keyword
MENU ▼
Read by QxMD icon Read
search

single-cell sequencing

keyword
https://www.readbyqxmd.com/read/29150045/spectrum-of-benzo-a-pyrene-induced-mutations-in-the-pig-a-gene-of-l5178ytk-cells-identified-with-next-generation-sequencing
#1
Javier Revollo, Yiying Wang, Page McKinzie, Azra Dad, Mason Pearce, Robert H Heflich, Vasily N Dobrovolsky
We used Sanger sequencing and next generation sequencing (NGS) for analysis of mutations in the endogenous X-linked Pig-a gene of clonally expanded L5178YTk(+/-) cells. The clones developed from single cells that were sorted on a flow cytometer based upon the expression pattern of the GPI-anchored marker, CD90, on their surface. CD90-deficient and CD90-proficient cells were sorted from untreated cultures and CD90-deficient cells were sorted from cultures treated with benzo[a]pyrene (B[a]P). Pig-a mutations were identified in all clones developed from CD90-deficient cells; no Pig-a mutations were found in clones of CD90-proficient cells...
December 2017: Mutation Research
https://www.readbyqxmd.com/read/29149987/inhibition-of-porcine-endogenous-retrovirus-by-multi-targeting-micro-rna-against-long-terminal-region
#2
H-C Chung, V-G Nguyen, W-T Oh, T-M-L Huynh, H-J Moon, J-H Lee, H-K Kim, S-J Park, B-K Park
BACKGROUND: There might be much benefit in xenotransplantation, however, the risk of infections across species barriers remains, especially porcine endogenous retrovirus (PERV). To date, many attempts have been made to knock down active PERVs by inhibitory RNA (RNAi) and micro RNA (miRNA), which target different genes of PERV. There are a few studies that have explored whether targeting promoter regions of PERV could exert an inhibition effect. METHODS: miRNAs were automatically selected based on an online program BLOCK-iT RNAi Designer...
November 2017: Transplantation Proceedings
https://www.readbyqxmd.com/read/29149607/classifying-drosophila-olfactory-projection-neuron-subtypes-by-single-cell-rna-sequencing
#3
Hongjie Li, Felix Horns, Bing Wu, Qijing Xie, Jiefu Li, Tongchao Li, David J Luginbuhl, Stephen R Quake, Liqun Luo
The definition of neuronal type and how it relates to the transcriptome are open questions. Drosophila olfactory projection neurons (PNs) are among the best-characterized neuronal types: different PN classes target dendrites to distinct olfactory glomeruli, while PNs of the same class exhibit indistinguishable anatomical and physiological properties. Using single-cell RNA sequencing, we comprehensively characterized the transcriptomes of most PN classes and unequivocally mapped transcriptomes to specific olfactory function for six classes...
November 16, 2017: Cell
https://www.readbyqxmd.com/read/29147724/glabrous-cmgl-encodes-a-hd-zip-iv-transcription-factor-playing-roles-in-multicellular-trichome-initiation-in-melon
#4
Huayu Zhu, Xiaofen Sun, Qi Zhang, Pengyao Song, Qianmei Hu, Xiaojing Zhang, Xiang Li, Jianbin Hu, Junsong Pan, Shouru Sun, Yiqun Weng, Luming Yang
Map-based cloning identified CmGL that encodes a HD-ZIP type IV transcription factor that controls multicellular trichome initiation in melon. Trichomes are small hairs covering the aerial parts of plants that originate from the epidermal cells, which can protect plants against the damage by insects and pathogens. The regulatory pathway of unicellular trichomes has been well studied in the model plant Arabidopsis. Little is known about the genetic control and regulation of trichome development in melon (Cucumis melo L...
November 17, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29146617/cure-in-advanced-renal-cell-cancer-is-it-an-achievable-goal
#5
Dhanusha Sabanathan, John J Park, Manuel Marquez, Louise Francisco, Natalie Byrne, Howard Gurney
BACKGROUND: Immunotherapy has historically been of interest in the management of metastatic renal cell cancer (mRCC) because of its relative chemoresistance and the reproducible but low incidence of spontaneous remission in metastatic disease. Recently, targeted immunotherapies in the form of checkpoint inhibitors have shown durable responses in approximately 20%-30% of patients with solid tumors, with a much more acceptable side-effect profile. Anti-programmed death receptor 1 (PD-1)/programmed death receptor ligand 1 antibodies rely on the presence of host T cells in the tumor microenvironment to be stimulated in order to activate an antitumor response...
