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https://www.readbyqxmd.com/read/29785028/the-reference-epigenome-and-regulatory-chromatin-landscape-of-chronic-lymphocytic-leukemia
#1
Renée Beekman, Vicente Chapaprieta, Núria Russiñol, Roser Vilarrasa-Blasi, Núria Verdaguer-Dot, Joost H A Martens, Martí Duran-Ferrer, Marta Kulis, François Serra, Biola M Javierre, Steven W Wingett, Guillem Clot, Ana C Queirós, Giancarlo Castellano, Julie Blanc, Marta Gut, Angelika Merkel, Simon Heath, Anna Vlasova, Sebastian Ullrich, Emilio Palumbo, Anna Enjuanes, David Martín-García, Sílvia Beà, Magda Pinyol, Marta Aymerich, Romina Royo, Montserrat Puiggros, David Torrents, Avik Datta, Ernesto Lowy, Myrto Kostadima, Maša Roller, Laura Clarke, Paul Flicek, Xabier Agirre, Felipe Prosper, Tycho Baumann, Julio Delgado, Armando López-Guillermo, Peter Fraser, Marie-Laure Yaspo, Roderic Guigó, Reiner Siebert, Marc A Martí-Renom, Xose S Puente, Carlos López-Otín, Ivo Gut, Hendrik G Stunnenberg, Elias Campo, Jose I Martin-Subero
Chronic lymphocytic leukemia (CLL) is a frequent hematological neoplasm in which underlying epigenetic alterations are only partially understood. Here, we analyze the reference epigenome of seven primary CLLs and the regulatory chromatin landscape of 107 primary cases in the context of normal B cell differentiation. We identify that the CLL chromatin landscape is largely influenced by distinct dynamics during normal B cell maturation. Beyond this, we define extensive catalogues of regulatory elements de novo reprogrammed in CLL as a whole and in its major clinico-biological subtypes classified by IGHV somatic hypermutation levels...
May 21, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29778791/evolutionary-transitions-in-controls-reconcile-adaptation-with-continuity-of-evolution
#2
REVIEW
Alexander V Badyaev
Evolution proceeds by accumulating functional solutions, necessarily forming an uninterrupted lineage from past solutions of ancestors to the current design of extant forms. At the population level, this process requires an organismal architecture in which the maintenance of local adaptation does not preclude the ability to innovate in the same traits and their continuous evolution. Representing complex traits as networks enables us to visualize a fundamental principle that resolves tension between adaptation and continuous evolution: phenotypic states encompassing adaptations traverse the continuous multi-layered landscape of past physical, developmental and functional associations among traits...
May 17, 2018: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29774116/human-papilloma-virus-global-research-architecture-assessed-by-density-equalizing-mapping
#3
Dörthe Brüggmann, Luise Kayser, Jenny Jaque, Matthias Bundschuh, Doris Klingelhöfer, David A Groneberg
Human papilloma virus (HPV) infection is linked to cervical cancer, which represents the world's fourth most common cancer in women. So far, no detailed map of the worldwide HPV research architecture has been constructed. Hence, this study focuses on the chronological development and geographical distribution of the global HPV-specific publications and evaluates citation-based parameters as well as socioeconomic features of the publishing countries. In total, 29,330 HPV-related publications were identified...
April 24, 2018: Oncotarget
https://www.readbyqxmd.com/read/29751068/multidimensional-brain-activity-dictated-by-winner-take-all-mechanisms
#4
Arturo Tozzi, James F Peters
A novel demon-based architecture is introduced to elucidate brain functions such as pattern recognition during human perception and mental interpretation of visual scenes. Starting from the topological concepts of invariance and persistence, we introduce a Selfridge pandemonium variant of brain activity that takes into account a novel feature, namely, demons that recognize short straight-line segments, curved lines and scene shapes, such as shape interior, density and texture. Low-level representations of objects can be mapped to higher-level views (our mental interpretations): a series of transformations can be gradually applied to a pattern in a visual scene, without affecting its invariant properties...
