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PubMed2004

Differential fitness of mitochondrial DNA in perturbation cage studies correlates with global abundance and population history in Drosophila simulans.

Mitochondria are often referred to as the powerhouse of the cell. However, research linking intraspecific differences in organismal fitness with genotypic mitochondrial DNA (mtDNA) variation has been hampered by the lack of variation in experimentally tractable species. This study examines whether fly lines harbouring three distinct Drosophila simulans mtDNA types (siI, -II and -III) exhibit differential fitness in laboratory perturbation cages. Comparison of the pre-perturbation and post-perturbation data shows that both the mtDNA and mitonuclear interactions have a significant and repeatable effect on the frequency of flies with specific genotypes in population cages (siII > -III > -I) and that coadapted mitonuclear interactions are greatest in the siI type. The rank order of mtDNA frequency correlates with the observed worldwide distribution of the haplogroups while mitonuclear interactions are most significant in the siI haplogroup that is likely to have been subject to repeated population bottlenecks. One possible explanation for the maintenance of the least fit siI haplogroup on Pacific islands is that it is protected from extinction by Wolbachia infection.

Animals↗
PubMed2005

A robust meta-classification strategy for cancer diagnosis from gene expression data.

One of the major challenges in cancer diagnosis from microarray data is to develop robust classification models which are independent of the analysis techniques used and can combine data from different laboratories. We propose a meta-classification scheme which uses a robust multivariate gene selection procedure and integrates the results of several machine learning tools trained on raw and pattern data. We validate our method by applying it to distinguish diffuse large B-cell lymphoma (DLBCL) from follicular lymphoma (FL) on two independent datasets: the HuGeneFL Affmetrixy dataset of Shipp et al. (www. genome.wi.mit.du/MPR /lymphoma) and the Hu95Av2 Affymetrix dataset (DallaFavera's laboratory, Columbia University). Our meta-classification technique achieves higher predictive accuracies than each of the individual classifiers trained on the same dataset and is robust against various data perturbations. We also find that combinations of p53 responsive genes (e.g., p53, PLK1 and CDK2) are highly predictive of the phenotype.

Algorithms↗
PubMed2005

HU-alpha binds to the putative double-stranded DNA mimic HI1450 from Haemophilus influenzae.

Recently, the solution structure of the hypothetical protein HI1450 from Haemophilus influenzae was solved as part of a structure-based effort to understand function. The distribution of its many negatively charged residues and weak structure and sequence homology to uracil DNA glycosylase inhibitor (Ugi) suggested that HI1450 may act as a double-stranded DNA (dsDNA) mimic. We present supporting evidence here and show that HI1450 interacts with the dsDNA-binding protein HU-alpha. The interaction between HI1450 and HU-alpha from H. influenzae is characterized using calorimetry and NMR spectroscopy. HU-alpha binds to HI1450 with a K(d) of 3.0 +/- 0.2 microM, which is similar in affinity to its interaction with dsDNA. Chemical shift perturbation data indicate that the beta1-strand of HI1450 and neighboring regions are most directly involved in interactions with HU-alpha. These results show that HI1450 and its structural homolog, Ugi, use similar parts of their structures to recognize DNA-binding proteins.

Bacterial Proteins↗
PubMed2004

Fair attribution of functional contribution in artificial and biological networks.

This letter presents the multi-perturbation Shapley value analysis (MSA), an axiomatic, scalable, and rigorous method for deducing causal function localization from multiple perturbations data. The MSA, based on fundamental concepts from game theory, accurately quantifies the contributions of network elements and their interactions, overcoming several shortcomings of previous function localization approaches. Its successful operation is demonstrated in both the analysis of a neurophysiological model and of reversible deactivation data. The MSA has a wide range of potential applications, including the analysis of reversible deactivation experiments, neuronal laser ablations, and transcranial magnetic stimulation "virtual lesions," as well as in providing insight into the inner workings of computational models of neurophysiological systems.

Algorithms↗
PubMed2005

Robust diagnosis of non-Hodgkin lymphoma phenotypes validated on gene expression data from different laboratories.

A major challenge in cancer diagnosis from microarray data is the need for robust, accurate, classification models which are independent of the analysis techniques used and can combine data from different laboratories. We propose such a classification scheme originally developed for phenotype identification from mass spectrometry data. The method uses a robust multivariate gene selection procedure and combines the results of several machine learning tools trained on raw and pattern data to produce an accurate meta-classifier. We illustrate and validate our method by applying it to gene expression datasets: the oligonucleotide HuGeneFL microarray dataset of Shipp et al. (www.genome.wi.mit.du/MPR/lymphoma) and the Hu95Av2 Affymetrix dataset (DallaFavera's laboratory, Columbia University). Our pattern-based meta-classification technique achieves higher predictive accuracies than each of the individual classifiers , is robust against data perturbations and provides subsets of related predictive genes. Our techniques predict that combinations of some genes in the p53 pathway are highly predictive of phenotype. In particular, we find that in 80% of DLBCL cases the mRNA level of at least one of the three genes p53, PLK1 and CDK2 is elevated, while in 80% of FL cases, the mRNA level of at most one of them is elevated.

