Babesia Bovis Ligand-Receptor Interaction: AMA-1 Contains Small Regions Governing Bovine Erythrocyte Binding

Apical membrane antigen 1 is a microneme protein which plays an indispensable role during Apicomplexa parasite invasion. The detailed mechanism of AMA-1 molecular interaction with its receptor on bovine erythrocytes has not been completely defined in Babesia bovis. This study was focused on identifying the minimum B. bovis AMA-1-derived regions governing specific and high-affinity binding to its target cells. Different approaches were used for detecting ama-1 locus genetic variability and natural selection signatures. The binding properties of twelve highly conserved 20-residue-long peptides were evaluated using a sensitive and specific binding assay based on radio-iodination. B. bovis AMA-1 ectodomain structure was modelled and refined using molecular modelling software. NetMHCIIpan software was used for calculating B- and T-cell epitopes. The B. bovis ama-1 gene had regions under functional constraint, having the highest negative selective pressure intensity in the Domain I encoding region. Interestingly, B. bovis AMA-1-DI (¹⁰⁰YMQKFDIPRNHGSGIYVDLG¹¹⁹ and ¹²⁰GYESVGSKSYRMPVGKCPVV¹³⁹) and DII (³⁰²CPMHPVRDAIFGKWSGGSCV³²¹)-derived peptides had high specificity interaction with erythrocytes and bound to a chymotrypsin and neuraminidase-treatment sensitive receptor. DI-derived peptides appear to be exposed on the protein’s surface and contain predicted B- and T-cell epitopes. These findings provide data (for the first-time) concerning B. bovis AMA-1 functional subunits which are important for establishing receptor-ligand interactions which could be used in synthetic vaccine development.     

Courses Based on iGEM/BIOMOD Competitions Are the Ideal Format for Research-Based Learning of Xenobiology

Synthetic biology and especially xenobiology, as emerging new fields of science, have reached an intellectual and experimental maturity that makes them suitable for integration into the university curricula of chemical and biological disciplines. Novel scientific fields that include laboratory work are perfect playgrounds for developing highly motivating research-based teaching modules. We believe that research-based learning enriched by digital tools is the best approach for teaching new emerging essentials of academic education. This is especially true when the scientific field as such is still not canonized with text books and best-practice examples. Our experience shows that iGEM/BIOMOD competitions represent an excellent basis for designing research-based courses in xenobiology. Therefore, we present a report on “iGEM–Synthetic Biology” offered at the Technische Universität Berlin as an example.     

Alteration of the Route to Menaquinone towards Isochorismate-Derived Metabolites

Chorismate and isochorismate constitute branch-point intermediates in the biosynthesis of many aromatic metabolites in microorganisms and plants. To obtain unnatural compounds, we modified the route to menaquinone in Escherichia coli. We propose a model for the binding of isochorismate to the active site of MenD ((1R,2S, 5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxycyclohex-3-ene-1-carboxylate (SEPHCHC) synthase) that explains the outcome of the native reaction with α-ketoglutarate. We have rationally designed variants of MenD for the conversion of several isochorismate analogues. The double-variant Asn117Arg–Leu478Thr preferentially converts (5S,6S)-5,6-dihydroxycyclohexa-1,3-diene-1-carboxylate (2,3-trans-CHD), the hydrolysis product of isochorismate, with a >70-fold higher ratio than that for the wild type. The single-variant Arg107Ile uses (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxylate (2,3-trans-CHA) as substrate with >6-fold conversion compared to wild-type MenD. The novel compounds have been made accessible in vivo (up to 5.3 g L⁻¹). Unexpectedly, as the identified residues such as Arg107 are highly conserved (>94 %), some of the designed variations can be found in wild-type SEPHCHC synthases from other bacteria (Arg107Lys, 0.3 %). This raises the question for the possible natural occurrence of as yet unexplored branches of the shikimate pathway.     

Lessons from a Minimal Genome: What Are the Essential Organizing Principles of a Cell Built from Scratch?

One of the primary challenges facing synthetic biology is reconstituting a living system from its component parts. A particularly difficult landmark is reconstituting a self-organizing system that can undergo autonomous chromosome compaction, segregation, and cell division. Here, we discuss how the syn3.0 minimal genome can inform us of the core self-organizing principles of a living cell and how these self-organizing processes can be built from the bottom up. The review underscores the importance of fundamental biology in rebuilding life from its molecular constituents.     

不同类型断层控制油气垂向富集的差异——以渤海湾盆地歧口凹陷歧南斜坡区为例

渤海湾盆地历经多期构造变动，断层圈闭发育普遍。断层作为断层圈闭的边界条件，在油气成藏过程中起着至关重要的作用。以断层圈闭较发育的歧南斜坡区为例分析了同向断层和反向断层控制油气垂向富集的差异，基于三维地震资料，从断层形成过程和断层圈闭分布出发，剖析了断层遮挡圈闭的成因及分布规律。结合油水分布规律，基于油藏解剖并应用储层定量荧光技术明确了不同类型断层控藏的差异及其形成机理。研究表明：①断层分段生长作用和断层上盘与下盘的差异活动是同向断层控制下断层遮挡圈闭形成的主要原因，斜坡区反向断层控制形成的断层圈闭则是断块掀斜翘倾作用所致；②同向断层圈闭发育在断层上盘分段点位置，只有当同向断层进入"硬连接"阶段方可形成断层圈闭，反向断层圈闭形成在断层下盘，在反向断层活动初期便可形成；③同向断层既可以控制油气在多套含油气系统中聚集成藏，也可在一套含油气系统中富集，而反向断层往往控制油气在一套含油气系统中富集；④不同类型断层控制油气垂向聚集的差异与圈闭发育位置以及断-盖配置有关。采用泥岩涂抹系数对沙河街组一段中部盖层控制的含油气系统的垂向调整进行定量评价，泥岩涂抹系数低于3.5时油气保存，泥岩涂抹系数高于3.5时油气垂向渗漏。     

