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3d genome

Awatef Ouertani, Ines Chaabouni, Amor Mosbah, Justine Long, Mohamed Barakat, Pascal Mansuelle, Olfa Mghirbi, Afef Najjari, Hadda-Imene Ouzari, Ahmed S Masmoudi, Marc Maresca, Philippe Ortet, Didier Gigmes, Kamel Mabrouk, Ameur Cherif
Milk and dairy products harbor a wide variety of bacterial species that compete for both limited resources and space. Under these competitive conditions, bacteria develop specialized mechanisms to protect themselves during niche colonization and nutrient acquisition processes. The bacterial antagonism mechanisms include the production of antimicrobial agents or molecules that facilitate competitor dispersal. In the present work, a bacterial strain designated RC6 was isolated from Ricotta and identified as Bacillus cereus ...
2018: Frontiers in Microbiology
Emma L Hesketh, Keith Saunders, Chloe Fisher, Joran Potze, John Stanley, George P Lomonossoff, Neil A Ranson
Geminiviruses are major plant pathogens that threaten food security globally. They have a unique architecture built from two incomplete icosahedral particles, fused to form a geminate capsid. However, despite their importance to agricultural economies and fundamental biological interest, the details of how this is realized in 3D remain unknown. Here we report the structure of Ageratum yellow vein virus at 3.3 Å resolution, using single-particle cryo-electron microscopy, together with an atomic model that shows that the N-terminus of the single capsid protein (CP) adopts three different conformations essential for building the interface between geminate halves...
June 18, 2018: Nature Communications
Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, Björn A Grüning
Galaxy HiCExplorer is a web server that facilitates the study of the 3D conformation of chromatin by allowing Hi-C data processing, analysis and visualization. With the Galaxy HiCExplorer web server, users with little bioinformatic background can perform every step of the analysis in one workflow: mapping of the raw sequence data, creation of Hi-C contact matrices, quality assessment, correction of contact matrices and identification of topological associated domains (TADs) and A/B compartments. Users can create publication ready plots of the contact matrix, A/B compartments, and TADs on a selected genomic locus, along with additional information like gene tracks or ChIP-seq signals...
June 13, 2018: Nucleic Acids Research
Eliza Li Shan Fong, Tan Boon Toh, Quy Xiao Xuan Lin, Zheng Liu, Lissa Hooi, Masturah Bte Mohd Abdul Rashid, Touati Benoukraf, Edward Kai-Hua Chow, The Hung Huynh, Hanry Yu
This data article presents datasets associated with the research article entitled "Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer" (Fong et al., 2018) [1]. A three-dimensional macroporous sponge system was used to generate in vitro counterparts to various hepatocellular carcinoma patient-derived xenograft (HCC-PDX) lines. This article describes the viability, proliferative capacity and molecular features (genomic and transcriptomic profiles) of the cultured HCC-PDX cells...
June 2018: Data in Brief
Philipp Metzger, Sabrina V Kirchleitner, Lars M Koenig, Christine Hörth, Sebastian Kobold, Stefan Endres, Max Schnurr, Peter Duewell
Checkpoint molecules such as programmed death 1 (PD-1) dampen excessive T cell activation to preserve immune homeostasis. PD-1-specific monoclonal antibodies have revolutionized cancer therapy, as they reverse tumour-induced T cell exhaustion and restore CTL activity. Based on this success, deciphering underlying mechanisms of PD-1-mediated immune functions has become an important field of immunological research. Initially described for T cells, there is emerging evidence of unconventional PD-1 expression by myeloid as well as tumor cells, yet, with cell-intrinsic functions in various animal tumor models...
June 11, 2018: Scientific Reports
Kepalee Saeng-Chuto, Christopher James Stott, Matthew Wegner, Pavita Kaewprommal, Jittima Piriyapongsa, Dachrit Nilubol
Senecavirus A (SVA) is a novel picornavirus that causes porcine idiopathic vesicular disease characterized by lameness, coronary band hyperemia, and vesicles on the snout and coronary bands. An increase in the detection rate of SVA in several countries suggests that the disease has become a widespread problem. Herein, we report the detection of SVA in Thailand and the characterization of full-length genomic sequences of six Thai SVA isolates. Phylogenetic, genetic, recombination, and evolutionary analyses were performed...
June 8, 2018: Infection, Genetics and Evolution
Sofia A Quinodoz, Noah Ollikainen, Barbara Tabak, Ali Palla, Jan Marten Schmidt, Elizabeth Detmar, Mason M Lai, Alexander A Shishkin, Prashant Bhat, Yodai Takei, Vickie Trinh, Erik Aznauryan, Pamela Russell, Christine Cheng, Marko Jovanovic, Amy Chow, Long Cai, Patrick McDonel, Manuel Garber, Mitchell Guttman
Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus...
