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https://www.readbyqxmd.com/read/28643254/gene-targeting-in-rabbits-single-step-generation-of-knock-out-rabbits-by-microinjection-of-crispr-cas9-plasmids
#1
Yoshihiro Kawano, Arata Honda
The development of genome editing technology has allowed gene disruptions to be achieved in various animal species and has been beneficial to many mammals. Gene disruption using pluripotent stem cells is difficult to achieve in rabbits, but thanks to advances in genome editing technology, a number of gene disruptions have been conducted. This paper describes a simple and easy method for carrying out gene disruptions in rabbits using CRISPR/Cas9 in which the gene to be disrupted is marked, the presence or absence of off-target candidates is checked, and a plasmid allowing simultaneous expression of Cas9 and sgRNA is constructed...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28643252/generation-of-knock-in-mouse-by-genome-editing
#2
Wataru Fujii
Knock-in mice are useful for evaluating endogenous gene expressions and functions in vivo. Instead of the conventional gene-targeting method using embryonic stem cells, an exogenous DNA sequence can be inserted into the target locus in the zygote using genome editing technology. In this chapter, I describe the generation of epitope-tagged mice using engineered endonuclease and single-stranded oligodeoxynucleotide through the mouse zygote as an example of how to generate a knock-in mouse by genome editing.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28642169/a-novel-method-to-quantify-base-substitution-mutations-at-the-10-6-per-bp-level-in-dna-samples
#3
Satoshi Yamashita, Naoko Iida, Hideyuki Takeshima, Naoko Hattori, Maeda Masahiro, Takayoshi Kishino, Reiko Nagano, Taichi Shimazu, Shoichiro Tsugane, Toshikazu Ushijima
Somatic base substitution mutations of frequencies at the 10(-6)/bp level are expected to be present in many biomedical samples, such as tissues exposed to carcinogenic factors and exhausted stem cells. However, measurement of such rare mutations has been very difficult in human DNA samples. Here, we invented the use of 100 copies of genomic DNA as a template for amplicon deep sequencing so that a real mutation in a single DNA molecule would be detected at a variant allele frequency of 1% while sequencing errors have less frequency...
June 19, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28641521/lncrna-hotair-polymorphisms-association-with-cancer-susceptibility-in-different-tumor-types
#4
Gerardo Botti, Francesca Collina, Giosuè Scognamiglio, Gabriella Aquino, Margherita Cerrone, Giuseppina Liguori, Vincenzo Gigantino, Maria Gabriella Malzone, Monica Cantile
Single nucleotide polymorphisms (SNPs) in non coding RNAs (ncRNA) molecules affect gene and protein expression and generate genetic variability influencing the risk of tumor diseases. HOTAIR is locates at the heart of the cell memory gene program and represents a prototype of long non coding RNA (LncRNA) due to its capacity to regulate in-trans a distant chromosome landscape. Aberrant expression of HOTAIR is frequently associated with pathogenesis and mostly with metastatic progression of several human cancers...
June 21, 2017: Current Drug Targets
https://www.readbyqxmd.com/read/28640939/global-transcriptome-and-co-expression-network-analyses-reveal-cultivar-specific-molecular-signatures-associated-with-seed-development-and-seed-size-weight-determination-in-chickpea
#5
Rohini Garg, Vikash K Singh, Mohan Singh Rajkumar, Vinay Kumar, Mukesh Jain
Seed development is an intricate process regulated via a complex transcriptional regulatory network. To understand the molecular mechanisms governing seed development and seed size/weight in chickpea, we performed a comprehensive analysis of transcriptome dynamics during seed development in two cultivars with contrasting seed size/weight (small seeded, Himchana 1 and large-seeded, JGK 3). Our analysis identified stage-specific expression for a significant proportion (>13%) of the genes. About one-fourth of total genes exhibited significant differential expression in JGK 3 as compared to Himchana 1...
June 22, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28640612/crispr-cas9-based-genome-editing-for-disease-modeling-and-therapy-challenges-and-opportunities-for-nonviral-delivery
#6
Hong-Xia Wang, Mingqiang Li, Ciaran M Lee, Syandan Chakraborty, Hae-Won Kim, Gang Bao, Kam W Leong
Genome editing offers promising solutions to genetic disorders by editing DNA sequences or modulating gene expression. The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) technology can be used to edit single or multiple genes in a wide variety of cell types and organisms in vitro and in vivo. Herein, we review the rapidly developing CRISPR/Cas9-based technologies for disease modeling and gene correction and recent progress toward Cas9/guide RNA (gRNA) delivery based on viral and nonviral vectors...
