Tag: mol
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…
Recombinant Feline EGF Protein, HEK293 Cells, hFc Tag, 62010-U01H
EGF Protein, Feline, Recombinant (ECD, hFc Tag): 产品信息 纯度 > 90 % as determined by SDS-PAGE. 生物活性 Testing in progress 蛋白构建 A DNA sequence encoding the Feline EGF (NP_001009381.1) (Asn969-Arg1020) was expressed with the fused Fc region of human IgG1 at the N-terminus. 表达宿主 HEK293 Cells 分子量 The…
Tempo and drivers of plant diversification in the European mountain system
Hughes, C. E. & Atchinson, G. W. The ubiquity of alpine plant radiations: from the Andes to the Hengduan Mountains. N. Phytol. 207, 275–282 (2015). Article Google Scholar Rahbek, C. et al. Humboldt’s enigma: what causes global patterns of mountain biodiversity? Science 365, 1108–1113 (2019). ADS CAS PubMed Article Google…
KEGG COMPOUND: C05924
KEGG COMPOUND: C05924 COMPOUND: C05924 Help Entry C05924 Compound Name Molybdopterin;Pyranopterin;H2Dtpp-mP Formula C10H14N5O6PS2 Exact mass 395.0123 Mol weight 395.3518 Structure Mol fileKCF fileDB search Reaction Pathway Module M00880 Molybdenum cofactor biosynthesis, GTP => molybdenum cofactor Enzyme Other DBs KCF data Show ATOM 24 1 S1a S 22.7500 -13.4003 2 S1a S 25.1308 -14.8087 3 C2y C 22.7383 -14.7666 4 C2y C 23.9353 -15.4866 5 C1y C 21.5555 -15.4809 6 C1y C 23.9236 -16.8776 7 C1y C 21.5496 -16.8718 8 N1x N 20.3269 -14.7608 9 C1b…
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…
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…
Detection of candidate gene LsACOS5 and development of InDel marker for male sterility by ddRAD-seq and resequencing analysis in lettuce
Ryder, E. J. Lettuce, Endive and Chicory (CABI Publishing, 1999). Google Scholar Seki, K. et al. A CIN-like TCP transcription factor (LsTCP4) having retrotransposon insertion associates with a shift from Salinas type to Empire type in crisphead lettuce (Lactuca sativa L.). Hortic. Res. 7, 1–14 (2020). Article Google Scholar Odland,…
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…
Optimized Protocol for Plasma-Derived Extracellular Vesicles Loading with Synthetic miRNA Mimic Using Electroporation
doi: 10.1007/978-1-0716-2341-1_16. Affiliations Expand Affiliations 1 Department of Medical Sciences, University of Turin, Turin, Italy. margheritaalbacarlotta.pomatto@unito.it. 2 Department of Medical Sciences, University of Turin, Turin, Italy. Item in Clipboard Margherita A C Pomatto et al. Methods Mol Biol. 2022. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1007/978-1-0716-2341-1_16. Affiliations 1…
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 …
Emerging Evidence of Pathological Roles of Very-Low-Density Lipoprotein (VLDL)
This article was originally published here Int J Mol Sci. 2022 Apr 13;23(8):4300. doi: 10.3390/ijms23084300. ABSTRACT Embraced with apolipoproteins (Apo) B and Apo E, triglyceride-enriched very-low-density lipoprotein (VLDL) is secreted by the liver into circulation, mainly during post-meal hours. Here, we present a brief review of the physiological role of…
7-Deaza-7-propargylamino-ddGTP, 7-Deazapurinas – Cellco
Structural formula of 7-Deaza-7-propargylamino-ddGTP For research use only! Envio: shipped on blue ice Condições de armazenamento: store at -20 °CShort term exposure (up to 1 week cumulative) to ambient temperature possible. Validade: 12 months after date of delivery Fórmula molecular: C14H20N5O12P3 (free acid) Peso molecular: 543.26 g/mol (free acid) Pureza:…
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…
KEGG COMPOUND: C05345
KEGG COMPOUND: C05345 COMPOUND: C05345 Help Entry C05345 Compound Name beta-D-Fructose 6-phosphate;beta-D-Fructofuranose 6-phosphate Formula C6H13O9P Exact mass 260.0297 Mol weight 260.1358 Structure Mol fileKCF fileDB search Reaction Pathway map00010 Glycolysis / Gluconeogenesis map00051 Fructose and mannose metabolism map00520 Amino sugar and nucleotide sugar metabolism map00541 O-Antigen nucleotide sugar biosynthesis map00997 …
