PCR candidate region mismatch scanning: adaptation to quantitative, high-throughput genotyping

Linkage and association analyses were performed to identify loci affecting disease susceptibility by scoring previously characterized sequence variations such as microsatellites and single nucleotide polymorphisms. Lack of markers in regions of interest, as well as difficulty in adapting various methods to high-throughput settings, often limits the effectiveness of the analyses. We have adapted the Escherichia coli mismatch detection system, employing the factors MutS, MutL and MutH, for use in PCR-based, automated, high-throughput genotyping and mutation detection of genomic DNA. Optimal sensitivity and signal-to-noise ratios were obtained in a straightforward fashion because the detection reaction proved to be principally dependent upon monovalent cation concentration and MutL concentration. Quantitative relationships of the optimal values of these parameters with length of the DNA test fragment were demonstrated, in support of the translocation model for the mechanism of action of these enzymes, rather than the molecular switch model. Thus, rapid, sequence-independent optimization was possible for each new genomic target region. Other factors potentially limiting the flexibility of mismatch scanning, such as positioning of dam recognition sites within the target fragment, have also been investigated. We developed several strategies, which can be easily adapted to automation, for limiting the analysis to intersample heteroduplexes. Thus, the principal barriers to the use of this methodology, which we have designated PCR candidate region mismatch scanning, in cost-effective, high-throughput settings have been removed.     

Checkpoint adaptation precedes spontaneous and damage-induced genomic instability in yeast

Despite the fact that eukaryotic cells enlist checkpoints to block cell cycle progression when their DNA is damaged, cells still undergo frequent genetic rearrangements, both spontaneously and in response to genotoxic agents. We and others have previously characterized a phenomenon (adaptation) in which yeast cells that are arrested at a DNA damage checkpoint eventually override this arrest and reenter the cell cycle, despite the fact that they have not repaired the DNA damage that elicited the arrest. Here, we use mutants that are defective in checkpoint adaptation to show that adaptation is important for achieving the highest possible viability after exposure to DNA-damaging agents, but it also acts as an entrée into some forms of genomic instability. Specifically, the spontaneous and X-ray-induced frequencies of chromosome loss, translocations, and a repair process called break-induced replication occur at significantly reduced rates in adaptation-defective mutants. This indicates that these events occur after a cell has first arrested at the checkpoint and then adapted to that arrest. Because malignant progression frequently involves loss of genes that function in DNA repair, adaptation may promote tumorigenesis by allowing genomic instability to occur in the absence of repair.     

Simulation of spontaneous discharge and short-term adaptation in acoustic nerve fibers

A model for firing of the auditory nerve fibres was carried out on a general purpose digital computer. In the model a noise with small correlation time and with assigned standard deviation (when modeling a spontaneous discharge) or a sum of a noise and a determinated signal (when modeling an elicited discharge) is compared with incremental threshold. When the threshold is exceeded a spike occurs and the threshold is increased. The threshold qualitative properties and quantitative values were chosen in a way to provide the most reliable patterns of spontaneous discharge, according to the literature data obtained from the cat's auditory nerve. When stimulated by tone-bursts the model reveals intrinsic ability of mimicking the phenomena of discharge rate short-term adaptation. Thus according to our model the short-term adaptation is entirely due to the properties of the incremental threshold.     

Single tube genotyping of sickle cell anaemia using PCR-based SNP analysis

Allele-specific amplification (ASA) is a generally applicable technique for the detection of known single nucleotide polymorphisms (SNPs), deletions, insertions and other sequence variations. Conventionally, two reactions are required to determine the zygosity of DNA in a two-allele system, along with significant upstream optimisation to define the specific test conditions. Here, we combine single tube bi-directional ASA with a ‘matrix-based’ optimisation strategy, speeding up the whole process in a reduced reaction set. We use sickle cell anaemia as our model SNP system, a genetic disease that is currently screened using ASA methods. Discriminatory conditions were rapidly optimised enabling the unambiguous identification of DNA from homozygous sickle cell patients (HbS/S), heterozygous carriers (HbA/S) or normal DNA in a single tube. Simple downstream mathematical analyses based on product yield across the optimisation set allow an insight into the important aspects of priming competition and component interactions in this competitive PCR. This strategy can be applied to any polymorphism, defining specific conditions using a multifactorial approach. The inherent simplicity and low cost of this PCR-based method validates bi-directional ASA as an effective tool in future clinical screening and pharmacogenomic research where more expensive fluorescence-based approaches may not be desirable.     