June 22, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28639307/anti-d-in-a-mother-hemizygous-for-the-variant-rhd-dnb-gene-associated-with-hemolytic-disease-of-the-fetus-and-newborn
#7
Kelli M Quantock, Genghis H Lopez, Catherine A Hyland, Yew-Wah Liew, Robert L Flower, Frans J Niemann, Arthur Joyce
BACKGROUND: Individuals with the partial D phenotype when exposed to D+ red blood cells (RBCs) carrying the epitopes they lack may develop anti-D specific for the missing epitopes. DNB is the most common partial D in Caucasians and the clinical significance for anti-D in these individuals is unknown. STUDY DESIGN AND METHODS: This article describes the serologic genotyping results and clinical manifestations in two group D+ babies of a mother presenting as group O, D+ with alloanti-D...
June 21, 2017: Transfusion
https://www.readbyqxmd.com/read/28639249/histone-post-translational-modifications-and-nucleosome-organisation-in-transcriptional-regulation-some-open-questions
#8
Josefa Castillo, Gerardo López-Rodas, Luis Franco
The organisation of chromatin is first discussed to conclude that nucleosomes play both structural and transcription-regulatory roles. The presence of nucleosomes makes difficult the access of transcriptional factors to their target sequences and the action of RNA polymerases. The histone post-translational modifications and nucleosome remodelling are first discussed, from a historical point of view, as mechanisms to remove the obstacles imposed by chromatin structure to transcription. Instead of reviewing the state of the art of the whole field, this review is centred on some open questions...
June 22, 2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28638221/prevalence-of-ifnl3-rs4803217-single-nucleotide-polymorphism-and-clinical-course-of-chronic-hepatitis-c
#9
Bogna Świątek-Kościelna, Ewelina Kałużna, Ewa Strauss, Jerzy Nowak, Iwona Bereszyńska, Ewelina Gowin, Jacek Wysocki, Jolanta Rembowska, Dominika Barcińska, Iwona Mozer-Lisewska, Danuta Januszkiewicz-Lewandowska
AIM: To evaluate the association of IFNL3 (IL28B) SNP rs4803217 with severity of disease and treatment outcome in chronic hepatitis C (CHC). METHODS: The study enrolled 196 CHC Polish patients (82 women and 114 men in age 20-64) infected with hepatitis C virus (HCV) genotype 1. They were treatment naïve and qualified to pegylated interferon alpha (PEG-IFN-α) and ribavirin (RBV) therapy. The analyzed baseline parameters included: degree of inflammation, stage of fibrosis, viral load as well as alanine aminotransferase (ALT), asparagine aminotransferase (AST) and total bilirubin (TBIL)...
June 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28638107/tracking-protein-function-with-sodium-multi-quantum%C3%A2-spectroscopy-in-a-3d-tissue-culture-based-on-microcavity-arrays
#10
Andreas Neubauer, Cordula Nies, Victor D Schepkin, Ruomin Hu, Matthias Malzacher, Jorge Chacón-Caldera, David Thiele, Eric Gottwald, Lothar R Schad
The aim of this study was to observe the effects of strophanthin induced inhibition of the Na-/K-ATPase in liver cells using a magnetic resonance (MR) compatible bioreactor. A microcavity array with a high density three-dimensional cell culture served as a functional magnetic resonance imaging (MRI) phantom for sodium multi quantum (MQ) spectroscopy. Direct contrast enhanced (DCE) MRI revealed the homogenous distribution of biochemical substances inside the bioreactor. NMR experiments using advanced bioreactors have advantages with respect to having full control over a variety of physiological parameters such as temperature, gas composition and fluid flow...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28637924/vp4-and-vp7-specific-antibodies-mediate-heterotypic-immunity-to-rotavirus-in-humans
#11
Nitya Nair, Ningguo Feng, Lisa K Blum, Mrinmoy Sanyal, Siyuan Ding, Baoming Jiang, Adrish Sen, John M Morton, Xiao-Song He, William H Robinson, Harry B Greenberg
Human rotaviruses (RVs) are the leading cause of severe diarrhea in young children worldwide. The molecular mechanisms underlying the rapid induction of heterotypic protective immunity to RV, which provides the basis for the efficacy of licensed monovalent RV vaccines, have remained unknown for more than 30 years. We used RV-specific single cell-sorted intestinal B cells from human adults, barcode-based deep sequencing of antibody repertoires, monoclonal antibody expression, and serologic and functional characterization to demonstrate that infection-induced heterotypic immunoglobulins (Igs) primarily directed to VP5*, the stalk region of the RV attachment protein, VP4, are able to mediate heterotypic protective immunity...
