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https://www.readbyqxmd.com/read/28936767/smc-complexes-orchestrate-the-mitotic-chromatin-interaction-landscape
#1
REVIEW
Yasutaka Kakui, Frank Uhlmann
Chromatin is a very long DNA-protein complex that controls the expression and inheritance of the genetic information. Chromatin is stored within the nucleus in interphase and further compacted into chromosomes during mitosis. This process, known as chromosome condensation, is essential for faithful segregation of genomic DNA into daughter cells. Condensin and cohesin, members of the structural maintenance of chromosomes (SMC) family, are fundamental for chromosome architecture, both for establishment of chromatin structure in the interphase nucleus and for the formation of condensed chromosomes in mitosis...
September 21, 2017: Current Genetics
https://www.readbyqxmd.com/read/28931935/alpha-tc1-and-beta-tc-6-genomic-profiling-uncovers-both-shared-and-distinct-transcriptional-regulatory-features-with-their-primary-islet-counterparts
#2
Nathan Lawlor, Ahrim Youn, Romy Kursawe, Duygu Ucar, Michael L Stitzel
Alpha TC1 (αTC1) and Beta-TC-6 (βTC6) mouse islet cell lines are cellular models of islet (dys)function and type 2 diabetes (T2D). However, genomic characteristics of these cells, and their similarities to primary islet alpha and beta cells, are undefined. Here, we report the epigenomic (ATAC-seq) and transcriptomic (RNA-seq) landscapes of αTC1 and βTC6 cells. Each cell type exhibits hallmarks of its primary islet cell counterpart including cell-specific expression of beta (e.g., Pdx1) and alpha (e.g., Arx) cell transcription factors (TFs), and enrichment of binding motifs for these TFs in αTC1/βTC6 cis-regulatory elements...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28928442/genome-wide-association-and-hla-region-fine-mapping-studies-identify-susceptibility-loci-for-multiple-common-infections
#3
Chao Tian, Bethann S Hromatka, Amy K Kiefer, Nicholas Eriksson, Suzanne M Noble, Joyce Y Tung, David A Hinds
Infectious diseases have a profound impact on our health and many studies suggest that host genetics play a major role in the pathogenesis of most of them. We perform 23 genome-wide association studies for common infections and infection-associated procedures, including chickenpox, shingles, cold sores, mononucleosis, mumps, hepatitis B, plantar warts, positive tuberculosis test results, strep throat, scarlet fever, pneumonia, bacterial meningitis, yeast infections, urinary tract infections, tonsillectomy, childhood ear infections, myringotomy, measles, hepatitis A, rheumatic fever, common colds, rubella and chronic sinus infection, in over 200,000 individuals of European ancestry...
September 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28916711/comparative-analysis-of-three-dimensional-chromosomal-architecture-identifies-a-novel-fetal-hemoglobin-regulatory-element
#4
Peng Huang, Cheryl A Keller, Belinda Giardine, Jeremy D Grevet, James O J Davies, Jim R Hughes, Ryo Kurita, Yukio Nakamura, Ross C Hardison, Gerd A Blobel
Chromatin structure is tightly intertwined with transcription regulation. Here we compared the chromosomal architectures of fetal and adult human erythroblasts and found that, globally, chromatin structures and compartments A/B are highly similar at both developmental stages. At a finer scale, we detected distinct folding patterns at the developmentally controlled β-globin locus. Specifically, new fetal stage-specific contacts were uncovered between a region separating the fetal (γ) and adult (δ and β) globin genes (encompassing the HBBP1 and BGLT3 noncoding genes) and two distal chromosomal sites (HS5 and 3'HS1) that flank the locus...
September 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28915487/genetic-backgrounds-and-hidden-trait-complexity-in-natural-populations
#5
REVIEW
Téo Fournier, Joseph Schacherer
Dissecting the genetic basis of natural phenotypic variation is a major goal in biology. We know that most traits are strongly heritable. However, their genetic architecture is a long-standing question, which is unfortunately confounded by the lack of complete knowledge of the genetic components as well as their phenotypic effect in a specific genetic background. Many genetic variants are known to affect phenotypes but the same functional variant can have a different effect on the phenotype in different individuals of the same species...
