Examination of the method for measuring soil respiration in cultivated land: Effect of carbon dioxide concentration on soil respiration

An acceleration of soil respiration with decreasing CO₂ concentration was suggested in the field measurements. The result supporrs that obtained in laboratory experiments in our previous study. The CO₂ concentrations in a chamber of the alkali absorption method (the AA-method) were about 150–250 parts/10⁶ lower than that in the atmosphere (about 350 parts/10⁶), while those observed in the open-flow IRGA method (the OF-method) were nearly equal to the soil surface CO₂ levels. The AA-method at such low CO₂ levels in the chamber appears to overestimate the soil respiration. Our results showed that the rates obtained by the AA-method were about twice as large as those by the OF-method in field and laboratory measurements. This finding has important consequences with respect to the validity of the existing data obtained by the AA-method and the estimation of changes in the terrestrial carbon flow with elevated CO₂     

任务驱动法在“微生物学实验”混合式教学中的实践

通过“微生物学实验”课程多年来的混合式教学实践发现,学生的主动性是学习效果的核心要素。鉴于在以往的教学实践中,无论采用何种教学手段,总有部分学生的学习主动性不能得到体现。我们近年来采用轮流组长责任制下的任务驱动教学法,极大地调动了所有学生的学习动力。每位学生在担任组长工作时从课前任务、课堂执行、课后总结等方面都发挥了重要作用,而不担任组长时也会积极主动地配合组长工作。最终,实验课程学习成绩优秀率占比、体现素质能力培养的成绩分项都显著提升。同时,课程教学也收获了良好的学生认可和反馈。     

Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: An alternative method for generating a high-resolution solution structure

Summary A new method, a restrained Monte Carlo (rMC) calculation, is demonstrated for generating high-resolution structures of DNA oligonucleotides in solution from interproton distance restraints and bounds derived from complete relaxation matrix analysis of two-dimensional nuclear Overhauser effect (NOE) spectral peak intensities. As in the case of restrained molecular dynamics (rMD) refinement of structures, the experimental distance restraints and bounds are incorporated as a pseudo-energy term (or penalty function) into the mathematical expression for the molecular energy. However, the use of generalized helical parameters, rather than Cartesian coordinates, to define DNA conformation increases efficiency by decreasing by an order of magnitude the number of parameters needed to describe a conformation and by simplifying the potential energy profile. The Metropolis Monte Carlo method is employed to simulate an annealing process. The rMC method was applied to experimental 2D NOE data from the octamer duplex d(GTA-TAATG)·d(CATTATAC). Using starting structures from different locations in conformational space (e.g. A-DNA and B-DNA), the rMC calculations readily converged, with a root-mean-square deviation (RMSD) of <0.3 Å between structures generated using different protocols and starting structures. Theoretical 2D NOE peak intensities were calculated for the rMC-generated structures using the complete relaxation matrix program CORMA, enabling a comparison with experimental intensities via residual indices. Simulation of the vicinal proton coupling constants was carried out for the structures generated, enabling a comparison with the experimental deoxyribose ring coupling constants, which were not utilized in the structure determination in the case of the rMC simulations. Agreement with experimental 2D NOE and scalar coupling data was good in all cases. The rMC structures are quite similar to that refined by a traditional restrained MD approach (RMSD<0.5 Å) despite the different force fields used and despite the fact that MD refinement was conducted with additional restraints imposed on the endocyclic torsion angles of deoxyriboses. The computational time required for the rMC and rMD calculations is about the same. A comparison of structural parameters is made and some limitations of both methods are discussed with regard to the average nature of the experimental restraints used in the refinement.Abbreviations MC Monte Carlo - rMC restrained Monte Carlo - MD molecular dynamics - rMD restrained molecular dynamics - DG distance geometry - EM energy minimization - 2D NOE two-dimensional nuclear Overhauser effect - DQF-COSY double-quantum-filtered correlation spectroscopy - RMSD root-mean-square deviation To whom correspondence should be addressed.     

信号分子在生物脱氮中的作用及检测方法

生物脱氮是由微生物主导的地球氮循环中的重要环节之一,主要包括硝化、反硝化和厌氧氨氧化(anaerobic ammonium oxidation,anammox)等过程。在微生物联合作用下,污水中的有机氮及氨氮经一系列作用转化为氮气,这种经济高效、环境友好的处理工艺在世界范围内得到广泛应用。群体感应(quorum sensing,QS)以信号分子为媒介通过改变菌群密度和周围环境变化来调节微生物的各种行为。大量的研究已证实调控QS信号分子在生物脱氮中具有应用潜力。本文介绍了各种信号分子类型,从基因组学、实际应用等方面综述了各类信号分子以及检测方法,同时针对酰基高丝氨酸内酯(acyl homoserine lactones,AHLs)类信号分子在生物脱氮中的作用进行详细介绍。然而不足之处在于信号分子研究只是停留在实验室阶段,仅仅研究了单一信号分子对生物脱氮的影响。未来可将信号分子应用于实际污水,研究多种信号分子共同作用以及多种微生物之间的QS现象。     

