小单孢菌属特异寡核苷酸探针的设计及杂交条件优化

小单孢菌在生态环境中占有重要地位,也是寻找新的抗生素的重要来源.为了探索小单孢菌的生态分布和在未培养情况下的生态位,在分离和鉴定一定数量的小单孢菌的情况下利用小单孢菌属的16S rDNA基因同源性,采用ClustalX软件进行序列分析,设计了小单孢菌属的16S rRNA特异寡核苷酸探针Mn1和Mn3两个序列,将这两个序列与GenBank中小单孢和非小单孢菌属的16S rRNA序列进行Blastn比对分析,先在理论上确认Mn1和Mn3对小单孢菌属是特异的.收集小单孢和非小单孢菌株19株,通过原位杂交试验的方法对设计的探针进行特异性验证,结果证明,Mn1能和试验用到的所有小单孢菌属的标准菌株杂交和非小单孢菌均不能杂交;Mn3能和所有小单孢菌属的标准菌株杂交,但也能与链霉菌CGMCC4.891(Streptomyces microflavus)杂交.初步证明Mn1可作为小单孢菌属的特异性探针.并通过杂交条件试验优化了Mn1荧光原位杂交的条件:甲酰胺浓度为30%,溶菌酶处理时间为37℃ 40 min,HCl处理时间为60 min,杂交时间为3 h.     

Structure and Disorder in an Unfolded State under Nondenaturing Conditions from Ensemble Models Consistent with a Large Number of Experimental Restraints

Obtaining detailed structural models of disordered states of proteins under nondenaturing conditions is important for a better understanding of both functional intrinsically disordered proteins and unfolded states of folded proteins. Extensive experimental characterization of the drk N-terminal SH3 domain unfolded state has shown that, although it appears to be highly disordered, it possesses significant nonrandom secondary and tertiary structure. In our previous attempts to generate structural models of the unfolded state using the program ENSEMBLE, we were limited by insufficient experimental restraints and conformational sampling. In this study, we have vastly expanded our experimental restraint set to include ¹H-¹⁵N residual dipolar couplings, small-angle X-ray scattering measurements, nitroxide paramagnetic relaxation enhancements, O₂-induced ¹³C paramagnetic shifts, hydrogen-exchange protection factors, and ¹⁵N R₂ data, in addition to the previously used nuclear Overhauser effects, amino terminal Cu²⁺-Ni²⁺ binding paramagnetic relaxation enhancements, J-couplings, chemical shifts, hydrodynamic radius, and solvent accessibility restraints. We have also implemented a new ensemble calculation methodology that uses iterative conformational sampling and seeks to calculate the simplest possible ensemble models. As a result, we can now generate ensembles that are consistent with much larger experimental data sets than was previously possible. Although highly heterogeneous and having broad molecular size distributions, the calculated drk N-terminal SH3 domain unfolded-state ensembles have very different properties than expected for random or statistical coils and possess significant nonnative α-helical structure and both native-like and nonnative tertiary structure.     

From Africa via Europe to South America: migrational route of a species‐rich genus of Neotropical lowland rain forest trees (Guatteria,Annonaceae)

Aim Several recent studies have suggested that a substantial portion of today’s plant diversity in the Neotropics has resulted from the dispersal of taxa into that region rather than by vicariance. In general, three routes have been documented for the dispersal of taxa onto the South American continent: (1) via the North Atlantic Land Bridge, (2) via the Bering Land Bridge, or (3) from Africa directly onto the continent. Here a species‐rich genus of Neotropical lowland rain forest trees (Guatteria, Annonaceae) is used as a model to investigate these three hypotheses. Location The Neotropics. Methods The phylogenetic relationships within the long‐branch clade of Annonaceae were reconstructed (using maximum parsimony, maximum likelihood and Bayesian inference) in order to gain insight in the phylogenetic position of Guatteria. Furthermore, Bayesian molecular dating and Bayesian dispersal–vicariance (Bayes‐DIVA) analyses were undertaken. Results Most of the relationships within the long‐branch clade of Annonaceae were reconstructed and had high support. However, the relationship between the Duguetia clade, the Xylopia–Artabotrys clade and Guatteria remained unclear. The stem node age estimate of Guatteria ranged between 49.2 and 51.3 Ma, whereas the crown node age estimate ranged between 11.4 and 17.8 Ma. For the ancestral area of Guatteria and its sister group, the area North America–Africa was reconstructed in 99% of 10,000 DIVA analyses, while South America–North America was found just 1% of the time. Main conclusions The estimated stem to crown node ages of Guatteria in combination with the Bayes‐DIVA analyses imply a scenario congruent with an African origin followed by dispersal across the North Atlantic Land Bridge in the early to middle Eocene and further dispersal into North and Central America (and ultimately South America) in the Miocene. The phylogenetically and morphologically isolated position of the genus is probably due to extinction of the North American and European stem lineages in the Tertiary.     

