Biomedical subjects

Matthew Spencer

Publications and source records attributed to Matthew Spencer.

12 recordsLinked to original sources

PubMed2006

Testing for covarion-like evolution in protein sequences.

The covarion hypothesis of molecular evolution proposes that selective pressures on an amino acid or nucleotide site change through time, thus causing changes of evolutionary rate along the edges of a phylogenetic tree. Several kinds of Markov models for the covarion process have been proposed. One model, proposed by Huelsenbeck (2002), has 2 substitution rate classes: the substitution process at a site can switch between a single variable rate, drawn from a discrete gamma distribution, and a zero invariable rate. A second model, suggested by Galtier (2001), assumes rate switches among an arbitrary number of rate classes but switching to and from the invariable rate class is not allowed. The latter model allows for some sites that do not participate in the rate-switching process. Here we propose a general covarion model that combines features of both models, allowing evolutionary rates not only to switch between variable and invariable classes but also to switch among different rates when they are in a variable state. We have implemented all 3 covarion models in a maximum likelihood framework for amino acid sequences and tested them on 23 protein data sets. We found significant likelihood increases for all data sets for the 3 models, compared with a model that does not allow site-specific rate switches along the tree. Furthermore, we found that the general model fit the data better than the simpler covarion models in the majority of the cases, highlighting the complexity in modeling the covarion process. The general covarion model can be used for comparing tree topologies, molecular dating studies, and the investigation of protein adaptation.

Algorithms↗

PubMed2006

Authenticated DNA from ancient wood remains.

BACKGROUND: The reconstruction of biological processes and human activities during the last glacial cycle relies mainly on data from biological remains. Highly abundant tissues, such as wood, are candidates for a genetic analysis of past populations. While well-authenticated DNA has now been recovered from various fossil remains, the final 'proof' is still missing for wood, despite some promising studies. SCOPE: The goal of this study was to determine if ancient wood can be analysed routinely in studies of archaeology and palaeogenetics. An experiment was designed which included blind testing, independent replicates, extensive contamination controls and rigorous statistical tests. Ten samples of ancient wood from major European forest tree genera were analysed with plastid DNA markers. CONCLUSIONS: Authentic DNA was retrieved from wood samples up to 1,000 years of age. A new tool for real-time vegetation history and archaeology is ready to use.

Base Sequence↗

PubMed2006

Sensitivity analysis of Markov models for communities of competing sessile organisms.

1. Communities of competing sessile organisms are often modelled using Markov chains. Sensitivity analysis of the stationary distribution of these models tells us how we expect the abundance of each organism to respond to changes in interactions between species. This is important for conservation and management. 2. Markov models for such communities have usually been formulated in discrete time. Each column of the discrete-time transition matrix must sum to 1 (column stochasticity). Sensitivity analysis therefore involves defining a pattern of compensation that maintains column stochasticity as a single transition probability changes. There is little biological theory about the appropriate compensation pattern, but the usual choices involve changing only the elements of a single column of the transition matrix. 3. I argue that if the underlying dynamics occur in continuous time, each transition probability is the net outcome of direct and many indirect interactions. 4. Determining the consequences of changing a single direct interaction will often be of interest. I show how this can be achieved using a continuous-time model. The resulting discrete-time compensation pattern is quite different from those that have been considered elsewhere, with changes occurring in many columns. 5. I also show how to determine which direct interactions are being changed under any discrete-time compensation pattern.

Ecosystem↗

PubMed2005

How many clones need to be sequenced from a single forensic or ancient DNA sample in order to determine a reliable consensus sequence?

Forensic and ancient DNA (aDNA) extracts are mixtures of endogenous aDNA, existing in more or less damaged state, and contaminant DNA. To obtain the true aDNA sequence, it is not sufficient to generate a single direct sequence of the mixture, even where the authentic aDNA is the most abundant (e.g. 25% or more) in the component mixture. Only bacterial cloning can elucidate the components of this mixture. We calculate the number of clones that need to be sampled (for various mixture ratios) in order to be confident (at various levels of confidence) to have identified the major component. We demonstrate that to be >95% confident of identifying the most abundant sequence present at 70% in the ancient sample, 20 clones must be sampled. We make recommendations and offer a free-access web-based program, which constructs the most reliable consensus sequence from the user's input clone sequences and analyses the confidence limits for each nucleotide position and for the whole consensus sequence. Accepted authentication methods must be employed in order to assess the authenticity and endogeneity of the resulting consensus sequences (e.g. quantification and replication by another laboratory, blind testing, amelogenin sex versus morphological sex, the effective use of controls, etc.) and determine whether they are indeed aDNA.

