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https://www.readbyqxmd.com/read/29780457/highly-efficient-base-editing-in-staphylococcus-aureus-using-an-engineered-crispr-rna-guided-cytidine-deaminase
#1
Tongnian Gu, Siqi Zhao, Yishuang Pi, Weizhong Chen, Chuanyuan Chen, Qian Liu, Min Li, Dali Han, Quanjiang Ji
Novel therapeutic means against Staphylococcus aureus infections are urgently needed due to the emergence of drug-resistant S. aureus . We report the development of a CRISPR RNA-guided cytidine deaminase (pnCasSA-BEC), enabling highly efficient gene inactivation and point mutations in S. aureus . We engineered a fusion of a Cas9 nickase (Cas9D10A) and a cytidine deaminase (APOBEC1) that can be guided to a target genomic locus for gene inactivation via generating a premature stop codon. The pnCasSA-BEC system nicks the non-edited strand of the genomic DNA, directly catalyzes the conversion of cytidine (C) to uridine (U), and relies on DNA replication to achieve C → T (G → A) conversion without using donor repair templates...
March 28, 2018: Chemical Science
https://www.readbyqxmd.com/read/29775408/lack-of-tone-in-mouse-small-mesenteric-arteries-leads-to-outward-remodeling-which-can-be-prevented-by-prolonged-agonist-induced-vasoconstriction
#2
Anika Klein, Philomeena Daphne Joseph, Vibeke Grøsfjeld Christensen, Lars Jørn Jensen, Jens Christian Brings Jacobsen
Inward remodeling of resistance vessels is an independent risk factor for cardiovascular events. Thus far, the remodeling process remains incompletely elucidated, but the activation level of the vascular smooth muscle cell (VSMC) appears to play a central role. Accordingly, previous data suggest that an antagonistic and, supposedly beneficial, response - outward remodeling - may follow prolonged vasodilatation. This study aims to determine if 1) outward remodeling follows 3 days of vessel culture without tone, 2) a similar response can be elicited in a much shorter 4-hour time frame and finally 3) a 4-hour response can be prevented or reversed by the presence of vasoconstrictors in the medium...
May 18, 2018: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/29772948/a-new-isoflavane-4-ol-derivative-from-melilotus-officinalis-l-pall
#3
Mert Ilhan, Zulfiqar Ali, Ikhlas A Khan, Esra Küpeli Akkol
A new isoflavane derivative, melilofficinaside together with seven other metabolites including coumarin, uridine, methyl-α-d-fructofuranoside, and flavonoid glucosides were isolated from the aerial parts of Melilotus officinalis (L.) Pall.
May 18, 2018: Natural Product Research
https://www.readbyqxmd.com/read/29769081/n-6-methyl-adenosine-level-in-nicotiana-tabacum-is-associated-with-tobacco-mosaic-virus
#4
Zhurui Li, Jing Shi, Lu Yu, Xiaozhen Zhao, Longlu Ran, Deyu Hu, Baoan Song
BACKGROUND: N 6 -methyl-adenosine (m6 A) is a prevalent RNA modification in many species. Abnormal m6 A methylation levels can lead to RNA dysfunction and can cause diseases. Tobacco mosaic virus (TMV) is one of the most devastating viruses for agricultural plants. It has many hosts, particularly including tobacco and other members the family Solanaceae. However, it remains unclear whether the abnormal growth induced by TMV is associated with the m6 A level. METHODS: A rapid and accurate analytical method using ultra-high-performance liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HR - MS/MS) was developed to analyse the adenosine (A), cytidine (C), guanosine (G), uridine (U), and m6 A contents in the tobacco leaf, and the m6 A/G ratio was used to evaluate the m6 A level...
May 16, 2018: Virology Journal
https://www.readbyqxmd.com/read/29768974/brain-phospholipid-precursors-administered-post-injury-reduce-tissue-damage-and-improve-neurological-outcome-in-experimental-traumatic-brain-injury
#5
Orli Thau-Zuchman, Rita Noutel Gomes, Simon Christopher Dyall, Meirion Davis, John V Priestley, Martine Groenendijk, Martijn DE Wilde, Jordi Lopez-Tremoleda, Adina T Michael-Titus
Traumatic brain injury (TBI) leads to cellular loss, destabilisation of membranes, disruption of synapses and altered brain connectivity, and increased risk of neurodegenerative disease. A significant and long-lasting decrease in phospholipids (PL), essential membrane constituents, has recently been reported in plasma and brain tissue, in human and experimental TBI. We hypothesised that supporting PL synthesis post-injury could improve outcome after TBI. We tested this hypothesis using a multi-nutrient combination designed to support the biosynthesis of phospholipids and available for clinical use...
