Acetogenic anthraquinones: biosynthetic convergence and chemical evidence of enzymatic cooperation in nature

Phenylanthraquinones belong to the quite rare class of fully unsymmetric biaryls, consisting of two different molecular portions, an anthraquinone part, chrysophanol, and a phenyl part, 2,4-dihydroxy-6-methoxyacetophenone, linked together by phenol-oxidative coupling. The biosynthesis of these two moieties, from eight and four acetate units, respectively, bears some unique features: Chrysophanol is the first example of an acetogenic natural product that is, in an organism-specific manner, formed via more than one folding mode: In eukaryotes, like, e.g., in fungi, in higher plants, and in insects, it is formed via folding mode F, while in prokaryotes it originates through mode S. It has, more recently, even been found to be synthesized by a third pathway, which we have named mode S′. It is thus the first example of biosynthetic convergence in polyketide biosynthesis. The monocyclic “southern” portion of the molecule, which is much simpler (arising from only four acetate units and without decarboxylation), unexpectedly does not show the anticipated randomization of the C₂-labeling in the aromatic ring, but has clearly localized C₂ units, excluding any symmetric intermediate like, e.g., 2,4,6-trihydroxyacetophenone. This is confirmed by competitive feeding experiments with specifically ¹³C₂-labeled acetophenones, showing the O-methylation to be the decisive symmetry-preventing step, which hints at a close collaboration of the participating enzymes. The results make knipholone an instructive example of structure, function, and evolution of polyketide synthases and O-methyltransferases, and their cooperation.

Evidence of gonochorism in a grouper, <Emphasis Type="Italic">Mycteroperca rosacea</Emphasis>, from the Gulf of California,Mexico

The sexual pattern and sexual development of the leopard grouper, Mycteroperca rosacea, were investigated from 483 specimens collected from the Gulf of California, Mexico. Histological and population data indicated a gonochoric sexual pattern. Some juveniles passed through an immature bisexual phase of gonadal development, but no evidence of post-maturational sex change was found. The immature bisexual phase is believed to be associated only with male development. The size distribution and size at sexual maturity were similar for both males and females. In accordance with predictions of the size-advantage model, the gonochoric sexual pattern of M. rosacea is likely influenced by its group-spawning mating system.

Progress in understanding the <Emphasis Type="Italic">N-</Emphasis>demethylation of alkaloids by exploiting isotopic techniques

The reaction of N-demethylation plays an important role in the degradation of some alkaloids in a number of organisms. This review presents how our understanding of the N-demethylation of nicotine in plants has been improved through studies in cell cultures of Nicotiana plumbaginifolia and N. glutinosa using a variety of isotopic techniques. The overall aim is to understand how metabolism recycles the alkaloid skeleton, both in terms of the metabolic route(s) exploited and the reaction mechanisms of the enzymes involved. The former has been approached using high-resolution 2-dimensional NMR and GC-MS methods; the latter by determining kinetic isotope effects and modelling the potential reaction steps. It appears that the mechanism for nicotine demethylation in plants is similar to but has significant differences from that described for mammals and Pseudomonas bacteria. These differences are discussed.

Leaf Chlorophyll Fluorescence: Background and Fundamentals for Plant Biologists

This review on chlorophyll a fluorescence starts with an overview of the primary photochemistry occurring at PSII and a characterization of the so-called “open” and “closed” states of its reaction centers. This provides the theoretical background for understanding the origin of PSII-emitted fluorescence and how its yield varies with the fraction of open reaction centers. The review proceeds to discuss the changes in fluorescence emission following illumination of a dark-adapted leaf and to define the PSII intrinsic quantum yield of photochemistry, which in turn provides an indication of PSII capacity. In light-adapted leaves, it is discussed how the use of modulated fluorometers and the double lighting technique allow an evaluation of photochemical and non-photochemical quenching, two parameters that give useful information about the plant’s photosynthetic performance under field conditions. Finally, it is described how the PSII operational efficiency can be used to calculate the photosynthetic electron transport rate and the conditions under which this is linearly related to the CO₂ assimilation rate. Some requirements for a valid application of the technique as well as some limitations in interpreting its results are discussed.

