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At least 109 records · Page 6Linked to original sources
PubMed2006

Evaluating the delayed effects of cellular exposure to ionizing radiation.

A number of ongoing delayed effects have now been described in the progeny of an irradiated cell. These are grouped under the rubric of radiation induced genomic instability. Perhaps the best characterized is the dynamic production of chromosomal rearrangements in some clonally expanded cells surviving irradiation. In this chapter we provide the protocols for irradiation, cell culture, chromosome analysis, and characterization of the status of genomic stability in the context of delayed radiation effects.

Cells, Cultured↗
PubMed2002

Cyclic dynamics in simulated plant populations.

Despite the general interest in nonlinear dynamics in animal populations, plant populations are supposed to show a stable equilibrium that is attributed to fundamental differences compared with animals. Some studies find more complex dynamics, but empirical studies usually are too short and most modelling studies ignore important spatial aspects of local competition and establishment. Therefore, we used a spatially explicit individual-based model of a hypothetical, non-clonal perennial to explore which mechanisms might generate complex dynamics, i.e. cycles. The model is based on the field-of-neighbourhood approach that describes local competition and establishment in a phenomenological manner. We found cyclic population dynamics for a wide spectrum of model variants, provided that mortality is determined by local competition and recruitment is virtually completely suppressed within the zone of influence of established plants. This destabilizing effect of local processes within plant populations might have wide-ranging implications for the understanding of plant community dynamics and coexistence.

Ecosystem↗
PubMed2006

Stochastic cancer progression driven by non-clonal chromosome aberrations.

Cancer research has previously focused on the identification of specific genes and pathways responsible for cancer initiation and progression based on the prevailing viewpoint that cancer is caused by a stepwise accumulation of genetic aberrations. This viewpoint, however, is not consistent with the clinical finding that tumors display high levels of genetic heterogeneity and distinctive karyotypes. We show that chromosomal instability primarily generates stochastic karyotypic changes leading to the random progression of cancer. This was accomplished by tracing karyotypic patterns of individual cells that contained either defective genes responsible for genome integrity or were challenged by onco-proteins or carcinogens that destabilized the genome. Analysis included the tracing of patterns of karyotypic evolution during different stages of cellular immortalization. This study revealed that non-clonal chromosomal aberrations (NCCAs) (both aneuploidy and structural aberrations) and not recurrent clonal chromosomal aberrations (CCAs) are directly linked to genomic instability and karyotypic evolution. Discovery of "transitional CCAs" during in vitro immortalization clearly demonstrates that karyotypic evolution in solid tumors is not a continuous process. NCCAs and their dynamic interplay with CCAs create infinite genomic combinations leading to clonal diversity necessary for cancer cell evolution. The karyotypic chaos observed within the cell crisis stage prior to establishment of the immortalization further supports the ultimate importance of genetic aberrations at the karyotypic or genome level. Therefore, genomic instability generated NCCAs are a key driving force in cancer progression. The dynamic relationship between NCCAs and CCAs provides a mechanism underlying chromosomal based cancer evolution and could have broad clinical applications.

Animals↗
PubMed2002

Population dynamics of a heterogeneous Borrelia burgdorferi B31 strain in an experimental mouse-tick infectious cycle.

We have recently shown that low-passage, infectious Borrelia burgdorferi strain B31 MI is a heterogeneous mixture of clones varying in colony morphology, growth rate, protein profiles, plasmid content and infectivity. In this study, we asked whether there is a selection for certain clonal populations during the infectious cycle when uncloned B31 MI is used as the starting strain. B31 MI derivatives were reisolated from various tissues of two mice after completion of a mouse-tick-mouse infectious cycle and their protein and plasmid profiles were analyzed. Both mice developed ostensibly clonal infections despite the fact that the infectious cycle was started with a heterogeneous strain. Moreover, the mice became infected with two different clones varying in protein profile and growth phenotype. Comparison of the mouse reisolates to uncloned B31 MI and clonal variants derived from B31 MI before mouse-tick-mouse passage suggests that they were derived from clonal populations present in the uncloned B31 MI. Our results indicate the presence of at least two distinct populations within B31 MI that are competent to complete an experimental mouse-tick infectious cycle. The study provides insight into infectivity profiles and infection dynamics of different clonal populations present in a low-passage, infectious B. burgdorferi strain.