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…
Antiplatelet response to clopidogrel is associated with a haplotype in CYP2C19 gene in Pakistani patients
Amsterdam, E. A. et al. 2014 AHA/ACC guideline for the management of patients with non-ST-elevation acute coronary syndromes: Executive summary: A report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines. Circulation 130, 2354–2394 (2014). Google Scholar Kernan, W. N. et al. Guidelines for the prevention…
A hypoxia-related signature in lung squamous cell carcinoma
Introduction Lung cancer is the major leading cause of tumour-related deaths throughout the world, while lung squamous cell carcinoma (LUSC) as the second most common histological type of lung cancer.1 Each year, almost 1.8 million people are diagnosed with lung cancer worldwide and 400,000 of these die from LUSC.2,3 Due to…
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,…
Parkinson’s disease motor symptoms rescue by CRISPRa-reprogramming astrocytes into GABAergic neurons
doi: 10.15252/emmm.202114797. Online ahead of print. Jessica Giehrl-Schwab # 1 2 , Florian Giesert # 1 2 , Benedict Rauser 1 2 , Chu Lan Lao 3 4 , Sina Hembach 1 2 , Sandrine Lefort 5 , Ignacio L Ibarra 6 , Christina Koupourtidou 3 7 , Malte Daniel Luecken 6 , Dong-Jiunn Jeffery…
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….
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…
Human distal lung maps and lineage hierarchies reveal a bipotent progenitor
Verleden, S. E. et al. Small airways pathology in idiopathic pulmonary fibrosis: a retrospective cohort study. Lancet Respir. Med. 8, 573–584 (2020). CAS PubMed PubMed Central Google Scholar Hogg, J. C., Macklem, P. T. & Thurlbeck, W. M. The resistance of small airways in normal and diseased human lungs. Aspen…
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…
ncRNA | Free Full-Text | Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions
Non-Coding RNA 2022, 8(2), 23; doi.org/10.3390/ncrna8020023 (registering DOI) Non-Coding RNA 2022, 8(2), 23; doi.org/10.3390/ncrna8020023 (registering DOI) Received: 1 March 2022 / Revised: 21 March 2022 / Accepted: 25 March 2022 / Published: 28 March 2022 Round 1 Reviewer 1 Report In recent years, a great process has been made in the research…
Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates | BMC Biology
Stölting KN, Wilson AB. Male pregnancy in seahorses and pipefish: beyond the mammalian model. Bioessays. 2007;29:884–96. PubMed Google Scholar Whittington CM, Friesen CR. The evolution and physiology of male pregnancy in syngnathid fishes. Biol Rev Camb Philos Soc. 2020;95:1252–72. PubMed Google Scholar Rosenqvist G, Berglund A. Sexual signals and mating…
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…
KEGG COMPOUND: C01380
Entry C01380 Compound Name Ethylene glycol;1,2-Ethanediol;Ethane-1,2-diol Formula C2H6O2 Exact mass 62.0368 Mol weight 62.0678 Structure Mol fileKCF fileDB search Reaction Pathway map00625 Chloroalkane and chloroalkene degradation map00630 Glyoxylate and dicarboxylate metabolism map01120 Microbial metabolism in diverse environments Enzyme Other DBs KCF data Show ATOM 4 1 C1b C 28.1392 -16.3327 2 C1b C 29.5408 -16.3327 3 O1a O 27.4444 -17.5473 4 O1a O 30.2356 -17.5473BOND 3 1 1 2 1 2 1 3 1 3 2 4 1…
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,…
AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice
Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019). CAS PubMed PubMed Central Google Scholar Li, C. & Samulski, R. J. Engineering adeno-associated virus vectors for gene therapy. Nat. Rev. Genet. 21, 255–272…
South-to-north migration preceded the advent of intensive farming in the Maya region