May 17, 2018: Journal of Neurotrauma
https://www.readbyqxmd.com/read/29768920/enzymatic-synthesis-of-the-ribosylated-glycyl-uridine-disaccharide-core-of-peptidyl-nucleoside-antibiotics
#6
Zheng Cui, Xiaodong Liu, Jonathan Overbay, Wenlong Cai, Xiachang Wang, Anke Lemke, Daniel Wiegmann, Giuliana Niro, Jon S Thorson, Christian Ducho, Steven G Van Lanen
Muraymycins belong to a family of nucleoside antibiotics that have a distinctive disaccharide core consisting of 5-amino-5-deoxyribofuranose (ADR) attached to 6'-N-alkyl-5'- C-glycyluridine (GlyU). Here we functionally assign and characterize six enzymes from the muraymycin biosynthetic pathway involved in the core assembly that starts from UMP. The biosynthesis is initiated by Mur16, a non-heme Fe(II)- and α-ketoglutarate-dependent dioxygenase, followed by four transferase enzymes-Mur17, a pyridoxal-5'-phosphate (PLP)-dependent transaldolase; Mur20, an aminotransferase; Mur26, a pyrimidine phosphorylase; and Mur18, a nucleotidylyltransferase...
May 17, 2018: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/29767200/nmr-analyses-on-n-hydroxymethylated-nucleobases-implications-for-formaldehyde-toxicity-and-nucleic-acid-demethylases
#7
S Shishodia, D Zhang, A H El-Sagheer, T Brown, T D W Claridge, C J Schofield, R J Hopkinson
Formaldehyde is produced in cells by enzyme-catalysed demethylation reactions, including those occurring on N-methylated nucleic acids. Formaldehyde reacts with nucleobases to form N-hydroxymethylated adducts that may contribute to its toxicity/carcinogenicity when added exogenously, but the chemistry of these reactions has been incompletely defined. We report NMR studies on the reactions of formaldehyde with canonical/modified nucleobases. The results reveal that hydroxymethyl hemiaminals on endocyclic nitrogens, as observed with thymidine and uridine monophosphates, are faster to form than equivalent hemiaminals on exocyclic nitrogens; however, the exocyclic adducts, as formed with adenine, guanine and cytosine, are more stable in solution...
May 16, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29766657/drug-drug-interaction-and-doping-effect-of-non-prohibited-drugs-on-the-urinary-excretion-profile-of-methandienone
#8
Monica Mazzarino, Franziska L Khevenhüller-Metsch, Ilaria Fiacco, Maria Kristina Parr, Xavier de la Torre, Francesco Botrè
The potential consequences of drug-drug interactions on the excretion profile of the anabolic androgenic steroid methandienone (17β-hydroxy-17α-methylandrosta-1,4-dien-3-one) are discussed here. More specifically, we have evaluated by in vitro and in vivo experiments the effects of seven non-prohibited drugs (fluconazole, ketoconazole, itraconazole, miconazole, fluoxetine, paroxetine and nefazodone) on the main metabolic pathways of methandienone. These are selected among those most commonly used by the athletes...
May 15, 2018: Drug Testing and Analysis
https://www.readbyqxmd.com/read/29761432/quantification-of-low-abundant-phosphorylated-carbohydrates-using-hilic-qqq-ms-ms
#9
Tiago F Jorge, Carla António
Phosphorylated carbohydrates are central metabolites involved in key plant metabolic pathways, such as glycolysis and central carbon metabolism. Such pathways influence plant growth, development, and stress responses to environmental changes, and ultimately, reflect the plant's energy status. The high polarity of these metabolites, the variety of isomeric structures (e.g., glucose-1-phosphate (G1P)/fructose-6-phosphate (F6P)/mannose-6-phosphate (M6P)/G6P, sucrose-6-phosphate (S6P)/T6P), and rapid metabolic turnover makes their analysis particularly challenging...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29761268/towards-a-comprehensive-picture-of-c-to-u-rna-editing-sites-in-angiosperm-mitochondria
#10
Alejandro A Edera, Carolina L Gandini, M Virginia Sanchez-Puerta
Our understanding of the dynamic and evolution of RNA editing in angiosperms is in part limited by the few editing sites identified to date. This study identified 10,217 editing sites from 17 diverse angiosperms. Our analyses confirmed the universality of certain features of RNA editing, and offer new evidence behind the loss of editing sites in angiosperms. RNA editing is a post-transcriptional process that substitutes cytidines (C) for uridines (U) in organellar transcripts of angiosperms. These substitutions mostly take place in mitochondrial messenger RNAs at specific positions called editing sites...
