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At least 667 records · Page 37Linked to original sources
PubMed2002

Segregation of the ND4/11778 and the ND1/3460 mutations in four heteroplasmic LHON families.

Leber hereditary optic neuropathy (LHON) is an ocular disease associated with mutations in the mitochondrial DNA (mtDNA). The level of heteroplasmy in the mtDNA mutations ND4/11778 and ND1/3460 was followed over a period of 4-12 years in blood samples taken from nine members of four heteroplasmic LHON families. In addition, hair follicle and urinary tract epithelium samples of one individual were studied. The quantification of heteroplasmy was performed using the solid-phase minisequencing method. Only minor and random shifts in the heteroplasmy levels were observed over time, but there were no systematic changes towards an increasing or decreasing proportion of either LHON mutant in the individuals. This indicates that there is no selection for either mtDNA genotype but the segregation of the wild-type mtDNAs and those carrying LHON mutations is a stochastic process governed by random genetic drift. In this respect, LHON mutations seem to behave like neutral polymorphisms.

DNA, Mitochondrial↗
PubMed2002

Endogenous mutagenesis and cancer.

Mutations in DNA accrue relentlessly, largely via stochastic processes. Random changes accumulate, eventually disabling genetic components which result in the formation of the cancer phenotype. Given the infrequency of measured nucleotide changes and the requirement for several mutations to occur in the same cell, it has been postulated that the rate of mutation must become elevated early in the course of evolution of the cancer. Recently, large scale sequencing of tumor DNA has sought to directly measure random mutations. We discuss the implications of these findings and the factors that must be considered in order for fruitful determination of whether a mutator phenotype is a necessary precursor for cancer.

Base Sequence↗
PubMed1996

Modelling the Chernobyl radioactive fallout (I): A fractal approach in northern Italy.

This paper deals with the 137Cs airborne radioactive concentration measured in Northern Italy after the Chernobyl accident. We devised a fractal model to aid in describing the space-time distribution of radioactivity. The model is based on the Fractal Sum of Pulses theory, involving additive stochastic processes. We use, as input source of information, the parametrization of the time trend of radioactive concentration in a few Italian Provinces we calculated in previous work. The results look promising, since realistic scenarios of environmental pollution are produced.

Air Pollutants, Radioactive↗
PubMed1996

Modelling the Chernobyl radioactive fallout (II): A multifractal approach in some European countries.

This paper deals with the 137Cs cumulative soil deposition measured in some European Countries after the Chernobyl accident. We devised a multifractal model to aid in describing the spatial distribution of radioactivity. The model is based the Fractal Sum of Pulses theory, involving additive stochastic processes. We use, as input source of information, the available data of radioactive deposition measured in some European Countries. The results look promising, since realistic scenarios of environmental pollution are produced.

Air Pollutants, Radioactive↗
PubMed2007

Mitochondrial DNA and the mammalian oocyte.

In mammals, mitochondria and mitochondrial DNA (mtDNA) are transmitted through the female germ line. Mature oocytes contain at least 100,000 copies of mtDNA, organized at 1-2 copies per organelle. Despite the high genome copy number, mtDNA sequence variants are observed to segregate rapidly between generations, and this has led to the concept of a developmental bottleneck for the transmission of mtDNA. Ultrastructural investigations of primordial germ cells show that they contain approximately 10 mitochondria, suggesting that mitochondrial biogenesis is arrested during early embryogenesis, and that the mitochondria contributing to the germ cell precursors are simply apportioned from those present in the zygote. Thus, as few as 0.01% of the mitochondria in the oocyte actually contribute to the offspring of the next generation. Mitochondrial replication restarts in the migrating primordial germ cells, and mitochondrial numbers steadily increase to a few thousand in primordial oocytes. Genetic evidence from both heteroplasmic mice and human pedigrees suggests that segregation of mtDNA sequence variants is largely a stochastic process that occurs during the mitotic divisions of the germ cell precursors. This process is essentially complete by the time the primary oocyte population is differentiated in fetal life. Analysis of the distribution of pathogenic mtDNA mutations in the offspring of carrier mothers shows that risk of inheriting a pathogenic mutation increases with the proportion in the mother, but there is no bias toward transmitting more or less of the mutant mtDNAs. This implies that there is no strong selection against oocytes carrying pathogenic mutations and that atresia is not a filter for oocyte quality based on oxidative phosphorylation capacity. The large number of mitochondria and mtDNAs present in the oocyte may simply represent a genetic mechanism to ensure their distribution to the gametes and somatic cells of the next generation. If true, mtDNA copy number, and by inference mitochondrial number, may be the most important determinant of oocyte quality, not because of the effects on oocyte metabolism, but because too few would result in a maldistribution in the early embryo.

