Untangling ecological complexity on different scales of space and time

Ecological systems are complex and essentially unpredictable, because of the multitude of interactions among their constituents. However, there are general statistical patterns emerging on particular spatial and temporal scales, which indicate the existence of some universal principles behind many ecological phenomena, and which can even be used for the prediction of phenomena occurring on finer scales of resolution. These generalities comprise regular frequency distributions of particular macroscopic variables within higher taxa (body size, abundance, range size), relationships between such variables, and general patterns in species richness. All the patterns are closely related to each other and although there are only a few major explanatory principles, there are plenty of alternative explanations. Reconciliation of different approaches cannot be obtained without careful formulation of testable hypotheses and rigorous quantitative empirical research. Two especially promising ways of untangling ecological complexity comprise: (1) analysis of invariances, i.e. universal quantitative relationships observed within many different systems, and (2) detailed analysis of the anatomy of macroecological phenomena, i.e. explorations of how emergent multispecies patterns are related to regular patterns concerning individual species.

Zusammenfassung

Ökologische Systeme sind komplex und im Wesentlichen aufgrund der Vielzahl von Interaktionen zwischen ihren Bestandteilen nicht vorhersagbar. Dennoch gibt es allgemeine statistische Muster, die in bestimmten räumlichen und zeitlichen Skalen auftreten. Dies weist auf die Existenz von einigen universellen Prinzipien hinter diesen ökologischen Phänomenen hin, die sogar für die Vorhersage von Phänomenen genutzt werden können, die auf kleineren Skalen auftreten. Diese Allgemeingültigkeiten bestehen aus Häufigkeitsverteilungen von bestimmten makroskopischen Variablen innerhalb höherer Taxa (Körpergröße, Abundanz, Arealgröße), den Beziehungen zwischen diesen Variablen und allgemeinen Mustern des Artenreichtums. Alle Muster stehen in enger Beziehung zueinander und obwohl es nur wenige bedeutende Erklärungsprinzipien gibt, existieren viele alternative Erklärungen. Die Abstimmung zwischen verschiedenen Ansätzen kann ohne eine sorgfältige Formulierung von testbaren Hypothesen und rigorose quantitative empirische Forschung nicht erreicht werden. Zwei besonders vielversprechende Wege ökologische Komplexität zu entwirren beinhalten (1) die Analyse von Invarianten, d.h. universellen quantitativen Beziehungen, die innerhalb verschiedener Systeme beobachtet werden, und (2) detaillierte Analysen der Anatomie von makroökologischen Phänomenen, d.h. Untersuchungen darüber, in welcher Beziehung die auftauchenden Muster von Multi-Arten-Systemen zu regulären Mustern individueller Arten stehen.     

Phosphorylation of the enteropathogenic E. coli receptor by the Src-family kinase c-Fyn triggers actin pedestal formation

Enteropathogenic Escherichia coli (EPEC) causes diarrhoeal disease worldwide. Pathogen adherence to host cells induces reorganization of the actin cytoskeleton into 'pedestal-like' pseudopods beneath the extracellular bacteria. This requires two bacterial virulence factors that mimic a ligand-receptor interaction. EPEC delivers its own receptor, the translocated intimin receptor (Tir), into the target cell plasma membrane, which is phosphorylated on interaction with the bacterial surface protein intimin. Tir phosphorylated on Tyr 474 (ref. 4) binds the cellular adaptor Nck, triggering actin polymerization. Nevertheless, despite its critical role, the mechanism of Tir Tyr 474 phosphorylation remains unknown. Here, by artificially uncoupling Tir delivery and activity, we show that Tir phosphorylation and Nck-dependent pedestal formation require the Src-family kinase (SFK) c-Fyn. SFK inhibitors prevent Tyr 474 phosphorylation, and cells lacking c-fyn are resistant to pedestal formation. c-Fyn exclusively phosphorylates clustered Tir in vitro, and kinase knockdown suppresses Tir phosphorylation and pedestal formation in cultured cells. These results identify the transient interaction with host c-Fyn as a pivotal link between bacterial Tir and the cellular Nck-WASP-Arp2/3 cascade, illuminating a tractable experimental system in which to dissect tyrosine kinase signalling.     

A web services choreography scenario for interoperating bioinformatics applications

Background  

Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow.     

Sucrose density gradient centrifugation and cross-flow filtration methods for the production of arbovirus antigens inactivated by binary ethylenimine

Background  

Sucrose density gradient centrifugation and cross-flow filtration methods have been developed and standardised for the safe and reproducible production of inactivated arbovirus antigens which are appropriate for use in diagnostic serological applications.     

