Flow Cytometric Analysis of Conidia of Fungi Isolated from Soybean Vascular Tissue

Flow cytometry was used to characterize isolates of Phialophora gregata using the fluorescence intensity of propidium iodide-stained conidia. The isolates differed in their mean fluorescence intensity, ranging from 100.0 to 129.7 arbitrary units (AU). When the number of fluorescent events was plotted against intensity of fluorescence, a single peak was observed. Fluorescent patterns of Acremonium isolates from soybean vascular tissue were compared with those of P. gregata. Their mean fluorescence intensity ranged from 76.4 to 88.0 AU. With some of these isolates, multiple peak histograms were observed, corresponding to multiple spore sizes as well as single and double nucleated conidia. Using flow cytometry, we were able to distinguish P. gregata isolates from those of Acremonium , based on mean fluorescence intensity and/or the presence of multiple peaks. Flow cytometric analysis of propidium-iodide stained conidia of Phialophora isolates should prove to be useful for determining the relative DNA content of different isolates collected from different geographic areas.     

Flow Cytometric Analysis of Marine Bacteria with Hoechst 33342

We investigated the accuracy and precision of flow cytometric (FCM) estimates of bacterial abundances using 4′, 6-diamidino-2-phenylindole (DAPI) and Hoechst 33342 (HO342, a bisbenzamide derivative) on paraformaldehyde-fixed seawater samples collected from two stations near Oahu, Hawaii. The accuracy of FCM estimates was assessed against direct counts by using epifluorescence microscopy. DAPI and HO342 differ in two aspects of their chemistry that make HO342 better suited for staining marine heterotrophic bacteria for FCM analysis. These differences are most important in studies of open-ocean ecosystems that require dual-beam FCM analysis to clearly separate heterotrophic bacterial populations from populations of photosynthetic Prochlorococcus spp. Bacterial populations were easier to distinguish from background fluorescence when stained with HO342 than when stained with DAPI, because HO342 has a higher relative fluorescence quantum yield. A substantially higher coefficient of variation of blue fluorescence, which was probably due to fluorescent complexes formed by DAPI with double-stranded RNA, was observed for DAPI-stained populations. FCM estimates averaged 2.0 and 12% higher than corresponding epifluorescence microscopy direct counts for HO342 and DAPI-stained samples, respectively. A paired-sample t test between FCM estimates and direct counts found no significant difference for HO342-stained samples but a significant difference for DAPI-stained samples. Coefficients of variation of replicate FCM abundance estimates ranged from 0.63 to 2.9% (average, 1.5%) for natural bacterial concentrations of 6 × 10⁵ to 15 × 10⁵ cells ml^-1.     

Directional Tests for the Analysis of Clinical Trials with Multiple Endpoints Allowing for Incomplete Data

Incomplete data are a serious problem in the multivariate analysis of clinical trials. Usually a complete-case analysis is performed: All incomplete observation vectors are excluded from the analysis. Provided that observations are missing randomly, an easy-to-handle available-case analysis is introduced, allowing the analysis of all data without insertion or deletion of observations. This method is applied to parametric and nonparametric test procedures of the O'Brien type, which are more powerful than the conventional Hotelling's T² for detecting alternatives where the (treatment) effect has the same direction for all observed variables. In addition, the applicability of these so-called directional tests, especially in the case of small samples, and their pros and cons are discussed.     

眼附属器MALT淋巴瘤临床病例分析

目的:探讨眼附属器MALT淋巴瘤的诊断、治疗、疗效及预后影响因素。方法:回顾性分析1997年1月至2008年1月68例病理确诊的ⅠE期眼附属器MALT淋巴瘤患者的临床表现、影像学结果、治疗经过、放疗疗效及预后情况。结果:本研究68例ⅠE期眼附属器MALT淋巴瘤中男性44例,女性24例,男女比例1.83:1。原发于眼眶40例,眼睑5例,泪腺11例,结膜12例。经过55月(28-135月)的随访,5年总生存率为91.3%,5年的局部控制率为97%。结论:眼附属器MALT淋巴瘤好发于老年男性,以侵及眼眶者居多,B超、CT、MRI仅可提供较好的定性、定位诊断,确诊仍需病理诊断。手术切除联合局部放射治疗对ⅠE期眼附属器MALT淋巴瘤有较好的疗效。眼附属器MALT淋巴瘤有转化为弥漫性大B细胞淋巴瘤的潜在危险,放射治疗后长期的随访仍然是必须的。放疗或化疗也可以作为成功的补救措施。     

Optimizing Viable Leukocyte Sampling from the Female Genital Tract for Clinical Trials: An International Multi-Site Study

Background

Functional analysis of mononuclear leukocytes in the female genital mucosa is essential for understanding the immunologic effects of HIV vaccines and microbicides at the site of HIV exposure. However, the best female genital tract sampling technique is unclear.

