Regulation of the Escherichia coli secA Gene Is Mediated by Two Distinct RNA Structural Conformations

Expression from the secA gene, encoding a key component of the general secretory pathway of Escherichia coli, is influenced by the secretion status of the cell, autogenous translational repression, and translational coupling to the upstream gene, X. SecA binds to its mRNA in a region overlapping its ribosome binding site, thus competing with ribosomes that would initiate secA translation. Mapping of the geneX-secA mRNA secondary structure has demonstrated that the RNA can adopt two distinct conformations in solution. The first conformation arises from the base-pairing of the secA Shine-Dalgarno (SD) sequence with the geneX terminus. The second conformation, in which the secA SD sequence is no longer paired with the geneX terminus, contains a GC-rich stem upstream of the secA SD sequence. The presence of this GC-rich stem is supported by structure mapping of a mutant RNA containing a deletion in the geneX terminus. The former structure appears to be involved in translational coupling by directly linking the geneX and secA sequences, where geneX translation activates secA translational initiation through the unpairing and unmasking of the secA SD sequence. As indicated by SecA-RNA binding assays, the latter structure is probably involved in SecA binding and translational repression of the secA gene. The stabilizing effect of magnesium ions toward occlusion of the secA SD sequence supports the presence of RNA tertiary structure in this regulatory domain. Received: 30 July 1998 / Accepted: 18 September 1998     

β‐amino acid substitution to investigate the recognition of angiotensin II (AngII) by angiotensin converting enzyme 2 (ACE2)

In spite of the important role of angiotensin converting enzyme 2 (ACE2) in the cardiovascular system, little is known about the substrate structural requirements of the AngII–ACE2 interaction. Here we investigate how changes in angiotensin II (AngII) structure affect binding and cleavage by ACE2. A series of C3 β‐amino acid AngII analogs were generated and their secondary structure, ACE2 inhibition, and proteolytic stability assessed by circular dichroism (CD), quenched fluorescence substrate (QFS) assay, and LC‐MS analysis, respectively. The β‐amino acid‐substituted AngII analogs showed differences in secondary structure, ACE2 binding and proteolytic stability. In particular, three different subsets of structure‐activity profiles were observed corresponding to substitutions in the N‐terminus, the central region and the C‐terminal region of AngII. The results show that β‐substitution can dramatically alter the structure of AngII and changes in structure correlated with ACE2 inhibition and/or substrate cleavage. β‐amino acid substitution in the N‐terminal region of AngII caused little change in structure or substrate cleavage, while substitution in the central region of AngII lead to increased β‐turn structure and enhanced substrate cleavage. β‐amino acid substitution in the C‐terminal region significantly diminished both secondary structure and proteolytic processing by ACE2. The β‐AngII analogs with enhanced or decreased proteolytic stability have potential application for therapeutic intervention in cardiovascular disease. Copyright © 2010 John Wiley & Sons, Ltd.     

Comparative neuromorphology of the telencephalon of sturgeon of the genera Acipenser, Huso and Scaphirhynchus (Actinopterygii; Acipenseridae)

Brain anatomy and structure, composition of the neurons, and cytoarchitectural maps were compared between five species of Acipenser, one species of Huso and two species of Scaphirhynchus. Morphological differences in the forebrain structure between species and genera were apparent. The evolutionary history of the Acipenseridae has been marked by an extensive mosaic radiation in the evolutionary development of the inner structure of their brains. Members of Scaphirhynchus have a very simple telencephalon structure differing significantly from that of Huso and Acipenser. It is clear that neuromorphological variation of sturgeon species will serve as an additional data useful in understanding the evolutionary processes and history associated with the speciation in Acipenseridae.     

Native and Introduced Ecosystem Engineers Produce Contrasting Effects on Estuarine Infaunal Communities

Cordgrasses in the genus Spartina are good examples of ecosystem engineers that modify habitat structure in estuaries throughout the world. In San Francisco Bay, California, USA, marshes containing native California cordgrass (Spartina foliosa) are being invaded by a hybrid (S. alterniflora × S. foliosa) formed after introduction of S. alterniflora. This study compared vegetation, sediment structure, and infaunal invertebrates in native and invaded marshes. We hypothesized that differences in the physical structure between S. foliosa and hybrid Spartina would be reflected in differences in density, biomass, diversity, and taxonomic composition of infauna. Hybrid Spartina modifies habitat structure more than S. foliosa by producing taller stems, and greater plant biomass both above- and belowground while occupying a much wider tidal range, thereby transforming open mudflats to a vegetated habitat. In general, S. foliosa areas contained significantly higher densities of benthic infauna than adjacent mudflats, while hybrid Spartina areas never contained greater infaunal densities than mudflats. This is because S. foliosa produces a moderate level of structure that can facilitate benthic invertebrates, whereas hybrid Spartina produces so much structure, particularly belowground, that it actually excludes invertebrates. Therefore, we suggest that these two closely related species both act as ecosystem engineers, but with opposing effects on invertebrate communities.     

