Learning from the past: palaeohydrology and palaeoecology

Attempts to increase European biodiversity by restoring rivers and floodplains are based on inadequate data on natural systems. This is particularly the case for NW European rivers because all catchments have been impacted by agriculture and river engineering. If river restoration is to have an ecological, as opposed to `cosmetic' design basis then baseline models are required. However, this poses three questions; (a) what is the natural river‐floodplain state, (b) how can it be defined and modelled and (c) can this state be recreated today? The first two questions can only be addressed by using palaeohydrological and palaeoecological data. A second and equally vital consideration is the stability/instability of any restored system to change in external forcing factors (e.g. climate) and in this context it may not be realistic to expect baseline models to provide equilibrium solutions but instead to define process‐form domains. Over the last two decades evidence has accumulated that the natural state of lowland rivers in much of NW Europe was multi rather than single thread‐braided, anastomosing or anabranching. Until recently our knowledge of floodplain palaeoecology was generally derived from pollen diagrams, which have source‐area of problems and lack of taxonomic specificity. The precision and breadth of palaeoecological reconstruction (including richness and structure) has been greatly increased by the use of multiple palaeo‐indicators including macrofossils, diatoms and beetles. The dynamics of small to medium sized, low‐energy, predeforestation floodplains were dominated by disturbance (windthrow, beavers, etc.) and large woody debris. In order to compare the hydrogeomorphological basis of floodplain ecology, both temporally and spatially, a simple index of fluvial complexity is presented. Palaeoecological and geomorphological investigations have the potential to provide in‐depth models of the natural range of channel conditions and sensitivity to external change that can be used to provide a scientific basis for floodplain restoration. There is also the possibility that floodplain‐channel restoration may be a valuable tool in the mitigation of future geomorphological change forced by climatic instability.     

Learning from the past: Diatoms as palaeoecological indicators of changes in marine environments

The North Sea is seriously threatened by a variety of pollution sources. Terrestrially derived effluents are causing extensive environmental damage and changes to ecosystems of both the offshore and coastal waters. Coastal and estuarine communities are being lost to reclamation projects, and there is the future threat of rising sea level associaed with global warming. The spatial and temporal extent of recent anthropogenic changes are largely unknown due to the paucity of background information. The possible role of palaeoecological methodology in providing ‘reference levels’ against which current status can be compared, and their importance for restoration and policy decisions, are presented. The usefulness of diatoms as environmental indicators is illustrated. The extent of natural and anthropogenic changes on coastal habitats are demonstrated by reference to the Holocene evolution of the coastline of The Netherlands. Possible profitable areas for further research are outlined,e.g. a diatom nutrient calibration data set for shallow marine embayments.     

Rho GTPases as targets of bacterial protein toxins

Several bacterial toxins target Rho GTPases, which constitute molecular switches in several signaling processes and master regulators of the actin cytoskeleton. The biological activities of Rho GTPases are blocked by C3-like transferases, which ADP-ribosylate Rho at Asn41, but not Rac or Cdc42. Large clostridial cytotoxins (e. g., Clostridium difficile toxin A and B) glucosylate Rho GTPases at Thr37 (Rho) or Thr35 (Rac/Cdc42), thereby inhibiting Rho functions by preventing effector coupling. The 'injected' toxins ExoS, YopE and SptP from Pseudomonas aeruginosa, Yersinia and Salmonella ssp., respectively, which are transferred into the eukaryotic target cells by the type-III secretion system, inhibit Rho functions by acting as Rho GAP proteins. Rho GTPases are activated by the cytotoxic necrotizing factors CNF1 and CNF2 from Escherichia coli and by the dermonecrotizing toxin DNT from B. bronchiseptica. These toxins deamidate/transglutaminate Gln63 of Rho to block the intrinsic and GAP-stimulated GTP hydrolysis, thereby constitutively activating the GTPases. Rho GTPases are also activated by SopE, a type-III system injected protein from Salmonella ssp., that acts as a GEF protein.     

BTXpred: prediction of bacterial toxins

This paper describes a method developed for predicting bacterial toxins from their amino acid sequences. All the modules, developed in this study, were trained and tested on a non-redundant dataset of 150 bacterial toxins that included 77 exotoxins and 73 endotoxins. Firstly, support vector machines (SVM) based modules were developed for predicting the bacterial toxins using amino acids and dipeptides composition and achieved an accuracy of 96.07% and 92.50%, respectively. Secondly, SVM based modules were developed for discriminating entotoxins and exotoxins, using amino acids and dipeptides composition and achieved an accuracy of 95.71% and 92.86%, respectively. In addition, modules have been developed for classifying the exotoxins (e.g. activate adenylate cyclase, activate guanylate cyclase, neurotoxins) using hidden Markov models (HMM), PSI-BLAST and a combination of the two and achieved overall accuracy of 95.75%, 97.87% and 100%, respectively. Based on the above study, a web server called 'BTXpred' has been developed, which is available at http://www.imtech.res.in/raghava/btxpred/. Supplementary information is available at http://www.imtech.res.in/raghava/btxpred/supplementary.html.     