May 8, 2018: Neuroscience Letters
https://www.readbyqxmd.com/read/29743253/modern-spandrels-the-roles-of-genetic-drift-gene-flow-and-natural-selection-in-the-evolution-of-parallel-clines
#5
James S Santangelo, Marc T J Johnson, Rob W Ness
Urban environments offer the opportunity to study the role of adaptive and non-adaptive evolutionary processes on an unprecedented scale. While the presence of parallel clines in heritable phenotypic traits is often considered strong evidence for the role of natural selection, non-adaptive evolutionary processes can also generate clines, and this may be more likely when traits have a non-additive genetic basis due to epistasis. In this paper, we use spatially explicit simulations modelled according to the cyanogenesis (hydrogen cyanide, HCN) polymorphism in white clover ( Trifolium repens ) to examine the formation of phenotypic clines along urbanization gradients under varying levels of drift, gene flow and selection...
May 16, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29728251/a-future-proof-architecture-for-telemedicine-using-loose-coupled-modules-and-hl7-fhir
#6
Kirstine Rosenbeck Gøeg, Rune Kongsgaard Rasmussen, Lasse Jensen, Christian Møller Wollesen, Søren Larsen, Louise Bilenberg Pape-Haugaard
BACKGROUND AND OBJECTIVES: Most telemedicine solutions are proprietary and disease specific which cause a heterogeneous and silo-oriented system landscape with limited interoperability. Solving the interoperability problem would require a strong focus on data integration and standardization in telemedicine infrastructures. Our objective was to suggest a future-proof architecture, that consisted of small loose-coupled modules to allow flexible integration with new and existing services, and the use of international standards to allow high re-usability of modules, and interoperability in the health IT landscape...
July 2018: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/29724048/neighbourhood-built-environment-influences-on-physical-activity-among-adults-a-systematized-review-of-qualitative-evidence
#7
REVIEW
Grazia Salvo, Bonnie M Lashewicz, Patricia K Doyle-Baker, Gavin R McCormack
Qualitative studies can provide important information about how and why the built environment impacts physical activity decision-making—information that is important for informing local urban policies. We undertook a systematized literature review to synthesize findings from qualitative studies exploring how the built environment influences physical activity in adults. Our review included 36 peer-reviewed qualitative studies published from 1998 onwards. Our findings complemented existing quantitative evidence and provided additional insight into how functional, aesthetic, destination, and safety built characteristics influence physical activity decision-making...
May 2, 2018: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29718366/intratumoral-heterogeneity-of-oxygen-metabolism-and-neovascularization-uncovers-two-survival-relevant-subgroups-of-idh1-wild-type-glioblastoma
#8
Andreas Stadlbauer, Max Zimmermann, Arnd Doerfler, Stefan Oberndorfer, Michael Buchfelder, Roland Coras, Melitta Kitzwögerer, Karl Roessler
Background: The intratumoral heterogeneity of oxygen metabolism in combination with variable patterns of neovascularization (NV) as well as reprogramming of energy metabolism affects the landscape of tumor microenvironments (TMEs) in glioblastoma. Knowledge of the hypoxic and perivascular niches within the TME is essential for understanding treatment failure. Methods: Fifty-two patients with untreated glioblastoma (IDH1 wildtype) were examined with a physiological MRI protocol including a multiparametric quantitative blood-oxygen-level-dependent (qBOLD) approach and vascular architecture mapping (VAM)...
April 28, 2018: Neuro-oncology
https://www.readbyqxmd.com/read/29712755/a-comparative-transcriptional-landscape-of-maize-and-sorghum-obtained-by-single-molecule-sequencing
#9
Bo Wang, Michael Regulski, Elizabeth Tseng, Andrew Olson, Sara Goodwin, W Richard McCombie, Doreen Ware
Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared expression profiles of both protein-coding and noncoding transcripts in 11 matched tissues using single-molecule, long-read, deep RNA sequencing. This comparative analysis revealed large numbers of novel isoforms in both species. Evolutionarily young genes were likely to be generated in reproductive tissues and usually had fewer isoforms than old genes...
April 30, 2018: Genome Research
https://www.readbyqxmd.com/read/29708965/topological-and-statistical-analyses-of-gene-regulatory-networks-reveal-unifying-yet-quantitatively-different-emergent-properties
#10
Wilberforce Zachary Ouma, Katja Pogacar, Erich Grotewold
Understanding complexity in physical, biological, social and information systems is predicated on describing interactions amongst different components. Advances in genomics are facilitating the high-throughput identification of molecular interactions, and graphs are emerging as indispensable tools in explaining how the connections in the network drive organismal phenotypic plasticity. Here, we describe the architectural organization and associated emergent topological properties of gene regulatory networks (GRNs) that describe protein-DNA interactions (PDIs) in several model eukaryotes...