GENETIC VARIATION AND POPULATION STRUCTURE IN THE FERN BLECHNUM SPICANT (BLECHNACEAE) FROM WESTERN NORTH AMERICA

Population genetic structure in the homosporous fern Blechnum spicant was analyzed in six populations from western North America. Each population was divided into approximately 10 m by 10 m subpopulations, and genetic variation within and among subpopulations was compared using enzyme electrophoresis and F statistics. These analyses indicated that there was no evidence of genetic structure in four of the six populations examined. However, significant genetic heterogeneity among subpopulations was observed for the other two populations. The genetic structure of these populations may be attributable, in part, to family structure resulting from high rates of intragametophytic selling and/or spatial patchiness in the distribution of individuals due to limited habitat availability in these areas. Outcrossing populations of B. spicant generally lack genetic structure, whereas the most highly inbreeding population maintains significant genetic structure. The information obtained in this investigation of population genetic structure in Blechnum spicant is consistent with data for angiosperms and gymnosperms. It appears that the outcrossing mating system and effective mechanism of spore dispersal in B. spicant may account for the general lack of genetic structure within populations of this species.     

Small-scale variability in the size structure of scleractinian corals around Moorea, French Polynesia: patterns across depths and locations

The size structure of coral populations is influenced by biotic and physical factors, as well as species-specific demographic rates (recruitment, colony growth, mortality). Coral reefs surrounding Moorea Island are characterized by strong environmental gradients at small spatial scales, and therefore, we expected that the size structure of coral populations would vary greatly at this scale. This study aimed at determining the degree of spatial heterogeneity in the population size structure of two coral taxa, Pocillopora meandrina and massive Porites spp., among depths (6, 12, and 18 m) and among locations (Vaipahu, Tiahura and Haapiti) representing different exposure to hydrodynamic forces. Our results clearly underlined the strong heterogeneity in the size structure of both P. meandrina and massive Porites spp., with marked variation among depths and among locations. However, the lack of any consistent and regular trends in the size structure along depths or among locations, and the lack of correlation between size structure and mean recruitment rates may suggest that other factors (e.g., stochastic life history processes, biotic interactions, and disturbances) further modify the structure of coral populations. We found that the size structure of P. meandrina was fundamentally different to that of massive Porites spp., reflecting the importance of life history characteristics in population dynamics. Handling editor: I. Nagelkerken     

Phylogeny of Sibling Species of Simulium venustrum and S. verecundum (Diptera: Simuliidae) Based on Sequences of the Mitochondrial 165 rRNA Gene

The phylogeny of four sibling species of Simulium venustum (CC, CC3, CC4, and AC(gB)) and two sibling species of S. verecundum (AA and ACD = S. rostratum) was reconstructed using nucleotide sequences of the mitochondrial large subunit rRNA gene. Separate phylogenetic analyses were performed by dividing the sequence data into: (1) helices of a computer-generated secondary structure of the rDNA; (2) loops of the computer-generated structure; (3) helices of a consensus secondary structure (deduced by comparing the computer-generated structure of black flies with the corresponding structures proposed for the fruit fly (Drosophila yakuba) and the mosquito (Aedes albopictus)); (4) loops of the consensus structure; (5) both helices and loops of the consensus secondary structure; and (6) the entire sequence regardless of secondary structure, including 11 variable sites in regions where the prediction of secondary structure was not possible. We found that different data sets led to different phylogenetic conclusions. The phylogenies based on data sets 4 and 6 were consistent with nonmolecular evidence, while the phylogenies based on other data sets were not. Our study suggests S. decorum, a morphospecies, might have shared a common ancestor with sibling species of S. venustum.     

