Clonal cells from embryonic retinal cell lines express qualitative electrophysiological differences.

Cells from the embryonic quail retina were immortalized with the v-mil oncogene and cloned by limiting dilution. Their phenotype was examined using the whole-cell patch clamp method. Three membrane currents, IK(IR), INa and IK, were found at different frequencies within a sample of 170 cells drawn from a large clone. Nearly all combinations of these three markers were found and the frequency of combinations showed that the markers assorted independently. Examination of clones of less than 10 cells showed that heterogeneity originates with a high probability within clones, arguing that chromosomal mutation, for example, is unlikely to account for phenotypic diversity. A possible explanation is that phenotypic differences between cells might reflect the local exchange of instructive signals. If so, then the genes for the three phenotypic markers are controlled independently.     

Bacterial Conjugation: An Analysis of Mixed Recombinant Clones

A fraction of recombinant colonies resulting from conjugation is heterogenetic for unselected markers. Constitutivity for alkaline phosphatase synthesis (phoR) is studied as the unselected marker. The frequency of phoR heterogeneity depends on the genetic distance between phoR and the selected marker. Various models are considered which explain the formation of heterogenetic colonies (mixed clones), and experiments are described which test these models. It is concluded that the Hfr fragment can replicate and participate more than once in recombination thus yielding heterogenetic colonies.     

Isolation and characterization of a diverse set of genes from carrot somatic embryos.

The early events in plant embryogenesis are critical for pattern formation, since it is during this process that the primary apical meristems and the embryo polarity axis are established. However, little is known about the molecular events that are unique to the early stages of embryogenesis. This study of gene expression during plant embryogenesis is focused on identifying molecular markers from carrot (Daucus carota) somatic embryos and characterizing the expression and regulation of these genes through embryo development. A cDNA library, prepared from polysomal mRNA of globular embryos, was screened using a subtracted probe; 49 clones were isolated and preliminarily characterized. Sequence analysis revealed a large set of genes, including many new genes, that are expressed in a variety of patterns during embryogenesis and may be regulated by different molecular mechanisms. To our knowledge, this group of clones represents the largest collection of embryo-enhanced genes isolated thus far, and demonstrates the utility of the subtracted-probe approach to the somatic embryo system. It is anticipated that many of these genes may serve as useful molecular markers for early embryo development.     

Preferential deletion of a specific region of mitochondrial DNA in Saccharomyces cerevisiae by ethidium bromide and 3-carbethoxy-psoralen: directional retention of DNA sequence.

Grande strains of Saccharomyces cerevisiae were mutagenized either by ethidium bromide or by 3-carbethoxy-psoralen (a monofunctional furocoumarin derivative) activated by 365nm light. 973 primary rho- clones induced were randomly collected and analyzed individually for the presence or absence of fifteen mitochondrial genetic markers. 1. Under mild conditions of mutagenesis, 83% of the primary clones showed single-deletion genotypes; a unique order of 14 markers could be deduced from the patterns of the deletion. The gene order confirmed our previous map constructed from the analysis of established non-random petite clones. From the frequencies of disjunction between markers, the distance separating 14 mitochondrial markers were estimated. 2. One region, carrying oxi-3, pho-1 and mit 175 loci, was preferentially lost in rho- mutants: there is a strong constraint in the frequencies of various genotypes found in rho- clones. On each side of this particular region, a bidirectionally oriented pattern of retention of markers is observed.     

