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https://www.readbyqxmd.com/read/28535409/mesial-temporal-lobe-epilepsy-diminishes-functional-connectivity-during-emotion-perception
#1
Bettina K Steiger, Angela M Muller, Esther Spirig, Gianina Toller, Hennric Jokeit
OBJECTIVES: Unilateral mesial temporal lobe epilepsy (MTLE) has been associated with impaired recognition of emotional facial expressions. Correspondingly, imaging studies showed decreased activity of the amygdala and cortical face processing regions in response to emotional faces. However, functional connectivity among regions involved in emotion perception has not been studied so far. METHODS: To address this, we examined intrinsic functional connectivity (FC) modulated by the perception of dynamic fearful faces among the amygdala and limbic, frontal, temporal and brainstem regions...
May 10, 2017: Epilepsy Research
https://www.readbyqxmd.com/read/28524624/pulmonary-arterial-hypertension-progress-in-understanding-the-disease-and-prioritizing-strategies-for-drug-development
#2
REVIEW
P Ghataorhe, C J Rhodes, L Harbaum, M Attard, J Wharton, M R Wilkins
Pulmonary arterial hypertension (PAH), at one time a largely overlooked disease, is now the subject of intense study in many academic and biotech groups. The availability of new treatments has increased awareness of the condition. This in turn has driven a change in the demographics of PAH, with an increase in the mean age at diagnosis. The diagnosis of PAH in more elderly patients has highlighted the need for careful phenotyping of patients and for further studies to understand how best to manage pulmonary hypertension associated with, for example, left heart disease...
May 19, 2017: Journal of Internal Medicine
https://www.readbyqxmd.com/read/28507139/long-read-sequencing-uncovers-the-adaptive-topography-of-a-carnivorous-plant-genome
#3
Tianying Lan, Tanya Renner, Enrique Ibarra-Laclette, Kimberly M Farr, Tien-Hao Chang, Sergio Alan Cervantes-Pérez, Chunfang Zheng, David Sankoff, Haibao Tang, Rikky W Purbojati, Alexander Putra, Daniela I Drautz-Moses, Stephan C Schuster, Luis Herrera-Estrella, Victor A Albert
Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains a tiny nuclear genome despite at least two rounds of whole genome duplication (WGD) since common ancestry with grapevine and other species. We used a third-generation genome assembly with several complete chromosomes to reconstruct the two most recent lineage-specific ancestral genomes that led to the modern U. gibba genome structure. Patterns of subgenome dominance in the most recent WGD, both architectural and transcriptional, are suggestive of allopolyploidization, which may have generated genomic novelty and led to instantaneous speciation...
May 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28505093/the-crucial-role-of-dna-methylation-and-mecp2-in-neuronal-function
#4
REVIEW
Maria Fasolino, Zhaolan Zhou
A neuron is unique in its ability to dynamically modify its transcriptional output in response to synaptic activity while maintaining a core gene expression program that preserves cellular identity throughout a lifetime that is longer than almost every other cell type in the body. A contributing factor to the immense adaptability of a neuron is its unique epigenetic landscape that elicits locus-specific alterations in chromatin architecture, which in turn influences gene expression. One such epigenetic modification that is sensitive to changes in synaptic activity, as well as essential for maintaining cellular identity, is DNA methylation...
May 13, 2017: Genes
https://www.readbyqxmd.com/read/28489315/mechanically-guided-deterministic-assembly-of-3d-mesostructures-assisted-by-residual-stresses
#5
Haoran Fu, Kewang Nan, Paul Froeter, Wen Huang, Yuan Liu, Yiqi Wang, Juntong Wang, Zheng Yan, Haiwen Luan, Xiaogang Guo, Yijie Zhang, Changqing Jiang, Luming Li, Alison C Dunn, Xiuling Li, Yonggang Huang, Yihui Zhang, John A Rogers
Formation of 3D mesostructures in advanced functional materials is of growing interest due to the widespread envisioned applications of devices that exploit 3D architectures. Mechanically guided assembly based on compressive buckling of 2D precursors represents a promising method, with applicability to a diverse set of geometries and materials, including inorganic semiconductors, metals, polymers, and their heterogeneous combinations. This paper introduces ideas that extend the levels of control and the range of 3D layouts that are achievable in this manner...
