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Dive into the research topics where Daniel A. Levy is active.

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Featured researches published by Daniel A. Levy.


Methods in Enzymology | 2003

Reconstitution of Membrane Proteins into Liposomes

Jean-Louis Rigaud; Daniel A. Levy

Publisher Summary The reconstitution of membrane proteins into liposomes is a powerful tool that can be used to identify the mechanism of the action of membrane proteins. The prospects of achieving optimal proteoliposome reconstitution are good when reliable methods and systematic experimental analysis are used. This chapter deals with the various strategies commonly used to reconstitute proteoliposomes and focuses on approaches that have led to the production of highly functional proteoliposomes. Four basic strategies are outlined—mechanical means, freeze-thawing, organic solvents, and detergents. The chapter also introduces a new method for membrane protein reconstitution. The new reconstitution strategy proceeds in four stages: (1) preparation of large, homogeneous, and unilamellar liposomes, (2) addition of detergent to the preformed liposomes, through all the range of the solubilization process, (3) addition of solubilized protein at each well-defined step of the solubilization process, and (4) detergent removal and characterization of the reconstituted products. Besides the need for measuring the activity of the protein, any method of membrane-protein reconstitution should fulfill a number of important criteria that must be analyzed to characterize unequivocally the efficiency of the reconstitution. The first parameter to analyze to check the efficiency of a reconstitution trial is the activity of the protein after reconstitution. The most accurate method to analyze the efficiency of membrane-protein incorporation is a density gradient.


Molecular Cell | 2008

Yap1 Phosphorylation by c-Abl Is a Critical Step in Selective Activation of Proapoptotic Genes in Response to DNA Damage

Daniel A. Levy; Yaarit Adamovich; Nina Reuven; Yosef Shaul

Cells undergo apoptosis upon exposure to severe DNA damage stress. Under this condition, p73 is phosphorylated and activated by c-Abl. The transcription coactivator Yap1 binds p73 to generate a complex that escapes p73 proteasomal degradation and recruits p300 to support transcription of proapoptotic genes. However, the mechanism of selective activation of proapoptotic genes by Yap1 remained unclear. In this study, we show that c-Abl directly phosphorylates Yap1 at position Y357 in response to DNA damage. Tyrosine-phosphorylated Yap1 is a more stable protein that displays higher affinity to p73 and selectively coactivates p73 proapoptotic target genes. Furthermore, we show that Yap1 switches between p73-mediated proapoptotic and growth arrest target genes based on its phosphorylation state. Thus, our data demonstrate that modification of a transcription coactivator, namely the DNA damage-induced phosphorylation of Yap1 by c-Abl, influences the specificity of target gene activation.


Proceedings of the National Academy of Sciences of the United States of America | 2003

Nanodissection and high-resolution imaging of the Rhodopseudomonas viridis photosynthetic core complex in native membranes by AFM

Simon Scheuring; Jérôme Seguin; Sergio Marco; Daniel A. Levy; Bruno Robert; Jean-Louis Rigaud

In photosynthesis, highly organized multiprotein assemblies convert sunlight into biochemical energy with high efficiency. A challenge in structural biology is to analyze such supramolecular complexes in native membranes. Atomic force microscopy (AFM) with high lateral resolution, high signal-to-noise ratio, and the possibility to nanodissect biological samples is a unique tool to investigate multiprotein complexes at molecular resolution in situ. Here we present high-resolution AFM of the photosynthetic core complex in native Rhodopseudomonas viridis membranes. Topographs at 10-Å lateral and ≈1-Å vertical resolution reveal a single reaction center (RC) surrounded by a closed ellipsoid of 16 light-harvesting (LH1) subunits. Nanodissection of the tetraheme cytochrome (4Hcyt) subunit from the RC allows demonstration that the L and M subunits exhibit an asymmetric topography intimately associated to the LH1 subunits located at the short ellipsis axis. This architecture implies a distance distribution between the antenna and the RC compared with a centered location of the RC within a circular LH1, which may influence the energy transfer within the core complex. The LH1 subunits rearrange into a circle after removal of the RC from the core complex.


