Chapter 10 Naturally Occurring Modified Nucleosides in DNA

1990 ◽  
pp. B327-B362 ◽  
Author(s):  
Melanie Ehrlich ◽  
Xian-Yang Zhang
Keyword(s):  
Modified Nucleosides ◽  
Naturally Occurring

scholarly journals Thermodynamic contribution of nucleoside modifications to yeast tRNA(Phe) anticodon stem loop analogs.

1999 ◽  
Vol 46 (1) ◽  
pp. 163-172 ◽  
Author(s):  
P F Agris ◽  
R Guenther ◽  
E Sochacka ◽  
W Newman ◽  
G Czerwińska ◽  
...  
Keyword(s):  
Thermodynamic Parameters ◽  
Atomic Level ◽  
Modified Nucleosides ◽  
Automated Synthesis ◽  
Modified Nucleotides ◽  
Stem Loop ◽  
Yeast Trna ◽  
Naturally Occurring ◽  
The Individual

The determination of the structural and functional contributions of natural modified nucleosides to tRNA has been limited by lack of an approach that can systematically incorporate the modified units. We have produced a number of oligonucleotide analogs, of the anticodon of yeast tRNA(Phe) by, combining standard automated synthesis for the major nucleosides with specialty chemistries for the modified nucleosides. In this study, both naturally occurring and unnatural modified nucleotides were placed in native contexts. Each oligonucleotide was purified and the nucleoside composition determined to validate the chemistry. The RNAs were denatured and analyzed to determine the van't Hoff thermodynamic parameters. Here, we report the individual thermodynamic contributions for Cm, Gm, m1G, m5C, psi. In addition m5m6U, m1psi, and m3psi, were introduced to gain additional understanding of the physicochemical contribution of psi and m5C at an atomic level. These oligonucleotides demonstrate that modifications have measurable thermodynamic contributions and that loop modifications have global contributions.

AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA

2007 ◽  
Vol 3 (4) ◽  
pp. 1464-1475 ◽  
Author(s):  
Raviprasad Aduri ◽  
Brian T. Psciuk ◽  
Pirro Saro ◽  
Hariprakash Taniga ◽  
H. Bernhard Schlegel ◽  
...  
Keyword(s):  
Force Field ◽  
Modified Nucleosides ◽  
Amber Force Field ◽  
Naturally Occurring ◽  
Force Field Parameters

scholarly journals Genetic Analysis Identifies a Function for the queC (ybaX) Gene Product at an Initial Step in the Queuosine Biosynthetic Pathway in Escherichia coli

2005 ◽  
Vol 187 (20) ◽  
pp. 6893-6901 ◽  
Author(s):  
Rahul Gaur ◽  
Umesh Varshney
Keyword(s):  
Escherichia Coli ◽  
Biosynthetic Pathway ◽  
Biological Activities ◽  
Single Gene ◽  
Initial Step ◽  
Modified Nucleosides ◽  
E Coli ◽  
Wobble Position ◽  
Naturally Occurring ◽  
Layer Chromatography

ABSTRACT Queuosine (Q), one of the most complex modifications occurring at the wobble position of tRNAs with GUN anticodons, is implicated in a number of biological activities, including accuracy of decoding, virulence, and cellular differentiation. Despite these important implications, its biosynthetic pathway has remained unresolved. Earlier, we observed that a naturally occurring strain of Escherichia coli B105 lacked Q modification in the tRNAs. In the present study, we developed a genetic screen to map the defect in E. coli B105 to a single gene, queC (renamed from ybaX), predicted to code for a 231-amino-acid-long protein with a pI of 5.6. As analyzed by mobility of tRNATyr on acid urea gels and two-dimensional thin-layer chromatography of the modified nucleosides, expression of QueC from a plasmid-borne copy confers a Q+ phenotype to E. coli B105. Further, analyses of tRNATyr from E. coli JE10651 (queA mutant), its derivative generated by deletion of chromosomal queC (queA ΔqueC), and E. coli JE7325, deficient in converting preQ0 to preQ1, have provided the first genetic evidence for the involvement of QueC at a step leading to production of preQ0, the first known intermediate in the generally accepted pathway that utilizes GTP as the starting molecule. In addition, we discuss the possibilities of collaboration of QueC with other cellular proteins in the production of preQ0.

