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PubMed2002

Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria.

Predation is a major mortality factor of planktonic bacteria and an important shaping force for the phenotypic and taxonomic structure of bacterial communities. In this paper we: (1) summarise current knowledge on bacterial phenotypic properties which affect their vulnerability towards grazers, and (2) review experimental evidence demonstrating that this phenotypic heterogeneity results in shifts of bacterial community composition during enhanced protist grazing pressure. Size-structured interactions are especially important in planktonic systems and bacterial cell size influences the mortality rate and the type of grazer to which bacteria are most susceptible. When protists are the major bacterivores, both very small and large bacterial cells gain some size refuge. Recent studies have revealed that also various non-morphological traits such as motility, physicochemical surface characters and toxicity affect bacterial vulnerability and protist feeding success. These properties are effective at different stages during the feeding process of interception feeding flagellates (encounter, capture, ingestion, digestion). Grazing-resistant bacteria in natural communities can account for a substantial portion of the total bacterial biomass at least in more productive aquatic systems. In field and laboratory experiments it has been demonstrated that increased protozoan grazing results in shifts in the phenotypic and genotypic composition of the bacterial assemblage. The importance of this shaping force for the bacterial community structure depends, however, on the overall food web structure, especially on the composition of the metazooplankton. Whereas the structuring impact of bacterial grazers is well documented, relatively little is known about how grazing-mediated changes in bacterial communities influence microbially mediated processes and biogeochemically important transformations.

Animals↗
PubMed1985

Expected time for random genetic drift of a population between stable phenotypic states.

Natural selection and random genetic drift are modeled by using diffusion equations for the mean phenotype of a quantitative (polygenic) character in a finite population with two available adaptive zones or ecological niches. When there is appreciable selection, the population is likely to spend a very long time drifting around the peak in its original adaptive zone. With the mean phenotype initially anywhere near the local optimum, the expected time until a shift between phenotypic adaptive peaks increases approximately exponentially with the effective population size. In comparison, the expected duration of intermediate forms in the actual transition between adaptive peaks is extremely short, generally below the level of resolution in the fossil record, and increases approximately logarithmically with the effective population size. The evolutionary dynamics of this model conform to the pattern of current paleontological concepts of morphological "stasis" and "punctuated equilibria."

Biological Evolution↗
PubMed1997

Asbestos and silica-induced changes in human alveolar macrophage phenotype.

The mechanism by which fibrogenic particulates induce inflammation that can progress to lung fibrosis is uncertain. The alveolar macrophage (AM) has been implicated in the inflammatory process because of its function and reported release of inflammatory mediators when isolated from fibrotic patients. It has been recently shown that fibrogenic, but not nonfibrogenic, particulates are highly potent in inducing apoptosis of human AM. In this study, we tested the hypothesis that fibrogenic particulates could shift the phenotypic ratio of human AM to a more inflammatory condition. The macrophage phenotypes were characterized by flow cytometry targeting the RFD1 and RFD7 epitopes. Results demonstrated that chrysotile and crocidolite asbestos, as well as crystalline silica, but not titanium dioxide or wollastonite, increased the RFD1+ phenotype (inducer or immune activator macrophages) and decreased the RFD1+ RFD7+ phenotype (suppressor macrophages). These results provide a mechanistic explanation that may link apoptosis (namely, suppressor macrophages) to a shift in the ratio of macrophage phenotypes that could initiate lung inflammation.

Apoptosis↗
PubMed1996

Ethanol neurotoxicity in culture: selective loss of cholinergic neurons.

Studies from our laboratory have shown that in ovo exposure of chick embryos to ethanol decreases neuronal survival in culture, and shifts neurotransmitter phenotypic from cholinergic to catecholaminergic and GABAergic. In this study we attempted to determine if the shift from cholinergic expression is a result of selective loss of cholinergic neurons. Neuron-enriched primary cultures were prepared from 3-day-old whole chick embryos. Cells proliferating during the first 3 days in culture were labeled with BrdU, and one half of the cultures were exposed to 50 mM ethanol during the same time period. Selective survival in vitro of the cholinergic, catecholaminergic. GABAergic, glutamatergic, and somatostatinergic phenotypes was determined by counting cells double-stained for BrdU and either ChAT, TH, GAD, Glu, or SRIF. We found that ethanol exposure resulted in a significant reduction in neuronal survival within the cholinergic phenotype, both in the total number of ChAT+ cells and in the subpopulation born between 0-3 DIV. In addition, survival of glutamatergic neurons "born" between 0-3 days in vitro was significantly enhanced, while survival in catecholaminergic, GABAergic, and somatostatinergic phenotypes was also enhanced slightly. These results corroborate our earlier biochemical findings and suggest that the differential cholinotoxic effect of ethanol is due, at least in part, to enhancement of cell-death of cholinergic neuroblasts. This does not preclude the possibility that multipotent neuroblasts are also influenced to express alternative phenotypes, and analyses of these data, in fact, support this notion as well.

