Physical Sciences and Mathematics Commons^™

Gene Expression Profiling In Salmonella Choleraesuis-Infected Porcine Lung Using A Long Oligonucleotide Microarray, Shu-Hong Zhao, Daniel Kuhar, Joan K. Lunney, Harry Dawson, Catherine Guidry, Jolita J. Uthe, Shawn M. D. Bearson, Justin Recknor, Dan Nettleton, Christopher K. Tuggle

Dan Nettleton

Understanding the transcriptional response to pathogenic bacterial infection within food animals is of fundamental and applied interest. To determine the transcriptional response to Salmonella enterica serovar Choleraesuis (SC) infection, a 13,297-oligonucleotide swine array was used to analyze RNA from control, 24-h postinoculation (hpi), and 48-hpi porcine lung tissue from pigs infected with SC. In total, 57 genes showed differential expression (p < 0.001; false discovery rate = 12%). Quantitative real-time PCR (qRT-PCR) of 61 genes was used to confirm the microarray results and to identify pathways responding to infection. Of the 33 genes identified by microarray analysis as differentially expressed, 23 were confirmed by qRT-PCR results. A novel finding was that two transglutaminase family genes (TGM1 and TGM3) showed dramatic increases in expression postinoculation; combined with several other apoptotic genes, they indicated the induction of apoptotic pathways during SC infection. A predominant T helper 1-type immune response occurred during infection, with interferon …

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Suppression Of Antiferromagnetic Spin Fluctuations In Superconducting Cr0.8 Ru0.2, M. Ramazanoglu, Benjamin G. Ueland, D. K. Pratt, L. W. Harringer, J. W. Lynn, G. Ehlers, G. E. Granroth, Sergey L. Bud’Ko, Paul C. Canfield, Deborah L. Schlagel, Alan I. Goldman, Thomas A. Lograsso, Robert J. Mcqueeney

A. I. Goldman

Unconventional superconductivity (SC) often develops in magnetic metals on the cusp of static antiferromagnetic (AFM) order where spin fluctuations are strong. This association is so compelling that many SC materials are labeled as unconventional by proximity to an ordered AFM state. The Cr-Ru alloy system possesses such a phase diagram [see Fig. 1(a)]. Here we use inelastic neutron scattering to show that spin fluctuations are present in a SC Cr0.8Ru0.2 alloy (Tc=1.35 K). However, the neutron spin resonance, a possible signature of unconventional SC, is not observed. Instead, data indicate a spin gap of order 2Δ (the superconducting gap) and …

Using Controlled Disorder To Probe The Interplay Between Charge Order And Superconductivity In Nbse2, Kyuil Cho, M. Kończykowski, Serafim Teknowijoyo, Makariy A. Tanatar, J. Guss, P. B. Gartin, John M. Wilde, A. Kreyssig, Robert Mcqueeney, Alan I. Goldman, V. Mishra, P. J. Hirschfeld, Ruslan Prozorov

A. I. Goldman

The interplay between superconductivity and charge-density wave (CDW) in 2H-NbSe2 is not fully understood despite decades of study. Artificially introduced disorder can tip the delicate balance between two competing long-range orders, and reveal the underlying interactions that give rise to them. Here we introduce disorder by electron irradiation and measure in-plane resistivity, Hall resistivity, X-ray scattering, and London penetration depth. With increasing disorder, the superconducting transition temperature, Tc, varies non-monotonically, whereas the CDW transition temperature, TCDW, monotonically decreases and becomes unresolvable above a critical irradiation dose where Tcdrops sharply. Our results imply that the CDW …

Magnetic-Field Effects On The Fragile Antiferromagnetism In Ybbipt, Benjamin G. Ueland, Andreas Kreyssig, E. D. Mun, J. W. Lynn, L. W. Harriger, D. K. Pratt, K. Prokeš, Z. Hüsges, R. Toft-Petersen, S. Sauerbrei, Scott M. Saunders, Yuji Furukawa, Sergey L. Bud’Ko, Robert J. Mcqueeney, Paul C. Canfield, Alan I. Goldman

