Transient Expression of β-Glucuronidase in Embryo Axes of Cotton by Agrobacterium and Particle Bombardment Methods

Transient expression of -glucuronidase (GUS) in zygotic embryo axes of two cotton (Gossypium hirsutum L.) cultivars NHH-44 and DCH-32 was induced by Agrobacterium mediated transformation or by particle bombardment. For Agrobacterium transformation, disarmed A. tumefaciens strain GV 2260/p35SGUSINT was used. In cv. NHH-44, the maximum frequency of transient expression (14.28 %) was achieved on spotting Agrobacterium paste on the apical regions of the split embryo axes. The method resulted in a transformed callus line, which showed strong GUS activity. Integration of NPTII gene was confirmed by Southern analysis. Transgene expression by particle bombardment was achieved with p35SGUSINT and pIBGUS plasmids independently. The maximum frequency of GUS expression in 29.16 % explants was observed in cultivar NHH-44 with gold microcarriers (1.1 µm) when bombarded once with rupture disc of 7586 kPa at target cell distance of 6 cm. A transformed callus line was obtained when explants were bombarded with p35SGUSINT and cultured on Murashige and Skoog's medium supplemented with B₅ vitamins, 0.1 mg dm^–3 1-phenyl-3-(1,2,3-thiadiazol-5-yl) urea, 0.01 mg dm^–3 -naphthaleneacetic acid, 3 % glucose + 50 mg dm^–3 kanamycin. High GUS activity was observed in callus tissue as well as in somatic embryo like structures achieved in liquid shake cultures.     

Current Status in Diagnosis of Scedosporium Infections: What Is the Impact of New Molecular Methods?

Scedosporium species are increasingly encountered as fungal pathogens. Species identification is important due to species-specific differences in epidemiology, antifungal susceptibility and virulence. Histology and culture-based identification are hampered by their low sensitivity and specificity. The use of new selective media has improved the recovery rate from clinical samples. Molecular methods, including multiplex PCR, PCR-RFLP analysis, DNA sequencing, oligonucleotide arrays, real-time PCR, rolling circle amplification, are increasingly used for species identification. Most recently, Matrix-Assisted Laser Desorption-Time of Flight Mass Spectrometry has been successfully applied as a tool for rapid identification of clinically relevant Scedosporium species. This review aims to summarize the methods currently used to guide the clinical microbiology laboratory in the selection of the most appropriate identification techniques. This will aid the laboratory in making a fast and reliable diagnosis that enables the clinician to make correct treatment choices.     

Methods Used in Economic Evaluations of Chronic Kidney Disease Testing — A Systematic Review

BackgroundThe prevalence of chronic kidney disease (CKD) is high in general populations around the world. Targeted testing and screening for CKD are often conducted to help identify individuals that may benefit from treatment to ameliorate or prevent their disease progression.AimsThis systematic review examines the methods used in economic evaluations of testing and screening in CKD, with a particular focus on whether test accuracy has been considered, and how analysis has incorporated issues that may be important to the patient, such as the impact of testing on quality of life and the costs they incur.MethodsArticles that described model-based economic evaluations of patient testing interventions focused on CKD were identified through the searching of electronic databases and the hand searching of the bibliographies of the included studies.ResultsThe initial electronic searches identified 2,671 papers of which 21 were included in the final review. Eighteen studies focused on proteinuria, three evaluated glomerular filtration rate testing and one included both tests. The full impact of inaccurate test results was frequently not considered in economic evaluations in this setting as a societal perspective was rarely adopted. The impact of false positive tests on patients in terms of the costs incurred in re-attending for repeat testing, and the anxiety associated with a positive test was almost always overlooked. In one study where the impact of a false positive test on patient quality of life was examined in sensitivity analysis, it had a significant impact on the conclusions drawn from the model.ConclusionFuture economic evaluations of kidney function testing should examine testing and monitoring pathways from the perspective of patients, to ensure that issues that are important to patients, such as the possibility of inaccurate test results, are properly considered in the analysis.     

How long is a piece of Strix? Methods in measuring and measuring the measurers

An experiment to quantify intra- and interobserver error in anatomical measurements found that interobserver measurements can vary by over 14% of mean specimen length; disparity in measurement increases logarithmically with the number of contributors; instructions did not reduce variation or measurement disparity; scale of the specimen influenced the precision of measurement (relative error increasing with specimen size); different methods of taking a measurement yielded different results, although they did not differ in terms of precision, and topographical complexity of the elements being considered may potentially influence error (error increasing with complexity). These results highlight concerns about introduction of noise and potential bias that should be taken into account when compiling composite datasets and meta-analyses.     

