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M James C Crabbe

Publications and source records attributed to M James C Crabbe.

16 recordsLinked to original sources
PubMed2025

Genomic analysis of Dasiphora on the Qinghai-Tibet Plateau provides insights into genetic divergence and flower color variation.

The Qinghai-Tibet Plateau (QTP) harbors diverse alpine flora, including the ecologically significant shrubs Dasiphora fruticosa and D. glabra, for which taxonomic uncertainties remain and adaptive mechanisms are still poorly understood. Based on high-quality genome assembly, population resequencing, and multi-omics integration, we elucidated their evolutionary divergence and flower color genetics. Chromosome-level haplotype-resolved genomes were assembled: autotetraploid D. fruticosa (929.99 Mb) and diploid D. glabra (450.89 Mb). Phylogenetic analysis showed that the tetraploid D. fruticosa and D. glabra in this study clustered together, while the diploid D. fruticosa sequenced by previous research formed a distinct lineage clustered outside. Consistently, population structure analysis of 55 samples revealed three major clades, with D. fruticosa further subdivided into two divergent branches. Additionally, hybridization events detected by Admixture, coupled with ploidy complexity identified via flow cytometry highlight the intricate genetic relationships within this genus. Adaptive gene families expanded in antioxidant (flavonoid synthesis) and secondary metabolism pathways, adapting to ultraviolet radiation and cold stress. Natural selection analysis identified 193 candidate genes (e.g., TFB5 in the DNA repair pathway), predominantly localized to chromosome 5, which are potential candidates for high-altitude adaptation. Transcriptome and metabolome analyses showed D. fruticosa's yellow petals derive from flavonol (quercetin) accumulation, while D. glabra's white petals result from proanthocyanidin biosynthesis via high LAR/ANR expression. This study provides insights into the taxonomic revision and adaptive genetic divergence of alpine plants, and offers a foundation for horticultural improvement of Dasiphora.

Flowers↗
PubMed2006

Modelling variations in corallite morphology of Galaxea fascicularis coral colonies with depth and light on coastal fringing reefs in the Wakatobi Marine National Park (S.E. Sulawesi, Indonesia).

Coastal environments in the tropics can suffer from high sedimentation and low light levels. Galaxea fascicularis is a hermatypic coral that is relatively resilient to stress from bleaching and from sedimentation. Corallite dimensions--width, height, corallite densities and inter-corallite distances--of Galaxea fascicularis colonies varied significantly with depth, and so with incident light at the Sampela reef in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. Modelling studies based on our data showed that corallite width decreased with the amount of incident light, while corallite height increased with the amount of incident light (r2 values of 0.835 for width and 0.869 for height). In all colonies, inter-corallite distance decreased significantly with the amount of incident light (r2 = 0.89). Colony width/height ratio increased in a linear fashion with inter-corallite distance for all colonies studied (r2 = 0.65). Current flow as judged using tags did not appear to be a factor in variations of corallite dimensions. Our results suggest that under low light conditions, distribution and size of corallites may optimise heterotrophic nutrition, while in conditions where light is not limiting, distribution and size of corallites may be optimal for photosynthesis.

Animals↗
PubMed2006

Metabolism of Maillard reaction products by the human gut microbiota--implications for health.

The human colonic microbiota imparts metabolic versatility on the colon, interacts at many levels in healthy intestinal and systemic metabolism, and plays protective roles in chronic disease and acute infection. Colonic bacterial metabolism is largely dependant on dietary residues from the upper gut. Carbohydrates, resistant to digestion, drive colonic bacterial fermentation and the resulting end products are considered beneficial. Many colonic species ferment proteins but the end products are not always beneficial and include toxic compounds, such as amines and phenols. Most components of a typical Western diet are heat processed. The Maillard reaction, involving food protein and sugar, is a complex network of reactions occurring during thermal processing. The resultant modified protein resists digestion in the small intestine but is available for colonic bacterial fermentation. Little is known about the fate of the modified protein but some Maillard reaction products (MRP) are biologically active by, e. g. altering bacterial population levels within the colon or, upon absorption, interacting with human disease mechanisms by induction of inflammatory responses. This review presents current understanding of the interactions between MRP and intestinal bacteria. Recent scientific advances offering the possibility of elucidating the consequences of microbe-MRP interactions within the gut are discussed.

