The structure of Clostridium difficile toxin A glucosyltransferase domain bound to Mn(2+) and UDP provides insights into glucosyltransferase activity and product release

Clostridium?difficile toxin?A (TcdA) is a member of the large clostridial toxin family, and is responsible, together with C.?difficile toxin?B (TcdB), for many clinical symptoms during human infections. Like other large clostridial toxins, TcdA catalyzes the glucosylation of GTPases, and is able to inactivate small GTPases within the host cell. Here, we report the crystal structures of the TcdA glucosyltransferase domain (TcdA-GT) in the apo form and in the presence of Mn(2+) and hydrolyzed UDP-glucose. These structures, together with the recently reported crystal structure of TcdA-GT bound to UDP-glucose, provide a detailed understanding of the conformational changes of TcdA that occur during the catalytic cycle. Indeed, we present a new intermediate conformation of a so-called 'lid' loop (residues?510-522 in TcdA), concomitant with the absence of glucose in the catalytic domain. The recombinant TcdA was expressed in Brevibacillus in the inactive apo form. High thermal stability of wild-type TcdA was observed only after the addition of both Mn(2+) and UDP-glucose. The glucosylhydrolase activity, which is readily restored after reconstitution with both these cofactors, was similar to that reported for TcdB. Interestingly, we found that ammonium, like K(+) , is able to activate the UDP-glucose hydrolase activities of TcdA. Consequently, the presence of ammonium in the crystallization buffer enabled us to obtain the first crystal structure of TcdA-GT bound to the hydrolysis product UDP. Database ??Coordinates of apo-TcdA-GT and Mn(2+) -UDP-TcdA-GT are available in the Protein Data Bank under the accession numbers 4DMV and 4DMW, respectively.     

Potential of Lariophagus distinguendus (Förster) (Hymenoptera: Pteromalidae) to suppress the maize weevil Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae) in bagged and bulk stored maize

Grains are often stored in jute bags in developing countries, especially in Africa, as well as in small quantities in bulk. Parasitoids suitable for biological control of stored-product pests should be able to find their hosts in bulk grain or in jute bags over a certain distance in a warehouse containing stacks of bagged grain. The potential of using Lariophagus distinguendus for the biological control of Sitophilus zeamais was assessed in maize stored in jute bags and bulk grain. The ability of the parasitoid to penetrate the jute cloth and the grain mass and parasitize its host was studied under controlled conditions of 25 ± 1 °C and 65 ± 5% RH. Experiments were carried out in small 5-kg jute bags containing 28 d old S. zeamais larvae within infested maize kernels, and in cylinders filled with maize grains and containing caged hosts at different depths. L. distinguendus parasitized S. zeamais in the jute bags and in the storage cylinders at various depths. In the jute bag experiment, out of the 60 L. distinguendus adults released, a mean ± SD of 7.03 ± 1.78% and 6.34 ± 1.01% of the 40 females and of the 20 males released, respectively, entered the jute bags. Significantly, no differences were found between the female and male L. distinguendus that entered the bags. Mean reduction of S. zeamais in the jute bags by parasitoids was 81%. The parasitic wasps also significantly reduced the emergence of S. zeamais in bulk maize. At depths of 20–45 cm from the grain surface, mean reduction of S. zeamais was 74%, while from 95 to 100 cm, mean reduction was 34%. When results from depths lower than 50 cm were pooled and compared with pooled data from depths higher than 90 cm, there was a significant reduction in parasitism at depths of more than 90 cm. For depths below 50 cm a mean of 5.3 L. distinguendus adult offspring per cage emerged compared with a mean of 2.6 at depths of more than 90 cm. These results support the approach to utilize L. distinguendus as a component in the integrated control of S. zeamais in bagged or bulk stored maize.     

Constraints and release at different scales – The role of adaptation in biological invasions

Attempts to find a consensus on traits promoting the invasiveness of exotic species have agreed on the idiosyncrasy of successful invasions. Despite considerable efforts to integrate aspects of context-dependency into theories of invasions, none of them has provided an evolutionary perspective taking consistently into account the direction of environmental changes in terms of ‘constraint’ vs. ‘release’. Applying the filter theory of species sorting, I consider different filters at different scales explaining evolutionary changes during invasions. Within this hierarchical approach, the focus is on the factorial filters climate, abiotic environment and biotic environment, distinguishing trophic interactions and plant-plant interactions. This review summarizes the evidence of adaptive shifts from native to exotic ranges, thereby differentiating the direction of shifts with regard to either constrained or released situations. Following this systematic approach, the present paper identifies further trade-offs within hierarchical levels complementing already existing hypotheses such as those for biotic interactions. In particular, the role of climatic changes should more explicitly be linked with evolutionary responses during invasions. Studying exotic species successfully invading several regions with different environmental conditions will be a promising starting point to enlarge the understanding of context-dependency of invasions.     