Methods and Findings

We enrolled women from four sites in Africa and the US to compare three genital leukocyte sampling methods: cervicovaginal lavages (CVL), endocervical cytobrushes, and ectocervical biopsies. Absolute yields of mononuclear leukocyte subpopulations were determined by flow cytometric bead-based cell counting. Of the non-invasive sampling types, two combined sequential cytobrushes yielded significantly more viable mononuclear leukocytes than a CVL (p<0.0001). In a subsequent comparison, two cytobrushes yielded as many leukocytes (∼10,000) as one biopsy, with macrophages/monocytes being more prominent in cytobrushes and T lymphocytes in biopsies. Sample yields were consistent between sites. In a subgroup analysis, we observed significant reproducibility between replicate same-day biopsies (r = 0.89, p = 0.0123). Visible red blood cells in cytobrushes increased leukocyte yields more than three-fold (p = 0.0078), but did not change their subpopulation profile, indicating that these leukocytes were still largely derived from the mucosa and not peripheral blood. We also confirmed that many CD4⁺ T cells in the female genital tract express the α4β7 integrin, an HIV envelope-binding mucosal homing receptor.

Conclusions

CVL sampling recovered the lowest number of viable mononuclear leukocytes. Two cervical cytobrushes yielded comparable total numbers of viable leukocytes to one biopsy, but cytobrushes and biopsies were biased toward macrophages and T lymphocytes, respectively. Our study also established the feasibility of obtaining consistent flow cytometric analyses of isolated genital cells from four study sites in the US and Africa. These data represent an important step towards implementing mucosal cell sampling in international clinical trials of HIV prevention.     

Improved Flow Cytometric Analysis of the Budding Yeast Cell Cycle

The budding yeast, Saccharomyces cerevisiae has been a remarkably useful model system for the study of eukaryotic cell cycle regulation. Flow cytometric analysis of DNA content in budding yeast has become a standard tool for the analysis of cell cycle progression. However, popular protocols utilizing the DNA binding dye, propidium iodide, suffer from a number of drawbacks that confound accurate analysis by flow cytometry. Here we show the utility of the DNA binding dye, SYTOX Green, in the cell cycle analysis of yeast. Samples analyzed using SYTOX Green exhibited better coefficients of variation, improved linearity between DNA content and fluorescence, and decreased peak drift associated with changes in dye concentration, growth conditions or cell size.

Key Words:

Flow cytometry, Cell cycle, Saccharomyces cerevisiae, SYTOX Green, Propidium iodide     

Ultra-Fast and Optimized Method for the Preparation of Rodent Testicular Cells for Flow Cytometric Analysis

Homogeneity of cell populations is a prerequisite for the analysis of biochemical and molecular events during male gamete differentiation. Given the complex organization of the mammalian testicular tissue, various methods have been used to obtain enriched or purified cell populations, including flow cell sorting. Current protocols are usually time-consuming and may imply loss of short-lived RNAs, which is undesirable for expression profiling. We describe an optimized method to speed up the preparation of suitable testicular cell suspensions for cytometric analysis of different spermatogenic stages from rodents. The procedure takes only 15 min including testis dissection, tissue cutting, and processing through the Medimachine System (Becton Dickinson). This method could be a substitute for the more tedious and time-consuming cell preparation techniques currently in use.     