Cloning, Molecular↗

PubMed2005

Likelihood, parsimony, and heterogeneous evolution.

Evolutionary rates vary among sites and across the phylogenetic tree (heterotachy). A recent analysis suggested that parsimony can be better than standard likelihood at recovering the true tree given heterotachy. The authors recommended that results from parsimony, which they consider to be nonparametric, be reported alongside likelihood results. They also proposed a mixture model, which was inconsistent but better than either parsimony or standard likelihood under heterotachy. We show that their main conclusion is limited to a special case for the type of model they study. Their mixture model was inconsistent because it was incorrectly implemented. A useful nonparametric model should perform well over a wide range of possible evolutionary models, but parsimony does not have this property. Likelihood-based methods are therefore the best way to deal with heterotachy.

Animals↗

PubMed2005

Short breath-hold, volumetric coronary MR angiography employing steady-state free precession in conjunction with parallel imaging.

An ECG-gated, 3D steady-state free precession (SSFP) technique in conjunction with sensitivity encoding (SENSE)-based parallel imaging was implemented for short breath-hold, volumetric coronary MR angiograpy (CMRA). Two parallel imaging acquisition strategies (employing 1 R-R and 2 R-R intervals, respectively) were developed to achieve 1) very short breath-hold times (12 s for a heart rate of 60 bpm), and 2) small acquisition windows to minimize sensitivity to physiologic motion. Both strategies were examined in CMRA applications over a range of heart rates. A four-point scale blinded reading (with 4 indicating the most desirable features) revealed substantial image quality improvements for the accelerated data as compared to the nonaccelerated approach. The 1 R-R interval scheme yielded an image score of 3.39 +/- 0.60, and was found to be particularly suitable for low heart rates (P = 0.0008). The 2 R-R interval strategy yielded an image score of 3.35 +/- 0.64, and was more appropriate for higher heart rates (P = 0.03). The results demonstrate that 3D SSFP combined with parallel imaging is a versatile method for short breath-hold CMRA while maintaining high spatial resolution. This strategy permits imaging of the major coronary artery distributions in two to three breath-holds using targeted slabs, and offers the potential for single breath-hold, large-volume CMRA.

Adult↗

PubMed2005

Laser capture microdissection for the analysis of gene expression during embryogenesis of Arabidopsis.

It is during embryogenesis that the body plan of the developing plant is established. Analysis of gene expression during embryogenesis has been limited due to the technical difficulty of accessing the developing embryo. Here we demonstrate that laser capture microdissection can be applied to the analysis of embryogenesis. We show how this technique can be used in concert with DNA microarray for the large-scale analysis of gene expression in apical and basal domains of the globular-stage and heart-stage embryo, respectively, when critical events of polarity, symmetry and biochemical differentiation are established. This high resolution spatial analysis shows that up to approximately 65% of the genome is expressed in the developing embryo, and that differential expression of a number of gene classes can be detected. We discuss the validity of this approach for the functional analysis of both published and previously uncharacterized essential genes.

Arabidopsis↗

PubMed2004

Authenticity of ancient-DNA results: a statistical approach.

Although there have been several papers recommending appropriate experimental designs for ancient-DNA studies, there have been few attempts at statistical analysis. We assume that we cannot decide whether a result is authentic simply by examining the sequence (e.g., when working with humans and domestic animals). We use a maximum-likelihood approach to estimate the probability that a positive result from a sample is (either partly or entirely) an amplification of DNA that was present in the sample before the experiment began. Our method is useful in two situations. First, we can decide in advance how many samples will be needed to achieve a given level of confidence. For example, to be almost certain (95% confidence interval 0.96-1.00, maximum-likelihood estimate 1.00) that a positive result comes, at least in part, from DNA present before the experiment began, we need to analyze at least five samples and controls, even if all samples and no negative controls yield positive results. Second, we can decide how much confidence to place in results that have been obtained already, whether or not there are positive results from some controls. For example, the risk that at least one negative control yields a positive result increases with the size of the experiment, but the effects of occasional contamination are less severe in large experiments.

Data Interpretation, Statistical↗

PubMed2004

Phylogenetics of artificial manuscripts.

