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  • Contrasting effects of ischemia on the kinetics of membrane voltage and intracellular calcium transient underlie electrical alternans.

    12 December 2017

    Repolarization alternans has been considered a strong marker of electrical instability. The objective of this study was to investigate the hypothesis that ischemia-induced contrasting effects on the kinetics of membrane voltage and intracellular calcium transient (Ca(i)T) can explain the vulnerability of the ischemic heart to repolarization alternans. Ischemia-induced changes in action potential (AP) and Ca(i)T resulting in alternans were investigated in perfused Langendorff guinea pig hearts subjected to 10-15 min of global no-flow ischemia followed by 10-15 min of reperfusion. The heart was stained with 100 microl of rhod-2 AM and 25 microl of RH-237, and AP and Ca(i)T were simultaneously recorded with an optical mapping system of two 16 x 16 photodiode arrays. Ischemia was associated with shortening of AP duration (D) but delayed upstroke, broadening of peak, and slowed decay of Ca(i)T resulting in a significant increase of Ca(i)T-D. The changes in APD were spatially heterogeneous in contrast to a more spatially homogeneous lengthening of Ca(i)T-D. Ca(i)T alternans could be consistently induced with the introduction of a shorter cycle when the upstroke of the AP occurred before complete relaxation of the previous Ca(i)T and generated a reduced Ca(i)T. However, alternans of Ca(i)T was not necessarily associated with alternans of APD, and this was correlated with the degree of spatially heterogeneous shortening of APD. Sites with less shortening of APD developed alternans of both Ca(i)T and APD, whereas sites with greater shortening of APD could develop a similar degree of Ca(i)T alternans but slight or no APD alternans. This resulted in significant spatial dispersion of APD. The study shows that the contrasting effects of ischemia on the duration of AP and Ca(i)T and, in particular, on their spatial distribution explain the vulnerability of ischemic heart to alternans and the increased dispersion of repolarization during alternans.

  • Global organization of dynamics in oscillatory heterogeneous excitable media.

    12 December 2017

    An oscillatory heterogeneous excitable medium undergoes a transition from periodic target patterns to a bursting rhythm driven by the spontaneous initiation and termination of spiral waves as coupling or density is reduced. We illustrate these phenomena in monolayers of chick embryonic heart cells using calcium-sensitive fluorescent dyes. These results are modeled in a heterogeneous cellular automaton in which the neighborhood of interaction and cell density is modified. Parameters that give rise to bursting rhythms are organized in distinct zones in parameter space, leading to a global organization that should be applicable to the dynamics in a large class of excitable media.

  • The role of photon scattering in voltage-calcium fluorescent recordings of ventricular fibrillation.

    12 December 2017

    Recent optical mapping studies of cardiac tissue suggest that membrane voltage (V(m)) and intracellular calcium concentrations (Ca) become dissociated during ventricular fibrillation (VF), generating a proarrhythmic substrate. However, experimental methods used in these studies may accentuate measured dissociation due to differences in fluorescent emission wavelengths of optical voltage/calcium (V(opt)/Ca(opt)) signals. Here, we simulate dual voltage-calcium optical mapping experiments using a monodomain-Luo-Rudy ventricular-tissue model coupled to a photon-diffusion model. Dissociation of both electrical, V(m)/Ca, and optical, V(opt)/Ca(opt), signals is quantified by calculating mutual information (MI) for VF and rapid pacing protocols. We find that photon scattering decreases MI of V(opt)/Ca(opt) signals by 23% compared to unscattered V(m)/Ca signals during VF. Scattering effects are amplified by increasing wavelength separation between fluorescent voltage/calcium signals and respective measurement-location misalignment. In contrast, photon scattering does not affect MI during rapid pacing, but high calcium dye affinity can decrease MI by attenuating alternans in Ca(opt) but not in V(opt). We conclude that some dissociation exists between voltage and calcium at the cellular level during VF, but MI differences are amplified by current optical mapping methods.

  • The role of heterogeneities and intercellular coupling in wave propagation in cardiac tissue.

    12 December 2017

    Electrical heterogeneities play a role in the initiation of cardiac arrhythmias. In certain pathological conditions such as ischaemia, current sinks can develop in the diseased cardiac tissue. In this study, we investigate the effects of changing the amount of heterogeneity and intercellular coupling on wavefront stability in a cardiac cell culture system and a mathematical model of excitable media. In both systems, we observe three types of behaviour: plane wave propagation without breakup, plane wave breakup into spiral waves and plane wave block. In the theoretical model, we observe a linear decrease in propagation velocity as the number of heterogeneities is increased, followed by a rapid, nonlinear decrease to zero. The linear decrease results from the heterogeneities acting independently on the wavefront. A general scaling argument that considers the degree of system heterogeneity and the properties of the excitable medium is used to derive a dimensionless parameter that describes the interaction of the wavefront with the heterogeneities.

