RESUMEN
Alkaline pH adaptation represents an important environmental stress response in Aspergillus nidulans. It is mediated by the pal signalling pathway and the PacC transcription factor. Although studied extensively experimentally, the activation mechanism of PacC has not been quantified, and it is not clear how this activation is regulated. Here, by constructing mathematical models, we first show that the pattern of PacC activation observed in previously published experiments cannot be explained based on existing knowledge about PacC activation. Extending the model with a negative feedback loop is necessary to produce simulation results that are consistent with the data, suggesting the existence of a negative feedback loop in the PacC activation process. This extended model is then validated against published measurements for cells with drug treatment and mutant cells. Furthermore, we investigate the role of an intermediate form of PacC in the PacC activation process, and propose experiments that can be used to test our predictions. Our work illustrates how mathematical models can be used to uncover regulatory mechanisms in the transcription regulation, and generate hypotheses that guide further laboratory investigations.
Asunto(s)
Aspergillus nidulans/genética , Retroalimentación Fisiológica/fisiología , Proteínas Fúngicas/agonistas , Modelos Biológicos , Factores de Transcripción/agonistas , Activación Transcripcional , Simulación por Computador , Regulación Fúngica de la Expresión Génica , Concentración de Iones de Hidrógeno , Estrés Fisiológico/genética , Estrés Fisiológico/fisiologíaRESUMEN
Pathogenic microbes exist in dynamic niches and have evolved robust adaptive responses to promote survival in their hosts. The major fungal pathogens of humans, Candida albicans and Candida glabrata, are exposed to a range of environmental stresses in their hosts including osmotic, oxidative and nitrosative stresses. Significant efforts have been devoted to the characterization of the adaptive responses to each of these stresses. In the wild, cells are frequently exposed simultaneously to combinations of these stresses and yet the effects of such combinatorial stresses have not been explored. We have developed a common experimental platform to facilitate the comparison of combinatorial stress responses in C. glabrata and C. albicans. This platform is based on the growth of cells in buffered rich medium at 30°C, and was used to define relatively low, medium and high doses of osmotic (NaCl), oxidative (H(2)O(2)) and nitrosative stresses (e.g., dipropylenetriamine (DPTA)-NONOate). The effects of combinatorial stresses were compared with the corresponding individual stresses under these growth conditions. We show for the first time that certain combinations of combinatorial stress are especially potent in terms of their ability to kill C. albicans and C. glabrata and/or inhibit their growth. This was the case for combinations of osmotic plus oxidative stress and for oxidative plus nitrosative stress. We predict that combinatorial stresses may be highly significant in host defences against these pathogenic yeasts.
Asunto(s)
Candida albicans/fisiología , Candida glabrata/fisiología , Viabilidad Microbiana/efectos de los fármacos , Estrés Fisiológico , Candida albicans/efectos de los fármacos , Candida albicans/crecimiento & desarrollo , Candida glabrata/efectos de los fármacos , Candida glabrata/crecimiento & desarrollo , Medios de Cultivo/química , Humanos , Micología/métodos , Compuestos Nitrosos/toxicidad , Presión Osmótica , Estrés Oxidativo , TemperaturaRESUMEN
Intraplaque hemorrhage accelerates atherosclerosis via oxidant stress and contributes to lesion development and destabilization. Normally, macrophages scavenge hemoglobin-haptoglobin (HbHp) complexes via CD163, and this process provokes the secretion of the anti-inflammatory atheroprotective cytokine interleukin (IL)-10. We therefore tested the hypothesis that HbHp complexes may drive monocyte differentiation to an atheroprotective phenotype. Examination of the macrophage phenotype in hemorrhaged atherosclerotic plaques revealed a novel hemorrhage-associated macrophage population (HA-mac), defined by high levels of CD163, but low levels of human leukocyte antigen-DR. HA-mac contained more iron, a pro-oxidant catalyst, but paradoxically had less oxidative injury, measured by 8-oxo-guanosine content. Differentiating monocytes with HbHp complexes reproduced the CD163(high) human leukocyte antigen-DR(low) HA-mac phenotype in vitro. These in vitro HA-mac cells cleared Hb more quickly, and consistently showed less hydrogen peroxide release, highly reactive oxygen species and oxidant stress, and increased survival. Differentiation to HA-mac was prevented by neutralizing IL-10 antibodies, indicating that IL-10 mediates an autocrine feedback mechanism in this system. Nonlinear dynamic modeling showed that an IL-10/CD163-positive feedback loop drove a discrete HA-mac lineage. Simulations further indicated an all-or-none switch to HA-mac at threshold levels of HbHp, and this conversion was experimentally verified. These data demonstrate the creation of a novel atheroprotective (HA-mac) macrophage subpopulation in response to intraplaque hemorrhage and raise the possibility that therapeutically reproducing this macrophage phenotype may be cardio-protective in cases of atherosclerosis.
