Pseudomonas duriflava sp nov., isolated from a desert soil

A Gram-negative, rod-shaped, non-motile, non-spore-forming bacterium, designated strain HR2(T) was isolated from a soil sample from the Talklimaken Desert in Xinjiang Province, China. Strain HR2(T) grew optimally at pH 7.0-8.0 and 30-37 degrees C in the presence of 0-1% (w/v) NaCl. An analysis of 16S rRNA gene sequences revealed that strain HR2(T) fell within the radiation of the genus Pseudomonas, the highest level of similarity being found with respect to Pseudomonas luteola IAM 13000(T) (97.5%); the levels of sequence similarity with respect to other recognized Pseudomonas species were < 96.4%. DNA-DNA hybridization showed that the genetic relatedness between strain HR2(T) and P. luteola IAM 13000(T) was 53.2%. The G + C content of the genomic DNA of strain HR2(T) was 55.2 mol%. The major fatty acids were 18: 1, summed feature 3 and 16:0. The hydroxylated fatty acids 10:0 3-OH, 12:0 3-OH and 12:0 2-OH were also present. The data obtained in this polyphasic study indicated that this isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas duriflava sp. nov. is proposed, The type strain is HR2(T) (=KCTC 221129(T) =CGMCC 1.6858(T)).

Sphingobacterium siyangense sp nov., isolated from farm soil

The taxonomic position of a novel Gram-negative strain, designated Sy1(T), isolated from a farm-soil sample obtained from Jiangsu Province, PR China, was characterized by using a polyphasic approach. The cells were non-motile, non-spore-forming rods. The organism grew optimally at 30-37 degrees C and at pH 6.0-8.0. Based on 16S rRNA gene sequence analysis, strain Sy1(T) is a member of the genus Sphingobacterium; Sphingobacterium multivorum JCM 21156(T) was the nearest relative (98.5% sequence similarity). The predominant fatty acids of strain Sy1T were isoC15:0 (32.90/o), C16:0 (10.9%) and summed feature 3 (iso-C-15:0 2-OH and/or C-16:1 omega 7c; 24.1%). The DNA G + C content was 38.5 mol%. The low level of DNA-DNA relatedness (2.2 %) to S. multivorum JCM 21156 T in combination with differential morphological and biochemical properties demonstrated that strain SY1(T) (=KCTC 22131(T)= CGMCC 1.6855(T)) should be classified as representing a novel species of the genus Sphingobacterium for which the name Sphingobacterium siyangense sp. nov. is proposed.

The evolution of cooperation in asymmetric systems

Explaining "Tragedy of the Commons" of evolution of cooperation remains one of the greatest problems for both biology and social science. Asymmetrical interaction, which is one of the most important characteristics of cooperative system, has not been sufficiently considered in the existing models of the evolution of cooperation. Considering the inequality in the number and payoff between the cooperative actors and recipients in cooperation systems, discriminative density-dependent interference competition will occur in limited dispersal systems. Our model and simulation show that the local but not the global stability of a cooperative interaction can be maintained if the utilization of common resource remains unsaturated, which can be achieved by density-dependent restraint or competition among the cooperative actors. More intense density dependent interference competition among the cooperative actors and the ready availability of the common resource, with a higher intrinsic contribution ratio of a cooperative actor to the recipient, will increase the probability of cooperation. The cooperation between the recipient and the cooperative actors can be transformed into conflict and, it oscillates chaotically with variations of the affecting factors under different environmental or ecological conditions. The higher initial relatedness (i.e. similar to kin or reciprocity relatedness), which is equivalent to intrinsic contribution ratio of a cooperative actor to the recipient, can be selected for by penalizing less cooperative or cheating actors but rewarding cooperative individuals in asymmetric systems. The initial relatedness is a pivot but not the aim of evolution of cooperation. This explains well the direct conflict observed in almost all cooperative systems.

