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Natural Isoforms Of The Photosystem Ii D1 Subunit Differ In Photoassembly Efficiency Of The Water-Oxidizing Complex, David J. Vinyard, Jennifer S. Sun, Javier Gimpel, Gennady M. Ananyev, Stephen P. Mayfield, G. Charles Dismukes May 2016

Natural Isoforms Of The Photosystem Ii D1 Subunit Differ In Photoassembly Efficiency Of The Water-Oxidizing Complex, David J. Vinyard, Jennifer S. Sun, Javier Gimpel, Gennady M. Ananyev, Stephen P. Mayfield, G. Charles Dismukes

Faculty Publications

© 2015 Springer Science+Business Media Dordrecht. Oxygenic photosynthesis efficiency at increasing solar flux is limited by light-induced damage (photoinhibition) of Photosystem II (PSII), primarily targeting the D1 reaction center subunit. Some cyanobacteria contain two natural isoforms of D1 that function better under low light (D1:1) or high light (D1:2). Herein, rates and yields of photoassembly of the Mn4CaO5 water-oxidizing complex (WOC) from the free inorganic cofactors (Mn2+, Ca2+, water, electron acceptor) and apo-WOC-PSII are shown to differ significantly: D1:1 apo-WOC-PSII exhibits a 2.3-fold faster rate-limiting step of photoassembly and up to seven-fold faster rate to the first light-stable Mn3+ intermediate, …

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Streptomyces Coelicolor Xdhr Is A Direct Target Of (P)Ppgpp That Controls Expression Of Genes Encoding Xanthine Dehydrogenase To Promote Purine Salvage, Smitha Sivapragasam, Anne Grove May 2016

Streptomyces Coelicolor Xdhr Is A Direct Target Of (P)Ppgpp That Controls Expression Of Genes Encoding Xanthine Dehydrogenase To Promote Purine Salvage, Smitha Sivapragasam, Anne Grove

Faculty Publications

© 2016 John Wiley & Sons Ltd. The gene encoding Streptomyces coelicolor xanthine dehydrogenase regulator (XdhR) is divergently oriented from xdhABC, which encodes xanthine dehydrogenase (Xdh). Xdh is required for purine salvage pathways. XdhR was previously shown to repress xdhABC expression. We show that XdhR binds the xdhABC-xdhR intergenic region with high affinity (Kd ∼ 0.5 nM). DNaseI footprinting reveals that this complex formation corresponds to XdhR binding the xdhR gene promoter at two adjacent sites; at higher protein concentrations, protection expands to a region that overlaps the transcriptional and translational start sites of xdhABC. While substrates for Xdh have …

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5-Lipoxygenase-Activating Protein Rescues Activity Of 5-Lipoxygenase Mutations That Delay Nuclear Membrane Association And Disrupt Product Formation, Jana Gerstmeier, Marcia E. Newcomer, Sophie Dennhardt, Erik Romp, Jana Fischer, Oliver Werz, Ulrike Garscha May 2016

5-Lipoxygenase-Activating Protein Rescues Activity Of 5-Lipoxygenase Mutations That Delay Nuclear Membrane Association And Disrupt Product Formation, Jana Gerstmeier, Marcia E. Newcomer, Sophie Dennhardt, Erik Romp, Jana Fischer, Oliver Werz, Ulrike Garscha

Faculty Publications

© FASEB. Leukotrienes (LTs) are proinflammatory lipid mediators formed from arachidonic acid in a 2-step reaction catalyzed by 5-lipoxygenase (5-LOX) requiring the formation of 5-HPETE [5(S)-hydroperoxy-6-trans-8,11,14-ciseicosatetraenoic acid] and its subsequent transformation to LTA4 . 5-LOX is thought to receive arachidonic acid from the nuclear membrane-embedded 5-LOX-activating protein (FLAP). The crystal structure of 5-LOX revealed an active site concealed by F177 and Y181 (FY cork). We examined the influence of the FY cork on 5-LOX activity and membrane binding in HEK293 cells in the absence and presence of FLAP. Uncapping the 5-LOX active site by mutation of F177 and/or Y181 to …

