Tag: mol

As cancer treatments have evolved, scientists have worked to improve 2 things: making the responses to therapy last longer, and limiting how much collateral damage the therapy does as it attacks the tumor. The arrival of immunotherapy has been monumental: across many types of cancers, response rates to immunotherapy are…

Bradley, B. A. et al. Cheatgrass (Bromus tectorum) distribution in the intermountain western United States and its relationship to fire frequency, seasonality, and ignitions. Biol. Invasions 20, 1493–1506 (2018). Article  Google Scholar  Balch, J. K., Bradley, B. A., D’Antonio, C. M. & Gomez-Dans, J. Introduced annual grass increases regional fire…

1 Introduction Modern plant breeding programs are collecting an increasing amount of data of various types from several sources such as multiple secondary phenotypic traits (other than the main trait of interest), high-throughput phenotyping data, weather data, hyper-spectral images, and different types of -omics data such as genomics, transcriptomics, proteomics,…

KEGG COMPOUND: C02059     COMPOUND: C02059 Help Entry C02059                      Compound                                Name Phylloquinone;Vitamin K1;Phytonadione;2-Methyl-3-phytyl-1,4-naphthoquinone Formula C31H46O2 Exact mass 450.3498 Mol weight 450.6957 Structure Mol fileKCF fileDB search Remark Reaction Pathway map00130   Ubiquinone and other terpenoid-quinone biosynthesis map01110   Biosynthesis of secondary metabolites map04977   Vitamin digestion and absorption Enzyme Brite Compounds with biological roles…

Srinivasan, S. et al. Enrichment of genetic markers of recent human evolution in educational and cognitive traits. Sci. Rep. 8, 12585 (2018). Ohi, K. et al. Genetic overlap between general cognitive function and schizophrenia: A review of cognitive GWASs. Int. J. Mol. Sci. 19, 3822 (2018). Savage, J. E. et…

KEGG COMPOUND: C11947     COMPOUND: C11947 Help Entry C11947                      Compound                                Name 3-Hydroxy-2,6-dimethyl-5-methylene-heptanoyl-CoA Formula C31H52N7O18P3S Exact mass 935.2302 Mol weight 935.767 Structure Mol fileKCF fileDB search Reaction Pathway map00907   Pinene, camphor and geraniol degradation Enzyme Brite Lipids [BR:br08002] FA  Fatty acyls  FA07 Fatty esters   FA0705 Fatty acyl CoAs    C11947  3-Hydroxy-2,6-dimethyl-5-methylene-heptanoyl-CoA BRITE hierarchy Other DBs KCF data Show ATOM        60            1   S2a…

Ross, J., Jiang, H., Kanost, M. R. & Wang, Y. Serine proteases and their homologs in the Drosophila melanogaster genome: An initial analysis of sequence conservation and phylogenetic relationships. Gene 304, 117–131 (2003). Article  CAS  PubMed  Google Scholar  Rawlings, N. D. & Barrett, A. J. Evolutionary families of peptidases. Biochem….

Davids D, Blouws T, Aboyade O, Gibson D, De Jong JT, Van’t Klooster C, Hughes G. Traditional health practitioners’ perceptions, herbal treatment and management of HIV and related opportunistic infections. J Ethnobiol Ethnomed. 2014;10:77. Article  PubMed  PubMed Central  Google Scholar  van Wyk BE, Albrecht C. A review of the taxonomy,…

Dev March 28, 2023, 6:07pm 1 I ran an example input file “in.tiny_polystyrene.stabilized’ located in a directory examples/PACKAGES/reaction/tiny_polystyrene shipped with Lammps version 8Feb2023The log file shows that the system has reacted with reaction values for f_rxn[1], f_rxn[2] and f_rxn[3]. When visualizing the trajectory, I was hoping to see some polyester…

MacDonald JR, Ziman R, Yuen RK, Feuk L, Scherer SW. The database of genomic variants: a curated collection of structural variation in the human genome. Nucleic Acids Res. 2014;42(Database issue):D986–992. Article  CAS  PubMed  Google Scholar  Zarrei M, MacDonald JR, Merico D, Scherer SW. A copy number variation map of the…

World Health Organization (2020) Lack of new antibiotics threatens global efforts to contain drug-resistant infections. World Health Organization, New release Geneva Google Scholar  Kmietowicz Z (2017) Few novel antibiotics in the pipeline, WHO warns. BMJ: British Medical Journal (Online) 358:1. doi.org/10.1136/bmj.j4339 Article  Google Scholar  Falagas ME, Lourida P, Poulikakos P,…

Naik RR, Singamaneni S. Introduction: bioinspired and biomimetic materials. Chem Rev. 2017;117(20):12581–3. Article  CAS  PubMed  Google Scholar  Huang G, Li F, Zhao X, Ma Y, Li Y, Lin M, et al. Functional and biomimetic materials for engineering of the three-dimensional cell microenvironment. Chem Rev. 2017;117(20):12764–850. Article  CAS  PubMed  PubMed Central …

Andrés, F. & Coupland, G. The genetic basis of flowering responses to seasonal cues. Nat. Rev. Genet. 13, 627–639 (2012). Article  PubMed  Google Scholar  Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S. & Shimamoto, K. Hd3a and RFT1 are essential for flowering in rice. Development 135, 767–774 (2008). Article  CAS …

Review . 2023 Mar 23;S1525-0016(23)00145-4. doi: 10.1016/j.ymthe.2023.03.024. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biomedicine, Aarhus University, 8000 Aarhus C., Denmark. 2 Department of Biomedicine, Aarhus University, 8000 Aarhus C., Denmark. Electronic address: bak@biomed.au.dk. Item in Clipboard Review Louise Bendixen et al. Mol Ther. 2023. Show details Display…

