Discovery of a new cellular structure--porosome

A new cell structure--"porosome", discovered by the American scientist Bhanu Jena and co-wokers, is described. Mechanisms of budding and fusion of transport vesicle are elucidated in addition to those of fusion of secretory vesicles at the cell plasma membrane, and of release of intravesicular contents. The morphology of porosomes, their contents and functional reconstruction in lipid bilayer membranes were examined at a near nanometer resolution. Using atomic force microscopy, the presence of circular "pits", measuring 400-1200 nm in diameter with small 100-150 nm wide "depressions" inside and 3-4 deep pores, called porosomes, was demonstrated. A porosome is cup-shaped and 15-30 nm wide. Porosomes are the places where secretory vesicles fuse with the plasma cell membrane, and where the intravesicular content is released.     

Punctualism, non-adaptationism, neutralism and evolution

In its further development the theory of evolution will incorporate molecular biology, synergetics and the theory of information. Using a simple model it is shown that speciation can be similar to phase transition. This is a thermodynamical statement which does not say anything concerning the sharpness and kinetic features of transition. Hence there is no contradiction between punctuated equilibrium and phyletic gradualism. The notion of punctualism can be used in the sense of phase transition. Evolution is directional because of constraints of natural selection due to the structure of organisms already existing and to the possible pathways of development. Correspondingly many characters are non-adaptative. Not only are the structures of proteins important for speciation but also the exact answers to the questions: "how much", "where" and "when"? These answers can be obtained as the results of regulation of genes, particularly of homeiotic regulation. The basis features of the structure of proteins are considered and the sense of the neutral theory is discussed in connection with degeneracy of correlation between the primary structure of a protein, its spatial structure and biological function. Informational aspects of evolution are discussed. Punctualism, non-adaptationism and neutralism form the triad of internally connected features of evolution. The Darwinian theory preserves its fundamental significance.     

On the origin and evolution of major morphological characters

Although the mathematical principles underpinning population-level evolution are now well studied, the origin and evolution of morphological novelties has received far less attention. Here, a broad but general theory for how this sort of change takes place is outlined, relying on functional continuity, least-constrained components of morphology, redundancy and preadaptation. At least four distinct sorts of redundancy are identified: (i) redundancy arising through duplication (amplification); (ii) redundancy arising through regionalisation (parcellation); (iii) redundancy arising through functional convergence; and (iv) redundancy arising from shared function (functional degeneracy). Although organisms are here recognised to be functionally constrained ("burdened", in Riedl's terminology), these constraints can be overcome through the combination of the four principles given above. Contrary to its common treatment, functional constraint is neither an ever-increasing restriction on the scope of evolution, nor does it require drastic events to overcome or "break" it. Rather, it is an evolutionary quantity, subject to selection at some level. The rules that govern morphological evolution are the primary controls on what is allowed to happen in the evolution of the overall genotype-phenotype system, suggesting strong controls on the sorts of developmental changes that might be associated with macroevolution. This model, then, sees organism functionality as the primary control on evolvability, with exact genetic make-up being of secondary importance. It should prove possible to recast traditional notions of body-plan evolution into the formulations of complex system analysis, which in the future may prove a unifying discipline for fields as disparate as palaeontology and gene regulatory networks. In particular, understanding how morphology can evolve may provide the critical link between the ecological and morphological networks that are currently the intense focus of evolutionary investigations.     

Conditions for cyanobacteria L-transformation

Anabaena variabilis and Chlorogloea fritschii can easily form L-like colonies that are characterized by their appearance and the morphology of component structures. The colonies consist of morphological elements typical of the L-variants of chemoheterotrophic bacteria: filaments, "grains", ring-shaped cells, etc. Data are presented pertinent to the functional activity of the photosynthetic apparatus of these organisms subjected to L-transformation.     