Phylogenetic studies of pantherine cats (Felidae) based on multiple genes, with novel application of nuclear beta-fibrinogen intron 7 to carnivores

The pantherine lineage of the cat family Felidae (order: Carnivora) includes five big cats of genus Panthera and a great many midsized cats known worldwide. Presumably because of their recent and rapid radiation, the evolutionary relationship among pantherines remains ambiguous. We provide an independent assessment of the evolutionary history of pantherine lineage using two complete mitochondrial (mt) genes (ND2 and ND4) and the nuclear beta-fibrmogen intron 7 gene, whose utility in carnivoran phylogeny was first explored. The available four mt (ND5, cytb, 12S, and 16SrRNA) and two nuclear (IRBP and TTR) sequence loci were also combined to reconstruct phylogeny of 14 closely related cat species. Our analyses of combined mt data (six genes; approximate to 3750 bp) and combined mt and nuclear data (nine genes; approximate to 6500 bp) obtained identical tree topologies, which were well-resolved and strongly supported for almost all nodes. Monophyly of Panthera genus in pantherine lineage was confirmed and interspecific affinities within this genus revealed a novel branching pattern, with P. tigris diverging first in Panthera genus, followed by P. onca, P. leo, and last two sister species P. pardus and P. uncia. In addition, close association of Neofelis nebulosa to Panthera, the phylogenetic redefinition of Otocolobus manil within the domestic cat group, and the relatedness of Acinonyx jubatus and Puma concolor were all important findings in the resulting phylogenies. The potential utilities of nine different genes for phylogenetic resolution of closely related pantherine species were also evaluated, with special interest in that of the novel nuclear beta-fibrinogen intron 7. (c) 2005 Elsevier Inc. All rights reserved.

DNA sequence analysis of the triose phosphate isomerase gene from isolates of Giardia lamblia

Objective To confirm the genetic relation between Giardia lamblia (G. lamblia) isolates from different geographic regions of China and other countries. Methods Genomic DNA were extracted from the trophozoites or cysts of Giardia lamblia. The triose phosphate isomerase (tim) gene was amplified using polymerase chain reaction (PCR) technique. PCR products were digested with endonuclease and sequenced. The data of sequencing were analyzed with the DNAstar software and compared with that of the isolates acquired from GenBank. Results Of nine isolates of Giardia lamblia from China (C1, C2, CH2 and CH3), Cambodia (CAM), Australia (A1 and A2) and America (BP and CDC), respectively, 3 (A1, A2 and CAM) fit into Group 1 (WB), 2 (CH2 and CH3) into Group 2, and 4 (C1, C2, BP and CDC) into Group 3 (GS). The results confirmed the genetic relatedness of G. lamblia isolates from all over the world. Conclusion Genotyping isolates of G. Lamblia provides important information for establishing the phylogenetic relationship or for the epidemiological evaluation of the spreading of this organism.

Parentage determination of an isolated Yangtze finless porpoise population Neophocaena phocaenoides asiaeorientalis in the Yangtze Tian-e-Zhou Baiji National Natural Reserve based on molecular data

Reproductive behaviors are poorly known for the Yangtze finless porpoise Neophocaena phocaenoides asiaeorientalis. In this study, the parentage of an isolated Yangtze finless porpoise population inhabiting the Yangtze Tian-e-Zhou Baiji National Natural Reserve is determined by analysis of microsatellite loci and mitochondrial DNA (mtDNA) control region sequences, and the porpoise's reproductive behaviors are studied. Overall 4 full parentage assignments and additional 3 single parentage assignments were determined for the population of 23 individuals. The analysis shows that their estimated reproductive cycle is shorter than that reported previously and there probably exists an overlapping between gestation and lactation period. The Study also shows that the female does not show fidelity to a particular male for breeding and vice versa, the oldest males did not monopolize mating and the dominance rank could not be so strict for the porpoise society. Moreover, the porpoise's mating pattern and relatedness among candidate parents are discussed here. These results provide important information for making guidelines of management and conservation for this protected population.

Common evolutionary origin of aquareoviruses and orthoreoviruses revealed by genome characterization of Golden shiner reovirus, Grass carp reovirus, Striped bass reovirus and golden ide reovirus (genus Aquareovirus, family Reoviridae)

Full-length and partial genome sequences of four members of the genus Aquareovirus, family Reoviridae (Golden shiner reovirus, Grass carp reovirus, Striped bass reovirus and golden ide reovirus) were characterized. Based on sequence comparison, the unclassified Grass carp reovirus was shown to be a member of the species Aquareovirus C The status of golden ide reovirus, another unclassified aquareovirus, was also examined. Sequence analysis showed that it did not belong to the species Aquareovirus A or C, but assessment of its relationship to the species Aquareovirus B, D, E and F was hampered by the absence of genetic data from these species. In agreement with previous reports of ultrastructural resemblance between aquareoviruses and orthoreoviruses, genetic analysis revealed homology in the genes of the two groups. This homology concerned eight of the 11 segments of the aquareovirus genome (amino acid identity 17-42%), and similar genetic organization was observed in two other segments. The conserved terminal sequences in the genomes of members of the two groups were also similar. These data are undoubtedly an indication of the common evolutionary origin of these viruses. This clear genetic relatedness between members of distinct genera is unique within the family Reoviridae. Such a genetic relationship is usually observed between members of a single genus. However, the current taxonomic classification of aquareoviruses and orthoreoviruses in two different genera is supported by a number of characteristics, including their distinct G+C contents, unequal numbers of genome segments, absence of an antigenic relationship, different cytopathic effects and specific econiches.

Rhodococcus qingshengii sp nov., a carbendazim-degrading bacterium

A Gram-positive, aerobic, non-motile, mesophilic strain, djl-6(T), able to degrade carbendazim, was isolated from a carbendazim-contaminated soil sample from Jiangsu province, China. The taxonomic position of this isolate was analysed by using a polyphasic approach. Chemotaxonomic analysis including peptidoglycan type, diagnostic sugar composition, fatty acid profile, menaquinones, polar lipids and mycolic acids showed that the characteristics of strain djl-6(T) were in good agreement with those of the genus Rhodococcus. DNA-DNA hybridization showed that it had low genomic relatedness with Rhodococcus baikonurensis DSM 44587(T) (31.8%), Rhodococcus erythropolis DSM 43066(T) (23.8%) and Rhodococcus globerulus DSM 43954(T) (117.7%), the three type strains to which strain djl-6(T) was most closely related based on 16S rRNA gene sequence analysis (99.78, 99.25 and 98.91% similarity, respectively). Based on the phenotypic properties and DNA-DNA hybridization data, strain djl-6(T) (=CGMCC 1.6580(T) =KCTC 19205(T)) is proposed as the type strain of a novel Rhodococcus species, Rhodococcus qingshengii sp. nov.

A linkage map of common carp (Cyprinus carpio) based on AFLP and microsatellite markers

P>Common carp (Cyprinus carpio) is an important fish for aquaculture, but genomics of this species is still in its infancy. In this study, a linkage map of common carp based on Amplified Fragment Length Polymorphism (AFLP) and microsatellite (SSR) markers has been generated using gynogenetic haploids. Of 926 markers genotyped, 151 (149 AFLPs, two SSRs) were distorted and eliminated from the linkage analyses. A total of 699 AFLP and 20 microsatellite (SSR) markers were assigned to the map, which comprised 64 linkage groups and covered 5506.9 cM Kosambi, with an average interval distance of 7.66 cM Kosambi. The normality tests on interval map distances showed a non-normal marker distribution. Visual inspection of the map distance distribution histogram showed a cluster of interval map distances on the left side of the chart, which suggested the occurrence of AFLP marker clusters. On the other hand, the lack of an obvious cluster on the right side showed that there were a few big gaps which need more markers to bridge. The correlation analysis showed a highly significant relatedness between the length of linkage group and the number of markers, indicating that the AFLP markers in this map were randomly distributed among different linkage groups. This study is helpful for research into the common carp genome and for further studies of genetics and marker-assisted breeding in this species.

