Interlayer Dependence of G-Modes in Semiconducting Double-Walled Carbon Nanotubes

A double-walled carbon nanotube (DWNT), a coaxial composite of two single-walled carbon nanotubes (SWNT), provides a unique model to study interactions between the two constituent SWNTs. Combining high resolution transmission electron microscopy (HRTEM), electron diffraction (ED), and resonant Raman scattering (RRS) experiments on the same individual suspended DWNT is the ultimate way to relate unambiguously its atomic structure, defined by the chiral indices of the coaxial outer/inner SWNTs, and its Raman-active vibration modes. This approach is used to investigate the intertube distance dependence of the G-modes of individual index-identified DWNTs composed of two semiconducting SWNTs. We state the main features of the dependence of the G-mode frequencies on the distance between the inner and outer layers: (i) When the interlayer distance is larger than the nominal van der Waals distance (close to 0.34 nm), a downshift of the inner-layer G-modes with respect to the G-modes in the equivalent SWNTs is measured. (ii) The amplitude of the downshift depends on the interlayer distance, or in other words, on the negative pressure felt by the inner layer in DWNT. (iii) No shift is observed for an intertube distance close to 0.34 nm

Accurate determination of the chiral indices of individual carbon nanotubes by combining electron diffraction and Resonant Raman spectroscopy

The experimental approach combining high resolution transmission electron microscopy (HRTEM), electron diffraction (ED) and resonant Raman spectroscopy (RRS) on the same free-standing individual carbon nanotubes (CNT) is the most efficient method to determine unambiguously the intrinsic features of the Raman-active phonons. In this paper, we review the main results obtained by the approach regarding the intrinsic features of the phonons of single-walled (SWNT) and double-walled carbon nanotubes (DWNT). First, we detail the different methods to identify the structure of SWNTs and DWNTs from the analysis of their electron diffraction patterns (EDP). In the following, we remind the principal features of the Raman response of SWNTs, unambiguously index-identified by ED. A special attention is devoted to the effect of the inter-layer interaction on the frequencies of the Raman-active phonons in index-identified DWNTs. The information obtained on index-identified SWNT and DWNT allows us to propose Raman criteria, which help identifying CNT when the ED fails to propose a single assignment. The efficiency of the Raman criteria as the complement to the ED information for the index-assignment of a few SWNTs and DWNTs is shown. The same approach to index-assign a triple-walled carbon nanotube (TWNT), by combining ED and RRS information, is reported

Study of collective radial breathing-like modes in double-walled carbon nanotubes: Combination of continuous two-dimensional membrane theory and Raman spectroscopy

Radial breathing modes (RBMs) are widely used for the atomic structure characterization and index assignment of single-walled carbon nanotubes (SWNTs) from resonant Raman spectroscopy. However, for double-walled carbon nanotubes (DWNTs), the use of conventional ¿RBM(d) formulas is complicated due to the van der Waals interaction between the layers, which strongly affects the frequencies of radial modes and leads to new collective vibrations. This paper presents an alternative way to theoretically study the collective radial breathing-like modes (RBLMs) of DWNTs and to account for interlayer interaction, namely the continuous two-dimensional membrane theory. We obtain an analytical ¿RBLM(do, di) relation, being the equivalent of the conventional ¿RBM(d) expressions, established for SWNTs. We compare our theoretical predictions with Raman data, measured on individual index-identified suspended DWNTs, and find a good agreement between experiment and theory. Moreover, we show that the interlayer coupling in individual DWNTs strongly depends on the interlayer distance, which is manifested in the frequency shifts of the RBLMs with respect to the RBMs of the individual inner and outer tubes. In terms of characterization, this means that the combination of Raman spectroscopy data and predictions of continuous membrane theory may give additional criteria for the index identification of DWNTs, namely the interlayer distance

Interlayer Dependence of G-Modes in Semiconducting Double-Walled Carbon Nanotubes

