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https://www.readbyqxmd.com/read/28202491/organoid-technologies-meet-genome-engineering
#1
REVIEW
Jing Nie, Eri Hashino
Three-dimensional (3D) stem cell differentiation cultures recently emerged as a novel model system for investigating human embryonic development and disease progression in vitro, complementing existing animal and two-dimensional (2D) cell culture models. Organoids, the 3D self-organizing structures derived from pluripotent or somatic stem cells, can recapitulate many aspects of structural organization and functionality of their in vivo organ counterparts, thus holding great promise for biomedical research and translational applications...
February 15, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28197972/prevalence-and-molecular-characterization-of-the-hepatitis-e-virus-in-retail-pork-products-marketed-in-canada
#2
Oksana Mykytczuk, Jennifer Harlow, Sabah Bidawid, Nathalie Corneau, Neda Nasheri
Infection with the hepatitis E virus (HEV) is very common worldwide. HEV causes acute viral hepatitis with approximately 20 million cases per year. While HEV genotypes 1 and 2 cause large waterborne and foodborne outbreaks with a significant mortality in developing countries, genotypes 3 and 4 are more prevalent in developed countries with transmission being mostly zoonotic. In North America and Europe, HEV has been increasingly detected in swine, and exposure to pigs and pork products is considered to be the primary source of infection...
February 14, 2017: Food and Environmental Virology
https://www.readbyqxmd.com/read/28194101/contribution-of-neuroepigenetics-to-huntington-s-disease
#3
REVIEW
Laetitia Francelle, Caroline Lotz, Tiago Outeiro, Emmanuel Brouillet, Karine Merienne
Unbalanced epigenetic regulation is thought to contribute to the progression of several neurodegenerative diseases, including Huntington's disease (HD), a genetic disorder considered as a paradigm of epigenetic dysregulation. In this review, we attempt to address open questions regarding the role of epigenetic changes in HD, in the light of recent advances in neuroepigenetics. We particularly discuss studies using genome-wide scale approaches that provide insights into the relationship between epigenetic regulations, gene expression and neuronal activity in normal and diseased neurons, including HD neurons...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28190810/visualization-of-the-spatial-arrangement-of-nuclear-organization-using-three-dimensional-fluorescence-in-situ-hybridization-in-early-mouse-embryos-a-new-easi-fish-chamber-glass-for-mammalian-embryos
#4
Masataka Nakaya, Hideyuki Tanabe, Shingo Takamatsu, Misaki Hosokawa, Tasuku Mitani
The fertilized oocyte begins cleavage, leading to zygotic gene activation (ZGA), which re-activates the resting genome to acquire totipotency. In this process, genomic function is regulated by the dynamic structural conversion in the nucleus. Indeed, a considerable number of genes that are essential for embryonic development are located near the pericentromeric regions, wherein the heterochromatin is formed. These genes are repressed transcriptionally in somatic cells. Three-dimensional fluorescence in situ hybridization (3D-FISH) enables the visualization of the intranuclear spatial arrangement, such as gene loci, chromosomal domains, and chromosome territories (CTs)...
February 11, 2017: Journal of Reproduction and Development
https://www.readbyqxmd.com/read/28188103/kidney-organoids-a-translational-journey
#5
REVIEW
Ryuji Morizane, Joseph V Bonventre
Human pluripotent stem cells (hPSCs) are attractive sources for regenerative medicine and disease modeling in vitro. Directed hPSC differentiation approaches have derived from knowledge of cell development in vivo rather than from stochastic cell differentiation. Moreover, there has been great success in the generation of 3D organ-buds termed 'organoids' from hPSCs; these consist of a variety of cell types in vitro that mimic organs in vivo. The organoid bears great potential in the study of human diseases in vitro, especially when combined with CRISPR/Cas9-based genome-editing...
February 7, 2017: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/28186153/superresolution-imaging-of-nanoscale-chromosome-contacts
#6
Yejun Wang, Prasuna Ratna, G V Shivashankar
Co-expression of a specific group of genes requires physical associations among these genes, which form functional chromosomal contacts. While DNA fluorescence in situ hybridization (FISH) pinpoints the localization of genes within the 3D nuclear architecture, direct evidence of physical chromosomal contacts is still lacking. Here, we report a method for the direct visualization of transcription-dependent chromosomal contacts formed in two distinct mechanical states of cells. We prepared open chromatin spreads from isolated nuclei, ensuring 2D rendering of chromosome organization...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28180292/3d-genome-structure-modeling-by-lorentzian-objective-function
#7
Tuan Trieu, Jianlin Cheng
No abstract text is available yet for this article.
