An efficient method for extraction of RNA from rice leaves at different ages using benzyl chloride.

With a conventional method of RNA extraction using an acid guanidinium thiocyanate-water-saturated phenol-chloroform mixture, extraction efficiency of extractable RNA to total RNA (extractable RNA+ residual RNA) in rice leaves at various ages was 54-69%. With a new method, an improvement of the above, using benzyl chloride instead of water-saturated phenol together with further maceration with a small amount of quartz sand, the efficiency was increased to 81-95%. When RNA fractions obtained with the improved method were subjected to agarose gel electrophoresis, intact bands of 25 S and 17 S rRNAs were detected. With a DNA probe for rice rbcS, only a single band was observed on the blotted membrane. These results indicate that the improved extraction method of RNA with benzyl chloride is useful for quantitative and qualitative analysis of RNA in plant tissues such as stiff leaves of rice.     

Multiplex RT-PCR with broad-range primers and an exogenous internal amplification control for the detection of honeybee viruses in bumblebees

Bumblebees are commercially reared and transported worldwide mainly for pollination of greenhouse tomatoes. Three honeybee viruses have been reported in bumblebees: Acute bee paralysis virus, Kashmir bee virus and Deformed wing virus. We developed a multiplex RT-PCR with primers designed on highly conserved regions of the RNA-dependent RNA polymerase in order to detect a maximum range of viral variants. Rearing facilities and governmental organizations can now thoroughly screen bumblebee colonies with a cost-effective technique with an integrated internal amplification control (IAC) implementable in laboratories that strive for International Organization for Standardization (ISO) certification.     

Comparison of different bead-beating RNA extraction strategies: an optimized method for filamentous fungi

Molecular studies, especially in relation to the activity of secondary metabolite gene clusters, require the ability to extract good quality RNA from fungal biomass. This is often hindered by the cell wall structure and endogenous RNase activity in filamentous fungi. There is thus a need for rapid methods for the extraction of good quality RNA for use in microarrays and for quantitative PCR assays. The objective of this study was to examine the use of different systems for the high throughput method to extract intact RNA from filamentous fungi. Two bead beating systems with different motion patterns and speed capacities were tested in the development of the extraction protocol. They were evaluated based on the total RNA yield and overall RNA quality. The high speed bead beating with glass beads associated with an automated purification method gave more than three times higher total RNA yields with less than a quarter of the amount of mycelium required. Furthermore the integrity and overall quality was conserved, with RNA Quality Indicator (RQI) numbers consistently >7.5. This method also reduced cross contamination risks and kept RNA handling to a minimum while still being capable of multiple sample processing, reducing the time required to obtain RNA from filamentous fungi.     

Evaluation of commercial kits for extraction of DNA and RNA from Clostridium difficile

Commercial nucleic acid extraction kits are a cost effective, efficient and convenient way to isolate DNA and RNA from bacteria. Despite the increasing importance of the gastrointestinal pathogen, Clostridium difficile, and the increased use of nucleic acids in its identification, characterization, and investigation of virulence factors, no standardized or recommended methods for nucleic acid isolation exist. Here, we sought to evaluate 4 commercial DNA extraction kits and 3 commercial RNA extraction kits assessing cost, labor intensity, purity, quantity and quality of nucleic acid preparations. The DNA extraction kits produced a range of concentrations (20.9–546 ng/ml) and A_260/280 ratios (1.92–2.11). All kits were suitable for DNA extraction with the exception of the Roche MagNA pure LC DNA isolation kit III which produced DNA of high yield but with substantial shearing, but that did not affect downstream PCR amplifications. For RNA extraction, the Qiagen RNeasy mini kit stood out producing preparations of consistently higher concentrations and higher RNA integrity numbers (RIN). The Roche MagNA pure LC RNA isolation kit produced preparations that could not be properly assigned RINs due to a failure to remove small RNAs which were interpreted as degradation. Good DNA and RNA yield are critical but methods are often overlooked. This study highlights the potential for critical variation between established commercial systems and the need for assessment of any extraction methods that are used.     