Asunto(s)
Aterosclerosis/genética , Aterosclerosis/prevención & control , Estenosis Coronaria/patología , Macrófagos/patología , Antígenos CD/análisis , Antígenos de Diferenciación Mielomonocítica/análisis , Autopsia , Estenosis Coronaria/complicaciones , Hemorragia/patología , Humanos , Microscopía Confocal , Monocitos/patología , Monocitos/fisiología , Estrés Oxidativo , Fenotipo , Receptores de Superficie Celular/análisisRESUMEN
Modern genomics technologies generate huge data sets creating a demand for systems level, experimentally verified, analysis techniques. We examined the transcriptional response to DNA damage in a human T cell line (MOLT4) using microarrays. By measuring both mRNA accumulation and degradation over a short time course, we were able to construct a mechanistic model of the transcriptional response. The model predicted three dominant transcriptional activity profiles-an early response controlled by NFkappaB and c-Jun, a delayed response controlled by p53, and a late response related to cell cycle re-entry. The method also identified, with defined confidence limits, the transcriptional targets associated with each activity. Experimental inhibition of NFkappaB, c-Jun and p53 confirmed that target predictions were accurate. Model predictions directly explained 70% of the 200 most significantly upregulated genes in the DNA-damage response. Genome-wide transcriptional modelling (GWTM) requires no prior knowledge of either transcription factors or their targets. GWTM is an economical and effective method for identifying the main transcriptional activators in a complex response and confidently predicting their targets.
Asunto(s)
Genoma Humano/genética , Modelos Genéticos , Transcripción Genética/genética , Línea Celular , Análisis por Conglomerados , Biología Computacional , Daño del ADN/genética , Perfilación de la Expresión Génica , Humanos , Análisis de Secuencia por Matrices de Oligonucleótidos , Estabilidad del ARN/efectos de la radiación , ARN Mensajero/genética , ARN Mensajero/metabolismo , Radiación Ionizante , Reproducibilidad de los Resultados , Factores de Tiempo , Factores de Transcripción/metabolismo , Transcripción Genética/efectos de la radiación , Proteína p53 Supresora de Tumor/metabolismo , Regulación hacia Arriba/genética , Regulación hacia Arriba/efectos de la radiaciónRESUMEN
BACKGROUND: Invasive aspergillosis (IA) is the most common cause of death associated with fungal infection in the developed world. Historically, susceptibility to IA has been associated with prolonged neutropenia; however, IA has now become a major problem in patients on calcineurin inhibitors and allogenic hematopoietic stem cell transplant patients following engraftment. These observations suggest complex cellular mechanisms govern immunity to IA. METHODS: To characterize the key early events that govern outcome from infection with Aspergillus fumigatus, we performed a comparative immunochip microarray analysis of the pulmonary transcriptional response to IA between cyclophosphamide-treated mice and immunocompetent mice at 24 h after infection. RESULTS: We demonstrate that death due to infection is associated with a failure to generate an incremental interferon-gamma response, increased levels of interleukin-5 and interleukin-17a transcript, coordinated expression of a network of tumor necrosis factor-alpha-related genes, and increased levels of tumor necrosis factor-alpha. In contrast, clearance of infection is associated with increased expression of a number genes encoding proteins involved in innate pathogen clearance, as well as apoptosis and control of inflammation. CONCLUSION: This first organ-level immune response transcriptional analysis for IA has enabled us to gain new insights into the mechanisms that govern fungal immunity in the lung.
