Tag: PubMed

Three families of Asgard archaeal viruses identified in metagenome-assembled genomes

Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021). CAS  PubMed  Google Scholar  Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018). PubMed  PubMed…

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COVID-19 mRNA vaccines linked to higher risk of side effects vs. traditional vaccines

Although the risk of adverse events (AEs) was increased for mRNA-based COVID-19 vaccines compared to traditional vaccines, the efficacy and benefits of mRNA vaccination outweighed the associated risks, according to a study in International Immunopharmacology. Researchers conducted a meta-analysis to evaluate the safety of several types of COVID-19 vaccines. They…

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Stabilizing and Anti-Repressor Elements Effectively Increases Transgene Expression in Transfected CHO Cells

doi: 10.3389/fbioe.2022.840600. eCollection 2022. Affiliations Expand Affiliations 1 School of Basic Medicine, Xinxiang Medical University, Xinxiang, China. 2 International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China. Free PMC article Item in Clipboard Qin Li et al. Front Bioeng Biotechnol. 2022. Free PMC…

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A highly sensitive fluorescent aptasensor for detection of prostate specific antigen based on the integration of a DNA structure and CRISPR-Cas12a

. 2022 Aug 1;1219:340031. doi: 10.1016/j.aca.2022.340031. Epub 2022 Jun 3. Affiliations Expand Affiliations 1 Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran. 2 Pharmaceutical Research Center, Pharmaceutical Technology Institute,…

Continue Reading A highly sensitive fluorescent aptasensor for detection of prostate specific antigen based on the integration of a DNA structure and CRISPR-Cas12a

Tramadol Therapy and CYP2D6 Genotype – Medical Genetics Summaries

Introduction Tramadol (brand names ConZip, Ultram, UltramER, Odolo) is an analgesic used to treat moderate to severe pain. It is used for a variety of pain conditions, including post-operative pain, cancer pain, and musculoskeletal pain. Tramadol is a centrally acting opioid analgesic with mu-opioid binding activity as well as weak…

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Genome-wide association study of musical beat synchronization demonstrates high polygenicity

Savage, P. E., Brown, S., Sakai, E. & Currie, T. E. Statistical universals reveal the structures and functions of human music. Proc. Natl Acad. Sci. USA 112, 8987–8992 (2015). CAS  PubMed  PubMed Central  Article  Google Scholar  Ravignani, A., Delgado, T. & Kirby, S. Musical evolution in the lab exhibits rhythmic…

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CRISPR-Cas technology a new era in genomic engineering

Review doi: 10.1016/j.btre.2022.e00731. eCollection 2022 Jun. Affiliations Expand Affiliation 1 Department of Agriculture and Natural Resources, College of Agriculture, Science, and Technology, Delaware State University, Dover, DE 19901, United States of America. Free PMC article Item in Clipboard Review Ali Parsaeimehr et al. Biotechnol Rep (Amst). 2022. Free PMC article Show…

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Tumorigenicity risk of iPSCs in vivo: nip it in the bud

Review . 2022 Feb 3;5(1):pbac004. doi: 10.1093/pcmedi/pbac004. eCollection 2022 Mar. Affiliations Expand Affiliations 1 Department of Cell Biology, Naval Medical University, Shanghai 200433, China. 2 Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University,…

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TwinEQTL: Ultra Fast and Powerful Association Analysis for eQTL and GWAS in Twin Studies

doi: 10.1093/genetics/iyac088. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA. 2 Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599, USA. 3 Department of Psychiatry, University of Utah, Salt Lake City, UT 84108, USA. 4 Gilead…

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Identification of the genetic elements involved in biofilm formation by Salmonella enterica serovar Tennessee using mini-Tn10 mutagenesis and DNA sequencing

doi: 10.1016/j.fm.2022.104043. Epub 2022 Apr 23. Affiliations Expand Affiliations 1 Department of Food Science and Technology, The University of Georgia, 1109 Experiment Street, Griffin, GA, 30223-1797, USA. 2 Department of Food Science and Technology, The University of Georgia, 1109 Experiment Street, Griffin, GA, 30223-1797, USA. Electronic address: jchen@uga.edu. Item in…

Continue Reading Identification of the genetic elements involved in biofilm formation by Salmonella enterica serovar Tennessee using mini-Tn10 mutagenesis and DNA sequencing

A desirable transgenic strategy using GGTA1 endogenous promoter-mediated knock-in for xenotransplantation model

Lai, L. et al. Production of alpha-1,3-galactosyltransferase knockout pigs by nuclear transfer cloning. Science 295, 1089–1092. doi.org/10.1126/science.1068228 (2002). ADS  CAS  Article  PubMed  Google Scholar  Kuwaki, K. et al. Heart transplantation in baboons using alpha1,3-galactosyltransferase gene-knockout pigs as donors: initial experience. Nat. Med. 11, 29–31. doi.org/10.1038/nm1171 (2005). CAS  Article  PubMed  Google…

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SMARCE1 deficiency generates a targetable mSWI/SNF dependency in clear cell meningioma

Clapier, C. R., Iwasa, J., Cairns, B. R. & Peterson, C. L. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat. Rev. Mol. Cell Biol. 18, 407–422 (2017). CAS  PubMed  PubMed Central  Article  Google Scholar  Mashtalir, N. et al. Modular organization and assembly of SWI/SNF family chromatin remodeling complexes….

