An Improved and Rapid Protocol for the Isolation of Polysaccharide- and Polyphenol-Free Sugarcane DNA

We have optimized a simple and rapid method for isolating milligram quantities of high quality DNA from polysaccharide- and polyphenolic-rich tissue such as sugarcane, lettuce and strawberry. The protocol utilizes fresh tissue without making use of liquid nitrogen or freeze-drying for initial grinding of the tissue and it significantly minimize the use of lab materials. At least one hundred samples can be processed daily by one person. The isolated DNA is essentially free of polysaccharides, polyphenols, RNA and other major contaminants, as judged by: its clear color, its viscosity, A260/A280 ratio, digestibility with restriction enzymes, and suitability for Restriction Fragment Length Polymorphism (RFLP)- and Polymerase Chain Reaction (PCR)-based techniques.     

An Improved Protocol for Intact Chloroplasts and cpDNA Isolation in Conifers

Background

Performing chloroplast DNA (cpDNA) isolation is considered a major challenge among different plant groups, especially conifers. Isolating chloroplasts in conifers by such conventional methods as sucrose gradient and high salt has not been successful. So far, plastid genome sequencing protocols for conifer species have been based mainly on long-range PCR, which is known to be time-consuming and difficult to implement.

Methodology/Principal Findings

We developed a protocol for cpDNA isolation using three different conifer families: Araucaria angustifolia and Araucaria bidwilli (Araucariaceae), Podocarpus lambertii (Podocarpaceae) and Pinus patula (Pinaceae). The present protocol is based on high salt isolation buffer followed by saline Percoll gradient. Combining these two strategies allowed enhanced chloroplast isolation, along with decreased contamination caused by polysaccharides, polyphenols, proteins, and nuclear DNA in cpDNA. Microscopy images confirmed the presence of intact chloroplasts in high abundance. This method was applied to cpDNA isolation and subsequent sequencing by Illumina MiSeq (2×250 bp), using only 50 ng of cpDNA. Reference-guided chloroplast genome mapping showed that high average coverage was achieved for all evaluated species: 24.63 for A. angustifolia, 135.97 for A. bidwilli, 1196.10 for P. lambertii, and 64.68 for P. patula.

Conclusion

Results show that this improved protocol is suitable for enhanced quality and yield of chloroplasts and cpDNA isolation from conifers, providing a useful tool for studies that require isolated chloroplasts and/or whole cpDNA sequences.     

根尖整体透明技术改良

整体透明观察技术是植物形态发育研究的基础手段之一, 是无需制作切片直接观察植物体内部形态结构的有效方法。该技术采用高折射率介质降低光在样品中的散射, 提高光通量, 增加视野深度, 从而实现组织样品透明观察。然而透明剂能改变透明液的渗透势和pH值, 从而对细胞形态保持产生负面影响。目前, 针对植物叶片和胚珠已建立了相对成熟的整体透明观察体系, 但根尖由于细胞壁较薄, 现有的整体透明方法常导致细胞形态改变, 不确定性增加(如根尖整体形态改变和细胞发生严重的质壁分离)。该研究以拟南芥(Arabidopsis thaliana)幼苗为实验材料, 通过检测根尖形态、细胞质壁分离情况和细胞清晰度, 对常用的透明液组分、pH值和透明时间进行优化, 旨在建立一种适用于根尖等较脆弱组织材料的整体透明方法。     

Improved Protocol for Rapid Identification of Certain Spa Types Using High Resolution Melting Curve Analysis