April 30, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29700467/digestion-ligation-only-hi-c-is-an-efficient-and-cost-effective-method-for-chromosome-conformation-capture
#11
Da Lin, Ping Hong, Siheng Zhang, Weize Xu, Muhammad Jamal, Keji Yan, Yingying Lei, Liang Li, Yijun Ruan, Zhen F Fu, Guoliang Li, Gang Cao
Chromosome conformation capture (3C) technologies can be used to investigate 3D genomic structures. However, high background noise, high costs, and a lack of straightforward noise evaluation in current methods impede the advancement of 3D genomic research. Here we developed a simple digestion-ligation-only Hi-C (DLO Hi-C) technology to explore the 3D landscape of the genome. This method requires only two rounds of digestion and ligation, without the need for biotin labeling and pulldown. Non-ligated DNA was efficiently removed in a cost-effective step by purifying specific linker-ligated DNA fragments...
April 26, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29695764/integrative-network-analyses-of-wilt-transcriptome-in-chickpea-reveal-genotype-dependent-regulatory-hubs-in-immunity-and-susceptibility
#12
Nasheeman Ashraf, Swaraj Basu, Kanika Narula, Sudip Ghosh, Rajul Tayal, Nagaraju Gangisetty, Sushmita Biswas, Pooja R Aggarwal, Niranjan Chakraborty, Subhra Chakraborty
Host specific resistance and non-host resistance are two plant immune responses to counter pathogen invasion. Gene network organizing principles leading to quantitative differences in resistant and susceptible host during host specific resistance are poorly understood. Vascular wilt caused by root pathogen Fusarium species is complex and governed by host specific resistance in crop plants, including chickpea. Here, we temporally profiled two contrasting chickpea genotypes in disease and immune state to better understand gene expression switches in host specific resistance...
April 25, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29691395/epigenetic-landscape-influences-the-liver-cancer-genome-architecture
#13
Natsuko Hama, Yasushi Totoki, Fumihito Miura, Kenji Tatsuno, Mihoko Saito-Adachi, Hiromi Nakamura, Yasuhito Arai, Fumie Hosoda, Tomoko Urushidate, Shoko Ohashi, Wakako Mukai, Nobuyoshi Hiraoka, Hiroyuki Aburatani, Takashi Ito, Tatsuhiro Shibata
The accumulations of different types of genetic alterations such as nucleotide substitutions, structural rearrangements and viral genome integrations and epigenetic alterations contribute to carcinogenesis. Here, we report correlation between the occurrence of epigenetic features and genetic aberrations by whole-genome bisulfite, whole-genome shotgun, long-read, and virus capture sequencing of 373 liver cancers. Somatic substitutions and rearrangement breakpoints are enriched in tumor-specific hypo-methylated regions with inactive chromatin marks and actively transcribed highly methylated regions in the cancer genome...
April 24, 2018: Nature Communications
https://www.readbyqxmd.com/read/29686034/topologically-associating-domains-in-chromosome-architecture-and-gene-regulatory-landscapes-during-development-disease-and-evolution
#14
Rafael Galupa, Edith Heard
The packaging of genetic material into chromatin and chromosomes has been recognized for more than a century, thanks to microscopy and biochemical approaches. This was followed by the progressive realization that chromatin organization is critical for genome functions such as transcription and DNA replication and repair. The recent discovery that chromosomes are partitioned at the submegabase scale into topologically associating domains (TADs) has implications for our understanding of gene regulation during developmental processes such as X-chromosome inactivation, as well as for evolution and for the search for disease-associated loci...
April 23, 2018: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29684403/white-matter-pathways-and-social-cognition
#15
REVIEW
Yin Wang, Athanasia Metoki, Kylie H Alm, Ingrid R Olson
There is a growing consensus that social cognition and behavior emerge from interactions across distributed regions of the "social brain". Researchers have traditionally focused their attention on functional response properties of these gray matter networks and neglected the vital role of white matter connections in establishing such networks and their functions. In this article, we conduct a comprehensive review of prior research on structural connectivity in social neuroscience and highlight the importance of this literature in clarifying brain mechanisms of social cognition...