May 10, 2017: Small
https://www.readbyqxmd.com/read/28475873/structure-and-dynamics-of-a-197%C3%A2-bp-nucleosome-in-complex-with-linker-histone-h1
#6
Jan Bednar, Isabel Garcia-Saez, Ramachandran Boopathi, Amber R Cutter, Gabor Papai, Anna Reymer, Sajad H Syed, Imtiaz Nisar Lone, Ognyan Tonchev, Corinne Crucifix, Hervé Menoni, Christophe Papin, Dimitrios A Skoufias, Hitoshi Kurumizaka, Richard Lavery, Ali Hamiche, Jeffrey J Hayes, Patrick Schultz, Dimitar Angelov, Carlo Petosa, Stefan Dimitrov
Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp nucleosome bearing symmetric 25 bp linker DNA arms in complex with vertebrate linker histone H1. We determined electron cryo-microscopy (cryo-EM) and crystal structures of unbound and H1-bound nucleosomes and validated these structures by site-directed protein cross-linking and hydroxyl radical footprinting experiments...
May 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28475225/the-adaptive-genomic-landscape-of-beak-morphology-in-darwin-s-finches
#7
Lucinda P Lawson, Kenneth Petren
Beak shape in Darwin's ground finches (Geospiza) is emblematic of natural selection and adaptive radiation, yet our understanding of the genetic basis of beak shape variation, and thus the genetic target of natural selection, is still evolving. Here we reveal the genomic architecture of beak shape variation using genome-wide comparisons of four closely related and hybridizing species across 13 islands subject to parallel natural selection. Pairwise contrasts among species were used to identify a large number of genomic loci that are consistently related to species differences across a complex landscape...
May 5, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28474175/the-hmga-gene-family-in-chordates-evolutionary-perspectives-from-amphioxus
#8
Matteo Bozzo, Simone Macrì, Daniela Calzia, Riccardo Sgarra, Guidalberto Manfioletti, Paola Ramoino, Thurston Lacalli, Robert Vignali, Mario Pestarino, Simona Candiani
High mobility group A proteins of vertebrates, HMGA1 and 2, are chromatin architectural factors involved in development, cell differentiation, and neoplastic transformation. Here, we characterize an amphioxus HMGA gene ortholog and analyze its expression. As a basal chordate, amphioxus is well placed to provide insights into the evolution of the HMGA gene family, particularly in the transition from invertebrates to vertebrates. Our phylogenetic analysis supports the basal position of amphioxus, echinoderm, and hemichordate HMGA sequences to those of vertebrate HMGA1 and HMGA2...
May 4, 2017: Development Genes and Evolution
https://www.readbyqxmd.com/read/28446118/motor-neurone-disease-progress-and-challenges
#9
REVIEW
Thanuja Dharmadasa, Robert D Henderson, Paul S Talman, Richard Al Macdonell, Susan Mathers, David W Schultz, Merrillee Needham, Margaret Zoing, Steve Vucic, Matthew C Kiernan
Major progress has been made over the past decade in the understanding of motor neurone disease (MND), changing the landscape of this complex disease. Through identifying positive prognostic factors, new evidence-based standards of care have been established that improve patient survival, reduce burden of disease for patients and their carers, and enhance quality of life. These factors include early management of respiratory dysfunction with non-invasive ventilation, maintenance of weight and nutritional status, as well as instigation of a multidisciplinary team including neurologists, general practitioners and allied health professionals...
May 1, 2017: Medical Journal of Australia
https://www.readbyqxmd.com/read/28436955/vitamin-a-mediates-conversion-of-monocyte-derived-macrophages-into-tissue-resident-macrophages-during-alternative-activation
#10
Uma Mahesh Gundra, Natasha M Girgis, Michael A Gonzalez, Mei San Tang, Hendrik J P Van Der Zande, Jian-Da Lin, Mireille Ouimet, Lily J Ma, Jordan Poles, Nikollaq Vozhilla, Edward A Fisher, Kathryn J Moore, P'ng Loke
It remains unclear whether activated inflammatory macrophages can adopt features of tissue-resident macrophages, or what mechanisms might mediate such a phenotypic conversion. Here we show that vitamin A is required for the phenotypic conversion of interleukin 4 (IL-4)-activated monocyte-derived F4/80(int)CD206(+)PD-L2(+)MHCII(+) macrophages into macrophages with a tissue-resident F4/80(hi)CD206(-)PD-L2(-)MHCII(-)UCP1(+) phenotype in the peritoneal cavity of mice and during the formation of liver granulomas in mice infected with Schistosoma mansoni...