Asunto(s)
Interferón gamma/metabolismo , Interleucina-17/metabolismo , Aspergilosis Pulmonar/inmunología , Aspergilosis Pulmonar/metabolismo , Factor de Necrosis Tumoral alfa/metabolismo , Animales , ADN Complementario , Regulación de la Expresión Génica/inmunología , Huésped Inmunocomprometido , Interferón gamma/genética , Interleucina-17/genética , Masculino , Ratones , Factor de Necrosis Tumoral alfa/genéticaRESUMEN
The malaria parasite causes lysis of red blood cells, resulting in anemia, a major cause of mortality and morbidity. Intuitively, one would expect the production of red blood cells to increase in order to compensate for this loss. However, it has been observed that this response is weaker than would be expected. Furthermore, iron supplementation for iron deficient children in malaria endemic regions can paradoxically adversely affect the clinical outcome of malaria infection. A possible explanation may lie in the preference that some malaria parasites show for infecting immature red blood cells (reticulocytes). In the presence of a parasite preference for immature red cells, a rise in red cell production can 'fuel the fire' of infection by increasing the availability of the parasite's preferred target cell. We present a mathematical model of red blood cell production and infection in order to explore this hypothesis. We assess the effect of varying the reticulocyte replacement rate and preference of the parasite for reticulocytes on four key outcome measures assessing anemia and parasitemia. For a given level of parasite preference for reticulocytes we uncover an optimal erythropoietic response which minimizes disease severity. Increasing red blood cell production much above this optimum confers no benefit to the patient, and in fact can increase the degree of anemia and parasitemia. These conclusions are consistent with epidemiological studies demonstrating that both iron deficiency and anemia are protective against severe malaria, whilst iron supplementation in malaria endemic regions is with an increased number of malaria related adverse effects. Thus, suppression of red blood cell production, rather than being an unfortunate side effect of inflammation, may be a host protective effect against severe malarial anemia.
Asunto(s)
Anemia/parasitología , Eritropoyesis/fisiología , Malaria/complicaciones , Modelos Biológicos , Anemia/sangre , Anemia/fisiopatología , Interacciones Huésped-Parásitos , Humanos , Malaria/sangre , Malaria/fisiopatología , Parasitemia/sangre , Parasitemia/parasitología , Parasitemia/fisiopatología , Reticulocitos/parasitologíaRESUMEN
Over the last few years, experimental data on the fluctuations in gene activity between individual cells and within the same cell over time have confirmed that gene expression is a "noisy" process. This variation is in part due to the small number of molecules taking part in some of the key reactions that are involved in gene expression. One of the consequences of this is that protein production often occurs in bursts, each due to a single promoter or transcription factor binding event. Recently, the distribution of the number of proteins produced in such bursts has been experimentally measured, offering a unique opportunity to study the relative importance of different sources of noise in gene expression. Here, we provide a derivation of the theoretical probability distribution of these bursts for a wide variety of different models of gene expression. We show that there is a good fit between our theoretical distribution and that obtained from two different published experimental datasets. We then prove that, irrespective of the details of the model, the burst size distribution is always geometric and hence determined by a single parameter. Many different combinations of the biochemical rates for the constituent reactions of both transcription and translation will therefore lead to the same experimentally observed burst size distribution. It is thus impossible to identify different sources of fluctuations purely from protein burst size data or to use such data to estimate all of the model parameters. We explore methods of inferring these values when additional types of experimental data are available.
