Viability of heterotrophic bacteria in the Bay of Marseilles

Marine microorganism activities are commonly assessed by bulk methods and assigned to the total cell count. The presence in significant amounts of ghost, dead, and damaged cells makes such as assignment a non-correct one. A Nucleic Acid Double Staining protocol (NADS) of fresh water bacteria (Barbesti et al., Cytometry 40 (2000) 214-218) has been adapted to resolve viable, damaged and dead cells in marine environments (Grégori et al., Appl. Environ. Microbiol. 67 (2001) 4662-4670). The present reports the first in situ application of this approach, conducted in the Bay of Marseilles in winter and spring periods at two sites with contrasted features.     

Head injuries in childhood: a 2-year survey.

A retrospective study was conducted of the 880 children with head injuries consecutively admitted to the Children''s Hospital of Eastern Ontario in Ottawa from July 1976 to June 1978. It confirmed a boy:girl ratio of about 2:1, with a peak of 3.5:1 around 7 years of age. The largest number of head injuries was in children under 1 year of age. Injuries were most common in summer and spring, and most were caused by falls. The most common place for head injuries was in the home, but the single most common cause of injuries was bicycle accidents, which were responsible for 12% of all the head injuries. Skull fractures were found in 30% of all the patients. Of the 34 patients with severe head injuries 8 (24%) died, 9 (26%) had a moderate residual disability and 17 (50%) made a good recovery. There were no other deaths, so the mortality for the entire group of 880 patients was 0.9%.     

Assessment of the dynamics of the physiological states of Lactococcus lactis ssp. cremoris SK11 during growth by flow cytometry

AIMS: The aim of this study was to improve knowledge about the dynamics of the physiological states of Lactococcus lactis ssp. cremoris SK11, a chain-forming bacterium, during growth, and to evaluate whether flow cytometry (FCM) combined with fluorescent probes can assess these different physiological states. METHODS AND RESULTS: Cellular viability was assessed using double labelling with carboxyfluorescein diacetate and propidium iodide. FCM makes it possible to discriminate between three cell populations: viable cells, dead cells and cells in an intermediate physiological state. During exponential and stationary phases, the cells in the intermediate physiological state were culturable, whereas this population was no longer culturable at the end of the stationary phase. CONCLUSIONS, AND IMPACT OF THE STUDY: We introduced a new parameter, the ratio of the means of the fluorescence cytometric index to discriminate between viable culturable and viable nonculturable cells. Finally, this work confirms the relevance of FCM combined with two fluorescent stains to evaluate the physiological states of L. lactis SK11 cells during their growth and to distinguish viable cells from viable but not culturable cells.     

Standardization of a flow cytometry SARS-CoV-2 serologic test

The SARS-CoV-2 virus is the causing agent of the coronavirus disease 2019 (COVID-19) pandemic responsible for millions of deaths worldwide. The development of the humoral response to the virus has been the subject of intensive research. A flow cytometry-based assay using native full-length SARS-CoV-2 Spike protein expressed in 293 T cells was recently proposed as a complementary seropositivity assay. The aim of our study was to further develop the flow cytometry assay and to standardize its parameters for reliable inter-laboratory use. We have optimized the protocol, established the Receiving Operating Characteristic (ROC) curve and tested reproducibility using pre-COVID and convalescent, SARS-CoV-2 individual plasma samples. The flow-based assay was simplified and standardized by cultivating the 293 T cells in suspension and expressing results in Mean Equivalent Soluble Fluorochrome (MESF) using an internal antibody positive control. The ROC curve was determined with an area under the curve (AUC) of 0.996 and the assay specificity and sensitivity were established at 100% and 97.7% respectively. Reproducibility was good as determined on multiple cytometers, on different days, and with data acquisition as far as 72 h post-staining. The standardized assay could be used as a high throughput confirmatory assay in flow cytometry laboratories involved in serological testing.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10616-021-00511-1.     

