Whatever happened to ecology?

The holistic ecology of the early days had much in common with the world-view of primal people and of the romantic poets. In the 1950s a revival of reductionist and mechanistic ideas took place. The living world, constantly changing in a total "chance direction", appeared by its very nature "totally indestructible". The view of ecological succession toward a "climax" (Odum) became unacceptable for its assumed metaphysical and teleological connotations. Ecological succession is indeed only one special instance of sequential development, that is a feature of all life processes at all levels of organisation. Even the principle of "balance" was rejected by reductionists, because it recalled divine-order. Finally, the principle that "the whole is more than the sum of its parts" was abandoned, thus denying the most basic feature of the living world: organisation. Mainstream scientific ecology no longer reflects the ecological movement of today and may serve to justify the destruction that the irresponsible activities of the multinationals are giving rise to.     

江苏省海滩植被演替的研究

江苏省海滩植被可分为滨海盐土植被、盐沼植被及海滩沙生植被三个基本类型。本文论述了这些植被类型的演替规律。滨海盐土植被与盐沼植被的演替,外因于土壤盐分含量递减与有机质含量的递增;海滩沙生植被的演替,外因于土壤沙颗粒大小及其相应的土壤含水量的变化,所以海滩植被演替为外因动态演替。     

Optical coherence tomography image denoising using a generative adversarial network with speckle modulation

Optical coherence tomography (OCT) is widely used for biomedical imaging and clinical diagnosis. However, speckle noise is a key factor affecting OCT image quality. Here, we developed a custom generative adversarial network (GAN) to denoise OCT images. A speckle‐modulating OCT (SM‐OCT) was built to generate low speckle images to be used as the ground truth. In total, 210 000 SM‐OCT images were used for training and validating the neural network model, which we call SM‐GAN. The performance of the SM‐GAN method was further demonstrated using online benchmark retinal images, 3D OCT images acquired from human fingers and OCT videos of a beating fruit fly heart. The denoise performance of the SM‐GAN model was compared to traditional OCT denoising methods and other state‐of‐the‐art deep learning based denoise networks. We conclude that the SM‐GAN model presented here can effectively reduce speckle noise in OCT images and videos while maintaining spatial and temporal resolutions.     

基于空间优先级的快速城市化地区绿色基础设施网络构建——以南京市浦口区为例

绿色基础设施是一个由自然区域和其他开放空间相互联系的网络。在城市空间极为有限的情况下,如何有效构建城市绿色基础设施网络并识别那些具关键性景观生态功能的网络要素显得极为重要。为了给城市绿色基础设施网络的建设和管理提供新的建模与分析理念,以快速城市化的南京市浦口区为例,采用MSPA方法并结合景观连通性指数,遴选出了对维持景观连通性贡献最大的生境斑块作为绿色基础设施网络的网络中心,进而采用最小路径方法构建了研究区潜在的绿色基础设施网络,并尝试利用空间句法分析,基于结构优化视角对绿色基础设施网络进行优先级的识别,从而使绿色基础设施网络的构建更科学。研究结果可为快速城市化地区绿色基础设施网络的构建提供一种研究思路与方法,对绿色基础设施网络要素的优先级评价也具有一定的借鉴意义。     

Growth Dynamics Explain the Development of Spatiotemporal Burst Activity of Young Cultured Neuronal Networks in Detail

A typical property of isolated cultured neuronal networks of dissociated rat cortical cells is synchronized spiking, called bursting, starting about one week after plating, when the dissociated cells have sufficiently sent out their neurites and formed enough synaptic connections. This paper is the third in a series of three on simulation models of cultured networks. Our two previous studies [26], [27] have shown that random recurrent network activity models generate intra- and inter-bursting patterns similar to experimental data. The networks were noise or pacemaker-driven and had Izhikevich-neuronal elements with only short-term plastic (STP) synapses (so, no long-term potentiation, LTP, or depression, LTD, was included). However, elevated pre-phases (burst leaders) and after-phases of burst main shapes, that usually arise during the development of the network, were not yet simulated in sufficient detail. This lack of detail may be due to the fact that the random models completely missed network topology .and a growth model. Therefore, the present paper adds, for the first time, a growth model to the activity model, to give the network a time dependent topology and to explain burst shapes in more detail. Again, without LTP or LTD mechanisms. The integrated growth-activity model yielded realistic bursting patterns. The automatic adjustment of various mutually interdependent network parameters is one of the major advantages of our current approach. Spatio-temporal bursting activity was validated against experiment. Depending on network size, wave reverberation mechanisms were seen along the network boundaries, which may explain the generation of phases of elevated firing before and after the main phase of the burst shape.In summary, the results show that adding topology and growth explain burst shapes in great detail and suggest that young networks still lack/do not need LTP or LTD mechanisms.     

