Alexander Silberman Institute of Life science

West Jerusalem, Israel

Alexander Silberman Institute of Life science

West Jerusalem, Israel
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Rabieh N.,Alexander Silberman Institute of Life Science | Ojovan S.M.,Alexander Silberman Institute of Life Science | Shmoel N.,Alexander Silberman Institute of Life Science | Erez H.,Alexander Silberman Institute of Life Science | And 2 more authors.
Scientific Reports | Year: 2016

In contrast to the extensive use of microelectrode array (MEA) technology in electrophysiological studies of cultured neurons and cardiac muscles, the vast field of skeletal muscle research has yet to adopt the technology. Here we demonstrate an empowering MEA technology for high quality, multisite, long-term electrophysiological recordings from cultured skeletal myotubes. Individual rat skeletal myotubes cultured on micrometer sized gold mushroom-shaped microelectrode (gMμE) based MEA tightly engulf the gMμEs, forming a high seal resistance between the myotubes and the gMμEs. As a consequence, spontaneous action potentials generated by the contracting myotubes are recorded as extracellular field potentials with amplitudes of up to 10 mV for over 14 days. Application of a 10 ms, 0.5-0.9 V voltage pulse through the gMμEs electroporated the myotube membrane, and transiently converted the extracellular to intracellular recording mode for 10-30 min. In a fraction of the cultures stable attenuated intracellular recordings were spontaneously produced. In these cases or after electroporation, subthreshold spontaneous potentials were also recorded. The introduction of the gMμE-MEA as a simple-to-use, high-quality electrophysiological tool together with the progress made in the use of cultured human myotubes opens up new venues for basic and clinical skeletal muscle research, preclinical drug screening, and personalized medicine. © 2016 The Author(s).


Moshitch D.,Alexander Silberman Institute of Life science | Nelken I.,Alexander Silberman Institute of Life science | Nelken I.,Hebrew University of Jerusalem
Cerebral Cortex | Year: 2016

Early representations of auditory features often involve neuronal populations whose tuning is substantially wider than behavioral discrimination thresholds. Although behavioral discrimination performance can be sometimes achieved by single neurons when using the appropriate part of their (wide) tuning curves, neurons that encode the resulting high-acuity representations have rarely been described. Here we demonstrate the existence of neurons with extremely narrow tuning for interaural time differences (ITDs), a major physical cue for the azimuth of sound sources. The tuning width of ITD-tuned brainstem neurons is mostly determined by the properties of their acoustic input, and may be 10-100 times wider than behavioral thresholds. In contrast, we show that tuning widths of some neurons in the primary auditory cortex in the cat high-frequency auditory cortex (measured using transposed stimulus) can be very sharp and approach behavioral thresholds. Furthermore, while best ITDs of brainstem neurons often lie outside the range of naturally encountered ITDs (the ethological range), the range of best ITDs of the narrowly tuned cortical neurons corresponds well to the ethological range. Thus, our results suggest that the auditory cortex contains a high-resolution representation of ITDs that explicitly decodes the widely tuned brainstem representations. © 2014 The Author 2014.


Zohar O.,Ben - Gurion University of the Negev | Shackleton T.M.,Medical Research Council Institute of Hearing Research | Nelken I.,Alexander Silberman Institute of Life science | Nelken I.,Hebrew University of Jerusalem | And 2 more authors.
Journal of Neuroscience | Year: 2011

First spike latency has been suggested as a source of the information required for fast discrimination tasks. However, the accuracy of such a mechanism has not been analyzed rigorously. Here, we investigate the utility of first spike latency for encoding information about the location of a sound source, based on the responses of inferior colliculus (IC) neurons in the guinea pig to interaural phase differences (IPDs). First spike latencies of many cells in the guinea pig IC show unimodal tuning to stimulus IPD. We investigated the discrimination accuracy of a simple latency code that estimates stimulus IPD from the preferred IPD of the single cell that fired first. Surprisingly, despite being based on only a single spike, the accuracy of the latency code is comparable to that of a conventional rate code computed over the entire response. We show that spontaneous firing limits the capacity of the latency code to accumulate information from large neural populations. This detrimental effect can be overcome by generalizing the latency code to estimate the stimulus IPD from the preferred IPDs of the population of cells that fired the first n spikes. In addition, we show that a good estimate of the neural response time to the stimulus, which can be obtained from the responses of the cells whose response latency is invariant to stimulus identity, limits the detrimental effect of spontaneous firing. Thus, a latency code may provide great improvement in response speed at a small cost to the accuracy of the decision. ©2011 the authors.


