Cardiovascular proteomic analysis

Here, we report on our proteomic studies in the field of cardiovascular medicine. Our research has been focused on understanding the role of proteins in cardiovascular disease with a particular focus on epigenetic regulation and biomarker discovery, with the objective of better understanding cardiovascular pathophysiology to lead to the development of new and better diagnostic and therapeutic methods. We have used mass spectrometry for over 5 years as a viable method to investigate protein-protein interactions and post-translational modifications in cellular proteins as well as a method to investigate the role of extra-cellular proteins. Use of mass spectrometry not only as a research tool but also as a potential diagnostic tool is a topic of interest. In addition to these functional proteomics studies, structural proteomic studies are also done with expectations to allow for pinpoint drug design and therapeutic intervention. Collectively, our proteomics studies are focused on understanding the functional role and potential therapeutically exploitable property of proteins in cardiovascular disease from both intra-cellular and extra-cellular aspects with both functional as well as structural proteomics approaches to allow for comprehensive analysis.     

叶脉网络功能性状及其生态学意义

叶脉网络结构是叶脉系统在叶片里的分布和排列样式。早期叶脉网络结构研究主要集中在其分类学意义上; 近年来叶脉网络功能性状及其在植物水分利用上的意义已成为植物生态学研究的热点。该文介绍了叶脉网络功能性状的指标体系(包括叶脉密度、叶脉直径、叶脉之间的距离、叶脉闭合度等), 综述了叶脉网络功能性状与叶脉系统功能(包括水分、养分和光合产物等物质运输、机械支撑和虫害防御等)的关系, 叶脉网络功能性状与叶片其他功能性状(包括比叶重、叶寿命、光合速率、叶片大小、气孔密度等)的协同变异和权衡关系, 以及叶脉网络功能性状随环境因子(包括水分、温度、光照等)的变化规律等方面的最新研究进展。此外, 叶脉网络功能性状的研究成果也被应用于古环境重建、城市交通规划、流域规划及全球变化研究中。由于叶脉网络功能性状是环境因子与系统发育共同作用的结果, 未来开展分子—叶片—植物—生态系统等多尺度的叶脉网络功能性状研究, 理清叶脉网络功能性状与气孔失水—茎干导水—根系吸水等植物水分利用的关系, 将为预测植物及生态系统对全球变化的响应提供新的启示。     

Photoaffinity labeling of P2-purinergic and H1-histamine receptors in intact smooth muscle

This paper discusses the general applicability of photoaffinity labels as pharmacological receptor antagonists in functional studies of intact smooth muscle preparations. Guidelines are suggested that take into account the criteria for photoaffinity labeling studies as well as those for use with conventional antagonists.     

Understanding mouse models of disease through metabolomics

Metabolomics is widely applicable to a number of fields including toxicology, plant metabolism and functional genomics. In the area of functional genomics, a number of studies have demonstrated the potential of this approach, which combines high-throughput metabolite profiling with computer-assisted pattern recognition approaches. In this review, recent applications of metabolomics to understanding mouse models of disease are considered. This includes studies on the impact of mouse strain on disease models, as well as metabolic profiling of cardiovascular, metabolic and neurodegenerative diseases. This versatile tool is set to increase in popularity as functional genomic approaches produce more mouse models for phenotyping.     

植物叶片功能性状及其环境适应研究

植物叶片是连接植物与外界环境的重要桥梁,其功能性状变化受外界环境和系统发育的共同影响。充分了解不同环境下叶片功能性状的变化对探讨植物对环境的适应性具有重要意义。本文阐述了叶片功能性状的类型及其功能意义,综述了影响叶片功能性状2个主要因素（环境因子和系统发育历史）的相关研究,探讨了叶片功能性状对植物适应环境的意义。最后,对叶片功能性状研究的现状及未来趋势进行了展望。     

Synthesis and structure-activity relationships of heteroaryl substituted-3,4-diamino-3-cyclobut-3-ene-1,2-dione CXCR2/CXCR1 receptor antagonists

Comprehensive SAR studies were undertaken in the 3,4-diaminocyclobut-3-ene-1,2-dione class of CXCR2/CXCR1 receptor antagonists to explore the role of the heterocycle on chemokine receptor binding affinities, functional activity, as well as oral exposure in rat. The nature of the heterocycle as well as the requisite substitution pattern around the heterocycle was shown to have a dramatic effect on the overall biological profile of this class of compounds. The furyl class, particularly the 4-halo adducts, was found to possess superior binding affinities for both the CXCR2 and CXCR1 receptors, functional activity, as well as oral exposure in rat versus other heterocyclic derivatives.     