Serological characterization of macrophage hybridomas: identification of an interferon-gamma-inducible surface marker

Macrophage hybridoma clones prepared by fusion of splenic adherent cells with P388D1 tumor cells have previously been shown to be heterogeneous with respect to function at the clonal level. In this study the macrophage clones were phenotypically characterized by indirect RIA using a battery of rat MAbs to murine myeloid and lymphoid cell surface markers. All macrophage clones expressed the common leukocyte antigen T200 and the Mac-1 alpha and beta chains. Markers which were differentially expressed among the clones included class II antigens and the antigens detected by MAbs MIV 55, MIV 38, and 14G8. The antigens detected by the latter three MAbs were referred to as MBR-1, -2 and -3, respectively. Functional heterogeneity did not correlate with phenotypic heterogeneity among the macrophage clones. Treatment of macrophage clones with IFN-gamma resulted in a significant increase in the expression of class II antigens and induced the expression of MBR antigens on some clones which were constitutively negative for these markers. The clonal distribution and induction patterns of class II antigen as compared to MBR antigen indicated that regulation of expression of these markers was independent. In addition, the clonal distribution and induction pattern of MBR antigens, along with competitive binding studies using radiolabeled MIV 38 and 14G8 MAbs, suggested that the three MBR antigens were similar or closely associated molecules.     

Regulation of idiotope expression. I. The effect of antigen dose on expression of certain T15 idiotopes during primary IgM response to S. pneumoniae R36a

Clonal heterogeneity among B cells reactive to the same epitope may be determined through differences in idiotypy. It appears that clones bearing distinct idiotopes may constitute functionally distinct subpopulations. Data suggest that idiotopically distinct clones of PC-reactive B cells may be regulated independently of one another. We have looked to see whether individual T15+ clones may also differ in their requirements for activation. Here we examine the effect of immunizing doses of antigen on expression of two T15 idiotopes, B36-82 and B39-38, during both in vivo and in vitro primary responses to Streptococcus pneumoniae R36a (Pn) in CB-20 mouse strain. The idiotopes were detected on the specific antibody plaque-forming cells (PFC) by using monoclonal anti-idiotopic antibodies. We find that distinct patterns of idiotope expression are generated by stimulation with different doses of antigen. Immunization with suboptimal and super-optimal doses of Pn produced responses dominated by PFC expressing both idiotopes, whereas PFC induced by optimal antigen concentrations were primarily B36-82+ and B39-38-. These data indicate that the varying of antigen concentration may induce the response of different B cells bearing distinct idiotypes.     

Molecular marker analysis of 24- and 25-chromosome plants obtained from Solanum tuberosum L. subsp. andigena (2n = 4x = 48) pollinated with a Solanum phureja haploid inducer.

Clones with 24 or 25 chromosomes were obtained by pollinating an Andean cultivated tetraploid potato (Solanum tuberosum subsp. andigena clone 94H94, 2n = 4x = 48) with the Solanum phureja haploid-inducer clone 1.22. Their genetic composition was analyzed in an RAPD assay using 135 decamer primers and in an RFLP assay using 45 single-copy DNA probes. In total, 22 RAPD and 20 RFLP markers were found to be specific to S. phureja. None of these markers were found in the 24- and 25-chromosome clones. RFLP genotypes for the 45 RFLP loci were further determined for each clone. Genotypes of the 24-chromosome clones were characterized using two alleles randomly selected from four alleles of the parental tetraploid clone for almost all RFLP loci. Five 25-chromosome clones had extra alleles for all of the RFLP loci of chromosomes 4, 8, 10, 11, and 12, respectively, suggesting primary trisomy for one of these chromosomes. Clones with genotypes showing double reduction were also identified. Therefore, the obtained clones likely originated from random samples of female gametes, and hence are euhaploids or aneuhaploids of S. tuberosum subsp. andigena, strongly supporting parthenogenesis to be a primary mechanism for haploid induction in potato.     

Clonal diversity of populations of Calamagrostis epigejos in relation to environmental stress and habitat heterogeneity

The clonal diversity of four populations of the vegetatively propagating grass Calamagrostis epigejos was studied with isozyme markers From each population, 100 individuals were sampled within a 10 × 10 m gnd In two populations of unpolluted sites 5 and 10 clones were distinguished, respectively Higher levels of clonal diversity were found m the populations at an abandoned sewage farm (59 clones) and around a copper smelter (92 clones) The level of clonal diversity observed suggests that sexual recruitment is important for the genetic structure in this species On the unpolluted, presumably more suitable habitats, the clonal diversity was lower than on the habitats polluted with heavy metals The results are discussed in relation to environmental stress and habitat heterogeneity, with the conclusion that in the unpolluted habitats intraspecific competition results in low clonal diversity On the other hand, stressful conditions decrease the importance of competition and facilitate the coexistence of a great number of clones     

Site-specific modification of the bovine genome using Cre recombinase-mediated gene targeting.

