基于蛋白质序列的泛素化位点预测研究进展

泛素化是目前广受关注的一种翻译后修饰过程,对蛋白质降解、DNA修复等多种细胞过程都具有重要的调控作用。本文根据国内外蛋白质泛素化位点预测的研究,分析了预测泛素化位点的特征属性,总结了对这些特征进行优化的特征选择方法,并对预测过程中所使用的各种机器学习分类器进行了概述。     

Evolution of postzygotic reproductive isolation in galliform birds: analysis of first and second hybrid generations and backcrosses

The process of speciation is a crucial aspect of evolutionary biology. In this study, we analysed the patterns of evolution of postzygotic reproductive isolation in Galliformes using information on hybridization and genetic distance among species. Four main patterns arose: (1) hybrid inviability and sterility in F₁ hybrids increase as species diverge; (2) the presence of geographical overlap does not affect the evolution of postzygotic isolation; (3) the galliforms follow Haldane's rule; (4) hybrid inviability is higher in F₂ than in F₁ hybrids, but does not appear to be increased in the backcrosses. This study contributes to the growing evidence suggesting that the patterns of evolution of postzygotic isolation and the process of speciation are shared among avian groups (and animals in general). In particular, our results support the notion of F₂ hybrid inviability as being key for the maintenance of species genetic integrity when prezygotic isolation barriers are overcome in closely related species, in which postzygotic isolation in the F₁ hybrid might still not be fully developed. To the contrary, hybrids from backcrosses did not show serious inviability problems (at least not more than F₁ hybrids), demonstrating that they could generate gene flow among bird species. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 528–542.     

Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites

O-GalNAc-glycosylation is one of the main types of glycosylation in mammalian cells. No consensus recognition sequence for the O-glycosyltransferases is known, making prediction methods necessary to bridge the gap between the large number of known protein sequences and the small number of proteins experimentally investigated with regard to glycosylation status. From O-GLYCBASE a total of 86 mammalian proteins experimentally investigated for in vivo O-GalNAc sites were extracted. Mammalian protein homolog comparisons showed that a glycosylated serine or threonine is less likely to be precisely conserved than a nonglycosylated one. The Protein Data Bank was analyzed for structural information, and 12 glycosylated structures were obtained. All positive sites were found in coil or turn regions. A method for predicting the location for mucin-type glycosylation sites was trained using a neural network approach. The best overall network used as input amino acid composition, averaged surface accessibility predictions together with substitution matrix profile encoding of the sequence. To improve prediction on isolated (single) sites, networks were trained on isolated sites only. The final method combines predictions from the best overall network and the best isolated site network; this prediction method correctly predicted 76% of the glycosylated residues and 93% of the nonglycosylated residues. NetOGlyc 3.1 can predict sites for completely new proteins without losing its performance. The fact that the sites could be predicted from averaged properties together with the fact that glycosylation sites are not precisely conserved indicates that mucin-type glycosylation in most cases is a bulk property and not a very site-specific one. NetOGlyc 3.1 is made available at www.cbs.dtu.dk/services/netoglyc.     

Rensch's rule, Bergmann's effect and adult sexual dimorphism in wild monogamous owl monkeys (Aotus azarai) of Argentina

Some monogamous primates are characterized by biparental care, territoriality, and a reduced level of physical dimorphism. In others, the relationship between those behavioral patterns and dimorphism is less clear. I tested Bergmann's and Rensch's rules using Aotus spp. body mass data and I characterized the extent of sexual dimorphism in body mass, dental and physical measurements in a socially monogamous owl monkey population (n = 91 adults) from the Argentinean Gran Chaco. A. azarai azarai from the Argentinean Chaco is larger than the more tropical owl monkey species (r = 0.7, N = 6 species), but there is no apparent increase in sexual dimorphism with increased body mass. The body masses of adult male and female A. a. azarai were remarkably similar (Mean = 1.26 kg); there were no marked sex differences in most skeletal measurements, but males had higher and wider upper and lower canines than did females. Body mass and neck circumference were positively and strongly related (r = 0.533, n = 52), and the body mass of adults was not a reliable indicator of their age (r = 0.03, n = 10). The data illustrate the complexities inherent in examining and summarizing within population variation in skeletal and nonskeletal measurements and contribute to a better understanding of the relationships between monogamous behavioral patterns and sexual dimorphism.     

Developmental Lead Exposure and Two-Way Active Avoidance Training Alter the Distribution of Protein Kinase C Activity in the Rat Hippocampus

Long-term exposure to a low level of lead is associated with learning deficits. Several types of learning have been correlated to hippocampal protein kinase C (PKC) activation. This study was designed to determine if there is a correlation between the effects of lead on hippocampal PKC activation and those on learning performance. Rats were exposed to 0.2% (w/v) lead acetate at different developmental stages including a maternally exposed group, a postweaning exposed group, and a continuously exposed group. The continuously lead exposed rats tended to avoid less frequently and not respond more frequently in two-way active avoidance training than did controls. This training process was associated with translocation of hippocampal PKC activity from cytosol to membrane. Two-way analysis of variance of data indicates that there is a significant training and lead treatment interaction in the ratio of membrane to cytosolic PKC activity (F_3,32 = 3.013; p = 0.044). The interaction is attributable to the absence of the training-induced PKC translocation in the continuously lead exposed rats. In addition, no significant changes were observed in learning performance and training-induced hippocampal PKC activation after maternal and postweaning lead exposure. Continuous and longer duration of lead exposure appears to affect the learning performance and hippocampal PKC activation. These data suggest that a change in the activation of hippocampal PKC may be involved in the lead-induced deficit in learning.     