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VCV000038126.28 Observations – ClinVar – NCBI

1 SCV000301220.2 Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Pathogenic reviewed by expert panel curation Breast-ovarian cancer, familial, susceptibility to, 2 (unknown ) germline Variant allele predicted to encode a truncated non-functional protein. 1 SCV000785901.2 Counsyl Pathogenic criteria provided,single submitter clinical testing Breast-ovarian cancer, familial, susceptibility to,…

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Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer

Torre, L. A., Siegel, R. L., Ward, E. M. & Jemal, A. Global cancer incidence and mortality rates and trends—an update. Cancer Epidemiol. Prev. Biomark. 25, 16–27 (2016). Article  Google Scholar  Gerasimova, E. et al. Wavelet-based multifractal analysis of dynamic infrared thermograms to assist in early breast cancer diagnosis. Front….

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Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)

Arlinghaus, R. et al. Governing the recreational dimension of global fisheries. Proc. Nat. Acad. Sci. USA 116, 5209–5213 (2019). CAS  PubMed  PubMed Central  Article  Google Scholar  Cowx, I. G. & Gerdeaux, D. The effects of fisheries management practises on freshwater ecosystems. Fish. Manag. Ecol. 11, 145–151 (2004). Article  Google Scholar …

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Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central  Google Scholar  Buniello, A. et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47,…

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Metagenomics – RPKM calculation

Normalization for comparing gene coverage values. RPKM corrects differences in both: sample sequencing depth and gene length. RPKM – Reads per kilo base per million mapped reads Formula RPKM = numReads / ( geneLength/1000 * totalNumReads/1,000,000 ) numReads – number of reads mapped to a gene sequence geneLength – length…

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A new functional ecological model reveals the nature of early plant management in southwest Asia

Willcox, G., Fornite, S. & Herveux, L. Early Holocene cultivation before domestication in northern Syria. Veg. Hist. Archaeobot. 17, 313–325 (2008). Article  Google Scholar  Fuller, D. Q., Willcox, G. & Allaby, R. G. Cultivation and domestication had multiple origins: arguments against the core area hypothesis for the origins of agriculture…

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Breast Reconstruction with Inferior Flap and Fat Transfer as Curative Treatment for BIA-ALCL

Araco A, Gravante G, Araco F, Delogu D, Cervelli V, Walgenbach K. A retrospective analysis of 3,000 primary aesthetic breast augmentations: postoperative complications and associated factors. Aesthet Plast Surg. 2007;31(5):532–9. doi.org/10.1007/s00266-007-0162-8. CAS  CrossRef  Google Scholar  Nahabedian MY, Patel K. Management of common and uncommon problems after primary breast augmentation. Clin…

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Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo

. 2022 May;24(5):783-792. doi: 10.1038/s41556-022-00900-4. Epub 2022 Apr 28. Affiliations Expand Affiliations 1 Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China. 2 Shanghai Institute of Stem…

Continue Reading Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo

Osteosarcoma Combination of Electroporation of Metabolic Modulators with Low dose chemotherapy

Osteosarcoma – Combination of Electroporation of Metabolic Modulators with Low dose chemotherapy Dr Kesh Gill Bone cancer particularly osteosarcoma can be an aggressive disease. Despite tremendous advances in diagnostic modalities, surgical procedures, and chemotherapy options, osteosarcoma confers a generally poor prognosis. The absence of an effective immune response to most…

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BAM file and no RNAME or POS information? : bioinformatics

Newbie here. Please, play nice. I got possession of a set of 4 .bam files that stores the exome of an individual, around 400 MB each. I used samtools to generate a 2.4 GB .sam file out of one of the .bam files, and I found it contains lines with…

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Tempo and drivers of plant diversification in the European mountain system

Hughes, C. E. & Atchinson, G. W. The ubiquity of alpine plant radiations: from the Andes to the Hengduan Mountains. N. Phytol. 207, 275–282 (2015). Article  Google Scholar  Rahbek, C. et al. Humboldt’s enigma: what causes global patterns of mountain biodiversity? Science 365, 1108–1113 (2019). ADS  CAS  PubMed  Article  Google…

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Oncolytic Adenovirus with SPAG9 shRNA Driven by DD3 Promoter Improved the Efficacy of Docetaxil for Prostate Cancer

. 2022 Apr 30;2022:7918067. doi: 10.1155/2022/7918067. eCollection 2022. Affiliations Expand Affiliations 1 Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu Province, China. 2 Department of Urology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China. Free PMC article Item in Clipboard Meng…

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Frontiers | Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data

Introduction Incipient species are critical for evolutionary biologists to study speciation, but they also challenge taxonomy due to gene flow or ancestral polymorphism. The former and contrasting population size lead to larger intraspecific than interspecific variations, a phenomenon called the species-definition anomaly zone (Jiao and Yang, 2021). The latter results…

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CORP: Gene delivery into murine skeletal muscle using in vivo electroporation

