Genome Structural Variation Landscape and Its Selection Signatures in the Fast-growing Strains of the Pacific Oyster,Crassostrea gigas

Marine Biotechnology - The Pacific oyster (Crassostrea gigas) genome is highly polymorphic and affluent in structural variations (SVs), a significant source of genetic variation underlying...     

Regulation of root secondary metabolites by partial root-associated microbiotas under the shaping of licorice ecotypic differentiation in northwest China

Interactions between plant hosts and their microbiotas are becoming increasingly evident, while the effects of plant communities on microbial communities in different geographic environments are poorly understood. Here, the differentiation of licorice plant ecotypes and the distribution of root-associated microbiotas were investigated across five sampling sites in northwest China. The interactions between the environment, plant and microbial communities, and their effects on licorice root secondary metabolites, were elucidated. The plant community was clearly differentiated into distinct ecotypes based on genotyping-by-sequencing and was primarily driven by geographic distance and available soil nitrogen. The bulk soil and root-associated microbiotas (rhizosphere soil and root endosphere) partially correlated with plant community, but all were significantly discriminated by plant clade. Moreover, these microbiotas were explained to different extents by distinct combinations of environment, geography, and plant community. Similarly, three structural equation models showed that licorice root secondary metabolites were complicatedly modulated by multiple abiotic and biotic factors, and were mostly explained by these factors in the rhizosphere model. Collectively, the results provide novel insights into the role of environment–plant–microbiota interactions in regulating root secondary metabolites. That should be accounted for when selecting appropriate licorice planting sites and management measures.     

Plant multiscale networks: charting plant connectivity by multi-level analysis and imaging techniques

In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological processes. Network analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain Project. In plant science, network analysis has similarly been applied to study the connectivity of plant components at the molecular, subcellular, cellular, organic, and organism levels. Analysis of these multiscale networks contributes to our understanding of how genotype determines phenotype. In this review, we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational modalities. We next discussed the currently available analytic methodologies and multi-level imaging techniques used to map multiscale networks in plants. Finally, we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field.     

How public reaction to disease information across scales and the impacts of vector control methods influence disease prevalence and control efficacy

With the development of social media, the information about vector-borne disease incidence over broad spatial scales can cause demand for local vector control before local risk exists. Anticipatory intervention may still benefit local disease control efforts; however, infection risks are not the only focal concerns governing public demand for vector control. Concern for environmental contamination from pesticides and economic limitations on the frequency and magnitude of control measures also play key roles. Further, public concern may be focused more on ecological factors (i.e., controlling mosquito populations) or on epidemiological factors (i.e., controlling infection-carrying mosquitoes), which may lead to very different control outcomes. Here we introduced a generic Ross-MacDonald model, incorporating these factors under three spatial scales of disease information: local, regional, and global. We tailored and parameterized the model for Zika virus transmitted by Aedes aegypti mosquito. We found that sensitive reactivity caused by larger-scale incidence information could decrease average human infections per patch breeding capacity, however, the associated increase in total control effort plays a larger role, which leads to an overall decrease in control efficacy. The shift of focal concerns from epidemiological to ecological risk could relax the negative effect of the sensitive reactivity on control efficacy when mosquito breeding capacity populations are expected to be large. This work demonstrates that, depending on expected total mosquito breeding capacity population size, and weights of different focal concerns, large-scale disease information can reduce disease infections without lowering control efficacy. Our findings provide guidance for vector-control strategies by considering public reaction through social media.     