Falkowski, P. G., Barber, R. T. & Smetacek, V. Biogeochemical controls and feedbacks on ocean primary production. Science (1979) 281, 200–206 (1998). CAS  Google Scholar  Nemergut, D. R. et al. Patterns and processes of microbial community assembly. Microbiol. Mol. Biol. Rev. 77, 342–356 (2013). Article  PubMed  PubMed Central  Google Scholar …

KEGG COMPOUND: C00916     COMPOUND: C00916 Help Entry C00916                      Compound                                Name Formula C16H21N3O8S Exact mass 415.1049 Mol weight 415.4182 Structure Mol fileKCF fileDB search Reaction Pathway map00311   Penicillin and cephalosporin biosynthesis map01110   Biosynthesis of secondary metabolites map07012   Cephalosporins – parenteral agents map07013   Cephalosporins – oral agents Enzyme Brite Compounds with biological…

KEGG COMPOUND: C00696     COMPOUND: C00696 Help Entry C00696                      Compound                                Name Prostaglandin D2;(5Z,13E)-(15S)-9alpha,15-Dihydroxy-11-oxoprosta-5,13-dienoate;(5Z,13E,15S)-9alpha,15-Dihydroxy-11-oxoprosta-5,13-dienoate;PGD2 Formula C20H32O5 Exact mass 352.225 Mol weight 352.4651 Structure Mol fileKCF fileDB search Reaction Pathway map04080   Neuroactive ligand-receptor interaction map04664   Fc epsilon RI signaling pathway Enzyme Brite Compounds with biological roles [BR:br08001] Lipids  Eicosanoids   Prostaglandins    C00696  Prostaglandin D2Lipids [BR:br08002] FA  Fatty acyls  FA03 Eicosanoids   FA0301 Prostaglandins    C00696  Prostaglandin D2…

Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol. 2018;3:754–66. Article  CAS  PubMed  Google Scholar  Suttle CA. Marine viruses—major players in the global ecosystem. Nat Rev Microbiol. 2007;5:801–12. Article  CAS  PubMed  Google Scholar  Breitbart M. Marine viruses: truth or dare. Ann…

Arranz AM, De Strooper B. The role of astroglia in Alzheimer’s disease: pathophysiology and clinical implications. Lancet Neurol. 2019;18(4):406–14. Article  CAS  PubMed  Google Scholar  Liao MC, Muratore CR, Gierahn TM, Sullivan SE, Srikanth P, De Jager PL, et al. Single-cell detection of secreted Aβ and sAPPα from human IPSC-derived neurons…

Böhm S, Fabian H, Welfle H (1982) Universal structural features of prokaryotic and eukaryotic ribosomal 5 S RNA derived from comparative analysis of their sequences. Acta Biol Med Ger 41:1–16 PubMed  Google Scholar  Dams E, Vandenberghe A, De Wachter R (1983) Sequences of the 5 S RNAs ofAzotobacter vinelandii, Pseudomonas…

Harden, V. A. Rocky mountain spotted fever: History of a twentieth-century disease Vol. 16 (Johns Hopkins University Press, 1990). Google Scholar  Maxey, E. E. M., G T; Leary, J W. (1899) Some observations on the so-called spotted fever of Idaho. Med Sentinel, 7: 433–438. Dantas-Torres, F. Rocky mountain spotted fever….

Review doi: 10.1038/s12276-023-00965-7. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul, 06591, South Korea. jhk@catholic.ac.kr. 2 Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul, 06591, South Korea. 3 Laboratory of Obesity and Aging Research,…

Fagagna, F. et al. A DNA damage checkpoint response in telomere-initiated senescence. Nature 426, 194–198 (2003). Article  Google Scholar  Takai, H., Smogorzewska, A. & de Lange, T. DNA damage foci at dysfunctional telomeres. Curr. Biol. 13, 1549–1556 (2003). Article  CAS  PubMed  Google Scholar  Olovnikov, A. M. A theory of marginotomy:…

Please cite Turkarslan et al., 2017 Mol. Sys. Biol. if you find Syntrophy Portal useful. Acknowledgement: “This material by ENIGMA- Ecosystems and Networks Integrated with Genes and Molecular Assemblies (enigma.lbl.gov), a Scientific Focus Area Program at Lawrence Berkeley National Laboratory is based upon work supported by the U.S. Department of…

Therapeutic antibodies are among the best-selling drug classes in the pharmaceutical market. The introduction of antibody engineering and recombinant production significantly enhanced the collection of therapeutics against acute and chronic diseases. Introduction The engineering and production of antibodies are vital in drug discovery, offering effective and precise therapeutics and diagnostic/prognostic…

GROMACS version: 2019.3GROMACS modification: No Dear all, I know that there are lots of topics about high RMSD value, sudden jumps or fluctuations. I’ve been scrolling through the topics and trying to apply several trjconv commands into my system but could not even get a smooth RMSD value and I…

Yin, H. et al. Non-viral vectors for gene-based therapy. Nat. Rev. Genet. 15, 541–555 (2014). Article  CAS  Google Scholar  Wu, S. Y., Lopez-Berestein, G., Calin, G. A. & Sood, A. K. RNAi therapies: drugging the undruggable. Sci. Transl. Med. 6, 240ps7 (2014). Article  Google Scholar  Mendes, B. B. et al….