A double-walled carbon nanotube (DWNT), a coaxial composite of two single walled carbon nanotubes (SWNT), provides a unique model to study interactions between thetwo constituent SWNTs. Combining high resolution transmission electron microscopy (HRTEM), electron diffraction (ED), and resonant Raman scattering (RRS) experiments on the same individual suspended DWNT is the ultimate way to relate unambiguously its atomicstructure, defined by the chiral indices of the coaxial outer/inner SWNTs, and its Raman-active vibration modes. This approach is used to investigate the intertube distance dependence of theG-modes of individual index-identified DWNTs composed of two semiconducting SWNTs.We state the main features of the dependence of the G-mode frequencies on the distance between the inner and outer layers: (i) When the interlayer distance is larger than the nominal van der Waals distance (close to 0.34 nm), a downshift of the inner-layer G-modes with respectto the G-modes in the equivalent SWNTs is measured. (ii) The amplitude of the downshiftdepends on the interlayer distance, or in other words, on the negative pressure felt by the innerlayer in DWNT. (iii) No shift is observed for an intertube distance close to 0.34 nm

Mild orotic aciduria in UMPS heterozygotes: a metabolic finding without clinical consequences

BACKGROUND: Elevated urinary excretion of orotic acid is associated with treatable disorders of the urea cycle and pyrimidine metabolism. Establishing the correct and timely diagnosis in a patient with orotic aciduria is key to effective treatment. Uridine monophosphate synthase is involved in de novo pyrimidine synthesis. Uridine monophosphate synthase deficiency (or hereditary orotic aciduria), due to biallelic mutations in UMPS, is a rare condition presenting with megaloblastic anemia in the first months of life. If not treated with the pyrimidine precursor uridine, neutropenia, failure to thrive, growth retardation, developmental delay, and intellectual disability may ensue. METHODS AND RESULTS: We identified mild and isolated orotic aciduria in 11 unrelated individuals with diverse clinical signs and symptoms, the most common denominator being intellectual disability/developmental delay. Of note, none had blood count abnormalities, relevant hyperammonemia or altered plasma amino acid profile. All individuals were found to have heterozygous alterations in UMPS. Four of these variants were predicted to be null alleles with complete loss of function. The remaining variants were missense changes and predicted to be damaging to the normal encoded protein. Interestingly, family screening revealed heterozygous UMPS variants in combination with mild orotic aciduria in 19 clinically asymptomatic family members. CONCLUSIONS: We therefore conclude that heterozygous UMPS-mutations can lead to mild and isolated orotic aciduria without clinical consequence. Partial UMPS-deficiency should be included in the differential diagnosis of mild orotic aciduria. The discovery of heterozygotes manifesting clinical symptoms such as hypotonia and developmental delay are likely due to ascertainment bias

Network-Free Inference of Knockout Effects in Yeast

Perturbation experiments, in which a certain gene is knocked out and the expression levels of other genes are observed, constitute a fundamental step in uncovering the intricate wiring diagrams in the living cell and elucidating the causal roles of genes in signaling and regulation. Here we present a novel framework for analyzing large cohorts of gene knockout experiments and their genome-wide effects on expression levels. We devise clustering-like algorithms that identify groups of genes that behave similarly with respect to the knockout data, and utilize them to predict knockout effects and to annotate physical interactions between proteins as inhibiting or activating. Differing from previous approaches, our prediction approach does not depend on physical network information; the latter is used only for the annotation task. Consequently, it is both more efficient and of wider applicability than previous methods. We evaluate our approach using a large scale collection of gene knockout experiments in yeast, comparing it to the state-of-the-art SPINE algorithm. In cross validation tests, our algorithm exhibits superior prediction accuracy, while at the same time increasing the coverage by over 25-fold. Significant coverage gains are obtained also in the annotation of the physical network

Chromatin signature of embryonic pluripotency is established during genome activation

available in PMC 2011 April 8.After fertilization the embryonic genome is inactive until transcription is initiated during the maternal–zygotic transition. This transition coincides with the formation of pluripotent cells, which in mammals can be used to generate embryonic stem cells. To study the changes in chromatin structure that accompany pluripotency and genome activation, we mapped the genomic locations of histone H3 molecules bearing lysine trimethylation modifications before and after the maternal–zygotic transition in zebrafish. Histone H3 lysine 27 trimethylation (H3K27me3), which is repressive, and H3K4me3, which is activating, were not detected before the transition. After genome activation, more than 80% of genes were marked by H3K4me3, including many inactive developmental regulatory genes that were also marked by H3K27me3. Sequential chromatin immunoprecipitation demonstrated that the same promoter regions had both trimethylation marks. Such bivalent chromatin domains also exist in embryonic stem cells and are thought to poise genes for activation while keeping them repressed. Furthermore, we found many inactive genes that were uniquely marked by H3K4me3. Despite this activating modification, these monovalent genes were neither expressed nor stably bound by RNA polymerase II. Inspection of published data sets revealed similar monovalent domains in embryonic stem cells. Moreover, H3K4me3 marks could form in the absence of both sequence-specific transcriptional activators and stable association of RNA polymerase II, as indicated by the analysis of an inducible transgene. These results indicate that bivalent and monovalent domains might poise embryonic genes for activation and that the chromatin profile associated with pluripotency is established during the maternal–zygotic transition.National Institutes of Health (U.S.) (grant 1R01 HG004069)National Institutes of Health (U.S.) (grant 5R01 GM56211)Human Frontier Science Program (Strasbourg, France) (LT-00090/2007)European Molecular Biology Organization (fellowship