合成生物学在生物基塑料制造中的应用

合成生物学是以工程学思想为指导，对天然生物基因组进行改造和重构，合成新的生物元件，构建新的代谢途径，生产新产品或获得新表型的新兴学科。生物基塑料是以天然物质为原料在微生物作用或化学反应下生成的塑料。利用合成生物学改造工程菌株的方法制备合成生物基塑料已经成为学术界和产业界关注的热点。本文综述了合成生物学的发展和重要的合成生物学技术，重点综述了利用合成生物学技术构建聚羟基烷酸酯、尼龙、聚乳酸和丁二酸丁二醇酯等生物基塑料聚合物单体及其衍生物的代谢途径和工程优化领域的研究进展。     

Land surface deformation parameter estimation using persistent scatterer interferometry approach in an underground metal mining environment

Persistent scatterer interferometry (PSI) is a major advancement in radar interferometry for detecting and monitoring land deformation. PSI is the most advanced class of differential interferometric synthetic aperture radar (DInSAR) techniques. The technique conquers the main drawbacks of the conventional DInSAR technique by identifying radar targets having stable backscattering characteristics in time. These targets are termed as persistent scatterers (PSs). The higher the number of PSs for a study area the higher the accuracy of the results will be, which is most common for deformation analysis in urban areas. However, for non-urban or highly de-correlated areas, PSs density collapses significantly, which needs to increase for optimal results. For this purpose, partially coherent/distributed scatterers (DSs) are being exploited in addition to the PSs. The field surface of this study is one of the copper-rich mining belts in India, which consists of two major underground metal mines. Scatterer characterziation of the field surface under study suggests that most of the scatterers are DSs and very few scatterers under the influence of the mining zone are PSs. In addition to this, a preliminary investigation of deformation characteristics of the field surface under study reveals that the spatial extent of deformation is small/localized along with slow and non-linear deformation. Keeping in view scatterer and deformation characteristics of the field surface under study, in this research paper, a Quasi-Persistent Scatterer based PSI approach has been applied using high-resolution TerraSAR-X interferometric data stack (10 images) to generate deformation time series and deformation velocity. Furthermore, results obtained from the applied PSI approach and ground-based observations (using GNSS) have shown good agreement with each other, in the order of ?5.20?mm/year (LOS) and ?5.38?mm/year (subsiding), respectively.     

松木颗粒热解与高温蒸汽气化半焦产率及形貌特征分析

以成型松木颗粒为原料，进行低温热解，研究了热解温度和升温速率对生成的松木半焦产率及官能团的影响。以试验得到的松木半焦进行蒸汽气化试验，对比分析了温度对半焦重整气化形貌特征、比表面积和平均孔径的影响。研究表明：随着热解温度升高，松木半焦脂肪族结构峰消失转化为烃等小分子物质及气化气，进而降低半焦产率。升温速率升高，半焦产率呈先下降后升高的趋势，在800℃升温速率为30K/min时半焦产率最低。不同温度热解和蒸汽气化对比试验表明，温度相对较低时（500℃）热解和蒸汽气化半焦孔隙结构相近，随着温度的升高，蒸汽气化半焦结构发生明显变化，900°C时出现了更小的孔道结构且比表面积增加明显。蒸汽引入使松木半焦和水蒸气发生热解反应的同时发生了脱氢反应，气化半焦形貌出现熔融和烧结现象。     

2种灰色模型在矿区地表沉陷预计中的适用性

目前矿区地表单点沉陷动态预计方法主要基于传统的水准测量数据,监测方法单一,成本高,观测点易破坏,不能保证地表形变信息的实时性,且采用灰色模型进行地表沉陷预计时只针对单一模型的应用,没有结合模型自身特点分析其适用性。以袁店二矿7221工作面为试验区域,采用合成孔径雷达差分干涉测量技术监测矿区地表沉陷量,分别建立了描述沉陷量与时间关系的GM(1,1)与灰色Verhulst模型进行地表沉陷量预计,实现了矿区地表沉陷监测与动态预计一体化。通过比较、分析GM(1,1)与灰色Verhulst模型对地表沉陷量的拟合及预计结果,得出了2种灰色模型在矿区地表沉陷预计中的适用性:在矿区开采沉陷开始至活跃前期,若地表单点沉陷量曲线呈近似单峰型,则宜采用GM(1,1)进行短期预计;当矿区地表沉陷进入衰退阶段,单点沉陷量曲线呈平底饱和状态,则宜采用灰色Verhulst模型进行中长期预计。