Van Doorslaer K, Chen Z, Bernard HU, Chan PKS, DeSalle R, Dillner J, Forslund O, Haga T, McBride AA, Villa LL, et al. ICTV Virus Taxonomy Profile: Papillomaviridae. J Gen Virol. 2018;99:989–90. Article  CAS  PubMed  PubMed Central  Google Scholar  McBride AA. Oncogenic human papillomaviruses. Philos Trans R Soc Lond B…

KEGG COMPOUND: C17594     COMPOUND: C17594 Help Entry C17594                      Compound                                Name Formula C21H24N2O4 Exact mass 368.1736 Mol weight 368.4263 Structure Mol fileKCF fileDB search Other DBs KCF data Show ATOM        27            1   C1y C    28.7700  -22.2600            2   C2y C    28.7700  -23.6600            3   C2x C    29.9600  -24.3600            4   O2x O    31.2200  -23.6600            5   C1y C    31.2200  -22.2600            6   C1y C    29.9600  -21.5600            7   C1x C    29.9600  -20.1600            8   N1y N    28.7700  -19.4600            9   C1y C    27.5800  -20.1600            10  C1x C    27.5800  -21.5600            11  C1x C    28.4900  -18.1300            12  C1x C    27.0900  -17.9900            13  C1z C    26.5300  -19.2500            14  C8y C    24.2900  -19.3200            15  N1x N    24.7800  -20.6500            16  C5x C    26.1800  -20.6500            17  C8y C    25.4100  -18.4800            18  C8x C    25.2000  -17.0800            19  C8x C    23.9400  -16.5900            20  C8x C    22.8200  -17.4300            21  C8x C    22.9600  -18.8300            22  C7a…

KEGG COMPOUND: C21717     COMPOUND: C21717 Help Entry C21717                      Compound                                Name Formula C30H48 Exact mass 408.3756 Mol weight 408.7021 Structure Mol fileKCF fileDB search Reaction Enzyme Other DBs KCF data Show ATOM        30            1   C2a C     4.3134  -16.5545            2   C2b C    30.4935  -17.1778            3   C2c C    31.7402  -16.4852            4   C1b C    29.2468  -16.4852            5   C1a C    31.7402  -15.1693            6   C2b C    25.5068  -17.1778            7   C2c C    26.7535  -16.4852            8   C1b C    24.2601  -16.4852            9   C1b C    28.0002  -17.1778            10  C1a C    26.7535  -15.1693            11  C2b C    20.4509  -17.1778            12  C2c C    21.7668  -16.4852            13  C1b C    19.2735  -16.4852            14  C1b C    23.0135  -17.1778            15  C1a C    21.7668  -15.1693            16  C2b C    15.4642  -17.1778            17  C2c C    16.7108  -16.4852            18  C1b C    14.2175  -16.4852            19  C1b C    17.9575  -17.1778            20  C1a…

Brown JS O’Carrigan B Jackson SP Yap TA Targeting DNA Repair in Cancer: Beyond PARP Inhibitors. Cancer Discov. 2017; 7: 20-37 Farmer H McCabe N Lord CJ Tutt AN Johnson DA Richardson TB Santarosa M Dillon KJ Hickson I Knights C Martin NM Jackson SP Smith GC Ashworth A Targeting…

Sanger, F., Nicklen, S., and Coulson, A. R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74, 5463–5467. Article  PubMed  CAS  Google Scholar  Drmanac, R., Dramanac, S., Strezoska, Z., et al. (1993) DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing. Science 260, 1649–1652. Article …

doi: 10.1007/s00438-023-01995-6. Online ahead of print. Affiliations Expand Affiliations 1 Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology (NIOT), Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, 600100, India. 2 Department of Biotechnology, School of Chemical and Biotechnology, SASTRA University, Tanjore,…

Introduction Cyanide-containing compounds are known as nitriles and are widely distributed in the natural environment. They are generated by different plants in various forms, such as ricinine, phenyl acetonitrile, cyanogenic glycosides, and β -cyanoalanine (Sewell et al., 2003). Anthropogenic activities have substantially influenced the production of vast quantities of nitrile…

Stephenson, W. et al. Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation. Nat. Commun. 9(1), 791 (2018). Article  ADS  PubMed  PubMed Central  Google Scholar  Schmidt, C. J. et al. Infection with Clostridioides difficile attenuated collagen-induced arthritis in mice and involved mesenteric Treg and Th2 polarization. Front. Immunol….

KEGG COMPOUND: C11898     COMPOUND: C11898 Help Entry C11898                      Compound                                Name Taxa-4(20),11(12)-dien-5alpha-acetoxy-10beta-ol;10beta-Hydroxytaxa-4(20),11-dien-5alpha-yl acetate;5alpha-Acetoxytaxa-4(20),11(12)-dien-10beta-ol Formula C22H34O3 Exact mass 346.2508 Mol weight 346.5036 Structure Mol fileKCF fileDB search Reaction Pathway map01110   Biosynthesis of secondary metabolites Enzyme Brite Lipids [BR:br08002] PR  Prenol lipids  PR01 Isoprenoids   PR0104 C20 isoprenoids (diterpenes)    PR010439 Taxane and Abeotaxane diterpenoids     C11898  Taxa-4(20),11(12)-dien-5alpha-acetoxy-10beta-ol BRITE hierarchy Other DBs KCF…

