Performance of positive pressure fan-pad cooling system and cooling load model for Chinese solar greenhouse

Year-round and efficient production for crop products of high yield, quality and cleanliness is the development trend of the Chinese solar greenhouse (CSG). However, this is limited by unfavorable climate conditions inside the CSG, such as high air temperature in warm seasons. The fan-pad cooling system, normally adopting negative pressure ventilation, has been widely used for greenhouse cultivation. But it generates a large air temperature gradient in greenhouse, limits the greenhouse dimensions. Above deficiencies are more serious in the CSG. Because CSG always has a long distance between the sidewalls, fans and gaskets are installed separately on the sidewalls. In order to overcome the limitations of negative fan-pad cooling system and improve ability of the CSG in coping with high temperature, a positive pressure fan-pad cooling system (PPFPCS) was designed in this study. By using this system, the cold and humid air enters the CSG from bottom of south roof, and then hot air leaves the CSG through roof vents. Performance of the PPFPCS was tested in a CSG without crops in Beijing area during summer. Results showed that in typical summer hot days, the PPFPCS cooperating with external shading net could decrease mean air temperature of the CSG experimental area to 30.7-33.4 ℃, which was lower than that in the CSG contrast area using natural ventilation combination with external shading net by 5.4-11.1 ℃. Air temperature of the CSG experimental area was also lower than that outside the CSG with a temperature difference of 2.4-5.4 ℃. Nevertheless, both natural and mechanical ventilations were tested to have limited cooling capacity to meet climate requirement for CSG cultivation. The PPFPCS could also decrease the CSG air temperature at night, but had a poorer performance in comparison with daytime cooling due to the smaller vapor pressure deficit (VPD). The contrast area of CSG encountered an extreme low air humidity state with mean VPD of 3.4-6.1 kPa. PPFPCS could effectively alleviate low humidity stress: the average relative humidity in CSG experimental area was between 49.8% and 62.3%, which was 13.6% - 21.2% higher than that in CSG control area and 13.6%-24.6% higher than that in outdoor area. Wind velocity inside the CSG experimental area ranged from 0.35 to 1 m/s, which indicated a relative uniform air flow distribution. Cooling efficiency of the PPFPCS was about 91%, which was over 10 percentage points higher than that of the traditional negative pressure fan-pad cooling system. Low temperature of the PPFPCS circling water contributed to the high cooling efficiency. Average water consumption rate of the PPFPCS used for CSG cooling was 0.035-0.079 g/(m2·s) during the test. It had a positive linear correlation with VPD of outdoor air, that is drier outdoor air anticipates larger water consumption and better cooling performance. Both cooling load model of the CSG and selection method for fan-pad cooling system were derived. Cooling load model is the basis for capacity calculation of cooling equipment to be installed. Cooling load of the CSG in summer was 299.1 W/m2. Contribution ratios of convective heat transfer between north wall and indoor air, convective heat transfer between greenhouse floor with indoor air, hot air infiltration, as well as heat transfer between indoor and outdoor air though south roof, north roof and side walls were 11.0%, 73.3%, 1.3% and 14.4%, respectively. The maximum specific ventilation rate of the PPFPCS used for CSG cooling was recommended to be 0.067 m/s. This study can provide technical support for the application of PPFPCS in CSG cultivation and provide theoretical basis for the climate control of CSG production in summer. 摘 要：负压湿帘风机降温被广泛应用于温室生产中，但存在降温均匀性差、限制温室长度及对温室密闭性要求高等不 足。为克服负压湿帘风机降温的局限性，提高日光温室降温能力，该研究设计了日光温室正压湿帘冷风降温系统，其气 流组织方式为湿冷空气从南屋面底部进入日光温室，热空气由顶开窗排出室外。在北京地区无作物的日光温室对系统夏 季降温增湿效果及性能进行试验，试验结果表明：在典型夏季高温白天，正压湿帘冷风降温系统配合遮阳网可将日光温 室试验区内平均气温控制在 30.7～33.4 ℃，比采用自然通风配合遮阳网的对照区低 5.4～11.1 ℃，比室外低 2.4～5.4 ℃， 降温效果良好；夜间系统对温室降温幅度减小。该系统可有效缓解低湿胁迫，日光温室试验区空气平均相对湿度为49.8%～ 62.3%，比对照区及室外分别高 13.6%～21.2%和 13.6%～24.6%。室内风速 0.35～1 m/s，气流分布差异性较小。试验条件 下，正压湿帘冷风降温系统的平均降温效率为91%，比传统的负压湿帘风机高10个百分点以上；实际平均耗水量为0.035～ 0.079 g/(m2 ·s)，且耗水量与室外空气水蒸气饱和压差（VPD，vapor pressure deficit）呈正相关（P<0.01，r=0.64）。同时， 研究构建了日光温室冷负荷计算模型及湿帘冷风降温设备合理选型方法，其中冷负荷模型是降温设备选型的基础，普遍 适用于各种日光温室降温方法的研究。计算得到日光温室夏季降温冷负荷为 299.1 W/m2，应安装的正压湿帘冷风降温系 统最大比通风量为 0.067 m/s。该研究为日光温室正压湿帘冷风降温方法的工程应用提供了技术参考，为日光温室安全越 夏生产环境控制提供了理论基础。 关键词：温室；温度；模型；日光温室；正压通风；湿帘风机；降温；冷负