The Journal of Neuroscience | 2008

Working Memory and the Organization of Brain Systems

Yael Shrager; Daniel A. Levy; Ramona O. Hopkins; Larry R. Squire

Working memory has historically been viewed as an active maintenance process that is independent of long-term memory and independent of the medial temporal lobe. However, impaired performance across brief time intervals has sometimes been described in amnesic patients with medial temporal lobe damage. These findings raise a fundamental question about how to know when performance depends on working memory and when the capacity for working memory has been exceeded and performance depends on long-term memory. We describe a method for identifying working memory independently of patient performance. We compared patients with medial temporal lobe damage to controls who were given either distraction or no distraction between study and test. In four experiments, we found concordance between the performance of patients and the effect of distraction on controls. The patients were impaired on tasks in which distraction had minimal effect on control performance, and the patients were intact on tasks in which distraction disrupted control performance. We suggest that the patients were impaired when the task minimally depended on working memory (and instead depended substantially on long-term memory), and they performed well when the task depended substantially on working memory. These findings support the conclusion that working memory (active maintenance) is intact after medial temporal lobe damage.


Neuroreport | 2001

Processing specificity for human voice stimuli: electrophysiological evidence.

Daniel A. Levy; Roni Y. Granot; Shlomo Bentin

Recent neuroimaging studies have provided evidence for localized perceptual specificity in the processing of human voice stimuli, paralleling the specificity for human faces. This study attempted to delineate the perceptual features of human voices yielding selective processing, and to characterize its time-course. Electrophysiological recordings revealed a positive potential peaking at 320 ms post-stimulus onset, in response to sung tones compared with fundamental-frequency-matched instrumental tones, when both categories were distracters in an oddball task. This voice-specific response (VSR) evoked under conditions different from those yielding positivity at that latency in other contexts, indicates the overriding salience of voice stimuli, possibly reflecting the operation of a gating system directing voice stimuli to be processed differently from other acoustic stimuli.


Psychological Science | 2004

Intact Conceptual Priming in the Absence of Declarative Memory

Daniel A. Levy; Craig E.L. Stark; Larry R. Squire

Priming is an unconscious (nondeclarative) form of memory whereby identification or production of an item is improved by an earlier encounter. It has been proposed that declarative memory and priming might be related---for example, that conceptual priming results in more fluent processing, thereby providing a basis for familiarity judgments. In two experiments, we assessed conceptual priming and recognition memory across a 5-min interval in 5 memory-impaired patients. All patients exhibited fully intact priming in tests of both free association (study tent; at test, provide an association to canvas) and category verification (study lemon; at test, decide: Is lemon a type of fruit?). Yet the 2 most severely amnesic patients performed at chance on matched tests of recognition memory. These findings count against the notion that conceptual priming provides feelings of familiarity that can support accurate recognition judgments. We suggest that priming is inaccessible to conscious awareness and does not influence declarative memory.


Neuropsychologia | 2008

The posterior parietal cortex in recognition memory: A neuropsychological study

Sharon Haramati; Nachum Soroker; Yadin Dudai; Daniel A. Levy

Several recent functional neuroimaging studies have reported robust bilateral activation (L>R) in lateral posterior parietal cortex and precuneus during recognition memory retrieval tasks. It has not yet been determined what cognitive processes are represented by those activations. In order to examine whether parietal lobe-based processes are necessary for basic episodic recognition abilities, we tested a group of 17 first-incident CVA patients whose cortical damage included (but was not limited to) extensive unilateral posterior parietal lesions. These patients performed a series of tasks that yielded parietal activations in previous fMRI studies: yes/no recognition judgments on visual words and on colored object pictures and identifiable environmental sounds. We found that patients with left hemisphere lesions were not impaired compared to controls in any of the tasks. Patients with right hemisphere lesions were not significantly impaired in memory for visual words, but were impaired in recognition of object pictures and sounds. Two lesion--behavior analyses--area-based correlations and voxel-based lesion symptom mapping (VLSM)---indicate that these impairments resulted from extra-parietal damage, specifically to frontal and lateral temporal areas. These findings suggest that extensive parietal damage does not impair recognition performance. We suggest that parietal activations recorded during recognition memory tasks might reflect peri-retrieval processes, such as the storage of retrieved memoranda in a working memory buffer for further cognitive processing.