Acrylamide↗
PubMed2005

GeneMCL in microarray analysis.

Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edges, where the nodes represent genes, and the edges represent the similarity in expression of those genes, as given by a proximity measurement. This measurement is taken to be the Pearson correlation coefficient combined with a local non-linear rescaling step. The resulting graph is input to the Markov Cluster (MCL) algorithm, which is an elegant, deterministic, non-specific and scalable method, which models stochastic flow through the graph. The algorithm is inherently affected by any cluster structure present, and rapidly decomposes a graph into cohesive clusters. The potential of the GeneMCL algorithm is demonstrated with a 5,730 gene subset (IGS) of the Van't Veer breast cancer database, for which the clusterings are shown to reflect underlying biological mechanisms.

Algorithms↗
PubMed2005

Novel experimental design for steady-state processes: a systematic Bayesian approach for enzymes, drug transport, receptor binding, continuous culture and cell transport kinetics.

We demonstrate that a Bayesian approach (the use of prior knowledge) to the design of steady-state experiments can produce major gains quantifiable in terms of information, productivity and accuracy of each experiment. Developing the use of Bayesian utility functions, we have used a systematic method to identify the optimum experimental designs for a number of kinetic model data sets. This has enabled the identification of trends between kinetic model types, sets of design rules and the key conclusion that such designs should be based on some prior knowledge of the kinetic model. We suggest an optimal and iterative method for selecting features of the design such as the substrate range, number of measurements and choice of intermediate points. The final design collects data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. It is equally applicable to enzymes, drug transport, receptor binding, microbial culture and cell transport kinetics.

Bayes Theorem↗
PubMed2004

Efficient and cost-effective experimental determination of kinetic constants and data: the success of a Bayesian systematic approach to drug transport, receptor binding, continuous culture and cell transport kinetics.

Details about the parameters of kinetic systems are crucial for progress in both medical and industrial research, including drug development, clinical diagnosis and biotechnology applications. Such details must be collected by a series of kinetic experiments and investigations. The correct design of the experiment is essential to collecting data suitable for analysis, modelling and deriving the correct information. We have developed a systematic and iterative Bayesian method and sets of rules for the design of enzyme kinetic experiments. Our method selects the optimum design to collect data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. The rules select features of the design such as the substrate range and the number of measurements. We show here that this method can be directly applied to the study of other important kinetic systems, including drug transport, receptor binding, microbial culture and cell transport kinetics. It is possible to reduce the errors in the estimated parameters and, most importantly, increase the efficiency and cost-effectiveness by reducing the necessary amount of experiments and data points measured.

Bayes Theorem↗
PubMed2003

A novel method for the transport and analysis of genetic material from polyps and zooxanthellae of scleractinian corals.

We have developed a new simple method for transport, storage, and analysis of genetic material from the corals Agaricia agaricites, Dendrogyra cylindrica, Eusmilia ancora, Meandrina meandrites, Montastrea annularis, Porites astreoides, Porites furcata, Porites porites, and Siderastrea siderea at room temperature. All species yielded sufficient DNA from a single FTA card (19 microg-43 ng) for subsequent PCR amplification of both coral and zooxanthellar DNA. The D1 and D2 variable region of the large subunit rRNA gene (LSUrDNA) was amplified from the DNA of P. furcata and S. siderea by PCR. Electrophoresis yielded two major DNA bands: an 800-base pair (bp) DNA, which represented the coral ribosomal RNA (rRNA) gene, and a 600-bp DNA, which represented the zooxanthellar srRNA gene. Extraction of DNA from the bands yielded between 290 microg total DNA (S. siderea coral DNA) and 9 microg total DNA (P. furcata zooxanthellar DNA). The ability to transport and store genetic material from scleractinian corals without resort to laboratory facilities in the field allows for the molecular study of a far wider range and variety of coral sites than have been studied to date.

