Introduction: patch clamp and single-cell voltage clamp techniques and selected data

Molecular and Cellular Biochemistry -     

利用单细胞RT-PCR体外克隆个体化乙型肝炎表面抗体重链

目的建立一种利用单细胞RT-PCR技术克隆乙型肝炎表面抗体重链的方法,为人源化、个体化的乙肝治疗性抗体研制奠定基础。方法利用单细胞分选技术从乙肝疫苗接种志愿者外周血中分选得到单个抗体分泌细胞（antibody-secreting cells,ASC）,用单细胞RT-PCR克隆其IgG重链全长到pEGFP-N1载体,转染COS-7细胞,上清液用乙肝表面抗原（hepatitis B surface antigen,HBsAg）通过Western blot进行结合力验证。结果克隆得到1 500 bp左右的重链全长,重链表达产物经验证能与乙肝表面抗原特异结合。结论克隆得到表达产物能与HBsAg特异结合的重链基因,为我们后期制备抗体轻链、连接轻重链和抗体亲和力鉴定奠定基础。     

Differential appearance of dynamin in constitutive and regulated exo-endocytosis: a single-cell multiplex RT-PCR study

Neurons in the central nervous system establish, via their axons and dendrites, an extended network that allows synaptic transmission. During developmental maturation and process outgrowth, membrane turnover is necessary for the enlargement and subsequent growth of axons and dendrites from the perikarya to the target cell (constitutive exocytosis/endocytosis). After targeting and synapse formation, small synaptic vesicles are needed for the quantal release of neurotransmitters from the presynaptic terminal with subsequent recycling by regulated exocytosis/endocytosis. An investigation of the onset of the appearance of mRNA and protein in dissociated cultures of neurons from mouse hippocampus or from chick retina has shown an early abundance of proteins involved in exocytosis, such as syntaxin 1, SNAP-25, and synaptotagmin 1, whereas dynamin 1, a protein necessary for clathrin-mediated endocytosis, can be detected only after neurons have established contacts with neighboring cells. The results reveal that constitutive membrane incorporation and regulated synaptic transmitter release is mediated by the same neuronal proteins. Moreover, the data exclude that dynamin 1 takes part in constitutive recycling before synapse formation, but dynamin 2 is present at this stage. Thus, dynamin 2 may be the constitutive counterpart of dynamin 1 in growing neurons. Synapse establishment is linked to an upregulation of dynamin 1 and thereby represents the beginning of the regulated recycling of membranes back into the presynaptic terminal.     

Microtechnologies and nanotechnologies for single-cell analysis

Many efforts are currently underway to try and mimic the properties of single cells with the aim of designing chips that are as efficient as cells. However, cells are nature's nanotechnology engineering at the scale of atoms and molecules, and it might be better to envision a microchip that utilizes a single cell as an experimentation platform. A novel, so-called laboratory-in-a-cell concept has been described, where advantage is taken of micro- and nanotechnological tools to enable precise control of the biochemical cellular environment; these tools also offer the possibility to analyse the composition of single cells. Methods for single-cell handling and analysis are being developed and will be required for this concept to progress further.     

Microbial analysis at the single-cell level: tasks and techniques

The heterogeneity of microorganisms themselves is orders of magnitude greater than the heterogeneity of perspectives from which they are contemplated by human observers. Even closely related species may exhibit marked differences in biochemistry and behavior, and, under many conditions, similar, striking heterogeneity may exist within a clonal population of organisms which, in the aggregate, occupy too small a region of space to be visible to the unaided human eye. Using methods of microscopy, microspectrophotometry, and cytometry developed and refined since the 1960s, it is now possible to characterize the physiology and pharmacology of individual microorganisms, and, in many cases, to isolate organisms with selected characteristics for culture and/or further analysis. These methods include fluorescent and confocal microscopy, scanning and image cytometry, and flow cytometry. Fluorescence measurements are particularly important in single-cell analysis; they allow demonstration and quantification of cells' nucleic acid content and sequence, of the presence of specific antigens, and of physiologic characteristics such as enzyme activity and membrane potential. Multiparameter cytometry, combined with cell sorting, provides insight into population heterogeneity and allows selected cells to be separated for further analysis and culture. The technology is applicable to a wide range of problems in contemporary microbiology, including strain selection and the development of antimicrobial agents.     

scdNet: a computational tool for single-cell differential network analysis

Background

Single-cell RNA sequencing (scRNA-Seq) is an emerging technology that has revolutionized the research of the tumor heterogeneity. However, the highly sparse data matrices generated by the technology have posed an obstacle to the analysis of differential gene regulatory networks.

Results

Addressing the challenges, this study presents, as far as we know, the first bioinformatics tool for scRNA-Seq-based differential network analysis (scdNet). The tool features a sample size adjustment of gene-gene correlation, comparison of inter-state correlations, and construction of differential networks. A simulation analysis demonstrated the power of scdNet in the analyses of sparse scRNA-Seq data matrices, with low requirement on the sample size, high computation efficiency, and tolerance of sequencing noises. Applying the tool to analyze two datasets of single circulating tumor cells (CTCs) of prostate cancer and early mouse embryos, our data demonstrated that differential gene regulation plays crucial roles in anti-androgen resistance and early embryonic development.

Conclusions

Overall, the tool is widely applicable to datasets generated by the emerging technology to bring biological insights into tumor heterogeneity and other studies. MATLAB implementation of scdNet is available at https://github.com/ChenLabGCCRI/scdNet.