Classification of cell signalling in tissue development

The traditional classification of signalling in biological systems is insufficient and outdated and novel efforts must take into account advances in systems theory, information theory and linguistics. We present some of the classification systems currently used both within and outside of the biological field and discuss some specific aspects of the nature of signalling in tissue development. The analytical methods used in understanding non-biological networks provide a valuable vocabulary, which requires integration and a system of classification to further facilitate development.     

Molecular characterization of spontaneous mesenchymal stem cell transformation

Background

We previously reported the in vitro spontaneous transformation of human mesenchymal stem cells (MSC) generating a population with tumorigenic potential, that we termed transformed mesenchymal cells (TMC).

Methodology/Principal Findings

Here we have characterized the molecular changes associated with TMC generation. Using microarrays techniques we identified a set of altered pathways and a greater number of downregulated than upregulated genes during MSC transformation, in part due to the expression of many untranslated RNAs in MSC. Microarray results were validated by qRT-PCR and protein detection.

Conclusions/Significance

In our model, the transformation process takes place through two sequential steps; first MSC bypass senescence by upregulating c-myc and repressing p16 levels. The cells then bypass cell crisis with acquisition of telomerase activity, Ink4a/Arf locus deletion and Rb hyperphosphorylation. Other transformation-associated changes include modulation of mitochondrial metabolism, DNA damage-repair proteins and cell cycle regulators. In this work we have characterized the molecular mechanisms implicated in TMC generation and we propose a two-stage model by which a human MSC becomes a tumor cell.     

Ultrastructural characteristics of mitochondria during cell adaptation to rotenone

A study was made of respiration, heat production, K+ output and ultrastructure of wheat root cells treated for 6 h with rotenone (10 microM), an inhibitor of HADH-ubiquinone oxidoreductase (Complex I). Besides, the involvement of alternative pathways for adaptation to this inhibitor was studied. After 20 min of treatment, a brightened mitochondrial matrix and mitochondria with torus shapes were observed. We propose that the outer area of mitochondria increases due to their torus shapes, and this can point to the activating of extremal NAD(P)H-dehydrogenase, which uses enternal NAD(P)H. Further on the normal ultrastructure of mitochondria was observed, which may result from activation of succinate dehydrogenase and rotenone resistant NAD(P)H-dehydrogenase. After 1 h of treatment, a decrease in respiration, heat production, K+ output and pH increase of incubation medium were observed. Starting from 2 h of incubation and up to the end of the experiment, an increase of respiration and heat production was observed, pointing to the activation of oxidative phosphorilation. Besides, re-entry of K+ and pH decrease in the incubation medium were observed. We conclude that these findings may indicate to a possible adaptation of root cells to this inhibitor. We propose that the torus shape of mitochondria may be associated with function of external NAD(P)H-dehydrogenase.     

Mechanism of spontaneous inside-out vesiculation of red cell membranes

In certain conditions, human red cell membranes spontaneously form inside out vesicles within 20 min after hypotonic lysis. Study of the geometry of this process now reveals that, contrary to earlier views of vesiculation by endocytosis or by the mechanical shearing of cytoskeleton-depleted membrane, lysis generates a persistent membrane edge which spontaneously curls, cuts, and splices the membrane surface to form single or concentric vesicles. Analysis of the processes by which proteins may stabilize a free membrane edge led us to formulate a novel zip-type mechanism for membrane cutting-splicing and fusion even in the absence of free edges. Such protein-led membrane fusion represents an alternative to mechanisms of membrane fusion based on phospholipid interactions, and may prove relevant to processes of secretion, endocytosis, phagocytosis, and membrane recycling in many cell types.     

