keyword
https://read.qxmd.com/read/38523431/an-oocyte-specific-cas9-expressing-mouse-for-germline-crispr-cas9-mediated-genome-editing
#1
JOURNAL ARTICLE
Denise G Lanza, Jianqiang Mao, Isabel Lorenzo, Lan Liao, John R Seavitt, M Cecilia Ljungberg, Elizabeth M Simpson, Francesco J DeMayo, Jason D Heaney
Cas9 transgenes can be employed for genome editing in mouse zygotes. However, using transgenic instead of exogenous Cas9 to produce gene-edited animals creates unique issues including ill-defined transgene integration sites, the potential for prolonged Cas9 expression in transgenic embryos, and increased genotyping burden. To overcome these issues, we generated mice harboring an oocyte-specific, Gdf9 promoter driven, Cas9 transgene (Gdf9-Cas9) targeted as a single copy into the Hprt1 locus. The X-linked Hprt1 locus was selected because it is a defined integration site that does not influence transgene expression, and breeding of transgenic males generates obligate transgenic females to serve as embryo donors...
April 2024: Genesis: the Journal of Genetics and Development
https://read.qxmd.com/read/38510975/comprehensive-analysis-of-m-6-a-methylome-alterations-after-azacytidine-plus-venetoclax-treatment-for-acute-myeloid-leukemia-by-nanopore-sequencing
#2
JOURNAL ARTICLE
Zaifeng Zhang, Lili Zhang, Jiangtao Li, Ru Feng, Chang Li, Ye Liu, Gaoyuan Sun, Fei Xiao, Chunli Zhang
N6 adenosine methylation (m6 A), one of the most prevalent internal modifications on mammalian RNAs, regulates RNA transcription, stabilization, and splicing. Growing evidence has focused on the functional role of m6 A regulators on acute myeloid leukemia (AML). However, the global m6 A levels after azacytidine (AZA) plus venetoclax (VEN) treatment in AML patients remain unclear. In our present study, bone marrow (BM) sample pairs (including pre-treatment [AML] and post-treatment [complete remission (CR)] samples) were harvested from three AML patients who had achieved CR after AZA plus VEN treatment for Nanopore direct RNA sequencing...
December 2024: Computational and Structural Biotechnology Journal
https://read.qxmd.com/read/38503737/comprehensive-blood-metabolomics-profiling-of-parkinson-s-disease-reveals-coordinated-alterations-in-xanthine-metabolism
#3
JOURNAL ARTICLE
Elisa Gómez de Lope, Rebecca Ting Jiin Loo, Armin Rauschenberger, Muhammad Ali, Lukas Pavelka, Tainá M Marques, Clarissa P C Gomes, Rejko Krüger, Enrico Glaab
Parkinson's disease (PD) is a highly heterogeneous disorder influenced by several environmental and genetic factors. Effective disease-modifying therapies and robust early-stage biomarkers are still lacking, and an improved understanding of the molecular changes in PD could help to reveal new diagnostic markers and pharmaceutical targets. Here, we report results from a cohort-wide blood plasma metabolic profiling of PD patients and controls in the Luxembourg Parkinson's Study to detect disease-associated alterations at the level of systemic cellular process and network alterations...
March 19, 2024: NPJ Parkinson's Disease
https://read.qxmd.com/read/38499035/applicability-of-gene-expression-in-saliva-as-an-alternative-to-blood-for-biodosimetry-and-prediction-of-radiation-induced-health-effects
#4
JOURNAL ARTICLE
P Ostheim, A Tichý, C Badie, M Davidkova, G Kultova, M Markova Stastna, I Sirak, S Stewart, D Schwanke, M Kasper, S A Ghandhi, S A Amundson, W Bäumler, C Stroszczynski, M Port, M Abend
As the great majority of gene expression (GE) biodosimetry studies have been performed using blood as the preferred source of tissue, searching for simple and less-invasive sampling methods is important when considering biodosimetry approaches. Knowing that whole saliva contains an ultrafiltrate of blood and white blood cells, it is expected that the findings in blood can also be found in saliva. This human in vivo study aims to examine radiation-induced GE changes in saliva for biodosimetry purposes and to predict radiation-induced disease, which is yet poorly characterized...