     

植物实时荧光定量PCR内参基因的特点及选择

实时荧光定量PCR(qRT-PCR)具有灵敏度高、特异性强、重复的动态定量范围和高通量等优点,是进行植物基因表达和转录分析最常用的技术手段之一.选择合适的内参基因是正确运用实时荧光定量PCR分析目标基因表达变化的前提.近年来,大量研究表明,内参基因的选择应取决于研究者的实验条件;随着实验条件的变化,内参基因的选择也随之变化.因此,实时荧光定量PCR结果分析的准确性在很大程度上依赖于所选择的内参基因是否适合.该文从内参基因的选择、常用内参基因的特点、新内参基因的挖掘、应用内参基因组合的优点和内参基因的稳定性评价等几方面进行综述,以期为研究者在实验中选择合适的内参基因提供参考和理论依据.     

Voltage-gated calcium and Ca2+-activated chloride channels and Ca2+ transients: voltage-clamp studies of perfused and intact cells of Chara

The voltage-clamp technique was used to study Ca²⁺ and Cl^– transient currents in the plasmalemma of tonoplast-free and intact Chara corallina cells. In tonoplast-free cells [perfused medium with ethylene glycol bis(2-aminoethyl ether)tetraacetic acid] long-term inward and outward currents through Ca channels consisted of two components: with and without time-dependent inactivation. The voltage dependence of the Ca channel activation ratio was found to be sigmoid-shaped, with about –140-mV activation threshold, reaching a plateau at V>50 mV. As the voltage increased, the characteristic activation time decreased from approximately 10³ ms in the threshold region to approximately 10 ms in the positive region. The positive pulse-activated channels can then be completely deactivated, which is recorded by the Ca²⁺ tail currents, at below-threshold negative voltages with millisecond-range time constants. This tail current is used for fast and brief Ca²⁺ injection into tonoplast-free and intact cells, to activate the chloride channels by Ca²⁺ . When cells are perfused with EDTA-containing medium in the presence of excess Mg²⁺, this method of injection allows the free submembrane Ca²⁺ concentration, [Ca²⁺]_c, to be raised rapidly to several tens of micromoles per liter. Then a chloride component is recorded in the inward tail current, with the amplitude proportional to . When Ca²⁺ is thus injected into an intact cell, it induces an inward current in the voltage-clamped plasmalemma, having activation–inactivation kinetics qualitatively resembling that in EDTA-perfused cells, but a considerably higher amplitude and duration (approximately 10 A m^–2 and _inact~0.5 s at –200 mV). Analysis of our data and theoretical considerations indicate that the [Ca²⁺]_c rise during cell excitation is caused mainly by Ca²⁺ entry through plasmalemma Ca channels rather than by Ca²⁺ release from intracellular stores.     

Reporter gene expression at single-cell level characterized with real-time RT-PCR, chemiluminescence, fluorescence, and electrochemical imaging

mRNA from single cells was quantified using real-time RT-PCR after recording the address and reporter protein activity with chemiluminescence, fluorescence, and electrochemical techniques, using luciferase, green fluorescent protein, and secreted alkaline phosphatase. mRNA copy number ranging from below 103 to 10⁷ in single cells showed a lognormal distribution for both externally introduced reporter genes and internally expressed genes. The fluctuation in the gene expression decreased with the increase of the number of cells picked but did not decrease with the increase of mRNA copy number per cell. We found that the correlation coefficients for mRNA and protein expression in logarithmic plot at single-cell level were much lower than 1.00.     

Action potential waveform voltage-clamp commands reveal striking differences in calcium entry via low and high voltage-activated calcium channels.

Calcium channels transduce natural voltage transients, like action potentials, into functionally important intracellular calcium transients. We have used digitally constructed waveforms that simulate natural action potentials as voltage-clamp commands to study channel function in transduction. Whole-cell calcium currents elicited by several action potential waveforms (APWs) were studied. The currents were subdivided into T (or low voltage-activated) and high voltage-activated components. Calcium entry through T channels constituted a disproportionately large fraction of the total during normal, brief APWs. Entry through high voltage-activated channels was much more responsive to APW, increasing more significantly as APW duration increased. Thus the results indicate that differences in the gating properties of these two channel classes combine to endow them with strikingly different transducer properties.     

Protein analysis of an individual Caenorhabditis elegans single-cell embryo by capillary electrophoresis

We present a simple one-dimensional electrophoretic map of the expressed proteins in a Caenorhabditis elegans embryo. The embryo was taken from an adult nematode, injected into a 50-μm I.D. capillary, and lysed. The proteins were fluorescently labeled and then separated by capillary electrophoresis and detected by laser-induced fluorescence. Over 20 components were resolved in the 22-min separation. The dynamic range was outstanding for this separation, noise in the baseline was less than 0.01% the amplitude of the largest component.     

Luminal chloride-dependent activation of endosome calcium channels: patch clamp study of enlarged endosomes

Although Ca(2+) release from early endosomes (EE) is important for the fusion of primary endosomes, the presence of an ion channel responsible for releasing calcium from the EE has not been shown. A recent proteomics study has identified the TRPV2 channel protein in EE, suggesting that transient receptor potential-like Ca(2+) channels may be in endosomes. The submicron size of endosomes has made it difficult to study their ion channels in the past. We have overcome this problem by generating enlarged EE with the help of a hydrolysis-deficient SKD1/VPS4B mutant in HEK293 cells. Here we report the first patch clamp recording of a novel endosome calcium channel (ECC) in these enlarged EE. The ECC shows a similar pharmacology to that of the TRPV2 channel. In addition, the ECC has a unique chloride-dependent regulation; it is inhibited by the endosome luminal chloride with a K(50) of 82 mm.