Comparison of carbon metabolism between chloramphenicol-treated and untreated cultures of Clostridium acetobutylicum

Summary Carbon distribution from substrates to products in Clostridium acetobutylicum ATCC 824 was investigated by adding ¹⁴C-labeled substrates as tracers. Comparison of carbon conversion between chloramphenicol (CAP)-treated and untreated cultures was also studied. The percentage of ¹⁴C recovery in butanol, acetone and ethanol from uniformly labeled [¹⁴C]glucose was increased by 17, 25 and 30%, respectively, after CAP addition. The incorporation of ¹⁴C in solvents from ¹⁴C-labeled acetate and butyrate was also increased by the antibiotic treatment. A total ¹⁴C recovery of 12% in all the products from added [¹⁴C]Na₂CO₃ indicates significant heterotrophic CO₂ fixation in this microorganism. The ratio of carbon in butanol derived from glucose, acetate and butyrate was about 71:6:18, and this ratio was unchanged by CAP treatment.This paper represents contribution No. 2685 of the Rhode Island Agricultural Experimental StationCorrespondence to: R. W. Traxler     

PHOSPHATIDYLSERINE SYNTHASE1 is Required for Inflorescence Meristem and Organ Development in Arabidopsis

<正>Phosphatidylserine(PS),a quantitatively minor membrane phospholipid,is involved in many biological processes besides its role in membrane structure.One PS synthesis gene,PHOSPHATIDYLSERINE SYNTHASE1(PSS1),has been discovered to be required for microspore development in Arabidopsis thaliana L.but how PSS1 affects postembryonic development is still largely unknown.Here,we show that PSS1 is also required for inflorescence meristem and organ development in Arabidopsis.Disruption of PSS1 causes severe dwarfism,smaller lateral organs and reduced size of inflorescence meristem. Morphological and molecular studies suggest that both cell division and cell elongation are affected in the pss1-1 mutant.RNA in situ hybridization and promoter GUS analysis show that expression of both WUSCHEL(WUS) and CLAVATA3(CLV3) depend on PSS1.Moreover,the defect in meristem maintenance is recovered and the expression of WUS and CLV3 are restored in the pss1-1 clv1-1 double mutant. Both SHOOTSTEMLESS(STM) and BREVIPEDICELLUS(BP) are upregulated,and auxin distribution is disrupted in rosette leaves of pss1-1.However,expression of BP,which is also a regulator of internode development,is lost in the pss1-1 inflorescence stem.Our data suggest that PSS1 plays essential roles in inflorescence meristem maintenance through the WUS-CLV pathway,and in leaf and internode development by differentially regulating the class I KNOX genes.     

Gene polymorphisms and chronic obstructive pulmonary disease

The genetic component was suggested to contribute to the development of chronic obstructive pulmonary disease (COPD), a major and growing public health burden. The present review aims to characterize the evidence that gene polymorphisms contribute to the aetiology of COPD and related traits, and explore the potential relationship between certain gene polymorphisms and COPD susceptibility, severity, lung function, phenotypes, or drug effects, even though limited results from related studies lacked consistency. Most of these studies were association studies, rather than confirmatory studies. More large‐sized and strictly controlled studies are needed to prove the relationship between gene polymorphisms and the reviewed traits. More importantly, prospective confirmatory studies beyond initial association studies will be necessary to evaluate true relationships between gene polymorphisms and COPD and help individualized treatment for patients with COPD.     

The wheat AGL6-like MADS-box gene is a master regulator for floral organ identity and a target for spikelet meristem development manipulation

The AGAMOUS-LIKE6 (AGL6)-like genes are ancient MADS-box genes and are functionally studied in a few model plants. The knowledge of these genes in wheat remains limited. Here, by studying a ‘double homoeolog mutant’ of the AGL6 gene in tetraploid wheat, we showed that AGL6 was required for the development of all four whorls of floral organs with dosage-dependent effect on floret fertility. Yeast two-hybrid analyses detected interactions of AGL6 with all classes of MADS-box proteins in the ABCDE model for floral organ development. AGL6 was found to interact with several additional proteins, including the G protein β and γ (DEP1) subunits. Analysis of the DEP1-B mutant showed a significant reduction in spikelet number per spike in tetraploid wheat, while overexpression of AGL6 in common wheat increased the spikelet number per spike and hence the grain number per spike. RNA-seq analysis identified the regulation of several meristem activity genes by AGL6, such as FUL2 and TaMADS55. Our work therefore extensively updated the wheat ABCDE model and proposed an alternative approach to improve wheat grain yield by manipulating the AGL6 gene.     

Targeted Next-Generation Sequencing for Clinical Diagnosis of 561 Mendelian Diseases

BackgroundTargeted next-generation sequencing (NGS) is a cost-effective approach for rapid and accurate detection of genetic mutations in patients with suspected genetic disorders, which can facilitate effective diagnosis.Conclusions/SignificanceResults of the evaluation showed that targeted NGS enabled to detect disease-causing mutations with high accuracy, stability, speed and throughput. Thus, the technology can be used for the clinical diagnosis of 561 Mendelian diseases.     

