Tag: KO

KEGG T07682: 118706260

Entry 118725205         ncRNA     T07682                                  Name (RefSeq) U1 spliceosomal RNA   KO K14276   U1 spliceosomal RNA Organism pkl  Pipistrellus kuhlii (Kuhl’s pipistrelle) Pathway pkl03040   Spliceosome Brite KEGG Orthology (KO) [BR:pkl00001] 09120 Genetic Information Processing  09121 Transcription   03040 Spliceosome    118725205 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03041 Spliceosome [BR:pkl03041]    118725205  09184 RNA family   03100 Non-coding RNAs [BR:pkl03100]    118725205Spliceosome [BR:pkl03041] Splicing related RNAs  118725205Non-coding RNAs [BR:pkl03100] Small non-coding…

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KEGG T01015: 4329963

Entry 4332822           CDS       T01015                                  Name (RefSeq) LOW QUALITY PROTEIN: nuclear cap-binding protein subunit 1-like   KO K12882   nuclear cap-binding protein subunit 1 Organism osa  Oryza sativa japonica (Japanese rice) (RefSeq) Pathway osa03013   Nucleocytoplasmic transport osa03015   mRNA surveillance pathway osa03040   Spliceosome Brite KEGG Orthology (KO) [BR:osa00001] 09120 Genetic Information Processing  09121 Transcription   03040 Spliceosome    4332822  09122 Translation   03013 Nucleocytoplasmic transport    4332822   03015 mRNA…

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KEGG ORTHOLOGY: K06121

KEGG ORTHOLOGY: K06121     ORTHOLOGY: K06121 Help Entry K06121                      KO                                      Symbol dhbC Name glycerol dehydratase medium subunit [EC:4.2.1.30] Pathway Reaction R01047   glycerol hydro-lyase (3-hydroxypropanal-forming) Brite KEGG Orthology (KO) [BR:ko00001] 09100 Metabolism  09103 Lipid metabolism   00561 Glycerolipid metabolism    K06121  dhbC; glycerol dehydratase medium subunitEnzymes [BR:ko01000] 4. Lyases  4.2  Carbon-oxygen lyases   4.2.1  Hydro-lyases    4.2.1.30  glycerol dehydratase     K06121  dhbC; glycerol dehydratase medium subunit BRITE hierarchy Other DBs Genes…

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KEGG T01710: 100306272

Entry 100782702         CDS       T01710                                  Symbol COX2 Name (RefSeq) cytochrome c oxidase subunit 2, mitochondrial   KO K02261   cytochrome c oxidase subunit 2 Organism gmx  Glycine max (soybean) Pathway gmx00190   Oxidative phosphorylation gmx01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:gmx00001] 09100 Metabolism  09102 Energy metabolism   00190 Oxidative phosphorylation    100782702 (COX2) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03029 Mitochondrial biogenesis…

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Proteomic analysis of SARS-CoV-2 particles unveils a key role of G3BP proteins in viral assembly

Capturing proteins associated with SARS-CoV-2 virions To identify host cell proteins potentially present in extracellular SARS-CoV-2 virions, viral particles were produced from two lung epithelial cell models, A549 cells overexpressing ACE2 receptor (A549-ACE2) and Calu-3 cells that naturally express ACE2 receptor and TMPRSS2. Following infection with the D614G SARS-CoV-2 strain32,…

Continue Reading Proteomic analysis of SARS-CoV-2 particles unveils a key role of G3BP proteins in viral assembly

Exosomes From IgE-Stimulated Mast Cells Aggravate Asthma-Mediated Atherosclerosis Through circRNA CDR1as-Mediated Endothelial Cell Dysfunction in Mice

Background: IgE has been known for mediating endothelial cell dysfunction and mast cell (MC) activation to fuel asthma-aggravated high-fat diet-induced atherosclerosis. However, it remains unclear for the mechanism of asthma-mediated atherosclerosis, especially the potential involvement of IgE in the exacerbation of asthma-mediated atherosclerosis with a standard laboratory diet, and the…

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Ten NK cell therapy companies to look out for this year

Natural killer (NK) cells are white blood cells that are a part of the body’s defense mechanism. These cells are on the lookout for any kind of disruption in the immune system, and can kill diseased cells like tumor cells. NK cells are being used in clinical applications to treat…

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Knockout of lipoprotein lipase with CRISPR/Cas9 causes severe developmental defects and affects lipid deposition in Japanese medaka (Oryzias latipes)

Abstract In mammals, lipoprotein lipase (LPL) has been found to play an important role in lipid mentalism and deposition. LPL deficiency in humans (Homo sapiens) and mice (Mus musculus) tends to cause hypertriglyceridemia. The lpl gene is not expressed in adult mammalian liver, but is in adult fish liver. The…

Continue Reading Knockout of lipoprotein lipase with CRISPR/Cas9 causes severe developmental defects and affects lipid deposition in Japanese medaka (Oryzias latipes)

csi-miR-96-5p delivered by Clonorchis sinensis extracellular vesicles promotes intrahepatic cholangiocarcinoma proliferation and migration via the ferroptosis-related PTEN/SLC7A11/GPX4 axis | Parasites & Vectors

Human tissue samples The preoperative diagnosis of CS mainly relies on stool microscopy, enzyme-linked immunosorbent assay, or endoscopy. Fresh liver and intrahepatic bile duct specimens were collected from ICC patients with (CS-ICC group) and without (NC-ICC group) CS infection during partial hepatectomy at the First Hospital of Jilin University. Tumor tissues…

Continue Reading csi-miR-96-5p delivered by Clonorchis sinensis extracellular vesicles promotes intrahepatic cholangiocarcinoma proliferation and migration via the ferroptosis-related PTEN/SLC7A11/GPX4 axis | Parasites & Vectors

Summary of Genomics and Transcriptomics – DNA sequencing I. Goal II. Methodology A. Sanger DNA

DNA sequencing I. Goal II. Methodology A. Sanger DNA sequencing ● Up to 900 base pairs ● Primer extension with labeled ddNTPs (radioactive or fluorescent) ● Prior knowledge on target needed ● Difficult to detect variation in mixtures ● High accuracy + still in use for genotyping When it is…

Continue Reading Summary of Genomics and Transcriptomics – DNA sequencing I. Goal II. Methodology A. Sanger DNA

KEGG T08053: IA203_01755

Entry IA203_01755       CDS       T08053                                  Name (GenBank) UDP-N-acetylmuramate dehydrogenase   KO K00075   UDP-N-acetylmuramate dehydrogenase [EC:1.3.1.98] Organism cwk  Corynebacterium wankanglinii Pathway cwk00520   Amino sugar and nucleotide sugar metabolism cwk00550   Peptidoglycan biosynthesis cwk01100   Metabolic pathways cwk01250   Biosynthesis of nucleotide sugars Brite KEGG Orthology (KO) [BR:cwk00001] 09100 Metabolism  09101 Carbohydrate metabolism   00520 Amino sugar and nucleotide sugar metabolism    IA203_01755  09107 Glycan biosynthesis and…

