酸感受性离子通道生物学特性及其调控

酸感受离子通道(ASICs)为H -门控的阳离子通道,是一类新的配体门控性离子通道,属于钠通道超家族的新成员.作为近来研究的热点,ASICs具有许多重要的生物学功能,并很有可能成为抗癫痫、镇痛、提高学习记忆能力和保护神经元缺血损伤作用药理学新靶点.近来,ASICs各个亚基已被克隆,它们在生物体内分布、表达、功能和相关调节因素的研究正受到广泛重视.     

Latency represents sound frequency in mouse IC

Frequency is one of the fundamental parameters of sound. The frequency of an acoustic stimulus can be represented by a neural response such as spike rate, and/or first spike latency (FSL) of a given neuron. The spike rates/frequency function of most neurons changes with different acoustic amplitudes, whereas FSL/frequency function is highly stable. This implies that FSL might represent the frequency of a sound stimulus more efficiently than spike rate. This study involved representations of acoustic frequency by spike rate and FSL of central inferior colliculus (IC) neurons responding to free-field pure-tone stimuli. We found that the FSLs of neurons responding to characteristic frequency (CF) of sound stimulus were usually the shortest, regardless of sound intensity, and that spike rates of most neurons showed a variety of function according to sound frequency, especially at high intensities.These results strongly suggest that FSL of auditory IC neurons can represent sound frequency more precisely than spike rate.     

Morphological and molecular identification of Colletotrichum species associated with cassava anthracnose in Thailand

The objective of this study was to identify the causal agent of anthracnose disease of cassava in Thailand. The study was carried out by collecting cassava samples with anthracnose symptoms from various planting areas including 10 districts of eight provinces in Thailand. One hundred and thirty‐six Colletotrichum samples were isolated from cassava anthracnose lesions on leaves, petioles and stems. Thirty‐eight single‐spore isolates were subsequently obtained and cultured on half potato dextrose agar for morphological and molecular characterizations. All 38 isolates were pathogenic with varying degrees of virulence when tested on detached leaves of Kasetsart 50, a susceptible cassava cultivar. Based on their growth habit, colony morphology, conidial morphology and the internal transcribed spacer sequences similarity to that of Colletotrichum accessions in the GenBank, one isolate was identified as C. capsici, one as C. lindemuthianum, two as C. aeschynomene, four as C. boninense and 28 C. gloeosporioides species complex. Geographically, the cosmopolitan C. gloeosporioides species complex was found in all regions, but other species were found only in particular regions. This is, so far, the first report of Colletotrichum complex species associated with cassava anthracnose in Thailand.     

华南地区亚热带树木叶面积指数的高光谱反演研究

为构建树种叶面积指数的估算模型,以NDVI、RVI、FREP、CIGreen、CIRed-edge、MSAVI2为高光谱特征变量,通过统计分析,确定反演树种叶面积指数的最佳光谱特征变量,构建华南农业大学校园内50种亚热带树木的叶片反射率和叶面积指数(LAI)模型。结果表明,6种高光谱特征变量与树种叶面积指数间都具有极显著相关性,其中红边位置反射率(FREP)和比值植被指数(RVI)与LAI的拟合方程的R2都大于0.8,决定系数分别为0.820和0.811。经过精度验证,FREP估算的均方根误差(RMSE)只有0.13,该回归模型为估测亚热带典型树种的叶片LAI最佳模型。从高光谱遥感的角度结合亚热带植被的群落结构特点来看,建立的红边位置光谱反射率与叶面积指数的回归模型普遍具有较高的拟合度,所以利用高光谱特征变量反演亚热带树木叶片的叶面积指数等植被参数的应用前景较好。     

In silico analysis of stomach lineage specific gene set expression pattern in gastric cancer

Stomach lineage specific gene products act as a protective barrier in the normal stomach and their expression maintains the normal physiological processes, cellular integrity and morphology of the gastric wall. However, the regulation of stomach lineage specific genes in gastric cancer (GC) is far less clear. In the present study, we sought to investigate the role and regulation of stomach lineage specific gene set (SLSGS) in GC. SLSGS was identified by comparing the mRNA expression profiles of normal stomach tissue with other organ tissue. The obtained SLSGS was found to be under expressed in gastric tumors. Functional annotation analysis revealed that the SLSGS was enriched for digestive function and gastric epithelial maintenance. Employing a single sample prediction method across GC mRNA expression profiles identified the under expression of SLSGS in proliferative type and invasive type gastric tumors compared to the metabolic type gastric tumors. Integrative pathway activation prediction analysis revealed a close association between estrogen-α signaling and SLSGS expression pattern in GC. Elevated expression of SLSGS in GC is associated with an overall increase in the survival of GC patients. In conclusion, our results highlight that estrogen mediated regulation of SLSGS in gastric tumor is a molecular predictor of metabolic type GC and prognostic factor in GC.     

Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences

Hot spot residues of proteins are fundamental interface residues that help proteins perform their functions. Detecting hot spots by experimental methods is costly and time‐consuming. Sequential and structural information has been widely used in the computational prediction of hot spots. However, structural information is not always available. In this article, we investigated the problem of identifying hot spots using only physicochemical characteristics extracted from amino acid sequences. We first extracted 132 relatively independent physicochemical features from a set of the 544 properties in AAindex1, an amino acid index database. Each feature was utilized to train a classification model with a novel encoding schema for hot spot prediction by the IBk algorithm, an extension of the K‐nearest neighbor algorithm. The combinations of the individual classifiers were explored and the classifiers that appeared frequently in the top performing combinations were selected. The hot spot predictor was built based on an ensemble of these classifiers and to work in a voting manner. Experimental results demonstrated that our method effectively exploited the feature space and allowed flexible weights of features for different queries. On the commonly used hot spot benchmark sets, our method significantly outperformed other machine learning algorithms and state‐of‐the‐art hot spot predictors. The program is available at http://sfb.kaust.edu.sa/pages/software.aspx . Proteins 2013; 81:1351–1362 © 2013 Wiley Periodicals, Inc.     

Towards fully automated structure-based function prediction in structural genomics: a case study

As the global Structural Genomics projects have picked up pace, the number of structures annotated in the Protein Data Bank as hypothetical protein or unknown function has grown significantly. A major challenge now involves the development of computational methods to assign functions to these proteins accurately and automatically. As part of the Midwest Center for Structural Genomics (MCSG) we have developed a fully automated functional analysis server, ProFunc, which performs a battery of analyses on a submitted structure. The analyses combine a number of sequence-based and structure-based methods to identify functional clues. After the first stage of the Protein Structure Initiative (PSI), we review the success of the pipeline and the importance of structure-based function prediction. As a dataset, we have chosen all structures solved by the MCSG during the 5 years of the first PSI. Our analysis suggests that two of the structure-based methods are particularly successful and provide examples of local similarity that is difficult to identify using current sequence-based methods. No one method is successful in all cases, so, through the use of a number of complementary sequence and structural approaches, the ProFunc server increases the chances that at least one method will find a significant hit that can help elucidate function. Manual assessment of the results is a time-consuming process and subject to individual interpretation and human error. We present a method based on the Gene Ontology (GO) schema using GO-slims that can allow the automated assessment of hits with a success rate approaching that of expert manual assessment.     

Evaluating the predictiveness of a continuous marker

Consider a continuous marker for predicting a binary outcome. For example, the serum concentration of prostate specific antigen may be used to calculate the risk of finding prostate cancer in a biopsy. In this article, we argue that the predictive capacity of a marker has to do with the population distribution of risk given the marker and suggest a graphical tool, the predictiveness curve, that displays this distribution. The display provides a common meaningful scale for comparing markers that may not be comparable on their original scales. Some existing measures of predictiveness are shown to be summary indices derived from the predictiveness curve. We develop methods for making inference about the predictiveness curve, for making pointwise comparisons between two curves, and for evaluating covariate effects. Applications to risk prediction markers in cancer and cystic fibrosis are discussed.     

A parametric comparison of diagnostic accuracy with three ordinal diagnostic groups

Many medical diagnostic studies involve three ordinal diagnostic groups in which the diagnostic accuracy can be summarized by the volume or partial volume under a Receiver Operating Characteristic (ROC) surface. We study in this paper the statistical comparison of diagnostic accuracy from multiple diagnostic tests when three ordinal diagnostic groups are involved. Under the assumption that the multiple diagnostic tests follow a multivariate normal distribution within each diagnostic group, we provide the asymptotic variance and covariance for the maximum likelihood estimates of the volumes under the ROC surfaces from multiple diagnostic tests and propose statistical tests to test whether the diagnostic accuracy as measured by the volume under the ROC surface is the same for multiple diagnostic tests. We also propose a confidence interval estimate to the difference of two volumes under two ROC surfaces. Our approach depends crucially on the assumptions of normal distributions on diagnostic tests, which might not be robust when such assumptions are violated. Finally, we apply our proposed methodology to a real data set of 118 subjects to compare the diagnostic accuracy of early stage Alzheimer's disease (AD) from multiple neuropsychological tests.     

Le Paléolithique supérieur du plateau de Musashino et les hauteurs de Tama aux alentours de Tokyo

The Upper Paleolithic at the region of Tokyo that itself called also the Japanese Preceramic age that possesses a large number of excavations and those studies during the dawn of Paleolithic study in this country. The Preceramic age or the Upper Paleolithic has been raised the curtain by the discovery of a piece in obsidian, in 1949, in the loam of Kantô, at Iwajyuku site. We explain above, on the stratigraphy, the chronology and the situation and the evolution of site around Tokyo. It is a region to the highest density of the Upper Paleolithic sites in the archipelago of Japan and the systematic excavation according to the stratigraphy of loam formation has been done for the first time in the country. The authentic chronology has been proposed to the years 60s that based on the discovered lithic industries on the plateau of Sagamino and Musashino. This chronology was used for a long time that it made a role like a norm for the whole country. Not only, after again an accumulation of the research until the present, we understand the different periodic activities between the Tama hills, the plateau of Musashino, the plateau of Sagamino, the North of Kantô district and the plateau of Simôssa. Of course, there is a complex circumstance that the apparition and the disappearance of various types of lithic instruments are different, and every type tools are not universal around Tokyo area, in the district of Kantô. The final of Upper Paleolithic on the archipelago of Japan divides extensively in two parts East-west that the East of Japan is characterized by the well-organized aspect microlithic tendency and the west is characterized by the trend of microlite, trapeze and tool on transverse blade. In such general tendency, the region of Kantô is located therefore in the center on the archipelago of Japan that it showed sets of every different time.