Moreno-Mayar, J. V. et al. Early human dispersals within the Americas. Science 362, eaav2621 (2018). ADS PubMed Google Scholar Posth, C. et al. Reconstructing the deep population history of Central and South America. Cell 175, 1185–1197.e22 (2018). CAS PubMed PubMed Central Google Scholar Raghavan, M. et al. Genomic evidence for…
Escherichia coli K-12 substr. MG1655 purA
BioCyc ID:TU00094 Synonyms: OP00133 Local Context (not to scale — see Genome Browser for correct scale) Transcription Unit Notes: Click on a binding site (if any) to navigate to the page for its transcription factor. Click on a gene to navigate to its gene page. Key to regulator colors: Green:…
KEGG COMPOUND: C02538
KEGG COMPOUND: C02538 COMPOUND: C02538 Help Entry C02538 Compound Name Formula C18H22O5S Exact mass 350.1188 Mol weight 350.4293 Structure Mol fileKCF fileDB search Reaction Pathway map00140 Steroid hormone biosynthesis Enzyme Brite Compounds with biological roles [BR:br08001] Hormones and transmitters Steroid hormones Estrogens C02538 Estrone 3-sulfateLipids [BR:br08002] ST Sterol lipids ST02 Steroids ST0201 C18 steroids (estrogens) and derivatives C02538 Estrone 3-sulfate ST05 Steroid…
IJMS | Free Full-Text | Systematic Discovery of FBXW7-Binding Phosphodegrons Highlights Mitogen-Activated Protein Kinases as Important Regulators of Intracellular Protein Levels
Int. J. Mol. Sci. 2022, 23(6), 3320; doi.org/10.3390/ijms23063320 (registering DOI) Int. J. Mol. Sci. 2022, 23(6), 3320; doi.org/10.3390/ijms23063320 (registering DOI) Received: 23 February 2022 / Revised: 16 March 2022 / Accepted: 17 March 2022 / Published: 19 March 2022 Round 1 Reviewer 1 Report This manuscript by Singh and co-workers defines a…
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,…
Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages
Díaz, S. et al. Summary for Policymakers of the Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES, 2019). Fisher, R. A. The correlation between relatives on the supposition of Mendelian inheritance. Earth Environ. Sci. Trans. R. Soc. Edinb. 52,…
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…
A genome-scale screen for synthetic drivers of T cell proliferation
Abramson, J. S. et al. Transcend NHL 001: immunotherapy with the CD19-directed CAR T-cell product JCAR017 results in high complete response rates in relapsed or refractory B-cell non-Hodgkin lymphoma. Blood 128, 4192–4192 (2016). Google Scholar Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators…
A single-cell atlas of human and mouse white adipose tissue
Rosen, E. D. & Spiegelman, B. M. What we talk about when we talk about fat. Cell 156, 20–44 (2014). CAS PubMed PubMed Central Google Scholar Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006)….
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…
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…
Type I Interferon Response Is Mediated by NLRX1-cGAS-STING Signaling in Brain Injury
doi: 10.3389/fnmol.2022.852243. eCollection 2022. Lauren E Fritsch 1 , Jing Ju 2 , Erwin Kristobal Gudenschwager Basso 3 , Eman Soliman 3 , Swagatika Paul 4 , Jiang Chen 2 , Alexandra M Kaloss 3 , Elizabeth A Kowalski 3 , Taylor C Tuhy 5 , Rachana Deven Somaiya 1 , Xia Wang 3 , Irving Coy Allen 3 , Michelle H…
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…
TargetScanHuman 7.1
TargetScanHuman 7.1 * broadly conserved = conserved across most vertebrates, usually to zebrafish conserved = conserved across most mammals, but usually not beyond placental mammals TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer, 7mer, and 6mer sites that match the seed region of each…
Prediction of histone post-translational modification patterns based on nascent transcription data
Allfrey, V. G., Faulkner, R. & Mirsky, A. E. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl Acad. Sci. USA 51, 786–794 (1964). CAS PubMed PubMed Central Google Scholar Ho, J. W. K. et al. Comparative analysis of metazoan chromatin organization….
