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Murine hematopoietic blast colony-forming cells (BL-CFCs) are able to generate up to 30,000 progeny blast cells within 10 d in agar cultures. Contained in these populations are large numbers of lineage-committed progenitor cells in the granulocytic and macrophage lineages. Sequential analyses of blast colonies revealed that self-generation of BL-CFCs occurs but is surprisingly late in clonal expansion, as is the emergence of progenitor cells committed to megakaryocytic and eosinophil lineages. Self-generating BL-CFCs were highly enriched in [lineage.sup.-] [Kit.sup.+] [Sca1.sup.+] [CD34.sup.-] [Flt3R.sup.-] populations, and colonies generated by such cells contained colony-forming units--spleen and formed erythroid and lymphoid progeny in vivo. The data suggest the existence of a hierarchical structure in BL-CFC populations with at least a subset being cells assayable as colony-forming units-spleen. Because BL-CFCs can self-generate and are able to generate lymphoid and myeloid populations, BL-CFCs appear to be ideal cells in which to analyze the processes of self-generation and lineage commitment in clonal in vitro cultures. colony-forming units-spleen | megakaryocytes | eosinophils www.pnas.org/cgi/doi/ 10.1073/pnas.1011881107

Sensorineural deafness and balance dysfunction are common impairments in humans frequently caused by defects in the sensory epithelium of the inner ear, composed of hair cells and supporting cells. Lineage studies have shown that hair Cells and supporting cells arise from a common progenitor, but how these progenitors are generated remains unknown. Although various molecules have been implicated in the development of the sensory progenitors, none has been shown to be required for the specification of these progenitors in the mammalian inner ear. Here, using both loss-of-function and gain-of-function approaches, we show that Jagged1 (JAG1)-mediated Notch signaling is both required and sufficient for the generation of the sensory progenitors. Specifically, we find that loss of JAG1 signaling leads to smaller sensory progenitor regions without initial effects on proliferation or cell death, indicating that JAG1 is involved in initial specification events. To further test whether Notch signaling is involved in specification of the sensory progenitors, we transiently expressed an activated form of the Notch1 receptor (NICD) using a combined Tet-On/Cre induction system in the mouse. NICD expression resulted in ectopic hair cells and supporting cells in the nonsensory regions of the cochlea and vestibule. These data indicate that Notch specifies sensory progenitors in the inner ear, and that induction of Notch may be important for regenerating or replacing hair cells and supporting cells in the mammalian inner ear. development | JAG1 | SOX2 | Tet-On | NICD doi/ 10.1073/pnas.1003089107

The number of reports per year on single-molecule imaging experiments has grown roughly exponentially since the first successful efforts to optically detect a single molecule were completed over two decades ago. Single-molecule spectroscopy has developed into a field that includes a wealth of experiments at room temperature and inside living cells. The fast growth of single-molecule biophysics has resulted from its benefits in probing heterogeneous populations, one molecule at a time, as well as from advances in microscopes and detectors. This Perspective summarizes the field of live-cell imaging of single biomolecules. 10.1021/ac9024889

This paper describes a rapid and sensitive strategy for the absolute and simultaneous quantification of specific pathogenic strain and total bacterial cells in a mixture. A laboratory-built compact, high-sensitivity, dual channel flow cytometer (HSDCFCM) was modified to enable dual fluorescence detection. A bacterial cell mixture comprising heat-killed pathogenic Escherichia coli E. coli O157: H7 and harmless E. coli DH5[alpha] was used as a model system. Pathogenic E. coli O157:H7 cells were selectively labeled by red fluorescent probe via antibody antigen interaction, and all bacterial cells were stained with membrane-permeable nucleic acid dye that fluoresces green. When each individual bacterium passes through the interrogating laser beam, E. coli O157:H7 emits both red and green fluorescence, while E. coli DH5[alpha] exhibits only green fluorescence. Because the fluorescence burst generated from each individual bacterial cell was easily distinguished from the background, accurate enumeration and consequently absolute quantification were achieved for both pathogenic and total bacterial cells. By using this strategy, accurate counting of bacteria at a density above 1.0 x [10.sup.5] cells/mL can be accomplished with 1 min of data acquisition time after fluorescent staining. Excellent correlation between the concentrations measured by the HSDCFCM and the conventional platecounting method were obtained for pure-cultured E. coli O157:H7 ([R.sup.2] = 0.9993) and E. coli DH5[alpha] ([R.sup.2] = 0.9998). Bacterial cell mixtures with varying proportions of E. coli O157:H7 and E. coli DH5[alpha] were measured with good ratio correspondence. We applied the established approach to detecting artificially contaminated drinking water samples; E. coli O157:H7 of 1.0 x [10.sup.2] cells/mL were accurately quantified upon sample enrichment. It is believed that the proposed method will find wide applications in many fields demanding bacterial identification and quantification. 10.1021/ac902524a