模拟水流扰动对香溪河库湾浮游病毒-宿主动态的影响

【背景】浮游病毒是淡水生态系统的重要组成部分,在调节浮游细菌和藻类群落结构及调控系统物质循环过程中起着重要的作用。水库具有不同于湖泊的水动力过程,产生的扰动可能影响浮游病毒的调控功能。【目的】研究水力扰动对浮游病毒-宿主动态的影响,为阐释水库生境下浮游病毒生态功能提供理论依据。【方法】以香溪河库湾原水为材料,模拟不同流速扰动对病毒-宿主动态的影响;通过病毒丰度、宿主丰度、宿主裂解率、宿主溶源诱导率等参数的变化反映这种动态变化过程,并分析其与环境因子间的关系。【结果】0.05 m/s和0.10 m/s的流速扰动强度对浮游植物和浮游细菌生长有显著促进作用,但扰动对浮游病毒丰度的影响不显著;扰动能促进病毒介导的浮游植物和细菌裂解率上升,而且0.05 m/s扰动强度的促进作用大于0.10 m/s;同时,扰动显著降低了浮游植物溶源诱导率,但引起浮游细菌溶源诱导率的显著上升(P<0.05)。【结论】模拟扰动对浮游病毒-宿主动态过程产生了显著的影响,表明水库浮游病毒维持种群延续的生态策略可能与湖泊浮游病毒存在差异。     

Population dynamics of a continuous fermentation of recombinant Saccharomyces cerevisiae using flow cytometry

The plasmid instability of genetically modified microorganisms during prolonged bioreactor operations is one of the major problems to be overcome in the production of recombinant proteins. The use of flow cytometry to monitor a fermentation process with recombinant cells in a CSTR is reported here. This technique has been applied to determine the fraction of plasmid-bearing cells (P+) of a recombinant Saccharomyces cerevisiae strain harboring the EXG1 gene in a continuous stirred tank bioreactor with a working volume of 2 L. The different levels in the expression of the EXG1 gene, which encodes the enzyme exo-beta-glucanase, were used to determine the P+ fraction. Other parameters such as viability, cellular protein, cell size and structure were also monitored using flow cytometry. This technique has two main advantages over the conventional method of determining the P+ fraction (plating in selective and non-selective solid media): (a) it takes a very short period of time to obtain a measurement that provides multiple parametric information; and (b) it is more representative of the bioreactor cell population since it can analyze thousands of cells in the same sample. A continuous operation (432 h) with the recombinant strain in a CSTR was carried out to test the application of this technique. Measurements of cellular exo-beta-glucanase activity and cellular protein content closely correlates to the measured fraction of plasmid-containing cells in the population. Moreover, the standard deviation of the fraction of P+ cells determined using this technique was very low (about 2%). Recombinant protein production also increased the size of the yeast cells, whereas the recombinant cells also had a more complex internal structure than the non-recombinant host strain.     

Resolution of viable and membrane-compromised bacteria in freshwater and marine waters based on analytical flow cytometry and nucleic acid double staining

The membrane integrity of a cell is a well-accepted criterion for characterizing viable (active or inactive) cells and distinguishing them from damaged and membrane-compromised cells. This information is of major importance in studies of the function of microbial assemblages in natural environments, in order to assign bulk activities measured by various methods to the very active cells that are effectively responsible for the observations. To achieve this task for bacteria in freshwater and marine waters, we propose a nucleic acid double-staining assay based on analytical flow cytometry, which allows us to distinguish viable from damaged and membrane-compromised bacteria and to sort out noise and detritus. This method is derived from the work of S. Barbesti et al. (Cytometry 40:214-218, 2000) which was conducted on cultured bacteria. The principle of this approach is to use simultaneously a permeant (SYBR Green; Molecular Probes) and an impermeant (propidium iodide) probe and to take advantage of the energy transfer which occurs between them when both probes are staining nucleic acids. A full quenching of the permeant probe fluorescence by the impermeant probe will point to cells with a compromised membrane, a partial quenching will indicate cells with a slightly damaged membrane, and a lack of quenching will characterize intact membrane cells identified as viable. In the present study, this approach has been adapted to bacteria in freshwater and marine waters of the Mediterranean region. It is fast and easy to use and shows that a large fraction of bacteria with low DNA content can be composed of viable cells. Admittedly, limitations stem from the unknown behavior of unidentified species present in natural environments which may depart from the established permeability properties with respect to the fluorescing dyes.     

DNA flow cytometry of isolated keratinized epithelia: a methodological study based on ultrasonic tissue disaggregation.