基于高光谱遥感的小麦叶干重和叶面积指数监测

生物量和叶面积指数(LAI)是描述作物长势的重要参数, 叶干重和LAI的实时动态监测对小麦(Triticum aestivum)生长诊断和管理调控具有重要意义。为分析多种高光谱参数估算小麦叶干重和LAI的效果, 建立小麦叶干重和LAI的定量监测模型, 该研究连续3年采用不同小麦品种进行不同施氮水平的大田试验, 于小麦不同生育期采集田间冠层高光谱数据并测定叶片叶干重和LAI。试验结果显示, 小麦叶干重和LAI随施氮水平的提高而增加, 随生育进程呈单峰动态变化模式。小麦叶干重和LAI与光谱反射率间相关性较好的区域主要位于红光波段(590~710 nm, r<-0.60)和近红外波段(745~1 130 nm, r>0.69)。对于不同试验条件下的叶干重和LAI, 可以使用统一的光谱参数进行定量反演, 其中基于RVI (810, 560)、FD755、GM1、SARVI (MSS)和TC3等光谱参数的方程拟合效果较好。经不同年际独立试验数据的检验表明, 以参数RVI (810, 560)、GM1、SARVI (MSS)、PSSRb、(R_750-800/R_695-740) -1、VOG2和MSR705为变量建立的叶干重和LAI监测模型均给出较好的检验结果。因此, 利用关键特征光谱参数可以有效地评价小麦叶片生长状况, 尤其是光谱参数RVI (810, 560)、GM1和SARVI (MSS)可以对不同条件下小麦叶干重和LAI进行准确可靠的监测。     

南亚热带人工林16种木本植物重要叶特征参数的相互关系

以南亚热带退化丘陵生态恢复进程中16种3 a生木本植物为对象,研究叶片重要特征参数间的相互关系.结果表明,植物叶片的N、P含量平均值低于全国平均值,N:P平均值则高于全国的平均水平;成熟叶片的N和P含量之间有极显著正相关关系(P<0.00001),N:P与N有弱的正相关关系(r=0.322,P<0.01),与P显著负相关,推断植物叶N:P主要由P决定(r=0/639,P<0.00001).含N量高的植物具有高的最大净光合速率(Pmax)、光合N利用效率(PNOE)和低的比叶重(LMA),反之,含N量低植物具有低的Pmax、PNUE和高的LMA;Pmax与PNUE极显著正相关,LMA与PNUE极显著负相关.     

Host genetic risk factors for community-acquired pneumonia

This study was conducted to establish the contribution of genetic host factors in the susceptibility to community acquired pneumonia (CAP) in the Russian population. Patients with CAP (n = 334), volunteers without a previous history of CAP, constantly exposed to infectious agents, control A group (n = 141) and a second control group B consisted of healthy persons (n = 314) were included in the study. All subjects were genotyped for 13 polymorphic variants in the genes of xenobiotics detoxification CYP1A1 (rs2606345, rs4646903, and rs1048943), GSTM1 (Ins/del), GSTT1 (Ins/del), ABCB1 rs1045642); immune and inflammation response IL-6 (rs1800795), TNF-a (rs1800629), MBL2 (rs7096206), CCR5 (rs333), NOS3 (rs1799983), angiotensin-converting enzyme ACE (rs4340), and occlusive vascular disease/hyperhomocysteinemia MTHFR (rs1801133). Seven polymorphic variants in genes CYP1A1, GSTM1, ABCB1, NOS3, IL6, CCR5 and ACE were associated with CAP. For two genes CYP1A1 and GSTM1 associations remained significant after correction for multiple comparisons. Multiple analysis by the number of all risk genotypes showed a highly significant association with CAP (P = 2.4 × 10^− 7, OR = 3.03, 95% CI 1.98–4.64) with the threshold for three risk genotypes. Using the ROC-analysis, the AUC value for multi-locus model was estimated as 68.38.     

