Methoxyspheroidene and methoxyspheroidenone,two carotenoids from Rhodopseudomonas spheroides

Two new carotenoids isolated from Rhodopseudomonas spheroides (Rhodospirillaceae) have been identified as methoxyspheroidene (1,1′-dimethoxy-3,4-didehydro-1,2,1′,2′,7$\text{,}\text{?}$8′-hexahydro-ψ,ψ-carotene) obtained from anaerobic cultures and methoxyspheroidenone (1,1′-dimethoxy-3,4-didehydro-1,2,1′,2′,7′,8′-hexahydro-ψ,ψ-caroten-2-one) recovered from aerobic cultures.     

Cross-conjugated carotenoid aldehydes in Rhodopseudomonas viridis

Two carotenoid aldehydes isolated from Rhodopseudomonas viridis (Rhodospirillaceae) have been identified as lycopen-20-al (13-cis-ψ, ψ-caroten-20-al) and the novel 3,4-didehydro-1,2-dihydrolycopen-20 (or 20′)-al (3,4-didehydro-1,2-dihydro-ψ,ψ-caroten-20-al or 3′, 4′-didehydro-1′,2′-dihydro-ψ,ψ-caroten-20-al). Some extracts also contained acetonyl derivatives, probably artefacts produced from the cross-conjugated carotenoid aldehydes and acetone under alkaline conditions. The distribution of cross-conjugated caroten-20-als in photosynthetic bacteria is discussed.     

Mammalian Granulocyte–Macrophage Colony-stimulating Factor Receptor Expressed in Primary Avian Hematopoietic Progenitors: Lineage-specific Regulation of Proliferation and Differentiation

The cytokine Granulocyte–Macrophage Colony-Stimulating Factor (GM-CSF) regulates proliferation, differentiation, and apoptosis during myelopoiesis and erythropoiesis. Structure–function relationships of GM-CSF interactions with its receptor (GM-R), the biochemistry of GM-R signal transduction, and GM-CSF action in vivo are relatively well understood. Much less is known, however, about GM-R function in primary hematopoietic cells. In this paper we show that expression of the human GM-R in a heterologous cell system (primary avian erythroid and myeloid cells) confirms respective results in murine or human cell lines, but also provides new insights how the GM-R regulates progenitor proliferation and differentiation. As expected, the hGM-CSF stimulated myeloid progenitor proliferation and differentiation and enhanced erythroid progenitor proliferation during terminal differentiation. In the latter cells, however, the hGM-R only partially substituted for the activities of the erythropoietin receptor (EpoR). It failed to replace the EpoR in its cooperation with c-Kit to induce long-term proliferation of erythroid progenitors. Furthermore, the hGM-R α chain specifically interfered with EpoR signaling, an activity neither seen for the β_c subunit of the receptor complex alone, nor for the α chain of the closely related Interleukin-3 receptor. These results point to a novel role of the GM-R α chain in defining cell type–specific functions of the GM-R.     

An apoptosis-related gene network induced by novel compound-cRGD in human breast cancer cells

Synthetic peptides with the arginine-glycine-aspartate (RGD) motif have been used widely as inhibitors of integrin-ligand interactions to study cell growth, adhesion, migration and differentiation. We designed cyclic-RGD peptide (Tpa-RGDWPC-, cRGD) which could cause cell death in MCF-7 cell line. In order to understand the mechanism involved in cRGD-induced apoptosis, we used microarray, real-time quantitative PCR (Q-PCR) and bioinformatics to study the effects of cRGD on breast cancer cell line MCF-7. By time-series gene expression measurements and our developed software BSIP and GeneNetwork, we reconstructed an apoptosis-related gene network. In the network, caspase-9, located at the upstream, activates downstream effector caspases such as caspase-7, leading to the induction of caspase-4. Combined our previous proteomics data with newly performed docking simulation, it indicated that the cell death induced by cRGD may be triggered through blocking integrin signaling to the extracellular matrix and activation of caspase pathway. This study provides a molecular explanation of cRGD treatment in breast cancer cells and set forth a constructive far-reaching impact on breast cancer therapy.     

