构建生物药物分析实验教学改革新模式

生物药物分析实验是生物药物分析理论课程的重要补充,是培养学生掌握和巩固理论知识以及实验操作技能的重要途径。为适应现代高等教育对本科生的培养要求,对生物药物分析原有单一的实验教学模式进行改革已势在必行。我学院生物药物分析实验教学改革从实验教学内容、实验教学方法、实验教学手段等方面进行实践探索,建立了"验证性-综合设计性实验教学"、"科研-实验教学相结合"、"开放式实验教学"等新型的实验教学模式,在近几年的本科实验教学活动中,对于培养学生的实际操作能力、独立分析问题和解决问题的能力,团队协作等方面的能力起到了明显的效果,受到学生好评。     

Modeling of dynamical systems through deep learning

This review presents a modern perspective on dynamical systems in the context of current goals and open challenges. In particular, our review focuses on the key challenges of discovering dynamics from data and finding data-driven representations that make nonlinear systems amenable to linear analysis. We explore various challenges in modern dynamical systems, along with emerging techniques in data science and machine learning to tackle them. The two chief challenges are (1) nonlinear dynamics and (2) unknown or partially known dynamics. Machine learning is providing new and powerful techniques for both challenges. Dimensionality reduction methods are used for projecting dynamical methods in reduced form, and these methods perform computational efficiency on real-world data. Data-driven models drive to discover the governing equations and give laws of physics. The identification of dynamical systems through deep learning techniques succeeds in inferring physical systems. Machine learning provides advanced new and powerful algorithms for nonlinear dynamics. Advanced deep learning methods like autoencoders, recurrent neural networks, convolutional neural networks, and reinforcement learning are used in modeling of dynamical systems.     

Male-male competition and repeated evolution of terrestrial breeding in Atlantic Coastal Forest frogs*

Terrestrial breeding is a derived condition in frogs, with multiple transitions from an aquatic ancestor. Shifts in reproductive mode often involve changes in habitat use, and these are typically associated with diversification in body plans, with repeated transitions imposing similar selective pressures. We examine the diversification of reproductive modes, male and female body sizes, and sexual size dimorphism (SSD) in the Neotropical frog genera Cycloramphus and Zachaenus, both endemic to the Atlantic rainforest of Brazil. Species in this clade either breed in rocky streams (saxicolous) or in terrestrial environments, allowing us to investigate reproductive habitat shifts. We constructed a multilocus molecular phylogeny and inferred evolutionary histories of reproductive habitats, body sizes, and SSD. The common ancestor was small, saxicolous, and had low SSD. Terrestrial breeding evolved independently three times and we found a significant association between reproductive habitat and SSD, with shifts to terrestrial breeding evolving in correlation with decreases in male body size, but not female body size. Terrestrial breeding increases the availability of breeding sites and results in concealment of amplexus, egg-laying, and parental care, therefore reducing male-male competition at all stages of reproduction. We conclude that correlated evolution of terrestrial reproduction and small males is due to release from intense male-male competition that is typical of exposed saxicolous breeding.     

Trait-dependency of trophic interactions in zooplankton food webs

Anthropogenic change in the abundance or identity of dominant top predators may induce reorganizations in whole food webs. Predicting these reorganizations requires identifying the biological rules that govern trophic niches. However, we still lack a detailed understanding of the respective contributions of body size, behaviour (e.g. match between predator hunting mode and prey antipredator strategy), phylogeny and/or ontogeny in determining both the presence and strength of trophic interactions. Here, we address this question by measuring zooplankton numerical response to fish predators in lake enclosures. We compared the fit to zooplankton count data of models grouping zooplankters based either on 1) body sizes, 2) antipredator behaviour, 3) body size combined with antipredator behaviour or on 4) phylogeny combined with ontogeny (i.e. different life stages of copepods). Body size was a better predictor of zooplankton numerical response to fish than antipredator behaviour, but combining body size and behaviour provided even better predictions. Models based on phylogeny combined with ontogeny clearly outperformed those based on other zooplankton grouping rules, except when phylogeny was poorly resolved. Removing ontogenetic information plagued the predictive power of the highly-resolved (genus-level) phylogenetic grouping but not of medium-resolved or poorly-resolved phylogenetic grouping. Our results support the recent use of phylogeny as a superior surrogate for traits controlling trophic niches, and further highlight the added value of combining phylogeny with ontogenetic traits. Further improvements in our mechanistic understanding of how trophic networks are shaped are bound to uncovering the trophic traits captured by phylogeny and ontogeny, but that currently remain hidden to us.     

