High Resolution Mapping of Enhancer-Promoter Interactions

RNA Polymerase II ChIA-PET data has revealed enhancers that are active in a profiled cell type and the genes that the enhancers regulate through chromatin interactions. The most commonly used computational method for analyzing ChIA-PET data, the ChIA-PET Tool, discovers interaction anchors at a spatial resolution that is insufficient to accurately identify individual enhancers. We introduce Germ, a computational method that estimates the likelihood that any two narrowly defined genomic locations are jointly occupied by RNA Polymerase II. Germ takes a blind deconvolution approach to simultaneously estimate the likelihood of RNA Polymerase II occupation as well as a model of the arrangement of read alignments relative to locations occupied by RNA Polymerase II. Both types of information are utilized to estimate the likelihood that RNA Polymerase II jointly occupies any two genomic locations. We apply Germ to RNA Polymerase II ChIA-PET data from embryonic stem cells to identify the genomic locations that are jointly occupied along with transcription start sites. We show that these genomic locations align more closely with features of active enhancers measured by ChIP-Seq than the locations identified using the ChIA-PET Tool. We also apply Germ to RNA Polymerase II ChIA-PET data from motor neuron progenitors. Based on the Germ results, we observe that a combination of cell type specific and cell type independent regulatory interactions are utilized by cells to regulate gene expression.National Institutes of Health (U.S.) (Grant 1U01HG007037

Unexpected effect of small viscosity on flow regimes in bubble columns

Bubble column contacting/reacting systems are widely used in many technologies of chemical and food industry, in biotechnology, and in environmental areas. The transport parameters of the system depend strongly on the flow regimes in the apparatus (homogeneous and heterogeneous regimes). One regime can change into the other at critical values of control parameters - system size and geometry, physico-chemical properties of the phases, etc. This study concerns the effect of the liquid phase viscosity on the extent the homogeneous regime. Experiments were performed in cylindrical bubble columns with solutions of different Newtonian viscosity. The data show that the uniform regime can be both supported and deteriorated with small changes in viscosity.Supported by GAČR (Grant No. 104/04/0827) and by the EC (BEMUSAC Project No. G1MA-CT-2002-04019 and Marie Curie Training Site Fellowship of P. C. Mena at the Institute of Chemical Process Fundamentals, Prague, CZ, Contract Number HPMT-CT-200000074). 31thinfo:eu-repo/semantics/publishedVersio

Effect of solid particles on flow regimes in bubble columns

Grantová agentura České republiky (GA ČR) - Grant No. 104/04/0827.Economic Community (EC) - BEMUSAC Project No. G1MA-CT-2002-04019.Institute of Chemical Process Fundamentals - Marie Curie Training Site Fellowship - Contract Number HPMT-CT-2000-00074

Stem Cells in the Nervous System

Given their capacity to regenerate cells lost through injury or disease, stem cells offer new vistas into possible treatments for degenerative diseases and their underlying causes. As such, stem cell biology is emerging as a driving force behind many studies in regenerative medicine. This review focuses on the current understanding of the applications of stem cells in treating ailments of the human brain, with an emphasis on neurodegenerative diseases. Two types of neural stem cells are discussed: endogenous neural stem cells residing within the adult brain and pluripotent stem cells capable of forming neural cells in culture. Endogenous neural stem cells give rise to neurons throughout life, but they are restricted to specialized regions in the brain. Elucidating the molecular mechanisms regulating these cells is key in determining their therapeutic potential as well as finding mechanisms to activate dormant stem cells outside these specialized microdomains. In parallel, patient-derived stem cells can be used to generate neural cells in culture, providing new tools for disease modeling, drug testing, and cell-based therapies. Turning these technologies into viable treatments will require the integration of basic science with clinical skills in rehabilitation

Exponential Distribution of Locomotion Activity in Cell Cultures

In vitro velocities of several cell types have been measured using computer controlled video microscopy, which allowed to record the cells' trajectories over several days. On the basis of our large data sets we show that the locomotion activity displays a universal exponential distribution. Thus, motion resulting from complex cellular processes can be well described by an unexpected, but very simple distribution function. A simple phenomenological model based on the interaction of various cellular processes and finite ATP production rate is proposed to explain these experimental results.Comment: 4 pages, 3 figure

Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity

Efficient transcriptional programming promises to open new frontiers in regenerative medicine. However, mechanisms by which programming factors transform cell fate are unknown, preventing more rational selection of factors to generate desirable cell types. Three transcription factors, Ngn2, Isl1 and Lhx3, were sufficient to program rapidly and efficiently spinal motor neuron identity when expressed in differentiating mouse embryonic stem cells. Replacement of Lhx3 by Phox2a led to specification of cranial, rather than spinal, motor neurons. Chromatin immunoprecipitation–sequencing analysis of Isl1, Lhx3 and Phox2a binding sites revealed that the two cell fates were programmed by the recruitment of Isl1-Lhx3 and Isl1-Phox2a complexes to distinct genomic locations characterized by a unique grammar of homeodomain binding motifs. Our findings suggest that synergistic interactions among transcription factors determine the specificity of their recruitment to cell type–specific binding sites and illustrate how a single transcription factor can be repurposed to program different cell types.Project ALS FoundationNational Institutes of Health (U.S.) (Grant P01 NS055923

