A5060914155- Lipid Membrane Structure and Behavior
- Spectroscopy and Quantum Chemical Studies
- Single-cell and spatial transcriptomics
- Plant Molecular Biology Research
- Gene Regulatory Network Analysis
- Evolution and Genetic Dynamics
- Bioinformatics and Genomic Networks
- Nanopore and Nanochannel Transport Studies
- Insect and Arachnid Ecology and Behavior
- Force Microscopy Techniques and Applications
- Plant Reproductive Biology
- Light effects on plants
- Enzyme Structure and Function
- Animal Behavior and Reproduction
- Electrostatics and Colloid Interactions
- Polysaccharides and Plant Cell Walls
- Cancer Genomics and Diagnostics
- Surfactants and Colloidal Systems
- Evolution and Paleontology Studies
- Evolutionary Game Theory and Cooperation
- Bat Biology and Ecology Studies
- Video Coding and Compression Technologies
- VLSI and Analog Circuit Testing
- Cell Image Analysis Techniques
- Advanced Image Processing Techniques
Duke University
2021-2024
Howard Hughes Medical Institute
2022-2023
Hebrew University of Jerusalem
2010-2019
Weizmann Institute of Science
2013-2019
Samsung (Israel)
2019
Technion – Israel Institute of Technology
2011
Brassinosteroids are plant steroid hormones that regulate diverse processes, such as cell division and elongation, through gene regulatory networks vary in space time. By using time series single-cell RNA sequencing to profile brassinosteroid-responsive expression specific different types developmental stages of the Arabidopsis root, we identified elongating cortex a site where brassinosteroids trigger shift from proliferation elongation associated with increased wall–related genes. Our...
Abstract Precise control of cell division is essential for proper patterning and growth during the development multicellular organisms. Coordination formative divisions that generate new tissue patterns with proliferative promote poorly understood. SHORTROOT (SHR) SCARECROW (SCR) are transcription factors required in stem niche Arabidopsis roots 1,2 . Here we show levels SHR SCR early cycle determine orientation plane, resulting either or division. We used 4D quantitative, long-term frequent...
Video frame interpolation is a long-studied problem in the video processing field. Recently, deep learning approaches have been applied to this problem, showing impressive results on low-resolution benchmarks. However, these methods do not scale-up favorably high resolutions. Specifically, when motion exceeds typical number of pixels, their quality degraded. Moreover, run time renders them impractical for real-time applications. In paper we propose IM-Net: an interpolated neural network. We...
There is a revolution in the ability to analyze gene expression of single cells tissue. To understand this data we must comprehend how are distributed high-dimensional space. One open question whether cell types form discrete clusters or forms continuum states. If such exists, what its geometry? Recent theory on evolutionary trade-offs suggests that need perform multiple tasks arranged polygon polyhedron (line, triangle, tetrahedron and so on, generally called polytopes) space, whose...
Abstract Recent advances have enabled powerful methods to sort tumors into prognosis and treatment groups. We are still missing, however, a general theoretical framework understand the vast diversity of tumor gene expression mutations. Here we present based on multi-task evolution theory, using fact that need perform multiple tasks contribute their fitness. find trade-offs between constrain gene-expression continuum bounded by polyhedron whose vertices profiles, each specializing in one...
In pure water, zwitterionic lipids form lamellar phases with an equilibrium water gap on the order of 2 to 3 nm as a result dominating van der Waals attraction between dipolar bilayers. Monovalent ions can swell those neutral lamellae by small amount. Divalent adsorb onto membranes and charge them. Using solution X-ray scattering, we studied how structure regulates membranes. We found that unlike monovalent weakly interact all examined membranes, divalent trivalent containing saturated...
X+ is a user-friendly multi-core accelerated program that fully analyses solution X-ray scattering radially integrated images. This software particularly useful for analysing supramolecular self-assemblies, often found in biology, and reconstructing the signal its entirety. The enables various ways of subtracting background noise. user selects geometric model defines as many layers shape needed. thickness electron density each layer are fitting parameters. An initial guess input by...
Biological regulatory systems face a fundamental tradeoff: they must be effective but at the same time also economical. For example, that are designed to repair damage in reducing damage, economical not making too many proteins because excessive carries fitness cost cell, called protein burden. In order see how biological compromise between two tasks of effectiveness and economy, we applied an approach from economics engineering Pareto optimality. This allows calculating best-compromise...
Zinc ions are highly abundant in biological systems and interact with various enzymes, proteins biomembranes. In this paper, an in-house state-of-the-art time-resolved solution X-ray scattering setup was used to study the interactions of divalent charged membranes. We show that unlike calcium strongly couple crystallize membranes very rapidly, zinc exhibit a fast time scale (seconds) for strong coupling bilayers much slower one (hours) 2D lateral crystallization bilayers. This is attributed...
In this paper, the analysis of several involved models, relevant for evaluating solution X-ray scattering form factors supramolecular self-assembled structures, is presented. Different geometrical models are discussed, and layers those shapes evaluated. The thickness electron density each layer parameters in models. include Gaussian profiles and/or uniform at layer. Various forms cuboid, layered, spherical, cylindrical, helical structures carefully treated. orientation-averaged intensities...