Impact of Firm-Based Environmental Standards on Subsidiaries and Their Suppliers: Evidence from Motorola-Penang

How successful are multinational corporations in extending their firm-based environmental standards to their subsidiaries and those subsidiaries' local suppliers in their global production networks in developing countries? We address this question through an in-depth case study of how Motorola, a prominent multinational electronics firm with an extensive global production network, is using a set of firm-based standards to meet several new stringent European Union environmental directives. The case study demonstrates that these firm-based standards appear to be enabling a major subsidiary and its suppliers in one developing economy to reduce the environmental intensities of their production activities. This finding suggests that the firm-based environmental standards of multinationals with extensive global production networks might contribute to a leveling up of environmental standards in subsidiaries and their local suppliers, rather than a "race to the bottom", thus reinforcing the technique or intensity effects associated with open trade, investment, and technology policies.     

Surprising complexity of the ancestral apoptosis network

Background

Apoptosis, one of the main types of programmed cell death, is regulated and performed by a complex protein network. Studies in model organisms, mostly in the nematode Caenorhabditis elegans, identified a relatively simple apoptotic network consisting of only a few proteins. However, analysis of several recently sequenced invertebrate genomes, ranging from the cnidarian sea anemone Nematostella vectensis, representing one of the morphologically simplest metazoans, to the deuterostomes sea urchin and amphioxus, contradicts the current paradigm of a simple ancestral network that expanded in vertebrates.

Results

Here we show that the apoptosome-forming CED-4/Apaf-1 protein, present in single copy in vertebrate, nematode, and insect genomes, had multiple paralogs in the cnidarian-bilaterian ancestor. Different members of this ancestral Apaf-1 family led to the extant proteins in nematodes/insects and in deuterostomes, explaining significant functional differences between proteins that until now were believed to be orthologous. Similarly, the evolution of the Bcl-2 and caspase protein families appears surprisingly complex and apparently included significant gene loss in nematodes and insects and expansions in deuterostomes.

Conclusion

The emerging picture of the evolution of the apoptosis network is one of a succession of lineage-specific expansions and losses, which combined with the limited number of 'apoptotic' protein families, resulted in apparent similarities between networks in different organisms that mask an underlying complex evolutionary history. Similar results are beginning to surface for other regulatory networks, contradicting the intuitive notion that regulatory networks evolved in a linear way, from simple to complex.     

Recognition of U1 and U2 small nuclear RNAs can be altered by a 5-amino-acid segment in the U2 small nuclear ribonucleoprotein particle (snRNP) B" protein and through interactions with U2 snRNP-A'' protein.

We have investigated the sequence elements influencing RNA recognition in two closely related small nuclear ribonucleoprotein particle (snRNP) proteins, U1 snRNP-A and U2 snRNP-B". A 5-amino-acid segment in the RNA-binding domain of the U2 snRNP-B" protein was found to confer U2 RNA recognition when substituted into the corresponding position in the U1 snRNP-A protein. In addition, B", but not A, was found to require the U2 snRNP-A' protein as an accessory factor for high-affinity binding to U2 RNA. The pentamer segment in B" that conferred U2 RNA recognition was not sufficient to allow the A' enhancement of U2 RNA binding by B", thus implicating other sequences in this protein-protein interaction. Sequence elements involved in these interactions have been localized to variable loops of the RNA-binding domain as determined by nuclear magnetic resonance spectroscopy (D. Hoffman, C.C. Query, B. Golden, S.W. White, and J.D. Keene, Proc. Natl. Acad. Sci. USA, in press). These findings suggest a role for accessory proteins in the formation of RNP complexes and pinpoint amino acid sequences that affect the specificity of RNA recognition in two members of a large family of proteins involved in RNA processing.     

