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Joaquin Espinosa-Garcia, Laurent Bonnet, Jose Carlos Corchado
The F + CHD3(v) reaction is a benchmark system in polyatomic reactions. Theoretical/experimental comparisons have been reported in recent years which present some controversies, specifically the role of the reactant CH stretching vibrational excitation, CHD3(v1=1), on the reactivity of both isotope channels, DF(v) + CHD2(v´) and HF(v) + CD3(v´). However, in many cases these comparisons are not made on an equal footing. Previous theoretical studies were concerned with overall reactivity of each isotope channel, while fine velocity map imaging experiments provided results in a product pair-correlated manner...
May 10, 2017: Journal of Physical Chemistry. A
Mario Mastrangelo
Lennox-Gastaut syndrome (LGS) is a severe age-dependent epileptic encephalopathy usually with onset between 1 and 8 years of age. Functional neuroimaging studies recently introduced the concept of Lennox-Gastaut as "secondary network epilepsy" resulting from dysfunctions of a complex system involving both cortical and subcortical structures (default-mode network, corticoreticular connections, and thalamus). These dysfunctions are produced by different disorders including hypoxic-ischemic encephalopathies, meningoencephalitis, cortical malformations, neurocutaneous disorders, or tumors...
March 27, 2017: Neuropediatrics
Yimin Wang, Xiaonan Du, Rao Bin, Shanshan Yu, Zhezhi Xia, Guo Zheng, Jianmin Zhong, Yunjian Zhang, Yong-Hui Jiang, Yi Wang
Genetic factors play a major role in the etiology of epilepsy disorders. Recent genomics studies using next generation sequencing (NGS) technique have identified a large number of genetic variants including copy number (CNV) and single nucleotide variant (SNV) in a small set of genes from individuals with epilepsy. These discoveries have contributed significantly to evaluate the etiology of epilepsy in clinic and lay the foundation to develop molecular specific treatment. However, the molecular basis for a majority of epilepsy patients remains elusive, and furthermore, most of these studies have been conducted in Caucasian children...
January 11, 2017: Scientific Reports
Jung-Ah Kim, Byungjin Hwang, Si Nae Park, Sunghoon Huh, Kyongok Im, Sungbin Choi, Hye Yoon Chung, JooRyung Huh, Eul-Ju Seo, Je-Hwan Lee, Duhee Bang, Dong Soon Lee
Chronic lymphocytic leukemia (CLL) is extremely rare in Asian countries and there has been one report on genetic changes for 5 genes (TP53, SF3B1, NOTCH1, MYD88, and BIRC3) by Sanger sequencing in Chinese CLL. Yet studies of CLL in Asian countries using Next generation sequencing have not been reported. We aimed to characterize the genomic profiles of Korean CLL and to find out ethnic differences in somatic mutations with prognostic implications. We performed targeted sequencing for 87 gene panel using next-generation sequencing along with G-banding and fluorescent in situ hybridization (FISH) for chromosome 12, 13q14...
2016: PloS One
Fengyan Wang, Kopin Liu
A complete set of four polarization-dependent differential cross sections in the reactions of Cl + aligned-CHD3(v1=1,jK)→DCl(v=0)+CHD2(v1=1) is reported here for two different, rotationally polarized states with j = 1: specifically the jK=10 state prepared via the R(0) excitation and the 1±1 state via Q(1). In stark contrast to the complicated situation of the HCl(v) + CD3(v = 0) channel reported in Paper-I, the stereo-requirement of this isotopic channel for both polarized reactants appears quite straightforward and consistent with a direct rebound mechanism...
October 14, 2016: Journal of Chemical Physics
Fengyan Wang, Kopin Liu
When a CHD3 molecule is pumped to the C-H stretching-excited state by absorbing a linearly polarized infrared (IR) photon via the R(0) branch of the v1 = 1←0 transition, the rotational angular momentum j of the prepared state jK=10 preferentially lies in a plane perpendicular to the IR polarization axis εIR. By way of contrast, when the Q(1) branch is used, the state of jK=1±1 is prepared with j aligned along the direction of εIR. Reported here is a detailed study of the title reaction by actively controlling the collision geometries under these two IR-excitation schemes at collision energy Ec = 8...
October 14, 2016: Journal of Chemical Physics
Ingo Helbig, Abou Ahmad N Tayoun
Epileptic encephalopathies are severe often intractable seizure disorders where epileptiform abnormalities contribute to a progressive disturbance in brain function. Often, epileptic encephalopathies start in childhood and are accompanied by developmental delay and various neurological and non-neurological comorbidities. In recent years, this concept has become virtually synonymous with a group of severe childhood epilepsies including West syndrome, Lennox-Gastaut syndrome, Dravet syndrome, and several other severe childhood epilepsies for which genetic factors are increasingly recognized...