February 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28180283/dynamic-chromatin-accessibility-modeled-by-markov-process-of-randomly-moving-molecules-in-the-3d-genome
#8
Yinan Wang, Caoqi Fan, Yuxuan Zheng, Cheng Li
No abstract text is available yet for this article.
February 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28179124/comparative-analysis-of-2d-and-3d-distance-measurements-to-study-spatial-genome-organization
#9
Elizabeth H Finn, Gianluca Pegoraro, Sigal Shachar, Tom Misteli
The spatial organization of eukaryotic genomes is non-random, cell-type specific, and has been linked to cellular function. The investigation of spatial organization has traditionally relied extensively on fluorescence microscopy. The validity of the imaging methods used to probe spatial genome organization often depends on the accuracy and precision of distance measurements. Imaging-based measurements may either use 2 dimensional datasets or 3D datasets including the z-axis information in image stacks. Here we compare the suitability of 2D versus 3D distance measurements in the analysis of various features of spatial genome organization...
February 4, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28165000/high-affinity-anchoring-of-the-decoration-protein-pb10-onto-the-bacteriophage-t5-capsid
#10
Emeline Vernhes, Madalena Renouard, Bernard Gilquin, Philippe Cuniasse, Dominique Durand, Patrick England, Sylviane Hoos, Alexis Huet, James F Conway, Anatoly Glukhov, Vladimir Ksenzenko, Eric Jacquet, Naïma Nhiri, Sophie Zinn-Justin, Pascale Boulanger
Bacteriophage capsids constitute icosahedral shells of exceptional stability that protect the viral genome. Many capsids display on their surface decoration proteins whose structure and function remain largely unknown. The decoration protein pb10 of phage T5 binds at the centre of the 120 hexamers formed by the major capsid protein. Here we determined the 3D structure of pb10 and investigated its capsid-binding properties using NMR, SAXS, cryoEM and SPR. Pb10 consists of an α-helical capsid-binding domain and an Ig-like domain exposed to the solvent...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28163093/picornaviral-polymerase-structure-function-and-fidelity-modulation
#11
REVIEW
Olve B Peersen
Like all positive strand RNA viruses, the picornaviruses replicate their genomes using a virally encoded RNA-dependent RNA polymerase enzyme known as 3D(pol). Over the past decade we have made tremendous advances in our understanding of 3D(pol) structure and function, including the discovery of a novel mechanism for closing the active site that allows these viruses to easily fine tune replication fidelity and quasispecies distributions. This review summarizes current knowledge of picornaviral polymerase structure and how the enzyme interacts with RNA and other viral proteins to form stable and processive elongation complexes...
February 2, 2017: Virus Research
https://www.readbyqxmd.com/read/28159004/software-tools-for-visualizing-hi-c-data
#12
REVIEW
Galip Gürkan Yardımcı, William Stafford Noble
High-throughput assays for measuring the three-dimensional (3D) configuration of DNA have provided unprecedented insights into the relationship between DNA 3D configuration and function. Data interpretation from assays such as ChIA-PET and Hi-C is challenging because the data is large and cannot be easily rendered using standard genome browsers. An effective Hi-C visualization tool must provide several visualization modes and be capable of viewing the data in conjunction with existing, complementary data. We review five software tools that do not require programming expertise...
February 3, 2017: Genome Biology
https://www.readbyqxmd.com/read/28158219/tissue-specific-features-of-the-x-chromosome-and-nucleolus-spatial-dynamics-in-a-malaria-mosquito-anopheles-atroparvus
#13
Semen M Bondarenko, Gleb N Artemov, Igor V Sharakhov, Vladimir N Stegniy
Spatial organization of chromosome territories is important for maintenance of genomic stability and regulation of gene expression. Recent studies have shown tissue-specific features of chromosome attachments to the nuclear envelope in various organisms including malaria mosquitoes. However, other spatial characteristics of nucleus organization, like volume and shape of chromosome territories, have not been studied in Anopheles. We conducted a thorough analysis of tissue-specific features of the X chromosome and nucleolus volume and shape in follicular epithelium and nurse cells of the Anopheles atroparvus ovaries using a modern open-source software...
2017: PloS One
https://www.readbyqxmd.com/read/28153045/visualizing-phylogenetic-tree-landscapes
#14
James C Wilgenbusch, Wen Huang, Kyle A Gallivan
BACKGROUND: Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems...