Asunto(s)
Expresión Génica , Modelos Genéticos , Biología Computacional , Interpretación Estadística de Datos , Perfilación de la Expresión Génica/estadística & datos numéricos , Modelos Estadísticos , Proteínas/genética , Proteínas/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismoRESUMEN
OBJECTIVES: Databases almost invariably contain some errors and improvements to the quality of recorded data are costly. We sought to assess the extent to which given levels of error in a clinical database can lead to misleading mortality rates being derived. METHODS: We deliberately seeded a large database concerning congenital heart surgery involving over 17,600 operations, which we assumed to be error free, with errors at known rates of 0-20%. The effects of three different types of random error were explored: data omission, outcome miscoding (alive or dead) and the miscoding of procedures. For each error type, we compared the mortality rates calculated from the 'seeded' database to those calculated from the pristine database. RESULTS: Outcome miscoding typically results in overestimated mortality rates which for low-risk procedures may well give estimates over double the true value. Random data omission has relatively little effect. If procedure types are miscoded, procedure-specific mortality estimates for high-risk operations tend to be underestimates and those for low-risk operations overestimates. A mathematical model developed to examine these effects accurately forecasted the results of such error-seeding experiments. Software to implement this model is available free of charge on the Internet. CONCLUSION: Even small levels of data error can substantially affect the accuracy of mortality rate estimates, especially for low-risk operations. Such inaccuracy could lead to misleading analysis of institutional and individual surgeons' results. Our results suggest that caution is warranted in interpreting the mortality estimates derived from clinical databases. Our analysis goes beyond the realms of surgical mortality and concerns all adverse events whose frequency is rare.
Asunto(s)
Procedimientos Quirúrgicos Cardíacos/mortalidad , Bases de Datos Factuales/normas , Cardiopatías Congénitas/cirugía , Mortalidad Hospitalaria , Mortalidad , Cardiopatías Congénitas/mortalidad , HumanosRESUMEN
BACKGROUND: Quantifying cell division and death is central to many studies in the biological sciences. The fluorescent dye CFSE allows the tracking of cell division in vitro and in vivo and provides a rich source of information with which to test models of cell kinetics. Cell division and death have a stochastic component at the single-cell level, and the probabilities of these occurring in any given time interval may also undergo systematic variation at a population level. This gives rise to heterogeneity in proliferating cell populations. Branching processes provide a natural means of describing this behaviour. RESULTS: We present a likelihood-based method for estimating the parameters of branching process models of cell kinetics using CFSE-labeling experiments, and demonstrate its validity using synthetic and experimental datasets. Performing inference and model comparison with real CFSE data presents some statistical problems and we suggest methods of dealing with them. CONCLUSION: The approach we describe here can be used to recover the (potentially variable) division and death rates of any cell population for which division tracking information is available.
Asunto(s)
Apoptosis/fisiología , Proliferación Celular , Células Cultivadas/citología , Células Cultivadas/fisiología , Fluoresceínas , Interpretación de Imagen Asistida por Computador/métodos , Microscopía Fluorescente/métodos , Succinimidas , Algoritmos , Simulación por Computador , Modelos BiológicosRESUMEN
CONTEXT: Polycystic ovary syndrome (PCOS) is the most common endocrine disorder in women, but its etiology remains obscure. Recent data suggest that an intrinsic abnormality of early follicle development in the ovary is key to the pathogenesis of PCOS. We have recently found that in PCOS the proportion of primordial follicles is decreased with a reciprocal increase in the proportion of primary follicles. OBJECTIVE: Our aim was to examine whether the accelerated transition of follicles from primordial to primary stages in polycystic ovaries (PCO) is due to increased granulosa cell (GC) division. DESIGN: This study is a comparison of expression of minichromosome maintenance protein 2 (MCM2) (present in the nuclei of cells that are licensed to divide) in archive tissue from normal and PCO. SETTING: This is a laboratory-based study. PATIENTS: There were 16 women with regular cycles (six with normal and 10 with PCO) and five anovulatory women with PCO, classified histologically, with reference to menstrual history and ultrasound. MAIN OUTCOME MEASURES: The presence of MCM2 expression in the GCs of 1,371 follicles was determined. RESULTS: GC proliferation was increased in anovulatory PCO compared with both normal and ovulatory PCO, with an increased proportion of preantral follicles with MCM2-positive GCs (P Asunto(s)