April 20, 2018: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/29683387/primary-transcriptome-analysis-reveals-importance-of-is-elements-for-the-shaping-of-the-transcriptional-landscape-of-bordetella-pertussis
#16
Fabian Amman, Alexandre D'Halluin, Rudy Antoine, Ludovic Huot, Ilona Bibova, Kristina Keidel, Stéphanie Slupek, Peggy Bouquet, Loïc Coutte, Ségolène Caboche, Camille Locht, Branislav Vecerek, David Hot
Bordetella pertussis is the causative agent of whooping cough, a respiratory disease still considered as a major public health threat and for which recent re-emergence has been observed. Constant reshuffling of Bordetella pertussis genome organization was observed during evolution. These rearrangements are essentially mediated by Insertion Sequences (IS), a mobile genetic elements present in more than 230 copies in the genome, which are supposed to be one of the driving forces enabling the pathogen to escape from vaccine-induced immunity...
April 23, 2018: RNA Biology
https://www.readbyqxmd.com/read/29681457/the-evolutionary-landscape-of-localized-prostate-cancers-drives-clinical-aggression
#17
Shadrielle Melijah G Espiritu, Lydia Y Liu, Yulia Rubanova, Vinayak Bhandari, Erle M Holgersen, Lesia M Szyca, Natalie S Fox, Melvin L K Chua, Takafumi N Yamaguchi, Lawrence E Heisler, Julie Livingstone, Jeff Wintersinger, Fouad Yousif, Emilie Lalonde, Alexandre Rouette, Adriana Salcedo, Kathleen E Houlahan, Constance H Li, Vincent Huang, Michael Fraser, Theodorus van der Kwast, Quaid D Morris, Robert G Bristow, Paul C Boutros
The majority of newly diagnosed prostate cancers are slow growing, with a long natural life history. Yet a subset can metastasize with lethal consequences. We reconstructed the phylogenies of 293 localized prostate tumors linked to clinical outcome data. Multiple subclones were detected in 59% of patients, and specific subclonal architectures associate with adverse clinicopathological features. Early tumor development is characterized by point mutations and deletions followed by later subclonal amplifications and changes in trinucleotide mutational signatures...
May 3, 2018: Cell
https://www.readbyqxmd.com/read/29674791/research-design-the-methodology-for-interdisciplinary-research-framework
#18
Hilde Tobi, Jarl K Kampen
Many of today's global scientific challenges require the joint involvement of researchers from different disciplinary backgrounds (social sciences, environmental sciences, climatology, medicine, etc.). Such interdisciplinary research teams face many challenges resulting from differences in training and scientific culture. Interdisciplinary education programs are required to train truly interdisciplinary scientists with respect to the critical factor skills and competences. For that purpose this paper presents the Methodology for Interdisciplinary Research (MIR) framework...
2018: Quality & Quantity
https://www.readbyqxmd.com/read/29670042/long-non-coding-rnas-in-neuronal-aging
#19
REVIEW
Diana Pereira Fernandes, Mainá Bitar, Frank M J Jacobs, Guy Barry
The expansion of long non-coding RNAs (lncRNAs) in organismal genomes has been associated with the emergence of sophisticated regulatory networks that may have contributed to more complex neuronal processes, such as higher-order cognition. In line with the important roles of lncRNAs in the normal functioning of the human brain, dysregulation of lncRNA expression has been implicated in aging and age-related neurodegenerative disorders. In this paper, we discuss the function and expression of known neuronal-associated lncRNAs, their impact on epigenetic changes, the contribution of transposable elements to lncRNA expression, and the implication of lncRNAs in maintaining the 3D nuclear architecture in neurons...
April 18, 2018: Non-Coding RNA
https://www.readbyqxmd.com/read/29663588/from-transects-to-transcripts-teasing-apart-the-architecture-of-reproductive-isolation
#20
Jill A Hamilton, Joshua M Miller
Understanding the processes underlying speciation has long been a challenge to evolutionary biologists. This spurs from difficulties teasing apart the various mechanisms that contribute to the evolution of barriers to reproduction. The study by Rafati et al. () in this issue of Molecular Ecology combines spatially explicit whole-genome resequencing with evaluation of differential gene expression across individuals with mixed ancestry to associate the genomic architecture of reproductive barriers with expression of reproductive incompatibilities...
March 2018: Molecular Ecology
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