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At least 451 records · Page 25Linked to original sources
PubMed2004

The yeast cell-cycle network is robustly designed.

The interactions between proteins, DNA, and RNA in living cells constitute molecular networks that govern various cellular functions. To investigate the global dynamical properties and stabilities of such networks, we studied the cell-cycle regulatory network of the budding yeast. With the use of a simple dynamical model, it was demonstrated that the cell-cycle network is extremely stable and robust for its function. The biological stationary state, the G1 state, is a global attractor of the dynamics. The biological pathway, the cell-cycle sequence of protein states, is a globally attracting trajectory of the dynamics. These properties are largely preserved with respect to small perturbations to the network. These results suggest that cellular regulatory networks are robustly designed for their functions.

Cell Cycle↗
PubMed2002

Redundancy, antiredundancy, and the robustness of genomes.

Genetic mutations that lead to undetectable or minimal changes in phenotypes are said to reveal redundant functions. Redundancy is common among phenotypes of higher organisms that experience low mutation rates and small population sizes. Redundancy is less common among organisms with high mutation rates and large populations, or among the rapidly dividing cells of multicellular organisms. In these cases, one even observes the opposite tendency: a hypersensitivity to mutation, which we refer to as antiredundancy. In this paper we analyze the evolutionary dynamics of redundancy and antiredundancy. Assuming a cost of redundancy, we find that large populations will evolve antiredundant mechanisms for removing mutants and thereby bolster the robustness of wild-type genomes; whereas small populations will evolve redundancy to ensure that all individuals have a high chance of survival. We propose that antiredundancy is as important for developmental robustness as redundancy, and is an essential mechanism for ensuring tissue-level stability in complex multicellular organisms. We suggest that antiredundancy deserves greater attention in relation to cancer, mitochondrial disease, and virus infection.

Biological Evolution↗
PubMed2005

Robust in vitro activity of RebF and RebH, a two-component reductase/halogenase, generating 7-chlorotryptophan during rebeccamycin biosynthesis.

The indolocarbazole antitumor agent rebeccamycin is modified by chlorine atoms on each of two indole moieties of the aglycone scaffold. These halogens are incorporated during the initial step of its biosynthesis from conversion of L-Trp to 7-chlorotryptophan. Two genes in the biosynthetic cluster, rebF and rebH, are predicted to encode the flavin reductase and halogenase components of an FADH2-dependent halogenase, a class of enzymes involved in the biosynthesis of numerous halogenated natural products. Here, we report that, in the presence of O2, chloride ion, and L-Trp as cosubstrates, purified RebH displays robust regiospecific halogenating activity to generate 7-chlorotryptophan over at least 50 catalytic cycles. Halogenation by RebH required the addition of RebF, which catalyzes the NADH-dependent reduction of FAD to provide FADH2 for the halogenase. Maximal rates were achieved at a RebF/RebH ratio of 3:1. In air-saturated solutions, a k(cat) of 1.4 min(-1) was observed for the RebF/RebH system but increased at least 10-fold in low-pO2 conditions. RebH was also able to use bromide ions to generate monobrominated Trp. The demonstration of robust chlorinating activity by RebF/RebH sets up this system for the probing of mechanistic questions regarding this intriguing class of enzymes.

Carbazoles↗
PubMed2005

Robust hepatitis C virus infection in vitro.

The absence of a robust cell culture model of hepatitis C virus (HCV) infection has severely limited analysis of the HCV life cycle and the development of effective antivirals and vaccines. Here we report the establishment of a simple yet robust HCV cell culture infection system based on the HCV JFH-1 molecular clone and Huh-7-derived cell lines that allows the production of virus that can be efficiently propagated in tissue culture. This system provides a powerful tool for the analysis of host-virus interactions that should facilitate the discovery of antiviral drugs and vaccines for this important human pathogen.

Antigens, CD↗
PubMed2006

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations.

By representing the high-resolution crystal structures of a number of enzymes using the elastic network model, it has been shown that only a few low-frequency normal modes are needed to describe the large-scale domain movements that are triggered by ligand binding. Here we explore a link between the nearly invariant nature of the modes that describe functional dynamics at the mesoscopic level and the large evolutionary sequence variations at the residue level. By using a structural perturbation method (SPM), which probes the residue-specific response to perturbations (or mutations), we identify a sparse network of strongly conserved residues that transmit allosteric signals in three structurally unrelated biological nanomachines, namely, DNA polymerase, myosin motor, and the Escherichia coli chaperonin. Based on the response of every mode to perturbations, which are generated by interchanging specific sequence pairs in a multiple sequence alignment, we show that the functionally relevant low-frequency modes are most robust to sequence variations. Our work shows that robustness of dynamical modes at the mesoscopic level is encoded in the structure through a sparse network of residues that transmit allosteric signals.

