Clathrin‐Dependent or Not: Is It Still the Question?

Whether the endocytic uptake of a given molecule is mediated through clathrin-coated pits or not is a classical criterion used to characterize its endocytic pathway(s). Hence, clathrin-dependent endocytosis has been associated with highly selective and efficient uptake, whereas clathrin-independent endocytosis appeared to be confined to bulk uptake of fluid-phase markers. This scholastic view has recently been challenged using newly developed molecular tools that allow for the first time a functional and mechanistic analysis of these less well-characterized clathrin-independent pathways, including caveolar uptake and macropinocytosis. Furthermore, several studies point to a critical role of lateral lipid asymmetry – lipid rafts/microdomains – in membrane sorting. We will discuss the potential role of these structures in endocytosis and the possibility that differential sorting at the plasma membrane predisposes the ensuing intracellular fate of a given molecule as well as its physiological function.     

Slowness: An Objective for Spike-Timing–Dependent Plasticity?

Our nervous system can efficiently recognize objects in spite of changes in contextual variables such as perspective or lighting conditions. Several lines of research have proposed that this ability for invariant recognition is learned by exploiting the fact that object identities typically vary more slowly in time than contextual variables or noise. Here, we study the question of how this “temporal stability” or “slowness” approach can be implemented within the limits of biologically realistic spike-based learning rules. We first show that slow feature analysis, an algorithm that is based on slowness, can be implemented in linear continuous model neurons by means of a modified Hebbian learning rule. This approach provides a link to the trace rule, which is another implementation of slowness learning. Then, we show analytically that for linear Poisson neurons, slowness learning can be implemented by spike-timing–dependent plasticity (STDP) with a specific learning window. By studying the learning dynamics of STDP, we show that for functional interpretations of STDP, it is not the learning window alone that is relevant but rather the convolution of the learning window with the postsynaptic potential. We then derive STDP learning windows that implement slow feature analysis and the “trace rule.” The resulting learning windows are compatible with physiological data both in shape and timescale. Moreover, our analysis shows that the learning window can be split into two functionally different components that are sensitive to reversible and irreversible aspects of the input statistics, respectively. The theory indicates that irreversible input statistics are not in favor of stable weight distributions but may generate oscillatory weight dynamics. Our analysis offers a novel interpretation for the functional role of STDP in physiological neurons.     

The hemolymph proteome of the honeybee: Gel‐based or gel‐free?

The honeybee has an invaluable economic impact and is a model for studying immunity, development and social behavior. The recent sequencing and annotation of the honeybee genome facilitates the study of its hemolymph, which reflects the physiological condition and mediates immune responses. We aimed at making a proteomic reference map of honeybee hemolymph and compared gel‐free and gel‐based techniques. One hundered and four 2‐DE spots corresponding to 62 different proteins were identified. Eight identical 2‐DLC experiments resulted in the identification of 32 unique proteins. One repeat was clearly not representative for the potential of the given 2‐DLC setup. Only 27% of the identified hemolymph proteins were found by both techniques. In addition, we found proteins of three different viruses which creates possibilities for biomarker design. Future hemolymph studies will benefit from this work.     

Alternaria-Induced Release of IL-18 from Damaged Airway Epithelial Cells: An NF-κB Dependent Mechanism of Th2 Differentiation?

Background

A series of epidemiologic studies have identified the fungus Alternaria as a major risk factor for asthma. The airway epithelium plays a critical role in the pathogenesis of allergic asthma. These reports suggest that activated airway epithelial cells can produce cytokines such as IL-25, TSLP and IL-33 that induce Th2 phenotype. However the epithelium-derived products that mediate the pro-asthma effects of Alternaria are not well characterized. We hypothesized that exposure of the airway epithelium to Alternaria releasing cytokines that can induce Th2 differentiation.

Methodology/Principal Finding

We used ELISA to measure human and mouse cytokines. Alternaria extract (ALT-E) induced rapid release of IL-18, but not IL-4, IL-9, IL-13, IL-25, IL-33, or TSLP from cultured normal human bronchial epithelial cells; and in the BAL fluids of naïve mice after challenge with ALT-E. Both microscopic and FACS indicated that this release was associated with necrosis of epithelial cells. ALT-E induced much greater IL-18 release compared to 19 major outdoor allergens. Culture of naïve CD4 cells with rmIL-18 induced Th2 differentiation in the absence of IL-4 and STAT6, and this effect was abrogated by disrupting NF- κB p50 or with a NEMO binding peptide inhibitor.