KEGG COMPOUND: C21832     COMPOUND: C21832 Help Entry C21832                      Compound                                Name (4S)- 2,3-Dehydroflavan-3,4-diol Formula C15H12O3 Exact mass 240.0786 Mol weight 240.254 Structure Mol fileKCF fileDB search Comment Generic compound in reaction hierarchy Reaction Enzyme KCF data Show ATOM        18            1   C8x C    14.4253  -15.8258            2   C8x C    14.4253  -17.2264            3   C8x C    15.6858  -17.9266            4   C8y C    16.8763  -17.2264            5   C8y C    16.8763  -15.8258            6   C8x C    15.6858  -15.1256            7   C1y C    18.0667  -17.9266            8   C2y C    19.3271  -17.2264            9   C2y C    19.3271  -15.8258            10  O2x O    18.0667  -15.1256            11  O1a O    18.0667  -19.3271            12  C8y C    20.5176  -15.1256            13  C8x C    21.7080  -15.8258            14  C8x…

doi: 10.1096/fj.202201891R. Affiliations Expand Affiliations 1 Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, South Korea. 2 Department of Biomedical Laboratory Science, College of Healthcare Medical Science and Engineering, Inje University, Gimhae, South Korea. Item in Clipboard Yea Woon Kim et al. FASEB J. 2023 Apr. Show…

GROMACS version:GROMACS modification: Yes/NoHere post your question Hi!I am currently facing a problem with erasing jumps from my system.I have tried several different combinations of the trjconv command which worked for other systems I have made, but not for my current system.I first tried only -pbc mol which worked fine…

Ahn S, Tanksley SD (1993) Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90:7980–7984 CAS  PubMed  Google Scholar  Ahuja MR, Devey ME, Groover AT, Jermstad KD, Neale DB (1994) Mapped DNA probes from loblolly pine can be used for restriction fragment length polymorphism in…

KEGG COMPOUND: C21131     COMPOUND: C21131 Help Entry C21131                      Compound                                Name Protodeoxyviolaceinic acid;Protodeoxyviolaceinate Formula C21H15N3O2 Exact mass 341.1164 Mol weight 341.3627 Structure Mol fileKCF fileDB search Reaction Pathway map01110   Biosynthesis of secondary metabolites Module M00808   Violacein biosynthesis, tryptophan => violacein Enzyme Other DBs KCF data Show ATOM        26            1   C8x C     8.7500  -18.2700            2   C8x C     8.7500  -19.6700            3   C8x C     9.9624  -20.3700            4   C8y C    11.1749  -19.6700            5   C8y…

Entry C06790                      Compound                                Name Trichloroethene;Trichloroethylene;TCE Formula C2HCl3 Exact mass 129.9144 Mol weight 131.3883 Structure Mol fileKCF fileDB search Remark Reaction Pathway map00625   Chloroalkane and chloroalkene degradation map00980   Metabolism of xenobiotics by cytochrome P450 map01120   Microbial metabolism in diverse environments map05207   Chemical carcinogenesis – receptor activation Enzyme Brite Anatomical Therapeutic Chemical (ATC)…

. 2023 Mar 16;18(3):e0282689. doi: 10.1371/journal.pone.0282689. eCollection 2023. Affiliations Expand Affiliations 1 Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia. 2 Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia. 3 Armand Hammer United World College of the American West, Montezuma, New Mexico, United Stated of…

Antin JH, Childs R, Filipovich A et al. (2001) Establishment of complete and mixed donor chimerism after allogenic lymphohematopoietic transplantation: recommendations for a workshop at the 2001 tandem meetings. BB&MM 7: 473–485. CAS  Google Scholar  Baldini A, Rocchi M, Archidiacono N, Miller OJ, Miller DA (1990) A human alpha satellite…

Guglielmone AA, Robbins RG, Apanaskevich DA, Petney TN, Estrada-Peña A, Horak IG. The hard ticks of the world. Dordrecht: Springer; 2014. p. 738. Book  Google Scholar  Estrada-Peña A, Pfäffle M, Baneth G, Kleinerman G, Petney TN. Ixodoidea of the western palaearctic: a review of available literature for identification of species….

Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014). Article  PubMed  PubMed Central  Google Scholar  Weyrich, L. S. et al. Laboratory contamination over time during low-biomass sample analysis. Mol. Ecol. Resour. 19, 982–996 (2019). Article  CAS  PubMed  PubMed Central …

KEGG COMPOUND: C13480     COMPOUND: C13480 Help Entry C13480                      Compound                                Name Formula C19H30N5O10P Exact mass 519.173 Mol weight 519.4428 Structure Mol fileKCF fileDB search Other DBs KCF data Show ATOM        35            1   C8y C    36.6859  -25.0034            2   C8y C    36.6859  -23.5438            3   N4y N    35.3654  -25.4206            4   N5x N    37.9370  -25.6290            5   N5x N    35.3654  -23.1268            6   C8y C    37.9370  -22.9182            7   C8x C    34.5312  -24.3083            8   C8x C    39.1187  -25.0034            9   N5x N    39.1187  -23.5438            10  N1a N    37.9370  -21.5280            11  C1b C    35.3654  -26.8138            12  C1c C    34.1647  -27.5069            13  O2a O    32.9516  -26.8063            14  C1b C    31.7298  -27.5121            15  P1b P    30.5115  -26.8097            16  O2b O    29.3047  -26.1131            17  O2b O    29.8184  -28.0101            18  O3b O    31.2109  -25.5978            19  C1b C    29.3047  -24.7149            20  C1b C    29.8184  -29.4083            21  O7a O    28.0932  -23.9875            22  C7a…

Andersen LO, Stensvold CR. Blastocystis in health and disease: are we moving from a clinical to a public health perspective? J Clin Microbiol. 2016;54:524–8. Article  CAS  PubMed  PubMed Central  Google Scholar  Hublin JSY, Maloney JG, Santin M. Blastocystis in domesticated and wild mammals and birds. Res Vet Sci. 2021;135:260–82. Article …