Allosteric Regulation↗
PubMed2006

Stable and robust polymer nanotubes stretched from polymersomes.

We create long polymer nanotubes by directly pulling on the membrane of polymersomes using either optical tweezers or a micropipette. The polymersomes are composed of amphiphilic diblock copolymers, and the nanotubes formed have an aqueous core connected to the aqueous interior of the polymersome. We stabilize the pulled nanotubes by subsequent chemical cross-linking. The cross-linked nanotubes are extremely robust and can be moved to another medium for use elsewhere. We demonstrate the ability to form networks of polymer nanotubes and polymersomes by optical manipulation. The aqueous core of the polymer nanotubes together with their robust character makes them interesting candidates for nanofluidics and other applications in biotechnology.

Chemical Phenomena↗
PubMed2006

Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer.

Predicting at the time of discovery the prognosis and metastatic potential of cancer is a major challenge in current clinical research. Numerous recent studies searched for gene expression signatures that outperform traditionally used clinical parameters in outcome prediction. Finding such a signature will free many patients of the suffering and toxicity associated with adjuvant chemotherapy given to them under current protocols, even though they do not need such treatment. A reliable set of predictive genes also will contribute to a better understanding of the biological mechanism of metastasis. Several groups have published lists of predictive genes and reported good predictive performance based on them. However, the gene lists obtained for the same clinical types of patients by different groups differed widely and had only very few genes in common. This lack of agreement raised doubts about the reliability and robustness of the reported predictive gene lists, and the main source of the problem was shown to be the small number of samples that were used to generate the gene lists. Here, we introduce a previously undescribed mathematical method, probably approximately correct (PAC) sorting, for evaluating the robustness of such lists. We calculate for several published data sets the number of samples that are needed to achieve any desired level of reproducibility. For example, to achieve a typical overlap of 50% between two predictive lists of genes, breast cancer studies would need the expression profiles of several thousand early discovery patients.

Breast Neoplasms↗
PubMed2007

A proposal for robust temperature compensation of circadian rhythms.

The internal circadian rhythms of cells and organisms coordinate their physiological properties to the prevailing 24-h cycle of light and dark on earth. The mechanisms generating circadian rhythms have four defining characteristics: they oscillate endogenously with period close to 24 h, entrain to external signals, suffer phase shifts by aberrant pulses of light or temperature, and compensate for changes in temperature over a range of 10 degrees C or more. Most theoretical descriptions of circadian rhythms propose that the underlying mechanism generates a stable limit cycle oscillation (in constant darkness or dim light), because limit cycles quite naturally possess the first three defining properties of circadian rhythms. On the other hand, the period of a limit cycle oscillator is typically very sensitive to kinetic rate constants, which increase markedly with temperature. Temperature compensation is therefore not a general property of limit cycle oscillations but must be imposed by some delicate balance of temperature dependent effects. However, "delicate balances" are unlikely to be robust to mutations. On the other hand, if circadian rhythms arise from a mechanism that concentrates sensitivity into a few rate constants, then the "balancing act" is likely to be more robust and evolvable. We propose a switch-like mechanism for circadian rhythms that concentrates period sensitivity in just two parameters, by forcing the system to alternate between a stable steady state and a stable limit cycle.

Circadian Rhythm↗
PubMed2001

Interlocked feedback loops contribute to the robustness of the Neurospora circadian clock.

Interlocked feedback loops may represent a common feature among the regulatory systems controlling circadian rhythms. The Neurospora circadian feedback loops involve white collar-1 (wc-1), wc-2, and frequency (frq) genes. We show that WC-1 and WC-2 proteins activate the transcription of frq gene, whereas FRQ protein plays dual roles: repressing its own transcription, probably by interacting with the WC-1/WC-2 complex, and activating the expression of both WC proteins. Thus, they form two interlocked feedback loops: one negative and one positive. We establish the physiological significance of the interlocked positive feedback loops by showing that the levels of WC-1 and WC-2 determine the robustness and stability of the clock. Our data demonstrate that with WC-1 being the limiting factor in the WC-1/WC-2 complex, the greater the levels of WC-1 and WC-2, the higher the level of the FRQ oscillation and the more robust the overt rhythms. Our data also show that, despite considerable changes in the levels of WC-1, WC-2, and FRQ, the period of the clock has been limited to a small range, suggesting that the interlocked circadian feedback loops are also important for determining the circadian period length of the clock.

Circadian Rhythm↗
PubMed2003

Information exchange and the robustness of organizational networks.