April 24, 2017: Nature Immunology
https://www.readbyqxmd.com/read/28413161/rapid-and-recent-evolution-of-ltr-retrotransposons-drives-rice-genome-evolution-during-the-speciation-of-aa-genome-oryza-species
#11
Qun-Jie Zhang, Li-Zhi Gao
The dynamics of LTR retrotransposons and their contribution to genome evolution during plant speciation have remained largely unanswered. Here, we perform a genome-wide comparison of all eight Oryza AA- genome species, and identify 3,911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ~4.8 Myr. Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes...
April 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28407093/non-random-inversion-landscapes-in-prokaryotic-genomes-are-shaped-by-heterogeneous-selection-pressures
#12
Jelena Repar, Tobias Warnecke
Inversions are a major contributor to structural genome evolution in prokaryotes. Here, using a novel alignment-based method, we systematically compare 1651 bacterial and 98 archaeal genomes to show that inversion landscapes are frequently biased towards (symmetric) inversions around the origin-terminus axis. However, symmetric inversion bias is not a universal feature of prokaryotic genome evolution but varies considerably across clades. At the extremes, inversion landscapes in Bacillus-Clostridium and Actinobacteria are dominated by symmetric inversions, while there is little or no systematic bias favouring symmetric rearrangements in archaea with a single origin of replication...
April 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28400425/the-logic-of-transcriptional-regulator-recruitment-architecture-at-cis-regulatory-modules-controlling-liver-functions
#13
Julie Dubois-Chevalier, Vanessa Dubois, Hélène Dehondt, Parisa Mazrooei, Claire Mazuy, Aurélien A Sérandour, Céline Gheeraert, Penderia Guillaume, Eric Baugé, Bruno Derudas, Nathalie Hennuyer, Réjane Paumelle, Guillemette Marot, Jason S Carroll, Mathieu Lupien, Bart Staels, Philippe Lefebvre, Jérôme Eeckhoute
Control of gene transcription relies on concomitant regulation by multiple transcriptional regulators (TRs). However, how recruitment of a myriad of TRs is orchestrated at cis-regulatory modules (CRMs) to account for coregulation of specific biological pathways is only partially understood. Here, we have used mouse liver CRMs involved in regulatory activities of the hepatic TR, NR1H4 (FXR; farnesoid X receptor), as our model system to tackle this question. Using integrative cistromic, epigenomic, transcriptomic, and interactomic analyses, we reveal a logical organization where trans-regulatory modules (TRMs), which consist of subsets of preferentially and coordinately corecruited TRs, assemble into hierarchical combinations at hepatic CRMs...
April 11, 2017: Genome Research
https://www.readbyqxmd.com/read/28390838/super-resolution-microscopy-approaches-to-nuclear-nanostructure-imaging
#14
Christoph Cremer, Aleksander Szczurek, Florian Schock, Amine Gourram, Udo Birk
The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has far-reaching functional consequences for gene regulation. Until recently, it appeared to be impossible to study this problem on the nanoscale by light microscopy. However, novel developments in optical imaging technology have radically surpassed the limited resolution of conventional far-field fluorescence microscopy (ca...
April 5, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28380286/folding-of-proteins-with-a-flavodoxin-like-architecture
#15
REVIEW
Joseline A Houwman, Carlo P M van Mierlo
The flavodoxin-like fold is a protein-architecture that can be traced back to the universal ancestor of the three kingdoms of life. Many proteins share this α-β parallel topology and hence it is highly relevant to illuminate how they fold. Here, we review experiments and simulations concerning the folding of flavodoxins and CheY-like proteins, which share the flavodoxin-like fold. These polypeptides tend to temporarily misfold during unassisted folding to their functionally active forms. This susceptibility to frustration is caused by the more rapid formation of an α-helix compared to a β-sheet, particularly when a parallel β-sheet is involved...