February 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28145590/molecular-modeling-and-dynamic-simulation-of-arabidopsis-thaliana-carotenoid-cleavage-dioxygenase-gene-a-comparison-with-bixa-orellana-and-crocus-sativus
#15
Priya R, Sneha P, Renata Rivera Madrid, George Priya Doss C, Pooja Singh, Siva Ramamoorthy
Carotenoid cleavage dioxygenase (CCD) gene, ubiquitously found in numerous types of plants, are eminent in synthesizing the various volatile compounds (β-ionone, C13 -norisoprenoid, geranylacetone) known as apocarotenoids. These apocarotenoids have various biological functions such as volatile signals, allelopathic interaction and plant defense. In Arabidopsis genome sequence, four potential CCD genes have been identified namely CCD1, CCD4, CCD7, and CCD8. These four genes give rise to diverse biological functions with almost similar sequence identity...
February 1, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28139771/a-new-model-of-sperm-nuclear-architecture-following-assessment-of-the-organization-of-centromeres-and-telomeres-in-three-dimensions
#16
Dimitrios Ioannou, Nicole M Millan, Elizabeth Jordan, Helen G Tempest
The organization of chromosomes in sperm nuclei has been proposed to possess a unique "hairpin-loop" arrangement, which is hypothesized to aid in the ordered exodus of the paternal genome following fertilization. This study simultaneously assessed the 3D and 2D radial and longitudinal organization of telomeres, centromeres, and investigated whether chromosomes formed the same centromere clusters in sperm cells. Reproducible radial and longitudinal non-random organization was observed for all investigated loci using both 3D and 2D approaches in multiple subjects...
January 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28137286/chrom3d-three-dimensional-genome-modeling-from-hi-c-and-nuclear-lamin-genome-contacts
#17
Jonas Paulsen, Monika Sekelja, Anja R Oldenburg, Alice Barateau, Nolwenn Briand, Erwan Delbarre, Akshay Shah, Anita L Sørensen, Corinne Vigouroux, Brigitte Buendia, Philippe Collas
Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational modeling framework that simulates positions of topologically-associated domains (TADs) relative to each other and to the nuclear periphery. Chrom3D integrates chromosome conformation capture (Hi-C) and lamin-associated domain (LAD) datasets to generate structure ensembles that recapitulate radial distributions of TADs detected in single cells...
January 30, 2017: Genome Biology
https://www.readbyqxmd.com/read/28137240/ascidians-an-emerging-marine-model-for-drug-discovery-and-screening
#18
Rémi Dumollard, Ievgeniia Gazo, Isa D L Gomes, Lydia Besnardeau, Alex McDougall
Ascidians (tunicates; sea squirts) are marine animals which provide a source of diverse, bioactive natural products, and a model for toxicity screenings. Compounds isolated from ascidians comprise an approved anti-tumor drug and many others are potent drug leads. Furthermore, the use of invertebrate embryos for toxicological screening tests or analysis offers the possibility to image a large number of samples for high throughput screens. Ascidians are members of a sister clade to the vertebrates and make a vertebrate-like tadpole larva composed of less than 3000 cells in 18 hours...
January 29, 2017: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/28135257/one-step-generation-of-conditional-and-reversible-gene-knockouts
#19
Amanda Andersson-Rolf, Roxana C Mustata, Alessandra Merenda, Jihoon Kim, Sajith Perera, Tiago Grego, Katie Andrews, Katie Tremble, José C R Silva, Juergen Fink, William C Skarnes, Bon-Kyoung Koo
Loss-of-function studies are key for investigating gene function, and CRISPR technology has made genome editing widely accessible in model organisms and cells. However, conditional gene inactivation in diploid cells is still difficult to achieve. Here, we present CRISPR-FLIP, a strategy that provides an efficient, rapid and scalable method for biallelic conditional gene knockouts in diploid or aneuploid cells, such as pluripotent stem cells, 3D organoids and cell lines, by co-delivery of CRISPR-Cas9 and a universal conditional intronic cassette...
January 30, 2017: Nature Methods
https://www.readbyqxmd.com/read/28131858/expansion-of-3d-human-induced-pluripotent-stem-cell-aggregates-in-bioreactors-bioprocess-intensification-and-scaling-up-approaches
#20
Bernardo Abecasis, Tiago Aguiar, Émilie Arnault, Rita Costa, Patricia Gomes-Alves, Anders Aspegren, Margarida Serra, Paula M Alves
Human induced pluripotent stem cells (hiPSC) are attractive tools for drug screening and disease modeling and promising candidates for cell therapy applications. However, to achieve the high numbers of cells required for these purposes, scalable and clinical-grade technologies must be established. In this study, we use environmentally controlled stirred-tank bioreactors operating in perfusion as a powerful tool for bioprocess intensification of hiPSC production. We demonstrate the importance of controlling the dissolved oxygen concentration at low levels (4%) and perfusion at 1...
January 25, 2017: Journal of Biotechnology
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