Animals↗
PubMed1984

Lyt phenotype of cytotoxic T cells: shift from Lyt-1+2+3+ to a mixed population of Lyt-1+2+3+ and Lyt-1-2+3+ during in vitro culture.

The Lyt phenotype of cytotoxic T cells generated in the primary H-2 response was investigated kinetically. The cytotoxicity generated in the early stage of culture was abolished by treatment with alpha Lyt-1,2,3, and complement (C), whereas that generated in the late stage was only partially eliminated by alpha Lyt-1, but was abolished by alpha Lyt-2, 3, and C. This suggested late expansion of the Lyt-1-2+3+ population. Lack of Lyt-1 antigen was confirmed with cells that were depleted of Lyt-1+ from primary culture and then stimulated in the secondary response by elimination of cytotoxicity and by direct Lyt typing. Results indicated that the response of proliferative and cytotoxic T cells of the Lyt-1+2+3+ phenotype in the early stage of culture was followed by activation of Lyt-1-2+3+ T cells. Cytotoxic T cells in the late stage were shown to be a mixture of Lyt-1+2+3+ and Lyt-1-2+3+ cells. This was confirmed with cytotoxic T cells from secondary culture and uncloned long-term T cell lines.

Animals↗
PubMed1993

Identification of a novel population of CD8 alpha+ beta- bone marrow-derived dendritic epidermal cells. This unique population is subsequently outnumbered by thymus-independent expansion of the CD8 alpha+ beta+ dendritic epidermal cells.

Maturation of some T cell populations has been suggested to occur in epithelial tissues. The CD8 molecule, which is expressed as heterodimers made of alpha/beta-chains on virtually all peripheral T cells, is preferentially expressed as homodimers made only of alpha-chains on a subset of CD8+ mouse gut intraepithelial lymphocytes, which arise from bone marrow (BM) precursors in a thymus-independent mechanism. This unique population of CD8 alpha+ beta- T cells, however, has not been identified in other lymphoid tissues in normal adult mice. Because our previous study demonstrated that reconstitution of thymectomized irradiated mice with T cell-depleted BM cells resulted in the appearance of CD8+, TCR-alpha beta+ dendritic epidermal cells (DEC) and suggested that a proportion of the BM-derived DEC may mature within the epidermis, we asked whether the unique phenotype of CD8 alpha+ beta- could be detected among the CD8+ BM-derived DEC. In this report for the first time we identified this unique population of CD8 alpha+ beta- cells among the DEC. Although this population comprised the predominant fraction of the BM-derived DEC in the early post-transfer period (2 to 3 mo), gradual shift from the CD8 alpha+ beta+ phenotypes occurred during the late post-transfer period (4 to 6 mo) independently of the presence of the thymus. Kinetic studies on the BM-derived DEC revealed that this phenotypic shift could be caused by the subsequent expansion of the CD8 alpha+ beta+ DEC. In contrast, the CD8 alpha+ beta- population was the major subset of the BM-derived intraepithelial lymphocytes throughout the entire observation period and the phenotypic shift with age was never observed. These results indicate that CD8 alpha+ beta- cells are preferentially detected on T cells that home to the epithelial tissues and that in the epidermis, but not in the gut epithelia, the subsequent expansion of the CD8 alpha+ beta+ DEC would dilute the high number of the CD8 alpha+ beta- cells.

Animals↗
PubMedDate not supplied

Predicting HIV-1 coreceptor usage with sequence analysis.

