Towards a more dynamic plant morphology

From the point of view of a dynamic morphology, form is not only the result of process(es) — it is process. This process may be analyzed in terms of two pairs of fundamental processes: growth and decay, differentiation and dedifferentiation. Each of these processes can be analyzed in terms of various modalities (parameters) and submodalities. This paper deals with those of growth (see Table 1). For the purpose of systematits and phylogenetic reconstruction the modalities and submodalities can be considered dynamic characters that have “states”. Each “state” of such a dynamic character is a more detailed process, hence not static. For example, determinate growth represents a “state” of the dynamic character (or modality) of growth duration. The processes of Table 1 can be applied to the whole plant kingdom (although in certain cases only some processes of the whole set may be applicable). Thus, the diversity of plant form is seen as a diversity of process combinations. From this point of view, change in form implies change in the process combination(s). Questions that arise are, for example, the following: Which process combinations actually occur? Which of these are the most frequent? How and why have process combinations changed during ontogeny and phylogeny? In comparative morphogenesis, process combinations are compared within an ontogeny or between ontogenies. The combinations may be repeated (i.e., conserved) or changed. Since repetition is limited, regularity that is the basis for structural categories is also limited or relative. With regard to change in process combinations, sequential change within an ontogeny and phylogenetic change between ontogenies can be distinguished. A large number of additional processes, such as heterochrony, that have been investigated by many zoologists and botanists, refer to these sequential and phylogenetic changes. General implications and consequences of the proposed approach are pointed out. As well, its limits, which are related to the language and concepts used, are discussed. The importance of a dynamic language is emphasized.     

Azathioprine, a genotoxic agent to be considered non-genotoxic in man

Azathioprine, an immunosuppressive drug, has been used for 25 years. Azathioprine is rapidly converted into a number of metabolites after absorption. Maximum blood levels in experimental animals (mice) were 11.3 micrograms/ml after a dosage of 33.3 mg/kg. Generally, levels of less than 1 microgram/ml are found. As azathioprine is ineffective in hypoxanthine guanine phosphoribosyltransferase (HPRT)-deficient patients, it will be clear that for immunosuppressive activity azathioprine must be metabolised. Regarding mutagenic activity, its mutagenicity for bacteria seems irrelevant for man because the nitroimidazole moiety can be reduced by bacteria but not or hardly at all by mammalian tissues. So 6-mercaptopurine (a metabolite of azathioprine) and its metabolites should be regarded as the active compounds. In vitro azathioprine can induce chromosome aberrations and other cytogenetic events at high, non-physiological doses. However, in view of the low blood levels it is unlikely that azathioprine can induce chromosome aberrations in kidney transplant patients. It is more probable that azathioprine inhibits the elimination of such aberrant cells through its immunosuppressive activity. It should be pointed out that in microbial mutagenicity systems also, azathioprine concentrations that are not reached in patients are needed to obtain an increased mutation rate.     

Towards a comprehensive model of feather regeneration

Understanding of the regeneration of feathers, despite a 140 year tradition of study, has remained substantially incomplete. Moreover, accumulated errors and mis‐statements in the literature have confounded the intrinsic difficulties in describing feather regeneration. Lack of allusion to Rudall's (Rudall [ 1947 ] Biochem Biophys Acta 1:549–562) seminal X‐ray diffraction study that revealed two distinct keratins, β‐ and α‐, in a mature feather, is one of the several examples where lack of citation long inhibited progress in understanding. This article reviews and reevaluates the available literature and provides a synthetic, comprehensive, morphological model for the regeneration of a generalized, adult contour feather. Particular attention is paid to several features that have previously been largely ignored. Some of these, such as the β‐keratogenic sheath and the α‐keratogenic, supra‐umbilical, pulp caps, are missing from mature, functional feathers sensu stricto because they are lost through preening, but these structures nevertheless play a critical role in development. A new developmental role for a tissue unique to feathers, the medullary pith of the rachis and barb rami, and especially its importance in the genesis of the superior umbilical region (SUR) that forms the transition from the spathe (rachis and vanes) to the calamus, is described. It is postulated that feathers form through an intricate interplay between cyto‐ and histodifferentiative processes, determined by patterning signals that emanate from the dermal core, and a suite of interacting biomechanical forces. Precisely regulated patterns of loss of intercellular adhesivity appear to be the most fundamental aspect of feather morphogenesis and regeneration: rather than a hierarchically branched structure, it appears more appropriate to conceive of feathers as a sheet of mature keratinocytes that is “full of holes. J. Morphol. 2009. © 2009 Wiley‐Liss, Inc.     

