Comparative analysis of microbial DNA extraction protocols for groundwater samples

A comparative analysis of four different DNA extraction protocols was performed to determine the best choice for groundwater microbial diversity studies using temperature gradient gel electrophoresis (TGGE) analysis. The methods used were a chelex-based method, a modified salting out procedure (MSOP), and the commercial kits Epicentre and FastDNA. Both commercial kits exhibited the greatest reproducibility in their methods; however, their band patterns were very different. The protocol that showed the highest diversity was the chelex-based method, and the one that showed the lowest diversity was the FastDNA kit.     

Aqueous biphasic systems composed of ionic liquids and sodium carbonate as enhanced routes for the extraction of tetracycline

Aqueous biphasic systems (ABS) using ionic liquids (ILs) offer an alternative approach for the extraction, recovery, and purification of biomolecules through their partitioning between two aqueous liquid phases. In this work, the ability of a wide range of ILs to form ABS with aqueous solutions of Na₂CO₃ was evaluated. The ABS formed by IL + water + Na₂CO₃ were determined at 25°C, and the respective solubility curves, tie‐lines, and tie‐line lengths are reported. The studied ILs share the common chloride anion, allowing the IL cation core, the cation isomerism, the presence of functionalized groups, and alkyl side chain length effects to be evaluated. An increase in the cation side alkyl chain length leads to a higher ability for liquid–liquid demixing whereas different positional isomers and the presence of an allyl group have no major influence in the phase diagrams behavior. Quaternary phosphonium‐ and ammonium‐based fluids are more able to form an ABS when compared with imidazolium‐, pyridinium‐, pyrrolidinium‐, and piperidium‐based ILs. Moreover, the presence of an aromatic cation core has no major contribution to the formation of ABS when compared to the respective nonaromatic counterparts. Finally, to appraise on the systems applicability in downstream processing, selected systems were used for the partitioning of tetracyclines (neutral and salt forms) — a class of antibiotics produced by bacteria fermentation. Single‐step extraction efficiencies for the IL‐rich phase were always higher than 99% and confirm the great potential of ILs to be applied in the biotechnological field. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:645–654, 2013     

Comparative computational analysis of ADP Glucose Pyrophosphorylase in plants

ADP-glucose pyrophosphorylase (AGPase), a key enzyme involved in higher plant starch biosynthesis, is composed of pairs of large (LS) and small subunits (SS). Ample evidence has shown that the AGPase catalyzes the rate limiting step in starch biosynthesis in higher plants. In this study, we compiled detailed comparative information about ADP glucose pyrophosphorylase in selected plants by analyzing their structural features e.g. amino acid content, physico-chemical properties, secondary structural features and phylogenetic classification. Functional analysis of these proteins includes identification of important 10 to 20 amino acids long motifs arise because specific residues and regions proved to be important for the biological function of a group of proteins, which are conserved in both structure and sequence during evolution. Phylogenetic analysis depicts two main clusters. Cluster I encompasses large subunits (LS) while cluster II contains small subunits (SS).     

A DNA extraction method for RAPD analysis from plants rich in soluble polysaccharides

A simple procedure for the isolation of DNA from mature leaf tissue was developed. This procedure purified DNA using Sephacryl S-1000 column and PEG 8000 precipitation. Polysaccharide-like components were successfully removed from DNA samples from species in which polysaccharides were found to be difficult to remove by phenol/chloroform extraction. The DNA obtained by this method was suitable for PCR, RAPD, enzyme digestion, and Southern-blot analyses.     