September 12, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28911083/multiregion-whole-exome-sequencing-of-matched-primary-and-metastatic-tumors-revealed-genomic-heterogeneity-and-suggested-polyclonal-seeding-in-colorectal-cancer-metastasis
#6
Q Wei, Z Ye, X Zhong, L Li, C Wang, R E Myers, J P Palazzo, D Fortuna, A Yan, S A Waldman, X Chen, J A Posey, A Basu-Mallick, B H Jiang, L Hou, J Shu, Y Sun, J Xing, B Li, H Yang
Background: Distant metastasis accounts for 90% of deaths from colorectal cancer (CRC). Genomic heterogeneity has been reported in various solid malignancies, but remains largely under-explored in metastatic CRC tumors, especially in primary to metastatic tumor evolution. Patients and methods: We conducted high-depth whole-exome sequencing in multiple regions of matched primary and metastatic CRC tumors. Using a total of 28 tumor, normal, and lymph node tissues, we analyzed inter- and intra-individual heterogeneity, inferred the tumor subclonal architectures, and depicted the subclonal evolutionary routes from primary to metastatic tumors...
September 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28910638/the-landscape-of-type-vi-secretion-across-human-gut-microbiomes-reveals-its-role-in-community-composition
#7
Adrian J Verster, Benjamin D Ross, Matthew C Radey, Yiqiao Bao, Andrew L Goodman, Joseph D Mougous, Elhanan Borenstein
Although gut microbiome composition is well defined, the mechanisms underlying community assembly remain poorly understood. Bacteroidales possess three genetic architectures (GA1-3) of the type VI secretion system (T6SS), an effector delivery pathway that mediates interbacterial competition. Here we define the distribution and role of GA1-3 in the human gut using metagenomic analysis. We find that adult microbiomes harbor limited effector and cognate immunity genes, suggesting selection for compatibility at the species (GA1 and GA2) and strain (GA3) levels...
September 13, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28905095/growing-canopy-on-a-college-campus-understanding-urban-forest-change-through-archival-records-and-aerial-photography
#8
Lara A Roman, Jason P Fristensky, Theodore S Eisenman, Eric J Greenfield, Robert E Lundgren, Chloe E Cerwinka, David A Hewitt, Caitlin C Welsh
Many municipalities are setting ambitious tree canopy cover goals to increase the extent of their urban forests. A historical perspective on urban forest development can help cities strategize how to establish and achieve appropriate tree cover targets. To understand how long-term urban forest change occurs, we examined the history of trees on an urban college campus: the University of Pennsylvania in Philadelphia, PA. Using a mixed methods approach, including qualitative assessments of archival records (1870-2017), complemented by quantitative analysis of tree cover from aerial imagery (1970-2012), our analysis revealed drastic canopy cover increase in the late 20th and early 21st centuries along with the principle mechanisms of that change...
