Digital Commons Network^™

Guidelines For The Use And Interpretation Of Assays For Monitoring Autophagy (3rd Edition), Daniel J. Klionsky, Rodrigo Franco, More Than 2,000 Co-Authors

School of Veterinary and Biomedical Sciences: Faculty Publications

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes.

For example, a key point that needs to be emphasized is that …

Expression And Distribution Of Thiol-Regulating Enzyme Glutaredoxin 2 (Grx2) In Porcine Ocular Tissues, Bijaya Upadhyaya, Xiaoli Tian, Hongli Wu, Marjorie F. Lou

School of Veterinary and Biomedical Sciences: Faculty Publications

Glutaredoxin2 (Grx2) is a mitochondrial isozyme of the cytosolic glutaredoxin1 (thioltransferase or TTase). Both belong to the large oxidoreductase family and play an important role in maintaining thiol/disulfide redox homeostasis in the cells. Grx2 is recently found in the lens where its activities of disulfide reductase and peroxidase, similar to TTase, can protect the lens against oxidative stress. Since other eye tissues are also highly sensitive to oxidative stress, and TTase’s distribution in the eye is known, we focused on this study by investigating the Grx2 distribution in the ocular tissues in comparison to the lens. Fresh porcine eyes were …

Horizontal Gene Acquisitions, Mobile Element Proliferation, And Genome Decay In The Host-Restricted Plant Pathogen Erwinia Tracheiphila, Lori R. Shapiro, Erin D. Scully, Timonthy J. Straub, Jihye Park, Andrew G. Stephenson, Gwyn A. Beattie, Mark L. Gleason, Roberto Kolter, Miguel C. Coelho, Consuelo M. De Moraes, Mark C. Mescher, Olga Zhaxybayeva

Department of Agronomy and Horticulture: Faculty Publications

Modern industrial agriculture depends on high-density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared with ecologically intact settings. Here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen Erwinia tracheiphila (Enterobacteriaceae) isolated from infected squash plants in New York, Pennsylvania, Kentucky, and Michigan. These genomes exhibit a high proportion of recent horizontal gene acquisitions, invasion and remarkable amplification of mobile genetic elements, and pseudogenization of approximately 20% of the coding sequences. These genome attributes indicate that E. tracheiphila recently emerged as a …

Nutrients In The Nexus, Eric A. Davidson, Rachel L. Nifong, Richard B. Ferguson, Cheryl Palm, Deanna L. Osmond, Jill S. Baron

Department of Agronomy and Horticulture: Faculty Publications

Synthetic nitrogen (N) fertilizer has enabled modern agriculture to greatly improve human nutrition during the twentieth century, but it has also created unintended human health and environmental pollution challenges for the twentyfirst century. Averaged globally, about half of the fertilizer-N applied to farms is removed with the crops, while the other half remains in the soil or is lost from farmers’ fields, resulting in water and air pollution. As human population continues to grow and food security improves in the developing world, the dual development goals of producing more nutritious food with low pollution will require both technological and socioeconomic …

Alkaline Stress And Iron Deficiency Regulate Iron Uptake And Riboflavin Synthesis Gene Expression Differently In Root And Leaf Tissue: Implications For Iron Deficiency Chlorosis, En-Jung Hsieh, Brian M. Waters

Department of Agronomy and Horticulture: Faculty Publications

Iron (Fe) is an essential mineral that has low solubility in alkaline soils, where its deficiency results in chlorosis. Whether low Fe supply and alkaline pH stress are equivalent is unclear, as they have not been treated as separate variables in molecular physiological studies. Additionally, molecular responses to these stresses have not been studied in leaf and root tissues simultaneously. We tested how plants with the Strategy I Fe uptake system respond to Fe deficiency at mildly acidic and alkaline pH by measuring root ferric chelate reductase (FCR) activity and expression of selected Fe uptake genes and riboflavin synthesis genes. …

Corn Response To Nitrogen Management Under Fully-Irrigated Vs. Water-Stressed Conditions, Bijesh Maharjan, Carl J. Rosen, John A. Lamb, Rodney T. Venterea

Department of Agronomy and Horticulture: Faculty Publications

Characterizing corn (Zea mays L.) grain yield (GY) response to N is critical for maximizing profits, increasing N use efficiency and minimizing environmental impacts. Although a large database of GY response to N exists for highly productive soils, few data exist for less productive soils. While changes in precipitation are expected in the future, few studies have compared GY response to varying N management practices under conditions of varying water availability. We measured GY and basal stalk nitrate nitrogen (BSN) at harvest using split-applied urea at eight N rates under fully-irrigated (FI) and water-stressed (WS) conditions in a loamy …

Inter-Row Robot Navigation Using 1d Ranging Sensors, Tyler A. Troyer, Santosh Pitla, Ethan Nutter

Department of Agricultural and Biological Systems Engineering: Faculty Publications

In this paper a fuzzy logic navigation controller for an inter-row agricultural robot is developed and evaluated in laboratory settings. The controller receives input from one-dimensional (1D) ranging sensors on the robotic platform, and operated on ten fuzzy rules for basic row-following behavior. The control system was implemented on basic hardware for proof of concept and operated on a commonly available microcontroller development platform and open source software libraries. The robot platform used for experimentation was a small tracked vehicle with differential steering control. Fuzzy inferencing and defuzzification, step response and cross track error were obtained from the test conducted …

Fatty Acid Transport Proteins: Targeting Fatp2 As A Gatekeeper Involved In The Transport Of Exogenous Fatty Acids, Paul N. Black, Constance Ahowesso, David Montefusco, Nipun Saini, Concetta C. Dirusso

Department of Biochemistry: Faculty Publications

The fatty acid transport proteins (FATP) are classified as members of the solute carrier 27 (Slc27) family of proteins based on their ability to function in the transport of exogenous fatty acids. These proteins, when localized to the plasma membrane or at intracellular membrane junctions with the endoplasmic reticulum, function as a gate in the regulated transport of fatty acids and thus represent a therapeutic target to delimit the acquisition of fatty acids that contribute to disease as in the case of fatty acid overload. To date, FATP1, FATP2, and FATP4 have been used as targets in the selection of …

Caloric Restriction Of Db/Db Mice Reverts Hepatic Steatosis And Body Weight With Divergent Hepatic Metabolism, Kyung Eun Kim, Youngae Jung, Soonki Min, Miso Nam, Rok Won Heo, Byeong Tak Jeon, Dae Hyun Song, Chin-Ok Yi, Eun Ae Jeong, Hwajin Kim, Jeonghyun Kim, Seon-Yong Jeong, Woori Kwak, Do Hyun Ryu, Tamas L. Horvath, Gu Seob Roh, Geum-Sook Hwang

Department of Biochemistry: Faculty Publications

Non-alcoholic fatty liver disease (NAFLD) is one of the most frequent causes of liver disease and its prevalence is a serious and growing clinical problem. Caloric restriction (CR) is commonly recommended for improvement of obesity-related diseases such as NAFLD. However, the effects of CR on hepatic metabolism remain unknown. We investigated the effects of CR on metabolic dysfunction in the liver of obese diabetic db/db mice. We found that CR of db/db mice reverted insulin resistance, hepatic steatosis, body weight and adiposity to those of db/m mice. H-NMR- and UPLC-QTOF-MS-based metabolite profiling data showed significant metabolic alterations related to lipogenesis, …

Evidence For Pipecolate Oxidase In Mediating Protection Against Hydrogen Peroxide Stress, Sathish Kumar Natarajan, Ezhumalai Muthukrishnan, Oleh Khalimonchuk, Justin L. Mott, Donald F. Becker

Department of Biochemistry: Faculty Publications

Pipecolate, an intermediate of the lysine catabolic pathway, is oxidized to Δ¹-piperideine-6-carboxylate (P6C) by the flavoenzyme lpipecolate oxidase (PIPOX). P6C spontaneously hydrolyzes to generate α-aminoadipate semialdehyde, which is then converted into α-aminoadipate acid by α-aminoadipatesemialdehyde dehydrogenase. l-pipecolate was previously reported to protect mammalian cells against oxidative stress. Here, we examined whether PIPOX is involved in the mechanism of pipecolate stress protection. Knockdown of PIPOX by small interference RNA abolished pipecolate protection against hydrogen peroxide-induced cell death in HEK293 cells suggesting a critical role for PIPOX. Subcellular fractionation analysis showed that PIPOX is localized in the mitochondria of HEK293 …

Engineering A Trifunctional Proline Utilization A Chimaera By Fusing A Dna-Binding Domain To A Bifunctional Puta, Benjamin W. Arentson, Erin L. Hayes, Weidong Zhu, John J. Tanner, Donald F. Becker

Department of Biochemistry: Faculty Publications

Proline utilization A (PutA) is a bifunctional flavoenzyme with proline dehydrogenase (PRODH) and Δ¹-pyrroline-5- carboxylate (P5C) dehydrogenase (P5CDH) domains that catalyses the two-step oxidation of proline to glutamate. Trifunctional PutAs also have an N-terminal ribbon–helix–helix (RHH) DNA-binding domain and moonlight as autogenous transcriptional repressors of the put regulon. A unique property of trifunctional PutA is the ability to switch functions from DNA-bound repressor to membrane-associated enzyme in response to cellular nutritional needs and proline availability. In the present study, we attempt to construct a trifunctional PutA by fusing the RHH domain of Escherichia coli PutA (EcRHH) to the …

Signal Traits And Oxidative Stress: A Comparative Study Across Populations With Divergent Signals, Maren N. Vitousek, Oldřich Tomášek, Tomáš Albrecht, Matt Wilkins, Rebecca Safran

School of Biological Sciences: Faculty Publications

Diverging populations often shift patterns of signal use – a process that can contribute to reproductive isolation and speciation. Yet it is not clear why most traits gain or lose signal value during divergence. One reason this could occur is because changes in the relationship between signals and relevant physiological parameters degrade the reliability of a signal, or even change its underlying information content. Here we test the hypothesis that the relationship between signal trait elaboration and a central component of organismal health – oxidative stress – differs across closely related populations that have diverged in signal use and preferences. …

Candida Albicans Isw2 Regulates Chlamydospore Suspensor Cell Formation And Virulence In Vivo In A Mouse Model Of Disseminated Candidiasis, Dhammika Navarathna, Ruvini U. Pathirana, Michail S. Lionakis, Kenneth W. Nickerson, David D. Roberts

School of Biological Sciences: Faculty Publications

Formation of chlamydospores by Candida albicans was an established medical diagnostic test to confirm candidiasis before the molecular era. However, the functional role and pathological relevance of this in vitro morphological transition to pathogenesis in vivo remain unclear. We compared the physical properties of in vitro-induced chlamydospores with those of large C. albicans cells purified by density gradient centrifugation from Candida infected mouse kidneys. The morphological and physical properties of these cells in kidneys of mice infected intravenously with wild type C. albicans confirmed that chlamydospores can form in infected kidneys. A previously reported chlamydospore-null Δisw2/ …

Experimental Microbial Evolution Of Extremophiles, Paul H. Blum, Deepak Rudrappa, Raghuveer Singh, Samuel Mccarthy, Benjamin J. Pavlik

School of Biological Sciences: Faculty Publications

Experimental microbial evolutions (EME) involves studying closely a microbial population after it has been through a large number of generations under controlled conditions (Kussell 2013). Adaptive laboratory evolution (ALE) selects for fitness under experimentally imposed conditions (Bennett and Hughes 2009; Dragosits and Mattanovich 2013). However, experimental evolution studies focusing on the contributions of genetic drift and natural mutation rates to evolution are conducted under non-selective conditions to avoid changes imposed by selection (Hindré et al. 2012).

To understand the application of experimental evolutionary methods to extremophiles it is essential to consider the recent growth in this field over the last …

A Stenotrophomonas Maltophilia Strain Evades A Major Caenorhabditis Elegans Defense Pathway, Corin V. White, Brian J. Darby, Robert J. Breeden, Robert J. Breeden, Michael A. Herman

School of Biological Sciences: Faculty Publications

Stenotrophomonas maltophilia is a ubiquitous bacterium and an emerging nosocomial pathogen. This bacterium is resistant to many antibiotics, associated with a number of infections, and a significant health risk, especially for immunocompromised patients. Given that Caenorhabditis elegans shares many conserved genetic pathways and pathway components with higher organisms, the study of its interaction with bacterial pathogens has biomedical implications. S. maltophilia has been isolated in association with nematodes from grassland soils, and it is likely that C. elegans encounters this bacterium in nature. We found that a local S. maltophilia isolate, JCMS, is more virulent than the other S. maltophilia …

Water Security And Rainwater Harvesting: A Conceptual Framework And Candidate Indicators, Patrick Bitterman, Eric Tate, Kimberly J. Meter, Nandita B. Basu

Geography Program: Faculty Publications

Rainwater-harvesting tanks (reservoirs) in Tamil Nadu, India support agricultural livelihoods, mitigate water insecurity, and enable ecosystem services. However, many tanks have fallen into disrepair, as private wells have supplanted collectively managed tanks as the dominant irrigation source. Meanwhile, encroachment by peri-urban development, landless farmers, and Prosopis juliflora has reduced inflow and tank capacity. This exploratory study presents a conceptual framework and proposed indicator set for measuring water security in the context of rainwater harvesting tanks. The primary benefits of tanks and threats to their functionality are profiled as a precursor to construction of a causal network of water security. The …

Will The Eastern Mediterranean Region Be The First To Prevent All Of Folic Acid-Preventable Spina Bifida And Anencephaly?, Godfrey P. Oakley, Vijaya Kancherla

Saudi Medical Journal

No abstract provided.

Assessment Of The Environmental And Genetic Factors Influencing Prevalence Of Metabolic Syndrome In Saudi Arabia, Ibrahim M. Gosadi

Saudi Medical Journal

Metabolic syndrome (MS) is a combination of factors that increases the risk of cardiovascular atherosclerotic diseases including diabetes, obesity, dyslipidemia, and high blood pressure. Cardiovascular diseases are one of the leading causes of death in the adult Saudi population where the increase in cardiovascular-related mortality is augmented by the rise in the prevalence of MS. Metabolic syndrome is a multi-factorial disorder influenced by interactions between genetic and environmental components. This review aims to provide a comprehensive assessment of studied environmental and genetic factors explaining the prevalence of MS in the Kingdom of Saudi Arabia. Additionally, this review aims to illustrate …

Low Oxytocin And Melatonin Levels And Their Possible Role In The Diagnosis And Prognosis In Iraqi Autistic Children, Haidar A. Abdulamir, Omar F. Abdul-Rasheed, Emad A. Abdulghani

Saudi Medical Journal

Objectives: To test the possible association between oxytocin and melatonin levels with the severity of social and cognitive dysfunctions, and to study the correlation between these parameters in children with autism. Methods: A case-control study was carried out in the Department of Chemistry and Biochemistry, College of Medicine, Al-Nahrain University, Baghdad, Iraq. The study was performed on 60 male autistic patients recruited from the Pediatric Department of Al-Sader General Hospital, Baghdad, Iraq between November 2014 and April 2015. The levels of oxytocin and melatonin were measured in the serum of these autistic male patients, and categorized as mild, moderate, and …

Evaluation Of Health Care Services Provided For Older Adults In Primary Health Care Centers And Its Internal Environments, Hakan Yaman

Saudi Medical Journal

No abstract provided.

Evaluating Categories Of Resistance In Soybean Genotypes From The United States And Brazil To Aphis Glycines (Hemiptera: Aphididae), Edison L. L. Baldin, Lia Marchi-Werle, Luiz E.R. Pannuti, Andre L. Lourencao, Tiffany M. Heng-Moss, Thomas E. Hunt

Department of Entomology: Faculty Publications

Aphis glycines Matsumura (Hemiptera: Aphididae), the soybean aphid, has become an important pest of soybeans, leading to significant yield losses in the United States. Host plant resistance is a viable alternative for managing A. glycines. The objectives of this study were to identify and categorize sources of resistance in soybean to A. glycines on genotypes from the United States and Brazil. An antixenosis assay was initially conducted with 8 genotypes to evaluate attractiveness to A. glycines. The selected soybean genotypes were further evaluated in a colonization assay to investigate the resistance of the genotypes at V1 (fully developed …

Parental Rnai Suppression Of Hunchback Gene To Control Hemipteran Pests, Blair D. Siegfried, Kenneth E. Narva, Kanika Arora, Sarah E. Worden, Chitvan Khajuria, Elane Fishilevich, Nicholas P. Storer, Meghan Frey, Ronda L. Hamm, Ana Velez

Department of Entomology: Faculty Publications

This disclosure concerns nucleic acid molecules and methods of use thereof for control of hemipteran pests through RNA interference-mediated inhibition of target coding and transcribed non-coding sequences in hemipteran pests. The dis closure also concerns methods for making transgenic plants that express nucleic acid molecules useful for the control of hemipteran pests, and the plant cells and plants obtained thereby.

Pronghorn Habitat Suitability In The Texas Panhandle, Nathan P. Duncan, Samantha S. Kahl, Shawn S. Gray, Christopher J. Salice, Richard D. Stevens

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Habitat quality is an important factor that can greatly affect wildlife populations. Pronghorn (Antilocapra americana) habitat in the Texas Panhandle, USA has been lost through growth of human settlements and agricultural lands. We determined the most pertinent environmental variables affecting habitat selection using multiple methods, including a search of peer-reviewed literature, expert opinion ranking, and habitat suitability modeling. We determined quality and extent of pronghorn habitat in the Texas Panhandle using the MAXENT modeling environment to build a presence-only habitat suitability model based on global positioning system (GPS) locations collected via aerial surveys. Our habitat suitability model indicated …

Dysphagia Management And Research In An Acute-Care Military Treatment Facility: The Role Of Applied Informatics, Nancy Pearl Solomon, Angela M. Dietsch, Katie E. Dietrich-Burns, Edda L. Styrmisdottir, Christopher S. Armao

Department of Special Education and Communication Disorders: Faculty Publications

Purpose: This report describes the development and preliminary analysis of a database for traumatically injured military service members with dysphagia.

Methods: A multidimensional database was developed to capture clinical variables related to swallowing. Data were derived from clinical records and instrumental swallow studies, and ranged from demographics, injury characteristics, swallowing biomechanics, medications, and standardized tools (e.g.. Glasgow Coma Scale, Penetration-Aspiration Scale). Bayesian Belief Network modeling was used to analyze the data at intermediate points, guide data collection, and predict outcomes. Predictive models were validated with independent data via receiver operating characteristic curves.

Results: The first iteration of …

Nutritional Effects On Reproductive Performance Of Captiveadult Female Coyotes (Canis Latrans), Eric M. Gese, Beth M. Roberts, Frederick F. Knowlton

United States Department of Agriculture Wildlife Services: Staff Publications

Interactions between animals and their environment are fundamental to ecological research. Field studies of coyote (Canis latrans) reproductive performance suggest mean litter size changes in response to prey abundance. However, this relationship has been assessed primarily by using carcasses collected from trappers. The objective of this study was to assess whether nutritional manipulation prior to mating affected reproduction in adult female coyotes. We examined the effects of caloric restriction during the 7 months prior to estrus on the reproductive rates of 11 captive female coyotes and the subsequent initial survival of pups through two reproductive cycles. This was …

Development Of Artificial Bait For Brown Treesnake Suppression, Bruce A. Kimball, Scott A. Sterling, Thomas W. Mcauliffe, Randal S. Stahl, Rafael A. Garcia, William C. Pitt

