bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Endogenously Anti-Inflammatory Role for Methylation in Mucosal Inflammation Identified through Metabolite Profiling
Authors: Kominsky Douglas J. , Keely Simon , MacManus Christopher F. , Glover Louise E. , Scully Melanie , Collins Colm B. , Bowers Brittelle E. , Campbell Eric L. , Colgan Sean P. 
Published: April 2011

Abstract
Tissues of the mucosa are lined by an epithelium that provides barrier and transport functions. It is now appreciated that inflammatory responses in inflammatory bowel diseases are accompanied by striking shifts in tissue metabolism. In this paper, we examined global metabolic consequences of mucosal inflammation using both in vitro and in vivo models of disease. Initial analysis of the metabolic signature elicited by inflammation in epithelial models and in colonic tissue isolated from murine colitis demonstrated that levels of specific metabolites associated with cellular methylation reactions are significantly altered by model inflammatory systems. Furthermore, expression of enzymes central to all cellular methylation, S-adenosylmethionine synthetase and S-adenosylhomocysteine hydrolase, are increased in response to inflammation. Subsequent studies showed that DNA methylation is substantially increased during inflammation and that epithelial NF-κB activity is significantly inhibited following treatment with a reversible S-adenosylhomocysteine hydrolase inhibitor, DZ2002. Finally, these studies demonstrated that inhibition of cellular methylation in a murine model of colitis results in disease exacerbation while folate supplementation to promote methylation partially ameliorates the severity of murine colitis. Taken together, these results identify a global change in methylation, which during inflammation, translates to an overall protective role in mucosal epithelia.
The effect of transport time from the assembly yard to the abattoir and resting time at the abattoir on pork quality
Authors: Fortin André 
Published: April 2011

Over 1900 pigs, supplied by two producers, were first delivered to an assembly yard and then transported to a commercial abattoir. Transport times were 50 min and 2 h, and resting periods at the abattoir were < 30 min, 3 h and 6 h. Times were chosen to represent normal practices in Ontario. The colour and structure of the boneless loins were as sessed subjectively 24 h postmortem. The shorter (50 min) transport time was associated with the highest (P ≤ 0.05) incidence of pale and soft/exudative loins. A longer transport time reduced the incidence of pale and soft/exudative loins; it also increased (P ≤ 0.05) the incidence of dark and firm/dry loins; particularly during winter. A resting period of < 30 min resulted in the highest (P ≤ 0.01) incidence of pale and soft/exudative loins. A 3 h resting period significantly improved (P ≤ 0.01) quality by reducing the incidence of pale loins and soft/exudative loins. Extending the resting period from 3 h to 6 h provided inconsistent improvements in quality due to interactions with season (P ≤ 0.05) and producer/management (P ≤ 0.05). Considering transport time and resting period together further highlighted the importance of resting period at the abattoir. Three h resting period always improved (P ≤ 0.05) quality regardless of transport time, season or producer. Key words: Transport, resting period, pork quality, pale, soft and exudative, DFD
Measurements of enzyme response with hulless barley-based diets full-fed to Leghorn and broiler chicks or restricted-fed broiler chicks
Authors: Scott T. A. , Leslie M. A. , Karimi A. 
Published: April 2011

