Coincidence between transcriptome analyses on different microarray platforms using a parametric framework

A parametric framework for the analysis of transcriptome data is demonstrated to yield coincident results when applied to data acquired using two different microarray platforms. Discrepancies among transcriptome studies are frequently reported, casting doubt on the reliability of collected data. The inconsistency among observations can be largely attributed to differences among the analytical frameworks employed for data analysis. The existing frameworks normalizes data against a standard determined from the data to be analyzed. In the present study, a parametric framework based on a strict model for normalization is applied to data acquired using an in-house printed chip and GeneChip. The framework is based on a common statistical characteristic of microarray data, and each data is normalized on the basis of a linear relationship with this model. In the proposed framework, the expressional changes observed and genes selected are coincident between platforms, achieving superior universality of data compared to other methods

Inherent-Structure Dynamics and Diffusion in Liquids

The self-diffusion constant D is expressed in terms of transitions among the local minima of the potential (inherent structure, IS) and their correlations. The formulae are evaluated and tested against simulation in the supercooled, unit-density Lennard-Jones liquid. The approximation of uncorrelated IS-transition (IST) vectors, D_{0}, greatly exceeds D in the upper temperature range, but merges with simulation at reduced T ~ 0.50. Since uncorrelated IST are associated with a hopping mechanism, the condition D ~ D_{0} provides a new way to identify the crossover to hopping. The results suggest that theories of diffusion in deeply supercooled liquids may be based on weakly correlated IST.Comment: submitted to PR

The Potential Energy Landscape and Mechanisms of Diffusion in Liquids

The mechanism of diffusion in supercooled liquids is investigated from the potential energy landscape point of view, with emphasis on the crossover from high- to low-T dynamics. Molecular dynamics simulations with a time dependent mapping to the associated local mininum or inherent structure (IS) are performed on unit-density Lennard-Jones (LJ). New dynamical quantities introduced include r2_{is}(t), the mean-square displacement (MSD) within a basin of attraction of an IS, R2(t), the MSD of the IS itself, and g_{loc}(t) the mean waiting time in a cooperative region. At intermediate T, r2_{is}(t) posesses an interval of linear t-dependence allowing calculation of an intrabasin diffusion constant D_{is}. Near T_{c} diffusion is intrabasin dominated with D = D_{is}. Below T_{c} the local waiting time tau_{loc} exceeds the time, tau_{pl}, needed for the system to explore the basin, indicating the action of barriers. The distinction between motion among the IS below T_{c} and saddle, or border dynamics above T_{c} is discussed.Comment: submitted to pr

Genetic Diversity, Inbreeding Level, and Genetic Load in Endangered Snub-Nosed Monkeys (Rhinopithecus)

The snub-nosed monkey genus (Rhinopithecus) comprises five closely related species (R. avunculus, R. bieti, R. brelichi, R. roxellana, and R. strykeri). All are among the world's rarest and most endangered primates. However, the genomic impact associated with their population decline remains unknown. We analyzed population genomic data of all five snub-nosed monkey species to assess their genetic diversity, inbreeding level, and genetic load. For R. roxellana, R. bieti, and R. strykeri, population size is positively correlated with genetic diversity and negatively correlated with levels of inbreeding. Other species, however, which possess small population sizes, such as R. brelichi and R. avunculus, show high levels of genetic diversity and low levels of genomic inbreeding. Similarly, in the three populations of R. roxellana, the Shennongjia population, which possesses the lowest population size, displays a higher level of genetic diversity and lower level of genomic inbreeding. These findings suggest that although R. brelichi and R. avunculus and the Shennongjia population might be at risk, it possess significant genetic diversity and could thus help strengthen their long-term survival potential. Intriguingly, R. roxellana with large population size possess high genetic diversity and low level of genetic load, but they show the highest recent inbreeding level compared with the other snub-nosed monkeys. This suggests that, despite its large population size, R. roxellana has likely been experiencing recent inbreeding, which has not yet affected its mutational load and fitness. Analyses of homozygous-derived deleterious mutations identified in all snub-nosed monkey species indicate that these mutations are affecting immune, especially in smaller population sizes, indicating that the long-term consequences of inbreeding may be resulting in an overall reduction of immune capability in the snub-nosed monkeys, which could provide a dramatic effect on their long-term survival prospects. Altogether, our study provides valuable information concerning the genomic impact of population decline of the snub-nosed monkeys. We revealed multiple counterintuitive and unexpected patterns of genetic diversity in small and large population, which will be essential for conservation management of these endangered species

