Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology

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Quercetin-induced yeast apoptosis through mitochondrial dysfunction under the accumulation of magnesium in Candida albicans

Latterly, the upsurge in use of antifungal drugs has brought about the emergence of several drug-resistance strains, making it skeptical to continue relying on current therapeutic regime. In the necessity of resistance-free antifungal agent, flavonoids presented possibilities of replacing existing drugs, displaying antifungal activity against pathogenic fungi. Among them, quercetin, one of the most representative flavonoids, exhibited antifungal activity against Candida albicans. To inspect the further understanding regarding quercetin, the antifungal mode of action of quercetin was investigated. In the initial step, the apoptosis was monitored after quercetin treatment. Moreover, intracellular levels of Mg²⁺ was assessed and was determined that Mg²⁺ increase occurred under the influence of quercetin. In addition, several features of mitochondrial dysfunction were monitored. Mitochondrial dysfunction triggers decrease in mitochondrial redox levels and leads to disruption in mitochondrial antioxidant system. Increased intracellular ROS and decreased intracellular redox levels were also displayed, indicating the occurrence of overall disruption in antioxidant systems. Sequentially, DNA fragmentation was observed and this DNA damage in turn induces apoptosis. In analyses, hexaamminecobalt(III) chloride (Cohex) was applied to inhibit Mg²⁺ transport between cytosol and mitochondria. Cohex attenuated the effects induced by quercetin, which demonstrates that the presence of Mg²⁺ is essential in quercetin-induced apoptosis.     

Antifungal effect of CopA3 monomer peptide via membrane-active mechanism and stability to proteolysis of enantiomeric d-CopA3

In our previous study, coprisin, a 43-mer defensin-like peptide, was derived from the dung beetle, Copris tripartitus, and a 9-mer CopA3 (monomer), truncated coprisin analog peptide, was designed. However, the antifungal effects of CopA3 are not known yet. In this study, the antifungal activity and mechanism of CopA3 were investigated and to develop a more effective antimicrobial peptide under physiological conditions, the enantiomeric d-CopA3 was designed. l- and d-CopA3 had a similar antifungal activity without chiral selectivity, and their activity was more potent than that of melittin used as a positive control. Furthermore, l- and d-CopA3 did not even show any hemolysis against human erythrocytes. Membrane studies using propidium iodide and bis-(1,3-dibutylbarbituric acid) trimethine oxonol [DiBAC₄(3)], suggested that the antifungal effect of l- and d-CopA3 was due to the membrane-active mechanism, by contrast with coprisin possessing apoptotic mechanism without membrane permeabilization. Finally, the proteolytic resistance and antifungal activity of l- and d-CopA3 against trypsin was analyzed by HPLC and colony count assay. The results showed that only d-CopA3 maintained a potent antifungal activity despite the proteolytic condition. Therefore, this study suggests that d-CopA3 has potential as a novel antimicrobial agent.     

Bridging the gap: How the National Core Arts Standards forge the divide between the arts and assessment-based learning

ABSTRACT

This article is a review and thematic analysis of the 2014 National Core Arts Standards (NCAS). Historically, there exists a gap between the arts and assessment-based educational practices. Thematic analysis of the NCAS reveals a policy striving to bridge the gap between the way arts educators envision arts in schools, and the current reality of assessment-based schooling in the United States. This policy could become the foundation for the recognition of the arts as academically rigorous subject matter, capable of existing and thriving in an assessment-oriented world; it remains to be seen as to how and if arts educators will use and adapt NCAS. Is the NCAS merely a symbolic policy or does it have the support behind it to be a material policy that truly creates change in the educational system?     

Quality Control and Assurance: crucial for the sustainability of the applied phycology industry

The chemical and nutritional properties of microalgae are well known, which has led to an ever expanding industry for foods and dietary supplements both in terms of quantity and products. Little has been done to regulate or control quality and assurance in the applied phycology industry and it is known that it varies considerably. Nutritional aspects of produced biomass and consumption as dietary supplements have become issues of concern, especially since the industry is lucrative and fast growing. Various claims are made regarding dietary and food supplements that include health, nutrition, structure and functioning, many often unsubstantiated. Although quality is a subjective term many organisations are involved in testing, controlling and determining criteria. Today quality is more than just standards where it is an "integrated quality management approach" involving amongst others "hazard analyses and critical control points" (HACCP) practices. Microalgae are not recognised as a food or food supplement and they are also not categorised under herbals or botanicals, but as "other supplements". Produced microalgal biomass is subject to contamination from the entire range of contaminants and pathogens. Contamination of products by algal toxins in mixed culture populations also occurs. The industry has largely regulated itself, but there is considerable scope for improvement. There is a need for support and dissemination of information in the industry.     

A rubber transfer gasket to improve the throughput of liquid–liquid extraction in 96-well plates: Application to vitamin D testing

Background

The unmitigated rise in demand for the assessment of vitamin D status has taxed the ability of clinical mass spectrometry laboratories to preserve turn-around times. We aimed to improve the throughput of liquid–liquid extraction of plasma/serum for the assay of 25-hydroxy vitamin D.

Methods

We designed and fabricated a flexible rubber gasket that seals two 96-well plates together to quantitatively transfer the contents of one plate to another. Using the transfer gasket and a dry-ice acetone bath to freeze the aqueous infranatant, we developed a novel liquid–liquid extraction workflow in a 96-well plate format. We applied the technology to the mass spectrometric quantification of 25-hydroxy vitamin D.

Results

Cross-contamination between wells was ≤0.13%. The interassay imprecision over 132 days of clinical implementation was less than 10%. The method compared favorably to a standard liquid–liquid extraction in glass tubes (Deming slope = 1.018, S_x|y = 0.022). The accuracy of the assay was 102–105% as assessed with the recently released control materials from NIST.

Conclusions

The development of a plate-sealing gasket permits the liquid–liquid extraction of clinical specimens in a moderate-throughput workflow and the reliable assay of vitamin D status. In the future, the gasket may also prove useful in other sample preparation techniques for HPLC or mass spectrometry.     

Ecological indicators of nutrient enrichment, freshwater wetlands, Midwestern United States (U.S.)

Vegetation and soil indicators of nutrient condition were evaluated in 30 wetlands, 10 each in 3 Nutrient Ecoregions (NE) (VI-Corn Belt and Northern Great Plains, VII-Mostly Glaciated Dairy Region, IX-Temperate Forested Plains and Hills) of the Midwestern United States (U.S.) to identify robust indicators for assessment of wetland nutrient enrichment and eutrophication. Nutrient condition was characterized by surface water inorganic N (NH₄-N, NO₃-N) and P (PO₄-P) concentrations measured seasonally for 1 year, plant available and total soil N and P, and aboveground biomass, leaf N and P and species composition of emergent vegetation measured at the end of the growing season. Aboveground biomass, nutrient uptake and species composition were positively related to surface water NH₄-N (N) but not to PO₄-P or NO₃-N. Aboveground biomass and biomass of aggressive species, Typha spp. plus Phalaris arundinacea, increased asymptotically with surface water N whereas leaf P, senesced leaf N and senesced leaf P increased linearly with N. And, species richness declined with surface water N. Soil total P was positively related to surface water PO₄-P but it was the only soil indicator related to wetland nutrient condition. Individual regressions for each NE generally were superior to a single regression for all NEs. In NE VI (Corn Belt), few indicators were related to surface water N because of the high degree of anthropogenic disturbance (85% of the landscape is cleared) as compared to NEs VII and IX (24–53% cleared). Of the indicators evaluated, stem height (r² = 0.42 for all NEs, r² = 0.56 for NE VII + IX) and percent biomass of aggressive species, Typha spp. plus Phalaris, (r² = 0.46 for all NEs, r² = 0.54 for NE VII + IX), were the best predictors of wetland nutrient enrichment. Vegetation-based indicators are a promising tool for assessment of wetland nutrient condition but they may not be effective in NEs where landscape disturbance is intense and widespread.     

The Science of Solubility: Using Reverse Engineering to Brew a Perfect Cup of Coffee

The Next Generation Science Standards call for the integration of science and engineering. Often, the introduction of engineering activities occurs after instruction in the science content. That is, engineering is used as a way for students to elaborate on science ideas that have already been explored. However, using only this sequence of instruction communicates a limited view of the relationship between science and engineering. In this article, we focus on the process of reverse engineering, and we provide a model 5E lesson in which we flip the typical science-to-engineering sequence and, instead, use principles of engineering design as a springboard from which to develop scientific concepts. Specifically, students use principles of engineering to deconstruct already engineered devices (i.e., different types of coffeemakers) in an effort to propose scientific explanations (i.e., factors affecting solubility) for the design features. These proposed explanations are then tested by isolating individual variables (e.g., solute size, temperature of solution) and testing the results. Students are provided whole coffee beans, grinders, water of different temperatures, timers, and apparatus for brewing samples of coffee and then test the effects of changing the variables by tasting, observing, or quantifying results of the individual samples.     

Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005)

The spring workshop of the HUPO-PSI convened in Siena to further progress the data standards which are already making an impact on data exchange and deposition in the field of proteomics. Separate work groups pushed forward existing XML standards for the exchange of Molecular Interaction data (PSI-MI, MIF) and Mass Spectrometry data (PSI-MS, mzData) whilst significant progress was made on PSI-MS' mzIdent, which will allow the capture of data from analytical tools such as peak list search engines. A new focus for PSI (GPS, gel electrophoresis) was explored; as was the need for a common representation of protein modifications by all workers in the field of proteomics and beyond. All these efforts are contextualised by the work of the General Proteomics Standards workgroup; which in addition to the MIAPE reporting guidelines, is continually evolving an object model (PSI-OM) from which will be derived the general standard XML format for exchanging data between researchers, and for submission to repositories or journals.     

关于植物DNA条形码研究技术规范

DNA条形码是利用标准的基因片段对物种进行快速鉴定的技术,已经成功用于生物物种分类和鉴定、生态学调查和生物多样性评估等研究领域。尽管生命条形码数据（BOLD）系统提供了主要针对动物类群DNA条形码研究的技术规范,但由于植物本身的生物学特性与所使用的条形码不同,因此已有技术规范并不完全适用于植物DNA条形码的研究。本文根据植物DNA条形码研究的特点与我国的实际情况,编写了植物DNA条形码研究技术标准和规范指南,具体包括十个方面的内容,即植物DNA条形码研究的样品采集策略;植物标本和野外数据的采集规范;植物标本图像信息的采集规范;植物DNA材料的采集规范;植物DNA材料的干燥与保存规范;植物总DNA的质量标准及保存规范;植物标准DNA条形码的选择与通用引物;DNA条形码的扩增与测序;DNA条形码数据的命名、编辑和提交规范;以及DNA条形码数据分析。我们期望通过这些标准规范的实施和在实践中的不断修订和完善,能为我国学者开展植物DNA条形码和iFlora研究提供参考和借鉴。
关键词：植物DNA条形码;技术规范;物种鉴定;标准;新一代植物志