Células de la Granulosa/patología
, Folículo Ovárico/patología
, Síndrome del Ovario Poliquístico/patología
, Adulto
, Recuento de Células
, Proteínas de Ciclo Celular/genética
, División Celular/fisiología
, Forma de la Célula/fisiología
, Femenino
, Células de la Granulosa/fisiología
, Humanos
, Inmunohistoquímica
, Componente 2 del Complejo de Mantenimiento de Minicromosoma
, Proteínas Nucleares/genética
, Oocitos/crecimiento & desarrollo
, Oocitos/patología
, Oocitos/ultraestructura
, Fijación del Tejido
RESUMEN
CONTEXT: In polycystic ovary syndrome (PCOS), an increased proportion of follicles leave the primordial (resting) pool and initiate growth. However, there is little evidence for a reduced reproductive life span (early menopause) in women with PCOS, suggesting that the dynamics of follicle growth, and of follicle loss by atresia, is altered in PCOS. OBJECTIVE: The aim of this study was to investigate the possibility that loss of preantral follicles by atresia is reduced in PCOS, leading to prolonged follicle survival. DESIGN: We compared follicle growth in normal and polycystic ovaries using cultures of small ovarian biopsies. SETTING: Tissue samples were obtained at routine laparoscopy from 12 patients with anovulatory PCOS and 16 controls and processed in an ovarian physiology laboratory. MAIN OUTCOME MEASURES: We performed morphometric analysis of follicle population in tissue fixed at time of biopsy (d 0) or after 5, 10, or 15 d in culture. Analyses included assessment of follicle and oocyte diameter, number and proportion of primordial and growing follicles, and number and proportion of atretic follicles. RESULTS: In tissue fixed on d 0, the proportion of healthy growing follicles was, as expected, greater in ovaries from PCOS patients than in normal ovaries (64 vs. 28%; P = 0.0005), but there were no differences between PCOS and normal tissue during culture. The rate of atresia throughout the period of culture in follicles was, however, significantly lower in PCOS tissue (P < 0.0001). After culture, 80% of follicles in normal ovarian tissue were atretic compared with 53% in PCOS biopsies. CONCLUSION: Follicles from polycystic ovaries demonstrate a decreased rate of atresia in culture, suggesting a mechanism for maintaining a larger follicle pool throughout reproductive life.
Asunto(s)
Folículo Ovárico/patología , Síndrome del Ovario Poliquístico/patología , Adulto , Supervivencia Celular/fisiología , Células Cultivadas , Femenino , Atresia Folicular/fisiología , Humanos , Laparoscopía , Técnicas de Cultivo de TejidosRESUMEN
BACKGROUND: The asymptomatic phase of HIV infection is characterised by a slow decline of peripheral blood CD4(+) T cells. Why this decline is slow is not understood. One potential explanation is that the low average rate of homeostatic proliferation or immune activation dictates the pace of a "runaway" decline of memory CD4(+) T cells, in which activation drives infection, higher viral loads, more recruitment of cells into an activated state, and further infection events. We explore this hypothesis using mathematical models. METHODS AND FINDINGS: Using simple mathematical models of the dynamics of T cell homeostasis and proliferation, we find that this mechanism fails to explain the time scale of CD4(+) memory T cell loss. Instead it predicts the rapid attainment of a stable set point, so other mechanisms must be invoked to explain the slow decline in CD4(+) cells. CONCLUSIONS: A runaway cycle in which elevated CD4(+) T cell activation and proliferation drive HIV production and vice versa cannot explain the pace of depletion during chronic HIV infection. We summarize some alternative mechanisms by which the CD4(+) memory T cell homeostatic set point might slowly diminish. While none are mutually exclusive, the phenomenon of viral rebound, in which interruption of antiretroviral therapy causes a rapid return to pretreatment viral load and T cell counts, supports the model of virus adaptation as a major force driving depletion.
