Biodegradation and detoxification of nicotine in tobacco solid waste by a Pseudomonas sp.

A Pseudomonas sp. grew with nicotine optimally 3 g l^–1 and at 30 °C and pH 7. Nicotine was fully degraded within 10 h. The resting cells degraded nicotine in tobacco solid waste completely within 6 h in 0.02 m sodium phosphate buffer (pH 7) at maximally 56 mg nicotine h^–1 g dry cell^–1.     

Development of genome-wide insertion and deletion markers for maize,based on next-generation sequencing data

Background

Insertions and deletions (indels) are the most abundant form of structural variation in all genomes. Indels have been increasingly recognized as an important source of molecular markers due to high-density occurrence, cost-effectiveness, and ease of genotyping. Coupled with developments in bioinformatics, next-generation sequencing (NGS) platforms enable the discovery of millions of indel polymorphisms by comparing the whole genome sequences of individuals within a species.

Results

A total of 1,973,746 unique indels were identified in 345 maize genomes, with an overall density of 958.79 indels/Mbp, and an average allele number of 2.76, ranging from 2 to 107. There were 264,214 indels with polymorphism information content (PIC) values greater than or equal to 0.5, accounting for 13.39 % of overall indels. Of these highly polymorphic indels, we designed primer pairs for 83,481 and 29,403 indels with major allele differences (i.e. the size difference between the most and second most frequent alleles) greater than or equal to 3 and 8 bp, respectively, based on the differing resolution capabilities of gel electrophoresis. The accuracy of our indel markers was experimentally validated, and among 100 indel markers, average accuracy was approximately 90 %. In addition, we also validated the polymorphism of the indel markers. Of 100 highly polymorphic indel markers, all had polymorphisms with average PIC values of 0.54.

Conclusions

The maize genome is rich in indel polymorphisms. Intriguingly, the level of polymorphism in genic regions of the maize genome was higher than that in intergenic regions. The polymorphic indel markers developed from this study may enhance the efficiency of genetic research and marker-assisted breeding in maize.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1797-5) contains supplementary material, which is available to authorized users.     

An extended conformation of calmodulin induces interactions between the structural domains of adenylyl cyclase from Bacillus anthracis to promote catalysis

The edema factor exotoxin produced by Bacillus anthracis is an adenylyl cyclase that is activated by calmodulin (CaM) at resting state calcium concentrations in infected cells. A C-terminal 60-kDa fragment corresponding to the catalytic domain of edema factor (EF3) was cloned, overexpressed in Escherichia coli, and purified. The N-terminal 43-kDa domain (EF3-N) of EF3, the sole domain of edema factor homologous to adenylyl cyclases from Bordetella pertussis and Pseudomonas aeruginosa, is highly resistant to protease digestion. The C-terminal 160-amino acid domain (EF3-C) of EF3 is sensitive to proteolysis in the absence of CaM. The addition of CaM protects EF3-C from being digested by proteases. EF3-N and EF3-C were expressed separately, and both fragments were required to reconstitute full CaM-sensitive enzyme activity. Fluorescence resonance energy transfer experiments using a double-labeled CaM molecule were performed and indicated that CaM adopts an extended conformation upon binding to EF3. This contrasts sharply with the compact conformation adopted by CaM upon binding myosin light chain kinase and CaM-dependent protein kinase type II. Mutations in each of the four calcium binding sites of CaM were examined for their effect on EF3 activation. Sites 3 and 4 were found critical for the activation, and neither the N- nor the C-terminal domain of CaM alone was capable of activating EF3. A genetic screen probing loss-of-function mutations of EF3 and site-directed mutations based on the homology of the edema factor family revealed a conserved pair of aspartate residues and an arginine that are important for catalysis. Similar residues are essential for di-metal-mediated catalysis in mammalian adenylyl cyclases and a family of DNA polymerases and nucleotidyltransferases. This suggests that edema factor may utilize a similar catalytic mechanism.     

