Tag: LIU
Burning Rock Receives CE Mark
SHANGHAI, June 1, 2022 /PRNewswire/ — Burning Rock Biotech Limited (NASDAQ: BNR, the “Company” or “Burning Rock”) announced that it has received CE marking for its OverC™ Multi-Cancer Detection Blood Test manufactured in both the US and China facilities (Identification Number: DE/CA20/01-IVD-Luxuslebenswelt-523/22, DE/CA20/01-IVD-Luxuslebenswelt-524/22). OverC™ Multi-Cancer Detection Blood Test is a…
Genetic characterization of two G8P[8] rotavirus strains isolated in Guangzhou, China, in 2020/21: evidence of genome reassortment | BMC Infectious Diseases
Mokomane M, Kasvosve I, Melo Ed, Pernica JM, Goldfarb DM. The global problem of childhood diarrhoeal diseases: emerging strategies in prevention and management. Ther Adv Infect Dis. 2018;5(1):29–43. PubMed Google Scholar Organization WH. Rotavirus vaccines: WHO position paper–July 2021. Weekly Epidemiol Rec. 2021;96(28):301–219. Google Scholar Bucardo F, Reyes Y, Svensson…
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses
Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017). CAS PubMed Article Google Scholar Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol….
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…
Joint analysis of functionally related genes yields further candidates associated with Tetralogy of Fallot
Bailliard F, Anderson RH. Tetralogy of Fallot. Orphanet J Rare Dis. 2009;4:2. Article Google Scholar Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, et al. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nat Genet. 2017;49:1593–601. CAS Article Google Scholar …
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…
Beam Therapeutics Stock: A Leader in Gene Editing Tech?
Don’t invest in stories. Don’t invest in a company before they have meaningful revenues. Don’t invest in drug developers that have a great deal of regulatory risk. These are all rules we need to break if we want exposure to a technology that allows mankind to start playing with the…
KEGG ENZYME: 1.14.19.32
Entry EC 1.14.19.32 Enzyme Name palmitoyl-CoA 14-(E/Z)-desaturase Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With oxidation of a pair of donors resulting in the reduction of O2 to two molecules of waterBRITE hierarchy Sysname palmitoyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (14,15 cis/trans-dehydrogenating) Reaction(IUBMB) (1) palmitoyl-CoA + 2 ferrocytochrome b5 + O2…
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…
Maintaining manganese in tumor to activate cGAS-STING pathway evokes a robust abscopal anti-tumor effect.
Affiliation Wang C(1), Sun Z(1), Zhao C(1), Zhang Z(1), Wang H(1), Liu Y(1), Guo Y(1), Zhang B(1), Gu L(2), Yu Y(2), Hu Y(3), Wu J(4).Author information: (1)State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, School of Life Sciences, Nanjing University, Nanjing 210093, PR China. (2)State…
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….
Researchers use nanotechnology to destroy and prevent relapse of solid tumor cancers
Generation and characterization of DCNV-rAd-Ag. a, Generation of DCNVs derived from adenovirus-infected mature dendritic cells. (1) The genes of tumor-specific antigen were genetically engineered into the adenovirus vector. (2) Recombinant adenovirus infected the immature DC2.4 cells to express the modified antigen on the cell surface and stimulate it. (3) Differentiation,…
Frontiers | Serum and Serum Exosomal CircRNAs hsa_circ_0001492, hsa_circ_0001439, and hsa_circ_0000896 as Diagnostic Biomarkers for Lung Adenocarcinoma
Introduction Lung cancer is associated with high morbidity and mortality and continues to be a major public health problem worldwide (1). Lung adenocarcinoma (LUAD) is the most common histological type of lung cancer. While the 5-year survival rates of patients with lung cancer are still <15%, rates are closer to…
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 …
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,…
Bioconductor – sSNAPPY (development version)