A. I. Goldman

We present neutron-diffraction data for the cubic-heavy-fermion YbBiPt that show broad magnetic diffraction peaks due to the fragile short-range antiferromagnetic (AFM) order persist under an applied magnetic-field H. Our results for H perpendicular to[(1) over bar 1 0] and a temperature of T = 0.14(1) K show that the (1/2,1/2,3/2) magnetic diffraction peak can be described by the same two-peak line shape found for mu H-0 = 0T below the Neel temperature of T-N = 0.4 K. Both components of the peak exist for mu H-0 less than or similar to 1.4 T, which is well past the AFM phase …

Automated Bioacoustics: Methods In Ecology And Conservation And Their Potential For Animal Welfare Monitoring, Michael P. Mcloughlin, Rebecca Stewart, Alan G. Mcelligott

Alan G. McElligott, PhD

Vocalizations carry emotional, physiological and individual information. This suggests that they may serve as potentially useful indicators for inferring animal welfare. At the same time, automated methods for analysing and classifying sound have developed rapidly, particularly in the fields of ecology, conservation and sound scene classification. These methods are already used to automatically classify animal vocalizations, for example, in identifying animal species and estimating numbers of individuals. Despite this potential, they have not yet found widespread application in animal welfare monitoring. In this review, we first discuss current trends in sound analysis for ecology, conservation and sound classification. Following this, …

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Laser Microdissection Of Narrow Sheath Mutant Maize Uncovers Novel Gene Expression In The Shoot Apical Meristem, Xiaolan Zhang, Shahinez Madi, Lisa Borsuk, Dan Nettleton, Robert J. Elshire, Brent Buckner, Diane Janick-Buckner, Jon Beck, Marja Timmermans, Patrick S. Schnable, Michael J. Scanlon

Dan Nettleton

Microarrays enable comparative analyses of gene expression on a genomic scale, however these experiments frequently identify an abundance of differentially expressed genes such that it may be difficult to identify discrete functional networks that are hidden within large microarray datasets. Microarray analyses in which mutant organisms are compared to nonmutant siblings can be especially problematic when the gene of interest is expressed in relatively few cells. Here, we describe the use of laser microdissection microarray to perform transcriptional profiling of the maize shoot apical meristem (SAM), a ~100-μm pillar of organogenic cells that is required for leaf initiation. Microarray analyses …

Scanning Microarrays At Multiple Intensities Enhances Discovery Of Differentially Expressed Genes, David S. Skibbe, Xiujuan Wang, Xuefeng Zhao, Lisa A. Borsuk, Dan Nettleton, Patrick S. Schnable

Dan Nettleton

Motivation: Scanning parameters are often overlooked when optimizing microarray experiments. A scanning approach that extends the dynamic data range by acquiring multiple scans of different intensities has been developed.

Results: Data from each of three scan intensities (low, medium, high) were analyzed separately using multiple scan and linear regression approaches to identify and compare the sets of genes that exhibit statistically significant differential expression. In the multiple scan approach only one-third of the differentially expressed genes were shared among the three intensities, and each scan intensity identified unique sets of differentially expressed genes. The set of differentially expressed genes from …

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Analysis, Optimization, And Characterization Of Magnetic Photonic Crystal Structures And Thin-Film Material Layers, Mikhail Vasiliev, Kamal Alameh, Mohammad Nur-E-Alam

Mikhail Vasiliev

Microarray Gene Expression Profiles Of Fasting Induced Changes In Liver And Adipose Tissues Of Pigs Expressing The Melanocortin-4 Receptor D298n Variant, Sender Lkhagvadorj, Long Qu, Weiguo Cai, Oliver P. Coutoure, C. Richard Barb, Gary J. Hausman, Dan Nettleton, Lloyd L. Anderson, Jack C. M. Dekkers, Christopher K. Tuggle

Dan Nettleton

Transcriptional profiling coupled with blood metabolite analyses were used to identify porcine genes and pathways that respond to a fasting treatment or to a D298N missense mutation in the melanocortin-4 receptor (MC4R) gene. Gilts (12 homozygous for D298 and 12 homozygous for N298) were either fed ad libitum or fasted for 3 days. Fasting decreased body weight, backfat, and serum urea concentration and increased serum nonesterified fatty acid. In response to fasting, 7,029 genes in fat and 1,831 genes in liver were differentially expressed (DE). MC4R genotype did not significantly affect gene expression, body weight, backfat depth, or any measured …