KEGG COMPOUND: C14800     COMPOUND: C14800 Help Entry C14800                      Compound                                Name 1-Nitronaphthalene-5,6-oxide Formula C10H7NO3 Exact mass 189.0426 Mol weight 189.1675 Structure Mol fileKCF fileDB search Reaction Pathway map00980   Metabolism of xenobiotics by cytochrome P450 Enzyme Other DBs KCF data Show ATOM        14            1   C2x C    22.8217  -19.9509            2   C1y C    22.8217  -21.3509            3   C1y C    24.0341  -22.0509            4   C8y C    25.2467  -21.3509            5   C8y C    25.2467  -19.9509            6   C2x C    24.0341  -19.2509            7   C8x C    26.4591  -22.0509            8   C8x C    27.6716  -21.3509            9   C8x C    27.6716  -19.9509            10  C8y C    26.4591  -19.2509            11  N2b…

Introduction Coronary heart disease (CHD) is the most common heart condition worldwide and the leading cause of death of elderly men and women (1). Despite recent declines in developed countries, both CHD morbidity and mortality continue to increase rapidly in developing countries. Various factors are involved in CHD pathogenesis, including…

Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007). Article  CAS  PubMed  PubMed Central  Google Scholar  Glöckner, J. et al. Phylogenetic diversity and metagenomics of candidate division OP3. Environ. Microbiol. 12, 1218–1229…

Other gene therapy strategies under preclinical investigation are mtDNA heteroplasmy shifting and mitochondrial base editing. (Adobe Stock image) By Benson S. Chen, MBChB, MSc, FRACP; Joshua P. Harvey, MA, BM BCh,Pg Cert, FRCOphth; and Patrick Yu-Wai-Man, PhD, BMedSci, MBBS,FRCPath, FRCOphth Inherited optic neuropathies (IONs) are disorders that result in degeneration…

Entry C06735                      Compound                                Name Aminoacetaldehyde;2-Aminoacetaldehyde Formula C2H5NO Exact mass 59.0371 Mol weight 59.0672 Structure Mol fileKCF fileDB search Reaction Pathway map00430   Taurine and hypotaurine metabolism Enzyme Other DBs KCF data Show ATOM        4            1   C1b C    27.3585  -20.5715            2   C4a C    28.6180  -19.8718            3   N1a N    26.1691  -19.8718            4   O4a O    29.8312  -20.5992BOND        3            1     1   2 1            2     1   3 1            3     2   4 2 Read more here: Source link

KEGG COMPOUND: C00369     COMPOUND: C00369 Help Entry C00369                      Compound                                Name Formula (C12H20O10)n Structure Mol fileKCF fileDB search Remark Reaction Pathway map00500   Starch and sucrose metabolism map00710   Carbon fixation in photosynthetic organisms map01110   Biosynthesis of secondary metabolites map04973   Carbohydrate digestion and absorption Module M00565   Trehalose biosynthesis, D-glucose 1P => trehalose M00854  …

Goldberg JL, Klassen MP, Hua Y, Barres BA. Amacrine-signaled loss of intrinsic axon growth ability by retinal ganglion cells. Science. 2002;296:1860–4. Article  CAS  PubMed  Google Scholar  Blackmore M, Letourneau PC. Changes within maturing neurons limit axonal regeneration in the developing spinal cord. J Neurobiol. 2006;66:348–60. Article  CAS  PubMed  Google Scholar …

. 2023 Mar 14;21(3):e3002023. doi: 10.1371/journal.pbio.3002023. eCollection 2023 Mar. Affiliations Expand Affiliations 1 Department of Biological Sciences, National University of Singapore, Singapore, Singapore. 2 Department of Haematology, University of Cambridge, Cambridge, United Kingdom. Free article Item in Clipboard Li Jianwei et al. PLoS Biol. 2023. Free article Show details Display options…

KEGG COMPOUND: C16967     COMPOUND: C16967 Help Entry C16967                      Compound                                Name Formula C30H48O Exact mass 424.3705 Mol weight 424.7015 Structure Mol fileKCF fileDB search Other DBs KCF data Show ATOM        31            1   C1x C    22.6102  -20.0902            2   C5x C    22.6102  -21.4902            3   C1z C    23.8226  -22.1902            4   C2y C    25.0351  -21.4902            5   C1y C    25.0351  -20.0902            6   C1x C    23.8226  -19.3902            7   C2x C    26.2475  -22.1902            8   C1x C    27.4599  -21.4902            9   C1y C    27.4599  -20.0902            10  C1z C    26.2475  -19.3902            11  C1z C    28.6724  -19.3902            12  C1z C    28.6724  -17.9902            13  C1x C    27.4599  -17.2902            14  C1x C    26.2475  -17.9902            15  C1x C    29.8848  -20.0902            16  C1x C    31.0972  -19.3902            17  C1z C    31.0972  -17.9902            18  C1y C    29.8848  -17.2902            19  C1x C    32.3097  -17.2902            20  C1x C    32.3097  -15.8902            21  C1z C    31.0972  -15.1902            22  C1x…

Kaper, J. B., Nataro, J. P. & Mobley, H. L. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2, 123–140 (2004). Article  CAS  PubMed  Google Scholar  Nataro, J. P. & Kaper, J. B. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11, 142–201 (1998). Article  CAS  PubMed  PubMed Central  Google Scholar  Croxen, M. A….

Bredesen DE, Rao RV, Mehlen P. Cell death in the nervous system. Nature. 2006;443:796–802. Article  CAS  PubMed  PubMed Central  Google Scholar  Fricker M, Tolkovsky AM, Borutaite V, Coleman M, Brown GC. Neuronal cell death. Physiol Rev. 2018;98:813–80. Article  CAS  PubMed  PubMed Central  Google Scholar  West MJ, Coleman PD, Flood DG,…

Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science. 2008;320:1647–51. Article  CAS  PubMed  PubMed Central  Google Scholar  Ochman H, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn BH, et al. Evolutionary relationships of wild hominids recapitulated…

Grabowski P, Zaug A, Cech T. The intervening sequence of the ribosomal RNA precursor is converted to a circular RNA in isolated nuclei of Tetrahymena. Cell. 1981;23(2):467–76. Article  CAS  PubMed  Google Scholar  Ye C, Chen L, Liu C, Zhu Q, Fan L. Widespread noncoding circular RNAs in plants. New Phytol….