Geographically structured genetic variation in the Medicago lupulina–Ensifer mutualism

Gene flow between genetically differentiated populations can maintain variation in species interactions, especially when population structure is congruent between interacting species. However, large‐scale empirical comparisons of the population structure of interacting species are rare, particularly in positive interspecific interactions (mutualisms). One agriculturally and ecologically important mutualism is the partnership between legume plants and rhizobia. Through characterizing and comparing the population genomic structure of the legume Medicago lupulina and two rhizobial species (Ensifer medicae and E. meliloti), we explored the spatial scale of population differentiation between interacting partners in their introduced range in North America. We found high proportions of E. meliloti in southeastern populations and high proportions of E. medicae in northwestern populations. Medicago lupulina and the Ensifer genus showed similar patterns of spatial genetic structure (isolation by distance). However, we detected no evidence of isolation by distance or population structure within either species of bacteria. Genome‐wide nucleotide diversity within each of the two Ensifer species was low, suggesting limited introduction of strains, founder events, or severe bottlenecks. Our results suggest that there is potential for geographically structured coevolution between M. lupulina and the Ensifer genus, but not between M. lupulina and either Ensifer species.     

粘质沙雷氏菌几丁质酶基因ChiA克隆及生物信息学分析

通过生物信息学技术对Chi A基因序列进行分析预测,了解Chi A的基因结构及蛋白质性质。从自有菌株(粘质沙雷氏菌Serratia mareescens S68)中克隆到几丁质酶基因Chi A,利用相关软件对Chi A基因序列进行分析预测。Chi A基因全长1 714 bp,开放阅读框编码563个氨基酸,推测其编码的蛋白质分子量为60 983.8Da,等电点为6.35,是一种稳定的亲水性蛋白质。预测Chi A可能存在信号肽,切割位点在第23~24位氨基酸之间,1~23位氨基酸为其跨膜结构,其余肽链位于细胞外。Chi A主要存在3种二级结构元件,在二级、三级结构中都有体现。该Chi A是一种水溶性蛋白质,结构稳定且可以分泌到胞外。     

COMPARATIVE STUDIES OF PYRENOID ULTRASTRUCTURE IN ALGAE OF THE MONOSTROMA COMPLEX123

The pyrenoid structure in 15 species of the Monostroma complex is very diverse us revealed by a study of the morphology of the pyrenoid matrix, associated starch shell, and pattern of intrapyrenoidalthylakoid bands. From these characteristics 8 types of pyrenoid structure were classified. The variation of pyrenoid structure was shown not only among the species studied, but also between the alternation of generations (M. angicava and M. nitidum). In M. fuscum var. splendens, M. groenlandicum, M. undulatum, and M. zostericola pyrenoid structure is the same throughout the life cycle. The pyrenoid matrix of M. zostericola is surrounded by a double membrane that prevents the direct connection of the pyrenoid matrix with chloroplast thylakoids. The pyrenoid also lacks a starch shell. These findings support the establishment of a new genus Kornmannia by Bliding to include M. zostericola. In addition, similarities in pyrenoid ultrastructure suggest an affinity of Capsosiphon fulvescens with M. groenlandicum.     

Microstructure and formation of the calcareous operculum in Pyrgopolonctenactis and Spirobranchusgiganteus (Annelida, Serpulidae)

The calcareous operculum of Pyrgopolon ctenactis is composed of spherulitic prismatic structures. The opercular cup consists of regular spherulitic prismatic crystals; the talon has two layers, an inner with an irregular spherulitic prismatic structure (150 μm thick) and an outer with a regular spherulitic prismatic structure (110 μm thick). The outer regular structure has thick (1 μm) organic interprismatic sheets unique in biomineralization of this group, but similar to that of Bivalvia. We infer that control over biomineralization is stronger during the formation of the outer regular layer, with its thick organic interprismatic sheets, than during the formation of the inner irregular spherulitic prismatic structure, without such sheets. In Spirobranchus giganteus, opercular formation differs from that of P. ctenactis. S. giganteus has numerous pores in its opercular plate, and calcification starts with the formation of an outer irregularly oriented prismatic structure followed by an oriented prismatic structure without interprismatic sheets.     

Patch occupancy of two hemipterans sharing a common host plant

Aim Two hemipteran species were chosen as a study system for the comparative analysis of patch occupancy and spatial population structure of insects sharing a common host plant. This study tested whether (1) the incidence in the host plant patches differed between the two species, and (2) the two species exhibited a different spatial population structure, i.e. were they affected differentially by isolation and area of the host plant patches. Location The porphyry landscape north of Halle (Saale) in Germany comprising 506 patches of the host plant Brachypodium pinnatum. Methods The host plant patches were surveyed for the two hemipterans. To assess the influence of patch quality on species occurrence the patches were characterized by mean cover abundance of B. pinnatum, type of subsoil, slope, exposure, and shading. The spatial configuration of the patches was considered by patch area and isolation. The influence of the habitat factors and the spatial configuration on the occupancy of the two species was analysed by logistic regression. Results Adarrus multinotatus was found in 441 patches, while Neophilaenus albipennis was found in only 90 patches. While A. multinotatus showed virtually no relationship to the habitat factors, the occupancy of N. albipennis was influenced by subsoil type, cover abundance, and shading. The effects of area and isolation on occupancy of the patches also differed between the two species. The occupancy of N. albipennis was determined largely by area and isolation, whereas in A. multinotatus no considerable effect of spatial configuration was found. Main conclusions The study revealed a marked difference between the two hemipteran species in respect of spatial population structure. Adarrus multinotatus built up a ‘patchy population’, whereas N. albipennis showed a ‘metapopulation’ structure within the same set of patches in the same landscape. Spatial population structure was found to be not only a function of spatial configuration of habitat patches, but population structure differed between the habitat generalist A. multinotatus and the habitat specialist N. albipennis.     