Cryopreservation of Endothelial Cells in Various Cryoprotective Agents and Media – Vitrification versus Slow Freezing Methods

Vitrification of endothelial cells (MHECT-5) has not previously been compared with controlled slow freezing methods under standardized conditions. To identify the best cryopreservation technique, we evaluated vitrification and standardized controlled-rate -1°C/minute cell freezing in a -80°C freezer and tested four cryoprotective agents (CPA), namely dimethyl sulfoxide (DMSO), ethylene glycol (EG), propylene glycol (PG), and glycerol (GLY), and two media, namely Dulbecco''s modified Eagle medium Ham’s F-12 (DMEM)and K⁺-modified TiProtec (K⁺TiP), which is a high-potassium-containing medium. Numbers of viable cells in proliferation were evaluated by the CellTiter 96® A_Queous One Solution Cell Proliferation Assay (Promega Corporation, Mannheim, Germany). To detect the exact frozen cell number per cryo vial, DNA content was measured by using Hoechst 33258 dye prior to analysis. Thus, results could be evaluated unconstrained by absolute cell number. Thawed cells were cultured in 25 cm² cell culture flasks to confluence and examined daily by phase contrast imaging. With regard to cell recovery immediately after thawing, DMSO was the most suitable CPA combined with K⁺TiP in vitrification (99 ±0.5%) and with DMEM in slow freezing (92 ±1.6%). The most viable cells in proliferation after three days of culture were obtained in cells vitrificated by using GLY with K⁺TiP (308 ±34%) and PG with DMEM in slow freezing (280 ±27%).     

Methods for recovery of ionic liquids—A review

Ionic liquids (ILs) have attracted much attention in both academics and industries as promising solvents for a diverse range of applications. However, there were little industrial processes employing ILs as current time due to the economical and efficient use of ILs. The economic efficiency can be improved by recycling and reuse of ILs. In the last few decades, several attempts have been made, by the researchers, for recovery and recycling of ILs. This review is intended to present a comprehensive summary on the methods used for recovery and recycling of ILs.     

The Ability of Different Imputation Methods to Preserve the Signi?cant Genes and Pathways in Cancer

Deciphering important genes and pathways from incomplete gene expression data could facilitate a better understanding of cancer. Different imputation methods can be applied to estimate the missing values. In our study, we evaluated various imputation methods for their performance in preserving signi?cant genes and pathways. In the ?rst step, 5% genes are considered in random for two types of ignorable and non-ignorable missingness mechanisms with various missing rates. Next,10 well-known imputation methods were applied to the complete datasets. The signi?cance analysis of microarrays(SAM) method was applied to detect the signi?cant genes in rectal and lung cancers to showcase the utility of imputation approaches in preserving signi?cant genes. To determine the impact of different imputation methods on the identi?cation of important genes, the chi-squared test was used to compare the proportions of overlaps between signi?cant genes detected from original data and those detected from the imputed datasets. Additionally, the signi?cant genes are tested for their enrichment in important pathways, using the Consensus Path DB. Our results showed that almost all the signi?cant genes and pathways of the original dataset can be detected in all imputed datasets, indicating that there is no signi?cant difference in the performance of various imputationmethods tested. The source code and selected datasets are available on http://pro?les.bs.ipm.ir/softwares/imputation_methods/.     

How to Preserve Plant Samples for Carbohydrate Analysis? Test of Suitable Methods Applicable in Remote Areas

Nonstructural carbohydrates (NSC) are frequently studied both by ecologists and plant physiologists because they serve as fundamental carbon and energy sources in plant metabolism. Because of the rapid enzymatic hydrolysis of NSC after harvest, plants are usually placed into liquid nitrogen until subsequent analyses in the laboratory. Nevertheless, when the research is performed in poorly accessible regions such as high mountains, tropical forests or deserts, the use of heavy containers containing vaporizing liquid nitrogen is problematic for logistical reasons. These places are particularly interesting as they harbor plant species with interesting physiological adaptations. In our study we aimed to develop a suitable storage method for plants intended for NSC analyses, which would require minimal equipment. These demands resulted in the idea of using the first step in NSC analyses – extraction in ethanol. Samples were extracted in 50 % and 96 % boiling or non-boiling ethanol and then stored for one month; they were compared with samples immediately frozen in liquid nitrogen. We discovered that for samples containing starch, fructans, soluble sugars and sugar alcohols, the best pretreatment for subsequent storage is extraction in 50 % or 96 % boiling ethanol. For total nonstructural carbohydrates (TNC) assessment, only extracting with 50 % ethanol without boiling gave very good results. Finally, we developed a method that could be used in any remote place without bulky laboratory equipment.     