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KEGG T09148: BWI76_09435

Entry BWI76_09435       CDS       T09148                                  Name (GenBank) glutaredoxin, GrxA family   KO K03674   glutaredoxin 1 Organism klm  Klebsiella sp. M5al Brite KEGG Orthology (KO) [BR:klm00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03110 Chaperones and folding catalysts [BR:klm03110]    BWI76_09435Chaperones and folding catalysts [BR:klm03110] Protein folding catalysts  Protein disulfide isomerase   BWI76_09435 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam:  Glutaredoxin Glrx-like Thioredoxin_3…

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Kris Bernal reacts to viral hairstyle from ‘Starstruck’

Kris Bernal couldn’t help but laugh at her hair mishap from years ago. A video of the actress and content creator from her time competing on “Starstruck” is making the rounds online. Posted on GMA Network’s Instagram page, it showed Kris getting a very short haircut with uneven bangs and…

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Sequential deregulation of histone marks, chromatin accessibility and gene expression in response to PROTAC-induced degradation of ASH2L

Loss of ASH2L prevents cell proliferation We have studied the molecular and cellular consequences of Ash2l loss in mouse embryo fibroblasts (MEFs) with floxed Ash2l alleles and an inducible Cre-ER recombinase (iMEF-Ash2lfl/fl-Cre-ER). While the knockout of Ash2l was rapid, the downstream effects, including the decrease in promoter-associated H3K4me3, altered gene…

Continue Reading Sequential deregulation of histone marks, chromatin accessibility and gene expression in response to PROTAC-induced degradation of ASH2L

Functional alterations and predictive capacity of gut microbiome in type 2 diabetes

Diversity and compositional analyses Regarding clinical differences (Table 1), T2DM individuals (mean 69.6 (± 12.3 sd) years) were significantly (p value < 0.01; Wilcoxon rank-sum test) older than the controls (46.9 (± 17.3 sd) years), showed higher BMI (mean 30.9 (± 7.01 sd) vs. mean 26.3 (± 6.12 sd) than the control…

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Identification of Differentially Expressed Genes in Human Colorectal Cancer Using RNASeq Data Validated on the Molecular Level with Real-Time PCR

Allam RM, Al-Abd AM, Khedr A, Sharaf OA, Nofal SM, Khalifa AE, Mosli HA, Abdel-Naim AB (2018) Fingolimod interrupts the cross talk between estrogen metabolism and sphingolipid metabolism within prostate cancer cells. Toxicol Lett 291:77–85 Article  CAS  PubMed  Google Scholar  Andrews S et al (2010) FastQC: a quality control tool…

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LOINC 16531-6 Campylobacter lari rRNA [Units/volume] in Serum by Probe

es-AR Spanish (Argentina) ARNr de Campylobacter lari:concentración arbitraria:punto en el tiempo:suero:cuantitativo:sonda es-ES Spanish (Spain) Campylobacter lari rRNA:Concentración arbitraria:Punto temporal:Suero:Qn:Sonda de DNASynonyms: Cuantitativo es-MX Spanish (Mexico) ARNr de Campylobacter lari:Concentración arbitraria:Punto temporal:Suero:Cuantitativo:Investigacion fr-CA French (Canada) Campylobacter lari , ARNr:Concentration arbitraire:Temps ponctuel:Sérum:Quantitatif:Sonde fr-FR French (France) Campylobacter lari ARNr:Arbitraire/Volume:Ponctuel:Sérum:Numérique:PCR fr-BE French (Belgium) Campylobacter…

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Evolution of lysine-specific demethylase 1 and REST corepressor gene families and their molecular interaction

The RCOR gene repertoire expanded in the ancestor of jawed vertebrates To understand the duplicative history of the RCOR genes, we reconstructed gene phylogenies with different taxonomic samplings. The first analysis aimed to understand the evolution of RCOR genes in vertebrates (Fig. 2), whereas in the second, our sampling effort included…

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Cancers | Free Full-Text | In Vitro Organoid-Based Assays Reveal SMAD4 Tumor-Suppressive Mechanisms for Serrated Colorectal Cancer Invasion

Original submission received: 21 November 2023 / Revised: 8 December 2023 / Accepted: 11 December 2023 / Published: 13 December 2023 Round 1 Reviewer 1 Report Comments and Suggestions for Authors Dear authors, thank you for this valuable piece of work. Should the other reviewer(s) recommend edits to your work,…

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Importance of a detailed anomaly scan after a cfDNA test indicating fetal trisomy 21, 18 or 13

Kagan KO, Sonek J, Kozlowski P (2022) Antenatal screening for chromosomal abnormalities. Arch Gynecol Obstet 305(4):825–835 Article  CAS  PubMed  PubMed Central  Google Scholar  Rose NC, Barrie ES, Malinowski J, Jenkins GP, McClain MR, LaGrave D et al (2022) Systematic evidence-based review: the application of noninvasive prenatal screening using cell-free DNA…

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Atg7 senses ATP levels and regulates AKT1-PDCD4 phosphorylation-ubiquitination axis to promote survival during metabolic stress

Atg7 interacts with PDCD4 and negatively regulates PDCD4 protein levels Previous studies have demonstrated the role of Atg7 in maintaining metabolic homeostasis by initiating autophagy and arresting the cell cycle17,18,22. Herein, the function of Atg7 was more comprehensively investigated and it was determined whether Atg7 reduces protein synthesis to save…

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Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe

Wang, W. T. Revision of Adonis (Ranunculaceae). Bull. Bot. Res. 14, 1–31 (1994). Google Scholar  Gao, T. et al. Evaluating the feasibility of using candidate DNA Barcodes in discriminating species of the large Asteraceae family. BMC Evol. Biol. 10, 324 (2016). Article  Google Scholar  Conti, F. et al. Adonis fucensis…

Continue Reading Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe

Glabridin improves autoimmune disease in Trex1-deficient mice by reducing type I interferon production | Molecular Medicine

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009;55:611–22. Article  CAS  PubMed  Google Scholar  Chen Q, Sun L, Chen ZJ….

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LOINC 17546-3 Bartonella quintana rRNA [Presence] in Specimen by Probe

de-DE German (Germany) Bartonella quintana rRNA:Nachweis oder Schwellenwert:Zeitpunkt:XXX:Ordinal:Sonde es-AR Spanish (Argentina) ADN de Bartonella quintana:concentración arbitraria:punto en el tiempo:XXX:ordinal:sonda es-ES Spanish (Spain) Bartonella quintana rRNA:PrThr:Punto temporal:XXX:Ord:Sonda de DNA es-MX Spanish (Mexico) ARNr de Bartonella quintana:Presencia o umbral:Punto temporal:XXX:Ordinal:Investigacion fr-CA French (Canada) Bartonella quintana , ARNr:Présence-Seuil:Temps ponctuel:XXX:Ordinal:Sonde fr-FR French (France) Bartonella…

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Psychological impact of additional findings detected by genome-wide Non-Invasive Prenatal Testing (NIPT): TRIDENT-2 study

Lo YMD, Corbetta N, Chamberlain PF, Rai V, Sargent IL, Redman CWG, et al. Presence of fetal DNA in maternal plasma and serum. Lancet. 1997;350:485–7. Article  CAS  PubMed  Google Scholar  Warsof SL, Larion S, Abuhamad AZ. Overview of the impact of noninvasive prenatal testing on diagnostic procedures. Prenat Diagn. 2015;35:972–9….