Asunto(s)
Linfocitos T CD4-Positivos/inmunología , Infecciones por VIH/inmunología , Memoria Inmunológica , Modelos Inmunológicos , Proliferación Celular , Progresión de la Enfermedad , Homeostasis , Humanos , Timo/inmunología , Carga ViralRESUMEN
Exposure to excess androgens in utero induces irreversible changes in gonadotrophin secretion and results in disrupted reproductive endocrine and ovarian function in adulthood, in a manner reminiscent of the common clinical endocrinopathy of polycystic ovary syndrome (PCOS). We have recently identified an abnormality in early follicle development in PCOS which we suggested might be an androgenic effect. We propose that altered ovarian function in androgenized ewes is due to prenatal androgens not only causing an abnormality of gonadotrophin secretion, but also exerting a direct effect on the early stages of folliculogenesis. Therefore, in this study, we explored the possible differences between small preantral follicles in the ovarian cortex of androgenized female lambs with those of normal lambs. At 8 months of age, small ovarian cortical biopsies (approximately 5 mm3) were obtained at laparotomy from nine female lambs that had been exposed to androgens in utero from embryonic days 30 to 90 of a 147-day pregnancy, and 11 control female lambs. Further, ovarian tissue was obtained at 20 months of age from ten androgenized and nine control animals. Tissue was either fixed immediately for histology or cultured for up to 15 days prior to fixing. The number of follicles in haematoxylin and eosin-stained sections was counted and recorded along with the stage of development. Before culture, the total follicle density (follicles/mm3 tissue) was not statistically significantly different between the two types of ovary at either 8 or 20 months of age. Furthermore, there were no statistically significant differences in the density of follicles at each stage of development. However, there was a lower percentage of primordial follicles, but a higher percentage of primary follicles, in biopsies taken at 8 months from androgenized lambs when compared with controls. At 20 months, the proportions of follicles at the primordial and primary stages were not significantly different between the two groups, but this was mainly attributable to an increase in the proportion of growing follicles in biopsies from control animals. Culture of ovarian cortex from 8-month-old lambs resulted in a progressive increase in the proportion of growing follicles when compared with tissue fixed on the day of surgery. However, there was no difference between androgenized and control tissue in the percentage of growing follicles. The increase in the proportion of growing follicles in the cortex of androgenized animals is reminiscent of similar observations in human polycystic ovaries and suggests that excess exposure to androgen in early life plays a part in the accelerated progression of follicle development from the primordial to the primary stage in polycystic ovaries.
Asunto(s)
Andrógenos/efectos adversos , Folículo Ovárico/fisiología , Síndrome del Ovario Poliquístico/etiología , Efectos Tardíos de la Exposición Prenatal , Andrógenos/metabolismo , Androstenodiona/análisis , Androstenodiona/metabolismo , Animales , Femenino , Genitales/patología , Modelos Animales , Folículo Ovárico/patología , Ovario , Síndrome del Ovario Poliquístico/metabolismo , Síndrome del Ovario Poliquístico/patología , Embarazo , Progesterona/análisis , Progesterona/metabolismo , Ovinos , Técnicas de Cultivo de Tejidos , VirilismoRESUMEN
BACKGROUND: Gene expression microarray data is notoriously subject to high signal variability. Moreover, unavoidable variation in the concentration of transcripts applied to microarrays may result in poor scaling of the summarized data which can hamper analytical interpretations. This is especially relevant in a systems biology context, where systematic biases in the signals of particular genes can have severe effects on subsequent analyses. Conventionally it would be necessary to replace the mismatched arrays, but individual time points cannot be rerun and inserted because of experimental variability. It would therefore be necessary to repeat the whole time series experiment, which is both impractical and expensive. RESULTS: We explain how scaling mismatches occur in data summarized by the popular MAS5 (GCOS; Affymetrix) algorithm, and propose a simple recursive algorithm to correct them. Its principle is to identify a set of constant genes and to use this set to rescale the microarray signals. We study the properties of the algorithm using artificially generated data and apply it to experimental data. We show that the set of constant genes it generates can be used to rescale data from other experiments, provided that the underlying system is similar to the original. We also demonstrate, using a simple example, that the method can successfully correct existing imbalances in the data. CONCLUSION: The set of constant genes obtained for a given experiment can be applied to other experiments, provided the systems studied are sufficiently similar. This type of rescaling is especially relevant in systems biology applications using microarray data.