Label-free chemical characterization of single cells is an important aim for biomedical research. Standard Raman spectroscopy provides intrinsic biochemical markers for noninvasive analysis of biological samples but is often hindered by the presence of fluorescence background. In this paper, we present an innovative modulated Raman spectroscopy technique to tilter out the Raman spectra from the fluorescence background. The method is based on the principle that the fluorescence background does not change whereas the Raman scattering is shifted by the periodical modulation of the laser wavelength. Exploiting this physical property and importantly the multichannel lock-in detection of the Raman signal, the modulation technique fulfills the requirements of an effective fluorescence subtraction method. Indeed, once the synchronization and calibration procedure is performed, minimal user intervention is required, making the method online and less time-consuming than the other fluorescent suppression methods. We analyze the modulated Raman signal and shifted excitation Raman difference spectroscopy (SERDS) signal of 2 pro-sized polystyrene beads suspended in a solution of fluorescent dye as a function of modulation rate. We show that the signal-to-noise ratio of the modulated Raman spectra at the highest modulation rate is 3 times higher than the SERDS one. To finally evaluate the real benefits of the modulated Raman spectroscopy, we apply our technique to Chinese hamster ovary ceils (CHO). Specifically, by analyzing separate spectra from the membrane, cytoplasm, and nucleus of CHO cells, we demonstrate the ability of this method to obtain localized sensitive chemical information from cells, away from the interfering fluorescence background. In particular, statistical analysis of the Raman data and classification using PCA (principal component analysis) indicate that our method allows us to distinguish between different cell locations with higher sensitivity and specificity, avoiding potential misinterpretation of the data obtained using standard background procedures. 10.1021/ac9026737

It is generally expected that the kinetics of reactions inside living cells differs from the situation in bulk solutions. Macromolecular crowding and specific binding interactions could change the diffusion properties and the availability of free molecules. Their impact on reaction kinetics in the relevant context of living cells is still elusive, mainly because the difficulty of capturing fast kinetics in vivo. This article shows spatially resolved measurements of DNA hybridization kinetics in single living cells. HeLa cells were transfected with a FRET-labeled dsDNA probe by lipofection. We characterized the hybridization reaction kinetics with a kinetic range of 10 [micro]s to 1 s by a combination of laser-driven temperature oscillations and stroboscopic fluorescence imaging. The time constant of the hybridization depended on DNA concentration within individual cells and between cells. A quantitative analysis of the concentration dependence revealed several-fold accelerated kinetics as compared with free solution for a 16-bp probe and decelerated kinetics for a 12-bp probe. We did not find significant effects of crowding agents on the hybridization kinetics in vitro. Our results suggest that the reaction rates in vivo are specifically modulated by binding interactions for the two probes, possibly triggered by their different lengths. In general, the presented imaging modality of temperature oscillation optical lock-in microscopy allows to probe biomolecular interactions in different cell compartments in living cells for systems biology. DNA | in vivo | molecular crowding | temperature oscillation | optical lock-in microscopy doi/10.1073/pnas.0901313106

Gene-transfected single HeLa cells were characterized using a scanning electrochemical/optical microscope (SECM/OM) system with shear-force-based probe-sample distance regulation to simultaneously capture electrochemical, fluorescent, and topographic images. The outer and inner states of single living cells were obtained as electrochemical and fluorescent signals, respectively, by using an optical fiber-nanoelectrode probe. A focused ion beam (FIB) was used to mill the optical aperture and the ring electrode at the probe apex (the inner and outer radii of the ring electrode were 37 and 112 nm, respectively). To apply an appropriate shear force between the probe tip and the living cell surface, we optimized the amplitude of oscillation of the tuning fork to which the probe was attached. Field-programmable gate arrays (FPGA) were adopted to drastically increase the feedback speed of the tip-sample distance regulation, shorten the scanning time for imaging, and enhance the accuracy and quality of the living cell images. In employing these improvements, we simultaneously measured the cellular expression activity of both secreted alkaline phosphatase outside and GFP inside by using the SECM/OM with shear force distance regulation. 10.1021/ac901796r

A microscopy system has been constructed that is capable of simultaneously acquiring both Raman spectra and angle-resolved elastic-scattering patterns in either epi- or transillumination modes with a 7 [micro]m spot size. The benefits and drawbacks of the epi- and transillumination modalities are discussed. Validation studies have been performed on single beads of a few micrometers in size, as well as on ensembles of submicrometer particles. In addition, transilluminated Raman and elastic-scattering spectra were obtained from single granulocytes and peripheral blood monocytes. Both the Raman- and the elastic-scattering channels show clear differences between the two types of immune cells. OCIS codes: 170.5660, 290.4020.