Conformational analysis corresponding to intra-chain disulfide bridged peptides in proteins of known three-dimensional structure

We have carried out a systematic analysis in order to evaluate whether Intra-Chain Disulfide Bridged Peptides (ICDBPs) observed in proteins of known three-dimensional structure adopt structurally similar conformations as they may correspond to structural/functional motifs. 406 representative ICDBPs comprising between 3 to 17 amino acid residues could be classified according to peptide sequence length and main-chain secondary structure conformation into 146 classes. ICDBPs comprising 6 amino acid residues are maximally represented in the Protein Data Bank. They also represent the maximum number of main-chain secondary structure conformational classes. Individual ICDBPs in each class represent different protein superfamilies and correspond to different amino acid sequences. We identified 145 ICDBP pairs that had not less-than 0.5 A root mean square deviation value corresponding to their equivalent peptide backbone atoms. We believe these ICDBPs represent structural motifs and possible candidates in order to further explore their structure/function role in the corresponding proteins. The common conformational classes observed for ICDBPs defined according to the main-chain secondary structure conformations; H (helix), B (residue in a isolated beta bridge), C (coil), E (extended beta strand), G (3(10) helix), I (pi helix), S (bend), T (hydrogen-bonded turn) were; "CHHH", "CTTC", "CSSS" and "CSSC" (for ICDBP length 4), "CSSCC" (length 5), "EETTEE", "CCSSCC", "CCSSSC" (length 6), "EETTTEE" (length 7), "EETTTTEE" (length 8), "EEEETTEEEE" (length 10), "EEEETTTEEEE" (length 11) and "EEEETTTTEEEE" (length 12).     

The association between functional and morphological assessments of endothelial function in patients with rheumatoid arthritis: a cross-sectional study

Introduction

Patients with rheumatoid arthritis (RA) are at an increased risk for cardiovascular disease (CVD). One of the earliest manifestations of CVD is endothelial dysfunction (ED), which can lead to functional and morphological vascular abnormalities. Several non-invasive assessments of vascular function and morphology can be utilised to assess vascular health, but little is known about the association between each of these assessments in patients with RA, and they tend to be used interchangeably in the literature. The objective of the present study was to examine associations between measures of vascular function and morphology in patients with RA.

Methods

A total of 201 RA patients (155 females, median (25^th to 75^th percentile) age: 67 (59 to 73)) underwent assessments of microvascular endothelium-dependent and endothelium-independent function (laser Doppler imaging with iontophoresis of acetylcholine and sodium-nitroprusside respectively), macrovascular endothelium-dependent and endothelium-independent function (flow-mediated dilatation and glyceryl-trinitrate-mediated dilation respectively), and vascular morphology (pulse wave analysis, carotid intima-media thickness (cIMT), and carotid plaque).

Results

Spearman''s correlations revealed that from the functional parameters, only macrovascular endothelium-independent function was inversely associated with cIMT (-0.294 (P < 0.001)) after applying the Bonferroni correction for multiple comparisons. For carotid plaque, t tests showed that macrovascular endothelium-independent function was lower in patients with plaque than without (15.5 ± 8.3 vs. 23.1 ± 9.1%, P = 0.002, respectively).

Conclusions

With the exception of macrovascular endothelium-independent function, all other measures of vascular function were not associated with vascular morphology. This suggests that different assessments of vascular function and morphology in patients with RA reflect quite distinct mechanisms and phases of the atherosclerotic process and should not be used interchangeably.     

The role of vocal self-stimulation in female responses to males: implications for state-reading

As research neurobiologists, we pursue specific questions, and the answers rendered are also correspondingly specific. Our goal, however, is to understand an entire system or the whole organism. To that end, it is not only useful, but sometimes also necessary, that we periodically reappraise a body of specific data in light of current knowledge of the field at large. In this spirit, the present paper reviews my work on the neural and hormonal mechanisms underlying the reproductive system of ring doves and others' studies of songbirds. By integrating these fields I then advance the concept that inherent in the avian breeding system is the mechanism of "state-reading" (a term fashioned after "mindreading", which was coined by cognitive neuroscientists). State-reading helps to coordinate a sequence of endocrine and behavioral events to realize a desired objective, in this case, successful reproduction.     