Machine Learning Approach to Detect Cardiac Arrhythmias in ECG Signals: A Survey

Cardiac arrhythmia is a condition when the heart rate is irregular either the beat is too slow or too fast. It occurs due to improper electrical impulses that coordinates the heart beats. Sudden cardiac death may occurs due to some dangerous arrhythmias conditions. Hence the main objective of the electrocardiogram (ECG) analysis is to detect the life-threatening arrhythmias accurately for appropriate treatment in order to save life. Since the last decades, several methods were reported for automatic ECG beat classifications. In this work, we present a systematic review of the current state-of-the-art methods used to detect cardiac arrhythmia using on ECG signals. It includes the signal decomposition, feature extraction and machine learning approaches used for automatic detection and decision making process. The articles covers the pre-processing, detection of QRS complex, feature extraction and classification of ECG beats. Based on the past studies, it is understood that the automated approach using computer-aided decision making process is highly required for real-time detection of cardiac arrhythmias. The advantages and limitations of different methods are discussed and also the future scopes is highlighted in the process of effective detection of cardiac arrhythmias. This study could be beneficial for researchers to analyze the existing state-of-art techniques used in detection of arrhythmia conditions.     

What makes a long tail short? Testing Allen's rule in the toque macaques of Sri Lanka

Allen's rule (1877) predicts ecogeographical anatomical variation in appendage proportions as a function of body temperature regulation. This phenomenon has been tested in a variety of animal species. In macaques, relative tail length (RTL) is one of the most frequently measured appendages to test Allen's rule. These studies have relied on museum specimens or the invasive and time-consuming capturing of free-ranging individuals. To augment sample size and lessen these logistical limitations, we designed and validated a novel noninvasive technique using digitalized photographs processed using LibreCAD, an open-source 2D-computer-aided design (CAD) application. This was used to generate pixelated measurements to calculate an RTL equivalent, the Tail to Trunk Index (TTI) = (tail [tail base to anterior tip] pixel count/trunk [neck to tail base] pixel count). The TTI of 259 adult free-ranging toque macaques (Macaca sinica) from 36 locations between 7 and 2,087 m above sea level (m.a.s.l.) was used in the analysis. Samples were collected from all three putative subspecies (M. s. sinica, aurifrons, and opisthomelas), at locations representing all altitudinal climatic zones where they are naturally distributed. These data were used to test whether toque macaque tail length variation across elevation follows Allen's rule, predicting that RTL decreases with increasing elevation and lower temperature. Our results strongly supported this prediction. There was also a statistically significant, negative correlation between elevation and annual average temperature. The best predictor for the TTI index was elevation. Significant subspecies differences in RTL are linked in part to their ecological and altitudinal niche separation, but overall the variation is seen as the species' adaptation to climate. The method developed for the quick morphometric assessment of relative body proportions, applicable for use on unhabituated free-ranging animals, widens the range of materials available for research studying morphological characteristics and their evolution in primates.     

9-Methyl-β-carboline-induced cognitive enhancement is associated with elevated hippocampal dopamine levels and dendritic and synaptic proliferation

β-Carbolines (BCs) belong to the heterogenous family of carbolines, which have been found exogenously, that is, in various fruits, meats, tobacco smoke, alcohol and coffee, but also endogenously, that is, blood, brain and CSF. These exogenous and endogenous BCs and some of their metabolites can exert neurotoxic effects, however, an unexpected stimulatory effect of 9-methyl-β-carboline (9-me-BC) on dopaminergic neurons in primary mesencephalic cultures was recently discovered. The aim of the present study was to extend our knowledge on the stimulatory effects of 9-me-BC and to test the hypothesis that 9-me-BC may act as a cognitive enhancer. We found that 10 days (but not 5 days) of pharmacological treatment with 9-me-BC (i) improves spatial learning in the radial maze, (ii) elevates dopamine levels in the hippocampal formation, and (iii) results after 10 days of treatment in elongated, more complex dendritic trees and higher spine numbers on granule neurons in the dentate gyrus of 9-me-BC-treated rats. Our results demonstrate that beyond its neuroprotective/neurorestorative and anti-inflammatory effects, 9-me-BC acts as a cognitive enhancer in a hippocampus-dependent task, and that the behavioral effects may be associated with a stimulatory impact on hippocampal dopamine levels and dendritic and synaptic proliferation.     

Issues and developments on the consumer recovery construct

The consumer recovery model has had increasing influence on mental healthpractices in the United States, Western Europe, and several other countries.However, adoption of the model has reflected political decisions rather thanempirical evidence of the validity of the model or its value for treatmentservices. The recovery construct is poorly defined, and until recently therehas been no reliable and valid measure with which to base a research program.We have developed an empirical measure that is well-suited for both researchand clinical applications: the Maryland Assessment of Recovery in SeriousMental Ill-ness (MARS). We briefly describe the MARS and present preliminarydata demonstrating that recovery is not a simple by-product of traditionaloutcome do-mains, but seems to be a distinct construct that may have importantimplications for understanding consumers with serious mental illness and forevaluating the outcome of treatment programs.