Biomarkers, Tumor↗
PubMed2005

Delay Fokker-Planck equations, perturbation theory, and data analysis for nonlinear stochastic systems with time delays.

We study nonlinear stochastic systems with time-delayed feedback using the concept of delay Fokker-Planck equations introduced by Guillouzic, L'Heureux, and Longtin. We derive an analytical expression for stationary distributions using first-order perturbation theory. We demonstrate how to determine drift functions and noise amplitudes of this kind of systems from experimental data. In addition, we show that the Fokker-Planck perspective for stochastic systems with time delays is consistent with the so-called extended phase-space approach to time-delayed systems.

Journal Article↗
PubMed1989

Point perturbation analysis of experimental data.

A new method of data analysis is proposed. The method is based on discrete perturbation of experimental data points, which is used to probe the metric of the parameter hyperspace. Perturbation-induced fluctuations in the residual values are analysed by discrete Fourier transform to yield the autocorrelation function and a relaxation length for each experimental point. This parameter provides a quantitative measure of correlation and hence nonrandomness of residuals. The method is applied to the analysis of measurements of the shear viscosity of a 2,6-lutidine/water mixture near the critical point, and to the oxygen and carbon monoxide binding reactions to human hemoglobin. Relaxation profiles are constructed for several experimental data sets. Departure from random behavior in the residuals is discussed in connection with the theoretical interpretations of the phenomenon under consideration.

Analysis of Variance↗
PubMed2003

On the normalization method in two-dimensional correlation spectra when concentration is used as a perturbation parameter.

Data pretreatment is of importance in two-dimensional (2D) correlation analysis when composition is used as a perturbation parameter. For composition-oriented studies, different normalization methods based on both external parameters (i.e., concentration) and internal parameters (i.e., absorbance from individual components) have been compared. It was found that when there is no overlapping between absorption bands of interest, no normalization is needed for data pretreatment. When overlapped bands must be used for 2D correlation analysis, the mean-centered normalization method could be used to obtain correct signs in synchronous spectra for a transformation process in the specific form of A-->kC. The intensity of the 2D spectrum, however, may not accurately reflect quantitative information of the overall extent of spectral intensity variation observed during experiments.

Algorithms↗
PubMed2003

Activation of pmar1 controls specification of micromeres in the sea urchin embryo.

pmar1 is a transcription factor in the paired class homeodomain family that was identified and found to be transcribed in micromeres beginning at the fourth cleavage of sea urchin development [Dev. Biol. 246 (2002), 209]. Based on in situ data, molecular perturbation studies, and QPCR data, the recently published gene regulatory network (GRN) model for endomesoderm specification [Science 295 (2002) 1669; Dev. Biol. 246 (2002), 162] places pmar1 early in the micromere specification pathway, and upstream of two important micromere induction signals. The goal of this study was to test these three predictions of the network model. A series of embryo chimeras were produced in which pmar1 activity was perturbed in one cell that was transplanted to control hosts. At the fourth cleavage, micromeres bearing altered pmar1 activity were combined with a normal micromereless host embryo. If beta-catenin signaling is blocked, the micromeres remain unspecified and are unable to signal to the host cells. When such beta-catenin-blocked micromeres also express Pmar1, all observed micromere functions are rescued. The rescue includes expression of the primary mesenchyme cell (PMC) differentiation program, expression and execution of the Delta signal to induce secondary mesoderm cell (SMC) specification in macromere progeny, and expression of the early endomesoderm induction signal necessary for full specification of the endoderm. Additionally, Pmar1 expressed mosaically from inserted DNA constructs causes induction of ectopic Endo 16 in adjacent cells, demonstrating further that Pmar1 controls expression of the early endomesoderm induction signal. Based on these experiments, Pmar1 is an important transcription factor necessary for initiating the micromere specification program and for the expression of two inductive signals produced by micromeres. Each of the tests we describe supports the placement and function of Pmar1 in the endomesoderm GRN model.

Animals↗
PubMed2001

Local structure and local compressibilities around Co2+ impurity in ZnSiF6.6H2O crystal determined from electron paramagnetic resonance data.