In temporal phase-shifting-based digital holographic microscopy, high-resolution phase contrast imaging requires optimized conditions for hologram recording and phase retrieval. To optimize the phase resolution, for the example of a variable three-step algorithm, a theoretical analysis on statistical errors, digitalization errors, uncorrelated errors, and errors due to a misaligned temporal phase shift is carried out. In a second step the theoretically predicted results are compared to the measured phase noise obtained from comparative experimental investigations with several coherent and partially coherent light sources. Finally, the applicability for noise reduction is demonstrated by quantitative phase contrast imaging of pancreas tumor cells. OCIS codes: 090.0090, 090.1995, 100.5070, 180.0180.

To precisely identify and screen target-specific protein--protein interactions at the endogenous level, here we introduce a novel quantitative proteomic method we have termed in vivo Profiling Endogenous Interactions with Knock-out (iPEIK). In our design, mouse embryonic fibroblasts (MEFs) derived from target gene knockout (KO) mice can be stable isotope-tagged and serve as a target-free background to 'light-up' the target protein-specific protein complex formed in the corresponding wild-type (WT) cells. In mass spectrometric analysis of the pairs of non-labeled versus heavy isotope-labeled peptide signals derived from WT versus KO cells, respectively, we then quantitatively measured the abundance differences of the proteins in the complex immunoprecipitated (IP) from the target-expressing WT versus target-absent KO cells, respectively. Those proteins detected with little or no presence in the cells of KO origin were determined as target-specific interacting partners. Further, dynamic interactors could be identified through different IP mixing schemes. Using iPEIK we identified multiple interacting partners both previously known and unknown to be associated with mitogen-activated protein kinase kinase kinase 2 (MEKK2). Because of the availability of a large library of knockout mice models with various target proteins of biological interests our method is generally applicable to screen any endogenous target-specific PPIs of physiological relevance.

Because of the ability to selectively reveal the objects of interest with subcellular resolution, fluorescence microscopy provides widespread applications from basic biological research to clinical diagnosis. However, challenges still remain in reducing the degree of photobleaching and increasing the contrast between signal and noise. Herein, we found that rare-earth nanophosphors exhibit a unique up-conversion luminescence mechanism and imaging modality and developed a new three-dimensional visualization method of laser scanning up-conversion luminescence microscopy (LSUCLM) with little photobleaching and no background fluorescence, by introducing a reverse excitation dichroic mirror and the confocal pinhole technique. Moreover, we demonstrated the up-conversion emission imaging of thin films containing embedded rare-earth nanophosphors and cells multilabeled with the nanophosphors and organic dyes. These data show that LSUCLM not only shares noninvasive benefits and deep penetration of two-photon microscopy but also offers some distinct advantages, such as little photobleaching of both organic dyes and rare-earth nanophosphors, no background fluorescence from either endogenous fluorophores or colabeled fluorescent probes, and excellent compatibility with conventional confocal microscopy.

It is widely accepted that the redox status of protein thiols is of central importance to protein structure and folding and that glutathione is an important low-molecular-mass redox regulator. However, the total cellular pools of thiols and disulfides and their relative abundance have never been determined. In this study, we have assembled a global picture of the cellular thiol--disulfide status in cultured mammalian cells. We have quantified the absolute levels of protein thiols, protein disulfides, and glutathionylated protein (PSSG) in all cellular protein, including membrane proteins. These data were combined with quantification of reduced and oxidized glutathione in the same cells. Of the total protein cysteines, 6% and 9.6% are engaged in disulfide bond formation in HEK and HeLa cells, respectively. Furthermore, the steady-state level of PSSG is 15% of all protein cysteine. Glutathione is typically characterized as the 'cellular redox buffer'; nevertheless, our data show that protein thiols represent a larger active redox pool than glutathione. Accordingly, protein thiols are likely to be directly involved in the cellular defense against oxidative stress. cysteine | glutathione | protein

Global metabolite analysis approaches, coupled with sophisticated data analysis and modeling procedures (metabolomics), permit a dynamic read-out of how cellular proteins interact with cellular and environmental conditions to determine cell status. This type of approach has profound potential for understanding, and subsequently manipulating, the regulation of cell function. As part of our study to define the regulatory events that may be used to maximize production of commercially valuable recombinant proteins from cultured mammalian cells, we have optimized the quenching process to allow retention of physiologically relevant intracellular metabolite profiles in samples from recombinant Chinese hamster ovary (CHO) cells. In a comparison of a series of candidate quenching procedures, we have shown that quenching in 60% methanol supplemented with 0.85% ammonium bicarbonate (AMBIC) at -40[degrees]C generates a profile of metabolites that is representative of a physiological status based upon examination of key labile cellular metabolites. This represents a key feature for any metabolomic study with suspension cultured mammalian cells and provides confidence in the validity of subsequent data analysis and modeling procedures.