Ultrasonication of keratinized, stratified, squamous epithelium, which had been separated from underlying tissue by means of acetic acid, resulted in disaggregation of all cellular layers in the epithelium, giving a suspension of single nuclei with mitoses preserved. This suspension was treated with RNAse and ethidium bromide for analysis by flow cytometry. From the resulting DNA histogram the G1, S and G2 + M fractions were estimated using the computer program of Fried (1976). Treatment with dithiothreitol before sonication increased the yield of nuclei in suspension and decreased the amount of debris and clumps, thereby suppressing overestimation of small S fractions. This method of preparation prior to DNA flow cytometry was useful for the study of the hamster cheek pouch epithelium and of normal and pathological human epidermis.     

基于流式细胞术的海菜花属植物基因组大小测定

利用改良的裂解液P1,以中国古代莲(Nelumbo nucifera Gaertn.Fruct.et Semin)为外标,采用流式细胞术(FCM)对海菜花属(Ottelia Pers.)6个代表性物种及3个存疑类群的基因组大小(C值)进行测定,并对海菜花属系统发育关系进行评估。结果显示:所测定的材料中,水菜花(Ottelia cordata(Wall.)Dandy)C值最小(6.759 pg),灌阳水车前(O.guanyangensis Z.Z.Li,S.Wu&Q.F.Wang)C值最大(12.929 pg);对基因组大小与该属系统发育树进行比较分析,结果发现该属植物基因组大小与系统发育关系具有一致性;对海菜花属3个存疑类群进行分子系统学研究,结果发现存疑类群与嵩明海菜花(Ottelia acuminata var.songmingensis Z.T.Jiang,H.Li&Z.L.Dao)及灌阳水车前的关系最近,而与水菜花的关系较远,这与基因组大小变异相一致。根据基因组大小进一步推测3个存疑类群很可能为二倍体。本研究结果可为海菜花属植物的系统学研究提供新资料,同时为该属植物基因组学研究提供基础数据。     

Spectra of cells in flow cytometry using a vidicon detector.

A TV type vidicon detector was interfaced to a flow cytometer (FCM) to obtain spectra of fluorophores in cells during flow. The normal operations of the FCM are undisturbed. A spectrograph spreads 320 nm of the fluorophore fluorescence emission across the 500 channels of the detector. Spectra of fluorescamine (a surface labeling agent) and of propidium iodide (a nuclear stain) were obtained from Balb 3T3 cells, and the chlorophyll and phycobilin peaks were resolved from flowing blue-green algae in the FCM. Under typical flow conditions, operation of the vidicon in the continuous mode gives for these fluorophores a S/N of several hundred to one in approximately 3 sec. The vidicon was also gated to obtain spectra of single cells and of cells in selected portions of the cell cycle. For example, the spectrum of fluorescamine was obtained from cells in the G1 phase of the growth cycle by using as a gate trigger the FCM discriminator output derived from the propidium iodide signal.     

Use of a high affinity DNA ligand in flow cytometry.

To investigate the feasibility of using oligonucleotides in flow cytometry we describe a model system consisting of human neutrophil elastase (HNE) coated on 3.3 micro beads and a high affinity DNA ligand for HNE isolated by in vitro selection (SELEX). In this system the fluoresceinated DNA ligand was equally effective as an anti- HNE antibody in detecting HNE on beads. The location on and the chemistry of attachment of fluorescein to the DNA ligand is critical for the sensitivity of detection. DNA constructs in which fluorescein was conjugated via an ethylene glycol tether to either the 5'-end or near the 3'-end gave much higher signals than did probes with fluorescein directly conjugated to either end. Second-step staining with strepavidin-conjugated phycoerythrin was accomplished using a biotinylated DNA ligand in the initial staining of HNE beads. These data suggest that instead of, or in addition to, antibodies high affinity oligonucleotide probes can be useful in diagnostic applications based on flow cytometry.     

Evaluation of a green laser pointer for flow cytometry.

Flow cytometers typically incorporate expensive lasers with high-quality (TEM00) output beam structure and very stable output power, significantly increasing system cost and power requirements. Red diode lasers minimize power consumption and cost, but limit fluorophore selection. Low-cost DPSS laser pointer modules could possibly offer increased wavelength selection but presumed emission instability has limited their use. A $160 DPSS 532 nm laser pointer module was first evaluated for noise characteristics and then used as the excitation light source in a custom-built flow cytometer for the analysis of fluorescent calibration and alignment microspheres. Eight of ten modules tested were very quiet (RMS noise < or = 0.6% between 0 and 5 MHz). With a quiet laser pointer module as the light source in a slow-flow system, fluorescence measurements from alignment microspheres produced CVs of about 3.3%. Furthermore, the use of extended transit times and < or =1 mW of laser power produced both baseline resolution of all 8 peaks in a set of Rainbow microspheres, and a detection limit of <20 phycoerythrin molecules per particle. Data collected with the transit time reduced to 25 micros (in the same instrument but at 2.4 mW laser output) demonstrated a detection limit of approximately 75 phycoerythrin molecules and CVs of about 2.7%. The performance, cost, size, and power consumption of the tested laser pointer module suggests that it may be suitable for use in conventional flow cytometry, particularly if it were coupled with cytometers that support extended transit times.     

