Studying molecular motor-based cargo transport: what is real and what is noise?

Noise is a major problem in analyzing tracking data of cargos moved by molecular motors. We use Bayesian statistics to incorporate what is known about the noise in parsing the trajectory of a cargo into a series of constant velocity segments. Tracks with just noise and no underlying motion are fit with constant velocity segments to produce a calibration curve of fit quality versus average segment duration. Fits to tracks of moving cargos are compared to the calibration curves with similar noise. The fit with the optimum number of constant velocity states has the least number of segments needed to match the fit quality of the calibration curve. We have tested this approach using tracks with known underlying motion generated by computer simulations and with a specially designed in vitro experiment. We present the results of using this parsing approach to analyze transport of lipid droplets in Drosophila embryos.     

Are culture-bound syndromes as real as universally-occurring disorders?

This paper asks what it means to say that a disorder is a "real" disorder and then considers whether culture-bound syndromes are real disorders. Following J.L. Austin I note that when we ask whether some supposed culture-bound syndrome is a real disorder we should start by specifying what possible alternatives we have in mind. We might be asking whether the reported behaviours genuinely occur, that is, whether the culture-bound syndrome is a genuine phenomenon as opposed to a myth. We might be wondering whether the condition should rightly be considered a disorder, as opposed to some sort of non-disorder condition (for example, a non-disorder form of deviance, or a potentially valuable condition). We might want to know whether the culture-bound syndrome is really a distinct disorder, in the sense that scientific classification systems should include it as a separate category, or whether it is just a variant of a universally occurring disorder. I argue that some specific difficulties can arise with determining whether a culture-bound syndrome is a real disorder in each of these three senses. However, the frequent assumption that real disorders will necessarily occur universally, and that those that occur only in certain environments are suspicious is not generally justified.     

Abiotic nitrate incorporation in soil: is it real?

In acid forest soils nitrate (NO₃⁻) from anthropogenic nitrogen deposition is retained at levels beyond what can be explained by known biological mechanisms. A number of researchers have hypothesized that abiotic NO₃⁻ incorporation into soil organic matter might be responsible for this phenomenon, however studies have been limited to a few temperate forest sites. The goal of this study was to determine if abiotic NO₃⁻ incorporation is important across a wide range of soil types. We collected 44 soils from a number of different ecosystem types in North and South America and measured the extent of abiotic NO₃⁻ incorporation. Significant abiotic nitrate incorporation did not occur in any of the soils examined. We show that the apparent abiotic incorporation observed in previous studies is likely the result of iron interference with NO₃⁻ measurements. Our results suggest that abiotic NO₃⁻ incorporation is not a likely explanation for the high rates of NO₃⁻ retention observed in some ecosystems.     

Nucleosome positioning: How is it established, and why does it matter?

Packaging of eukaryotic genomes into chromatin affects every process that occurs on DNA. The positioning of nucleosomes on underlying DNA plays a key role in the regulation of these processes, as the nucleosome occludes underlying DNA sequences. Here, we review the literature on mapping nucleosome positions in various organisms, and discuss how nucleosome positions are established, what effect nucleosome positioning has on control of gene expression, and touch on the correlations between chromatin packaging, sequence evolution, and the evolution of gene expression programs.     

Inositol trisphosphate receptor in higher plants: is it real?

The receptor for D-myo-inositol 1,4,5-trisphosphate (InsP3-R) has been well documented in animal cells. It constitutes an important component of the intracellular calcium signalling system. Today the corresponding genes in many species have been sequenced and the antibodies against some of the InsP3-Rs are available. In contrast, very little is known about its plant counterpart. Only a few published works have dealt directly with this topic. This review summarizes the available relevant data and determines some properties of putative plant receptor(s) including the in silico search for its gene in plant genomes, in vivo evidence, its electrophysiology, the parameters of InsP3-induced calcium release and InsP3 binding, immunological cross-reactivity, and subcellular localization. Future progress in this area seems to be inevitable as, despite the efforts, its gene in plants has not been identified yet.     

Responsibility and punishment: whose mind? A response.