Conclusion/Significance

Rapid and specific release of IL-18 from Alternaria-exposed damaged airway epithelial cells can directly initiate Th2 differentiation of naïve CD4⁺ T-cells via a unique NF-κB dependent pathway.     

Male genes: X‐pelled or X‐cluded?

Two recent studies by Parisi et al. and Ranz et al., catalogue sex differences in gene expression across the whole genome of the fruit fly Drosophila melanogaster. Both report striking associations of sex-biased gene expression with the X chromosome. Genes with male-biased expression are depauperate on the X chromosome, whereas genes with female-biased expression show weaker evidence of being in excess. A number of evolutionary hypotheses for the expulsion or exclusion of male-biased genes from the X chromosome have been suggested. None is entirely consistent with the available evidence.     

Trophic control of mesopredators in terrestrial ecosystems: top‐down or bottom‐up?

It has been argued that widespread extinctions of top predators have changed terrestrial ecosystem structures through mesopredator release, where increased abundances of medium-sized predators have detrimental effects on prey communities. This top-down concept has received much attention within conservation biology, but few studies have demonstrated the phenomenon. The concept has been criticized since alternative explanations involving bottom-up impacts from bioclimatic effects on ecosystem productivity and from anthropogenic habitat change are rarely considered. We analyse the response of a mesopredator (the red fox) to declines in top predators (wolf and Eurasian lynx) and agricultural expansion over 90 years in Sweden, taking bioclimatic effects into account. We show a top-down mesopredator release effect, but ecosystem productivity determined its strength. The impacts of agricultural activity were mediated by their effects on top predator populations. Thus, both top-down and bottom-up processes need to be understood for effective preservation of biodiversity in anthropogenically transformed ecosystems.     

Does the Type of Disturbance Matter When Restoring Disturbance‐Dependent Grasslands?

The reintroduction of burning is usually viewed as critical for grassland restoration; but its ecological necessity is often untested. On the one hand, fire may be irreplaceable because it suppresses dominant competitors, eliminates litter, and modifies resource availability. On the other hand, its impacts could be mimicked by other disturbances such as mowing or weeding that suppress dominants but without the risks sometimes associated with burning. Using a 5‐year field experiment in a degraded oak savanna, we tested the impacts of fire, cutting and raking, and weeding on two factors critical for restoration: controlling dominant invasive grasses and increasing subordinate native flora. We manipulated the season of treatment application and used sites with different soil depths because both factors influence fire behavior. We found no significant difference among the treatments—all were similarly effective at suppressing exotics and increasing native plant growth. This occurred because light is the primary limiting resource for many native species and each treatment increased its availability. The effectiveness of disturbance for restoration depended more on the timing of application and site factors than on the type of treatment used. Summer disturbances occurred near their reproductive peak of the exotics, so their mortality approached 100%. Positive responses by native species were significantly greater on shallow soils because these areas had higher native diversity prior to treatment. Although likely not applicable to all disturbance‐dependent ecosystems, these results emphasize the importance of testing the effectiveness of alternative restoration treatments prior to their application.     

Analysis of cause of death: Competing risks or progressive illness‐death model?

The analysis of cause of death is increasingly becoming a topic in oncology. It is usually distinguished between disease‐related and disease‐unrelated death. A frequently used approach is to define death as disease‐related when a progression to advanced phases has occurred before, otherwise as disease‐unrelated. The data are often analyzed as competing risks, while a progressive illness‐death model might in fact describe the situation more precisely. In this study, we investigated under which circumstances this misspecification leads to biased estimations of the state occupation probabilities. We simulated data according to the progressive illness‐death model in various settings, analyzed them with a competing risks model and with a progressive illness‐death model and compared them to the true state occupation probabilities. Censoring was either added independently of the status or based on the patients' status. The simulations showed that the censoring mechanism was decisive for the bias while neither the progression hazard nor the Markov property was important. Further, we found a slightly increased standard deviation for the competing risk estimator when censoring was independent of the patients' status. For illustration, both methods were applied to two practical examples of chronic myeloid leukemia (CML): one randomized controlled trial and one registry data set. While in the first case both estimators yielded almost identical results, in the latter case, visible differences were found between both methods.     