The ramification of Apinagia riedelii: A key to the understanding of the plant architecture of Podostemaceae,subfamily Podostemoideae

The study of the ramification pattern of Apinagia riedelii results in a new concept of the architecture of this species, with general implications to members of subfamily Podostemoideae with dithecous leaves. The presence of a subtending leaf below the floriferous shoot proves axillary branching also for species with dithecous leaves. Previous opinions of an unusual ramification mode by subfoliar or non-axillary branching or stem bifurcation in combination with dithecous leaves hitherto pleaded for Podostemoideae is refuted. Moreover, the view of the so-called dithecous leaves with one sheath (theca) at the ventral and one at the dorsal side of the leaf, previously regarded as initially connected with branching, has to be changed. The dithecous leaf arises from the branch and not from the mother shoot axis – as previously believed – and represents the addorsed hypsophyll, i.e., the first leaf (prophyll) of the floriferous branch. This finding leads to the conclusion that the lower sheath of the dithecous leaf is the ventral (not dorsal) sheath pointing to the branch and surrounding its flower bud with a ligule or an ochrea and a hood upon the bud. In this way, the branch and its flower bud become seemingly sunk in the leaf base. At the fusion of leaf basis and shoot results this enigmatic common tissue. The wings of the dorsal (upper) sheath of the dithecous leaf point to the mother shoot axis of the branch. Successive floriferous branches along the main stem disclose the shoot axis of A. riedelii as a monopodium (not sympodium) that develops an anthocladial (foliated) inflorescence in the form of a botrys or a compound botrys, respectively. Since it is generally difficult to define cymose or racemose inflorescences if subtending leaves are absent – which occur in most other species of subfamily Podostemoideae with dithecous leaves – the nature of these inflorescences is discussed anew. The findings on A. riedelii have consequences on our comprehension of the shoot architecture of Podostemoideae.     

Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network

This article attempts to increase the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins through improved learning. Most methods developed for improving the backpropagation algorithm of artificial neural networks are limited to small neural networks. Here, we introduce a guided-learning method suitable for networks of any size. The method employs a part of the weights for guiding and the other part for training and optimization. We demonstrate this technique by predicting residue solvent accessibility and real-value backbone torsion angles of proteins. In this application, the guiding factor is designed to satisfy the intuitive condition that for most residues, the contribution of a residue to the structural properties of another residue is smaller for greater separation in the protein-sequence distance between the two residues. We show that the guided-learning method makes a 2-4% reduction in 10-fold cross-validated mean absolute errors (MAE) for predicting residue solvent accessibility and backbone torsion angles, regardless of the size of database, the number of hidden layers and the size of input windows. This together with introduction of two-layer neural network with a bipolar activation function leads to a new method that has a MAE of 0.11 for residue solvent accessibility, 36 degrees for psi, and 22 degrees for phi. The method is available as a Real-SPINE 3.0 server in http://sparks.informatics.iupui.edu.     

Mitochondrial DNA variation and the evolutionary history of the Mediterranean species of Cicada L. (Hemiptera,Cicadoidea)

Cicadas are widely distributed in the Mediterranean area and are mainly distinguished by male acoustic signals, which act as specific mate recognition systems. Within the genus Cicada L. several species have diverged in their calling songs without showing external morphological differences, so acoustic recordings and genetic studies are particularly useful for systematic, biogeography and evolutionary studies. This study assesses sequence variation in closely related species of Cicada from the Mediterranean area, using domain III of the 12S rRNA mitochondrial gene in order to determine the phylogenetic relationships and the evolutionary history of this group, as well as the population structure of the two most common species, C. orni and C. barbara. Five distinct haplogroups were identified, C. orni, C. barbara, C. mordoganensis, C. cretensis and C. lodosi, each corresponding to a distinct evolutionary group. C. barbara was the most divergent species within this group, while C. orni and C. mordoganensis were the most similar. The population structure and demographic parameters of the species were not completely resolved. However, there is evidence for the separation of the C. orni Greek populations from the rest of Europe and also for demographic expansions probably related to Pleistocene climate changes. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 266–288.