Optimization of Single-Cell Electroporation Protocol for Forced Gene Expression in Primary Neuronal Cultures

The development and function of the central nervous system (CNS) are realized through interactions between many neurons. To investigate cellular and molecular mechanisms of the development and function of the CNS, it is thus crucial to be able to manipulate the gene expression of single neurons in a complex cell population. We recently developed a technique for gene silencing by introducing small interfering RNA into single neurons in primary CNS cultures using single-cell electroporation. However, we had not succeeded in forced gene expression by introducing expression plasmids using single-cell electroporation. In the present study, we optimized the experimental conditions to enable the forced expression of green fluorescent protein (GFP) in cultured cerebellar Purkinje neurons using single-cell electroporation. We succeeded in strong GFP expression in Purkinje neurons by increasing the inside diameter of micropipettes or by making the size of the original plasmid smaller by digestion and cyclizing it by ligation. Strong GFP expression in Purkinje neurons electroporated under the optimal conditions continued to be observed for more than 25 days after electroporation. Thus, this technique could be used for forced gene expression in single neurons to investigate cellular and molecular mechanisms of the development, function, and disease of the CNS.     

Long-Term Gene-Silencing Effects of siRNA Introduced by Single-Cell Electroporation into Postmitotic CNS Neurons

To explore how long the gene-silencing effects of siRNA introduced into postmitotic neurons continue, we transferred siRNA against GFP into GFP-expressing Purkinje and Golgi cells in cerebellar cell cultures by single-cell electroporation. The temporal changes in the intensity of GFP fluorescence in the same electroporated cells were monitored in real time using GFP imaging. Under standard conditions, GFP fluorescence was reduced to under one-tenth of the initial levels 4–7 days after electroporation. Such effects continued at least up to 14 days after electroporation. The effects of siRNAs against endogenous genes also continued for the same period. Thus, this method could be an effective tool for silencing gene expression for a long period in postmitotic neurons.     

Numerical Modeling of Bi-polar (AC) Pulse Electroporation of Single Cell in Microchannel to Create Nanopores on its Membrane

AC electroporation of a single cell in a microchannel was numerically studied. A \(15\,\upmu\) m diameter cell was considered in a microchannel \(25\,\upmu\) m in height and the influences of AC electric pulse on its membrane were numerically investigated. The cell was assumed to be suspended between two electroporative electrodes embedded on the walls of a microchannel. An amplitude and a time span of applied electric pulse were chosen to be 80 kV/m and \(10\,\upmu\) s, respectively. For different frequency values (50, 100, 200, and 500 kHz), simulations were performed to show how the cell membrane was electroporated and the creation of nanopores. Obtained numerical results show that the most and the largest nanopores are created around poles of cell (nearest points of cell membrane to the electrodes). The numerical simulations also demonstrate that increased frequency will slightly decrease electroporated area of the cell membrane; additionally, growth of the created nanopores will be stabilized. It has also been proven that size and number of the created nanopores will be decreased by moving from the poles to the equator of the cell. There is almost no nanopore created in the vicinity of the equator. Frequency affects the rate of generation of nanopores. In case of AC electroporation, creation of nanopores has two phases that periodically repeat over time. In each period, the pore density sharply increases and then becomes constant. Enhancement of the frequency will result in decrease in time span of the periods. In each period, size of the created nanopores sharply increases and then slightly decreases. However, until the AC electric pulse is present, overall trends of creation and development of nanopores will be ascending. Variation of the size and number of created nanopores can be explained by considering time variation of transmembrane potential (difference of electric potential on two sides of cell membrane) which is clear in the results presented in this study.     

A Parametric Study Delineating Irreversible Electroporation from Thermal Damage Based on a Minimally Invasive Intracranial Procedure

Background  

Irreversible electroporation (IRE) is a new minimally invasive technique to kill undesirable tissue in a non-thermal manner. In order to maximize the benefits from an IRE procedure, the pulse parameters and electrode configuration must be optimized to achieve complete coverage of the targeted tissue while preventing thermal damage due to excessive Joule heating.     

A Numerical Study on Pressure Drop in Microchannel Flow with Different Bionic Micro-Grooved Surfaces

The studies of bionics reveal that some aquatic animals and winged insects have developed an unsmoothed surface possessing good characteristics of drag reduction.In this paper,four types of bionic surfaces,placoid-shaped,V-shaped,riblet-shaped,and ridge-shaped grooved surfaces,are employed as the microchannel surfaces for the purpose of reducing pressure loss.Lattice Boltzmann Method (LBM),a new numerical approach on mescoscopic level,is used to conduct the numerical investigations.The results show that the micro-grooved surfaces possess the drag reduction performance.The existence of the vortices formed within the grooves not only decrease the shear force between fluid and wall but also minimize the contact area between fluid and walls,which can lead to a reduction of pressure loss.The drag reduction coefficient (η) for these four types of　micro-structures could be generalized as follows:ηridge-shaped ＞ ηV-shaped ＞ ηplacoid-shaped ＞ ηriblet-shaped.Besides,the geometrical optimizations for the ridge-shaped grooves,which have the highest drag reduction performance,are performed as well.The results suggest that,for the purpose of drag reduction,the ridge-shaped grooves with smaller width to height ratio are recommended for the lower Reynolds number flow,while the ridge-shaped grooves with larger width to height ratio are be more suitable for the larger Reynolds number flow.     