Individual variability of behavioural responses by Wandering Albatrosses (Diomedea exulans) to human disturbance

Sub-Antarctic Marion Island has had a permanent research station for 50 years and the islands Wandering Albatrosses have been intensively studied for 20 years. The reactions of breeding birds to approaches by a human on foot were recorded. Three response variables were calculated: intensity of vocal reaction (IVR), intensity of non-vocal reaction (INR) and overall response index (ORI). At 5 m from the nest, twice as many birds stood and/or vocalised as at 15 m. Nearest neighbour distance, age and gender did not explain individual variability of responses. Study colony birds had higher IVR scores than non-study colony birds; birds at colonies closest to the station had the highest ORI scores. A better breeding record was associated with lower IVR and ORI scores, but a causative relationship remains to be demonstrated. A minimum viewing distance of 25 m is recommended for breeding Wandering Albatrosses.

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Does Off-Farm Work Discourage Soil Conservation? Incentives and Disincentives Throughout Two Honduran Hillside Communities

   Soil conservation is widely regarded a critical component of sustainable livelihood strategies for the hillsides of Honduras. However, neoliberal polices have reduced economic incentives for agricultural intensification. Recent studies indicate off-farm work opportunities address poverty in a way conservation and development efforts do not. Yet off-farm work may discourage poor farmers from practicing soil conservation. A middle ground is needed. This study indicates micro-credit can substitute for off-farm work and encourage soil conservation practice. Many regions throughout Honduras have had extensive contact with soil conservation programs and would benefit more from credit services than redundant technological extension.

Does climate change influence the availability and quality of reindeer forage plants?

The northward and upward movement of the tree line and gradual replacement of lichens with vascular plants associated with increasing temperatures and nutrient availability may change the reindeer pastures in Northern Fennoscandia. The productivity of reindeer forage will most probably increase, but their protein (nitrogen) concentrations may decrease because of higher temperatures and CO₂ concentration. In the long term, the nutritive value of forage will depend on the mineralization rate and nutrient uptake from the soil. Enhanced UV-B is likely to increase the concentration of phenolics, decreasing forage quality and choice, but reindeer may adapt to increased phenolics. Increased winter precipitation, the occurrence of ice layers, deeper snow cover, and the appearance of molds beneath the snow cover may reduce the availability and/or quality of reindeer forage, but prolongation of snowless periods might have the opposite effect. The net balance of negative and positive effects will vary regionally depending on the climate, bedrock, vegetation, reindeer herding systems and socio-political factors. Multidisciplinary research is needed most importantly on the effects of the changing winter climate on reindeer forage, and the effect of modified forage quality on reindeer physiology.

One oxidant,many pathways: a theoretical perspective of monooxygenation mechanisms by cytochrome P450 enzymes

Density functional theoretical studies of monooxygenation reactivity of the high-valent oxoiron(IV) porphyrin cation-radical compound of cytochrome P450, the so-called Compound I, and of its precursor, the ferric(III)-hydroperoxide species, are described. The degeneracy of the spin states of Compound I, its electron deficiency, and dense orbital manifold lead to two-state and multi-state reactivity scenarios and may thereby create reactivity patterns as though belonging to two or more different oxidants. Most of the controversies in the experimental data are reconciled using Compound I as the sole competent oxidant. Theory finds ferric(III)-hydroperoxide to be a very sluggish oxidant, noncompetitive with Compound I. If and when Compound I is absent, P450 oxidation will logically proceed by another form, but this has to be more reactive than ferric(III)-hydroperoxide. Theoretical studies are conducted to pinpoint such an oxidant for P450.

Is it a revolution?

Jablonka and Lamb's claim that evolutionary biology is undergoing a ‘revolution’ is queried. But the very concept of revolutionary change has uncertain application to a field organized in the manner of contemporary biology. The explanatory primacy of sequence properties is also discussed.

Piaroa Manioc Varietals: Hyperdiversity or Social Currency?