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Advanced Emerging Techniques for Forensic DNA Analysis: STRs, SNPs, and mtDNA Analysis

Alshehhi A, Almarzooqi A, Alhammadi K, Werghi N, Tay GK, Alsafar H (2023) Advancement in human face prediction using DNA. Genes (Basel) 14:136. doi.org/10.3390/genes14010136 CrossRef  CAS  PubMed  Google Scholar  Amorim A, Fernandes T, Taveira N (2019) Mitochondrial DNA in human identification: a review. PeerJ 7:e7314. doi.org/10.7717/peerj.7314 CrossRef  PubMed Central  PubMed …

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Map of disease-causing mutations in neurodevelopmental disorders and cancer revealed

Experimental design overview. a Two independent sgRNAs and associated HDR variant libraries are designed at the 5′ and 3′ end of each exon. b The sgRNA, together with the HDR template library are transfected into LIG4-KO Cas9-expressing HAP1 cells. HDR utilizes the library as a template for repair of the…

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tRNA therapeutics for genetic diseases

Huang, X. et al. The landscape of mRNA nanomedicine. Nat. Med. 28, 2273–2287 (2022). Article  CAS  Google Scholar  Rohner, E., Yang, R., Foo, K. S., Goedel, A. & Chien, K. R. Unlocking the promise of mRNA therapeutics. Nat. Biotechnol. 40, 1586–1600 (2022). Article  CAS  Google Scholar  Brown, A., Shao, S.,…

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Targeting the epigenome to reinvigorate T cells for cancer immunotherapy | Military Medical Research

Tsui C, Kretschmer L, Rapelius S, Gabriel SS, Chisanga D, Knöpper K, et al. MYB orchestrates T cell exhaustion and response to checkpoint inhibition. Nature. 2022;609(7926):354–60. Article  CAS  PubMed  PubMed Central  Google Scholar  Zhu L, Zhou X, Gu M, Kim J, Li Y, Ko CJ, et al. Dapl1 controls NFATc2…

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Developing more advanced renal organoids to model polycystic kidney disease

Credit: Cell Reports (2023). DOI: 10.1016/j.celrep.2023.113431 A team of CiRA researchers, building upon their previous work on differentiating iPS cells into kidney organoids, have made significant improvements to build a better model of kidney development and diseases for use as a robust platform for drug discovery. Autosomal dominant polycystic kidney…

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KEGG ORTHOLOGY: K17062

KEGG ORTHOLOGY: K17062     ORTHOLOGY: K17062 Help Entry K17062                      KO                                      Symbol bgtB Name arginine/lysine/histidine/glutamine transport system substrate-binding and permease protein Pathway Brite KEGG Orthology (KO) [BR:ko00001] 09130 Environmental Information Processing  09131 Membrane transport   02010 ABC transporters    K17062  bgtB; arginine/lysine/histidine/glutamine transport system substrate-binding and permease protein 09180 Brite Hierarchies  09183 Protein families: signaling and cellular processes   02000 Transporters    K17062  bgtB; arginine/lysine/histidine/glutamine transport…

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KEGG ORTHOLOGY: K06665

KEGG ORTHOLOGY: K06665     ORTHOLOGY: K06665 Help Entry K06665                      KO                                      Symbol SSN6, CYC8 Name general transcriptional corepressor CYC8 Pathway map04011   MAPK signaling pathway – yeast Brite KEGG Orthology (KO) [BR:ko00001] 09130 Environmental Information Processing  09132 Signal transduction   04011 MAPK signaling pathway – yeast    K06665  SSN6, CYC8; general transcriptional corepressor CYC8 09140 Cellular Processes  09143 Cell growth and death   04111…

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How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.

How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package. 0 @3e18707b Last seen 10 hours ago India I have transcriptome data of an inhouse sequenced bacterial genome. I made the database for my bacteria using makeOrgPackageFromNCBI command. How can I use…

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A Reliable Method for Quantifying Plasma Cell-Free DNA Using an Internal Standard Strategy: Evaluation in a Cohort of Non-Pregnant and Pregnant Women

Martignano F. Cell-free DNA: an overview of sample types and isolation procedures. In: Casadio V, Salvi S, editors. Cell-free DNA as diagnostic markers. Methods in molecular biology, Vol. 1909. New York, NY: Humana Press; 2019. p. 13–27. doi.org/10.1007/978-1-4939-8973-7_2. Volckmar AL, Sültmann H, Riediger A, Fioretos T, Schirmacher P, Endris V,…

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Potential use of iPSCs for disease modeling, drug screening, and cell-based therapy for Alzheimer’s disease | Cellular & Molecular Biology Letters

Tarawneh R, Holtzman DM. The clinical problem of symptomatic Alzheimer disease and mild cognitive impairment. Cold Spring Harb Perspect Med. 2012;2(5): a006148. Article  PubMed  PubMed Central  Google Scholar  van der Flier WM, Scheltens P. Epidemiology and risk factors of dementia. J Neurol Neurosurg Psychiatry. 2005;76(suppl 5):v2-7. Article  PubMed  PubMed Central …

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KEGG T01005: 473325

Entry 473325            CDS       T01005                                  Symbol RNASE2 Name (RefSeq) non-secretory ribonuclease precursor   KO K01168   pancreatic ribonuclease [EC:4.6.1.18] Organism ptr  Pan troglodytes (chimpanzee) Brite KEGG Orthology (KO) [BR:ptr00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03019 Messenger RNA biogenesis [BR:ptr03019]    473325 (RNASE2)   04131 Membrane trafficking [BR:ptr04131]    473325 (RNASE2)Enzymes [BR:ptr01000] 4. Lyases  4.6  Phosphorus-oxygen lyases   4.6.1  Phosphorus-oxygen lyases (only sub-subclass identified to date)    4.6.1.18  pancreatic ribonuclease     473325 (RNASE2)Messenger…

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Precise base editing without unintended indels in human cells and mouse primary myoblasts

Base editors cause unintended indels at the target sites Several types of evolved base editors based on the CRISPR system have been developed for more accurate and efficient genome engineering21,37. Among these, AncBE4max and ABEmax were evolved by modifying codon usage, NLSs, and ancestral deaminase reconstructions21. These modifications greatly improve…

