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https://www.readbyqxmd.com/read/29332168/efficient-crispr-cas9-based-genome-editing-in-carrot-cells
#1
Magdalena Klimek-Chodacka, Tomasz Oleszkiewicz, Levi G Lowder, Yiping Qi, Rafal Baranski
The first report presenting successful and efficient carrot genome editing using CRISPR/Cas9 system. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas9) is a powerful genome editing tool that has been widely adopted in model organisms recently, but has not been used in carrot-a model species for in vitro culture studies and an important health-promoting crop grown worldwide. In this study, for the first time, we report application of the CRISPR/Cas9 system for efficient targeted mutagenesis of the carrot genome...
January 13, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29331962/splicing-variant-of-wdfy4-augments-mda5-signalling-and-the-risk-of-clinically-amyopathic-dermatomyositis
#2
Yuta Kochi, Yoichiro Kamatani, Yuya Kondo, Akari Suzuki, Eiryo Kawakami, Ryosuke Hiwa, Yukihide Momozawa, Manabu Fujimoto, Masatoshi Jinnin, Yoshiya Tanaka, Takashi Kanda, Robert G Cooper, Hector Chinoy, Simon Rothwell, Janine A Lamb, Jiří Vencovský, Heřman Mann, Koichiro Ohmura, Keiko Myouzen, Kazuyoshi Ishigaki, Ran Nakashima, Yuji Hosono, Hiroto Tsuboi, Hidenaga Kawasumi, Yukiko Iwasaki, Hiroshi Kajiyama, Tetsuya Horita, Mariko Ogawa-Momohara, Akito Takamura, Shinichiro Tsunoda, Jun Shimizu, Keishi Fujio, Hirofumi Amano, Akio Mimori, Atsushi Kawakami, Hisanori Umehara, Tsutomu Takeuchi, Hajime Sano, Yoshinao Muro, Tatsuya Atsumi, Toshihide Mimura, Yasushi Kawaguchi, Tsuneyo Mimori, Atsushi Takahashi, Michiaki Kubo, Hitoshi Kohsaka, Takayuki Sumida, Kazuhiko Yamamoto
OBJECTIVES: Idiopathic inflammatory myopathies (IIMs) are a heterogeneous group of rare autoimmune diseases in which both genetic and environmental factors play important roles. To identify genetic factors of IIM including polymyositis, dermatomyositis (DM) and clinically amyopathic DM (CADM), we performed the first genome-wide association study for IIM in an Asian population. METHODS: We genotyped and tested 496 819 single nucleotide polymorphism for association using 576 patients with IIM and 6270 control subjects...
January 13, 2018: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/29331932/cnv-biology-in-neurodevelopmental-disorders
#3
REVIEW
Toru Takumi, Kota Tamada
Copy number variants (CNVs), characterized in recent years by cutting-edge technology, add complexity to our knowledge of the human genome. CNVs contribute not only to human diversity but also to different kinds of diseases including neurodevelopmental delay, autism spectrum disorder and neuropsychiatric diseases. Interestingly, many pathogenic CNVs are shared among these diseases. Studies suggest that pathophysiology of disease may not be simply attributed to a single driver gene within a CNV but also that multifactorial effects may be important...
January 10, 2018: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/29331751/comprehensive-genomic-profiling-of-head-and-neck-squamous-cell-carcinoma-reveals-fgfr1-amplifications-and-tumour-genomic-alterations-burden-as-prognostic-biomarkers-of-survival
#4
C Dubot, V Bernard, M P Sablin, S Vacher, W Chemlali, A Schnitzler, G Pierron, K Ait Rais, N Bessoltane, E Jeannot, J Klijanienko, O Mariani, T Jouffroy, V Calugaru, C Hoffmann, M Lesnik, N Badois, F Berger, C Le Tourneau, M Kamal, I Bieche
BACKGROUND: We aimed at identifying deleterious genomic alterations from untreated head and neck squamous cell carcinoma (HNSCC) patients, and assessing their prognostic value. PATIENTS AND METHODS: We retrieved 122 HNSCC patients who underwent primary surgery. Targeted NGS was used to analyse a panel of 100 genes selected among the most frequently altered genes in HNSCC and potential therapeutic targets. We selected only deleterious (activating or inactivating) single nucleotide variations, and copy number variations for analysis...