Review doi: 10.1152/japplphysiol.00088.2022. Online ahead of print. Affiliations Expand Affiliations 1 Division of Endocrinology and Metabolism, Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, United States. 2 Centre for Muscle Research (CMR), Department of Anatomy and Physiology, The University of Melbourne, Victoria, Australia. 3…

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Detection of candidate gene LsACOS5 and development of InDel marker for male sterility by ddRAD-seq and resequencing analysis in lettuce

Ryder, E. J. Lettuce, Endive and Chicory (CABI Publishing, 1999). Google Scholar  Seki, K. et al. A CIN-like TCP transcription factor (LsTCP4) having retrotransposon insertion associates with a shift from Salinas type to Empire type in crisphead lettuce (Lactuca sativa L.). Hortic. Res. 7, 1–14 (2020). Article  Google Scholar  Odland,…

Continue Reading Detection of candidate gene LsACOS5 and development of InDel marker for male sterility by ddRAD-seq and resequencing analysis in lettuce

Recent developments in miRNA based recombinant protein expression in CHO

Aguiar TQ, Santos SB, Martins IM, Domingues L, Oliveira C (2019) Production and bioengineering of recombinant pharmaceuticals. Proteins: sustainable source, processing and applications. Elsevier, Amsterdam, pp 259–293 Chapter  Google Scholar  Amadi IM, Agrawal V, Christianson T, Bardliving C, Shamlou P, LeBowitz JH (2020) Inhibition of endogenous miR-23a/miR-377 in CHO cells…

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Landscape of helper and regulatory antitumour CD4+ T cells in melanoma

Sallusto, F. & Lanzavecchia, A. Heterogeneity of CD4+ memory T cells: functional modules for tailored immunity. Eur. J. Immunol. 39, 2076–2082 (2009). CAS  PubMed  Article  Google Scholar  Swain, S. L., McKinstry, K. K. & Strutt, T. M. Expanding roles for CD4+ T cells in immunity to viruses. Nat. Rev. Immunol….

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Multiplexed genome regulation in vivo with hyper-efficient Cas12a

. 2022 Apr;24(4):590-600. doi: 10.1038/s41556-022-00870-7. Epub 2022 Apr 12. Lucie Y Guo #  1   2 , Jing Bian #  3 , Alexander E Davis  4 , Pingting Liu  4 , Hannah R Kempton  3 , Xiaowei Zhang  3 , Augustine Chemparathy  3 , Baokun Gu  3 , Xueqiu Lin  3 , Draven A Rane  3 , Xiaoshu Xu  3 , Ryan M…

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Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites

Van Treuren, W. & Dodd, D. Microbial contribution to the human metabolome: implications for health and disease. Annu. Rev. Pathol. 15, 345–369 (2020). PubMed  Article  CAS  Google Scholar  Russell, W. R. et al. Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein. Mol. Nutr. Food…

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Optimized Protocol for Plasma-Derived Extracellular Vesicles Loading with Synthetic miRNA Mimic Using Electroporation

doi: 10.1007/978-1-0716-2341-1_16. Affiliations Expand Affiliations 1 Department of Medical Sciences, University of Turin, Turin, Italy. margheritaalbacarlotta.pomatto@unito.it. 2 Department of Medical Sciences, University of Turin, Turin, Italy. Item in Clipboard Margherita A C Pomatto et al. Methods Mol Biol. 2022. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1007/978-1-0716-2341-1_16. Affiliations 1…

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Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data | Clinical Epigenetics

Experimental design and processing steps For the EpiSCOPE study [20], DHA supplementation and gender were balanced as much as possible across the 12 450K BeadChips on each glass slide, with these factors also randomly distributed over the 6 rows and 2 columns of 31 slides (Additional file 1: Fig. S1). Blood…

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Mining Curated Databases for Literature in VSClinical

Curated databases are a real-time saver when compiling published evidence to support your variant evaluations and classifications. Leveraging the curated databases at your fingertips in our VSClinical variant interpretation hub is even more efficient. Not only does VSClinical provides users with automated variant classification for germline variants according to the…

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MouseMine: Report page

Your browser does not have JavaScript enabled. Some parts of this website may require JavaScript to function correctly First Author  Kuchta K Year  2016 Journal  Nucleic Acids Res Volume  44 Issue  8 Pages  3534-48 PubMed ID  27060136 Mgi Id    Expression Publication –> Expression annotations Returns expression annotations for the…

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Circulating cell-free mtDNA release is associated with the activation of cGAS-STING pathway and inflammation in mitochondrial diseases

Craven L, Alston C, Taylor R, Turnbull D (2017) Recent advances in mitochondrial disease. Annu Rev Genomics Hum Genet 18:257–275. doi.org/10.1146/annurev-genom-091416-035426 CAS  Article  PubMed  Google Scholar  El-Hattab AW, Adesina AM, Jones J, Scaglia F (2015) MELAS syndrome: clinical manifestations, pathogenesis, and treatment options. Mol Genet Metab 116(1–2):4–12. doi.org/10.1016/j.ymgme.2015.06.004 CAS  Article …

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Electroporation and Electrochemotherapy in Gynecological and Breast Cancer Treatment

Review . 2022 Apr 12;27(8):2476. doi: 10.3390/molecules27082476. Affiliations Expand Affiliation 1 Department of Molecular and Cellular Biology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland. Free PMC article Item in Clipboard Review Zofia Łapińska et al. Molecules. 2022. Free PMC article Show details Display options Display options Format…

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Full Text Journal Article: Exploiting the orthogonal CRISPR-Cas12a/Cas13a trans-cleavage for dual-gene virus detection using a handheld device.