Towards a more versatile alpha-glucan biosynthesis in plants

Starch is an important storage polysaccharide in many plants. It is composed of densely packed alpha-glucans, consisting of 1,4- and 1,4,6-linked glucose residues. The starch polymers are used in many industrial applications. The biosynthetic machinery for assembling the granule has been manipulated in many different ways to gain insight into the process of starch biosynthesis and to engineer starches with improved functionalities. With respect to the latter, two generic technologies with great potential have been developed: (i) introduction of new linkage types in starch polymers (1,3- and 1,6-linkages), and (ii) engineering granule-boundness. The toolbox to engineer this new generation of starch polymers is discussed.     

Towards more effective acetylcholinesterase inhibitors: a comprehensive modelling study based on human acetylcholinesterase protein–drug complex

Abstract

Alzheimer's disease is a progressive neurodegenerative disorder and as the exact cause of the disease remains unknown, it still has no cure to date. Due to the fact that, until recently, there has been no crystal structure of human AChE in complex with drugs, researchers have had to use mainly Torpedo californica homologues which were later reported to have significantly different binding sites. In this study, an energy-based pharmacophore model that has the advantages of both ligand- and structure-based approaches was generated using hAChE crystal structures in complex with drugs. This model was validated utilizing several commonly used statistical measures such as the enrichment factor, BEDROC, RIE and AUAC. A huge database consisting of around 7 million compounds with approximately 150,000,000 conformations from 8 vendors was used in virtually screening workflow, in which Lipinski’s filter and basic and precise docking algorithms were utilized. A rigorous MM-GBSA binding affinity calculation was also applied to accurately predict relative free energy that produced 361 hits. The selected top ranked 15 compounds were shown to have extra intermolecular interactions with hAChE which is an indication of a more stable complex and high binding affinity. The e-pharmacophore model and overall results obtained might be used for further experimental studies in designing the next generation of hAChE inhibitors.

Communicated by Ramaswamy H. Sarma     

Towards a comprehensive view of the bacterial cell wall

Direct in vivo visualization, in full atomic detail, of the microbial cell wall and its stress-bearing structural architecture remains one of the prime challenges in microbiology. In the meantime, molecular modeling can provide a framework for explaining and predicting mechanisms involved in morphogenesis, bacterial cell growth and cell division, during which the wall and its major structural component--murein--have to protect the cell from osmotic pressure and multiple tensile forces. Here, we illustrate why the scaffold concept of murein architecture provides a more comprehensive representation of bacterial cell wall physiology than previous models.     

Towards a more environmentally sustainable production of graphene-based materials

The International Journal of Life Cycle Assessment - This study compares prior life cycle assessment (LCA) studies on graphene-based materials (GBMs) with new results from original data on ball...     

Semi-quantitative evaluation of genotoxic activity of chemical substances and evidence for a biological threshold of genotoxic activity

Oxidative DNA damage caused by a cysteine metal-catalyzed oxidation system (Cys-MCO) comprised of Fe(3+), O(2), and a cysteine as an electron donor was enhanced by copper, zinc superoxide dismutase (CuZnSOD) in a concentration-dependent manner, as reflected by the formation of 8-hydroxy-2'-deoxyguanosine (8-OH-dG) and strand breaks. Unlike CuZnSOD, manganese SOD (MnSOD) as well as iron SOD (FeSOD) did not enhance DNA damage. The capacity of CuZnSOD to enhance damage to DNA was inhibited by a spin-trapping agent, 5, 5-dimethyl-1-pyrroline N-oxide (DMPO) and a metal chelator, diethylenetriaminepentaacetic acid (DETAPAC). The deoxyribose assay showed that hydroxyl free radicals were generated in the reaction of CuZnSOD with Cys-MCO. We found that the Cys-MCO system caused the release of free copper from CuZnSOD. CuZnSOD also caused the two-fold enhancement of a mutation in the pUC18 lacZ' gene in the presence of Cys-MCO when measured as a loss of alpha-complementation. Based on these results, we interpret the effects of CuZnSOD on Cys-MCO-induced DNA damage and mutation as due to reactive oxygen species, probably hydroxyl free radicals, formed by the reaction of free Cu(2+), released from oxidatively damaged CuZnSOD, and H(2)O(2) produced by the Cys-MCO system.     