Bioinformatics approaches are increasingly being used to identify and understand the genetic variation underlying changes in HIV-1 biological phenotype. The variable regions of the viral envelope are the major determinant of virus coreceptor usage and cell tropism. Specifically, amino acids 11 and 25 in the 3rd variable (V3) loop have been found to strongly influence viral syncytium inducing capacity and coreceptor usage. Many additional V3 loop changes, however, as well as changes elsewhere in Env, are thought to contribute to phenotype. In this review we describe several recently developed methods to analyze this variability and their use to predict biological phenotype based on sequence information. These approaches have identified changes in the V3 loop, in addition to the known changes at positions 11 and 25, that affect phenotype and significantly enhance our ability to predict phenotype from genotype. Besides improving phenotype prediction, methods that score V3 sequences on a continuous scale can also assist in the interpretation of evolutionary information about shifts in phenotype, and the relationship between that evolution and pathogenesis. Several examples and potential practical applications of this scoring are discussed. We conclude that advances in computational approaches have enhanced both our ability to predict and to understand HIV-1 biological phenotype evolution. Further development of these methods, by extending analysis to regions outside the V3 loop and to clades beyond subtype B, will extend our understanding of HIV-1 pathogenesis and inform treatment strategies.

Computational Biology↗
PubMed1999

Surgical stress, bacteria, and mucosal immune function.

Bacteria share a benign coexistence with host mucosal surfaces in the gastrointestinal tract during periods of health. Both host epithelial defense function and bacterial virulence phenotypes are significantly affected by stress. Via discreet and specific sensory input signals to bacteria, the molecular machinery of otherwise commensal strains of bacteria can shift the phenotypes of residential colonizers to more virulent and invasive strains. This occurs at a time when the host may be relatively immunosuppressed by the injury. This adaptive response demonstrates the duplicitous nature of bacteria residing on mucosal surfaces whose ability to shift their virulence characteristics may play an important role in infectious-related morbidity following surgical stress.

Animals↗
PubMed1981

Immunological definition of leukemic cell surface phenotypes.

Immunological phenotyping of blasts from over 200 children with acute lymphocytic leukemia (ALL) reveals both interpatient differences and phenotypic heterogeneity in the blast population from individual patients. A battery of five independent lymphocyte differentiation markers, erythrocyte-forming rosettes. T-cell antigens, Ia-like antigens, the common ALL antigen, and surface immunoglobulin, permit classification of all ALL specimens into four major marker groups. These are common, T-cell, B-cell, and undifferentiated ALL. Heterogeneity in the marker phenotypes within each of the major groups is observed. Within individual erythrocyte receptor-positive ALL specimens, phenotypic heterogeneity in the blast population is demonstrated. Sequential determinations of the blast phenotype during periods of active disease reveal a second example of intrapatient blast cell heterogeneity. Differences in phenotype of the dominant blast populations present prior to treatment and at relapse are observed in sequential studies of individual patients. These shifts in phenotype are nonrandom. They result most frequently from losses in single differentiation markers. A unifying hypothesis which explains these observations of phenotypic heterogeneity is that ALL blasts manifest limited lymphoid-like differentiation.

Antigens, Neoplasm↗
PubMed1992

Interaction between the Saccharomyces cerevisiae CDC25 gene product and mammalian ras.

In order to characterize the interaction between the Saccharomyces cerevisiae Cdc25 protein and Harvey-ras (p21H-ras), we have constructed a yeast strain disrupted at the RAS1 and RAS2 loci, expressing both p21H-ras and the catalytic domain of the bovine GTPase activating protein (GAP) and containing the cdc25-2 mutation. Such a strain exhibits a temperature-sensitive phenotype. The shift to the nonpermissive temperature is accompanied by the loss of guanyl nucleotide-dependent activity of adenylylcyclase in vitro. The temperature-sensitive phenotype can be rescued by CDC25 itself, as well as by a plasmid containing a truncated SDC25 gene. In addition, wild type CDC25 significantly improves the guanyl nucleotide response observed in the background of the cdc25ts allele at the permissive temperature in a dosage-dependent manner and restores the guanyl nucleotide response at the restrictive temperature. Both CDC25 and a truncated SDC25 also restored p21H-ras-dependent guanyl nucleotide response in a strain isogenic to the one described above but containing a disrupted CDC25 locus instead of the temperature-sensitive allele. These results suggest that the S. cerevisiae Cdc25 protein interacts with p21H-ras expressed in yeast by promoting GDP-GTP exchange. It follows that the yeast system can be used for characterizing the interaction between guanyl nucleotide exchangers of Ras proteins and mammalian p21H-ras.

Adenylyl Cyclases↗
PubMed2002

Critical role for cataplerosis via citrate in glucose-regulated insulin release.