  • Dynamical mechanism for subcellular alternans in cardiac myocytes.

    12 December 2017

    RATIONALE: Cardiac repolarization alternans is an arrhythmogenic rhythm disturbance, manifested in individual myocytes as a beat-to-beat alternation of action potential durations and intracellular calcium transient magnitudes. Recent experimental studies have reported "subcellular alternans," in which distinct regions of an individual cell are seen to have counterphase calcium alternations, but the mechanism by which this occurs is not well understood. Although previous theoretical work has proposed a possible dynamical mechanism for subcellular alternans formation, no direct evidence for this mechanism has been reported in vitro. Rather, experimental studies have generally invoked fixed subcellular heterogeneities in calcium-cycling characteristics as the mechanism of subcellular alternans formation. OBJECTIVE: In this study, we have generalized the previously proposed dynamical mechanism to predict a simple pacing algorithm by which subcellular alternans can be induced in isolated cardiac myocytes in the presence or absence of fixed subcellular heterogeneity. We aimed to verify this hypothesis using computational modeling and to confirm it experimentally in isolated cardiac myocytes. Furthermore, we hypothesized that this dynamical mechanism may account for previous reports of subcellular alternans seen in statically paced, intact tissue. METHODS AND RESULTS: Using a physiologically realistic computational model of a cardiac myocyte, we show that our predicted pacing algorithm induces subcellular alternans in a manner consistent with theoretical predictions. We then use a combination of real-time electrophysiology and fluorescent calcium imaging to implement this protocol experimentally and show that it robustly induces subcellular alternans in isolated guinea pig ventricular myocytes. Finally, we use computational modeling to demonstrate that subcellular alternans can indeed be dynamically induced during static pacing of 1D fibers of myocytes during tissue-level spatially discordant alternans. CONCLUSION: Here we provide the first direct experimental evidence that subcellular alternans can be dynamically induced in cardiac myocytes. This proposed mechanism may contribute to subcellular alternans formation in the intact heart.

  • Spiral wave generation in heterogeneous excitable media.

    12 December 2017

    As the coupling in a heterogeneous excitable medium is reduced, three different types of behavior are encountered: plane waves propagate without breaking up, plane waves break up into spiral waves, and plane waves block. We illustrate these phenomena in monolayers of chick embryonic heart cells using calcium sensitive fluorescent dyes. Following the addition of heptanol, an agent that reduces the electrical coupling between cells, we observe breakup of spiral waves. These results are modeled in a heterogeneous cellular automaton model in which the neighborhood of interaction is modified.

  • The Pfam protein families database

    12 December 2017

    Pfam is a widely used database of protein families, currently containing more than 13 000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that have occurred since our 2010 NAR paper (release 24.0). Over the last 2 years, we have generated 1840 new families and increased coverage of the UniProt Knowledgebase (UniProtKB) to nearly 80%. Notably, we have taken the step of opening up the annotation of our families to the Wikipedia community, by linking Pfam families to relevant Wikipedia pages and encouraging the Pfam and Wikipedia communities to improve and expand those pages. We continue to improve the Pfam website and add new visualizations, such as the 'sunburst' representation of taxonomic distribution of families. In this work we additionally address two topics that will be of particular interest to the Pfam community. First, we explain the definition and use of family-specific, manually curated gathering thresholds. Second, we discuss some of the features of domains of unknown function (also known as DUFs), which constitute a rapidly growing class of families within Pfam. © The Author(s) 2011. Published by Oxford University Press.

  • The Pfam protein families database.

    12 December 2017

    Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).

  • PairsDB atlas of protein sequence space

    27 October 2017

    Sequence similarity/database searching is a cornerstone of molecular biology. PairsDB is a database intended to make exploring protein sequences and their similarity relationships quick and easy. Behind PairsDB is a comprehensive collection of protein sequences and BLAST and PSI-BLAST alignments between them. Instead of running BLAST or PSI-BLAST individually on each request, results are retrieved instantaneously from a database of pre-computed alignments. Filtering options allow you to find a set of sequences satisfying a set of criteria-for example, all human proteins with solved structure and without transmembrane segments. PairsDB is continually updated and covers all sequences in Uniprot. The data is stored in a MySQL relational database. Data files will be made available for download at ftp://nic.funet.fi/pub/sci/molbio. PairsDB can also be accessed interactively at. PairsDB data is a valuable platform to build various downstream automated analysis pipelines. For example, the graph of all-against-all similarity relationships is the starting point for clustering protein families, delineating domains, improving alignment accuracy by consistency measures, and defining orthologous genes. Moreover, query-anchored stacked sequence alignments, profiles and consensus sequences are useful in studies of sequence conservation patterns for clues about possible functional sites. © 2007 The Author(s).