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…
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…
Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution
de Visser, J. A. G. M. & Krug, J. Empirical fitness landscapes and the predictability of evolution. Nat. Rev. Genet. 15, 480–490 (2014). PubMed PubMed Central Google Scholar Lässig, M., Mustonen, V. & Walczak, A. M. Predicting evolution. Nat. Ecol. Evol. 1, 77 (2017). PubMed PubMed Central Google Scholar Mas,…
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…
HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps
doi: 10.1186/s13059-022-02626-w. Affiliations Expand Affiliations 1 Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA. 2 Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA. fsun@usc.edu. Item in Clipboard Yuxuan Du et al. Genome Biol. 2022. Show details Display options Display options Format…
KEGG COMPOUND: C01113
KEGG COMPOUND: C01113 COMPOUND: C01113 Help Entry C01113 Compound Name D-Galactose 6-phosphate;6-Phospho-D-galactose Formula C6H13O9P Exact mass 260.0297 Mol weight 260.1358 Structure Mol fileKCF fileDB search Reaction Pathway map02060 Phosphotransferase system (PTS) Enzyme Other DBs KCF data Show ATOM 16 1 P1b P 25.9015 -16.0011 2 O2b O 27.3009 -16.0070 3 O1c O 25.8898 -17.4005 4 O1c O 24.5021 -16.0011 5 O1c O 25.8898 -14.6076 6 C1b C 28.3679 -15.0973 7 C1y C 29.5748 -15.8029 8 C1y C 29.5748 -17.2021 9 O2x O 30.7818 -15.0973 10 C1y C 30.7818 -17.9018 11 O1a O 28.3679 -17.9018 12 C1y C 32.0005 -15.8029 13 C1y…
Escherichia coli K-12 substr. MG1655 EC 7.2.2.8
BioCyc ID: RXN-14455 EC Number: 7.2.2.8 Transporters and Genes: Cu+ exporting P-type ATPase: copA Supersedes EC number: 3.6.3.54 Reaction Locations: inner membrane The reaction direction shown is in accordance with the direction in which it was curated. Most BioCyc compounds have been protonated to a reference pH value of 7.3….
KEGG COMPOUND: C00469
KEGG COMPOUND: C00469 COMPOUND: C00469 Help Entry C00469 Compound Name Ethanol;Ethyl alcohol;Methylcarbinol Formula C2H6O Exact mass 46.0419 Mol weight 46.0684 Structure Mol fileKCF fileDB search Remark Reaction Pathway map00010 Glycolysis / Gluconeogenesis map01110 Biosynthesis of secondary metabolites map01120 Microbial metabolism in diverse environments map04750 Inflammatory mediator regulation of TRP channels…
KEGG COMPOUND: C00565
Entry C00565 Compound Name Trimethylamine;(CH3)3N;N,N-Dimethylmethanamine Formula C3H9N Exact mass 59.0735 Mol weight 59.1103 Structure Mol fileKCF fileDB search Reaction Pathway map01120 Microbial metabolism in diverse environments Module M00563 Methanogenesis, methylamine/dimethylamine/trimethylamine => methane Enzyme Other DBs KCF data Show ATOM 4 1 N1c N 22.1200 -15.8200 2 C1a C 23.3299 -15.1185 3 C1a C 20.9101 -15.1185 4 C1a C 22.1200 -17.2929BOND 3 1 1 2 1 2 1 3 1 3 1 4 1 Read more here: Source link
KEGG COMPOUND: C00247
KEGG COMPOUND: C00247 COMPOUND: C00247 Help Entry C00247 Compound Name L-Sorbose;L-xylo-Hexulose Formula C6H12O6 Exact mass 180.0634 Mol weight 180.1559 Structure Mol fileKCF fileDB search Comment Reaction Pathway map00051 Fructose and mannose metabolism Enzyme Brite Compounds with biological roles [BR:br08001] Carbohydrates Monosaccharides Ketoses C00247 L-Sorbose BRITE hierarchy Other DBs KCF data Show ATOM 12 1 C1z C 26.2968 -14.4371 2 C1y C 26.2968 -15.8376 3 O2x O 25.0888 -13.7368 4 C1b…
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)….
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…
KEGG COMPOUND: C21620
KEGG COMPOUND: C21620 COMPOUND: C21620 Help Entry C21620 Compound Name S-[(E)-N-Hydroxy(indol-3-yl)acetimidoyl]-L-glutathione Formula C20H25N5O7S Exact mass 479.1475 Mol weight 479.5068 Structure Mol fileKCF fileDB search Reaction Enzyme Other DBs KCF data Show ATOM 33 1 C8y C 17.0403 -15.7134 2 C8y C 18.3672 -15.9928 3 C8y C 16.3420 -16.9006 4 C8x C 16.3420 -14.4564 5 C8x C 18.4371 -17.3895 6 N4x N 17.1800 -17.9482 7 C8x C 14.8754 -16.9006 8 C8x C 14.9452 -14.4564 9 C8x C 14.1770 -15.7134 10 O1b O 19.6829 -18.0281 11 N2b N 20.8589 -17.2684 12 C2c C 20.7891 -15.8717 13 C1b C 19.5432 -15.2331 14 C1b C 23.2109 -15.7506 15 S2a S 21.9650 -15.1120 16 C1c C 24.3869 -14.9909 17 N1b N 24.3170 -13.5927 18 C5a C 25.6328 -15.6295 19 O5a…
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 …
The epigenetic dimension of protein structure
References [1] Tunyasuvunakool K, Adler J, Wu Z, Green T, Zielinski M, Žídek A, et al. Highly accurate protein structure prediction for the human proteome. Nature. 2021;596:590–6.10.1038/s41586-021-03828-1Search in Google Scholar [2] Hardy J, Allsop D. Amyloid deposition as the central event in the aetiology of Alzheimer’s disease. Trends Pharmacol Sci….