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Discovery Of A New Repeat Family In The Callithrix Jacchus Genome, Miriam K. Konkel, Brygg Ullmer, Erika L. Arceneaux, Sreeja Sanampudi, Sarah A. Brantley, Robert Hubley, Arian F.A. Smit, Mark A. Batzer May 2016

Discovery Of A New Repeat Family In The Callithrix Jacchus Genome, Miriam K. Konkel, Brygg Ullmer, Erika L. Arceneaux, Sreeja Sanampudi, Sarah A. Brantley, Robert Hubley, Arian F.A. Smit, Mark A. Batzer

Faculty Publications

© 2016 Konkel et al. We identified a novel repeat family, termed Platy-1, in the Callithrix jacchus (common marmoset) genome that arose around the time of the divergence of platyrrhines and catarrhines and established itself as a repeat family in New World monkeys (NWMs). A full-length Platy-1 element is ~100 bp in length, making it the shortest known short interspersed element (SINE) in primates, and harbors features characteristic of non-LTR retrotransposons. We identified 2268 full-length Platy-1 elements across 62 subfamilies in the common marmoset genome. Our subfamily reconstruction and phylogenetic analyses support Platy-1 propagation throughout the evolution of NWMs in …

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Identification And Characterization Of Putative Translocated Effector Proteins Of The Edwardsiella Ictaluri Type Iii Secretion System, Lidiya P. Dubytska, Matthew L. Rogge, Ronald L. Thune May 2016

Identification And Characterization Of Putative Translocated Effector Proteins Of The Edwardsiella Ictaluri Type Iii Secretion System, Lidiya P. Dubytska, Matthew L. Rogge, Ronald L. Thune

Faculty Publications

© 2016 Dubytska et al. Edwardsiella ictaluri, a major pathogen in channel catfish aquaculture, encodes a type III secretion system (T3SS) that is essential for intracellular replication and virulence. Previous work identified three putative T3SS effectors in E. ictaluri, and in silico analysis of the E. ictaluri genome identified six additional putative effectors, all located on the chromosome outside the T3SS pathogenicity island. To establish active translocation by the T3SS, we constructed translational fusions of each effector to the amino-terminal adenylate cyclase (AC) domain of the Bordetella pertussis adenylate cyclase toxin CyaA. When translocated through the membrane of the Edwardsiella-containing …

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Methods For Efficient Elimination Of Mitochondrial Dna From Cultured Cells, Domenico Spadafora, Nataliya Kozhukhar, Vladimir N. Chouljenko, Konstantin G. Kousoulas, Mikhail F. Alexeyev May 2016

Methods For Efficient Elimination Of Mitochondrial Dna From Cultured Cells, Domenico Spadafora, Nataliya Kozhukhar, Vladimir N. Chouljenko, Konstantin G. Kousoulas, Mikhail F. Alexeyev

Faculty Publications

© 2016 Spadafora 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. Here, we document that persistent mitochondria DNA (mtDNA) damage due to mitochondrial overexpression of the Y147A mutant uracil-N-glycosylase as well as mitochondrial overexpression of bacterial Exonuclease III or Herpes Simplex Virus protein UL12.5M185 can induce a complete loss of mtDNA (ρ0 phenotype) without compromising the viability of cells cultured in media supplemented with uridine and pyruvate. Furthermore, we use these observations …

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Comparative Risk Predictions Of Second Cancers After Carbon-Ion Therapy Versus Proton Therapy, John G. Eley, Thomas Friedrich, Kenneth L. Homann, Rebecca M. Howell, Michael Scholz, Marco Durante, Wayne D. Newhauser May 2016

Comparative Risk Predictions Of Second Cancers After Carbon-Ion Therapy Versus Proton Therapy, John G. Eley, Thomas Friedrich, Kenneth L. Homann, Rebecca M. Howell, Michael Scholz, Marco Durante, Wayne D. Newhauser

Faculty Publications

Purpose This work proposes a theoretical framework that enables comparative risk predictions for second cancer incidence after particle beam therapy for different ion species for individual patients, accounting for differences in relative biological effectiveness (RBE) for the competing processes of tumor initiation and cell inactivation. Our working hypothesis was that use of carbon-ion therapy instead of proton therapy would show a difference in the predicted risk of second cancer incidence in the breast for a sample of Hodgkin lymphoma (HL) patients. Methods and Materials We generated biologic treatment plans and calculated relative predicted risks of second cancer in the breast …

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The Cytoplasmic Carbonic Anhydrases Βca2 And Βca4 Are Required For Optimal Plant Growth At Low Co2, Robert J. Dimario, Jennifer C. Quebedeaux, David J. Longstreth, Maheshi Dassanayake, Monica M. Hartman, James V. Moroney May 2016

The Cytoplasmic Carbonic Anhydrases Βca2 And Βca4 Are Required For Optimal Plant Growth At Low Co2, Robert J. Dimario, Jennifer C. Quebedeaux, David J. Longstreth, Maheshi Dassanayake, Monica M. Hartman, James V. Moroney

Faculty Publications

© 2016 American Society of Plant Biologists. All Rights Reserved. Carbonic anhydrases (CAs) are zinc metalloenzymes that interconvert CO2 and HCO3-. In plants, both α-and β-type CAs are present. We hypothesize that cytoplasmic bCAs are required to modulate inorganic carbon forms needed in leaf cells for carbonrequiring reactions such as photosynthesis and amino acid biosynthesis. In this report, we present evidence that βCA2 and βCA4 are the two most abundant cytoplasmic CAs in Arabidopsis (Arabidopsis thaliana) leaves. Previously, βCA4 was reported to be localized to the plasma membrane, but here, we show that two forms of βCA4 are expressed in …

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Direct And Indirect Targeting Of Pp2a By Conserved Bacterial Type-Iii Effector Proteins, Lin Jin, Jong Hyun Ham, Rosemary Hage, Wanying Zhao, Jaricelis Soto-Hernández, Sang Yeol Lee, Seung Mann Paek, Min Gab Kim, Charles Boone, David L. Coplin, David Mackey May 2016

Direct And Indirect Targeting Of Pp2a By Conserved Bacterial Type-Iii Effector Proteins, Lin Jin, Jong Hyun Ham, Rosemary Hage, Wanying Zhao, Jaricelis Soto-Hernández, Sang Yeol Lee, Seung Mann Paek, Min Gab Kim, Charles Boone, David L. Coplin, David Mackey

Faculty Publications

Bacterial AvrE-family Type-III effector proteins (T3Es) contribute significantly to the virulence of plant-pathogenic species of Pseudomonas, Pantoea, Ralstonia, Erwinia, Dickeya and Pectobacterium, with hosts ranging from monocots to dicots. However, the mode of action of AvrE-family T3Es remains enigmatic, due in large part to their toxicity when expressed in plant or yeast cells. To search for targets of WtsE, an AvrE-family T3E from the maize pathogen Pantoea stewartii subsp. stewartii, we employed a yeast-two-hybrid screen with non-lethal fragments of WtsE and a synthetic genetic array with full-length WtsE. Together these screens indicate that WtsE targets maize protein phosphatase 2A (PP2A) …

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Fibroblast Growth Factor-23 (Fgf-23) Levels Differ Across Populations By Degree Of Industrialization, Shennin N. Yuen, Kramer Holly, Amy Luke, Pascal Bovet, Jacob Plange-Rhule, Terrence Forrester, Vicki Lambert, Myles Wolf, Pauline Camacho, Regina Harders, Lara Dugas, Richard Cooper, Ramon Durazo-Arvizu May 2016

Fibroblast Growth Factor-23 (Fgf-23) Levels Differ Across Populations By Degree Of Industrialization, Shennin N. Yuen, Kramer Holly, Amy Luke, Pascal Bovet, Jacob Plange-Rhule, Terrence Forrester, Vicki Lambert, Myles Wolf, Pauline Camacho, Regina Harders, Lara Dugas, Richard Cooper, Ramon Durazo-Arvizu

Faculty Publications

Context: Compensatory increases in fibroblast growth factor 23 (FGF23) with increasing phosphate intake may adversely impact health. However, population and clinical studies examining the link between phosphate intake and FGF23 levels have focused mainly on populations living in highly industrialized societies in which phosphate exposure may be homogenous. Objective: The objective of the study was to contrast dietary phosphate intake, urinary measures of phosphate excretion, and FGF23 levels across populations that differ by the level of industrialization. Design: This was a cross-sectional analysis of three populations. Setting: The study was conducted in Maywood, Illinois; Mahé Island, Seychelles; and Kumasi, Ghana. …

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Discovery Of A New Repeat Family In The Callithrix Jacchus Genome, Miriam Konkel, Mark Batzer, Brygg Ullmer, Erika L. Arceneaux, Sreeja Sanampudi, Sarah A. Brantley, Robert Hubley, Arian F.A. Smit May 2016

Discovery Of A New Repeat Family In The Callithrix Jacchus Genome, Miriam Konkel, Mark Batzer, Brygg Ullmer, Erika L. Arceneaux, Sreeja Sanampudi, Sarah A. Brantley, Robert Hubley, Arian F.A. Smit

Faculty Publications

We identified a novel repeat family, termed Platy-1, in the Callithrix jacchus (common marmoset) genome that arose around the time of the divergence of platyrrhines and catarrhines and established itself as a repeat family in New World monkeys (NWMs). A full-length Platy-1 element is ∼100 bp in length, making it the shortest known short interspersed element (SINE) in primates, and harbors features characteristic of non-LTR retrotransposons. We identified 2268 full-length Platy-1 elements across 62 subfamilies in the common marmoset genome. Our subfamily reconstruction and phylogenetic analyses support Platy-1 propagation throughout the evolution of NWMs in the lineage leading to C. …

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Potential And Timescales For Oxygen Depletion In Coastal Upwelling Systems: A Box‐Model Analysis, C. S. Harrison, B. Hales, S. Siedlecki, R. M. Samelson May 2016

Potential And Timescales For Oxygen Depletion In Coastal Upwelling Systems: A Box‐Model Analysis, C. S. Harrison, B. Hales, S. Siedlecki, R. M. Samelson

Faculty Publications

No abstract provided.

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Mitochondrial Dna Variation In Southeastern Pre-Columbian Canids, Kristin E. Brzeski, Melissa B. Debiasse, David R. Rabon, Michael J. Chamberlain, Sabrina S. Taylor May 2016

Mitochondrial Dna Variation In Southeastern Pre-Columbian Canids, Kristin E. Brzeski, Melissa B. Debiasse, David R. Rabon, Michael J. Chamberlain, Sabrina S. Taylor

Faculty Publications

The taxonomic status of the red Wolf (Canis rufus) is heavily debated, but could be clarified by examining historic specimens from the southeastern United States. We analyzed mitochondrial DNA (mtDNA) from 3 ancient (350-1900 year olds) putative Wolf samples excavated from middens and sinkholes within the historic red Wolf range. We detected 3 unique mtDNA haplotypes, which grouped with the coyote mtDNA clade, suggesting that the canids inhabiting southeastern North America prior to human colonization from Europe were either coyotes, which would vastly expand historic coyote distributions, an ancient coyote-Wolf hybrid, or a North American evolved red Wolf lineage related …

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The Use Of Marine Aquaculture Solid Waste For Nursery Production Of The Salt Marsh Plants Spartina Alterniflora And Juncus Roemerianus, Heather M. Joesting, Reginald B. Blaylock, Patrick Biber, Andrew Ray May 2016

The Use Of Marine Aquaculture Solid Waste For Nursery Production Of The Salt Marsh Plants Spartina Alterniflora And Juncus Roemerianus, Heather M. Joesting, Reginald B. Blaylock, Patrick Biber, Andrew Ray

Faculty Publications

Recent technological advances in marine shrimp and finfish aquaculture alleviate many of the environmental risks associated with traditional aquaculture, but challenges remain in cost-effective waste management. Liquid effluent from freshwater aquaculture systems has been shown to be effective in agricultural crop production (i.e., aquaponics), but few studies have explored the potential for reuse of marine aquaculture effluent, particularly the solid fraction. The purpose of this study was to investigate the use of marine aquaculture solid waste as a nutrient source for the nursery production of two salt tolerant plants commonly used in coastal salt marsh restoration, Spartina alterniflora (smooth cordgrass) …

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Chesapeake Aquaculture, Garth Woodruff May 2016

Chesapeake Aquaculture, Garth Woodruff

Faculty Publications

No abstract provided.

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Dynamic Simulation And Numerical Analysis Of Hurricane Storm Surge Under Sea Level Rise With Geomorphologic Changes Along The Northern Gulf Of Mexico, Matthew V. Bilskie, S. C. Hagen, Karim Alizad, S. C. Medeiros, D. L. Passeri, H. F. Needham, A. Cox May 2016

Dynamic Simulation And Numerical Analysis Of Hurricane Storm Surge Under Sea Level Rise With Geomorphologic Changes Along The Northern Gulf Of Mexico, Matthew V. Bilskie, S. C. Hagen, Karim Alizad, S. C. Medeiros, D. L. Passeri, H. F. Needham, A. Cox

Faculty Publications

This work outlines a dynamic modeling framework to examine the effects of global climate change, and sea level rise (SLR) in particular, on tropical cyclone-driven storm surge inundation. The methodology, applied across the northern Gulf of Mexico, adapts a present day large-domain, high resolution, tide, wind-wave, and hurricane storm surge model to characterize the potential outlook of the coastal landscape under four SLR scenarios for the year 2100. The modifications include shoreline and barrier island morphology, marsh migration, and land use land cover change. Hydrodynamics of 10 historic hurricanes were simulated through each of the five model configurations (present day …

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Ubisol-Q10 Prevents Glutamate-Induced Cell Death By Blocking Mitochondrial Fragmentation And Permeability Transition Pore Opening, Santosh Kumari, Suresh L. Mehta, Gaolin Z. Milledge, Xinyu Huang, P Andy Li Apr 2016

Ubisol-Q10 Prevents Glutamate-Induced Cell Death By Blocking Mitochondrial Fragmentation And Permeability Transition Pore Opening, Santosh Kumari, Suresh L. Mehta, Gaolin Z. Milledge, Xinyu Huang, P Andy Li

Faculty Publications

Mitochondrial dysfunction and oxidative stress are the major events that lead to the formation of mitochondrial permeability transition pore (mPTP) during glutamate-induced cytotoxicity and cell death. Coenzyme Q10 (CoQ10) has widely been used for the treatment of mitochondrial disorders and neurodegenerative diseases. Comparing to traditional lipid-soluble CoQ10, water soluble CoQ10 (Ubisol-Q10) has high intracellular and intra-mitochondrial distribution. The aims of the present study are to determine the neuroprotective effects of Ubisol-Q10 on glutamate-induced cell death and to explore its functional mechanisms. HT22 neuronal cells were exposed to glutamate. Cell viability was measured and mitochondrial fragmentation was assessed by mitochondrial imaging. …

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Integrative Analysis Reveals Clinical Phenotypes And Oncogenic Potentials Of Long Non-Coding Rnas Across 15 Cancer Types, Ze-Lin Wang, Bin Li, Stephen R. Piccolo, Xiao-Qin Zhang, Jun-Hao Li, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu Apr 2016

Integrative Analysis Reveals Clinical Phenotypes And Oncogenic Potentials Of Long Non-Coding Rnas Across 15 Cancer Types, Ze-Lin Wang, Bin Li, Stephen R. Piccolo, Xiao-Qin Zhang, Jun-Hao Li, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu

Faculty Publications

Long non-coding RNAs (lncRNAs) have been shown to contribute to tumorigenesis. However, surprisingly little is known about the comprehensive clinical and genomic characterization of lncRNAs across human cancer. In this study, we conducted comprehensive analyses for the expression profile, clinical outcomes, somatic copy number alterations (SCNAs) profile of lncRNAs in ~7000 clinical samples from 15 different cancer types. We identified significantly differentially expressed lncRNAs between tumor and normal tissues from each cancer. Notably, we characterized 47 lncRNAs which were extensively dysregulated in at least 10 cancer types, suggesting a conserved function in cancer development. We also analyzed the associations between …

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Transmission Mechanisms Of An Emerging Insect-Borne Rickettsial Pathogen, Lisa D. Brown, Kaikhushroo H. Banajee, Lane D. Foil, Kevin R. Macaluso Apr 2016

Transmission Mechanisms Of An Emerging Insect-Borne Rickettsial Pathogen, Lisa D. Brown, Kaikhushroo H. Banajee, Lane D. Foil, Kevin R. Macaluso

Faculty Publications

© 2016 Brown et al. Background: Vector-borne pathogens must overcome arthropod infection and escape barriers (e.g. midgut and salivary glands) during the extrinsic incubation period (EIP) before subsequent transmission to another host. This particular timespan is undetermined for the etiological agent of flea-borne spotted fever (Rickettsia felis). Artificial acquisition of R. felis by blood-feeding cat fleas revealed dissemination to the salivary glands after seven days; however, this length of time is inconsistent with co-feeding studies that produced infectious cat fleas within 24 h of infection. In the current study, we demonstrated that an alternative mechanism is responsible for the early-phase …

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Structure, Organization And Evolution Of Adp-Ribosylation Factors In Rice And Foxtail Millet, And Their Expression In Rice, Mehanathan Muthamilarasan, Venkata R. Mangu, Hana Zandkarimi, Manoj Prasad, Niranjan Baisakh Apr 2016

Structure, Organization And Evolution Of Adp-Ribosylation Factors In Rice And Foxtail Millet, And Their Expression In Rice, Mehanathan Muthamilarasan, Venkata R. Mangu, Hana Zandkarimi, Manoj Prasad, Niranjan Baisakh

Faculty Publications

ADP-ribosylation factors (ARFs) have been reported to function in diverse physiological and molecular activities. Recent evidences also demonstrate the involvement of ARFs in conferring tolerance to biotic and abiotic stresses in plant species. In the present study, 23 and 25 ARF proteins were identified in C 3 model-rice and C 4 model-foxtail millet, respectively. These proteins are classified into four classes (I-IV) based on phylogenetic analysis, with ARFs in classes I-III and ARF-like proteins (ARLs) in class IV. Sequence alignment and domain analysis revealed the presence of conserved and additional motifs, which may contribute to neo-and sub-functionalization of these proteins. …

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Alternative Promoters Of Peg3 With Maternal Specificity, Bambarendage P.U. Perera, Joomyeong Kim Apr 2016

Alternative Promoters Of Peg3 With Maternal Specificity, Bambarendage P.U. Perera, Joomyeong Kim

Faculty Publications

Peg3 (paternally expressed gene 3) is an imprinted gene localized within an evolutionarily conserved 500-kb domain in human chromosome 19q13.4 and mouse proximal chromosome 7. In the current study, we have identified three alternative promoters for mouse Peg3 and one alternative promoter for human PEG3. These alternative promoters are localized within the 200-kb upstream region of human and mouse PEG3, which is well conserved and thus predicted to harbor several cis-regulatory elements for the PEG3 domain. In the mouse, two of these alternative promoters drive maternal-specific expression of Peg3 specifically in the hypothalamus of the adult brain, while the remaining …

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Robustness Of Multiple Indicators In Automated Screening Systems For Deception Detection, Ryan M. Schuetzler, Nathan W. Twyman, Jeffery Gainer Proudfoot, Aaron C. Elkins, Douglas C. Derrik Apr 2016

Robustness Of Multiple Indicators In Automated Screening Systems For Deception Detection, Ryan M. Schuetzler, Nathan W. Twyman, Jeffery Gainer Proudfoot, Aaron C. Elkins, Douglas C. Derrik

Faculty Publications

This study investigates the effectiveness of an automatic system for detection of deception by individuals with the use of multiple indicators of such potential deception. Deception detection research in the information systems discipline has postulated increased accuracy through a new class of screening systems that automatically conduct interviews and track multiple indicators of deception simultaneously. Understanding the robustness of this new class of systems and the limitations of its theoretical improved performance is important for refinement of the conceptual design. The design science proof-of-concept study presented here implemented and evaluated the robustness of these systems for automated screening for deception …

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Protein Synthesis Directly From Pcr: Progress And Applications Of Cell-Free Protein Synthesis With Linear Dna, Song-Min Schinn, Andrew Broadbent, William T. Bradley, Bradley Charles Bundy Apr 2016

Protein Synthesis Directly From Pcr: Progress And Applications Of Cell-Free Protein Synthesis With Linear Dna, Song-Min Schinn, Andrew Broadbent, William T. Bradley, Bradley Charles Bundy

Faculty Publications

A rapid, versatile method of protein expression and screening can greatly facilitate the future development of therapeutic biologics, proteomic drug targets and biocatalysts. An attractive candidate is cell-free protein synthesis (CFPS), a cell-lysate-based in vitro expression system, which can utilize linear DNA as expression templates, bypassing time-consuming cloning steps of plasmid-based methods. Traditionally, such linear DNA expression templates (LET) have been vulnerable to degradation by nucleases present in the cell lysate, leading to lower yields. This challenge has been significantly addressed in the recent past, propelling LET-based CFPS as a useful tool for studying, screening and engineering proteins in a …

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The Removal Kinetics Of Dissolved Organic Matter And The Optical Clarity Of Groundwater, Francis H. Chapelle, Yuan Shen, Eric W. Strom, Ronald Benner Apr 2016

The Removal Kinetics Of Dissolved Organic Matter And The Optical Clarity Of Groundwater, Francis H. Chapelle, Yuan Shen, Eric W. Strom, Ronald Benner

Faculty Publications

Concentrations of dissolved organic matter (DOM) and ultraviolet/visible light absorbance decrease systematically as groundwater moves through the unsaturated zones overlying aquifers and along flowpaths within aquifers. These changes occur over distances of tens of meters (m) implying rapid removal kinetics of the chromophoric DOM that imparts color to groundwater. A one-compartment input-output model was used to derive a differential equation describing the removal of DOM from the dissolved phase due to the combined effects of biodegradation and sorption. The general solution to the equation was parameterized using a 2-year record of dissolved organic carbon (DOC) concentration changes in groundwater at …

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Eating Increases Oxidative Damage In A Reptile, Michael W. Butler, Thomas J. Lutz, Haralambos Fokidis, Zachary R. Stahlschmidt Apr 2016

Eating Increases Oxidative Damage In A Reptile, Michael W. Butler, Thomas J. Lutz, Haralambos Fokidis, Zachary R. Stahlschmidt

Faculty Publications

While eating has substantial benefits in terms of both nutrient and energy acquisition, there are physiological costs associated with digesting and metabolizing a meal. Frequently, these costs have been documented in the context of energy expenditure while other physiological costs have been relatively unexplored. Here, we tested whether the seemingly innocuous act of eating affects either systemic pro-oxidant (reactive oxygen metabolite, ROM) levels or antioxidant capacity of corn snakes (Pantherophis guttatus) by collecting plasma during absorptive (peak increase in metabolic rate due to digestion of a meal) and non-absorptive (baseline) states. When individuals were digesting a meal, there was a …

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The Ecologist's Field Guide To Sequence-Based Identification Of Biodiversity, Simon Creer, Kristy Deiner, Serita D. Frey, Dorota Porazinska, Pierre Taberlet, W. Kelley Thomas, Caitlin Potter, Holly M. Bik Apr 2016

The Ecologist's Field Guide To Sequence-Based Identification Of Biodiversity, Simon Creer, Kristy Deiner, Serita D. Frey, Dorota Porazinska, Pierre Taberlet, W. Kelley Thomas, Caitlin Potter, Holly M. Bik

Faculty Publications

The past 100 years of ecological research has seen substantial progress in understanding the natural world and likely effects of change, whether natural or anthropogenic. Traditional ecological approaches underpin such advances, but would additionally benefit from recent developments in the sequence-based quantification of biodiversity from the fields of molecular ecology and genomics. By building on a long and rich history of molecular taxonomy and taking advantage of the new generation of DNA sequencing technologies, we are gaining previously impossible insights into alpha and beta diversity from all domains of life, irrespective of body size. While a number of complementary reviews …

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The Response Of Runoff And Sediment Loading In The Apalachicola River, Florida To Climate And Land Use Land Cover Change, Paige A. Hovenga, Dingbao Wang, Stephen C. Medeiros, Scott C. Hagen, Karim Alizad Apr 2016

The Response Of Runoff And Sediment Loading In The Apalachicola River, Florida To Climate And Land Use Land Cover Change, Paige A. Hovenga, Dingbao Wang, Stephen C. Medeiros, Scott C. Hagen, Karim Alizad

Faculty Publications

The response of runoff and sediment loading in the Apalachicola River under projected climate change scenarios and land use land cover (LULC) change is evaluated. A hydrologic model using the Soil and Water Assessment Tool was developed for the Apalachicola region to simulate daily runoff and sediment load under present (circa 2000) and future conditions (2100) to understand how parameters respond over a seasonal time frame to changes in climate, LULC, and coupled climate/LULC. The Long Ashton Research Station-Weather Generator was used to downscale temperature and precipitation from three general circulation models, each under Intergovernmental Panel on Climate Change (IPCC) …

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Tidal Hydrodynamics Under Future Sea Level Rise And Coastal Morphology In The Northern Gulf Of Mexico, Davina L. Passeri, Scott C. Hagen, Nathaniel G. Plant, Matthew V. Bilskie, Stephen C. Medeiros, Karim Alizad Apr 2016

Tidal Hydrodynamics Under Future Sea Level Rise And Coastal Morphology In The Northern Gulf Of Mexico, Davina L. Passeri, Scott C. Hagen, Nathaniel G. Plant, Matthew V. Bilskie, Stephen C. Medeiros, Karim Alizad

Faculty Publications

This study examines the integrated influence of sea level rise (SLR) and future morphology on tidal hydrodynamics along the Northern Gulf of Mexico (NGOM) coast including seven embayments and three ecologically and economically significant estuaries. A large-domain hydrodynamic model was used to simulate astronomic tides for present and future conditions (circa 2050 and 2100). Future conditions were simulated by imposing four SLR scenarios to alter hydrodynamic boundary conditions and updating shoreline position and dune heights using a probabilistic model that is coupled to SLR. Under the highest SLR scenario, tidal amplitudes within the bays increased as much as 67% (10.0 …

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Truly Quantitative Analysis Of The Firefly Luciferase Complementation Assay, Renee Dale, Naohiro Kato Apr 2016

Truly Quantitative Analysis Of The Firefly Luciferase Complementation Assay, Renee Dale, Naohiro Kato

Faculty Publications

© 2016 The Authors. Luciferase complementation assays detect protein-protein interactions within living cells using bioluminescence. Since the first report using plant cells was published in 2007, over 100 peer-reviewed articles have been published describing the detection of protein-protein interactions within plant cells by the assays. The assays have also been used to analyze networks of protein-protein interactions in plants. Although the assays have a high dynamic range, they remain qualitative with respect to determining the affinities of interactions. In this article, we first summarize the luciferase complementation assays developed in the past years. We then describe the mechanism of the …

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Genome Content And Phylogenomics Reveal Both Ancestral And Lateral Evolutionary Pathways In Plant-Pathogenic Streptomyces Species, Jose C. Huguet-Tapia, Tristan Lefebure, Jonathan H. Badger, Dongli Guan, Gregg S. Pettis, Michael J. Stanhope, Rosemary Loria Apr 2016

Genome Content And Phylogenomics Reveal Both Ancestral And Lateral Evolutionary Pathways In Plant-Pathogenic Streptomyces Species, Jose C. Huguet-Tapia, Tristan Lefebure, Jonathan H. Badger, Dongli Guan, Gregg S. Pettis, Michael J. Stanhope, Rosemary Loria

Faculty Publications

© 2016, American Society for Microbiology. All Rights Reserved. Streptomyces spp. are highly differentiated actinomycetes with large, linear chromosomes that encode an arsenal of biologically active molecules and catabolic enzymes. Members of this genus are well equipped for life in nutrient-limited environments and are common soil saprophytes. Out of the hundreds of species in the genus Streptomyces, a small group has evolved the ability to infect plants. The recent availability of Streptomyces genome sequences, including four genomes of pathogenic species, provided an opportunity to characterize the gene content specific to these pathogens and to study phylogenetic relationships among them. Genome …

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