Combining inference from evolution and geometric probability in protein structure evaluation

Starting from the hypothesis that evolutionarily important residues form a spatially limited cluster in a protein's native fold, we discuss the possibility of detecting a non-native structure based on the absence of such clustering. The relevant residues are determined using the Evolutionary Trace method. We propose a quantity to measure clustering of the selected residues on the structure and show that the exact values for its average and variance over several ensembles of interest can be found. This enables us to study the behavior of the associated z-scores. Since our approach rests on an analytic result, it proves to be general, customizable, and computationally fast. We find that clustering is indeed detectable in a large representative protein set. Furthermore, we show that non-native structures tend to achieve lower residue-clustering z-scores than those attained by the native folds. The most important conclusion that we draw from this work is that consistency between structural and evolutionary information, manifested in clustering of key residues, imposes powerful constraints on the conformational space of a protein.     

Pathological shear stress directly regulates platelet alphaIIbbeta3 signaling

Integrin mechanotransduction is a ubiquitous biological process. Mechanical forces are transduced transmembranously by an integrin's ligand-bound extracellular domain through its -subunit's cytoplasmic domain connected to the cytoskeleton. This often culminates in the activation of tyrosine kinases directing cell responses. The delicate balance between hemostasis and thrombosis requires exquisitely fine-tuned integrin function, and balance is maintained in vivo despite that the major platelet integrin _IIb3 is continuously subjected to frictional or shearing forces generated by laminar blood flow. To test the hypothesis that platelet function is regulated by the direct effects of mechanical forces on _IIb3, we examined _IIb3/cytoskeletal interactions in human platelets exposed to shear stress in a cone-plate viscometer. We observed that -actinin, myosin heavy chain, and Syk coimmunoprecipitate with _IIb3 in resting platelets and that 120 dyn/cm² shear stress leads to their disassociation from _IIb3. Shear-induced disassociation of -actinin and myosin heavy chain from the ₃ tail is unaffected by blocking von Willebrand factor (VWF) binding to glycoprotein (Gp) Ib-IX-V but abolished by blocking VWF binding to _IIb3. Syk's disassociation from ₃ is inhibited when VWF binding to either GpIb-IX-V or _IIb3 is blocked. Shear stress-induced phosphorylation of SLP-76 and its association with tyrosine-phosphorylated adhesion and degranulation-promoting adapter protein are inhibited by blocking ligand binding to _IIb3 but not by blocking ligand binding to GpIb-IX-V. Chinese hamster ovary cells expressing _IIb3 with ₃ truncated of its cytoskeletal binding domains demonstrate diminished shear-dependent adhesion and cohesion. These results support the hypothesis that shear stress directly modulates _IIb3 function and suggest that shear-induced _IIb3-mediated signaling contributes to the regulation of platelet aggregation by directing the release of constraining cytoskeletal elements from the ₃-tail. platelets; mechanoreceptor; integrin; shear stress; signal transduction     

Rapid detection of Mycoplasma pneumoniae in clinical samples by real-time PCR

M. pneumoniae is a common causative agent of community-acquired pneumonia in children. The diagnosis of such infections is usually based on serology using complement fixation or, more recently, enzyme-immuno assays. PCR has been shown to be a promising alternative. We have evaluated a real-time PCR assay targeting the P1 adhesion protein gene and compared it to a conventional semi-nested PCR assay with the 16S rDNA as target. Comparison of 147 specimens from 48 patients showed an overall agreement of 97.4%. Real-time PCR proved to be of equal value on clinical specimens as conventional PCR regarding sensitivity and specificity, but is clearly advantageous regarding speed, handling and number of samples that can be analyzed per run.     

Survival synchronicity in two avian insectivore communities

Climate change is forecast to increase climatic variability, in particular the occurrence of extreme events. Consequently, it is imperative to understand how climatic variation influences the dynamics of communities. We investigated synchronicity in survival in response to climatic variation among bird communities occupying habitats that differed in climatic seasonality: a more seasonal wetland and a less seasonal fynbos shrubland in South Africa. We predicted higher synchronicity at the wetland than at the shrubland because there was more potential for weather to induce variation in survival at this climatically more variable site. We estimated survival from ringing data for four wetland species and three fynbos species in hierarchical models with an asynchronous (species-specific) variance component and a synchronous (common) variance component. Comparing models including and excluding a climatic covariate enabled us to estimate the effect of climatic variation as a synchronizing and desynchronizing agent on survival. As hypothesized, synchronicity in survival was substantially greater at the more seasonal wetland than at the climatically more stable fynbos site: 0.50 (95% credible interval 0.01–1.92 on the logit scale) and 0.03 (0.00001–0.19), respectively. Similarly, asynchronicity in survival was greater for wetland species than for fynbos species. However, we found no clear evidence that weather affected survival. We provide the first survival estimates of several African endemic birds and the first estimates of synchronicity and asynchronicity in survival of communities outside the strongly seasonal northern temperate zone. Our results suggest that the relative magnitude of synchronicity and asynchronicity varies among communities and support the idea that environmental variability induces synchronicity.     