Significance Analysis of Time Course Microarray Experiments

Characterizing the genome-wide dynamic regulation of gene expression is important and will be of much interest in the future. However, there is currently no established method for identifying differentially expressed genes in a time course study. Here we propose a significance method for analyzing time course microarray studies that can be applied to the typical types of comparisons and sampling schemes. This method is applied to two studies on humans. In one study, genes are identified that show differential expression over time in response to in vivo endotoxin administration. Using our method 7409 genes are called significant at a 1% FDR level, whereas several existing approaches fail to identify any genes. In another study, 417 genes are identified at a 10% FDR level that show expression changing with age in the kidney cortex. Here it is also shown that as many as 47% of the genes change with age in a manner more complex than simple exponential growth or decay. The methodology proposed here has been implemented in the freely distributed and open-source EDGE software package

Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes

<p>Abstract</p> <p>Background</p> <p>The GeneChip^®<it>Medicago </it>Genome Array, developed for <it>Medicago truncatula</it>, is a suitable platform for transcript profiling in tetraploid alfalfa [<it>Medicago sativa </it>(L.) subsp. <it>sativa</it>]. However, previous research involving cross-species hybridization (CSH) has shown that sequence variation between two species can bias transcript profiling by decreasing sensitivity (number of expressed genes detected) and the accuracy of measuring fold-differences in gene expression.</p> <p>Results</p> <p>Transcript profiling using the <it>Medicago </it>GeneChip^®was conducted with elongating stem (ES) and post-elongation stem (PES) internodes from alfalfa genotypes 252 and 1283 that differ in stem cell wall concentrations of cellulose and lignin. A protocol was developed that masked probes targeting inter-species variable (ISV) regions of alfalfa transcripts. A probe signal intensity threshold was selected that optimized both sensitivity and accuracy. After masking for both ISV regions and previously identified single-feature polymorphisms (SFPs), the number of differentially expressed genes between the two genotypes in both ES and PES internodes was approximately 2-fold greater than the number detected prior to masking. Regulatory genes, including transcription factor and receptor kinase genes that may play a role in development of secondary xylem, were significantly over-represented among genes up-regulated in 252 PES internodes compared to 1283 PES internodes. Several cell wall-related genes were also up-regulated in genotype 252 PES internodes. Real-time quantitative RT-PCR of differentially expressed regulatory and cell wall-related genes demonstrated increased sensitivity and accuracy after masking for both ISV regions and SFPs. Over 1,000 genes that were differentially expressed in ES and PES internodes of genotypes 252 and 1283 were mapped onto putative orthologous loci on <it>M. truncatula </it>chromosomes. Clustering simulation analysis of the differentially expressed genes suggested co-expression of some neighbouring genes on <it>Medicago </it>chromosomes.</p> <p>Conclusions</p> <p>The problems associated with transcript profiling in alfalfa stems using the <it>Medicago </it>GeneChip as a CSH platform were mitigated by masking probes targeting ISV regions and SFPs. Using this masking protocol resulted in the identification of numerous candidate genes that may contribute to differences in cell wall concentration and composition of stems of two alfalfa genotypes.</p

Association of Genetic Variants of Melatonin Receptor 1B with Gestational Plasma Glucose Level and Risk of Glucose Intolerance in Pregnant Chinese Women

BACKGROUND: This study aimed to explore the association of MTNR1B genetic variants with gestational plasma glucose homeostasis in pregnant Chinese women. METHODS: A total of 1,985 pregnant Han Chinese women were recruited and evaluated for gestational glucose tolerance status with a two-step approach. The four MTNR1B variants rs10830963, rs1387153, rs1447352, and rs2166706 which had been reported to associate with glucose levels in general non-pregnant populations, were genotyped in these women. Using an additive model adjusted for age and body mass index (BMI), association of these variants with gestational fasting and postprandial plasma glucose (FPG and PPG) levels were analyzed by multiple linear regression; relative risk of developing gestational glucose intolerance was calculated by logistic regression. Hardy-Weinberg Equilibrium was tested by Chi-square and linkage disequilibrium (LD) between these variants was estimated by measures of D' and r(2). RESULTS: In the pregnant Chinese women, the MTNR1B variant rs10830963, rs1387153, rs2166706 and rs1447352 were shown to be associated with the increased 1 hour PPG level (p=8.04 × 10(-10), 5.49 × 10(-6), 1.89 × 10(-5) and 0.02, respectively). The alleles were also shown to be associated with gestational glucose intolerance with odds ratios (OR) of 1.64 (p=8.03 × 10(-11)), 1.43 (p=1.94 × 10(-6)), 1.38 (p=1.63 × 10(-5)) and 1.24 (p=0.007), respectively. MTNR1B rs1387153, rs2166706 were shown to be associated with gestational FPG levels (p=0.04). Our data also suggested that, the LD pattern of these variants in the studied women conformed to that in the general populations: rs1387153 and rs2166706 were in high LD, they linked moderately with rs10830963, but might not linked with rs1447352;rs10830963 might not link with rs1447352, either. In addition, the MTNR1B variants were not found to be associated with any other traits tested. CONCLUSIONS: The MTNR1B is likely to be involved in the regulation of glucose homeostasis during pregnancy

