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Ben Clark

Publications and source records attributed to Ben Clark.

8 recordsLinked to original sources
PubMed2006

Shedding light on plant competition: modelling the influence of plant morphology on light capture (and vice versa).

A plant's morphology is both strongly influenced by local light availability and, simultaneously, strongly influences this local light availability. This reciprocal relationship is complex, but lies at the heart of understanding plant growth and competition. Here, we develop a sub-individual-based simulation model, cast at the level of interacting plant components. The model explicitly simulates growth, development and competition for light at the level of leaves, branches, etc., located in 3D space. In this way, we are able to explore the manner in which the low-level processes governing plant growth and development give rise to individual-, cohort-, and community-level phenomena. In particular, we show that individual-level trade-offs between growing up and growing out arise naturally in the model, and robustly give rise to cohort-level phenomena such as self-thinning, and community processes such as the effect of ecological disturbance on the maintenance of biodiversity. We conclude with a note on our methodology and how to interpret the results of simulation models such as this one.

Algorithms↗
PubMed2006

Quinolactacins revisited: from lactams to imide and beyond.

Chemical analysis of a solid phase fermentation of an Australian Penicillium citrinum strain has returned all known examples of a rare class of N-methyl quinolone lactams, quinolactacins A2 (1), B2 (2), C2 (3) and A1 (4), together with the new quinolactacins B1 (5), C1 (6), D1 (7) and D2 (8), and the novel derivatives quinolonimide (9) and quinolonic acid (10). Complete stereostructures were assigned to all these compounds by detailed spectroscopic analysis and chemical interconversion. Carefully controlled and monitored decomposition studies have confirmed that quinolactacins readily undergo C-3 epimerization and oxidation, and under appropriate conditions convert to quinolonimide and quinolonic acid. Mechanisms for key transformations are proposed. The decomposition studies suggested that only quinolactacins A2 (1) and B2 (2) are genuine natural products, with all other isolated compounds being decomposition artefacts. Quinolactacins C1 (6), C2 (3), and the racemic mixture of quinolactacins D1/D2 (8/7) all displayed notable cytotoxic activity.

Imides↗
PubMed2006

Hepatitis C virus genotype and HIV coinfection affect cytokine mRNA levels in unstimulated PBMC but do not shift the T1/T2 balance.

Rapid progression of hepatitis C virus (HCV) disease in patients with HIV/HCV may reflect different cytokine responses and be influenced by HCV genotype. This is addressed by a study of patients with HIV/HCV coinfection and infection with HCV genotype 2 or 3 (2/3). They are compared with coinfected patients infected with genotype 1 and HCV monoinfected patients matched for HCV genotype. IFN-gamma, IL-10, IL-4 and IL-4delta2 mRNA were quantified by real-time PCR in unstimulated PBMC and after in vitro stimulation with HCV core or nonstructural 3/4A antigen. In unstimulated PBMC, levels of IFN-gamma and IL-4 mRNA were lowest in HIV/HCV genotype 1 patients, intermediate in HIV/HCV genotype 2/3 patients and highest in HCV genotype 2/3 patients. Neither HCV genotype nor HIV affected levels of IL-10 mRNA in unstimulated PBMC or IFN-gamma, IL-4 and IL-10 mRNA in PBMC stimulated with HCV antigens. Levels of IL-4 and IL-4delta2 mRNA correlated in mitogen-stimulated PBMC from all patient groups but both were low in HIV/HCV genotype 1 patients. Serum soluble CD30 levels (a putative marker of a T2 cytokine environment) did not differ between patient groups. The data do not suggest a shift in the T1/T2 balance driven by HIV coinfection or HCV genotype but either may affect IL-4 bioavailability.

Adult↗
PubMed2005

Gymnoascolides A-C: aromatic butenolides from an Australian isolate of the soil ascomycete Gymnoascus reessii.

Three new aromatic butenolides, gymnoascolides A-C (1-3), have been isolated from the Australian soil ascomycete Gymnoascus reessii and assigned structures on the basis of detailed spectroscopic analysis. The absolute configurations of gymnoascolides B (2) and C (3) at C-5 were solved using a combination of chemical derivatization and quantum chemical simulations.

4-Butyrolactone↗
PubMed2005

Roquefortine E, a diketopiperazine from an Australian isolate of Gymnoascus reessii.

The new isoprenylated diketopiperazine roquefortine E (6) has been isolated from an Australian soil isolate of the ascomycete Gymnoascus reessii. The known fungal metabolite roquefortine C (1) was also recovered as the major antibacterial principle, and all structures were assigned by detailed spectroscopic analysis.

Anti-Bacterial Agents↗
PubMed2004

Blanchaquinone: a new anthraquinone from an Australian Streptomyces sp.

Chemical analysis of an Australian Streptomyces species yielded a range of known anthracyclines and biosynthetically related metabolites, including daunomycin (1), epsilon-rhodomycinone (2), 11-hydroxyauramycinone (3), 11-hydroxysulfurmycinone (4), aklavinone (5), bisanhydro-gamma-rhodomycinone (6), and the anthraquinone 7, as well as the hitherto unreported blanchaquinone (8). The structure assigned to 8 was secured by detailed spectroscopic analysis and correlation to known analogues, such as the anthraquinone 7. This account also represents the first natural occurrence of 3, 4, and 7 and the first spectroscopic characterization of 11-hydroxysulfurmycinone (4).

Anthracyclines↗