青稞B组醇溶蛋白基因与上游调控区的克隆及基因表达

高等植物种子胚乳贮藏蛋白是种子发芽时的主要氮源，也是人类和动物食用植物蛋白的主要来源。大麦种子胚乳贮藏蛋白主要是醇溶蛋白（hordeins），占大麦胚乳总蛋白的50–60%。根据大麦醇溶蛋白的大小和组成特点，大麦醇溶蛋白被划分为三种类型：富硫蛋白亚类(B，γ-hordeins)、贫硫蛋白亚类（C-hordeins)以及高分子量蛋白亚类(D-hordeins)。B组和C组醇溶蛋白是大麦胚乳的两类主要贮藏蛋白，它们分别占大麦总醇溶蛋白成分的70–80%和10–12%。遗传分析表明，大麦B、C、D和γ-组醇溶蛋白分别是由位于大麦第五染色体1H（5）上的Hor2、Hor1、Hor3和Hor5位点编码。Hor2位点编码大量分子量相同但组成不同的B组醇溶蛋白（B-hordein）。B-hordein的种类、数量和分布是影响大麦酿造、食用及饲养品质的重要因素之一。为深入了解B-hordein基因家族的结构和染色体组织，探明Hor2位点基因表达的发育调控机制，最终达到改良禾谷类作物籽粒品质的目的，本研究以青藏高原青稞为材料，采用同源克隆法，分别克隆B-hordein基因和启动子，通过原核生物表达验证B-hordein基因功能，并利用实时定量PCR探索B-hordein基因表达时空关系，取得如下研究结果： 1. 以具有特殊B组醇溶蛋白亚基组成的9份青藏高原青稞为材料，根据GenBank中三个B-hordein基因序列（GenBank No. X03103, X53690和X53691）设计一对引物，通过PCR扩增，获得23个B-hordein基因克隆并对其进行了序列分析。核苷酸序列分析表明，所有克隆均包含完整的开放阅读框。有11个克隆都存在一个框内终止密码子，推测这11个克隆可能是假基因。推测的氨基酸序列分析表明，所有大麦B-hordein具有相似的蛋白质基本结构，均包括一个高度保守的信号肽、中间重复区以及C-端结构域。不同大麦种重复区内重复基元的数目有较大差异。青稞材料Z07–2和Z26的B-hordeins仅具有12个重复基元结构，更接近于野生大麦。这些重复基元数目的差异导致了重复区序列长度和结构的变异。这种现象极可能是由于醇溶谷蛋白基因在进化过程中染色体的不平衡交换或复制滑动所造成的。对所克隆基因和禾本科代表性醇溶谷蛋白基因进行聚类分析，结果表明所有来自栽培大麦的B-hordeins聚类成一个亚家族，来自野生大麦的B-hordeins以及普通小麦的LMW-GS聚类成另外一个亚家族，表明这两个亚家族的成员存在显著差异。此外，我们发现B-hordein基因推测的C-末端序列具有一些有规律的特征：即具有相同C-末端序列的B-hordein基因在系统发生树中聚类为同一个亚组（除BXQ053，BZ09-1，BZ26-5分别单独聚为一类外）。这个特征将有助于我们对所有B组醇溶蛋白基因家族成员进行分类，避免了在SDS-PAGE电泳图谱上仅依靠大小分类的局限性。 2. 根据上述克隆的青稞B-hordein基因的5’端序列设计三条基因特异的反向引物，以青稞Z09和Z26的基因组DNA为模板，采用SON-PCR和TAIL-PCR技术分离克隆出8个B-hordein基因的上游调控序列（命名为Z09P和Z26P）。序列分析表明，推测的TATA box位于–80 bp，CAAT–like box位于–140 bp处。此外，Z09P和Z26P中有六个序列在–300 bp处均存在一个由高度保守的EM基序和类GCN4基序构成的胚乳盒(Endosperm Box，EB)，在约–560 bp处存在一个胚乳盒类似结构。而Z09P-2和Z26P-3不存在保守的胚乳盒或其类似结构，预示着这两个启动子所调控的基因表达可能受不同类型反式作用因子的调节，推测该启动子对基因的表达调控具有多样性。 3. 将B-hordein基因的开放阅读框定向克隆到表达载体pET-30a中，将其导入大肠杆菌表达菌株BL21中进行外源基因的诱导表达以验证所克隆基因的功能。结果表明仅含重组子pET-BZ07-2和pET-BZ26-5的BL21细菌有目的表达蛋白产生。在诱导3 h时的蛋白表达量最高；3 mM IPTG诱导的蛋白表达量要高于1 mM IPTG诱导的表达量。这为分离纯化B-hordein蛋白以及进一步研究其对大麦籽粒品质的影响奠定基础。 4. 根据从青稞Z09和Z26中分离克隆的B-hordein基因序列设计一对基因特异的引物，同时，选择大麦α-微管蛋白基因（GenBank no. U40042）为看家基因并设计特异引物，利用实时荧光定量PCR检测了青稞籽粒4个胚乳发育时间段的B-hordein基因表达，荧光定量结果显示：两份材料中B-hordein基因的表达量均随发育过程的进行而逐渐升高。Z09中B-hordein基因在开花后7天开始转录，而Z26开花4天后就有低水平B-hordein的表达，这表明Z26中B-hordein基因可能比Z09表达的较早或者Z09中B-hordein基因表达水平较低以致于不能被检测到。此外，在4个不同的胚乳发育时期中，Z26中B-hordein基因的表达量均高于Z09材料。在开花12天到18天的过程中，Z09和Z26中B-hordein基因的表达水平有一个急剧性的升高。这说明在不同胚乳发育时期，Hor2位点的B-hordein等位基因变异体存在mRNA的差异表达。 Seed endosperm storage proteins in higher plants are the main resources of nitrogen for germinating and plant proteins for human and animals. Barley prolamins (also called hordeins) are the major storage proteins in the endosperm and account for 50–60% of total proteins. Hordeins are classically divided into three groups: sulphur-rich (B, γ-hordeins), sulphur-poor (C-hordeins) and high molecular weight (HMW, D-hordeins) hordeins based on the size and composition. B-hordeins and C-hordeins are two major groups and each respectively account for about 70-80% and 10-12% of the total hordein fraction in barley endosperm. Genetic analysis showed that B-, C-, C-, γ-hordeins are encoded by Hor2, Hor1, Hor3 and Hor5 locus on the chromosome 1H (5). Hor2 locus is rich in alleles that encode numerous heterogeneous B-hordein polypeptides. It is reported that B-hordein species, quantity and distribution are significant factors affecting malting, food and feed quality of barley. To understand comprehensively the structure and organization of B-hordein gene family in hull-less barley and explore the developmental control mechanisms of Hor2 locus gene expression and eventually to better exploitation in crop grain quality improvement, we isolated and cloned B-hordein genes and promotors of hull-less barley from Qinghai-Tibet Plateau by PCR, and testified their expression founction in bacteria expression system and explore their spatial and temporal expression pattern by quantitative real time PCR. Our results are as followed, 1. Twenty-three copies of B-hordein gene were cloned from nine hull-less barley cultivars of Qinghai-Tibet Plateau with special B-hordein subunits and molecularly characterized by PCR, based on three B-hordein genes published previously (GenBank No. X03103, X53690 and X53691). DNA sequences analyses confirmed that the