基于设计的生物大分子成药性优化策略研究进展

目前生物药物正处在高速发展阶段,但生物大分子的一些固有特性限制了其成药性,使得很多具有良好治疗潜能的生物大分子 最终不能开发成药物,因而严重制约了生物药物的发展。生物药物开发的瓶颈已从“新分子的产生”转向“如何获得具有优良生理特性 和预期治疗效果的有效药物”。近年来,通过合理设计改造生物大分子高级结构以优化其成药性的研究获得了快速发展。综述基于设计 的生物大分子成药性优化策略研究进展。     

EST-based in silico identification and in vitro test of antimicrobial peptides in Brassica napus

Background

Brassica napus is the third leading source of vegetable oil in the world after soybean and oil palm. The accumulation of gene sequences, especially expressed sequence tags (ESTs) from plant cDNA libraries, has provided a rich resource for genes discovery including potential antimicrobial peptides (AMPs). In this study, we used ESTs including those generated from B. napus cDNA libraries of seeds, pathogen-challenged leaves and deposited in the public databases, as a model, to perform in silico identification and consequently in vitro confirmation of putative AMP activities through a highly efficient system of recombinant AMP prokaryotic expression.

Results

In total, 35,788 were generated from cDNA libraries of pathogen-challenged leaves and 187,272 ESTs from seeds of B. napus, and the 644,998 ESTs of B. napus were downloaded from the EST database of PlantGDB. They formed 201,200 unigenes. First, all the known AMPs from the AMP databank (APD2 database) were individually queried against all the unigenes using the BLASTX program. A total of 972 unigenes that matched the 27 known AMP sequences in APD2 database were extracted and annotated using Blast2GO program. Among these unigenes, 237 unigenes from B. napus pathogen-challenged leaves had the highest ratio (1.15 %) in this unigene dataset, which is 13 times that of the unigene datasets of B. napus seeds (0.09 %) and 2.3 times that of the public EST dataset. About 87 % of each EST library was lipid-transfer protein (LTP) (32 % of total unigenes), defensin, histone, endochitinase, and gibberellin-regulated proteins. The most abundant unigenes in the leaf library were endochitinase and defensin, and LTP and histone in the pub EST library. After masking of the repeat sequence, 606 peptides that were orthologous matched to different AMP families were found. The phylogeny and conserved structural motifs of seven AMPs families were also analysed. To investigate the antimicrobial activities of the predicted peptides, 31 potential AMP genes belonging to different AMP families were selected to test their antimicrobial activities after bioinformatics identification. The AMP genes were all optimized according to Escherichia coli codon usage and synthetized through one-step polymerase chain reaction method. The results showed that 28 recombinant AMPs displayed expected antimicrobial activities against E. coli and Micrococcus luteus and Sclerotinia sclerotiorum strains.

Conclusion

The study not only significantly expanded the number of known/predicted peptides, but also contributed to long-term plant genetic improvement for increased resistance to diverse pathogens of B.napus. These results proved that the high-throughput method developed that combined an in silico procedure with a recombinant AMP prokaryotic expression system is considerably efficient for identification of new AMPs from genome or EST sequence databases.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1849-x) contains supplementary material, which is available to authorized users.     

Spatial variability in the amount of forest litter at the local scale in northeastern China: Kriging and cokriging approaches to interpolation

Litter is essential to promote nutrient cycling and maintain the sustainability of forest resources. However, its variability has not been sufficiently studied at the local scale. The prediction of litter amount using ordinary cokriging with Pearson correlation analysis (COK_P) and ordinary cokriging with principal component analysis (COK_PCA) was compared with that using ordinary kriging (OK) based on cross‐validation at the local scale of a 1‐ha plot over natural spruce–fir mixed forest in Jilin Province, China. Litter samples in semidecomposed (F) and complete decomposed (H) horizons were collected using an equidistant grid point sampling of 10 m × 10 m. Pearson correlation analysis and principal component analysis (PCA) were used to confirm auxiliary variables. The results showed that the amount of litter was 19.65 t/ha in the F horizon and 10.37 t/ha in the H horizon. The spatial structure variance ratio in the H horizon was smaller than that in the F horizon, indicative of its stronger spatial autocorrelation. Spatial distributions of litter amount in both horizons exhibited a patchy and heterogeneous pattern. Of the selected stand characteristics and litter properties, litter moisture content indicated the strongest relationship with litter amount. Cross‐validation revealed that COK_PCA using the comprehensive score as an auxiliary variable produced the most accurate map. The average standard error and root‐mean‐square error between the predicted and measured values were always smaller, the mean error and mean standardized error were much closer to 0, and the root‐mean‐square standardized error was closer to 1 than COK_P using litter moisture and OK. Therefore, a clear advantage of cokriging based on principal component analysis was observed and COK_PCA was found to be a very useful approach for further interpolation prediction.