A proteomic analysis of the statocyst endolymph in common cuttlefish (Sepia officinalis): an assessment of acoustic trauma after exposure to sound

Here, the proteomic analysis of the endolymph was performed before and after sound exposure to assess the efects of exposure to low intensity, low frequency sounds on the statocyst endolymph of the Mediterranean common cuttlefsh (Sepia ofcinalis), determining changes in the protein composition of the statocyst endolymph immediately and 24h after sound exposure. Signifcant diferences in protein expression were observed, especially 24h after exposure. A total of 37 spots were signifcantly diferent in exposed specimens, 17 of which were mostly related to stress and cytoskeletal structure. Among the stress proteins eight spots corresponding to eight hemocyanin isoforms were under-expressed possible due to lower oxygen consumption. In addition, cytoskeletal proteins such as tubulin alpha chain and intermediate flament protein were also down-regulated after exposure. Thus, endolymph analysis in the context of acoustic stress allowed us to establish the efects at the proteome level and identify the proteins that are particularly sensitive to this type of trauma.Postprint (published version

Soliton structures in a molecular chain model with saturation

In the present work, we study, by means of a one-dimensional lattice model, the collective excitations corresponding to intra molecular ones of a chain like proteins. It is shown that such excitations are described by the Nonlinear Schrodinger equation with saturation. The solutions obtained here are the bell solitons, bubbles, kinks and crowdons. Since they belong to different sectors on the parametric space, the bubble condensation could give place to some important changes of face in this kind of nonlinear system. Additionally, it is shown that the limiting velocity of the solitons is the velocity of sound waves corresponding to longitudinal vibrations of molecules.Comment: 12 pages, 4 figure

The evolutionary tuning of hearing

After the transition to life on land, tympanic middle ears emerged separately in different groups of tetrapods, facilitating the efficient detection of airborne sounds and paving the way for high frequency sensitivity. The processes that brought about high-frequency hearing in mammals are tightly linked to the accumulation of coding sequence changes in inner ear genes; many of which were selected during evolution. These include proteins involved in hair bundle morphology, mechanotransduction and high endolymphatic potential, somatic electromotility for sound amplification, ribbon synapses for high-fidelity transmission of sound stimuli, and efferent synapses for the modulation of sound amplification. Here, we review the molecular evolutionary processes behind auditory functional innovation. Overall, the evidence to date supports the hypothesis that changes in inner ear proteins were central to the fine tuning of mammalian hearing

A proteomic analysis of the statocyst endolymph in common cuttlefish (Sepia officinalis): an assessment of acoustic trauma after exposure to sound

Recent studies, both in laboratory and sea conditions, have demonstrated damage after sound exposure in the cephalopod statocyst sensory epithelium, which secretes endolymph protein. Here, the proteomic analysis of the endolymph was performed before and after sound exposure to assess the effects of exposure to low intensity, low frequency sounds on the statocyst endolymph of the Mediterranean common cuttlefish (Sepia officinalis), determining changes in the protein composition of the statocyst endolymph immediately and 24 h after sound exposure. Significant differences in protein expression were observed, especially 24 h after exposure. A total of 37 spots were significantly different in exposed specimens, 17 of which were mostly related to stress and cytoskeletal structure. Among the stress proteins eight spots corresponding to eight hemocyanin isoforms were under-expressed possible due to lower oxygen consumption. In addition, cytoskeletal proteins such as tubulin alpha chain and intermediate filament protein were also down-regulated after exposure. Thus, endolymph analysis in the context of acoustic stress allowed us to establish the effects at the proteome level and identify the proteins that are particularly sensitive to this type of trauma

Semiclassical and quantum polarons in crystaline acetanilide

Crystalline acetanilide is a an organic solid with peptide bond structure similar to that of proteins. Two states appear in the amide I spectral region having drastically different properties: one is strongly temperature dependent and disappears at high temperatures while the other is stable at all temperatures. Experimental and theoretical work over the past twenty five years has assigned the former to a selftrapped state while the latter to an extended free exciton state. In this article we review the experimental and theoretical developments on acetanilide paying particular attention to issues that are still pending. Although the interpretation of the states is experimentally sound, we find that specific theoretical comprehension is still lacking. Among the issues that that appear not well understood is the effective dimensionality of the selftrapped polaron and free exciton states.Comment: 28 pages 13 figure

Global Network Alignment

Motivation: High-throughput methods for detecting molecular interactions have lead to a plethora of biological network data with much more yet to come, stimulating the development of techniques for biological network alignment. Analogous to sequence alignment, efficient and reliable network alignment methods will improve our understanding of biological systems. Network alignment is computationally hard. Hence, devising efficient network alignment heuristics is currently one of the foremost challenges in computational biology. 