DOI: 10.18129/B9.bioc.sSNAPPY This is the development version of sSNAPPY; for the stable release version, see sSNAPPY. Single Sample directioNAl Pathway Perturbation analYsis Bioconductor version: Development (3.16) A single sample pathway pertrubation testing methods for RNA-seq data. The method propagate changes in gene expression down gene-set topologies to compute…
Frontiers | A Mutated Nme1Cas9 Is a Functional Alternative RNase to Both LwaCas13a and RfxCas13d in the Yeast S. cerevisiae
Introduction The clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) protein systems naturally exist in prokaryotes. They are RNA-mediated defense mechanisms to protect bacteria and archaea from invading nucleic acids (Barrangou et al., 2007). CRISPR–Cas systems are classified into two classes (1 and 2). Class 2 CRISPR–Cas require a single…
Roles of circRNAs | CMAR
Introduction Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, with an increasing global incidence, and a leading cause of cancer-related mortality.1 Although hepatitis B and C virus infections, cirrhosis, alcohol intake, and non-alcoholic fatty liver disease (NAFLD) are the main risk factors contributing to HCC.1,2 Approximately…
Specific High-Sensitivity Enzymatic Molecular Detection System Termed RPA-Based CRISPR-Cas13a for Duck Tembusu Virus Diagnostics
journal contribution posted on 19.05.2022, 07:04 by Dalin He, Gang Liu, Jing Yang, Xiaoning Jiang, Hongzhi Wang, Yaru Fan, Shangyu Gong, Feng Wei, Youxiang Diao, Yi Tang In China, drastic losses in the economy have been caused by the Tembusu virus (TMUV), the causative agent of the egg-drop syndrome, to…
In vivo hypermutation and continuous evolution
Arnold, F. H. Design by directed evolution. Acc. Chem. Res. 31, 125–131 (1998). Google Scholar Packer, M. S. & Liu, D. R. Methods for the directed evolution of proteins. Nat. Rev. Genet. 16, 379–394 (2015). Google Scholar Drake, J. W., Charlesworth, B., Charlesworth, D. & Crow, J. F. Rates of…
Crispr/Cas12a-Based Fluorescence Biosensor for Detection of Exosomal Mir-21 Derived from Lung Cancer by Yulin Zhang, Zhe Lu, wei Ni, Nian Liu, Dan Jin, Tingxian Li, Kun Li, Yuling Zhang, Qunfeng Yao, Guo-Jun Zhang :: SSRN
30 Pages Posted: 17 May 2022 See all articles by Yulin Zhang Hubei University of Chinese Medicine Hubei University of Chinese Medicine Hubei Provincial Hospital of Traditional Chinese Medicine Hubei Provincial Hospital of Traditional Chinese Medicine Hubei University of Chinese Medicine…
Single-cell eQTL models reveal dynamic T cell state dependence of disease loci – Nature – Alert Breaking News
Wei, K. et al. Notch signalling drives synovial fibroblast identity and arthritis pathology. Nature 582, 259–264 (2020). ADS CAS PubMed PubMed Central Article Google Scholar Cembrowski, M. S. & Menon, V. Continuous variation within cell types of the nervous system. Trends Neurosci. 41, 337–348 (2018). CAS PubMed Article Google Scholar Maurano, M. T. et al. Systematic localization of…
MND1 Expression as a Predictor of Breast Cancer Survival
Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…
Single-Cell Transcriptome Resource From Human Cell Atlas Team Yields Immune, Disease Insights
NEW YORK – A large international team came up with single-cell and single-nucleus transcriptomic resources to characterize the diverse cell types found in the human body, along with related gene expression and splicing features that offer clues to processes at play within and across tissues and organs. In a series…
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…
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…
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…
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…
Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma
Introduction Liver hepatocellular carcinoma (LIHC) is the most common type of primary cancer in the liver and third leading cause of cancer-related mortality worldwide (1). Although substantial improvements have been made in LIHC therapy, particularly in molecular targeted therapy and immunotherapy (2, 3), the 5-year survival rate of LIHC is…
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 …
Endometriosis-related functional modules and hub genes