Methicillin-resistant Staphylococcus aureus is one of the most significant pathogens associated with health care. For efficient surveillance, control and outbreak investigation, S. aureus typing is essential. A high resolution melting curve analysis was developed and evaluated for rapid identification of the most frequent spa types found in an Austrian hospital consortium covering 2,435 beds. Among 557 methicillin-resistant Staphylococcus aureus isolates 38 different spa types were identified by sequence analysis of the hypervariable region X of the protein A gene (spa). Identification of spa types through their characteristic high resolution melting curve profiles was considerably improved by double spiking with genomic DNA from spa type t030 and spa type t003 and allowed unambiguous and fast identification of the ten most frequent spa types t001 (58%), t003 (12%), t190 (9%), t041 (5%), t022 (2%), t032 (2%), t008 (2%), t002 (1%), t5712 (1%) and t2203 (1%), representing 93% of all isolates within this hospital consortium. The performance of the assay was evaluated by testing samples with unknown spa types from the daily routine and by testing three different high resolution melting curve analysis real-time PCR instruments. The ten most frequent spa types were identified from all samples and on all instruments with 100% specificity and 100% sensitivity. Compared to classical spa typing by sequence analysis, this gene scanning assay is faster, cheaper and can be performed in a single closed tube assay format. Therefore it is an optimal screening tool to detect the most frequent endemic spa types and to exclude non-endemic spa types within a hospital.     

An Improved Method for Rapid Intubation of the Trachea in Mice

Despite some anatomical and physiological differences, mouse models continue to be an essential tool for studying human lung disease. Bleomycin toxicity is a commonly used model to study both acute lung injury and fibrosis, and multiple methods have been developed for administering bleomycin (and other toxic agents) into the lungs. However, many of these approaches, such as transtracheal instillation, have inherent drawbacks, including the need for strong anesthetics and survival surgery. This paper reports a quick, reproducible method of intratracheal intubation that involves mild inhaled anesthesia, visualization of the trachea, and the use of a surrogate spirometer to confirm exposure. As a proof of concept, 8-12 week old C57BL/6 mice were administered either 2.0 U/kg of bleomycin or an equivalent volume of PBS, and both damage and fibrotic endpoints were measured post-exposure. This procedure allows researchers to treat a large cohort of mice in a relatively short period with little expense and minimal post-procedure care.     

An Improved Medium for the Rapid Growth of Isolated Potato Buds

As a result of varying several components, a medium has beendeveloped which sustains fast continuous growth of small potatobuds in tissue culture. Growth-rates were increased with highconcentrations of inorganic nutrients. Gibberellic acid and8-hydroxyquinoline were required for the maintenance of thestem organization. In the absence of gibberellic acid the apicalmeristem degenerated to a callus. Without 8-hydroxyquinolinegrowth stopped when the stem was 6–10 mm long. Growthwas faster following addition of indole-3-acetic acid.     

一种有效纯化低拷贝质粒DNA的改良硅藻土法

碱法制备的低拷贝质粒因含有大量杂质而无法获得有效的测序结果。为此,以纯λDNA为样品,对硅藻土纯化DNA的方法进行了优化,表明硅藻土悬液的最佳用量是20μl／μgλDNA,回收率达77．31％。应用此改良硅藻土法纯化一长为14953bp的低拷贝质粒pLZ14,所得质粒纯度达23．87％,比未纯化前提高了11．06倍。经纯化的pLZ14质粒测序信号强、无误认碱基,而未经纯化的质粒测序时信号弱、错误普遍存在。     

An Improved Protocol for Quantification of Freshwater Actinobacteria by Fluorescence In Situ Hybridization

We tested a previously described protocol for fluorescence in situ hybridization of marine bacterioplankton with horseradish peroxidase-labeled rRNA-targeted oligonucleotide probes and catalyzed reporter deposition (CARD-FISH) in plankton samples from different lakes. The fraction of Bacteria detected by CARD-FISH was significantly lower than after FISH with fluorescently monolabeled probes. In particular, the abundances of aquatic Actinobacteria were significantly underestimated. We thus developed a combined fixation and permeabilization protocol for CARD-FISH of freshwater samples. Enzymatic pretreatment of fixed cells was optimized for the controlled digestion of gram-positive cell walls without causing overall cell loss. Incubations with high concentrations of lysozyme (10 mg ml⁻¹) followed by achromopeptidase (60 U ml⁻¹) successfully permeabilized cell walls of Actinobacteria for subsequent CARD-FISH both in enrichment cultures and environmental samples. Between 72 and >99% (mean, 86%) of all Bacteria could be visualized with the improved assay in surface waters of four lakes. For freshwater samples, our method is thus superior to the CARD-FISH protocol for marine Bacteria (mean, 55%) and to FISH with directly fluorochrome labeled probes (mean, 67%). Actinobacterial abundances in the studied systems, as detected by the optimized protocol, ranged from 32 to >55% (mean, 45%). Our findings confirm that members of this lineage are among the numerically most important Bacteria of freshwater picoplankton.     