Results: We present a superior heuristic network alignment algorithm, called Matching-based GRAph ALigner (M-GRAAL), which can process and integrate any number and type of similarity measures between network nodes (e.g., proteins), including, but not limited to, any topological network similarity measure, sequence similarity, functional similarity, and structural similarity. This is efficient in resolving ties in similarity measures and in finding a combination of similarity measures yielding the largest biologically sound alignments. When used to align protein-protein interaction (PPI) networks of various species, M-GRAAL exposes the largest known functional and contiguous regions of network similarity. Hence, we use M-GRAAL’s alignments to predict functions of un-annotated proteins in yeast, human, and bacteria _C. jejuni_ and _E. coli_. Furthermore, using M-GRAAL to compare PPI networks of different herpes viruses, we reconstruct their phylogenetic relationship and our phylogenetic tree is the same as sequenced-based one

EF-hand protein Ca²⁺ buffers regulate Ca²⁺ influx and exocytosis in sensory hair cells

EF-hand Ca²⁺-binding proteins are thought to shape the spatiotemporal properties of cellular Ca²⁺ signaling and are prominently expressed in sensory hair cells in the ear. Here, we combined genetic disruption of parvalbumin-α, calbindin-D28k, and calretinin in mice with patch-clamp recording, in vivo physiology, and mathematical modeling to study their role in Ca²⁺ signaling, exocytosis, and sound encoding at the synapses of inner hair cells (IHCs). IHCs lacking all three proteins showed excessive exocytosis during prolonged depolarizations, despite enhanced Ca²⁺-dependent inactivation of their Ca²⁺ current. Exocytosis of readily releasable vesicles remained unchanged, in accordance with the estimated tight spatial coupling of Ca²⁺ channels and release sites (effective “coupling distance” of 17 nm). Substitution experiments with synthetic Ca²⁺ chelators indicated the presence of endogenous Ca²⁺ buffers equivalent to 1 mM synthetic Ca²⁺-binding sites, approximately half of them with kinetics as fast as 1,2-Bis(2-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid (BAPTA). Synaptic sound encoding was largely unaltered, suggesting that excess exocytosis occurs extrasynaptically. We conclude that EF-hand Ca²⁺ buffers regulate presynaptic IHC function for metabolically efficient sound coding

Non-linear solitary sound waves in lipid membranes and their possible role in biological signaling.

Thesis (Ph. D.)--Boston UniversityBiological macromolecules self-assemble under entropic forces to form a dynamic 20 interfacial medium where the elastic properties arise from the curvature of the entropic potential of the interface. Elastic interfaces should be capable of propagating localized perturbations analogous to sound waves. However, (1) the existence and (2) the possible role of such waves in affecting biological functions remain unexplored. Both these aspects of "sound' as a signaling mechanism in biology are explored experimentally on mixed monolayers of lipids-fluorophores-proteins at the air/water interface as a model biological interface. This study shows - for the first time - that the nonlinear susceptibility near a thermodynamic transition in a lipid monolayer results in nonlinear solitary sound waves that are of 'all or none ' nature. The state dependence of the nonlinear propagation is characterized by studying the velocity-amplitude relationship and results on distance dependence, effect of geometry and collision of solitary waves are presented. Given that the lipid bilayers and real biological membranes have such nonlinearities in their susceptibility diagrams, similar solitary phenomenon should be expected in biological membranes. In fact the observed characteristics of solitary sound waves such as, their all or none nature, a biphasic pulse shape with a long tail and optp-mechano-electro-thermal coupling etc. are strikingly similar to the phenomenon of nerve pulse propagation as observed in single nerve fibers. Finally given the strong correlation between the activity of membrane bound enzymes and the susceptibility and the fact that the later varies within a single solitary pulse, a new thermodynamic basis for biological signaling is proposed. The state of the interface controls both the nature of sound propagation and its impact on incorporated enzymes and proteins. The proof of concept is demonstrated for acetylcholine esterase embedded in a lipid monolayer, where the enzyme is spatiotemporally "knocked out" by a propagating sound wave