On a density-dependent model of competition for one resource

We use the concept of steady-state characteristic of a population using a single limiting resource, in order to discuss the issue of the competition of many species for the same resource. The steady-state characteristic is a curve that is associated to each species, likely to be determined empirically. Once one knows the steady-state characteristics and the dynamic of the renewal of the resource, it is possible to predict to some extent the issue of the competition and to give sufficient conditions for coexistence.     

Purification of the recombinant human serotonin N-acetyltransferase (EC 2.3.1.87): further characterization of and comparison with AANAT from other species

Melatonin is synthesized by a series of enzymes, the penultimate one, serotonin N-acetyltransferase, catalyzing the limiting reaction. In the present study, we compared the recombinant serotonin N-acetyltransferases from rat, ovine, and human. The human protein is particularly difficult to purify because it interacts strongly with a putative chaperone protein from bacteria whereas the rat and sheep enzymes, which interact less strongly with this protein, have been purified close to homogeneity. We identified the contaminating protein as GroEL, the bacterial equivalent of Hsp60. We present numerous catalytic activities (substrate and cosubstrate specificities as well as inhibitor specificities) measured on the three species enzymes from which we deduced that the presence of the chaperone might partly explain the differences between the various species enzyme characteristics, beside the inter-species ones resulting from sequence differences. Despite several trials reported in the literature, a purification to homogeneity of the human (recombinant) enzyme has never been described. We present a new purification method, by using an original denaturation/renaturation process in which the enzyme is immobilized on an affinity chromatography column. The enzyme is then eluted in an active and pure form (i.e., absence of chaperone). The up-scaled system permitted us to perform the necessary experiments for the measurement of more accurate affinities of human serotonin N-acetyltransferase towards its main natural substrates, showing that only the activity of the enzyme towards phenylethylamine was modified.     

Character displacement and the origins of diversity

In The Origin of Species, Darwin proposed his principle of divergence of character (a process now termed "character displacement") to explain how new species arise and why they differ from each other phenotypically. Darwin maintained that the origin of species and the evolution of differences between them is ultimately caused by divergent selection acting to minimize competitive interactions between initially similar individuals, populations, and species. Here, we examine the empirical support for the various claims that constitute Darwin's principle, specifically that (1) competition promotes divergent trait evolution, (2) the strength of competitively mediated divergent selection increases with increasing phenotypic similarity between competitors, (3) divergence can occur within species, and (4) competitively mediated divergence can trigger speciation. We also explore aspects that Darwin failed to consider. In particular, we describe how (1) divergence can arise from selection acting to lessen reproductive interactions, (2) divergence is fueled by the intersection of character displacement and sexual selection, and (3) phenotypic plasticity may play a key role in promoting character displacement. Generally, character displacement is well supported empirically, and it remains a vital explanation for how new species arise and diversify.     

Cupressus dupreziana A. Camus: distribution,decline and regeneration on the Tassili n'Ajjer,central Sahara

As soon as it was first discovered in 1924, on the heights of the Tassili n'Ajjer, Cupressus dupreziana (A. Camus) was declared an endangered species. The few ancient trees to be seen in the beds of wadis gave reason to suppose that they were isolated individuals left behind from a forest that had flourished in a damper climate. Attempts at a census of the trees were made on a number of occasions, the fullest, in 1972, reporting a total of 230 living specimens. The revision of this inventory between 1997 and 2001 has now enabled us to draw the boundaries of the present range of this species, to assess its rate of decline over the last three decades and, for the first time, to record some regeneration, with the presence of new, young trees.     

The release of genetically engineered micro-organisms and viruses into the environment

This review considers the reasons for, and research governing, the regulation and monitoring of genetically engineered micro-organisms and viruses (GEMs) released into the environment. The hazards associated with releasing GEMs into the environment are the creation and evolution of new pests and diseases, and damage to the ecosystem and non target species. The similarities and differences between GEMs and conventional micro-organisms are discussed in relation to risk assessment. Other issues covered include the persistence of micro-organisms in the environment, transgene dispersal to non-engineered microbes and other organisms, the effects of transgenes and transformation on fitness, and the evolution of pests and pathogens that are given or acquire transgenes. Areas requiring further research are identified and recommendations for risk assessment made.     

