单菌落PCR法直接快速鉴定重组克隆

利用单菌落PCR法直接筛选含有GFP、LTB-ST外源基因的重组克隆,阳性克隆可以扩增出目的条带,和质粒PCR扩增的结果一致。同时,单菌落PCR法也可应用于重组质粒转化后的农杆菌的筛选,单菌落PCR法的扩增结果和农杆菌液扩增的结果一致。结果表明,单菌落PCR法是一个有效简便的鉴定重组阳性克隆的方法。     

Improved protocols for the isolation and in-situ cryopreservation of cell colonies

Stable transfection and cloning of cells often require physical separation of cell colonies. In order to conveniently isolate cell clones from petri dishes, we developed a protocol starting with a soft agar overlay of cells. This reduces the risk of cell diffusion between different colonies. Cells from individual colonies are mechanically removed, incubated with trypsin, and cell suspensions are seeded onto parallel microtiter plates. The cell clones on one microtiter plate can be cryopreserved in situ using the protocol described here which was tested for a variety of cell lines. Replica plates can be used for screening and further expansion of interesting clones. If screening can also be performed in situ, e.g., by immunocytochemistry, immunofluorescence, or the polymerase chain reaction, it is possible to perform most steps necessary in cell cloning experiments on microtiter plates.     

A simple PCR procedure for discovering microsatellites from small insert libraries

Microsatellite discovery from genomic libraries is tedious because of the low number of clones that contain inserts and costly because of screening methodologies. A new procedure for screening clones for microsatellite DNA is described herein. Instead of colony hybridization, a polymerase chain reaction (PCR) with two vector standard primers and one synthesized repeat primer was used to directly screen colonies. PCR of colonies that produced a strong smear in gels contained the desired motif, whereas a single strong band indicated the lack of the desired motif. This simple screening method is a cost‐effective way to identify microsatellite‐containing colonies.     

Rapid cloning of mammalian cells with honeycomb cloning plates and nonlethal vital stains

A rapid and technically simple method for cloning both adhesive and nonadhesive mammalian cells is described. The procedure employs (a) honeycomb cloning plates and (b) nonlethal vital stains. Instead of placing cloning rings around colonies, cells are initially seeded at clonal density directly into a plate containing an array of cloning rings (the honeycomb plate). Hence, the time involved in placing cloning rings around colonies is eliminated. Second, clone-containing wells of the honeycomb plate are easily identified by staining plates with the nonlethal vital stains, MTT or INT tetrazolium. Vital staining eliminates the time involved in searching for clones. Last, clones are transferred with a cotton-tipped swab thereby eliminating the time involved in trypsinization of cells. In this fashion, one can pick and transfer clones of substrate adherent mammalian cells at a rate of one clone/10 to 15 s. Thus, mammalian cells can be cloned as rapidly as cloning can be carried out in microbial systems.     

Chromosomal assignment of human YAC clones by fluorescence in situ hybridization: use of single-yeast-colony PCR and multiple labeling.

Alu-PCR provides a convenient tool for amplification of human-specific sequences from yeast DNA containing yeast artificial chromosomes (YAC) clones. PCR products can be labeled nonisotopically and hybridized in situ, and the chromosomal origin of the clones can be determined. This avoids time-consuming gel purification of the yeast artificial chromosome and the low-efficiency procedure of labeling whole yeast DNA containing the YAC. The application of Alu-PCR to single-yeast colonies permits the mapping of YACs at a very early stage of their characterization. In situ hybridization can detect clones with noncontiguous fragments of DNA, and these can be discarded without further time-consuming characterization. To increase further the potential of the method, we show the application of multicolor hybridization techniques.     

A modified procedure for replica plating of mammalian cells allowing selection of clones based on gene expression.

The polyester cloth replica-plating technique for selection of mammalian cell clones was modified by growing cells in colonies on a flexible polytetrafluoroethylene membrane and then transferring them completely to polyester cloth (27-microns mesh), from which a replica was made by allowing cells to transfer to a cloth of smaller pore size (17-microns mesh). Using this technique, two phenotype selection methods are demonstrated here: in situ hybridization for detection of a specific mRNA and a photographic film assay for detection of luciferase expression. Cells were transfected with pSV2AL-A delta 5' in which firefly luciferase cDNA is under the control of the simian virus 40 promoter. The luciferase assay was adapted for colonies on polyester cloth; cells were permeabilized with digitonin to allow access of ATP and luciferin to the cell without disruption of colonies. Clones selected for expression or nonexpression of luciferase by the photographic film assay were positive or negative for expression after isolation from the cloth replica and subsequent growth under conventional culture conditions. The replica-plating procedure described here should be generally applicable to most mammalian cell types. The ability to produce replicas of colonies, combined with in situ hybridization or assays that can be adapted to in situ detection, provides phenotype selection for clones based on gene expression independent of growth characteristics.     