January 10, 2018: European Journal of Cancer
https://www.readbyqxmd.com/read/29331642/protein-adaptations-in-extremophiles-an-insight-into-extremophilic-connection-of-mycobacterial-proteome
#5
REVIEW
Ashutosh Kumar, Anwar Alam, Deeksha Tripathi, Mamta Rani, Hafeeza Khatoon, Saurabh Pandey, Nasreen Z Ehtesham, Seyed E Hasnain
The biological paradox about how extremophiles persist at extreme ecological conditions throws a fascinating picture of the enormous potential of a single cell to adapt to homeostatic conditions in order to propagate. Unicellular organisms face challenges from both environmental factors and the ecological niche provided by the host tissue. Although the existence of extremophiles and their physiological properties were known for a long time, availability of whole genome sequence has catapulted the study on mechanisms of adaptation and the underlying principles that have enabled these unique organisms to withstand evolutionary and environmental pressures...
January 10, 2018: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29331569/salinivibrio-kushneri-sp-nov-a-moderately-halophilic-bacterium-isolated-from-salterns
#6
Clara López-Hermoso, Rafael R de la Haba, Cristina Sánchez-Porro, Antonio Ventosa
Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184T, IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37°C, at pH 7.2-7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAGT (99...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29330484/single-cell-rna-sequencing-resolves-self-antigen-expression-during-mtec-development
#7
Ricardo J Miragaia, Xiuwei Zhang, Tomás Gomes, Valentine Svensson, Tomislav Ilicic, Johan Henriksson, Gozde Kar, Tapio Lönnberg
The crucial capability of T cells for discrimination between self and non-self peptides is based on negative selection of developing thymocytes by medullary thymic epithelial cells (mTECs). The mTECs purge autoreactive T cells by expression of cell-type specific genes referred to as tissue-restricted antigens (TRAs). Although the autoimmune regulator (AIRE) protein is known to promote the expression of a subset of TRAs, its mechanism of action is still not fully understood. The expression of TRAs that are not under the control of AIRE also needs further characterization...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330186/effect-of-plasmid-design-and-type-of-integration-event-on-recombinant-protein-expression-in-pichia-pastoris
#8
Thomas Vogl, Leigh Gebbie, Robin W Palfreyman, Robert Speight
Pichia pastoris (syn. Komagataella phaffii) is one of the most common eukaryotic expression systems for heterologous protein production. Expression cassettes are typically integrated in the genome to obtain stable expression strains. In contrast to Saccharomyces cerevisiae, where short overhangs are sufficient to target highly specific integration, long overhangs are more efficient in P. pastoris and ectopic integration of foreign DNA can occur. Here, we aimed to elucidate the influence of ectopic integration by high throughput screening of >700 transformants and whole genome sequencing of 27 transformants...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29328909/single-cell-genomics-a-stepping-stone-for-future-immunology-discoveries
#9
REVIEW
Amir Giladi, Ido Amit
The immunology field has invested great efforts and ingenuity to characterize the various immune cell types and elucidate their functions. However, accumulating evidence indicates that current technologies and classification schemes are limited in their ability to account for the functional heterogeneity of immune processes. Single-cell genomics hold the potential to revolutionize the way we characterize complex immune cell assemblies and study their spatial organization, dynamics, clonal distribution, pathways, function, and crosstalks...
January 11, 2018: Cell
https://www.readbyqxmd.com/read/29328552/changes-in-chromosome-counts-and-patterns-in-cho-cell-lines-upon-generation-of-recombinant-cell-lines-and-subcloning
#10
Sabine Vcelar, Michael Melcher, Norbert Auer, Astrid Hrdina, Anja Puklowski, Friedrich Leisch, Vaibhav Jadhav, Till Wenger, Martina Baumann, Nicole Borth
Chinese hamster ovary cells are the number one production system for therapeutic proteins. A pre-requirement for their use in industrial production of biopharmaceuticals is to be clonal, thus originating from a single cell in order to be phenotypically and genomically identical. In the present study it was evaluated whether standard procedures, such as the generation of a recombinant cell line in combination with selection for a specific and stable phenotype (expression of the recombinant product) or subcloning have any impact on karyotype stability or homogeneity in CHO cells...