Relaxational study of poly(vinylpyrrolidone-co-butyl acrylate) membrane by dielectric and dynamic mechanical spectroscopy

[EN] A poly(vinylpyrrolidone-co-butyl acrylate) (60VP-40BA) membrane is synthesized as a tractable and hydrophilic material, obtaining a water-swelling percentage around 60%. An investigation of molecular mobility by means of differential scanning calorimetry, dynamic mechanical analysis and broadband dielectric relaxation spectroscopy (DRS) is fulfilled in the dry membrane. Dielectric and viscoelastic relaxation measurements are carried out on the 60VP-40BA sample at several frequencies between -150 and 150 degrees C. The dielectric spectrum shows several relaxation processes labelled gamma, beta and alpha in increasing order of temperature, whereas in the mechanical spectrum only the beta and alpha relaxation processes are completely defined. In the dielectric measurements, conductive contributions overlap the alpha-relaxation. The apparent activation energies have similar values for the beta-relaxation in both, the mechanical and the dielectric measurements. The beta process is a Johari-Golstein secondary relaxation and it is related to the local motions of the pyrrolidone group accompanied by the motion of the segments of the polymer backbone. The gamma process is connected with the butyl unit's motions, both located in the side chains of the polymer.BRF, MC, PO and MJS are grateful to CICYT for grant MAT2012-33483. FG and JMG thank the Spanish Ministerio de Economia y Competitividad-FEDER (MAT2011-22544) and the Consejeria de Educacion-Junta de Castilla y Leon (BU001A10-2).Redondo Foj, MB.; Carsí Rosique, M.; Ortiz Serna, MP.; Sanchis Sánchez, MJ.; García, FC.; García. José Miguel (2013). Relaxational study of poly(vinylpyrrolidone-co-butyl acrylate) membrane by dielectric and dynamic mechanical spectroscopy. JOURNAL OF PHYSICS D-APPLIED PHYSICS. 46(29):295304-1-295304-12. https://doi.org/10.1088/0022-3727/46/29/295304S295304-1295304-12462

Global Control of Motor Neuron Topography Mediated by the Repressive Actions of a Single Hox Gene

In the developing spinal cord, regional and combinatorial activities of Hox transcription factors are critical in controlling motor neuron fates along the rostrocaudal axis, exemplified by the precise pattern of limb innervation by more than fifty Hox-dependent motor pools. The mechanisms by which motor neuron diversity is constrained to limb levels are, however, not well understood. We show that a single Hox gene, Hoxc9, has an essential role in organizing the motor system through global repressive activities. Hoxc9 is required for the generation of thoracic motor columns, and in its absence, neurons acquire the fates of limb-innervating populations. Unexpectedly, multiple Hox genes are derepressed in Hoxc9 mutants, leading to motor pool disorganization and alterations in the connections by thoracic and forelimb-level subtypes. Genome-wide analysis of Hoxc9 binding suggests that this mode of repression is mediated by direct interactions with Hox regulatory elements, independent of chromatin marks typically associated with repressed Hox genes.National Institutes of Health (U.S.) (P01NS055923

Retinoic Acid Functions as a Key GABAergic Differentiation Signal in the Basal Ganglia

Retinoic acid (RA) is essential for the generation of GABAergic inhibitory neurons in the mouse forebrain, and RA treatment of embryonic stem cells induces the production of GABAergic neurons

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

Hox genes controlling motor neuron subtype identity are expressed in rostrocaudal patterns that are spatially and temporally collinear with their chromosomal organization. Here we demonstrate that Hox chromatin is subdivided into discrete domains that are controlled by rostrocaudal patterning signals that trigger rapid, domain-wide clearance of repressive histone H3 Lys27 trimethylation (H3K27me3) polycomb modifications. Treatment of differentiating mouse neural progenitors with retinoic acid leads to activation and binding of retinoic acid receptors (RARs) to the Hox1–Hox5 chromatin domains, which is followed by a rapid domain-wide removal of H3K27me3 and acquisition of cervical spinal identity. Wnt and fibroblast growth factor (FGF) signals induce expression of the Cdx2 transcription factor that binds and clears H3K27me3 from the Hox1–Hox9 chromatin domains, leading to specification of brachial or thoracic spinal identity. We propose that rapid clearance of repressive modifications in response to transient patterning signals encodes global rostrocaudal neural identity and that maintenance of these chromatin domains ensures the transmission of positional identity to postmitotic motor neurons later in development.Leona M. and Harry B. Helmsley Charitable TrustNational Institutes of Health (U.S.) (Grant P01 NS055923)Smith Family Foundatio