Enzymatic studies during spontaneous cell rupture of Saccharomyces cerevisiae

Summary Some of the extract and intracellular enzyme activities in K2nB strain of Saccharomyces cerevisiae that growing in the condition which induce spontaneous cell rupture, were measured. B-1-3-glucanase, invertase, acid phosphatase and active chitin synthetase zymogen showed a reduced activity in ruptured cell while alkaline phosphatase shows no differences in its activity.     

On spontaneous mutagenesis and cell cultivation conditions.

The leu2 revertant content of a Saccharomyces cerevisiae cell culture increases as the leucine concentration in the nutrient solid medium decreases. Reversions form in the S-phase of the cell cycle. If a cell culture from a medium with a low concentration of leucine containing the revertants which have just formed is transferred on a medium with a normal or higher than normal leucine content, these 'newborn' revertants disappear at the end of the G1-phase or at the beginning of the S-phase of the next cell cycle. These data can be explained either by a difference in the ability of revertants formed in the culture to compete with the cells of the initial strain on different media, or on the basis of the intermediate heteroduplex model proposed by F.W. Stahl (1988).     

High-throughput genotyping in citrus accessions using an SNP genotyping array

We developed a 384 multiplexed SNP array, named CitSGA-1, for the genotyping of Citrus cultivars, and evaluated the performance and reliability of the genotyping. SNPs were surveyed by direct sequence comparison of the sequence tagged site (STS) fragment amplified from genomic DNA of cultivars representing the genetic diversity of citrus breeding in Japan. Among 1497 SNPs candidates, 384 SNPs for a high-throughput genotyping array were selected based on physical parameters of Illumina’s bead array criteria. The assay using CitSGA-1 was applied to a hybrid population of 88 progeny and 103 citrus accessions for breeding in Japan, which resulted in 73,726 SNP calls. A total of 351 SNPs (91 %) could call different genotypes among the DNA samples, resulting in a success rate for the assay comparable to previously reported rates for other plant species. To confirm the reliability of SNP genotype calls, parentage analysis was applied, and it indicated that the number of reliable SNPs and corresponding STSs were 276 and 213, respectively. The multiplexed SNP genotyping array reported here will be useful for the efficient construction of linkage map, for the detection of markers for marker-assisted breeding, and for the identification of cultivars.     

Classification of cell types: Agglutination and chromosomal properties

Summary The properties of agglutination by plant lectins, along with chromosome patterns, were examined in a variety of mammalian cell types. Untransformed adult and embryonic cells in culture, direct mouse spleen cell preparations, SV40-transformed 3T3 cells, and trypsinized 3T3 cells were all highly agglutinable with concanavalin A and with wheat germ agglutinin. In contrast, untreated cells of the contact-inhibited 3T3 line were alone among the cells tested in their low agglutinability. Chromosome analysis of the cultured cells showed that karyotypic variation from the diploid to an aneuploid state in mouse and rat embryo cultures was not accompanied by a change in agglutinability. Adult rat lung, adult monkey kidney, and embryonic human lung cells, which were all highly agglutinable, showed the normal diploid pattern. Thus, agglutination of cells by plant lectins appears to be a cellular property often associated with non-neo-plastic cells. This investigation was supported by Grants CA-12503 and ES-00260 from the National Institutes of Health, United States Public Health Service.     

Non-invasive genotyping of primates

Using DNA amplified from shed or plucked hair follicles it is now possible to genotype individual primates at many nuclear and mitochondrial gene loci. Sequence specific primers and the polymerase chain reaction permit the rapid production of sufficient DNA from a single hair for numerous analyses. The direct sequencing of relatively conservative mtDNA sequences like cytochromeb is proving useful in establishing species and subspecies-level relationships. More variable sequences (e.g. the mtDNA control region or D-loop) are useful at the population and social community levels. Paternity exclusion, pedigree relationships, and community structure can be determined using simple sequence length polymorphisms (SSLPs) of multiple hypervariable nuclear microsatellite or simple sequence repeat (SSR) loci. Studies involving captive and free-ranging chimpanzees, gibbons, and macaques illustrate the resolving power of these new non-invasive molecular genetic genotyping techniques.     