September 13, 2017: Environmental Management
https://www.readbyqxmd.com/read/28883174/a-decentralized-it-architecture-for-locating-and-negotiating-access-to-biobank-samples
#9
Rumyana Proynova, Diogo Alexandre, Martin Lablans, David Van Enckevort, Sebastian Mate, Niina Eklund, Kaisa Silander, Michael Hummel, Petr Holub, Frank Ückert
There is a need among researchers for the easy discoverability of biobank samples. Currently, there is no uniform way for finding samples and negotiate access. Instead, researchers have to communicate with each biobank separately. We present the architecture for the BBMRI-CS IT platform, whose goal is to facilitate sample location and access. We chose a decentral approach, which allows for strong data protection and provides the high flexibility needed in the highly heterogeneous landscape of European biobanks...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28854635/partner-drug-resistance-and-population-substructuring-of-artemisinin-resistant-plasmodium-falciparum-in-cambodia
#10
Christian M Parobek, Jonathan B Parr, Nicholas F Brazeau, Chanthap Lon, Suwanna Chaorattanakawee, Panita Gosi, Eric J Barnett, Lauren D Norris, Steven R Meshnick, Michele D Spring, Charlotte A Lanteri, Jeffrey A Bailey, David L Saunders, Jessica T Lin, Jonathan J Juliano
Plasmodium falciparum in western Cambodia has developed resistance to artemisinin and its partner drugs, causing frequent treatment failure. Understanding this evolution can inform the deployment of new therapies. We investigated the genetic architecture of 78 falciparum isolates using whole-genome sequencing, correlating results to in vivo and ex vivo drug resistance and exploring the relationship between population structure, demographic history, and partner drug resistance. Principle component analysis, network analysis and demographic inference identified a diverse central population with three clusters of clonally expanding parasite populations, each associated with specific K13 artemisinin resistance alleles and partner drug resistance profiles which were consistent with the sequential deployment of artemisinin combination therapies in the region...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28832066/the-structural-landscape-in-14-vertex-clusters-of-silicon-m-si14-when-two-bonding-paradigms-collide
#11
Xiao Jin, Vaida Arcisauskaite, John E McGrady
The structural chemistry of the title clusters has been the source of controversy in the computational literature because the identity of the most stable structure appears to be pathologically dependent on the chosen theoretical model. The candidate structures include a D3h-symmetric 'fullerene-like' isomer with 3-connected vertices (A), an 'arachno' architecture (B) and an octahedral isomer with high vertex connectivities typical of 'closo' electron-deficient clusters (C). The key to understanding these apparently very different structures is the fact that they make use of the limited electron density available from the endohedral metal in very different ways...
September 12, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28825727/condensin-mediated-remodeling-of-the-mitotic-chromatin-landscape-in-fission-yeast
#12
Yasutaka Kakui, Adam Rabinowitz, David J Barry, Frank Uhlmann
The eukaryotic genome consists of DNA molecules far longer than the cells that contain them. They reach their greatest compaction during chromosome condensation in mitosis. This process is aided by condensin, a structural maintenance of chromosomes (SMC) family member. The spatial organization of mitotic chromosomes and how condensin shapes chromatin architecture are not yet fully understood. Here we use chromosome conformation capture (Hi-C) to study mitotic chromosome condensation in the fission yeast Schizosaccharomyces pombe...
August 21, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28783060/a-diagnostic-post-occupancy-evaluation-of-the-nacadia%C3%A2-therapy-garden
#13
Ulrik Sidenius, Patrik Karlsson Nyed, Victoria Linn Lygum, Ulrika K Stigsdotter
The design of the Nacadia® therapy garden is based on a model for evidence-based health design in landscape architecture (EBHDL). One element of the model is a diagnostic post-occupancy evaluation (DPOE), which has not previously been fully developed. The present study develops a generic DPOE for therapy gardens, with a focus on studying the effects of the design on patients' health outcomes. This is done in order to identify successes and failures in the design. By means of a triangulation approach, the DPOE employs a mixture of methods, and data is interpreted corroborating...
August 5, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28777140/the-molecular-landscape-of-noninvasive-follicular-thyroid-neoplasm-with-papillary-like-nuclear-features-niftp-a-literature-review
#14
Fulvio Basolo, Elisabetta Macerola, Clara Ugolini, David N Poller, Zubair Baloch
The encapsulated and noninvasive follicular variant of papillary thyroid carcinoma has been recently reclassified as noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP). These tumors demonstrate indolent behavior. This change in nomenclature will have great clinical impact by avoiding overtreatment of patients with NIFTP lesions who in the past were diagnosed with thyroid carcinoma and typically received completion thyroidectomy followed by radioactive iodine ablation. The pathologic diagnosis of NIFTP requires surgical removal of the thyroid lesion or the lobe harboring it, and thorough sampling of the complete interface between the tumor capsule and the thyroid parenchyma, to exclude foci of invasion...