Pennsylvania Folklife Vol. 31, No. 3

• Jamison City • Domestic Architecture in Lancaster County • Conversation with Marguerite de Angeli • Who Put the Turnip on the Grave? • Pennsylfawnisch Deitsch un Pfalzer: Dialect Comparisons Old and New • John Philip Boehm: Pioneer Pennsylvania Pastor • The Search for our German Ancestors • Aldes un Neieshttps://digitalcommons.ursinus.edu/pafolklifemag/1095/thumbnail.jp

Helminth Coinfection Does Not Affect Therapeutic Effect of a DNA Vaccine in Mice Harboring Tuberculosis

From 14 diseases considered by WHO as Neglected Tropical Diseases, four involve helminth infections, such as schistosomiasis and soil-transmitted helminthiasis. Toxocariasis is a soil-transmitted worm highly prevalent in many developing countries, while schistosomiasis causes an annual mortality of 14,000 deaths per year, with 200–300 million infected people and 10% at risk of infection worldwide. Additionally, tuberculosis (TB) remains one of the leading causes of morbidity and mortality in many settings, particularly in the world's poorest countries. Mycobacteria and helminths are co-endemic and induce opposing patterns of immune responses in the host, recognized as Th1 and Th2 respectively. These co-existing patterns could be associated with the failure of TB vaccines. In this sense, we investigated the inflammatory and immune response in a coinfection model with T. canis or S. mansoni and M. tuberculosis analyzing the effects of an immunotherapy that has previously shown efficacy in experimental TB. This immunotherapy is based on a DNA vaccine that codifies a mycobacterial heat shock protein (hsp65), which can prevent TB in a prophylactic and also therapeutic setting. In this work, we show that helminth coinfection does not abrogate the therapeutic effects of DNAhsp65 vaccine against TB

Evaluation of different soy protein concentrate sources on growth performance of weanling pigs

Three experiments were conducted using 486 weanling pigs (216 in Experiment 1; 210 in Experiment 2; 60 in Experiment 3) to determine the effects of different soy protein concentrate (SPC) sources on growth performance. Soy protein concentrate source 1 is dried with a torus disk following the concentration of soy proteins. This drying procedure will generate some degree of heat and possibly mechanical forces somewhat similar to extrusion processing (Soycomil P®, ADM). Soy protein concentrate source 2 is dried by a different process, and then it is moist extruded (Profine E, Central Soya). Therefore, the objective of our study was to determine the relative feeding value of the different SPC sources compared with a complex diet containing milk and other specialty proteins (no soy protein), or a diet containing 40% soybean meal. In Experiment 1, each SPC source (28.6%) replaced all the soybean meal (SBM) in the control diet on a lysine basis. Pigs fed the diet containing 40% SBM had similar performance to pigs fed the milk-protein based diet from d 0 to 14. Pigs fed either SPC source had lower ADG and ADFI compared to pigs fed either the diet containing 40% SBM or the milkprotein based diet. Pigs fed the diet containing 40% SBM and SPC from source 2 had better F/G than pigs fed the milk-protein based diet or SPC from source 1. In Experiment 2, either all or half of the soybean meal was replaced by the 28.6 or 14.3% SPC from source 1 and 2. From d 0 to 14 and d 0 to 28, an SPC source by level interaction was observed for ADG (P<0.01) and ADFI (P<0.07). Replacing soybean meal with SPC from source 1 did not influence pig performance. However, replacing soybean meal with SPC from source 2 resulted in a quadratic (P<0.05) improvement in ADG with performance being improved for the diet containing 14.3% SPC, but no benefit to replacing all the soybean meal with SPC. Replacing soybean meal with SPC from either source influenced feed efficiency in a quadratic (P<0.01) manner with feed efficiency being optimal for pigs consuming the diet with half the soybean meal replaced by SPC. Because replacing all of the soybean meal with SPC reduced ADFI in Experiments 1 and 2, we hypothesized that pigs may not prefer the taste of a diet with a high inclusion rate of SPC (28.6%). To test this theory, a 7-day preference test was conducted to determine feed intake of weanling pigs provided the option of consuming diets containing either 40% soybean meal or 28.6% SPC (from source 2). Average daily feed intake was 0.41 and 0.01 lb for the 40% soybean meal and 28.6% soy protein concentrate diets, respectively (P<0.0001). The poor intake of the SPC diet may indicate a palatability problem when high levels of SPC are included in the diet. Our results suggest replacing a portion of the soybean meal in the diet with SPC from source 2 improves ADG and feed efficiency; however, high levels (28.6%) of SPC should not be included in the diet