Animals↗
PubMed2003

Efficient and accurate experimental design for enzyme kinetics: Bayesian studies reveal a systematic approach.

In areas such as drug development, clinical diagnosis and biotechnology research, acquiring details about the kinetic parameters of enzymes is crucial. The correct design of an experiment is critical to collecting data suitable for analysis, modelling and deriving the correct information. As classical design methods are not targeted to the more complex kinetics being frequently studied, attention is needed to estimate parameters of such models with low variance. We demonstrate that a Bayesian approach (the use of prior knowledge) can produce major gains quantifiable in terms of information, productivity and accuracy of each experiment. Developing the use of Bayesian Utility functions, we have used a systematic method to identify the optimum experimental designs for a number of kinetic model data sets. This has enabled the identification of trends between kinetic model types, sets of design rules and the key conclusion that such designs should be based on some prior knowledge of K(M) and/or the kinetic model. We suggest an optimal and iterative method for selecting features of the design such as the substrate range, number of measurements and choice of intermediate points. The final design collects data suitable for accurate modelling and analysis and minimises the error in the parameters estimated.

Bayes Theorem↗
PubMed2003

Expression profiles in the progression of ductal carcinoma in the breast.

An understanding of the multi-step nature of cancer as it is in the breast, as a series of pivotal genetic/epigenetic modifications is irrefutably a milestone in diagnostics, prognostics and eventually providing a cure. Here we have utilised a variant of analysis of variance (ANOVA) as a model for the identification and tracking of specific mRNA species whose transcription has been significantly altered at each grade in the progression of ductal carcinoma, making it possible to correlate histological progression with the genetic events underlying breast cancer. We show that in the progression of ductal carcinomas, from grade 1 to 3, there is a reduction in the actual number of mRNA species, which are significantly over or under expressed. We also show that this technique can be employed to generate differential gene expression patterns, whereby the combined expression profile of the tailored spectra of genes in the comparison of each ductal grade is sufficient to render them on clearly separate arms of an array-wise hierarchical cluster dendrogram.

Analysis of Variance↗
PubMed2003

Use of a novel Hill-climbing genetic algorithm in protein folding simulations.

We have developed a novel Hill-climbing genetic algorithm (GA) for simulation of protein folding. The program (written in C) builds a set of Cartesian points to represent an unfolded polypeptide's backbone. The dihedral angles determining the chain's configuration are stored in an array of chromosome structures that is copied and then mutated. The fitness of the mutated chain's configuration is determined by its radius of gyration. A four-helix bundle was used to optimise simulation conditions, and the program was compared with other, larger, genetic algorithms on a variety of structures. The program ran 50% faster than other GA programs. Overall, tests on 100 non-redundant structures gave comparable results to other genetic algorithms, with the Hill-climbing program running from between 20 and 50% faster. Examples including crambin, cytochrome c, cytochrome B and hemerythrin gave good secondary structure fits with overall alpha carbon atom rms deviations of between 5 and 5.6 A with an optimised hydrophobic term in the fitness function.

Algorithms↗
PubMed2003

Use of essential and molecular dynamics to study gammaB-crystallin unfolding after non-enzymic post-translational modifications.

Essential and Molecular Dynamics (ED/MD) have been used to model the conformational changes of a protein implicated in a conformational disease--cataract, the largest cause of blindness in the world-after non-enzymic post-translational modification. Cyanate modification did not significantly alter flexibility, while the Schiff's base adduct produced a more flexible N-terminal domain, and intra-secondary structure regions, than either the cyanate adduct or the native structure. Glycation also increased linker flexibility and disrupted the charge network. A number of post-translational adducts showed structural disruption around Cys15 and increased linker flexibility; this may be important in subsequent protein aggregation. Our modelling results are in accord with experimental evidence, and show that ED/MD is a useful tool in modelling conformational changes in proteins implicated in disease processes.

Computer Simulation↗
PubMed2003

Non-steroidal anti-inflammatory drugs (NSAIDs) inhibit vascular smooth muscle cell proliferation via differential effects on the cell cycle.