Broiler chicks fed diets high in soluble non-starch polysaccharides (NSP; e.g., wheat- and/or barley-based diets) have a higher capacity to ingest, digest and absorb nutrients when diets are supplemented with appropriate NSP enzymes. However, this same enzyme response is typically reduced or non-significant in older birds, Leghorn chicks and turkey poults. We hypothesise that the enzyme response in the latter classes of poultry is reduced because feed intake is lower in comparison to feed intake by broilers. In the present study, the hypothesis that restricted feeding of broilers would reduce the enzyme response typically observed in full-fed broilers was tested. Two experiments were conducted to determine the feeding value of hulless barley supplemented or not supplemented with enzyme (Avizyme 1100, Finnfeeds Int, UK). In Study 1, eight sources of hulless barley were included at 80% in each diet and fed to four groups of six male broilers or Leghorn chicks from 4 to 17 d of age. The response to enzyme in hulless barley-based diets by broilers was approximately twofold that of Leghorns for growth and feed intake. The Leghorns had higher digesta viscosity than broilers, although the relative drop in digesta viscosity with enzyme supplementation was equal. In a second study (Study 2) broiler chicks were fed one of four diets (two hulless barley cultivars with or without enzyme) at three feed allotment levels (ad libitum, R1 and R2) from 4 to 21 d of age. The R1 and R2 feed allotments were pre-determined fixed daily feed amounts. Actual feed restriction in the R1 group was only achieved for diets with, but not without, an enzyme. At the lowest feed allotment (R2) actual feed intake of diets with or without enzyme were lower than that recorded for ad libitum fed birds. Study 2 demonstrated that restricted-fed broilers had a lower growth response to enzyme supplementation compared to birds allowed ad libitum intake, in part due to improved retention of energy, either directly in response to feed restriction or because digesta viscosity in diets without enzyme was lowered. Although digesta viscosity of restricted-fed birds was lower, it is still high enough to be considered problematic. In determining feeding value of cereal grains or supplements such as enzymes, especially those directed for use with broilers, it is imperative that a broiler chick bioassay be used and that they have ad libitum access to the diets. Key words: Enzyme, hulless barley, viscosity, feed intake
Performance of laying hens fed wheat, wheat-barley or wheat-barley-wheat bran based diets supplemented with xylanase
Authors: Mathlouthi N. , Larbier M. , Mohamed M. A. , Lessire M. 
Published: April 2011

Two experiments were conducted to study the response of laying hens to a commercial enzyme preparation (Safizyme XP20) containing 70 000 IU g-1 xylanase. In the first experiment, 270 laying hens (ISA Brown), aged 28 wk, were fed basal diets of wheat (W), wheat-barley (WB) or wheat-barley and wheat bran (WBB) without xylanase, or supplemented with 1400 IU xylanase kg-1 in 3 × 2 factorial arrangement. In the second experiment, 180 ISA Brown laying hens, aged 28 wk, were assigned to 2 × 2 factorial arrangement and fed wheat-based diets containing 2753 or 2653 kcal metabolizable energy (ME) kg-1 without xylanase, or supplemented with 1400 IU xylanase kg-1. Egg production (% hen-day), egg weight, egg mass, feed conversion ratio and changes in body weight were recorded for 12 wk. The effects of xylanase on true metabolizable energy (TME) values of wheat, barley and wheat bran were determined using roosters. Layers fed W-, WB- or WBB-based diets had similar egg mass. The feed conversion ratio of layers fed the WBB-based diet was better (P ≤ 0.05) than that of the other groups. Xylanase improved (P ≤ 0.05) egg mass of layers fed W- or WB-based diets, but it did not affect the performance of hens fed the WBB-based diet. Low dietary ME significantly (P ≤ 0.05) reduced the performance of laying hens. Xylanase supplementation improved (P ≤ 0.05) egg production, egg mass and feed conversion ratio of layers fed the low energy diet. It did improve the feed conversion ratio of layers fed the high-energy diet. Addition of 1400 IU xylanase kg-1 to the low-energy diet was equivalent to an increase of at least 100 kcal ME kg-1. Xylanase increased (P ≤ 0.05) the TME values by 5.2 and 2.44% for wheat and barley, respectively, and did not affect the TME value of wheat bran. Key words: Xylanase, hens, laying, wheat, barley, wheat bran, metabolizable energy.
Challenges related to soil biodiversity research in agroecosystems - Issues within the context of scale of observation
Authors: Fox C. A. , MacDonald K. B. 
Published: April 2011