果蝇细胞凋亡核心机制的基因组比较

基因组比较研究是从基因组序列推测调控网络的主要途径。细胞凋亡信号网络是调控网络的一个典型代表。ＥＧＬ１、ＣＥＤ３、ＣＥＤ４和ＣＥＤ９及其同源蛋白质的线虫和哺乳动物构成保守的凋亡核心机制。目前果蝇细胞凋亡核心机制尚不完整,还未找到ＥＧＬ１和ＣＥＤ９类似蛋白质。通过一系列基于生物信息学的基因组比较分析,在果蝇的基因组数据库中发现了两个ＢＣＬ２／ＣＥＤ９和一个ＥＧＬ１的同源蛋白质的编码基因,并重构了果蝇     

Evaluation of some methods for hybrid analysis, exemplified by hybridization in Argyrantheimim (Asteraceae)

A grouping of transformations is proposed: 1) "Element transformations", aimed at changing relations between elements within a single character vector; and 2) "vector transformations", aimed at changing relations between different character vectors. Logarithmic element transformation seemed suitable for revealing variation in size characters.
Principal coordinate analysis (PCO) was appropriate for determination of dimensionality and structural extremes (parentage). Due to polynomial distortions, however, variation in extreme populations was underestimated and variation in intermediate populations exaggerated.
A "character index", the mean of a specimen's ranged characters, is suggested to replace Anderson's hybrid index. Knowledge of parentage and parental maxima, but not of variation in pure parental populations, is required. The character index combined with modified Gay triangles was found suitable for revealing the structure of the material, which showed mainly one-dimensional variation. The material analysed comprised Argyranthemum broussonetü, A. frutescens , a hybrid swarm and experimental F₁ hybrids between these species; and A. sundingü , which was found to be a stabilized hybrid derivative, probably evolved by hybrid speciation with external barriers.     

GENERAL PATTERN, 35SO4-INCORPORATION AND INTRACELLULAR LOCALIZATION OF GLYCANS IN DEVELOPING SEA URCHIN (ANTHOCIDARIS) EMBRYOS

Glycosaminoglycan (GAG) prepared from sea urchin embryos ( Anthocidaris crassispina ) at various stages with or without pulse ³⁵SO₄-labelling was separated into various fractions by chromatography on DEAE-cellulose with a linear NaCl concentration gradient: fraction "P" (nonacidic) and fractions "A" through "F" (of increasing acidities). The ³⁵SO₄-radioactivity was negligible in "P" and "A", largest in "B" and "C", and decreased in the other fractions three alphabetical order. During development (hatched blastulae to gastrulae) the glycans in fractions "P" and "A" decreased in amount, whereas those in "E" and "F" increased. "E" contained heparin-like (AMPS-1) and dermatanpolysulfate-like (AMPS-2) GAG in addition to a sulfated fucogalactan-like (E₁) glycan. Another sulfated fucogalactan-like (F₁) glycan was found in "F". A sulfated polysialic acid-like (S₁) glycan was found in "C". An EDTA-extract of gastrulae gave AMPS-2, E₁ and F₁. The mitochondria-rich fraction gave AMPS-1, whereas the yolk granule-rich fraction gave S₁. Most of the other still unidentified components in "B", "C", and "D" appeared to be derived from glycoproteins and were mainly located in the crude yolk-mitochondrial and cytosol fractions.     

Scaling of differentiation in networks: nervous systems,organisms, ant colonies,ecosystems, businesses,universities, cities,electronic circuits,and Legos

Nodes in networks are often of different types, and in this sense networks are differentiated. Here we examine the relationship between network differentiation and network size in networks under economic or natural selective pressure, such as electronic circuits (networks of electronic components), Legos (networks of Lego pieces), businesses (networks of employees), universities (networks of faculty), organisms (networks of cells), ant colonies (networks of ants), and nervous systems (networks of neurons). For each of these we find that (i) differentiation increases with network size, and (ii) the relationship is consistent with a power law. These results are explained by a hypothesis that, because nodes are costly to build and maintain in such "selected networks", network size is optimized, and from this the power-law relationship may be derived. The scaling exponent depends on the particular kind of network, and is determined by the degree to which nodes are used in a combinatorial fashion to carry out network-level functions. We find that networks under natural selection (organisms, ant colonies, and nervous systems) have much higher combinatorial abilities than the networks for which human ingenuity is involved (electronic circuits, Legos, businesses, and universities). A distinct but related optimization hypothesis may be used to explain scaling of differentiation in competitive networks (networks where the nodes themselves, rather than the entire network, are under selective pressure) such as ecosystems (networks of organisms).     