PDF.MPro – Full Text Journal Article: Exploiting the orthogonal CRISPR-Cas12a/Cas13a trans-cleavage for dual-gene virus detection using a handheld device. Home / Search / Abstract 34653714 (Page 1) Advertisement Find full text journal articles PMID: 34653714 (view PubMed database entry)DOI: 10.1016/j.bios.2021.113701 (read at publisher’s website ) Tian Tian, Zhiqiang Qiu, Yongzhong…

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Full Text Journal Article: Androgen receptor transcriptional activity and chromatin modifications on the ABCB1/MDR gene are critical for taxol resistance in ovarian cancer cells.

PDF.MPro – Full Text Journal Article: Androgen receptor transcriptional activity and chromatin modifications on the ABCB1/MDR gene are critical for taxol resistance in ovarian cancer cells. Home / Search / Abstract 30317630 (Page 1) Advertisement Find full text journal articles PMID: 30317630 (view PubMed database entry)DOI: 10.1002/jcp.27535 (read at publisher’s…

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Full Text Journal Articles by Author Qi Pei Li (Page 1)

PDF.MPro – Full Text Journal Articles by Author Qi Pei Li (Page 1) Home / Search / Author Qi Pei Li (Page 1) Advertisement Find full text journal articles Disclaimer ‘ManuscriptPro PDF Search’ digitally communicates with online databases that contain selected information from scientific journals. The service’s predominant goal is…

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Full Text Journal Articles by Author And Robin Andersson (Page 1)

PDF.MPro – Full Text Journal Articles by Author And Robin Andersson (Page 1) Home / Search / Author And Robin Andersson (Page 1) Advertisement Find full text journal articles The GBAF chromatin remodeling complex binds H3K27ac and mediates enhancer transcription Kirill Jefimov, Nicolas Alcaraz, Susan Kloet, Signe Värv, Siri Aastedatter…

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CircRNA and miRNA expression profiles during remote ischemic postconditioning attenuate brain ischemia/reperfusion injury

. 2022 Apr 19;S0361-9230(22)00098-3. doi: 10.1016/j.brainresbull.2022.04.006. Online ahead of print. Chun-Yan Li  1 , Wei Ma  2 , Kuang-Pin Liu  2 , Jin-Wei Yang  3 , Xian-Bin Wang  2 , Zhen Wu  3 , Tong Zhang  3 , Jia-Wei Wang  3 , Wei Liu  2 , Jie Liu  2 , Yu Liang  2 , Xing-Kui Zhang  2 , Jun-Jun Li  2 , Jian-Hui…

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Primary Extra Nodal Diffuse Large B-Cell Lymphoma of the Maxillary Sinus with Symptoms of Acute Pulpitis

Case Reports . 2022 Apr 7;2022:8875832. doi: 10.1155/2022/8875832. eCollection 2022. Affiliations Expand Affiliation 1 Department of Stomatology, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China. Item in Clipboard Case Reports Jian-Tong Cui et al. Case Rep Dent. 2022. Show details Display options Display options Format AbstractPubMedPMID . 2022…

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A conditional gene-based association framework integrating isoform-level eQTL data reveals new susceptibility genes for schizophrenia

doi: 10.7554/eLife.70779. Affiliations Expand Affiliations 1 Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China. 2 Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China. 3 Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China. 4 Research…

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Transcriptional and H3K27ac related genome profiles in oral squamous cell carcinoma cells treated with metformin

. 2022 Mar 21;13(6):1859-1870. doi: 10.7150/jca.63234. eCollection 2022. Affiliations Expand Affiliations 1 State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, China. 2 Department of Oral and Maxillofacial Surgery, Binzhou…

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Generation of iPSCs from mouse fibroblasts with a single gene, Oct4, and small molecules

Li, Zhang, Yin, Yang, Du, Hou, Ge, Liu, Zhang, Zhang, Wu, Li, Liu, Wu, Song, Zhao, Shi, Deng (2011) Generation of iPSCs from mouse fibroblasts with a single gene, Oct4, and small molecules Cell Res 21(1) 196-204 Full text Abstract The introduction of four transcription factors Oct4,…

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Does Norepinephrine Metabolite DOPEGAL Turn Tau Toxic?