January 12, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29327728/diverse-modes-of-clonal-evolution-in-hbv-related-hepatocellular-carcinoma-revealed-by-single-cell-genome-sequencing
#11
Meng Duan, Junfeng Hao, Sijia Cui, Daniel L Worthley, Shu Zhang, Zhichao Wang, Jieyi Shi, Longzi Liu, Xiaoying Wang, Aiwu Ke, Ya Cao, Ruibin Xi, Xiaoming Zhang, Jian Zhou, Jia Fan, Chong Li, Qiang Gao
Hepatocellular carcinoma (HCC) is a cancer of substantial morphologic, genetic and phenotypic diversity. Yet we do not understand the relationship between intratumor heterogeneity and the associated morphologic/histological characteristics of the tumor. Using single-cell whole-genome sequencing to profile 96 tumor cells (30-36 each) and 15 normal liver cells (5 each), collected from three male patients with HBV-associated HCC, we confirmed that copy number variations occur early in hepatocarcinogenesis but thereafter remain relatively stable throughout tumor progression...
January 12, 2018: Cell Research
https://www.readbyqxmd.com/read/29327208/analysis-of-dna-modifications-in-aging-research
#12
REVIEW
Dustin R Masser, Niran Hadad, Hunter Porter, Michael B Stout, Archana Unnikrishnan, David R Stanford, Willard M Freeman
As geroscience research extends into the role of epigenetics in aging and age-related disease, researchers are being confronted with unfamiliar molecular techniques and data analysis methods that can be difficult to integrate into their work. In this review, we focus on the analysis of DNA modifications, namely cytosine methylation and hydroxymethylation, through next-generation sequencing methods. While older techniques for modification analysis performed relative quantitation across regions of the genome or examined average genome levels, these analyses lack the desired specificity, rigor, and genomic coverage to firmly establish the nature of genomic methylation patterns and their response to aging...
January 11, 2018: GeroScience
https://www.readbyqxmd.com/read/29327017/a-significant-role-of-non-thermal-equilibrated-electrons-in-the-formation-of-deleterious-complex-dna-damage
#13
Takeshi Kai, Akinari Yokoya, Masatoshi Ukai, Kentaro Fujii, Tomohiro Toigawa, Ritsuko Watanabe
Although most of the radiation damage to genomic DNA could be rendered harmless using repair enzymes in a living cell, a certain fraction of the damage is persistent resulting in serious genetic effects, such as mutation induction. In order to understand the mechanisms of the deleterious DNA damage formation in terms of its earliest physical stage at the radiation track end, dynamics of low energy electrons and their thermalization processes around DNA molecules were investigated using a dynamic Monte Carlo code...
January 12, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29325248/-survival-of-patients-with-primary-central-nervous-system-diffuse-large-b-cell-lymphoma-impact-of-gene-aberrations-and-protein-overexpression-of-bcl-2-and-c-myc-and-selection-of-chemotherapy-regimens
#14
W J Yin, X Zhu, H Y Yang, W Y Sun, M J Wu
Objective: To investigate the impact of clinicopathological features, gene rearrangements and protein expression of bcl-6, bcl-2, C-MYC and chemotherapy regime on the prognosis of patients with primary central nervous system diffuse large B-cell lymphoma (PCNS-DLBCL). Methods: Thirty-three cases of PCNS-DLBCL diagnosed from January 2006 to December 2016 at Zhejiang Cancer Hospital were collected. The expression of CD10, bcl-6, bcl-2, MUM1 and MYC were detected by immunohistochemical staining (IHC). The presence of EB virus was detected by in situ hybridization(EBER)...
January 8, 2018: Zhonghua Bing Li Xue za Zhi Chinese Journal of Pathology
https://www.readbyqxmd.com/read/29325035/amplicon-based-next-generation-sequencing-of-plasma-cell-free-dna-for-detection-of-driver-and-resistance-mutations-in-advanced-non-small-cell-lung-cancer
#15
N Guibert, Y Hu, N Feeney, Y Kuang, V Plagnol, G Jones, K Howarth, J F Beeler, C P Paweletz, G R Oxnard
Background: Genomic analysis of plasma cell-free DNA is transforming lung cancer care, however available assays are limited by cost, turnaround time, and imperfect accuracy. Here we study amplicon-based plasma next-generation sequencing (NGS), rather than hybrid-capture-based plasma NGS, hypothesizing this would allow sensitive detection and monitoring of driver and resistance mutations in advanced non-small cell lung cancer (NSCLC). Methods: Plasma samples from patients with NSCLC and a known targetable genotype (EGFR, ALK/ROS1 and other rare genotypes) were collected while on therapy and analyzed, blinded to tumor genotype...