Nestboxes and immigration drive the growth of an urban Peregrine Falcon Falco peregrinus population

Drivers of wildlife population dynamics are generally numerous and interacting. Some of these drivers may impact demographic processes that are difficult to estimate, such as immigration into the focal population. Populations may furthermore be small and subject to demographic stochasticity. All of these factors contribute to blur the causal relationship between past management action and current population trends. The urban Peregrine Falcon Falco peregrinus population in Cape Town, South Africa, increased from three pairs in 1997 to 18 pairs in 2010. Nestboxes were installed over this period to manage the interface between new urban pairs of Falcons and the human users of colonized buildings, and incidentally to improve breeding success. We used integrated population models (IPMs) formally to combine information from a capture–mark–recapture study, monitoring of reproductive success and counts of population size. As all local demographic processes were directly observed, the IPM approach also allowed us to estimate immigration by difference. The provision of nestboxes, as a possible stimulant of population growth, improved breeding success and accounted for an estimated 3–26% of the population increase. The most important driver of growth, however, was immigration. Despite low sample sizes, the IPM approach allowed us to obtain relatively precise estimates of the population‐level impact of nestbox deployment. The goal of conservation interventions is often to increase population size, so the effectiveness of such interventions should ideally be assessed at the population level. IPMs are powerful tools in this context for combining demographic information that may be limited due to small population size or practical constraints on monitoring. Our study quantitatively documented both the immigration process that led to growth of a small population and the effect of a management action that helped the process.     

Age-specific fitness components and their temporal variation in the barn owl

Theory predicts that temporal variability plays an important role in the evolution of life histories, but empirical studies evaluating this prediction are rare. In constant environments, fitness can be measured by the population growth rate lambda, and the sensitivity of lambda to changes in fitness components estimates selection on these traits. In variable environments, fitness is measured by the stochastic growth rate lambda(S), and stochastic sensitivities estimate selection pressure. Here we examine age-specific schedules for reproduction and survival in a barn owl population (Tyto alba). We estimated how temporal variability affected fitness and selection, accounting for sampling variance. Despite large sample sizes of old individuals, we found no strong evidence for senescence. The most variable fitness components were associated with reproduction. Survival was less variable. Stochastic simulations showed that the observed variation decreased fitness by about 30%, but the sensitivities of lambda and lambda(S) to changes in all fitness components were almost equal, suggesting that temporal variation had negligible effects on selection. We obtained these results despite high observed variability in the fitness components and relatively short generation time of the study organism, a situation in which temporal variability should be particularly important for natural selection and early senescence is expected.     

Patterns of bird migration phenology in South Africa suggest northern hemisphere climate as the most consistent driver of change

Current knowledge of phenological shifts in Palearctic bird migration is largely based on data collected on migrants at their breeding grounds; little is known about the phenology of these birds at their nonbreeding grounds, and even less about that of intra‐African migrants. Because climate change patterns are not uniform across the globe, we can expect regional disparities in bird phenological responses. It is also likely that they vary across species, as species show differences in the strength of affinities they have with particular habitats and environments. Here, we examine the arrival and departure of nine Palearctic and seven intra‐African migratory species in the central Highveld of South Africa, where the former spend their nonbreeding season and the latter their breeding season. Using novel analytical methods based on bird atlas data, we show phenological shifts in migration of five species – red‐backed shrike, spotted flycatcher, common sandpiper, white‐winged tern (Palearctic migrants), and diederik cuckoo (intra‐African migrant) – between two atlas periods: 1987–1991 and 2007–2012. During this time period, Palearctic migrants advanced their departure from their South African nonbreeding grounds. This trend was mainly driven by waterbirds. No consistent changes were observed for intra‐African migrants. Our results suggest that the most consistent drivers of migration phenological shifts act in the northern hemisphere, probably at the breeding grounds.     

Beiträge zur Lichtkeimung von Amarantus caudatus L. und Phacelia tanacetifolia Benth

Ohne ZusammenfassungMit 10 Textabbildungen.     

Untersuchungen über die Symbiose von Tieren mit Pilzen und Bakterien

Ohne ZusammenfassungEs ist mir eine angenehme Pflicht, auch an dieser Stelle der Deutschen Forschungsgemeinschaft, mit deren Unterstützung die vorliegenden Untersuchungen durchgeführt wurden, meinen besten Dank auszusprechen. Zu besonderem Dank fühle ich mich Herrn Prof. Dr. W. Schwartz für die Anregung zu dieser Arbeit, für viele Ratschläge und alle erhaltene Förderung verpflichtet.