March 19, 2024: Radiation Research
https://read.qxmd.com/read/38485739/purine-salvage-associated-metabolites-as-biomarkers-for-early-diagnosis-of-esophageal-squamous-cell-carcinoma-a-diagnostic-model-based-study
#5
JOURNAL ARTICLE
Yawen Sun, Wenjuan Liu, Mu Su, Tao Zhang, Xia Li, Wenbin Liu, Yuping Cai, Deli Zhao, Ming Yang, Zhengjiang Zhu, Jialin Wang, Jinming Yu
Esophageal squamous cell carcinoma (ESCC) remains an important health concern in developing countries. Patients with advanced ESCC have a poor prognosis and survival rate, and achieving early diagnosis remains a challenge. Metabolic biomarkers are gradually gaining attention as early diagnostic biomarkers. Hence, this multicenter study comprehensively evaluated metabolism dysregulation in ESCC through an integrated research strategy to identify key metabolite biomarkers of ESCC. First, the metabolic profiles were examined in tissue and serum samples from the discovery cohort (n = 162; ESCC patients, n = 81; healthy volunteers, n = 81), and ESCC tissue-induced metabolite alterations were observed in the serum...
March 14, 2024: Cell Death Discovery
https://read.qxmd.com/read/38484140/network-pharmacology-and-experimental-evaluation-strategies-to-decipher-the-underlying-pharmacological-mechanism-of-traditional-chinese-medicine-cff-1-against-prostate-cancer
#6
JOURNAL ARTICLE
Yong Wei, Mingxia Zhu, Ye Chen, Qianying Ji, Jun Wang, Luming Shen, Xin Yang, Haibin Hu, Xin Zhou, Qingyi Zhu
Prostate cancer (PCa) is a common malignancy in elderly men. We have applied Traditional Chinese Medicine CFF-1 in clinical treatments for PCa for several years. Here, we aimed to identify the underlying mechanism of CFF-1 on PCa using network pharmacology and experimental validation. Active ingredients, potential targets of CFF-1 were acquired from the public databases. Subsequently, protein-protein interaction (PPI) and the herbs-active ingredients-target network was constructed. A prognostic model for PCa was also constructed based on key targets...
March 13, 2024: Aging
https://read.qxmd.com/read/38474154/validation-of-rna-extraction-methods-and-suitable-reference-genes-for-gene-expression-studies-in-developing-fetal-human-inner-ear-tissue
#7
JOURNAL ARTICLE
Claudia Steinacher, Dietmar Rieder, Jasmin E Turner, Nita Solanky, Shin-Ya Nishio, Shin-Ichi Usami, Barbara Hausott, Anneliese Schrott-Fischer, Jozsef Dudas
A comprehensive gene expression investigation requires high-quality RNA extraction, in sufficient amounts for real-time quantitative polymerase chain reaction and next-generation sequencing. In this work, we compared different RNA extraction methods and evaluated different reference genes for gene expression studies in the fetal human inner ear. We compared the RNA extracted from formalin-fixed paraffin-embedded tissue with fresh tissue stored at -80 °C in RNAlater solution and validated the expression stability of 12 reference genes (from gestational week 11 to 19)...