Amphiphilic model conetworks based on cross-linked star copolymers of benzyl methacrylate and 2-(dimethylamino)ethyl methacrylate: synthesis, characterization, and DNA adsorption studies

Six amphiphilic model conetworks of a new structure, that of cross-linked "in-out" star copolymers, were synthesized by the group transfer polymerization (GTP) of the hydrophobic monomer benzyl methacrylate (BzMA) and the ionizable hydrophilic monomer 2-(dimethylamino)ethyl methacrylate (DMAEMA) in a one-pot preparation. The synthesis took place in tetrahydrofuran (THF) using tetrabutylammonium bibenzoate (TBABB) as the catalyst, 1-methoxy-1-(trimethylsiloxy)-2-methyl-propene (MTS) as the initiator, and ethylene glycol dimethacrylate (EGDMA) as the cross-linker. Three heteroarm star-, two star block-, one statistical copolymer star-, and one homopolymer star-based networks were prepared. The synthesis of these star-based networks involved four to six steps, including the preparation of the linear (co)polymers, the "arm-first" and the "in-out" star copolymers, and finally the network. The precursors and the extractables were characterized using gel permeation chromatography (GPC) and proton nuclear magnetic resonance (1H NMR) spectroscopy. The degrees of swelling (DSs) of all the networks were measured in THF, while the aqueous DSs were measured as a function of pH. The DSs at low pH were higher than those at neutral or high pH because of the protonation of the DMAEMA units and were found to be dependent on the structure of the network. The DSs in THF were higher than those in neutral water and were independent of the structure. Finally, DNA adsorption studies onto the networks indicated that the DNA binding was governed by electrostatics.     

黄曲霉群菌种产生黄曲霉毒素B1的调查研究

本文对来自我国20个省、市、自治区的不同基物上分离的和中国科学院微生物研究所菌种保藏室以及其他单位提供的黄曲霉群菌种,经随机选取82株进行了黄曲霉毒素B_1的测定,证明在测试的9个已知分类群中产生黄曲霉毒素B_1的菌种只限于寄生曲霉和黄曲霉,另外4株种名未定者也能产生此种毒素。在黄曲霉中产毒菌株约占30％(28.3％),其在GAN(葡萄糖硝酸铵)和大米培养基中的黄曲霉毒素B_1的最高产量分别为133,333.3和160,000.0ppb。总的来说,大体上可以反映在我国一般基物上黄曲霉产毒菌株存在的现状。在实验过程中,还对黄曲霉群菌种在GAN和大米培养基中黄曲霉毒素B_1的产量和产毒菌株数作了比较。发现在大米培养基中黄曲霉毒素B_1的产量高于GAN,而且测试的黄曲霉产毒菌株在这两种培养基中均各有不能产毒的菌株,因此,在测定产毒菌株时,若仅采用其中一种产毒培养基,往往会有漏掉产毒菌株的可能性。     

黄曲霉群菌种产生黄曲霉毒素B_1的调查研究

本文对来自我国20个省、市、自治区的不同基物上分离的和中国科学院微生物研究所菌种保藏室以及其他单位提供的黄曲霉群菌种,经随机选取82株进行了黄曲霉毒素B_1的测定,证明在测试的9个已知分类群中产生黄曲霉毒素B_1的菌种只限于寄生曲霉和黄曲霉,另外4株种名未定者也能产生此种毒素。在黄曲霉中产毒菌株约占30％(28.3％),其在GAN(葡萄糖硝酸铵)和大米培养基中的黄曲霉毒素B_1的最高产量分别为133,333.3和160,000.0ppb。总的来说,大体上可以反映在我国一般基物上黄曲霉产毒菌株存在的现状。在实验过程中,还对黄曲霉群菌种在GAN和大米培养基中黄曲霉毒素B_1的产量和产毒菌株数作了比较。发现在大米培养基中黄曲霉毒素B_1的产量高于GAN,而且测试的黄曲霉产毒菌株在这两种培养基中均各有不能产毒的菌株,因此,在测定产毒菌株时,若仅采用其中一种产毒培养基,往往会有漏掉产毒菌株的可能性。     

Comparative strategies in the investigation of neural networks.