Influence of the mode of reactor operation on the rate and yield of fermentation of the model solid substrate,wheat bran,by a microbial consortium under non-axenic anaerobic conditions

Summary Anaerobic fermentation of wheat bran, a model solid substrate, was conducted under non-axenic conditions, in two reactors operated under different modes, all other conditions being strictly identical. The first reactor was a completely-mixed batch reactor. The second reactor was a percolator into which the liquid phase was recirculated in closed loop through the solid substrate acting as a stationary bed. The final yield of fermentation was obtained after 27 days in the completely-mixed batch reactor, and after 14 days only in the percolator. Scanning electron microscopy revealed that numerous micro-organisms adhered to the solid substrate acting as a carrier in the percolator, whereas only very few micro-organisms adhered to the solid substrate in the completely-mixed batch reactor. The results show that obtaining a durable direct contact between micro-organisms and their solid substrate improves the rate of solids degradation.     

Influence of the feeding pattern on the glucose metabolism of Arthrobacter sp. and Sphaerotilus natans,growing in chemostat culture,simulating activated sludge bulking

Summary Changing from a continuous feeding to an intermittent feeding selects for floc-forming micro-organisms in activated sludge systems. Previous research stressed the importance of the substrate uptake rate. In order to explain this shift in population the uptake kinetics of pure cultures of Sphaerotilus natans (filament) and Arthrobacter (floc-former) were examined with glucose as C-source.Batch experiments indicated a severe decrease in uptake capacity at the end of the declining growth phase.The results with continuously and intermittently fed chemostats indicated a profound influence of periodic feeding on the metabolism of pure cultures; steady state dry weights were lower, substrate uptake over-capacity was larger, more over-flow metabolites were produced. Higher K_m values for substrate uptake were recorded and more reserve materials were built. More important, the over-capacity in I-fed cultures of the floc-forming micro-organism was larger than for the filamentous bacterium. In ecological perspective this may explain the selection of a floc-forming biomass in activated sludge systems with temporary higher BOD-concentrations or operating in plug-flow.     

Evolution and selection of reproduction

The examination of the official records from Artas, Isère (North Dauphiné, France), provides nearly continuous information from 1540 to 1900. These allowed us to study the twinning during this period, to specify its importance, its evolution, and its links with diverse other characteristics of reproduction. The number of twins per 1000 births is on a general average very close to 11. It seems to decrease during the last four centuries. However, the variability is very high from one year to another or one decade to another, including the composition of twins (identical or different sex), with the result that no statistical argument allows us to reject the null hypothesis. Numerous data have been collected that support a partially genetic determinism in twinning. The number of children in families with twins is clearly higher that in other families. Age of death of the mother of twins is higher than that of the mother of single births. With the result that 'gemellity', fecundity and longevity are related. On the other hand, the perinatal and infant death rate is much higher for twins than for single births, so that the percentage of 'useful' children is very low for twins. There is therefore, at the same time, selection and counter-selection. The momentary importance of either could explain the extent of variation of the 'gemellity' rate. The compensations, at short or long time, between the two processes could explain the roughly constant rate of 'gemellity' during the last four centuries.     

The species of Aspidorhynchus Agassiz, 1833 (Neopterygii,Aspidorhynchiformes) from the Jurassic plattenkalks of Southern Germany

The fishes of the genus Aspidorhynchus (Aspidorhynchidae) are among the most abundant predators in the palaeolagoons of the Solnhofen archipelago (Late Jurassic, southern Germany). They have been known since the end to the nineteenth century and the last revision of the genus was published more than 20 years ago. During these last two decades, numerous complete and excellently preserved specimens have been collected. The high morphological diversity shown by the new material made a new revision of these fishes necessary. This new taxonomic revision led us to revalidate the species A. ornatissimus Agassiz, 1834, which has hitherto been considered a junior synonym of the type species of the genus, A. acutirostris (Blainville, 1818), as well as to recognize high intraspecific variation in the latter species. These results helped to improve the distinction and, thus, the diagnoses of A. acutirostris, A. ornatissimus, and A. sanzenbacheri Brito and Ebert, 2009, which are the three valid species of this genus in the Solnhofen archipelago. We have been able to explain most of the intraspecific diversity of A. acutirostris by means of patterns of ontogenetic variation that encompass most of the other nominal species, thus largely reflecting early taxonomic hypotheses. Furthermore, the detailed morphological study led us to the recognition of some important anatomical structures previously unknown for aspidorhynchids: a connection between the temporal, infraorbital and supraorbital sensory canals in the frontal bone, the presence of an Y-shaped antorbital bone, and the presence of an interoperculum.     