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DNA methylation change in blood cells of FB and CFS patients

Introduction Fibromyalgia (FM) and Chronic Fatigue Syndrome (CFS) are characterized by chronic pain, fatigue, and weakness. Patients with these symptoms also suffer from sleep abnormalities and report affected cognitive processes such as memory. The diagnosis of these two syndromes is challenging and is based on questionnaires that make the diagnosis…

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KEGG T01007: 415125

Entry 415125            CDS       T01007                                  Symbol FGFR2 Name (RefSeq) fibroblast growth factor receptor 2 precursor   KO K05093   fibroblast growth factor receptor 2 [EC:2.7.10.1] Organism cfa  Canis lupus familiaris (dog) Pathway cfa01521   EGFR tyrosine kinase inhibitor resistance cfa04010   MAPK signaling pathway cfa04014   Ras signaling pathway cfa04015   Rap1 signaling pathway cfa04020   Calcium signaling pathway cfa04144   Endocytosis…

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KEGG T02994: 18601618

Entry 18601618          CDS       T02994                                  Name (RefSeq) alpha-glucan phosphorylase 1   KO K00688   glycogen phosphorylase [EC:2.4.1.1] Organism tcc  Theobroma cacao (cacao) Pathway tcc00500   Starch and sucrose metabolism tcc01100   Metabolic pathways tcc01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:tcc00001] 09100 Metabolism  09101 Carbohydrate metabolism   00500 Starch and sucrose metabolism    18601618Enzymes [BR:tcc01000] 2. Transferases  2.4  Glycosyltransferases   2.4.1  Hexosyltransferases    2.4.1.1  glycogen phosphorylase     18601618 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT…

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KEGG T00196: STH138

Entry STH138            CDS       T00196                                  Name (GenBank) putative N-acetyl-mannosamine transferase   KO K05946   N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase [EC:2.4.1.187] Organism sth  Symbiobacterium thermophilum Pathway sth00552   Teichoic acid biosynthesis Brite KEGG Orthology (KO) [BR:sth00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00552 Teichoic acid biosynthesis    STH138 09180 Brite Hierarchies  09181 Protein families: metabolism   01003 Glycosyltransferases [BR:sth01003]    STH138Enzymes [BR:sth01000] 2. Transferases  2.4  Glycosyltransferases   2.4.1  Hexosyltransferases    2.4.1.187  N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase     STH138Glycosyltransferases [BR:sth01003] Polysaccharide  Bacterial polysaccharide (excluding LPS)   STH138 BRITE hierarchy SSDB…

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Proteomics and metabolomics analyses of Streptococcus agalactiae isolates from human and animal sources

Shen, C.-H. Molecular diagnosis of infectious diseases in Diagnostic Molecular Biology Ch. 15, 387–411 (Academic Press, C 2019). Katholm, J., Bennedsgaard, T. W., Koskinen, M. T. & Rattenborg, E. Quality of bulk tank milk samples from Danish dairy herds based on real-time polymerase chain reaction identification of mastitis pathogens. J….

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KEGG T02920: 102247935

Entry 102247935         CDS       T02920                                  Symbol TRMT44 Name (RefSeq) tRNA methyltransferase 44 homolog (S. cerevisiae)   KO K15447   tRNASer (uridine44-2′-O)-methyltransferase [EC:2.1.1.211] Organism myb  Myotis brandtii (Brandt’s bat) Brite KEGG Orthology (KO) [BR:myb00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03016 Transfer RNA biogenesis [BR:myb03016]    102247935 (TRMT44)Enzymes [BR:myb01000] 2. Transferases  2.1  Transferring one-carbon groups   2.1.1  Methyltransferases    2.1.1.211  tRNASer (uridine44-2′-O)-methyltransferase     102247935 (TRMT44)Transfer RNA biogenesis [BR:myb03016] Eukaryotic type  tRNA modification…

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Cytoplasmic Escape of Mitochondrial DNA Mediated by Mfn2 Downregulation Promotes Microglial Activation via cGas-Sting Axis in Spinal Cord Injury

doi: 10.1002/advs.202305442. Online ahead of print. Fei-Long Wei  1 , Tian-Fu Wang  1 , Chao-Li Wang  2 , Zhen-Peng Zhang  3 , Jing-Wei Zhao  1 , Wei Heng  1 , Zhen Tang  1 , Ming-Rui Du  1 , Xiao-Dong Yan  1 , Xiao-Xiang Li  1 , Zheng Guo  1 , Ji-Xian Qian  1 , Cheng-Pei Zhou  1 Affiliations Expand Affiliations 1 Department…

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KEGG T03531: KR75_11080

Entry KR75_11080        CDS       T03531                                  Name (GenBank) xylose isomerase   KO K01805   xylose isomerase [EC:5.3.1.5] Organism kvd  Klebsiella variicola DX120E Pathway kvd00040   Pentose and glucuronate interconversions kvd00051   Fructose and mannose metabolism kvd01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:kvd00001] 09100 Metabolism  09101 Carbohydrate metabolism   00040 Pentose and glucuronate interconversions    KR75_11080   00051 Fructose and mannose metabolism    KR75_11080Enzymes [BR:kvd01000] 5. Isomerases  5.3  Intramolecular oxidoreductases   5.3.1  Interconverting aldoses and…

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KEGG T01001: 1474

Entry 1474              CDS       T01001                                  Symbol CST6, ECTD15 Name (RefSeq) cystatin E/M   KO K13902   cystatin-M Organism hsa  Homo sapiens (human) Disease H00651   Hypohidrotic ectodermal dysplasia Brite KEGG Orthology (KO) [BR:hsa00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:hsa01002]    1474 (CST6)Peptidases and inhibitors [BR:hsa01002] Peptidase inhibitors  Family I25: cystatin family   1474 (CST6) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif…

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KEGG T01001: 637

Entry 637               CDS       T01001                                  Symbol BID, FP497 Name (RefSeq) BH3 interacting domain death agonist   KO K04726   BH3 interacting domain death agonist Organism hsa  Homo sapiens (human) Pathway hsa01524   Platinum drug resistance hsa04071   Sphingolipid signaling pathway hsa04115   p53 signaling pathway hsa04210   Apoptosis hsa04215   Apoptosis – multiple species hsa04217   Necroptosis hsa04650   Natural killer cell mediated…

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Complex design with a mixture of male and female mice

DEseq2 : Complex design with a mixture of male and female mice 0 @2bfe541c Last seen 4 hours ago France Hello everyone, I’m working on a scientific project that poses a particular problem. The experimental design includes 3 times and 2 conditions (WT and KO). Each time*condition has 3 mice….