Rho GTPase-activating bacterial toxins: from bacterial virulence regulation to eukaryotic cell biology

Studies on the interactions of bacterial pathogens with their host have provided an invaluable source of information on the major functions of eukaryotic and prokaryotic cell biology. In addition, this expanding field of research, known as cellular microbiology, has revealed fascinating examples of trans-kingdom functional interplay. Bacterial factors actually exploit eukaryotic cell machineries using refined molecular strategies to promote invasion and proliferation within their host. Here, we review a family of bacterial toxins that modulate their activity in eukaryotic cells by activating Rho GTPases and exploiting the ubiquitin/proteasome machineries. This family, found in human and animal pathogenic Gram-negative bacteria, encompasses the cytotoxic necrotizing factors (CNFs) from Escherichia coli and Yersinia species as well as dermonecrotic toxins from Bordetella species. We survey the genetics, biochemistry, molecular and cellular biology of these bacterial factors from the standpoint of the CNF1 toxin, the paradigm of Rho GTPase-activating toxins produced by urinary tract infections causing pathogenic Escherichia coli. Because it reveals important connections between bacterial invasion and the host inflammatory response, the mode of action of CNF1 and its related Rho GTPase-targetting toxins addresses major issues of basic and medical research and constitutes a privileged experimental model for host-pathogen interaction.     

Mammalian membrane trafficking as seen through the lens of bacterial toxins

A fundamental question of eukaryotic cell biology is how membrane organelles are organised and interact with each other. Cell biologists address these questions by characterising the structural features of membrane compartments and the mechanisms that coordinate their exchange. To do so, they must rely on variety of cargo molecules and treatments that enable targeted perturbation, localisation, and labelling of specific compartments. In this context, bacterial toxins emerged in cell biology as paradigm shifting molecules that enabled scientists to not only study them from the side of bacterial infection but also from the side of the mammalian host. Their selectivity, potency, and versatility made them exquisite tools for uncovering much of our current understanding of membrane trafficking mechanisms. Here, we will follow the steps that lead toxins until their intracellular targets, highlighting how specific events helped us comprehend membrane trafficking and establish the fundamentals of various cellular organelles and processes. Bacterial toxins will continue to guide us in answering crucial questions in cellular biology while also acting as probes for new technologies and applications.     

Thiol-dependent cytolytic bacterial toxins: streptolysin O and prominent toxins

Streptolysin O is the prototype of fifteen bacterial cytolytic protein toxins elaborated by gram-positive bacteria of species Streptococcus, Clostridium, Bacillus and Listeria. These toxins share a number of common properties: they are antigenically related as shown by cross-neutralization and immunoprecipitation; their cytolytic and other reducing agents; these toxins are inactivated by cholesterol and certain related sterols. This group of oxygen-labile cytolytic toxins has been named sulfyhdryl-activated toxins or thiol-activated cytolysins. The mechanism of action of these toxins is very likely identical or at least closely similar.     

Actin as target for modification by bacterial protein toxins

Various bacterial protein toxins and effectors target the actin cytoskeleton. At least three groups of toxins/effectors can be identified, which directly modify actin molecules. One group of toxins/effectors causes ADP-ribosylation of actin at arginine-177, thereby inhibiting actin polymerization. Members of this group are numerous binary actin-ADP-ribosylating exotoxins (e.g. Clostridium botulinum C2 toxin) as well as several bacterial ADP-ribosyltransferases (e.g. Salmonella enterica SpvB) which are not binary in structure. The second group includes toxins that modify actin to promote actin polymerization and the formation of actin aggregates. To this group belongs a toxin from the Photorhabdus luminescens Tc toxin complex that ADP-ribosylates actin at threonine-148. A third group of bacterial toxins/effectors (e.g. Vibrio cholerae multifunctional, autoprocessing RTX toxin) catalyses a chemical crosslinking reaction of actin thereby forming oligomers, while blocking the polymerization of actin to functional filaments. Novel findings about members of these toxin groups are discussed in detail.     