Soil biodiversity, the study of the variety of life in the soil, has received increasing attention as an outcome of recent national and international initiatives, such as the Convention on Biological Diversity, and various programs related to sustainable development of agroecosystems. The broad objectives of this paper are to set the stage for a “state of the art” review of soil biodiversity research in Canadian agricultural systems, to highlight the relevance of soil biodiversity studies at various scales of observation, to acknowledge the importance of soil biodiversity to the soil system with respect to soil functions, and processes and to suggest research challenges and opportunities. Study scale is of critical importance as it determines both the kind of soil biodiversity information and the feasible level of detail (spatially and temporally). At all scales from global to national to regional to landscape to ecosystems ranging to even fine scales of habitat niches at soil particle level, soil biota respond to the physical, chemical and biological constraints of their environment as mediated by environmental and anthropogenic influences. For example, at the landscape level, there exists a mosaic of ecosystems that can be characterized as a continuum ranging from unmanaged (natural), uncontrolled systems regulated primarily by environmental influences to managed, controlled systems regulated primarily by anthropogenic influences. In agroecosystems, soil biota contribute to the decomposition of crop residues and nutrient cycling, soil aggregation and water infiltration, suppression of soil-borne diseases and pests, and detoxification of chemicals. The intensity and duration of environmental and anthropogenic influences on these soil biota will affect their spatial and temporal distribution within this continuum of ecosystems occurring in the landscape and thereby also affect the extent of their capability for contributing towards soil functions and processes. Within this spatial and temporal context, research challenges are discussed. Key words: Soil biodiversity, scale of observation, agroecosystems, soil quality
Growing season nitrogen dynamics in manured soils in south coastal British Columbia: Implications for a soil nitrate test for silage corn
Authors: Zebarth B. J. , Paul J. W. 
Published: April 2011

Spring soil nitrate and ammonium dynamics in south coastal British Columbia soils were examined with respect to the potential to develop a soil nitrate test for silage corn (Zea mays, L.). Soil nitrate and ammonium contents were measured to 90 cm depth in two soils from April to July of two growing seasons. Treatments included a control, spring application of either 300 or 600 kg total N ha−1 as liquid dairy manure, or 200 kg N ha−1 as inorganic fertilizer. Significant amounts of ammonium were present until late May following manure and until mid-June following fertilizer application, requiring simultaneous determination of both nitrate and ammonium concentrations to assess soil inorganic N contents during this period. Most of the changes in soil nitrate over time occurred in the top 30 cm, suggesting that sampling to 30 cm depth would be sufficient in most cases for a soil nitrate test in this region. Most of the increase in soil inorganic N associated with the spring application of manure occurred by 1 June. A soil nitrate test in early to mid-June when the corn is at the six leaf stage appeared to be most suitable for use in south coastal British Columbia to determine if additional fertilizer N is required. A sample taken at this time will measure soil nitrate contents just before the period of rapid corn N uptake, after most of the additional inorganic N associated with spring manure application is already present in the soil as nitrate, and after nitrification of the manure ammonium has occurred. Key words: N recovery, preplant nitrate test, pre-sidedress soil nitrate test
An artificial neural network to estimate soil temperature
Authors: Yang Chun-Chieh , Prasher Shiv O. , Mehuys Guy R. 
Published: April 2011

This study was undertaken to develop an artificial neural network (ANN) model for transient simulation of soil temperature at different depths in the profile. The capability of ANN models to simulate the variation of temperature in soils was investigated by considering readily available meteorologic parameters. The ANN model was constructed by using five years of meteorologic data, measured at a weather station at the Central Experimental Farm in Ottawa, Ontario, Canada. The model inputs consisted of daily rainfall, potential evapotranspiration, and the day of the year. The model outputs were daily soil temperatures at the depths of 100, 500 and 1500 mm. The estimated values were found to be close to the measured values, as shown by a root-mean-square error ranging from 0.59 to 1.82 °C, a standard deviation of errors from 0.61 to 1.81 °C, and a coefficient of determination from 0.937 to 0.987. Therefore, it is concluded that ANN models can be used to estimate soil temperature by considering routinely measured meteorologic parameters. In addition, the ANN model executes faster than a comparable conceptual simulation model by several orders of magnitude. Key words: Artificial neural networks, soil temperature, precipitation, potential evapotranspiration
Evaluating the suitability of coupled biophysical models for fishery management
Authors: Hinrichsen Hans-Harald , Dickey-Collas Mark , Huret Martin , Peck Myron A. , Vikebø Frode B. 
Published: April 2011

