The design of potent and selective inhibitors of thrombin utilizing a piperazinedione template: part 2.

Potent and selective thrombin inhibitors have been prepared with a piperazinedione template and L-amino acids. Likewise, incorporation of D-amino acids led to potent inhibitors with a novel mode of binding. Herein, the structure activity relationships and structural aspects of these compounds will be described.     

Crystal structure of Methanococcus voltae RadA in complex with ADP: hydrolysis-induced conformational change

Members of a superfamily of RecA-like recombinases facilitate a central strand exchange reaction in the DNA repair process. Archaeal RadA and Rad51 and eukaryal Rad51 and meiosis-specific DMC1 form a closely related group of recombinases distinct from bacterial RecA. Nevertheless, all such recombinases share a conserved core domain which carries the ATPase site and putative DNA-binding sites. Here we present the crystal structure of an archaeal RadA from Methanococcus voltae (MvRadA) in complex with ADP and Mg2+ at 2.1 A resolution. The crystallized RadA-ADP filament has an extended helical pitch similar to those of previously determined structures in the presence of nonhydrolyzable ATP analogue AMP-PNP. Structural comparison reveals two recurrent conformations with an extensive allosteric effect spanning the ATPase site and the putative DNA-binding L2 region. Varied conformations of the L2 region also imply a dynamic nature of recombinase-bound DNA.     

Impact of Precipitation Patterns on Biomass and Species Richness of Annuals in a Dry Steppe

Annuals are an important component part of plant communities in arid and semiarid grassland ecosystems. Although it is well known that precipitation has a significant impact on productivity and species richness of community or perennials, nevertheless, due to lack of measurements, especially long-term experiment data, there is little information on how quantity and patterns of precipitation affect similar attributes of annuals. This study addresses this knowledge gap by analyzing how quantity and temporal patterns of precipitation affect aboveground biomass, interannual variation aboveground biomass, relative aboveground biomass, and species richness of annuals using a 29-year dataset from a dry steppe site at the Inner Mongolia Grassland Ecosystem Research Station. Results showed that aboveground biomass and relative aboveground biomass of annuals increased with increasing precipitation. The coefficient of variation in aboveground biomass of annuals decreased significantly with increasing annual and growing-season precipitation. Species richness of annuals increased significantly with increasing annual precipitation and growing-season precipitation. Overall, this study highlights the importance of precipitation for aboveground biomass and species richness of annuals.     

高产申嗪霉素和吩嗪-1-酰胺的水稻根际铜绿假单胞菌PA1201分离、鉴定与应用潜力

【目的】从水稻根际筛选能高效抑制水稻病原菌的细菌,分析和鉴定其形态和生化特征,为开发新型绿色农药奠定基础。【方法】从水稻根际分离能以1-氨基环丙烷-1-羧酸(ACC)为唯一碳源的菌株,根据菌株形态和生化特性、16S r DNA序列比对和磷脂脂肪酸图谱,对该菌株进行鉴定。通过氯仿萃取抽提、高效液相色谱分析,确定菌株PA1201在PPM培养基和黄豆粉培养基中申嗪霉素和吩嗪-1-酰胺的产量。【结果】菌株PA1201能有效抑制水稻纹枯病菌和水稻白叶枯病菌的生长,属于铜绿假单胞菌(Pseudomonas aeruginosa sp.PA1201);PA1201产生两种抑菌代谢产物申嗪霉素和吩嗪-1-酰胺,在PPM和黄豆粉培养基中申嗪霉素的产量可达81.7 mg/L和926.9 mg/L,吩嗪-1-酰胺的产量亦可达18.1 mg/L和489.5 mg/L;PA1201产生大量胞外蛋白酶,对人肺腺癌细胞系A549和黑腹果蝇具有一定毒性。【结论】PA1201的申嗪霉素产量比现有生产菌株的出发菌株M18高3-4倍,还能产生另一种抑菌活性更高的衍生物吩嗪-1-酰胺,具有进一步开发的潜力。     

Emotional Noun Processing: An ERP Study with Rapid Serial Visual Presentation

Reading is an important part of our daily life, and rapid responses to emotional words have received a great deal of research interest. Our study employed rapid serial visual presentation to detect the time course of emotional noun processing using event-related potentials. We performed a dual-task experiment, where subjects were required to judge whether a given number was odd or even, and the category into which each emotional noun fit. In terms of P1, we found that there was no negativity bias for emotional nouns. However, emotional nouns elicited larger amplitudes in the N170 component in the left hemisphere than did neutral nouns. This finding indicated that in later processing stages, emotional words can be discriminated from neutral words. Furthermore, positive, negative, and neutral words were different from each other in the late positive complex, indicating that in the third stage, even different emotions can be discerned. Thus, our results indicate that in a three-stage model the latter two stages are more stable and universal.     