Tal-Gan Y.,Institute of Chemistry | Hurevich M.,Institute of Chemistry | Klein S.,Alexander Silberman Institute of Life science | Ben-Shimon A.,Hebrew University | And 6 more authors.
Journal of Medicinal Chemistry | Year: 2011

Elevated levels of activated protein kinase B (PKB/Akt) have been detected in many types of cancer. Substrate-based peptide inhibitors have the advantage of selectivity due to their extensive interactions with the kinase-specific substrate binding site but often lack necessary pharmacological properties. Chemical modifications of potent peptide inhibitors, such as cyclization, may overcome these drawbacks while maintaining potency. We present an extensive structure-activity relationship (SAR) study of a potent peptide-based PKB/Akt inhibitor. Two backbone cyclic (BC) peptide libraries with varying modes of cyclization, bridge chemistry, and ring size were synthesized and evaluated for in vitro PKB/Akt inhibition. Backbone-to-backbone urea BC peptides were more potent than N-terminus-to-backbone amide BC peptides. Several analogues were up to 10-fold more active than the parent linear peptide. Some activity trends could be rationalized using computational surface mapping of the PKB/Akt kinase catalytic domain. The novel molecules have enhanced pharmacological properties which make them promising lead candidates. © 2011 American Chemical Society.


Neuman H.,Alexander Silberman Institute of Life science | Galpaz N.,Alexander Silberman Institute of Life science | Cunningham Jr. F.X.,University of Maryland University College | Zamir D.,Hebrew University of Jerusalem | Hirschberg J.,Alexander Silberman Institute of Life science
Plant Journal | Year: 2014

Carotenoid pigments are indispensable for plant life. They are synthesized within plastids where they provide essential functions in photosynthesis. Carotenoids serve as precursors for the synthesis of the strigolactone phytohormones, which are made from β-carotene, and of abscisic acid (ABA), which is produced from certain xanthophylls. Despite the significant progress that has been made in our understanding of the carotenoid biosynthesis pathway, the synthesis of the xanthophyll neoxanthin has remained unknown. We report here on the isolation of a tomato (Solanum lycopersicum) mutant, neoxanthin-deficient 1 (nxd1), which lacks neoxanthin, and on the cloning of a gene that is necessary for neoxanthin synthesis in both tomato and Arabidopsis. The locus nxd1 encodes a gene of unknown function that is conserved in all higher plants. The activity of NXD1 is essential but cannot solely support neoxanthin synthesis. Lack of neoxanthin does not significantly reduce the fitness of tomato plants in cultivated field conditions and does not impair the synthesis of ABA, suggesting that in tomato violaxanthin is a sufficient precursor for ABA production in vivo. © 2014 John Wiley & Sons Ltd.


Moran Y.,Center for Organismal Systems Biology | Moran Y.,University of Bergen | Fredman D.,Center for Organismal Systems Biology | Fredman D.,Alexander Silberman Institute of Life science | And 7 more authors.
Genome Research | Year: 2014

In bilaterians, which comprise most of extant animals, microRNAs (miRNAs) regulate the majority of messenger RNAs (mRNAs) via base-pairing of a short sequence (the miRNA "seed") to the target, subsequently promoting translational inhibition and transcript instability. In plants, many miRNAs guide endonucleolytic cleavage of highly complementary targets. Because little is known about miRNA function in nonbilaterian animals, we investigated the repertoire and biological activity of miRNAs in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister phylum of Bilateria. Our work uncovers scores of novel miRNAs in Nematostella, increasing the total miRNA gene count to 87. Yet only a handful are conserved in corals and hydras, suggesting that microRNA gene turnover in Cnidaria greatly exceeds that of other metazoan groups. We further show that Nematostella miRNAs frequently direct the cleavage of their mRNA targets via nearly perfect complementarity. This mode of action resembles that of small interfering RNAs (siRNAs) and plant miRNAs. It appears to be common in Cnidaria, as several of the miRNA target sites are conserved among distantly related anemone species, and we also detected miRNA-directed cleavage in Hydra. Unlike in bilaterians, Nematostella miRNAs are commonly coexpressed with their target transcripts. In light of these findings, we propose that post-transcriptional regulation by miRNAs functions differently in Cnidaria and Bilateria. The similar, siRNA-like mode of action of miRNAs in Cnidaria and plants suggests that this may be an ancestral state. © 2014 Moran et al.


Lis H.,Interuniversity Institute for Marine science | Lis H.,Hebrew University of Jerusalem | Shaked Y.,Interuniversity Institute for Marine science | Shaked Y.,Hebrew University of Jerusalem | And 4 more authors.
ISME Journal | Year: 2015

Phytoplankton are often limited by iron in aquatic environments. Here we examine Fe bioavailability to phytoplankton by analyzing iron uptake from various Fe substrates by several species of phytoplankton grown under conditions of Fe limitation and comparing the measured uptake rate constants (Fe uptake rate/substrate concentration). When unchelated iron, Fe′, buffered by an excess of the chelating agent EDTA is used as the Fe substrate, the uptake rate constants of all the eukaryotic phytoplankton species are tightly correlated and proportional to their respective surface areas (S.A.). The same is true when FeDFB is the substrate, but the corresponding uptake constants are one thousand times smaller than for Fe′. The uptake rate constants for the other substrates we examined fall mostly between the values for Fe′ and FeDFB for the same S.A. These two model substrates thus empirically define a bioavailability envelope with Fe′ at the upper and FeDFB at the lower limit of iron bioavailability. This envelope provides a convenient framework to compare the relative bioavailabilities of various Fe substrates to eukaryotic phytoplankton and the Fe uptake abilities of different phytoplankton species. Compared with eukaryotic species, cyanobacteria have similar uptake constants for Fe′ but lower ones for FeDFB. The unique relationship between the uptake rate constants and the S.A. of phytoplankton species suggests that the uptake rate constant of Fe-limited phytoplankton has reached a universal upper limit and provides insight into the underlying uptake mechanism. © 2015 International Society for Microbial Ecology All rights reserved.