June 21, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28637869/heat-shock-proteins-stimulate-apobec-3-mediated-cytidine-deamination-in-the-hepatitis-b-virus
#12
Zhigang Chen, Thomas L Eggerman, Alexander V Bocharov, Irina N Baranova, Tatyana G Vishnyakova, Roger Kurlander, Amy P Patterson
Apolipoprotein B mRNA-editing enzyme catalytic subunit 3 (APOBEC-3) enzymes are cytidine deaminases that are broadly and constitutively expressed. They are often upregulated during carcinogenesis and candidate genes for causing the major single-base substitution in cancer-associated DNA mutations. Moreover, APOBEC-3s are involved in host innate immunity against many viruses. However, how APOBEC-3 mutational activity is regulated in normal and pathological conditions remains largely unknown. Heat shock protein levels are often elevated in both carcinogenesis and viral infection and are associated with DNA mutations...
June 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28637867/full-length-cellular-beta-secretase-has-a-trimeric-subunit-stoichiometry-and-its-sulfur-rich-transmembrane-interaction-site-modulates-cytosolic-copper-compartmentalization
#13
Filip Liebsch, Mark R P Aurousseau, Tobias Bethge, Hugo McGuire, Silvia Scolari, Andreas Herrmann, Rikard Blunck, Derek Bowie, Gerd Multhaup
The beta-secretase (BACE1) initiates processing of the amyloid precursor protein (APP) into Aβ peptides, which have been implicated as central players in the pathology of Alzheimer disease. BACE1 has been described as a copper-binding protein and its oligomeric state as being monomeric, dimeric, and/or multimeric, but the native cellular stoichiometry has remained elusive. Here, by using single-molecule fluorescence and in vitro cross-linking experiments with photo-activatable unnatural amino acids, we show that full-length BACE1, independently of its subcellular localization, exists as trimers in human cells...
June 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28637761/mother-to-child-hiv-transmission-bottleneck-selects-for-consensus-virus-with-lower-gag-protease-driven-replication-capacity
#14
Vanessa L Naidoo, Jaclyn K Mann, Christie Noble, Emily Adland, Jonathan M Carlson, Jake Thomas, Chanson J Brumme, Christina F Thobakgale-Tshabalala, Zabrina L Brumme, Mark A Brockman, Philip J R Goulder, Thumbi Ndung'u
HIV infection is in the large majority of cases established by a single variant and understanding the characteristics of successfully transmitted variants is relevant to prevention strategies. Few studies have investigated the viral determinants of mother-to-child transmission. To determine the impact of Gag-protease driven viral replication capacity on mother-to-child transmission, the replication capacities of 148 recombinant viruses encoding plasma derived Gag-protease from 53 non-transmitter mothers, 48 transmitter mothers and 47 infected infants were assayed in an HIV-1 inducible green fluorescent protein reporter cell line...
June 21, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28637749/cell-cycle-dependent-spatial-segregation-of-telomerase-from-sites-of-dna-damage
#15
Faissal Ouenzar, Maxime Lalonde, Hadrien Laprade, Geneviève Morin, Franck Gallardo, Samuel Tremblay-Belzile, Pascal Chartrand
Telomerase can generate a novel telomere at DNA double-strand breaks (DSBs), an event called de novo telomere addition. How this activity is suppressed remains unclear. Combining single-molecule imaging and deep sequencing, we show that the budding yeast telomerase RNA (TLC1 RNA) is spatially segregated to the nucleolus and excluded from sites of DNA repair in a cell cycle-dependent manner. Although TLC1 RNA accumulates in the nucleoplasm in G1/S, Pif1 activity promotes TLC1 RNA localization in the nucleolus in G2/M...