Analysis of Longitudinal Clinical Trials with Missing Data Using Multiple Imputation in Conjunction with Robust Regression

Summary In a typical randomized clinical trial, a continuous variable of interest (e.g., bone density) is measured at baseline and fixed postbaseline time points. The resulting longitudinal data, often incomplete due to dropouts and other reasons, are commonly analyzed using parametric likelihood‐based methods that assume multivariate normality of the response vector. If the normality assumption is deemed untenable, then semiparametric methods such as (weighted) generalized estimating equations are considered. We propose an alternate approach in which the missing data problem is tackled using multiple imputation, and each imputed dataset is analyzed using robust regression (M‐estimation; Huber, 1973 , Annals of Statistics 1, 799–821.) to protect against potential non‐normality/outliers in the original or imputed dataset. The robust analysis results from each imputed dataset are combined for overall estimation and inference using either the simple Rubin (1987 , Multiple Imputation for Nonresponse in Surveys, New York: Wiley) method, or the more complex but potentially more accurate Robins and Wang (2000 , Biometrika 87, 113–124.) method. We use simulations to show that our proposed approach performs at least as well as the standard methods under normality, but is notably better under both elliptically symmetric and asymmetric non‐normal distributions. A clinical trial example is used for illustration.     

Isolation and Flow Cytometric Analysis of Immune Cells from the Ischemic Mouse Brain

Ischemic stroke initiates a robust inflammatory response that starts in the intravascular compartment and involves rapid activation of brain resident cells. A key mechanism of this inflammatory response is the migration of circulating immune cells to the ischemic brain facilitated by chemokine release and increased endothelial adhesion molecule expression. Brain-invading leukocytes are well-known contributing to early-stage secondary ischemic injury, but their significance for the termination of inflammation and later brain repair has only recently been noticed.Here, a simple protocol for the efficient isolation of immune cells from the ischemic mouse brain is provided. After transcardial perfusion, brain hemispheres are dissected and mechanically dissociated. Enzymatic digestion with Liberase is followed by density gradient (such as Percoll) centrifugation to remove myelin and cell debris. One major advantage of this protocol is the single-layer density gradient procedure which does not require time-consuming preparation of gradients and can be reliably performed. The approach yields highly reproducible cell counts per brain hemisphere and allows for measuring several flow cytometry panels in one biological replicate. Phenotypic characterization and quantification of brain-invading leukocytes after experimental stroke may contribute to a better understanding of their multifaceted roles in ischemic injury and repair.     

Electronic Data Processing System for the Clinical Microbiology Laboratory

Owing to the increased volume of laboratory services and the shortage of skilled medical microbiologists who presently spend up to 30% of their time in clerical matters, pragmatic applications of electronic sorting techniques and computers should be considered to alleviate this problem. Moreover, surveillance of the hospital community, with particular reference to changing patterns of microbial resistance and the distribution of potentially infectious pathogens, requires detailed information which can be readily supplied by electronic sorting analysis. Mark-sense and prescored Port-A-Punch IBM cards were used to: (i) analyze antibiotic susceptibility data; (ii) tabulate total test loads according to conditions set down by the American Society for Clinical Pathologists; and (iii) to prepare a bacteriological report on the surveillance of hospital infections. After proper sorting and analysis, the cards also serve as a convenient reference file in the laboratory for pertinent information recorded by either blackening the appropriate areas (mark-sense style) or pushing out the preperforated rectangular holes with a simple inexpensive board and stylus (Port-A-Punch). No one scheme can fulfill the requirements of all laboratories or purposes, but ideas contained herein might serve as starting points for the design of similar systems in other laboratories.     

猴艾滋病急性期肠粘膜相关淋巴组织NK细胞表型及功能

目的研究猴艾滋病毒感染急性期恒河猴肠道相关淋巴组织（mucosal associated lymphoid tissues,MALTs）NK细胞亚群和功能变化。方法 SIV静脉感染恒河猴后,定期进行动物感染指标测定,并在感染后不同时间点取肠组织,分离派氏淋巴结单个核细胞（peyer＇s patch mononuclear cells,PPMC）和粘膜固有层单个核细胞（lamina propria mononuclear cells,LPMC）,进行T细胞和NK细胞表面抗体染色,流式分析。结果 SIV感染急性期MALTs CD56CD16＋NK细胞亚群比例增幅明显,同时细胞毒性功能增强;CD56-CD16-NK细胞亚群数量减少,功能无明显变化;CD56＋CD16＋和CD56＋CD16-NK细胞数量比例略有增加趋势,但免疫调节功能显著降低。结论SIV感染急性期恒河猴肠道MALTs中NK细胞脱颗粒作用增强,表型功能呈现出较强可塑性。该研究对探索艾滋病粘膜免疫机理、抗病毒治疗及药物研发具有参考意义。     

A Likelihood-Based Approach for the Analysis of Longitudinal Clinical Trials with Return-to-Baseline Imputation

Statistics in Biosciences - Discontinuation of assigned therapy in longitudinal clinical trials is often inevitable due to various reasons such as intolerability or lack of efficacy. When the...     