AnzeH March 13, 2023, 1:09pm 1 Hi all, I know that the following has been discussed in the past but it still confuses me. I am modelling a zeolite with a force field that has harmonic springs for bonds and angles (e.g. a CHARMM type of a FF). Inevitably due…

Roughly 2 million Americans will be diagnosed with cancer in 2023, and approximately 610,000 will die from the disease.1 A majority of those deaths will be due to advanced cancer progression, where tumor cells have spread to distant parts of the body and formed additional lesions.1 However, venturing through the…

Bray, F. et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 68, 394–424 (2018). Article  PubMed  Google Scholar  Sung, H. et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers…

R.L. Siegel, K.D. Miller, H.E. Fuchs, A. Jemal, CA Cancer J. Clin 72 (2022). doi.org/10.3322/caac.21708 J.M. Llovet, F. Castet, M. Heikenwalder, M.K. Maini, V. Mazzaferro, D.J. Pinato, E. Pikarsky, A.X. Zhu, R.S. Finn, Nat. Rev. Clin. Oncol 19, 151–172 (2022). doi.org/10.1038/s41571-021-00573-2 Article  CAS  PubMed  Google Scholar  J.M. Llovet, T. De Baere, L. Kulik,…

KEGG COMPOUND: C03274     COMPOUND: C03274 Help Entry C03274                      Compound                                Name Formula C6H15O8P Exact mass 246.0505 Mol weight 246.1523 Structure Mol fileKCF fileDB search Other DBs KCF data Show ATOM        15            1   P1b P    17.7298  -15.4438            2   O2b O    19.1277  -15.4438            3   O2b O    17.7362  -14.0523            4   O1c O    16.3319  -15.4438            5   O1c O    17.7298  -16.8481            6   C1b C    20.3385  -16.1459            7   C1b C    17.7362  -12.6481            8   C1c C    20.3385  -17.6137            9   C1c C    16.5251  -11.9524            10  C1b C    19.1277  -18.3159            11  O1a O    21.5561  -18.3159            12  C1b C    16.5251  -10.5482            13  O1a O    15.3142  -12.6481            14  O1a O    19.1277  -19.7201            15  O1a O    17.7362   -9.8460BOND        14            1     1   2 1            2     1   3 1            3     1   4 1            4     1   5 2            5     2   6 1            6     3   7 1            7     6   8…

KEGG COMPOUND: C21543     COMPOUND: C21543 Help Entry C21543                      Compound                                Name Formula C24H26N6O3 Exact mass 446.2066 Mol weight 446.5016 Structure Mol fileKCF fileDB search Remark Brite Drug groups [BR:br08330] Cardiovascular agent  DG01925  Renin-angiotensin system inhibitor   DG01495  Angiotensin II receptor antagonist    DG01544  Olmesartan     D05246  Olmesartan  DG03231  Antihypertensive   DG01495  Angiotensin II receptor antagonist    DG01544  Olmesartan     D05246  Olmesartan Transporter substrate  DG01665  ABCB1 substrate   DG01544  Olmesartan    D05246  Olmesartan  DG02861  ABCC2 substrate   DG01544  Olmesartan    D05246  Olmesartan  DG01913  ABCG2 substrate   DG01544  Olmesartan    D05246  OlmesartanTarget-based classification of drugs [BR:br08310] G Protein-coupled receptors  Rhodopsin family   Angiotensin    AGTR1     D05246  Olmesartan (USAN/INN)Drug metabolizing…

doi: 10.15252/msb.202311587. Online ahead of print. Affiliations Expand Affiliations 1 Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany. 2 Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany. 3 Biozentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany. 4 Institute of Chemical Biology, National…

. 2023 Mar 6;24(3):e55536. doi: 10.15252/embr.202255536. Epub 2023 Jan 27. Niklas Kuhl #  1   2 , Andreas Linder #  1   2 , Nora Philipp  1   3 , Daniel Nixdorf  1   3 , Hannah Fischer  1 , Simon Veth  4 , Gunnar Kuut  1 , Teng Teng Xu  1   3 , Sebastian Theurich  1   3…

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Baek, M. et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 871–876 (2021). Article  ADS  CAS  PubMed  PubMed Central  Google…

By Benson S. Chen, MBChB, MSc, FRACP; Joshua P. Harvey, MA, BM BCh, Pg Cert, FRCOphth; and Patrick Yu-Wai-Man, PhD, BMedSci, MBBS, FRCPath, FRCOphth; Special to Ophthalmology Times® Inherited optic neuropathies (IONs) are a group of disorders that result in degeneration of the retinal ganglion cells (RGCs) and optic atrophy,1…

Azad A (1979) Intermolecular base-paired interaction between complementary sequences present near the 3′ ends of 5S rRNA and 18S (16S) rRNA might be involved in the reversible association of ribosomal subunits. Nucleic Acids Res 7:1913–1929 PubMed  Google Scholar  Blanken R, Klotz L, Hinnebusch A (1982) Computer comparison of new and…

Affiliations Expand Affiliations 1 University of Wisconsin-Madison, Madison, Wisconsin. 2 New England Biolabs, Ipswich, Massachusetts. Item in Clipboard Alexander T Duckworth et al. Curr Protoc. 2023 Mar. Show details Display options Display options Format AbstractPubMedPMID Affiliations 1 University of Wisconsin-Madison, Madison, Wisconsin. 2 New England Biolabs, Ipswich, Massachusetts. Item in Clipboard…