Visualization of multidimensional spectra in flow cytometry.

Flow data from a cell sorter have been processed by hardwired circuits which include amplification, discrimination, coincidence requirements, peak sensing and holding, A-D conversion, and a computerized pulse height analysis with storage of the spectra obtained. Two dimensional spectra can be stored directly in memory, on tape and disk. Three and four parametric cellular events can be recorded on line during the flow measurement in a sequential mode on tape for subsequent recall. Simple processing of these data can be performed for displaying of two dimensional projections from these multidimensional spaces based on threshold conditions for the remaining parameters. Interfaced transmission of the stored data to a large scale computer enables more sophisticated data analysis. Data reduction by means of a multidimensional probability analysis has been carried out in order to transfer the spectra to a computerized picture system for display. This system creates perspective two-dimensional images from a three-dimensional data space. Frequency can be converted into grey levels. Hard copy in color (color as the third dimension and color intensity as frequency) simplifies the visualization of multiparametric flow data sets.     

An analytical system based on a compact flow cytometer for DNA fragment sizing and single-molecule detection.

BACKGROUND: Previous reports have demonstrated accurate DNA fragment sizing of linear DNA fragments, from 564 to approximately 4 x 10(5) bp, in a flow system. B-phycoerythrin (B-PE), commonly used in conventional cytometric applications that require high-sensitivity, was the first fluorophore detected in flow at the single-molecule level. METHODS: Dilute solutions of stained DNA fragments or B-PE were analyzed in a simplified, compact flow system, with enhanced performance and lower cost, utilizing a solid-state laser and a single-photon sensing avalanche photodiode detector (SSAPD). Extensive data processing and display software, developed specifically for the photon-counting data stream, extracts correlated height, width, and area features from bursts of photons due to discrete molecules passing through the sensing region in the flow channel. RESULTS: DNA fragment sizing in flow has now been demonstrated for SYTOX-orange-stained fragments ranging in size over 3.4 orders of magnitude, from 125 to 5 x 10(5) bp. For Lambda bacteriophage DNA (lambda DNA; 48.5 kbp) a CV of 1.2 % has been achieved. Analysis of a femtomolar B-PE solution demonstrates that the bursts of photons from individual molecules can be baseline-resolved with 0.5 mW of laser power at a signal to noise ratio (SNR) of approximately 30, with approximately 100 photons detected from each molecule. CONCLUSIONS: A compact, low-power, high-sensitivity system detects DNA fragments as small as 125 bp or individual B-PE molecules in a flowing liquid stream. Demonstrated linearity, sensitivity, and resolution indicate that <1.0 mW of laser power is optimal, permitting further miniaturization of the system and additional cost reduction. Comprehensive analytical software exploits the standard cytometric paradigm of multiple 2D graphs and gating to extract features from classes of individually analyzed biomolecules. This complete system is thus poised to engage high-sensitivity applications not amenable to conventional flow cytometric instrumentation.     

Phytoplankton seasonal dynamics in a Mediterranean coastal lagoon: emphasis on the picoeukaryote community

The dynamics of the phytoplankton community were investigatedin a marine coastal lagoon (Thau, NW Mediterranean) from February1999 to January 2000. Dilution experiments, chlorophyll a (Chla) size-fractionation and primary production measurements wereconducted monthly. Maximum growth and microzooplankton grazingrates were estimated from Chl a biomass fractions to separatepico- from nano- and microphytoplankton and by flow cytometryto distinguish between picoeukaryotes and picocyanobacteria.In spring, the phytoplankton community was dominated by Chaetocerossp. and Skeletonema costatum, which represented most of biomass(B) and primary production (P). Nano- and microphytoplanktongrowth was controlled by nutrient availability and exceededlosses due to microzooplankton grazing (g). Picoeukaryote andcyanobacteria growth was positively correlated with water temperatureand/or irradiance, reaching maximum values in the summer (2.38and 1.44 day^–1 for picoeukaryotes and cyanobacteria, respectively).Picophytoplankton accounted for 57% of the biomass-specificprimary productivity (P/B). Picophytoplankton was strongly controlledby protist grazers (g = 0.09–1.66 day^–1 for picoeukaryotes,g = 0.25–1.17 day^–1 for cyanobacteria), and microzooplanktonconsumption removed 71% of the daily picoplanktonic growth.Picoeukaryotes, which numerically dominate the picoplanktoncommunity, are an important source of organic carbon for theprotistan community and contribute to the carbon flow to highertrophic levels.     