The SV40 Capsid Is Stabilized by a Conserved Pentapeptide Hinge of the Major Capsid Protein VP1

The simian virus 40 (SV40) outer shell is composed of 72 pentamers of VP1. The core of the VP1 monomer is a β-barrel with jelly-roll topology and extending N- and C-terminal arms. A pentapeptide hinge, KNPYP, tethers the C-arm to the VP1 β-barrel core. The five C-arms that extend from each pentamer insert into the neighbouring pentamers, tying them together through different types of interactions. In the mature virion, this element adopts either of six conformations according to their location in the capsid. We found that the hinge is conserved among 16 members of the Polyomaviridae, attesting to its importance in capsid assembly and/or structure. We have used site-directed mutagenesis to gain an understanding into the structural requirements of this element: Y299 was changed to A, F, and T, and P300 to A and G. The mutants showed reduction in viability to varying degrees. Unexpectedly, assembly was reduced only to a small extent. However, the data showed that the mutants were highly unstable. The largest effect was observed for mutations of P300, indicating a role of the proline in the virion structure. P300G was more unstable than P300A, indicating a requirement for rigidity of the pentapeptide hinge. Y299T and Y299A were more defective in viability than Y299F, highlighting the importance of an aromatic ring at this position. Structural inspection showed that this aromatic ring contacts C-arms of neighbouring pentamers. Computational modelling predicted loss of stability of the Y mutants in concordance with the experimental results. This study provides insights into the structural details of the pentapeptide hinge that are responsible for capsid stability.     

Protrusion and actin assembly are coupled to the organization of lamellar contractile structures

Directed cell migration requires continuous cycles of protrusion of the leading edge and contraction to pull up the cell rear. How these spatially distributed processes are coordinated to maintain a state of persistent protrusion remains unknown. During wound healing responses of epithelial sheets, cells along the wound edge display two distinct morphologies: ‘leader cells’ exhibit persistent edge protrusions, while the greater majority of ‘follower cells’ randomly cycle between protrusion and retraction. Here, we exploit the heterogeneity in cell morphodynamic behaviors to deduce the requirements in terms of cytoskeleton dynamics for persistent and sporadic protrusion events. We used quantitative Fluorescent Speckle Microscopy (qFSM) to compare rates of F-actin assembly and flow relative to the local protrusion and retraction dynamics of the leading edge. Persistently protruding cells are characterized by contractile actomyosin structures that align with the direction of migration, with converging F-actin flows interpenetrating over a wide band in the lamella. Conversely, non-persistent protruders have their actomyosin structures aligned perpendicular to the axis of migration, and are characterized by prominent F-actin retrograde flows that end into transverse arcs. Analysis of F-actin kinetics in the lamellipodia showed that leader cells have three-fold higher assembly rates when compared to followers. To further investigate a putative relationship between actomyosin contraction and F-actin assembly, myosin II was inhibited by blebbistatin. Treated cells at the wound edge adopted a homogeneously persistent protrusion behavior, with rates matching those of leader cells. Surprisingly, we found that disintegration of actomyosin structures led to a significant decrease in F-actin assembly. Our data suggests that persistent protrusion in these cells is achieved by a reduction in overall F-actin retrograde flow, with lower assembly rates now sufficient to propel forward the leading edge. Based on our data we propose that differences in the protrusion persistence of leaders and followers originate in the distinct actomyosin contraction modules that differentially regulate leading edge protrusion-promoting F-actin assembly, and retraction-promoting retrograde flow.     

Genetic variation, population structure, and linkage disequilibrium in European elite germplasm of perennial ryegrass