Cognitive neuroscience is challenging the Anglo-American approach to criminal responsibility. Critiques, in this issue and elsewhere, are pointing out the deeply flawed psychological assumptions underlying the legal tests for mental incapacity. The critiques themselves, however, may be flawed in looking, as the tests do, at the psychology of the offender. Introducing the strategic structure of punishment into the analysis leads us to consider the psychology of the punisher as the critical locus of cognition informing the responsibility rules. Such an approach both helps to make sense of the counterfactual assumptions about offender psychology embodied in the law and provides a possible explanation for the human conviction of the existence of free will, at least in others.     

Synaptic vesicles: is kissing a matter of competence?

The "kiss-and-run" model of exocytosis and endocytosis predicts that synaptic vesicles can undergo fast and efficient recycling, after fusion with the plasmalemma, without intermixing of membranes. Evidence is mounting from several new experimental approaches that kiss-and-run occurs at synapses. Distinct vesicle pools, which initially were identified in morphological terms, are now being characterized in biochemical and functional terms. In addition, at least two functional recycling pathways, operating on different time scales (from milliseconds to tens of seconds), have been shown to coexist in the same synaptic system, and the two pathways appear to be differentially regulated. Taken together, these data suggest that kiss-and-run operates in parallel with the classical, coated-vesicle recycling. Here, we review recent evidence for kiss-and-run recycling and discuss whether it is a distinct process, dependent on the molecular organization of the fusing vesicle. We propose that vesicles undergo a process of "competence maturation". According to this view, the specific molecular make-up of the vesicles, their location and their interactions with nerve terminal proteins might determine not only the differential availability of the vesicles for fusion and neurotransmitter release but also the recycling path that they will follow.     

Antisense therapeutics: is it as simple as complementary base recognition?

Antisense oligonucleotides provide a simple and efficient approach for developing target-selective drugs because they can modulate gene expression sequence-specifically. Antisense oligonucleotides have also become efficient molecular biological tools to investigate the function of any protein in the cell. As the application of antisense oligonucleotides has expanded, multiple mechanisms of oligonucleotides have been characterized that impede their routine use. Here, we discuss different mechanisms of action of oligonucleotides and the possible ways of minimizing non-antisense-related [corrected] effects to improve their specificity.     

Toxoplasma gondii infection: What is the real situation?

The prevalence of chronic Toxoplasma infections reported in the literature varies enormously. We hypothesize that one factor could be due to the different methods used in the evaluation of infections. Serological evidence of Toxoplasma infections in 450 pregnant women (PW) and 300 HIV-infected patients (HIV) were investigated by the Sabin–Feldman dye test and two other commercial ELISA kits (kit1 and kit2). Anti-Toxoplasma IgG antibodies obtained from the Sabin–Feldman dye test, ELISA kit1 and ELISA kit2 in the PW subjects were 14.7%, 29.6% and 38.7%, and in the HIV subjects were 13%, 34.7% and 36.3%, respectively. So there were significant differences in the seroprevalences when different diagnostic tests were used (P < 0.05). Regarding Sabin–Feldman dye test as the gold standard for anti-Toxoplasma antibodies detection, we found that the sensitivity and specificity of the ELISA kit1 and kit2 was in the range of their specification. However as the two ELISA kits used in our study identified a much higher prevalence of Toxoplasma infections which indicated that false positive cases were being reported. Based on results obtained, it is therefore highly recommended that research workers should be aware that the reports of serological studies in terms of high positive results should be treated with some skepticism until additional precise diagnostic tools are developed.     

Who is where in the Plastisphere,and why does it matter?

To fully understand how plastic is affecting the ocean, we need to understand how marine life interacts directly with it. Besides their ecological relevance, microbes can affect the distribution, degradation and transfer of plastics to the rest of the marine food web. From amplicon sequencing and scanning electron microscopy, we know that a diverse array of microorganisms rapidly associate with plastic marine debris in the form of biofouling and biofilms, also known as the “Plastisphere.” However, observation of multiple microbial interactions in situ, at small spatial scales in the Plastisphere, has been a challenge. In this issue of Molecular Ecology Resources, Schlundt et al. apply the combination labelling and spectral imaging – fluorescence in situ hybridization to study microbial communities on plastic marine debris. The images demonstrate the colocalization of abundant bacterial groups on plastic marine debris at a relatively high taxonomic and spatial resolution while also visualizing biofouling of eukaryotes, such as diatoms and bryozoans. This modern imaging technology provides new possibilities to address questions regarding the ecology of marine microbes on plastic marine debris and describe more specific impacts of plastic pollution in the marine food webs.     