March 2, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38471523/pum1-and-pgk1-are-favorable-housekeeping-genes-over-established-biodosimetry-related-housekeeping-genes-such-as-hprt1-itfg1-dpm1-mrps5-18s-rrna-and-others-after-radiation-exposure
#8
JOURNAL ARTICLE
R Muhtadi, S Stewart, F Bunert, O O Fatanmi, S Y Wise, C Gärtner, S Motzke, C Ruf, P Ostheim, S Schüle, D Schwanke, V K Singh, M Port, M Abend
In gene expression (GE) studies, housekeeping genes (HKGs) are required for normalization purposes. In large-scale inter-laboratory comparison studies, significant differences in dose estimates are reported and divergent HKGs are employed by the teams. Among them, the 18S rRNA HKG is known for its robustness. However, the high abundance of 18S rRNA copy numbers requires dilution, which is time-consuming and a possible source of errors. This study was conducted to identify the most promising HKGs showing the least radiation-induced GE variance after radiation exposure...
March 13, 2024: Radiation Research
https://read.qxmd.com/read/38448583/synthetic-reversed-sequences-reveal-default-genomic-states
#9
JOURNAL ARTICLE
Brendan R Camellato, Ran Brosh, Hannah J Ashe, Matthew T Maurano, Jef D Boeke
Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or 'noise'1-4 . Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity...
March 6, 2024: Nature
https://read.qxmd.com/read/38421481/reference-gene-validation-in-the-embryonic-and-postnatal-brain-in-the-rat-hyperhomocysteinemia-model
#10
JOURNAL ARTICLE
Anna A Kovalenko, Alexander P Schwarz, Anastasiia D Shcherbitskaia, Anastasiia V Mikhel, Dmitrii S Vasilev, Alexander V Arutjunyan
Maternal hyperhomocysteinemia (HCY) induced by genetic defects in methionine cycle enzymes or vitamin imbalance is known to be a pathologic factor that can impair embryonal brain development and cause long-term consequences in the postnatal brain development as well as changes in the expression of neuronal genes. Studies of the gene expression on this model requires the selection of optimal housekeeping genes. This work aimed to analyze the expression stability of housekeeping genes in offspring brain. Pregnant female Wistar rats were treated daily with a 0...
February 29, 2024: Neurotoxicity Research
https://read.qxmd.com/read/38411699/epigenetic-related-transcriptional-reprogramming-elucidated-by-identification-and-validation-of-a-novel-reference-gene-combination-for-rt-qpcr-studies-in-porcine-oocytes-of-contrasting-quality
#11
JOURNAL ARTICLE
Linda Marijke Haug, Robert C Wilson, Anne Hege Alm-Kristiansen
BACKGROUND: Reliable RT-qPCR results are dependent on appropriate normalisation. Oocyte maturation studies can be challenging in this respect, as the stage of development can distinctively affect reference gene transcript abundance. The aim of this study was to validate the use of reference genes in oocyte in vitro maturation RT-qPCR studies, and thereafter, examine the abundance of transcripts supporting histone modification during oocyte and early embryo development in oocytes of contrasting quality...
February 27, 2024: Molecular Biology Reports
https://read.qxmd.com/read/38397141/validation-of-endogenous-control-genes-by-real-time-quantitative-reverse-transcriptase-polymerase-chain-reaction-for-acute-leukemia-gene-expression-studies
#12
JOURNAL ARTICLE
Flávia Melo Cunha de Pinho Pessoa, Vitória Beatriz de Jesus Viana, Marcelo Braga de Oliveira, Beatriz Maria Dias Nogueira, Rodrigo Monteiro Ribeiro, Deivide de Sousa Oliveira, Germison Silva Lopes, Ricardo Parente Garcia Vieira, Manoel Odorico de Moraes Filho, Maria Elisabete Amaral de Moraes, André Salim Khayat, Fabiano Cordeiro Moreira, Caroline Aquino Moreira-Nunes
Reference genes are used as internal reaction controls for gene expression analysis, and for this reason, they are considered reliable and must meet several important criteria. In view of the absence of studies regarding the best reference gene for the analysis of acute leukemia patients, a panel of genes commonly used as endogenous controls was selected from the literature for stability analysis: Glyceraldehyde-3-phosphate dehydrogenase ( GAPDH ), Abelson murine leukemia viral oncogene human homolog 1 ( ABL ), Hypoxanthine phosphoribosyl-transferase 1 ( HPRT1 ), Ribosomal protein lateral stalk subunit P0 ( RPLP0 ), β-actin ( ACTB ) and TATA box binding protein ( TBP )...
