Preparation of capacitor’s electrode from sunflower seed shell

Series of nanoporous carbons are prepared from sunflower seed shell (SSS) by two different strategies and used as electrode material for electrochemical double-layer capacitor (EDLC). The surface area and pore-structure of the nanoporous carbons are characterized intensively using N₂ adsorption technique. The results show that the pore-structure of the carbons is closely related to activation temperature and dosage of KOH. Electrochemical measurements show that the carbons made by impregnation-activation process have better capacitive behavior and higher capacitance retention ratio at high drain current than the carbons made by carbonization-activation process, which is due to that there are abundant macroscopic pores and less interior micropore surface in the texture of the former. More importantly, the capacitive performances of these carbons are much better than ordered mesoporous carbons and commercial wood-based active carbon, thus highlighting the success of preparing high performance electrode material for EDLC from SSS.     

An optimized technique for rapid genome modifications of Bacillus subtilis

The transformation efficiency of naturally competent Bacillus subtilis cells can be significantly increased using β recombinase binding sequences, as revealed by the results of this study. Plasmids containing different variations of these so called six-site-marker-cassettes were investigated. Furthermore, an optimized protocol for knock-out or knock-in mutations combining the Cre–lox-system and the six-sites is presented, which can be used for multiple genome modifications of B. subtilis.     

基于单链DNA开关调控的多功能生物电路

合成生物电路在生物传感及生物计算方面成为了广泛应用的工具。工程化生物电路系统具有良好的灵活性,同时也具备模块化的特征。在本文中,研究了基于单链DNA开关调控的多功能生物电路的构建方法。通过将计算机辅助设计的单链DNA开关作为核心控制元件,并利用长度为20 bp的toehold区域来激活单链DNA开关,驱动了简单的单向式、循环式以及级联的多层次的生物电路系统。在级联式电路系统中,通过调整单链DNA开关的结构,使信噪比从2.996变成5.274。同时,单链DNA开关作为长单链DNA（784 bp）的一部分,在无细胞蛋白质系统中实现了基因表达调控。因此,本文研究的工程化方法为今后复杂的人工生物电路的构建提供了坚实的技术基础。     

糯玉米胚乳淀粉粒粒度分布形成的酶学机理

以7个糯玉米品种为材料,测定其籽粒发育过程中淀粉粒粒度分布及淀粉合成相关酶活性的变化,分析两者之间的关系。结果表明,随着籽粒发育,糯玉米淀粉粒平均粒径逐渐增大,可溶性淀粉合成酶(SSS)和淀粉分支酶(SBE)活性呈单峰曲线变化。籽粒发育前期,小淀粉粒(≤7.4μm)所占体积较大;随着籽粒发育,小淀粉粒所占体积减少,大淀粉粒(>7.4μm)所占体积增多;籽粒发育后期,大淀粉粒所占体积较大。相关分析表明, SSS和SBE活性与大淀粉粒体积增大速率和平均粒径增大速率均呈显著或极显著正相关。因此, SSS和SBE是影响糯玉米胚乳淀粉粒粒度分布形成的主要酶, SSS和SBE活性越高,淀粉粒平均粒径越大,大淀粉粒所占体积越多。     

植物支链淀粉生物合成研究进展

植物支链淀粉占贮存淀粉的70%～80%,是决定植物果实或种子品质的关键成分.对植物支链淀粉生物合成途径及其代谢酶基因的研究,可大大推动支链淀粉结构的改造和在食品工业上的应用.该文介绍了植物支链淀粉的结构组成,详细阐述了参与支链淀粉生物合成的三类酶,即淀粉分支酶(starch branchingenzyme,SBE)、可溶性淀粉合酶(soluble starch synthase,SSS)和淀粉脱支酶(starch debranching enzyme,SDBE)的编码基因、酶学特性及其在支链淀粉合成中的作用,并就植物支链淀粉的合成模型加以探讨.同时提出了该研究领域尚待解决的问题,对其应用前景作了展望.     

Occurrence of sucrose and sucrose metabolizing enzymes in achlorophyllous algae

The presence of sucrose and the enzymes related to sucrose metabolism, i.e. sucrose synthase (SS) (UDP-glucose: D-fructose-2-glucosyl transferase, EC 2.4.1.13), sucrose phosphate synthase (SPS) (UDP-glucose: D-fructose-6-phosphate-2-glucosyl transferase, EC 2.4.1.14) and invertase (β-D-fructofuranoside fructohydrolase, EC 3.2.1.26) was demonstrated in Prototheca zopfii, a colorless alga. The levels of enzyme activities were lower than those obtained in Chlorella vulgaris, which is generally considered the photosynthetic counterpart of P. zopfii. Whem enzyme activities were measured in bleached cells of C. vulgaris, the levels were of the same order than those found in P. zopfii. These results would indicate that the sucrose metabolizing enzymes are not related to the algae ability to carry on photosynthesis.     

