The population genetic test Tajima's D identifies genes encoding pathogen‐associated molecular patterns and other virulence‐related genes in Ralstonia solanacearum

The detection of pathogen‐associated molecular patterns (PAMPs) by plant pattern recognition receptors (PRRs) is an essential part of plant immunity. Until recently, elf18, an epitope of elongation factor‐Tu (EF‐Tu), was the sole confirmed PAMP of Ralstonia solanacearum, the causal agent of bacterial wilt disease, limiting our understanding of R. solanacearum–plant interactions. Therefore, we set out to identify additional R. solanacearum PAMPs based on the hypothesis that genes encoding PAMPs are under selection to avoid recognition by plant PRRs. We calculated Tajima's D, a population genetic test statistic which identifies genes that do not evolve neutrally, for 3003 genes conserved in 37 R. solanacearum genomes. The screen flagged 49 non‐neutrally evolving genes, including not only EF‐Tu but also the gene for Cold Shock Protein C, which encodes the PAMP csp22. Importantly, an R. solanacearum allele of this PAMP was recently identified in a parallel independent study. Genes coding for efflux pumps, some with known roles in virulence, were also flagged by Tajima's D. We conclude that Tajima's D is a straightforward test to identify genes encoding PAMPs and other virulence‐related genes in plant pathogen genomes.     

Dialect Discrimination by Male Orange-Tufted Sunbirds (Nectarinia osea): Reactions to Own vs. Neighbor Dialects

Male orange-tufted sunbirds ( Nectarinia osea ) exhibit distinct song dialects throughout Israel. Recently, two distinct local dialects with a sharp boundary were discovered in a small (1.5 km²) urban neighborhood densely inhabited by 63 territorial sunbird pairs. We conducted playback experiments to determine song dialect discrimination capability by sunbird males in this neighborhood. Males of both dialects responded significantly more strongly to playback of their own dialect than to that of the adjacent dialect. In spite of the extreme proximity between the two dialect areas, we found no effect of distance to the neighboring dialect on the intensity of any the behavioral responses. We suggest that due to the complex acoustic properties of this urban neighborhood, sunbirds are extremely limited in the number of neighboring males they can assess to establish what the local song is. A stronger response to one's own dialect is therefore expected, and we discuss how local dialects could be maintained via this mechanism regardless of the very small distances between territories and dialect populations.     

Assembling an arsenal,the scorpion way

Background  

For survival, scorpions depend on a wide array of short neurotoxic polypeptides. The venoms of scorpions from the most studied group, the Buthida, are a rich source of small, 23–78 amino acid-long peptides, well packed by either three or four disulfide bridges that affect ion channel function in excitable and non-excitable cells.     

Predicting the receptive range of olfactory receptors

Although the family of genes encoding for olfactory receptors was identified more than 15 years ago, the difficulty of functionally expressing these receptors in an heterologous system has, with only some exceptions, rendered the receptive range of given olfactory receptors largely unknown. Furthermore, even when successfully expressed, the task of probing such a receptor with thousands of odors/ligands remains daunting. Here we provide proof of concept for a solution to this problem. Using computational methods, we tune an electronic nose to the receptive range of an olfactory receptor. We then use this electronic nose to predict the receptors' response to other odorants. Our method can be used to identify the receptive range of olfactory receptors, and can also be applied to other questions involving receptor–ligand interactions in non-olfactory settings.     

2-Aminoethoxydiphenyl-borate (2-APB) increases excitability in pyramidal neurons

Calcium ions (Ca²⁺) released from inositol trisphosphate (IP₃)-sensitive intracellular stores may participate in both the transient and extended regulation of neuronal excitability in neocortical and hippocampal pyramidal neurons. IP₃ receptor (IP₃R) antagonists represent an important tool for dissociating these consequences of IP₃ generation and IP₃R-dependent internal Ca²⁺ release from the effects of other, concurrently stimulated second messenger signaling cascades and Ca²⁺ sources. In this study, we have described the actions of the IP₃R and store-operated Ca²⁺ channel antagonist, 2-aminoethoxydiphenyl-borate (2-APB), on internal Ca²⁺ release and plasma membrane excitability in neocortical and hippocampal pyramidal neurons. Specifically, we found that a dose of 2-APB (100 μM) sufficient for attenuating or blocking IP₃-mediated internal Ca²⁺ release also raised pyramidal neuron excitability. The 2-APB-dependent increase in excitability reversed upon washout and was characterized by an increase in input resistance, a decrease in the delay to action potential onset, an increase in the width of action potentials, a decrease in the magnitude of afterhyperpolarizations (AHPs), and an increase in the magnitude of post-spike afterdepolarizations (ADPs). From these observations, we conclude that 2-APB potently and reversibly increases neuronal excitability, likely via the inhibition of voltage- and Ca²⁺-dependent potassium (K⁺) conductances.     

