Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene region

Background  

PPE38 (Rv 2352c) is a member of the large PPE gene family of Mycobacterium tuberculosis and related mycobacteria. The function of PPE proteins is unknown but evidence suggests that many are cell-surface associated and recognised by the host immune system. Previous studies targeting other PPE gene members suggest that some display high levels of polymorphism and it is thought that this might represent a means of providing antigenic variation. We have analysed the genetic variability of the PPE38 genomic region on a cohort of M. tuberculosis clinical isolates representing all of the major phylogenetic lineages, along with the ancestral M. tuberculosis complex (MTBC) member M. canettii, and supplemented this with analysis of publicly available whole genome sequences representing additional M. tuberculosis clinical isolates, other MTBC members and non tuberculous mycobacteria (NTM). Where possible we have extended this analysis to include the adjacent plcABC and PPE39/40 genomic regions.     

Airborne Pollen Grains of Bozuyuk （Bilecik, Turkey）

Airborne pollen grains in the atmosphere of Bozuyuk were investigated over a 2 yr period from 2000 to 2001 using a Durham sampler. A total number of pollen grains of 5 170 pollen grains belonging to 32 taxa were identified and recorded along with some unidentified pollen grains. Of all the pollen grains, 78.66% were arboreal, 19.20% were non-arboreal, and 2.12% were unidentified. The majority of pollen grains investigated were Pinus, Platanus, Quercus, Cupressaceae, Poaceae, Fagus, Salix, Rosaceae, Urticaceae, Asteraceae, and Chenopodiaceae. The maximum number of pollen grains was recorded in May.     

Polymorphic microsatellites for the study of Aconitum napellus L. (Ranunculaceae), a rare species in France

Aconitum napellus is a perennial European Ranunculaceae that is currently decreasing in France. Six polymorphic microsatellite markers were characterized to study the polymorphism among individuals sampled from six populations in France. The total number of alleles per locus varied from two to four. Mean observed heterozygosities at each microsatellite locus ranged from 0.05 to 0.19. This set of microsatellites offers an efficient tool for more detailed investigations on population genetic structure of a rare species that can reproduce both sexually and by vegetative spread.     

How much time can herbivore protection buy for coral reefs under realistic regimes of hurricanes and coral bleaching?

Coral reefs have been more severely impacted by recent climate instability than any other ecosystem on Earth. Corals tolerate a narrow range of physical environmental stress, and increases in sea temperature of just 1 °C over several weeks can result in mass coral mortality, often exceeding 95% of individuals over hundreds of square kilometres. Even conservative climate models predict that mass coral bleaching events could occur annually by 2050. Unfortunately, managers of coral‐reef resources have few options available to meet this challenge. Here, we investigate the role that fisheries conservation tools, including the designation of marine reserves, can play in altering future trajectories of Caribbean coral reefs. We use an individual‐based model of the ecological dynamics to test the influence of spatially realistic regimes of disturbance on coral populations. Two major sources of disturbance, hurricanes and coral bleaching, are simulated in contrasting regions of the Caribbean: Belize, Bonaire, and the Bahamas. Simulations are extended to 2099 using the HadGEM1 climate model. We find that coral populations can maintain themselves under all levels of hurricane disturbance providing that grazing levels are high. Regional differences in hurricane frequency are found to cause strikingly different spatial patterns of reef health with greater patchiness occurring in Belize, which has less frequent disturbance, than the Bahamas. The addition of coral bleaching led to a much more homogenous reef state over the seascape. Moreover, in the presence of bleaching, all reefs exhibited a decline in health over time, though with substantial variation among regions. Although the protection of herbivores does not prevent reef degradation it does delay rates of coral loss even under the most severe thermal and hurricane regimes. Thus, we can estimate the degree to which local conservation can help buy time for reefs with values ranging between 18 years in the Bahamas and over 50 years in Bonaire, compared with heavily fished systems. Ultimately, we demonstrate that local conservation measures can benefit reef ecosystem services but that their impact will vary spatially and temporally. Recognizing where such management interventions will either help or fail is an important step towards both achieving sustainable use of coral‐reef resources and maximizing resource management investments.     

Evolutionary dynamics of tandem repeats in the mitochondrial DNA control region of the minnow Cyprinella spiloptera

Length variation due to tandem repeats is now recognized as a common feature of animal mitochondrial DNA; however, the evolutionary dynamics of repeated sequences are not well understood. Using phylogenetic analysis, predictions of three models of repeat evolution were tested for arrays of 260-bp repeats in the cyprinid fish Cyprinella spiloptera. Variation at different nucleotide positions in individual repeats supported different models of repeat evolution. One set of characters included several nucleotide variants found in all copies from a limited number of individuals, while the other set included an 8- bp deletion found in a limited number of copies in all individuals. The deletion and an associated nucleotide change appear to be the result of a deterministic, rather than stochastic, mutation process. Parallel origins of repeat arrays in different mitochondrial lineages, possibly coupled with a homogenization mechanism, best explain the distribution of nucleotide variation.      

Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA

Secondary structure models are an important step for aligning sequences, understanding probabilities of nucleotide substitutions, and evaluating the reliability of phylogenetic reconstructions. A set of conserved sequence motifs is derived from comparative sequence analysis of 184 invertebrate and vertebrate taxa (including many taxa from the same genera, families, and orders) with reference to a secondary structure model for domain III of animal mitochondrial small subunit (12S) ribosomal RNA. A template is presented to assist with secondary structure drawing. Our model is similar to previous models but is more specific to mitochondrial DNA, fitting both invertebrate and vertebrate groups, including taxa with markedly different nucleotide compositions. The second half of the domain III sequence can be difficult to align precisely, even when secondary structure information is considered. This is especially true for comparisons of anciently diverged taxa, but well-conserved motifs assist in determining biologically meaningful alignments. Patterns of conservation and variability in both paired and unpaired regions make differential phylogenetic weighting in terms of "stems" and "loops" unsatisfactory. We emphasize looking carefully at the sequence data before and during analyses, and advocate the use of conserved motifs and other secondary structure information for assessing sequencing fidelity.      

31种木本植物开花物候与系统发育的关系

植物物候通常被认为是由环境因素,如降水、温度和日照长度所决定,然而环境因素是否是物候唯一的决定因素仍然存在很大争议。谱系结构表征了植物在进化上的顺序,该发育时序是否对物候产生影响,当前仍然未知。在调查2016年春季新疆乌鲁木齐市最常见的31种木本植物的初始开花时间、败花时间和开花持续时间的基础上,通过分析植物开花物候的分布特征、开花物候在乔灌木间的差别、以及植物谱系距离与开花物候距离间的关系,试图揭示植物的开花物候和物种谱系(进化)顺序间的关系。结果表明:(1)新疆乌鲁木齐市31种木本植物的初始开花时间为4月18日±9d、败花时间为5月5日±12d、开花持续时间为(16±8)d;(2)乔木的初始开花时间和败花时间的标准差分别均低于灌木,乔木开花物候相对灌木更稳定;(3)乔木的初始开花和败花时间均显著早于灌木(P0.05),但开花持续时间在两者间未有显著性差异(P0.05);(3)31种木本植物间的初始开花时间距离、败花时间距离和开花持续时间距离均与物种谱系距离存在显著线性回归关系(P0.05)。综上可知:乔灌木在垂直空间上的分化使得木本植物的开花物候在植物生活型间存在不同。对植物的开花物候,除已被证明的降水、温度和日照长度等环境因素的影响外,物种进化顺序也可能造成了它在植物种间、时间和空间上的变异。     

Heterologous expression of bacteriocin E-760 in Chlamydomonas reinhardtii and functional analysis

The use of antimicrobial peptides (AMPs) synthesized by bacteria (bacteriocins) is an alternative for combating multidrug resistant bacterial strains and their production by recombinant route is a viable option for their mass production. The bacteriocin E-760 isolated from the genus Enterococcus sp. has been shown to possess inhibitory activity against Gram-negative and Gram-positive bacteria. In this study, the expression of a chimeric protein coding for E-760 in the nucleus of C. reinhardtii was evaluated, as well as, its antibacterial activity. The synthetic gene E-760S was inserted into the genome of C. reinhardtii using Agrobacterium tumefaciens. A transgenic line was identified in TAP medium with hygromycin and also by PCR. The increment in the culture medium temperature of the transgenic strain at 35 °C for 10 minutes, increased the production level of the recombinant protein from 0.14 (Noninduced culture, NIC) to 0.36% (Induced culture, IC) of total soluble proteins (TSP); this was quantified by an ELISA assay. Recombinant E-760 possesses activity against Staphylococcus aureus in 0.34 U log, Streptococcus agalactiae in 0.48 U log, Enterococcus faecium in 0.36 U log, Pseudomonas aeruginosa in 2 U log and for Klebsiella pneumoniae, the activity was 0.07 U log. These results demonstrate that the nucleus transformation of C. reinhardtii can function as a stable expression platform for the production of the synthetic gene E-760 and it can potentially be used as an antibacterial agent.     

Ixodes (Pholeoixodes) hexagonus, an efficient vector of Borrelia burgdorferi in the laboratory

Borrelia burgdorferi Johnson et al. was first isolated from the midgut of Ixodes dammini Spielman et al. in the U.S.A. and from the midgut of I.ricinus (L.) in Europe. I.ricinus was considered to be the only tick vector of this borrelia, in Europe, until I.hexagonus Leach, the hedgehog tick, was found to harbour spirochaetes. This paper reports an evaluation of the vector competence of I.hexagonus for the spirochaete B.burgdorferi. Transovarial and trans-stadial survival were demonstrated and the spirochaete was transmitted to laboratory mice via the bites of trans-stadially infected I.hexagonus females.