Biological evolution has parallels with the development of natural languages, man-made artifacts, and manuscript texts. As a result, phylogenetic methods developed for evolutionary biology are increasingly being used in linguistics, anthropology, archaeology, and textual criticism. Despite this popularity, there have been few critical tests of their suitability. Here, we apply phylogenetic methods to artificial manuscripts with a known true phylogeny, produced by modern 'scribes'. Although the survival of ancestral forms and multiple descendants from a single ancestor are probably much more common in manuscript evolution than biological evolution, we were able to reconstruct most of the true phylogeny. This is important because phylogenetic methods are influencing the production of critical editions of major written works. We also show that the variation in rates of change at different locations in the text follows a gamma distribution, as is often the case in DNA sequences.

Language↗

PubMed2003

The effect of an intermittent, high-intensity warm-up on supramaximal kayak ergometer performance.

It has previously been shown that the metabolic acidaemia induced by a continuous warm-up at the 'lactate threshold' is associated with a reduced accumulated oxygen deficit and decreased supramaximal performance. The aim of this study was to determine if an intermittent, high-intensity warm-up could increase oxygen uptake (VO2) without reducing the accumulated oxygen deficit, and thus improve supramaximal performance. Seven male 500 m kayak paddlers, who had represented their state, volunteered for this study. Each performed a graded exercise test to determine VO2max and threshold parameters. On subsequent days and in a random, counterbalanced order, the participants then performed a continuous or intermittent, high-intensity warm-up followed by a 2 min, all-out kayak ergometer test. The continuous warm-up consisted of 15 min of exercise at approximately 65% VO2max. The intermittent, high-intensity warm-up was similar, except that the last 5 min was replaced with five 10 s sprints at 200% VO2max, separated by 50 s of recovery at approximately 55% VO2max. Significantly greater (P < 0.05) peak power (intermittent vs continuous: 629 +/- 199 vs 601 +/- 204 W) and average power (intermittent vs continuous: 328 +/- 39.0 vs 321 +/- 42.4 W) were recorded after the intermittent warm-up. There was no significant difference between conditions for peak VO2, total VO2 or the accumulated oxygen deficit. The results of this study indicate that 2 min all-out kayak ergometer performance is significantly better after an intermittent rather than a continuous warm-up.

Adaptation, Physiological↗

PubMed2002

Role of electrostatics in the interaction between plastocyanin and photosystem I of the cyanobacterium Phormidium laminosum.

The interactions between photosystem I and five charge mutants of plastocyanin from the cyanobacterium Phormidium laminosum were investigated in vitro. The dependence of the overall rate constant of reaction, k2, on ionic strength was investigated using laser flash photolysis. The rate constant of the wild-type reaction increased with ionic strength, indicating repulsion between the reaction partners. Removing a negative charge on plastocyanin (D44A) accelerated the reaction and made it independent of ionic strength; removing a positive charge adjacent to D44 (K53A) had little effect. Neutralizing and inverting the charge on R93 slowed the reaction down and increased the repulsion. Specific effects of MgCl2 were observed for mutants K53A, R93Q and R93E. Thermodynamic analysis of the transition state revealed positive activation entropies, suggesting partial desolvation of the interface in the transition state. In comparison with plants, plastocyanin and photosystem I of Phormidium laminosum react slowly at low ionic strength, whereas the two systems have similar rates in the range of physiological salt concentrations. We conclude that in P. laminosum, in contrast with plants in vitro, hydrophobic interactions are more important than electrostatics for the reactions of plastocyanin, both with photosystem I (this paper) and with cytochrome f[Schlarb-Ridley, B.G., Bendall, D.S. & Howe, C.J. (2002) Biochemistry41, 3279-3285]. We discuss the implications of this conclusion for the divergent evolution of cyanobacterial and plant plastocyanins.

Cyanobacteria↗

PubMedDate not supplied

Impact of replicate types on proteomic expression analysis.

In expression proteomics, the samples utilized within an experimental design may include technical, biological, or pooled replicates. This manuscript discusses various experimental designs and the conclusions that can be drawn from them. Specifically, it addresses the impact of mixing replicate types on the statistical analysis which can be performed. This study focuses on difference gel electrophoresis (DiGE), but the issues are equally applicable to all quantitative methodologies assessing relative changes in protein expression.

Analysis of Variance↗