Dynamic Chromatin Organization during Foregut Development Mediated by the Organ Selector Gene PHA-4/FoxA

Central regulators of cell fate, or selector genes, establish the identity of cells by direct regulation of large cohorts of genes. In Caenorhabditis elegans, foregut (or pharynx) identity relies on the FoxA transcription factor PHA-4, which activates different sets of target genes at various times and in diverse cellular environments. An outstanding question is how PHA-4 distinguishes between target genes for appropriate transcriptional control. We have used the Nuclear Spot Assay and GFP reporters to examine PHA-4 interactions with target promoters in living embryos and with single cell resolution. While PHA-4 was found throughout the digestive tract, binding and activation of pharyngeally expressed promoters was restricted to a subset of pharyngeal cells and excluded from the intestine. An RNAi screen of candidate nuclear factors identified emerin (emr-1) as a negative regulator of PHA-4 binding within the pharynx, but emr-1 did not modulate PHA-4 binding in the intestine. Upon promoter association, PHA-4 induced large-scale chromatin de-compaction, which, we hypothesize, may facilitate promoter access and productive transcription. Our results reveal two tiers of PHA-4 regulation. PHA-4 binding is prohibited in intestinal cells, preventing target gene expression in that organ. PHA-4 binding within the pharynx is limited by the nuclear lamina component EMR-1/emerin. The data suggest that association of PHA-4 with its targets is a regulated step that contributes to promoter selectivity during organ formation. We speculate that global re-organization of chromatin architecture upon PHA-4 binding promotes competence of pharyngeal gene transcription and, by extension, foregut development

Differential Localization and Independent Acquisition of the H3K9me2 and H3K9me3 Chromatin Modifications in the Caenorhabditis elegans Adult Germ Line

Histone methylation is a prominent feature of eukaryotic chromatin that modulates multiple aspects of chromosome function. Methyl modification can occur on several different amino acid residues and in distinct mono-, di-, and tri-methyl states. However, the interplay among these distinct modification states is not well understood. Here we investigate the relationships between dimethyl and trimethyl modifications on lysine 9 of histone H3 (H3K9me2 and H3K9me3) in the adult Caenorhabditis elegans germ line. Simultaneous immunofluorescence reveals very different temporal/spatial localization patterns for H3K9me2 and H3K9me3. While H3K9me2 is enriched on unpaired sex chromosomes and undergoes dynamic changes as germ cells progress through meiotic prophase, we demonstrate here that H3K9me3 is not enriched on unpaired sex chromosomes and localizes to all chromosomes in all germ cells in adult hermaphrodites and until the primary spermatocyte stage in males. Moreover, high-copy transgene arrays carrying somatic-cell specific promoters are highly enriched for H3K9me3 (but not H3K9me2) and correlate with DAPI-faint chromatin domains. We further demonstrate that the H3K9me2 and H3K9me3 marks are acquired independently. MET-2, a member of the SETDB histone methyltransferase (HMTase) family, is required for all detectable germline H3K9me2 but is dispensable for H3K9me3 in adult germ cells. Conversely, we show that the HMTase MES-2, an E(z) homolog responsible for H3K27 methylation in adult germ cells, is required for much of the germline H3K9me3 but is dispensable for H3K9me2. Phenotypic analysis of met-2 mutants indicates that MET-2 is nonessential for fertility but inhibits ectopic germ cell proliferation and contributes to the fidelity of chromosome inheritance. Our demonstration of the differential localization and independent acquisition of H3K9me2 and H3K9me3 implies that the trimethyl modification of H3K9 is not built upon the dimethyl modification in this context. Further, these and other data support a model in which these two modifications function independently in adult C. elegans germ cells