Construction of tomato genomic DNA libraries in a binary-BAC (BIBAC) vector

This is the first report of large insert genomic DNA libraries constructed in a binary-BAC (BIBAC) vector. Genomic DNA libraries containing approximately 4.6 haploid nuclear genomic equivalents were constructed for Lycopersicon esculentum (cv. Mogeor) and Lycopersicon pennellii (LA716) in the BIBAC2 vector. The L. esculentum library has an average insert size of 125 kb and is comprised of 42 272 individual colonies stored as frozen cultures in a 384-well format (108 plates). The L. pennellii library has an average insert size of 90 kb and is comprised of 53 760 individual clones (140 384-well plates). In each of the libraries, it is estimated that 90% of the colonies contain genomic DNA inserts. The composition of the L. esculentum and L. pennellii libraries was determined by analyzing a series of randomly selected clones. The L. esculentum library was surveyed for clones containing chloroplast DNA (1.4%), mitochondrial DNA (0.012%) and repetitive DNA motifs. BIBAC clones that may contain a gene of interest can be identified from these libraries by colony hybridization with homologous or heterologous probes or by PCR pooling techniques. Once identified, BIBAC genomic DNA library clones are immediately suitable for Agrobacterium tumefaciens-mediated plant transformation.     

Rapid cloning of mammalian cells with honeycomb cloning plates and nonlethal vital stains

Summary A rapid and technically simple method for cloning both adhesive and nonadhesive mammalian cells is described. The procedure employs (a) honeycomb cloning plates and (b) nonlethal vital stains. Instead of placing cloning rings around colonies, cells are initially seeded at clonal density directly into a plate containing an array of cloning rings (the honeycomb plate). Hence, the time involved in placing cloning rings around colonies is eliminated. Second, clone-containing wells of the honeycomb plate are easily identified by staining plates with the nonlethal vital stains, MTT or INT tetrazolium. Vital staining eliminates the time involved in searching for clones. Last, clones are transferred with a cotton-tipped swab thereby eliminating the time involved in trypsinization of cells. In this fashion, one can pick and transfer clones ofsubstrate adherent mammalian cells at a rate of one clone/ 10 to 15 s. Thus, mammalian cells can be cloned as rapidly as cloning can be carried out in microbial systems. This study was supported, in part, by Grant CA 33074 from the National Cancer Institute, Bethesda, MD, Grant PCM-8218137 from the National Science Foundation, Washington, D.C., and a grant from the National March of Dimes.     

Selection strategies for the establishment of recombinant Chinese hamster ovary cell line with dihydrofolate reductase-mediated gene amplification

To evaluate the efficacy of selection strategies for recombinant Chinese hamster ovary (rCHO) clones undergone with dihydrofolate reductase-mediated gene amplification, rCHO cell lines producing a chimeric antibody were established using two strategies, one based on individual clones and the other based on cell pools. In a selection based on individual clones, cell cloning by limiting dilution method was performed twice, once after a round of selection of parental cell clones and once after obtaining high-producer clones. Thirty parental clones selected from 300 parental clones were cultivated independently throughout the gene amplification procedure. Using this labor-intensive strategy, it took approximately 17 weeks to obtain high-producing clones such as CS11-8 and CS18-3 clones. A selection based on cell pools, in which cell cloning was performed once at the final selection stage, required less effort and time to amplify large numbers of individual parental clones within the pool. However, high-producing clones were lost during the amplification procedure. The antibody expression level of high-producing clones such as PS7-2 and PS7-32 chosen on the basis of cell pools was less than one third of that of CS11-8 and CS18-3 clones. Taken together, a selection strategy based on individual clones is favored for establishment of high-producing rCHO clones because it is more efficient to perform cell cloning at the initial selection stage of parental cell clones.     