松叶猪毛菜NADP-苹果酸酶基因家族及启动子克隆分析北大核心CSCD

NADP-苹果酸酶(NADP-ME)是C_(4)植物的关键光合酶,在生物和非生物胁迫中发挥了重要的作用。为了进一步研究该酶编码基因的功能,该研究以典型荒漠C_(3)-C_(4)中间型植物松叶猪毛菜为研究对象,在克隆得到NADP-ME家族基因序列的基础上,研究其表达部位及在非生物胁迫下的表达模式,并克隆其启动子序列分析响应非生物胁迫的元件差异。结果表明:(1)成功获得松叶猪毛菜3个NADP-MEs,命名为SaNADP-ME1、SaNADP-ME2和SaNADP-ME4,CDS序列长度分别为1755、1758和1941 bp。(2)SaNADP-ME1主要在根中表达,SaNADP-ME2和SaNADP-ME4主要在叶中表达;在ABA、NaCl、NAHCO_(3)和PEG_(6000)胁迫下松叶猪毛菜幼苗中3个NADP-MEs均可被诱导表达,且SaNADP-ME2和SaNADP-ME4的响应表达模式相似。(3)成功克隆得到SaNADP-ME1、SaNADP-ME2和SaNADP-ME4启动子区域2351、1655和2887 bp。生物信息学分析发现它们都含有基本启动子元件以及响应外界刺激的元件。     

High histone variant H3.3 content in mouse prospermatogonia suggests a role in epigenetic reformatting

Histone variants can incorporate into the nucleosome outside of S-phase. Some are known to play important roles in mammalian germ cell development, this cell lineage being characterized by long phases of quiescence, a protracted meiotic phase, and genome-wide epigenetic reformatting events. The best known example of such an event is the global-scale erasure of DNA methylation in sexually indifferent primordial germ cells, then its re-establishment in fetal prospermatogonia and growing oocytes. Histone H3 and its post-translationally modified forms provide important waypoints in the establishment of epigenetic states. Using mass spectrometry and immunoblotting, we show that the H3.3 replacement variant is present at an unusually high amount in mouse prospermatogonia at the peak stage of global DNA methylation re-establishment. We speculate that H3.3 facilitates this process through achieving a greater level of accessibility of chromatin modifiers to DNA.     

Seroprevalence of pandemic (H1N1) 2009 in pregnant women in China: an observational study

Background

We investigated the seropositive rates and persistence of antibody against pandemic (H1N1) 2009 virus (pH1N1) in pregnant women and voluntary blood donors after the second wave of the pandemic in Nanjing, China.

Methodology/Principal Findings

Serum samples of unvaccinated pregnant women (n = 720) and voluntary blood donors (n = 320) were collected after the second wave of 2009 pandemic in Nanjing. All samples were tested against pH1N1 strain (A/California/7/2009) with hemagglutination inhibition assay. A significant decline in seropositive rates, from above 50% to about 20%, was observed in pregnant women and voluntary blood donors fifteen weeks after the second wave of the pandemic. A quarter of the samples were tested against a seasonal H1N1 strain (A/Brisbane/59/2007). The antibody titers against pH1N1 strain were found to correlate positively with those against seasonal H1N1 strain. The correlation was modest but statistically significant.

Conclusions and Significance

The high seropositive rates in both pregnant women and voluntary blood donors suggested that the pH1N1 virus had widely spread in these two populations. Immunity derived from natural infection seemed not to be persistent well.     

Spatial pattern changes in aboveground plant biomass in a grazing pasture

Using gamma distribution and spatial autocorrelation, it was demonstrated that plant biomass per unit area of a pasture grazed by cattle exhibited two kinds of spatial heterogeneity: small-scale heterogeneity caused by grazing and large-scale heterogeneity caused by topography, land aspect, etc. For each of the 10 measurement times from May to August, 100 quadrats 50cm × 50cm were arranged along a straight line 50m long in a pasture, and the plants within the quadrats were harvested at the height of 3cm above the ground surface to measure the dry weight. The data were aggregated into frequency distributions, and gamma distribution and the parameter values were estimated. This analysis showed that with the progression of grazing the amount of biomass decreased and the degree of spatial heterogeneity in biomass, measured per 0.25m², increased, and due to plant regrowth the trends were reversed. By rearranging the 100 biomass data in order of weight, it was suggested that plots with an extremely large biomass were not grazed by cattle and remained in the pasture. For the same data, variations of biomass along the straight line were divided into two parts based on the moving average: the spatial trend and the residuals which cannot be explained by the trend. In this analysis, 48–75% of the total spatial variation was explained by the trend along the straight line. Analysis using spatial autocorrelation for the actual biomass changes showed that the biomass changes within a range of about 10m on the straight line gave a positive correlation, which indicates a topographical trend in biomass. Spatial autocorrelation for residuals suggested that the spatial changes in biomass along the straight line followed a wave-like or checker-board pattern. Small-scale spatial heterogeneity in plant biomass may be caused by the uneven deposition of excreta by grazing animals, uneven use of the grassland by grazing animals, and uneven dispersal of plant seeds through faeces over the grassland. The possibility that such unevenness might accelerate energy flow in the grassland ecosystem and contribute to grassland sustainability is discussed.