免疫球蛋白G(IgG)分子结构的扫描隧道显微镜观察

把溶于双蒸水的兔IgG铺展在高定向石墨(HOPG)底载上,直接用扫描隧道显微镜(Scanning Tunneling Microscopy,简称STM)在大气环境中观察,得到了IgG分子的表面结构图像。从图像上可清晰地分辨出IgG分子的Fab及Fc片段,片段连接处的"铰链区"以及Fab和F_e片段的某些精细结构(IgG分子功能辖区)。本工作表明STM在研究生物大分子天然结构方面有巨大潜力。     

Predicting functional divergence in protein evolution by site-specific rate shifts

Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs.     

Computer simulation on the cooperation of functional molecules during the early stages of evolution

It is very likely that life began with some RNA (or RNA-like) molecules, self-replicating by base-pairing and exhibiting enzyme-like functions that favored the self-replication. Different functional molecules may have emerged by favoring their own self-replication at different aspects. Then, a direct route towards complexity/efficiency may have been through the coexistence/cooperation of these molecules. However, the likelihood of this route remains quite unclear, especially because the molecules would be competing for limited common resources. By computer simulation using a Monte-Carlo model (with "micro-resolution" at the level of nucleotides and membrane components), we show that the coexistence/cooperation of these molecules can occur naturally, both in a naked form and in a protocell form. The results of the computer simulation also lead to quite a few deductions concerning the environment and history in the scenario. First, a naked stage (with functional molecules catalyzing template-replication and metabolism) may have occurred early in evolution but required high concentration and limited dispersal of the system (e.g., on some mineral surface); the emergence of protocells enabled a "habitat-shift" into bulk water. Second, the protocell stage started with a substage of "pseudo-protocells", with functional molecules catalyzing template-replication and metabolism, but still missing the function involved in the synthesis of membrane components, the emergence of which would lead to a subsequent "true-protocell" substage. Third, the initial unstable membrane, composed of prebiotically available fatty acids, should have been superseded quite early by a more stable membrane (e.g., composed of phospholipids, like modern cells). Additionally, the membrane-takeover probably occurred at the transition of the two substages of the protocells. The scenario described in the present study should correspond to an episode in early evolution, after the emergence of single "genes", but before the appearance of a "chromosome" with linked genes.     

Functional states of neutrophils as suggested by whole blood chemiluminescence

Luminol-enhanced chemiluminescence (CL) of whole blood was examined in order to distinguish between activation states of phagocytic cells. The CL response of these cells was provoked by a phagocytic stimulus--polystyrene particles. Four functional states of phagocytes were proposed: "resting", "stand by", "activated" and "exhausted". The distinction was done on the basis of extent of the CL response to the particles, time pattern of the process, inhibition of CL by plasma and appearance of spontaneous light emission. Freshly drawn blood of healthy individuals exhibits the "resting" profile of CL, but that of patients with bacterial infection reveals CL patterns ascribed in this paper to the "stand by", "activated" or "exhausted" states of phagocytes. The "stand by", "activated" and "exhausted" behaviour of phagocytes in extravasated blood may be induced by preincubation of blood, stimulation with saline extract of Escherichia coli or N-formyl-Met-Leu-Phe, and by some manipulations involved in preparation of the purified neutrophils.     

Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs

The function of most proteins is not determined experimentally, but is extrapolated from homologs. According to the "ortholog conjecture", or standard model of phylogenomics, protein function changes rapidly after duplication, leading to paralogs with different functions, while orthologs retain the ancestral function. We report here that a comparison of experimentally supported functional annotations among homologs from 13 genomes mostly supports this model. We show that to analyze GO annotation effectively, several confounding factors need to be controlled: authorship bias, variation of GO term frequency among species, variation of background similarity among species pairs, and propagated annotation bias. After controlling for these biases, we observe that orthologs have generally more similar functional annotations than paralogs. This is especially strong for sub-cellular localization. We observe only a weak decrease in functional similarity with increasing sequence divergence. These findings hold over a large diversity of species; notably orthologs from model organisms such as E. coli, yeast or mouse have conserved function with human proteins.     