Stimulation of Na⁺/H⁺ Exchanger Isoform 1 Promotes Microglial Migration

Regulation of microglial migration is not well understood. In this study, we proposed that Na+/H+ exchanger isoform 1 (NHE-1) is important in microglial migration. NHE-1 protein was co-localized with cytoskeletal protein ezrin in lamellipodia of microglia and maintained its more alkaline intracellular pH (pHi). Chemoattractant bradykinin (BK) stimulated microglial migration by increasing lamellipodial area and protrusion rate, but reducing lamellipodial persistence time. Interestingly, blocking NHE-1 activity with its potent inhibitor HOE 642 not only acidified microglia, abolished the BK-triggered dynamic changes of lamellipodia, but also reduced microglial motility and microchemotaxis in response to BK. In addition, NHE-1 activation resulted in intracellular Na+ loading as well as intracellular Ca2+ elevation mediated by stimulating reverse mode operation of Na+/Ca2+ exchange (NCXrev). Taken together, our study shows that NHE-1 protein is abundantly expressed in microglial lamellipodia and maintains alkaline pHi in response to BK stimulation. In addition, NHE-1 and NCXrev play a concerted role in BK-induced microglial migration via Na+ and Ca2+ signaling. © 2013 Shi et al

Innate immunity and remodelling

A wide variety of cardiac disease states can induce remodelling and lead to the functional consequence of heart failure. These complex disease states involve a plethora of parallel signal transduction events, which may be associated with tissue injury or tissue repair. Innate immunity is activated in hearts injured in different ways, evident as cytokine release from the heart, activation of toll-like receptors involved in recognizing danger, and activation of the transcription factor nuclear factor kappa B. Nuclear factor kappa B regulates gene programmes involved in inflammation as well as the resolution of inflammation. The impact of this is an enigma; while cytokines, toll-like receptors, and nuclear factor kappa B appear to elicit myocardial protection in studies of preconditioning, the literature strongly indicates a detrimental role for activation of innate immunity in studies of acute ischaemia–reperfusion injury. The impact of activation of cardiac innate immunity on the long-term outcome in in vivo models of hypertrophy and remodelling is less clear, with conflicting results as to whether it is beneficial or detrimental. More research using genetically engineered mice as tools, different models of evoking remodelling, and long-term follow-up is required for us to conclude whether activation of the innate immune system is good, bad, or unimportant in chronic injury models

Scope and Mechanistic Study of the Coupling Reaction of α,β-Unsaturated Carbonyl Compounds with Alkenes: Uncovering Electronic Effects on Alkene Insertion vs Oxidative Coupling Pathways

The cationic ruthenium-hydride complex [(C6H6)(PCy3)(CO)RuH]+BF4– (1) was found to be a highly effective catalyst for the intermolecular conjugate addition of simple alkenes to α,β-unsaturated carbonyl compounds to give (Z)-selective tetrasubstituted olefin products. The analogous coupling reaction of cinnamides with electron-deficient olefins led to the oxidative coupling of two olefinic C–H bonds in forming (E)-selective diene products. The intramolecular version of the coupling reaction efficiently produced indene and bicyclic fulvene derivatives. The empirical rate law for the coupling reaction of ethyl cinnamate with propene was determined as follows: rate = k[1]1[propene]0[cinnamate]−1. A negligible deuterium kinetic isotope effect (kH/kD = 1.1 ± 0.1) was measured from both (E)-C6H5CH═C(CH3)CONHCH3 and (E)-C6H5CD═C(CH3)CONHCH3 with styrene. In contrast, a significant normal isotope effect (kH/kD = 1.7 ± 0.1) was observed from the reaction of (E)-C6H5CH═C(CH3)CONHCH3 with styrene and styrene-d8. A pronounced carbon isotope effect was measured from the coupling reaction of (E)-C6H5CH═CHCO2Et with propene (13C(recovered)/13C(virgin) at Cβ = 1.019(6)), while a negligible carbon isotope effect (13C(recovered)/13C(virgin) at Cβ = 0.999(4)) was obtained from the reaction of (E)-C6H5CH═C(CH3)CONHCH3 with styrene. Hammett plots from the correlation of para-substituted p-X-C6H4CH═CHCO2Et (X = OCH3, CH3, H, F, Cl, CO2Me, CF3) with propene and from the treatment of (E)-C6H5CH═CHCO2Et with a series of para-substituted styrenes p-Y-C6H4CH═CH2 (Y = OCH3, CH3, H, F, Cl, CF3) gave the positive slopes for both cases (ρ = +1.1 ± 0.1 and +1.5 ± 0.1, respectively). Eyring analysis of the coupling reaction led to the thermodynamic parameters, ΔH⧧ = 20 ± 2 kcal mol–1 and ΔS⧧ = −42 ± 5 eu. Two separate mechanistic pathways for the coupling reaction have been proposed on the basis of these kinetic and spectroscopic studies