Animals↗
PubMed2006

Cell polarity in filamentous fungi: shaping the mold.

The formation of highly polarized hyphae that grow by apical extension is a defining feature of the filamentous fungi. High-resolution microscopy and mathematical modeling have revealed the importance of the cytoskeleton and the Spitzenkorper (an apical vesicle cluster) in hyphal morphogenesis. However, the underlying molecular mechanisms remain poorly characterized. In this review, the pathways and functions known to be involved in polarized hyphal growth are summarized. A central theme is the notion that the polarized growth of hyphae is more complex than in yeast, though similar sets of core pathways are likely utilized. In addition, a model for the establishment and maintenance of hyphal polarity is presented. Key features of the model include the idea that polarity establishment is a stochastic process that occurs independent of internal landmarks. Moreover, the stabilization of nascent polarity axes may be the critical step that permits the emergence of a new hypha.

Actins↗
PubMed1985

Cell biology of the asialoglycoprotein receptor system: a model of receptor-mediated endocytosis.

Substantial information about the ASGP-R has accumulated in the 10 years following the initial studies of this receptor by Ashwell and Morell. Many of its biochemical properties, its structure, and its orientation within the plasma membrane are now known. The pathways of ASGP ligand and receptor, with the CURL organelle being a central component, are summarized in Fig. 18. The major pathway of the ligand through the cell, beginning with binding at the cell surface and ending with degradation in lysosomes, has been investigated in detail. Recently, alternate routes of the ligand such as the ligand recycling pathway have been observed. With regard to the itinerary of the receptor, there is now biochemical, kinetic, and morphological evidence to support receptor recycling. The new concept of CURL as an important intracellular organelle has originated from studies of ASGP-R recycling. Its importance in the dissociation and segregation of ligand and receptor as well as in receptor recycling is now evident. In addition, there has been a concurrent investigation of other receptor systems that participate in receptor-mediated endocytosis, providing parallels and contrasts to the ASGP-R of hepatocytes. Many critical issues still exist in the cell biology of the ASGP-R. What are the structural requirements of the receptor for ligand binding and subsequent endocytosis of the receptor-ligand complex? Very little is known about the interactions between the receptor and the lipid bilayer in which it resides. How does the receptor move laterally in the plasma membrane? Are there proteins or glycolipids closely associated with the ASGP-R and, if so, what is their function? What is the mechanism that causes receptor clustering into coated pits? Although the existence of a pathway for ligand recycling has been demonstrated, there are still many issues to be addressed. What signals a particular ligand molecule for recycling? Is it a stochastic process? What is the function of this route of ligand movement? How are the various ligand pathways coordinated and regulated? In addition, there are many unanswered questions regarding the receptor pathway. How does CURL mediate the sorting of ASGP-R from ligand? How are receptors with different destinations (e.g., ASGP-R and IgA receptor) sorted in CURL? What is the mechanism of ASGP-R degradation and how is it regulated? Finally, how does the Golgi function in the ASGP system and what is the relationship between the Golgi and CURL? Future investigation of these issues will require further observations with existing techniques as well as new approaches.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed2002

Linkage disequilibrium: what history has to tell us.

Linkage disequilibrium has become important in the context of gene mapping. We argue that to understand the pattern of association between alleles at different loci, and of DNA sequence polymorphism in general, it is useful first to consider the underlying genealogy of the chromosomes. The stochastic process known as the coalescent is a convenient way to model such genealogies, and in this paper we set out the theory behind the coalescent and its implications for understanding linkage disequilibrium.

Genetic Variation↗
PubMed1997

A quantitative analysis of single protein-ligand complex separation with the atomic force microscope.