Parallel multiplicity and error discovery rate (EDR) in microarray experiments

<p>Abstract</p> <p>Background</p> <p>In microarray gene expression profiling experiments, differentially expressed genes (DEGs) are detected from among tens of thousands of genes on an array using statistical tests. It is important to control the number of false positives or errors that are present in the resultant DEG list. To date, more than 20 different multiple test methods have been reported that compute overall Type I error rates in microarray experiments. However, these methods share the following dilemma: they have low power in cases where only a small number of DEGs exist among a large number of total genes on the array.</p> <p>Results</p> <p>This study contrasts parallel multiplicity of objectively related tests against the traditional simultaneousness of subjectively related tests and proposes a new assessment called the Error Discovery Rate (EDR) for evaluating multiple test comparisons in microarray experiments. Parallel multiple tests use only the negative genes that parallel the positive genes to control the error rate; while simultaneous multiple tests use the total unchanged gene number for error estimates. Here, we demonstrate that the EDR method exhibits improved performance over other methods in specificity and sensitivity in testing expression data sets with sequence digital expression confirmation, in examining simulation data, as well as for three experimental data sets that vary in the proportion of DEGs. The EDR method overcomes a common problem of previous multiple test procedures, namely that the Type I error rate detection power is low when the total gene number used is large but the DEG number is small.</p> <p>Conclusions</p> <p>Microarrays are extensively used to address many research questions. However, there is potential to improve the sensitivity and specificity of microarray data analysis by developing improved multiple test comparisons. This study proposes a new view of multiplicity in microarray experiments and the EDR provides an alternative multiple test method for Type I error control in microarray experiments.</p

Involvement of Skeletal Muscle Gene Regulatory Network in Susceptibility to Wound Infection Following Trauma

Despite recent advances in our understanding the pathophysiology of trauma, the basis of the predisposition of trauma patients to infection remains unclear. A Drosophila melanogaster/Pseudomonas aeruginosa injury and infection model was used to identify host genetic components that contribute to the hyper-susceptibility to infection that follows severe trauma. We show that P. aeruginosa compromises skeletal muscle gene (SMG) expression at the injury site to promote infection. We demonstrate that activation of SMG structural components is under the control of cJun-N-terminal Kinase (JNK) Kinase, Hemipterous (Hep), and activation of this pathway promotes local resistance to P. aeruginosa in flies and mice. Our study links SMG expression and function to increased susceptibility to infection, and suggests that P. aeruginosa affects SMG homeostasis locally by restricting SMG expression in injured skeletal muscle tissue. Local potentiation of these host responses, and/or inhibition of their suppression by virulent P. aeruginosa cells, could lead to novel therapies that prevent or treat deleterious and potentially fatal infections in severely injured individuals

Integrative Analysis of the Mitochondrial Proteome in Yeast

In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans

A genomic storm in critically injured humans

Critical injury in humans induces a genomic storm with simultaneous changes in expression of innate and adaptive immunity genes

SUMOylation Represses Nanog Expression via Modulating Transcription Factors Oct4 and Sox2

Nanog is a pivotal transcription factor in embryonic stem (ES) cells and is essential for maintaining the pluripotency and self-renewal of ES cells. SUMOylation has been proved to regulate several stem cell markers' function, such as Oct4 and Sox2. Nanog is strictly regulated by Oct4/Sox2 heterodimer. However, the direct effects of SUMOylation on Nanog expression remain unclear. In this study, we reported that SUMOylation repressed Nanog expression. Depletion of Sumo1 or its conjugating enzyme Ubc9 increased the expression of Nanog, while high SUMOylation reduced its expression. Interestingly, we found that SUMOylation of Oct4 and Sox2 regulated Nanog in an opposing manner. SUMOylation of Oct4 enhanced Nanog expression, while SUMOylated Sox2 inhibited its expression. Moreover, SUMOylation of Oct4 by Pias2 or Sox2 by Pias3 impaired the interaction between Oct4 and Sox2. Taken together, these results indicate that SUMOylation has a negative effect on Nanog expression and provides new insights into the mechanism of SUMO modification involved in ES cells regulation