Evaluation of a shortened QIAsymphony DNA extraction protocol for stool samples using a multiplex real-time PCR for the detection of enteric pathogens

A shortened DNA extraction protocol for the QIAsymphony SP was evaluated by quantitative and qualitative comparison of real-time PCR results of 150 co-extracted stool samples. The average ?Cycle threshold value for positive pathogenic targets was 0.28 Ct. A consensus of 96.91%, with a correlation coefficient of 0.9880 was recorded.     

The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase

The RNA-dependent RNA polymerase of bacteriophage phi6 transcribes mRNA from the three segments of the dsRNA viral genome. We have cocrystallized RNA oligonucleotides with the polymerase, revealing the mode of binding of RNA templates. This binding is somewhat different from that previously seen for DNA oligomers, leading to additional RNA-protein hydrogen bonds, consistent with a preference for RNA. Activation of the RNA/polymerase complex by the addition of substrate and Mg2+ initiates a single round of reaction within the crystal to form a dead-end complex that partially collapses within the enzyme active site. By replacing Mg2+ with Ca2+, we have been able to capture the inhibited complex which shows distortion that explains the structural basis for the inhibition of such polymerases by Ca2+.     

Extended application of an efficient method for RNA isolation from different organisms

Summary We have extended the use of the triisopropylnaphthalene sulfonic acid and p-aminosalicylic acid (TNS-PAS) method for RNA isolation to a wide range of different tissues and microorganisms including bacteria, yeast, filamentous fungi, animal and plant tissues. This method has proved successful for isolating high quality, pure RNA in a simple and reproducible manner for use in Biochemical and Molecular Biology approaches.     

Evaluation of four protocols for the detection and isolation of thermophilic Campylobacter from different matrices

Aims: To identify the optimal method for detection of thermophilic Campylobacter at various stages in the food chain, three culture‐dependent (direct plating, Bolton and Preston enrichment) and one molecular method (qPCR) were compared for three matrices: poultry faeces (n = 38), neck skin (n = 38) and packed fresh meat (n = 38). Methods and Results: Direct plating was compared to enrichment with either Bolton broth (ISO 10272:2006‐1) or Preston broth, followed by culture on two selective agars: modified charcoal cefoperazone desoxycholate agar (mCCDA) and Campyfood agar (CFA). Direct plating on CFA provided the highest number of positive samples for faeces and neck skin samples. Enrichment of meat samples in Preston followed by plating on mCCDA gave significantly higher number of positives than the recommended ISO method. Real‐time qPCR yielded the highest number of positive samples. Conclusion: Direct plating on CFA is optimal for Campylobacter isolation from highly contaminated samples such as faeces or neck skin. When enrichment is required for less‐contaminated samples such as poultry meat, Preston broth is the best choice. The maximum of detectable cells predicted by qPCR is a sensitive and powerful evaluation tool. Significance and impact of the study: The recommended ISO protocol had the least sensitivity, and application of this method could result in underreporting. We detected a high prevalence of Campylobacter on packed meat to be distributed, which suggests this is still a significant risk for consumers.     

Predicting worldwide invasiveness for four major problematic decapods: an evaluation of using different calibration sets

Recently, there has been much debate whether niche based models (NBM) can predict biological invasions into new areas. These studies have chiefly focused on the type of occurrence data to use for model calibration. Additionally, pseudo‐absences are also known to cause uncertainty in NBM, but are rarely tested for predicting invasiveness. Here we test the implications of using different calibration sets for building worldwide invasiveness models for four major problematic decapods: Cherax destructor, Eriocheir sinensis, Pacifastacus leniusculus and Procambarus clarkii. Using Artificial Neural Networks models we compared predictions containing either native range occurrences (NRO), native and invasive occurrences (NIO) and invasive only (IRO) coupled with three types of pseudo‐absences – based on sampling only 1) the native range (NRA), 2) native and invasive ranges (NIA), and 3) worldwide random (WRA). We further analysed the potential gains in accuracy obtained through averaging across multiple models. Our results showed that NRO and IRO provided the best predictions for native and invaded ranges, respectively. Still, NIO provided the best balance in predicting both ranges. Pseudo‐absences had a large influence on the predictive performance of the models, and were more important for predictiveness than types of occurrences. Specifically, WRA performed the best and NRA and NIA performed poorly. We also found little benefit in combining predictions since best performing single‐models showed consistently higher accuracies. We conclude that NBM can provide useful information in forecasting invasiveness but are largely dependent on the type of initial information used and more efforts should be placed on recognizing its implications. Our results also show extensive areas which are highly suitable for the studied species worldwide. In total these areas reach from three to nine times the species current ranges and large portions of them are contiguous with currently invasive populations.     