Animals↗
PubMed2005

Scaling, genetic drift, and clonal interference in the extinction pattern of asexual population.

We investigate the dynamics of loss of favorable mutations in an asexual haploid population. In the current work, we consider homogeneous as well as spatially structured population models. We focus our analysis on statistical measurements of the probability distribution of the maximum population size N(sb) achieved by those mutations that have not reached fixation. Our results show a crossover behavior which demonstrates the occurrence of two evolutionary regimes. In the first regime, which takes place for small N(sb) , the probability distribution is described by a power law with characteristic exponent theta(d) =1.8 +/- 0.01. This power law is not influenced by the rate of beneficial mutations. The second regime, which occurs for intermediate to large values of N(sb), has a characteristic exponent theta(c) which increases as the rate of beneficial mutations grows. These results establish where genetic drift and clonal interference become the main underlying mechanism in the extinction of advantageous mutations.

Demography↗
PubMed2005

In vivo measurements document the dynamic cellular kinetics of chronic lymphocytic leukemia B cells.

Due to its relatively slow clinical progression, B cell chronic lymphocytic leukemia (B-CLL) is classically described as a disease of accumulation rather than proliferation. However, evidence for various forms of clonal evolution suggests that B-CLL clones may be more dynamic than previously assumed. We used a nonradioactive, stable isotopic labeling method to measure B-CLL cell kinetics in vivo. Nineteen patients drank an aliquot of deuterated water (2H2O) daily for 84 days, and 2H incorporation into the deoxyribose moiety of DNA of newly divided B-CLL cells was measured by gas chromatography/mass spectrometry, during and after the labeling period. Birth rates were calculated from the kinetic profiles. Death rates were defined as the difference between calculated birth and growth rates. These analyses demonstrated that the leukemic cells of each patient had definable and often substantial birth rates, varying from 0.1% to greater than 1.0% of the entire clone per day. Those patients with birth rates greater than 0.35% per day were much more likely to exhibit active or to develop progressive disease than those with lower birth rates Thus, B-CLL is not a static disease that results simply from accumulation of long-lived lymphocytes. Rather, it is a dynamic process composed also of cells that proliferate and die, often at appreciable levels. The extent to which this turnover occurs has not been previously appreciated. A correlation between birth rates and disease activity and progression appears to exist, which may help identify patients at risk for worsening disease in advance of clinical deterioration.

Aged↗
PubMed2003

Genetic structure and reproduction dynamics of Salix reinii during primary succession on Mount Fuji, as revealed by nuclear and chloroplast microsatellite analysis.

The early stage of volcanic desert succession is underway on the southeastern slope of Mount Fuji. We used markers of nuclear microsatellites (simple sequence repeats; SSR) and chloroplast microsatellites (cpSSR) to investigate the population genetic structure and reproduction dynamics of Salix reinii, one of the dominant pioneer shrubs in this area. The number of S. reinii genets in a patch and the area of the largest genet within the patch increased with patch area, suggesting that both clonal growth and seedling recruitment are involved in the reproduction dynamics of S. reinii. Five polymorphic cpSSR markers were developed for S. reinii by sequencing the noncoding regions between universal sequences in the chloroplast genome. Nineteen different cpSSR haplotypes were identified, indicating that S. reinii pioneer genets were created by the long-distance dispersal of seeds originating from different mother genets around the study site, where all vegetation was destroyed during the last eruption. Furthermore, the clustered distributions of different haplotypes within each patch or plot suggested that newly colonized genets tended to be generated from seeds dispersed near the initially established mother genets. These results revealed that the establishment of the S. reinii population on the southeastern slope of Mount Fuji involved two sequential modes of seed dispersal: long-distance dispersal followed by short-distance dispersal.