June 4, 2018: Cell
Josée Dostie, Mathieu Blanchette
No abstract text is available yet for this article.
June 1, 2018: Methods: a Companion to Methods in Enzymology
Anuj Kumar, Mansi Sharma, Sanjay Kumar, Pankaj Tyagi, Shabir Hussain Wani, M N V Prasad Gajula, Krishna Pal Singh
An extensive bioinformatics based study has been performed to gain insight into the structural and functional aspects of candidate genes involved in Nitrogen and Phosphorus nutrition in wheat. Based on our study, 37 N and P nutrition candidate genes were identified (24 NUE and 13 inorganic phosphate transporters) in wheat genome. 23 gene specific novel microsatellites were discovered using genomic sequences of identified N and P nutrition genes. We also identified the microRNAs that target ten candidate genes including TaAS1-3A, TaAS1-3D, TaASN2-1A, TaASN2-1B, TaANR1-6A, TaANR1-6B, TaNRT2...
June 4, 2018: International Journal of Biological Macromolecules
Nelle Varoquaux
The development of new ways to probe samples for the three-dimensional (3D) structure of DNA paves the way for in depth and systematic analyses of the genome architecture. 3C-like methods coupled with high-throughput sequencing can now assess physical interactions between pairs of loci in a genome-wide fashion, thus enabling the creation of genome-by-genome contact maps. The spreading of such protocols creates many new opportunities for methodological development: how can we infer 3D models from these contact maps? Can such models help us gain insights into biological processes? Several recent studies applied such protocols to P...
June 7, 2018: International Journal of Biostatistics
Jung-Hee Lee, Seon-Joo Park, Gurusamy Hariharasudhan, Min-Ji Kim, Sung Mi Jung, Seo-Yeon Jeong, In-Youb Chang, Cheolhee Kim, Eunae Kim, Jihyeon Yu, Sangsu Bae, Ho Jin You
This Article contains errors in Fig. 3, Fig. 4 and Fig. 7, for which we apologize. In Fig. 3, panel 'b', the 0.5 hour time point after Ku55933 treatment images were inadvertently replaced with duplicates of the 3 hour time point after Ku55933 treatment images in Fig. 3b. Additionally, in panel 'b', the 0.5 hour time point after Nu7026 treatment images were inadvertently replaced with duplicates of the 180 min time point after siMDC1 treatment images in Fig. 3d. In Fig. 4, panel 'g', RNF168 foci in U2OS cell images were inadvertently replaced with duplicates of RNF168 foci in HeLa cell images in Fig...
June 6, 2018: Nature Communications
Maaike V J Braham, Monique C Minnema, Tineke Aarts, Zsolt Sebestyen, Trudy Straetemans, Anna Vyborova, Jurgen Kuball, F Cumhur Öner, Catherine Robin, Jacqueline Alblas
Bone marrow niches support multiple myeloma, providing signals and cell-cell interactions essential for disease progression. A 3D bone marrow niche model was developed, in which supportive multipotent mesenchymal stromal cells and their osteogenic derivatives were co-cultured with endothelial progenitor cells. These co-cultured cells formed networks within the 3D culture, facilitating the survival and proliferation of primary CD138+ myeloma cells for up to 28 days. During this culture, no genetic drift was observed within the genomic profile of the primary myeloma cells, indicating a stable outgrowth of the cultured CD138+ population...
2018: Oncoimmunology
Kundan Sengupta
The genome of higher eukaryotes is non-randomly organized in the interphase nucleus. However, notwithstanding the absence of membrane bound sub-compartments, the nucleus coordinates a number of functions largely by organizing chromatin in a non-random but dynamic manner. The plasticity of chromatin structure and function relies on epigenetic modifications as well as its association with nuclear landmarks such as the nuclear envelope, nuclear lamina, nuclear pore complex and nuclear bodies such as the nucleolus among others...
June 2018: Journal of Biosciences
Kumarasamy Jayakumar, María Belén Camarada, Venkataraman Dharuman, Rajendiran Rajesh, Rengarajan Venkatesan, Huangxian Ju, Mahalingam Maniraj, Abhishek Rai, Sudipta Roy Barman, Yangping Wen
The structure and electrochemical properties of layer-by-layer assembled gold nanoparticles (AuNPs) decorated the first generation (G1) poly(amidoamine) dendrimer (PD) with reduced graphene oxide (rGO) core as a highly-sensitive and label-free biosensing platform with a controllable three-dimensional (3D) nanoarchitecture for the rapid voltammetric analysis of DNA hybridization at ultra-trace levels were characterized. The mercaptopropinoic acid (MPA) was self-assembled onto Au substrate, then GG1PD that was formed by the covalent functionalization between amino terminals of G1PD and carboxyl terminals of rGO was covalently linked onto MPA, and finally AuNPs were decorated onto GG1PD by strong physicochemical interaction between AuNPs and -OH of rGO in GG1PD, which was characterized through different techniques and confirmed by the computational calculation...