Prediction of functional phosphorylation sites by incorporating evolutionary information

Protein phosphorylation is a ubiquitous protein post-translational modification, which plays an important role in cellular signaling systems underlying various physiological and pathological processes. Current in silico methods mainly focused on the prediction of phosphorylation sites, but rare methods considered whether a phosphorylation site is functional or not. Since functional phosphorylation sites are more valuable for further experimental research and a proportion of phosphorylation sites have no direct functional effects, the prediction of functional phosphorylation sites is quite necessary for this research area. Previous studies have shown that functional phosphorylation sites are more conserved than non-functional phosphorylation sites in evolution. Thus, in our method, we developed a web server by integrating existing phosphorylation site prediction methods, as well as both absolute and relative evolutionary conservation scores to predict the most likely functional phosphorylation sites. Using our method, we predicted the most likely functional sites of the human, rat and mouse proteomes and built a database for the predicted sites. By the analysis of overall prediction results, we demonstrated that protein phosphorylation plays an important role in all the enriched KEGG pathways. By the analysis of protein-specific prediction results, we demonstrated the usefulness of our method for individual protein studies. Our method would help to characterize the most likely functional phosphorylation sites for further studies in this research area.     

Functional morphology of the head of Hawaiian and Mid-Pacific butterflyfishes (Perciformes,Chaetodontidae)

Synopsis The functional morphology of the jaws of six species of butterflyfishes was investigated and related to their feeding behaviors. Utilizing observations and measurements of fresh-killed specimens as well as scanning electron microscopy of their dentitions, interspecific differences in the size, shape, orientation of the mouth, dentition, degree and function of jaw protrusion were related to their different feeding behaviors. The jaws of the six species showed a variety of adaptations for feeding on or over the reef as well as a repertoire of modulated jaw movements hitherto unnoticed in many studies. This radiation in morphologies was believed to be due to relatively simple changes of a few structural elements, changes that could occur relatively rapidly in the evolutionary time scale. The benefit of naturalistic observations in such functional morphological studies was emphasized.     

微生物蛋白质组学的定量分析

越来越多的微生物基因组序列数据为系统地研究基因的调节和功能创造了有利条件.由于蛋白质是具有生物功能的分子,蛋白质组学在微生物基因组的功能研究中异军突起、蓬勃发展.微生物蛋白质组学的基本原则是,用比较研究来阐明和理解不同微生物之间或不同生长条件下基因的表达水平.显而易见,定量分析技术是比较蛋白质组学中急需发展的核心技术.对蛋白质组学定量分析技术在微生物蛋白质组研究中的进展进行了综述.     

Functional diversity: a review of methodology and current knowledge in freshwater macroinvertebrate research

Although several studies have examined the functional diversity of freshwater macroinvertebrates, the variety of methodologies combined with the absence of a synthetic review make our understanding of this field incomplete. Therefore, we reviewed the current methodology for assessing functional diversity in freshwater macroinvertebrate research. Our review showed that most papers quantified functional diversity using biological traits, among which feeding habits were the most common traits probably due to the assumed links between feeding and ecosystem functions. A large number of diversity measures have been applied for quantifying functional diversity of freshwater macroinvertebrate assemblages, among which Rao’s quadratic entropy looks like the most frequent. In most papers, functional diversity was positively related to taxon richness, and functional redundancy was a key concept in explaining this correlation. Most studies detected strong influence of the environmental factors as well as human impact on functional diversity. Finally, our review revealed that functional diversity research is biased towards European running waters and is hindered by yet insufficient information on the autecology of macroinvertebrates.     

Unraveling the relative contribution of inter‐ and intrapopulation functional variability in wild populations of a tadpole species

Functional traits are increasingly recognized as an integrative approach by ecologists to quantify a key facet of biodiversity. And these traits are primarily expressed as species means in previous studies, based on the assumption that the effects of intraspecific variability can be overridden by interspecific variability when studying functional ecology at the community level. However, given that intraspecific variability could also have important effects on community dynamics and ecosystem functioning, empirical studies are needed to investigate the importance of intraspecific variability in functional traits. In this study, 256 Scutiger boulengeri tadpole individuals from four different populations are used to quantify the functional difference between populations within a species, and the relative contribution of inter‐ and intrapopulation variability in functional traits. Our results demonstrate that these four populations differ significantly in functional attributes (i.e., functional position, functional richness, and low functional overlap), indicating that individuals from different populations within a species should be explicitly accounted for in functional studies. We also find similar relative contribution of inter‐ (~56%) and intrapopulation (~44%) variation to the total variability between individuals, providing evidence that individuals within populations should also be incorporated in functional studies. Overall, our results support the recent claims that intraspecific variability cannot be ignored, as well as the general idea of “individual level” research in functional ecology.     

Xenopus white papers and resources: folding functional genomics and genetics into the frog

The frog Xenopus has been vital for biomedical science for over 80 years, contributing to diverse fields from cell signaling, cell and developmental biology, to ion channel physiology and toxicology. Its experimentally manipulable oocytes and embryos provide abundant material for molecular and biochemical approaches for a wide range of gene discovery and protein function studies. In recent years, the Xenopus community has invested in key resources for functional genomics, including genome-wide full-length cDNA collections and genome assemblies as well as genetic tools. These assets combine with Xenopus' extensive range of functional assays to create exciting new research avenues with medical as well as basic applications. This review describes how these resources were developed and what new tools are on the horizon.     