January 24, 2024: Genes
https://read.qxmd.com/read/38364877/evaluation-of-reference-genes-for-gene-expression-analysis-by-real-time-quantitative-pcr-qpcr-in-different-tissues-from-mice-infected-by-ascaris-suum
#13
JOURNAL ARTICLE
Jorge Lucas Nascimento Souza, Camila de Almeida Lopes, Thais Leal-Silva, Flaviane Vieira-Santos, Chiara Cássia Oliveira Amorim, Luiza de Lima Silva Padrão, Ana Rafaela Antunes Porto, Ricardo Toshio Fujiwara, Remo Castro Russo, Lilian Lacerda Bueno
Human ascariasis is the most prevalent helminth infection, affecting 445 million people worldwide. To better understand the impact of the immune system on the pathophysiology of individuals infected with Ascaris suum, mice have been used as experimental models. The RT-qPCR technique is a critical auxiliary tool of investigation used to quantify mRNA levels. However, proper normalization using reference genes is essential to ensure reliable outcomes to avoid analytical errors and false results. Despite the importance of reference genes for experimental A...
February 14, 2024: Microbial Pathogenesis
https://read.qxmd.com/read/38302649/comprehensive-evaluation-and-validation-of-optimal-reference-genes-for-normalization-of-qpcr-data-in-different-caprine-tissues
#14
JOURNAL ARTICLE
Sonika Ahlawat, Mahanthi Vasu, Vikas Choudhary, Reena Arora, Rekha Sharma, M A Mir, Manoj Kumar Singh
BACKGROUND: Quantitative real-time PCR (qPCR) is a highly reliable method for validating gene expression data in molecular studies due to its sensitivity, specificity, and efficiency. To ensure accurate qPCR results, it's essential to normalize the expression data using stable reference genes. METHODS: This study aimed to identify suitable reference genes for qPCR studies in goats by evaluating 18 candidate reference genes (ACTB, BACH1, B2M, GAPDH, HMBS, HPRT1, PGK1, PPIA, PPIB, RPLP0, RPL19, RPS9, RPS15, RPS28, SDHA, TBP, UXT, and YWHAZ) in 10 different caprine tissues (heart, intestine, kidney, liver, lung, muscle, rumen, skin, spleen, and testis)...
February 1, 2024: Molecular Biology Reports
https://read.qxmd.com/read/38287074/selection-of-suitable-reference-genes-for-gene-expression-studies-in-hmc3-cell-line-by-quantitative-real-time-rt-pcr
#15
JOURNAL ARTICLE
Martina Fazzina, Matteo Bergonzoni, Francesca Massenzio, Barbara Monti, Flavia Frabetti, Raffaella Casadei
Microglia represent the primary immune defense system within the central nervous system and play a role in the inflammatory processes occurring in numerous disorders, such as Parkinson's disease (PD). PD onset and progression are associated with factors considered possible causes of neuroinflammation, i.e. genetic mutations. In vitro models of microglial cells were established to identify specific molecular targets in PD through the analysis of gene expression data. Recently, the Human Microglial Clone 3 cell line (HMC3) has been characterized and a new human microglia model has emerged...
January 29, 2024: Scientific Reports
https://read.qxmd.com/read/38275668/inflammation-and-starvation-affect-housekeeping-gene-stability-in-adipose-mesenchymal-stromal-cells
#16
JOURNAL ARTICLE
Enrico Ragni, Simona Piccolo, Michela Taiana, Caterina Visconte, Giulio Grieco, Laura de Girolamo
Due to the scientific success of in vitro and in vivo model studies, the interest in using mesenchymal stromal cells (MSCs) for the treatment of orthopaedic conditions is growing. In the context of osteoarthritis (OA), MSCs, and, in particular, those derived from adipose tissues (ASCs), have found broader access to clinical use as active components of minimally manipulated orthobiologics, as well as clinically expanded cell preparations, or to collect their released factors (secretome) for cell-free approaches...