Introduction Endometriosis (EMS) is a chronic gynecological disease defined as implantation and periodic growth of the endometrial glands and stroma outside the uterine cavity, causing chronic pelvic pain, severe dysmenorrhea, and infertility in 10% reproductive-age women, among which the infertility rate is approximately 30–50%.1,2 Surgical excision is commonly used for…
Crispr/Cas13a Induced Exponential Amplification for Highly Sensitive and Specific Detection of Circular Rna by Pengfei Song, Pengbo Zhang, Ke Qin, Fengxia Su, Kejian Gao, Xin Liu, Zhengping Li :: SSRN
19 Pages Posted: 23 Mar 2022 See all articles by Pengfei Song University of Science and Technology Beijing University of Science and Technology Beijing University of Science and Technology Beijing University of Science and Technology Beijing University of Science and Technology…
Whole-genome analysis of coxsackievirus B3 reflects its genetic diversity in China and worldwide | Virology Journal
Song Y, Zhang Y, Han Z, Xu W, Xiao J, Wang X, et al. Genetic recombination in fast-spreading coxsackievirus A6 variants: a potential role in evolution and pathogenicity. Virus Evol. 2020;6:2. doi.org/10.1093/ve/veaa048. Article Google Scholar Chen J, Han Z, Wu H, Xu W, Yu D, Zhang Y. A large-scale outbreak…
KEGG MODULE: M00567
MODULE: M00567 Help Entry M00567 Pathway Module Name Methanogenesis, CO2 => methane Definition (K00200+K00201+K00202+K00203-K11261+(K00205,K11260,K00204)) K00672 K01499 (K00319,K13942) K00320 (K00577+K00578+K00579+K00580+K00581-K00582-K00583+K00584) (K00399+K00401+K00402) (K22480+K22481+K22482,K03388+K03389+K03390,K08264+K08265,K03388+K03389+K03390+K14127+(K14126+K14128,K22516+K00125)) Diagram Orthology 4Fe-4S ferredoxin formylmethanofuran–tetrahydromethanopterin N-formyltransferase [EC:2.3.1.101] [RN:R03390] methenyltetrahydromethanopterin cyclohydrolase [EC:3.5.4.27] [RN:R03464] methylenetetrahydromethanopterin dehydrogenase [EC:1.5.99.9] [RN:R04456] 5,10-methenyltetrahydromethanopterin hydrogenase [EC:1.12.98.2] [RN:R04455] coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase [EC:1.5.99.11] [RN:R04464] Ortholog tableTaxonomyModule table…
CRISPRi for specific inhibition of miRNA clusters and miRNAs with high sequence homology
Bartel, D. P. MicroRNAs: Target recognition and regulatory functions. Cell 136, 215–233 (2009). CAS Article Google Scholar Bassett, A. R. et al. Understanding functional miRNA–target interactions in vivo by site-specific genome engineering. Nat. Commun. 5, 4640 (2014). ADS CAS Article Google Scholar Moore, M. J. et al. miRNA–target chimeras reveal…
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,…
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…
circRNA rtcisE2F regulates the self-renewal o
image: rt-circRNA rtcisE2F is originated from two adjacent genes CYP2C18 and CYP2C19, involves in the binding between m6A E2F6/E2F3 mRNAs and m6A readers IGF2BP2/YTHDF2, and finally promotes the stability of E2F6/E2F3 mRNAs. E2F6 and E2F3 drive the activation of Wnt/β-catenin signaling and the self-renewal of liver TICs. view more Credit: ©Science…
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…
Innovative site-specific anti-HER2 antibody-drug conjugate
Introduction Antibody-drug conjugates (ADCs) have been studied for decades as a promising cancer treatment. As compared to conventional chemotherapy, ADCs have a larger therapeutic window because of their ability to target antigen-expressing tumor cells.1 As ADC drug development technology continues to evolve, several ADC drugs are being introduced to the…
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…
Bioinformatics analysis identifies widely expressed genes
1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…
Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure
Date created: | Last Updated: : DOI | ARK Creating DOI. Please wait… Create DOI Category: Data Description: Supplementary data for publication: Juber Herrera-Uribe, Haibo Liu, Kristen A. Byrne, Zahra F. Bond, Crystal L. Loving and Christopher K. Tuggle. (2020). Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar…
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….