The molecular mechanisms mediating acute regulation of insulin release by glucose are partially known. The process involves at least two pathways that can be discriminated on basis of their (in)dependence of closure of ATP-sensitive potassium (K+(ATP)) channels. The mechanism of the K+(ATP) channel-independent pathway was proposed to involve cataplerosis, the export of mitochondrial intermediates into the cytosol and in the induction of fatty acid-derived signaling molecules. In the present article, we have explored in fluorescence-activated cell sorter (FACS)-purified rat beta-cells the molecular steps involved in chronic glucose regulation of the insulin secretory response. When compared with culture in 10 mmol/l glucose, 24 h culture in 3 mmol/l glucose shifts the phenotype of the cells into a state with low further secretory responsiveness to glucose, lower rates of glucose oxidation, and lower rates of cataplerosis. Microarray mRNA analysis indicates that this shift can be attributed to differences in expression of genes involved in the K+(ATP) channel-dependent pathway, in cataplerosis and in fatty acid/cholesterol biosynthesis. This response was paralleled by glucose upregulation of the transcription factor sterol regulatory element binding protein 1c (SREBP1c) (ADD1) and downregulation of peroxisome proliferator-activated receptor (PPAR)-alpha and PPAR-beta (PPARdelta). The functional importance of cataplerosis via citrate for glucose-induced insulin release was further supported by the observation that two ATP-citrate lyase inhibitors, radicicol and (-)-hydroxycitrate, block part of glucose-stimulated release in beta-cells. In conclusion, chronic glucose regulation of the glucose-responsive secretory phenotype is associated with coordinated changes in gene expression involved in the K+(ATP) channel-dependent pathway, in cataplerosis via citrate and in acyl CoA/cholesterol biosynthesis.

Animals↗
PubMed1991

Effects of retinoic acid and bromodeoxyuridine on human melanoma-associated antigen expression in small cell lung carcinoma cells.

The dispersed neuroendocrine system includes cells with different embryological derivations, sharing a common neuroendocrine (NE) program, as indicated by the expression of NE markers, some of which are shared antigenic determinants. We report here that the small cell lung carcinoma cells NCI-H69 express the two human melanoma-associated antigens (HMAA) NGA/LS62 an LS109. Incubation of NCI-H69 cells with maturational inducers, such as retinoic acid and bromodeoxyuridine (BrdU), upregulated the expression of both HMAA. Exposure to BrdU for 4 weeks induced the appearance of a different phenotype in subpopulations of NCI-H69 cells, which became epithelioid, substrate-adherent, grew in monolayer and continued to express NE-associated antigens in variable amount. The shift in phenotype was not reversible after BrdU withdrawal and was maintained for at least 6 months in continuous culture. The substrate adhesion of NCI-H69 cells was paralleled by a change in NGA glycosylation pattern, thus suggesting a possible functional role for NGA in cell substrate adhesion/recognition.

Antigens, Neoplasm↗
PubMed1989

TCDD alters medial epithelial cell differentiation during palatogenesis.

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a widely distributed, persistent environmental contaminant that is teratogenic in mice, where it induces hydronephrosis and cleft palate. The incidence of clefting has been shown to be dose dependent after exposure on either gestation Day (GD) 10 or 12, although the embryo is more susceptible on GD 12. TCDD-exposed palatal shelves meet but do not fuse, and programmed cell death of the medial epithelial cells is inhibited. The mechanism of action through which TCDD alters the program of medial cell development has not been examined in earlier studies, and it is not known whether the mechanism is the same regardless of the dose or developmental stage of exposure. In this study, C57BL/6N mice, a strain sensitive to TCDD, were dosed orally on GD 10 or 12 with 0, 6, 12, 24, or 30 micrograms/kg body wt, in 10 ml corn oil/kg. Embryonic palatal shelves were examined on GD 14, 15, or 16. The degree of palatal closure, epithelial surface morphology, and cellular ultrastructure, the incorporation of [3H]TdR, the expression of EGF receptors, and the binding of 125I-EGF were assessed. After exposure on GD 10 or 12, TCDD altered the differentiation pathway of the medial epithelial cells. The palatal shelves were of normal size and overall morphology, but fusion of the medial epithelia of the opposing shelves did not occur. TCDD prevented programmed cell death of the medial peridermal cells. The expression of EGF receptors by medial cells continued through Day 16 and the receptors were able to bind ligand. The medial cells differentiated into a stratified, squamous, keratinizing epithelium. The shift in phenotype to an oral-like epithelium occurred after exposure on either GD 10 or 12. At the lower dose (6 micrograms/kg), fewer cleft palates were produced, but those shelves which did respond had a fully expressed shift in differentiation. Whether the exposure begins on GD 10 or 12 or whether the dosing level produces only a few cleft palates within a litter, TCDD produced cleft palate by altering the differentiation program of the medial cells.

