impact nature of WMD, failures of counter-WMD (C-WMD) missions can have catastrophic consequences.To ensure robot's success in carrying out C-WMD missions, we have developed a novel verification framework in providing performance guarantees for behavior-based and probabilistic robot algorithms in complex real-world environments. This paper describes the system architecture and discusses how the verification framework can be used to provide pre-mission performance guarantees for robots in executing C-WMD missions.

Chemical Attraction Of Dermacentor Variabilis Ticks Parasitic To Peromyscus Leucopus Based On Host Body Mass And Sex, Tad Dallas, Stephanie Foré

Faculty Publications

Macroparasites are commonly aggregated on a small subset of a host population. Previous explanations for this aggregation relate to differences in immunocompetence or the degree to which hosts encounter parasites. We propose active tick host choice through chemical attraction as a potential mechanism leading to aggregated tick burdens. We test this hypothesis using a Y-maze olfactometer, comparing chemical attraction responses of larval and nymphal Dermacentor variabilis ticks parasitic to the white-footed mouse, Peromyscus leucopus, as a function of host sex and host body mass. We hypothesized that larger hosts and male hosts would be most attractive to searching ticks, as …

Social Descent With Territory Loss Causes Rapid Behavioral, Endocrine And Transcriptional Changes In The Brain, Karen P. Maruska, Lisa Becker, Anoop Neboori, Russell D. Fernald

Faculty Publications

In social species that form hierarchies where only dominant males reproduce, lower-ranking individuals may challenge higherranking ones, often resulting in changes in relative social status. How does a losing animal respond to loss of status? Here, using the African cichlid fish Astatotilapia burtoni, we manipulated the social environment, causing males to descend in rank, and then examined changes in behavior, circulating steroids and immediate early gene (IEG) expression (cfos, egr-1) in micro-dissected brain regions as a proxy for neuronal activation. In particular, we examined changes in the conserved 'social behavior network' (SBN), a collection of brain nuclei known to regulate …

Silencing Histone Deacetylase-Specific Isoforms Enhances Expression Of Pluripotency Genes In Bovine Fibroblasts, Jaroslaw Staszkiewicz, Rachel A. Power, Lettie L. Harkins, Christian W. Barnes, Karen L. Strickler, Jong S. Rim, Kenneth R. Bondioli, Kenneth J. Eilersten

Faculty Publications

Histone deacetylases (HDACs) catalyze deacetylation of histones that results in altered transcriptional activity. Inhibitors of HDACs have been shown to induce transcriptional changes that contribute positively to reprogramming somatic cells either by nuclear transfer or inducing a pluripotent state. However, the exact molecular mechanisms whereby HDAC inhibitors function and the specificity of the HDAC isoforms in cell reprogramming are not yet fully understood. Herein, we report the ability of individual isoform-specific HDACs to modulate endogenous expression of pluripotency-associated genes in bovine somatic cells. This in vitro study showed that a transient selective depletion of HDACs resulted in elevated mRNA levels …

Sin-Dependent Phosphoinhibition Of Formin Multimerization Controls Fission Yeast Cytokinesis, K. Adam Bohnert, Agnieszka P. Grzegorzewska, Alaina H. Willet, Craig W. Vander Kooi, David R. Kovar, Kathleen L. Gould

Faculty Publications

Many eukaryotes accomplish cell division by building and constricting a medial actomyosin-based cytokinetic ring (CR). In Schizosaccharomyces pombe, a Hippo-related signaling pathway termed the septation initiation network (SIN) controls CR formation, maintenance, and constriction. However, how the SIN regulates integral CR components was unknown. Here, we identify the essential cytokinetic formin Cdc12 as a key CR substrate of SIN kinase Sid2. Eliminating Sid2-mediated Cdc12 phosphorylation leads to persistent Cdc12 clustering, which prevents CR assembly in the absence of anillin-like Mid1 and causes CRs to collapse when cytokinesis is delayed. Molecularly, Sid2 phosphorylation of Cdc12 abrogates multimerization of a previously unrecognized …

Symposium Foreword: Bombshell Or Baby Step? The Ramifications Of Miller V. Alabama For Sentencing Law And Juvenile Crime Policy, Paul J. Litton

Faculty Publications

This short essay, which serves as the Symposium Foreword, argues that the rationale of Miller is incoherent insofar as it permits juvenile LWOP sentences and that the Court misidentifies the foundational principle of Roper. First, in banning mandatory juvenile LWOP sentences, the Court invokes Woodson, which bans mandatory death sentences. The Court maintains that Woodson, from its capital jurisprudence, applies because juvenile LWOP is “akin to the death penalty” for juveniles. But if the Court’s capital jurisprudence is binding based on that equivalence, Roper should imply that juvenile LWOP, like the death penalty, is unconstitutional for juveniles. This essay briefly …

Triacylglycerol Mobilization Is Suppressed By Brefeldin A In Chlamydomonas Reinhardtii, Naohiro Kato, Trung Dong, Michael Bailey, Tony Lum, Drury Ingram

Faculty Publications

Brefeldin A suppresses vesicle trafficking by inhibiting exchange of GDP for GTP in ADP-ribosylation factor. We report that brefeldin A suppresses mobilization of triacylglycerols in Chlamydomonas reinhardtii, a model organism of green microalgae. Analyses revealed that brefeldin A causes Chlamydomonas to form lipid droplets in which triacylglycerols accumulate in a dose-dependent manner. Pulse labeling experiment using fluorescent fatty acids suggested that brefeldin A inhibits the cells from degrading fatty acids. The experiment also revealed that the cells transiently form novel compartments that accumulate exogenously added fatty acids in the cytoplasm, designated fatty acid-induced microbodies (FAIMs). Brefeldin A up-regulates the formation …

Homologous Rig-I-Like Helicase Proteins Direct Rnaimediated Antièiral Immunity In C. Elegans By Distinct Mechanisms, Xunyang Guo, Rui Zhang, Jeffrey Wang, Shou Wei Ding, Rui Lu

Faculty Publications

RNAi-mediated antièiral immunity in Caenorhabditis elegans requires Dicer-related helicase 1 (DRH-1), which encodes the helicase and C-terminal domains homologous to the mammalian retinoic acid inducible gene I (RIG-I)-like helicase (RLH) family of cytosolic immune receptors. Here we show that the antièiral function of DRH-1 requires the RIG-I homologous domains as well as its wormspecific N-terminal domain. We also demonstrate that the helicase and C-terminal domains encoded by either worm DRH-2 or human RIG-I can functionally replace the corresponding domains of DRH-1 to mediate antièiral RNAi in C. elegans. Notably, substitutions in a three-residue motif of the C-terminal regulatory domain of …

Characterization Of Microsatellites For Population Genetic Analyses Of The Fungus-Growing Termite Odontotermes Formosanus (Isoptera: Termitidae), Claudia Husseneder, Susan P. Garner, Qiuying Huang, Warren Booth, Edward L. Vargo

Faculty Publications

The fungus-growing subterranean termite Odontotermes formosanus Shiraki (Isoptera: Termitidae) is a destructive pest in Southeast Asia. To facilitate studies on the biology, ecology, and control of O. formosanus, we isolated and characterized nine novel microsatellite loci from a mixed partial genomic library of O. formosanus and the sympatric Macrotermes barneyi Light enriched for di-, tri-, and tetranucleotide repeats. We screened these loci in three populations of O. formosanus from China. All loci were polymorphic. Three loci showed heterozygote deficit possibly because of the presence of null alleles. The remaining six loci with 4-15 alleles per locus and an average observed …