PCR-Based Methods for the Diagnosis of Invasive Candidiasis: Are They Ready for Use in the Clinic?

Purpose of Review

We review the performance of Candida PCR and the T2Candida panel (T2Biosystems, Lexington, MA) in diagnosing invasive candidiasis, consider how these tests may be incorporated into patient care, and determine if they are ready to be used in the clinic.

Recent Findings

PCR and T2Candida sensitivity/specificity for diagnosing candidemia are ~?90%/90% and ~?90%/98%, respectively. Limited data for intra-abdominal candidiasis suggest PCR sensitivity of ~?85–90%, but specificity has varied from 33 to 97%. T2Candida data are lacking for infections other than candidemia.

Summary

PCR and T2Candida will have the greatest value if their use is restricted to cases in which positive and negative predictive values differ in a clinically meaningful way from the pre-test likelihood. Studies are needed to establish that patient care and stewardship strategies incorporating Candida PCR or T2Candida improve patients’ outcomes, reduce unnecessary antifungal usage, limit emergence of resistance, and are cost-effective. The development and validation of standardized PCR assays is a top priority.

     

Non–Culture-Based Methods for the Diagnosis of Invasive Candidiasis

Given the limitations of current fungal diagnostics, the use of non–culture-based methods for the diagnosis of invasive candidiasis (IC) is highly warranted. The implementation of molecular diagnostic strategies could permit the timely onset of appropriate therapy and may be expected to pave the way for improved clinical outcome of IC. Polymerase chain reaction (PCR) may have higher sensitivity for the diagnosis of IC than conventional blood cultures. The detection of fungal antigens generally requires a large fungal burden, and the presence of fungus-specific antibodies may not correlate with the underlying diseases. Therefore, the combined mannan and anti-mannan antibody testing is recommended. No single test has been shown convincingly to compensate for all the limitations of culture. Real-time PCR coupled with fungal culture and/or antigen detection will likely be required to significantly ameliorate the diagnostic problems in IC.     

Methods in Primate Nutritional Ecology: A User’s Guide

An important goal of primatology is to identify the ecological factors that affect primate abundance, diversity, demography, and social behavior. Understanding the nutritional needs of primates is central to understanding primate ecology because adequate nutrition is a prerequisite for successful reproduction. Here, we review nutritional methods and provide practical guidelines to measure nutrient intake by primates in field settings. We begin with an assessment of how to estimate food intake by primates using behavioral observations. We then describe how to collect, prepare, and preserve food samples. Finally, we suggest appropriate nutritional assays for estimating diet nutritional quality and point to the merits and limitations of each. We hope this review will inspire primatologists to use nutritional ecology to answer many unresolved questions in primatology.     

Enzyme Characteristics of β-d-Galactosidase- and β-d-Glucuronidase-Positive Bacteria and Their Interference in Rapid Methods for Detection of Waterborne Coliforms and Escherichia coli