April 5, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28360231/combination-of-short-read-long-read-and-optical-mapping-assemblies-reveals-large-scale-tandem-repeat-arrays-with-population-genetic-implications
#16
Matthias H Weissensteiner, Andy W C Pang, Ignas Bunikis, Ida Höijer, Olga Vinnere-Petterson, Alexander Suh, Jochen B W Wolf
Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow...
May 2017: Genome Research
https://www.readbyqxmd.com/read/28330771/deciphering-the-molecular-architecture-of-membrane-contact-sites-by-cryo-electron-tomography
#17
REVIEW
Javier Collado, Rubén Fernández-Busnadiego
At membrane contact sites (MCS) two cellular membranes form tight appositions that play critical roles in fundamental phenomena such as lipid metabolism or Ca(2+) homeostasis. The interest for these structures has surged in recent years, bringing about the characterization of a plethora of MCS-resident molecules. How those molecules are structurally organized at MCS remains enigmatic, limiting our understanding of MCS function. Whereas such molecular detail is obscured by conventional electron microscopy sample preparation, cryo-electron tomography (cryo-ET) allows high resolution imaging of cellular landscapes in close-to-native conditions...
March 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28317958/the-collective-behavior-of-spring-like-motifs-tethered-to-a-dna-origami-nanostructure
#18
E-C Schöneweiß, B Saccà
Dynamic DNA nanotechnology relies on the integration of small switchable motifs at suitable positions of DNA nanostructures, thus enabling the manipulation of matter with nanometer spatial accuracy in a trigger-dependent fashion. Typical examples of such motifs are hairpins, whose elongation into duplexes can be used to perform long-range, translational movements. In this work, we used temperature-dependent FRET spectroscopy to determine the thermal stabilities of distinct sets of hairpins integrated into the central seam of a DNA origami structure...
March 20, 2017: Nanoscale
https://www.readbyqxmd.com/read/28315713/maternal-senp7-programs-meiosis-architecture-and-embryo-survival-in-mouse
#19
Chun-Jie Huang, Di Wu, Xiao-Fei Jiao, Faheem Ahmed Khan, Cheng-Liang Xiong, Xiao-Ming Liu, Jing Yang, Tai-Lang Yin, Li-Jun Huo
Understanding the mechanisms underlying abnormal egg production and pregnancy loss is significant for human fertility. SENP7, a SUMO poly-chain editing enzyme, has been regarded as a mitotic regulator of heterochromatin integrity and DNA repair. Herein, we report the roles of SENP7 in mammalian reproductive scenario. Mouse oocytes deficient in SENP7 experienced meiotic arrest at prophase I and metaphase I stages, causing a substantial decrease of mature eggs. Hyperaceylation and hypomethylation of histone H3 and up-regulation of Cdc14B/C accompanied by down-regulation of CyclinB1 and CyclinB2 were further recognized as contributors to defective M-phase entry and spindle assembly in oocytes...
March 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28302711/precision-and-prognostic-value-of-clone-specific-minimal-residual-disease-in-acute-myeloid-leukemia
#20
Pierre Hirsch, Ruoping Tang, Nassera Abermil, Pascale Flandrin, Hannah Moatti, Fabrizia Favale, Ludovic Suner, Florence Lorre, Christophe Marzac, Fanny Fava, Anne-Claire Mamez, Simona Lapusan, Françoise Isnard, Mohamad Mohty, Ollivier Legrand, Luc Douay, Chrystele Bilhou-Nabera, François Delhommeau
The genetic landscape of adult acute myeloid leukemias has been recently unraveled. However, due to their genetic heterogeneity, only a handful of markers are currently used for the evaluation of minimal residual disease. Recent studies using multi-target strategies indicate that detection of residual mutations in less than 5% of cells in complete remission is associated with a better survival. Here, in a series of 69 acute myeloid leukemias with known clonal architecture, we design a clone-specific strategy based on fluorescent in situ hybridization and high-sensitivity next generation sequencing to detect chromosomal aberrations and mutations, respectively, in follow-up samples...
March 16, 2017: Haematologica
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