A network analysis of plant–pollinator interactions in temperate rain forests of Chiloé Island, Chile

This study characterizes the structure of a plant–pollinator network in a temperate rain forest of Chiloé Island, southern Chile, where woody species are strongly dependent on biotic pollinators, and analyzes its robustness to the loss of participating species. Degree distribution, nestedness, and expected species persistence were evaluated. In addition, we assessed the roles of predefined subsets of plants (classified by life forms) and pollinators (grouped by taxonomic orders) in the network’s structure and dynamics. For this, we simulated the complete removal of each plant and pollinator subset and analyzed the resultant connectivity patterns, as well as the expected long-term species losses by running a stochastic model. Finally, we evaluated the sensitivity of the network structure to the loss of single species in order to identify potential targets for conservation. Our results show that the plant–pollinator network of this Chilean temperate rain forest exhibits a nested structure of interactions, with a degree distribution best described by a power law model. Model simulations revealed the importance of trees and hymenopterans as pivotal groups that maintain the core structure of the pollination network and guarantee overall species persistence. The hymenopterans Bombus dahlbomii and Diphaglossa gayi, the shrubs Tepualia stipularis and Ugni molinae, the vines Mitraria coccinea and Asteranthera ovata, and the entire set of tree species exerted a disproportionately large influence on the preservation of network structure and should be considered as focal species for conservation programs given current threats from selective logging and habitat loss.     

外来入侵植物与人工林下层植被结构的关联性

为有效防控外来入侵植物,在广西陆川县人工林区进行植被嵌套样方调查,分析群落物种组成与植被结构和环境因子之间的相关性。Mantel检验表明样方物种组成与样方植被结构的相关性(r=0.208, P=0.002)高于其与环境因子相关性(r=0.084, P=0.051)。MRPP分析表明,有入侵植物阔叶丰花草(Spermacoce alata)、假臭草(Praxelis clematidea)和胜红蓟(Ageratum conyzoides)样方的植被结构与无这3种植物样方的有极显著不同(P 0.01),而有无薇甘菊(Mikainamicrantha)样方的植被结构相似。t检验表明林冠盖度(3.0 m)与这4种植物入侵均无显著相关性(P0.073)。通过增加垂直高度1.5 m以下的植被密度,可以减少阔叶丰花草、假臭草和胜红蓟的入侵,但对抑制薇甘菊入侵无效。因此,植被结构作为过滤器,可能主要作用于植物的种子产生时间、萌发周期和生长习性;以种子方式繁殖的入侵植物能否定植相对更依赖干扰、暴露的裸地;兼具无性和有性繁殖且能攀援和匍匐生长使得薇甘菊能够在不同植被结构的群落中相对随机地定植。     

The Microbial <Emphasis Type="BoldItalic">Phyllo</Emphasis>geography of the Carnivorous Plant <Emphasis Type="BoldItalic">Sarracenia alata</Emphasis>

Carnivorous pitcher plants host diverse microbial communities. This plant–microbe association provides a unique opportunity to investigate the evolutionary processes that influence the spatial diversity of microbial communities. Using next-generation sequencing of environmental samples, we surveyed microbial communities from 29 pitcher plants (Sarracenia alata) and compare community composition with plant genetic diversity in order to explore the influence of historical processes on the population structure of each lineage. Analyses reveal that there is a core S. alata microbiome, and that it is similar in composition to animal gut microfaunas. The spatial structure of community composition in S. alata (phyllogeography) is congruent at the deepest level with the dominant features of the landscape, including the Mississippi river and the discrete habitat boundaries that the plants occupy. Intriguingly, the microbial community structure reflects the phylogeographic structure of the host plant, suggesting that the phylogenetic structure of bacterial communities and population genetic structure of their host plant are influenced by similar historical processes.     