Evaluation of optimization techniques for variable selection in logistic regression applied to diagnosis of myocardial infarction

Logistic regression is often used to help make medical decisions with binary outcomes. Here we evaluate the use of several methods for selection of variables in logistic regression. We use a large dataset to predict the diagnosis of myocardial infarction in patients reporting to an emergency room with chest pain. Our results indicate that some of the examined methods are well suited for variable selection in logistic regression and that our model, and our myocardial infarction risk calculator, can be an additional tool to aid physicians in myocardial infarction diagnosis.     

Dynein light chain regulates axonal trafficking and synaptic levels of Bassoon

Bassoon and the related protein Piccolo are core components of the presynaptic cytomatrix at the active zone of neurotransmitter release. They are transported on Golgi-derived membranous organelles, called Piccolo-Bassoon transport vesicles (PTVs), from the neuronal soma to distal axonal locations, where they participate in assembling new synapses. Despite their net anterograde transport, PTVs move in both directions within the axon. How PTVs are linked to retrograde motors and the functional significance of their bidirectional transport are unclear. In this study, we report the direct interaction of Bassoon with dynein light chains (DLCs) DLC1 and DLC2, which potentially link PTVs to dynein and myosin V motor complexes. We demonstrate that Bassoon functions as a cargo adapter for retrograde transport and that disruption of the Bassoon–DLC interactions leads to impaired trafficking of Bassoon in neurons and affects the distribution of Bassoon and Piccolo among synapses. These findings reveal a novel function for Bassoon in trafficking and synaptic delivery of active zone material.     

Cluster analysis and classification of heart sounds

Acoustic heart signals, generated by the mechanical processes of the cardiac cycle, carry significant information about the underlying functioning of the cardiovascular system. We describe a computational analysis framework for identifying distinct morphologies of heart sounds and classifying them into physiological states. The analysis framework is based on hierarchical clustering, compact data representation in the feature space of cluster distances and a classification algorithm. We applied the proposed framework on two heart sound datasets, acquired during controlled alternations of the physiological conditions, and analyzed the morphological changes induced to the first heart sound (S1), and the ability to predict physiological variables from the morphology of S1. On the first dataset of 12 subjects, acquired while modulating the respiratory pressure, the algorithm achieved an average accuracy of 82 ± 7% in classifying the level of breathing resistance, and was able to estimate the instantaneous breathing pressure with an average error of 19 ± 6%. A strong correlation of 0.92 was obtained between the estimated and the actual breathing efforts. On the second dataset of 11 subjects, acquired during pharmacological stress tests, the average accuracy in classifying the stress stage was 86 ± 7%. The effects of the chosen raw signal representation, distance metrics and classification algorithm on the performance were studied on both real and simulated data. The results suggest that quantitative heart sound analysis may provide a new non-invasive technique for continuous cardiac monitoring and improved detection of mechanical dysfunctions caused by cardiovascular and cardiopulmonary diseases.     

Assembly of active zone precursor vesicles: obligatory trafficking of presynaptic cytomatrix proteins Bassoon and Piccolo via a trans-Golgi compartment

Neurotransmitter release from presynaptic nerve terminals is restricted to specialized areas of the plasma membrane, so-called active zones. Active zones are characterized by a network of cytoplasmic scaffolding proteins involved in active zone generation and synaptic transmission. To analyze the modes of biogenesis of this cytomatrix, we asked how Bassoon and Piccolo, two prototypic active zone cytomatrix molecules, are delivered to nascent synapses. Although these proteins may be transported via vesicles, little is known about the importance of a vesicular pathway and about molecular determinants of cytomatrix molecule trafficking. We found that Bassoon and Piccolo co-localize with markers of the trans-Golgi network in cultured neurons. Impairing vesicle exit from the Golgi complex, either using brefeldin A, recombinant proteins, or a low temperature block, prevented transport of Bassoon out of the soma. Deleting a newly identified Golgi-binding region of Bassoon impaired subcellular targeting of recombinant Bassoon. Overexpressing this region to specifically block Golgi binding of the endogenous protein reduced the concentration of Bassoon at synapses. These results suggest that, during the period of bulk synaptogenesis, a primordial cytomatrix assembles in a trans-Golgi compartment. They further indicate that transport via Golgi-derived vesicles is essential for delivery of cytomatrix proteins to the synapse. Paradigmatically this establishes Golgi transit as an obligatory step for subcellular trafficking of distinct cytoplasmic scaffolding proteins.