Administration, Oral↗
PubMed2006

Normal expression of myelin protein zero with frame-shift mutation correlates with mild phenotype.

Mutations in the gene encoding for myelin protein zero (MPZ) cause inherited demyelinating peripheral neuropathies of different severity. The molecular and cellular mechanisms by which the MPZ mutations cause neuropathy are incompletely understood. We investigated MPZ, myelin basic protein, and peripheral myelin protein 22 (PMP22) protein expression levels in a nerve biopsy of a Charcot-Marie-Tooth type 1B patient heterozygous for the Val 102 frame-shift mutation. We demonstrate by quantitative immunohistochemical as well as by Western blot analyses that MPZ expression levels were not reduced in myelin membranes, a finding that is in accordance with the mild phenotype of this patient. Our data show that heterozygous 'loss-of-function' of MPZ may not necessarily lead to reduced protein levels. In conclusion, we demonstrate that careful analysis of protein expression levels in peripheral nerve tissues provides important information with respect to the understanding of the molecular basis of these neuropathies.

Adult↗
PubMed2003

Marrow stem cells shift gene expression and engraftment phenotype with cell cycle transit.

We studied the genetic and engraftment phenotype of highly purified murine hematopoietic stem cells (lineage negative, rhodamine-low, Hoechst-low) through cytokine-stimulated cell cycle. Cells were cultured in interleukin (IL)-3, IL-6, IL-11, and steel factor for 0 to 48 h and tested for engraftment capacity in a lethally irradiated murine competitive transplant model. Engraftment showed major fluctuations with nadirs at 36 and 48 h of culture and recovery during the next G1. Gene expression of quiescent (0 h) or cycling (48 h) stem cells was compared with lineage positive cells by 3' end PCR differential display analysis. Individual PCR bands were quantified using a 0 to 9 scale and results were visually compared using color-coded matrices. We defined a set of 637 transcripts expressed in stem cells and not expressed in lineage positive cells. Gene expression analyzed at 0 and 48 h showed a major shift from "stem cell genes" being highly expressed at 0 h and turned off at 48 h, while "cell division" genes were turned on at 48 h. These observations suggest stem cell gene expression shifts through cell cycle in relation to cell cycle related alterations of stem cell phenotype. The engraftment defect is related to a major phenotypic change of the stem cell.

Animals↗
PubMed2002

Population depletion activates autonomous CD154-dependent survival in biopsylike Burkitt lymphoma cells.

Population size is governed through cells reacting to a variety of intrinsic and extrinsic cues. Tumors, while liberated from many of the homeostatic constraints placed on physiologic counterparts, can nonetheless remain subject to both social and environmental control. Burkitt lymphoma cells faithful to the biopsy phenotype were used to model the reliance of the colony, if any, on an inbuilt population sensor. Below a normally suicidal threshold number of cells, low picomolar quantities of exogenous CD40 ligand (CD40L/CD154) were found to sustain the clone without the discernible shift in phenotype that accompanies high CD40L encounter. Although CD154 was undetectable in populous cultures, message was induced as numbers became limiting. Correspondingly, attempts to neutralize endogenous CD40L activity failed to perturb cells at optimal densities but resulted in their marked decline as the critical threshold was approached. These data reveal an auto-inducible survival mechanism seemingly regulated through the monitoring of population size, a process somewhat akin to that of "quorum sensing" among gram-negative bacteria in which diffusible molecules provide a means of communication to coordinate gene expression with population density. This process could be activated as cells discern depletions in their community or when deprived of signals otherwise furnished within an appropriate environmental niche.

Biopsy↗
PubMed2001

Are the Phenotypes of Preneoplastic Lesions of Significance for Cancer Prevention? 1. Liver.

Preneoplastic lesions have been described for most major sites of human tumour development. They appear to be share characteristics like monoclonality, induction by all classes of carcinogens and some quantitative relationship to actual tumours. Extensive studies of preneoplasia in the liver of the rat has indicated that a directed shift in phenotype occurs, commensurate with greater physiological emphasis on growth potential. One characteristic change is increase in the key enzyme of the pentose phosphate pathway, glucose 6 phosphatase dehydrogenase as well as elevation in glycolysis, reduction of gluconeogenesis. In general, the changes observed in preneoplastic liver lesions appear reminiscent of the effects of insulin or other hormones on hepatocytes, pointing to possible application of specific inhibitors for cancer chemoprevention.

Journal Article↗