Perennial ryegrass (Lolium perenne L.) is a highly valued temperate climate grass species grown as forage crop and for amenity uses. Due to its outbreeding nature and recent domestication, a high degree of genetic diversity is expected among cultivars. The aim of this study was to assess the extent of linkage disequilibrium (LD) within European elite germplasm and to evaluate the appropriate methodology for genetic association mapping in perennial ryegrass. A high level of genetic diversity was observed in a set of 380 perennial ryegrass elite genotypes when genotyped with 40 SSRs and 2 STS markers. A Bayesian structure analysis identified two subpopulations, which were confirmed by principal coordinate analysis (PCoA). One subpopulation consisted mainly of genotypes originating from the UK, while germplasm mostly from Continental Europe was grouped into the second subpopulation. LD (r²) decay was rapid and occurred within 0.4 cM across European varieties, when population structure was taken into consideration. However, an extended LD of up to 6.6 cM was detected within the variety Aberdart. High genetic diversity and rapid LD decay provide means for high resolution association mapping in elite materials of perennial ryegrass. However, different strategies need to be applied depending on the material used. Genome-wide association study (GWAS) with several hundred markers can be applied within synthetic varieties to identify large (up to 10 cM) genomic regions affecting trait variation. A combination of available and novel DNA markers is needed to achieve resolution required for GWAS in elite breeding materials. An even higher marker density of several million SNPs might be needed for GWAS in diverse ecotype collections, potentially resulting in quantitative trait polymorphism (QTP) identification.     

家蚕吡哆醛激酶基因干扰降低转氨酶基因的转录表达

【目的】维生素B₆在氨基酸代谢中是多种酶的辅酶,维持氨基酸代谢的正常运行。磷酸吡哆醛（pyridoxal-5′-phosphate, PLP）是维生素B₆的主要辅酶形式,吡哆醛激酶（pyridoxal kinase, PLK）是PLP的重要生成酶,本研究试图明确PLK基因与PLP依赖酶之间转录水平的调节关系。【方法】本研究采用RNA干扰（RNA interference, RNAi）方法对家蚕 Bombyx mori 的PLK基因进行干扰,通过体外合成PLK基因的3个干扰片段（siRNA1, siRNA2和siRNA3）,将siRNA从体腔注入5龄第3天的家蚕幼虫体内诱导RNAi。利用荧光定量PCR测定不同干扰片段、不同时间点及不同组织中PLK基因表达量的变化;并测定家蚕体内磷酸丝氨酸转氨酶（phosphoserine aminotransferase, SerB）和天门冬氨酸氨基转移酶（asparate aminotransferase, AST）基因的表达量。【结果】注射干扰片段后48 h干扰效果达到最佳。3个干扰片段干扰效果从高到低依次为siRNA1, siRNA2和siRNA3。RNAi效果最好的是中肠组织,其PLK基因的相对表达量下降了55%。RNA干扰PLK基因后,后部丝腺中SerB和AST基因相对表达量分别下降了90%和29%。【结论】本研究通过RNAi实现了家蚕PLK基因干扰,并进一步证明了家蚕PLK基因和SerB基因及AST基因存在联动调节关系。     

Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus

Ostreococcus is a marine picophytoeukaryote for which culture studies indicate there are ‘high-light'' and ‘low-light'' adapted ecotypes. Representatives of these ecotypes fall within two to three 18S ribosomal DNA (rDNA) clades for the former and one for the latter. However, clade distributions and relationships to this form of niche partitioning are unknown in nature. We developed two quantitative PCR primer-probe sets and enumerated the proposed ecotypes in the Pacific Ocean as well as the subtropical and tropical North Atlantic. Statistical differences in factors such as salinity, temperature and NO₃ indicated the ecophysiological parameters behind clade distributions are more complex than irradiance alone. Clade OII, containing the putatively low-light adapted strains, was detected at warm oligotrophic sites. In contrast, Clade OI, containing high-light adapted strains, was present in cooler mesotrophic and coastal waters. Maximal OI abundance (19 555±37 18S rDNA copies per ml) was detected in mesotrophic waters at 40 m depth, approaching the nutricline. OII was often more abundant at the deep chlorophyll maximum, when nutrient concentrations were significantly higher than at the surface (stratified euphotic zone waters). However, in mixed euphotic-zone water columns, relatively high numbers (for example, 891±107 18S rDNA copies per ml, Sargasso Sea, springtime) were detected at the surface. Both Clades OI and OII were found at multiple euphotic zone depths, but co-occurrence at the same geographical location appeared rare and was detected only in continental slope waters. In situ growth rate estimates using these primer-probes and better comprehension of physiology will enhance ecological understanding of Ostreococcus Clades OII and OI which appear to be oceanic and coastal clades, respectively.     

