Optimization of random amplification of polymorphic DNA analysis for molecular subtyping of Escherichia coli O157

Random amplification of polymorphic DNA (RAPD) analysis using the polymerase chain reaction has proved to be a useful technique in the epidemiological investigation of micro-organisms but may suffer from a lack of reproducibility in poorly optimized protocols. In this study a method of obtaining reproducible genomic fingerprints using RAPD analysis of Escherichia coli O157 is described. By systematic optimization of reaction conditions and selection of suitable primers, reproducible and discriminatory profiles could be obtained from all E. coli O157 strains tested. In addition, two other methods of obtaining reproducible profiles from E. coli O157 strains without the need to purify genomic DNA are described.     

Microtissue Culture Plaque Assay for Herpesvirus saimiri

A microtissue culture method for the plaque assay of Herpesvirus saimiri has been developed. Virus titrations carried out in Microtest II tissue culture plates (Falcon) yielded reproducible results that agreed well with those obtained by employing macrocultures. The described method is quantitative, reproducible, economical, and suitable for routine assay of large numbers of virus samples.     

Motility evaluation of human spermatozoa by photon correlation spectroscopy.

The application of photon correlation spectroscopy for the evaluation of motility parameters of undiluted human sperm is investigated. Measurements on semen samples, selected visually as good (i.e., fraction motile spermatozoa larger than 0.6 and a positive appreciation of the motion), gave estimates of the fraction motile spermatozoa, reproducible within 10%, and of the mean velocity of the motile cells, reproducible within 5%.     

Rapid and reproducible deactivation of rhodopsin requires multiple phosphorylation sites

Efficient single-photon detection by retinal rod photoreceptors requires timely and reproducible deactivation of rhodopsin. Like other G protein-coupled receptors, rhodopsin contains multiple sites for phosphorylation at its COOH-terminal domain. Transgenic and electrophysiological methods were used to functionally dissect the role of the multiple phosphorylation sites during deactivation of rhodopsin in intact mouse rods. Mutant rhodopsins bearing zero, one (S338), or two (S334/S338) phosphorylation sites generated single-photon responses with greatly prolonged, exponentially distributed durations. Responses from rods expressing mutant rhodopsins bearing more than two phosphorylation sites declined along smooth, reproducible time courses; the rate of recovery increased with increasing numbers of phosphorylation sites. We conclude that multiple phosphorylation of rhodopsin is necessary for rapid and reproducible deactivation.     

A mouse model of intracerebral hemorrhage using autologous blood infusion

The development of controllable and reproducible animal models of intracerebral hemorrhage (ICH) is essential for the systematic study of the pathophysiology and treatment of hemorrhagic stroke. In recent years, we have used a modified version of a murine ICH model to inject blood into mouse basal ganglia. According to our protocol, autologous blood is stereotactically infused in two stages into the right striatum to mimic the natural events of hemorrhagic stroke. Following ICH induction, animals demonstrate reproducible hematomas, brain edema formation and marked neurological deficits. Our technique has proven to be a reliable and reproducible means of creating ICH in mice in a number of acute and chronic studies. We believe that our model will serve as an ideal paradigm for investigating the complex pathophysiology of hemorrhagic stroke. The protocol for establishing this model takes about 2 h.     

Plant leaf and stem proteins. I. Extraction and electrophoretic separation of the basic, water-soluble fraction

Simplified but highly reproducible extraction and electrophoretic procedures have been developed for plant stem and leaf proteins using recent chemical and technical advances. The method is applied to the separation of the basic, water-soluble proteins found in stem and leaf tissues of 3 Dianthus clones. While most of the highly reproducible protein bands appear in all 3 selections, and many are also common to both leaf and stem tissue, others are characteristic for the variety or tissue.     

Microculture System for Detection of Newcastle Disease Virus Antibodies

A microculture system utilizing cytopathic effect (CPE) and hemadsorption (HAd) end points was effective in determining the level of Newcastle disease virus (NDV) antibodies. The microculture system was of comparable sensitivity to the plaque reduction test for the detection of NDV antibodies. The standards by which the CPE and HAd microculture tests would be considered reproducible were defined. The results indicate that the CPE and HAd microculture tests are reproducible within one twofold dilution.     