Comparative studies on nervous systems, though infrequently undertaken for the purpose of comparison, have yielded some important generalities about the formats of nervous networks, and about the cell biology of certain neural types. In the first category, it is clear that convergent evolutionary processes arrived at very similar networks to accomplish reciprocal and lateral inhibition, and load-compensation in "resistance reflexes." A newer general network format is described, command-derived inhibition, in which the central nervous elements controlling a rapid movement deliver presynaptic inhibition to the terminals of sensory neurons that carry reafferent excitation from the movement. It is argued that such circuits occur in several groups of animals, and that they include as a special class the efferent inhibitory neurons innervating acoustico-lateralis receptors in vertebrates. The properties of circuit elements that now seem to constitute useful generalizations include size principle (the inverse relationship between size and excitability in a variety of neurons), and the late differentiation of sensory neurons, failure to decussate, and their inability to mediate inhibition. Many other generalities have emerged, only to fall; one conclusion from such searches is that many supposedly "basic" properties of cell types or neural circuits are in fact not phylogenetically conservative, however much the physiologist may expect them to be.     

Systematic synthesis of four epicatechin series procyanidin trimers and their inhibitory activity on the Maillard reaction and antioxidant activity

A systematic synthesis of four natural epicatechin series procyanidin trimers [[4,8:4",8"]-2,3-cis-3,4-trans: 2",3"-cis-3",4"-trans: 2,3-trans-(-)-epi-catechin-(-)-epicatechin-(+)-catechin, [4,8:4",8"]-2,3-cis-3,4-trans: 2",3"-cis-3",4"-trans: 2,3-cis-tri-(-)-epicatechin: procyanidin C1, [4,8:4",8"]-2,3-cis-3,4-trans: 2",3"-trans-3",4"-trans: 2,3-trans-(-)-epicatechin-(+)-catechin-(+)-catechin: procyanidin C4, and [4,8:4",8"]-2,3-cis-3,4-trans: 2",3"-trans-3",4"-trans: 2,3-cis-(-)-epicatechin-(+)-catechin-(-)-epicatechin] is described. Condensation of (2R,3R,4S)-5,7,3'4'-tetra-O-benzyl-4-(2"-ethoxyethyloxy)flavan derived from (-)-epicatechin as an electrophile with the dimeric nucleophiles in the presence of TMSOTf followed by deprotection yielded trimers. Inhibitory activities on the Maillard reaction and antioxidant activity on lipid peroxide of the synthesized oligomers were also investigated.     

Tension and robustness in multitasking cellular networks

Cellular networks multitask by exhibiting distinct, context-dependent dynamics. However, network states (parameters) that generate a particular dynamic are often sub-optimal for others, defining a source of "tension" between them. Though multitasking is pervasive, it is not clear where tension arises, what consequences it has, and how it is resolved. We developed a generic computational framework to examine the source and consequences of tension between pairs of dynamics exhibited by the well-studied RB-E2F switch regulating cell cycle entry. We found that tension arose from task-dependent shifts in parameters associated with network modules. Although parameter sets common to distinct dynamics did exist, tension reduced both their accessibility and resilience to perturbation, indicating a trade-off between "one-size-fits-all" solutions and robustness. With high tension, robustness can be preserved by dynamic shifting of modules, enabling the network to toggle between tasks, and by increasing network complexity, in this case by gene duplication. We propose that tension is a general constraint on the architecture and operation of multitasking biological networks. To this end, our work provides a framework to quantify the extent of tension between any network dynamics and how it affects network robustness. Such analysis would suggest new ways to interfere with network elements to elucidate the design principles of cellular networks.