Towards a more plant physiological perspective on soil ecology

Soil respiration almost balances carbon fixation by terrestrial photosynthesis and exceeds all anthropogenic carbon emissions by an order of magnitude, yet we lack precise knowledge of the sources of, and controls upon, the release of carbon dioxide from soils. Here, we discuss the increasing evidence that half of this carbon release is from living plant roots, their mycorrhizal fungi and other root-associated microbes, and that this release is driven directly by recent photosynthesis. The new studies challenge the widespread view that soil activity is dominated by decomposer organisms using older detrital material and that root litter inputs equal those of aboveground litter. The new observations emphasize the physiological continuity and dynamic interdependence of the plant-microbe-soil system and highlight the need for closer cooperation between plant and soil scientists.     

Towards a more rapid diagnosis of rapidly progressive glomerulonephritis.

An attempt was made to provide simple practical guidelines to alert general practitioners to the diagnosis of rapidly progressive glomerulonephritis and lead to early referral to hospital. The duration of illness before referral to this hospital and its effect on outcome in patients with crescentic nephritis were assessed retrospectively from the case notes of 24 patients referred over two years. Four patients had Goodpasture''s syndrome, 11 Wegener''s granulomatosis, seven microscopic polyarteritis, and two idiopathic progressive glomerulonephritis. The duration of symptoms before referral to the local hospital was similar in the four groups of patients and varied from one week to 28 months (mean 10 months). The duration of stay in the local hospital was two, nine, 11, and 180 days in the patients with Goodpasture''s syndrome and a mean of four days (range one to eight) in those with Wegener''s granulomatosis and 10 days (one to 18 days) in those with microscopic polyarteritis. In the local hospital the diagnosis was based on the results of renal biopsy and detection of antibodies to glomerular basement membrane in two patients with Goodpasture''s syndrome and on the results of renal biopsy in seven of the other patients aided by the detection of antibodies to the cytoplasm of neutrophils (ANCA) in 10. Three of the 24 patients died and four required maintenance haemodialysis. Patients who present to their general practitioners with persistent non-specific symptoms should have a urine dipstick test and then blood tests and emergency referral to hospital if necessary. Hospital physicians should be aware of the speed and accuracy with which current assays can confirm a diagnosis of rapidly progressive glomerulonephritis.     

Towards a comprehensive simulation model of malaria epidemiology and control

Planning of the control of Plasmodium falciparum malaria leads to a need for models of malaria epidemiology that provide realistic quantitative prediction of likely epidemiological outcomes of a wide range of control strategies. Predictions of the effects of control often ignore medium- and long-term dynamics. The complexities of the Plasmodium life-cycle, and of within-host dynamics, limit the applicability of conventional deterministic malaria models. We use individual-based stochastic simulations of malaria epidemiology to predict the impacts of interventions on infection, morbidity, mortality, health services use and costs. Individual infections are simulated by stochastic series of parasite densities, and naturally acquired immunity acts by reducing densities. Morbidity and mortality risks, and infectiousness to vectors, depend on parasite densities. The simulated infections are nested within simulations of individuals in human populations, and linked to models of interventions and health systems. We use numerous field datasets to optimise parameter estimates. By using a volunteer computing system we obtain the enormous computational power required for model fitting, sensitivity analysis, and exploration of many different intervention strategies. The project thus provides a general platform for comparing, fitting, and evaluating different model structures, and for quantitative prediction of effects of different interventions and integrated control programmes.     

Towards a more precise therapy in cancer: Exploring epigenetic complexity

A plethora of preclinical evidences suggests that pharmacological targeting of epigenetic dysregulation is a potent strategy to combat human diseases. Nevertheless, the implementation of epidrugs in clinical practice is very scarce and mainly limited to haematological malignancies. In this review, we discuss cutting-edge strategies to foster the chemical design, the biological rationale and the clinical trial development of epidrugs. Specifically, we focus on the development of dual hybrids to exploit multitargeting of key epigenetic molecules deregulated in cancer; the study of epigenetic-synthetic lethality interactions as a mechanism to address loss-of-function mutations, and the combination of epidrugs with other therapies such as immunotherapy to avoid acquired chemoresistance and increase therapy sensitivity. By exploring these challenges, among others, the field of epigenetic chemical biology will increase its potential for clinical benefit, and more effective strategies targeting the aberrant epigenome in cancer are likely to be developed both in haematological and solid tumours.