Isolation of Human Atrial Myocytes for Simultaneous Measurements of Ca2+ Transients and Membrane Currents

The study of electrophysiological properties of cardiac ion channels with the patch-clamp technique and the exploration of cardiac cellular Ca²⁺ handling abnormalities requires isolated cardiomyocytes. In addition, the possibility to investigate myocytes from patients using these techniques is an invaluable requirement to elucidate the molecular basis of cardiac diseases such as atrial fibrillation (AF).¹ Here we describe a method for isolation of human atrial myocytes which are suitable for both patch-clamp studies and simultaneous measurements of intracellular Ca²⁺ concentrations. First, right atrial appendages obtained from patients undergoing open heart surgery are chopped into small tissue chunks ("chunk method") and washed in Ca²⁺-free solution. Then the tissue chunks are digested in collagenase and protease containing solutions with 20 μM Ca²⁺. Thereafter, the isolated myocytes are harvested by filtration and centrifugation of the tissue suspension. Finally, the Ca²⁺ concentration in the cell storage solution is adjusted stepwise to 0.2 mM. We briefly discuss the meaning of Ca²⁺ and Ca²⁺ buffering during the isolation process and also provide representative recordings of action potentials and membrane currents, both together with simultaneous Ca²⁺ transient measurements, performed in these isolated myocytes.     

Fast Micro-iontophoresis of Glutamate and GABA: A Useful Tool to Investigate Synaptic Integration

One of the fundamental interests in neuroscience is to understand the integration of excitatory and inhibitory inputs along the very complex structure of the dendritic tree, which eventually leads to neuronal output of action potentials at the axon. The influence of diverse spatial and temporal parameters of specific synaptic input on neuronal output is currently under investigation, e.g. the distance-dependent attenuation of dendritic inputs, the location-dependent interaction of spatially segregated inputs, the influence of GABAergig inhibition on excitatory integration, linear and non-linear integration modes, and many more.With fast micro-iontophoresis of glutamate and GABA it is possible to precisely investigate the spatial and temporal integration of glutamatergic excitation and GABAergic inhibition. Critical technical requirements are either a triggered fluorescent lamp, light-emitting diode (LED), or a two-photon scanning microscope to visualize dendritic branches without introducing significant photo-damage of the tissue. Furthermore, it is very important to have a micro-iontophoresis amplifier that allows for fast capacitance compensation of high resistance pipettes. Another crucial point is that no transmitter is involuntarily released by the pipette during the experiment.Once established, this technique will give reliable and reproducible signals with a high neurotransmitter and location specificity. Compared to glutamate and GABA uncaging, fast iontophoresis allows using both transmitters at the same time but at very distant locations without limitation to the field of view. There are also advantages compared to focal electrical stimulation of axons: with micro-iontophoresis the location of the input site is definitely known and it is sure that only the neurotransmitter of interest is released. However it has to be considered that with micro-iontophoresis only the postsynapse is activated and presynaptic aspects of neurotransmitter release are not resolved. In this article we demonstrate how to set up micro-iontophoresis in brain slice experiments.     

Divalent cations permeation in a Ca2+ non-conducting skeletal muscle dihydropyridine receptor mouse model

In response to excitation of skeletal muscle fibers, trains of action potentials induce changes in the configuration of the dihydropyridine receptor (DHPR) anchored in the tubular membrane which opens the Ca²⁺ release channel in the sarcoplasmic reticulum membrane. The DHPR also functions as a voltage-gated Ca²⁺ channel that conducts L-type Ca²⁺ currents routinely recorded in mammalian muscle fibers, which role was debated for more than four decades. Recently, to allow a closer look into the role of DHPR Ca²⁺ influx in mammalian muscle, a knock-in (ki) mouse model (ncDHPR) carrying mutation N617D (adjacent to domain II selectivity filter E) in the DHPRα_1S subunit abolishing Ca²⁺ permeation through the channel was generated [Dayal et al., 2017]. In the present study, the Mn²⁺ quenching technique was initially intended to be used on voltage-clamped muscle fibers from this mouse to determine whether Ca²⁺ influx through a pathway distinct from DHPR may occur to compensate for the absence of DHPR Ca²⁺ influx. Surprisingly, while N617D DHPR muscle fibers of the ki mouse do not conduct Ca²⁺, Mn²⁺ entry and subsequent quenching did occur because Mn²⁺ was able to permeate and produce L-type currents through N617D DHPR. N617D DHPR was also found to conduct Ba²⁺ and Ba²⁺ currents were strongly blocked by external Ca²⁺. Ba²⁺ permeation was smaller, current kinetics slower and Ca²⁺ block more potent than in wild-type DHPR. These results indicate that residue N617 when replaced by the negatively charged residue D is suitably located at entrance of the pore to trap external Ca²⁺ impeding in this way permeation. Because Ba²⁺ binds with lower affinity to D, Ba²⁺ currents occur, but with reduced amplitudes as compared to Ba²⁺ currents through wild-type channels. We conclude that mutations located outside the selectivity filter influence channel permeation and possibly channel gating in a fully differentiated skeletal muscle environment.     

Architecture of the Pol III–clamp–exonuclease complex reveals key roles of the exonuclease subunit in processive DNA synthesis and repair

DNA polymerase III (Pol III) is the catalytic α subunit of the bacterial DNA Polymerase III holoenzyme. To reach maximum activity, Pol III binds to the DNA sliding clamp β and the exonuclease ε that provide processivity and proofreading, respectively. Here, we characterize the architecture of the Pol III–clamp–exonuclease complex by chemical crosslinking combined with mass spectrometry and biochemical methods, providing the first structural view of the trimeric complex. Our analysis reveals that the exonuclease is sandwiched between the polymerase and clamp and enhances the binding between the two proteins by providing a second, indirect, interaction between the polymerase and clamp. In addition, we show that the exonuclease binds the clamp via the canonical binding pocket and thus prevents binding of the translesion DNA polymerase IV to the clamp, providing a novel insight into the mechanism by which the replication machinery can switch between replication, proofreading, and translesion synthesis.     