An Improved Rapid Method for Selecting Monoclonal Antibodies with High Catalytic Activities

Monoclonal antibodies were raised against a -naphthyl phosphonate hapten (1) to elicit antibodies capable of catalyzing the hydrolysis of -naphthyl acetate (3). After cell fusion, potential catalytic antibody-producing hybridomas were selected, by use of a competitive inhibition assay on the basis of the binding activity for a short transition-state analogue (inhibitor 5), followed by use of high-performance liquid chromatography analysis for the hybridoma supernatants to screen the antibodies processing catalytic activities. It was shown that supernatants of 12 wells had high binding activity with inhibitor and of them, 7 had catalytic activities. After cloning by limiting dilution, we got two hybridoma clones producing monoclonal antibodies which catalyzed the hydrolysis of -naphthyl acetate. This combination of competitive inhibition assay with high-performance liquid chromatography analysis represents an improved rapid approach for the screening of potential catalytic antibodies and significantly increases the possibility of obtaining efficient catalytic monoclonal antibodies. Further study of the catalytic antibodies revealed significant rate enhancement (K _cat/K _uncat 10⁶) and specificity.     

An Improved Method for Rapid Fixation and Embedding of Pteridophyte Plant Materials

A rapid method for fixation and embedding of plant materials, especially pterido-phytes, is suggested. Addition of tannic acid following osmication improved the visualization of membranes. Staining en bloc with uranyl acetate between osmication and tannic acid is suggested for tissues infected with fungi and bacteria.     

Homologous-Restraint Polymerase Chain Reaction: An Efficient and Rapid Protocol to Clone Multiple Homologous Genes

In this article, we present a novel protocol, called homologous-restraint polymerase chain reaction (HRPCR), for cloning multiple homologous genes. One of the homologous genes was cloned by consensus-degenerate hybrid oligonucleotide (CODEHOP) polymerase chain reaction (PCR) and sequenced. Primers of HRPCR were designed with 20 to 30 nt inverted to the known gene before the 5' end of the CODEHOP primers. The amplification of the known gene was restricted owing to the loop of the PCR product or the incorrect binding of the primers and the template. As a result, only unknown genes could be cloned. This protocol proved to be simple, rapid, and efficient. We applied this protocol to clone the multiple homologous genes of beta-1,4-N,6-O-diacetylmuramidase from the genomic DNA of Streptomyces griseus.     

An Improved Method for Accurate and Rapid Measurement of Flight Performance in Drosophila

Drosophila has proven to be a useful model system for analysis of behavior, including flight. The initial flight tester involved dropping flies into an oil-coated graduated cylinder; landing height provided a measure of flight performance by assessing how far flies will fall before producing enough thrust to make contact with the wall of the cylinder. Here we describe an updated version of the flight tester with four major improvements. First, we added a "drop tube" to ensure that all flies enter the flight cylinder at a similar velocity between trials, eliminating variability between users. Second, we replaced the oil coating with removable plastic sheets coated in Tangle-Trap, an adhesive designed to capture live insects. Third, we use a longer cylinder to enable more accurate discrimination of flight ability. Fourth we use a digital camera and imaging software to automate the scoring of flight performance. These improvements allow for the rapid, quantitative assessment of flight behavior, useful for large datasets and large-scale genetic screens.     

Trachoma Rapid Assessments in Unity and Northern Bahr-el-Ghazal States,Southern Sudan

Background

Trachoma is thought to be endemic over large parts of Southern Sudan, but empirical evidence is limited. While some areas east of the Nile have been identified as highly endemic, few trachoma surveys have been conducted in the remainder of the country. This study aimed to determine whether trachoma constitutes a problem to public health in Northern Bahr-el-Ghazal and Unity State, both located west of the Nile.

Methods and Principal Findings

Trachoma rapid assessments (TRA) were conducted between July and September 2009. Seven villages in Northern Bahr-el-Ghazal State and 13 villages in Unity State were surveyed; an average of 50 children (age 1–9 years) and 44 women (age 15 years and above) were examined per village. Samples for analysis using the APTIMA Combo-2 nucleic acid amplification test (NAAT) were collected from participants with active trachoma in eight villages in Unity State. In Northern Bahr-el-Ghazal State, only three children with active trachoma (trachomatous inflammation follicular (TF) and/or trachomatous inflammation intense (TI)) and two women with trichiasis (TT) were found, in two of the seven villages surveyed. In Unity State, trachoma was endemic in all thirteen villages surveyed; the proportion of children with active trachoma ranged from 33% to 75% between villages, while TF in children ranged from 16% to 44%. Between 4% to 51% of examined women showed signs of TT. Samples from active trachoma cases tested using the NAAT were positive for Chlamydia trachomatis infection for 46.6% of children and 19.0% of women.

Conclusions

Trachoma presents a major problem to public health Unity State, while the disease is of low priority in Northern-Bahr-el-Ghazal State. Implementation of a population-based prevalence survey is now required in Unity State to generate baseline prevalence data so that trachoma interventions can be initiated and monitored over time.     

Rapid and Efficient Gene Splicing Using Megaprimer-Based Protocol

Megaprimer-based methodology has been widely applied in site-directed mutagenesis, but rarely used in gene splicing. In this article, we describe a modification of the megaprimer PCR method, which can efficiently create and amplify a specific ligated chimeric gene segment in a PCR reaction and under a common PCR program that is widely used by researchers. More importantly, this modified method for splicing two or more gene fragments together revealed the mechanism of the megaprimer PCR method, by elucidating the key factor in the megaprimer-based protocol. In this method, the denatured megaprimer divided into two strands. One strand was used as template DNA to regenerate megaprimer and the other strand was used as an oligonucleotide primer to create a ligated chimeric gene product. In this article, we detail the modified megaprimer protocol for creating and amplifying these chimeric gene products, including a specific protocol for large chimeric gene products. We also provide additional tips to increase specificity and efficiency of the protocols. In conclusion, the improved megaprimer PCR protocol is a simple, broadly applicable protocol for splicing two different gene fragments together without relying on restriction sites. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

一种水稻幼苗单株DNA的快速提取及PAGE银染改良法

目的:为了提高SSR分子标记技术在水稻遗传育种中的研究效率,介绍一种快速的适于SSR-PCR扩增的水稻幼苗单株DNA提取法及PAGE银染法。方法:在常温下加入少量SDS提取液将单株叶片迅速捣碎,再加入300μLSDS提取液,65℃水浴10min后离心,取上清用乙醇沉淀后离心,超净工作台吹干后用100μLTE回溶即可。改进的PAGE银染法只需染色、冲洗、显影等3步,用乙醇和硝酸银作为染色液,去离子水快速冲洗1次后置显影液中即可显影。结果:本法可快速提取DNA,不须液氮研磨、氯仿抽提,提取的DNA经0.8%琼脂糖凝胶电泳检测表明质量较好,且扩增结果稳定可靠,满足了SSR-PCR的需要。改良的银染法与常规银染法的检出结果相同,但快速方便,整个过程只需10min,且背景较浅,灵敏度高。结论:快速提取法及PAGE银染改良法结合SSR分子标记技术,可有效地用于杂种后代的遗传连锁分析和分子标记辅助育种时的单株检测。     

Assessing an Improved Protocol for Plasma microRNA Extraction

The first step in biomarkers discovery is to identify the best protocols for their purification and analysis. This issue is critical when considering peripheral blood samples (plasma and serum) that are clinically interesting but meet several methodological problems, mainly complexity and low biomarker concentration. Analysis of small molecules, such as circulating microRNAs, should overcome these disadvantages. The present study describes an optimal RNA extraction method of microRNAs from human plasma samples. Different reagents and commercially available kits have been analyzed, identifying also the best pre-analytical conditions for plasma isolation. Between all of them, the column-based approaches were shown to be the most effective. In this context, miRNeasy Serum/Plasma Kit (from Qiagen) rendered more concentrated RNA, that was better suited for microarrays studies and did not require extra purification steps for sample concentration and purification than phenol based extraction methods. We also present evidences that the addition of low doses of an RNA carrier before starting the extraction process improves microRNA purification while an already published carrier dose can result in significant bias over microRNA profiles. Quality controls for best protocol selection were developed by spectrophotometry measurement of contaminants and microfluidics electrophoresis (Agilent 2100 Bioanalyzer) for RNA integrity. Selected donor and patient plasma samples and matched biopsies were tested by Affymetrix microarray technology to compare differentially expressed microRNAs. In summary, this study defines an optimized protocol for microRNA purification from human blood samples, increasing the performance of assays and shedding light over the best way to discover and use these biomarkers in clinical practice.     

一种改进的快速PCR定点突变技术

在基因工程与蛋白质工程研究中常常用到基因突变技术制备突变体,用于研究基因调控、蛋白质的结构与功能。本项研究在快速PCR定点突变技术的基础上,改进实验方法,简化实验步骤,以适用蛋白质结构改造研究的需要。建立的突变技术仅需一次PCR反应即可完成基因的定点突变,突变效率为79.6%左右。该法对1～3个连续碱基的突变和对间隔4个甚至多达15个碱基的数个密码子突变效果都很好。     

一种快速提取植物病毒DNA的方法

介绍在PCR检测体系中一种快速提取病毒DNA的方法。利用高盐缓冲液溶液释放病毒DNA,同时利用葡聚糖凝胶微柱纯化提取液,有效消除样品中PCR抑制物质并直接作为PCR反应模板扩增检测病毒。该法无需任何特殊设备,适合对大量植株进行大通量的检测分析。     

An Improved Protocol for Microcallus Production and Whole Plant Regeneration from Recalcitrant Banana Protoplasts (Musa spp.)

One important limitation for routine production of somatic hybrids in banana (Musa spp.) is the difficulty in protoplast regeneration. To facilitate protoplast regeneration in banana, the crucial step of microcallus production was optimised for the following parameters: nurse culture medium, duration of microcalli on nurse culture, differing nurse cells, and filter composition. A comparative study between two nurse cell media, Ma₂ and PCM, significantly affected the number of microcalli produced, which was 90 × 10³ per Petri dish on Ma₂ with 0.5 μM zeatin and 9.0 μM 2,4 D, and 30 × 10³ per Petri dish on PCM. Moreover, continuous production of microcalli was achieved on Ma₂ and the frequency of embryogenic cell aggregates was higher among microcalli on Ma₂-medium. However, no cell division was observed in protoplasts cultured on Ma₂ in which nurse cells were maintained for 2 weeks suggesting a requirement of effective presence of nurse cells for cell division of banana protoplasts. Use of a filter in conjugation with nurse cells resulted in greater than 7-fold increase in the number of microcalli. Flow cytometry analysis of 124 protoplast-derived plants showed the presence of hexaploid plants (mother plant is triploid) at the frequency of 4%. Together, these data are indicative of the complex factors involved in the regulation of plant cell division and growth. Each individual aspect must be optimised for efficient protocol development.