Pathology of Bone Cells in Pigs with Experimental Turbinate Osteoporosis (Atrophic Rhinitis)

1971 ◽  
Vol 29 ◽  
pp. 304-305
Author(s):  
A. W. Fetter ◽  
C. C. Capen
Keyword(s):  
Mucous Membrane ◽  
Bone Cells ◽  
Atrophic Rhinitis ◽  
Infectious Agents ◽  
Metabolic Disturbances ◽  
Progressive Reduction ◽  
Naturally Occurring ◽  
Fundamental Cause ◽  
Osteocytic Osteolysis ◽  
Uncertain Etiology

Atrophic rhinitis in swine is a disease of uncertain etiology in which infectious agents, hereditary predisposition, and metabolic disturbances have been reported to be of primary etiologic importance. It shares many similarities, both clinically and pathologically, with ozena in man. The disease is characterized by deformity and reduction in volume of the nasal turbinates. The fundamental cause for the localized lesion of bone in the nasal turbinates has not been established. Reduced osteogenesis, increased resorption related to inflammation of the nasal mucous membrane, and excessive resorption due to osteocytic osteolysis stimulated by hyperparathyroidism have been suggested as possible pathogenetic mechanisms.The objectives of this investigation were to evaluate ultrastructurally bone cells in the nasal turbinates of pigs with experimentally induced atrophic rhinitis, and to compare these findings to those in control pigs of the same age and pigs with the naturally occurring disease, in order to define the fundamental lesion responsible for the progressive reduction in volume of the osseous core.

High Resolution Replication of Organoclay Surfaces

1982 ◽  
Vol 40 ◽  
pp. 576-577
Author(s):  
W. W. Barker ◽  
W. E. Rigsby ◽  
V. J. Hurst ◽  
W. J. Humphreys
Keyword(s):  
Clay Mineral ◽  
Organic Molecule ◽  
Organic Molecules ◽  
X Ray Diffraction ◽  
Xrd Pattern ◽  
X Ray ◽  
Naturally Occurring ◽  
Silicate Layers ◽  
Mineral Identification

Experimental clay mineral-organic molecule complexes long have been known and some of them have been extensively studied by X-ray diffraction methods. The organic molecules are adsorbed onto the surfaces of the clay minerals, or intercalated between the silicate layers. Natural organo-clays also are widely recognized but generally have not been well characterized. Widely used techniques for clay mineral identification involve treatment of the sample with H2 O2 or other oxidant to destroy any associated organics. This generally simplifies and intensifies the XRD pattern of the clay residue, but helps little with the characterization of the original organoclay. Adequate techniques for the direct observation of synthetic and naturally occurring organoclays are yet to be developed.

SEM study of the morphological effects of kinetin and zeatin on the growth and development of the apical meristem in wheat

1995 ◽  
Vol 53 ◽  
pp. 978-979
Author(s):  
G. M. Hutchins ◽  
J. S. Gardner
Keyword(s):  
Growth And Development ◽  
Furfuryl Alcohol ◽  
Apical Meristem ◽  
Plant Cells ◽  
Triticum Aestivum L ◽  
Morphological Development ◽  
Naturally Occurring ◽  
Chinese Spring Wheat ◽  
Sem Study ◽  
Moist Environment

Cytokinins are plant hormones that play a large and incompletely understood role in the life-cycle of plants. The goal of this study was to determine what roles cytokinins play in the morphological development of wheat. To achieve any real success in altering the development and growth of wheat, the cytokinins must be applied directly to the apical meristem, or spike of the plant. It is in this region that the plant cells are actively undergoing mitosis. Kinetin and Zeatin were the two cytokinins chosen for this experiment. Kinetin is an artificial hormone that was originally extracted from old or heated DNA. Kinetin is easily made from the reaction of adenine and furfuryl alcohol. Zeatin is a naturally occurring hormone found in corn, wheat, and many other plants.Chinese Spring Wheat (Triticum aestivum L.) was used for this experiment. Prior to planting, the seeds were germinated in a moist environment for 72 hours.