Internalization of the TGF-β type I receptor into caveolin-1 and EEA1 double-positive early endosomes

Endocytosis and intracellular sorting of transforming growth factor-β (TGF-β) receptors play an important regulatory role in TGF-β signaling. Two major endocytic pathways, clathrin- and caveolae-mediated endocytosis, have been reported to independently mediate the internalization of TGF-β receptors. In this study, we demonstrate that the clathrin- and caveolae-mediated endocytic pathways can converge during TGF-β receptor endocytic trafficking. By tracking the intracellular dynamics of fluorescently-labeled TGF-β type I receptor (TβRI), we found that after mediating TβRI internalization, certain clathrin-coated vesicles and caveolar vesicles are fused underneath the plasma membrane, forming a novel type of caveolin-1 and clathrin double-positive vesicles. Under the regulation of Rab5, the fused vesicles are targeted to early endosomes and thus deliver the internalized TβRI to the caveolin-1 and EEA1 double-positive early endosomes (caveolin-1-positive early endosomes). We further showed that the caveolin-1-positive early endosomes are positive for Smad3/SARA, Rab11 and Smad7/Smurf2, and may act as a multifunctional device for TGF-β signaling and TGF-β receptor recycling and degradation. Therefore, these findings uncover a novel scenario of endocytosis, the direct fusion of clathrin-coated and caveolae vesicles during TGF-β receptor endocytic trafficking, which leads to the formation of the multifunctional sorting device, caveolin-1-positive early endosomes, for TGF-β receptors.     

Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses

Background

Members of the genera Prevotella, Veillonella and Fusobacterium are the predominant culturable obligate anaerobic bacteria isolated from periodontal abscesses. When determining the cumulative number of clinical anaerobic isolates from periodontal abscesses, ambiguous or overlapping signals were frequently encountered in 16S rRNA gene sequencing chromatograms, resulting in ambiguous identifications. With the exception of the genus Veillonella, the high intra-chromosomal heterogeneity of rrs genes has not been reported.

Methods

The 16S rRNA genes of 138 clinical, strictly anaerobic isolates and one reference strain were directly sequenced, and the chromatograms were carefully examined. Gene cloning was performed for 22 typical isolates with doublet sequencing signals for the 16S rRNA genes, and four copies of the rrs-ITS genes of 9 Prevotella intermedia isolates were separately amplified by PCR, sequenced and compared. Five conserved housekeeping genes, hsp60, recA, dnaJ, gyrB1 and rpoB from 89 clinical isolates of Prevotella were also amplified by PCR and sequenced for identification and phylogenetic analysis along with 18 Prevotella reference strains.

Results

Heterogeneity of 16S rRNA genes was apparent in clinical, strictly anaerobic oral bacteria, particularly in the genera Prevotella and Veillonella. One hundred out of 138 anaerobic strains (72%) had intragenomic nucleotide polymorphisms (SNPs) in multiple locations, and 13 strains (9.4%) had intragenomic insertions or deletions in the 16S rRNA gene. In the genera Prevotella and Veillonella, 75% (67/89) and 100% (19/19) of the strains had SNPs in the 16S rRNA gene, respectively. Gene cloning and separate amplifications of four copies of the rrs-ITS genes confirmed that 2 to 4 heterogeneous 16S rRNA copies existed.

Conclusion

Sequence alignment of five housekeeping genes revealed that intra-species nucleotide similarities were very high in the genera Prevotella, ranging from 94.3–100%. However, the inter-species similarities were relatively low, ranging from 68.7–97.9%. The housekeeping genes rpoB and gyrB1 were demonstrated to be alternative classification markers to the species level based on intra- and inter-species comparisons, whereas based on phylogenetic tree rpoB proved to be reliable phylogenetic marker for the genus Prevotella.