September 2016: Molecular Syndromology
Alexandra Gauthier-Vasserot, Christel Thauvin-Robinet, Ange-Line Bruel, Yannis Duffourd, Judith St-Onge, Thibaud Jouan, Jean-Baptiste Rivière, Delphine Heron, Jean Donadieu, Christine Bellanné-Chantelot, Claire Briandet, Frédéric Huet, Paul Kuentz, Daphné Lehalle, Laurence Duplomb-Jego, Elodie Gautier, Isabelle Maystadt, Lucile Pinson, Daniel Amram, Salima El Chehadeh, Judith Melki, Sophia Julia, Laurence Faivre, Julien Thevenon
Neutropenia can be qualified as congenital when of neonatal onset or when associated with extra-hematopoietic manifestations. Overall, 30% of patients with congenital neutropenia (CN) remain without a molecular diagnosis after a multidisciplinary consultation and tedious diagnostic strategy. In the rare situations when neutropenia is identified and associated with intellectual disability (ID), there are few diagnostic hypotheses to test. This retrospective multicenter study reports on a clinically heterogeneous cohort of 10 unrelated patients with CN associated with ID and no molecular diagnosis prior to whole-exome sequencing (WES)...
January 2017: American Journal of Medical Genetics. Part A
Changjian Xie, Bin Jiang, Minghui Yang, Hua Guo
The F + CHD3 → HF/DF + CD3/CHD2 reaction is studied using a state-to-state quasi-classical trajectory method on a recently developed ab initio based full-dimensional potential energy surface. Consistent with sudden vector projection model predictions, the HF/DF products are highly excited in both vibrational and rotational modes, while the CD3/CHD2 product internal excitation is mostly in the umbrella/out-of-plane mode. Furthermore, the C-H stretching vibration in the CHD3 reactant is found to behave as an active mode for the HF + CD3 channel, leading to additional excitation in the HF product but having almost no impact on CD3 vibrational state distributions...
August 25, 2016: Journal of Physical Chemistry. A
Vilius Kurauskas, Elodie Crublet, Pavel Macek, Rime Kerfah, Diego F Gauto, Jérôme Boisbouvier, Paul Schanda
Solid-state NMR spectroscopy allows the characterization of the structure, interactions and dynamics of insoluble and/or very large proteins. Sensitivity and resolution are often major challenges for obtaining atomic-resolution information, in particular for very large protein complexes. Here we show that the use of deuterated, specifically CH3-labelled proteins result in significant sensitivity gains compared to previously employed CHD2 labelling, while line widths increase only marginally. We apply this labelling strategy to a 468 kDa-large dodecameric aminopeptidase, TET2, and the 1...
July 21, 2016: Chemical Communications: Chem Comm
Willem Ma Verhoeven, Jos Im Egger, Alida C Knegt, José Zuydam, Tjitske Kleefstra
Deletions of the 15q26 region encompassing the chromodomain helicase DNA binding domain 2 (CHD2) gene have been associated with intellectual disability, behavioral problems, and several types of epilepsy. Including the cases mentioned in ECARUCA (European cytogeneticists association register of unbalanced chromosome aberrations) and DECIPHER (database of genomic variation and phenotype in humans using ensembl resources), so far, a total of 13 intellectually disabled patients with a genetically proven deletion of the CHD2 gene are described, of whom eleven had a history of severe forms of epilepsy starting from a young age...
2016: Neuropsychiatric Disease and Treatment
Enrico Rennella, Anne K Schuetz, Lewis E Kay
Methyl groups have emerged as powerful probes of protein dynamics with timescales from picoseconds to seconds. Typically, studies involving high molecular weight complexes exploit (13)CH3- or (13)CHD2-labeling in otherwise highly deuterated proteins. The (13)CHD2 label offers the unique advantage of providing (13)C, (1)H and (2)H spin probes, however a disadvantage has been the lack of an experiment to record (13)C Carr-Purcell-Meiboom-Gill relaxation dispersion that monitors millisecond time-scale dynamics, implicated in a wide range of biological processes...
June 2016: Journal of Biomolecular NMR
Nisar A Amin, Erlene Seymour, Kamlai Saiya-Cork, Brian Parkin, Kerby Shedden, Sami N Malek
PURPOSE: Chronic lymphocytic leukemia (CLL)-associated gene mutations that influence CLL cell fitness and chemotherapy resistance should increase in clonal representation when measured before therapy and at relapse. EXPERIMENTAL DESIGN: To uncover mutations associated with CLL relapse, we have performed whole-exome sequencing in a discovery cohort of 61 relapsed CLL patients identifying 86 recurrently mutated genes. The variant allele fractions (VAF) of 19 genes with mutations in ≥3 of 61 cases were measured in 53 paired pre- and posttreatment CLL samples sorted to purity using panel-based deep resequencing or by droplet digital PCR...