Kinetic study in the transient phase of the suicide inactivation of frog epidermis tyrosinase

This paper deals with the kinetic study of a multisubstrate mechanism with enzyme inactivation induced by a suicide substrate. A transient phase approach has been developed that enables the deduction of explicit equations of product concentration vs. time. From these equations kinetic constants which characterize the suicide substrate can be obtained. This study with tyrosinase enzyme, which acts on L-dopa and catechol allowed us to determine the corresponding kinetic parameters, indicating that catechol is about 8-times more powerful as a suicide substrate than is L-dopa.     

Metabolic analysis in drug design

Biotechnology is often presented as if progress in the past two decades represented a major success, but the reality is quite different. For example, ten major classes of antibiotics were discovered between 1935 and 1963, but after 1963 there has been just one, the oxazolidones. To illustrate the possibilities of doing better by taking account of the real behaviour of metabolic systems, we can examine how one might modify the activity of an enzyme in the cell (for example by genetic manipulation, or by the action of an inhibitor, etc.) to satisfy a technological aim. For example, if the objective is to eliminate a pest, one might suppose that the effect of an inhibitor could be to depress an essential flux to a level insufficient for life, or to raise the concentration of an intermediate to a toxic level. The former may seem the more obvious, but the latter is easier to achieve in practice, and there are some excellent examples of industrial products that work in that way, such as the herbicide 'Roundup' and antimalarials of the quinine class. A study of glycolysis in the parasite Trypanosoma brucei (which causes African sleeping sickness) indicates that for this approach to work the selected target enzyme must have a substrate with a concentration that is not limited by stoichiometric constraints. That is not necessarily easy to find in a complicated system, and typically needs the metabolic network to be analysed in the computer.     

Effect of disulfide-bond introduction on the activity and stability of the extended-spectrum class A beta-lactamase Toho-1

The production of class A beta-lactamases is a major cause of clinical resistance to beta-lactam antibiotics. Some of class A beta-lactamases are known to have a disulfide bridge. Both narrow spectrum and extended spectrum beta-lactamases of TEM and the SHV enzymes possess a disulfide bond between Cys77 and Cys123, and the enzymes with carbapenem-hydrolyzing activity have a well-conserved disulfide bridge between Cys69 and Cys238. We produced A77C/G123C mutant of the extended-spectrum beta-lactamase Toho-1 in order to introduce a disulfide bond between the cysteine residues at positions 77 and 123. The result of 5,5'-dithiobis-2-nitrobenzoic acid (DTNB) titrations confirmed formation of a new disulfide bridge in the mutant. The results of irreversible heat inactivation and circular dichroism (CD) melting experiments indicated that the disulfide bridge stabilized the enzyme significantly. Though kinetic analysis indicated that the catalytic properties of the mutant were quite similar to those of the wild-type enzyme, E. coli producing this mutant showed drug resistance significantly higher than E. coli producing the wild-type enzyme. We speculate that the stability of the enzymes provided by the disulfide bond may explain the wide distribution of TEM and SHV derivatives and explain how various mutations can cause broadened substrate specificity without loss of stability.     

Competition between phytoplankton and bacteria: exclusion and coexistence

Resource-based competition between microorganisms species in continuous culture has been studied extensively both experimentally and theoretically, mostly for bacteria through Monod and Contois “constant yield” models, or for phytoplankton through the Droop “variable yield” models. For homogeneous populations of N bacterial species (Monod) or N phytoplanktonic species (Droop), with one limiting substrate and under constant controls, the theoretical studies indicated that competitive exclusion occurs: only one species wins the competition and displaces all the others (Armstrong and McGehee in Am Nat 115:151, 1980; Hsu and Hsu in SIAM J Appl Math 68:1600–1617, 2008). The winning species expected from theory is the one with the lowest “substrate subsistence concentration” \(s^{\star }\), such that its corresponding equilibrium growth rate is equal to the dilution rate \(D\). This theoretical result was validated experimentally with phytoplankton (Tilman and Sterner in Oecologia 61(2):197–200, 1984) and bacteria (Hansen and Hubell in Science 207(4438):1491–1493, 1980), and observed in a lake with microalgae (Tilman in Ecology 58(22):338–348, 1977). On the contrary for aggregating bacterial species described by a Contois model, theory predicts coexistence between several species (Grognard et al. in Discrete Contin Dyn Syst Ser B 8(1):73–93, 2007). In this paper we present a generalization of these results by studying a competition between three different types of microorganisms: planktonic (or free) bacteria (represented by a generalized Monod model), aggregating bacteria (represented by a Contois model) and free phytoplankton (represented by a Droop model). We prove that the outcome of the competition is a coexistence between several aggregating bacterial species with a free species of bacteria or phytoplankton, all the other free species being washed out. This demonstration is based mainly on the study of the substrate concentration’s evolution caused by competition; it converges towards the lowest subsistence concentration \(s^{\star }\), leading to three different types of competition outcomes: (1) the best free bacteria or phytoplankton competitor excludes all other species; (2) only some aggregating bacterial species coexist in the chemostat; (3) A coexistence between the single best free species, with one or several aggregating species.     