November 16, 2017: Oncologist
https://www.readbyqxmd.com/read/29146449/an-integrated-metabolic-consequence-of-hepatospora-eriocheir-infection-in-the-chinese-mitten-crab-eriocheir-sinensis
#6
Zhengfeng Ding, Jing Pan, Hua Huang, Gongcheng Jiang, Jianqin Chen, Xueshen Zhu, Renlei Wang, Guohua Xu
Despite the economic and evolutionary importance of aquatic host-infecting microsporidian species, at present, limited information has been provided about the microsporidia-host interactions. This study focused on Hepatospora eriocheir, an emerging microsporidian pathogen for the Chinese mitten crab Eriocheir sinensis. Hypertrophy of hepatopancreas cells was a common feature of H. eriocheir infection. More importantly, mitochondria of the hepatopancreas were drawn around the H. eriocheir, most likely to aid the uptake of ATP directly from the host...
November 13, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29144536/isolation-and-whole-genome-sequencing-of-fetal-cells-from-maternal-blood-towards-the-ultimate-non-invasive-prenatal-testing
#7
Fang Chen, Ping Liu, Ying Gu, Zhu Zhu, Amulya Nanisetti, Zhangzhang Lan, Zhiwei Huang, Sophie Jia Liu, Xiongbin Kang, Yuqing Deng, Liqiong Luo, Dan Jiang, Yong Qiu, Jianchang Pan, Jun Xia, Ken Xiong, Chao Liu, Lin Xie, Qianyu Shi, Jing Li, Xiuqing Zhang, Wei Wang, Snezana Drmanac, Hui Jiang, Radoje Drmanac, Xun Xu
OBJECTIVE: To develop a methodology of isolating fetal cells from maternal blood and use deep sequencing demonstrating the promise for more complete and accurate genetic screening compared to other non-invasive prenatal testing (NIPT). METHODS: Here in this study, we developed a double negative selection (DNS) procedure to unbiasedly enrich fetal cells. After validated by short tandem repeat (STR), the isolated CFCs were subjected to deep whole genome sequencing analysis (WGS)...
November 16, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/29144389/effects-of-infrared-optical-trapping-on-saccharomyces-cerevisiae-in-a-microfluidic-system
#8
Zdeněk Pilát, Alexandr Jonáš, Jan Ježek, Pavel Zemánek
Baker's yeast (Saccharomyces cerevisiae) represents a very popular single-celled eukaryotic model organism which has been studied extensively by various methods and whose genome has been completely sequenced. It was also among the first living organisms that were manipulated by optical tweezers and it is currently a frequent subject of optical micromanipulation experiments. We built a microfluidic system for optical trapping experiments with individual cells and used it for the assessment of cell tolerance to phototoxic stress...
November 16, 2017: Sensors
https://www.readbyqxmd.com/read/29143729/thalassotalea-coralli-sp-nov-isolated-from-the-torch-coral-euphyllia-glabrescens
#9
Der-Shyan Sheu, Shih-Yi Sheu, Pei-Bei Xie, Sen-Lin Tang, Wen-Ming Chen
Strain Eup a-8(T), isolated from a torch coral Euphyllia glabrescens, was characterized using a polyphasic taxonomy approach. Cells of strain Eup a-8(T) were Gram-staining-negative, aerobic, motile by means of a single polar flagellum, poly-β-hydroxybutyrate-containing, rod-shaped and formed white colonies. Optimal growth occurred at 25-30 °C, pH 7-8, and in the presence of 2 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Eup a-8(T) belonged to the genus Thalassotalea and showed the highest levels of sequence similarity with respect to Thalassotalea ganghwensis JC2041(T) (97...
November 16, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29143727/characterization-of-clinically-isolated-thymidine-dependent-small-colony-variants-of-escherichia-coli-producing-extended-spectrum-%C3%AE-lactamase
#10
Tatsuya Negishi, Takehisa Matsumoto, Kazuki Horiuchi, Eriko Kasuga, Tatsuya Natori, Mina Matsuoka, Naoko Ogiwara, Mitsutoshi Sugano, Takeshi Uehara, Noriyuki Nagano, Takayuki Honda
PURPOSE: Thymidine-dependent small-colony variants (TD-SCVs) are difficult to detect or test for antimicrobial susceptibility. We investigated the characteristics of clonal TD-SCVs of Escherichia coli, both with and without blaCTX-M-3, isolated from a patient. METHODOLOGY: Mutation in the thyA gene was analysed by sequencing, and morphological abnormalities in the colonies and cells of the isolates were examined. Additionally, conjugational transfer experiments were performed to prove the horizontal transferability of plasmids harbouring resistance genes...