The maintenance of exceptionally high numbers of folk varieties by the Piaroa people of the Venezuelan Amazon is considered. We cataloged 113 manioc folk varieties, their nomenclature, use and relevant characters, revealing significant insights into the role of manioc in Piaroa social life. Through a qualitative investigation of the cultivation, processing and symbolic significance of manioc (Manihot esculenta) in two Piaroa regions over a period of 18 years, we have found that such agrobiodiversity can only be fully explained by a combination of multiple factors, including pragmatic and ecological considerations, the subtle and complex diversity of Piaroa manioc preparations and a variety of sociocultural factors, such as manioc’s role as a mediator of social relationships and as a marker of cultural and social heritage.

Steps towards sustainable harvest of Ophiocordyceps sinensis in Bhutan

The insect-pathogenic fungus Ophiocordyceps sinensis (better known as Cordyceps sinensis) is harvested over much of the Himalayan plateau as a highly prized remedy in traditional Oriental medicine. Over the past 10 years its financial value has increased dramatically, with collectors paid as much as US $12,500 kg⁻¹ for top-quality material. This is causing significant distortion to local economies, and there is widespread concern that the current rate of collection is unsustainable. This paper introduces the fungus and its insect hosts, documents some of the biological and social constraints to achieving sustainability, describes the socioeconomic climate within which harvest and sale occurs in Bhutan, and details the measures put in place by the Royal Government of Bhutan to promote wise management of this valuable natural resource.

Responses of marine organisms to physical and chemical impacts

Studies on the effects of a variety of exogenous and anthropogenic environmental factors, including endocrine disruptors, heavy metals, UV light, high temperature, and others, on marine organisms have been presented at the 2nd Bilateral Seminar Italy–Japan held in November 2006. Reports were discussed in order to reveal the current situation of marine ecosystems, aiming at evaluation and prediction of environmental risks.

Nootkatone—a biotechnological challenge

Due to its pleasant grapefruit-like aroma and various further interesting molecular characteristics, (+)-nootkatone represents a highly sought-after specialty chemical. (+)-Nootkatone is accumulated in its producer plants in trace amounts only, and the demand of the food, cosmetics and pharmaceutical industry is currently predominantly met by chemical syntheses. These typically require environmentally critical reagents, catalysts and solvents, and the final product must not be marketed as a “natural flavour” compound. Both the market pull and the technological push have thus inspired biotechnologists to open up more attractive routes towards natural (+)-nootkatone. The multifaceted approaches for the de novo biosynthesis or the biotransformation of the precursor (+)-valencene to (+)-nootkatone are reviewed. Whole-cell systems of bacteria, filamentous fungi and plants, cell extracts or purified enzymes have been employed. A prominent biocatalytic route is the allylic oxidation of (+)-valencene. It allows the production of natural (+)-nootkatone in high yields under mild reaction conditions. The first sequence data of (+)-valencene-converting activities have just become known.

“Berry Patch” As a Kind of Place—the Ethnoecology of Black Huckleberry in Northwestern Canada

The Gitksan and Wet’suwet’en of Northwestern British Columbia formerly used landscape burning to manage patches of black huckleberry (Vaccinium membranaceum), the most important plant resource of their seasonal round. In view of its significance one might postulate that managed sites would conform to a biophysical or ecological type to maximize return for effort. However, a survey of a number of traditionally managed sites indicated that managed sites are characterized by wide variation in biophysical attributes including elevation, aspect and moisture regime, while proximity to fishing sites, village sites, or sites for harvest of alpine resources proved to be a common factor in known historic berry patch sites. We conclude that characterization of the ideal site type for aboriginal V. membranaceum management must include the economy and social institutions of the local First Nations and requires an enhanced appreciation for the sophistication of the strategies and techniques employed in their management and utilization of the species.

The connectionist framework for gene regulation

I show that gene regulation networks are qualitatively consistent and therefore sufficiently similar to linearly seperable connectionist networks to warrant that the connectionist framework be applied to gene regulation. On this view, natural selection designs gene regulation networks to overcome the difficulty of development. I offer some general lessons about their evolvability that can be learned by examining the generic features of connectionist networks.