Classification of coupling patterns among spontaneous rhythms and ventilation in the sympathetic discharge of decerebrate cats

 The spontaneous low- and high-frequency rhythms in the sympathetic discharge of decerebrate artificially ventilated cats are affected by external ventilation. Two graphical methods (i.e. the space-time separation plot and the frequency tracking locus) are used to classify the non-linear interactions. The observed behaviours in the sympathetic discharge consist of phase-locked periodic dynamics (at various frequency ratios with ventilation), quasiperiodic and aperiodic patterns. They depend on the experimental condition. In control condition the sympathetic discharge appears more frequently locked to each ventilatory cycle (1 : 1 dynamics). However, some cases of quasiperiodic dynamics are found. A sympathetic activation stimulus, such as inferior vena cava occlusion, is able to synchronise slow rhythms in the sympathetic discharge to a subharmonic of ventilation. During a sympathetic inhibition stimulus, such as aortic constriction, 1 : 1 dynamics is detected but the amplitude of the sympathetic responses can be modulated by unlocked slow rhythms. Moreover, some cases of aperiodic dynamics are observed. Vagotomy reduces the 1 : 1 coupling between sympathetic outflow and ventilation. Vagotomy plus spinalisation disrupts periodic dynamics in the sympathetic discharge so that irregular and complex patterns are found. Received: 19 July 1995/Accepted in revised form: 20 May 1996     

Functional analysis of spontaneous cell movement under different physiological conditions

Cells can show not only spontaneous movement but also tactic responses to environmental signals. Since the former can be regarded as the basis to realize the latter, playing essential roles in various cellular functions, it is important to investigate spontaneous movement quantitatively at different physiological conditions in relation to a cell's physiological functions. For that purpose, we observed a series of spontaneous movements by Dictyostelium cells at different developmental periods by using a single cell tracking system. Using statistical analysis of these traced data, we found that cells showed complex dynamics with anomalous diffusion and that their velocity distribution had power-law tails in all conditions. Furthermore, as development proceeded, average velocity and persistency of the movement increased and as too did the exponential behavior in the velocity distribution. Based on these results, we succeeded in applying a generalized Langevin model to the experimental data. With this model, we discuss the relation of spontaneous cell movement to cellular physiological function and its relevance to behavioral strategies for cell survival.     

The adaptation of a two-compartment cell renewal system to external demands

Summary The inner enamel epithelium (IEE) covers the labial tooth aspect as a one cell layer which, when cut sagittally, appears as a longitudinal cell column extending from the tooth origin toward the periphery. Following sudden tooth shortening, the IEE responds by an increased cell production which later declines below normal values. The perturbation affects all cell kinetic parameters; the progenitor compartment, which initially increases, diminishes in size toward end of the experiment. The cell cycle transition times, which initially decline, rise toward the end of the experiment. The mean normal daily cell production rate of 70 cell % (i.e. 70 cells are produced by 100 progenitors) increases to 111 cell % and then declines to a low of 51 cell %. The IEE response typifies the behavior of other cell renewal systems such as intestinal epithelium and epidermis.     

Single cell translocations in couples with multiple spontaneous abortions

Summary Single cell translocations have been previously reported to occur in normal lymphocyte cultures. Comparison of the frequency of these in 140 individuals referred for a history of multiple miscarriages and 415 individuals referred for other reasons showed a significantly greater number of single cell translocations in the former group. This group also had a significantly greater number of other types of single cell structural abnormalities. Increased chromosome instability, chromosome mosaicism, residual fetal trophoblasts, and immunological differences are discussed in considering the possible etiology.