May 14, 2018: Plant Molecular Biology
https://www.readbyqxmd.com/read/29759223/effects-of-hydrophilic-monomers-on-sorptive-properties-of-divinylbenzene-based-reversed-phase-sorbents
#11
Hiroya Murakami, Takuya Aoyanagi, Yuta Miki, Hiroki Tomita, Yukihiro Esaka, Yoshinori Inoue, Norio Teshima
Solid phase extraction (SPE) has been extensively used as a pretreatment method. In SPE methods, commercially available reversed phase type sorbents, which consist of macroporus styrene-divinylbenzene or copolymers including divinylbenzene (DVB) and hydrophilic monomers, have been applied to a variety of samples. The later sorbents are called hydrophilic lipophilic balanced (HLB) type sorbents. Hydrophilic monomers in hydrophilic lipophilic balanced type sorbents contribute to the increase in retention of polar compounds, because hydrophilic monomers improve the wettability and increase the interaction with polar compounds as analytes...
August 1, 2018: Talanta
https://www.readbyqxmd.com/read/29753787/studying-sparsely-populated-conformational-states-in-rna-combining-chemical-synthesis-and-solution-nmr-spectroscopy
#12
Elisabeth Strebitzer, Felix Nußbaumer, Johannes Kremser, Martin Tollinger, Christoph Kreutz
Using chemical synthesis and solution NMR spectroscopy, RNA structural ensembles including a major ground state and minor populated excited states can be studied at atomic resolution. In this work, atom-specific 13 C labeled RNA building blocks - a 5-13 C-uridine and a 2,8-13 C2 -adenosine building block - are used to introduce isolated 13 C-1 H-spin topologies into a target RNA to probe such structural ensembles via NMR spectroscopy. First, the 5-13 C-uridine 2'-O-TBDMS-phosphoramidite building block was introduced into a 21 nucleotide (nt) tP5c stem construct of the tP5abc subdomain of the Tetrahymena group I ribozyme...
May 10, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29753740/2-deoxy-d-glucose-increases-gfat1-phosphorylation-resulting-in-endoplasmic-reticulum-related-apoptosis-via-disruption-of-protein-n-glycosylation-in-pancreatic-cancer-cells
#13
Kousuke Ishino, Mitsuhiro Kudo, Wei-Xia Peng, Shoko Kure, Kiyoko Kawahara, Kiyoshi Teduka, Yoko Kawamoto, Taeko Kitamura, Takenori Fujii, Tetsushi Yamamoto, Ryuichi Wada, Zenya Naito
The glycolytic inhibitor 2-deoxy-d-glucose (2DG) causes energy starvation, affecting cell viability in a wide range of cancer cell lines. To determine the action of 2DG in pancreatic cancer, we performed proteomic analysis of pancreatic cancer cell line after 2DG treatment. Eighty proteins showed differential expression and among these, proteins involved in phosphohexose metabolism were upregulated. Up-regulation of glutamine: fructose 6-phosphate aminotransferase 1 (GFAT1), which belongs to the hexosamine biosynthesis pathway (HBP) that produces uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) to maintain glycoprotein, was validated by evaluation of mRNA and protein levels...
May 10, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29751715/-study-on-quality-evaluation-of-dihuang-rehmannia-glutinosa-by-two-dimension-hplc-fingerprints-and-chemometrics-methods
#14
Chun-Yue Huang, Dan-Wei Ouyang, Li-Xin Niu, Jing Zhou, Shan Lin, Xiao Hu
The study is to establish the two-dimension HPLC fingerprints of Dihuang (Rehmannia glutinosa), by HPLC-PDA and HPLC-ELSD methods. The separations were performed on Waters Atlantis®T3(4.6 mm× 250 mm,5 μm)and Welch Ultimate®Hilic-NH₂(4.6 mm× 250 mm,5 μm)columns with the gradient elution of acetonitrile-0.01% phosphoric acid and acetonitrile-water, respectively. The chromatographic display wavelength for PDA detector was set at 203 nm. For HPLC-ELSD, the nebulizer was set as cooling mode, the drift tube temperature was set at 60 °C and the gas pressure was 35...
April 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29749563/zinc-supplementation-decreases-galactosylation-of-recombinant-igg-in-cho-cells
#15
Anuja Prabhu, Ramchandra Gadre, Mugdha Gadgil
Trace element composition of culture medium can be altered to modulate glycoform of recombinant glycoproteins. In this study, we show that Zn2+ supplementation at or above 100 μM decreases galactosylation of recombinant IgG expressed in Chinese Hamster Ovary cells. This decrease in galactosylation is not due to reduced galactosyltransferase expression. This effect persists upon supplementation of galactose and uridine to the culture, indicating that it may not be due to reduced UDP-Gal availability. Measurements of galactosyltransferase activity in the cell lysate show that activity decreases with increasing Zn2+ /Mn2+ ratio...