Behavioral and anatomical consequences of early versus late symbol training in macaques

Distinct brain regions, reproducible from one person to the next, are specialized for processing different kinds of human expertise, such as face recognition?and reading. Here, we explore the relationship between age of learning, learning ability, and specialized brain structures. Specifically, we ask whether the existence of reproducible cortical domains necessarily means that certain abilities are innate, or innately easily learned, or whether reproducible domains can be formed, or refined, by interactions between genetic programs and common early experience. Functional MRI showed that intensive early, but not late, experience caused the formation of category-selective regions in macaque temporal lobe for stimuli never naturally encountered by monkeys. And behaviorally, early training produced more fluent processing of these stimuli than the same training in adults. One explanation for these results is that in higher cortical areas, as in early sensory areas, experience drives functional clustering and functional clustering determines how that information is processed.     

Chiral HPLC method for chiral purity determination of paroxetine drug substance

This article describes a chiral HPLC method for (+) trans isomer of paroxetine in a paroxetine drug substance. The method development was performed to establish a suitable HPLC system in order to separate both enantiomers. It was found that a system based on a Chiralpak AD column was suitable for the analysis. Proper column maintenance and the optimized eluent composition allowed good reproducibility and sensitivity for the method. The method was also checked on a number of different columns using different HPLC equipment and gave both reproducible chromatography and reproducible quantitative results.     

Optimization of RAPD for fingerprinting Salmonella

Random amplification of polymorphic DNA (RAPD) is proving to be a useful technique in studying the epidemiology of micro-organisms. The technique can be troublesome and time consuming to establish due to the essentially empirical approach to optimization. By standardization of certain parameters and use of a commercially available PCR buffer optimization kit, a particularly promising primer was identified and RAPD conditions for a highly discriminatory and reproducible characterization of Salmonella isolates was achieved. In addition, a technique to obtain reproducible RAPD fingerprints of Salmonella isolates without the need to purify genomic DNA is described.     

Determination of N-acetyl tryptophan in albumin solutions. Use of a F.P.L.C. method

We developed a simple and reproducible technique for measuring N-Acetyl tryptophane in albumin after chromatography.     

Measurement of the rate of stomach emptying using Indium-113m and a 10-crystal rectilinear scanner

Accurate reproducible measurements of the rate of gastric emptying have only been possible since the advent of external radionuclide detection techniques. Indium-113m and a 10-crystal rectilinear scanner have been employed to measure stomach emptying rates. The technique is simple, the results reproducible and it has proved ideal for assessing the results of drug therapy in patients with gastric retention. In the normal individual the T50% was 42 to 95 minutes, and the relationship between counts and time was, to first approximation, a linear function.     

Principles for data analysis workflows

A systematic and reproducible “workflow”—the process that moves a scientific investigation from raw data to coherent research question to insightful contribution—should be a fundamental part of academic data-intensive research practice. In this paper, we elaborate basic principles of a reproducible data analysis workflow by defining 3 phases: the Explore, Refine, and Produce Phases. Each phase is roughly centered around the audience to whom research decisions, methodologies, and results are being immediately communicated. Importantly, each phase can also give rise to a number of research products beyond traditional academic publications. Where relevant, we draw analogies between design principles and established practice in software development. The guidance provided here is not intended to be a strict rulebook; rather, the suggestions for practices and tools to advance reproducible, sound data-intensive analysis may furnish support for both students new to research and current researchers who are new to data-intensive work.     

Reproducible and inducible knockdown of gene expression in mice

RNA interference (RNAi) has emerged as an efficient approach for rapid analysis of gene function. In mammalian cells, vector-based expression of small hairpin RNAs (shRNA) produces potent and stable gene knockdown effects. An inducible RNAi system with reproducible levels of siRNA expression will extend the usefulness of this methodology to the identification of gene functions within the developing or adult mouse. We present evidence that an RNA polymerase III-driven U6 promoter with stuffer sequences flanked by loxP sites inserted at three different sites within the promoter drives shRNA expression in a Cre recombinase-dependent manner. We utilized this approach to develop a generic strategy for the reproducible knockdown of gene expression in mice. By placing the inducible shRNA cassette into the ROSA26 locus of the mouse, we were able to generate reproducible levels of controlled expression of shRNA to produce discernable phenotypes in vitro and in vivo. This approach circumvents the prescreening of random integration in embryonic stem cell clones and further enables conditional gene knockdown with temporal and/or tissue specificity. This methodology should expedite large-scale functional studies.     