Force measurements on and within single macromolecular complexes utilizing techniques such as atomic force microscopy, optical trapping, flexible glass fibers, and magnetic beads provide a rich source of quantitative data on biomolecular processes. Stochastic thermal fluctuations, an undesirable source of noise in macroscopic biochemical experiments, are an essential element of these sensitive and novel experiments. With the proper analysis, a great deal of information can be gleaned from measurements of these fluctuations. A quantitative framework for analyzing such measurements, based on Kramers' theory of molecular dissociation, is developed. The analysis reveals the kinetic origin and stochastic nature of the measurements. This framework is presented in the context of protein-ligand separation with the atomic force microscope.

Journal Article↗
PubMed1999

Quantitative Doppler measures in coiled vessels: investigation on excised umbilical veins.

Quantitative assessment of umbilical venous blood velocity with Doppler ultrasound (US) must cope with the coiled structure of the vein inside the cord. Both an experimental and a theoretical approach showed remarkable variations in the insonation angle when the probe was moved along the vein, provided the inclination between the Doppler probe and the cord was kept constant. Inaccurate signal processing, stochastic variability and flow disturbances could, however, mask the influence of the geometry. The above hypotheses were assessed by investigating five cords in vitro a few hours after delivery from normal pregnancies at term. The Doppler signal was sampled at different sites along each cord and the mean Doppler shift estimated by FFT spectral analysis, both directly and through the noise rejection D'Alessio's algorithm, which proved effective in improving the Doppler shift estimate in condition of low signal-to-noise ratio (SNR).

Blood Flow Velocity↗
PubMedDate not supplied

Quantification of sensory information transmission using timeseries decorrelation techniques.

To estimate the information transmitted across a neuronal sensory system one has to deal with serial dependence among consecutive samples of the stimulus and the response signal. Common methods usually require a huge amount of data, or are restricted to Gaussian stimuli. Here, we describe stimulus and response as stochastic processes, i.e. as sequences of random variables, in the same coordinate system. Stimulus-response pairs of these random variables must not be considered independently because otherwise the transinformation is overestimated. To account for the linear fraction of the serial dependence, we present two decorrelation techniques based on coordinate transformation. They provide a representation of the processes with uncorrelated random variables and yield a more precise estimate of the transinformation.

Animals↗
PubMedDate not supplied

Cross-correlation between neurons: a source of information about the nervous system.

Impulse trains of spiking neurons are a stochastic process; however, the impulse trains of related neurons are generally not statistically independent. Cross-correlation may be due to either a common input that affects the firing of both cells, or to direct synaptic influence of the one neuron upon the other. By analyzing the distributions of intervals preceding and those following the coincident firings relative to that of all the intervals between impulses in each train, it is possible to infer restrictions upon the ways in which the correlating influence interacts with other sources of variability for each cell. This is applied to pairs of cells in two systems, one in which the coincident firing is due to an input common to the two cells, and one in which one cell is presynaptic to the other.

Action Potentials↗
PubMed2003

Detecting excess radical replacements in phylogenetic trees.

There are a few instances in which positive Darwinian selection has been convincingly demonstrated at the molecular level. In this study, we present a novel test for detecting excess of radical amino-acid replacements. Such excess is usually indicative of positive Darwinian selection, but may also be due to relaxed functional constraints or model misspecification. In our test, each amino-acid replacement is characterized in terms of a physicochemical distance, i.e., the degree of dissimilarity between the exchanged amino-acid residues. By using phylogenetic trees based on protein sequences, our test identifies statistically significant deviations of the mean physicochemical distance from the random expectation, either along a taxonomic lineage or across a subtree. The mean inferred distance is calculated as the average physicochemical distance over all possible ancestral sequence reconstructions weighted by their likelihood. Our method substantially improves over previous approaches by taking into account the stochastic process, tree phylogeny, among-site rate variation, and alternative ancestral reconstructions. We provide a fast linear time algorithm for applying this test to all branches and all subtrees of a given phylogenetic tree. We validate this approach by applying it to two well-studied datasets: the MHC class I glycoproteins serving as a positive control, and the house-keeping gene carbonic anhydrase I serving as a negative control.