High prevalence of cerebral venous sinus thrombosis (CVST) as presentation of cystathionine beta-synthase deficiency in childhood: Molecular and clinical findings of Turkish probands

Classical homocystinuria is the most commonly inherited disorder of sulfur metabolism, caused by the genetic alterations in human cystathionine beta-synthase (CBS) gene. In this study, we present comprehensive clinical findings and the genetic basis of homocystinuria in a cohort of Turkish patients. Excluding some CBS mutations, detailed genotype–phenotype correlation for different CBS mutations has not been established in literature. We aimed to make clinical subgroups according to main clinical symptoms and discussed these data together with mutational analysis results from our patients. Totally, 16 different mutations were identified; twelve of which had already been reported, and four are novel (p.N93Y, p.L251P, p.D281V and c.829−2A>T). The probands were classified into three major groups according to the clinical symptoms caused by these mutations. A psychomotor delay was the most common diagnostic symptom (n = 12, 46.2% neurological presentation), followed by thromboembolic events (n = 6, 23.1% vascular presentation) and lens ectopia, myopia or marfanoid features (n = 5, 19.2% connective tissue presentation). Pyridoxine responsiveness was 7.7%; however, with partial responsive probands, the ratio was 53.9%.     

Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations

Worldwide structural genomics projects are increasing structure coverage of sequence space but have not significantly expanded the protein structure space itself (i.e., number of unique structural folds) since 2007. Discovering new structural folds experimentally by directed evolution and random recombination of secondary-structure blocks is also proved rarely successful. Meanwhile, previous computational efforts for large-scale mapping of protein structure space are limited to simple model proteins and led to an inconclusive answer on the completeness of the existing observed protein structure space. Here, we build novel protein structures by extending naturally occurring circular (single-loop) permutation to multiple loop permutations (MLPs). These structures are clustered by structural similarity measure called TM-score. The computational technique allows us to produce different structural clusters on the same naturally occurring, packed, stable core but with alternatively connected secondary-structure segments. A large-scale MLP of 2936 domains from structural classification of protein domains reproduces those existing structural clusters (63%) mostly as hubs for many nonredundant sequences and illustrates newly discovered novel clusters as islands adopted by a few sequences only. Results further show that there exist a significant number of novel potentially stable clusters for medium-size or large-size single-domain proteins, in particular, > 100 amino acid residues, that are either not yet adopted by nature or adopted only by a few sequences. This study suggests that MLP provides a simple yet highly effective tool for engineering and design of novel protein structures (including naturally knotted proteins). The implication of recovering new-fold targets from critical assessment of structure prediction techniques (CASP) by MLP on template-based structure prediction is also discussed. Our MLP structures are available for download at the publication page of the Web site http://sparks.informatics.iupui.edu.     

Density-dependent effects of prey defenses and predator offenses

Defenses protect prey, while offenses arm predators. Some defenses and offenses are constitutive (e.g. tortoise shells), while others are phenotypically plastic and not always expressed (e.g. neckteeth in water fleas). All of them are costly and only adaptive at certain prey densities. Here, I analyse such density-dependent effects, applying a functional response model to categorize defenses and offenses and qualitatively predict at which prey densities each category should evolve (if it is constitutive) or be expressed (if it is phenotypically plastic). The categories refer to the step of the predation cycle that a defense or offense affects: (1) search, (2) encounter, (3) detection, (4) attack, or (5) meal. For example, prey warning signals such as red coloration prevent predator attacks and are hence step 4 defenses, while sharp predator eyes enhance detection and are step 3 offenses. My theoretical analyses predict that step 1 defenses, which prevent predators from searching for their next meal (e.g. toxic substances), evolve or are expressed at intermediate prey densities. Other defenses, however, should be most beneficial at low prey densities. Regarding predators, step 1 offenses (e.g. immunity against prey toxins) are predicted to evolve or be expressed at high prey densities, other offenses at intermediate densities. I provide evidence from the literature that supports these predictions.     

Predicting and testing functional responses: An example from a tardigrade–nematode system

Numerous studies have empirically measured consumer functional responses or theoretically developed response models, but whether these models can quantitatively predict observed data has hardly been tested. We perform such a test for the terrestrial predator–prey system Macrobiotus richtersi (Tardigrada)–Acrobeloides nanus (Nematoda). For two different size classes of A. nanus, we report a functional response as measured in the laboratory and quantitatively compare it to predictions of three models with different degrees of complexity: (1) the disc equation which does not include satiation effects; (2) the steady-state satiation (SSS) equation which assumes a constant level of predator satiation; and (3) the satiation model which accounts for prey depletion and increasing predator satiation over the course of the experiments. We parameterized these models with data that were measured independently of the functional response experiments. In both prey-size classes, the predictions of the satiation model matched the observations best, and the match came close to that of logistic regressions fitted to the observations. Thus, the parameterized satiation model seems to include the most important determinants of the functional response in our focal system. For understanding functional responses, we need more studies that compare data to independently derived model predictions.