MAGeCK – BioGrids Consortium – Supported Software
AllHigh-Throughput SequencingGenomicsProteomicsVisualizationOther MAGeCK Description (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. Installation Use the following command to install this title with the CLI client: $ biogrids-cli install mageck Copy to clipboard Primary Citation* W….
Bug#1008752: avifile: autopkgtest regression on armhf: Bus error
Hi, On 01-04-2022 14:53, Ying-Chun Liu (PaulLiu) wrote: I need some help. Actually I know this bug for a while but I just cannot fix it. I’ve tried to reproduce the bug on qemu-user-static armhf chroot envorionment and PorterBox (abel.debian.org), on both platform the autopkgtest just passed without problem. I…
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…
An Introduction to the Biopharmaceutical Industry – Features
David Gemmell looks at key unit operations, and why chemical engineers are heavily involved in their design, troubleshooting or optimisation TO DATE, the Covid-19 pandemic has taken the lives of over 5.7m1 people and impacted global trade, travel, and the livelihoods of billions. It also sparked a vaccine…
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…
Accurate assembly of multi-end RNA-seq data with Scallop2
Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010). Article Google Scholar Guttman, M. et al. Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28,…
Extensively drug resistant E. coli LZ00114
Introduction Escherichia coli is a common Gram-negative opportunistic pathogen that causes invasive host infections through virulence factors such as flagella, toxin secretion, and adhesins. According to the source of the infection, pathogenic E. coli can be classified as intestinal (diarrheagenic) and extraintestinal (ExPEC). Uropathogenic E. coli (UPEC) is the most…
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,…
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…
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,…
Probing the microscopic structure and flexibility of oxidized DNA by molecular simulations
A R Poetsch, Comput. Struct. Biotechnol. J 18 207 (2020) Google Scholar S Steenken, and S V Jovanovic, J. Am. Chem. Soc. 119 617 (1997). Google Scholar P Diamantis, I Tavernelli, and U Rothlisberger, J. Chem. Theory Comput. 16 6690 (2020). Google Scholar J M Berg, J L Tymoczko, and…
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…
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…
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….
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…
ETSformer-pytorch 0.0.1 on PyPI – Libraries.io
ETSformer – Pytorch (wip) Implementation of ETSformer, state of the art time-series Transformer, in Pytorch Install $ pip install etsformer-pytorch Python import torch from etsformer_pytorch.etsformer_pytorch import ETSFormer model = ETSFormer( time_features = 4, model_dim = 512, # in paper they use 512 embed_kernel_size = 3, # kernel size for 1d…
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…
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…
BTG2 gene predicts poor outcome in PT-DLBCL
Introduction Primary testicular diffuse large B-cell lymphoma (PT-DLBCL) is a rare and aggressive form of mature B-cell lymphoma.1–3 PT-DLBCL was the most common type of testicular tumor in men aged over 60 and characterized by painless uni- or bilateral testicular masses with infrequent constitutional symptoms.4–6 PT-DLBCL shows significant extranodal tropism,…
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…
The long non-coding RNA LNC_000397 negatively regulates PRRSV replication through induction of interferon-stimulated genes | Virology Journal
Badaoui B, Rutigliano T, Anselmo A, Vanhee M, Nauwynck H, Giuffra E, Botti S. RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence. PLOS ONE. 2014;9:91918. Article Google Scholar Bateman A, Birney E, Cerruti L, Durbin R, Etwiller…
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…
Identification of Hub Genes Associated with COPD Through Integrated Bi
Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…
The Clam Cyclina sinensis (Gmelin) Phylogeography Study with 28S rRNA Gene and Potential of Nuclear rRNA Genes in Genetic Assessments of Molluscs
Avise, J. C., 2009. Phylogeography: Retrospect and prospect. Journal of Biogeography, 36: 3–15. Article Google Scholar Beheregaray, L. B., 2008. Twenty years of phylogeography: The state of the field and the challenges for the Southern Hemisphere. Molecular Ecology, 17: 3754–3774. Google Scholar Clement, M., Posada, D., and Crandall, K. A.,…
EFFICACY AND SAFETY OF CYCLOPHOSPHAMIDE LOW-DOSE PRE-PHASE CHEMOTHERAPY IN DIFFUSE LARGE B CELL LYMPHOMA WITH GASTROINTESTINAL INVOLVEMENT
Luca Guarnera Hematology, Department of Biomedicine and Prevention, University Tor Vergara, Rome, Italy Federico Meconi Hematology, Department of Biomedicine and Prevention, University Tor Vergara, Rome, Italy Roberto Secchi Hematology, Department of Biomedicine and Prevention, University Tor Vergara, Rome, Italy Maria Rosaria Pascale Hematology, Department of Biomedicine and Prevention, University Tor…
LAMP-CRISPR-Cas12a-lateral flow immunochromatographic strip | IDR
Introduction About 700,000 people die from “superbugs” globally every year. Antibiotic abuse is the culprit of extensive spread of superbugs. Currently, carbapenemase-producing organisms are among the most important pathogens of hospital infections. Especially the plasmid-mediated highly transmissible carbapenem-resistant Enterobacterales (CRE) has become an important public health issue of global concern….
