In vitro development and transfer of resistance to chlortetracycline in Bacillus subtilis

The present criteria and rules controlling the approval of the use of probiotics are limited to antibiotic resistance patterns and the presence of antibiotic resistance genes in bacteria. There is little information available in the literature regarding the risk of the usage of probiotics in the presence of antibiotic pressure. In this study we investigated the development and transfer of antibiotic resistance in Bacillus subtilis selected in vitro by chlortetracycline in a stepwise manner. Bacillus subtilis was exposed to increasing concentrations of chlortetracyclineto induce in vitro resistance to chlortetracycline, and the minimal inhibitory concentrations were determinedfor the mutants. Resistant B. subtilis were conjugated with Escherichia coli NK5449 and Enterococcus faecalis JH2-2 using the filter mating. Three B. subtilis tetracycline resistant mutants (namely, BS-1, BS-2, and BS-3) were derived in vitro. A tetracycline resistant gene, tet (K), was found in the plasmids of BS-1 and BS-2. Three conjugates (BS-1N, BS-2N, and BS-3N) were obtained when the resistant B. subtilis was conjugated with E. coli NK5449. The conjugation frequencies for the BS-1N, BS-2N, and BS-3N conjugates were 4.57×10^?7, 1.4×10^?7, and 1.3×10^?8, respectively. The tet(K) gene was found only in the plasmids of BS-1N. These results indicate that long-term use of probiotics under antibiotic selection pressure could cause antibiotic resistance, and the resistance gene could be transferred to other bacteria. The risk arising from the use of probiotics under antibiotic pressure should be considered in the criteria and rules for the safety assessment of probiotics.     

PSMD: An extensive database for pan‐species microsatellite investigation and marker development

Microsatellites are widely distributed throughout nearly all genomes which have been extensively exploited as powerful genetic markers for diverse applications due to their high polymorphisms. Their length variations are involved in gene regulation and implicated in numerous genetic diseases even in cancers. Although much effort has been devoted in microsatellite database construction, the existing microsatellite databases still had some drawbacks, such as limited number of species, unfriendly export format, missing marker development, lack of compound microsatellites and absence of gene annotation, which seriously restricted researchers to perform downstream analysis. In order to overcome the above limitations, we developed PSMD (Pan‐Species Microsatellite Database, http://big.cdu.edu.cn/psmd/ ) as a web‐based database to facilitate researchers to easily identify microsatellites, exploit reliable molecular markers and compare microsatellite distribution pattern on genome‐wide scale. In current release, PSMD comprises 678,106,741 perfect microsatellites and 43,848,943 compound microsatellites from 18,408 organisms, which covered almost all species with available genomic data. In addition to interactive browse interface, PSMD also offers a flexible filter function for users to quickly gain desired microsatellites from large data sets. PSMD allows users to export GFF3 formatted file and CSV formatted statistical file for downstream analysis. We also implemented an online tool for analysing occurrence of microsatellites with user‐defined parameters. Furthermore, Primer3 was embedded to help users to design high‐quality primers with customizable settings. To our knowledge, PSMD is the most extensive resource which is likely to be adopted by scientists engaged in biological, medical, environmental and agricultural research.     

海南五针松人工林分生物量的研究

 本文是对海拔930m的17年生海南五针松(Pinus fanzeliana)人工林分生物量和生产力进行了测定和研究。按平均标准木法和样方收获法分别调查了乔木层,灌木层,草本地被物层和枯枝落叶层。据调查数,建立了估测乔木层单株林木各器官干重的回归方程。方程的相关系数和估测精度都较高,具有参考价值．分析结果表明：林分总生物量平均为161.152t／ha,生产力为10630.69kg／(ha·a),其中：乔木层生物量为149.351t／ha,生产力为11095kg／(ha·a),叶面积为199248.734m2／ha,叶面积指数为19.9149m2／m2。     

Analysis of variable sites between two complete South China tiger (Panthera tigris amoyensis) mitochondrial genomes

In order to investigate the mitochondrial genome of Panthera tigris amoyensis, two South China tigers (P25 and P27) were analyzed following 15 cymt-specific primer sets. The entire mtDNA sequence was found to be 16,957 bp and 17,001 bp long for P25 and P27 respectively, and this difference in length between P25 and P27 occurred in the number of tandem repeats in the RS-3 segment of the control region. The structural characteristics of complete P. t. amoyensis mitochondrial genomes were also highly similar to those of P. uncia. Additionally, the rate of point mutation was only 0.3% and a total of 59 variable sites between P25 and P27 were found. Out of the 59 variable sites, 6 were located in 6 different tRNA genes, 6 in the 2 rRNA genes, 7 in non-coding regions (one located between tRNA-Asn and tRNA-Tyr and six in the D-loop), and 40 in 10 protein-coding genes. COI held the largest amount of variable sites (9 sites) and Cytb contained the highest variable rate (0.7%) in the complete sequences. Moreover, out of the 40 variable sites located in 10 protein-coding genes, 12 sites were nonsynonymous.     