We have combined nonresonant Raman microspectroscopy and spectral imaging with stable isotope labeling by amino acids in cell culture (SILAC) to selectively detect the incorporation of deuterium-labeled phenylalanine, tyrosine, and methionine into proteins in intact, single HeLa cells. The C-D stretching vibrational bands in these amino acids are observed in the 2100-2300 [cm.sup.-1] spectral region that is devoid of vibrational contributions from other, nondeuterated intracellular constituents. We found that incubation with deuterated amino acids for 8 h in cell culture already led to clearly detectable isotope-related signals in Raman spectra of HeLa cells. As expected, the level of isotope incorporation into proteins increased with incubation time, reaching 55% for deuterated phenylalanine after 28 h. Raman spectral imaging of HeLa cells incubated with deuterium-labeled amino acids showed similar spatial distributions for both isotope-labeled and unlabeled proteins, as evidenced by Raman ratio imaging. The SILAC-Raman methodology presented here combines the strengths of stable isotopic labeling of cells with the nondestructive and quantitative nature of Raman chemical imaging and is likely to become a powerful tool in both cell biology applications and research on tissues or whole organisms.

Two types of blast colonies can be stimulated to develop in semisolid agar cultures of murine bone marrow cells. Typically, these are either multicentric colonies stimulated by stem cell factor (SCF) plus interleukin-6 (IL-6) or dispersed colonies stimulated by Fit3 ligand (FL) plus IL-6. Both types of blast colony-forming ceils (BL-CFCs) can generate large numbers of lineage-committed granulocyte-macrophage progenitor cells and exhibit some capacity for self-generation and the formation of eosinophil and megakaryocyte progenitor cells. However, the two populations of BL-CFCs are largely distinct and partially separable by fluorescence-activated cell sorting and are distinguished by differing capacity to form granulocyte-committed progeny. Both types of BL-CFCs can generate dendritic cells and small numbers of lymphocytes but the FL-responsive BL-CFCs have a greater capacity to form both B and T lymphocytes. Both types of blast colonies offer remarkable opportunities to analyze muitilineage commitment at a clonal level in vitro. blast colonies | T and B lymphocytes

One of the limitations on imaging fluorescent proteins within living cells is that they are usually present in small numbers and need to be detected over a large background. We have developed the means to isolate specific fluorescence signals from background by using lock-in detection of the modulated fluorescence of a class of optical probe termed 'optical switches.' This optical lock-in detection (OLID) approach involves modulating the fluorescence emission of the probe through deterministic, optical control of its fluorescent and nonfluorescent states, and subsequently applying a lock-in detection method to isolate the modulated signal of interest from nonmodulated background signals. Cross-correlation analysis provides a measure of correlation between the total fluorescence emission within single pixels of an image detected over several cycles of optical switching and a reference waveform detected within the same image over the same switching cycles. This approach to imaging provides a means to selectively detect the emission from optical switch probes among a larger population of conventional fluorescent probes and is compatible with conventional microscopes. OLID using nitrospirobenzopyran-based probes and the genetically encoded Dronpa fluorescent protein are shown to generate high-contrast images of specific structures and proteins in labeled cells in cultured and explanted neurons and in live Xenopus embryos and zebrafish larvae. high-contrast | optical switches | 'ac'-imaging | fluorescence microscopy

The effect of sampling time in the context of growth conditions on a dynamic metabolic system was investigated in order to assess to what extent a single sampling time may be sufficient for general application, as well as to determine if useful kinetic information could be obtained. A wild type yeast strain (W) was compared to a snf1[DELTA] mutant yeast strain (S) grown in high-glucose medium (R) and in low-glucose medium containing ethanol (DR). Under these growth conditions, different metabolic pathways for utilizing the different carbon sources are expected to be active. Thus, changes in metabolite levels relating to the carbon source in the growth medium were anticipated. Furthermore, the Snf1 protein kinase complex is required to adapt cellular metabolism from fermentative R conditions to oxidative DR conditions. So, differences in intracellular metabolite levels between the W and S yeast strains were also anticipated. Cell extracts were collected at four time points (0.5, 2, 4, 6 h) after shifting half of the cells from R to DR conditions, resulting in 16 sample classes (WR, WDR, SR, SDR) x (0.5, 2, 4, 6 h). The experimental design provided time course data, so temporal dependencies could be monitored in addition to carbon source and strain dependencies. Comprehensive two-dimensional (2D) gas chromatography coupled to time-of-flight mass spectrometry (GC x GC-TOFMS) was used with discovery-based data mining algorithms (Anal Chem. 2006, 78, 5068-5075 (ref 1); J. Chromatogr., A 2008, 1186, 401-411 (ref 2)) to locate regions within the 2D chromatograms (i.e., metabolites) that provided chemical selectivity between the 16 sample classes. These regions were mathematically resolved using parallel factor analysis to positively identify the metabolites and to acquire quantitative results. With these tools, 51 unique metabolites were identified and quantified. Various time course patterns emerged from these data, and principal component analysis (PCA) was utilized as a comparison tool to determine the sources of variance between these 51 metabolites. The effect of sampling time was investigated with separate PCA analyses using various subsets of the data. PCA utilizing all of the time course data, averaged time course data, and each individual time point data set independently were performed to discern the differences. For the yeast strains examined in the current study, data collection at either 4 or 6 h provided information comparable to averaged time course data, albeit with a few metabolites missing using a single sampling time point.