Cre recombinase (Cre)-mediated targeted insertion of a transgene is a powerful technique that can be used to tailor genomes. When combined with somatic cell nuclear transfer it could offer an efficient way to generate transgenic livestock with site-specific genetic modifications that are free of antibiotic selection markers. We have engineered primary bovine fibroblasts to contain a chromosomal acceptor site with incompatible loxP/lox2272 sites for Cre-mediated cassette exchange and show for the first time that Cre-mediated targeting can be applied in these acceptor cells. Molecular characterization of the resulting cell clones revealed Cre-mediated transgene insertion efficiencies of up to 98% when antibiotic selection was used to identify transgene containing cell clones. Most clonal lines also contained random insertions of the targeting and Cre expression plasmids with only about 10% of the clones being exclusively modified by the intended targeted insertion. This targeting efficiency was sufficient to enable the isolation of correctly targeted clones without the help of antibiotic selection. Therefore, this recombinase-mediated insertion strategy has the potential to produce transgenic cattle from antibiotic selection marker-free somatic cells with transgenes inserted into proven genomic loci ensuring reliable expression levels.     

The plasmid of Salmonella typhimurium LT2

Summary Methods of clonal analysis were applied to the study of heterogeneity of the progeny after crosses of 4 donor strains (Hfr H, Hfr C, KL 16 and KL 99) with 3 recipient strains (PC 0212, AB 712 and ECK 022). Three markers were used in each cross. The distal one was the selective marker. The inheritance of two additional proximal markers characterized the heterogeneity of clones originating from particular zygotes. In most crosses the percentage of heterogeneity exceeded 30. One of the recipient strains, obtained by conjugation of the conventional strain PC 0212 with the donor Hfr H revealed unusual properties in respect to heterogeneity. Exconjugants derived from this recipient (ECK 022) and donor Hfr H and Hfr C had a heterogeneity index of about 5%. It is shown that this unusual behavior reflects a very fast process of segregation of recombinants.In crosses with the donors KL 16 and KL 99 the same recipient revealed normal indices of heterogeneity. All these data are explained assuming that there exists a specific genetic marker which determines the process of decay of merozygotes. Tentatively it is called het. Its approximate localization was deduced from specifically designed experiments, in which the heterogeneity of the progeny was found very different, when the donor KL 16 transmitted different parts of its chromosome to the recipient ECK 022.     

A general statistical model for detecting complex-trait loci by using affected relative pairs in a genome search.

Scanning of the human genome by use of affected relative pairs and dense sets of highly polymorphic markers or by emerging techniques such as genomic mismatch scanning. (GMS) is making it possible to identify the genetic etiology of a disease through detection of susceptibility loci. We present a general statistical model and test to detect disease genes, using affected relative pairs and either markers or GMS technologies in a genome search. There are an exact test and large-sample normal approximation that control for the elevated probability of false detection of linkage in a genome search. The approach can be used to determine the sample size needed to obtain a prespecified power to detect a disease gene in the presence of etiologic heterogeneity for a single class or mixture of relative classes, with any number of markers, or clones, markers PIC values, or mapping function. The approach is used to examine differences in performance of markers and GMS technologies in a common statistical framework and to provide practical information for designing studies of complex traits.     