six clones all contained a full-length coding region of the barley B-hordein genes. Eleven clones all contain an in-frame stop codon and they are probably pseudogenes. The analysis of deduced amino acid sequences of the genes shows that they have similar structures including signal peptide domain, central repetitive domain, and C-terminal domain. The number of the repeats was largerly variable and resulted in polypeptides in different sizes or structures among the genes. Twelve such repeated motifs were found in Z07–2 and Z26, and they are close to those of the wild barleys, and it is most probably caused by unequal crossing-over and/or slippage during replication as suggested for the evolution of other prolamins. The relatedness of prolamin genes of barley and wheat was assessed in the phylogenetic tree based on their polypeptides comparison. Our phylogenetic analysis suggested that the predicted B-hordeins of cultivated barley formed a subfamily, while the B-hordeins of wild barleys and the two most similar sequences of LMW-GS of T. aestivum formed another subfamily. This result indicated that the members of the two subfamilys have a distinctive difference. In addition, we found the B-hordeins with identical C-terminal end sequences were clustered into a same subgroup (except BXQ053，BZ09-1 and BZ26-5 as a sole group, respectively), so we believe that B-hordein gene subfamilies possibly can be classified on the basis of the conserved C-terminal end sequences of predicted polypeptide and without the limit of SDS-PAGE protein banding patterns. 2. The specific primers were designed according to the published sequences of barley B-hordein genes from Z09 and Z26. Using total DNA isolated from them as the templates, eight clones (designated Z09Pand Z26P) of upstream sequences of the known B-hordein genes was obtained by TAIL-PCR and SON-PCR. Sequences analysis shows that the putative TATA box was present at position –80 bp and CAAT-like box at position –140 bp. Besides, a putative Endosperm Box including an Endosperm Motif (EM) and a GCN4-Like Motif was found at position –300 bp in six clones, and another Endosperm-like box was found at positon –560 bp. While the Endosperm Box or Endosperm-like box was not found in Z09P-2 and Z26P-3. This may indicate that gene expression drived by the two promtors was probably controlled by different trans-acting factors and the genetic control mechanism of corresponding gene expression may be diverse. 3. The B-hordein genic region coding for the mature peptide was cloned into expression vector pET-30a and transformed into bacterial strain BL21 for identifying gene expression fountion. Protein SDS–PAGE analysis showed that only the transformed lysate with the pET-BZ07-2 and pET-BZ26-5 constructs produced proteins related to B-group hordeins of barley, and the mounts of proteins induced by 3 mM IPTG and 3 h were higher than other conditions. This established a base for isolating and putifying B-hordein and further exploring their effects on barley grain quality. 4. The gene-specific primers of B-hordein genes from Z09 and Z26 were used for the quantification of B-hordein gene expression. The α-tubulin gene from Hordeum vulgare subsp. vulgare (GenBank accession number U40042) was used as a control gene. The result shows the transcription of the B-hordein genes in Z09 was found 7 days after flowering, while the transcription of the B-hordein genes in Z26 was found 4 days after flowering, but at a very low level, and it suggested that the B-hordein genes in Z26 probably expressed earlier than those in Z09, or the B-hordein genes in Z09 expressed at so a lower level than Z26 that it can not detected. In addition, B-hordein genes in Z26 accession showed higher expression levels than those in Z09 in four developing stages. Furthermore, a progressive increase in the expression levels of the B-hordein genes between 12 and 18 days after anthesis was observed in both Z09 and Z26. It implies that the B-hordein allelic variants encoded by Hor2 locus exist the differential expression in mRNA levels of during barley endosperm development.