Single-stranded DNA or RNA aptamer molecules have usually been selected against purified target molecules. To eliminate the need of purifying target molecules on the cell surface, we have developed a selection technique using live bacterial cells in suspension as targets, to select for ssDNA aptamers specific to cell surface molecules. Lactobacillus acidophilus cells were chosen to demonstrate proof of principle based on their high abundance of surface molecules (potential targets). Aptamer pools obtained after 6-8 rounds of selection demonstrated high affinity for and selective binding with L. acidophilus cells when tested via flow cytometry, microscopy, and fluorescence measurements. Out of 27 aptamers that were cloned and sequenced, one sequence, hemag1P, was found to bind to L. acidophilus much more strongly and specifically than other cells tested. This aptamer was predicted to have a tight hairpin secondary structure. On average, an estimated 164 [+ or -] 47 aptamer molecules were bound to a target cell with an apparent [K.sub.d] of 13 [+ or -] 3 nM. A likely putative molecular target of hemag1P is the S-layer protein on the cell surface.

Many types of ceils are able to accurately sense shallow gradients of chemicals across their diameters, allowing the ceils to move toward or away from chemical sources. This chemotactic ability relies on the remarkable capacity of cells to infer gradients from particles randomly arriving at cell-surface receptors by diffusion. Whereas the physical limits of concentration sensing by cells have been explored, there is no theory for the physical limits of gradient sensing. Here, we derive such a theory, using as models a perfectly absorbing sphere and a perfectly monitoring sphere, which, respectively, infer gradients from the absorbed surface particle density or the positions of freely diffusing particles inside a spherical volume. We find that the perfectly absorbing sphere is superior to the perfectly monitoring sphere, both for concentration and gradient sensing, because previously observed particles are never remeasured. The superiority of the absorbing sphere helps explain the presence at the surfaces of cells of signal-degrading enzymes, such as PDE for cAMP in Dictyostelium discoideum (Dicty) and BAR1 for mating factor [alpha] in Saccharomyces cerevisiae (budding yeast). Quantitatively, our theory compares favorably with recent measurements of Dicty moving up a cAMP gradient, suggesting these cells operate near the physical limits of gradient detection. chemotaxis | receptors | noise

The interaction of particles with cells is known to be strongly influenced by particle size, but little is known about the interdependent role that size, shape, and surface chemistry have on cellular internalization and intracellular trafficking. We report on the internalization of specially designed, monodisperse hydrogel particles into HeLa cells as a function of size, shape, and surface charge. We employ a top-down particle fabrication technique called PRINT that is able to generate uniform populations of organic micro- and nanoparticles with complete control of size, shape, and surface chemistry. Evidence of particle internalization was obtained by using conventional biological techniques and transmission electron microscopy. These findings suggest that HeLa cells readily internalize nonspherical particles with dimensions as large as 3 [micro]m by using several different mechanisms of endocytosis. Moreover, it was found that rod-like particles enjoy an appreciable advantage when it comes to internalization rates, reminiscent of the advantage that many rod-like bacteria have for internalization in nonphagocytic cells. PRINT | shape | size | surface charge

Marbling, or i.m. fat, is an important factor determining beef quality. Both adipogenesis and hypertrophy of existing adipocytes contribute to enhanced marbling. We hypothesized that the fetal stage is important for the formation of i.m. adipocytes and that AMP-activated protein kinase (AMPK) has a key role in adipogenesis during this stage. The objective of this study was to assess the role of AMPK in adipogenesis in fetal sheep muscle and 3T3-L1 cells. Nonpregnant ewes were randomly assigned to a control (Con, 100% of NRC recommendations, n = 7) or overfed (OF, 150% of NRC, n = 7) diet from 60 d before to 75 d after conception, when the ewes were killed. The fetal LM was collected at necropsy for biochemical analyses. The activity of AMPK was less in the fetal muscle of OF sheep. The expression of peroxisome proliferator-activated receptor (PPAR)[gamma], a marker of adipogenesis, was greater in OF fetal muscle compared with Con fetal muscle. To further show the role of AMPK in adipogenesis, we used 3T3-L1 cells. The 3T3-L1 cells were incubated in a standard adipogenic medium for 24 h and 10 d. Activation of AMPK by 5-aminoimidazole-4-carboxamide-1-[beta]-d-ribonucleoside dramatically inhibited the expression of PPAR[gamma] and reduced the presence of adipocytes after 10 d of differentiation. Inhibition of AMPK by compound C enhanced the expression of PPAR[gamma]. In conclusion, these data show that AMPK activity is inversely related to adipogenesis in fetal sheep muscle and 3T3-L1 cells. Key words: 3T3-L1 cells, adipogenesis, AMP-activated protein kinase, fetus, sheep, skeletal muscle

