Effects of Spirogyra arcta on biomass and structure of submerged macrophyte communities

The presence of algae can greatly reduce the amount of light that reaches submerged macrophytes, but few experimental studies have been conducted to examine the effects of algae on biomass and structure of submerged macrophyte communities. We constructed communities with four submerged macrophytes (Hydrilla verticillata, Egeria densa, Ceratophyllum demersum, and Chara vulgaris) in three environments in which 0 (control), 50 and 100% of the water surface was covered by Spirogyra arcta. Compared to the control treatment, the 100% spirogyra treatment decreased biomass of the submerged macrophyte communities and of all the four macrophytes except C. demersum. Compared to the control and 50% treatments, the 100% treatment significantly increased relative abundance of C. demersum and decreased that of E. densa. Therefore, the presence of S. arcta can greatly affect the productivity and alter the structure of submerged macrophyte communities. To restore submerged macrophyte communities in conditions with abundant algae, assembling communities consisting of C. demersum or similar species may be a good practice.     

Molecular Evolution of the Pathogenicity Island of Enterotoxigenic Bacteroides fragilis Strains

Enterotoxigenic Bacteroides fragilis (ETBF) strains, which produce a 20-kDa zinc metalloprotease toxin (BFT), have been associated with diarrheal disease in animals and young children. Studying a collection of ETBF and nontoxigenic B. fragilis (NTBF) strains, we found that bft and a second metalloprotease gene (mpII) are contained in an approximately 6-kb pathogenicity island (termed B. fragilis pathogenicity island or BfPAI) which is present exclusively in all 113 ETBF strains tested (pattern I). Of 191 NTBF strains, 100 (52%) lack both the BfPAI and at least a 12-kb region flanking BfPAI (pattern II), and 82 of 191 NTBF strains (43%) lack the BfPAI but contain the flanking region (pattern III). The nucleotide sequence flanking the left end of the BfPAI revealed a region with the same organization as the mobilization region of the 5-nitroimidazole resistance plasmid pIP417 and the clindamycin resistance plasmid pBFTM10, that is, two mobilization genes (bfmA and bfmB) organized in one operon and a putative origin of transfer (oriT) located in a small, compact region. The region flanking the right end of the BfPAI contains a gene (bfmC) whose predicted protein shares significant identity to the TraD mobilization proteins encoded by plasmids F and R100 from Escherichia coli. Nucleotide sequence analysis of one NTBF pattern III strain (strain I-1345) revealed that bfmB and bfmC are adjacent to each other and separated by a 16-bp GC-rich sequence. Comparison of this sequence with the appropriate sequence of ETBF strain 86-5443-2-2 showed that in this ETBF strain the 16-bp sequence is replaced by the BfPAI. This result defined the BfPAI as being 6,036 bp in length and its precise integration site as being between the bfmB and bfmC stop codons. The G+C content of the BfPAI (35%) and the flanking DNA (47 to 50%) differ greatly from that reported for the B. fragilis chromosome (42%), suggesting that the BfPAI and its flanking region are two distinct genetic elements originating from very different organisms. ETBF strains may have evolved by horizontal transfer of these two genetic elements into a pattern II NTBF strain.     

Functional interactions between herpesvirus oncoprotein MEQ and cell cycle regulator CDK2