08 Apr 2022 What makes tau toxic? In the March 24 Nature Structural & Molecular Biology, researchers led by Keqiang Ye at Shenzhen Institute of Advanced Technology, China, suggest a new culprit, a norepinephrine metabolite known as DOPEGAL, which is produced only in the locus coeruleus (LC). The authors found…

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Activation of STING by targeting a pocket in the transmembrane domain

Zhang, X., Bai, XC & Chen, ZJ Structures and mechanisms of the cGAS-STING innate immunity pathway. Immunity 5343–53 (2020). CAS PubMed Google Scholar Article Ishikawa, H. & Barber, GN STING is an endoplasmic reticulum adapter that facilitates innate immune signaling. Nature 455674–678 (2008). ADS CAS PubMed PubMed Central Article Google…

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Gene variants of the SLC2A5 gene encoding GLUT5, the major fructose transporter, do not contribute to clinical presentation of acquired fructose malabsorption | BMC Gastroenterology

Fassio F, Facioni MS, Guagnini F. Lactose maldigestion, malabsorption, and intolerance: a comprehensive review with a focus on current management and future perspectives. Nutrients. 2018. doi.org/10.3390/nu10111599. Article  PubMed  PubMed Central  Google Scholar  Gibson PR, Newnham E, Barrett JS, et al. Review article: fructose malabsorption and the bigger picture. Aliment Pharmacol…

Continue Reading Gene variants of the SLC2A5 gene encoding GLUT5, the major fructose transporter, do not contribute to clinical presentation of acquired fructose malabsorption | BMC Gastroenterology

Parkinson’s disease motor symptoms rescue by CRISPRa-reprogramming astrocytes into GABAergic neurons

doi: 10.15252/emmm.202114797. Online ahead of print. Jessica Giehrl-Schwab #  1   2 , Florian Giesert #  1   2 , Benedict Rauser  1   2 , Chu Lan Lao  3   4 , Sina Hembach  1   2 , Sandrine Lefort  5 , Ignacio L Ibarra  6 , Christina Koupourtidou  3   7 , Malte Daniel Luecken  6 , Dong-Jiunn Jeffery…

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SAWRPI: A Stacking Ensemble Framework With Adaptive Weight for Predicting ncRNA-Protein Interactions Using Sequence Information

doi: 10.3389/fgene.2022.839540. eCollection 2022. Affiliations Expand Affiliations 1 School of Information Engineering, Xijing University, Xi’an, China. 2 School of Computer Science, Northwestern Polytechnical University, Xi’an, China. Item in Clipboard Zhong-Hao Ren et al. Front Genet. 2022. Show details Display options Display options Format AbstractPubMedPMID doi: 10.3389/fgene.2022.839540. eCollection 2022. Affiliations 1 School…

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A multi-omics approach to elucidate the mechanisms of action of a dietary muramidase administered to broiler chickens

Gadde, U., Kim, W. H., Oh, S. T. & Lillehoj, H. S. Alternatives to antibiotics for maximizing growth performance and feed efficiency in poultry: a review. Animal Health Res. Rev. 18, 26–45 (2017). CAS  Google Scholar  Smits, C. H. M., Li, D., Patience, J. F. & den Hartog, L. A….

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Skin cutaneous melanoma properties of immune-related lncRNAs identifying potential prognostic biomarkers

. 2022 Mar 31;14(undefined). doi: 10.18632/aging.203982. Online ahead of print. Affiliations Expand Affiliations 1 Department of Breast Surgery, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, P.R. China. 2 Department of Plastic Surgery, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, P.R. China. 3…

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Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class

Pereira, S. L. Mitochondrial genome organization and vertebrate phylogenetics. Genet. Mol. Biol. 23, 745–752 (2000). CAS  Google Scholar  Boore, J. L. Animal mitochondrial genomes. Nucl. Acids Res. 27, 1767–1780 (1999). CAS  PubMed  PubMed Central  Google Scholar  Formenti, G. et al. Complete vertebrate mitogenomes reveal widespread gene duplications and repeats. BioRxiv…

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Human distal lung maps and lineage hierarchies reveal a bipotent progenitor

Verleden, S. E. et al. Small airways pathology in idiopathic pulmonary fibrosis: a retrospective cohort study. Lancet Respir. Med. 8, 573–584 (2020). CAS  PubMed  PubMed Central  Google Scholar  Hogg, J. C., Macklem, P. T. & Thurlbeck, W. M. The resistance of small airways in normal and diseased human lungs. Aspen…

Continue Reading Human distal lung maps and lineage hierarchies reveal a bipotent progenitor

Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing

Fricke, R., Eschmeyer, W. N. & van der Laan, R. (eds). Eschmeyer’s Catalog of Fishes: Genera, Species, Rererences. researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp. Electronic version, Accessed 15 October 2021. Nelson, J. S. Fishes of the World 4th edn, 372 (Wiley, 2006). Google Scholar  Chen, X. H., Lin, K. B. & Wang, X. W. Outbreaks…

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Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates | BMC Biology

Stölting KN, Wilson AB. Male pregnancy in seahorses and pipefish: beyond the mammalian model. Bioessays. 2007;29:884–96. PubMed  Google Scholar  Whittington CM, Friesen CR. The evolution and physiology of male pregnancy in syngnathid fishes. Biol Rev Camb Philos Soc. 2020;95:1252–72. PubMed  Google Scholar  Rosenqvist G, Berglund A. Sexual signals and mating…

Continue Reading Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates | BMC Biology

Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis

Rawla, P., Sunkara, T., Muralidharan, P. & Raj, J. P. Update in global trends and aetiology of hepatocellular carcinoma. Contemp. Oncol. (Poznan, Poland) 22, 141–150 (2018). CAS  Google Scholar  Kong, D. et al. Current statuses of molecular targeted and immune checkpoint therapies in hepatocellular carcinoma. Am. J. Cancer Res. 10,…

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AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice

Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019). CAS  PubMed  PubMed Central  Google Scholar  Li, C. & Samulski, R. J. Engineering adeno-associated virus vectors for gene therapy. Nat. Rev. Genet. 21, 255–272…

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South-to-north migration preceded the advent of intensive farming in the Maya region

Moreno-Mayar, J. V. et al. Early human dispersals within the Americas. Science 362, eaav2621 (2018). ADS  PubMed  Google Scholar  Posth, C. et al. Reconstructing the deep population history of Central and South America. Cell 175, 1185–1197.e22 (2018). CAS  PubMed  PubMed Central  Google Scholar  Raghavan, M. et al. Genomic evidence for…

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Towards the Genetic Architecture of Complex Gene Expression Traits: Challenges and Prospects for eQTL Mapping in Humans

Review doi: 10.3390/genes13020235. Affiliations Expand Affiliation 1 Department of Bioinformatics and Life Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul 06978, Korea. Free PMC article Item in Clipboard Review Chaeyoung Lee. Genes (Basel). 2022. Free PMC article Show details Display options Display options Format AbstractPubMedPMID doi: 10.3390/genes13020235. Affiliation 1 Department of…

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Mitogenomics provides new insights into the phylogenetic relationships and evolutionary history of deep-sea sea stars (Asteroidea)

Mah, C. L. & Blake, D. B. Global diversity and phylogeny of the asteroidea (Echinodermata). PLoS ONE 7, e35644. doi.org/10.1371/journal.pone.0035644 (2012). ADS  CAS  Article  PubMed  PubMed Central  Google Scholar  WoRMS. Asteroidea. Accessed at: www.marinespecies.org/aphia.php?p=taxdetails&id=123080. on 2021-08-02. Blake, D. B. Adaptive zones of the class Asteroidea (Echinodermata). Bull. Mar. Sci. 46,…

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Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages

Díaz, S. et al. Summary for Policymakers of the Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES, 2019). Fisher, R. A. The correlation between relatives on the supposition of Mendelian inheritance. Earth Environ. Sci. Trans. R. Soc. Edinb. 52,…

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A genome-scale screen for synthetic drivers of T cell proliferation

Abramson, J. S. et al. Transcend NHL 001: immunotherapy with the CD19-directed CAR T-cell product JCAR017 results in high complete response rates in relapsed or refractory B-cell non-Hodgkin lymphoma. Blood 128, 4192–4192 (2016). Google Scholar  Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators…

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A single-cell atlas of human and mouse white adipose tissue

Rosen, E. D. & Spiegelman, B. M. What we talk about when we talk about fat. Cell 156, 20–44 (2014). CAS  PubMed  PubMed Central  Google Scholar  Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006)….

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Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species

Tan, M. H. et al. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci. Rep. 9, 1–16 (2019). ADS  Google Scholar  Zhang, Y. et al. Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida). Mol. Phylogenet. Evol. 125, 220–231 (2018). CAS  PubMed  Google…

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Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases

Cooper, G. S., Bynum, M. L. K. & Somers, E. C. Recent insights in the epidemiology of autoimmune diseases: improved prevalence estimates and understanding of clustering of diseases. J. Autoimmun. 33, 197–207 (2009). PubMed  PubMed Central  Google Scholar  El-Gabalawy, H., Guenther, L. C. & Bernstein, C. N. Epidemiology of immune-mediated…

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Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape

Karesh, W. B. et al. Ecology of zoonoses: natural and unnatural histories. Lancet 380, 1936–1945 (2012). PubMed  PubMed Central  Google Scholar  Wolfe, N. D., Dunavan, C. P. & Diamond, J. Origins of major human infectious diseases. Nature 447, 279–283 (2007). CAS  PubMed  PubMed Central  Google Scholar  Allen, T. et al….

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Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

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Type I Interferon Response Is Mediated by NLRX1-cGAS-STING Signaling in Brain Injury

doi: 10.3389/fnmol.2022.852243. eCollection 2022. Lauren E Fritsch  1 , Jing Ju  2 , Erwin Kristobal Gudenschwager Basso  3 , Eman Soliman  3 , Swagatika Paul  4 , Jiang Chen  2 , Alexandra M Kaloss  3 , Elizabeth A Kowalski  3 , Taylor C Tuhy  5 , Rachana Deven Somaiya  1 , Xia Wang  3 , Irving Coy Allen  3 , Michelle H…

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CRISPR/Cas12a-Enhanced Loop-Mediated Isothermal Amplification for the Visual Detection of Shigella flexneri

doi: 10.3389/fbioe.2022.845688. eCollection 2022. Affiliations Expand Affiliations 1 Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China. 2 Clinical Laboratory Department, Yan’an Hospital Affiliated to Kunming Medical University, Kunming, China. 3 Department of Emergency, The Traditional…

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Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

. 2022 Mar 3;220(3):iyac017. doi: 10.1093/genetics/iyac017. Affiliations Expand Affiliations 1 Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA. 2 Presidential Initiative in Data Science, University of Oregon, Eugene, OR 97403, USA. Item in Clipboard Hope M Healey et al. Genetics. 2022. Show details Display options Display options…