January 19, 2024: Current Issues in Molecular Biology
https://read.qxmd.com/read/38233393/x-chromosome-and-kidney-function-evidence-from-a-multi-trait-genetic-analysis-of-908-697-individuals-reveals-sex-specific-and-sex-differential-findings-in-genes-regulated-by-androgen-response-elements
#17
JOURNAL ARTICLE
Markus Scholz, Katrin Horn, Janne Pott, Matthias Wuttke, Andreas Kühnapfel, M Kamal Nasr, Holger Kirsten, Yong Li, Anselm Hoppmann, Mathias Gorski, Sahar Ghasemi, Man Li, Adrienne Tin, Jin-Fang Chai, Massimiliano Cocca, Judy Wang, Teresa Nutile, Masato Akiyama, Bjørn Olav Åsvold, Nisha Bansal, Mary L Biggs, Thibaud Boutin, Hermann Brenner, Ben Brumpton, Ralph Burkhardt, Jianwen Cai, Archie Campbell, Harry Campbell, John Chalmers, Daniel I Chasman, Miao Ling Chee, Miao Li Chee, Xu Chen, Ching-Yu Cheng, Renata Cifkova, Martha Daviglus, Graciela Delgado, Katalin Dittrich, Todd L Edwards, Karlhans Endlich, J Michael Gaziano, Ayush Giri, Franco Giulianini, Scott D Gordon, Daniel F Gudbjartsson, Stein Hallan, Pavel Hamet, Catharina A Hartman, Caroline Hayward, Iris M Heid, Jacklyn N Hellwege, Bernd Holleczek, Hilma Holm, Nina Hutri-Kähönen, Kristian Hveem, Berend Isermann, Jost B Jonas, Peter K Joshi, Yoichiro Kamatani, Masahiro Kanai, Mika Kastarinen, Chiea Chuen Khor, Wieland Kiess, Marcus E Kleber, Antje Körner, Peter Kovacs, Alena Krajcoviechova, Holly Kramer, Bernhard K Krämer, Mikko Kuokkanen, Mika Kähönen, Leslie A Lange, James P Lash, Terho Lehtimäki, Hengtong Li, Bridget M Lin, Jianjun Liu, Markus Loeffler, Leo-Pekka Lyytikäinen, Patrik K E Magnusson, Nicholas G Martin, Koichi Matsuda, Yuri Milaneschi, Pashupati P Mishra, Nina Mononen, Grant W Montgomery, Dennis O Mook-Kanamori, Josyf C Mychaleckyj, Winfried März, Matthias Nauck, Kjell Nikus, Ilja M Nolte, Raymond Noordam, Yukinori Okada, Isleifur Olafsson, Albertine J Oldehinkel, Brenda W J H Penninx, Markus Perola, Nicola Pirastu, Ozren Polasek, David J Porteous, Tanja Poulain, Bruce M Psaty, Ton J Rabelink, Laura M Raffield, Olli T Raitakari, Humaira Rasheed, Dermot F Reilly, Kenneth M Rice, Anne Richmond, Paul M Ridker, Jerome I Rotter, Igor Rudan, Charumathi Sabanayagam, Veikko Salomaa, Neil Schneiderman, Ben Schöttker, Mario Sims, Harold Snieder, Klaus J Stark, Kari Stefansson, Hannah Stocker, Michael Stumvoll, Patrick Sulem, Gardar Sveinbjornsson, Per O Svensson, E-Shyong Tai, Kent D Taylor, Bamidele O Tayo, Andrej Teren, Yih-Chung Tham, Joachim Thiery, Chris H L Thio, Laurent F Thomas, Johanne Tremblay, Anke Tönjes, Peter J van der Most, Veronique Vitart, Uwe Völker, Ya Xing Wang, Chaolong Wang, Wen Bin Wei, John B Whitfield, Sarah H Wild, James F Wilson, Thomas W Winkler, Tien-Yin Wong, Mark Woodward, Xueling Sim, Audrey Y Chu, Mary F Feitosa, Unnur Thorsteinsdottir, Adriana M Hung, Alexander Teumer, Nora Franceschini, Afshin Parsa, Anna Köttgen, Pascal Schlosser, Cristian Pattaro