June 5, 2018: ACS Applied Materials & Interfaces
Aleksandar Kojic, Ana Cuadrado, Magali De Koninck, Daniel Giménez-Llorente, Miriam Rodríguez-Corsino, Gonzalo Gómez-López, François Le Dily, Marc A Marti-Renom, Ana Losada
Two variant cohesin complexes containing SMC1, SMC3, RAD21 and either SA1 (also known as STAG1) or SA2 (also known as STAG2) are present in all cell types. We report here their genomic distribution and specific contributions to genome organization in human cells. Although both variants are found at CCCTC-binding factor (CTCF) sites, a distinct population of the SA2-containing cohesin complexes (hereafter referred to as cohesin-SA2) localize to enhancers lacking CTCF, are linked to tissue-specific transcription and cannot be replaced by the SA1-containing cohesin complex (cohesin-SA1) when SA2 is absent, a condition that has been observed in several tumors...
June 2018: Nature Structural & Molecular Biology
Mark R Segal, Henrik L Bengtsson
BACKGROUND: Three dimensional (3D) genome spatial organization is critical for numerous cellular functions, including transcription, while certain conformation-driven structural alterations are frequently oncogenic. Genome conformation had been difficult to elucidate but the advent chromatin conformation capture assays, notably Hi-C, has transformed understanding of chromatin architecture and yielded numerous biological insights. Although most of these findings have flowed from analysis of proximity data produced by these assays, added value in generating 3D reconstructions has been demonstrated, deriving, in part, from superposing genomic features on the reconstruction...
May 30, 2018: BMC Bioinformatics
Antonio Z Politi, Yin Cai, Nike Walther, M Julius Hossain, Birgit Koch, Malte Wachsmuth, Jan Ellenberg
The ability to tag a protein at its endogenous locus with a fluorescent protein (FP) enables quantitative understanding of protein dynamics at the physiological level. Genome-editing technology has now made this powerful approach routinely applicable to mammalian cells and many other model systems, thereby opening up the possibility to systematically and quantitatively map the cellular proteome in four dimensions. 3D time-lapse confocal microscopy (4D imaging) is an essential tool for investigating spatial and temporal protein dynamics; however, it lacks the required quantitative power to make the kind of absolute and comparable measurements required for systems analysis...
June 2018: Nature Protocols
Johanna Gassler, Ilya M Flyamer, Kikuë Tachibana
The 3D folding of the genome is linked to essential nuclear processes including gene expression, DNA repair, and replication. Chromatin conformation capture assays such as Hi-C are providing unprecedented insights into higher-order chromatin structure. Bulk Hi-C of millions of cells enables detection of average chromatin features at high resolution but is challenging to apply to rare cell types. This chapter describes our recently developed single-nucleus Hi-C (snHi-C) approach for detection of chromatin contacts in single nuclei of murine oocytes and one-cell embryos (zygotes)...
2018: Methods in Cell Biology
Xiaoji Sun, Xuya Wang, Zuojian Tang, Mark Grivainis, David Kahler, Chi Yun, Paolo Mita, David Fenyö, Jef D Boeke
Transposable elements (TEs) represent a substantial fraction of many eukaryotic genomes, and transcriptional regulation of these factors is important to determine TE activities in human cells. However, due to the repetitive nature of TEs, identifying transcription factor (TF)-binding sites from ChIP-sequencing (ChIP-seq) datasets is challenging. Current algorithms are focused on subtle differences between TE copies and thus bias the analysis to relatively old and inactive TEs. Here we describe an approach termed "MapRRCon" (mapping repeat reads to a consensus) which allows us to identify proteins binding to TE DNA sequences by mapping ChIP-seq reads to the TE consensus sequence after whole-genome alignment...
May 25, 2018: Proceedings of the National Academy of Sciences of the United States of America
Bhavna S Rao, Samdani Ansar, Tharigopala Arokiasamy, Rachapalli R Sudhir, Vetrivel Umashankar, Rama Rajagopal, Nagasamy Soumittra
BACKGROUND: Fuchs' endothelial corneal dystrophy (FECD) is a complex degenerative disease of the corneal endothelium with genetic predisposition. Pathogenic rare variants have been identified in SLC4A11, LOXHD1, ZEB1, and AGBL1. Association of single nucleotide polymorphisms (SNPs) and CTG trinucleotide repeat expansions in the intron of TCF4 gene to FECD has been studied across multiple ethnicities. Recently, genome-wide association studies have also identified KANK4, LAMC1, and ATP1B1 as novel loci for FECD...
May 25, 2018: Ophthalmic Genetics
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