铜绿假单胞菌最佳电转化条件的研究

以临床分离的一株铜绿假单胞菌 (Pseudomonasaeruginosa)PA68作受体菌 ,将具有卡那霉素抗性标记的质粒pSMC2 8通过电转化导入到受体菌中 ,研究细胞生长状态、电击电压、细胞浓度、感受态细胞的贮备方式对转化效率的影响。结果表明 ,在细胞生长至OD5 40 =0 7～ 0 8时收集菌体 ,在低温 (2℃ )条件下 ,制备浓度为 10 11个细胞 mL的感受态细胞 ,在较高的电压 (2 6kV)电击下 ,能获得较高的转化效率。最高可达 1 68× 10 8个转化子 μgDNA(CFU μgDNA)。用此优化的转化条件 ,在国际上首次成功地将Mu转座复合物导入到P .aeruginosa中 ,并获得 2 4× 10 4 CFU μgDNA的高转化效率。由于Mu转座重组技术具有随机单点插入的优点 ,克服了传统转座子能在染色体上迁移的缺点 ,保证了表型的改变与转座子插入位点所在的基因突变的一一对应关系 ,为进一步研究P .aerugi nosa的基因组功能奠定基础     

Electroporation in dense cell suspension—Theoretical and experimental analysis of ion diffusion and cell permeabilization

Electroporation is a process where increased permeability of cells exposed to an electric field is observed. It is used in many biomedical applications including electrogene transfection and electrochemotherapy. Although the increased permeability of the membrane is believed to be the result of pores due to an induced transmembrane voltage U_m, the exact molecular mechanisms are not fully explained.     

A Single-Cell Genome for Thiovulum sp.

We determined a significant fraction of the genome sequence of a representative of Thiovulum, the uncultivated genus of colorless sulfur Epsilonproteobacteria, by analyzing the genome sequences of four individual cells collected from phototrophic mats from Elkhorn Slough, California. These cells were isolated utilizing a microfluidic laser-tweezing system, and their genomes were amplified by multiple-displacement amplification prior to sequencing. Thiovulum is a gradient bacterium found at oxic-anoxic marine interfaces and noted for its distinctive morphology and rapid swimming motility. The genomic sequences of the four individual cells were assembled into a composite genome consisting of 221 contigs covering 2.083 Mb including 2,162 genes. This single-cell genome represents a genomic view of the physiological capabilities of isolated Thiovulum cells. Thiovulum is the second-fastest bacterium ever observed, swimming at 615 μm/s, and this genome shows that this rapid swimming motility is a result of a standard flagellar machinery that has been extensively characterized in other bacteria. This suggests that standard flagella are capable of propelling bacterial cells at speeds much faster than typically thought. Analysis of the genome suggests that naturally occurring Thiovulum populations are more diverse than previously recognized and that studies performed in the past probably address a wide range of unrecognized genotypic and phenotypic diversities of Thiovulum. The genome presented in this article provides a basis for future isolation-independent studies of Thiovulum, where single-cell and metagenomic tools can be used to differentiate between different Thiovulum genotypes.     

A Single-Cell Transcriptomic Atlas of Human Skin Aging

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Expression of Oat-phyA-cDNA in a Suspension Cell Culture of Transgenic Tobacco: A Single-Cell System for the Study of Phytochrome Function

A culture of callus cells has been developed from a transgenicline of tobacco which contains an introduced phyA-cDNA encodingphytochrome A. Suspension cultures of the cells were shown toaccumulate a significant immunodetectable level of the heterologousphytochrome, but not of the native phyA-gene product. The red-irradiatedform (P_fr) of the heterologous phytochrome was specificallydegraded in vivo, and the red-irradiated (P_fr) and far-red-irradiated(P_r) forms demonstrated different patterns of in vitro proteolyticcleavage. These results strongly suggested that the phytochromeapoprotein was associated with a chromophore moiety which mediatedred/far-red sensitive conformational changes of the molecule.Exogenous application of 4-amino-5-hexynoic acid (AHA) to thetransgenic suspension cultures resulted in the accumulationof a population of phytochrome which was stable under red lightand gave identical patterns of in vitro digestion in the redand far-red irradiated forms, i.e. the spectral activity ofphytochrome was inhibited. Application of exogenous 5-aminolevulinicacid (ALA) or biliverdin overcame the inhibitory effects ofAHA to restore spectral sensitivity of the phytochrome pool.These results are consistent with the proposed pathway of phytochromechromophore biosynthesis in intact plant systems. Thus, thetransgenic suspension cultures provided a single-cell systemin which spectrally-active phytochrome, apparently indistinguishablefrom the native phytochrome synthesized in etiolated seedlings,was accumulated. Photoregulation of expression of the genesencoding the small subunit of ribulose-1,5-bisphosphate carboxylaseand chlorophyll a/b binding proteins demonstrated that the heterologousphytochrome population mediated rapid changes in gene expressionin the de-differentiated cells. It is therefore proposed thatsuch a suspension culture of transgenic cells offers a modelsystem for the study of phytochrome function. Key words: Cell cultures, transgenic tobacco, phytochrome, oat-phy A-cDNA, gene expression     