热带雨林和亚热带季雨林灌木光合作用对水分胁迫的反应

生长在热带植物温室的热带雨林植物Piper hispidum和亚热带季风常绿阔叶林植物九节(Psychotria rubra),在灌水、环境的CO_2浓度和26℃下,饱和光强的最大光合速率(PN)分别为6.3和9.8μmol·m~(-2)·s~(-1)。在低的叶片/空气水蒸汽压陡度(△w=10毫巴·巴~(-1))情况下,每降低叶片水势(ψ)1巴,P.hispidum的PN降低0.38μmol·m~(-2)·s~(-1);当ψ为-8巴时,PN随△w增高而降低,其关系PN=7.02-0.06△w(r~2=0.7);ψ为—13巴时,PN与△w关系的直线斜率变小(0.02)。对于九节,PN对△w变化的反应更为敏感。在ψ为-8.75巴时,PN=11.16—0.1△w(r~2=0.65)。在高ψ(-8和-8.75巴)情况下,两种灌木的气孔传导率(g)随△w的变化而相近;但ψ降低时,九节的g对△w的变化反应较P.hispidum敏感。ψ降低导致两种灌木的水分利用效率(WUE,μmol·m~(-2)·s~(-1)CO_2同化/mmol·m~(-2)·s~(-1)水散失)增高;而△w增高,WUE降低。九节的PN对△w增高的反应较P.hispidum敏感。     

Carotenoids of Phaffia rhodozyma, a red-pigmented fermenting yeast

The red-pigmented fermenting yeast Phaffia rhodozyma contains astaxanthin as the principal carotenoid pigment. Echinenone, 3-hydroxyechinenone and phoenicoxanthin were also isolated and identified; isocryptoxanthin and canthaxanthin were absent. Evidence is presented for a new carotenoid, 3-hydroxy-3′4′-didehydro-β,ψ-caroten-4-one. A possible biosynthetic scheme for the formation of astaxanthin in P. rhodozyma is suggested.     

Genetic Architecture and Functional Characterization of Genes Underlying the Rapid Diversification of Male External Genitalia Between Drosophila simulans and Drosophila mauritiana

Male sexual characters are often among the first traits to diverge between closely related species and identifying the genetic basis of such changes can contribute to our understanding of their evolutionary history. However, little is known about the genetic architecture or the specific genes underlying the evolution of male genitalia. The morphology of the claspers, posterior lobes, and anal plates exhibit striking differences between Drosophila mauritiana and D. simulans. Using QTL and introgression-based high-resolution mapping, we identified several small regions on chromosome arms 3L and 3R that contribute to differences in these traits. However, we found that the loci underlying the evolution of clasper differences between these two species are independent from those that contribute to posterior lobe and anal plate divergence. Furthermore, while most of the loci affect each trait in the same direction and act additively, we also found evidence for epistasis between loci for clasper bristle number. In addition, we conducted an RNAi screen in D. melanogaster to investigate if positional and expression candidate genes located on chromosome 3L, are also involved in genital development. We found that six of these genes, including components of Wnt signaling and male-specific lethal 3 (msl3), regulate the development of genital traits consistent with the effects of the introgressed regions where they are located and that thus represent promising candidate genes for the evolution these traits.     

Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial

Advancements in mass spectrometry‐based proteomics have enabled experiments encompassing hundreds of samples. While these large sample sets deliver much‐needed statistical power, handling them introduces technical variability known as batch effects. Here, we present a step‐by‐step protocol for the assessment, normalization, and batch correction of proteomic data. We review established methodologies from related fields and describe solutions specific to proteomic challenges, such as ion intensity drift and missing values in quantitative feature matrices. Finally, we compile a set of techniques that enable control of batch effect adjustment quality. We provide an R package, "proBatch", containing functions required for each step of the protocol. We demonstrate the utility of this methodology on five proteomic datasets each encompassing hundreds of samples and consisting of multiple experimental designs. In conclusion, we provide guidelines and tools to make the extraction of true biological signal from large proteomic studies more robust and transparent, ultimately facilitating reliable and reproducible research in clinical proteomics and systems biology.     