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)….
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…
Validation of hub genes in acute pancreatitis
Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…
Hot Plasmids – February 2022
Every few months we highlight a subset of the new plasmids and viral preps in the repository through our hot plasmids articles. These articles provide brief summaries of recent plasmid deposits and we hope they’ll make it easier for you to find and use the plasmids you need. If you’d ever…
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 …
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…
Fatty infiltration after rotator cuff tear
Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…
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…
Spatial components of molecular tissue biology
1. Okabe, Y. & Medzhitov, R. Tissue biology perspective on macrophages. Nat. Immunol. 17, 9–17 (2016). CAS PubMed Google Scholar 2. Xia, C., Fan, J., Emanuel, G., Hao, J. & Zhuang, X. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc. Natl Acad. Sci. USA…
dCas9-VPR-mediated transcriptional activation of functionally equivalent genes for gene therapy
1. Dunbar, C. E. et al. Gene therapy comes of age. Science 359, eaan4672 (2018). PubMed Google Scholar 2. 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 3. Eid, A.,…
Identification of a four-gene signature & PTC.
Introduction Thyroid carcinoma (THCA) is the most common type of endocrine malignancy and its incidence is increasing.1 Based on its histopathological characteristics, thyroid carcinoma can be classified into multiple subtypes, such as papillary thyroid carcinoma (PTC), follicular thyroid carcinoma, and anaplastic thyroid carcinoma.2 PTC is the most common subtype of…
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…
Genome Study Finds Unexpected Variation in a Fundamental RNA Gene
Newswise — A genome study undertaken by Johns Hopkins Kimmel Cancer Center researchers to look for variants in a gene considered a fundamental building block for microscopic structures that synthesize proteins took a surprising twist. Human ribosomal RNA (rRNA) genes are essential for building ribosomes, or machineries that translate proteins….
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…
Novel diagnostic biomarkers for keloid based on GEO database
Introduction Keloid is excessive fibrosis of the skin that extends beyond the area of injury and does not regress.1 Keloid can occur in the joints and mouth after several years of severe injury, including burns, chemical injury, wound, and surgical incision.2 Keloids on the joints affect the quality of life,…
Novel gene rearrangement in the mitochondrial genome of Anastatus fulloi (Hymenoptera Chalcidoidea) and phylogenetic implications for Chalcidoidea
1. Osellame, L. D., Blacker, T. S. & Duchen, M. R. Cellular and molecular mechanisms of mitochondrial function. Best Pract. Res. Clin. Endocrinol. Metab. 26, 711–723 (2012). CAS PubMed PubMed Central Google Scholar 2. Bernt, M., Braband, A., Schierwater, B. & Stadler, P. F. Genetic aspects of mitochondrial genome evolution….