Cell Nucleus↗
PubMed2003

Sexual recombination and clonal evolution of virulence in Toxoplasma.

The protozoan parasite Toxoplasma gondii is endemic worldwide. For such a widespread pathogen that has few geographic or host boundaries, it possess an unexpected population structure comprised principally of three clonally propagated lineages. The origin and the evolutionary dynamics of these three lines are unclear. Recent population genetic analyses suggest that a meiotic recombination between two discrete gene pools produces a pandemic outbreak of three super-successful lines, which have recently come to dominate most other strains worldwide.

Animals↗
PubMed1998

T-cell receptor variable gene analysis of renal allograft-infiltrating cells in biopsy specimens using a nonradioisotopic micromethod.

BACKGROUND: A sensitive micromethod for T-cell receptor (TCR) analysis is needed for clonality analysis of renal allograft-infiltrating T cells (RAITs) obtained by needle biopsy. METHODS: TCR cDNA was amplified by the anchored polymerase chain reaction and was hybridized with 28 different TCR beta variable (TCRBV) genes fixed on nylon membranes, and the percentage of each TCRBV gene was measured spectrophotometrically. RESULTS: The specificity and linearity of the hybridization technique and the constancy of the TCRBV percentages over a wide range of sample amounts were demonstrated by control experiments. Analysis of RAITs of biopsy specimens from four patients showed broad or skewed TCRBV usage, indicating the presence of polyclonal and oligoclonal RAIT populations, respectively. In one patient who received OKT3 immunosuppressive treatment, the TCRBV skewness was dramatically reduced after the treatment. CONCLUSION: We have established a powerful method for analyzing RAIT clonality, which is especially useful for monitoring RAIT dynamics after immunosuppression therapy.

Acute Disease↗
PubMed1997

Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts.

Clonal diversifications of HIV virus were monitored by periodic samplings on each of the six patients with regard to 183- to 335-bp segments of the env gene, which invariably included the functionally critical V3 region. Subsequently, six individual phylogenetic trees of viral variants were constructed. It was found that at one time or another during the course of disease progression, viral variants were inexplicably released from a strong negative selection against nonsynonymous base substitutions, possibly indicating positive selection. This resulted in concentrated amino acid substitutions at five specific sites within the V3 region. It was noted that these sites were often involved as antigenic determinants that provoked the host immune response and that these sites were also involved in the determination of viral phenotypes as to their cell tropism, syncytium formation capability, and replication rates.

Amino Acid Sequence↗
PubMed1994

Dynamic actin structures stabilized by profilin.

We describe the production and analysis of clonal cell lines in which we have overexpressed human profilin, a small ubiquitous actin monomer binding protein, to assess the role of profilin on actin function in vivo. The concentration of filamentous actin is increased in cells with higher profilin levels, and actin filament half-life measured in these cells is directly proportional to the steady-state profilin concentration. The distribution of actin filaments is altered by profilin overexpression. While parallel actin bundles crossing the cells are virtually absent in cells overexpressing profilin, the submembranous actin network of these cells is denser than in control cells. These results suggest that in vivo profilin regulates the stability, and thereby distribution, of specific dynamic actin structures.

Actins↗
PubMed1988

Current concepts of autoimmune disease.

Our concepts of autoimmune disease have evolved with our changing understanding of the immune response. In recent years, clonal deletion theories have gradually given way to more dynamic views of the regulation of anti-self immune reactions. It is now clear that self-reactive B cells and some self-reactive T cells persist in the body, and there is every reason to believe that antigen-presenting cells are fully capable of presenting self-antigens in the same manner as foreign antigens. The critical event in the induction of autoimmune disease, therefore, is the quantitative balance of active suppression v the induction of self-reactive help. This help provided a helper T cell response requires that the self-antigens be presented in the context of self-MHC with sufficient affinity and avidity. The antireaction must be potent enough to overcome the totality of suppressive factors, including specific and non-specific suppressor T cells and anti-idiotypic or anti-T-cell-receptor responses.