Stress induces tRNA cleavage by angiogenin in mammalian cells

tRNAs play a central role in protein translation, acting as the carrier of amino acids. By cloning microRNAs, we unexpectedly obtained some tRNA fragments generated by tRNA cleavage in the anticodon loop. These tRNA fragments are present in many cell lines and different mouse tissues. In addition, various stress conditions can induce this tRNA cleavage event in mammalian cells. More importantly, angiogenin (ANG), a member of RNase A superfamily, appears to be the nuclease which cleaves tRNAs into tRNA halves in vitro and in vivo. These results imply that angiogenin plays an important physiological role in cell stress response, except for the known function of inducing angiogenesis.     

Integrated and independent evolution of heteromorphic sperm types

Sperm are a simple cell type with few components, yet they exhibit tremendous between-species morphological variation in those components thought to reflect selection in different fertilization environments. However, within a species, sperm components are expected to be selected to be functionally integrated for optimal fertilization of eggs. Here, we take advantage of within-species variation in sperm form and function to test whether sperm components are functionally and genetically integrated both within and between sperm morphologies using a quantitative genetics approach. Drosophila pseudoobscura males produce two sperm types with different functions but which positively interact together in the same fertilization environment; the long eusperm fertilizes eggs and the short parasperm appear to protect eusperm from a hostile female reproductive tract. Our analysis found that all sperm traits were heritable, but short sperm components exhibited evolvabilities 10 times that of long sperm components. Genetic correlations indicated functional integration within, but not between, sperm morphs. These results suggest that sperm, despite sharing a common developmental process, can become developmentally and functionally non-integrated, evolving into separate modules with the potential for rapid and independent responses to selection.     

Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog Ranitomeya imitator

The number of genes controlling mimetic traits has been a topic of much research and discussion. In this paper, we examine a mimetic, dendrobatid frog Ranitomeya imitator, which harbours extensive phenotypic variation with multiple mimetic morphs, not unlike the celebrated Heliconius system. However, the genetic basis for this polymorphism is unknown, and not easy to determine using standard experimental approaches, for this hard-to-breed species. To circumvent this problem, we first develop a new protocol for automatic quantification of complex colour pattern phenotypes from images. Using this method, which has the potential to be applied in many other systems, we define a phenotype associated with differences in colour pattern between different mimetic morphs. We then proceed to develop a maximum-likelihood method for estimating the number of genes affecting a quantitative trait segregating in a hybrid zone. This method takes advantage of estimates of admixture proportions obtained using genetic data, such as microsatellite markers, and is applicable to any other system where a phenotype has been quantified in an admixture/introgression zone. We evaluate the method using extensive simulations and apply it to the R. imitator system. We show that probably one or two, or at most three genes, control the mimetic phenotype segregating in a R. imitator hybrid zone identified using image analyses.     

中华按蚊气味结合蛋白基因AsinOBP1的克隆和表达分析

【目的】蚊虫的行为在很大程度上依赖于嗅觉系统, 例如寻找宿主和产卵场所等。中华按蚊Anopheles sinensis是我国最重要的传疟媒介之一, 但有关中华按蚊嗅觉信号传递过程的研究甚少。本研究旨在克隆和表达分析中华按蚊的气味结合蛋白（odorant binding proteins, OBPs）基因, 为进一步研究中华按蚊嗅觉传递的分子机制奠定基础。【方法】通过分析中华按蚊的转录组数据克隆气味结合蛋白基因, 采用RT-PCR和实时定量PCR技术分析该基因在成虫不同组织和在吸血前后的表达模式。【结果】克隆到一个气味结合蛋白基因, 命名为AsinOBP1 (GenBank登录号为KJ958382)。AsinOBP1基因开放阅读框长435 bp, 编码144个氨基酸, 具有典型的6个半胱氨酸位点。RT-PCR组织表达谱分析发现, AsinOBP1在检测的所有成虫触角、下颚须、喙和头部组织中都有表达, 而在足和去掉头部以外的躯体组织中不表达。定量分析发现AsinOBP1在雌蚊触角中的表达水平最高, 吸食血液后, AsinOBP1的表达水平显著下降; 仅用小鼠气味处理后, AsinOBP1的表达水平也显著下降。【结论】研究结果说明AsinOBP1可能是嗅觉组织特异性表达的基因, 与雌蚊寻找宿主等行为有关, 其功能还需深入研究。