June 21, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28637323/evolution-of-transcription-activator-like-effectors-in-xanthomonas-oryzae
#16
Annett Erkes, Maik Reschke, Jens Boch, Jan Grau
Transcription activator-like effectors (TALEs) are secreted by plant-pathogenic Xanthomonas bacteria into plant cells where they act as transcriptional activators and, hence, are major drivers in reprogramming the plant for the benefit of the pathogen. TALEs possess a highly repetitive DNA-binding domain of typically 34 amino acid tandem repeats, where amino acid 12 and 13, termed repeat variable di-residue (RVD), determine target specificity. Different Xanthomonas strains possess different repertoires of TALEs...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28636592/quantifiable-predictive-features-define-epitope-specific-t-cell-receptor-repertoires
#17
Pradyot Dash, Andrew J Fiore-Gartland, Tomer Hertz, George C Wang, Shalini Sharma, Aisha Souquette, Jeremy Chase Crawford, E Bridie Clemens, Thi H O Nguyen, Katherine Kedzierska, Nicole L La Gruta, Philip Bradley, Paul G Thomas
T cells are defined by a heterodimeric surface receptor, the T cell receptor (TCR), that mediates recognition of pathogen-associated epitopes through interactions with peptide and major histocompatibility complexes (pMHCs). TCRs are generated by genomic rearrangement of the germline TCR locus, a process termed V(D)J recombination, that has the potential to generate marked diversity of TCRs (estimated to range from 10(15) (ref. 1) to as high as 10(61) (ref. 2) possible receptors). Despite this potential diversity, TCRs from T cells that recognize the same pMHC epitope often share conserved sequence features, suggesting that it may be possible to predictively model epitope specificity...
June 21, 2017: Nature
https://www.readbyqxmd.com/read/28635411/single-nucleotide-polymorphisms-in-the-human-rad21l-gene-may-be-a-genetic-risk-factor-for-japanese-patients-with-azoospermia-caused-by-meiotic-arrest-and-sertoli-cell-only-syndrome
#18
Gaku Minase, Toshinobu Miyamoto, Yasushi Miyagawa, Masashi Iijima, Hiroto Ueda, Yasuaki Saijo, Mikio Namiki, Kazuo Sengoku
Genetic mechanisms are implicated in some cases of male infertility. Recently, it was demonstrated that male mice lacking the gene for RAD21L exhibited azoospermia caused by meiotic arrest. Mouse RAD21L is a functionally relevant meiotic α-kleisin that is essential for male fertility. Therefore, we hypothesized that RAD21L mutations or polymorphisms may be associated with male infertility, especially azoospermia secondary to meiotic arrest. To determine if RAD21L defects are associated with azoospermia in groups of patients with meiotic arrest, we performed direct sequencing of the RAD21L coding regions in 38 Japanese patients with meiotic arrest and in 200 normal controls...
February 21, 2017: Human Fertility: Journal of the British Fertility Society
https://www.readbyqxmd.com/read/28634471/a-chitin-binding-protein-purified-from-moringa-oleifera-seeds-presents-anticandidal-activity-by-increasing-cell-membrane-permeability-and-reactive-oxygen-species-production
#19
João X S Neto, Mirella L Pereira, Jose T A Oliveira, Lady C B Rocha-Bezerra, Tiago D P Lopes, Helen P S Costa, Daniele O B Sousa, Bruno A M Rocha, Thalles B Grangeiro, José E C Freire, Ana Cristina O Monteiro-Moreira, Marina D P Lobo, Raimunda S N Brilhante, Ilka M Vasconcelos
Candida species are opportunistic pathogens that infect immunocompromised and/or immunosuppressed patients, particularly in hospital facilities, that besides representing a significant threat to health increase the risk of mortality. Apart from echinocandins and triazoles, which are well tolerated, most of the antifungal drugs used for candidiasis treatment can cause side effects and lead to the development of resistant strains. A promising alternative to the conventional treatments is the use of plant proteins...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28634269/human-development-heredity-and-evolution
#20
REVIEW
Ryuichi Nishinakamura, Minoru Takasato
From March 27-29 2017, the RIKEN Center for Developmental Biology held a symposium entitled 'Towards Understanding Human Development, Heredity, and Evolution' in Kobe, Japan. Recent advances in technologies including stem cell culture, live imaging, single-cell approaches, next-generation sequencing and genome editing have led to an expansion in our knowledge of human development. Organized by Yoshiya Kawaguchi, Mitinori Saitou, Mototsugu Eiraku, Tomoya Kitajima, Fumio Matsuzaki, Takashi Tsuji and Edith Heard, the symposium covered a broad range of topics including human germline development, epigenetics, organogenesis and evolution...
June 15, 2017: Development
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