Biomedical subjects

Adam G Marsh

Publications and source records attributed to Adam G Marsh.

4 recordsLinked to original sources

PubMed2006

Profiling transcriptome complexity and secondary metabolite synthesis in a benthic soft coral, Sinularia polydactyla.

Sinularia polydactyla, an abundant Indo-Pacific soft coral species, exhibits biochemical phenotypic plasticity, prompting investigations into differences in mRNA diversity and complexity in response to predation stress. Changes in transcriptome complexity of S. polydactyla cDNA libraries were measured using reannealing rate assays that employ an informatics-based analysis of kinetic profiles. This method allows for quick, high-throughput analysis of sequence complexity and has been used to compare transcriptome-level differences in other marine invertebrates. Here, S. polydactyla colonies were transplanted between two sites exhibiting high and low predation levels. Statistically significant differences between bite scar counts found on different transplant groups suggest site-specific variation in predation. Changes in mRNA pool complexity were quantified to indicate shifts in secondary metabolite concentration between treatment groups. Examining the complexity of the mRNA pool in this soft coral is one of the first steps toward understanding the mechanisms of phenotypic plasticity at a biochemical and molecular level.

Animals↗

PubMed2005

Genome complexity and repetitive DNA in metazoans from extreme marine environments.

As genomics converges with ecology and evolution to identify the fundamental linkages between genome structure and function, genome and transcriptome complexity will need to be measured in organisms from more diverse habitats, most often in the absence of complete sequence data. Here, we describe the complexity of ten genomes measured by a novel, high-throughput fluorescence-based kinetic hybridization assay. We applied the Shannon information index, H, and a related, fluorescence-adjusted index, H(f), as unique metrics of the hybridization kinetics to complement the conventional rate constant, k. A strong, positive relationship was present between H(f), and the repetitive DNA content of five eukaryotic genomes previously determined by Cot kinetic analyses (Onchorynchus keta, Ilyanassa obsoleta, Bos taurus, Limulus polyphemus, Saccharyomyces cerevisiae). This relationship was used to characterize the complexity of previously unstudied genomic samples in five metazoan taxa from three marine environments, including deep-sea hydrothermal vents (Alvinella pompejana), the temperate subtidal (Streblospio benedicti), and Antarctic coastal bays (Sterechinus neumayeri, Odontaster validus, Tritonia antarctica). Contrary to the predictions of nucleotypic theory, Antarctic invertebrates consistently had the lowest quantities of repetitive DNA in conjunction with low metabolic rates and highly protracted rates of cell division and larval development. Conversely, hydrothermal vent species with rapid cell division and growth do not have significantly different genome sizes or particularly low amounts of repetitive DNA as compared to non-vent, deep-sea taxa. Furthermore, there appears to be a positive correlation between the temperature at which the most abundant repetitive sequence classes anneal and habitat thermal stability. Thus, our study reveals a potential shift in repetitive sequence representation between these extreme environments that may be related to genome function in species living at these different thermal regimes.

Animals↗

PubMed2005

Transcriptome profiling of individual larvae of two different developmental modes in the poecilogonous polychaete Streblospio benedicti (Spionidae).

Understanding the range of biochemical and physiological phenotypes in a cohort of embryos or larvae is crucial to understanding the lifespan, dispersal potential, and recruitment success of the early life history stages of a species. In this study, a novel kinetic assay has been employed to profile the transcriptome pool complexity in individual larvae of both planktotrophic and lecithotrophic developmental modes in the poecilogonous polycheate Streblospio benedicti. Using a nano-scale synthesis strategy, the mRNA pool in a single embryo or larva can be amplified into cDNA for quantitative characterization in a high-throughput, kinetic reannealing assay in a 96-well, microtiterplate format. This assay generates transcript-pool complexity estimates at 1 degrees C temperature increments for each sample producing 3,360 quantitative measurements per 96-well plate. Measuring transcriptome complexity on 8 individual planktotrophic and 8 individual lecithotrophic larvae (with 4 duplicate assays for each individual) reveals a more complex gene expression profile in planktotrophic larvae and a lower level of interindividual variation in expression patterns in lecithotrophic larvae. Although differences in these gene expression patterns are more likely due to physiological differences between feeding and non-feeding larval types in these late-stage individuals, this is one of the first assessments of inter-individual variation in gene expression patterns in marine invertebrate larvae and indicates a large potential for developmental variability.

Animal Nutritional Physiological Phenomena↗

PubMed2003

eXPatGen: generating dynamic expression patterns for the systematic evaluation of analytical methods.

MOTIVATION: Experimental gene expression data sets, such as those generated by microarray or gene chip experiments, typically have significant noise and complicated interconnectivities that make understanding even simple regulatory patterns difficult. Given these complications, characterizing the effectiveness of different analysis techniques to uncover network groups and structures remains a challenge. Generating simulated expression patterns with known biological features of expression complexity, diversity and interconnectivities provides a more controlled means of investigating the appropriateness of different analysis methods. A simulation-based approach can systematically evaluate different gene expression analysis techniques and provide a basis for improved methods in dynamic metabolic network reconstruction. RESULTS: We have developed an on-line simulator, called eXPatGen, to generate dynamic gene expression patterns typical of microarray experiments. eXPatGen provides a quantitative network structure to represent key biological features, including the induction, repression, and cascade regulation of messenger RNA (mRNA). The simulation is modular such that the expression model can be replaced with other representations, depending on the level of biological detail required by the user. Two example gene networks, of 25 and 100 genes respectively, were simulated. Two standard analysis techniques, clustering and PCA analysis, were performed on the resulting expression patterns in order to demonstrate how the simulator might be used to evaluate different analysis methods and provide experimental guidance for biological studies of gene expression. AVAILABILITY: http://www.che.udel.edu/eXPatGen/

Algorithms↗