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Immune-privileged tissues formed from immunologically cloaked mouse embryonic stem cells survive long term in allogeneic hosts

Mice C57BL/6N (strain 005304), C3H/HeJ (strain 000659), FVB/NJ (strain 001800), BALB/cJ (strain 000651) and NSG mice (stock 005557) were purchased from the Jackson Laboratory. CD-1 (stock 022) mice were purchased from Charles River. Mice (6–20-week-old) of each strain/background were used for teratoma assays. Mice were housed in a pathogen-free facility…

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High-throughput screening of genetic and cellular drivers of syncytium formation induced by the spike protein of SARS-CoV-2

Plasmid construction All the constructs used in this study were generated with standard cloning strategies, including PCR, overlapping PCR, oligo annealing, digestion and ligation. Primers were purchased from Genewiz. The plasmid sequence was verified by Sanger sequencing. The pCAG-spike(D614G)-GFP11-mCherry plasmid was modified from Addgene plasmid 158761. Briefly, GFP11 and mCherry…

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Gene expression profiles separate endometriosis lesion subtypes and indicate a sensitivity of endometrioma to estrogen suppressive treatments through elevated ESR2 expression | BMC Medicine

Cea Soriano L, López-Garcia E, Schulze-Rath R, Garcia Rodríguez LA. Incidence, treatment and recurrence of endometriosis in a UK-based population analysis using data from The Health Improvement Network and the Hospital Episode Statistics database. Eur J Contracept Reprod Health Care. 2017;22(5):334–43. Article  PubMed  Google Scholar  Guo SW. Recurrence of endometriosis…

Continue Reading Gene expression profiles separate endometriosis lesion subtypes and indicate a sensitivity of endometrioma to estrogen suppressive treatments through elevated ESR2 expression | BMC Medicine

Megakaryocytes possess a STING pathway that is transferred to platelets to potentiate activation

Introduction Host defence against infection relies on two important systems: the immune and the coagulation systems. Platelets are anucleate cells produced by megakaryocytes and are responsible for blood clotting and haemostasis (Lefrancais et al, 2017). They are also very abundant and play unexpected roles in immune responses (Maouia et al,…

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KEGG T00046: PM0721

Entry PM0721            CDS       T00046                                  Symbol ttrA Name (GenBank) TtrA   KO K08357   tetrathionate reductase subunit A Organism pmu  Pasteurella multocida subsp. multocida Pm70 Pathway pmu00920   Sulfur metabolism pmu01100   Metabolic pathways pmu01120   Microbial metabolism in diverse environments pmu02020   Two-component system Brite KEGG Orthology (KO) [BR:pmu00001] 09100 Metabolism  09102 Energy metabolism   00920 Sulfur metabolism    PM0721 (ttrA) 09130 Environmental Information Processing  09132 Signal…

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Herpes Zoster Pipeline Analysis Demonstrates Novel 18+

Herpes Zoster Pipeline DelveInsight’s, “Herpes Zoster Pipeline Insight 2023,” report provides comprehensive insights about 18+ companies and 20+ pipeline drugs in the Herpes Zoster pipeline landscape. It covers the Herpes Zoster pipeline drug profiles, including Herpes Zoster clinical trials and nonclinical stage products. It also covers the therapeutics assessment by…

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KEGG module and abundance of its KEGG Orthologs for functioning

KEGG module and abundance of its KEGG Orthologs for functioning 0 Hi all, I’m trying to interpret KEGG Orholog (KO) abundance data from two different groups. As you know, KEGG module is composed of multiple KOs. Then, if I want to say “this KEGG module functions well and actively”, does…

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A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei

Cell growth and transfections Procyclic form (PCF) T. brucei, strain 29-1354, which carries integrated genes for the T7 polymerase and the tetracycline repressor, was grown in SDM-79 medium supplemented with 10% fetal calf serum, in the presence of 50 μg/ml hygromycin. Cells were grown in the presence of 15 μg/ml G418 for…

Continue Reading A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei

[Kernel-packages] [Bug 2007050] Autopkgtest regression report (initramfs-tools/0.142ubuntu15.1)

All autopkgtests for the newly accepted initramfs-tools (0.142ubuntu15.1) for mantic have finished running. The following regressions have been reported in tests triggered by the package: initramfs-tools/0.142ubuntu15.1 (armhf) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-

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KEGG T06063: 106511269

Entry 106522761         CDS       T06063                                  Symbol pak1 Name (RefSeq) serine/threonine-protein kinase PAK 1   KO K04409   p21-activated kinase 1 [EC:2.7.11.1] Organism alim  Austrofundulus limnaeus (annual killifish) Pathway alim04010   MAPK signaling pathway alim04012   ErbB signaling pathway alim04510   Focal adhesion alim04625   C-type lectin receptor signaling pathway alim04810   Regulation of actin cytoskeleton alim05132   Salmonella infection Brite KEGG Orthology…

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GDF11 slows excitatory neuronal senescence and brain ageing by repressing p21

Experimental model and subject details Mice Male ICR mice (Laboratory Animal Center of Zhejiang Academy of Medical Sciences) at age of 3 months (M), 9 M and 36 M, male C57BL/B6 wild‐type (WT) mice (Shanghai Slac Laboratory) at age of 3 M and 10 M, male GDF11-flox mice (GDF11f/f, mice carrying the “floxed” GDF11…

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KEGG T00183: SAS2563

Entry SAS2563           CDS       T00183                                  Name (GenBank) putative histidinol dehydrogenase   KO K00013   histidinol dehydrogenase [EC:1.1.1.23] Organism sas  Staphylococcus aureus subsp. aureus MSSA476 (MSSA) Pathway sas00340   Histidine metabolism sas01100   Metabolic pathways sas01110   Biosynthesis of secondary metabolites sas01230   Biosynthesis of amino acids Brite KEGG Orthology (KO) [BR:sas00001] 09100 Metabolism  09105 Amino acid metabolism   00340 Histidine metabolism    SAS2563Enzymes [BR:sas01000] 1. Oxidoreductases  1.1  Acting on…

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KEGG T00918: Mlut_12280

Entry Mlut_12280        CDS       T00918                                  Name (GenBank) Undecaprenyl pyrophosphate synthetase   KO K00806   undecaprenyl diphosphate synthase [EC:2.5.1.31] Organism mlu  Micrococcus luteus Pathway mlu00550   Peptidoglycan biosynthesis mlu00900   Terpenoid backbone biosynthesis mlu01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:mlu00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00550 Peptidoglycan biosynthesis    Mlut_12280  09109 Metabolism of terpenoids and polyketides   00900 Terpenoid backbone biosynthesis    Mlut_12280 09180 Brite…

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The analysis of the genotype of Sapovirus outbreaks in Zhejiang Province | Virology Journal

Leblanc D, Inglis GD, Boras VF, Brassard J, Houde A. The prevalence of enteric RNA viruses in stools from diarrheic and non-diarrheic people in southwestern Alberta, Canada. Arch Virol. 2017;162(1):117–28. Article  CAS  PubMed  Google Scholar  Becker-Dreps S, González F, Bucardo F. Sapovirus: an emerging cause of childhood diarrhea. Curr Opin…