Structural dynamics of pentapeptide repeat proteins

Pentapeptide repeat proteins (PRPs) represent a large superfamily with more than 38 000 sequences in nearly 3500 species, the majority belonging to cyanobacteria but represented among all branches of life. PRPs contain at least eight consecutive pentapeptide repeats with the consensus (A/C/S/V/T/L/I)(D/N/S/K/E/I/R)(L/F)(S/T/R/E/Q/K/V/D)(G/D/E/N/R/Q/K). PRPs fold into right-handed quadrilateral β helices, also known as repeat-five-residue (Rfr)-folds, with four consecutive pentapeptide repeats comprising a single coil, the ~90° change in polypeptide direction in square-shaped coils achieved by type I, II and IV β turns, and hydrogen bonds between coils establishing β ladders on each Rfr-fold face. PRPs are broadly categorized into group 1 and 2 involved in antibiotic resistance and group 3 currently having unknown functions. Motivated by their intriguing structures, we are investigating PRP biophysical characteristics, including Rfr-fold thermal stability, β turn and β ladder hydrogen bond amide exchange rates and backbone dynamics. Here, we present analysis of 20 ns molecular dynamics (MD) simulations and all atom normal mode analysis (aaNMA) calculations for four group 1 and group 2 and four group 3 PRPs whose structures have been determined by X-ray crystallography. The MD cross-correlation matrices and aaNMA indicated strong correlated motion between adjacent coils and weak coupled motion between coils separated by one or more intervening coils. Slow anticorrelated motions were detected between adjacent coils in aaNMA modes that we hypothesize are requisite to access exchange-competent states necessary to permit solvent exchange of amide hydrogens involved in β-ladder and β-turns hydrogen bonds, which can have lifetimes on the order of months.     

Binding mechanism of spinosine and venenatine molecules with p300 HAT enzyme: Molecular screening,molecular dynamics and free-energy analysis

The chromatin modification is regulated by the histone acetyltransferase (HAT) and histone deacetyltransferase (HDAC) enzymes; abnormal function of these enzymes leads to several malignant diseases. The inhibition of these enzymes using natural ligand molecules is an emerging technique to cure these diseases. The in vitro analysis of natural molecules, venenatine, spinosine, palmatine and taxodione are giving the best inhibition rate against p300 HAT enzyme. However, the detailed understanding of binding and the stability of these molecules with p300 HAT is not yet known. The aim of the present study is focused to determine the binding strength of the molecules from molecular dynamics simulation analysis. The docking analysis confirms that, the venenatine (−6.97 kcal/mol - conformer 8), spinosine (−6.52 kcal/mol conformer −10), palmatine (−5.72 kcal/mol conformer-3) and taxodione (−4.99 kcal/mol conformer-4) molecules form strong hydrogen bonding interactions with the key amino acid residues (Arg1410, Thr1411 and Trp1466) present in the active site of p300. In the molecular dynamics (MD) simulation, the spinosine retain these key interactions with the active site amino acid residues (Arg1410, Thr1411, and Trp1466) than venenatine and are stable throughout the simulation. The RMSD value of spinosine (0.5 to 1.3 Å) and venenatine (0.3 to 1.3 Å) are almost equal during the MD simulation. However, during the MD simulation, the intermolecular interaction between venenatine and the active site amino acid residues (Arg1410, Thr1411, and Trp1466) decreased on comparing with the spinosine-p300 interaction. The binding free energy of the spinosine (−15.30 kcal/mol) is relatively higher than the venenatine (−11.8 kcal/mol); this increment is attributed to the strong hydrogen bonding interactions of spinosine molecule with the active site amino acid residues of p300.     