Bone marrow osteogenic stem cells: in vitro cultivation and transplantation in diffusion chambers

Fibroblast colonies (clones) were obtained by explantation of bone marrow single-cell suspensions and were used to establish multicolony and single-colony derived fibroblast cultures by successive passaging of either pooled or individual colonies. When transplanted in diffusion chambers after 20-30 cell doublings in vitro, the descendants of fibroblast colony-forming cells (FCFC), whether grown from single or pooled colonies, retained the ability for bone and cartilage formation. The content of osteogenic precursors in the cultured progeny significantly outnumbered the initiating FCFC. Thus the high proliferative potential of bone marrow FCFC and their ability to serve as common precursors of bone and cartilage-forming cells makes them probable candidates for the role of osteogenic stem cells.     

Genotype-Based Recognition Among Individuals of the Social Insect Pristomyrmex Punctatus (Japanese Queenless Ant) from Geographically Divergent Populations

The queenless ant, Pristomyrmex punctatus (F. Smith) reproduces parthenogenetically. The workers lay unfertilized eggs, which develop into female workers. This mode of reproduction generates hereditary clones. A previous research shows that when genetically monomorphic colonies were split, the workers tended to reassemble after being split into two groups, but when genetically polymorphic colonies split, they remained as two separate colonies. However, it remains unclear whether the workers can recognize individual genotype. Here, it was investigated whether individuals from geographically divergent, genetically monomorphic colonies would assemble with individuals of the same genotype. Two artificially fused colonies were prepared, A and B, comprising 200 individuals and 100 individuals, respectively. Each half of the artificially fused colony was composed of workers from two different genetically monomorphic source colonies. The workers assembled as a single colony when the genotype of the source colonies was identical. However, when the genotypes of source colonies were different, the workers did not assemble into one colony, but split into two groups according to genotype. These results suggest that P. punctatus can potentially recognize individual genotype, and select colony members based on an individual’s genotype.     

Correlation between bizarre colony morphology and metastatic potential of tumor cells

The morphology of colonies developing from cells of UV-2237 fibrosarcoma clones grown in an unattached state correlated with their experimental metastatic potential in vivo. The frequency of bizarre-shaped (non-symmetrical) colonies was increased in colonies that developed from cells of highly metastatic clones growing in an overlay of media on agar, in 1.3% Methocel, or in 0.3% Noble agar. These bizarre-shaped colonies rarely developed from cells of clones with low metastatic frequency. In addition, when tested for in vivo experimental metastasis, the cells from the bizarre colonies were highly metastatic.     

Bone marrow osteogenic stem cells: in vitro cultivation and transplantation in diffusion chambers

Abstract. Fibroblast colonies (clones) were obtained by explantation of bone marrow single-cell suspensions and were used to establish multicolony and single-colony derived fibroblast cultures by successive passaging of either pooled or individual colonies. When transplanted in diffusion chambers after 20–30 cell doublings in vitro , the descendants of fibroblast colony-forming cells (FCFC), whether grown from single or pooled colonies, retained the ability for bone and cartilage formation. The content of osteogenic precursors in the cultured progeny significantly outnumbered the initiating FCFC. Thus the high proliferative potential of bone marrow FCFC and their ability to serve as common precursors of bone and cartilage-forming cells makes them probable candidates for the role of osteogenic stem cells.     

Procedure for the isolation of mutants of Bacillus subtilis with defective cytoplasmic membranes

A procedure has been devised to isolate mutants of Bacillus subtilis with structurally defective membranes. The procedure used to screen for the mutants involved comparison of the stability of protoplasts of the mutant with those of the wild type in a medium of sufficient osmotic strength to stabilize wild-type protoplasts. Mutagenized cells were grown as clones on agar plates, and then replicated onto plates containing 0.5 m lactose, which is sufficient to stabilize wild-type protoplasts. The colonies on the lactose-containing plates were then treated with lysozyme to convert the cells to protoplasts. Colonies of wild-type protoplasts remained opaque; however, colonies of mutant protoplasts lysed and became clear. Twenty-nine osmotically fragile mutants were isolated in this manner; the membranes of several mutants were found to contain alterations in the composition of their proteins or lipids.     

