Bioconvection in Casson nanofluid flow with Gyrotactic microorganisms and variable surface heat flux

This paper presents a two-dimensional unsteady laminar boundary layer mixed convection flow heat and mass transfer along a vertical plate filled with Casson nanofluid located in a porous quiescent medium that contains both nanoparticles and gyrotactic microorganisms. This permeable vertical plate is assumed to be moving in the same direction as the free stream velocity. The flow is subject to a variable heat flux, a zero nanoparticle flux and a constant density of motile microorganisms on the surface. The free stream velocity is time-dependent resulting in a non-similar solution. The transport equations are solved using the bivariate spectral quasilinearization method. A grid independence test for the validity of the result is given. The significance of the inclusion of motile microorganisms to heat transfer processes is discussed. We show, inter alia, that introducing motile microorganisms into the flow reduces the skin friction coefficient and that the random motion of the nanoparticles improves the rate of transfer of the motile microorganisms.     

Stability analysis of drugdynamics model: A mat hematical approach

In this paper, a mathematical model of drug release from polymeric matrix and consequent intracellular drug transport is proposed and analyzed. Modeling of drug release is done through solubilization dynamics of drug particles, diffusion of the solubilized drug through the polymeric matrix in addition to reversible dissociation/recrystallization process. The interaction between drug-receptor, drug-plasma proteins along with other intracellular endosomal events is modeled. This leads to a mixed system of partial and ordinary differential equations with associated pertinent set of initial and boundary conditions. Furthermore, besides the stability of the proposed model, several sub-models are also studied for their stability criteria. Prominence is provided to the reduced model system having requisite relevance to the original system where quasi steady state approximation (QSSA) theory is utilized. For the model to be potent enough to generate appropriate predictive results for drug delivery, the stability properties of equilibrium in the mathematical model are analyzed both analytically and numerically. Numerical simulation in the embodiment of graphical representations speaks about various vital characteristics of the underlying physical phenomena along with the importance and sensitized impact of the model parameters controlling significant biological functions. Probed new therapies and clinical procedures could be assessed considering the present mathematical model and its analysis as the basis framework in order to effectively enhance therapeutic efficacy and improved patient compliance. The present study confirms the necessity of stability analysis study so that advocated mathematical model can effectively complement the real physiological behavior of pharmacokinetics.     

Discontinuous phenomena in bioreactor and membrane reactor systems

In this work, we analyze the existence of discontinuous bifurcation and stability issues in discontinuous flow of bioreactor and membrane reactor models with or without recycle. The reaction is assumed to be governed by certain types of discontinuities in Monod growth kinetics curve leading to discontinuous dynamical system. The criteria for the existence and stability of steady-states of these models are established. More generally, our analysis highlights the presence of several types of bifurcation depending upon the effect of the dilution factor (residence time), biomass concentration and solid-liquid-gas separator efficiency. As well, we present bifurcation conditions defining the dynamics near steady-state branches on the border, providing a possible framework for existing of saddle-node, nonsmooth fold, persistence and grazing-sliding scenarios. It is shown that the critical values of residence time dependence upon recycle ratio, decay rate and existence of discontinuity surface. Further, the performance of the reactor at largest residence times will be discussed. In addition, numerical simulations to illustrate and confirm the results will be carried out.     

Modeling control of foot and mouth disease with two time delays

We develop a delay ordinary differential equation model that captures the effects of prophylactic vaccination, reactive vaccination, prophylactic treatment and reactive culling on the spread of foot and mouth disease (FMD) with time delays. Simulation results from the study suggest that increasing time delay while increasing the control strategies decreases the burden of FMD. Further, the results reveal, that decreasing time delay while decreasing the control strategies increases the burden of FMD. The intermediate scenarios of either (i) increasing time delay while decreasing control or (ii) decreasing time delay while increasing control have intermediate effects on burden reduction. Thus, the implementation of effective control strategies combination can play an important role in mitigating against the FMD burden.     