Aaronson Y.,Alexander Silberman Institute of Life science | Livyatan I.,Alexander Silberman Institute of Life science | Gokhman D.,Alexander Silberman Institute of Life science | Meshorer E.,Alexander Silberman Institute of Life science | Meshorer E.,Hebrew University of Jerusalem
Nucleic Acids Research | Year: 2016

Pluripotent self-renewing embryonic stem cells (ESCs) have been the focus of a growing number of high-throughput experiments, revealing the genome-wide locations of hundreds of transcription factors and histone modifications. While most of these datasets were used in a specific context, all datasets combined offer a comprehensive view of chromatin characteristics and regulatory elements that govern cell states. Here, using hundreds of datasets in ESCs, we generated colocalization maps of chromatin proteins and modifications, and built a discovery pipeline for regulatory proteins of gene families. By comparing genome-wide binding data with over-expression and knockdown analysis of hundreds of genes, we discovered that the pluripotency-related factor NR5A2 separates mitochondrial from cytosolic ribosomal genes, regulating their expression. We further show that genes with a common chromatin profile are enriched for distinct Gene Ontology (GO) categories. Our approach can be generalized to reveal common regulators of any gene group; discover novel gene families, and identify common genomic elements based on shared chromatin features. © 2016 The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.


PubMed | Johannes Gutenberg University Mainz, Alexander Silberman Institute of Life science and Hebrew University of Jerusalem
Type: Journal Article | Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience | Year: 2015

Dynamic remodeling of connectivity is a fundamental feature of neocortical circuits. Unraveling the principles underlying these dynamics is essential for the understanding of how neuronal circuits give rise to computations. Moreover, as complete descriptions of the wiring diagram in cortical tissues are becoming available, deciphering the dynamic elements in these diagrams is crucial for relating them to cortical function. Here, we used chronic in vivo two-photon imaging to longitudinally follow a few thousand dendritic spines in the mouse auditory cortex to study the determinants of these spines lifetimes. We applied nonlinear regression to quantify the independent contribution of spine age and several morphological parameters to the prediction of the future survival of a spine. We show that spine age, size, and geometry are parameters that can provide independent contributions to the prediction of the longevity of a synaptic connection. In addition, we use this framework to emulate a serial sectioning electron microscopy experiment and demonstrate how incorporation of morphological information of dendritic spines from a single time-point allows estimation of future connectivity states. The distinction between predictable and nonpredictable connectivity changes may be used in the future to identify the specific adaptations of neuronal circuits to environmental changes. The full dataset is publicly available for further analysis. Significance statement: The neural architecture in the neocortex exhibits constant remodeling. The functional consequences of these modifications are poorly understood, in particular because the determinants of these changes are largely unknown. Here, we aimed to identify those modifications that are predictable from current network state. To that goal, we repeatedly imaged thousands of dendritic spines in the auditory cortex of mice to assess the morphology and lifetimes of synaptic connections. We developed models based on morphological features of dendritic spines that allow predicting future turnover of synaptic connections. The dynamic models presented in this paper provide a quantitative framework for adding putative temporal dynamics to the static description of a neuronal circuit from single time-point connectomics experiments.


PubMed | Alexander Silberman Institute of Life science
Type: Journal Article | Journal: The Plant journal : for cell and molecular biology | Year: 2014

Carotenoid pigments are indispensable for plant life. They are synthesized within plastids where they provide essential functions in photosynthesis. Carotenoids serve as precursors for the synthesis of the strigolactone phytohormones, which are made from -carotene, and of abscisic acid (ABA), which is produced from certain xanthophylls. Despite the significant progress that has been made in our understanding of the carotenoid biosynthesis pathway, the synthesis of the xanthophyll neoxanthin has remained unknown. We report here on the isolation of a tomato (Solanum lycopersicum) mutant, neoxanthin-deficient 1 (nxd1), which lacks neoxanthin, and on the cloning of a gene that is necessary for neoxanthin synthesis in both tomato and Arabidopsis. The locus nxd1 encodes a gene of unknown function that is conserved in all higher plants. The activity of NXD1 is essential but cannot solely support neoxanthin synthesis. Lack of neoxanthin does not significantly reduce the fitness of tomato plants in cultivated field conditions and does not impair the synthesis of ABA, suggesting that in tomato violaxanthin is a sufficient precursor for ABA production in vivo.

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