Attenuation of dengue virus infection by adeno-associated virus-mediated siRNA delivery

BACKGROUND: The need for safe and effective treatment of dengue virus (DEN), a class A agent that causes dengue hemorrhagic fever/dengue shock syndrome, has been a critical global priority. An effective vaccine for DEN is not yet available. In this study the possibility of attenuating DEN infection using adeno-associated virus (AAV)-encoded short interfering RNAs (siRNA) was examined in Vero cells and human dendritic cells (DCs). METHODS: A cassette encoding siRNA targeted to a 3' untranslated sequence common to all DEN serotypes was designed and tested for its ability to attenuate DEN infection by use of AAV delivery. RESULTS: Vero cells or DCs infected with AAV-siRNA showed a significant, dose-dependent reduction in DEN infection. Treatment of DCs with AAV-siRNA also decreased the DEN-induced apoptosis of DCs and did not induce significant inflammation. CONCLUSION: These results demonstrate that AAV-mediated siRNA delivery is capable of reducing DEN infection in cells and may be useful in decreasing DEN replication in humans.     

Differential accumulation and pigmenting ability of dietary carotenoids in colorful finches

Many animals develop bright red, orange, or yellow carotenoid pigmentation that they use to attract mates. Colorful carotenoid pigments are acquired from the diet and are either directly incorporated as integumentary colorants or metabolized into other forms before deposition. Because animals often obtain several different carotenoids from plant and animal food sources, it is possible that these pigments are accumulated at different levels in the body and may play unique roles in shaping the ultimate color expression of individuals. We studied patterns of carotenoid accumulation and integumentary pigmentation in two colorful finch species--the American goldfinch (Carduelis tristis) and the zebra finch (Taeniopygia guttata). Both species acquire two main hydroxycarotenoids, lutein and zeaxanthin, from their seed diet but transform these into a series of metabolites that are used as colorful pigments in the plumage (goldfinches only) and beak (both species). We conducted a series of carotenoid-supplementation experiments to investigate the relative extent to which lutein and zeaxanthin are accumulated in blood and increase carotenoid coloration in feathers and bare parts. First, we supplemented the diets of both species with either lutein or zeaxanthin and measured plasma pigment status, feather carotenoid concentration (goldfinches only), and integumentary color. Zeaxanthin-supplemented males grew more colorful feathers and beaks than lutein-supplemented males, and in goldfinches incorporated a different ratio of carotenoids in feathers (favoring the accumulation of canary xanthophyll B). We also fed goldfinches different concentrations of a standard lutein-zeaxanthin mix and found that at physiologically normal and high concentrations, birds circulated proportionally more zeaxanthin over lutein than occurred in the diet. Collectively, these results demonstrate that zeaxanthin is preferentially accumulated in the body and serves as a more potent substrate for pigmentation than lutein in these finches.     

Beyond prostate-specific antigen: new serologic biomarkers for improved diagnosis and management of prostate cancer

The use of total prostate-specific antigen (tPSA) measurement has dramatically improved the ability to detect prostate cancer at earlier stages. However, as the number of men presenting with advanced disease (and high tPSA levels) has decreased, and given the fact that tPSA is highly reflective of benign prostatic hyperplasia, the need has emerged for novel biomarkers specifically associated with prostate cancer in order to improve predictive models. Several new biomarkers have shown promise, and studies continue to investigate the role of these markers in the detection, staging, and prognosis of prostate cancer. As new useful biomarkers continue to emerge, guidelines for their employment, as well as coordination of further research studies, are needed; a systematic, phased, nomogram-based model is a rational way to manage these efforts.     

Endothermy in African platypleurine cicadas: the influence of body size and habitat (Hemiptera: Cicadidae)

The platypleurine cicadas have a wide distribution across Africa and southern Asia. We investigate endothermy as a thermoregulatory strategy in 11 South African species from five genera, with comparisons to the lone ectothermic platypleurine we found, in an attempt to ascertain any influence that habitat and/or body size have on the expression of endothermy in the platypleurine cicadas. Field measurements of body temperature (T(b)) show that these animals regulate T(b) through endogenous heat production. Heat production in the laboratory elevated T(b) to the same range as in animals active in the field. Maximum T(b) measured during calling activity when there was no access to solar radiation ranged from 13.2 degrees to 22.3 degrees C above ambient temperature in the five species measured. The mean T(b) during activity without access to solar radiation did not differ from the mean T(b) during diurnal activity. All platypleurines exhibit a unique behavior for cicadas while warming endogenously, a temperature-dependent telescoping pulsation of the abdomen that probably functions in ventilation. Platypleurines generally call from trunks and branches within the canopy and appear to rely on endothermy even when the sun is available to elevate T(b), in contrast to the facultative endothermy exhibited by New World endothermic species. The two exceptions to this generalization we found within the platypleurines are Platypleura wahlbergi and Albanycada albigera, which were the smallest species studied. The small size of P. wahlbergi appears to have altered their thermoregulatory strategy to one of facultative endothermy, whereby they use the sun when it is available to facilitate increases in T(b). Albanycada albigera is the only ectothermic platypleurine we found. The habitat and host plant association of A. albigera appear to have influenced the choice of ectothermy as a thermoregulatory strategy, as the species possesses the metabolic machinery to elevate to the T(b) range observed in the endothermic species. Therefore, size and habitat appear to influence the expression of thermoregulatory strategies in African platypleurine cicadas.