Migration of red‐backed shrikes from the Iberian Peninsula: optimal or sub‐optimal detour?

The current Northern Hemisphere migration systems are believed to have arisen since the last glaciation. In many cases, birds do not migrate strait from breeding to non‐breeding areas but fly via a detour. All western European populations of red‐backed shrikes Lanius collurio are assumed to reach their southern African wintering grounds detouring via southeast Europe. Based on theoretical considerations under an optimality framework this detour is apparently optimal. Here, we use individual geolocator data on red‐backed shrikes breeding in Spain to show that these birds do indeed detour via southeast Europe en route to southern Africa where they join other European populations of red‐backed shrikes and return via a similar route in spring. Disregarding potential wind assistance, the routes taken for the tracked birds in autumn were not optimal compared to crossing the barrier directly. For spring migration the situation was quite different with the detour apparently being optimal. However, when considering potential wind assistance estimated total air distances during autumn migration were overall similar and the barrier crossing shorter along the observed routes. We conclude that considering the potential benefit of wind assistance makes the route via southeast Europe likely to be less risky in autumn. However, it cannot be ruled out that other factors, such as following a historical colonisation route could still be important.     

The small‐island effect: fact or artefact?

Positive relationships between species richness and sampling area are perhaps the most pervasive patterns in nature. However, the shape of species–area relationships is often highly variable, for reasons that are poorly understood. One such source of variability is the "small-island effect", which refers to a decrease in the capacity of sampling area to predict species richness on small islands. Small-island effects have been attributed to a variety of processes, including spatial subsidies, habitat characteristics and ocean-born disturbances. Here, we show that small-island effects can be generated by logarithmic data transformations, which are commonly applied to both axes of species–area relationships. To overcome this problem, we derive several null models to test for non-random variability in the capacity of island area to predict species richness and apply them to data sets on island plant communities in Canada and New Zealand. Both archipelagos showed evidence for small-island effects using traditional breakpoint regression techniques on log-log axes. However, null model analyses revealed different results. The capacity of sampling area to predict species richness in the Canadian archipelago was actually lowest at intermediate island size classes. In the New Zealand archipelago, island area was similarly capable of predicting species richness across the full range of island sizes, indicating the small-island effect detected by breakpoint regression is an artifact of logarithm data transformation. Overall results show that commonly used regression techniques can generate spurious small-island effects and that alternative analytic procedures are needed to detect non-random patterns in species richness on small islands.     

Mechanism of Chromosomal Boundary Action: Roadblock,Sink, or Loop?

Boundary elements or insulators subdivide eukaryotic chromosomes into a series of structurally and functionally autonomous domains. They ensure that the action of enhancers and silencers is restricted to the domain in which these regulatory elements reside. Three models, the roadblock, sink/decoy, and topological loop, have been proposed to explain the insulating activity of boundary elements. Strong predictions about how boundaries will function in different experimental contexts can be drawn from these models. In the studies reported here, we have designed assays that test these predictions. The results of our assays are inconsistent with the expectations of the roadblock and sink models. Instead, they support the topological loop model.     

Intrinsic values in nature: Objective good or simply half of an unhelpful dichotomy?

Two generations of conservationists and philosophers have built a strong case for intrinsic values in nature; they are the basis of the normative postulates of conservation biology. I argue that the recognition of intrinsic natural value is a fundamental and non-negotiable aspect of an eco-evolutionary worldview. Recently, relational values, “preferences, principles, and virtues associated with relationships”, have been proposed as a third category of values in nature, which may help to resolve the debate between instrumental and intrinsic valuation. By depicting intrinsic values as part of an unhelpful dichotomy between anthropocentric and ecocentric values, the current assessment of relational values fails to adequately account for the modern philosophical view of intrinsic natural value. The recognition of intrinsic natural value is not merely an academic exercise, but rather a vital aspect of conservation of the biosphere; recognition of value entails the obligation to do what is right, i.e., protect the good. Any attempt to reframe the discussion about values and environmental protection through more formal recognition of relational values will need to more clearly address how relational and intrinsic values coexist and how they can jointly form the basis for nature conservation.     

A Curcumin‐Based 1‐Week Triple Therapy for Eradication of Helicobacter pylori Infection: Something to Learn From Failure?