Towards a quantitative grading of bladder tumors.

The histological inspection of tumor tissue for the purpose of reporting a tumor grade is a problem of significant clinical importance. The grading by a pathologist is only partly reproducible due to vaguely defined, subjective criteria. In this article we describe and evaluate a set of measurable features that quantitate the differences in tumor tissue. Different aspects of the reproducibility of the measurements under varying conditions of image selection, focus, and noise have been investigated. Three hundred thirty-three images were digitized from 111 bladder tissue sections (4 microns thick, Feulgen stained), using the ICAS microscope-camera platform. A segmentation routine was developed to segment the images into nuclei and background without any user interaction. Size, shape, optical density, and texture features were measured on and among the objects found by this segmentation routine using the image analysis package Acuity. The results of the measurements showed that there is a significant quantitative difference between grade 1 and grade 3 tumors. Grade 2 tumors can be described as "in between grade 1 and grade 3" and falling somewhere on an increasing scale between grades 1 and 3. Grade 2 tumors do not seem to represent a statistically distinct population. The procedure described here is shown to be quite reproducible in the presence of noise, reasonably reproducible in the event of a modest amount of defocusing (with grade 3 tumors exhibiting the most sensitivity), and less reproducible in the context of which fields-of-view are chosen for analysis.     

Importance of carbon dioxide for the cultivation of Thermoactinomyces vulgaris from spores

Thermoactinomyces vulgaris has been used for the production of the serine protease Thermitase [EC 3.4.21.14] by fermentation. Spore germination of this strain is influenced by the gas composition of the medium. Since the outgrowth of the germ tubes occurs only in the presence of a raised CO₂ concentration, the cultivation in aerated stirred fermenters is not reproducible. However, if cultivation takes place in a closed fermentation system, initially unaerated, in which the CO₂ formed by spore respiration accumulates, reproducible germination can be obtained. From an O₂-balance, indirect conclusions can be drawn with regard to the effect of CO₂, and the process of germination can be described. The cultivation method described permits almost complete germination of all inoculated spores and reproducible rates of biomass and enzyme production in the subsequent fermentation. Thus, stabilization of the procedure with increased enzyme yields is ensured.     

Phenol Extraction Op 28 S Ribosomal RNA Prom Rat Liver Cytoplasm

A simple and reproducible phenol method for the isolation of 28 S ribosomal RNA from rat liver cytoplasm, free from poly(A)-RNA is described. The procedure is based on the observation that at lower pH of the homogenate (pH 5.5) 28 S ribosomal RNA is extracted, while 18 S ribosomal RNA remains in the interphase layer.

Isolation of pure 28 S or 18 S ribosomal RNA in preparative amounts requires density gradient cen-trifugation or preparative gel electrophoresis. In this communication a rapid and reproducible method for the isolation of 28 S ribosomal RNA is proposed.     

应用DNA指纹图谱技术鉴定整肠生菌株BL63516的研究

目的建立应用DNA指纹图谱技术鉴定微生态制剂——整肠生菌株BL63516的方法,提高菌种鉴别水平。方法应用RAPD（随机扩增多态性）方法,采用50条随机引物对7株地衣芽胞杆菌进行基因组DNA指纹图谱分析,选择多态性好、重复性好、稳定性强的随机引物,对BL63516与其他地衣芽胞杆菌进行区分。结果发现选用引物$87或$88分别对7株地衣芽胞杆菌进行基因组DNA指纹图谱分析,BL63516菌株扩增的DNA片段的大小、数量均与其他地衣芽胞杆菌有明显差异。结论此方法具有可重复性,方便、快速和准确的优势,可用于微生态制剂整肠生菌株的鉴别。