Prediction of potential drivers connecting different dysfunctional levels in lung adenocarcinoma via a protein–protein interaction network

Lung cancer is a serious disease that threatens an affected individual's life. Its pathogenesis has not yet to be fully described, thereby impeding the development of effective treatments and preventive measures. “Cancer driver” theory considers that tumor initiation can be associated with a number of specific mutations in genes called cancer driver genes. Four omics levels, namely, (1) methylation, (2) microRNA, (3) mutation, and (4) mRNA levels, are utilized to cluster cancer driver genes. In this study, the known dysfunctional genes of these four levels were used to identify novel driver genes of lung adenocarcinoma, a subtype of lung cancer. These genes could contribute to the initiation and progression of lung adenocarcinoma in at least two levels. First, random walk with restart algorithm was performed on a protein–protein interaction (PPI) network constructed with PPI information in STRING by using known dysfunctional genes as seed nodes for each level, thereby yielding four groups of possible genes. Second, these genes were further evaluated in a test strategy to exclude false positives and select the most important ones. Finally, after conducting an intersection operation in any two groups of genes, we obtained several inferred driver genes that contributed to the initiation of lung adenocarcinoma in at least two omics levels. Several genes from these groups could be confirmed according to recently published studies. The inferred genes reported in this study were also different from those described in a previous study, suggesting that they can be used as essential supplementary data for investigations on the initiation of lung adenocarcinoma. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.     

5种光合细菌种间原生质体融合及优良农用融合子的筛选鉴定

处于对数生长期的光合细菌球形红假单胞菌(Rhodopseudomonassphaeroides)、沼泽红假单胞菌(Rhodopseudomonaspalustris)、嗜酸红假单胞菌(Rhodopseudomdnasacidophila)、深红红螺菌(Rhodospirarubrum)、万尼氏红微菌(Rhodomocrobiumvannielii),经溶菌酶(3mg/L)处理50min后,获得了它们的菌体形成的原生质体,其再生率分别为80%、71%、82%、61%、74%.取等量的亲本菌株在35%的PEG(MW6000)诱导下两两融合5min,共10种组合.其融合率为球×沼2.5×10-4、球×嗜2.1×10-4、球×深2.0×10-4、球×万2.1×10-4、沼×嗜2.8×10-4、沼×深2.4×10-4、沼×万2.6×10-4、嗜×深2.0×10-4、嗜×万2.3×10-4、深×万2.4×10-4.经影印法鉴定:形成的融合子可以分别生长于以相应的有机物为唯一碳源的培养基上,所有融合子体积均相当于两亲本株体积之和,融合子菌落形态特征介于两亲本株之间.从中随机挑选100个融合子,以辣椒苗作为靶标植物,从上述融合子中筛选到了1株具有显著促进作物生长、提高抗病性的融合子.     

Immobilization of cellulases on the reversibly soluble polymer Eudragit S‐100 for cotton treatment

Cellulases can penetrate into the fiber, causing tensile strength loss of the cellulosic fibers or fabrics. To minimize the tensile strength loss, we have immobilized cellulases on Eudragit S‐100. The characteristics of covalent Eudragit cellulase were evaluated using gel filtration analysis and UV spectra. Gel filtration analysis revealed that the cellulases were covalently bound to the polymer. Covalent Eudragit cellulase was loaded with the enzyme of about 40% and had a relative activity about 80% at a Eudragit S‐100 concentration of 15 g/L. When cellulase is bound to the polymer, the solubility profile becomes similar to the one of Eudragit. In addition, the effects of the enzyme on the cotton yarns and fabric using cellulases have been investigated. Native and immobilized cellulases caused improvements in whiteness and wrinkle recovery angle of the fabric in comparison to the control samples. The bending stiffness results show that native and immobilized cellulase treated cotton fabric has an improved softness than the control samples. It was found that using the immobilized cellulase reduced the weight and tensile strength, because the hydrolytic attack is only limited to the surfaces of cotton fibers.     

基于生态效率理论和TOPSIS法的工业园区循环经济发展评价

工业园区层面的生态效率评价是生态效率研究领域有待深入探索的课题。TOPSIS方法则可能是适用于生态效率评价的一种方法,它以空间统计学为基础,借助于多目标决策问题的理想解和负理想解来进行排序,能够客观地比较和评价不同样本点综合指标的优劣。本文根据生态效率和循环经济理论,结合《综合类生态工业园区标准（试行）》,建立工业园区循环经济评价指标体系,运用TOPSIS方法对苏州高新区、苏州工业园区生态工业园和无锡新区生态工业示范园区的生态效率进行综合评价,结果表明：三者的生态效率综合排名由高到低依次为：无锡新区生态工业示范园区> 苏州工业园区生态工业园> 苏州高新区,且3园区在经济发展、资源能源利用率、物质循环利用、环境污染控制等子系统有所优劣。并针对各园区的各自存在的不足提出了相应的改进和发展建议。