BACKGROUND: Curcumin is the principal element of turmeric powder extracted from the root of Curcuma longa. Studies on curcumin have demonstrated some anti-Helicobacter pylori activity as well as immunomodulating properties. N-acetylcysteine and lactoferrin with their respective mucolytic and antibacterial activities might also be effective in H. pylori eradication therapy. AIM: To determine if a 7-day non-antibiotic therapy comprised of curcumin, lactoferrin, N-acetylcysteine, and pantoprazole was effective for eradication of H. pylori infection and reduction of gastric inflammation, assessed by serum pepsinogens and relief of symptoms. SUBJECTS AND METHODS: Twenty-five consecutive H. pylori-positive patients (12 males, mean age 50 +/- 12 years, range 31-76) with functional dyspepsia were enrolled. Patients were administered for 7 days curcumin 30 mg b.i.d., bovine lactoferrin 100 mg b.i.d., N-acetylcysteine 600 mg b.i.d., and pantoprazole 20 mg b.i.d. H. pylori status and upper gastrointestinal symptoms were assessed by (13)C-urea breath test and a scale of upper gastrointestinal symptoms intensity (absent, mild, moderate, and severe), as well as a blood test for serum pepsinogens (sPGI, sPGII), gastrin-17 (G-17), and anti-H. pylori IgG (IgG-Hp) at baseline (T0) and after 2 months (T1). RESULTS: Three of 25 patients (12%) were cured of H. pylori infection. A significant decrease in the overall severity of symptoms (T0: 6, interquartile range [IQR]: 4.5-8; T1: 2, IQR: 2-3; p < or = .001), and sPGII (T0: 16 microg/L, IQR: 13-22; T1: 10 microg/L, IQR: 8-16; p < or = .001) and sPGI (T0: 82 microg/L, IQR: 67-97; T1: 74 microg/L, IQR: 62-94; p = .02) levels were observed after 2 months of the treatment. IgG and G-17 values did not significantly decrease after 2 months. CONCLUSIONS: This novel therapy was not effective for H. pylori eradication. However, despite the bacterium persistence, significant improvement of dyspeptic symptoms and reduction of serologic signs of gastric inflammation were observed after 2 months at the end of the 7-day treatment schedule.     

ADARs: allies or enemies? The importance of A‐to‐I RNA editing in human disease: from cancer to HIV‐1

Adenosine deaminases acting on RNA (ADARs) are enzymes that convert adenosine (A) to inosine (I) in nuclear‐encoded RNAs and viral RNAs. The activity of ADARs has been demonstrated to be essential in mammals and serves to fine‐tune different proteins and modulate many molecular pathways. Recent findings have shown that ADAR activity is altered in many pathological tissues. Moreover, it has been shown that modulation of RNA editing is important for cell proliferation and migration, and has a protective effect on ischaemic insults. This review summarises available recent knowledge on A‐to‐I RNA editing and ADAR enzymes, with particular attention given to the emerging role played by these enzymes in cancer, some infectious diseases and immune‐mediated disorders.     

Macro and Microhabitat Associations of the Peter's Tent‐Roosting Bat (Uroderma bilobatum): Human‐Induced Selection and Colonization?

Understanding species‐specific habitat selection is essential to identify how natural systems are assembled and maintained, and how emerging natural and anthropogenic disturbances will affect ecosystem function. In the Neotropics, Peter's tent‐roosting bat (Uroderma bilobatum), known to roost in forests, has become abundant in human‐modified areas. To understand how habitat characteristics in both intact forest and human‐modified areas influence the presence and density of U. bilobatum, we characterized habitat use at two scales (macrohabitat and microhabitat) and used logistic and poisson regressions to determine which habitat characteristics best predicted the presence and density of U. bilobatum within each scale. Moreover, we performed a redundancy analysis to determine which habitat scale explained more variation. As these bats are obligate tent roosters, we used tent as a surrogate for bat presence and density. We found that both macrohabitat and microhabitat scales explained variation in presence and density. Characteristics of the microhabitat scale, however, had higher predictive power, revealing that U. bilobatum preferentially inhabits areas with high density of coconut palms. Coconut palms were introduced recently in the Neotropics and are found only in human‐modified areas. Therefore, we hypothesize that U. bilobatum is expanding its range into these areas following the expanded distribution of this exotic plant species.