Asunto(s)
Algoritmos , Perfilación de la Expresión Génica , Análisis de Secuencia por Matrices de Oligonucleótidos , Línea Celular , Perfilación de la Expresión Génica/métodos , Regulación de la Expresión Génica , Humanos , Modelos Genéticos , Modelos Estadísticos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Reproducibilidad de los Resultados , Proyectos de Investigación , Linfocitos T/metabolismo , Linfocitos T/efectos de la radiaciónRESUMEN
BACKGROUND: A number of publications have recently examined the occurrence and properties of the feed-forward motif in a variety of networks, including those that are of interest in genome biology, such as gene networks. The present work looks in some detail at the dynamics of the bi-fan motif, using systems of ordinary differential equations to model the populations of transcription factors, mRNA and protein, with the aim of extending our understanding of what appear to be important building blocks of gene network structure. RESULTS: We develop an ordinary differential equation model of the bi-fan motif and analyse variants of the motif corresponding to its behaviour under various conditions. In particular, we examine the effects of different steady and pulsed inputs to five variants of the bifan motif, based on evidence in the literature of bifan motifs found in Saccharomyces cerevisiae (commonly known as baker's yeast). Using this model, we characterize the dynamical behaviour of the bi-fan motif for a wide range of biologically plausible parameters and configurations. We find that there is no characteristic behaviour for the motif, and with the correct choice of parameters and of internal structure, very different, indeed even opposite behaviours may be obtained. CONCLUSION: Even with this relatively simple model, the bi-fan motif can exhibit a wide range of dynamical responses. This suggests that it is difficult to gain significant insights into biological function simply by considering the connection architecture of a gene network, or its decomposition into simple structural motifs. It is necessary to supplement such structural information by kinetic parameters, or dynamic time series experimental data, both of which are currently difficult to obtain.
Asunto(s)
Biología Computacional , Modelos Biológicos , Saccharomyces cerevisiae/genética , Secuencias de Aminoácidos/genética , Regulación Fúngica de la Expresión Génica , Genes Fúngicos/genética , Transcripción Genética/genéticaRESUMEN
BACKGROUND: We postulated that during ontogenesis cortical surface area and cerebral volume are related by a scaling law whose exponent gives a quantitative measure of cortical development. We used this approach to investigate the hypothesis that premature termination of the intrauterine environment by preterm birth reduces cortical development in a dose-dependent manner, providing a neural substrate for functional impairment. METHODS AND FINDINGS: We analyzed 274 magnetic resonance images that recorded brain growth from 23 to 48 wk of gestation in 113 extremely preterm infants born at 22 to 29 wk of gestation, 63 of whom underwent neurodevelopmental assessment at a median age of 2 y. Cortical surface area was related to cerebral volume by a scaling law with an exponent of 1.29 (95% confidence interval, 1.25-1.33), which was proportional to later neurodevelopmental impairment. Increasing prematurity and male gender were associated with a lower scaling exponent (p < 0.0001) independent of intrauterine or postnatal somatic growth. CONCLUSIONS: Human brain growth obeys an allometric scaling relation that is disrupted by preterm birth in a dose-dependent, sexually dimorphic fashion that directly parallels the incidence of neurodevelopmental impairments in preterm infants. This result focuses attention on brain growth and cortical development during the weeks following preterm delivery as a neural substrate for neurodevelopmental impairment after premature delivery.
Asunto(s)
Encéfalo/crecimiento & desarrollo , Corteza Cerebral/crecimiento & desarrollo , Discapacidades del Desarrollo/etiología , Recien Nacido Prematuro , Biometría , Encéfalo/anatomía & histología , Corteza Cerebral/anatomía & histología , Estudios de Cohortes , Femenino , Edad Gestacional , Humanos , Recién Nacido , Imagen por Resonancia Magnética , Masculino , Modelos Neurológicos , Factores SexualesRESUMEN
CONTEXT: Polycystic ovary syndrome, the most common cause of anovulatory infertility, is characterized by disordered folliculogenesis, notably increased progression from the primordial to the primary stages. This ovarian phenotype is similar to that observed in mice lacking anti-müllerian hormone (AMH). OBJECTIVE: The objective of this study is to investigate whether AMH is involved in accelerating the transition of follicles from primordial to primary stages in polycystic ovaries. DESIGN: This study compares AMH expression in archive tissue from normal and polycystic ovaries. SETTING: This is a laboratory-based study. PATIENTS: Ovarian tissue from seven normoovulatory women and 16 women with polycystic ovaries (five of whom were anovulatory) was used in this study. Ovaries were classified by histology and with reference to menstrual cycle history and ultrasound. MAIN OUTCOME MEASURE: Presence and intensity of AMH expression in 1403 follicles was the main outcome measure. RESULTS: AMH was observed from the primordial stage onward. AMH immunostaining was observed in significantly fewer primordial (P = 0.007) and transitional follicles (P = 0.001) in ovaries from anovulatory women with polycystic ovaries compared with women with regular cycles and either normal or polycystic ovaries. AMH-negative follicles had fewer pregranulosa cells in the largest cross-section of the follicle at both the primordial (median, four and six for AMH-negative and -positive follicles, respectively; P < 0.0001) and transitional stages (median six and nine; P < 0.0007) in normal tissue, and fewer at the transitional stage (median, seven and 11; P < 0.0001) in tissue from anovulatory women with polycystic ovaries. This suggests that AMH expression is associated with granulosa cell mitosis. CONCLUSIONS: These findings indicate a relative deficiency of AMH in primordial and transitional follicles in ovaries from anovulatory women with polycystic ovaries. This may contribute to disordered early follicle development in polycystic ovary syndrome.