LJ parameters – User discussions
GROMACS version: 2021.3GROMACS modification: NoHere post your question I have a very basic question on parameterization of non-bonded parameters (LJ) of atoms. The target system is a cluster/aggregate of metal atoms. From experimental data, I can get the atomic radius and vdw radius of the atoms. However, looking at the…
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…
What is the molarity of a solution made from 325.4g of AlCl 3 with enough water to make 500.0 mL? (MM of AlCl3 = 133.34 g/mol)
Home What is the molarity of a solution made from 325.4g of AlCl 3 with enough water to make 500.0 mL? (MM of AlCl3 = 133.34 g/mol) What is the molarity of a solution made from 325.4g of AlCl3 with enough water to make 500.0 mL? (MM of AlCl3 =…
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…
Investigating binding dynamics of trans resveratrol to HSA for an efficient displacement of aflatoxin B1 using spectroscopy and molecular simulation
Spectroscopic studies The binding and interactive mode of flavonoid trans-resveratrol with HSA was investigated before its use as a dislodging agent for HSA bound AFB1. The binding behavior was studied using spectroscopic tools like fluorescence spectroscopy and UV–visible spectroscopy. UV-absorption spectroscopy was used to ascertain the structural changes induced by…
molecular dynamics – How to generate a .tpr file from a .pdb or .xyz file in gromacs
For generating a tpr file, you need a topology file (.top), a coordinate file (.gro/.pdb) and a input parameter file (.mdp). Assuming, you are working with amber forcefield (a99ffSBdisp), Here’s how I do it. gmx pdb2gmx -ff a99SBdisp -f yourpdbfile.pdb -o water_1.gro -ignh -p topol.top gmx grompp -f water.mdp -c…
Glutamine synthetase licenses APC/C-mediated mitotic progression to drive cell growth
Altman, B. J., Stine, Z. E. & Dang, C. V. From Krebs to clinic: glutamine metabolism to cancer therapy. Nat. Rev. Cancer 16, 619–634 (2016). CAS Article Google Scholar Hensley, C. T., Wasti, A. T. & DeBerardinis, R. J. Glutamine and cancer: cell biology, physiology, and clinical opportunities. J. Clin….
RefSeq: XP_007190711
LOCUS XP_007190711 296 aa linear MAM 12-FEB-2019 DEFINITION reticulon-4-interacting protein 1, mitochondrial isoform X3 [Balaenoptera acutorostrata scammoni]. ACCESSION XP_007190711 VERSION XP_007190711.1 DBLINK BioProject: PRJNA237330 DBSOURCE REFSEQ: accession XM_007190649.2 KEYWORDS RefSeq. SOURCE Balaenoptera acutorostrata scammoni ORGANISM Balaenoptera acutorostrata scammoni Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Whippomorpha; Cetacea;…
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.,…
KEGG COMPOUND: C06070
KEGG COMPOUND: C06070 COMPOUND: C06070 Help Entry C06070 Compound Name Iridotrial;(1S,2R,3S)-2-Formyl-alpha-(hydroxymethylene)-3-methylcyclopentaneacetaldehyde Formula C10H14O3 Exact mass 182.0943 Mol weight 182.2164 Structure Mol fileKCF fileDB search Reaction Pathway map01110 Biosynthesis of secondary metabolites Enzyme Brite Lipids [BR:br08002] PR Prenol lipids PR01 Isoprenoids PR0102 C10 isoprenoids (monoterpenes) PR010207 Iridoid, 10-alkyliridoid and secoiridoid monoterpenoids C06070 IridotrialPhytochemical compounds [BR:br08003] Terpenoids Monoterpenoids (C10) Iridoids C06070 Iridotrial BRITE hierarchy…
UniProtKB/SwissProt variant VAR_081680
Sequence information Variant position: 126 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length: 230 The length of the canonical sequence. Location on the sequence: GLYQCQSLHGSEADTLRKVL V EVLADPLDHRDAGDLWFPGE The residue change on the sequence. Unless the variant is located at the beginning or at the end of…
[Solved] ) What is the theoretical yield (in moles) of aluminum chloride (AlCl 3 -133.34 g/mol) if 0.385 mol of aluminum are reacted with 0.800 mol o…
1.) What is the theoretical yield (in moles) of aluminum chloride… – 133.34 g/mol) if 0.385 mol of aluminum are reacted with 0.800 mol of chlorine. (g) —> 2AlCl(s) 2.) A sample of impure potassium chloride weighing 0.4260 grams is dissolved in water and treated with an excess of silver…
Postdoctoral Fellow job with EMBL