A Bayesian functional data model for surveys collected under informative sampling with application to mortality estimation using NHANES

Functional data are often extremely high-dimensional and exhibit strong dependence structures but can often prove valuable for both prediction and inference. The literature on functional data analysis is well developed; however, there has been very little work involving functional data in complex survey settings. Motivated by physical activity monitor data from the National Health and Nutrition Examination Survey (NHANES), we develop a Bayesian model for functional covariates that can properly account for the survey design. Our approach is intended for non-Gaussian data and can be applied in multivariate settings. In addition, we make use of a variety of Bayesian modeling techniques to ensure that the model is fit in a computationally efficient manner. We illustrate the value of our approach through two simulation studies as well as an example of mortality estimation using NHANES data.     

慢性疼痛与皮层-边缘系统

慢性疼痛作为最常见的临床症状之一,已被认为是全球性的公共健康问题.然而,目前急性疼痛转化为慢性疼痛(即疼痛慢性化)的机制尚不清楚,如何防治急性疼痛转化为慢性疼痛仍然是临床亟待解决的问题.影像学研究表明,编码疼痛情绪、动机和记忆的脑区涉及皮层-边缘系统,而编码持续性疼痛的脑区也主要涉及该系统.基于此,本文概述了慢性疼痛患者在情绪、动机和记忆等方面的行为异常,并详细讨论了慢性疼痛患者皮层-边缘系统的结构和功能变化.其次,本文以慢性腰背痛为例,总结了可能预测疼痛慢性化的影像学指标,如内侧前额叶皮层与伏隔核以及海马的功能连接、背内侧前额叶皮层-杏仁核-伏隔核之间的功能连接均可预测1年后腰背痛疼痛慢性化的发展.此外,基于现有的疼痛慢性化理论模型,本文指出疼痛慢性化可能涉及患者对负面情绪的强化学习以及奖赏和应激系统的功能失调.最后,根据目前研究仍存在的问题和局限,本文对未来的研究方向和方法提出了建议.     

Neutrophil programming dynamics and its disease relevance

Neutrophils are traditionally considered as first responders to infection and provide antimicrobial host defense. However, recent advances indicate that neutrophils are also critically involved in the modulation of host immune environments by dynamically adopting distinct functional states. Functionally diverse neutrophil subsets are increasingly recognized as critical components mediating host pathophysiology. Despite its emerging significance, molecular mechanisms as well as functional relevance of dynamically programmed neutrophils remain to be better defined. The increasing complexity of neutrophil functions may require integrative studies that address programming dynamics of neutrophils and their pathophysiological relevance. This review aims to provide an update on the emerging topics of neutrophil programming dynamics as well as their functional relevance in diseases.     

Challenging the three-dimensional structure of ribosomes

A prerequisite for understanding the detailed mechanism of the intricate process of protein biosynthesis is the determination of the molecular structure of ribosomes. This may be obtained by crystallographic analysis. Although such studies, in general, provide static pictures, they do indicate how to design subsequent functional and dynamic experiments. Thus, investigating models obtained by three-dimensional image reconstruction have stimulated further biochemical as well as crystallographic studies.     

Current issues in x-ray diagnosis of cervical osteochondrosis in the course of medical rehabilitation

The results of studying 500 patients with neurological manifestations of cervical osteochondrosis are presented. All the patients underwent in the vertical position X-ray studies in the frontal, lateral, and axial projections, as well as functional spondylography. The development of radiological signs in patients with cervical osteochondrosis and that of the morphological and functional signs of degenerative and dystrophic changes in the cervical spine are discussed. Comprehensive evaluation of osteochondrosis used criteria for cervical motor disorders and impaired disk amortizing and spinal fixing functions. The degree of intradural space compression was also estimated. The studies have yielded a new classification of osteochondrosis and recommendations at the stages of medical rehabilitation.     

The good, the bad, the ugly: validating the mass spectrometric analysis of modified peptides

Mass spectrometric characterization of protein modifications is usually based on single peptides. With the advent of large-scale PTM-focussed MS studies, vast amounts of data are generated continuously, providing biologists extremely valuable and virtually never-ending sources for targeted functional research. However, even more than for proteomics in general, appropriate strategies for quality control of the different steps of the analytical strategy are imperative to prevent functional researchers from doing Sisyphos work on false-positive and unconfident PTM assignments. Here, we describe strategies to address the important issue of quality control for PTM analysis on various levels of the analytical pipeline: sample preparation/processing, analysis/identification and finally data interpretation, for qualitative as well as quantitative studies.