The perturbation formulas of g-factors gparallel, gperpendicular and hyperfine structure constants Aparallel, Aperpendicular for 3d7 ion in trigonal octahedral crystal field are established on the basis of a cluster approach. These formulas consist of the contributions from configuration interaction and covalency effect and the parameters related to both effects can be estimated from the optical spectra and the structural data of the system under study. According to these formulas, the local trigonal distortion angle beta at pressure P = 0 and the local compressibilities d ln beta/dP in two pressure regions around Co2+ impurity in ZnSiF6.6H2O crystal are estimated by fitting the calculated electron paramagnetic resonance parameters gi, Ai and their pressure coefficients to the observed values. The results show that these local values are different from those of the host crystal because of the influence of impurity.

Cations, Divalent↗
PubMed2006

Pressure perturbation calorimetry of helical peptides.

Pressure perturbation calorimetry quantifies the temperature dependence of a solute's thermal expansion coefficient, providing information about solute-solvent interactions. We tested the idea that pressure perturbation calorimetry can provide information about solvent-accessible surface area by studying peptides with different secondary structures. The peptides comprised two host-guest series: one predominately an alpha-helix, the other predominately a polyproline II helix. In aqueous buffer, we find a correlation between the amount of secondary structure as assessed by circular dichroism spectropolarimetry and the pressure perturbation calorimetry data. We conclude that pressure perturbation calorimetry can provide information about the exposure of polar and nonpolar surface area. Data acquired in a buffered urea solution, however, are not as easily interpreted.

Calorimetry↗
PubMed1990

Point perturbation analysis of experimental data: II. The statistics of relaxation length values of pseudo-random errors.

The statistics of relaxation lengths for pseudo-random deviates as determined by point perturbation analysis (E. Di Cera, F. Andreasi Bassi and G. Arcovito Biophys. Chem. 34 (1989)239),has been constructed by a Monte Carlo study. The values of the relaxation length, L, approximately follow a Gamma distribution. The results allow for a statistical estimation of relaxation profiles and provide a test for randonmess of residuals which is more accurate than other standard procedures.

Journal Article↗
PubMed2005

Support versus corroboration.

Numerous metrics have been developed that attempt to assess the reliability of phylogenetic trees. Several of these commonly used measures of tree and tree branch support are described and discussed in the context of their relationship to Popperian corroboration. Claims that measures of support indicate the accuracy of phylogenetic trees or provide information for tree choice are rebutted. Measures of support are viewed as being of heuristic value within a given phylogenetic framework for describing the precision of the data based on perturbations to the data. However, no direct link is observed between the calculation of measures of support and corroboration. Direct measures of support, but not re-sampling or randomization methods, may play a more specific role in phylogenetic inference by providing the tools to search for falsifiers that could be the subject of future rounds of hypothesis testing.

Algorithms↗
PubMed2006

Scalable implementation of analytic gradients for second-order Z-averaged perturbation theory using the distributed data interface.

The analytic gradient expression for second-order Z-averaged perturbation theory is revised and its parallel implementation is described in detail. The distributed data interface is used to access molecular-orbital integral arrays stored in distributed memory. The algorithm is designed to maximize the use of local data and reduce communication costs. The iterative solution and the preconditioner used to induce the convergence of the coupled-perturbed Hartree-Fock equations are presented. Several illustrative timing examples are discussed.

Journal Article↗
PubMed2006

Analyzing gastrocnemius EMG-activity and sway data from quiet and perturbed standing.

In an experiment, we combined force plate measurements and surface EMG in studying quiet and perturbed standing, involving MS (Multiple sclerosis) and controls. The aim of this paper is to report the results thus obtained on the relation between filtered gastrocnemius (GA) EMG and the anterior-posterior center-of-pressure (A/P COP) coordinate. The main finding is the good correspondence between A/P COP and the filtered GA EMG in the low frequency range. The EMG envelope was calculated using a zero-lag filter. Combining this with time shifts around 250-350 ms produced a high correlation (85.5+/-8.4%) between the GA-EMG envelope and the A/P COP. This EMG-COP relation was closest when using a low cut-off frequency value around 1 Hz in calculating the EMG envelope. Based on this filtering procedure we estimated the average EMG-COP time shift to be 283+/-43 ms between the GA-EMG envelope and A/P COP (which "lags" behind EMG envelope). This shift is consistent with the 1 Hz cut-off and phase shift produced by a corresponding critically damped second-order filter, and is about twice the corresponding twitch time. These results suggest that GA is to a large extent responsible for the phasic control of the anterior-posterior balance during quiet standing. A small difference (p<0.03) was found between mean time shift thus obtained for controls (n=4) and MS (n=6) while sway area showed a major difference (p<0.01). The paper also compares three alternative filters for numerical calculation of the EMG-envelope.

Adult↗