Monitoring of excitation activity of nerve cells is very useful for not only brain research but also assessment of the effects of various chemicals, including drugs and toxins.We previouslyreported anovelenzyme luminescence method for real-time monitoring of L-glutamate release from C6 glioma cells with high levels of sensitivity (approximately equal to] 10 nM) and temporal resolution (

We describe the development of an enzyme assay inside picoliter microdroplets. The enzyme alkaline phosphatase is expressed in Escherichia coli cells and presented in the periplasm. Droplets act as discrete reactors which retain and localize any reaction product. The catalytic turnover of the substrate is measured in individual droplets by monitoring the fluorescence at several time points within the device and exhibits kinetic behavior similar to that observed in bulk solution. Studies on wild type and a mutant enzyme successfully demonstrated the feasibility of using microfluidic droplets to provide time-resolved kinetic measurements.

A high-throughput single copy genetic amplification (SCGA) process is developed that utilizes a microfabricated droplet generator ([micro]DG) to rapidly encapsulate individual DNA molecules or cells together with primer functionalized microbeads in uniform PCR mix droplets. The nanoliter volume droplets uniquely enable quantitative high-yield amplification of DNA targets suitable for long-range sequencing and genetic analysis. A hybrid glass--polydimethylsiloxane (PDMS) microdevice assembly is used to integrate a micropump into the [micro]DG that provides uniform droplet size, controlled generation frequency, and effective bead incorporation. After bulk PCR amplification, the droplets are lysed and the beads are recovered and rapidly analyzed via flow cytometry. DNA targets ranging in size from 380 to 1139 bp at single molecule concentrations are quantitatively amplified using SCGA. Long-range sequencing results from beads each carrying ~100 amol of a 624 bp product demonstrate that these amplicons are competent for achieving attomole-scale Sanger sequencing from a single bead and for advancing pyrosequencing read-lengths. Successful single cell analysis of the glyceraldehyde 3 phosphate dehydrogenase (GAPDH) gene in human lymphocyte cells and of the gyr B gene in bacterial Escherichia coil K12 cells establishes that SCGA will also be valuable for performing high-throughput genetic analysis on single cells.

Synaptic vesicles release neurotransmitter by following a process of vesicle docking and exocytosis. Although these steps are well established, it has been difficult to observe and measure these rates directly in living synapses. Here, by combining the direct imaging of single synaptic vesicles and synaptic ribbons, I measure the properties of vesicle docking and evoked and spontaneous release from ribbon and extraribbon locations in a ribbon-type synaptic terminal, the goldfish retinal bipolar cell. In the absence of a stimulus, captured vesicles near ribbons associate tightly and only rarely undock or undergo spontaneous exocytosis. By contrast, vesicle capture at outlier sites is less stable and spontaneous exocytosis occurs at a higher rate. In response to a stimulus, exocytic events cluster near ribbons, but show no evidence of clustering away from ribbon sites. Together, the results here indicate that, although vesicles can associate and fuse both near and away from synaptic sites, vesicles at synaptic ribbons associate more stably and fusion is more tightly linked to stimuli. imaging | neurotransmitter release | retina I synapse | synaptic vesicle

Interaction of the neuropeptide substance P (SP) with its high-affinity neurokinin-1 receptor (NK1R) plays an important role in the pathophysiology of acute pancreatitis. SP is known to stimulate the production of chemokines monocyte chemoattractant protein-1 (MCP-1), macrophage inflammatory protein (MIP)-1[alpha], and MIP-2 in pancreatic acinar cells via the activation of NF-[kappa]B. However, the signaling mechanisms by which the SP-NK1R interaction induces NF-[kappa]B activation and chemokine production remain unclear. To that end, in the present study, we investigated the participation of PKC in SP-induced chemokine production in pancreatic acinar cells. In this study, we showed that SP stimulated an early phosphorylation of PKC isoform PKC-[delta] followed by increased activation of MAPKKK MEKK1 and MAPK ERK and JNK as well as transcription factor NF-[kappa]B and activator protein-1 driven chemokine production. Depletion of PKC-[delta] with its inhibitor rottlerin or the specific PKC-[delta] translocation inhibitor peptide dose dependently decreased SP-induced PKC-[delta], MEKK1, ERK, JNK, NF-[kappa]B, and AP-1 activation. Moreover, rottlerin as well as PKC-[delta] translocation inhibitor inhibited SP-induced chemokine production in a concentration-dependent manner. We also demonstrated that PKC-[delta] activation was attenuated by CP96345, a selective NK1R antagonist, thus showing that PKC-[delta] activation was indeed mediated by SP in pancreatic acinar cells. These results show that PKC-[delta] is an important proinflammatory signal transducer for SP-NK1R-induced chemokine production in pancreatic acinar cells. protein kinse C-[delta]; mitogen-activated protein kinase kinase kinase-1; extracellular signal-regulated kinase; c-Jun N[H.sub.2]-terminal kinase; nuclear factor-[kappa]B; activator protein-1

