ILLUMINA Golden Gate DNA甲基化芯片的KL-FCM聚类分析

DNA甲基化作为一种重要的表观遗传修饰,其甲基化水平被发现与疾病的发生发展密切相关,对其进行聚类分析有希望发现新的疾病亚型并建立有效的疾病预测预后方法。传统的聚类分析方法之一模糊C-均值（FCM：Fuzzy C-means）适用于特征空间呈球形或椭球形分布的场景,缺乏普适性。而Illumina Golden Gate平台通过计算基因的各甲基化位点的甲基化百分比描述其甲基化程度,其值位于（0,1）之间,服从混合贝塔分布,不能直接采用FCM进行聚类分析。鉴于此,本文提出基于KL特征测度的KL-FCM聚类算法,采用各样本间的K-L距离作为样本划分时的度量准则。最后,本文基于KL-FCM算法实现IRIS测试数据集和基因的DNA甲基化水平数据的聚类分析。实验结果表明该方法可以以更低的计算负荷获得优于k-均值（k-means）和传统FCM的分类效果。     

Golden Rice--five years on the road--five years to go?

Provitamin A accumulates in the grain of Golden Rice as a result of genetic transformation. In developing countries, where vitamin A deficiency prevails, grain from Golden Rice is expected to provide this important micronutrient sustainably through agriculture. Since its original production, the prototype Golden Rice has undergone intense research to increase the provitamin A content, to establish the scientific basis for its carotenoid complement, and to better comply with regulatory requirements. Today, the current focus is on how to get Golden Rice effectively into the hands of farmers, which is a novel avenue for public sector research, carried out with the aid of international research consortia. Additional new research is underway to further increase the nutritional value of Golden Rice.     

Adventitious shoot regeneration from ovaries of Hosta ‘Golden Scepter’

Summary The objective of this study was to evaluate the ability ofHosta Golden Scepter (GS) ovary explants to generate adventitious shootsin vitro. Ovaries were transversely cut into halves and transferred to petri dishes containingHosta initiation medium supplemented with naphthaleneacetic acid (NAA) at 2.5 μM and N⁶-benzyladenine (BA) at 10 μM. GS produced adventitious shoots from the ovary base via organogenesis. The number of adventitious shoots regenerated from callus increased linearly with repeated subculturing on Murashige and Skoog (MS) medium supplemented with 2.5 μM NAA and 10 μM BA. The number of multiple shoots developing from callus (15.8), shoot tip (8.4), leaf (6.7), and root (4.3) occurred on MS medium supplemented with 2.5 μM NAA and 20–30 μM BA. There were significant differences in the number of shoots regenerated from shoot tips and callus on MS medium with 50 and 100 mgmyo-inositol per l. Similarly, there were significant differences in the number of axillary shoots and adventitious shoots produced with 20 g/l sucrose treatment.     

葡萄Golden2-like转录因子家族的鉴定及其表达分析

本研究对葡萄（Vitis vinifera L.）的Golden2-like （GLK）转录因子家族进行了全基因组鉴定和表达模式分析,并利用品种‘玫瑰香’（V.vinifera cv.Muscat Hamburg）进一步验证其在低温胁迫下的响应。结果显示,葡萄Golden2-like家族共46个成员,分为5个亚族,同一亚族的保守结构域相似。46个VvGLK分别定位于细胞核、叶绿体、细胞质和过氧化物酶体中,其启动子区域含多种逆境应答顺式作用元件。基因芯片分析结果表明,22个Golden2-like基因在果实发育过程中变化显著。同时,有15、15和9个基因分别响应盐、干旱和低温胁迫。qRT-PCR分析发现26个基因参与低温应答。VvGLK41在所有胁迫处理中均下调表达。     

Marker-assisted characterization of durum wheat Langdon–Golden Ball disomic substitution lines