. 2023 Mar;11(3):e006648. doi: 10.1136/jitc-2022-006648. Affiliations Expand Affiliations 1 Department of Hepatic Surgery and Liver Transplantation Center, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China. 2 Department of Biotherapy Center, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China. 3 Department of Hepatic Surgery and Liver Transplantation…

Review doi: 10.1038/s41594-023-00933-9. Online ahead of print. Affiliations Expand Affiliations 1 Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA. pateld@mskcc.org. 2 Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA. 3 College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China. Item in Clipboard Review Dinshaw…

Introduction Chronic obstructive pulmonary disease (COPD) is a common chronic respiratory condition that mostly occurs in middle-aged and elderly people. COPD manifests as a progressive airflow limitation associated with an abnormal lung inflammatory response.1 As a disease with high incidence, disability rate, long disease course, and multiple comorbidities, COPD has…

Entry C00244                      Compound                                Name Formula HNO3 Exact mass 62.9956 Mol weight 63.0128 Structure Mol fileKCF fileDB search Remark Reaction Pathway map01120   Microbial metabolism in diverse environments Module M00529   Denitrification, nitrate => nitrogen M00530   Dissimilatory nitrate reduction, nitrate => ammonia M00531   Assimilatory nitrate reduction, nitrate => ammonia M00804   Complete nitrification, comammox, ammonia…

KEGG COMPOUND: C11512     COMPOUND: C11512 Help Entry C11512                      Compound                                Name Methyl jasmonate;(-)-Methyl jasmonate Formula C13H20O3 Exact mass 224.1412 Mol weight 224.2961 Structure Mol fileKCF fileDB search Reaction Pathway map00592   alpha-Linolenic acid metabolism map01110   Biosynthesis of secondary metabolites Enzyme Brite Lipids [BR:br08002] FA  Fatty acyls  FA02 Octadecanoids   FA0202 Jasmonic acids    C11512  (-)-Methyl jasmonate BRITE hierarchy Other DBs…

Introduction Osteoporosis is a frequently diagnosed disease of the bone featured by reduced bone tissue quality as well as a reduced mass of bone tissues. It was determined that > 20 million people suffer from various degrees of osteoporosis at any moment.1,2 Although various therapeutic approaches and agents, such as…

mjksho March 10, 2023, 3:58am 1 Hi All,I have a mixture system of water and an alcohol which I want to put between two walls to simulate a channel. The problem is I have the LAMMPS data file containing the mixture system but I need to create a wall of…

Doudna JA, Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346(6213):1258096. Article  PubMed  Google Scholar  Doudna JA. The promise and challenge of therapeutic genome editing. Nature. 2020;578(7794):229–36. Article  CAS  PubMed  PubMed Central  Google Scholar  Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing…

Bergwerk, M. et al. Covid-19 breakthrough infections in vaccinated health care workers. N. Engl. J. Med. 385, 1474–1484 (2021). Article  CAS  PubMed  Google Scholar  V’Kovski, P., Kratzel, A., Steiner, S., Stalder, H. & Thiel, V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat. Rev. Microbiol. 19, 155–170 (2021). Article  PubMed …

doi: 10.1038/s41586-023-05767-5. Online ahead of print. Lin Shan #  1 , Guang Xu #  1 , Run-Wen Yao  1   2 , Peng-Fei Luan  1 , Youkui Huang  1 , Pei-Hong Zhang  3 , Yu-Hang Pan  1 , Lin Zhang  4 , Xiang Gao  1   5 , Ying Li  6 , Shi-Meng Cao  1 , Shuai-Xin Gao  7 , Zheng-Hu Yang  1  …

doi: 10.1007/978-1-0716-3084-6_12. Affiliations Expand Affiliation 1 Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, South Korea. tyroh@postech.edu. Item in Clipboard Tae-Young Roh. Methods Mol Biol. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1007/978-1-0716-3084-6_12. Affiliation 1 Department of Life Sciences, Pohang University of Science…

Balietti M, Giuli C, Fattoretti P, Fabbietti P, Papa R, Postacchini D, Conti F. Effect of a Comprehensive Intervention on Plasma BDNF in Patients with Alzheimer’s Disease. Journal of Alzheimer’s disease : JAD. 2017;57(1):37–43. Bagyinszky E, Giau VV, Shim K, Suk K, An SSA, Kim S. Role of inflammatory molecules in…

Backgrounds Secondary to war wounds, surgery, trauma, etc., wound healing depends on the continuous proliferation of fibroblasts and collagen synthesis in the dermis.1,2 Skin scarring is considered as a natural outcome of the wound repair process. The incidence of scars after skin burns, trauma, and operations can be as high…

Mice Mice were of mixed genetic background C57BL/6 and 129/SvJ. Mice were bred and maintained under specific-pathogen-free conditions at the Breeding Unit (BRU) at the CRUK Cambridge Institute. Fh1fl/fl (ref. 4) and R26-Cre-ERT2 (ref. 5) mice were gifts from E. Gottlieb and D. Winton, respectively. Experimental mice were homozygous for…