THE STRUCTURE OF GRANA IN FLOWERING PLANTS

A model of granum structure, consisting of multiple helical frets wound around each cylindrical granum, is proposed as a representation of granum structure for flowering plants in general. This model was originally formulated for grana in the mesophyll plastids of Zea mays and was subsequently extended to grana of Phaseolus vulgaris by additional studies. The model is now shown to be applicable also to grana in the plastids of Cannabis sativa, Elodea canadensis, Nicotiana rustica, Pisum sativum, and Spinacia oleracea. This sample of seven angiosperms includes genera commonly studied by other workers in their ultrastructural investigations of plastid structure.     

Pollen morphology of JapaneseSymplocos (Symplocaceae)

The pollen morphology of all 23 Japanese species ofSymplocos (1 of subgenusEusymplocos, and 22 of subgenusHopea) was comprehensively studied using LM, SEM and TEM, and found to be classifiable into two types (Type I and II) primarily on the basis of wall structure. Type I, characterized by a thick tectum lacking a supratectal structure and reduced columellae, occurs in subgenusEusymplocos, while Type II, characterized by a thin tectum with a supratectal structure and generally distinct columellae, occurs in subgenusHopea. Resemblances in wall structure suggest a closer relationship of subgenusEusymplocos to subgenusMicrosymplocos as well as of subgenusHopea to subgenusEpigenia. This fact contradicts the earlier proposed infrageneric classification, and may require its revision. Within Type II, five subtypes are recognized primarily on the basis of sculpture combined with other pollen characters. Systematic value of sculpture (i.e., subtype), aperture morphology and “globules”, as well as certain species relationships based on those characters, are also discussed.     

Structure of a Novel Drug-Nucleic Acid Crystalline Complex: 1,10-Phenanthroline-Platinum(II) Ethylenediamine—5′-Phosphoryl-Thymidylyl(3′-5′) Deoxyadenosine

Abstract

1,10-Phenanthroline-platinum (II) ethylenediamine (PEPt) forms a 1:2 crystalline complex with 5′-phosphorylthymidylyl (3′-5′) deoxyadenosine (d-pTpA). Crystals are monoclinic, P2₁, with a - 10.204 Å, b =24.743 Å, c = 21.064 Å, β = 94.6°. The structure has been determined by Patterson and Fourier methods, and refined by least squares to a residual of 0.128 on 2,367 observed reflections.

PEPt molecules form sandwich-like stacks with adenine-thymine hydrogen-bonded pairs along the a axis. Intercalation in the classic sense is not observed in this structure. Instead, d-pTpA molecules form an open chain structure in which adenine-thymine residues hydrogen- bond together with the reversed Hoogsteen type base-pairing configuration. Deoxyadenosine residues exist in the syn conformation and are C3′ endo and C1′ exo. Thymidine residues are in the high anti conformation with C2′ endo puckers. The structure is heavily hydrated, forming a channel-like water network along the a axis. Other features of the structure are described.     

基于结构方程模型分析林分空间结构对草本物种多样性的影响

林分空间结构的改变直接影响林下草本物种的多样性。以针叶纯林、针阔混交林和常绿阔叶林为研究对象,采用结构方程模型研究了林分空间结构对林下草本物种多样性的影响,并探讨了林分水平空间结构,垂直空间结构以及林木竞争态势对林下草本物种多样性的影响的相对重要性。结果表明,林分水平空间结构对林下草本的物种多样性指数和物种均匀性指数均存在极显著的影响（P < 0.001）,影响系数高达0.96和0.89,对林下草本物种丰富度存在显著影响（P < 0.01）,影响系数为0.22;林分垂直空间结对林下草本丰富度和物种均匀性指数均存在极显著的影响（P < 0.001）,影响系数分别为0.86和0.43,对林下草本物种多样性指数存在显著影响（P < 0.01）,影响系数为0.16;林木竞争指数与林下草本丰富度和物种多样性指数也均存在极显著的影响（P < 0.001）,但影响系数较小,分别为-0.47和-0.30,而对林下草本物种均匀性指数未达到显著影响作用（P > 0.05）,影响系数仅为-0.04。整体上看,林分水平空间结构、垂直空间结构和林木竞争态势均对林下草本物种多样性有较强的影响作用,但从影响系数看,林分水平空间结构的影响作用最大,垂直空间结构次之,林木竞争态势的影响作用最小。因此,欲维持或改善林下草本物种多样性,应采取调整林分水平空间结构为主,垂直空间结构调整为辅,并适当降低林木竞争程度的综合经营措施。