Antigen-Presenting Cells↗
PubMed1984

Dynamic heterogeneity: rapid generation of metastatic variants in mouse B16 melanoma cells.

The ability of clonally derived lines of B16F1 and B16F10 melanoma cells to form experimental metastases in C57BL mice after intravenous injection was examined. Luria- Delbruck fluctuation analysis was applied to the results obtained with parallel subclones grown to small population sizes before testing for metastatic ability. The analysis demonstrated that variant cells capable of forming experimental metastases were generated in B16F1 cell populations at an effective rate of about 1.3 X 10(-5) per cell per generation while in B16F10 cell populations the effective rate of production was about 5 X 10(-5) per cell per generation. These results are consistent with a dynamic heterogeneity model of tumor progression. They suggest that the majority of cells in both lines are effectively nonmetastatic and that the higher metastatic ability of the B16F10 population may be due in part to a higher rate of generation of metastatic variants.

Animals↗
PubMed2003

Real-time imaging of gene promoter activity using an adenoviral reporter construct demonstrates transcriptional dynamics in normal anterior pituitary cells.

Although analysis of luciferase activity using luminescence imaging has provided new insights into the dynamic regulation of gene expression in living tIssues, studies in vitro have relied on stably transfected clonal cell lines, limiting the choice of cell type and species, or DNA microinjection, which is arduous and highly selective. We report here the first use of a recombinant adenovirus in which the firefly luciferase reporter gene was regulated by the prolactin gene promoter, to study temporal dynamics of promoter activity. This vector was used to infect the pituitary GH3 cell line, and also primary cultures of Syrian hamster pituitary cells. We show that adenovirally transduced cells retained normal regulation of the promoter-reporter transgene by appropriate signals. Furthermore, microscopic imaging studies indicated that both clonal and primary pituitary cells were transduced efficiently, giving readily detectable luminescence signals in real-time over long periods. Finally, analysis of single-cell expression patterns indicated that prolactin promoter activity was highly dynamic with pulses in gene expression, revealing that the transcriptional instability seen in clonal cells is a feature of normal pituitary cells. Adenoviral vectors offer a valuable tool for studies of gene regulation where conventional transgenesis and clonal cell lines are not available.

Adenoviridae↗
PubMed2006

Clonal senescence alters endothelial ICAM-1 function.

Little is known how age alters the dynamics and function of cell adhesion molecules, especially under inflammatory and stressful conditions. One membrane constituent, intercellular adhesion molecule-1 (ICAM-1) is a transmembrane glycoprotein of the immunoglobulin (Ig) superfamily that regulates key outside-->in and inside-->out signals associated with cell-to-cell interactions. If conditions such as age and inflammation change usual ICAM-1 action then important downstream effects ultimately perturb endothelial cell function. In this report, ICAM-1 accumulates in late passage endothelial cells when compared to early passage endothelial cells, yet ICAM-1 protein expression is attenuated when senescent cells are challenged by TNF-alpha (10ng/ml). Importantly, age alters ICAM-1 dynamic properties from directed to random receptor motion within the membrane. Single particle tracking reveals that the average ICAM-1 mobility is 44% less in late than early passage cells after its motion is stimulated by the Protein Kinase C (PKC) activator, phorbol myristate acetate (PMA). The mechanism for altered ICAM-1 mobility partly can be explained by a reduced rate of alpha-actinin linking with ICAM-1 in late passage Human Pulmonary Artery Endothelial Cells (HPAECs). Furthermore, tyrosine phosphorylation of alpha-actinin, a requirment for ICAM-1 clustering, is markedly reduced in senescent cells. These findings support a hypothesis that senescence results in changes of ICAM-1 activation and clustering, thus resulting in an age-dependent transmembrane signaling disorder. Therefore, further understanding of age-dependent disturbances of ICAM-1 regulation during inflammation can provide important clues as to appropriate targets for therapeutic interventions and prevention of vascular disorders in elderly at the level of the endothelial surface membrane.