Analysis Of Porcine Transcriptional Response To Salmonella Enterica Serovar Choleraesuis Suggests Novel Targets Of Nfkappab Are Activated In The Mesenteric Lymph Node, Yanfang Wang, Olivre P. Couture, Long Qu, Jolita J. Uthe, Shawn M. D. Bearson, Daniel Kuhar, Joan K. Lunney, Dan Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle

Dan Nettleton

Background: Specific knowledge of the molecular pathways controlling host-pathogen interactions can increase our understanding of immune response biology as well as provide targets for drug development and genetic improvement of disease resistance. Toward this end, we have characterized the porcine transcriptional response to Salmonella enterica serovar Choleraesuis (S. Choleraesuis), a Salmonella serovar that predominately colonizes swine, yet can cause serious infections in human patients. Affymetrix technology was used to screen for differentially expressed genes in pig mesenteric lymph nodes (MLN) responding to infection with S. Choleraesuis at acute (8 hours (h), 24 h and 48 h post-inoculation (pi)) and chronic …

Comparative Gene Expression Profiles Between Heterotic And Non-Heterotic Hybrids Of Tetraploid Medicago Sativa, Xuehui Li, Yanling Wei, Dan Nettleton, E. Charles Brummer

Dan Nettleton

Background: Heterosis, the superior performance of hybrids relative to parents, has clear agricultural value, but its genetic control is unknown. Our objective was to test the hypotheses that hybrids expressing heterosis for biomass yield would show more gene expression levels that were different from midparental values and outside the range of parental values than hybrids that do not exhibit heterosis.

Results: We tested these hypotheses in three Medicago sativa (alfalfa) genotypes and their three hybrids, two of which expressed heterosis for biomass yield and a third that did not, using Affymetrix M. truncatula GeneChip arrays. Alfalfa hybridized to approximately 47% …

A Survey Of Sierra Nevada Magmatism Using Great Valley Detrital Zircon Trace-Element Geochemistry: View From The Forearc, Kathleen D. Surpless, D. Clemens-Knott, A. P. Barth, M. Gevedon

Kathleen D. Surpless

The well-characterized Sierra Nevada magmatic arc offers an unparalleled opportunity to improve our understanding of continental arc magmatism, but present bedrock exposure provides an incomplete record that is dominated by Cretaceous plutons, making it challenging to decipher details of older magmatism and the dynamic interplay between plutonism and volcanism. Moreover, the forearc detrital record includes abundant zircon formed during apparent magmatic lulls, suggesting that understanding the long-term history of arc magmatism requires integrating plutonic, volcanic, and detrital records. We present trace-element geochemistry of detrital zircon grains from the Great Valley forearc basin to survey Sierra Nevadan arc magmatism through Mesozoic …

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Use Of Legume Green Manures As Nitrogen Sources For Corn Production, Matt Liebman, Rhonda L. Graef, Daniel Nettleton, Cynthia A. Cambardella

Dan Nettleton

Recent volatility in supplies and prices of natural gas and synthetic nitrogen (N) fertilizer suggests a need to develop and refine alternative strategies for supplying N to corn. In this study, conducted in north-eastern Iowa, we examined the use of red clover and alfalfa green manures as means of supplying N to a succeeding corn crop. Red clover intercropped with oat produced significantly more biomass and contained more N than alfalfa intercropped with oat. Tilling green manures in the fall or delaying tillage until the following spring did not have a consistent effect on green manure N content. Without N …

Distinct Peripheral Blood Rna Responses To Salmonella In Pigs Differing In Salmonella Shedding Levels: Intersection Of Ifng, Tlr And Mirna Pathways, Ting-Hua Huang, Jolita J. Uthe, Shawn M. D. Bearson, Cumhur Yusuf Demirkale, Dan Nettleton, Susan Knetter, Curtis Christian, Amanda E. Ramer-Tait, Michael J. Wannemeuhler, Christopher K. Tuggle