Algorithmica | 2009

Why Neighbor-Joining Works

Radu Mihaescu; Daniel A. Levy; Lior Pachter

Abstract We show that the neighbor-joining algorithm is a robust quartet method for constructing trees from distances. This leads to a new performance guarantee that contains Atteson’s optimal radius bound as a special case and explains many cases where neighbor-joining is successful even when Atteson’s criterion is not satisfied. We also provide a proof for Atteson’s conjecture on the optimal edge radius of the neighbor-joining algorithm. The strong performance guarantees we provide also hold for the quadratic time fast neighbor-joining algorithm, thus providing a theoretical basis for inferring very large phylogenies with neighbor-joining.


Psychophysiology | 2003

Neural sensitivity to human voices: ERP evidence of task and attentional influences

Daniel A. Levy; Roni Y. Granot; Shlomo Bentin

In an earlier study, we found that human voices evoked a positive event-related potential (ERP) peaking at approximately 320 ms after stimulus onset, distinctive from those elicited by instrumental tones. Here we show that though similar in latency to the Novelty P3, this Voice-Sensitive Response (VSR) differs in antecedent conditions and scalp distribution. Furthermore, when participants were not attending to stimuli, the response to voices was undistinguished from other harmonic stimuli (strings, winds, and brass). During a task requiring attending to a feature other than timbre, voices were not distinguished from voicelike stimuli (strings), but were distinguished from other harmonic stimuli. We suggest that the component elicited by voices and similar sounds reflects the allocation of attention on the basis of stimulus significance (as opposed to novelty), and propose an explanation of the task and attentional factors that contribute to the effect.


Proceedings of the National Academy of Sciences of the United States of America | 2013

Detergent-mediated incorporation of transmembrane proteins in giant unilamellar vesicles with controlled physiological contents

Manuela Dezi; Aurelie Di Cicco; Patricia Bassereau; Daniel A. Levy

Giant unilamellar vesicles (GUVs) are convenient biomimetic systems of the same size as cells that are increasingly used to quantitatively address biophysical and biochemical processes related to cell functions. However, current approaches to incorporate transmembrane proteins in the membrane of GUVs are limited by the amphiphilic nature or proteins. Here, we report a method to incorporate transmembrane proteins in GUVs, based on concepts developed for detergent-mediated reconstitution in large unilamellar vesicles. Reconstitution is performed either by direct incorporation from proteins purified in detergent micelles or by fusion of purified native vesicles or proteoliposomes in preformed GUVs. Lipid compositions of the membrane and the ionic, protein, or DNA compositions in the internal and external volumes of GUVs can be controlled. Using confocal microscopy and functional assays, we show that proteins are unidirectionally incorporated in the GUVs and keep their functionality. We have successfully tested our method with three types of transmembrane proteins. GUVs containing bacteriorhodopsin, a photoactivable proton pump, can generate large transmembrane pH and potential gradients that are light-switchable and stable for hours. GUVs with FhuA, a bacterial porin, were used to follow the DNA injection by T5 phage upon binding to its transmembrane receptor. GUVs incorporating BmrC/BmrD, a bacterial heterodimeric ATP-binding cassette efflux transporter, were used to demonstrate the protein-dependent translocation of drugs and their interactions with encapsulated DNA. Our method should thus apply to a wide variety of membrane or peripheral proteins for producing more complex biomimetic GUVs.

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Roni Tibon

Cognition and Brain Sciences Unit

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Nurit Gronau

Open University of Israel

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Lior Pachter

University of California

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Yael Shrager

University of California

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