The durum wheat cultivar ‘Golden Ball’ (GB) is a source of resistance to wheat sawfly due to its superior solid stem. In the late 1980s, Dr. Leonard Joppa developed a complete set of 14 ‘Langdon’ (LDN)–GB disomic substitution (DS) lines by using GB as the chromosome donor and LDN as the recipient. However, these substitution lines have not been previously characterized and reported in the literature. The objectives of this study were to confirm the authenticity of the substituted chromosomes and to analyze the genetic background of the 14 LDN–GB DS lines with the aid of molecular markers, and to further use the substitution lines for chromosomal localization of DNA markers and genes conferring the superior stem solidness in GB. Results from simple sequence repeat marker analysis validated the authenticity of the substituted chromosomes in 14 LDN–GB DS lines. Genome-wide scans using the target region amplification polymorphism (TRAP) marker system produced a total of 359 polymorphic fragments that were used to compare the genetic background of substitution lines with that of LDN. Among the polymorphic TRAP markers, 134 (37.3%) and 185 (51.5%) were present in LDN and GB, respectively, with only 10 (2.8%) derived from Chinese Spring. Therefore, marker analysis demonstrated that each LDN–GB DS line had a pair of chromosomes from GB with a genetic background similar to that of LDN. Of the TRAP markers generated in this study, 200 were successfully assigned to specific chromosomes based on their presence or absence in the corresponding LDN–GB DS lines. Also, evaluation of stem solidness in the substitution lines verified the presence of a major gene for stem solidness in chromosome 3B. Results from this research provides useful information for the utilization of GB and LDN–GB DS lines for genetic and genomic studies in tetraploid wheat and for the improvement of stem solidness in both durum and bread wheat.     

基于Golden Gate技术的齐整小核菌转录单元高效组装系统

【目的】为齐整小核菌代谢工程研究建立高效的转录单元组装系统。【方法】通过应用Golden Gate技术,以mobius assembly为基础,分别设计并构建DNA元件标准化接口改造、单转录单元组装、应用质粒(多转录单元)组装等功能的载体,从而形成一套完整的多转录单元组装系统。【结果】构建了2个用于DNA元件标准化接口改造的Level 0载体,4个用于单转录单元组装的Level 1载体,4个用于应用质粒组装的Level 2载体和13个应用质粒组装的辅助质粒。然后应用此系统为齐整小核菌组装了若干经过标准化接口改造的DNA元件质粒、单转录单元质粒和硬葡聚糖相关基因的功能分析质粒。所构建的最终应用质粒可以同时适用于齐整小核菌的根癌农杆菌介导转化法、电穿孔转化法和原生质体转化法。【结论】此质粒系统具有强大的DNA设计、组装和容纳能力,为未来齐整小核菌代谢工程和功能基因组学研究提供了高效的质粒构建技术平台。     

Golden GATEway Cloning – A Combinatorial Approach to Generate Fusion and Recombination Constructs

The design and generation of DNA constructs is among the necessary but generally tedious tasks for molecular biologists and, typically, the cloning strategy is restricted by available restriction sites. However, increasingly sophisticated experiments require increasingly complex DNA constructs, with an intricacy that exceeds what is achievable using standard cloning procedures. Many transgenes such as inducible gene cassettes or recombination elements consist of multiple components that often require precise in-frame fusions. Here, we present an efficient protocol that facilitates the generation of these complex constructs. The golden GATEway cloning approach presented here combines two established cloning methods, namely golden Gate cloning and Multisite Gateway^TM cloning. This allows efficient and seamless assembly as well as reuse of predefined DNA elements. The golden Gate cloning procedure follows clear and simple design rules and allows the assembly of multiple fragments with different sizes into one open reading frame. The final product can be directly integrated into the widely used Multisite Gateway^TM cloning system, granting more flexibility when using a transgene in the context of multiple species. This adaptable and streamlined cloning procedure overcomes restrictions of “classical construct generation” and allows focusing on construct design.     

Cost-Effectiveness of “Golden Mustard” for Treating Vitamin A Deficiency in India

Background

Vitamin A deficiency (VAD) is an important nutritional problem in India, resulting in an increased risk of severe morbidity and mortality. Periodic, high-dose vitamin A supplementation is the WHO-recommended method to prevent VAD, since a single dose can compensate for reduced dietary intake or increased need over a period of several months. However, in India only 34 percent of targeted children currently receive the two doses per year, and new strategies are urgently needed.