January 9, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29324905/strains-of-bacterial-species-induce-a-greatly-varied-acute-adaptive-immune-response-the-contribution-of-the-accessory-genome
#16
Uri Sela, Chad W Euler, Joel Correa da Rosa, Vincent A Fischetti
A fundamental question in human susceptibility to bacterial infections is to what extent variability is a function of differences in the pathogen species or in individual humans. To focus on the pathogen species, we compared in the same individual the human adaptive T and B cell immune response to multiple strains of two major human pathogens, Staphylococcus aureus and Streptococcus pyogenes. We found wide variability in the acute adaptive immune response induced by various strains of a species, with a unique combination of activation within the two arms of the adaptive response...
January 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29323295/alcohol-and-endogenous-aldehydes-damage-chromosomes-and-mutate-stem-cells
#17
Juan I Garaycoechea, Gerry P Crossan, Frédéric Langevin, Lee Mulderrig, Sandra Louzada, Fentang Yang, Guillaume Guilbaud, Naomi Park, Sophie Roerink, Serena Nik-Zainal, Michael R Stratton, Ketan J Patel
Haematopoietic stem cells renew blood. Accumulation of DNA damage in these cells promotes their decline, while misrepair of this damage initiates malignancies. Here we describe the features and mutational landscape of DNA damage caused by acetaldehyde, an endogenous and alcohol-derived metabolite. This damage results in DNA double-stranded breaks that, despite stimulating recombination repair, also cause chromosome rearrangements. We combined transplantation of single haematopoietic stem cells with whole-genome sequencing to show that this damage occurs in stem cells, leading to deletions and rearrangements that are indicative of microhomology-mediated end-joining repair...
January 11, 2018: Nature
https://www.readbyqxmd.com/read/29323274/apobec3-induces-mutations-during-repair-of-crispr-cas9-generated-dna-breaks
#18
Liqun Lei, Hongquan Chen, Wei Xue, Bei Yang, Bian Hu, Jia Wei, Lijie Wang, Yiqiang Cui, Wei Li, Jianying Wang, Lei Yan, Wanjing Shang, Jimin Gao, Jiahao Sha, Min Zhuang, Xingxu Huang, Bin Shen, Li Yang, Jia Chen
The APOBEC-AID family of cytidine deaminase prefers single-stranded nucleic acids for cytidine-to-uridine deamination. Single-stranded nucleic acids are commonly involved in the DNA repair system for breaks generated by CRISPR-Cas9. Here, we show in human cells that APOBEC3 can trigger cytidine deamination of single-stranded oligodeoxynucleotides, which ultimately results in base substitution mutations in genomic DNA through homology-directed repair (HDR) of Cas9-generated double-strand breaks. In addition, the APOBEC3-catalyzed deamination in genomic single-stranded DNA formed during the repair of Cas9 nickase-generated single-strand breaks in human cells can be further processed to yield mutations mainly involving insertions or deletions (indels)...
January 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29322456/method-for-detecting-and-studying-genome-wide-mutations-in-single-living-cells-in-real-time
#19
Marina Elez, Lydia Robert, Ivan Matic
DNA sequencing and fluctuation test have been choice methods for studying DNA mutations for decades. Although invaluable tools allowing many important discoveries on mutations, they are both highly influenced by fitness effects of mutations, and therefore suffer several limits. Fluctuation test is for example limited to mutations that produce an identifiable phenotype, which is the minority of all generated mutations. Genome-wide extrapolations using this method are therefore difficult. DNA sequencing detects almost all DNA mutations in population of cells...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29321601/crispr-cas9-mediated-gene-modification-and-gene-knock-out-in-the-human-infective-parasite-trichomonas-vaginalis
#20
Brian D Janssen, Yi-Pei Chen, Brenda M Molgora, Shuqi E Wang, Augusto Simoes-Barbosa, Patricia J Johnson
The sexually-transmitted parasite Trichomonas vaginalis infects ~1/4 billion people worldwide. Despite its prevalence and myriad adverse outcomes of infection, the mechanisms underlying T. vaginalis pathogenesis are poorly understood. Genetic manipulation of this single-celled eukaryote has been hindered by challenges presented by its complex, repetitive genome and inefficient methods for introducing DNA (i.e. transfection) into the parasite. Here, we have developed methods to increase transfection efficiency using nucleofection, with the goal of efficiently introducing multiple DNA elements into a single T...
January 10, 2018: Scientific Reports
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