September 1, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Rebecca García Sosa, Srishti Nangia
Investigators from multinational institutions hypothesized that disruption of CHD2, which encodes chromodomain helicase DNA-binding protein 2, would be associated with common forms of photosensitive epilepsy or photosensitivity manifesting as a photoparoxysmal response alone.
September 2015: Pediatric neurology briefs
Martijn S Luijsterburg, Inge de Krijger, Wouter W Wiegant, Rashmi G Shah, Godelieve Smeenk, Anton J L de Groot, Alex Pines, Alfred C O Vertegaal, Jacqueline J L Jacobs, Girish M Shah, Haico van Attikum
The response to DNA double-strand breaks (DSBs) requires alterations in chromatin structure to promote the assembly of repair complexes on broken chromosomes. Non-homologous end-joining (NHEJ) is the dominant DSB repair pathway in human cells, but our understanding of how it operates in chromatin is limited. Here, we define a mechanism that plays a crucial role in regulating NHEJ in chromatin. This mechanism is initiated by DNA damage-associated poly(ADP-ribose) polymerase 1 (PARP1), which recruits the chromatin remodeler CHD2 through a poly(ADP-ribose)-binding domain...
February 18, 2016: Molecular Cell
Maud de Dieuleveult, Kuangyu Yen, Isabelle Hmitou, Arnaud Depaux, Fayçal Boussouar, Daria Bou Dargham, Sylvie Jounier, Hélène Humbertclaude, Florence Ribierre, Céline Baulard, Nina P Farrell, Bongsoo Park, Céline Keime, Lucie Carrière, Soizick Berlivet, Marta Gut, Ivo Gut, Michel Werner, Jean-François Deleuze, Robert Olaso, Jean-Christophe Aude, Sophie Chantalat, B Franklin Pugh, Matthieu Gérard
ATP-dependent chromatin remodellers allow access to DNA for transcription factors and the general transcription machinery, but whether mammalian chromatin remodellers target specific nucleosomes to regulate transcription is unclear. Here we present genome-wide remodeller-nucleosome interaction profiles for the chromatin remodellers Chd1, Chd2, Chd4, Chd6, Chd8, Chd9, Brg1 and Ep400 in mouse embryonic stem (ES) cells. These remodellers bind one or both full nucleosomes that flank micrococcal nuclease (MNase)-defined nucleosome-free promoter regions (NFRs), where they separate divergent transcription...
February 4, 2016: Nature
J Espinosa-Garcia
To analyze the role of CH-stretching vibrational excitation on the reactivity and dynamics of the F((2)P) + CHD3(v1=0,1) reactions, quasiclassical trajectory calculations using a full-dimensional analytical potential energy surface at different collision energies were performed. The extra energy of the CH excitation had almost no effect on the reactivity for the DF + CHD2 channel, although it increased the reactivity for the HF + CD3 channel, with the net effect being that CH excitation barely modified overall reactivity...
January 14, 2016: Journal of Physical Chemistry. A
Roei Levy, Richard F Mott, Fuad A Iraqi, Yankel Gabet
BACKGROUND: The microstructure of trabecular bone is a composite trait governed by a complex interaction of multiple genetic determinants. Identifying these genetic factors should significantly improve our ability to predict of osteoporosis and its associated risks. Genetic mapping using collaborative cross mice (CC), a genetically diverse recombinant inbred mouse reference panel, offers a powerful tool to identify causal loci at a resolution under one mega base-pairs, with a relatively small cohort size...
November 26, 2015: BMC Genomics
Enrico Rennella, Rui Huang, Algirdas Velyvis, Lewis E Kay
An NMR experiment for quantifying slow (millisecond) time-scale exchange processes involving the interconversion between visible ground state and invisible, conformationally excited state conformers is presented. The approach exploits chemical exchange saturation transfer (CEST) and makes use of (13)CHD2 methyl group probes that can be readily incorporated into otherwise highly deuterated proteins. The methodology is validated with an application to a G48A Fyn SH3 domain that exchanges between a folded conformation and a sparsely populated and transiently formed unfolded ensemble...
October 2015: Journal of Biomolecular NMR
Juliana Palma, Uwe Manthe
Quasiclassical trajectories (QCT) have been employed to elucidate the effect of exciting the C-H bond in F + CHD3 collisions. The calculations were performed on a new potential energy surface that accurately describes the van der Waals complexes in the entrance channel of the reaction. It was found that exciting the C-H bond significantly enhances the yield of HF + CD3, whereas it has a minor effect on the production of DF + CHD2. Therefore, the net effect is that the total reactivity increases upon excitation...
December 17, 2015: Journal of Physical Chemistry. A
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