Missense mutation in the amino terminus of phytochrome A disrupts the nuclear import of the photoreceptor

Phytochromes are the red/far-red photoreceptors in higher plants. Among them, phytochrome A (PHYA) is responsible for the far-red high-irradiance response and for the perception of very low amounts of light, initiating the very-low-fluence response. Here, we report a detailed physiological and molecular characterization of the phyA-5 mutant of Arabidopsis (Arabidopsis thaliana), which displays hyposensitivity to continuous low-intensity far-red light and shows reduced very-low-fluence response and high-irradiance response. Red light-induced degradation of the mutant phyA-5 protein appears to be normal, yet higher residual amounts of phyA-5 are detected in seedlings grown under low-intensity far-red light. We show that (1) the phyA-5 mutant harbors a new missense mutation in the PHYA amino-terminal extension domain and that (2) the complex phenotype of the mutant is caused by reduced nuclear import of phyA-5 under low fluences of far-red light. We also demonstrate that impaired nuclear import of phyA-5 is brought about by weakened binding affinity of the mutant photoreceptor to nuclear import facilitators FHY1 (for FAR-RED ELONGATED HYPOCOTYL1) and FHL (for FHY1-LIKE). Finally, we provide evidence that the signaling and degradation kinetics of constitutively nuclear-localized phyA-5 and phyA are identical. Taken together, our data show that aberrant nucleo/cytoplasmic distribution impairs light-induced degradation of this photoreceptor and that the amino-terminal extension domain mediates the formation of the FHY1/FHL/PHYA far-red-absorbing form complex, whereby it plays a role in regulating the nuclear import of phyA.     

Is Bagging Effective in the Classification of Small-Sample Genomic and Proteomic Data?

There has been considerable interest recently in the application of bagging in the classification of both gene-expression data and protein-abundance mass spectrometry data. The approach is often justified by the improvement it produces on the performance of unstable, overfitting classification rules under small-sample situations. However, the question of real practical interest is whether the ensemble scheme will improve performance of those classifiers sufficiently to beat the performance of single stable, nonoverfitting classifiers, in the case of small-sample genomic and proteomic data sets. To investigate that question, we conducted a detailed empirical study, using publicly-available data sets from published genomic and proteomic studies. We observed that, under t-test and RELIEF filter-based feature selection, bagging generally does a good job of improving the performance of unstable, overfitting classifiers, such as CART decision trees and neural networks, but that improvement was not sufficient to beat the performance of single stable, nonoverfitting classifiers, such as diagonal and plain linear discriminant analysis, or 3-nearest neighbors. Furthermore, as expected, the ensemble method did not improve the performance of these classifiers significantly. Representative experimental results are presented and discussed in this work.     

A dual fluorochrome probe for imaging proteases

Near-infrared fluorescence (NIRF) optical probes have been able to provide a noninvasive assessment of enzyme activity for a number of different enzymes and types of pathology. Here we describe a dual fluorochrome enzyme-activatable probe featuring one NIRF fluorochrome that is activated by protease activity and a second fluorochrome that is protease resistant and serves as an internal standard. The probe was prepared by attaching Cy7 directly to an amino-CLIO, an amine functional cross-linked iron oxide (CLIO) nanoparticle carrier, in a protease resistant manner. Cy5.5 was attached to a protease sensitive polyarginine peptide spacer, also attached to amino-CLIO. In vitro and in vivo the ratio of the Cy5.5 to Cy7 fluorescence was increased by protease, reflecting the increase in Cy5.5 fluorescence by protease in the vicinity of the probe. In vitro and in vivo the absolute values of the Cy5.5 and Cy7 fluorescence reflected lesion size and the distance of lesions from the surface, while the ratio of Cy5.5 to Cy7 fluorescence obtained was constant and independent of lesion size and depth. The dual fluorochrome probe, and related dual wavelength imaging method, represents a novel approach for imaging protease activity in vivo.     

Self-Regulation of Anterior Insula with Real-Time fMRI and Its Behavioral Effects in Obsessive-Compulsive Disorder: A Feasibility Study

Introduction

Obsessive-compulsive disorder (OCD) is a common and chronic condition that can have disabling effects throughout the patient''s lifespan. Frequent symptoms among OCD patients include fear of contamination and washing compulsions. Several studies have shown a link between contamination fears, disgust over-reactivity, and insula activation in OCD. In concordance with the role of insula in disgust processing, new neural models based on neuroimaging studies suggest that abnormally high activations of insula could be implicated in OCD psychopathology, at least in the subgroup of patients with contamination fears and washing compulsions.