Asunto(s)
Glicoproteínas/biosíntesis , Glicoproteínas/genética , Folículo Ovárico/fisiología , Síndrome del Ovario Poliquístico/genética , Síndrome del Ovario Poliquístico/metabolismo , Hormonas Testiculares/biosíntesis , Hormonas Testiculares/genética , Adulto , Anovulación/genética , Anovulación/patología , Hormona Antimülleriana , Recuento de Células , Femenino , Células de la Granulosa/fisiología , Humanos , Inmunohistoquímica , Folículo Ovárico/patología , Ovario/patología , Síndrome del Ovario Poliquístico/patologíaRESUMEN
True quantitative and predictive biology requires the ability to interpret increasingly complex datasets in new ways to reveal underlying functional interactions. This has come a step closer with two recent articles that describe a 'top-down' modelling approach to reconstructing functional networks from microarray data.
Asunto(s)
Perfilación de la Expresión Génica/métodos , Regulación de la Expresión Génica/fisiología , Modelos Biológicos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Proteómica/métodos , Transducción de Señal/fisiología , Simulación por ComputadorRESUMEN
The specificity and sensitivity of T-cell recognition is vital to the immune response. Ligand engagement with the T-cell receptor (TCR) results in the activation of a complex sequence of signalling events, both on the cell membrane and intracellularly. Feedback is an integral part of these signalling pathways, yet is often ignored in standard accounts of T-cell signalling. Here we show, using a mathematical model, that these feedback loops can explain the ability of the TCR to discriminate between ligands with high specificity and sensitivity, as well as provide a mechanism for sustained signalling. The model also explains the recent counter-intuitive observation that endogenous 'null' ligands can significantly enhance T-cell signalling. Finally, the model may provide an archetype for receptor switching based on kinase-phosphatase switches, and thus be of interest to the wider signalling community.
Asunto(s)
Retroalimentación Fisiológica/inmunología , Modelos Inmunológicos , Receptores de Antígenos de Linfocitos T/metabolismo , Transducción de Señal/inmunología , Animales , Ligandos , Monoéster Fosfórico Hidrolasas/metabolismo , Fosfotransferasas/metabolismo , Receptores de Antígenos de Linfocitos T/inmunología , Sensibilidad y Especificidad , Procesos EstocásticosRESUMEN
Performance monitoring is playing an increasing role in modern congenital heart surgery. We present a number of examples to show the kinds of benefits that it can lead to. Conversely, we discuss some of the potential pitfalls including: errors in the collection of data; use of inappropriate data originally collected for a different purpose; assessment based on inadequate sample size; lack of confidence intervals in reported results; failure to include all members of the team in the assessment; and others. We emphasize that apparent changes in performance from year to year or between different units can be purely due to chance. However, despite these difficulties, we believe that performance monitoring, if carried out carefully, with clearly specified goals, can have many benefits in improving patient care. We suggest that statistical analysis of results should not be taken as a definitive indication of inadequate performance; confidence intervals for any performance measurements should always be clearly indicated; small groups of patients/operations should not be used as a basis for assessment; and that performance measurements should be assigned to the whole team, rather than individual members.