Fine structure and properties of defects in naturally occurring silicates and oxides

1990 ◽  
Vol 48 (4) ◽  
pp. 460-461
Author(s):  
David R. Veblen
Keyword(s):  
Chemical Reactions ◽  
High Resolution Electron Microscopy ◽  
Extended Defects ◽  
Single Chain ◽  
Naturally Occurring ◽  
Resolution Electron ◽  
Fine Structures ◽  
Image Simulations ◽  
Similar Crystal Structure

Extended defects and interfaces control many processes in rock-forming minerals, from chemical reactions to rock deformation. In many cases, it is not the average structure of a defect or interface that is most important, but rather the structure of defect terminations or offsets in an interface. One of the major thrusts of high-resolution electron microscopy in the earth sciences has been to identify the role of defect fine structures in reactions and to determine the structures of such features. This paper will review studies using HREM and image simulations to determine the structures of defects in silicate and oxide minerals and present several examples of the role of defects in mineral chemical reactions. In some cases, the geological occurrence can be used to constrain the diffusional properties of defects.The simplest reactions in minerals involve exsolution (precipitation) of one mineral from another with a similar crystal structure, and pyroxenes (single-chain silicates) provide a good example. Although conventional TEM studies have led to a basic understanding of this sort of phase separation in pyroxenes via spinodal decomposition or nucleation and growth, HREM has provided a much more detailed appreciation of the processes involved.

Flavonoids in adipose tissue inflammation and atherosclerosis: one arrow, two targets

2020 ◽  
Vol 134 (12) ◽  
pp. 1403-1432 ◽  
Author(s):  
Manal Muin Fardoun ◽  
Dina Maaliki ◽  
Nabil Halabi ◽  
Rabah Iratni ◽  
Alessandra Bitto ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Fruits And Vegetables ◽  
Metabolic Diseases ◽  
Therapeutic Agents ◽  
Adipose Tissue Inflammation ◽  
Cellular Mechanisms ◽  
Tissue Inflammation ◽  
Cholesterol Levels ◽  
Naturally Occurring ◽  
Pro Inflammatory Cytokines

Abstract Flavonoids are polyphenolic compounds naturally occurring in fruits and vegetables, in addition to beverages such as tea and coffee. Flavonoids are emerging as potent therapeutic agents for cardiovascular as well as metabolic diseases. Several studies corroborated an inverse relationship between flavonoid consumption and cardiovascular disease (CVD) or adipose tissue inflammation (ATI). Flavonoids exert their anti-atherogenic effects by increasing nitric oxide (NO), reducing reactive oxygen species (ROS), and decreasing pro-inflammatory cytokines. In addition, flavonoids alleviate ATI by decreasing triglyceride and cholesterol levels, as well as by attenuating inflammatory mediators. Furthermore, flavonoids inhibit synthesis of fatty acids and promote their oxidation. In this review, we discuss the effect of the main classes of flavonoids, namely flavones, flavonols, flavanols, flavanones, anthocyanins, and isoflavones, on atherosclerosis and ATI. In addition, we dissect the underlying molecular and cellular mechanisms of action for these flavonoids. We conclude by supporting the potential benefit for flavonoids in the management or treatment of CVD; yet, we call for more robust clinical studies for safety and pharmacokinetic values.

Molecular Mechanism of Apoptosis Induction by Resveratrol, a Natural Cancer Chemopreventive Agent

2008 ◽  
Vol 78 (1) ◽  
pp. 3-8 ◽  
Author(s):  
Fan ◽  
Jiang ◽  
Zhang ◽  
Bai
Keyword(s):  
Cancer Treatment ◽  
Molecular Mechanism ◽  
Apoptosis Induction ◽  
Protective Agents ◽  
Chemopreventive Agent ◽  
Naturally Occurring ◽  
Apoptosis Pathways ◽  
Present Understanding

In efforts to identify naturally occurring compounds that act as protective agents, resveratrol, a phytoalexin existing in wine, has attracted much interest because of its diverse pharmacological characteristics. Considering that apoptosis induction is the most potent defense approach for cancer treatment, we have tried to summarize our present understanding of apoptosis induction by resveratrol based on the two major apoptosis pathways.

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