Abstract
Hinrichsen, H-H., Dickey-Collas, M., Huret, M., Peck, M. A., and Vikebø, F. B. 2011. Evaluating the suitability of coupled biophysical models for fishery management. – ICES Journal of Marine Science, 68: 1478–1487. The potential role of coupled biophysical models in enhancing the conservation, management, and recovery of fish stocks is assessed, with emphasis on anchovy, cod, herring, and sprat in European waters. The assessment indicates that coupled biophysical models are currently capable of simulating transport patterns, along with temperature and prey fields within marine ecosystems; they therefore provide insight into the variability of early-life-stage dynamics and connectivity within stocks. Moreover, the influence of environmental variability on potential recruitment success may be discerned from model hindcasts. Based on case studies, biophysical modelling results are shown to be capable of shedding light on whether stock management frameworks need re-evaluation. Hence, key modelling products were identified that will contribute to the development of viable stock recovery plans and management strategies. The study also suggests that approaches combining observation, process knowledge, and numerical modelling could be a promising way forward in understanding and simulating the dynamics of marine fish populations.
PERSISTENT TAPETAL CELL1Encodes a PHD-Finger Protein That Is Required for Tapetal Cell Death and Pollen Development in Rice
Authors: Li Hui , Yuan Zheng , Vizcay-Barrena Gema , Yang Caiyun , Liang Wanqi , Zong Jie , Wilson Zoe A. , Zhang Dabing 
Published: April 2011

AbstractIn higher plants, timely degradation of tapetal cells, the innermost sporophytic cells of the anther wall layer, is a prerequisite for the development of viable pollen grains. However, relatively little is known about the mechanism underlying programmed tapetal cell development and degradation. Here, we report a key regulator in monocot rice (Oryza sativa), PERSISTANT TAPETAL CELL1 (PTC1), which controls programmed tapetal development and functional pollen formation. The evolutionary significance of PTC1 was revealed by partial genetic complementation of the homologous mutation MALE STERILITY1 (MS1) in the dicot Arabidopsis (Arabidopsis thaliana). PTC1 encodes a PHD-finger (for plant homeodomain) protein, which is expressed specifically in tapetal cells and microspores during anther development in stages 8 and 9, when the wild-type tapetal cells initiate a typical apoptosis-like cell death. Even though ptc1 mutants show phenotypic similarity to ms1 in a lack of tapetal DNA fragmentation, delayed tapetal degeneration, as well as abnormal pollen wall formation and aborted microspore development, the ptc1 mutant displays a previously unreported phenotype of uncontrolled tapetal proliferation and subsequent commencement of necrosis-like tapetal death. Microarray analysis indicated that 2,417 tapetum- and microspore-expressed genes, which are principally associated with tapetal development, degeneration, and pollen wall formation, had changed expression in ptc1 anthers. Moreover, the regulatory role of PTC1 in anther development was revealed by comparison with MS1 and other rice anther developmental regulators. These findings suggest a diversified and conserved switch of PTC1/MS1 in regulating programmed male reproductive development in both dicots and monocots, which provides new insights in plant anther development.
The Influence of Low Oxygen on Macrophage Response to Leishmania Infection
Authors: Degrossoli A. , Arrais‐Silva W. W. , Colhone M. C. , Gadelha F. R. , Joazeiro P. P. , Giorgio S. 
Published: April 2011