A queueing model for predicting message latency in uni-directional <Emphasis Type="Italic">k</Emphasis>-ary <Emphasis Type="Italic">n</Emphasis>-cubes with deterministic routing and non-uniform traffic

The interconnection network is one of the key architectural components in any parallel computer. The distribution of the traffic injected into the network is among the factors that greatly influences network performance. The uniform traffic pattern has been adopted in many existing network performance evaluation studies due to the tractability of the resulting analytical modelling approach. However, many real applications exhibit non-uniform traffic patterns such as hot-spot traffic. K-ary n-cubes have been the mostly widely used in the implementation of practical parallel systems. Extensive research studies have been conducted on the performance modelling and evaluation of these networks. Nonetheless, most of these studies have been confined to uniform traffic distributions and have been based on software simulation. The present paper proposes a new stochastic model to predict message latency in k-ary n-cubes with deterministic routing in the presence of hot-spot traffic. The model has been validated through simulation experiments and has shown a close agreement with simulation results.

Activation of Apical K<Superscript>+</Superscript> Conductances by Muscarinic Receptor Stimulation in Rat Distal Colon: Fast and Slow Components

In the epithelium of rat distal colon the acetylcholine analogue carbachol induces a transient increase of short-circuit current (I_sc) via stimulation of cellular K⁺ conductances. Inhibition of the turnover of inositol-1,4,5-trisphosphate (IP₃) by LiCl significantly reduced both the amplitude and the duration of this response. When the apical membrane was permeabilized with nystatin, LiCl nearly abolished the carbachol-induced activation of basolateral K⁺ conductances. In contrast, in epithelia, in which the basolateral membrane was bypassed by a basolateral depolarization, carbachol induced a biphasic increase in the K⁺ current across the apical membrane consisting of an early component carried by charybdotoxin- and tetraethylammonium-sensitive K⁺ channels followed by a sustained plateau carried by channels insensitive against these blockers. Only the latter was sensitive against LiCl or inhibition of protein kinases. In contrast, the stimulation of the early apical K⁺ conductance by carbachol proved to be resistant against inhibition of phospholipase C or protein kinases. However, apical dichlorobenzamil, an inhibitor of Na⁺/Ca²⁺ exchangers, or a Ca²⁺-free mucosal buffer solution significantly reduced the early component of the carbachol-induced apical K⁺ current. The presence of an apically localized Na⁺/Ca²⁺-exchanger was proven immunohistochemically. Taken together these experiments reveal divergent regulatory mechanisms for the stimulation of apical Ca²⁺-dependent K⁺ channels in this secretory epithelium, part of them being activated by an inflow of Ca²⁺ across the apical membrane.

Impact of an alien octocoral, Carijoa riisei, on black corals in Hawaii

In 2001 Carijoa riisei, an octocoral native to the tropical Western Atlantic, was discovered overgrowing black corals in the Au’au Channel in Hawaii. In this paper data from a 2001 survey are reanalyzed and combined with new data from 2003 and 2004 to assess the ecological impact in greater detail. C. riisei differentially affected reproductively mature black coral colonies with maximum impact between 80 and 105 m. The pattern of C. riisei overgrowth on black corals and C. riisei on the substrata appears to be bounded by high irradiance in shallow water and cold temperature in deep water. Evidence suggests that the C. riisei settlement on black corals is facilitated by other epifauna. Once established, C. riisei spreads vegetatively and smothers the coral. The success of the C. riisei invasion appears to be unaided by anthropogenic disturbance and is at least partially attributable to Hawaii’s depauperate shallow-water (<100 m) octocoral fauna.

Predictive performance modelling of parallel component compositions

Large-scale scientific computing applications frequently make use of closely-coupled distributed parallel components. The performance of such applications is therefore dependent on the component parts and their interaction at run-time. This paper describes a methodology for predictive performance modelling and evaluation of parallel applications composed of multiple interacting components. In this paper, the fundamental steps and required operations involved in the modelling and evaluation process are identified—including component decomposition, component model combination, M×N communication modelling, dataflow analysis and overall performance evaluation. A case study is presented to illustrate the modelling process and the methodology is verified through experimental analysis.