Interactions between charged and neutral self-assembled phospholipid membranes are well understood take into account temperature dependence. Yet, the manner in which structure of membrane is affected by was hardly studied. Here we study effect on thickness, area per lipid, volume lipid membranes. Two types were studied: composed lipids dipolar (neutral) that adsorbed divalent cations became charged. Small-angle X-ray scattering data demonstrate thickness decreases with temperature....
When organisms need to perform multiple tasks they face a fundamental tradeoff: no phenotype can be optimal at all tasks. This situation was recently analyzed using Pareto optimality, showing that tradeoffs between lead phenotypes distributed on low dimensional polygons in trait space. The vertices of these are archetypes—phenotypes single task. theory applied examples from animal morphology and gene expression. Here we ask whether optimality apply life history traits, which include...
Like-charged solid interfaces repel and separate from one another as much possible. Charged composed of self-assembled charged-molecules such lipids or proteins are ubiquitous. The present study shows that although charged lipid-membranes sufficiently rigid, in order to swell possible, they deviate markedly the behavior typical like-charged solids when diluted below a critical concentration (ca. 15 wt %). Unexpectedly, into lamellar structures with spacing is up four times shorter than...
Populations of organisms show genetic differences called polymorphisms. Understanding the effects polymorphisms is important for biology and medicine. Here, we ask which occur at high frequency when evolve under trade-offs between multiple tasks. Multiple tasks present a problem, because it not possible to be optimal all simultaneously hence compromises are necessary. Recent work indicates that lead simple geometry phenotypes in space traits: fall on Pareto front, shaped as polytope: line,...
Bacteria often face complex environments. We asked how gene expression in conditions relates to simpler conditions. To address this, we obtained accurate promoter activity dynamical measurements on 94 genes E. coli environments made up of all possible combinations four nutrients and stresses. find that the dynamics across is well described by two principal component curves specific each promoter. As a result, combination weighted average condition alone. The weights tend sum approximately...
It is well-known that phospholipids in aqueous environment self-assemble into lamellar structures with a repeat distance governed by the interactions between them. Yet, understanding of these incomplete. In this paper, we study effect temperature on interlamellar dipolar membranes. Using solution small-angle X-ray scattering (SAXS), measured 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) bilayers at different temperatures and osmotic stresses. We found when no pressure applied distance, D,...
When aqueous salt solutions contain multivalent ions (like Ca2+ or Mg2+), strong correlation effects may lead to ion-bridging, net attraction, and tight-coupling between like-charged interfaces. To examine the of surface charge density, temperature, type, concentration on structures tightly coupled charged interfaces, we have used mixed lipid membranes, containing either saturated unsaturated tails in presence ions. We discovered that membrane lamellar phases, dominated by attractive...
Understanding the tradeoffs faced by organisms is a major goal of evolutionary biology. One main approaches for identifying these Pareto task inference (ParTI). Two recent papers claim that results obtained in ParTI studies are spurious due to phylogenetic dependence (Mikami T, Iwasaki W. 2021. The flipping t-ratio test: phylogenetically informed assessment theory phenotypic evolution. Methods Ecol Evol. 12(4):696-706) or hypothetical p-hacking and population-structure concerns (Sun M, Zhang...
Abstract Populations of organisms show prevalent genetic differences called polymorphisms. Understanding the effects polymorphisms is central importance in biology and medicine. Here, we ask which occur at high frequency when evolve under tradeoffs between multiple tasks. Multiple tasks present a problem, because it not possible to be optimal all simultaneously hence compromises are necessary. Recent work indicates that lead simple geometry phenotypes space traits: fall on Pareto front,...
Brassinosteroids (BRs) are plant steroid hormones that regulate diverse processes such as cell division and elongation. BRs control thousands of genes through gene regulatory networks vary in space time. By using time-series single-cell RNA-sequencing to identify BR-responsive expression specific different types developmental stages the Arabidopsis root, we uncovered elongating cortex a site where trigger shift from proliferation elongation associated with increased wall-related genes. Our...
Precise control of cell division is essential for proper patterning and growth during the development multicellular organisms. Coordination formative (asymmetric) divisions that generate new tissue patterns with proliferative (symmetric) promote poorly understood. Here, we employed quantitative 4D light sheet confocal microscopy to probe in vivo dynamics two transcription factors, SHORTROOT (SHR) SCARECROW (SCR), which are required asymmetric stem niche Arabidopsis roots [1,2]. Long-term (up...
Abstract Recent advances have led to an appreciation of the vast molecular diversity cancer. Detailed data has enabled powerful methods sort tumors into groups with benefits for prognosis and treatment. We are still missing, however, a general theoretical framework understand tumor gene-expression mutations. To address this, we present based on multi-task evolution theory, using fact that evolve in body, faced multiple tasks contribute their fitness. In accordance find tradeoff between...