Generation of initial molecular dynamics configurations in arbitrary geometries and in parallel

A computational pre-processing tool for generating initial configurations of molecules for molecular dynamics simulations in geometries described by a mesh of unstructured arbitrary polyhedra is described. The mesh is divided into separate zones and each can be filled with a single crystal lattice of atoms. Each zone is filled by creating an expanding cube of crystal unit cells, initiated from an anchor point for the lattice. Each unit cell places the appropriate atoms for the user-specified crystal structure and orientation. The cube expands until the entire zone is filled with the lattice; zones with concave and disconnected volumes may be filled. When the mesh is spatially decomposed into portions for distributed parallel processing, each portion may be filled independently, meaning that the entire molecular system never needs to fit onto a single processor, allowing very large systems to be created. The computational time required to fill a zone with molecules scales linearly with the number of cells in the zone for a fixed number of molecules, and better than linearly with the number of molecules for a fixed number of mesh cells. Our tool, molConfig, has been implemented in the open source C++ code OpenFOAM.     

EDISON-WMW: Exact Dynamic Programing Solution of the Wilcoxon–Mann–Whitney Test

In many research disciplines, hypothesis tests are applied to evaluate whether findings are statistically significant or could be explained by chance. The Wilcoxon–Mann–Whitney(WMW) test is among the most popular hypothesis tests in medicine and life science to analyze if two groups of samples are equally distributed. This nonparametric statistical homogeneity test is commonly applied in molecular diagnosis. Generally, the solution of the WMW test takes a high combinatorial effort for large sample cohorts containing a significant number of ties. Hence, P value is frequently approximated by a normal distribution. We developed EDISON-WMW, a new approach to calculate the exact permutation of the two-tailed unpaired WMW test without any corrections required and allowing for ties. The method relies on dynamic programing to solve the combinatorial problem of the WMW test efficiently. Beyond a straightforward implementation of the algorithm, we presented different optimization strategies and developed a parallel solution. Using our program,the exact P value for large cohorts containing more than 1000 samples with ties can be calculated within minutes. We demonstrate the performance of this novel approach on randomly-generated data, benchmark it against 13 other commonly-applied approaches and moreover evaluate molecular biomarkers for lung carcinoma and chronic obstructive pulmonary disease(COPD). We foundthat approximated P values were generally higher than the exact solution provided by EDISONWMW. Importantly, the algorithm can also be applied to high-throughput omics datasets, where hundreds or thousands of features are included. To provide easy access to the multi-threaded version of EDISON-WMW, a web-based solution of our algorithm is freely available at http://www.ccb.uni-saarland.de/software/wtest/.     

Hybrid Flora of the British Isles by Clive A. Stace,Chris D. Preston and David A. Pearman. Bristol: Botanical Society of Britain and Ireland, 2015. 500 pp. Hardback. ISBN 978‐0‐901158‐48‐2. £45.00.

In this commentary, we discuss evidence for the phylogenetic affiliations of Tortotubus protuberans, the subject of Martin Smith's 2016 paper in the Botanical Journal of the Linnean Society entitled, ‘Cord‐forming Palaeozoic fungi in terrestrial assemblages’. We agree that the fossilized, branching, somatic filaments probably represent fungal hyphae. We were not convinced by Smith's proposal that T. protuberans represents Dikarya, the clade of fungi that includes most modern moulds, yeasts and mushrooms. To justify classification, Smith relied on structures that are analogous between T. protuberans and modern fungi, and argued ‘that Dikarya can produce the range of morphologies expressed by T. protuberans’. We review available information about homologies of the characteristics of T. protuberans, including mycelial cords, retrograde growth, septal pores and ornamented hyphae. Retrograde growth in T. protuberans is intriguing from an evolutionary developmental point of view, but it differs sufficiently in fine detail when compared with growth patterns in croziers or clamp connections of Dikarya, so that homologies are unclear. Tortotubus protuberans is an important fossil form, but we suggest taking a step back and relating it to the distribution of character evolution through the fungal phylogeny rather than to derived characters of modern taxa.     

适用于磁压榨吻合的平移钳的设计

目的:提出了磁压榨吻合操作中可用于磁体夹持固定的平移钳的结构设计方案。方法:分析本团队多种原创性磁压榨吻合技术操作中存在的缺陷和不足,认为目前磁压榨吻合操作中依靠术者徒手控制或利用现有血管钳对磁体进行夹持和固定,是造成操作中诸多不便的主要原因。从力学角度分析了常规血管钳夹持磁体易导致磁体滑脱的原因,指出设计加工磁吻合专用钳是解决目前磁吻合操作不便的有效措施。在此基础上提出了利用平移钳来固定磁体的结构设计方案,并从力学角度进行了受力分析,设计出了用于磁压榨吻合操作中磁体夹持固定的平移钳。结果:平移钳的结构设计能够稳定夹持磁体,避免磁体滑脱;同时,借助齿轮传动结构控制钳头的平行移动能够更好地控制磁体的精准对吸和分离,可进一步简化操作,避免副损伤,节省手术操作时间。结论:平移钳能满足多种形状及大小的磁体的夹持和固定,可有效控制磁体的吸合与分离,极大地方便操作。该平移钳加工简单,使用方便,有助于推动磁压榨吻合技术在临床广泛开展。