Molecules into Cells: Specifying Spatial Architecture

A living cell is not an aggregate of molecules but an organized pattern, structured in space and in time. This article addresses some conceptual issues in the genesis of spatial architecture, including how molecules find their proper location in cell space, the origins of supramolecular order, the role of the genes, cell morphology, the continuity of cells, and the inheritance of order. The discussion is framed around a hierarchy of physiological processes that bridge the gap between nanometer-sized molecules and cells three to six orders of magnitude larger. Stepping stones include molecular self-organization, directional physiology, spatial markers, gradients, fields, and physical forces. The knowledge at hand leads to an unconventional interpretation of biological order. I have come to think of cells as self-organized systems composed of genetically specified elements plus heritable structures. The smallest self that can be fairly said to organize itself is the whole cell. If structure, form, and function are ever to be computed from data at a lower level, the starting point will be not the genome, but a spatially organized system of molecules. This conclusion invites us to reconsider our understanding of what genes do, what organisms are, and how living systems could have arisen on the early Earth.     

Nutrients determine the spatial architecture of Paracoccus sp. biofilm

Bacterial biofilms adapt and shape their structure in response to varied environmental conditions. A statistical methodology was adopted in this study to empirically investigate the influence of nutrients on biofilm structural parameters deduced from confocal scanning laser microscope images of Paracoccus sp.W1b, a denitrifying bacterium. High concentrations of succinate, Mg⁺⁺, Ca⁺⁺, and Mn⁺⁺ were shown to enhance biofilm formation whereas higher concentration of iron decreased biofilm formation. Biofilm formed at high succinate was uneven with high surface to biovolume ratio. Higher Mg⁺⁺ or Ca⁺⁺ concentrations induced cohesion of biofilm cells, but contrasting biofilm architectures were detected. Biofilm with subpopulation of pillar-like protruding cells was distributed on a mosaic form of monolayer cells in medium with 10 mM Mg⁺⁺. 10 mM Ca⁺⁺ induced a dense confluent biofilm. Denitrification activity was significantly increased in the Mg⁺⁺- and Ca⁺⁺-induced biofilms. Chelator treatment of various biofilm ages indicated that divalent cations are important in the initial stages of biofilm formation.     

New insights into the molecular mechanisms specifying neuronal polarity in vivo

The polarization of axon and dendrites underlies the ability of neurons to integrate and transmit information in the brain. Important progress has been made toward the identification of the molecular mechanisms regulating neuronal polarization using primarily in vitro approaches such as dissociated culture of rodent hippocampal neurons. The predominant view emerging from this paradigm is that neuronal polarization is initiated by intrinsic activation of signaling pathways underlying the initial break in neuronal symmetry that precedes the future asymmetric growth of the axon. Recent evidence shows that (i) axon-dendrite polarization is specified when neurons engage migration in vivo, (ii) that a kinase pathway defined by LKB1and SAD-kinases (Par4/Par1 dyad) is required for proper neuronal polarization in vivo and that (iii) extracellular cues can play an instructive role during neuronal polarization. Here, we review some of these recent results and highlight future challenges in the field including the determination of how extracellular cues control intracellular responses underlying neuronal polarization in vivo.     

Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: mixed linear modelling of repeated spatial and temporal measures

The present study aimed to dissect tree architectural plasticity into genetic, ontogenetic and environmental effects over the first 4 yr of growth of an apple (Malus x domestica) F1 progeny by means of mixed linear modelling of repeated data. Traits related to both growth and branching processes were annually assessed on different axes of the trees planted in a staggered-start design. Both spatial repetitions, (i.e. different axis types) and temporal repetitions (i.e. successive ages of trees) were considered in a mixed linear model of repeated data. A significant genotype effect was found for most studied traits and interactions between genotype and year and/or age were also detected. The analysis of repeated temporal measures highlighted that the magnitude of the decrease in primary growth is mainly determined by the first year of growth, and the decrease in bottom diameter increment is concomitant with the first fruiting occurrence. This approach allowed us to distinguish among the traits that were under genetic control, those for which this control is exerted differentially throughout tree life or depending on climatic conditions or an axis type. Mapping quantitative trait loci (QTL) that are specific to these different effects will constitute the next step in the research.     

Ecological networks: delving into the architecture of biodiversity

In recent years, the analysis of interaction networks has grown popular as a framework to explore ecological processes and the relationships between community structure and its functioning. The field has rapidly grown from its infancy to a vibrant youth, as reflected in the variety and quality of the discussions held at the first international symposium on Ecological Networks in Coimbra—Portugal (23–25 October 2013). The meeting gathered 170 scientists from 22 countries, who presented data from a broad geographical range, and covering all stages of network analyses, from sampling strategies to effective ways of communicating results, presenting new analytical tools, incorporation of temporal and spatial dynamics, new applications and visualization tools.¹ During the meeting it became evident that while many of the caveats diagnosed in early network studies are successfully being tackled, new challenges arise, attesting to the health of the discipline.     