September 2017: Advances in Anatomic Pathology
https://www.readbyqxmd.com/read/28752247/breast-cancer-complexity-implications-of-intratumoral-heterogeneity-in-clinical-management
#15
REVIEW
Brittany Haynes, Ashapurna Sarma, Pratima Nangia-Makker, Malathy P Shekhar
Generation of intratumoral phenotypic and genetic heterogeneity has been attributed to clonal evolution and cancer stem cells that together give rise to a tumor with complex ecosystems. Each ecosystem contains various tumor cell subpopulations and stromal entities, which, depending upon their composition, can influence survival, therapy responses, and global growth of the tumor. Despite recent advances in breast cancer management, the disease has not been completely eradicated as tumors recur despite initial response to treatment...
July 27, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/28740156/mapping-the-dynamics-of-the-glucocorticoid-receptor-within-the-nuclear-landscape
#16
Martin Stortz, Diego M Presman, Luciana Bruno, Paolo Annibale, Maria V Dansey, Gerardo Burton, Enrico Gratton, Adali Pecci, Valeria Levi
The distribution of the transcription machinery among different sub-nuclear domains raises the question on how the architecture of the nucleus modulates the transcriptional response. Here, we used fluorescence fluctuation analyses to quantitatively explore the organization of the glucocorticoid receptor (GR) in the interphase nucleus of living cells. We found that this ligand-activated transcription factor diffuses within the nucleus and dynamically interacts with bodies enriched in the coregulator NCoA-2, DNA-dependent foci and chromatin targets...
July 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28727195/patterns-of-divergence-across-the-geographic-and-genomic-landscape-of-a-butterfly-hybrid-zone-associated-with-a-climatic-gradient
#17
Sean F Ryan, Michael C Fontaine, J Mark Scriber, Michael E Pfrender, Shawn T O'Neil, Jessica J Hellmann
Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and nonecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations...
July 20, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28726930/competition-and-selectivity-in-supramolecular-synthesis-structural-landscape-around-1-pyridylmethyl-2-2-biimidazoles
#18
C A Gunawardana, J Desper, A S Sinha, M Ðaković, C B Aakeröy
Three isomeric forms of 1-(pyridylmethyl)-2,2'-biimidazole, A1-A3, have been synthesized and subjected to systematic co-crystallizations with selected hydrogen- and halogen-bond donors in order to explore the impact of electrostatics and geometry on the resulting supramolecular architectures. The solid-state supramolecular behavior of A1-A3 is largely consistent in halogen-bonded co-crystals. Only two types of primary interactions, the N-HN/NH-N homomeric hydrogen-bond interactions responsible for the pairing of biimidazole moieties and the IN(pyridine) halogen bonds responsible for the co-crystal formation and structure extension, are present in these systems...
July 20, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28701277/the-epigenetic-architecture-at-gene-promoters-determines-cell-type-specific-lps-tolerance
#19
Kerstin Klein, Mojca Frank-Bertoncelj, Emmanuel Karouzakis, Renate E Gay, Christoph Kolling, Adrian Ciurea, Nagihan Bostanci, Georgios N Belibasakis, Lih-Ling Lin, Oliver Distler, Steffen Gay, Caroline Ospelt
Synovial fibroblasts (SF) drive inflammation and joint destruction in chronic arthritis. Here we show that SF possess a distinct type of LPS tolerance compared to macrophages and other types of fibroblasts. In SF and dermal fibroblasts, genes that were non-tolerizable after repeated LPS stimulation included pro-inflammatory cytokines, chemokines and matrix metalloproteinases, whereas anti-viral genes were tolerizable. In macrophages, all measured genes were tolerizable, whereas in gingival and foreskin fibroblasts these genes were non-tolerizable...
July 9, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28698678/prototype-of-a-bistable-polariton-field-effect-transistor-switch
#20
H Suchomel, S Brodbeck, T C H Liew, M Amthor, M Klaas, S Klembt, M Kamp, S Höfling, C Schneider
Microcavity exciton polaritons are promising candidates to build a new generation of highly nonlinear and integrated optoelectronic devices. Such devices range from novel coherent light emitters to reconfigurable potential landscapes for electro-optical polariton-lattice based quantum simulators as well as building blocks of optical logic architectures. Especially for the latter, the strongly interacting nature of the light-matter hybrid particles has been used to facilitate fast and efficient switching of light by light, something which is very hard to achieve with weakly interacting photons...
July 11, 2017: Scientific Reports
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