AbstractHypoxia (low oxygen tension) is a common feature of inflamed and infected tissues. The influence of hypoxia on macrophage responses to micro‐organisms has only recently been studied. This study demonstrates that hypoxia induced macrophages to control Leishmania amazonensis, an intracellular parasite that causes cutaneous and cutaneous metastatic lesions. The mechanisms that contribute to the control of macrophages against L. amazonensis infection under a hypoxic microenvironment are not known. Nitric oxide, TNF‐α, IL‐10 or IL‐12 is not responsible for the decrease in parasitism under hypoxia. Live L. amazonensis entry or exocytosis of internalized particles as well as energetic metabolism was not impaired in infected macrophages; no apoptosis‐like death was detected in intracellular parasites. Reactive oxygen species (ROS) is likely to be involved, because treatment with antioxidants N‐acetylcysteine (NAC) and ebselen inhibits the leishmanicidal effect of macrophages under hypoxia. Leishmania amazonensis infection induces macrophages to express hypoxia‐inducible factor‐1 (HIF‐1α) and ‐2 (HIF‐2α). Data indicate that hypoxia affects the microbial activities and protein expression of macrophages leading to a different phenotype from that of the normoxic counterpart and that it plays a role in modulating Leishmania infection.
Of Stem Cells and Germ Cells
Authors: Roelen BAJ 
Published: April 2011

ContentsStem cells have an intrinsic capacity to self‐renew and can differentiate to at least one specialized cell type. Different types of stem cells exist that can be culturedin vitro. The identity of the stem cells is marked by their origin and differentiation potential. Germ cells have similarities with pluripotent stem cells but are of a special order: They do not self‐renew and are already differentiated, but they have the capacity to form a complete new organism after fertilization. This review focuses on pluripotent stem cells and discusses possibilities of generating pluripotent stem cells from germ cell precursors and possibilities of generating germ cells from stem cells. As it accompanies a plenary lecture at the 15th annual ESDAR Conference 2011, the overview is focused on stem cells from farm animal species and on results from my own research group.
Genomic Analysis of Xanthomonas oryzae Isolates from Rice Grown in the United States Reveals Substantial Divergence from Known X. oryzae Pathovars
Authors: Triplett L. R. , Hamilton J. P. , Buell C. R. , Tisserat N. A. , Verdier V. , Zink F. , Leach J. E. 
Published: April 2011

ABSTRACT

The species
Xanthomonas oryzae
is comprised of two designated pathovars, both of which cause economically significant diseases of rice in Asia and Africa. Although
X. oryzae
is not considered endemic in the United States, an
X. oryzae
-like bacterium was isolated from U.S. rice and southern cutgrass in the late 1980s. The U.S. strains were weakly pathogenic and genetically distinct from characterized
X. oryzae
pathovars. In the current study, a draft genome sequence from two U.S.
Xanthomonas
strains revealed that the U.S. strains form a novel clade within the
X. oryzae
species, distinct from all strains known to cause significant yield loss. Comparative genome analysis revealed several putative gene clusters specific to the U.S. strains and supported previous reports that the U.S. strains lack transcriptional activator-like (TAL) effectors. In addition to phylogenetic and comparative analyses, the genome sequence was used for designing robust U.S. strain-specific primers, demonstrating the usefulness of a draft genome sequence in the rapid development of diagnostic tools.
Genotype Distribution of Human Sapoviruses in Wastewater in Japan
Authors: Kitajima Masaaki , Haramoto Eiji , Phanuwan Chanetta , Katayama Hiroyuki 
Published: April 2011

ABSTRACT
Human sapovirus sequences were identified in 12 (100%) influent and 7 (58%) effluent wastewater samples collected once a month for a year. The strains were characterized based on their partial capsid gene sequences and classified into 10 genotypes, demonstrating that genetically diverse sapovirus strains infect humans in the study area.
Continuous Monitoring of Ammonia Removal Activity and Observation of Morphology of Microbial Complexes in a Microdevice
Authors: Toda Kensuke , Yawata Yutaka , Setoyama Erika , Fukuda Junji , Nomura Nobuhiko , Suzuki Hiroaki 
Published: April 2011

ABSTRACT

Continuous monitoring of ammonia removal by microbial complexes and observation of their morphology were carried out using a microdevice. Consumption of NH
4
+
ions by active sludge could clearly be recorded over 48 h. Aggregation of the sludge could be observed in parallel by using confocal reflection microscopy.