情绪对创造力影响的发展性特点

Although robust findings have been that positive mood leads to greater creativity, several other literatures have found that negative mood sometimes results in more creative performance than positive or neutral mood. Several possible explanations for this emotion–creativity link have been proposed by researchers, but there has not yet been definitive research identifying the mechanism(s) behind this relationship. This research represents an initial step in this direction, examining the possibility that Intelligence Current may be a contributing mechanism in the emotion–creativity link from the perspective of development. The object of the present study was to do the followings 1) the effects and mechanism(s) of emotions on creativity development from adolescence to young adulthood by Unusual Uses Test; 2) the possibility that Intelligence Current may be a contributing mechanism in the emotion–creativity link. The participants were 849 adolescents in high schools and 267 undergraduates in the university aged from 11 to 22 years old. The mechanism(s) for emotion-creativity link was explored by cognitive flexibility (assessed using Abstract Match Task), tolerance (inclusive) ratings (assessed using Categorization of Analogy Task), uses originality ratings, and confidence ratings. Results indicated that: 1) The level of creativity varied with age. It increased from 11 years on, but decreased at about 14 to improve again from 15 to 22 years. 2) The different effects of emotions on creativity development among adolescents and undergraduates emerged, but the effects of positive and negative emotions on creativity didn’t differ from each other for the whole participants. Furthermore, compared with positive and negative emotions, the neutral emotions produced the lowest creativity for 11.00-13.99 years old group, but produced the highest creativity for 14.00-14.99 and 17.00-21.99years old. 3) Positive emotions have been shown to enable individuals to higher level of cognitive flexibility and better performance than negative emotions by Abstract Match Task, which could be considered that the Intelligence Current may be a contributing mechanism in the emotion–creativity link. 4) Positive emotions have been shown to enable individuals to own higher confidence, to categorize items with more flexibility, to see more potential relatedness among unusual and atypical members of categories, to evaluate items more originality than negative emotions among most of participants, especially the group of 14.00-14.99 years old. In sum, the present study helps us to further understand that the term ‘Intelligence Current’ is further explained and the problems found in relationships between creativity and emotions. However, further research is required to explore and confirm the conclusions of the present study.