The dynamics of information exchange is an important but understudied aspect of collective communication, coordination, and problem solving in a wide range of distributed systems, both physical (e.g., the Internet) and social (e.g., business firms). In this paper, we introduce a model of organizational networks according to which links are added incrementally to a hierarchical backbone and test the resulting networks under variable conditions of information exchange. Our main result is the identification of a class of multiscale networks that reduce, over a wide range of environments, the likelihood that individual nodes will suffer congestion-related failure and that the network as a whole will disintegrate when failures do occur. We call this dual robustness property of multiscale networks "ultrarobustness." Furthermore, we find that multiscale networks attain most of their robustness with surprisingly few link additions, suggesting that ultrarobust organizational networks can be generated in an efficient and scalable manner. Our results are directly relevant to the relief of congestion in communication networks and also more broadly to activities, like distributed problem solving, that require individuals to exchange information in an unpredictable manner.

Journal Article↗
PubMed2003

A natural class of robust networks.

As biological studies shift from molecular description to system analysis we need to identify the design principles of large intracellular networks. In particular, without knowing the molecular details, we want to determine how cells reliably perform essential intracellular tasks. Recent analyses of signaling pathways and regulatory transcription networks have revealed a common network architecture, termed scale-free topology. Although the structural properties of such networks have been thoroughly studied, their dynamical properties remain largely unexplored. We present a prototype for the study of dynamical systems to predict the functional robustness of intracellular networks against variations of their internal parameters. We demonstrate that the dynamical robustness of these complex networks is a direct consequence of their scale-free topology. By contrast, networks with homogeneous random topologies require fine-tuning of their internal parameters to sustain stable dynamical activity. Considering the ubiquity of scale-free networks in nature, we hypothesize that this topology is not only the result of aggregation processes such as preferential attachment; it may also be the result of evolutionary selective processes.

Biophysical Phenomena↗
PubMed2003

Robust singular value decomposition analysis of microarray data.

In microarray data there are a number of biological samples, each assessed for the level of gene expression for a typically large number of genes. There is a need to examine these data with statistical techniques to help discern possible patterns in the data. Our technique applies a combination of mathematical and statistical methods to progressively take the data set apart so that different aspects can be examined for both general patterns and very specific effects. Unfortunately, these data tables are often corrupted with extreme values (outliers), missing values, and non-normal distributions that preclude standard analysis. We develop a robust analysis method to address these problems. The benefits of this robust analysis will be both the understanding of large-scale shifts in gene effects and the isolation of particular sample-by-gene effects that might be either unusual interactions or the result of experimental flaws. Our method requires a single pass and does not resort to complex "cleaning" or imputation of the data table before analysis. We illustrate the method with a commercial data set.

Cluster Analysis↗
PubMed2004

Early-onset and robust cerebral microvascular accumulation of amyloid beta-protein in transgenic mice expressing low levels of a vasculotropic Dutch/Iowa mutant form of amyloid beta-protein precursor.

Cerebrovascular deposition of amyloid beta-protein (Abeta) is a common pathological feature of Alzheimer's disease and related disorders. In particular, the Dutch E22Q and Iowa D23N mutations in Abeta cause familial cerebrovascular amyloidosis with abundant diffuse amyloid plaque deposits. Both of these charge-altering mutations enhance the fibrillogenic and pathogenic properties of Abeta in vitro. Here, we describe the generation of several transgenic mouse lines (Tg-SwDI) expressing human neuronal Abeta precursor protein (AbetaPP) harboring the Swedish K670N/M671L and vasculotropic Dutch/Iowa E693Q/D694N mutations under the control of the mouse Thy1.2 promoter. Tg-SwDI mice expressed transgenic human AbetaPP only in the brain, but at levels below those of endogenous mouse AbetaPP. Despite the paucity of human AbetaPP expression, quantitative enzyme-linked immunosorbent assay measurements revealed that Tg-SwDI mice developed early-onset and robust accumulation of Abeta in the brain with high association with isolated cerebral microvessels. Tg-SwDI mice exhibited striking perivascular/vascular Abeta deposits that markedly increased with age. The vascular Abeta accumulations were fibrillar, exhibiting strong thioflavin S staining, and occasionally presented signs of microhemorrhage. In addition, numerous largely diffuse, plaque-like structures were observed starting at 3 months of age. In vivo transport studies demonstrated that Dutch/Iowa mutant Abeta was more readily retained in the brain compared with wild-type Abeta. These results with Tg-SwDI mice demonstrate that overexpression of human AbetaPP is not required for early-onset and robust accumulation of both vascular and parenchymal Abeta in mouse brain.

Amyloid beta-Peptides↗
PubMed2004

A single-headed recombinant fragment of Dictyostelium cytoplasmic dynein can drive the robust sliding of microtubules.