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Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis

Hallam, S. J., Goncharov, A., McEwen, J., Baran, R. & Jin, Y. Syd-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains specifies axon identity in C. elegans. Nat. Neurosci. 5, 1137–1146 (2002). CAS  PubMed  Google Scholar  Xu, Y. & Quinn, C. C. SYD-1 promotes multiple developmental steps leading to…

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Prediction of histone post-translational modification patterns based on nascent transcription data

Allfrey, V. G., Faulkner, R. & Mirsky, A. E. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl Acad. Sci. USA 51, 786–794 (1964). CAS  PubMed  PubMed Central  Google Scholar  Ho, J. W. K. et al. Comparative analysis of metazoan chromatin organization….

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Expression profiling of N 6-methyladenosine modified circRNAs in acute myeloid leukemia

Biochem Biophys Res Commun . 2022 Feb 23;601:137-145. doi: 10.1016/j.bbrc.2022.02.087. Online ahead of print. Affiliations Expand Affiliations 1 Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001,…

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Text string using Biopython – Stack Overflow

I’m using Biopython in my code and i need to extract the abstract out of articles. For searching the article I’m using the function: def search(query): Entrez.email=”your.email@example.com” handle = Entrez.esearch(db=’pubmed’, sort=”relevance”, retmax=’20’, retmode=”xml”, term=query) results = Entrez.read(handle) return results I’m looking for the simpliest way to get the text as…

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Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics | Environmental Microbiome

Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, Cameron TJ. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13:3126–30. PubMed  PubMed Central  Google Scholar  Goh KM, Shahar S, Chan K-G, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current…

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Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM

Wu, W. et al. NDM metallo-β-lactamases and their bacterial producers in health care settings. Clin. Microbiol. Rev. 32, e00115–18 (2019). Yong, D. et al. Characterization of a new metallo-β-lactamase gene, bla NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14…

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Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution

de Visser, J. A. G. M. & Krug, J. Empirical fitness landscapes and the predictability of evolution. Nat. Rev. Genet. 15, 480–490 (2014). PubMed  PubMed Central  Google Scholar  Lässig, M., Mustonen, V. & Walczak, A. M. Predicting evolution. Nat. Ecol. Evol. 1, 77 (2017). PubMed  PubMed Central  Google Scholar  Mas,…

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METASnake: a Snakemake workflow to facilitate…

Introduction As sequencing technology has become cheaper and more readily accessible, the need for the increased computational capacity to process these data has become apparent. In particular, high-throughput sequencing has been particularly useful when applied to the field of metagenomics. Substantial effort has been devoted to developing software and computational…

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HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps

doi: 10.1186/s13059-022-02626-w. Affiliations Expand Affiliations 1 Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA. 2 Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA. fsun@usc.edu. Item in Clipboard Yuxuan Du et al. Genome Biol. 2022. Show details Display options Display options Format…

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Genomic variation from an extinct species is retained in the extant radiation following speciation reversal

Vamosi, J. C., Magallon, S., Mayrose, I., Otto, S. P. & Sauquet, H. Macroevolutionary patterns of flowering plant speciation and extinction. Annu. Rev. Plant Biol. 69, 685–706 (2018). CAS  PubMed  Google Scholar  Rhymer, J. M. & Simberloff, D. Extinction by hybridization and introgression. Annu. Rev. Ecol. Syst. 27, 83–109 (1996)….

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Frontiers | Hair Graying Regulators Beyond Hair Follicle

Introduction Hair graying is one of the representative signs of aging. It has been considered to be triggered by a decreased number of follicular melanocyte stem cells (MeSCs; Nishimura et al., 2005; Iida et al., 2020) or dysfunction of MeSCs such as decreased oxidation resistance capacity with aging (Shi et…

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rs532111960 RefSNP Report – dbSNP

Help Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When…

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Notch activation suppresses endothelial cell migration and sprouting via miR-223-3p targeting Fbxw7

Alabi RO, Farber G, Blobel CP (2018) Intriguing roles for endothelial ADAM10/Notch signaling in the development of organ-specific vascular beds. Physiol Rev 98:2025–2061 CAS  Article  Google Scholar  Autiero M, De Smet F, Claes F, Carmeliet P (2005) Role of neural guidance signals in blood vessel navigation. Cardiovasc Res 65:629–638 CAS …

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Highly Efficient Genome Editing in Plant Protoplasts by Ribonucleoprotein Delivery of CRISPR-Cas12a Nucleases

Review doi: 10.3389/fgeed.2022.780238. eCollection 2022. Affiliations Expand Affiliations 1 Department of Plant Science and Landscape Architecture, University of Maryland, College Park, College Park, MD, United States. 2 College of Agriculture, Nanjing Agricultural University, Nanjing, China. 3 Integrated DNA Technologies, Coralville, IA, United States. 4 U.S. Horticultural Research Laboratory, USDA-Agricultural Research…

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CRISPR-Cas9 Gene Therapy for Duchenne Muscular Dystrophy