The organs of multicellular species consist of cell types that must function together to perform specific tasks. One critical organ function is responding to internal or external change. Some cell-specific responses to changes in environmental conditions are known, but the scale of cell-specific responses within an entire organ as it perceives an environmental flux has not been well characterized in plants or any other multicellular organism. Here, we use cellular profiling of five Arabidopsis root cell types in response to an influx of a critical resource, nitrogen, to uncover a vast and predominantly cell-specific response. We show that cell-specific profiling increases sensitivity several-fold, revealing highly localized regulation of transcripts that were largely hidden from previous global analyses. The cell-specific data revealed responses that suggested a coordinated developmental response in distinct cell types or tissues. One example is the cell-specific regulation of a transcriptional circuit that we showed mediates lateral root outgrowth in response to nitrogen via microRNA167, linking small RNAs to nitrogen responses. Together, these results reveal a previously cryptic component of cell-specific responses to nitrogen. Thus, the results make an important advance in our understanding of how multicellular organisms cope with environmental change at the cell level. cell sorting | microRNA | lateral roots | auxin response | transcriptional analysis

Retinal progenitor cells have been shown to be multipotent throughout development. Similarly, many other structures of the developing central nervous system have been found to contain multipotent progenitor cells. Previous lineage studies did not address whether these multipotent progenitor cells were biased in their production of neuronal subtypes. This question is of interest because subtypes are the basis of distinct types of circuits. Here, lentivirus-mediated gene transfer was used to mark single retinal progenitor cells in vivo, and the different subtypes of horizontal cells (HCs) in each clone were quantified. Clones with two HCs consistently contained a single HC subtype, a pair of either H1 or H3 cells. This suggests that a multipotent progenitor cell produces a mitotic cell fated to make a terminal division that produces two HCs of only one subtype. This bias in production of one HC subtype suggests a previously undescribed mechanism of cell fate determination in at least a subset of retinal cells that involves decisions made by mitotic cells that are inherited in a symmetric manner by both neuronal daughter cells. chick | lentivirus | lineage | retina

Cell binding assays on antibody arrays permit the rapid immunophenotyping of living cells. The throughput of the analysis, however, is still limited due to our inability to perform parallel and quantitative detection of cells captured on the array. To address this limitation, we employed here an imaging technique based on surface plasmon resonance (SPR). SPR has been frequently used to monitor capture of proteins on antibody microarrays, while few cases were reported for capture of cells. Antibody arrays were prepared through the photopatterning of an alkanethiol monolayer on a gold-evaporated glass plate and the subsequent immobilization of various antibodies onto 4-9 separate spots created by photopatterning. A glass slip was mounted onto the array with a thin spacer to construct a parallel-plate chamber. Leukemia cells were injected into the chamber to conduct a binding assay, while refractive index changes at the vicinity of the array surface were monitored by SPR imaging. We observed that SPR signals were intensified on specific antibody spots but not on nonspecific spots. Confocal laser scanning microscopy revealed that the observed SPR signals were attributed to cell deformations caused by multivalent interactions with immobilized antibody, which effectively elevated the refractive index of a medium phase within an evanescent field. This effect could be suitably utilized to monitor quantitatively cell binding to multiple spots from a heterogeneous cell population.