X-chromosomal genetic variants are understudied but can yield valuable insights into sexually dimorphic human traits and diseases. We performed a sex-stratified cross-ancestry X-chromosome-wide association meta-analysis of seven kidney-related traits (n = 908,697), identifying 23 loci genome-wide significantly associated with two of the traits: 7 for uric acid and 16 for estimated glomerular filtration rate (eGFR), including four novel eGFR loci containing the functionally plausible prioritized genes ACSL4, CLDN2, TSPAN6 and the female-specific DRP2...
January 18, 2024: Nature Communications
https://read.qxmd.com/read/38165476/selection-of-reference-genes-in-liproxstatin-1-treated-k562-leukemia-cells-via-rt-qpcr-and-rna-sequencing
#18
JOURNAL ARTICLE
Hai-Qun Dong, Xue-Ying Hu, Shi-Jing Liang, Ren-Sheng Wang, Peng Cheng
BACKGROUND: Reverse transcription quantitative polymerase chain reaction (RT-qPCR) can accurately detect relative gene expression levels in biological samples. However, widely used reference genes exhibit unstable expression under certain conditions. METHODS AND RESULTS: Here, we compared the expression stability of eight reference genes (RPLP0, RPS18, RPL13, EEF1A1, β-actin, GAPDH, HPRT1, and TUBB) commonly used in liproxstatin-1 (Lip-1)-treated K562 cells using RNA-sequencing and RT-qPCR...
January 2, 2024: Molecular Biology Reports
https://read.qxmd.com/read/38159260/prognostic-significance-and-immunological-role-of-hprt1-in-human-cancers
#19
JOURNAL ARTICLE
Yiwen Lu, Ruixue Chen, Han Zhang, Xu Sun, Xiangjun Li, Mengyuan Yang, Xudong Zhang
Hypoxanthine phosphoribosyl transferase 1 (HPRT1), once considered a housekeeping gene, has been identified as playing an important role in several tumors. Its role in pan-cancer, however, has not been systematically studied. This study evaluates the relationship between HPRT1 and clinical parameters, survival prognosis, and tumor immunity based on multi omics data from the Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Drug sensitivity analysis screened 16 effective drugs against HPRT1, exploring the interactions with chemicals and genes...
December 14, 2023: Biomol Biomed
https://read.qxmd.com/read/38154384/generation-of-an-ipsc-line-sdqlchi030-a-derived-from-pbmcs-of-a-patient-with-lesch-nyhan-syndrome-caused-by-hprt1-mutation
#20
JOURNAL ARTICLE
Yue Li, Huawei Zhang, Jingyun Guan, Bin Wang, Haiyan Zhang, Yi Liu, Zhongtao Gai
Lesch-Nyhan syndrome (LNS, MIM300322) is a rare inherited disorder caused by mutations in HPRT1 gene. Here we describe the generation of induced pluripotent stem cells (iPSCs) from an infected child carrying the HPRT1 mutation c.508C > T(p.R170X) by reprogramming peripheral blood mononuclear cells (PBMCs) with episomal vectors. The obtained hiPSCs exhibited normal karyotype, expressed pluripotency markers, and possessed trilineage differentiation capacity.
February 2024: Stem Cell Research
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