Marek's disease virus, an avian alphaherpesvirus, has been used as an excellent model to study herpesvirus oncogenesis. One of its potential oncogenes, MEQ, has been demonstrated to transform a rodent fibroblast cell line, Rat-2, in vitro by inducing morphological transformation and anchorage- and serum-independent growth and by protecting cells from apoptosis induced by tumor necrosis factor alpha, C2-ceramide, UV irradiation, or serum deprivation. In this report, we show that there is a cell cycle-dependent colocalization of MEQ protein and cyclin-dependent kinase 2 (CDK2) in coiled bodies and the nucleolar periphery during the G1/S boundary and early S phase. To our knowledge, this is the first demonstration that CDK2 is found to localize to coiled bodies. Such an in vivo association and possibly subsequent phosphorylation may result in the cytoplasmic translocation of MEQ protein. Indeed, MEQ is expressed in both the nucleus and the cytoplasm during the G1/S boundary and early S phase. In addition, we were able to show in vitro phosphorylation of MEQ by CDKs. We have mapped the CDK phosphorylation site of MEQ to be serine 42, a residue in the proximity of the bZIP domain. An indirect-immunofluorescence study of the MEQ S42D mutant, in which the CDK phosphorylation site was mutated to a charged residue, reveals more prominent cytoplasmic localization. This lends further support to the notion that the translocation of MEQ is regulated by phosphorylation. Furthermore, phosphorylation of MEQ by CDKs drastically reduces the DNA binding activity of MEQ, which may in part account for the lack of retention of MEQ oncoprotein in the nucleus. Interestingly, the localization of CDK2 in coiled bodies and the nucleolar periphery is observed only in MEQ-transformed Rat-2 cells, implicating MEQ in modifying the subcellular localization of CDK2. Taken together, our data suggest that there is a novel reciprocal modulation between the herpesvirus oncoprotein MEQ and CDK2.     

Pharmacophore modeling of human adenosine receptor A2A antagonists

Three-dimensional pharmacophore models of human adenosine receptor A_2A antagonists were developed based on 23 diverse compounds selected from a large number of A_2A antagonists. The best pharmacophore model, Hypo1, contained five features: one hydrogen bond donor , three hydrophobic points and one ring aromatic. Its correlation coefficient, root mean square deviation, and cost difference values were 0.955, 0.921 and 84.4, respectively, suggested that the Hypo1 model was reasonable and reliable. This model was validated by three methods: a test set of 106 diverse compounds, a simulated virtual screening, and superimposition with the crystal structure of A_2A receptor. The results showed that Hypo1 was not only in agreement with the A_2A crystal structure and literature reports, but also well identified active A_2A antagonists from the virtual database. This methodology provides helpful information and a robust tool for the discovery of potent A_2A antagonists.     

Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1)

Ignisphaera aggregans Niederberger et al. 2006 is the type and sole species of genus Ignisphaera. This archaeal species is characterized by a coccoid-shape and is strictly anaerobic, moderately acidophilic, heterotrophic hyperthermophilic and fermentative. The type strain AQ1.S1(T) was isolated from a near neutral, boiling spring in Kuirau Park, Rotorua, New Zealand. This is the first completed genome sequence of the genus Ignisphaera and the fifth genome (fourth type strain) sequence in the family Desulfurococcaceae. The 1,875,953 bp long genome with its 2,009 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

黄土高原根瘤菌数值分类及DNA-DNA杂交

黄土高原位于我国内陆,气候比较干旱,生长的植被较少,水土流失严重,而有些豆科植物如锦鸡儿(Caragana sinica)、苦豆子(Sophora alopecuroides)、甘草(Glycyrrhiza uralensis)、苦马豆(Swainsoniasalsula)、洋槐(Robinia pseudoacacia)等却能很好生长.这些豆科植物的生长,在防风固沙、保持水土、绿化环境、作为饲用牧草等方面起着很重要的作用.但人们对于黄土高原野生豆科植物根瘤菌的研究尚很少.为此,作者在地处黄土高原的陕西、宁夏及甘肃的部分地区进行了广泛的根瘤菌资源调查.在此基础上,对分离的部分菌株进行了数值分类和DNA同源性分析.     

锦橙汁囊的超微结构

用常规电镜方法观察了锦橙［Ｃｉｔｒｕｓｓｉｎｅｎｓｉｓ （Ｌ．） Ｏｓｂ．］汁囊从原始细胞到发育为一个具柄的成熟汁囊的过程中,汁囊构成细胞超微结构的变化。锦橙汁囊原始细胞及发育为球状体时的构成细胞以及柱状结构顶端的细胞都是一种典型的分生组织细胞。在细胞质中有包括线粒体、质体、内质网、核糖体等丰富的细胞器,但没有观察到高尔基体。这些分生细胞分裂一段时期后就停止活动,逐渐分化为适应贮藏功能的液泡化薄壁细胞。分生细胞开始分化时,在细胞中出现许多小液泡和高尔基体。这些小液泡逐渐地融合,同时细胞质变少,最后形成一个有中央大液泡的薄壁细胞,在紧贴细胞膜的薄薄的一层细胞质中有线粒体、质体、高尔基体以及含有许多脂滴的杂色体。但成熟果实中汁囊的薄壁细胞中几乎没有任何细胞器。     