Another method for specifying furanose ring puckering.

A set of pseudorotation coordinates is proposed for characterizing the puckering of the furanose ring. These are defined from the curvilinear displacements of the C1' and C4' atoms from the planar conformation. The present coordinates have some practical advantages over the ones currently used.     

Neuronal development: specifying a hard-wired circuit

The formation of neuronal circuits that relay distinct olfactory information is thought to depend on cues provided by pre-synaptic receptor neurons. But direct visualization of second order neurons in Drosophila now suggests that dendritic targeting occurs independently of interactions with incoming sensory neurons.     

不同空间尺度三维建筑景观变化

以沈阳市铁西区建筑物三维信息为基础数据,从建筑高度、密度、体积与体形、分布均匀度与空间拥挤度等方面构建了三维建筑景观评价指标,分别从区域、功能分区和梯度带3个角度分析了三维建筑景观的变化特征.结果表明:从1997年到2008年,铁西区建筑向垂直方向扩张,建筑空间分布越来越不均匀,空间拥挤度、建筑平均体积与容积率逐渐增大;居住区平均高度、平均体积、覆盖率、容积率、空间拥挤程度最小,建筑分布最均匀;商业区除建筑高度变异系数和平均体形系数最小外,其余指标值最大;工业区高度变异系数和平均体形系数最大,空间分布最不均匀;从梯度带上看,建筑使用类型的差异决定了三维建筑景观的变化特征.     

Four-Stranded Intercalated Cytosine-Rich Molecules: Novel Insights into DNA Structure and Stability

Abstract

DNA fragments with stretches of cytosine residues can form four-stranded intercalated i-DNA molecules stabilized by hemiprotonated cytosine·cytosine⁺ (C·C⁺) base pairs. Intriguing features of this motif are the accomodation of base stacking that is unfavorable due to electrostatic repulsion and the close approach of phosphates in narrow grooves of the molecule. Unusual sources of stability in this structure involve sugar-base stacking and CH-O interribose short contacts between the backbones of adjacent strands.     

Language: specifying the site of modality-independent meaning

Language processing can be triggered by auditory, visual or somatosensory input. A recent study has provided new insight into a fundamental issue raised by this observation: how is knowledge of language implemented in the human brain such that speakers can use any type of sensory-motor input-output system for comprehension and production?     

Toxoplasma gondii: penetration into differentiating Friend erythroleukemia cells.

The ability of Toxoplasma gondii tachyzoites to penetrate erythroid-differentiating Friend erythroleukemia cells (FL cells) was examined in vitro. The parasites were incubated for 4 hr with FL cells which had been induced to synthesize spectrin, a major erythrocyte membrane protein, or hemoglobin by culturing the cells in the presence of dimethylsulfoxide (DMSO) or sodium butyrate. The penetration rate, in terms of both the average number of T. gondii per cell and the percentage of cells containing parasities, observed in the DMSO-treated FL cells was depressed as compared with that found in untreated cells. However, this depression was not related to the presence of spectrin or hemoglobin. This conclusion was based on the fact that the penetration rate in the butyrate-treated cells was the same as that in untreated cells. These results suggest that it is not the presence of spectrin and hemoglobin that inhibits penetration by T. gondii. The failure of T. gondii to enter mammalian erythrocytes is discussed in relation to surface changes in FL cells undergoing erythroid differentiation.     

Sequences of three genes specifying xylanases in Streptomyces lividans.

The entire nucleotide (nt) sequences of three genes (xlnA, xlnB and xlnC) of Streptomyces lividans encoding three distinct xylanases (Xln) have been determined. The nt sequences were confirmed by comparing the deduced amino acid (aa) sequences with the ones derived from the N-terminal aa sequences of the mature purified proteins. The N-terminus of the XlnA showed some homology with either the N-termini or the C-termini of eight other Xln and of two exo-glucanases. The N-terminus of XlnB is homologous to that of XlnC and to Xln of seven other microorganisms.     

Newly characterized crystal structures: further insights into the architecture of GPCRs

正G protein-coupled receptors (GPCRs), also known as seven-transmembrane (7TM) receptors, are crucial components of numerous cellular signaling cascades. There are about 900 GPCRs in the human genome, making GPCRs the largest family of cell-surface receptors (Lappano and Maggiolini, 2011). GPCRs are classified into six classes based on sequence homology and functional similarity: rhodopsin-like receptors (Class A ), the secretin receptor family (Class B), metabotropic glutamate receptors (Class C), fungal mating pheromone receptors (Class D),