Manipulation of thiol contents in plants

As sulfur constitutes one of the macronutrients necessary for the plant life cycle, sulfur uptake and assimilation in higher plants is one of the crucial factors determining plant growth and vigour, crop yield and even resistance to pests and stresses. Inorganic sulfate is mostly taken up as sulfate from the soil through the root system or to a lesser extent as volatile sulfur compounds from the air. In a cascade of enzymatic steps inorganic sulfur is converted to the nutritionally important sulfur-containing amino acids cysteine and methionine (Hell, 1997; Hell and Rennenberg, 1998; Saito, 1999). Sulfate uptake and allocation between plant organs or within the cell is mediated by specific transporters localised in plant membranes. Several functionally different sulfate transporters have to be postulated and have been already cloned from a number of plant species (Clarkson et al., 1993; Hawkesford and Smith, 1997; Takahashi et al., 1997; Yamaguchi, 1997). Following import into the plant and transport to the final site of reduction, the plastid, the chemically relatively inert sulfate molecule is activated through binding to ATP forming adenosine-5'-phosphosulfate (APS). This enzymatic step is controlled through the enzyme ATP-sulfurylase (ATP-S). APS can be further phosphorylated to form 3'-phosphoadenosine-5'-phosphosulfate (PAPS) which serves as sulfate donor for the formation of sulfate esters such as the biosynthesis of sulfolipids (Schmidt and J?ger, 1992). However, most of the APS is reduced to sulfide through the enzymes APS-reductase (APR) and sulfite reductase (SIR). The carbon backbone of cysteine is provided through serine, thus directly coupling photosynthetic processes and nitrogen metabolism to sulfur assimilation. L-serine is activated by serine acetyltransferase (SAT) through the transfer to an acetyl-group from acetyl coenzyme A to form O-acetyl-L-serine (OAS) which is then sulhydrylated using sulfide through the enzyme O-acetyl-L-serine thiol lyase (OAS-TL) forming cysteine. Cysteine is the central precursor of all organic molecules containing reduced sulfur ranging from the amino acid methionine to peptides as glutathione or phytochelatines, proteines, vitamines, cofactors as SAM and hormones. Cysteine and derived metabolites display essential roles within plant metabolism such as protein stabilisation through disulfide bridges, stress tolerance to active oxygen species and metals, cofactors for enzymatic reactions as e.g. SAM as major methylgroup donor and plant development and signalling through the volatile hormone ethylene. Cysteine and other metabolites carrying free sulfhydryl groups are commonly termed thioles (confer Fig. 1). The physiological control of the sulfate reduction pathway in higher plants is still not completely understood in all details. The objective of this paper is to summarise the available data on the molecular analysis and control of cysteine biosynthesis in plants, and to discuss potentials for manipulating the pathway using transgenic approaches.     

Forms of silicon in medicinal plants

The contents of three forms of silicon (organic, soluble mineral, and polymeric) were determined in leaves of 21 medicinal plants. At a total content of silicon 0.74 to 3.59% the organic, soluble mineral, and polymeric forms accounted for 0.51-1.91%, 0.05-0.51%, and 0.1-1.21%, respectively. An analysis of silicon in the condensed polyphenol fraction was performed for the first time revealing the presence of a covalently bound form in the amounts of 0.1 to 0.2% of the total silicon content in the leaves. These results are of interest for food or medical applications of the plants studied.     

植物硅营养的研究进展

阐述了植物吸收硅的机理、硅与其它营养元素的关系及其对非胁迫和胁迫条件下植物生长发育的有益作用 .植物吸收硅的机制目前尚不是很清楚 ,不同植物吸收硅的方式不同 .硅可影响植物中其它营养元素的含量 .在非胁迫条件下 ,硅可促进植物的生长 ;硅也参与了植物抗病、抗虫等生物胁迫 ,以及抗金属毒害、盐害、温度胁迫、干旱、抗倒伏等非生物胁迫的反应 .目前 ,应从多种植物上深入研究硅的吸收方式与机理 ;同时 ,应该改变硅在细胞壁的沉积仅仅起增强组织机械强度作用的观点 ,而应从生理代谢调控的角度进行硅作用机制的研究 ,为生产实践中硅肥的应用奠定理论基础     

Methodology: a modified method for high-quality DNA extraction for molecular analysis in cereal plants

Cereal crops that have rigid non-cellulose components in the cell wall tissues of leaves and high starch and protein content in grains face limitations in DNA extraction. Advanced molecular genetic techniques such as mapping and marker-assisted selection programs require pure and quick DNA extraction. In this study, we developed methods for isolating high-quality genomic DNA from leaves and seeds of major cereal crops with minor modifications. DNA yields ranged from 300 to 1800 ng for 0.01 g seed or leaf tissue.     

Comparative quantification of sphingolipids and analogs in biological samples by high-performance liquid chromatography after chloroform extraction

Sphingosine 1-phosphate (S1P) is an extra- and intracellular messenger that specifically activates five G-protein-coupled cell surface receptors designated S1P_1-5. The S1P₁ receptor is particularly important for the maintenance of immune surveillance by regulating egress of lymphocytes from thymus and secondary lymphoid organs. S1P is generated through phosphorylation of sphingosine which is catalyzed by sphingosine kinase types 1 and 2. The immunosuppressant and sphingosine analog Fingolimod (2-amino-2-(2-[4-octylphenyl]ethyl)-1,3-propanediol, FTY720) can also be phosphorylated and induces lymphopenia by downregulating cell surface expression of the S1P₁ receptor on lymphocytes. To analyze the role of S1P in lymphocyte circulation and distribution we established a high-performance-liquid-chromatography-based method for parallel detection and quantification of Fingolimod, sphingosine, and dihydrosphingosine together with their phosphorylated derivatives Fingolimod-phosphate, S1P, and dihydrosphingosine 1-phosphate. Phosphorylated and nonphosphorylated lipids were efficiently isolated from biological samples such as cells, tissues, serum, plasma, and media by simple chloroform extraction. Fluorescence labeling with 9-fluorenylmethyl chloroformiate ensured high selectivity and enhanced sensitivity for sphingolipid detection. The described method provides an accurate approach to investigate phosphorylation, dephosphorylation, hydrolyzation, and dehydrolyzation of sphingolipids and analogs. In addition it works independently from enzymatic conversions, measuring actual concentrations rather than enzymatic activities.     

不同粪便DNA提取方法比较分析北大核心CSCD

肠道微生物群落结构和多样性与人体疾病密切相关。然而,相关群落结构分析结果可能受到DNA提取质量等实验因素影响。因此,评估不同DNA提取方法对肠道特定种属的提取效果,对于全面、准确获取人体肠道微生物谱,深入探究肠道微生物群落结构具有指导意义。本研究旨在借助实时荧光定量PCR(real-time quantitative polymerase chain reaction,RT qPCR)技术,以DNA提取纯度、浓度,以及对肠道中特定种属微生物基因组DNA的提取丰度为指标,对5种DNA提取方法进行比较分析。结果表明,试剂盒Q的提取效果最佳,特别是对乳杆菌属和双歧杆菌属等革兰氏阳性菌的提取效果较好。N试剂盒的平均DNA提取浓度较Q试剂盒低,但在纯度方面,二者无显著性差异。与其他3种商用试剂盒(M、PSP、TG)相比,N方法对肠道内指定微生物基因组的提取效果仅次于Q试剂盒,位居第二。相比之下,M试剂盒提取所得DNA,质量较高,但浓度偏低,对于肠道内革兰氏阳性菌的提取效果不很理想。TG试剂盒和PSP试剂盒提取所得DNA在浓度、质量以及细菌丰度方面均不及其他验证的试剂盒。综上,Q试剂盒可作为肠道微生态研究相关实验中获取高质量基因组DNA的提取方法。本研究结果为肠道微生态研究相关实验中基因组DNA提取方法的选择提供参考依据。     

Comparative analysis of cation/proton antiporter superfamily in plants

The cation/proton antiporter superfamily is associated with the transport of monovalent cations across membranes. This superfamily was annotated in the Arabidopsis genome and some members were functionally characterized. In the present study, a systematic analysis of the cation/proton antiporter genes in diverse plant species was reported. We identified 240 cation/proton antiporters in alga, moss, and angiosperm. A phylogenetic tree was constructed showing these 240 members are separated into three families, i.e., Na⁺/H⁺ exchangers, K⁺ efflux antiporters, and cation/H⁺ exchangers. Our analysis revealed that tandem and/or segmental duplications contribute to the expansion of cation/H⁺ exchangers in the examined angiosperm species. Sliding window analysis of the nonsynonymous/synonymous substitution ratios showed some differences in the evolutionary fate of cation/proton antiporter paralogs. Furthermore, we identified over-represented motifs among these 240 proteins and found most motifs are family specific, demonstrating diverse evolution of the cation/proton antiporters among three families. In addition, we investigated the co-expressed genes of the cation/proton antiporters in Arabidopsis thaliana. The results showed some biological processes are enriched in the co-expressed genes, suggesting the cation/proton antiporters may be involved in these biological processes. Taken together, this study furthers our knowledge on cation/proton antiporters in plants.     

Power analysis for real-time PCR quantification of genes in activated sludge and analysis of the variability introduced by DNA extraction

The aims of this study were to determine the power of discrimination of the real-time PCR assay for monitoring fluctuations in microbial populations within activated sludge and to identify sample processing points where methodological changes are needed to minimize the variability in target quantification. DNA was extracted using a commercially available kit from mixed liquor samples taken from the aeration tank of four bench-scale activated-sludge reactors operating at 2-, 5-, 10-, and 20-day solid retention times, with mixed-liquor volatile suspended solid (MLVSS) values ranging from 260 to 2,610 mg/liter. Real-time PCR assays for bacterial and Nitrospira 16S rRNA genes were chosen because they represent, respectively, a highly abundant and a less-abundant bacterial target subject to clustering within the activated sludge matrix. The mean coefficient of variation in DNA yields (measured as microgram of DNA per milligram of MLVSS) in triplicate extractions of 12 different samples was 12.2%. Based on power analyses, the variability associated with DNA extraction had a small impact on the overall variability of the real-time PCR assay. Instead, a larger variability was associated with the PCR assay. The less-abundant target (Nitrospira 16S rRNA gene) had more variability than the highly abundant target (bacterial 16S rRNA gene), and samples from the lower-biomass reactors had more variability than samples from the higher-biomass reactors. Power analysis of real-time PCR assays indicated that three to five samples were necessary to detect a twofold increase in bacterial 16S rRNA genes, whereas three to five samples were required to detect a fivefold increase in Nitrospira 16S rRNA genes.     

Simultaneous quantification of jasmonic acid and salicylic acid in plants by vapor-phase extraction and gas chromatography-chemical ionization-mass spectrometry

Jasmonic acid and salicylic acid represent important signaling compounds in plant defensive responses against other organisms. Here, we present a new method for the easy, sensitive, and reproducible quantification of both compounds by vapor-phase extraction and gas chromatography-positive ion chemical ionization-mass spectrometry. The method is based on a one-step extraction, phase partitioning, methylation with HCl/methanol, and collection of methylated and, thus, volatilized compounds on Super Q filters, thereby omitting further purification steps. Eluted samples are analyzed and quantified by GC/MS with chemical ionization. Standard curves were linear over a range of 5-1000 ng for jasmonic acid and salicylic acid. The correlation coefficients were greater than 0.999 and the recovery rates estimated between 70 and 90% for salicylic acid and 90 and 100% for jasmonic acid. The limit of detection was about 500 fg by using single ion detection mode. Both, cis- and trans-isomers for jasmonic acid can be detected. A comparison with established methods indicates the new method to be highly efficient, allowing reliable quantification of both compounds from small amounts of plant material (5-400mg fresh weight).     

Emerging technologies for non-invasive quantification of physiological oxygen transport in plants

Oxygen plays a critical role in plant metabolism, stress response/signaling, and adaptation to environmental changes (Lambers and Colmer, Plant Soil 274:7–15, 2005; Pitzschke et al., Antioxid Redox Signal 8:1757–1764, 2006; Van Breusegem et al., Plant Sci 161:405–414, 2001). Reactive oxygen species (ROS), by-products of various metabolic pathways in which oxygen is a key molecule, are produced during adaptation responses to environmental stress. While much is known about plant adaptation to stress (e.g., detoxifying enzymes, antioxidant production), the link between ROS metabolism, O₂ transport, and stress response mechanisms is unknown. Thus, non-invasive technologies for measuring O₂ are critical for understanding the link between physiological O₂ transport and ROS signaling. New non-invasive technologies allow real-time measurement of O₂ at the single cell and even organelle levels. This review briefly summarizes currently available (i.e., mainstream) technologies for measuring O₂ and then introduces emerging technologies for measuring O₂. Advanced techniques that provide the ability to non-invasively (i.e., non-destructively) measure O₂ are highlighted. In the near future, these non-invasive sensors will facilitate novel experimentation that will allow plant physiologists to ask new hypothesis-driven research questions aimed at improving our understanding of physiological O₂ transport.     

Quantification of cyanamide contents in herbaceous plants

Cyanamide (NH2CN) is found in nature, although it has long been recognized as an industrial product. Distribution of cyanamide in the plant kingdom was investigated using a direct quantitative determination method to detect and measure cyanamide by stable isotope dilution gas chromatography-mass spectrometry (the SID-GC-MS method). The SID-GC-MS method proved to be a robust way to quantify cyanamide contents in the extracts of 101 species of herbaceous plants. The average recovery of cyanamide from all plants tested was 55.6+/-20.3%. Vicia villosa and V. cracca contained cyanamide at 369-498 microg/gFW and 3,460-3,579 microg/gFW respectively, while the other 99 species contained no detectable cyanamide (<1 microg/gFW). This result suggests that distribution of cyanamide in the plant kingdom is limited and uneven.     

白木香不同抗黄野螟植株代谢物质对比分析

白木香Aquilaria sinensis Lour.为国家濒危保护植物,在其受创伤后产生的沉香是一种珍贵药材和香料,而黄野螟Heortia vitessoides Moore虫害的频繁发生严重影响了沉香产业的发展。为了探究白木香对黄野螟的抗虫生理机制,本研究利用指标含量测定、GC-MS分析及非靶向性代谢组学分析等方法,对6种不同抗虫性植株叶片的理化性质、挥发性物质及差异代谢产物进行对比分析。结果表明,抗虫植株（A01）的单宁酸含量（0.39 mg/g）、类黄酮含量（1.48 mg/g）最高,而可溶性蛋白含量（4.5 mg/g）和可溶性糖含量（6.7 mg/g）最低。白木香感虫植株（S）诱虫成分含量显著高于其它5个植株,而驱虫成分含量显著低于其它5个植株。白木香抗虫植株叶片中的营养物质和挥发性成分与普通感虫植株具有明显差异,抗虫植株叶片中的营养物质和诱虫活性挥发性成分偏低而驱虫活性挥发性成分普遍偏高。抗虫植株与普通感虫植株的差异代谢产物主要集中在黄酮与黄酮醇生物合成、苯丙氨酸生物合成、苯丙氨酸代谢、酪氨酸代谢和异喹啉生物碱生物合成通路。本研究可为确定白木香的抗虫机制及今后发掘新型无公害的黄野螟防控方法提供理论指导。     

Phytotoxic analysis of coastal medicinal plants and quantification of phenolic compounds using HPLC

Abstract

Medicinal plants are rich sources of bioactive phytochemicals. Production of such chemicals usually increased under unfavorable conditions. This study investigated the phytotoxic potential of 105 medicinal plants distributed in arid/semiarid areas along Arabian Sea coast of Pakistan. Total polyphenols, flavonoids, tannins and composition of individual phenolic compounds were also determined in species which showed high phytotoxic potential. Sandwich method was used to determine the phytotoxicity of medicinal plants on the growth of lettuce seedlings. Radicle growth was inhibited more than the hypocotyl growth. In general, halophytes showed higher phytotoxic potential than non-halophytes. Capparis cartilaginea, Indigofera hochstetteri, Parkinsonia aculeata and Prosopis glandulosa showed highest degree of inhibition. Higher amount of total phenols (16.35–25.33?mg GAE g^?1), flavonoids (3.32-6.41?mg QE g^?1) and tannins (1.54–2.54?mg TAE g^?1) were found in these species. Pyrocatechol, quercetin, gallic, hydroxybenzoic and ferulic acids were detected as major phytotoxins, of which, gallic acid, pyrocatechol and quercetin were most abundant. These phytochemicals could be used for the production of natural, safe, healthy and eco-friendly agro-chemicals. Furthermore, these plants can be grown without encroaching agricultural lands, and can convert vast areas of arid/saline lands into economically viable resources, which also helps to halt climate change and desertification.     

Comparative analysis of sequences preceding protein-coding mitochondrial genes in flowering plants

We examined the nucleotide sequences preceding 23 mitochondrial protein-coding genes held in common by maize, rice, wheat, sugar beet, tobacco, Arabidopsis, and Brassica to look for features related to translation initiation and to assess the degree of conservation in mitochondrial mRNA leaders among these plants. We observed broad variation in sequence similarity as illustrated by dot plot analysis, ranging from a level rivaling that of coding sequences to complete absence of homology due to lineage-specific DNA rearrangements. Genes encoding ATP synthase subunits predominated in the latter category, whereas ones encoding cytochrome c biogenesis proteins and NADH dehydrogenase subunits were primarily of the highly conserved type. Within the region immediately preceding initiation codons, in most cases we did not observe motifs consistent with a bacterial-type Shine-Dalgarno interaction to assist in ribosome binding, nor was any other consensus sequence evident. In fact, indels in the form of tandem repeats were seen among homologues from different plants. We did, however, observe a bias for high adenosine and low cytosine in the proximal approximately 30 nt compared with further upstream. Duplicates of some sequences in our data set were found to be associated with more than one gene within a genome. Indeed, 3 such families of upstream cassettes were identified, and they exhibit a lineage-specific distribution among plants. Moreover, the presence of related sequences at genomic sites distant from known genes raises the possibility of future recruitment as regulatory elements. Our observations point to a dynamic nature in the makeup of the 5' leaders of plant mitochondrial mRNAs and an apparent plasticity in translational control elements.