Evaluation of different parameters for the purification of inulinase using an ion exchange fixed bed

The main conditions affecting the downstream process for purification of inulinase from Kluyveromyces marxianus var. bulgaricus ATCC 16045 were investigated. Parameters including the elution mode, linear rate, ionic strength, and elution pH were evaluated in order to achieve the best purification factor and recovery. The best purification factor and recovery were achieved in run 6 using a gradient elution mode with concentrations of NaCl ranging from 0 to 1 M, a linear flow rate of 100 cm/h and a pH value of 4.1. Under these conditions, the recovery was ∼ 67.5% and the purification factor ∼ 6.6-fold.     

Evaluation of different methods for the extraction of DNA from fungal conidia by quantitative competitive PCR analysis.

Five different DNA extraction methods were evaluated for their effectiveness in recovering PCR templates from the conidia of a series of fungal species often encountered in indoor air. The test organisms were Aspergillus versicolor, Penicillium chrysogenum, Stachybotrys chartarum, Cladosporium herbarum and Alternaria alternata. The extraction methods differed in their use of different cell lysis procedures. These included grinding in liquid nitrogen, grinding at ambient temperature, sonication, glass bead milling and freeze-thawing. DNA purification and recovery from the lysates were performed using a commercially available system based on the selective binding of nucleic acids to glass milk. A simple quantitative competitive polymerase chain reaction (QC-PCR) assay was developed for use in determining copy numbers of the internal transcribed spacer (ITS) regions of the ribosomal RNA operon (rDNA) in the total DNA extracts. These quantitative analyses demonstrated that the method using glass bead milling was most effective in recovering PCR templates from each of the different types of conidia both in terms of absolute copy numbers recovered and also in terms of lowest extract to extract variability. Calculations of average template copy yield per conidium in this study indicate that the bead milling method is sufficient to support the detection of less than ten conidia of each of the different organisms in a PCR assay.     

Comparison of analytical methods for extraction of chloride from plant tissue using36Cl as tracer

Eleven published and unpublished methods for extraction of chloride from plant tissue were compared, using a homogeneous sample of dried, ground maize leaves previously labelled with³⁶Cl. The most effective method of extraction of Cl^–, estimated by liquid scintillation counting of³⁶Cl, was with hot water. However, six other methods, including either cold water extraction, or dry-ashing at 500°C of plant material previously treated to give an alkaline pH, gave³⁶Cl values that were not statistically different from that obtained with hot water extraction. The lowest estimates of³⁶Cl content were obtained either by wet digestion in nitric/acetic acid or by dry-ashing following Mg(NO₃)₂ treatment of the plant material.     

Comparative analysis of different TaqMan real-time RT-PCR assays for the detection of swine Hepatitis E virus and integration of Feline calicivirus as internal control

Aims:  The aim of this study was to compare the performance of four TaqMan RT-PCR assays with a commonly used nested RT-PCR and to include the Feline calicivirus (FCV) as an internal control.
Methods and Results:  RNA extracted from 87 swine faecal samples and 103 swine blood samples was subjected to different detection systems. Faecal samples naturally contaminated with Hepatitis E virus (HEV) and negative samples were artificially inoculated with 3·2 × 10³ PFU of FCV. Detection results obtained on faecal and plasma samples were 35·6% and 4·9% with the nested RT-PCR assay, 8·0% and 0%, 0% and 0%, 13·8% and 0% and 36·8% and 3·9% with TaqMan systems A, B, C and D respectively. The Ct means obtained with the multiplex TaqMan assay were 30·11 and 30·43 for the detection of FCV with HEV contaminated samples and negative samples.
Conclusions:  The TaqMan system D was more suitable for the detection of swine HEV strains than the three others and FCV was integrated successfully as an internal control.
Significance and Impact of the Study:  FCV was demonstrated as an efficient control to monitor the RNA extraction process and HEV amplification procedure in a multiplex HEV/FCV TaqMan assay. This control would be helpful in limiting false negative results.