Catalytic transformations of supercoiled DNA as studied by flow linear dichroism technique

A catalytic turnover of supercoiled DNA (scDNA) transformation mediated by topoisomerases leads to changes in the linking number (Lk) of the polymeric substrate by 1 or 2 per cycle. As a substrate of the topoisomerization reaction it is chemically identical to its product; even a single catalytic event results in the quantum leap in the scDNA topology. Non-intrusive continuous assay to measure the kinetics of the scDNA topoisomerization was performed. The development of such a technique was hindered because of multiple DNA species of intermediate topology present in the reaction mixture. The interrelation of DNA topology, its hydrodynamics, and optical anisotropy enable us to use the flow linear dichroism technique (FLD) for continuous monitoring of the scDNA topoisomerization reaction. This approach permits us to study the kinetics of DNA transformation catalyzed by eukaryotic topoisomerases I and II, as well as mechanistic characteristics of these enzymes and their interactions with anticancer drugs. Moreover, FLD assay can be applied to any enzymatic reaction that involves scDNA as a substrate. It also provides a new way of screening drugs dynamically and is likely to be potent in various biomedical applications.     

Crystal structure of Trypanosoma cruzi trypanothione reductase in complex with trypanothione, and the structure-based discovery of new natural product inhibitors.

BACKGROUND: Trypanothione reductase (TR) helps to maintain an intracellular reducing environment in trypanosomatids, a group of protozoan parasites that afflict humans and livestock in tropical areas. This protective function is achieved via reduction of polyamine-glutathione conjugates, in particular trypanothione. TR has been validated as a chemotherapeutic target by molecular genetics methods. To assist the development of new therapeutics, we have characterised the structure of TR from the pathogen Trypanosoma cruzi complexed with the substrate trypanothione and have used the structure to guide database searches and molecular modelling studies. RESULTS: The TR-trypanothione-disulfide structure has been determined to 2.4 A resolution. The chemical interactions involved in enzyme recognition and binding of substrate can be inferred from this structure. Comparisons with the related mammalian enzyme, glutathione reductase, explain why each enzyme is so specific for its own substrate. A CH***O hydrogen bond can occur between the active-site histidine and a carbonyl of the substrate. This interaction contributes to enzyme specificity and mechanism by producing an electronic induced fit when substrate binds. Database searches and molecular modelling using the substrate as a template and the active site as receptor have identified a class of cyclic-polyamine natural products that are novel TR inhibitors. CONCLUSIONS: The structure of the TR-trypanothione enzyme-substrate complex provides details of a potentially valuable drug target. This information has helped to identify a new class of enzyme inhibitors as novel lead compounds worthy of further development in the search for improved medicines to treat a range of parasitic infections.     

Amber microfossils: On the validity of species concept

Do terrestrial micro-organisms evolve morphologically? A recent concept suggests that morphological stasis over dozens of millions of years has persisted in microbial lineages. However, it is based on a weak fossil record. Indeed, it is already difficult to define a species with extant microbes, and this task is even harder when dealing with fossil micro-organisms. Based on research on fossils in amber, we highlighted the different problems that are raised when describing a new fossil species of micro-organisms and we discuss the concept of morphological stasis.     

A new species of wild mice on the Island of Cyprus

A mitochondrial and nuclear gene analysis allowed us to precise the taxonomical position of the two sympatric species of mice known to be present on Cyprus. One of them is the commensal house mouse M. m. domesticus, and the other revealed to be a new taxon that is a sister species of M. spicilegus and M. macedonicus. The new species is equidistant from each of these, the divergence dating around 0.5-1 Myr. Its origin either results from an ancient accidental colonisation of the island or from a recent transportation by the first epipalaeolithic settlers. In this last eventuality, the new species would also exist somewhere else in Asia Minor.     