Actinin↗
PubMed2006

Defining the actual sensitivity and specificity of the neurosphere assay in stem cell biology.

For more than a decade the 'neurosphere assay' has been used to define and measure neural stem cell (NSC) behavior, with similar assays now used in other organ systems and in cancer. We asked whether neurospheres are clonal structures whose diameter, number and composition accurately reflect the proliferation, self-renewal and multipotency of a single founding NSC. Using time-lapse video microscopy, coculture experiments with genetically labeled cells, and analysis of the volume of spheres, we observed that neurospheres are highly motile structures prone to fuse even under ostensibly 'clonal' culture conditions. Chimeric neurospheres were prevalent independent of ages, species and neural structures. Thus, the intrinsic dynamic of neurospheres, as conventionally assayed, introduces confounders. More accurate conditions (for example, plating a single cell per miniwell) will be crucial for assessing clonality, number and fate of stem cells. These cautions probably have implications for the use of 'cytospheres' as an assay in other organ systems and with other cell types, both normal and neoplastic.

Animals↗
PubMed2006

Plant population growth and competition in a light gradient: a mathematical model of canopy partitioning.

Can a difference in the heights at which plants place their leaves, a pattern we call canopy partitioning, make it possible for two competing plant species to coexist? To find out, we examine a model of clonal plants living in a nonseasonal environment that relates the dynamical behavior and competitive abilities of plant populations to the structural and functional features of the plants that form them. This examination emphasizes whole plant performance in the vertical light gradient caused by self-shading. This first of three related papers formulates a prototype single species Canopy Structure Model from biological first principles and shows how all plant properties work together to determine population persistence and equilibrium abundance. Population persistence is favored, and equilibrium abundance is increased, by high irradiance, high maximum photosynthesis rate, rapid saturation of the photosynthetic response to increased irradiance, low tissue respiration rate, small amounts of stem and root tissue necessary to support the needs of leaves, and low density of leaf, stem, and root tissues. In particular, equilibrium abundance decreases as mean leaf height increases because of the increased cost of manufacturing and maintaining stem tissue. All conclusions arise from this formulation by straightforward analysis. The argument concludes by stating this formulation's straightforward extension, called a Canopy Partitioning Model, to two competing species.

Ecosystem↗
PubMed2001

Direct genotyping and nucleotide sequence analysis of VS1 and VS2 of the Omp1 gene of Chlamydia trachomatis from Moroccan trachomatous specimens.

To determine the range of ocular strains of Chlamydia trachomatis circulating in southern Morocco, where trachoma is endemic, and to compare the value of the molecular methods for genotyping C. trachomatis, ocular specimens were subjected to a direct Omp1 PCR-restriction fragment length polymorphism (RFLP)-based analysis and direct sequencing. PCR-RFLP analysis shows that the Ba genotype represents the most frequent one (63%), followed by genotype A (45%), whereas no B or C genotypes were identified among the 53 out of 108 specimens that were strongly positive in the Omp1 CT1-CT5 PCR. Our results further show that the notion of interfamily and intrafamily transmission is very likely. To confirm the genotype identity of C. trachomatis as determined by PCR-RFLP, 16 selected specimens were sequenced across variable sequence 1 (VS1) and 2 (VS2). No discrepancies were found between PCR-RFLP typing and the genotype identity confirmed by nucleotide sequencing of the PCR product. Our results clearly indicate that both molecular methods of typing chlamydiae (i.e., PCR-RFLP and sequencing) are important and have specific applications for clinical epidemiological purposes. This is the case for individuals infected with more than one clonal population of C. trachomatis. The unambiguous nucleotide sequencing therefore defines an important epidemiologic descriptor for the infected patient whether the source is from a clonal population of organisms or whether it represents a more dynamic process of strain dominance or genetic change. Furthermore, Omp1 genotyping affords the necessary approach to epidemiologic investigations in areas of the world endemic for trachoma, where only one or two serovars are known to predominate.

Bacterial Outer Membrane Proteins↗