We are offering a 2-year postdoc position in the group of Dr. Marco Marcia (www.embl.org/groups/marcia/) at the European Molecular Biology Laboratory (EMBL), one of the highest-ranked scientific research organisations worldwide. The group is based in Grenoble, France. We are carrying out an exciting pioneering project that will decipher the molecular…
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…
First Report of Jacobsen Syndrome with Dextrocardia Diagnosed with del(11)(q24q25) – Abstract – Molecular Syndromology
Log in to MyKarger to check if you already have access to this content. Buy FullText & PDF Unlimited re-access via MyKarger Unrestricted printing, no saving restrictions for personal use read more CHF 38.00 * EUR 35.00 * USD 39.00 * …
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…
[gmx-users] sudden jumps in RMSD etc.
Hi all, I am doing duplicate MD simulations with a protein-ligand system. After processing one trajectory by trjconv with the optioin -pbc nojump, Istill find abrupt jumps (on the scale of nm) in RMSDs and COM distances. Then I tried -pbc mol -ur compact, which did not work. And then…
UniProtKB/SwissProt variant VAR_082098
Sequence information Variant position: 729 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length: 1053 The length of the canonical sequence. Location on the sequence: CELCVKSFVTKRSLQEHMSI H TGESKYLCSVCGKSFHRGSG The residue change on the sequence. Unless the variant is located at the beginning or at the end of…
SETDB1/NSD-dependent H3K9me3/H3K36me3 dual heterochromatin maintains gene expression profiles by bookmarking poised enhancers
. 2022 Jan 17;S1097-2765(21)01142-4. doi: 10.1016/j.molcel.2021.12.037. Online ahead of print. Affiliations Expand Affiliations 1 DNA Repeat Lab, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, 34000 Montpellier, France. 2 Chromatin and Cell Biology Lab, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141…
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….
Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits
1. Jansen, I. E. et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat. Genet. 51, 404–413 (2019). CAS PubMed PubMed Central Google Scholar 2. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed…
Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics
1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed Google Scholar 2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed PubMed Central Google Scholar 3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….
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….
CRISPR-Cas12a ribonucleoprotein-mediated gene editing in the plant pathogenic fungus Magnaporthe oryzae
. 2021 Dec 24;3(1):101072. doi: 10.1016/j.xpro.2021.101072. eCollection 2022 Mar 18. Affiliations Expand Affiliation 1 Department of Plant Pathology, Kansas State University, Manhattan, KS, USA. Free PMC article Item in Clipboard Jun Huang et al. STAR Protoc. 2021. Free PMC article Show details Display options Display options Format AbstractPubMedPMID . 2021 Dec…
ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes | BMC Bioinformatics
1. Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, et al. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016;17:66. Article Google Scholar 2. Minio A, Lin J, Gaut BS, Cantu D. How single…
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…
Decoding gene regulation in the fly brain
1. Li, H. et al. Classifying Drosophila olfactory projection neuron subtypes by single-cell RNA sequencing. Cell 171, 1206–1220 (2017). CAS PubMed PubMed Central Google Scholar 2. Davie, K. et al. A single-cell transcriptome atlas of the aging Drosophila brain. Cell 174, 982–998 (2018). CAS PubMed PubMed Central Google Scholar 3….
Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr
Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…
computational chemistry – Troubleshooting an Autodock Vina Error on Chimera: “Could not find an atomic number for Hn Hn”
After having minimized a ligand (that I prepared on Marvinsketch), and after having prepared a target enzyme to dock said ligand onto (collected from RCSP PDB), I was met with an error by the reply log stating that it “could not find atomic number for Hn Hn”. As a new…
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 …