Bacteria which were β-d-galactosidase and β-d-glucuronidase positive or expressed only one of these enzymes were isolated from environmental water samples. The enzymatic activity of these bacteria was measured in 25-min assays by using the fluorogenic substrates 4-methylumbelliferyl-β-d-galactoside and 4-methylumbelliferyl-β-d-glucuronide. The enzyme activity, enzyme induction, and enzyme temperature characteristics of target and nontarget bacteria in assays aimed at detecting coliform bacteria and Escherichia coli were investigated. The potential interference of false-positive bacteria was evaluated. Several of the β-d-galactosidase-positive nontarget bacteria but none of the β-d-glucuronidase-positive nontarget bacteria contained unstable enzyme at 44.5°C. The activity of target bacteria was highly inducible. Nontarget bacteria were induced much less or were not induced by the inducers used. The results revealed large variations in the enzyme levels of different β-d-galactosidase- and β-d-glucuronidase-positive bacteria. The induced and noninduced β-d-glucuronidase activities of Bacillus spp. and Aerococcus viridans were approximately the same as the activities of induced E. coli. Except for some isolates identified as Aeromonas spp., all of the induced and noninduced β-d-galactosidase-positive, noncoliform isolates exhibited at least 2 log units less mean β-d-galactosidase activity than induced E. coli. The noncoliform bacteria must be present in correspondingly higher concentrations than those of target bacteria to interfere in the rapid assay for detection of coliform bacteria.Indicators of pollution (e.g., coliforms, fecal coliforms, and Escherichia coli) are traditionally used for monitoring the microbiological safety of water supplies and recreational water. Several techniques for detection of coliforms and E. coli are based on enzymatic hydrolysis of fluorogenic or chromogenic substrates for β-d-galactosidase and β-d-glucuronidase (9, 20). Current methods of recovery are usually culture based, and the analysis time is 18 to 24 h. In addition to enzymatic activity, these techniques use growth at appropriate temperatures in the presence of inhibitors, combined with demonstration of enzymatic activity, to selectively detect target bacteria.Rapid methods which require less than 6 h and are based on chromogenic, fluorogenic, or chemiluminogenic substrates for detection of coliforms, fecal coliforms, or E. coli have been described (1–3, 10, 27, 28). These rapid assays are based on the assumption that β-d-galactosidase and β-d-glucuronidase are markers for coliforms and E. coli, respectively. However, when the incubation time is 1 h or less, growth is not a selective step, and all β-d-galactosidase-positive or β-d-glucuronidase-positive microorganisms in a water sample contribute to the activity measured. At low initial concentrations of target bacteria (i.e., E. coli and total coliforms), increasing the preincubation time to 5 to 6 h did not result in a predominance of target bacteria compared to nontarget bacteria (28).The β-d-galactosidase or β-d-glucuronidase activity calculated per cultivable coliform or fecal coliform bacterium in environmental samples can be 1 to 2 log units higher than the activity per induced E. coli cell in pure culture (11, 26). The presence of active, noncultivable bacteria can be one reason for this. Studies of survival (7, 24, 25) and disinfection (26) of E. coli have shown that loss of cultivability does not necessarily result in a loss of β-d-galactosidase activity. The presence of false-positive bacteria can be another reason.β-d-Galactosidase has been found in numerous microorganisms, including gram-negative bacteria (e.g., strains belonging to the Enterobacteriaceae, Vibrionaceae, Pseudomonadaceae, and Neisseriaceae), several gram-positive bacteria, yeasts, protozoa, and fungi (17, 29). β-d-Glucuronidase is produced by most E. coli strains and also by other members of the Enterobacteriaceae, including some Shigella and Salmonella strains and a few Yersinia, Citrobacter, Edwardia, and Hafnia strains. Production of β-d-glucuronidase by Flavobacterium spp., Bacteroides spp., Staphylococcus spp., Streptococcus spp., anaerobic corynebacteria, and Clostridium has also been reported (12).High numbers of false-positive bacteria in sewage and contaminated water have been revealed by enumeration of β-d-galactosidase- and β-d-glucuronidase-positive CFU on nonselective agar supplemented with fluorogenic or chromogenic substrates (11, 28). Whether the activity from nontarget organisms can be neglected in a rapid assay depends on the number of nontarget organisms compared with the number of target bacteria and also on the level of their enzyme activity. Plant and algal biomass must be present at high concentrations to interfere in rapid bacterial β-d-galactosidase and β-d-glucuronidase assays (8).The main objective of this study was to investigate the enzyme characteristics of β-d-galactosidase- and β-d-glucuronidase-positive bacteria isolated from environmental water samples and to evaluate the potential influence of false-positive bacteria in rapid assays for coliform bacteria or E. coli in water. The effect of temperature on enzyme activity and on the interference of nontarget bacteria in the rapid assays was investigated as an important factor.(Some of the results were presented at the 97th General Meeting of the American Society for Microbiology 1997, Miami Beach, Fla., 4 to 8 May 1997.)     

Research Methods Leading to a Perception of Knowledge Loss—One Century of Plant Use Documentation Among the Chácobo in Bolivia

The loss of traditional knowledge, concomitant with changes in livelihoods, languages, and demographics of indigenous and local groups, is a global concern. However, documenting such loss poses serious methodological challenges. Comparing the results of contemporary studies with past research is often problematic due to methodological differences. Here, comparing studies that attempted to document the traditional ethnobotanical knowledge of the Chácobo of Bolivia, we tried to examine whether knowledge loss was really occurring across more than 100 years or was only researcher’s perception. The Chácobo are a Panoan-speaking tribe of about 1000 members, first visited by researchers in 1911, and subsequently in the 1950s, 1960s, 1970s, 1980s, and 1990s. Each study had different foci, but all recorded ethnobotanical data. The first more detailed anthropological report exists from the late 1960s, and ecological-ethnobotanical studies were conducted in the 1980s and 1990s. Based on available literature, in particular the botanical studies of Boom (1987) and Bergeron (1998), it seemed that Chácobo plant use now centers on income generation. Both Boom (1987) and Bergeron (1998) perceived that traditional plant use related to household artifacts and medicine, as well as traditional crop varieties had almost disappeared. Here, we hypothesized that plant knowledge documented and the perception of so-called knowledge loss observed in these depended completely on the background of the interviewers and the methods employed, and that in a sufficiently comprehensive ethnobotanical study, we would be able to document all species and uses mentioned in previous studies. We tested this hypothesis by conducting a complete ethnobotanical inventory of almost the entire adult Chácobo population, with interviews and plant collection conducted directly by Chácobo counterparts. The results verify our initial hypothesis and showed that the loss of knowledge perceived in previous studies simply was an artifact of the research methods employed. Traditional crop varieties are still widely grown, most Chácobo know, and can name, traditional artifacts, and many still know the names and uses of medicinal species. However, some knowledge, including the manufacture of artifacts and proficient identification of many medicinal plants, is limited to the older generation.     

Systematic Comparative Evaluation of Methods for Investigating the TCRβ Repertoire

High-throughput sequencing has recently been applied to profile the high diversity of antibodyome/B cell receptors (BCRs) and T cell receptors (TCRs) among immune cells. To date, Multiplex PCR (MPCR) and 5’RACE are predominately used to enrich rearranged BCRs and TCRs. Both approaches have advantages and disadvantages; however, a systematic evaluation and direct comparison of them would benefit researchers in the selection of the most suitable method. In this study, we used both pooled control plasmids and spiked-in cells to benchmark the MPCR bias. RNA from three healthy donors was subsequently processed with the two methods to perform a comparative evaluation of the TCR β chain sequences. Both approaches demonstrated high reproducibility (R² = 0.9958 and 0.9878, respectively). No differences in gene usage were identified for most V/J genes (>60%), and an average of 52.03% of the CDR3 amino acid sequences overlapped. MPCR exhibited a certain degree of bias, in which the usage of several genes deviated from 5’RACE, and some V-J pairings were lost. In contrast, there was a smaller rate of effective data from 5’RACE (11.25% less compared with MPCR). Nevertheless, the methodological variability was smaller compared with the biological variability. Through direct comparison, these findings provide novel insights into the two experimental methods, which will prove to be valuable in immune repertoire research and its interpretation.     

Usual and Unusual Methods for Detection of Lipid Peroxides as Indicators of Tissue Injury in Cerebral Ischemia: What Is Appropriate and Useful?

1. Free radical-dependent lipid peroxidation processes have long been thought to contribute to brain damage following stroke or cerebral ischemia/reperfusion.2. The preponderance of evidence for this belief has been derived indirectly, through diminution of tissue injury indices (e.g., brain infarct volume) facilitated by application of free radical scavenger substances.3. Direct, unequivocal evidence for lipid peroxidation in terms of classical assays (detection of conjugated diene absorbance or thiobarbituric acid-reactive substances) is considerably less common, and its validity can be questioned.4. Correlations of treatment-induced diminishment of brain injury indices with reductions in lipid peroxidation level are rarer still.5. Reasons underlying the disparity between the belief that lipid peroxidation contributes to ischemic brain injury and direct evidence for this contribution (at least acutely) are proposed, along with evidence that new methods are being developed which should provide the basis for obtaining a definitive answer.     

Sensitive and Simple Methods for Determination of l-Lysine with l-Lysine α-Oxidase

l-Lysine could be determined satisfactorily with a new fungal enzyme, l-Iysine α-oxidase (EC 1.4.3). The method consists of the oxidative deamination of l-Iysine with l-lysine α-oxidase and the spectrophotometric determination of one of the reaction products: α-keto-ε-aminocaproate, its intramolecular dehydrated form, Δ¹-piperideine-2-carboxylate or hydrogen peroxide. The method on the basis of the color reaction of hydrogen peroxide formed from l-lysine with 4-aminoantipyrine and phenol in the presence of peroxidase was most sensitive and simple. The method could be used for the direct assay of l-lysine levels in serums from several animals without pretreatments.     

α4β2-Nicotinic Receptor Binding with 5-IA in Alzheimer’s Disease: Methods of Scan Analysis

Five patients with Alzheimer’s disease and five healthy volunteers were examined by SPECT with the nicotinic receptor ligand ¹²³I-5-IA-85380. Patients were scanned before and after 6 weeks of treatment with donepezil. Quantification by regions of interest was reliable and the optimal normalisation procedure used cerebellar ratios. We found relative reductions in 5-IA binding capacity in patients in thalamus, frontal and central regions of interest of approximately one standard deviation unit (Cohen’s d = 1). Reductions in binding after treatment with the acetylcholinesterase inhibitor donepezil of the same magnitude occurred in the brain stem. The study was clearly too small to confirm group differences, but it suggests that 5-IA can be used to examine both group differences and treatment effects in patients with Alzheimer’s disease. Special issue article in honor of George Fink.