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KEGG T00139: BP3287

Entry BP3287            CDS       T00139                                  Symbol atpG Name (GenBank) ATP synthase gamma chain   KO K02115   F-type H+-transporting ATPase subunit gamma Organism bpe  Bordetella pertussis Tohama I Pathway bpe00190   Oxidative phosphorylation bpe01100   Metabolic pathways Module bpe_M00157   F-type ATPase, prokaryotes and chloroplasts Brite KEGG Orthology (KO) [BR:bpe00001] 09100 Metabolism  09102 Energy metabolism   00190 Oxidative phosphorylation    BP3287 (atpG) 09180 Brite Hierarchies  09181 Protein…

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KEGG T01028: 706234

Entry 706234            CDS       T01028                                  Symbol TRAP1 Name (RefSeq) heat shock protein 75 kDa, mitochondrial   KO K09488   TNF receptor-associated protein 1 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc05012   Parkinson disease mcc05022   Pathways of neurodegeneration – multiple diseases Brite KEGG Orthology (KO) [BR:mcc00001] 09160 Human Diseases  09164 Neurodegenerative disease   05012 Parkinson disease    706234 (TRAP1)   05022 Pathways of neurodegeneration –…

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KEGG T03271: 103675060

Entry 103675060         CDS       T03271                                  Symbol APPL1 Name (RefSeq) DCC-interacting protein 13-alpha   KO K08733   DCC-interacting protein 13 alpha Organism umr  Ursus maritimus (polar bear) Pathway umr04211   Longevity regulating pathway umr05200   Pathways in cancer umr05210   Colorectal cancer Brite KEGG Orthology (KO) [BR:umr00001] 09150 Organismal Systems  09149 Aging   04211 Longevity regulating pathway    103675060 (APPL1) 09160 Human Diseases  09161 Cancer: overview   05200 Pathways in…

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Inhibition of providencia vermicola FabD

Introduction Microbial resistance has become a problem in the contemporary medical environment due to the inadequate development of new antibiotics and the asinine prescription of antibiotics in both developed and developing nations. Antimicrobial resistance (AMR), which affects wealthy and developing nations, is a global concern.1 AMR is a problem for…

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Loss of SETD2 aggravates colorectal cancer progression caused by SMAD4 deletion through the RAS/ERK signalling pathway

Backgound: Colorectal cancer (CRC) is a complex, multistep disease that arises from the interplay genetic mutations and epigenetic alterations. The histone H3K36 trimethyltransferase SET domain-containing 2 (SETD2), as an epigenetic signalling molecule, has a 5% mutation rate in CRC. SETD2 expression is decreased in the development of human CRC and…

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transformers 4.35.1 – Download, Browsing & More

transformers 4.35.1 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of transformers-4.35.1.tar.gz (14 Nov 15:37, 15700182 Bytes) About: Transformers supports Machine Learning for Pytorch, TensorFlow, and JAX by providing thousands of pretrained models to perform tasks on different modalities such as…

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Potential Y-H? – LAMMPS General Discussion

Xtof November 14, 2023, 8:00am 1 Dear all, Would anyone know where to find the potential for Y-H? I found some potential for Y-Y in an article from 2013 but so far nothing about Y-H. Many thanks in advance and best regards,Christophe It’s good practice to reference the articles you…

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KEGG T01001: 257194

Entry 257194            CDS       T01001                                  Symbol NEGR1, DMML2433, IGLON4, KILON, Ntra Name (RefSeq) neuronal growth regulator 1   KO K06775   neuronal growth regulator 1 Organism hsa  Homo sapiens (human) Pathway hsa04514   Cell adhesion molecules Brite KEGG Orthology (KO) [BR:hsa00001] 09130 Environmental Information Processing  09133 Signaling molecules and interaction   04514 Cell adhesion molecules    257194 (NEGR1) 09180 Brite Hierarchies  09183 Protein families: signaling…

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Forecasting the dynamics of a complex microbial community using integrated meta-omics

Characterization of the microbial community From the experimental period between 21 March 2011 and 3 May 2012 (ref. 27), we previously obtained and analysed 51 weekly samples, to which we added 21 samples collected in the month of June during the years 2012–2016. The 72 samples were submitted to the…

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KEGG T08541: 104528229

Entry 104528229         CDS       T08541                                  Symbol SLC15A4 Name (RefSeq) solute carrier family 15 member 4   KO K14638   solute carrier family 15 (peptide/histidine transporter), member 3/4 Organism acar  Antrostomus carolinensis (chuck-will’s-widow) Brite KEGG Orthology (KO) [BR:acar00001] 09180 Brite Hierarchies  09183 Protein families: signaling and cellular processes   02000 Transporters [BR:acar02000]    104528229 (SLC15A4)Transporters [BR:acar02000] Solute carrier family (SLC)  SLC15: Proton oligopeptide cotransporter   104528229 (SLC15A4)…

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KEGG T01011: 100038077

Entry 100038077         CDS       T01011                                  Symbol nkx2-2 Name (RefSeq) homeobox protein Nkx-2.2 isoform X1   KO K08029   homeobox protein Nkx-2.2 Organism xtr  Xenopus tropicalis (tropical clawed frog) Brite KEGG Orthology (KO) [BR:xtr00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03000 Transcription factors [BR:xtr03000]    100038077 (nkx2-2)Transcription factors [BR:xtr03000] Eukaryotic type  Helix-turn-helix   Homeo domain ANTP: NKL    100038077 (nkx2-2) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT…

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KEGG T09424: 118385109

Entry 118385109         CDS       T09424                                  Name (RefSeq) adenylosuccinate synthetase isozyme 2-like   KO K01939   adenylosuccinate synthase [EC:6.3.4.4] Organism oke  Oncorhynchus keta (chum salmon) Pathway oke00230   Purine metabolism oke00250   Alanine, aspartate and glutamate metabolism oke01100   Metabolic pathways oke01232   Nucleotide metabolism oke01240   Biosynthesis of cofactors Module oke_M00049   Adenine ribonucleotide biosynthesis, IMP => ADP,ATP Brite KEGG Orthology (KO)…

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KEGG T08782: 127423656

Entry 127423656         CDS       T08782                                  Name (RefSeq) heparan sulfate glucosamine 3-O-sulfotransferase 3B1-like   KO K07809   [heparan sulfate]-glucosamine 3-sulfotransferase 3 [EC:2.8.2.30] Organism masi  Myxocyprinus asiaticus (Chinese sucker) Pathway masi00534   Glycosaminoglycan biosynthesis – heparan sulfate / heparin Brite KEGG Orthology (KO) [BR:masi00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00534 Glycosaminoglycan biosynthesis – heparan sulfate / heparin    127423656 09180 Brite Hierarchies  09181 Protein…

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The mystery of the ‘black box’ at the MacBook event. What is that object?