Are Treatments More Effective than Placebos? A Systematic Review and Meta-Analysis

BackgroundPlacebos are widely used in clinical practice in spite of ethical restrictions. Whether such use is justified depends in part on the relative benefit of placebos compared to ‘active’ treatments. A direct test for differences between placebo and ‘active’ treatment effects has not been conducted.ObjectivesWe aimed to test for differences between treatment and placebo effects within similar trial populations.ResultsIn trials with continuous outcomes (n = 115) we found no difference between treatment and placebo effects (MD = −0.29, 95% CI −0.62 to 0.05, P = 0.10). In trials with binary outcomes (n = 37) treatments were significantly more effective than placebos (RRR = 0.72, 95%CI = 0.61 to 0.86, P = 0.0003). Treatment and placebo effects were not different in 22 out of 28 predefined subgroup analyses. Of the six subgroups with differences treatments were more effective than placebos in five. However when all criteria for reducing bias were ruled out (continuous outcomes) placebos were more effective than treatments (MD = 1.59, 95% CI = 0.40 to 2.77, P = 0.009).

Conclusions and Implications

Placebos and treatments often have similar effect sizes. Placebos with comparatively powerful effects can benefit patients either alone or as part of a therapeutic regime, and trials involving such placebos must be adequately blinded.     

Review article. Ozone depletion and increased UV-B radiation: is there a real threat to photosynthesis?

This critical review of recent literature questions earlier predictions that photosynthetic productivity of higher plants is vulnerable to increased ultraviolet-B (UV-B) radiation as a result of stratospheric ozone (O3) depletion. Direct UV-B-induced inhibition of photosynthetic competence is observed only at high UV-B irradiances and primarily involves the loss of soluble Calvin cycle enzymes and adaxial stomatal closure in amphistomatous plants. However, even under these extreme UV-B exposures, acclimation (e.g. induction of UV-B absorbing flavonoids) can protect the photosynthetic processes. In plants irradiated with UV-B throughout development a reduction in productivity is usually associated with a reduced ability to intercept light (i.e. smaller leaf area) and not an inhibition of photosynthetic competence. Finally, a review of field experiments utilizing realistic UV-B enhancement is made to evaluate whether the mechanisms involved in UV-B-induced depressions of photosynthesis are likely to impact on the photosynthetic productivity of crops and natural vegetation in the future. Predictions of plant responses to O3 depletion are suspect from square-wave irradiance experiments due to the increased sensitivity of plants to UV-B at relatively low photosynthetically-active photon flux densities (PPFD) and ultraviolet-A (UV-A) irradiances. Realistic modulated UV-B irradiances in the field do not appear to have any significant effects on photosynthetic competence or light-interception. It is concluded that O3 depletion and the concurrent rise in UV-B irradiance is not a direct threat to photosynthetic productivity of crops and natural vegetation.Key words: Biomass, development, ozone depletion, photosynthesis, ultraviolet-B.      

Xenotransplantation: is the risk of viral infection as great as we thought?

Two major hurdles remain before xenotransplantation can enter the clinic. The first is the more technical issue of being able to overcome the human immune response that leads to rejection of transplanted organs/cells from other species. The second, reviewed here, concerns the potential risk of inadvertent transfer of animal viruses present in the xenotransplant that are able to infect the human recipient. The threat from viruses is a particularly contentious topic because it poses a risk not only to those individuals who receive xenotransplants, but also to healthy individuals who come into contact, either directly or indirectly, with the xenotransplant recipient. In this review, we describe some of the virus types, in addition to the much discussed porcine endogenous retroviruses that might cross the species barrier, and assess the risk of such viruses causing disease in human hosts.