United States Department of Agriculture Wildlife Services: Staff Publications

The brown treesnake (Boiga irregularis) was accidentally introduced to Guam in the 1940s from the Admiralty Islands. A native of Australia, Papua New Guinea, and the Solomon Islands, the brown treesnake (BTS) continues to threaten the economy and ecology of Guam and is currently the subject of a cooperative program to control snake populations on the island and prevent its spread throughout the Pacific Rim. Delivery of toxic baits is a primary component of population suppression efforts. While many food items tested as baits for toxicant delivery provide relevant food prey cues leading to investigatory behaviors in BTS, …

Using Satellite Vegetation And Compound Topographic Indices To Maphighly Erodible Cropland Buffers For Cellulosic Biofuel Cropdevelopments In Eastern Nebraska, Usa, Yingxin Gu, Bruce K. Wylie

United States Geological Survey: Staff Publications

Cultivating annual row crops in high topographic relief waterway buffers has negative environmental effects and can be environmentally unsustainable. Growing perennial grasses such as switchgrass(Panicum virgatum L.) for biomass (e.g., cellulosic biofuel feedstocks) instead of annual row crops in these high relief waterway buffers can improve local environmental conditions (e.g., reduce soil erosion and improve water quality through lower use of fertilizers and pesticides) and ecosystem services (e.g.,minimize drought and flood impacts on production; improve wildlife habitat, plant vigor, and nitro-gen retention due to post-senescence harvest for cellulosic biofuels; and serve as carbon sinks). The main objectives of this …

Supplementary Feeding And Endangered Avian Scavengers: Benefits, Caveats, And Controversies, Ainara Cortés- Avizanda, Guillermo Blanco, Travis L. Devault, Anil Markandya, Munir Z Virani, Joseph Brandt, José A Donázar

United States Department of Agriculture Wildlife Services: Staff Publications

Large avian scavengers are among the most vulnerable vertebrates, and many of their populations have declined severely in recent decades. To help mitigate this marked reduction in abundance, supplementary feeding stations (SFS; colloquially termed “vulture restaurants”) have been created worldwide, often without consideration of the scientific evidence supporting the suitability of the practice. SFS have been effective and important tools for conservation and reintroduction of avian scavengers. However, negative consequences can result from large aggregations of individual birds, disrupting intraguild processes and promoting density-dependent decreases in productivity. At the community level, SFS favor the congregation of predators (ie facultative scavengers), …

American Robins (Turdus Migratorius) And Cedar Waxwings (Bombycilla Cedrorum) Vary In Use Of Cultivated Cherry Orchards, Rachael A. Eaton, Catherine A. Lindell, Jeffrey Homan, George M. Linz, Brian A. Maurer

United States Department of Agriculture Wildlife Services: Staff Publications

Some fruit-eating bird species commonly consume cultivated fruit. Species-specific variation in diet preferences could result in varying use of orchards and impacts on the fruit-producing industry. However, species specific studies of avian orchard use are lacking, particularly throughout the fruit-growing season. Our objectives were to quantify the frequency of daily bird visits to orchards and the amount of time birds spent visiting orchards each day over the fruit-ripening season. Birds are well-documented consumers of cultivated sweet cherries (Prunus avium), which are relatively high in sugar and low in proteins and lipids. American Robins (Turdus migratorius) and …

Ecosystem Services Provided By Avian Scavengers, Travis L. Devault, James C. Beasley, Zachary H. Olson, Marcos Moleón, Martina Carrete, Antoni Margalida, José Antonio Sánchez-Zapata

United States Department of Agriculture Wildlife Services: Staff Publications

Food webs developed under classical theoretical models often depict simplistic interactions among trophic levels linked by predation (Hairston et al. 1960). As a result, extensive research efforts have been devoted to studying predator-prey interactions, often ignoring the contribution of scavenging in food-web dynamics. However, recent advancements in food-web theory have recognized the widespread and critical role that scavenging plays in stabilizing food webs in ecosystems throughout the world, thus suggesting that previous models may have greatly underestimated the importance of scavenging in food web research ( Wilson and Wolkovich 2011; Barton et al. 2013). Such disregard for the importance of …