November 16, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29143621/identification-and-characterization-of-regulatory-network-components-for-anthocyanin-synthesis-in-barley-aleurone
#11
Ksenia V Strygina, Andreas Börner, Elena K Khlestkina
BACKGROUND: Among natural populations, there are different colours of barley (Hordeum vulgare L.). The colour of barley grains is directly related to the accumulation of different pigments in the aleurone layer, pericarp and lemma. Blue grain colour is due to the accumulation of anthocyanins in the aleurone layer, which is dependent on the presence of five Blx genes that are not sequenced yet (Blx1, Blx3 and Blx4 genes clustering on chromosome 4HL and Blx2 and Blx5 on 7HL). Due to the health benefits of anthocyanins, blue-grained barley can be considered as a source of dietary food...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29141659/rescue-of-high-specificity-cas9-variants-using-sgrnas-with-matched-5-nucleotides
#12
Sojung Kim, Taegeun Bae, Jaewoong Hwang, Jin-Soo Kim
We report that engineered Cas9 variants with improved specificity-eCas9-1.1 and Cas9-HF1-are often poorly active in human cells, when complexed with single guide RNAs (sgRNAs) with a mismatch at the 5' terminus, relative to target DNA sequences. Because the nucleotide at the 5' end of sgRNAs, expressed under the control of the commonly-used U6 promoter, is fixed to a guanine, these attenuated Cas9 variants are not useful at many target sites. By using sgRNAs with matched 5' nucleotides, produced by linking them to a self-cleaving ribozyme, the editing activity of Cas9 variants can be rescued without sacrificing high specificity...
November 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/29141638/diffusion-weighted-imaging-of-the-brains-of-dogs-with-idiopathic-epilepsy
#13
Antje Hartmann, Steffen Sager, Klaus Failing, Marion Sparenberg, Martin J Schmidt
BACKGROUND: Idiopathic epilepsy is one of the most common neurological disorders in dogs. Unfortunately, up to 30% of dogs with idiopathic epilepsy show no improvement under antiepileptic drug treatment. Diffusion-weighted imaging is used in human medicine to identify epileptogenic foci in the brain to allow for more invasive treatments such as deep brain stimulation or surgical removal. The aim of this study was to ass the feasibility of interictal diffusion-weighted MRI in dogs and to evaluate the distribution of diffusion in the brains of dogs with idiopathic epilepsy (IE) and to compare these values to previously published values from healthy beagle dogs...
November 15, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/29141374/-association-of-pd-1-tim-3-and-trem-1-single-nucleotide-polymorphisms-with-pulmonary-tuberculosis-susceptibility
#14
F M Wang, X Zhang, L Lan, J M Ji, H B Tang, X J Yao, Y Jiang, J Qian, X G Xu, Q Li, P Yao, J H Li, Y P Shen
Objective: To investigate the association of programmed cell death 1(PD-1), T cell immunoglobulin mucin 3 (TIM-3) and triggering receptor expressed on myeloid cells-1 (TREM-1) genes polymorphisms with pulmonary tuberculosis susceptibility. Methods: In this case-control study, peripheral venous blood of 100 pulmonary tuberculosis patients (pulmonary tuberculosis group) in the Jintan People's Hospital of Changzhou and of community physical examination volunteers (health control group) was collected from Mar 2015 to Sep 2016...
November 14, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/29141156/plasmid-azobr_p1-borne-fabg-gene-for-putative-3-oxoacyl-acyl-carrier-protein-reductase-is-essential-for-proper-assembly-and-work-of-the-dual-flagellar-system-in-the-alphaproteobacterium-azospirillum-brasilense-sp245
#15
Yulia A Filip'echeva, Andrei V Shelud'ko, Alexei G Prilipov, Gennady L Burygin, Elizaveta M Telesheva, Stella S Yevstigneyeva, Marina P Chernyshova, Lilia P Petrova, Elena I Katsy
Azospirillum brasilense can swim and swarm owing to the activity of a constitutive polar flagellum (Fla) and inducible lateral flagella (Laf), respectively. Experimental data on the regulation of the Fla and Laf assembly in azospirilla are scarce. Here, the coding sequence (CDS) AZOBR_p1160043 (fabG1) for a putative 3-oxoacyl-[acyl-carrier protein (ACP)] reductase was found essential for the construction of both types of flagella. In an immotile leaky Fla- Laf- fabG1::Omegon-Km mutant, Sp245.1610, defects in flagellation and motility were fully complemented by expressing the CDS AZOBR_p1160043 from plasmid pRK415...