The mystery of the ‘black box’ at the MacBook event. What is that object? On October 30th, during the latter part of Apple’s new MacBook Pro unveiling event, a black machine box connected to the MacBook was briefly captured on camera. The presenter at the event was discussing the speed…

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A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

40,039 MAGs reconstructed from large-scale genome-resolved metagenomics To reconstruct previously unexplored bacterial and archaeal genomes, we performed a large-scale single-sample metagenomic assembly on 3304 soil metagenomes across the globe (Fig. 1a), including 363 metagenomes from the in-house dataset and 2941 from publicly available metagenomes. The soil samples were mainly collected from…

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RNAseq from P4 murine whole kidneys with Polycystic Kidney Disease

Snap frozen Postnatal day4 murine kidney tissues were crushed using micropestles in RLT Buffer and RNA was extracted from these tissues using QiaShredders followed by Qiagen RNAeasy Mini Kits according to manufacturer’s protocol. RNA concentration and integrity were determined by Aligent bioanalyzer. cDNA library preparation was carried out using NEB…

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KEGG T00186: ECA0055

Entry ECA0055           CDS       T00186                                  Symbol prlC Name (GenBank) oligopeptidase A   KO K01414   oligopeptidase A [EC:3.4.24.70] Organism eca  Pectobacterium atrosepticum SCRI1043 Brite KEGG Orthology (KO) [BR:eca00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:eca01002]    ECA0055 (prlC)Enzymes [BR:eca01000] 3. Hydrolases  3.4  Acting on peptide bonds (peptidases)   3.4.24  Metalloendopeptidases    3.4.24.70  oligopeptidase A     ECA0055 (prlC)Peptidases and inhibitors [BR:eca01002] Metallo peptidases  Family M3   ECA0055 (prlC) BRITE hierarchy SSDB OrthologParalogGene…

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KEGG T00644: APJL_0327

Entry APJL_0327         CDS       T00644                                  Symbol rumA Name (GenBank) 23S rRNA (Uracil-5-)-methyltransferase   KO K03215   23S rRNA (uracil1939-C5)-methyltransferase [EC:2.1.1.190] Organism apj  Actinobacillus pleuropneumoniae JL03 (serotype 3) Brite KEGG Orthology (KO) [BR:apj00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03009 Ribosome biogenesis [BR:apj03009]    APJL_0327 (rumA)Enzymes [BR:apj01000] 2. Transferases  2.1  Transferring one-carbon groups   2.1.1  Methyltransferases    2.1.1.190  23S rRNA (uracil1939-C5)-methyltransferase     APJL_0327 (rumA)Ribosome biogenesis [BR:apj03009] Prokaryotic type  rRNA modification factors   23S rRNA…

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KEGG T00186: ECA2422

Entry ECA2422           CDS       T00186                                  Symbol thrS Name (GenBank) threonyl-tRNA synthetase   KO K01868   threonyl-tRNA synthetase [EC:6.1.1.3] Organism eca  Pectobacterium atrosepticum SCRI1043 Pathway eca00970   Aminoacyl-tRNA biosynthesis Brite KEGG Orthology (KO) [BR:eca00001] 09120 Genetic Information Processing  09122 Translation   00970 Aminoacyl-tRNA biosynthesis    ECA2422 (thrS) 09180 Brite Hierarchies  09181 Protein families: metabolism   01007 Amino acid related enzymes [BR:eca01007]    ECA2422 (thrS)  09182 Protein families: genetic information processing   03016 Transfer…

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Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens

Developing an epigenetic screening platform in human T cells Staphylococcus aureus Cas9 (SaCas9) has been extensively used for genome editing in vivo as its compact size (3,159 bp) relative to the conventional Streptococcus pyogenes Cas9 (SpCas9) enables packaging into adeno-associated virus26,27,28. However, SaCas9 has not been widely used for targeted gene…

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KEGG T01028: 701915

Entry 701915            CDS       T01028                                  Symbol KRT25 Name (RefSeq) keratin, type I cytoskeletal 25   KO K07604   type I keratin, acidic Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04915   Estrogen signaling pathway mcc05150   Staphylococcus aureus infection Brite KEGG Orthology (KO) [BR:mcc00001] 09150 Organismal Systems  09152 Endocrine system   04915 Estrogen signaling pathway    701915 (KRT25) 09160 Human Diseases  09171 Infectious disease: bacterial   05150 Staphylococcus…

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KEGG T05390: C3V38_02785

Entry C3V38_14330       CDS       T05390                                  Name (GenBank) GTP pyrophosphokinase   KO K01139   GTP diphosphokinase / guanosine-3′,5′-bis(diphosphate) 3′-diphosphatase [EC:2.7.6.5 3.1.7.2] Organism dit  Dietzia sp. oral taxon 368 Pathway dit00230   Purine metabolism dit01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:dit00001] 09100 Metabolism  09104 Nucleotide metabolism   00230 Purine metabolism    C3V38_14330 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03009 Ribosome biogenesis [BR:dit03009]    C3V38_14330Enzymes [BR:dit01000] 2. Transferases  2.7  Transferring…

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KEGG T01028: 698365

Entry 698365            CDS       T01028                                  Symbol AMACR Name (RefSeq) alpha-methylacyl-CoA racemase   KO K01796   alpha-methylacyl-CoA racemase [EC:5.1.99.4] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00120   Primary bile acid biosynthesis mcc01100   Metabolic pathways mcc04146   Peroxisome Module mcc_M00104   Bile acid biosynthesis, cholesterol => cholate/chenodeoxycholate Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09103 Lipid metabolism   00120 Primary bile acid biosynthesis    698365 (AMACR) 09140…

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KEGG T01028: 703937

Entry 703937            CDS       T01028                                  Symbol PTPRG Name (RefSeq) receptor-type tyrosine-protein phosphatase gamma isoform X2   KO K16667   receptor-type tyrosine-protein phosphatase gamma [EC:3.1.3.48] Organism mcc  Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01009 Protein phosphatases and associated proteins [BR:mcc01009]    703937 (PTPRG)Enzymes [BR:mcc01000] 3. Hydrolases  3.1  Acting on ester bonds   3.1.3  Phosphoric-monoester hydrolases    3.1.3.48  protein-tyrosine-phosphatase     703937 (PTPRG)Protein phosphatases and…

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FAT10 is phosphorylated by IKK{beta} to inhibit the antiviral type-I interferon response

Introduction The innate immune system represents the host´s first-line defense against viral infections (Koyama et al, 2008). In this context, IFN-I are produced by all nucleated cells and represent the principal cytokines that counteract viral replication (Ivashkiv & Donlin, 2014). In fact, several receptors of the infected cell can recognize…

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KEGG T07278: 119316072

Entry 119322531         CDS       T07278                                  Name (RefSeq) porphobilinogen deaminase, chloroplastic-like   KO K01749   hydroxymethylbilane synthase [EC:2.5.1.61] Organism tdc  Triticum dicoccoides (wild emmer wheat) Pathway tdc00860   Porphyrin metabolism tdc01100   Metabolic pathways tdc01110   Biosynthesis of secondary metabolites tdc01240   Biosynthesis of cofactors Module tdc_M00121   Heme biosynthesis, plants and bacteria, glutamate => heme Brite KEGG Orthology (KO) [BR:tdc00001] 09100 Metabolism  09108…