Pre-Darwinian Taxonomy and Essentialism – A Reply to MaryWinsor

Mary Winsor (2003) argues against the received view that pre-Darwinian taxonomy was characterized mainly by essentialism. She argues, instead, that the methods of pre-Darwinian taxonomists, in spite of whatever their beliefs, were that of clusterists, so that the received view, propagated mainly by certain modern biologists and philosophers of biology, should at last be put to rest as a myth. I argue that shes right when it comes to higher taxa, but wrong when it comes the most important category of all, the species category.     

ROXAS – A new tool to build centuries-long tracheid-lumen chronologies in conifers

Measurements of tree-ring features (ring width, density, isotopes concentration, etc.) are well-established proxies of environmental variability and, in particular, climate fluctuation at local, regional and continental scales. In recent years, tree-ring anatomical structure (conduit size, density, cell wall thickness, ray abundance, etc.) has been recognized as a novel source of valuable ecological information. However, despite the high potential interest, these kinds of investigations have been significantly constrained by the methodological limitations and time-consuming procedures of data collection.In this paper, we present ROXAS: an image analysis tool specifically designed to automatically recognize and measure conduit lumen area and calculate reliable statistics in a reasonable amount of time. With ROXAS, many of the aforementioned limitations in analyzing tree-ring anatomical structure can potentially be overcome. While ROXAS was previously used exclusively for angiosperm analysis, we demonstrate in this paper for the first time how it can also be used to analyze an entire sample of a conifer wood.The use of ROXAS for the analysis of conifer anatomy is exemplified by a 120-year long Pinus leucodermis sample including about 75,000 tracheid cells. The results of ROXAS fully automatic tracheid detection are compared to the results obtained after using in-built manual editing capabilities. While both approaches proved to be efficient, the quality of the fully automatic tracheid detection is found to be generally sufficient for most research applications.     

A new approach to insect-pest control—combination of neurotoxins interacting with voltage sensitive sodium channels to increase selectivity and specificity

Voltage-sensitive sodium channels are responsible for the generation of electrical signals in most excitable tissues and serve as specific targets for many neurotoxins. At least seven distinct classes of neurotoxins have been designated on the basis of physiological activity and competitive binding studies. Although the characterization of the neurotoxin receptor sites was predominantly performed using vertebrate excitable preparations, insect neuronal membranes were shown to possess similar receptor sites. We have demonstrated that the two mutually competing antiinsect excitatory and depressant scorpion toxins, previously suggested to occupy the same receptor site, bind to two distinct receptors on insect sodium channels. The latter provides a new approach to their combined use in insect control strategy. Although the sodium channel receptor sites are topologically separated, there are strong allosteric interactions among them. We have shown that the lipid-soluble sodium channel activators, veratridine and brevetoxin, reveal divergent allosteric modulation on scorpion α-toxins binding at homologous receptor sites on mammalian and insect sodium channels. The differences suggest a functionally important structural distinction between these channel subtypes. The differential allosteric modulation may provide a new approach to increase selective activity of pesticides on target organisms by simultaneous application of allosterically interacting drugs, designed on the basis of the selective toxins. Thus, a comparative study of neurotoxin receptor sites on mammalian and invertebrate sodium channels may elucidate the structural features involved in the binding and activity of the various neurotoxins, and may offer new targets and approaches to the development of highly selective pesticides.     

A new journal – "Theoretical Biology and Medical Modelling"

Biology has a conceptual basis that allows one to build models and theorize across many life sciences, including medicine and medically-related disciplines. A dearth of good venues for publication has been perceived during a period when bioinformatics, systems analysis and biomathematics are burgeoning.     