Lonomia genus caterpillar toxins: biochemical aspects

In 1967 we reported for the first time five cases of an acquired bleeding disorder in humans which developed after contact with saturnidae caterpillars. Since that time, other cases have been reported in Brazil, French Guyana, Peru, Paraguay and Argentina. The caterpillars have been identified as Lonomia achelous (LA) in Venezuela and northern Brazil and as Lonomia obliqua (LO) in southern Brazil. All patients present pain and a burning sensation at the site of contact. Within a few hours hematomas and hematuria are seen in combination with intracerebral and intraperitoneal hemorrhage (in some cases also renal failure). Hematological tests show: mild anemia with leucocytosis; prolonged PT, PTT and ThT; decreased fibrinogen, factor V, factor XIII, plasminogen and alpha2-antiplasmin levels; increased factor VIII:c, von Willebrand factor, and FDPs/D-dimers levels with normal ATIII and platelets. Factor VII, factor II and PC levels varied. Several activities similar to or directed against blood clotting factors have been identified in LA: fibrinolytic enzymes, which degrade fibrinogen producing abnormal FDPs; prothrombin activators: one direct and one factor Xa-like; a thermostable factor V activator; a thermolabile factor V inhibitor; a factor XIII proteolytic/urokinase-like activity; and a kallikrein-like activitiy. In LO three activities have been described: a prothrombin activator called 'Lonomia obliqua prothrombin activator protease' (LOPAP); a factor X activator; and a phospholipase A(2)-like activity called Lonomiatoxin. No fibrinolytic activity has been described in LO. Subcutaneous injection of crude hemolymph and some chromatographic fractions of LA induce a decrease in fibrinogen, plasminogen and factor XIII. Intravenous injection of factor XIII proteolytic/urokinase-like activity induce a dose-dependent thrombolysis with a decrease in plasmatic factor XIII without hemorrhagic manifestations. Intradermal injection of LO bristle extracts in rats and rabbits produce incoagulability whereas intravenous injection of LOPAP induced DIC in mice.     

Recombinant pharmaceuticals from plants: the plant endomembrane system as bioreactor

The production of safe pharmaceuticals at affordable costs is one of the great challenges of our times. Research has proven that transgenic plants can fulfill this need. This review focuses on the peculiar features of plant cells that allow high accumulation of recombinant proteins. The endomembrane system and the secretory pathway of plant cells in themselves offer a fascinating model of protein sorting, and in practical terms, represent the potential for the facile and very low-cost purification of recombinant pharmaceutical proteins.     

Cholesterol and the activity of bacterial toxins

Cholesterol may affect the activity of microbial toxins in a direct, specific way, or it may exert indirect effects because of its role in membrane fluidity, membrane line tension, and in the stabilization of rafts in the cytoplasmic membrane. The thiol-activated toxins of gram-positive bacteria, and the cytolysin of Vibrio cholerae are presented as examples of specific toxin-cholesterol interaction. Several mechanisms of indirect effects of cholesterol are discussed using examples such as Staphylococcus aureus alpha-hemolysin, aerolysin, and diphtheria toxin.     

Circadian and infradian aspects of the cell cycle: from past to future

A review of some aspects of circadian and infradian rhythms of the cell cycle is given. The background is that the research of the last decade has given entirely new insights into the cell cycle as a dynamic process which occurs in waves. After some short historical notes on the development of methodology for study of cell kinetics, it is reviewed how the strong variability of this function was recognized from the 1960's. This again led to an increasing understanding of the rhythmic pattern of cell renewal in various tissues of the body. Conventional methods for studying cell population kinetics gave general insights into both circadian and infradian rhythms, but were hampered by several shortcomings. The techniques were time consuming, and usually one and only one parameter could be studied at a time. However, this general knowledge both had a strong impact on the understanding of cell kinetics and provided a basis for designing cancer chemotherapy. Today we are facing a new area in the study of cell population kinetics. New, rapid and automated methods for multiparameter studies of both cell kinetics and other biological properties of cell populations have given entirely new possibilities for cell kinetic research. Methods, mainly connected to analytical cytology, can discriminate subpopulations with varying kinetic properties, and also enable monitoring of cell proliferation in normal and malignant tissues of patients. Chronobiology has had a strong impact on the understanding of cell population kinetics in the body. In the light of the new developments in the fields of growth factors and their regulatory influences on the cell cycle, important and fundamental aspects of biological rhythms are now being elucidated.     

Bioassays for evaluation of medical products derived from bacterial toxins

Bioassays play central role in evaluation of biological products and those derived from bacterial toxins often rely exclusively on in vivo models for assurance of safety and potency. This chapter reviews existing regulatory approved methods designed to provide information on potency and safety of complex biological medicines with an insight into strategies considered for alternative procedures.