Intratumor heterogeneity: Nature and biological significance

Intratumor heterogeneity inherent in the majority of human cancers is a major obstacle for a highly efficient diagnosis and successful prognosis and treatment of these diseases. Being a result of clonal diversity within the same tumor, intratumor heterogeneity can be manifested in variability of genetic and epigenetic status, gene and protein expression, morphological structure, and other features of the tumor. It is most likely that the appearance of this diversity is a source for the adaptation of the tumor to changes in microenvironmental conditions and/or a tool for changing its malignant potential. In any case, both processes result in the appearance of cell clones with different undetermined sets of hallmarks. In this review, we describe the heterogeneity of molecular disorders in various human tumors and consider modern viewpoints of its development including genetic and non-genetic factors of heterogeneity origin and the role of cancer stem cells and clonal evolution. We also systematize data on the contribution of tumor diversity to progression of various tumors and the efficiency of their treatment. The main problems are indicated in the diagnosis and therapy of malignant tumors caused by intratumor heterogeneity and possible pathways for their solution. Moreover, we also suggest the key goals whose achievement promises to minimize the problem of intratumor heterogeneity and to identify new prognostic, predictive, and target markers for adequate and effective treatment of cancer.     

Evidence of distinct tumour-propagating cell populations with different properties in primary human hepatocellular carcinoma

Background and Aims

Increasing evidence that a number of malignancies are characterised by tumour cell heterogeneity has recently been published, but there is still a lack of data concerning liver cancers. The aim of this study was to investigate and characterise tumour-propagating cell (TPC) compartments within human hepatocellular carcinoma (HCC).

Methods

After long-term culture, we identified three morphologically different tumour cell populations in a single HCC specimen, and extensively characterised them by means of flow cytometry, fluorescence microscopy, karyotyping and microarray analyses, single cell cloning, and xenotransplantation in NOD/SCID/IL2Rγ^−/− mice.

Results

The primary cell populations (hcc-1, -2 and -3) and two clones generated by means of limiting dilutions from hcc-1 (clone-1/7 and -1/8) differently expressed a number of tumour-associated stem cell markers, including EpCAM, CD49f, CD44, CD133, CD56, Thy-1, ALDH and CK19, and also showed different doubling times, drug resistance and tumorigenic potential. Moreover, we found that ALDH expression, in combination with CD44 or Thy-1 negativity or CD56 positivity identified subpopulations with a higher clonogenic potential within hcc-1, hcc-2 and hcc-3 primary cell populations, respectively. Karyotyping revealed the clonal evolution of the cell populations and clones within the primary tumour. Importantly, the primary tumour cell population with the greatest tumorigenic potential and drug resistance showed more chromosomal alterations than the others and contained clones with epithelial and mesenchymal features.

Conclusions

Individual HCCs can harbor different self-renewing tumorigenic cell types expressing a variety of morphological and phenotypical markers, karyotypic evolution and different gene expression profiles. This suggests that the models of hepatic carcinogenesis should take into account TPC heterogeneity due to intratumour clonal evolution.     

Molecular mapping of wheat. Homoeologous group 3.

A prerequisite for molecular level genetic studies and breeding in wheat is a molecular marker map detailing its similarities with those of other grass species in the Gramineae family. We have constructed restriction fragment length polymorphism maps of the A-, B-, and D-genome chromosomes of homoeologous group 3 of hexaploid wheat (Triticum aestivum L. em. Thell) using 114 F7-8 lines from a synthetic x bread wheat cross. The map consists of 58 markers spanning 230 cM on chromosome 3A, 62 markers spanning 260 cM on 3B, and 40 markers spanning 171 cM on 3D. Thirteen libraries of genomic or cDNA clones from wheat, barley, and T. tauschii, the wheat D genome donor, are represented, facilitating the alignment and comparison of these maps with maps of other grass species. Twenty-four clones reveal homoeoloci on two of the three genomes and the associated linkages are largely comparable across genomes. A consensus sequence of orthologous loci in grass species genomes is assembled from this map and from existing maps of the chromosome-3 homoeologs in barley (Hordeum spp.), T. tauschii, and rice (Oryza spp.). It illustrates the close homoeology among the four species and the partial homoeology of wheat chromosome 3 with oat (Avena spp.) chromosome C. Two orthologous red grain color genes, R3 and R1, are mapped on chromosome arms 3BL and 3DL.     