Epipolarization Microscopic Immunogold Assay: a Combination of Immunogold Silver Staining, Enzyme-Linked-Immunosorbent Assay and Epipolarization Microscopy

We describe a new immunoassay which combines an immunosorbent assay, Immunogold silver staining and epipolarization microscopy. Our new assay procedure features multiple samples on a single microscope slide, and high sensitivity of epipolarization microscope for detection of silver-enhanced colloidal gold as a final immunoassay product. We call the new immunoassay “on slide immunogold assay” (OSIGA). This new method uses biotinylated antibody and streptavidin-gold reaction with silver enhancement technique. With OSIGA it is possible to investigate 30 samples on a single microscopic slide. Our preliminary studies used 10-20 μ1 samples and detected nanogram quantities of a standardized protein solution. Unlike enzyme linked immunosorbent assay (ELISA), which has a limited time for reading the final color products, the OSIGA specimens can be dried or resin mounted for longer storage and future reference.     

Interaction between programmed cell death 5 and calcineurin B-like interacting protein kinase 23 in Oryza sativa

Programmed cell death (PCD) is crucial for plants during development and stress survival. OsPDCD5, an ortholog to mammalian-programmed cell death 5, was previously cloned from rice (Oryza sativa, cv Zhenxian 97A), and its overexpression can induce PCD in transgenic rice. In the present study, immunoblotting analysis revealed that the OsPDCD5 protein was widely expressed in the tassel, leaf, leaf sheath, and different parts of the stem but not in the anther. RT-PCR analysis showed that OsPDCD5 was related to the senescence of leaf and root tissues as well as the development of stem tissues. Furthermore, OsPDCD5 was up-regulated by UV-B irradiation. Calcineurin B-like interacting protein kinase 23 (OsCIPK23), which is involved in the calcineurin B-like proteins (CLBs)/CBL-interacting protein kinases (CIPKs) signaling network, was identified as interacting with OsPDCD5 by yeast two-hybrid screening and subsequently confirmed by pull-down assay in vitro. Present findings may shed light on the investigation of the biochemical function of OsPDCD5 in rice.     

Sequences variation and classification of B-hordein genes in hull-less barley from the Qinghai-Tibet Plateau

The goal of this study is to understand the evolution relationship of the members of the B-hordein gene family in hull-less barley by analysis of their structure and to explore their utility in grain quality improvement. Six copies of the B-hordein gene (Hn1-Hn3, Hn7-Hn9) were cloned from six hull-less barley cultivars collected from Qinghai-Tibet Plateau and molecularly characterized. Comparison of their predicted polypeptide sequences with the published data suggested that they all share the same basic protein structures. In addition, we found that the C-terminal end sequences of all B-hordeins shared a similar feature. In the six clones and the other three published genes (Hn4, Hn5, and Hn6) from hull-less barley, Hn2 and Hn7 contained the identical C-terminal end sequence DIMPVDFWH. Hn3, Hn4, Hn5, Hn8 and Hn9 also shared the common sequence DIMPPDFWH, which was similar to that of a B-hordein reported previously. Both Hn1 and Hn6 exhibited differences in their C-terminal end sequences, and they clustered into different subgroups. The B-hordeins with identical C-terminal end sequences were clustered into the same subgroup, 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. Phylogenetic analysis also indicated that there is a relatively weak identity between our predicted B-hordeins and those reported from H. chilense and H. brevisubulatum. All of our nine predicted B-hordeins were clustered together and other B-hordeins formed another cluster. The possible use of these genes in relation to barley quality is discussed. Published in Russian in Molekulyarnaya Biologiya, 2008, Vol. 42, No. 1, pp. 63–70. The text was submitted by the authors in English