Management to control citrus greening alters the soil food web and severity of a pest–disease complex

Since 2005, the Florida citrus industry has faced the need to control the devasting bacterial disease huanglongbing (HLB). Advanced production systems (APS) were designed to grow citrus trees more quickly than conventional citriculture (CC) methods in order to mitigate the impact of HLB. Daily fertigation required by APS produces changes in the soil physical–chemical properties compared to those in conventionally managed orchards. We used real-time PCR in an ongoing field experiment to compare the effects of APS and CC on more than a dozen metazoan and microorganism species in soil food webs that affect larvae of a major arthropod pest of citrus, Diaprepes abbreviatus. Soil chemical properties, citrus performance, weevil occurrence, and abundance of free-living and plant-parasitic nematodes were also evaluated. The effects of polypropylene mulch that provides a barrier to soil entry by D. abbreviatus larvae were also investigated in each of the two cultural systems. Trees grew significantly larger in APS and mulching increased tree growth and reduced tree mortality, thereby increasing fruit yield per ha. APS increased the fruit yield in 2011; however, by 2013 the number of fruit per tree was not affected by any of the treatments. Root mass density increased in APS, but decreased under mulch. The numbers of plant-parasitic and free-living nematodes and some natural enemies of nematodes such as Catenaria sp. and Paecilomyces lilacinus were more abundant in the treatments with greater root mass density. Both organisms in the D. abbreviatus–Phytophthora nicotianae pest–disease complex were more abundant in APS than in CC, whereas fewer steinernematid entomopathogenic nematodes (EPNs) that prey on insect larvae occurred in APS. By contrast, heterorhabditid EPNs tended to be more numerous in APS than in CC, although they comprised <25% of the EPN communities in any treatment. Major differences between APS and CC in almost all of the measured physical and chemical soil properties provide a basis for controlled studies to understand why EPN taxa responded differently to these treatments and how APS and soils generally might be modified to conserve the beneficial activities of nematodes.     

The facultative bimodal growth pattern in Quercus ilex – A simple model to predict sub-seasonal and inter-annual growth

In Mediterranean climates, bimodal growth patterns, corresponding to two peaks in radial increment during favorable seasons, have been described in several tree species. However, we lack a better mechanistic understanding of bimodality and its potential responses to the predicted warming and aridification trends. Filling this research gap is important since growth duration affects the capacity of trees to form wood and uptake carbon. Here we used an 11-year (1994–2004) long record of dendrometer data of the Mediterranean Holm oak (Quercus ilex) and compared how climate related to radial increment in trees from the south- and the north-facing slopes. We also related climate variables to tree-ring width and the production of intra-annual density fluctuations (IADFs), which reflects bimodality. In this paper, we introduce a model called VS-Lite2 to simulate tree-growth dynamics, which is a modified version of the process-based Vaganov-Shashkin Lite model. The VS-Lite2 model adequately reproduced the bimodal intra‐annual pattern of radial growth, IADFs, and annual tree growth. Trees from the south-oriented slope grew more, produced more IADFs and showed a more marked bimodal pattern than trees from the north-facing slope. These differences agree with the observation that late-summer drought constrained growth. Therefore, radial-growth models should consider plastic bimodality and micro-environmental conditions in areas subjected to seasonal droughts.     

The Stopped-flow Method and Chemical Intermediates in Enzyme Reactions – A Personal Essay

My perspective does not deal directly with photosynthesis research. However, the methods evolved have played an important role in several areas of biochemistry and biophysics including photosynthesis. Improvements of rapid reaction methods, based upon the pioneering studies of Hamilton Hartridge and F.J.W. Roughton, and Glenn Millikan, required a detailed study of the hydraulics of small-bore tubes and jet mixers, taking into account, that economy of reactants was demanded by the sparcity of enzyme preparations in the 1930s. This Personal perspective recites the steps taken to minimize the volumes expended in rapid flow studies, together with the improvements in electronic technology of rapid and sensitive spectrophotometry of labile intermediates in enzyme reactions. Of the methods studied, continuous, accelerated and stopped flow, the latter was designed for the highest fluid economy and subsequently proved to be of wide use for studying biochemical kinetics. Advances in fast spectrophotometry of dilute solutions led to great improvements in Millikan's dual-wavelength system, both in speed of recording and decreases of background noise level, largely due to electronic stabilization of light sources and sensitive amplifiers. The application of these technologies to studies of hemoglobin, myoglobin and heme enzymes was, more recently, followed by studies of suspensions of organelles, cells, and tissues not only in vivo but also at low temperatures with cryoprotectants, leading to the use of flash activation in carbon monoxide inhibited heme enzymes. Laser technology allowed photosynthetic systems to be studied at cryotemperatures, leading to the development of electron tunneling theories for biological reactions (not discussed in this paper). All in all, the many fundamental developments of electronics, optics and hydraulics indicate how technology can respond effectively to the needs of biology in general, and photobiology in particular.