A cytoplasmic dynein is a microtubule-based motor protein involved in diverse cellular functions, such as organelle transport and chromosome segregation. The dynein has two ring-shaped heads that contain six repeats of the AAA domain responsible for ATP hydrolysis. It has been proposed that the ATPase-dependent swing of a stalk and a stem emerging from each of the heads generates the power stroke (Burgess, S.A. (2003) Nature 421, 715-718). To understand the molecular mechanism of the dynein power stroke, it is essential to establish an easy and reproducible method to express and purify the recombinant dynein with full motor activities. Here we report the expression and purification of the C-terminal 380-kDa fragment of the Dictyostelium cytoplasmic dynein heavy-chain fused with an affinity tag and green fluorescent protein. The purified single-headed recombinant protein drove the robust minus-end-directed sliding of microtubules at a velocity of 1.2 microm/s. This recombinant protein had a high basal ATPase activity (approximately 4s(-1)), which was further activated by >15-fold on the addition of 40 microM microtubules. These results show that the 380-kDa recombinant fragment retains all the structures required for motor functions, i.e. the ATPase activity highly stimulated by microtubules and the robust motility.

Animals↗
PubMed2006

Robustness testing of a tablet formulation using multivariate design.

A total of 45 experiments were carried out to evaluate the robustness of two similar tablet formulations--a product of two strengths--with respect to normal batch-to-batch variation of the excipients and the active pharmaceutical ingredient. The formulations consist of 10 ingredients. Because of the differing amounts of active pharmaceutical ingredients, the two formulations also differ in the amounts of two of the diluents and one of the binders. The excipients and active pharmaceutical ingredient were characterized in terms of multiple variables, and principal properties were calculated with principal component analysis. A Plackett and Burman design was applied to the principal properties. The relationships between the design factors and two responses, mean disintegration time and mean crushing strength, were evaluated by using regression methods. Both formulations were found to be robust under controlled conditions.

Chemistry, Pharmaceutical↗
PubMed1997

Robustness of bioequivalence procedures under Box-Cox alternatives.

This study investigates the robustness of Schuirmann's two one-sided tests procedure under a set of Box-Cox alternatives. A simulation is conducted to study the level of significance and the power of the procedure. Empirical results show that Schuirmann's procedure is robust under Box-Cox alternatives when the mean of the underlying distribution of the reference formulation is known, which suggests that the assumptions of normality or lognormality are sufficient but may not be necessary. It appears that Schuirmann's procedure cannot maintain the proper level of significance when the mean of the reference formulation is unknown, even under the normality or lognormality assumptions.

Chemistry, Pharmaceutical↗
PubMed2002

Robustness of ancestral state estimates: evolution of life history strategy in ichneumonoid parasitoids.

We test hypotheses for the evolution of a life history trait among a group of parasitoid wasps (Hymenoptera: Ichneumonoidea), namely, the transition among koinobiont parasitoids (parasitoids whose hosts continue development after oviposition) between attacking exposed hosts and attacking hosts that are concealed within plant tissue. Using a range of phylogeny estimates based on 28S rDNA sequences, we use maximum parsimony (MP) and maximum likelihood (ML) methods to estimate the ancestral life history traits for the main clades in which both traits occur (using the programs MacClade and Discrete, respectively). We also assess the robustness of these estimates; for MP, we use step matrices in PAUP* to find the minimum weight necessary to reverse estimates or make them ambiguous, and for ML, we measure the differences in likelihood after fixing the ancestral nodes at the alternative states. We also measure the robustness of the MP ancestral state estimate against uncertainties in the phylogeny estimate, manipulating the most-parsimonious tree in MacClade to find the shortest suboptimal tree in which the ancestral state estimate is reversed or made ambiguous. Using these methods, we find strong evidence supporting two transitions among koinobiont Ichneumonoidea: (1) to attacking exposed hosts in a clade consisting of the Helconinae and related subfamilies, and (2) the reverse transition in a clade consisting of the Euphorinae and related subfamilies. In exploring different methods of analyzing variable-length DNA sequences, we found that direct optimization with POY gave some clearly erroneous results that had a profound effect on the overall phylogeny estimate. We also discuss relationships within the superfamily and expand the Mesostoinae to include all the gall-associated braconids that form the sister group of the Aphidiinae.

Animals↗
PubMed2004

Exaggeration index for an expanded version of the auditory verbal learning test: robustness to coaching.

Recent research suggests that effort detection measures based on patterns of neuropsychological performance may be more robust to coaching than traditional effort detection measures. In the present study, we evaluated the Exaggeration Index for an extended version of the Auditory Verbal Learning Test (EI-AVLTX), a recently developed effort detection instrument based on patterns of performance on the AVLT using a simulated malingering paradigm. In two independent samples, the EI-AVLTX was1 found to be relatively sensitive and specific to malingering, and robust to the effects of a warning about malingering detection.

Acoustic Stimulation↗