Interactions of Candida albicans with other Candida spp. and bacteria in the biofilms

AIMS: To study the interactions between Candida albicans and 12 other species of Candida and bacteria in biofilms. METHODS AND RESULTS: The number of cells within growing biofilms in a polystyrene tube model was measured after adding C. albicans to preformed biofilms of other micro-organisms and vice versa. It was also measured after simultaneous biofilm formation of C. albicans and other micro-organisms. The number of cells of C. albicans within the growing biofilms decreased significantly (P < 0.05) when the fungus was added to preformed biofilms of Candida spp. and bacteria except, with C. parapsilosis, Torulopsis glabrata and the glycocalyx producer Pseudomonas aeruginosa. When C. parapsilosis, Staphylococcus epidermidis (nonglycocalyx producer) or Serratia marcescens was added to preformed biofilms of C. albicans, the number of cells of these micro-organisms increased in the growing biofilms. CONCLUSIONS: Biofilms of C. albicans are capable of holding other micro-organisms and more likely to be heterogeneous with other bacteria and fungi in the environment and on medical devices. SIGNIFICANCE AND IMPACT OF THE STUDY: Recognition of the heterogeneity of biofilm-associated organisms can influence treatment decisions, particularly in patients who do not respond to initial appropriate therapy.     

Influence of the colonizing substrate on diatom assemblages and implications for bioassessment: a mesocosm experiment

Although diatoms are important bioindicators of ecological quality, their ecological traits are still not well understood. A major issue is that of substrate preferences, which may result in differences in production, and assemblage structure and composition, and which should therefore be taken into account for ecological quality assessment studies. Thus, in this work, the periphyton grown on sand and ceramic tiles in indoor controlled channels were compared to understand whether substrate differences lead to differences in: periphyton production (chlorophyll-a), chlorophyll-b and c concentrations, diatom assemblages (diversity-Shannon-Wiener, cell density, taxonomic composition, trait proportions), and ecological quality assessments (IPS-‘Indice de Polluosensibilité Spécifique’). A combined inoculum of periphyton from four Portuguese streams was introduced to the running channels (six sand and six tile) and left to colonize for 35 days. Epilithic (tiles) and epipsammic (sand) assemblages were sampled at days 14 and 35. We verified that there were no differences in chlorophyll-a concentration over time and between substrates. On both sampling occasions, the epipsammic assemblages had higher concentration of chlorophyll-c and diatom density but without significant differences over time in each substrate. The taxonomic composition was different between substrates and over time. However, these differences were not reflected in ecological quality assessment. The diversity was also similar between substrates in both sampling occasions, but it was higher at day 14. Mobile and stalked species were more abundant over the entire study and differed significantly between substrates, with the epipsammic assemblages presenting higher abundances of both traits. We concluded that the colonizing substrate influences diatom assemblages but not the ecological quality assessment.     

Nutrients and Trace Elements Content of Wood Decay Fungi Isolated from Oak (Quercus ilex)

The presence of chemical elements and the differences in their concentration in the fruiting bodies of wood decay fungi may reflect their activity either as saprobes or parasites and the intimate physiological relation with the substrate from which they extract their nutrients. In order to test this hypothesis, we carried out a systematic sampling of eight species of wood decay fungi on oak (Quercus ilex). The data show that the concentration of some elements exhibits a very wide range of values for the species tested, which could mean that the relative content of some elements may provide clues about the nature of the substrate and, moreover, about the nutritional physiology. The comparison between the foliar analysis (FA) and the elemental content of fungi may shed light on the specific physiological behaviour of the species. Potassium is an element accumulated in fungal biomass in higher quantities than in the FA. By contrast, calcium appears in foliar analysis in much higher quantities than in fungal fruiting bodies' biomass. Concerning this element, we have also found profound differences between the two species phylogenetic groups and lifestyle. Of all elements measured, we believe that the relative accumulation of K and Ca may be related to the close connection between fungi and the substrate on which they live and may also explain their physiological role as saprobes or parasites. When the lifestyle and the systematic position of the different species sampled were compared, differences also emerged in the content of Na and Ca.