直刺变豆菜叶绿体全基因组及其特征

直刺变豆菜(Sanicula orthacantha)是中国广泛分布的多年生草本植物, 也是一味著名的民族药。本文通过二代高通量测序平台Illumina HiSeq PE150对直刺变豆菜叶绿体全基因组进行测序, 并通过生物信息学方法对其结构特征进行分析。结果表明: 直刺变豆菜叶绿体全基因组大小为157,163 bp, 包括大单拷贝区(large single copy, LSC)、小单拷贝区(small single copy, SSC)和2个反向重复序列(inverted repeat sequence, IRa和IRb), 长度分别为87,547 bp、17,122 bp和26,247 bp, 具有典型被子植物叶绿体基因组环状四分体结构; 共注释得到129个基因, 包括8个核糖体RNA (rRNA)基因、37个转运RNA (tRNA)基因和84个蛋白质编码基因。直刺变豆菜在叶绿体基因组结构、基因种类、排列顺序上与其他伞形科植物基本一致。直刺变豆菜叶绿体全基因组测序的成功为变豆菜属植物完整叶绿体基因组组装及其特征分析提供了新的方法。     

基于Nextflow构建的宏条形码自动化分析流程EPPS

基于宏条形码技术的物种快速检测有助于生物多样性的评估、预测和保护。本文介绍了常用宏条形码分析的步骤和参数设定方法。我们利用Nextflow搭建了一款宏条形码分析流程EPPS, 可以自动化地运行从原始数据的质量控制到环境多样性的比较。Nextflow软件还拥有流程监控的功能, 可视化输出每个进程所消耗的时间与内存。本文还使用测试数据和已发表数据证明该平台能够有效地分析宏条形码数据并可靠地分析环境生物多样性的相似性。     

变豆菜属15种植物的果实微形态特征及其分类学意义

采用扫描电镜对来自北美和东亚的变豆菜属植物(美国7个种,中国8个种)的果实表面微形态进行观察,结合前人对伞形科其他类群果实微形态特征的研究及近年来分子系统学证据,对变豆菜属的种间分类进行研究。结果显示,变豆菜属植物果实的形态大小、皮刺弯曲程度和果柄蜡质纹饰丰富多样。研究表明变豆菜属是一个自然类群,果实表面钩刺结构有利于该属植物的传播及扩散,果实微形态特征具有分类学价值,可作为种间分类的依据。根据变豆菜属果实表面微形态特征,编制了该属植物分种检索表。     

Endo-β-1,4-glucanases impact plant cell wall development by influencing cellulose crystallization

Cell walls are vital to the normal growth and development of plants as they protect the protoplast and provide rigidity to the stem. Here, two poplar and Arabidopsis orthologous endoglucanases, which have been proposed to play a role in secondary cell wall development, were examined. The class B endoglucanases, Pt GH9B5 and At GH9B5, are secreted enzymes that have a predicted glycosylphosphatidylinositol anchor, while the class C endoglucanases, Pt GH9C2 and At GH9C2, are also predicted to be secreted but instead contain a carbohydrate-binding module.The poplar endoglucanases were expressed in Arabidopsis using both a 35 S promoter and the Arabidopsis secondary cell wall-specific Ces A8 promoter. Additionally, Arabidopsis t-DNA insertion lines and an RNAiconstruct was created to downregulate At GH9C2 in Arabidopsis. All of the plant lines were examined for changes in cell morphology and patterning, growth and development, cell wall crystallinity, micro fibril angle, and proportion of cell wall carbohydrates. Misregulation of Pt GH9B5/At GH9B5 resulted in changes in xylose content, while misregulation of Pt GH9C2/At GH9C2 resulted in changes in crystallinity, which was inversely correlated with changes in plant height and rosette diameter. Together, these results suggest that these endoglucanases affect secondary cell wall development by contributing to the cell wall crystallization process.     

YPED:An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database(YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry(LC–MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring(MRM)/selective reaction monitoring(SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.