Algorithms↗
PubMed2000

Reactive oxygen species, cell signaling, and cell injury.

Oxidative stress has traditionally been viewed as a stochastic process of cell damage resulting from aerobic metabolism, and antioxidants have been viewed simply as free radical scavengers. Only recently has it been recognized that reactive oxygen species (ROS) are widely used as second messengers to propagate proinflammatory or growth-stimulatory signals. With this knowledge has come the corollary realization that oxidative stress and chronic inflammation are related, perhaps inseparable phenomena. New pharmacological strategies aimed at supplementing antioxidant defense systems while antagonizing redox-sensitive signal transduction may allow improved clinical management of chronic inflammatory or degenerative conditions, including Alzheimer's disease. Introduction of antioxidant therapies into mainstream medicine is possible and promising, but will require significant advances in basic cell biology, pharmacology, and clinical bioanalysis.

Antioxidants↗
PubMed2003

Real-time imaging of lymphocytes in vivo.

New preparations, fluorescent probes and imaging techniques are providing the means to observe the behavior of cells in the tissue environment of lymphoid organs. In particular, when combined with two-photon laser microscopy, intravital imaging of surgically exposed lymph nodes provides a unique view of lymphocyte migration and antigen presentation as it occurs within the living animal. The view is emerging that lymphocytes migrate randomly within lymphoid organs, and that lymphocyte contact with antigen-presenting cells may be a stochastic process rather than one guided by chemokine gradients.

Animals↗
PubMed2001

Steered molecular dynamics and mechanical functions of proteins.

Atomic force microscopy of single molecules, steered molecular dynamics and the theory of stochastic processes have established a new field that investigates mechanical functions of proteins, such as ligand-receptor binding/unbinding and elasticity of muscle proteins during stretching. The combination of these methods yields information on the energy landscape that controls mechanical function and on the force-bearing components of proteins, as well as on the underlying physical mechanisms.

Avidin↗
PubMed2003

Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator.

BACKGROUND: The pattern of somites is traced out by a mechanism involving oscillating gene expression at the tail end of the embryo. In zebrafish, two linked oscillating genes, her1 and her7, coding for inhibitory gene regulatory proteins, are especially implicated in genesis of the oscillations, while Notch signaling appears necessary for synchronization of adjacent cells. RESULTS: I show by mathematical simulation that direct autorepression of her1 and her7 by their own protein products provides a mechanism for the intracellular oscillator. This mechanism operates robustly even when one allows for the fact that gene regulation is an essentially noisy (stochastic) process. The predicted period is close to the observed period (30 min) and is dictated primarily by the transcriptional delay, the time taken to make an mRNA molecule. Through its coupling to her1/her7 expression, Notch signaling can keep the rapid oscillations in adjacent cells synchronized. When the coupling parameters are varied, however, the model system can switch to oscillations of a much longer period, resembling that of the mouse or chick somitogenesis oscillator and governed by the delays in the Notch pathway. Such Notch-mediated synchronous oscillations are predicted even in the absence of direct her1/her7 autoregulation, through operation of the standard Notch signaling pathway that is usually assumed simply to give lateral inhibition. CONCLUSIONS: Direct autorepression of a gene by its own product can generate oscillations, with a period determined by the transcriptional and translational delays. Simple as they are, such systems show surprising behaviors. To understand them, unaided intuition is not enough: we need mathematics.

Animals↗
PubMed1999

Real time monitoring of muscular fatigue from dynamic surface myoelectric signals using a complex covariance approach.

A method aimed at the real-time monitoring of muscular fatigue was implemented and optimized. The method is based on an estimate of the complex covariance function in order to evaluate, in real time, the mean frequency of the myoelectric signal spectrum. Real-time implementation is guaranteed by a recursive computation of the complex covariance and then of the mean frequency. The results show good performance on both synthetic and experimental non-stationary myoelectric signals recorded during fatiguing dynamic protocols. Performance in the presence of noise is highly satisfactory on both deterministic signals and stochastic processes, even when there are strong non-stationarities. Moreover, the computational complexity is highly reduced with respect to that offered by traditional methods based on short time Fourier transform.

Adult↗