Methodology

Recent advancements in biotechnology permit alternative strategies for increasing the vitamin A content of common foods. Mustard (Brassica juncea), which is consumed widely in the form of oil by VAD populations, can be genetically modified to express high levels of beta-carotene, a precursor to vitamin A. Using estimates for consumption, we compare predicted costs and benefits of genetically modified (GM) fortification of mustard seed with high-dose vitamin A supplementation and industrial fortification of mustard oil during processing to alleviate VAD by calculating the avertable health burden in terms of disability-adjusted life years (DALY).

Principal Findings

We found that all three interventions potentially avert significant numbers of DALYs and deaths. Expanding vitamin A supplementation to all areas was the least costly intervention, at $23–$50 per DALY averted and $1,000–$6,100 per death averted, though cost-effectiveness varied with prevailing health subcenter coverage. GM fortification could avert 5 million–6 million more DALYs and 8,000–46,000 more deaths, mainly because it would benefit the entire population and not just children. However, the costs associated with GM fortification were nearly five times those of supplementation. Industrial fortification was dominated by both GM fortification and supplementation. The cost-effectiveness ratio of each intervention decreased with the prevalence of VAD and was sensitive to the efficacy rate of averted mortality.

Conclusions

Although supplementation is the least costly intervention, our findings also indicate that GM fortification could reduce the VAD disease burden to a substantially greater degree because of its wider reach. Given the difficulties in expanding supplementation to areas without health subcenters, GM fortification of mustard seed is an attractive alternative, and further exploration of this technology is warranted.     

Ethylene action blockade and cold storage affect ripening of ‘Golden’ papaya fruit

The purpose of this work was to evaluate the effects of ethylene action blockade and cold storage on the ripening of ‘Golden’ papaya fruit. Papayas harvested at maturity stage 1 (up to 15% yellow skin) were evaluated. Half of the fruits, whether treated or not treated with 100 nL L⁻¹ of 1-methylcyclopropene (1-MCP), were stored at 23°C, while the other half were stored at 11°C for 20 days prior to being stored at 23°C. Non-refrigerated fruits receiving 1-MCP application presented a reduction in respiratory activity, ethylene production, skin color development and pectinmethylesterase activity. Even with a gradual increase in ethylene production at 23°C, fruits treated with 1-MCP maintained a high firmness, but presented a loss of green skin color. Cold storage caused a decrease in ethylene production when fruits were transferred to 23°C. The results suggest that pulp softening is more dependent on ethylene than skin color development, and that some processes responsible for loss of firmness do not depend on ethylene.     

Effect of potassium humate on apple cv. ‘Golden Delicious’ cultured in vitro

The effects of humic substances on in vitro culture of Golden Delicious apple are reported. Potassium humate (KH) when used in proliferation showed a negative interaction with BA while it enhanced rooting when IBA was not present in the culture medium. In the presence of IBA, KH increased root number and reduced root growth. The highest concentration tested, 500 mg l^-1, caused a drastic reduction in root system development. 50 mg l^-1 KH hastened rooting and plants grew more rapidly when transferred to soil.     

Stage-specific protein regulation during somatic embryo development of Carica papaya L. ‘Golden’