Seven technologies to watch in 2022
The Telomere-to-Telomere Consortium is sequencing whole chromosomes.Credit: Adrian T. Sumner/SPL From gene editing to protein-structure determination to quantum computing, here are seven technologies that are likely to have an impact on science in the year ahead. Fully finished genomes Roughly one-tenth of the human genome remained uncharted when genomics researchers…
Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells
Aghamohseni H, Ohadi K, Spearman M, Krahn N, Moo-Young M, Scharer JM, Butler M, Budman HM (2014) Effects of nutrient levels and average culture pH on the glycosylation pattern of camelid-humanized monoclonal antibody. J Biotechnol 186:98–109. doi.org/10.1016/j.jbiotec.2014.05.024 CAS Article PubMed Google Scholar Altamirano C, Illanes A, Casablancas A, Gámez X,…
Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence
Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….
Long non-coding RNA MSTRG.81401 short hairpin RNA relieves diabetic neuropathic pain and behaviors of depression by inhibiting P2X4 receptor expression in type 2 diabetic rats
1. Nicodemus JM, Enriquez C, Marquez A, Anaya CJ, Jolivalt CG (2017) Murine model and mechanisms of treatment-induced painful diabetic neuropathy. Neuroscience 354:136–145. doi.org/10.1016/j.neuroscience.2017.04.036 CAS Article PubMed Google Scholar 2. Morimoto SS, Kanellopoulos D, Manning KJ, Alexopoulos GS (2015) Diagnosis and treatment of depression and cognitive impairment in late life….
FDA Grants Regenerative Medicine Advanced Therapy, Fast Track Designations to Novel CAR T-Cell Therapy for Relapsed, Refractory B-cell Non-Hodgkin Lymphoma
C-CAR039 showed positive efficacy and safety data in patients with relapsed or refractory B-cell non-Hodgkin lymphoma. Officials with the FDA have granted both Regenerative Medicine Advanced Therapy (RMAT) Designation and Fast Track Designation to C-CAR039, a novel autologous bi-specific chimeric antigen receptor (CAR) T-cell therapy, for the treatment of patients…
Immune-related Prognostic Genes of ccRCC
Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…
The Genetic Architecture of Sleep Health Scores in the UK
Introduction Sleep is a complex neurological and physiological state. It is defined as a natural and reversible state of reduced responsiveness to external stimuli and relative inactivity, accompanied by a loss of consciousness.1 Sleep disorders can be classified as seven major categories: insomnia disorders, sleep-related breathing disorders, central disorders of…
Identification of differentially expressed genes in AF
Defeng Pan,1,* Yufei Zhou,2,* Shengjue Xiao,1,* Yue Hu,3,* Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…
Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome
1. Wang, J. & Jia, H. Metagenome-wide association studies: fine-mining the microbiome. Nat. Rev. Microbiol. 14, 508–522 (2016). CAS PubMed Google Scholar 2. Moschen, A. R. et al. Lipocalin 2 protects from inflammation and tumorigenesis associated with gut microbiota alterations. Cell Host Microbe 19, 455–469 (2016). CAS PubMed Google Scholar …
Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet
1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS PubMed PubMed Central Google Scholar 2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …
Phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein PINLYP regulates type I interferon innate immunity
Significance Interferon (IFN)-mediated antiviral responses serve as the first line of the host innate immune defense against viral infection. Here we identify a previously uncharacterized protein designated phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein (PINLYP), which is essential for embryonic development and plays an important role in type I IFN…
Bioconductor – ChIPQC
This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see ChIPQC. Quality metrics for ChIPseq data Bioconductor version: 3.1 Quality metrics for ChIPseq data Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark Maintainer: Tom Carroll <tc.infomatics at gmail.com>, Rory Stark <rory.stark…
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics
1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article Google Scholar 2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…
Valine tRNA levels and availability regulate complex I assembly in leukaemia
1. Rapino, F. et al. Codon-specific translation reprogramming promotes resistance to targeted therapy. Nature 558, 605–609 (2018). CAS PubMed Google Scholar 2. Goodarzi, H. et al. Modulated expression of specific tRNAs drives gene expression and cancer progression. Cell 165, 1416–1427 (2016). CAS PubMed PubMed Central Google Scholar 3. Wolfe, A….