不同耕作方式对内蒙古旱作农田土壤微生物量和作物指标的影响

研究了不同耕作方式下土壤微生物量碳、氮、磷及玉米全生育期叶面积指数、株高和干物质积累量的动态变化,并对土壤指标与作物指标之间的关系进行分析.结果表明:免耕有利于提高土壤微生物量碳、氮、磷含量.不同处理微生物量均表现为:免耕留高茬覆盖>免耕留低茬覆盖>免耕留高茬>免耕留低茬>传统耕翻;土壤微生物量碳、氮、磷含量随土层深度的增加而呈降低趋势.除传统耕翻微生物量碳在10～20 cm土层深度含量提高外,其他处理微生物量碳、氮、磷均表现为0～10 cm>10～20 cm>20～30 cm>30～40cm土层深度;土壤生物量碳、氮、磷随季节的变化趋势基本一致,不同处理土壤生物量含量均为7月份含量最高、6月份次之、10月份最低;叶面积指数全生育期呈单峰曲线变化,株高和干物质积累呈S曲线变化.不同处理之间作物指标均表现为免耕留高茬覆盖>免耕留低茬覆盖>免耕留高茬>免耕留低茬>传统耕翻;土壤微生物量与作物指标之间的相关度较高,特别是微生物量磷,土壤微生物量在一定程度上可以反映作物的生长状况.研究结果能够很好地揭示在黄河流域内蒙古农田旱作区实施免耕的优势.

Abstract：

This paper studied the dynamic changes of soil microbial biomass and crop indices on a degraded rain-fed maize field in the Qingshuihe County of Inner Mongolia under no tillage with low stubble (NL), no tillage with high stubble (NH), no tillage with low stubble and residues (NLS), no tillage with high stubble and residues (NHS), and conventional tillage (CT). No tillage increased the soil microbial biomass C, N, and P, with the sequence of treatments NHS > NLS > NH > NL > CT. Except that the soil microbial biomass C in CT had an increase in 10-20 cm soil layer, the soil microbial biomass C, N, and P in all treatments decreased with soil depth. The soil microbial biomass C, N, and P had the same seasonal pattern, being the highest in July, secondly in June, and the lowest in October. The LAI in whole growth period varied in unimodal form, while the plant height and dry matter accumulation were in "S" form. All the crop indices followed the order of NHS > NLS > NH > NL > CT. Soil microbial biomass, its P in particular, had positive correlations with crop indices. Our results revealed the advantages of no tillage on rain-fed farmlands in Inner Mongolia.     

植物生理学双语教学的实践与创新

对近几年来植物生理学课程双语教学内容、教学方法、教学手段及考核方式等方面的改革进行了较深入的探讨与实践。通过研制双语教学网络课件,选择正确的国外原版教材和国内教材、编写合适的双语教学讲义,采用形式多样的双语教学模式,正确处理专业词汇和建立有效的考核机制等途径来提高双语教学质量,实现教学目标。     

V型羊毛硫肽雷可肽的抑菌机制

【背景】雷可肽(Lexapeptide)为首例V型羊毛硫肽家族化合物,具有较好的抗革兰氏阳性菌活性,对耐甲氧西林金黄色葡萄球菌(Methicillin-Resistant Staphylococcus aureus,MRSA)和表皮葡萄球菌(Methicillin-Resistant Staphylococcus epidermidis,MRSE)的抑制作用强于广泛应用的食品防腐剂乳酸链球菌素,其对pH和高温的稳定性也优于乳酸链球菌素,具有较好的应用前景。由于抑菌机制不明确,限制了雷可肽的开发应用。【目的】探究雷可肽抑菌作用特征以及作用机制,为雷可肽开发应用奠定基础。【方法】通过菌落计数法与Mg2+试验表征雷可肽抑菌动力学曲线;采用流式细胞仪和透射电子显微镜研究雷可肽在靶细胞表面的成孔性;利用高效液相色谱与基质辅助激光解吸电离的时间飞行质谱分析雷可肽处理对革兰氏阳性菌肽聚糖前体积累的影响。【结果】雷可肽在抑菌动力学上与乳酸链球菌素没有显著差别,但在更宽的Mg2+浓度范围内仍可保持抑菌活性。雷可肽处理后的细胞具有透过荧光染料的能力,生物型透射电镜观察到细胞发生破损。此外,在雷可肽作用后的细胞中检测到肽聚糖合成的前体尿嘧啶核苷二磷酸-N-乙酰胞壁酸五肽。【结论】雷可肽能够通过抑制细胞壁肽聚糖生物合成并造成细胞损伤进而获得通透性,以此来抑制革兰氏阳性菌生长。