Electroporation of cells

By measuring uptake of the membrane impermeable dye. phenosafranine, it can be shown that the plasma membrane of intact cells within cell aggregates can be reversibly permeabilized by electroporation. However, the plant cell wall is a barrier to DNA uptake by intact cells, although under certain circumstances expression of DNA, electroporated into intact cells, can be demonstrated. The level of expression is about 20–50 times lower than that obtained by electroporation of protoplasts, and depends on cell wall properties and pretreatments of cell aggregates. In contrast, efficient transformation of whole cells of bacteria and yeasts can be achieved by electroporation. Factors which influence DNA transfer into whole plant cells and the possibility of stable transformation are discussed.     

Electroporation of a lipid bilayer as a chemical reaction

When a cell's transmembrane potential is increased from a physiological one to more than 370 mV, the transmembrane current increases more than hundredfold within a millisecond. This is due to the formation of conductive pores in the membrane. We construct a model in which we conceive of pore formation as a voltage sensitive chemical reaction. The model predicts the logarithm of the pore formation rate to increase proportionally to the square of the voltage. We measure currents through frog muscle cell membranes under 8 ms pulses of up to 440 mV. The experimental data appear consistent with the model.     

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods

Single-cell sequencing is emerging as an important tool for studies of genomic heterogeneity. Whole genome amplification (WGA) is a key step in single-cell sequencing workflows and a multitude of methods have been introduced. Here, we compare three state-of-the-art methods on both bulk and single-cell samples of E. coli DNA: Multiple Displacement Amplification (MDA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC), and the PicoPLEX single-cell WGA kit (NEB-WGA). We considered the effects of reaction gain on coverage uniformity, error rates and the level of background contamination. We compared the suitability of the different WGA methods for the detection of copy-number variations, for the detection of single-nucleotide polymorphisms and for de-novo genome assembly. No single method performed best across all criteria and significant differences in characteristics were observed; the choice of which amplifier to use will depend strongly on the details of the type of question being asked in any given experiment.     

A Single-Cell Atlas of Tumor-Infiltrating Immune Cells in Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies with limited treatment options. To guide the design of more effective immunotherapy strategies, mass cytometry was employed to characterize the cellular composition of the PDAC-infiltrating immune cells. The expression of 33 protein markers was examined at the single-cell level in more than two million immune cells from four types of clinical samples, including PDAC tumors, normal pancreatic tissues, chronic pancreatitis tissues, and peripheral blood. Based on the analyses, we identified 23 distinct T-cell phenotypes, with some cell clusters exhibiting aberrant frequencies in the tumors. Programmed cell death protein 1 (PD-1) was extensively expressed in CD4⁺ and CD8⁺ T cells and coexpressed with both stimulatory and inhibitory immune markers. In addition, we observed elevated levels of functional markers, such as CD137L and CD69, in PDAC-infiltrating immune cells. Moreover, the combination of PD-1 and CD8 was used to stratify PDAC tumors from The Cancer Genome Atlas database into three immune subtypes, with S1 (PD-1⁺CD8⁺) exhibiting the best prognosis. Further analysis suggested distinct molecular mechanisms for immune exclusion in different subtypes. Taken together, the single-cell protein expression data depicted a detailed cell atlas of the PDAC-infiltrating immune cells and revealed clinically relevant information regarding useful cell phenotypes and targets for immunotherapy development.     

Estimating Single-Cell Lag Times via a Bayesian Scheme

Network models offer computationally efficient tools for estimating the variability of single-cell lag phases. Currently, optical methods for estimating the variability of single-cell lag phases use single-cell inocula and are technically challenging. A Bayesian network model incorporating small uncertain inocula addresses these limitations.     

Oligotrophic Bacterioplankton with a Novel Single-Cell Life Strategy

A large fraction of the marine bacterioplankton community is unable to form colonies on agar surfaces, which so far no experimental evidence can explain. Here we describe a previously undescribed growth behavior of three non-colony-forming oligotrophic bacterioplankton, including a SAR11 cluster representative, the world's most abundant organism. We found that these bacteria exhibit a behavior that promotes growth and dispersal instead of colony formation. Although these bacteria do not form colonies on agar, it was possible to monitor growth on the surface of seawater agar slides containing a fluorescent stain, 4′,6′-diamidino-2-phenylindole (DAPI). Agar slides were prepared by pouring a solution containing 0.7% agar and 0.5 μg of DAPI per ml in seawater onto glass slides. Prompt dispersal of newly divided cells explained the inability to form colonies since immobilized cells (cells immersed in agar) formed microcolonies. The behavior observed suggests a life strategy intended to optimize access of individual cells to substrates. Thus, the inability to form colonies or biofilms appears to be part of a K-selected population strategy in which oligotrophic bacteria explore dissolved organic matter in seawater as single cells.