May 10, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29742281/analyzing-the-clinical-actionability-of-germline-pharmacogenomic-findings-in-oncology
#16
Rebecca Wellmann, Brittany A Borden, Keith Danahey, Rita Nanda, Blase N Polite, Walter M Stadler, Mark J Ratain, Peter H O'Donnell
BACKGROUND: Germline and tumor pharmacogenomics impact drug responses, but germline markers less commonly guide oncology prescribing. The authors hypothesized that a critical number of clinically actionable germline pharmacogenomic associations exist, representing clinical implementation opportunities. METHODS: In total, 125 oncology drugs were analyzed for positive germline pharmacogenomic associations in journals with impact factors ≥5. Studies were assessed for design and genotyping quality, clinically relevant outcomes, statistical rigor, and evidence of drug-gene effects...
May 9, 2018: Cancer
https://www.readbyqxmd.com/read/29737521/age-and-genotype-dependent-variability-in-the-protein-abundance-and-activity-of-six-major-uridine-diphosphate-glucuronosyltransferases-in-human-liver
#17
Deepak Kumar Bhatt, Aanchal Mehrotra, Andrea Gaedigk, Revathi Chapa, Abdul Basit, Haeyoung Zhang, Prachi Choudhari, Mikael Boberg, Robin E Pearce, Roger Gaedigk, Ulrich Broeckel, J Steven Leeder, Bhagwat Prasad
The ontogeny of hepatic uridine diphosphate-glucuronosyltransferases (UGTs) was investigated by LC-MS/MS proteomics to determine UGT protein abundance in human liver microsomes isolated from 136 pediatric (0-18 years) and 35 adult (age 18-67 years) donors. Microsomal protein abundances of UGT1A1, UGT1A4, UGT1A6, UGT1A9, UGT2B7 and UGT2B15 increased by ∼8, 55, 35, 33, 8 and 3-fold from neonates to adults, respectively. The estimated age at which 50% of the adult protein abundance is observed for UGT isoforms was between 2...
May 8, 2018: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/29721784/subtractive-genomics-molecular-docking-and-molecular-dynamics-simulation-revealed-lpxc-as-a-potential-drug-target-against-multi-drug-resistant-klebsiella-pneumoniae
#18
Sajjad Ahmad, Afifa Navid, Amina Saleem Akhtar, Syed Sikander Azam, Abdul Wadood, Horacio Pérez-Sánchez
The emergence and dissemination of pan drug resistant clones of Klebsiella pneumoniae are great threat to public health. In this regard new therapeutic targets must be highlighted to pave the path for novel drug discovery and development. Subtractive proteomic pipeline brought forth UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC), a Zn+2 dependent cytoplasmic metalloprotein and catalyze the rate limiting deacetylation step of lipid A biosynthesis pathway. Primary sequence analysis followed by 3-dimensional (3-D) structure elucidation of the protein led to the detection of K...
May 2, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29718364/the-dyw-domains-of-pentatricopeptide-repeat-rna-editing-factors-contribute-to-discriminate-target-and-non-target-editing-sites
#19
Mizuho Ichinose, Mamoru Sugita
In land plant organelles, many transcripts are modified by cytidine-to-uridine RNA editing. Target cytidines are specifically recognized by nuclear-encoded pentatricopeptide repeat (PPR) proteins via their sequence-specific RNA binding motifs. In the moss Physcomitrella patens, all PPR editing factors have C-terminal E and DYW domains. To examine the contribution of E and DYW domains in RNA editing, we performed a complementation assay using mutated PpPPR_56 and PpPPR_71, which are responsible for mitochondrial editing sites...
April 27, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29718331/the-uba4-domain-interplay-is-mediated-via-a-thioester-that-is-critical-for-trna-thiolation-through-urm1-thiocarboxylation
#20
Martin Termathe, Sebastian A Leidel
Eukaryotic ubiquitin-like proteins (UBLs) have evolved from prokaryotic sulfur-carrier proteins (SCPs). Ubiquitin related modifier 1 (Urm1) shares biochemical and structural features of UBLs and SCPs and is essential for 2-thiolation of cytoplasmic tRNA. This chemical modification of wobble uridine is highly conserved amongst species and is achieved via Urm1 thiocarboxylation by the non-canonical ubiquitin activating 4 enzyme (Uba4), which contains an E1- and a Rhodanese (RHD) domain. While the RHD catalyzes the last step in Urm1-thiocarboxylate formation, the previous steps in Urm1 activation and the interplay between the two domains have remained elusive...
April 30, 2018: Nucleic Acids Research
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