Clonal variation and aging of diploid fibroblasts : Cinematographic studies of cell pedigrees

Time-lapse cinematographic (TLC) analysis of clones of human diploid fibroblasts indicate heterogeneity in clonal division behaviour. Variations are noted in interdivision time, clone size and generations per clone. Correlation coefficients for interdivision times of sister pairs are high in young clones and generally low in aged clones. A consistent division pattern at all population doubling levels is one of low average interdivision time for early and late generations of a clone and high average interdivision time for the middle range of generations of a clone. The clonal division patterns observed experimentally have been duplicated in computer simulated pedigrees. The computer model is based on an oscillating system which allows for flux of regulator substances. The critical concentrations of regulator substances determine the clonal division pattern for a given progenitor cell.     

Clonal cells from embryonic retinal cell lines express qualitative electrophysiological differences

Cells from the embryonic quail retina were immortalized with the v-mil oncogene and cloned by limiting dilution. Their phenotype was examined using the whole-cell patch clamp method. Three membrane currents, I_k(IR), I_Na and I_K, were found at different frequencies within a sample of 170 cells drawn from a large clone. Nearly all combinations of these three markers were found and the frequency of combinations showed that the markers assorted independently. Examination of clones of less than 10 cells showed that heterogeneity originates with a high probability within clones, arguing that chromosomal mutation, for example, is unlikely to account for phenotypic diversity. A possible explanation is that phenotypic differences between cells might reflect the local exchange of instructive signals. If so, then the genes for the three phenotypic markers are controlled independently.     

Model misspecification and multipoint linkage analysis.

Pairwise linkage analysis is robust to genetic model misspecification provided dominance is correctly specified, the primary effect being inflation of the recombination fraction. By contrast, we show that multipoint analysis under misspecified models is not robust when a putative disease locus is placed between close flanking markers, with potentially spuriously negative multipoint lod scores being produced. The problem is due to incorrect attribution of segregation of a disease allele and the consequent conclusion of (unlikely) double crossovers between flanking markers. As a possible solution, we propose the use of high disease allele frequencies, as this allows probabilistically for nonsegregation (through parental homozygosity or dual matings). We show analytically and through analysis of pedigree data simulated under a two-locus heterogeneity model that using a disease allele frequency of 0.05 in the dominant case and 0.25 in the recessive case is quite robust in producing positive multipoint lod scores with close flanking markers across a broad range of conditions including varying allele frequencies, epistasis, genetic heterogeneity and phenocopies.     

Solving the puzzle of metastasis: the evolution of cell migration in neoplasms

Background

Metastasis represents one of the most clinically important transitions in neoplastic progression. The evolution of metastasis is a puzzle because a metastatic clone is at a disadvantage in competition for space and resources with non-metastatic clones in the primary tumor. Metastatic clones waste some of their reproductive potential on emigrating cells with little chance of establishing metastases. We suggest that resource heterogeneity within primary tumors selects for cell migration, and that cell emigration is a by-product of that selection.

Methods and Findings

We developed an agent-based model to simulate the evolution of neoplastic cell migration. We simulated the essential dynamics of neoangiogenesis and blood vessel occlusion that lead to resource heterogeneity in neoplasms. We observed the probability and speed of cell migration that evolves with changes in parameters that control the degree of spatial and temporal resource heterogeneity. Across a broad range of realistic parameter values, increasing degrees of spatial and temporal heterogeneity select for the evolution of increased cell migration and emigration.

Conclusions

We showed that variability in resources within a neoplasm (e.g. oxygen and nutrients provided by angiogenesis) is sufficient to select for cells with high motility. These cells are also more likely to emigrate from the tumor, which is the first step in metastasis and the key to the puzzle of metastasis. Thus, we have identified a novel potential solution to the puzzle of metastasis.