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.     

The role of LPA1 in formation of synapses among cultured hippocampal neurons

We studied the lysophosphatidic acid receptor-1 (LPA1) gene, which we found to be expressed endogenously in cultured hippocampal neurons, and in vivo in young (1-week-old) rat brain slices. Overexpressed green fluorescent protein (GFP)-tagged, membrane-associated LPA1 accumulated in a punctate manner over the entire dendritic tree and caused an increase in dendritic spine density. About half of the dendritic spines in the LPA1-transfected neurons displayed distinct fluorescent puncta, and this subset of spines was also substantially larger than puncta-free, LPA1-transfected or control GFP spines. This phenotype could also be seen in cells transfected with a ligand-binding, defective mutant and is therefore not dependent on interaction with an ambient ligand. While spontaneous miniature excitatory synaptic currents were of the same amplitudes, they decayed slower in LPA1-transfected neurons compared with GFP controls. We propose that LPA1 may play a role in the formation and modulation of the dendritic spine synapse.     

Strain driven transport for bone modeling at the periosteal surface

Bone modeling and remodeling has been the subject of extensive experimental studies. There have been several mathematical models proposed to explain the observed behavior, as well. A different approach is taken here in which the bone is treated from a macroscopic view point. In this investigation, a one-dimensional analytical model is used to shed light on the factors which play the greatest role in modeling or growth of cortical bone at the periosteal surface. It is presumed that bone growth is promoted when increased amounts of bone nutrients, such as nitric oxide synthase (NOS) or messenger molecules, such as prostaglandin E₂ (PGE₂), seep out to the periosteal surface of cortical bone and are absorbed by osteoblasts. The transport of the bone nutrients is assumed to be a strain controlled process. Equations for the flux of these nutrients are written for a one-dimensional model of a long bone. The obtained partial differential equation is linearized and solved analytically. Based upon the seepage of nutrients out of the bone, the effect of loading frequency, number of cycles and strain level is examined for several experiments that were found in the literature. It is seen that bone nutrient seepage is greatest on the tensile side of the bone; this location coincides with the greatest amount of bone modeling.     

First structures of an active bacterial tyrosinase reveal copper plasticity

Tyrosinase is a member of the type 3 copper enzyme family that is involved in the production of melanin in a wide range of organisms. The crystal structures of a tyrosinase from Bacillus megaterium were determined at a resolution of 2.0-2.3 Å. The enzyme crystallized as a dimer in the asymmetric unit and was shown to be active in crystal. The overall monomeric structure is similar to that of the monomer of the previously determined tyrosinase from Streptomyces castaneoglobisporus, but it does not contain an accessory Cu-binding “caddie” protein. Two Cu(II) ions, serving as the major cofactors within the active site, are coordinated by six conserved histidine residues. However, determination of structures under different conditions shows varying occupancies and positions of the copper ions. This apparent mobility in copper binding modes indicates that there is a pathway by which copper is accumulated or lost by the enzyme. Additionally, we suggest that residues R209 and V218, situated in a second shell of residues surrounding the active site, play a role in substrate binding orientation based on their flexibility and position. The determination of a structure with the inhibitor kojic acid, the first tyrosinase structure with a bound ligand, revealed additional residues involved in the positioning of substrates in the active site. Comparison of wild-type structures with the structure of the site-specific variant R209H, which possesses a higher monophenolase/diphenolase activity ratio, lends further support to a previously suggested mechanism by which monophenolic substrates dock mainly to CuA.