The characteristics of an anchorage-independent clonal agar assay for primary explanted bovine granulosa cells

Normal, primary explanted, bovine granulosa cells grow reproducibly in agar culture as anchorage-independent clones. Epidermal growth factor (EGF) and rat erythrocytes are effective stimulators of colony formation, and when both are added to the culture medium at optimal concentrations, there is an enhancement of colony numbers and colony size, indicative of an independent, and operationally additive, mode of action for the two factors. The ability of cells propagated from agar clones to secrete progesterone, and to augment progesterone secretion 4-fold in the presence of 1 mM dbcAMP is proof that colonies originate from and are composed of functional granulosa cells. Maximal colony numbers are present at day 10 of incubation, and colony forming cells undergo self-renewal as assessed by the ability of cells from primary colonies to reclone in agar. Absolute cloning efficiency, however, is dependent on a number of factors. Inherent variability exists in cloning efficiency of granulosa cells from individual follicles. Quantitative and qualitative clonal growth was improved at an osmolality of less than 300 mOsm when compared with higher osmolalities. Cl-1 medium and the alpha modification of Eagle's medium were equally effective in supporting agar clonogenic growth, whereas both Ham's F12 and NCTC 135 media exhibited poor clonogenic growth supporting properties. The substitution of agarose for agar did not affect colony numbers but colonies grown in the presence of agarose tended to be smaller and more uniform in size.     

Investigation of the mesenchymal stem cell compartment by means of a lentiviral barcode library

The hematopoietic bone marrow microenvironment is formed by proliferation and differentiation of mesenchymal stem cells (MSCs). The MSC compartment has been less studied than the hematopoietic stem cell compartment. To characterize the structure of the MSC compartment, it is necessary to trace the fate of distinct mesenchymal cells. To do so, mesenchymal progenitors need to be marked at the single-cell level. A method for individual marking of normal and cancer stem cells based on genetic “barcodes” has been developed for the last 10 years. Such approach has not yet been applied to MSCs. The aim of this study was to evaluate the possibility of using such barcoding strategy to mark MSCs and their descendants, colony-forming units of fibroblasts (CFU-Fs). Adherent cell layers (ACLs) of murine long-term bone marrow cultures (LTBMCs) were transduced with a lentiviral library with barcodes consisting of 32 + 3 degenerate nucleotides. Infected ACLs were suspended, and CFU-F-derived clones were obtained. DNA was isolated from each individual colony, and barcodes were analyzed in marked CFU-F-derived colonies by means of conventional polymerase chain reaction and Sanger sequencing. Barcodes were identified in 154 marked colonies. All barcodes appeared to be unique: there were no two distinct colonies bearing the same barcode. It was shown that ACLs included CFU-Fs with different proliferative potential. MSCs are located higher in the hierarchy of mesenchymal progenitors than CFU-Fs, so the presented data indicate that MSCs proliferate rarely in LTBMCs. A method of stable individual marking and comparing the markers in mesenchymal progenitor cells has been developed in this work. We show for the first time that a barcoded library of lentiviruses is an effective tool for studying stromal progenitor cells.     

应用抑制性差减杂交法分离法分离阜豆苗期根系镉胁迫诱导表达的基因

以1/2Hoagland溶液培养的阜豆幼苗根系为对照群体,含Cd2+浓度为100μM营养液处理的为目标群体,进行抑制差减杂交。用经过对照组cDNA差减目标组cDNA构建了一个含有大约600个独立克隆的差减文库。随机挑取部分克隆进行菌落PCR鉴定,表明插入的片段大小均在250～800 bp。对已确认的6个阳性克隆测序,序列分析和同源性比较,表明它们与镉胁迫有关。     

Hypervariability, a new phenomenon of genetic instability, related to DNA amplification in Streptomyces ambofaciens.

The wild-type strain Streptomyces ambofaciens DSM 40697 exhibits a high degree of genetic instability. Pigment-defective colonies were observed in the progeny of wild-type colonies at a frequency of about 0.01. While only 13% of these pigment-defective colonies gave rise to homogeneous progeny exhibiting the mutant parental phenotype, 87% of the mutant colonies gave rise to hetergeneous progeny without a preponderant phenotype. This new phenomenon of instability was called hypervariability. In addition, 21% of the mutant strains arising in hypervariable progeny contained highly reiterated DNA sequences, while amplified DNA sequences could be detected in neither stable pigment-defective mutant clones nor in wild-type clones. These results indicate a frequent association between genetic instability and hypervariability and a frequent association between hypervariability and amplification of DNA sequences.