November 15, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/29140455/a-sparse-differential-clustering-algorithm-for-tracing-cell-type-changes-via-single-cell-rna-sequencing-data
#16
Martin Barron, Siyuan Zhang, Jun Li
Cell types in cell populations change as the condition changes: some cell types die out, new cell types may emerge and surviving cell types evolve to adapt to the new condition. Using single-cell RNA-sequencing data that measure the gene expression of cells before and after the condition change, we propose an algorithm, SparseDC, which identifies cell types, traces their changes across conditions and identifies genes which are marker genes for these changes. By solving a unified optimization problem, SparseDC completes all three tasks simultaneously...
November 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29139543/molecular-cloning-and-expression-analysis-of-sox3-during-gonad-and-embryonic-development-in-misgurnus-anguillicaudatus
#17
Xiaohua Xia, Weiran Huo, Ruyan Wan, Linxia Zhang, Xiaopei Xia, Zhongjie Chang
Sox3 is a single-exon gene located on the X chromosome in most vertebrates. It belongs to the SoxB1 subfamily, which is part of the larger Sox family. Previous studies have revealed that Sox3 is expressed in many fish species. However, how Sox3 influences the development of Misgurnus anguillicaudatus remains unknown. In this study, a Sox3 homologue, termed MaSox3, was cloned from the brain of M. anguillicaudatus using homology-based cloning and the rapid amplification of cDNA ends method. Sequence analysis reveals that MaSox3 encodes a hydrophilic protein, which contains a characteristic HMG-box DNA-binding domain of 79 amino acids, and shares high homology with Sox3 in other species...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/29139141/developing-novel-species-specific-dna-markers-for-pcr-based-species-identification-of-the-lactobacillus-sakei-group
#18
Chien-Hsun Huang, Jong-Shian Liou, Lina Huang, Koichi Watanabe
Identification members of the Lactobacillus sakei group (LSG) by common phenotypic and genotypic methods is generally inadequate and time-consuming. The objective of this study was to develop novel species-specific primers based on sequence-characterized amplified region (SCAR) markers using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) analysis. Three species-specific fragments were gel-purified, cloned, and sequenced after preliminary screening of 80 random primers. Accordingly, three pairs of primers Lcur-F/R, Lgram-F/R, and Lsakei-F/R were designed based on single species-specific bands (281, 278, and 472 bp) that were obtained from L...
November 14, 2017: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/29138535/comparable-pharmacokinetics-and-pharmacodynamics-of-two-epoetin-alfa-formulations-eporon-%C3%A2-and-eprex-%C3%A2-following-a-single-subcutaneous-administration-in-healthy-male-volunteers
#19
Sumin Yoon, Su-Jin Rhee, Sun Ju Heo, Tae Young Oh, Seo Hyun Yoon, Joo-Youn Cho, SeungHwan Lee, Kyung-Sang Yu
Purpose: This study aimed to assess and compare the pharmacokinetic (PK) and pharmacodynamic (PD) properties following a single subcutaneous injection of epoetin alfa (Eporon(®)) with those of the comparator (Eprex(®)) in healthy male subjects. Subjects and methods: A randomized, double-blind, two-sequence, crossover study was conducted. Subjects were randomly assigned to receive a single dose, that is, 4,000 IU, of the test or comparator epoetin alfa. After 4 weeks, all subjects received the alternative formulation...
2017: Drug Design, Development and Therapy
https://www.readbyqxmd.com/read/29138417/association-of-predicted-pathogenic-mutations-in-mitochondrial-nd-genes-with-distant-metastasis-in-nsclc-and-colon-cancer
#20
Nobuko Koshikawa, Miho Akimoto, Jun-Ichi Hayashi, Hiroki Nagase, Keizo Takenaga
Cancer cells have more mutations in their mitochondrial DNA (mtDNA) than do normal cells, and pathogenic mutations in the genes encoding mitochondrial NADH dehydrogenase (ND) subunits have been found to enhance the invasive and metastatic ability of various tumour cells in animal experiments. However, it is unknown whether single-nucleotide variants (SNVs) of the ND genes that decrease complex I activity are involved in distant metastasis in human clinical samples. Here, we demonstrated the enhancement of the distant metastasis of Lewis lung carcinoma cells by the ND6 13885insC mutation, which is accompanied by the overexpression of metastasis-related genes, metabolic reprogramming, the enhancement of tumour angiogenesis and the acquisition of resistance to stress-induced cell death...
November 14, 2017: Scientific Reports
keyword
keyword
45265
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"