Methods

In the current study, we used a Brain Computer Interface (BCI) based on real-time functional magnetic resonance imaging (rtfMRI) to aid OCD patients to achieve down-regulation of the Blood Oxygenation Level Dependent (BOLD) signal in anterior insula. Our first aim was to investigate whether patients with contamination obsessions and washing compulsions can learn to volitionally decrease (down-regulate) activity in the insula in the presence of disgust/anxiety provoking stimuli. Our second aim was to evaluate the effect of down-regulation on clinical, behavioural and physiological changes pertaining to OCD symptoms. Hence, several pre- and post-training measures were performed, i.e., confronting the patient with a disgust/anxiety inducing real-world object (Ecological Disgust Test), and subjective rating and physiological responses (heart rate, skin conductance level) of disgust towards provoking pictures.

Results

Results of this pilot study, performed in 3 patients (2 females), show that OCD patients can gain self-control of the BOLD activity of insula, albeit to different degrees. In two patients positive changes in behaviour in the EDT were observed following the rtfMRI trainings. Behavioural changes were also confirmed by reductions in the negative valence and in the subjective perception of disgust towards symptom provoking images.

Conclusion

Although preliminary, results of this study confirmed that insula down-regulation is possible in patients suffering from OCD, and that volitional decreases of insula activation could be used for symptom alleviation in this disorder.     

Interior decoration: Tropomyosin in actin dynamics and cell migration

Cell migration and invasion requires the precise temporal and spatial orchestration of a variety of biological processes. Filaments of polymerized actin are critical players in these diverse processes, including the regulation of cell anchorage points (both cell-cell and cell-extracellular matrix), the uptake and delivery of molecules via endocytic pathways and the generation of force for both membrane protrusion and retraction. How the actin filaments are specialized for each of these discrete functions is yet to be comprehensively elucidated. The cytoskeletal tropomyosins are a family of actin associating proteins that form head-to-tail polymers which lay in the major groove of polymerized actin filaments. In the present review we summarize the emerging isoform-specific functions of tropomyosins in cell migration and invasion and discuss their potential roles in the specialization of actin filaments for the diverse cellular processes that together regulate cell migration and invasion.Key words: tropomyosin, actin, migration, invasion, cytoskeleton, actin dynamics, adhesionActin is the most abundant protein in eukaryotic cells and is critical for maintaining structural integrity. The polymerization of globular (G)-actin monomers forms actin filaments (F-actin),¹ which play a role in diverse and complex cellular functions including intercellular transport of organelles and vesicles,^2,3 cytokinesis,⁴ apoptosis⁵ and cell motility.⁶ Intricate details describing the molecular scale interactions between regulatory proteins and actin have been extensively investigated but the mechanistic control of diverse actin filament functions remain largely unclear. Recent improvements in analysis techniques⁷ and the use of physiologically relevant models of 3D cell culturing⁸ have now begun to reveal mechanisms of actin cytoskeleton regulation. Accruing evidence suggests that the actin decorating protein tropomyosin is a key regulator of actin filament specialization. Of particular interest is the impact that tropomyosin regulation has on actin filament activity during cell migration and invasion that underpins immunological cell homing, development, wound healing and metastasis.     

Your flaws are my pain: linking empathy to vicarious embarrassment

People vicariously experience embarrassment when observing others' public pratfalls or etiquette violations. In two consecutive studies we investigated the subjective experience and the neural correlates of vicarious embarrassment for others in a broad range of situations. We demonstrated, first, that vicarious embarrassment was experienced regardless of whether the observed protagonist acted accidentally or intentionally and was aware or unaware that he/she was in an embarrassing situation. Second, using functional magnetic resonance imaging (fMRI), we showed that the anterior cingulate cortex and the left anterior insula, two cortical structures typically involved in vicarious feelings of others' pain, are also strongly implicated in experiencing the 'social pain' for others' flaws and pratfalls. This holds true even for situations that engage protagonists not aware of their current predicament. Importantly, the activity in the anterior cingulate cortex and the left anterior insula positively correlated with individual differences in trait empathy. The present findings establish the empathic process as a fundamental prerequisite for vicarious embarrassment experiences, thus connecting affect and cognition to interpersonal processes."When we are living with people who have a delicate sense of propriety, we are in misery on their account when anything unbecoming is committed. So I always feel for and with Charlotte when a person is tipping his chair. She cannot endure it." [Elective Affinities, J. W. Goethe].     

Active-site mobility revealed by the crystal structure of arylmalonate decarboxylase from Bordetella bronchiseptica

Arylmalonate decarboxylase (AMDase) from Bordetella bronchiseptica catalyzes the enantioselective decarboxylation of arylmethylmalonates without the need for an organic cofactor or metal ion. The decarboxylation reaction is of interest for the synthesis of fine chemicals. As basis for an analysis of the catalytic mechanism of AMDase and for a rational enzyme design, we determined the X-ray structure of the enzyme up to 1.9 Å resolution. Like the distantly related aspartate or glutamate racemases, AMDase has an aspartate transcarbamoylase fold consisting of two α/β domains related by a pseudo dyad. However, the domain orientation of AMDase differs by about 30° from that of the glutamate racemases, and also significant differences in active-site structures are observed. In the crystals, four independent subunits showing different conformations of active-site loops are present. This finding is likely to reflect the active-site mobility necessary for catalytic activity.