Levofloxacin susceptibility testing for Helicobacter pylori in China: comparison of E-test and disk diffusion method

Background: The aims of this study were to compare disk diffusion with E‐test method for levofloxacin susceptibility testing of Helicobacter pylori and standardized breakpoints for disk diffusion as a stable and reliable method for determining qualitative levofloxacin susceptibility. Materials and Methods: We determined the levofloxacin susceptibility of 45 H. pylori strains isolated from Chinese patients by the E‐test method. Disk diffusion was evaluated as an alternative method to determine susceptibility and compared with the E‐test results by linear regression analysis. Results: The minimum inhibitory concentration (MIC) values tested by E‐test method ranged from 0.047 to 32 μg/mL. Resistance to levofloxacin was detected in 16 (35.6%) isolates. The levofloxacin disk zone sizes obtained by disk diffusion method correlated well (r² = .877) with the MICs obtained by E‐test method. As a consequence of regression analysis, isolates with inhibition diameters <12 mm were considered resistant to levofloxacin. There was 100% agreement between the two methods for levofloxacin, applying the regression‐based breakpoints. Conclusions: The disk diffusion method is equivalent to the E‐test method for testing levofloxacin susceptibility of H. pylori strains; it is more practical and inexpensive, and it is suitable for the analysis of a small number of isolates compared with the E‐test method.     

Non-invasive limb ischemic pre-conditioning reduces oxidative stress and attenuates myocardium ischemia-reperfusion injury in diabetic rats

This study was to explore whether repeated non-invasive limb ischemic pre-conditioning (NLIP) can confer an equivalent cardioprotection against myocardial ischemia-reperfusion (I/R) injury in acute diabetic rats to the extent of conventional myocardial ischemic pre-conditioning (MIP) and whether or not the delayed protection of NLIP is mediated by reducing myocardial oxidative stress after ischemia-reperfusion. Streptozotocin-induced diabetic rats were randomized to four groups: Sham group, the I/R group, the MIP group and the NLIP group. Compared with the I/R group, both the NLIP and MIP groups showed an amelioration of ventricular arrhythmia, reduced myocardial infarct size, increased activities of total superoxide dismutase (SOD), manganese-SOD and glutathione peroxidase, increased expression of manganese-SOD mRNA and decreased xanthine oxidase activity and malondialdehyde concentration (All p < 0.05 vs I/R group). It is concluded that non-invasive limb ischemic pre-conditioning reduces oxidative stress and attenuates myocardium ischemia-reperfusion injury in diabetic rats.     

电转化法构建变形链球菌UA159 comD缺陷菌株

目的构建变形链球菌UAl59密度感应相关的comD基因缺陷菌株,为进一步研究该基因功能做准备。方法根据同源重组原理,利用变形链球菌UAl59comD基因同源重组DNA片段,采用电击转化方法获取转化菌落,通过形态学观察、生化特性检测、PCR及测序、RT-PCR对缺陷菌进行鉴定。结果在含有红霉素（10μg/mL）的琼脂平板上出现转化菌落,鉴定结果均显示转化菌为comD缺陷菌。结论成功构建了变形链球菌UA159comD基因缺陷菌株。     

Upregulation of p21-activated Kinase 6 in rat brain cortex after traumatic brain injury

p21-activated Kinase 6 (PAK6) is a serine/threonine kinase belonging to the p21-activated kinase (PAK) family. PAK kinases are well-known regulators of a wide variety of cellular functions, including regulation of cytoskeleton rearrangement, cell survival, apoptosis and the mitogen-activated protein kinase signaling pathway. To elucidate the expressions and possible functions of PAK6 in central nervous system (CNS) lesion and repair, we performed a traumatic brain injury (TBI) model in adult rats. Western blot analysis revealed that PAK6 level significantly increased at day 3 after damage, and then declined during the following days. Besides, double immunofluorescence staining showed PAK6 was primarily expressed in the neurons and a few of glial cells in the normal group. While after injury, the expression of PAK6 was increased significantly in the astrocytes and neurons, and the astrocytes had largely proliferated. We also examined the expression of proliferating cell nuclear antigen (PCNA) whose change was correlated with the expression of PAK6. Importantly, double immunofluorescence staining revealed that cell proliferation evaluated by PCNA appeared in many PAK6-expressing cells at day 3 after injury. In addition, injury-induced expression of PAK6 was co-labeled by active caspase-3 during neuronal apoptosis after injury. Collectively, we hypothesized PAK6 may play important roles in CNS pathophysiology after TBI and further research is needed to have a good understanding of its function and mechanism.