Effects of functional group changes in the EcoRI recognition site on the cleavage reaction catalyzed by the endonuclease

Oligodeoxynucleotides have been prepared that contain changes in the functional group pattern present in the EcoRI recognition site. These changes involve "functional group deletions", "functional group reversals", and "displaced functional groups". Steady-state kinetic parameters have been used to characterize the interaction of these modified recognition sites with the EcoRI endonuclease. Changes in the functional group pattern have varying effects upon the cleavage reaction. Both the exocyclic amino groups of the two adenine residues and the methyl groups of the thymine residues appear to interact with the endonuclease quite differently. In both cases efficient catalysis was observed when these functional groups were present at the "outer" dA-dT base pair. Selectivity was decreased by over an order of magnitude largely via increases in Km when these functional groups were deleted. Similar modifications at the "inner" dA-dT base pair did not alter the kinetic parameters significantly from those observed with the native sequence. Addition of an amino group to the minor groove at the outer dA-dT base pair resulted in a modified recognition site that interacted with the enzyme, on the basis of observed competitive inhibition kinetics, but was not cleaved.     

基于植物功能群的生态系统服务形成与维持机制研究

生态系统可以从“结构-功能-服务”3个层次来理解,其中服务是人类的主观感受或效用。维持高质量的生态系统服务还需从生态系统的自然属性入手。结构和功能是生态系统服务形成和维持的内在机制,而植物是生态系统结构和功能的核心驱动力。植物功能群具有特定功能的植物组合,其中优势植物功能群控制着生态系统的结构和功能。生态系统服务的概念、分类与植物功能群密切相关,植物功能群是生态系统与生态系统服务间更直接的桥梁。建立生态系统服务与植物功能群间的联系,使相关研究有更明确的指向,在深化理论研究的同时使研究成果更容易落地。生态系统服务的形成、维持机制与植物功能群的内在联系主要体现在4个主要方面：(1)植物功能群的内在适应性特征和外在效应是生态系统服务形成的基础;(2)植物功能群的多功能特性为生态系统服务协同提供了可能;(3)植物功能群间替代和互补效应可以提升生态系统服务质量和稳定性;(4)植物功能群能够提供基于自然的生态系统服务修复问题解决方案。     

用《组合中药学》的理论开发新型中药

我们以现代科技理论为出发点,提出了<组合中药学>新理论体系,试图使中外学者对中药的认识趋于一致.中药的本质就是"组合".无论是单方或复方都是一个庞大的分子库.具有相同或相似功能的分子组合成一个群体.这些群体表现出特定的药效."组合"有三层意思生药的组合、活性分子群的组合与特定疗效的组合.分子群是特定药效功能的物质基础.<组合中药学>就是从<组合分子>水平上研究中药及其药效的物质基础,阐明中药活性部位的相互作用与药效的相互关系及其作用机制.<组合中药学>的三个新概念中药功效分子族具有相似药效作用的一类分子的组合,其骨架及功能团相同或相似.单味中药表征性组合分子单味中药药效的代表性功效分子族,即主要药效分子组合.单味中药非表性组合分子单味中药表征性分子以外的其它功效分子族,即辅助药效分子的组合.<组合中药学>的主要研究范围中药药效的组合分子学基础(植物化学,天然产物);组合分子的药理学基础(分子生物学,细胞生物学,药理学).本文提出了应用<组合中药学>研究新型中药的新方法.     

On the brotherhood of the mitochondrial chaperones mortalin and heat shock protein 60

The heat shock chaperones mortalin/mitochondrial heat shock protein 70 (mtHsp70) and Hsp60 are found in multiple subcellular sites and function in the folding and intracellular trafficking of many proteins. The chaperoning activity of these 2 proteins involves different structural and functional mechanisms. In spite of providing an excellent model for an evolutionarily conserved molecular "brotherhood", their individual functions, although overlapping, are nonredundant. As they travel to various locations, both chaperones acquire different binding partners and exert a more divergent involvement in tumorigenesis, cellular senescence, and immunology. An understanding of their functional biology may lead to novel designing and development of therapeutic strategies for cancer and aging.