Cells respond to mechanical forces whether applied externally or generated internally via the cytoskeleton. To study the cellular response to forces separately, we applied external forces to cells via microfabricated magnetic posts containing cobalt nanowires interspersed among an array of elastomeric posts, which acted as independent sensors to cellular traction forces. A magnetic field induced torque in the nanowires, which deflected the magnetic posts and imparted force to individual adhesions of cells attached to the array. Using this system, we examined the cellular reaction to applied forces and found that applying a step force led to an increase in local focal adhesion size at the site of application but not at nearby nonmagnetic posts. Focal adhesion recruitment was enhanced further when cells were subjected to multiple force actuations within the same time interval. Recording the traction forces in response to such force stimulation revealed two responses: a sudden loss in contractility that occurred within the first minute of stimulation or a gradual decay in contractility over several minutes. For both types of responses, the subcellular distribution of loss in traction forces was not confined to locations near the actuated micropost, nor uniformly across the whole cell, but instead occurred at discrete locations along the cell periphery. Together, these data reveal an important dynamic biological relationship between external and internal forces and demonstrate the utility of this microfabricated system to explore this interaction. focal adhesions | magnetic nanowires | mechanotransduction | microfabrication | traction forces

Haptotaxis is a mechanism proposed at the end of the 1960s to explain cell motility. It describes cell movement induced by an adhesion gradient. In this work, we present evidence for self-induced haptotaxis using negatively charged giant vesicles interacting with positively charged supported lipid bilayers, which has not been previously described. Depending on the charge of the vesicle, we observed different behaviors. At low charge, no adhesion occurs. At high charge, the vesicle adheres but does not move. In a restricted range of intermediate charge densities, we found that the vesicle moves spontaneously with velocities of the order of a few micrometers per second over distances of >100 [micro]m. We show that a local lipid transfer between the giant vesicle and the supported lipid bilayer takes place during the adhesion, breaking the symmetry and inducing a lateral charge gradient. This charge gradient polarizes the giant vesicle and induces its motion. To explain our observations, we propose a scaling model that relates the adhesion energy to the velocity of vesicle motion and to the characteristic lipid transfer time. Our measurements indicate that the effective adhesion energy is strongly reduced by counterions, which are dynamically trapped between the vesicle and the supported bilayer. adhesion | electrostatic interaction | giant unilameilar vesicles | haptotaxis | lipid membrane

Adhesive properties of cells undergoing morphogenetic rearrangements can be regulated either at the cellular level or by altering the environment in which rearrangements occur. Here, we describe the identification of a mutation ([my.sup.F11]) in the mouse extracellular matrix component Frem2, and provide evidence that suggests Frem2 expression creates an environment conducive to morphogenetic events. Loss of Frem2 function results in defects in developmental events associated with morphogenetic rearrangements of the vasculature and of tissues arising from all germ layers. The Frem2 transcript is restricted both spatially and temporally and appears in advance of cell rearrangement events. Thus, expression of Frem2 may dynamically alter the extracellular matrix to provide a substrate for cell migration and rearrangements during embryogenesis. extracellular matrix | hemorrhage | Frem | CALX[beta] | neural tube defect

Byline: V. P. Nikitin (1), S. A. Kozyrev (1) Abstract: Studies on semi-intact common snail preparations addressed the involvement of intracellular calcium in changes in the excitability and responses to sensory stimuli of defensive behavior command neurons LPl1 and RPl1 during the acquisition of nociceptive sensitization. Application of sensitizing stimuli to the heads of control snails led to depolarization of neuron membranes, increases in neuron excitability, and depression of the responses of neurons to sensory stimuli during the short-term stage, and marked facilitation of responses in the long-term stage of sensitization. Acquisition of sensitization during profound hyperpolarization of neurons led to suppression of the increase in excitability, along with depression of responses to chemical stimulation of the head in the short- and long-term stages of sensitization. Neuron responses to tactile stimulation of the head and foot showed synaptic facilitation, similar to that seen in neurons of control animals. Acquisition of sensitization during intracellular injection of the calcium chelators EGTA and BAPTA led to suppression of synaptic facilitation in the responses of neurons to both chemical and tactile stimulation. In these conditions, membrane excitability increased to a greater extent than in neurons of control animals. The results of these experiments suggest that changes in responses to sensory stimulation in sensitized snails are associated with postsynaptic calcium-dependent mechanisms of plasticity in neurons LPl1 and RPl1. Author Affiliation: (1) P. K. Anokhin Science Research Institute of Normal Physiology, Russian Academy of Medical Sciences, Moscow Article History: Registration Date: 12/10/2004

A microfabricated device is described for the capture and injection of a single mammalian cell into a fused silica capillary for subsequent analysis by chemical cytometry. The device consists of a 500 [micro]m diameter well made from polydimethylsiloxane on an indium--tin oxide coated microscope slide. The bottom of the well contains a 2 [micro]m high aperture, which was designed to block passage of cells. A cellular suspension was allowed to settle on the device, and aspiration through the aperture was used to trap a single NG-108 cell. Untrapped cells were washed from the device, and a 150 [micro]m outer diameter and 50 [micro]m inner diameter capillary was placed in the well. To inject a cell, voltage was applied to the indium--tin oxide while simultaneously applying vacuum at the distal end of the capillary. 10.1021/ac1022716

A new method is developed for protein-protein interaction (PPI) detection in vitro and in cells based on proximity biotinylation. The studies have shown that proximity biotinylation can be applied to different protein pairs.