Ishino Y, Shinagawa H, Makino K, et al. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol. 1987;169:5429–33. CAS  PubMed  PubMed Central  Google Scholar  Jansen R, van Embden JDA, Gaastra W, et al. Identification of genes…

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RFLP mapping and race specificity of bacterial blight resistance genes (QTLs) in rice

RFLP mapping and race specificity of bacterial blight resistance genes (QTLs) in rice – Texas A&M University (TAMU) Scholar Search form   Overview   Research   Identity   Additional Document Info   View All   Overview abstract By using a set of 315 recombinant inbred lines (RILs) from the cross…

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STING Agonist-Mediated Cytokine Secretion Is Accompanied by Monocyte Apoptosis

doi: 10.1021/acsinfecdis.1c00554. Online ahead of print. Affiliations Expand Affiliations 1 Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, Prague 16000, Czech Republic. 2 Faculty of Science, Charles University, Albertov 6, Prague 12800, Czech Republic. Item in Clipboard Marketa Pimkova Polidarova et al. ACS Infect…

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Addgene: lentiCRISPR v2 puro – CRBN (#1)

These plasmids were created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the plasmids were described, and include Addgene in the Materials and Methods of your future publications. For your Materials & Methods section: lentiCRISPR v2 puro – CRBN (#1) was a gift from Günter…

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Novel technologies in cfDNA analysis and potential utility in clinic

. 2021 Dec 31;33(6):708-718. doi: 10.21147/j.issn.1000-9604.2021.06.07. Affiliations Expand Affiliations 1 Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China. 2 Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China. 3 Department of Medical…

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Generation of NKX2.5 GFP Reporter Human iPSCs and Differentiation Into Functional Cardiac Fibroblasts

doi: 10.3389/fcell.2021.797927. eCollection 2021. Leyre López-Muneta  1 , Javier Linares  1 , Oscar Casis  2 , Laura Martínez-Ibáñez  3 , Arantxa González Miqueo  3   4 , Jaione Bezunartea  5 , Ana Maria Sanchez de la Nava  6   7 , Mónica Gallego  2 , María Eugenia Fernández-Santos  6   7 , Juan Roberto Rodriguez-Madoz  8 , Xabier L Aranguren …

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rs9789283 RefSNP Report – dbSNP

Help Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When…

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Frontiers | Association of Maternal Dietary Habits and MTHFD1 Gene Polymorphisms With Ventricular Septal Defects in Offspring: A Case-Control Study

Introduction Congenital heart disease (CHD) refers to a group of anatomic heart and great vessel malformations that arise during the embryologic development of the fetus. CHD is one of the most prevalent birth defects, affecting around 2.50 out of every 1,000 births in China (1), and it imposes a substantial…

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Immune microenvironment-related gene mapping predicts immunochemotherapy response and prognosis in diffuse large B-cell lymphoma

doi: 10.1007/s12032-021-01642-3. Affiliations Expand Affiliations 1 Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. 2 Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China. 3 Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China. 4 Department of Blood Transfusion, Nanfang Hospital, Southern…

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SETDB1/NSD-dependent H3K9me3/H3K36me3 dual heterochromatin maintains gene expression profiles by bookmarking poised enhancers

. 2022 Jan 17;S1097-2765(21)01142-4. doi: 10.1016/j.molcel.2021.12.037. Online ahead of print. Affiliations Expand Affiliations 1 DNA Repeat Lab, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, 34000 Montpellier, France. 2 Chromatin and Cell Biology Lab, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141…

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Mouse Cre drivers: Tools for studying disorders of the human female neuroendocrine-reproductive axis

doi: 10.1093/biolre/ioac012. Online ahead of print. Affiliations Expand Affiliations 1 Department of Obstetrics, Gynecology and Reproductive Health, Rutgers Biomedical and Health Sciences, Newark, NJ, USA. 2 Rutgers New Jersey Medical School, Newark, NJ, USA. 3 Department of Pediatrics, Robert Wood Johnson Medical School, Rutgers Biomedical and Health Sciences, New Brunswick,…

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Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis

1. Parte, A. C. LPSN–list of prokaryotic names with standing in nomenclature. Nucleic Acids Res. 42, D613-616 (2014). CAS  PubMed  Google Scholar  2. Krzyściak, W., Pluskwa, K. K., Jurczak, A. & Kościelniak, D. The pathogenicity of the Streptococcus genus. Eur. J. Clin. Microbiol. Infect. Dis. 32, 1361–1376 (2013). PubMed  PubMed…

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16S rRNA gene sequence diversity in Faecalibacterium prausnitzii-complex taxa has marked impacts on quantitative analysis

doi: 10.1093/femsec/fiac004. Online ahead of print. Affiliations Expand Affiliations 1 Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, 099-2493 Hokkaido, Japan. 2 Functional Food Forum, University of Turku, 20014 Turku, Finland. 3 Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, 33300 Villaviciosa, Spain….

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A high-throughput assay for directly monitoring nucleolar rRNA biogenesis

doi: 10.1098/rsob.210305. Epub 2022 Jan 26. Affiliations Expand Affiliations 1 Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 333 Cedar Street, New Haven, CT, USA. 2 Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA. 3 Department of Genetics, Yale School of Medicine, New Haven, CT,…

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