Nitrogen dynamics in lower Narragansett Bay. II. Phytoplankton uptake, depletion rates of nitrogenous nutrient pools, and estimates of ecosystem remineralization

Phytoplankton nitrogen demand in lower Narragansett Bay, RhodeIsland, measured during the winter-spring of 1977–78 andsummers of 1978 and 1979, is compared with estimates of zooplanktonand the benthic nitrogen remineralization drawn from the resultsof ekperimental field studies. Measured uptake rates would generallylead to the depletion of available nitrogenous nutrient stockswithin hours, and usually exceeded estimates of benthic pluszooplankton remineralization. Additional estimates of nitrogeninputs from sewage and riverine sources appear insufficientto make up the difference. The discrepancy lends support tothe paradigm that water column remineralization by microheterotrophsmay supply much, if not most, of the nitrogen needs of coastalphytoplankton.     

Identification of a small molecule yeast TORC1 inhibitor with a multiplex screen based on flow cytometry

TOR (target of rapamycin) is a serine/threonine kinase, evolutionarily conserved from yeast to human, which functions as a fundamental controller of cell growth. The moderate clinical benefit of rapamycin in mTOR-based therapy of many cancers favors the development of new TOR inhibitors. Here we report a high-throughput flow cytometry multiplexed screen using five GFP-tagged yeast clones that represent the readouts of four branches of the TORC1 signaling pathway in budding yeast. Each GFP-tagged clone was differentially color-coded, and the GFP signal of each clone was measured simultaneously by flow cytometry, which allows rapid prioritization of compounds that likely act through direct modulation of TORC1 or proximal signaling components. A total of 255 compounds were confirmed in dose-response analysis to alter GFP expression in one or more clones. To validate the concept of the high-throughput screen, we have characterized CID 3528206, a small molecule most likely to act on TORC1 as it alters GFP expression in all five GFP clones in a manner analogous to that of rapamycin. We have shown that CID 3528206 inhibited yeast cell growth and that CID 3528206 inhibited TORC1 activity both in vitro and in vivo with EC(50)'s of 150 nM and 3.9 μM, respectively. The results of microarray analysis and yeast GFP collection screen further support the notion that CID 3528206 and rapamycin modulate similar cellular pathways. Together, these results indicate that the HTS has identified a potentially useful small molecule for further development of TOR inhibitors.     

Three probe flow cytometry of a human foam-cell forming macrophage.

A human cell line THP-1 was differentiated into macrophages expressing the scavenger receptor for uptake of modified lipoproteins. The cells were exposed to native low-density lipoprotein (n-LDL), acetylated-low-density lipoprotein (Ac-LDL), oxidised-LDL, or 25-OH cholesterol, leading to the accumulation of cholesteryl esters within the cells. Harvested macrophages were studied using three separate probes: 1) 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (diI)-labelled LDL to study lipoprotein uptake; 2) the lipophilic fluorescent dye Nile Red to study cholesteryl ester accumulation within the cells; and 3) the polyene antibiotic Filipin III to study free cholesterol homeostasis. Cells were analysed using fluorescence flow cytometry and the three signals analysed separately. THP-1 macrophages incubated with diI-labelled modified lipoproteins produced a concentration dependent increase in the fluorescence emissions, consistent with accumulation of the labelled particles. Macrophages exposed to unlabelled modified LDLs were demonstrated, by staining with Nile Red, to accumulate cholesteryl esters within their cytoplasm and to alter their cholesterol content as judged by staining with Filipin. The foam-cell forming macrophage and its response to modified lipoproteins is considered a key step in the development of atherosclerosis. The use of these three probes during the formation of foam-cells in vitro offers a way of studying their behaviour at the single cell level.