Abnormal vascular smooth muscle cell (VSMC) proliferation plays an important role in the pathogenesis of both atherosclerosis and restenosis. Recent studies suggest that high-dose salicylates, in addition to inhibiting cyclooxygenase activity, exert an antiproliferative effect on VSMC growth both in-vitro and in-vivo. However, whether all non-steroidal anti-inflammatory drugs (NSAIDs) exert similar antiproliferative effects on VSMCs, and do so via a common mechanism of action, remains to be shown. In this study, we demonstrate that the NSAIDs aspirin, sodium salicylate, diclofenac, ibuprofen, indometacin and sulindac induce a dose-dependent inhibition of proliferation in rat A10 VSMCs in the absence of significant cytotoxicity. Flow cytometric analyses showed that exposure of A10 cells to diclofenac, indometacin, ibuprofen and sulindac, in the presence of the mitotic inhibitor, nocodazole, led to a significant G0/G1 arrest. In contrast, the salicylates failed to induce a significant G1 arrest since flow cytometry profiles were not significantly different from control cells. Cyclin A levels were elevated, and hyperphosphorylated p107 was present at significant levels, in salicylate-treated A10 cells, consistent with a post-G1/S block, whereas cyclin A levels were low, and hypophosphorylated p107 was the dominant form, in cells treated with other NSAIDs consistent with a G1 arrest. The ubiquitously expressed cyclin-dependent kinase (CDK) inhibitors, p21 and p27, were increased in all NSAID-treated cells. Our results suggest that diclofenac, indometacin, ibuprofen and sulindac inhibit VSMC proliferation by arresting the cell cycle in the G1 phase, whereas the growth inhibitory effect of salicylates probably affects the late S and/or G2/M phases. Irrespective of mechanism, our results suggest that NSAIDs might be of benefit in the treatment of certain vasculoproliferative disorders.

Animals↗
PubMed2002

Effective experimental design: enzyme kinetics in the bioinformatics era.

Acquiring details about the kinetic parameters of enzymes is crucial to both drug development and clinical diagnosis. The correct design of an experiment is crucial to collecting data suitable for analysis, modelling and deriving the correct information. As classical design methods are not targeted to the more complex kinetics now frequently studied, further work is required to estimate parameters of such models with low variance. This review examines the different options available to produce major gains in information, productivity and the accuracy of each experiment.

Animals↗
PubMed2002

Heterologous expression and topography of the main intrinsic protein (MIP) from rat lens.

Wild type rat lens main intrinsic protein (MIP) and MIP mutated (F73I, F75L) to resemble the glycerol facilitator of Escherichia coli in the region of the NPA1 box were used to investigate the topology of MIP in the membrane of Spodoptera frugiperda (Sf21) cells using the baculovirus expression system and expression in mouse erythroid leukaemia cells (MEL C88). Differential fixation for staining was used, with paraformaldehyde for externally exposed antigenic sites, and acetone for both externally and internally exposed protein antigenic sites. Immunofluorescence using antibodies to synthetic MIP peptides showed that wild type MIP had a six transmembrane topography. The N- and C-termini were intracellular in both expression systems, and both NPA boxes were found to be extracellular. These results show that residues around the NPA1 box can influence the folding of the MIP in the membrane, and provide structural evidence for the poor water transport properties of MIP, as the NPA boxes lie outside the plane of the membrane.

Amino Acid Sequence↗
PubMed2002

pH-Dependent channel activity of heterologously-expressed main intrinsic protein (MIP) from rat lens.

Wild-type rat lens main intrinsic protein (MIP) was heterologously expressed in the membrane of Spodoptera frugiperda (Sf21) cells using the baculovirus expression system and in mouse erythroid leukaemia cells (MEL C88). Both MEL and Sf21 cell lines expressing wild-type MIP were investigated for the conductance of ions using a whole cell patch clamp technique. An increase in conductance was seen in both expression systems, particularly on lowering the pH to 6.3. In Sf21 cells, addition of antibodies to the NPA1 box resulted in a reduction of current flow. These results suggest that MIP has pH-dependent ion channel activity, which involves the NPA1 box domain.

Animals↗