Dan Nettleton

Transcriptomic analysis of the response to bacterial pathogens has been reported for several species, yet few studies have investigated the transcriptional differences in whole blood in subjects that differ in their disease response phenotypes. Salmonella species infect many vertebrate species, and pigs colonized with Salmonella enterica serovar Typhimurium (ST) are usually asymptomatic, making detection of these Salmonella-carrier pigs difficult. The variable fecal shedding of Salmonella is an important cause of foodborne illness and zoonotic disease. To investigate gene pathways and biomarkers associated with the variance in Salmonellashedding following experimental inoculation, we initiated the first analysis of the whole …

Unique Genome-Wide Transcriptome Profiles Of Chicken Macrophages Exposed To Salmonella-Derived Endotoxin, Ceren Ciraci, Christopher K. Tuggle, Michael J. Wannemeuhler, Dan Nettleton, Susan J. Lamont

Dan Nettleton

Background: Macrophages play essential roles in both innate and adaptive immune responses. Bacteria require endotoxin, a complex lipopolysaccharide, for outer membrane permeability and the host interprets endotoxin as a signal to initiate an innate immune response. The focus of this study is kinetic and global transcriptional analysis of the chicken macrophage response to in vitro stimulation with endotoxin from Salmonella typhimurium-798.

Results: The 38535-probeset Affymetrix GeneChip Chicken Genome array was used to profile transcriptional response to endotoxin 1, 2, 4, and 8 hours post stimulation (hps). Using a maximum FDR (False Discovery Rate) of 0.05 to declare genes as differentially …

Complementation Contributes To Transcriptome Complexity In Maize (Zea Mays L.) Hybrids Relative To Their Inbred Parents, Anja Paschold, Yi Jia, Caroline Marcon, Steve Lund, Nick B. Larson, Cheng-Ting Yeh, Stephan Ossowski, Christa Lanz, Dan Nettleton, Patrick S. Schnable, Frank Hochholdinger

Dan Nettleton

Typically, F₁-hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study, the transcriptomes of the reciprocal maize (Zea mays L.) hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were surveyed in primary roots, early in the developmental manifestation of heterotic root traits. The application of statistical methods and a suitable experimental design established that 34,233 (i.e., 86%) of all high-confidence maize genes were expressed in at least one genotype. Nearly 70% of all expressed genes were differentially expressed between the two parents and 42%–55% …

The Urban Infrastructure For Sustainability: Learning From Kigali, Marwan Ghandour

Marwan Ghandour

Until 2013, when a new master plan for the city was approved, Kigali had very few urban regulations in place. Incremental constructions, usually associated with informal urbanization, were the norm rather than the exception. Most of the city fabric grew organically creating a unique configuration of urban adjacencies, which would be improbable for planners and designers to imagine. This configuration is particular to the geographic, economic and social conditions of the city as incremental urbanization slowly adjusted to the living conditions, through the actions of thousands of city residents over a long period of time. These actions were formed in …

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Hemilabile Bonding Of 1-Oxa-4,7-Dithiacyclononane In Cyclometallated Palladium(Ii) Complexes, Daron E. Janzen, Meaghan A. Bruening, A. A. Mamiya, Laura E. Driscoll, Demetrio A. De Silva Filho

Daron E Janzen, Ph.D.

The Birth Of A Forearc: The Basal Great Valley Group, California, Usa, D. A. Orme, Kathleen D. Surpless

Kathleen D. Surpless

The Great Valley basin of California (USA) is an archetypal forearc basin, yet the timing, structural style, and location of basin development remain controversial. Eighteen of 20 detrital zircon samples (3711 new U-Pb ages) from basal strata of the Great Valley forearc basin contain Cretaceous grains, with nine samples yielding statistically robust Cretaceous maximum depositional ages (MDAs), two with MDAs that overlap the Jurassic-Cretaceous boundary, suggesting earliest Cretaceous deposition, and nine with Jurassic MDAs consistent with latest Jurassic deposition. In addition, the pre-Mesozoic age populations of our samples are consistent with central North America sources and do not require a …

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