制药工程“微生物学实验”课程的项目化教学探索与实践

为了培养学生的自主学习能力和实践创新能力,按照工程教育专业认证要求基于成果导向教育(outcome based education, OBE)理念设计课程教学,将制药工程微生物学实验课实验教学项目设置成入门、进阶和自主3种项目等级。实验项目内容由浅入深、逐级递进、层层相关,教学过程以学生为中心,并结合线上教学手段和竞赛机制的支持。实践结果表明,经过项目化教学改革,在教师教学和学生学习成效两个方面均得到明显提升,学生在论文撰写能力、动手能力等方面也有了明显的进步,值得后续进一步总结和推广。     

基于微波热声层析成像定量重建生物组织电导率的改进方法

目的 生物电磁学参数中的电导率与组织的功能性信息直接相关,精准重建生物组织电导率在医学成像技术和医学诊断领域中有着重要意义。本文改进定量微波热声层析成像（microwave-induced thermoacoustic tomography,MTAT）算法,使组织电导率的重建精度提高。方法 本文在利用有限元离散法求解热声波动方程和亥姆霍兹方程的基础之上,提出了一种基于正则化牛顿迭代法（regularized Newton iteration method,RNIM）定量重建组织电导率的改进方法。结果 通过数值模拟实验和含不同浓度NaCl溶液的仿体实验,验证了算法改进的有效性。组织仿体实验结果表明,目标在不同位置、不同大小、不同对比度情况下,相比于定量微波热声层析成像采用拟合（fitting）的方法,采用正则化牛顿法定量重建的仿体电导率相对误差明显降低,重建目标精度提高。在仿体实验中采用RNIM方法重建相同浓度的单目标在不同位置的电导率变化幅度更小,以及重建多目标电导率的相对比值与实际更接近,实验结果验证了改进方法的稳定性。结论 研究结果表明优化算法能更加准确地定量重建组织仿体的电导率,...     

电场对完整青蛙横纹肌收缩机理的椭圆偏振法研究

利用能反映肌纤维内部结构的椭圆偏振参数研究恒定电场,脉冲电场对完整的青蛙横纹肌收缩的影响,研究表明,电场对肌纤维作用后,肌质网释放钙离子,致使肌纤维中蛋白质分子运动后出现收缩效应。实验发现：椭圆偏参数的测量灵敏度和肌小节长度有关,蛋白质运动规律和电场的性质的关系无的差异,只有量的不同。它们的共同特点是,随着电场强度的逐渐增强,其退偏率的变化呈先下降一上升的凹形曲线,这是由于电场引起的肌球蛋白分子极     

酵母样真菌快速分型诊断

为进一步解决感染酵母样真菌病患者的早期诊断和治疗,我们采用了一种快速、简便、准确鉴定和分类酵母样真菌的方法——纸片法,同时对纸片法与传统的方法(生长图谱法)进行了比较。217株酵母样真菌的鉴定结果准确率达100％,其中白念珠菌检出率最高155株占71.42％,为最常见菌,其次是热带念珠20株占9.22％,其它四种念珠菌16株占7.37％,还有分类及种未定酵母菌26株占11.98％。以上观察结果其检出率和国内外报道的资料相似。我们认为用纸片法鉴定酵母样真菌,操作过程简单易行、费用低廉、准确快速,可尽早为临床提供治疗依据。     

iBench: A ground truth approach for advanced validation of mass spectrometry identification method

The discovery of many noncanonical peptides detectable with sensitive mass spectrometry inside, outside, and on cells shepherded the development of novel methods for their identification, often not supported by a systematic benchmarking with other methods. We here propose iBench, a bioinformatic tool that can construct ground truth proteomics datasets and cognate databases, thereby generating a training court wherein methods, search engines, and proteomics strategies can be tested, and their performances estimated by the same tool. iBench can be coupled to the main database search engines, allows the selection of customized features of mass spectrometry spectra and peptides, provides standard benchmarking outputs, and is open source. The proof-of-concept application to tryptic proteome digestions, immunopeptidomes, and synthetic peptide libraries dissected the impact that noncanonical peptides could have on the identification of canonical peptides by Mascot search with rescoring via Percolator (Mascot+Percolator).     

Milk metabolites can characterise individual differences in animal resilience to a nutritional challenge in lactating dairy goats

The aim of this study is built in two phases: to quantify the ability of novel milk metabolites to measure between-animal variability in response and recovery profiles to a short-term nutritional challenge, then to derive a resilience index from the relationship between these individual variations. At two different stages of lactation, sixteen lactating dairy goats were exposed to a 2-d underfeeding challenge. The first challenge was in late lactation, and the second was carried out on the same goats early in the following lactation. During the entire experiment period, samples were taken at each milking for milk metabolite measures. For each metabolite, the response profile of each goat was characterised using a piecewise model for describing the dynamic pattern of response and recovery profiles after the challenge relative to the start of the nutritional challenge. Cluster Analysis identified three types of response/recovery profiles per metabolite. Using cluster membership, multiple correspondence analyses (MCAs) were performed to further characterise response profile types across animals and metabolites. This MCA analysis identified three groups of animals. Further, discriminant path analysis was able to separate these groups of multivariate response/recovery profile type based on threshold levels of three milk metabolites: β-hydroxybutyrate, free glucose and uric acid. Further analyses were done to explore the possibility of developing an index of resilience from milk metabolite measures. Different types of performance response to short-term nutritional challenge can be distinguished using multivariate analyses of a panel of milk metabolites.