Utilities of the P‐value Distribution Associated with Effect Size in Clinical Trials

The P‐value, which is widely used for assessing statistical evidence in randomized comparative clinical trials, is a function of the observed effect size of the experimental treatment relative to the control treatment. The relationship of the P‐value with the observed effect size at study completion and the effect size anticipated at the design stage has potential usefulness in providing guidance for planning and interpretation of a clinical trial. The post‐trial power associated with a statistically significant P‐value from a completed study is also a random variable and its use may assist in planning a follow‐up trial to confirm the statistically significant findings in an initial study. A measure of robustness is explored to quantify the degree of sensitivity of the observed P‐value to potential bias that may be contained in the observed effect size.     

Bacteria Associated with the Surface and Gut of Marine Copepods

Little is known about the nature of bacteria associated with the surface and gut of marine copepods, either in laboratory-reared animals or in the natural environment. Nor is it known whether such animals possess a gut flora. The present report deals with studies of microorganisms isolated from healthy, laboratory-reared copepods of the species Acartia tonsa Dana, from several species of wild copepods collected from a marine or estuarine environment, and from laboratory dishes containing moribund copepods. Evidence for a unique gut flora in laboratory-reared animals is presented; the predominant bacteria were represented by the genus Vibrio. Other organisms such as Pseudomonas and Cytophaga were found less abundantly associated with the copepods and not specifically associated with the gut.     

Processing of Primary Brain Tumor Tissue for Stem Cell Assays and Flow Sorting

Brain tumors are typically comprised of morphologically diverse cells that express a variety of neural lineage markers. Only a relatively small fraction of cells in the tumor with stem cell properties, termed brain tumor initiating cells (BTICs), possess an ability to differentiate along multiple lineages, self-renew, and initiate tumors in vivo. We applied culture conditions originally used for normal neural stem cells (NSCs) to a variety of human brain tumors and found that this culture method specifically selects for stem-like populations. Serum-free medium (NSC) allows for the maintenance of an undifferentiated stem cell state, and the addition of bFGF and EGF allows for the proliferation of multi-potent, self-renewing, and expandable tumorspheres.To further characterize each tumor''s BTIC population, we evaluate cell surface markers by flow cytometry. We may also sort populations of interest for more specific characterization. Self-renewal assays are performed on single BTICs sorted into 96 well plates; the formation of tumorspheres following incubation at 37 °C indicates the presence of a stem or progenitor cell. Multiple cell numbers of a particular population can also be sorted in different wells for limiting dilution analysis, to analyze self-renewal capacity. We can also study differential gene expression within a particular cell population by using single cell RT-PCR.The following protocols describe our procedures for the dissociation and culturing of primary human samples to enrich for BTIC populations, as well as the dissociation of tumorspheres. Also included are protocols for staining for flow cytometry analysis or sorting, self-renewal assays, and single cell RT-PCR.     

Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota

Soil-transmitted helminths colonize more than 1.5 billion people worldwide, yet little is known about how they interact with bacterial communities in the gut microbiota. Differences in the gut microbiota between individuals living in developed and developing countries may be partly due to the presence of helminths, since they predominantly infect individuals from developing countries, such as the indigenous communities in Malaysia we examine in this work. We compared the composition and diversity of bacterial communities from the fecal microbiota of 51 people from two villages in Malaysia, of which 36 (70.6%) were infected by helminths. The 16S rRNA V4 region was sequenced at an average of nineteen thousand sequences per samples. Helminth-colonized individuals had greater species richness and number of observed OTUs with enrichment of Paraprevotellaceae, especially with Trichuris infection. We developed a new approach of combining centered log-ratio (clr) transformation for OTU relative abundances with sparse Partial Least Squares Discriminant Analysis (sPLS-DA) to enable more robust predictions of OTU interrelationships. These results suggest that helminths may have an impact on the diversity, bacterial community structure and function of the gut microbiota.