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KEGG T01028: 704242

Entry 704242            CDS       T01028                                  Symbol CYP39A1 Name (RefSeq) 24-hydroxycholesterol 7-alpha-hydroxylase   KO K07439   24-hydroxycholesterol 7alpha-hydroxylase [EC:1.14.14.26] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00120   Primary bile acid biosynthesis Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09103 Lipid metabolism   00120 Primary bile acid biosynthesis    704242 (CYP39A1) 09180 Brite Hierarchies  09181 Protein families: metabolism   00199 Cytochrome P450 [BR:mcc00199]    704242 (CYP39A1)Enzymes [BR:mcc01000] 1. Oxidoreductases  1.14  Acting on paired…

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KEGG T01028: 694719

Entry 694719            CDS       T01028                                  Symbol RPL23 Name (RefSeq) 60S ribosomal protein L23   KO K02894   large subunit ribosomal protein L23e Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc03010   Ribosome mcc05171   Coronavirus disease – COVID-19 Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing  09122 Translation   03010 Ribosome    694719 (RPL23) 09160 Human Diseases  09172 Infectious disease: viral   05171 Coronavirus disease – COVID-19    694719…

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KEGG T08540: 104459063

Entry 104463828         CDS       T08540                                  Symbol ACOX3 Name (RefSeq) peroxisomal acyl-coenzyme A oxidase 3   KO K00232   acyl-CoA oxidase [EC:1.3.3.6] Organism pguu  Pterocles gutturalis (yellow-throated sandgrouse) Pathway pguu00071   Fatty acid degradation pguu00410   beta-Alanine metabolism pguu00592   alpha-Linolenic acid metabolism pguu00640   Propanoate metabolism pguu01040   Biosynthesis of unsaturated fatty acids pguu01100   Metabolic pathways pguu01200   Carbon metabolism pguu01212   Fatty…

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An FcRn-targeted mucosal vaccine against SARS-CoV-2 infection and transmission

Mice and Golden Syrian hamsters All research experiments in this study comply with all relevant ethical regulations. The Institutional Animal Care and Use Committee approved the animal protocol at the University of Maryland (#R-APR-20-18 and #R-MAR-21-19). The animals were acclimatized at the animal facility for 4–6 days before initiating experiments….

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KEGG T01028: 704366

Entry 704366            CDS       T01028                                  Symbol ZDHHC15 Name (RefSeq) palmitoyltransferase ZDHHC15   KO K20028   palmitoyltransferase ZDHHC2/15/20 [EC:2.3.1.225] Organism mcc  Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:mcc04131]    704366 (ZDHHC15)Enzymes [BR:mcc01000] 2. Transferases  2.3  Acyltransferases   2.3.1  Transferring groups other than aminoacyl groups    2.3.1.225  protein S-acyltransferase     704366 (ZDHHC15)Membrane trafficking [BR:mcc04131] SNARE  SNARE associated proteins   Palmitoyltransferases    704366 (ZDHHC15) BRITE hierarchy…

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KEGG T05489: A6B45_00495

Entry A6B45_05465       CDS       T05489                                  Name (GenBank) diacetyl reductase   KO K03366   meso-butanediol dehydrogenase / (S,S)-butanediol dehydrogenase / diacetyl reductase [EC:1.1.1.- 1.1.1.76 1.1.1.304] Organism lsu  Leuconostoc suionicum Pathway lsu00650   Butanoate metabolism lsu01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:lsu00001] 09100 Metabolism  09101 Carbohydrate metabolism   00650 Butanoate metabolism    A6B45_05465Enzymes [BR:lsu01000] 1. Oxidoreductases  1.1  Acting on the CH-OH group of donors   1.1.1  With NAD+…

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KEGG T01028: 695442

Entry 695442            CDS       T01028                                  Symbol RPLP1 Name (RefSeq) 60S acidic ribosomal protein P1   KO K02942   large subunit ribosomal protein LP1 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc03010   Ribosome mcc05171   Coronavirus disease – COVID-19 Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing  09122 Translation   03010 Ribosome    695442 (RPLP1) 09160 Human Diseases  09172 Infectious disease: viral   05171 Coronavirus disease –…

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KEGG T01028: 717682

Entry 717682            CDS       T01028                                  Symbol SEPTIN2 Name (RefSeq) septin-2 isoform X1   KO K16942   septin 2 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc05100   Bacterial invasion of epithelial cells Brite KEGG Orthology (KO) [BR:mcc00001] 09160 Human Diseases  09171 Infectious disease: bacterial   05100 Bacterial invasion of epithelial cells    717682 (SEPTIN2) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking…

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Molecular diagnosis, phylogenetic analysis, and antifungal susceptibility profiles of Candida species isolated from neutropenic oncological patients | BMC Infectious Diseases

Eissa S, Khedr R, Romeih M, Halaby L, Elanany M, Madney Y. Clinical characteristics and outcome of invasive fungal sinusitis in children with hematological malignancies. Med Mycol. 2022;60(4):myac010. Article  PubMed  Google Scholar  Lin G-L, Chang H-H, Lu C-Y, Chen C-M, Lu M-Y, Lee P-I, Jou S-T, Yang Y-L, Huang L-M,…

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systemtap: autopkgtest regression: Pass 4: compilation failed. [man error::pass4]

Source: systemtap Version: 4.9-1 Severity: serious User: debi…@lists.debian.org Usertags: regression Dear maintainer(s), Your package has an autopkgtest, great. However, it fails since a couple of months. Can you please investigate the situation and fix it? I copied some of the output at the bottom of this report. The release team…

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KEGG T01028: 699325

Entry 699325            CDS       T01028                                  Symbol OSBP Name (RefSeq) oxysterol-binding protein 1   KO K20456   oxysterol-binding protein 1 Organism mcc  Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:mcc04131]    699325 (OSBP)Membrane trafficking [BR:mcc04131] Endoplasmic reticulum (ER) – Golgi transport  Others   Oxysterol-binding proteins    699325 (OSBP) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif…

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KEGG T04128: 106346836

Entry 111199314         CDS       T04128                                  Name (RefSeq) GDP-L-fucose synthase 1 isoform X2   KO K02377   GDP-L-fucose synthase [EC:1.1.1.271] Organism bna  Brassica napus (rape) Pathway bna00051   Fructose and mannose metabolism bna00520   Amino sugar and nucleotide sugar metabolism bna01100   Metabolic pathways bna01250   Biosynthesis of nucleotide sugars Brite KEGG Orthology (KO) [BR:bna00001] 09100 Metabolism  09101 Carbohydrate metabolism   00051 Fructose and mannose…

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