Somatic embryogenesis is an important biotechnological technique for large-scale propagation of elite genotypes. Identifying stage-specific compounds associated with somatic embryo development can help elucidate the ontogenesis of Carica papaya L. somatic embryos and improve tissue culture protocols. To identify the stage-specific proteins that are present during the differentiation of C. papaya somatic embryos, proteomic analyses of embryos at the globular, heart, torpedo and cotyledonary developmental stages were performed. Mass spectrometry data have been deposited in the ProteomeXchange with the dataset identifier PXD021107. Comparative proteomic analyses revealed a total of 801 proteins, with 392 classified as differentially accumulated proteins in at least one of the developmental stages. The globular-staged presented a higher number of unique proteins (16), and 7 were isoforms of 60S ribosomal proteins, suggesting high translational activity at the beginning of somatic embryogenesis. Proteins related to mitochondrial metabolism accumulated to a high degree at the early developmental stages and then decreased with increasing development, and they contributed to cell homeostasis in early somatic embryos. A progressive increase in the accumulation of vicilin, late embryogenesis abundant proteins and chloroplastic proteins that lead to somatic embryo maturation was also observed. The differential accumulation of acetylornithine deacetylase and S-adenosylmethionine synthase 2 proteins was correlated with increases in putrescine and spermidine contents, which suggests that both polyamines should be tested to determine whether they increase the conversion rates of globular- to cotyledonary-staged somatic embryos. Taken together, the results showed that somatic embryo development in C. papaya is regulated by the differential accumulation of proteins, with ribosomal and mitochondrial proteins more abundant during the early somatic embryo stages and seed maturation proteins more abundant during the late stages.     

Methyl jasmonate vapor promotes β-carotene synthesis and chlorophyll degradation in Golden Delicious apple peel

Methyl jasmonate (JAMe) vapors (8 ppm) for 4 h at 25°C dramatically increased Golden Delicious apple peel -carotene synthesis by nearly threefold to 35 ng/mm², while control fruits remained nearly constant at 11 ng/mm² during the 10 day measurement period. Chlorophyll a and to a lesser extent chlorophyll b and lutein degradation were accelerated by JAMe treatment, but all showed some recovery after 6 days. Peel chlorophyll ab ratio held almost constant at 4.2–4.5 in control fruits during 10 days, while JAMe-treated apple chl ab ratio decreased linearly to 2.9 during 10 days.     

Cosmopolitan theology: Fethullah Gülen and the making of a ‘Golden Generation’

Global conditions, under which an increasing number of Muslims in the world currently live, do not just generate idioms of purity often adduced to global Islam, but also new and diverse forms of sociability and notions of global citizenship. This article addresses, as an example in case, Hizmet, one of the fastest growing contemporary Islamic movements. Hizmet and its founder Fethullah Gülen propagate a global Islamic doctrine with explicitly cosmopolitan underpinnings. However, there seems to be a contradiction between the cosmopolitan inclusiveness and universality of Gülen's global message, and strong internal hierarchical structures and the disciplining modes of teaching and training that are applied by the movement to teach the doctrine. I will argue that there is no contradiction between these two aspects when we focus on the central position of ‘hermeneutics of the self’ and civic responsibility in Gülen's theology.     

Ray Wu’s Golden Rules: How he achieved greatness in work, and in life

Overview When Ray Wu passed away on February 10, 2008, he was 79, working full-time in his lab at Cornell University, and was at or near the top of his long and noteworthy career. He had developed the first method for DNA sequencing and pioneered recombinant DNA technology. He had identified key genes related to stress tolerance in plants and was poised to apply these to boost crop yields of rice and other     

Population Dynamics of the Critically Endangered Golden Lancehead Pitviper,Bothrops insularis: Stability or Decline?

Little is known about vital rates of snakes generally because of the difficulty in collecting data. Here we used a robust design mark-recapture model to estimate survival, behavioral effects on capture probability, temporary emigration, abundance and test the hypothesis of population decline in the golden lancehead pitviper, Bothrops insularis, an endemic and critically endangered species from southeastern Brazil. We collected data at irregular intervals over ten occasions from 2002 to 2010. Survival was slightly higher in the wet season than in the dry season. Temporal emigration was high, indicating the importance of accounting for this parameter both in the sampling design and modeling. No behavioral effects were detected on capture probability. We detected an average annual population decrease ( = 0.93, CI = 0.47–1.38) during the study period, but estimates included high uncertainty, and caution in interpretation is needed. We discuss the potential effects of the illegal removal of individuals and the implications of the vital rates obtained for the future persistence and conservation of this endemic, endangered species.