KEGG COMPOUND: C00561     COMPOUND: C00561 Help Entry C00561                      Compound                                Name Mandelonitrile;Benzaldehyde cyanohydrin;(R)-Mandelonitrile Formula C8H7NO Exact mass 133.0528 Mol weight 133.1473 Structure Mol fileKCF fileDB search Reaction Pathway map01110   Biosynthesis of secondary metabolites Enzyme Other DBs KCF data Show ATOM        10            1   C8y C    18.0269  -16.1638            2   C1c C    18.0269  -14.7745            3   C8x C    16.8232  -16.8615            4   C8x C    19.2496  -16.8615            5   C3b C    19.2303  -14.0703            6   O1a O    16.8167  -14.0766            7   C8x C    16.8232  -18.2699            8   C8x C    19.2496  -18.2699            9   N3a N    20.4340  -13.3724            10  C8x C    18.0269  -18.9806BOND        10            1     1   2 1            2     1   3…

KEGG COMPOUND: C00526     COMPOUND: C00526 Help Entry C00526                      Compound                                Name Deoxyuridine;2-Deoxyuridine;2′-Deoxyuridine Formula C9H12N2O5 Exact mass 228.0746 Mol weight 228.202 Structure Mol fileKCF fileDB search Reaction Pathway Enzyme Brite Compounds with biological roles [BR:br08001] Nucleic acids  Nucleosides   Deoxyribonucleosides    C00526  Deoxyuridine (dU) BRITE hierarchy Other DBs KCF data Show ATOM        16            1   C1y C    25.8014  -16.2807            2   N4y N    27.1414  -15.8321            3   O2x O    24.7119  -15.4709            4   C1x C    25.3935  -17.6383            5   C8y C    28.1902  -16.7643            6   C8x C    27.4327  -14.4688            7   C1y C    23.5757  -16.3040            8   C1y…

Foucault C, Brouqui P, Raoult D. Bartonella quintana characteristics and clinical management. Emerg Infect Dis. 2006;12:217–23. Article  PubMed  PubMed Central  Google Scholar  Kostrzewski J. The epidemiology of trench fever. Bull Acad Pol Sci. 1949;7:233–63. CAS  Google Scholar  Maurin M, Raoult D. Bartonella (Rochalimaea) quintana infections. Clin Microbiol Rev. 1996;9:273–92. Article …

Amann, R. I., Ludwig, W., Schleifer, K. H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143–169. CrossRef  CAS  PubMed  PubMed Central  Google Scholar  Bench, S. R., Hanson, T. E., Williamson, K. E., Ghosh, D., Radosovich, M., Wang, K., Wommack, K. E. 2007….

Here is the database with 3,898 ncRNA that was compared to the set of lncRNA indentified by us. The database was built based on the papers below: Berretta J, Pinskaya M, Morillon A (2008) A cryptic unstable transcript mediates transcriptional trans -silencing of the Ty1 retrotransposon in S. cerevisiae. Genes…

GBD 2017 Disease and Injury Incidence and Prevalence Collaborators. Global, regional, and national incidence, prevalence, and years lived with disability for 354 diseases and injuries for 195 countries and territories, 1990-2017: a systematic analysis for the Global Burden of Disease Study 2017. Lancet. 2018;392:1789–858. Article  Google Scholar  Smoller JW, Finn…

Stairs CW, Leger MM, Roger AJ. Diversity and origins of anaerobic metabolism in mitochondria and related organelles. Philos Trans R Soc B: Biol Sci. 2015;370:20140326. Article  Google Scholar  Eme L, Spang A, Lombard J, Stairs CW, Ettema TJG. Archaea and the origin of eukaryotes. Nat Rev Microbiol. 2017;15:711–23. Article  CAS …

Chan, K. S. et al. Identification, molecular characterization, clinical prognosis, and therapeutic targeting of human bladder tumor-initiating cells. Proc. Natl Acad. Sci. USA 106, 14016–14021 (2009). Article  CAS  PubMed  PubMed Central  Google Scholar  Adams, S. et al. Signal-regulatory protein is selectively expressed by myeloid and neuronal cells. J. Immunol. 161,…

Review . 2023 Feb 25;15:245-255. doi: 10.2147/CMAR.S400013. eCollection 2023. Affiliations Expand Affiliation 1 Department of Hematology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People’s Republic of China. Item in Clipboard Review Jing Zhang et al. Cancer Manag Res. 2023. Show details Display options Display options Format AbstractPubMedPMID . 2023…

Jones HB. Pathology. In: Wexler P. (eds). Information resources in toxicology (Fourth Edition). Academic Press: San Diego, 2009, pp 357–63. Griesinger W. Die Pathologie und therapie der psychischen krankheiten. (Krabbe:Stuttgart, 1861). Kraepelin E. Psychiatrie: ein Lehrbuch für Studierende und Aerzte. (Verlag von Johann Ambrosius Barth:Leipzig, 1899). Jauhar S, Johnstone M,…

Manzin, A., Mallus, F., Macera, L., Maggi, F. & Blois, S. Global impact of Torque teno virus infection in wild and domesticated animals. J. Infect. Dev. Countries 9, 562–570 (2015). Article  CAS  Google Scholar  Biagini, P. et al. Family Anelloviridae. In Virus Taxonomy: Ninth Report of the International Committee on…

Miles JH. Autism spectrum disorders-a genetics review. Genet Med. 2011;13:278–94. Article  PubMed  Google Scholar  Betancur C. Etiological heterogeneity in autism spectrum disorders: more than 100 genetic and genomic disorders and still counting. Brain Res. 2011;1380:42–77. Article  CAS  PubMed  Google Scholar  Satterstrom FK, Kosmicki JA, Wang J, Breen MS, De Rubeis…

Yan Sha,1,* An-qi Mao,1,* Yuan-jie Liu,2 Jie-pin Li,2 Ya-ting Gong,3 Dong Xiao,1 Jun Huang,1 Yan-wei Gao,1 Mu-yao Wu,3 Hui Shen1 1Departments of Dermatology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, People’s Republic of China; 2Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu…