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Sample records for deoxyribonucleic acid base

  1. Deoxyribonucleic acid base compositions of dermatophytes.

    PubMed

    Davison, F D; Mackenzie, D W; Owen, R J

    1980-06-01

    DNA was extracted and purified from 55 dermatophyte isolates representing 34 species of Trichophyton, Microsporum and Epidermophyton. The base compositions of the chromosomal DNA were determined by CsCl density gradient centrifugation and were found to be in the narrow range of 48.7 to 50.3 mol % G + C. A satellite DNA component assumed to be of mitochondrial origin was present in most strains, with a G + C content ranging from 14.7 to 30.8 mol % G + C. Heterogeneity in microscopic and colonial characteristics was not reflected in differences in the mean G + C content of the chromosomal DNAs. Strains varied in the G + C contents of satelite DNA, but these did not correlate with traditional species concepts.

  2. A novel chaotic based image encryption using a hybrid model of deoxyribonucleic acid and cellular automata

    NASA Astrophysics Data System (ADS)

    Enayatifar, Rasul; Sadaei, Hossein Javedani; Abdullah, Abdul Hanan; Lee, Malrey; Isnin, Ismail Fauzi

    2015-08-01

    Currently, there are many studies have conducted on developing security of the digital image in order to protect such data while they are sending on the internet. This work aims to propose a new approach based on a hybrid model of the Tinkerbell chaotic map, deoxyribonucleic acid (DNA) and cellular automata (CA). DNA rules, DNA sequence XOR operator and CA rules are used simultaneously to encrypt the plain-image pixels. To determine rule number in DNA sequence and also CA, a 2-dimension Tinkerbell chaotic map is employed. Experimental results and computer simulations, both confirm that the proposed scheme not only demonstrates outstanding encryption, but also resists various typical attacks.

  3. Agreement Between Deoxyribonucleic Acid Base Composition and Taxometric Classification of Gram-Positive Cocci1

    PubMed Central

    Silvestri, L. G.; Hill, L. R.

    1965-01-01

    Silvestri, L. G. (Università Statale, Milan, Italy), and L. R. Hill. Agreement between deoxyribonucleic acid base composition and taxometric classification of gram-positive cocci. J. Bacteriol. 90:136–140. 1965.—It had been previously proposed, from taxometric analyses, that gram-positive, catalase-positive cocci be divided into two subgroups. Thirteen strains, representative of both subgroups, were examined for deoxyribonucleic acid (DNA) base composition, determined from melting temperatures. Per cent GC (guanine + cytosine/total bases) values fell into two groups: 30.8 to 36.5% GC and 69 to 75% GC. Strains with low per cent GC values belonged to the Staphylococcus aureus–S. saprophyticus–S. lactis taxometric subgroups, and those with high per cent GC values belonged to the S. roseus–S. afermentans subgroup. The hypothetical nature of any classification is emphasized, and, in the present work, the hypothesis derived from taxometric analyses of division into two subgroups is confirmed by the study of DNA base ratios. The two subgroups correspond, respectively, to the genera Staphylococcus and Micrococcus. PMID:16562008

  4. BASE COMPOSITION OF THE DEOXYRIBONUCLEIC ACID OF SULFATE-REDUCING BACTERIA.

    PubMed

    SIGAL, N; SENEZ, J C; LEGALL, J; SEBALD, M

    1963-06-01

    Sigal, Nicole (Laboratoire de Chimie Bactérienne du CNRS, Marseille, France), Jacques C. Senez, Jean Le Gall, and Madeleine Sebald. Base composition of the deoxyribonucleic acid of sulfate-reducing bacteria. J. Bacteriol. 85:1315-1318. 1963-The deoxyribonucleic acid constitution of several strains of sulfate-reducing bacteria has been analytically determined. The results of these studies show that this group of microorganisms includes at least four subgroups characterized by significantly different values of the adenine plus thymine to guanine plus cytosine ratio. The nonsporulated forms with polar flagellation, containing both cytochrome c(3) and desulfoviridin, are divided into two subgroups. One includes the fresh-water, nonhalophilic strains with base ratio from 0.54 to 0.59, and the other includes the halophilic or halotolerant strains with base ratio from 0.74 to 0.77. The sporulated, peritrichous strains without cytochrome and desulfoviridin ("nigrificans" and "orientis") are distinct from the above two types and differ from each other, having base ratios of 1.20 and 1.43, respectively.

  5. Optoelectronic studies on heterocyclic bases of deoxyribonucleic acid for DNA photonics.

    PubMed

    El-Diasty, Fouad; Abdel-Wahab, Fathy

    2015-10-01

    The optoelectronics study of large molecules, particularly π-stacking molecules, such as DNA is really an extremely difficult task. We perform first electronic structure calculations on the heterocyclic bases of 2'-deoxyribonucleic acid based on Lorentz-Fresnel dispersion theory. In the UV-VIS range of spectrum, many of the optoelectronic parameters for DNA four bases namely adenine, guanine, cytosine and thymine are calculated and discussed. The results demonstrate that adenine has the highest hyperpolarizability, whereas thymine has the lowest hyperpolarizability. Cytosine has the lower average oscillator energy and the higher lattice energy. Thymine infers the most stable nucleic base with the lower phonon energy. Thymine also has the highest average oscillator energy and the lower lattice energy. Moreover, the four nucleic acid bases have large band gap energies less than 5 eV with a semiconducting behavior. Guanine shows the smallest band gap and the highest Fermi level energy, whereas adenine elucidates the highest band gap energy.

  6. Performance of an electro-optic waveguide modulator fabricated using a deoxyribonucleic-acid-based biopolymer

    NASA Astrophysics Data System (ADS)

    Heckman, Emily M.; Grote, James G.; Hopkins, F. Kenneth; Yaney, Perry P.

    2006-10-01

    An electro-optic (EO) planar waveguide modulator using a deoxyribonucleic acid (DNA)-based biopolymer for both the waveguide core and cladding layers has been fabricated and its performance evaluated. A cross-linked DNA-surfactant biopolymer was used for the top and bottom cladding layers and the core layer was a cross-linked DNA-surfactant biopolymer with 3wt% Disperse Red 1. The EO coefficient r33 was induced through contact poling. The fabricated device was found to exhibit EO modulating behavior. Using an estimated value of r33=0.5pm/V, a sine-squared fit to the modulating data was obtained with Vπ=263V±10%.

  7. Deoxyribonucleic Acid Base Sequence Homologies of Some Budding and Prosthecate Bacteria

    PubMed Central

    Moore, Richard L.; Hirsch, Peter

    1972-01-01

    The genetic relatedness of a number of budding and prosthecate bacteria was determined by deoxyribonucleic acid (DNA) homology experiments of the direct binding type. Strains of Hyphomicrobium sp. isolated from aquatic habitats were found to have relatedness values ranging from 9 to 70% with strain “EA-617,” a subculture of the Hyphomicrobium isolated by Mevius from river water. Strains obtained from soil enrichments had lower values with EA-617, ranging from 3 to 5%. Very little or no homology was detected between the amino acid-utilizing strain Hyphomicrobium neptunium and other Hyphomicrobium strains, although significant homology was observed with the two Hyphomonas strains examined. No homology could be detected between prosthecate bacteria of the genera Rhodomicrobium, Prosthecomicrobium, Ancalomicrobium, or Caulobacter, and Hyphomicrobium strain EA-617 or H. neptunium LE-670. The grouping of Hyphomicrobium strains by their relatedness values agrees well with a grouping according to the base composition of their DNA species. It is concluded that bacteria possessing cellular extensions represent a widely diverse group of organisms. PMID:5018022

  8. Heat shock protein 70 stimulation of the deoxyribonucleic acid base excision repair enzyme polymerase β

    PubMed Central

    Mendez, Frances; Kozin, Elliott; Bases, Robert

    2003-01-01

    Base excision repair (BER) of damaged deoxyribonucleic acid (DNA) is a multistep process during which potentially lethal abasic sites temporarily exist. Repair of these lesions is greatly stimulated by heat shock protein 70 (Hsp70), which enhances strand incision and removal of the abasic sites by human apurinic-apyrimidinic endonuclease (HAP1). The resulting single-strand gaps must then be filled in. Here, we show that Hsp70 and its 48- and 43-kDa N-terminal domains greatly stimulated filling in the single-strand gaps by DNA polymerase β, a novel finding that extends the role of Hsps in DNA repair. Incorporation of deoxyguanosine monophosphate (dGMP) to fill in single-strand gaps in DNA phagemid pBKS by DNA polymerase β was stimulated by Hsp70. Truncated proteins derived from the C-terminus of Hsp70 as well as unrelated proteins were less effective, but proteins derived from the N-terminus of Hsp70 remained efficient stimulators of DNA polymerase β repair of DNA single-strand gaps. In agreement with these results, repair of a gap in a 30-bp oligonucleotide by polymerase β also was strongly stimulated by Hsp70 although not by a truncated protein from the C-terminus of Hsp70. Sealing of the repaired site in the oligonucleotide by human DNA ligase 1 was not specifically stimulated by Hsp-related proteins. Results presented here now implicate and extend the role of Hsp70 as a partner in the enzymatic repair of damaged DNA. The participation of Hsp70 jointly with base excision enzymes improves repair efficiency by mechanisms that are not yet understood. PMID:14627201

  9. BASE COMPOSITION OF DEOXYRIBONUCLEIC ACID OF SULFATE-REDUCING BACTERIA DEDUCED FROM BUOYANT DENSITY MEASUREMENTS IN CESIUM CHLORIDE

    PubMed Central

    Saunders, Grady F.; Campbell, L. Leon; Postgate, John R.

    1964-01-01

    Saunders, Grady F. (University of Illinois, Urbana), L. Leon Campbell, and John R. Postgate. Base composition of deoxyribonucleic acid of sulfate-reducing bacteria deduced from buoyant density measurements in cesium chloride. J. Bacteriol. 87:1073–1078. 1964.—The base composition of the deoxyribonucleic acid (DNA) of sulfate-reducing bacteria was calculated from buoyant density measurements in CsCl. The sporulating sulfate-reducing bacteria fell into two groups: Desulfovibrio orientis with a DNA base composition of 42% guanine plus cytosine (G + C), and Clostridium nigrificans with a DNA base composition of 45% G + C. The mesophilic relative of C. nigrificans had a DNA base composition of 46% G + C. Thirty strains of nonsporulating sulfate-reducing bacteria called D. desulfuricans were studied. They fell into three groups as judged by DNA base composition: group I (11 strains), 60 to 62% G + C; group II (13 strains), 54 to 56% G + C; and group III (6 strains), 46 to 47% G + C. These data underline the need for a taxonomic revision of this group of microorganisms. PMID:5874533

  10. Role of Ribonucleic Acid Synthesis in Replication of Deoxyribonucleic Acid

    PubMed Central

    Pato, Martin L.

    1975-01-01

    An experiment previously interpreted to show a ribonucleic acid requirement for propagation of deoxyribonucleic replication is reexamined and the earlier interpretation is shown to be incorrect. PMID:1090599

  11. Deoxyribonucleic Acid Base Composition and Biochemical Properties of Certain Coagulase-Negative Enterotoxigenic Cocci

    PubMed Central

    Lotter, Leonard P.; Genigeorgis, Constantin A.

    1975-01-01

    Eight coagulase-negative, enterotoxigenic strains of cocci and one weakly coagulase-positive strain isolated from a number of different sources, including cases of food poisoning incidents, were evaluated for their relationship to Staphylococcus aureus on the basis of deoxyribonucleic acid (DNA) buoyant density and physiological studies. One strain of cocci produced enterotoxins A and C, two strains produced types B and C, four strains produced only type C, and one strain only type D. The enterotoxin produced by one strain of cocci was serologically untypable. None of the test organisms produced detectable amounts of enterotoxin in broth cultures. The test strains of cocci exhibited the following profile: all produced catalase; all grew anaerobically and fermented glucose; five were sensitive to lysostaphin; the percentage of guanine plus cytosine content of their DNA varied from 32.7 to 37.6; five produced acid from mannitol both aerobically and anaerobically; two formed δ-hemolysin; five produced phosphatase and acetoin; and all produced heat-stable nuclease. None of the organisms exhibited typical characteristics of S. aureus, S. epidermidis, or S. saprophyticus. On the basis of the present data and data reported elsewhere, these organisms should be considered as variants or mutants of S. aureus. PMID:803812

  12. Deoxyribonucleic acid base composition and biochemical properties of certain coagulase-negative enterotoxigenic cocci.

    PubMed

    Lotter, L P; Genigeorgis, C A

    1975-02-01

    Eight coagulase-negative, enterotoxigenic strains of cocci and one weakly coagulase-positive strain isolated from a number of different sources, including cases of food poisoning incidents, were evaluated for their relationship to Staphylococcus aureus on the basis of deoxyribonucleic acid (DNA) buoyant density and physiological studies. One strain of cocci produced enterotoxins A and C, two strains produced types B and C, four strains produced only type C, and one strain only type D. The enterotoxin produced by one strain of cocci was serologically untypable. None of the test organisms produced detectable amounts of enterotoxin in broth cultures. The test strains of cocci exhibited the following profile: all produced catalase; all grew anaerobically and fermented glucse; five were sensitive to lysostaphin; the percentage of guanine plus cytosine content of their DNA varied from 32.7 to 37.6; five produced acid from mannitol both aerobically and anaerobically; two formed delta-hemolysin; five produced phosphatase and acetoin; and all produced heat-stable nuclease. None of the organisms exhibited typical characteristics of S. aureus, S. epidermidis, or S. saprophyticus. On the basis of the present data and data reported elsewhere, these organisms should be considered as variants or mutants of S. aureus.

  13. High mobility organic field-effect transistor based on water-soluble deoxyribonucleic acid via spray coating

    SciTech Connect

    Shi, Wei; Han, Shijiao; Huang, Wei; Yu, Junsheng

    2015-01-26

    High mobility organic field-effect transistors (OFETs) by inserting water-soluble deoxyribonucleic acid (DNA) buffer layer between electrodes and pentacene film through spray coating process were fabricated. Compared with the OFETs incorporated with DNA in the conventional organic solvents of ethanol and methanol: water mixture, the water-soluble DNA based OFET exhibited an over four folds enhancement of field-effect mobility from 0.035 to 0.153 cm{sup 2}/Vs. By characterizing the surface morphology and the crystalline structure of pentacene active layer through atomic force microscope and X-ray diffraction, it was found that the adoption of water solvent in DNA solution, which played a key role in enhancing the field-effect mobility, was ascribed to both the elimination of the irreversible organic solvent-induced bulk-like phase transition of pentacene film and the diminution of a majority of charge trapping at interfaces in OFETs.

  14. Transcription of single base oligonucleotides by ribonucleic acid-directed deoxyribonucleic acid polymerase.

    PubMed Central

    Falvey, A K; Weiss, G B; Krueger, L J; Kantor, J A; Anderson, W F

    1976-01-01

    The synthesis of DNA products complementary to artificial templates by the enzyme RNA-directed DNA polymerase isolated from avian myeloblastosis virus has been studied. Of the single base polyribonucleotides, poly (rC), poly(rA), and poly(rI) were active while poly (rG) and poly (rU) were almost inactive. The minimum length showing activity for an oligo (rC) template was 9; the minimum primer length of oligo(dG) was 3 or 4. In order to examine the fidelity of transcription, single base oligoribonucleotides of defined length were studied. Using (rC)13 as template and (dG)8as primer, the oligo (dG) product coelectrophoresed with the template. However, using (rA)-20 as template and (dT)10 as primer, a large (10-16s) product was formed. Similarly, using oligo (rI) (2.5S) as template and (dC)10 as primer, a large (greater than 22s) product was formed. No significant activity was obtained with oligo (rU) templates. RNA-directed DNA polymerase transcribes the various oligonucleotides differently: slippage with oligo (rA) and oligo (rI), faithful transcription with oligo (rC), and poor transcription with oligo (rU). PMID:55999

  15. Determination of the base composition of deoxyribonucleic acid by measurement of the adenine-granine ratio.

    PubMed

    Kirk, J T

    1967-11-01

    A method is described for determination of the base composition (as guanine+cytosine or adenine+thymine content) of DNA by accurate measurement of the adenine/guanine ratio. The DNA is hydrolysed with 0.03n-hydrochloric acid for 40min. to release the purines. The hydrolysate is subjected to ion-exchange chromatography on Zeo-Karb 225. Apurinic acids are eluted with 0.03n-hydrochloric acid and then guanine and adenine are eluted separately with 2n-hydrochloric acid. Guanine and adenine are each collected as a single fraction, and the amount of base in each case is determined by measuring the volume and the extinction at suitable wavelengths. For use in the calculations, millimolar extinction coefficients in 2n-hydrochloric acid of 12.09 for adenine at 262mmu, and 10.77 for guanine at 248mmu, were determined with authentic samples of bases. The method gives extremely reproducible results: from 12 determinations with calf thymus DNA the adenine/guanine molar ratio had a standard deviation of 0.011; this corresponds to a standard deviation in guanine+cytosine content of 0.2% guanine+cytosine.

  16. Determination of the base composition of deoxyribonucleic acid by measurement of the adenine/guanine ratio

    PubMed Central

    Kirk, J. T. O.

    1967-01-01

    A method is described for determination of the base composition (as guanine+cytosine or adenine+thymine content) of DNA by accurate measurement of the adenine/guanine ratio. The DNA is hydrolysed with 0·03n-hydrochloric acid for 40min. to release the purines. The hydrolysate is subjected to ion-exchange chromatography on Zeo-Karb 225. Apurinic acids are eluted with 0·03n-hydrochloric acid and then guanine and adenine are eluted separately with 2n-hydrochloric acid. Guanine and adenine are each collected as a single fraction, and the amount of base in each case is determined by measuring the volume and the extinction at suitable wavelengths. For use in the calculations, millimolar extinction coefficients in 2n-hydrochloric acid of 12·09 for adenine at 262mμ, and 10·77 for guanine at 248mμ, were determined with authentic samples of bases. The method gives extremely reproducible results: from 12 determinations with calf thymus DNA the adenine/guanine molar ratio had a standard deviation of 0·011; this corresponds to a standard deviation in guanine+cytosine content of 0·2% guanine+cytosine. PMID:5626094

  17. Attitude to Human Papillomavirus Deoxyribonucleic Acid-Based Cervical Cancer Screening in Antenatal Care in Nigeria: A Qualitative Study.

    PubMed

    Filade, Temitope E; Dareng, Eileen O; Olawande, Toyosi; Fagbohun, Tolani A; Adebayo, Amos O; Adebamowo, Clement A

    2017-01-01

    Human papillomavirus (HPV) deoxyribonucleic acid (DNA)-based testing is increasingly used for cervical cancer screening in developed countries, but the best approach to utilizing it in low- and middle-income countries (LMIC) is unclear. Incorporation of HPV DNA-based testing into routine antenatal care (ANC) is a potential yet poorly explored strategy for cervical cancer screening in LMIC. We explored the attitude of health care workers and pregnant women to the incorporation of HPV DNA-based tests into routine ANC in Nigeria. We conducted nine focus group discussions with 82 pregnant women and 13 in-depth interviews with obstetricians and midwives at four health care facilities in Abuja, Nigeria. We used qualitative content analysis to analyze the data and the theory of planned behavior as a theoretical framework to examine the responses. Pregnant women expressed a favorable attitude toward HPV DNA testing for cervical cancer screening as part of routine ANC. Acceptability of this approach was motivated by the expected benefits from early detection and treatment of cervical cancer. The factors most commonly cited as likely to influence acceptability and uptake of HPV DNA-based tests are recommendations by their care providers and mandating testing as part of ANC services. Discussants mentioned lack of awareness and affordability as factors that may inhibit uptake of HPV DNA-based cervical cancer screening. Midwives expressed concerns about the safety of sampling procedure in pregnancy, while obstetricians fully support the integration of HPV DNA-based testing into routine ANC. Our results show that incorporating HPV DN-based cervical cancer screening into routine ANC is acceptable to pregnant women and health care providers. Making the test affordable and educating health care workers on its efficacy and safety if performed during ANC will enhance their willingness to recommend it and increase its uptake.

  18. Reversible phospholipid nanogels for deoxyribonucleic acid fragment size determinations up to 1500 base pairs and integrated sample stacking.

    PubMed

    Durney, Brandon C; Bachert, Beth A; Sloane, Hillary S; Lukomski, Slawomir; Landers, James P; Holland, Lisa A

    2015-06-23

    Phospholipid additives are a cost-effective medium to separate deoxyribonucleic acid (DNA) fragments and possess a thermally-responsive viscosity. This provides a mechanism to easily create and replace a highly viscous nanogel in a narrow bore capillary with only a 10°C change in temperature. Preparations composed of dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) self-assemble, forming structures such as nanodisks and wormlike micelles. Factors that influence the morphology of a particular DMPC-DHPC preparation include the concentration of lipid in solution, the temperature, and the ratio of DMPC and DHPC. It has previously been established that an aqueous solution containing 10% phospholipid with a ratio of [DMPC]/[DHPC]=2.5 separates DNA fragments with nearly single base resolution for DNA fragments up to 500 base pairs in length, but beyond this size the resolution decreases dramatically. A new DMPC-DHPC medium is developed to effectively separate and size DNA fragments up to 1500 base pairs by decreasing the total lipid concentration to 2.5%. A 2.5% phospholipid nanogel generates a resolution of 1% of the DNA fragment size up to 1500 base pairs. This increase in the upper size limit is accomplished using commercially available phospholipids at an even lower material cost than is achieved with the 10% preparation. The separation additive is used to evaluate size markers ranging between 200 and 1500 base pairs in order to distinguish invasive strains of Streptococcus pyogenes and Aspergillus species by harnessing differences in gene sequences of collagen-like proteins in these organisms. For the first time, a reversible stacking gel is integrated in a capillary sieving separation by utilizing the thermally-responsive viscosity of these self-assembled phospholipid preparations. A discontinuous matrix is created that is composed of a cartridge of highly viscous phospholipid assimilated into a separation matrix

  19. Deoxyribonucleic acid base composition and taxonomy of Moniliella and allied genera.

    PubMed

    de Hoog, G S; Guého, E

    1984-01-01

    DNA base compositions of representative (type) strains of Moniliella, Trichosporonoides and Hyalodendron were determined. Within Trichosporonoides over 16% variance was found. Most species separated well, but M. suaveolens showed considerable heterogeneity. The standard 2% G + C differences for species distinction is probably not applicable to these yeasts. The new combination M. pollinis is proposed for M. tomentosa var. pollinis on the basis of slight ecological, morphological and physiological differences, supported by a marked difference in % G + C.

  20. Base composition, size and sequence similarities of genoma deoxyribonucleic acids from clinical isolates of Pseudomonas putrefaciens.

    PubMed

    Owen, R J; Legors, R M; Lapage, S P

    1978-01-01

    The mean base compositions of DNA from 27 strains of Pseudomonas putrefaciens, P. rubescens and P. piscicida ranged from 43-4 to 53-2 mol% GC with genome sizes from 3.04 X 10(9) to 4.23 X 10(9) daltons. On the basis of in vitro DNA-DNA binding, estimated spectrophotometrically from initial renaturation rates, P. putrefaciens strains were heterogenous in the extent to which they shared similar nucleotide sequences, and were divided into four DNA homology groups. The DNA characteristics of strains in these groups correlated with several biochemical characteristics that facilitated identification of clinical isolates of P. putrefaciens. The two species P. putrefaciens and P. rubescens appear to be synonymous and none of the four groups of P. putrefaciens was related in DNA sequences to P. pisicida. Pseudomonas putrefaciens should theretofore be retained as a single species and characteristics for identifying the various groups within the species are listed.

  1. Graphene-based polyaniline arrays for deoxyribonucleic acid electrochemical sensor: effect of nanostructure on sensitivity.

    PubMed

    Yang, Tao; Meng, Le; Zhao, Jinlong; Wang, Xinxing; Jiao, Kui

    2014-01-01

    DNA detection sensitivity can be improved by carefully controlling the texture of the sensor substrate, which was normally investigated on metal or metal oxide nanostructured platform. Morphology effects on the biofunctionalization of polymer micro/nanoelectrodes have not been investigated in detail. To extend this topic, we used graphene oxide (GNO) as the supporting material to prepare graphene-based polyaniline nanocomposites with different morphologies as a model for comparing their DNA sensing behaviors. Owing to GNO serving as an excellent support or template for nucleation and growth of polyaniline (PANI), PANI nanostructures grown on GNO substrate were successfully obtained. However, if GNO supporting was absent, the obtained PANI nanowires showed a connected network. Furthermore, adjustment of reaction time can be used for dominating the topographies of PANI-GNO nanocomposites, meaning that different reaction times resulted in various formations of PANI-GNO nanocomposites, including small horns (5 and 12 h), vertical arrays (18 h), and nanotips (24 h). The next-step electrochemical data showed that the DNA electrochemical sensors constructed on the different morphologies possessed different ssDNA surface coverage and hybridization efficiency. Compared with other morphologies of PANI-GNO nanocomposite (5, 12, and 24 h), vertical arrays (18 h) exhibited the highest sensitivity (2.08 × 10(-16) M, 2 orders of magnitude lower than others). It is can be concluded that this nanocomposite with higher surface area and more accessible space can provide an optimal balance for DNA immobilization and DNA hybridization detection.

  2. 21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... ANIMALS § 528.1070 Bc6 recombinant deoxyribonucleic acid construct. (a) Specifications and indications for use. Five copies of a human Bc6 recombinant deoxyribonucleic acid (rDNA) construct located at the GTC... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Bc6 recombinant deoxyribonucleic acid...

  3. Ribonucleotides Covalently Linked to Deoxyribonucleic Acid in T4 Bacteriophage

    PubMed Central

    Speyer, J. F.; Chao, J.; Chao, L.

    1972-01-01

    Bacteriophage T4 was grown in the presence of labeled uridine. The deoxyribonucleic acid (DNA) of the phage was shown to contain covalently attached ribonucleotides. The label appears not to be internal in the DNA strands. Presumably, it is at the ends of the DNA strands and this may be related to DNA initiation. PMID:4564585

  4. Determination of triadimenol based on the quenching effect on resonance light scattering from the triadimenol-deoxyribonucleic acid-hydrochloric acid system.

    PubMed

    Du, Fengpei; Luo, Xiaolin; Jiang, Guibin; Hou, Shicong; Liu, Gang; Ren, Liping; Zhang, Li; Huang, Qin; Jie, Nianqin

    2007-05-01

    Analysis of triadimenol was carried out using deoxyribonucleic acids (DNA) via the resonance light scattering (RLS) technique. After adding triadimenol into aqueous medium of pH 1.72, the RLS of DNA was remarkably quenched. A resonance light scattering peak at 310 nm was found, and the quenched intensity of RLS at this wavelength was proportional to the concentration of triadimenol. The linear range of the calibration curve was approximately 0-3 microg mL-1 with a detection limit (S/N=3) of 0.07 microg mL-1. The triadimenol in samples of water, cucumber and human serum was determined. The results were satisfactory, and the recovery rates were in the range of 96.3-106.0%, 94.8-105.9% and 92.3-100.5%, respectively. The interaction mechanism was also studied.

  5. Fundamental Interaction Between Au Nanoparticles and Deoxyribonucleic Acid (DNA)

    DTIC Science & Technology

    2010-06-01

    Fundamental Interaction Between Au Nanoparticles and Deoxyribonucleic Acid (DNA) by Molly Karna, Govind Mallick, and Shashi P. Karna ARL...Karna Science and Mathematics Academy at Aberdeen High School Govind Mallick and Shashi P. Karna Weapons and Materials Research Directorate, ARL...GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Molly Karna, Govind Mallick, and Shashi P. Karna 5d. PROJECT NUMBER 5e. TASK NUMBER

  6. Maximizing Deoxyribonucleic Acid Yield from Dried Blood Spots

    PubMed Central

    Lane, Julie A.; Noble, Janelle A.

    2010-01-01

    Background One source of deoxyribonucleic acid (DNA) for genetic studies is the utilization of dried blood spots stored on paper cards (Guthrie cards) collected shortly after birth. These cards represent an important source of material for epidemiologic and population-based genetic studies. Extraction of DNA from these cards can lead to variable amounts of recovered DNA. We report here results of our efforts to maximize yield from this valuable, but nonrenewable, resource. Method Commercial methods of DNA extraction from blood cards were used, and protocol modifications were introduced that enhanced DNA yield. Results Use of a commercial solvent prior to DNA extraction steps gave greater yields than extraction without the solvent. Modification of the elution step by use of prewarmed extraction buffer and a soaking step at an elevated temperature increased yield by 6- to 10-fold. Conclusions The modified DNA extraction method yielded as much as 660 ng of DNA from a single 5-mm-diameter punch of a blood spot card. The DNA performed well in downstream, polymerase chain reaction-based applications. PMID:20307384

  7. Electrophoresis-Enhanced Detection of Deoxyribonucleic Acids on a Membrane-Based Lateral Flow Strip Using Avian Influenza H5 Genetic Sequence as the Model

    PubMed Central

    Wu, Jui-Chuang; Chen, Chih-Hung; Fu, Ja-Wei; Yang, Huan-Ching

    2014-01-01

    This study reports a simple strategy to detect a deoxyribonucleic acid (DNA) on a membrane-based lateral flow (MBLF) strip without tedious gel preparation, gel electrophoresis, and EtBr-staining processes. The method also enhances the detection signal of the genetic sample. A direct electric field was applied over two ends of the MBLF strips to induce an electrophoresis of DNAs through the strips. The signal enhancement was demonstrated by the detection of the H5 subtype of avian influenza virus (H5 AIV). This approach showed an excellent selectivity of H5 AIV from other two control species, Arabidopsis thaliana and human PSMA5. It also showed an effective signal repeatability and sensitivity over a series of analyte concentrations. Its detection limit could be enhanced, from 40 ng to 0.1 ng by applying 12 V. The nano-gold particles for the color development were labeled on the capture antibody, and UV-VIS and TEM were used to check if the labeling was successful. This detection strategy could be further developed to apply on the detection of drug-allergic genes at clinics or detection of infectious substances at incident sites by a simple manipulation with an aid of a mini-PCR machine and auxiliary kits. PMID:24603637

  8. Highly Sensitive Detection of Deoxyribonucleic Acid Hybridization Using Au-Gated AlInN/GaN High Electron Mobility Transistor-Based Sensors

    NASA Astrophysics Data System (ADS)

    Zhan, Xiang-Mi; Hao, Mei-Lan; Wang, Quan; Li, Wei; Xiao, Hong-Ling; Feng, Chun; Jiang, Li-Juan; Wang, Cui-Mei; Wang, Xiao-Liang; Wang, Zhan-Guo

    2017-03-01

    Gallium nitride- (GaN) based high electron mobility transistors (HEMTs) provide a good platform for biological detection. In this work, both Au-gated AlInN/GaN HEMT and AlGaN/GaN HEMT biosensors are fabricated for the detection of deoxyribonucleic acid (DNA) hybridization. The Au-gated AlInN/GaN HEMT biosensor exhibits higher sensitivity in comparison with the AlGaN/GaN HEMT biosensor. For the former, the drain-source current ( {V}{DS}=0.5 V) shows a clear decrease of 69 μA upon the introduction of 1 μmolL {}-1 (μM) complimentary DNA to the probe DNA at the sensor area, while for the latter it is only 38 μA. This current reduction is a notable indication of the hybridization. The high sensitivity can be attributed to the thinner barrier of the AlInN/GaN heterostructure, which makes the two-dimensional electron gas channel more susceptible to a slight change of the surface charge. Supported by the National Key Research and Development Program of China under Grant Nos 2016YFB0400104 and 2016YFB0400301, the National Natural Sciences Foundation of China under Grant No 61334002, and the National Science and Technology Major Project.

  9. Cell-free deoxyribonucleic acid as a prognostic marker of bowel ischemia in patients with small bowel obstruction.

    PubMed

    Netz, Uri; Perry, Zvi; Mizrahi, Solly; Kirshtein, Boris; Czeiger, David; Sebbag, Gilbert; Reshef, Avraham; Douvdevani, Amos

    2017-08-07

    Patients with strangulation small bowel obstruction are at a high risk for serious morbidity and mortality due to ischemic bowel. Measuring serum, cell-free deoxyribonucleic acid levels could help recognize early cell death. Our hypothesis was that small bowel ischemia or necrosis is associated with increases in serum cell-free deoxyribonucleic acid and that recovery is associated with a decrease in cell-free deoxyribonucleic acid levels. A prospective cohort study in addition to standard treatment of patients admitted with a diagnosis of small bowel obstruction. The participants were divided into groups depending on the presence of ischemic or necrotic bowel according to operative and clinical outcome. Clinical data and serum-based cell-free deoxyribonucleic acid levels were compared. Cell-free deoxyribonucleic acid levels from these 2 groups also were compared with a third group of healthy controls. In the study, 58 patients were enrolled, and 18 patients (31%) underwent operation. During the operative procedure, ischemic or necrotic bowel was found in 10 cases (17%). Serum levels of cell-free deoxyribonucleic acid at the time of admission in the ischemic/necrotic bowel group were increased compared with patients with well perfused or spontaneously recovered bowel (P = .03). Cell-free deoxyribonucleic acid levels decreased on the day after admission in 88% of the nonoperated patients. No significant differences were found in demographics, medical background, imaging performed, and cause of obstruction nor in clinical admission data. Surgeons currently rely on imprecise clinical parameters, including degree of pain, abdominal tenderness, leukocytosis etc to decide when operative intervention is needed. The association of cell-free deoxyribonucleic acid with small bowel obstruction, ischemia, and recovery supports our hypothesis and suggests that this biomarker is a potential surrogate of small bowel perfusion. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Stabilizing and destabilizing effects of arginine on deoxyribonucleic acid.

    PubMed

    Arakawa, Tsutomu; Hirano, Atsushi; Shiraki, Kentaro; Kita, Yoshiko; Koyama, A Hajime

    2010-03-01

    Aqueous arginine solution now finds a wide range of applications in biotechnology fields, including protein refolding, chromatography and virus inactivation. While progress has been made for mechanistic understanding of the effects of arginine on proteins, we have little understanding on how arginine inactivates viruses. One of the viral components is nucleic acid. We have examined the effects of arginine on the structure and thermal stability of calf thymus deoxyribonucleic acid (DNA) using circular dichroism (CD). Both NaCl and arginine reduced CD intensity. At low concentrations, arginine showed a stronger effect on CD intensity than NaCl. Both NaCl and arginine sharply increased the melting temperature at low concentrations (below 0.25 M). However, they had an opposite effect at higher concentrations. Above this concentration, NaCl gradually increased the melting temperature, leading to the onset melting temperature above 90 degrees C. On the other hand, the thermal stability in the presence of arginine reached a maximum at 0.2-0.5 M, after which further addition of arginine caused decreased melting temperature. It is most likely that the increased melting temperature at low concentration is due to electrostatic stabilization of DNA structure by both NaCl and arginine and that the opposite effects at higher salt concentration are due to salt-specific effects, i.e., stabilizing (salting-out) effects of NaCl and destabilizing (salting-in) effects of arginine. Solubility measurements of nucleic acid bases showed that arginine, but not NaCl, increases the solubilities of the bases, supporting their effects on DNA stability at higher concentration.

  11. The binding of echinomycin to deoxyribonucleic acid.

    PubMed Central

    Wakelin, S P; Waring, M J

    1976-01-01

    Echinomycin is a peptide antibiotic which binds strongly to double-helical DNA up to a limit of approximately one molecule per five base-pairs. There is no detectable interaction with rRNA and only extremely feeble non-specific interaction with poly(rA)-poly(rU). Heat denaturation of DNA greatly decreases the binding, and similarly limited interaction is observed with naturally occurring single-stranded DNA. Association constants for binding to nine double-helical DNA species from different sources are presented; they vary by a factor of approximately 10, but are not simply related to the gross base composition. The interaction with DNA is ionic-strength-dependent, the binding constant falling by a factor of 4 when the ionic strength is raised from 0.01 to 0.10mol/litre. From the effect of temperature on the association constant for calf thymus DNA, the enthalpy of interaction is calculated to be about -13kJ/mol (-3kcal/mol). Binding of echinomycin persists in CsCl gradients and the buoyant density of nicked bacteriophage PM2 DNA is decreased by 25 mg/ml. Echinomycin interacts strongly with certain synthetic poly-deoxynucleotides, the binding constant decreasing in the order poly(dG)-poly(dC) greater than poly(dG-dC) greater than poly(dA-dT). For the latter two polymers the number of base-pairs occluded per bound antibiotic molecule is calculated to be three, whereas for poly(dG)-poly(dC) it is estimated to be four to five. Poly(dA)-poly(dT) and poly(dI)-poly(dC) interact only very weakly with the antibiotic. Poly(dI-dC) interacts to a slightly greater extent, but the binding curve is quite unlike that seen with the three strongly binding synthetic polynucleotides. Echinomycin affects the supercoiling of closed circular duplex bacteriophage PM2 DNA in the characteristic fashion of intercalating drugs. At low ionic strength the unwinding angle is almost twice that of ethidium. Likewise the extension of the helix, determined from changes in the viscosity of rod

  12. Incorporation of Deoxyribonucleic Acid Precursors by T4 Deoxyribonucleic Acid-Protein Complexes Retained on Glass Fiber Filters

    PubMed Central

    Miller, Robert C.; Kozinski, Andrzej W.

    1970-01-01

    Bacteriophage T4 deoxyribonucleic acid (DNA)-protein complexes were retained preferentially on glass fiber filters. DNA polymerase activity in the complex was detected through the incorporation of 3H-labeled DNA precursors. The primer-product DNA hybridized with both phage and Escherichia coli DNA. Density labeling experiments showed that about 30% of incorporated 3H-deoxyadenosine triphosphate was found in DNA which hybridized with phage DNA; this DNA was found to be covalently attached to the primer DNA. PMID:5497903

  13. Photochemical Inactivation of Deoxyribonucleic and Ribonucleic Acid Viruses by Chlorpromazine

    PubMed Central

    Hanson, Carl Veith

    1979-01-01

    Chlorpromazine, a widely used tranquilizing drug of the phenothiazine group, was found to be a very potent photochemical inactivator of both deoxyribonucleic acid and ribonucleic acid viruses in the presence of long-wave ultraviolet light (320 to 380 nm). Neither the light alone nor chlorpromazine alone caused any appreciable inactivation. The known chlorpromazine photoreactions with nucleic acids are somewhat similar to those of psoralen (furocoumarin) derivatives. As in the case of the psoralens, chlorpromazine is capable of photoinactivating viruses totally within a few minutes under near-physiological or other gentle conditions. The antiviral effects of the chlorpromazine photoreaction could make it valuable for the development of inactivated viral vaccines as well as for use in the photochemotherapy of viral dermatoses. PMID:464574

  14. recA gene product is responsible for inhibition of deoxyribonucleic acid synthesis after ultraviolet irradiation.

    PubMed Central

    Trgovcević, Z; Petranović, D; Petranović, M; Salaj-Smic, E

    1980-01-01

    Deoxyribonucleic acid synthesis after ultraviolet irradiation was studied in wild-type, uvrA, recB, recA recB, and recA Escherichia coli strains. Inhibition of deoxyribonucleic acid synthesis, which occurs almost immediately after exposing the cells to ultraviolet radiation, depends on the functional gene recA. PMID:6997276

  15. Petite mutation in yeast. II. Isolation of mutants containing mitochondrial deoxyribonucleic acid of reduced size.

    PubMed

    Goldring, E S; Grossman, L I; Marmur, J

    1971-07-01

    A series of petite mutants of Saccharomyces cerevisiae, generated after treatment for various times with ethidium bromide, was isolated, and the mitochondrial deoxyribonucleic acid size for each member was estimated. It was found that, as the treatment time with ethidium bromide was increased, the mitochondrial deoxyribonucleic acid isolated from the petite series was increasingly reduced in size.

  16. Role of deoxyribonucleic acid technology in forensic dentistry.

    PubMed

    Datta, Pankaj; Datta, Sonia Sood

    2012-01-01

    In the last few years, Deoxyribonucleic Acid (DNA) analysis methods have been applied to forensic cases. Forensic dental record comparison has been used for human identification in cases where destruction of bodily tissues or prolonged exposure to the environment has made other means of identification impractical, that is, after fire exposure or mass disaster. Teeth play an important role in identification and criminology, due to their unique characteristics and relatively high degree of physical and chemical resistance. The use of a DNA profile test in forensic dentistry offers a new perspective in human identification. The DNA is responsible for storing all the genetic material and is unique to each individual. The currently available DNA tests have high reliability and are accepted as legal proofs in courts. This article gives an overview of the evolution of DNA technology in the last few years, highlighting its importance in cases of forensic investigation.

  17. Electrical conduction in macroscopically oriented deoxyribonucleic and hyaluronic acid samples

    NASA Astrophysics Data System (ADS)

    Kutnjak, Zdravko; Lahajnar, Gojmir; Filipič, Cene; Podgornik, Rudolf; Nordenskiöld, Lars; Korolev, Nikolay; Rupprecht, Allan

    2005-04-01

    Measurements of the quasistatic and frequency dependent electrical conductivity below 1 MHz were carried out on wet-spun, macroscopically oriented, calf thymus deoxyribonucleic (DNA) and umbilical cord hyaluronic acid (HA) bulk samples. The frequency dependence of the electrical conductivity in the frequency range of approximately 10-3-106Hz of both materials is surprisingly rather similar. Temperature dependence of the quasistatic electrical conductivity above the low temperature saturation plateau can be well described by the activated Arrhenius law with the activation energy of ≈0.8eV for both DNA and HA. We discuss the meaning of these findings for the possible conduction mechanism in these particular charged polyelectrolytes.

  18. Role of deoxyribonucleic acid technology in forensic dentistry

    PubMed Central

    Datta, Pankaj; Datta, Sonia Sood

    2012-01-01

    In the last few years, Deoxyribonucleic Acid (DNA) analysis methods have been applied to forensic cases. Forensic dental record comparison has been used for human identification in cases where destruction of bodily tissues or prolonged exposure to the environment has made other means of identification impractical, that is, after fire exposure or mass disaster. Teeth play an important role in identification and criminology, due to their unique characteristics and relatively high degree of physical and chemical resistance. The use of a DNA profile test in forensic dentistry offers a new perspective in human identification. The DNA is responsible for storing all the genetic material and is unique to each individual. The currently available DNA tests have high reliability and are accepted as legal proofs in courts. This article gives an overview of the evolution of DNA technology in the last few years, highlighting its importance in cases of forensic investigation. PMID:23087582

  19. Endonuclease from Micrococcus luteus Which Has Activity Toward Ultraviolet-Irradiated Deoxyribonucleic Acid: Its Action on Transforming Deoxyribonucleic Acid

    PubMed Central

    Setlow, R. B.; Setlow, Jane K.; Carrier, W. L.

    1970-01-01

    An endonuclease purified from Micrococcus luteus makes single-strand breaks in ultraviolet (UV)-irradiated, native deoxyribonucleic acid (DNA). The purified endonuclease is able to reactivate UV-inactivated transforming DNA of Haemophilus influenzae, especially when the DNA is assayed on a UV-sensitive mutant of H. influenzae. After extensive endonuclease action, there is a loss of transforming DNA when assayed on both UV-sensitive and -resistant cells. The endonuclease does not affect unirradiated DNA. The results indicate that the endonuclease function is involved in the repair of biological damage resulting from UV irradiation and that the UV-sensitive mutant is deficient in this step. We interpret the data as indicating that the various steps in the repair of DNA must be well coordinated if repair is to be effective. PMID:4314478

  20. Absence of Strand Breaks in Deoxyribonucleic Acid Treated with Metronidazole

    PubMed Central

    LaRusso, Nicholas F.; Tomasz, Maria; Kaplan, David; Müller, Miklós

    1978-01-01

    The deoxyribonucleic acid (DNA)-degrading potential of metronidazole was evaluated in vitro by three techniques: determination of melting curve, measurement of viscosity, and centrifugation in neutral or alkaline sucrose gradients. Studies were performed on calf thymus DNA and on 3H-labeled or unlabeled pneumococcal and T7 phage DNA after treatment with metronidazole alone or metronidazole reduced by sodium dithionite in the presence of DNA. This latter process is known to elicit covalent binding of metronidazole to DNA. Reduced or unreduced metronidazole had no effect on the melting properties, viscosity, or sedimentation velocity of the nucleic acids studied. Sodium dithionite alone, however, caused a 25% decrease in the intrinsic viscosity of pneumococcal DNA, and decreased the sedimentation velocity of pneumococcal and T7 phage DNA in both neutral and alkaline sucrose gradients. These data suggest that degradation of DNA is not important in the interaction of metronidazole with nucleic acids, an interaction assumed relevant to the cytotoxic, radiosensitizing, and mutagenic activities of this compound. PMID:626487

  1. Unambiguous typing of canine adenovirus isolates by deoxyribonucleic acid restriction-endonuclease analysis.

    PubMed Central

    Assaf, R; Marsolais, G; Yelle, J; Hamelin, C

    1983-01-01

    Viral deoxyribonucleic acid extracted from a limited number of cells infected with canine adenovirus type 1 or type 2 was cleaved with several restriction endonucleases. Agarose gel electrophoresis of the limit digests showed stable differences between the canine adenovirus type 1 and type 2 cleavage patterns. Rapid and accurate typing of large numbers of clinical isolates may thus be done by deoxyribonucleic acid restriction-endonuclease analysis. Images Fig. 1. Fig. 2. PMID:6321002

  2. Genetic Control of the Secondary Modification of Deoxyribonucleic Acid in Escherichia coli1

    PubMed Central

    Mamelak, Linda; Boyer, Herbert W.

    1970-01-01

    The wild-type restriction and modification alleles of Escherichia coli K-12 and B were found to have no measurable effect on the patterns of methylated bases in the deoxyribonucleic acid (DNA) of these strains. The genetic region controlling the methylation of cytosine in E. coli K-12 was mapped close to his, and the presence or absence of this gene in E. coli B or E. coli K had no effect on the restriction and modification properties of these strains. Thus, only a few of the methylated bases in the DNA of these strains are involved in host modification, and the biological role of the remainder remains obscure. PMID:4919756

  3. Influence of surfactant on dynamics of photoinduced motions in a dye-doped deoxyribonucleic acid

    NASA Astrophysics Data System (ADS)

    Mysliwiec, Jaroslaw; Parafiniuk, Kacper; Miniewicz, Andrzej; Rau, Ileana; Kajzar, Francois; Niziol, Jacek; Hebda, Edyta; Pielichowski, Jan; Sahraoui, Bouchta

    2012-10-01

    Pure deoxyribonucleic acid (DNA) is known to be soluble in water only and exhibits poor temperature stability. In contrary, it is well known that the complex of DNA - with cetyltrimethyl ammonium (CTMA) is soluble in alcohols and can be processed into very good optical quality thin films by solution casting and spin deposition. Despite the success of DNA-CTMA, there is still need for new cationic surfactants which would extend the range of available solvents for DNA complex. We test and present experimental results of influence of new surfactants based on benzalkonium chloride (BA), and didecyldimethylammonium chloride (DDCA) for applications in all optical switching.

  4. Excretion of glutamic acid in Citrobacter intermedius C3 associated with plasmid deoxyribonucleic acid.

    PubMed Central

    Jofre, J; Prieto, M J; Tomás, J; Parés, R

    1979-01-01

    Several mutants of Citrobacter intermedius C3 lacking both the ability to synthesize proline and the ability to excrete glutamic acid were isolated by treatment with nitrosoguanidine. No revertants for either characteristic were obtained from these mutants. The ability to excrete glutamic acid was transferred to those mutants with very high frequencies in mating experience by using auxotropic excreting strains as donors. Moreover, the ability to synthesize proline was transferred together with the ability to excrete glutamic acid when an excreting strain was used as donor. The transconjugants showed a rapid spontaneous curing of both genetic markers. It was shown by two different methods that a band of covalently closed circular deoxyribonucleic acid is present in the cesium chloride gradients corresponding to the wild type and excretor mutants. Nonexcretor mutants described herein lacked such a band. Pro + transformants that were also excretors were obtained with plasmid deoxyribonucleic acid isolated either from wild type or from an excretor mutant. These data strongly indicate that glutamic acid excretion in C. intermedius C3 is related to the presence of extrachromosomal deoxyribonucleic acid. PMID:457593

  5. First-trimester fetal sex prediction by deoxyribonucleic acid analysis of maternal peripheral blood.

    PubMed

    Falcinelli, C; Battafarano, S; Neri, C; Mazza, V; Ranzi, A; Volpe, A; Forabosco, A

    1999-09-01

    We investigated whether the number of weeks of gestation influences the accuracy of first-trimester fetal sex prediction by analysis of deoxyribonucleic acid extracted from whole maternal blood. A comparison was also made to determine whether a difference exists between this approach and the deoxyribonucleic acid analysis of transcervical cells performed on the same group of subjects. Deoxyribonucleic acid was isolated from 50 maternal blood samples taken between gestational weeks 7 and 11. The sex of the fetus was assessed by nested polymerase chain reaction specific for the amelogenin gene. A receiver-operating characteristic curve analysis was used to correlate the accuracy of fetal gender prediction with the gestational age and also to compare the goodness of the 2 methods under investigation. Analysis of the receiver-operating characteristic curve provided a cutoff value of 9 weeks 4 days of gestation for both tests, indicating that a higher degree of accuracy in the sex assignment was obtained in those samples taken before or at this time. However, this difference was statistically significant only for analysis of deoxyribonucleic acid from maternal blood. The comparison between tests of deoxyribonucleic acid from maternal blood and from transcervical cells showed that the first approach is better, although a statistically significant difference was not found. Analysis of maternal blood deoxyribonucleic acid is a better approach than analysis of trans-cervical cell deoxyribonucleic acid in fetal sex prediction. The highest degree of accuracy is obtained when blood is drawn before 10 weeks of gestation. This can be important when sampling of chorionic villi should be avoided because of the risk of an X-linked disease when the fetal sex is female.

  6. Synthesis and properties of novel 2'-C,4'-C-ethyleneoxy-bridged 2'-deoxyribonucleic acids with exocyclic methylene groups.

    PubMed

    Osawa, Takashi; Obika, Satoshi; Hari, Yoshiyuki

    2016-10-12

    Three 2'-C,4'-C-ethyleneoxy-bridged 2'-deoxyribonucleic acids possessing six-membered bridges with 6'-oxygen and 8'-exocyclic methylene groups (methylene-EoDNAs) were designed and synthesized in nine to ten steps from 5-methyluridine. The methylene-EoDNA-modified oligonucleotides showed excellent binding affinity with target ssRNA and extremely high nuclease resistance compared with natural oligonucleotides. These results proved the potential of methylene-EoDNAs for nucleic acid based technology.

  7. Application of Markov chain to the pattern of mitochondrial deoxyribonucleic acid mutations

    NASA Astrophysics Data System (ADS)

    Vantika, Sandy; Pasaribu, Udjianna S.

    2014-03-01

    This research explains how Markov chain used to model the pattern of deoxyribonucleic acid mutations in mitochondrial (mitochondrial DNA). First, sign test was used to see a pattern of nucleotide bases that will appear at one position after the position of mutated nucleotide base. Results obtained from the sign test showed that for most cases, there exist a pattern of mutation except in the mutation cases of adenine to cytosine, adenine to thymine, and cytosine to guanine. Markov chain analysis results on data of mutations that occur in mitochondrial DNA indicate that one and two positions after the position of mutated nucleotide bases tend to be occupied by particular nucleotide bases. From this analysis, it can be said that the adenine, cytosine, guanine and thymine will mutate if the nucelotide base at one and/or two positions after them is cytosine.

  8. Inhibition of Deoxyribonucleic Acid Synthesis and Bud Formation by Nalidixic Acid in Hyphomicrobium neptunium

    PubMed Central

    Weiner, Ronald M.; Blackman, Marcia A.

    1973-01-01

    The relationship between chromosome replication and morphogenesis in the budding bacterium Hyphomicrobium neptunium has been investigated. Nalidixic acid was found to completely inhibit deoxyribonucleic acid synthesis, but not ribonucleic acid synthesis. The antibiotic was bacteriostatic to the organism for the initial 5 h of exposure; thereafter it was bacteriocidal. Observation of inhibited cultures revealed cells that had produced abnormally long stalks, but no buds. These results indicate that bud formation is coupled to chromosome replication in H. neptunium. They do not exclude the possibilities that cross wall formation and bud separation may also be coupled to chromosome replication. Images PMID:4127631

  9. Four proteins synthesized in response to deoxyribonucleic acid damage in Micrococcus radiodurans.

    PubMed Central

    Hansen, M T

    1980-01-01

    Four proteins, alpha beta, gamma, and delta, preferentially synthesized in ultraviolet light-treated cells of Micrococcus radiodurans, were characterized in terms of their molecular weights and isoelectric points. Within the sublethal-dose range, the differential rate of synthesis for these proteins increased linearly with the inducing UV dose. The degree of induction reached 100-fold, and the most abundant protein beta, amounted to approximately 2% of the total newly synthesized protein after irradiation. Damage caused by ionizing radiation or by treatment with mitomycin C also provoked the synthesis of the four proteins. The proportions between the individual proteins, however, varied strikingly with the damaging agent. In contrast to treatments which introduced damage in the cellular deoxyribonucleic acid, the mere arrest of deoxyribonucleic acid replication, caused by nalidixic acid or by starvation for thymine, failed to elicit the synthesis of either protein. Repair of deoxyribonucleic acid damage requires that a number of versatile and efficient processes by employed. It is proposed that the induced proteins participate in deoxyribonucleic acid repair in M. radiodurans. Mechanisms are discussed which would allow a differentiated cellular response to damages of sufficiently distinctive nature. Images PMID:7354007

  10. 21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... use. Five copies of a human Bc6 recombinant deoxyribonucleic acid (rDNA) construct located at the GTC.... 528.1070 Section 528.1070 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... hircus) directing the expression of the human gene for antithrombin (which is intended for the treatment...

  11. 21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... use. Five copies of a human Bc6 recombinant deoxyribonucleic acid (rDNA) construct located at the GTC.... 528.1070 Section 528.1070 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... hircus) directing the expression of the human gene for antithrombin (which is intended for the treatment...

  12. 21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... use. Five copies of a human Bc6 recombinant deoxyribonucleic acid (rDNA) construct located at the GTC.... 528.1070 Section 528.1070 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... hircus) directing the expression of the human gene for antithrombin (which is intended for the treatment...

  13. 21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... use. Five copies of a human Bc6 recombinant deoxyribonucleic acid (rDNA) construct located at the GTC.... 528.1070 Section 528.1070 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... hircus) directing the expression of the human gene for antithrombin (which is intended for the treatment...

  14. Role of polyadenylic acid in a deoxyribonucleic acid-membrane fraction extracted from pneumococci.

    PubMed Central

    Firshein, W; Meyer, B; Epner, E; Viggiani, J

    1976-01-01

    After the addition of radioactive polyadenylic acid to cell suspensions of pneumocci, part of the radioactivity becomes associated with a deoxyribonucleic acid (DNA)-membrane fraction extracted from the cells. A variety of techniques show that a portion of this associated radioactivity may represent oligoadenylates complexed to DNA, probaby as part of a ribonucleic acid (RNA) component. Polyadenylic acid, which had previously been shown to enhance DNA synthesis in cell suspensions (Firshein and Benson, 1968), also enhances the extent of DNA synthesis by the DNA-membrane fraction in vitro under specific conditions of concentration and conformation. The mechanism of action of this enhancement may be related to the ability of oligoadenylates to increase the number of initiation sites for DNA replication by stimulating the production of an RNA primer, thus providing additional 3'-OH groups with which DNA polymerase can react. PMID:6428

  15. Simultaneous Rates of Ribonucleic Acid and Deoxyribonucleic Acid Syntheses for Estimating Growth and Cell Division of Aquatic Microbial Communities

    PubMed Central

    Karl, David M.

    1981-01-01

    A method for measuring rates of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) syntheses using a single radioactive precursor has been devised and tested using bacterial cultures and natural assemblages of marine and freshwater microorganisms. The procedure is based upon the uptake and incorporation of exogenous [3H]adenine into cellular adenosine triphosphate and deoxyadenosine triphosphate pools which serve as the immediate precursors for the adenine incorporated into RNA and DNA, respectively. It is proposed that the DNA/RNA rate ratio is correlated with the specific growth rate of microorganisms and can be used as an index for estimating and comparing the productivities of microbial assemblages in nature. This technique can also be used to detect discontinuous growth and cell division processes which frequently occur in surface plankton populations. The DNA/RNA rate ratios measured in a variety of aquatic ecosystems ranged from 3.3 to 31.8% without significant correlation to total microbial biomass. PMID:16345882

  16. Excision of pyrimidine dimers from nuclear deoxyribonucleic acid in ultraviolet-irradiated Dictyostelium discoideum

    SciTech Connect

    Clark, J.M.; Deering, R.A.

    1987-02-01

    A sensitive endonuclease assay was used to study the fate of pyrimidine dimers introduced by ultraviolet irradiation into the nuclear deoxyribonucleic acid of the cellular slime mold Dictyostellium discoideum. Analysis of the frequency of T4 endonuclease V-induced single-strand breaks by alkaline sucrose gradient sedimentation showed that strain NC4 (rad/sup +/) removed >98% of the dimers induced by irradiation at 40 J/m/sup 2/ (254 nm) within 215 min after irradiation. HPS104 (radC44), a mutant sensitive to ultraviolet irradiation, removed 91% under these conditions, although at a significantly slower rate than NC4: only 8% were removed during the 10- to 15- min period immediately after irradiation, whereas NC4 excised 64% during this interval. HPS104 thus appears to be deficient in the activity(ies) responsible for rapidly incising ultraviolet-irradiated nuclear deoxyribonucleic acid at the sites of pyrimidine dimers.

  17. INCORPORATION OF DEOXYRIBONUCLEIC ACID IN THE BACILLUS SUBTILIS TRANSFORMATION SYSTEM1

    PubMed Central

    Young, F. E.; Spizizen, John

    1963-01-01

    Young, F. E. (Western Reserve University Cleveland, Ohio) and John Spizizen. Incorporation of deoxyribonucleic acid in the Bacillus subtilis transformation system. J. Bacteriol. 86:392–400. 1963.—The optimal conditions for the incorporation of deoxyribonucleic acid (DNA) were studied. In competent cells, the irreversible binding of DNA was influenced by temperature, hydrogen ion concentration, and aeration. Divalent cations, such as barium, strontium, calcium, or magnesium, were required. Under suboptimal environmental conditions and with metabolic inhibitors, the process of transformation was decreased to a greater extent than was incorporation of DNA. Under conditions of phosphate depletion, the incorporation of P32 increased. However, the frequency of transformation decreased. This inducible process was not related to competence. PMID:14066414

  18. Blood lymphocyte ultrastructure and deoxyribonucleic acid content in children with systemic lupus erythematosis.

    PubMed

    Ptasekas, R; Matulis, A; Urmonas, V; Graziene, V; Zukiene, G

    1980-01-01

    Two varieties of peripheral blood lymphocytes have been disclosed in systemic lupus erythematosus (SLE) cases: one showing signs of degradation and nuclear chromatine elimination and the other one manifesting a state of biological activation, possibly of an immunologic nature. This karyostructural lymphocyte heterogeneity in SLE may cause a great scattering of these cells on histograms in respect to their nuclear deoxyribonucleic acid content determined by cytophotometry. On the other hand, the expressiveness of the scattering and the degree of predominance of negative tendency towards proliferation (with a shift to the left from 2 n) may thereby serve as a very objective quantitative indication of nuclear structure degradation and of loss by lymphocytes of chromatine with deoxyribonucleic acid during SLE.

  19. Electrochemical deoxyribonucleic acid biosensor based on the self-assembly film with nanogold decorated on ionic liquid modified carbon paste electrode.

    PubMed

    Gao, Hongwei; Qi, Xiaowei; Chen, Ying; Sun, Wei

    2011-10-17

    An electrochemical DNA biosensor was fabricated by self-assembling probe single-stranded DNA (ssDNA) with a nanogold decorated on ionic liquid modified carbon paste electrode (IL-CPE). IL-CPE was fabricated using 1-butylpyridinium hexafluorophosphate as the binder and the gold nanoparticles were electrodeposited on the surface of IL-CPE (Au/IL-CPE). Then mercaptoacetic acid was self-assembled on the Au/IL-CPE to obtain a layer of modified film, and the ssDNA probe was further covalently-linked with mercaptoacetic acid by the formation of carboxylate ester with the help of N-(3-dimethylamino-propyl)-N'-ethylcarbodiimide hydrochloride and N-hydroxysuccinimide. The hybridization reaction with the target ssDNA was monitored with methylene blue (MB) as the electrochemical indicator. Under the optimal conditions, differential pulse voltammetric responses of MB was proportional to the specific ssDNA arachis sequences in the concentration range from 1.0×10(-11) to 1.0×10(-6) mol L(-1) with the detection limit as 1.5×10(-12) mol L(-1) (3σ). This electrochemical DNA sensor exhibited good stability and selectivity with the discrimination ability of the one-base and three-base mismatched ssDNA sequences. The polymerase chain reaction product of arachis Arabinose operon D gene was successfully detected by the proposed method, which indicated that the electrochemical DNA sensor designed in this paper could be further used for the detection of specific ssDNA sequence. Copyright © 2011 Elsevier B.V. All rights reserved.

  20. Self-assembled ternary complexes of neutral liposomes, deoxyribonucleic acid, and bivalent metal cations. Promising vectors for gene transfer?

    NASA Astrophysics Data System (ADS)

    Bruni, P.; Pisani, M.; Amici, A.; Marchini, C.; Montani, M.; Francescangeli, O.

    2006-02-01

    By means of synchrotron x-ray diffraction we demonstrate the self-assembled formation of the neutral ternary dioleoyl-phosphatidylcholine-deoxyribonucleic acid (plasmid)-Me2+ (Me=Ca and Mn) complexes in the liquid-crystalline Lα phase. We also report an attempt of an in vitro transfection on mouse fibroplast NIH 3T3 cell lines, which shows the capability of these complexes to transfect DNA. Based on the reported results, efficient encapsulation of DNA plasmids in these ternary neutral complexes may represent an important alternative to current systemic gene approaches.

  1. pH-responsive deoxyribonucleic acid capture/release by polydopamine functionalized magnetic nanoparticles.

    PubMed

    Wang, Yu; Ma, Xiangdong; Ding, Chun; Jia, Li

    2015-03-03

    Polydopamine functionalized magnetic nanoparticles (PDA@Fe3O4) were prepared and characterized by transmission electron microscopy, scanning electron microscopy, zeta potential and vibrating sample magnetometry. They were found to enable highly efficient capture of genomic deoxyribonucleic acid (DNA). The adsorption capacity of PDA@Fe3O4 for genomic DNA can reach 161 mg g(-1). The extraction protocol used aqueous solutions for DNA binding to and releasing from the surface of the magnetic particles based on the pH inducing the charge switch of amino and phenolic hydroxyl groups on PDA@Fe3O4. The extracted DNA with high quality (A260/A280=1.80) can be directly used as templates for polymerase chain reaction (PCR) followed by capillary electrophoresis (CE) analysis. None of the toxic chemical reagents and PCR inhibitors was used throughout the whole procedure. PDA@Fe3O4 based magnetic solid phase extraction (MSPE) method was superior to those using commercial kit and traditional phenol-chloroform extraction methods in yield of DNA. The developed PDA@Fe3O4 based MSPE-PCR-CE method was applied for simultaneous and fast detection of Listeria monocytogenes and Escherichia coli O157:H7 in milk. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Motion of megabase deoxyribonucleic acid during field-inversion gel electrophoresis: Investigation by nonlocal Monte Carlo

    NASA Astrophysics Data System (ADS)

    Duke, T. A. J.; Viovy, J. L.

    1992-06-01

    We give a detailed description of a new Monte Carlo method for the simulation of the forced dynamics of long chain polymers in a constrictive environment. The model is based on the reptation theory but admits, in addition, the possibility that loops of the chain (``hernias'') may escape laterally out of the tube. A discrete representation of the molecule, in which individual chain segments are either taut or slack, permits the extensional mode of the molecule within the tube to be taken into consideration. The dynamics is modeled by the nonlocal hopping of ``defects'' (regions of slack) along the chain, with Monte Carlo rules based on the stochastic equations of motion of the taut portions of the molecule. We use the technique to investigate the motion of long deoxyribonucleic acid (DNA) molecules, containing millions of base pairs, during field-inversion gel electrophoresis. For the pulse ratios most commonly used in practice, we find that the separation patterns display two regions of band-inversion. This anomalous behavior is linked to the strong transient response of the molecules when the field is reversed; sudden field inversion induces the formation of a chain configuration shaped like an extended V after an interval of time that increases linearly with the chain length. The DNA molecules that have the minimum and the maximum migration speeds are those whose transient response times are approximately equal to the forward and the reverse pulse time, respectively.

  3. Tetracycline Inhibits Propagation of Deoxyribonucleic Acid Replication and Alters Membrane Properties

    PubMed Central

    Pato, Martin L.

    1977-01-01

    Tetracycline, at concentrations greater than required for inhibition of protein synthesis, rapidly and completely inhibits replication of deoxyribonucleic acid (DNA) in Escherichia coli and Bacillus subtilis. At these concentrations of tetracycline, synthesis of ribonucleic acid is not appreciably altered. In addition to inhibiting DNA replication, tetracycline causes alterations of the cytoplasmic membrane resulting in leakage of intracellular pools of nucleotides, amino acids, and the non-metabolizable sugar analogue, thiomethylgalactoside. As DNA is synthesized at a site on the membrane, alterations of membrane structure by tetracycline may be responsible for the observed inhibition of DNA replication. PMID:403855

  4. Lambda bacteriophage-mediated transduction of ColE1 deoxyribonucleic acid having a lambda bacteriophage-cohesive end site: selection of packageable-length deoxyribonucleic acid.

    PubMed Central

    Umene, K; Shimada, K; Tsuzuki, T; Mori, R; Takagi, Y

    1979-01-01

    An in vitro recombinant ColE1-cos lambda deoxyribonucleic acid (DNA) molecule, pKY96, has 70% of the length of lambda phage DNA. The process of lambda phage-mediated transduction of pKY96 generated a small amount of transducing phage particles containing ColE1-cos lambda DNA molecules of 80 or 101% of the length of lambda phage DNA, in addition to those containing original pKY96 DNA molecules. The newly isolated larger plasmid DNAs were transduced 100 times more efficiently than pKY96 DNA. Their structures were compared with that of a prototype pKY96 DNA, and the mechanism of the formation of these molecules is discussed. Images PMID:158007

  5. Study on the interaction of morphine chloride with deoxyribonucleic acid by fluorescence method

    NASA Astrophysics Data System (ADS)

    Li, J. F.; Dong, C.

    2009-01-01

    The mode and mechanism of the interaction of morphine chloride, an important alkaloid compound to calf thymus deoxyribonucleic acid (ct DNA) was investigated from absorption and fluorescence titration techniques. Hypochromic effect was founded in the absorption spectra of morphine when concentration of DNA increased. The decreased fluorescence study revealed non-cooperative binding of the morphine to DNA with an affinity of 3.94 × 10 3 M -1, and the stoichiometry of binding was characterized to be about one morphine molecule per nucleotide. Stern-Volmer plots at different temperatures proved that the quenching mechanism was static. Ferrocyanide quenching study showed that the magnitude of KSV of the bound morphine was lower than that of the free one. In addition, it was found that ionic strength could affect the binding of morphine and DNA. Fluorescence polarization and denatured DNA studies also applied strong evidences that morphine molecule was partially intercalated between every alternate base pairs of ct DNA. As observed from above experiments, intercalation was well supported as the binding mode of morphine and ct DNA.

  6. Integrity of nuclear genomic deoxyribonucleic acid in cooked meat: Implications for food traceability.

    PubMed

    Aslan, O; Hamill, R M; Sweeney, T; Reardon, W; Mullen, A M

    2009-01-01

    It is essential to isolate high-quality DNA from muscle tissue for PCR-based applications in traceability of animal origin. We wished to examine the impact of cooking meat to a range of core temperatures on the quality and quantity of subsequently isolated genomic (specifically, nuclear) DNA. Triplicate steak samples were cooked in a water bath (100 degrees C) until their final internal temperature was 75, 80, 85, 90, 95, or 100 degrees C, and DNA was extracted. Deoxyribonucleic acid quantity was significantly reduced in cooked meat samples compared with raw (6.5 vs. 56.6 ng/microL; P < 0.001), but there was no relationship with cooking temperature. Quality (A(260)/A(280), i.e., absorbance at 260 and 280 nm) was also affected by cooking (P < 0.001). For all 3 genes, large PCR amplicons (product size >800 bp) were observed only when using DNA from raw meat and steak cooked to lower core temperatures. Small amplicons (<200 bp) were present for all core temperatures. Cooking meat to high temperatures thus resulted in a reduced overall yield and probable fragmentation of DNA to sizes less than 800 bp. Although nuclear DNA is preferable to mitochondrial DNA for food authentication, it is less abundant, and results suggest that analyses should be designed to use small amplicon sizes for meat cooked to high core temperatures.

  7. Coordination of deoxyribonucleic acid by ions of alkaline-earth elements

    SciTech Connect

    Tikhonova, L.I.

    1986-05-01

    The interaction of deoxyribonucleic acid (DNA) isolated from salmonid fish milt with Ca/sup 2 +/ and Sr/sup 2 +/ has been studied by conductometric, ion-exchange, and spectroscopic (circular dichroism, CD) methods at ambient ionic strengths equal to 0.0025, 0.0036, 0.0005, 0.01, and 0.165 (NaCl) and pH 6.5-6.6 and and.4 (buffer). The molecular weights of the biopolymer were 9.1 x 10/sup 6/ and 15.35 x 10/sup 6/ (ion exchange was carried out with the native and denatured forms with the use of /sup 45/Ca and /sup 85/Sr). The discontinuities on the conductometric titration curves correspond to M/sup 2 +/:DNA ratios equal to 0.125, 0.3, and 0.5. The calculated values of the associated constants are close for the two samples in the native and denatured forms over a broad range of concentrations of the cations. An anticooperature process has been established in the interaction of the cations with phosphate groups in both forms of the biopolymer. It has been concluded that the phosphate groups and purine bases of the DNA participate in coordination when the ionic strength is low or when the excess of the cations is great (..mu.. = 0.165). This attests to the influence of the concentration of the sodium ion on the interaction processes of DNA.

  8. Particle acceleration for delivery deoxyribonucleic acid vaccine into skin in vivo

    NASA Astrophysics Data System (ADS)

    Xinglong, Yu; Xiwen, Zhang; Yuan, Wang; Junshi, Xie; Pengfei, Hao

    2001-08-01

    Skin represents an important immunogenic inductive site, 3%-4% epidermis cells are special antigen-presenting cells. Deoxyribonucleic acid (DNA) vaccine can elicit vigorous immune responses in epidermis cells. The means of delivering DNA vaccine into epidermis cells becomes an important step in DNA vaccine applications. This article presents a new type of gene gun based on the principle of two-stage injector acceleration. DNA coated particles are attached on an screen-type carrier located at the negative pressure inlet, the particles will be sucked into the accelerating channel by negative pressure and be accelerated at a great speed. FLUENT, a computation fluid dynamic application software is used to simulate the flow condition of the injector. Distribution of Mach number, total pressure on exit cross section, and negative pressure on negative pressure inlet are analyzed, by which the process of acceleration of particles is determined. We also measured these parameters in this study. The data show that the particle velocity can be up to 500 m/s and the particles distribute evenly over a circle of Φ 20 mm. The numerical simulation results coincide with experimental data well. Therefore, the results of numerical simulation can be served as guidance for an optimal design of the gene gun and for practical operations. When gene coated particles are distributed evenly, they can penetrate into or even through epidermis cells where the gene can be expressed and subsequently elicits host immune responses. This device may be evaluated in human objects in future.

  9. Photodynamic Action on Native and Denatured Transforming Deoxyribonucleic Acid from Haemophilus influenzae

    PubMed Central

    León, Manuel Ponce-De; Cabrera-Juárez, Emiliano

    1970-01-01

    The photodynamic inactivation of native or denatured transforming deoxyribonucleic acid (DNA) from Haemophilus influenzae is described. The inactivation at the same pH was higher for denatured than native DNA. At acidic pH, the inactivation both for native and denatured DNA was faster than at alkaline pH. The guanine content of photoinactivated native DNA at neutral pH was less than untreated DNA. The inactivation of biological activity was more extensive than the alteration of guanine. The absorption spectrum of photoinactivated native or denatured DNA was only slightly different than the control DNA at the different experimental conditions. PMID:5309576

  10. The complementary deoxyribonucleic acid sequence of guinea pig endometrial prorelaxin.

    PubMed

    Lee, Y A; Bryant-Greenwood, G D; Mandel, M; Greenwood, F C

    1992-03-01

    The nucleotide sequence of the relaxin gene transcript in the endometrium of the late pregnant guinea pig has been determined. The strategy used was a combination of polymerase chain reaction (PCR) with primers designed from the mRNA sequence of porcine preprorelaxin, rapid amplification of cDNA ends-PCR, and blunt end cloning in M13 mp18. With heterologous primers, a 226-basepair (bp) segment of the guinea pig relaxin gene sequence was obtained and was used to design a guinea pig-specific primer for use with the rapid amplification of cDNA ends-PCR method. The latter allowed completion of the sequence of 336 bp, with a 96-bp overlap. The sequence obtained shows greater homology at both the nucleotide and amino acid levels with porcine and human relaxins H1 and H2 than with rat relaxin, supporting the thesis that the guinea pig is not a rodent. The transcription of the guinea pig endometrial relaxin gene during pregnancy was confirmed by Northern analysis of guinea pig endometrial tissues with a species-specific cDNA probe. The endometrial relaxin gene is transcribed during pregnancy, but not in lactation, consistent with the observed immunostaining for relaxin.

  11. Kinetic and spectrophotometric studies on the renaturation of deoxyribonucleic acid.

    PubMed

    Thrower, K J; Peacocke, A R

    1968-10-01

    The kinetics of the renaturation of Escherichia coli DNA in 0.4-1.0m-sodium chloride at temperatures from 60 degrees to 90 degrees have been studied. The extent of renaturation was a maximum at 65 degrees to 75 degrees and increased with ionic strength, and the rate constant increased with both ionic strength and temperature. The energy and entropy of activation of renaturation were calculated to be 6-7kcal.mole(-1) and -40cal.deg.(-1)mole(-1) respectively. It has been shown that renaturation is a second-order process for 5hr. under most conditions. The results are consistent with a reaction in which the rate-controlling step is the diffusion together of two separated complementary DNA strands and the formation of a nucleus of base pairs between them. The kinetics of the renaturation of T7-phage DNA and Bordetella pertussis DNA have also been studied, and their rates of renaturation related quantitatively to the relative heterogeneity of the DNA samples. By analysis of the spectra of DNA at different stages during renaturation it was shown that initially the renatured DNA was rich in guanine-cytosine base pairs and non-random in base sequence, but that, as equilibrium was approached, the renatured DNA gradually resembled native DNA more closely. The rate constant for the renaturation of guanine-cytosine base pairs was slightly higher than for adenine-thymine base pairs.

  12. Semiconductor sensor embedded microfluidic chip for protein biomarker detection using a bead-based immunoassay combined with deoxyribonucleic acid strand labeling.

    PubMed

    Lin, Yen-Heng; Peng, Po-Yu

    2015-04-15

    Two major issues need to be addressed in applying semiconductor biosensors to detecting proteins in immunoassays. First, the length of the antibody on the sensor surface surpasses the Debye lengths (approximately 1 nm, in normal ionic strength solution), preventing certain specifically bound proteins from being tightly attached to the sensor surface. Therefore, these proteins do not contribute to the sensor's surface potential change. Second, these proteins carry a small charge and can be easily affected by the pH of the surrounding solution. This study proposes a magnetic bead-based immunoassay using a secondary antibody to label negatively charged DNA fragments for signal amplification. An externally imposed magnetic force attaches the analyte tightly to the sensor surface, thereby effectively solving the problem of the analyte protein's distance to the sensor surface surpassing the Debye lengths. In addition, a normal ion intensity buffer can be used without dilution for the proposed method. Experiments revealed that the sensitivity can be improved by using a longer DNA fragment for labeling and smaller magnetic beads as solid support for the antibody. By using a 90 base pair DNA label, the signal was 15 times greater than that without labeling. In addition, by using a 120 nm magnetic bead, a minimum detection limit of 12.5 ng mL(-1) apolipoprotein A1 can be measured. Furthermore, this study integrates a semiconductor sensor with a microfluidic chip. With the help of microvalves and micromixers in the chip, the length of the mixing step for each immunoassay has been reduced from 1h to 20 min, and the sample volume has been reduced from 80 μL to 10 μL. In practice, a protein biomarker in a urinary bladder cancer patient's urine was successfully measured using this technique. This study provides a convenient and effective method to measure protein using a semiconductor sensor.

  13. “BLACK LIGHT” INACTIVATION OF TRANSFORMING DEOXYRIBONUCLEIC ACID FROM HAEMOPHILUS INFLUENZAE

    PubMed Central

    Cabrera-Juárez, Emiliano

    1964-01-01

    Cabrera-Juárez, Emiliano (Instituto Politecnico Nacional, Mexico, D.F., Mexico). “Black light” inactivation of transforming deoxyribonucleic acid from Haemophilus influenzae. J. Bacteriol. 87:771–778. 1964.—The biological activity (intrinsic genetic markers or nitrous acid mutable regions) of transforming deoxyribonucleic acid (DNA) from Haemophilus influenzae has been inactivated by “black light” (BL) by two mechanisms: (i) photodynamic action (oxygen-dependent) and (ii) “BL inactivation” (oxygen-independent). The BL inactivation is greater in denatured than in native DNA, and it is dependent on the pH. It does not depend on the temperature, and the damage produced is stable. The effective wavelength of inactivation is between 330 and 360 mμ. The BL inactivation is not reactivated by photoreactivating enzyme or nitrous acid. The BL and ultraviolet inactivations are additive, suggesting that the changes produced by BL and ultraviolet irradiation on transforming DNA are different. T2 phage was also inactivated by BL. The nature of the photochemical changes produced in DNA by BL is not known. PMID:14139527

  14. Individual identification from semen by the deoxyribonucleic acid (DNA) fingerprint technique.

    PubMed

    Honma, M; Yoshii, T; Ishiyama, I; Mitani, K; Kominami, R; Muramatsu, M

    1989-01-01

    For individual identification from semen, the deoxyribonucleic acid (DNA) fingerprint technique was used. In a blind trial, we succeeded in determining the semen donors among several volunteers comparing the DNA fingerprints of the blood and semen samples, respectively. Thereafter, we examined semen in a condom left beside a naked female dead body. The DNA fingerprint of the semen was recognized to be identical to that of the blood from a suspected man arrested later. This is the first report that the DNA fingerprint technique was practically used in a criminal investigation in Japan.

  15. Survival, Deoxyribonucleic Acid Breakdown, and Synthesis in Salmonella typhimurium as Compared with Escherichia coli B Strains

    PubMed Central

    Hudnik-Plevnik, Tamara A.; Djordjević, Nadežda

    1970-01-01

    Salmonella typhimurium LT-2 was compared with radioresistant (B/r) and radiosensitive (Bs−2) strains of Escherichia coli in respect to the survival, deoxyribonucleic acid (DNA) breakdown, and DNA synthesis after X irradiation. It is shown that S. typhimurium LT-2 is about four times more sensitive than E. coli B/r but less sensitive than Bs−2. The DNA breakdown is in S. typhimurium LT-2 lower than the postirradiation breakdown of DNA in both E. coli strains and DNA synthesis proceeds in this bacterium in spite of a much lower survival, as in the radioresistant E. coli B/r. PMID:4916313

  16. Mechanisms of Inhibition of Pyrimidine Dimer Formation in Deoxyribonucleic Acid by Acridine Dyes

    PubMed Central

    Sutherland, B. M.; Sutherland, J. C.

    1969-01-01

    The ultraviolet (UV)-induced formation of cyclobutyl pyrimidine dimers in Escherichia coli deoxyribonucleic acid (DNA) in vitro has been investigated in terms of the mechanism of inhibition by acridine dyes, the effect on dimer yield of specific singlet and triplet quenchers, and the mechanism of dimer formation. Our results indicate that (a) energy transfer is important in dimer reduction by acridines, (b) this transfer occurs from the singlet (S1) of DNA, and (c) at room temperature triplet quenchers do not reduce dimer yield in DNA. PMID:4888976

  17. Some Unique Properties of the Deoxyribonucleic Acid-Bearing Portion of the Bacterial Membrane

    PubMed Central

    Ballesta, J. P.; Cundliffe, E.; Daniels, M. J.; Silverstein, Judith L.; Susskind, Miriam M.; Schaechter, M.

    1972-01-01

    By using the M-band technique we have shown that portions of the membranes of Bacillus megaterium and Escherichia coli vary in their affinity for magnesium-Sarkosyl crystals and in phospholipid composition. The portion to which deoxyribonucleic acid is attached comprises as little as 4% of the total cell membrane, has a particularly high degree of affinity for magnesium-Sarkosyl crystals, and is rich in phosphatidylethanolamine. The M-band fractionation does not depend on the use of lysozyme. PMID:4627921

  18. Role of deoxyribonucleic acid ligase in a doxyribonucleic acid membrane fraction extracted from pneumococci.

    PubMed Central

    Greene, M; Firshein, W

    1976-01-01

    Deoxyribonucleic acid (DNA) ligase has been detected in a DNA membrane fraction extracted from Pneumococcus. The specific activity of the enzyme in this fraction is 10-fold greater than in the remaining cell extract. It remains firmly bound (with other enzymes) to the complex after a purification procedure in which a considerable percentage of the macromolecules are dissociated. The ligase acts in two ways in the DNA membrane fraction in vitro. One, it catalyzes the linkage of small-molecular-weight pieces of newly synthesized DNA into heavier-molecular-weight DNA strands as shown by others (M Gellert, 1976; R. Okazaki, A. Sugino, S. Hirose, T. Okazaki, Y. Imae, R. Kainuma-Kuroda, T. Ogawa, M. Arisawa, and Y. Kurosowa, 1973; B. Olivera and I. Lehman, 14; and A. Sugino, S. Hirose, and R. Okazaki, 1972) and, two, it protects DNA from degradation by deoxyribonucleases. This latter effect is due to a competition between the ability of the nucleases to degrade DNA and the ability of DNA ligase to seal the nicks produced by these degradative enzymes. The ligase acts cooperatively with other enzymes in the DNA membrane fraction to synthesize DNA. PMID:4433

  19. Intracellular Forms of Adenovirus Deoxyribonucleic Acid I. Evidence for a Deoxyribonucleic Acid-Protein Complex in Baby Hamster Kidney Cells Infected with Adenovirus Type 12

    PubMed Central

    Doerfler, Walter; Lundholm, Ulla; Hirsch-Kauffmann, Monica

    1972-01-01

    The total intracellular deoxyribonucleic acid (DNA) from baby hamster kidney cells abortively infected with 3H-adenovirus type 12 was analyzed in dye-buoyant density gradients. Between 10 and 20% of the cell-associated radioactivity derived from viral DNA bands in a density position which is 0.043 to 0.085 g/cm3 higher than that of viral DNA extracted from purified virions. The DNA in the high-density region (HP-fraction) is almost completely absent when DNA, ribonucleic acid (RNA) or protein synthesis is chemically inhibited in separate experiments. The HP-fraction is not found when the virus does not adsorb to and enter the cell. The DNA in the HP-fraction appears as early as 2 hr after inoculation. At 2 hr after infection, the HP-fraction is present both in the nucleus and the cytoplasm. This DNA hybridizes exclusively with viral DNA and sediments at approximately the same rate in both neutral and alkaline sucrose density gradients. Electron microscopy has revealed no circular DNA molecules in this fraction. Evidence indicates that the viral DNA in the HP-fraction exists in a complex with protein and possibly RNA. The protein component of the complex is resistant to enzymatic digestion, whereas the complex is susceptible to ribonuclease treatment. Digestion with deoxyribonuclease reduces the amount of DNA found in the HP-fraction. The structure and biological function of this complex are currently being investigated. PMID:5062681

  20. Influence of Bacteriophage PBS1 and φW-14 Deoxyribonucleic Acids on Homologous Deoxyribonucleic Acid Uptake and Transformation in Competent Bacillus subtilis

    PubMed Central

    López, Paloma; Espinosa, Manuel; Piechowska, Mirosława; Shugar, David

    1980-01-01

    Both bacteriophage PBS1 deoxyribonucleic acid (DNA) (in which all the thymine residues are replaced by uracil) and phage φW-14 DNA [in which half the thymine residues are replaced by 5-(aminobutylaminomethyl)uracil or 5-putrescinylthymine] exhibit comparable competing abilities for uptake of homologous DNA in a Bacillus subtilis competent system. But, whereas PBS1 DNA leads to a decrease in transformation frequencies compatible with its competing ability for DNA uptake, φW-14 DNA decreases transformation frequencies by a factor up to eightfold higher. The effect of φW-14 DNA on transformation frequencies is visible even at a concentration level that does not decrease transforming DNA uptake. No such effect was observed with heterologous DNA containing presumably ionically bound putrescine. Low concentrations of φW-14 DNA decreased the number of double (nonlinked) transformants more than single transformants. The influence on transformation was abolished when φW-14 DNA was added 20 min after addition of transforming DNA, i.e., when the recombination process was terminated. The putrescine-containing DNA also decreased retention of trichloroacetic acid-precipitable radioactivity of homologous DNA taken up. We conclude that φW-14 DNA inhibits some intracellular process(es) at the level of recombination. In addition, there is evidence that φW-14 DNA, but not heterologous DNA with ionically bound putrescine, binds also to site(s) on the cell surface other than receptors for homologous DNA. PMID:6772635

  1. Further Evidence Concerning the Configuration of Transforming Deoxyribonucleic Acid During Entry into Bacillus subtilis1

    PubMed Central

    Strauss, Norman

    1966-01-01

    Strauss, Norman (State University of New York at Buffalo, Buffalo, N.Y.). Further evidence concerning the configuration of transforming deoxyribonucleic acid during entry into Bacillus subtilis. J. Bacteriol 91:702–708. 1966.—The appearance of linked, unselected traits with selected markers was followed as a function of time after the exposure of competent cells to transforming deoxyribonucleic acid (DNA). It was found that the per cent cotransfer of a linked, unselected trait with a single selected trait increased sharply soon after the lag period characterizing the appearance of the selected trait. Similar results were obtained when cotransfer of a linked unselected trait with a pair of selected traits was examined. The results are taken as an unequivocal demonstration that the entry of transforming DNA into competent Bacillus subtilis occurs in longitudinal fashion. The nature of the linkage between try2 and his9 was characterized. It was found that, although these two traits had been found to be unlinked on the basis of recombination tests, the saturation curves showed these two traits to be present on the same fragment of DNA. PMID:4956757

  2. PENICILLIN RESISTANCE OF COMPETENT CELLS IN DEOXYRIBONUCLEIC ACID TRANSFORMATION OF BACILLUS SUBTILIS.

    PubMed

    NESTER, E W

    1964-04-01

    Nester, E. W. (University of Washington, Seattle). Penicillin resistance of competent cells in deoxyribonucleic acid transformation of Bacillus subtilis. J. Bacteriol. 87:867-875. 1964.-Transformants are resistant to penicillin killing for several hours after deoxyribonucleic acid (DNA) addition. The present study indicates that this resistance is a consequence of such cells still remaining competent and is not the result of any interaction of donor DNA with the recipient cell. The following data support this conclusion: (i) the frequency of transformation can be increased five- to tenfold if penicillin acts on a competent culture prior to DNA addition; (ii) the percentage of competent cells in such a penicillin-treated culture calculated on the basis of a random coincidence of DNA molecules entering the same cell increases some 25-fold over that of a penicillin-nontreated population; (iii) the kinetics of penicillin killing of a recipient culture are identical whether or not transforming DNA has been added; (iv) the extent of killing by penicillin is related to the level of competence of the recipient culture; and (v) the kinetics of appearance and disappearance of competence in a population as well as in individual cells indicate that a cell may remain competent for 3 to 4 hr.

  3. A MapReduce approach to diminish imbalance parameters for big deoxyribonucleic acid dataset.

    PubMed

    Kamal, Sarwar; Ripon, Shamim Hasnat; Dey, Nilanjan; Ashour, Amira S; Santhi, V

    2016-07-01

    In the age of information superhighway, big data play a significant role in information processing, extractions, retrieving and management. In computational biology, the continuous challenge is to manage the biological data. Data mining techniques are sometimes imperfect for new space and time requirements. Thus, it is critical to process massive amounts of data to retrieve knowledge. The existing software and automated tools to handle big data sets are not sufficient. As a result, an expandable mining technique that enfolds the large storage and processing capability of distributed or parallel processing platforms is essential. In this analysis, a contemporary distributed clustering methodology for imbalance data reduction using k-nearest neighbor (K-NN) classification approach has been introduced. The pivotal objective of this work is to illustrate real training data sets with reduced amount of elements or instances. These reduced amounts of data sets will ensure faster data classification and standard storage management with less sensitivity. However, general data reduction methods cannot manage very big data sets. To minimize these difficulties, a MapReduce-oriented framework is designed using various clusters of automated contents, comprising multiple algorithmic approaches. To test the proposed approach, a real DNA (deoxyribonucleic acid) dataset that consists of 90 million pairs has been used. The proposed model reduces the imbalance data sets from large-scale data sets without loss of its accuracy. The obtained results depict that MapReduce based K-NN classifier provided accurate results for big data of DNA. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  4. Molecular beacon mediated circular strand displacement strategy for constructing a ratiometric electrochemical deoxyribonucleic acid sensor.

    PubMed

    Gao, Fenglei; Du, Lili; Zhang, Yu; Tang, Daoquan; Du, Yan

    2015-07-09

    A novel ratiometric electrochemical sensor for sensitive and selective determination of deoxyribonucleic acid (DNA) had been developed based on signal-on and signal-off strategy. The target DNA hybridized with the loop portion of ferrocene (Fc) labeled hairpin probe immobilized on the gold electrode (GE), the Fc away from the surface of GE and the methylene blue (MB) was attached to an electrode surface by hybridization between hairpin probe and MB labeled primer. Such conformational changes resulted in the oxidation peak current of Fc decreased and that of MB increased, and the changes of dual signals are linear with the concentration of DNA. Furthermore, with the help of strand-displacement polymerization, polymerase catalyzed the extension of the primer and the sequential displacement of the target DNA, which led to the release of target and another polymerization cycle. Thus the circular strand displacement produced the multiplication of the MB confined near the GE surface and Fc got away from the GE surface. Therefore, the recognition of target DNA resulted in both the "signal-off" of Fc and the "signal-on" of MB for dual-signal electrochemical ratiometric readout. The dual signal strategy offered a dramatic enhancement of the stripping response. The dynamic range of the target DNA detection was from 10(-13) to 10(-8) mol L(-1) with a detection limit down to 28 fM level. Compared with the single signaling electrochemical sensor, the dual-signaling electrochemical sensing strategy developed in this paper was more selective. It would have important applications in the sensitive and selective electrochemical determination of other small molecules and proteins.

  5. Absence of Circular Plasmid Deoxyribonucleic Acid Attributable to a Genetic Determinant for Methicillin Resistance in Staphylococcus aureus

    PubMed Central

    Stiffler, Paul W.; Sweeney, H. M.; Cohen, Sidney

    1973-01-01

    Plasmid deoxyribonucleic acid was not detected by centrifugal analysis of lysates of penicillinase-negative strains of Staphylococcus aureus harboring a determinant of methicillin resistance derived from strain Villaluz. When these strains contained a penicillinase plasmid, the plasmid deoxyribonucleic acid of methicillin-resistant and methicillin-susceptible strains was indistinguishable by the methods employed. The results indicate that the genetic determinant for methicillin resistance in the strains examined was not associated with a circular plasmid comparable to those that have been shown to determine resistance to benzylpenicillin, tetracycline, and chloramphenicol in S. aureus. PMID:4490525

  6. Protein Synthesis and Deoxyribonucleic Acid-Membrane Attachment During Thymineless Death in Escherichia coli

    PubMed Central

    Dankberg, Frances; Cummings, Donald J.

    1973-01-01

    The proteins synthesized during thymineless death in Escherichia coli B and B/r were analyzed by polyacrylamide gel elctrophoresis. It was found that the amount of a protein of molecular weight 80,000 to 88,000 is greatly increased during thymineless death compared to the amounts of other cell proteins. A technique for the isolation of cell membrane-deoxyribonucleic acid (DNA)-nascent ribonucleic acid (RNA) complex on detergent crystals was used to determine whether DNA might be detached from the cell membrane as a result of thymineless death. It was found that under no conditions of thymineless death or immunity to thymineless death was there any change in the attachment of DNA or pulse-labeled RNA to cell membrane. Images PMID:4570604

  7. Influence of surfactant on dynamics of photoinduced motions and light emission of a dye-doped deoxyribonucleic acid

    NASA Astrophysics Data System (ADS)

    Sznitko, Lech; Parafiniuk, Kacper; Miniewicz, Andrzej; Rau, Ileana; Kajzar, Francois; Niziol, Jacek; Hebda, Edyta; Pielichowski, Jan; Sahraoui, Bouchta; Mysliwiec, Jaroslaw

    2013-10-01

    Pure deoxyribonucleic acid (DNA) is known to be soluble in water only and exhibits poor temperature stability. In contrary, it is well known that the complex of DNA - with cetyltrimethyl ammonium (CTMA) is insoluble in water but soluble in alcohols and can be processed into very good optical quality thin films by solution casting or spin deposition. Despite the success of DNA-CTMA, there is still need for new cationic surfactants which would extend the range of available solvents for DNA complex. We test and present experimental results of influence of new surfactants replacing CTMA in the DNA complex and based on benzalkonium chloride (BA) and didecyldimethylammonium chloride (DDCA) on their optical properties. Particularly, we were interested in all optical switching and light generation in amplified spontaneous emission process in these materials.

  8. Respiratory-deficient mutants of Torulopsis glabrata, a yeast with circular mitochondrial deoxyribonucleic acid of 6 mu m.

    PubMed Central

    O'Connor, R M; McArthur, C R; Clark-Walker, G D

    1976-01-01

    Purified mitochondria from the petite positive yeast Torulopsis glabrata contain a circular deoxyribonucleic acid (DNA) with a length of 6 mum and a buoyant density of 1.686 g/cm3. This DNA is absent from ethidium bromide induced respiratory-deficient mutants. Images PMID:944184

  9. Fluorescence, spectroscopic and NLO properties of green tea extract in deoxyribonucleic acid

    NASA Astrophysics Data System (ADS)

    Manea, Ana-Maria; Rau, Ileana; Kajzar, Francois; Meghea, Aurelia

    2013-11-01

    Natural, purely biological deoxyribonucleic acid (DNA)-green tea extract (GTE) complexes at different concentrations were prepared and characterized for their spectroscopic, fluorescent, linear and nonlinear optical properties. The complexes can be processed into good optical quality thin films by solution casting. They fluoresce when excited in UV absorption band, with a significantly larger quantum yield for the DNA-GTE complex than for a pure GTE solution. The thin film refractive indices were determined by Fabry-Perot (FP) interference patterns. The third-order nonlinear optical (NLO) properties of thin films were determined by the optical third-harmonic generation technique at 1064.2 nm fundamental wavelength. The phase of THG susceptibility was determined from the concentration variation of THG susceptibility. It reveals presence of a two-photon resonance with a band lying in the optical gap.

  10. New Deoxyribonucleic Acid Polymerase Induced by Bacillus subtilis Bacteriophage PBS2

    PubMed Central

    Price, Alan R.; Cook, Sandra J.

    1972-01-01

    The deoxyribonucleic acid (DNA) of Bacillus subtilis phage PBS2 has been confirmed to contain uracil instead of thymine. PBS2 phage infection of wild-type cells or DNA polymerase-deficient cells results in an increase in the specific activity of DNA polymerase. This induction of DNA polymerase activity is prevented by actinomycin D and chloramphenicol. In contrast to the major B. subtilis DNA polymerase, which prefers deoxythymidine triphosphate (dTTP) to deoxyuridine triphosphate (dUTP), the DNA polymerase in crude extracts of PBS2-infected cells is equally active whether dTTP or dUTP is employed. This phage-induced polymerase may be responsible for the synthesis of uracil-containing DNA during PBS2 phage infection. PMID:4623224

  11. Features of the damage produced by proflavine on transforming deoxyribonucleic acid.

    PubMed

    Cabrera-Juárez, E; Sánchez-Rincón, D A

    1979-03-01

    Proflavine formed a complex with transforming deoxyribonucleic acid (DNA) from Haemophilus influenzae, with optimal formation at a ratio of proflavine to DNA of 0.06. The rate of dissociation of the complex by dialysis increased in the order: native, denatured, renatured DNA. The transforming activity of the DNA was reduced by its interaction with proflavine. This inactivation was dependent on the physical state of the DNA, the proflavine concentration, and the temperature. DNA that had been denatured and renatured was most sensitive; native DNA was much less sensitive. The inactivation remained after dialysis and was stable to prolonged storage. It is concluded that the inactivation of transforming DNA by proflavine takes place by a mechanism different from that of DNA-proflavine complex formation.

  12. Capsid Size and Deoxyribonucleic Acid Length: the Petite Variant of Bacteriophage T4

    PubMed Central

    Eiserling, Frederick A.; Geiduschek, E. Peter; Epstein, Richard H.; Metter, E. Jeffrey

    1970-01-01

    A mutant which produces a small-headed (“petite”) variant of bacteriophage T4 is described. The mutation (E920g) maps in a new gene (66) between genes 23 and 24. Petite phage particles composed up to 70% of the phage yield. The petite phage was nonviable upon single infection but produced progeny when two or more infected a cell. Its genome was shortened by a random deletion of about 30%, and deoxyribonucleic acid (DNA) extracted from the particles was 0.68 the length of normal T4 DNA. The reduction in DNA length was accompanied by a proportional reduction in head volume. Double mutants between E920g and head-defective mutants in gene 21 produced unusually high frequencies of spherical capsidlike structures (τ-particles). Images PMID:4924630

  13. Anomalies in the Sedimentation of Deoxyribonucleic Acid from Haemophilus influenzae in Alkaline Sucrose Gradients

    PubMed Central

    Kantor, George J.

    1972-01-01

    Difficulties were experienced in obtaining reproducible results for the sedimentation in alkaline sucrose gradients of Haemophilus influenzae deoxyribonucleic acid (DNA). The technique of McGrath and Williams of lysing whole cells on top of an alkaline sucrose gradient was employed. The addition of 0.2% sodium lauryl sulfate to the 0.2 n NaOH lysing solution and reduction of the hemin concentration in the growth medium increased the reproducibility to 100% for log-phase cells handled in a manner mimicking the handling procedure used for irradiating cells with ultraviolet light. Distributions of DNA with number average molecular weights of 200 × 106 were routinely obtained by using these modifications. PMID:4539243

  14. Number of Deoxyribonucleic Acid Uptake Sites in Competent Cells of Bacillus subtilis

    PubMed Central

    Singh, R. N.

    1972-01-01

    Two direct methods are presented for estimating the average number of deoxyribonucleic acid (DNA) uptake sites in competent cells of Bacillus subtilis from measurement of 14C- or 3H-thymine-labeled DNA uptake by competent culture. Advantage is taken of two facts: (i) effective contact between competent cells and transforming DNA molecules is established within a short time after mixing them together, and (ii) DNA molecules enter the competent B. subtilis cells in a linear fashion at a finite speed. From the number of DNA molecules initially attached to competent cells by brief exposure to transforming DNA in the first method or from the rate of DNA uptake by competent culture in the second method, the average number of DNA uptake sites is calculated to be 20 to 53 per competent cell. PMID:4622899

  15. Deoxyribonucleic acid damage induced by doxorubicin in peripheral blood mononuclear cells: possible roles for the stress response and the deoxyribonucleic acid repair process

    PubMed Central

    Nadin, Silvina B.; Vargas-Roig, Laura M.; Cuello-Carrión, F. Darío; Ciocca, Daniel R.

    2003-01-01

    Doxorubicin is an antineoplastic drug widely used in cancer treatment. However, many tumors are intrinsically resistant to the drug or show drug resistance after an initial period of response. Among the different molecules implicated with doxorubicin resistance are the heat shock proteins (Hsps). At present we do not know with certainty the mechanism(s) involved in such resistance. In the present study, to advance our knowledge on the relationship between Hsps and drug resistance, we have used peripheral blood mononuclear cells obtained from healthy nonsmoker donors to evaluate the capacity of a preliminary heat shock to elicit the Hsp response and to establish the protection against the deoxyribonucleic acid (DNA) damage induced by doxorubicin. DNA damage and repair were determined using the alkaline comet assay. We also measured the expression of Hsp27, Hsp60, Hsp70, Hsp90, hMLH1, hMSH2, and proliferating cell nuclear antigen by immunocytochemistry. The damage induced by doxorubicin was more efficiently repaired when the cells were previously heat shocked followed by a resting period of 24 hours before drug exposure, as shown by (1) the increased number of undamaged cells (P < 0.05), (2) the increased DNA repair capacity (P < 0.05), and (3) the high expression of the mismatch repair (MMR) proteins hMLH1 and hMSH2 (P < 0.05). In addition, in the mentioned group of cells, we confirmed by Western blot high expression levels of Hsp27 and Hsp70. We also noted a nuclear translocation of Hsp27 and mainly of Hsp70. Furthermore, inducible Hsp70 was more expressed in the nucleus than Hsc70, showing a possible participation of Hsp70 in the DNA repair process mediated by the MMR system. PMID:15115288

  16. Transcription of exogenous and endogenous deoxyribonucleic acid templates in cold-shocked Bacillus subtilis.

    PubMed Central

    Kuhl, S J; Brown, L R

    1980-01-01

    Ribonucleic acid (RNA) synthesis was examined in cold-shocked Bacillus subtilis cells. The cells were grown to mid-log stage, harvested, and cold shocked. RNA synthesis was monitored by the incorporation of [3H]uridine triphosphate or [alpha 32P]adenosine triphosphate into trichloroacetic acid-precipitable material in the presence of all four nucleoside triphosphates. The inhibition of RNA synthesis in cold-shocked cells by lipiarmycin, ethidium bromide, rifampin. or streptolydigin was analyzed using mutant or wild-type cells. Also examined were the effects of temperature, salt concentration, and the addition of polyamines or highly phosphorylated nucleotides. In ultraviolet-irradiated and cold-shocked cells, RNA wynthesis decreased to low levels. The addition of exogenous phi 29 or TSP-1 template to these cells caused a 13- to 20-fold increase in RNA synthesis, as monitored by trichloroacetic acid-precipitable counts. RNA synthesized in the presence of phi 29 deoxyribonucleic acid (DNA) hybridizes mainly to EcoRI fragments A and C of phi 29 DBA, These two fragments direct transcription by purified RNA polymerase in vitro and hybridize to early phi 29 DNA produced in vivo. Our results with TSP-1 DNA in this system indicated that the RNA produced hybridizes to the same fragments as early RNA produced in vivo. Plasmic pUB110 DNA was not transcribed in this system. Images PMID:6157674

  17. Spermidine-Deoxyribonucleic acid interaction in vitro and in Escherichia coli.

    PubMed Central

    Rubin, R L

    1977-01-01

    The binding of spermidine to deoxyribonucleic acid (DNA) was studied by equilibrium dialysis in a wide range of salt concentrations. The association constants ranged from 6 x 10(5) M-1 in 1 mM sodium cacodylate, pH 7.5, to 3 x 10(2) M-1 in 0.3 M NaCl. MgCl2 reduced spermidine-DNA interaction even more than NaCl so that in moderate-ionic-strength solutions (0.3 M NaCl, 0.002 M MgCl2) there was little detectable binding. Low-ionic-strength media were used to isolate DNA from Escherichia coli by a method shown to minimize loss of spermidine from the DNA. Considerable spermidine was associated with E. coli DNA, but control experiments indicated that complex formation had taken place during or after lysis of the cells. Exogenous DNA or ribonucleic acid added to spheroplasts at the time of their lysis caused most of the cellular spermidine to be scavenged by the extra nucleic acid. The data suggest that spermidine is relatively free in the cell and thereby capable of strong (high-affinity) associations with nucleic acids only after the ionic strength of the cell environment is lowered. PMID:320196

  18. Deoxyribonucleic Acid Polymerase of Rous Sarcoma Virus: Reaction Conditions and Analysis of the Reaction Product Nucleic Acids

    PubMed Central

    Bishop, D. H. L.; Ruprecht, Ruth; Simpson, R. W.; Spiegelman, S.

    1971-01-01

    Reaction conditions for Rous sarcoma virus ribonucleic acid (RNA)-instructed deoxyribonucleic acid (DNA) polymerase activity are described whereby the viral RNA is relatively protected from endogenous or added nuclease activity. Three analyses of reaction product nucleic acids (3H-RNA, 32P-DNA) were compared, namely, gel electrophoresis, Cs2SO4 gradient centrifugation, and hydroxyapatite column chromatography. It was found that hydroxyapatite analysis could be misleading unless the state of the template RNA was monitored concomitantly with the DNA analysis. Gel electrophoresis and Cs2SO4 gradient centrifugation gave comparable results. It was concluded that analyses of the product of reverse transcriptase reactions should not only refer to the template RNA and product DNA species, but also be performed with virus or viral RNA which do not have or obtain nicks in the 60S RNA. Otherwise, interpretation of the results would have the ambiguity of potential artifacts caused by those degraded RNA molecules. PMID:4332143

  19. Properties of the Deoxyribonucleic Acid Contained in the Defective Particle Coliphage 15 1

    PubMed Central

    Frampton, E. W.; Mandel, M.

    1970-01-01

    Escherichia coli strain 15 TAU, which requires thymine, arginine, and uracil for growth and harbors an apparently defective prophage, was induced by exposure to ultraviolet light (580 ergs/mm2) or to mitomycin C (5 μg/ml). Phage particles (coliphage 15) were recovered from the resulting lysate by treatment with deoxyribonuclease, filtration, and several cycles of differential centrifugation. Analysis of the phage particles obtained by using cesium chloride density gradient centrifugation in a preparative ultracentrifuge resulted in the resolution of three components. The major component had a peak density of 1.52 to 1.53 g/cm3 followed by components with densities of 1.5 and 1.49 g/cm3. The guanine plus cytosine content of coliphage 15 deoxyribonucleic acid (DNA) was determined by both analytical ultracentrifugation in cesium chloride and by thermal denaturation in standard saline citrate buffer. Respective values of 46.4 ± 1% and 46.6 ± 1% guanine plus cytosine content were obtained. Coliphage 15 DNA formed molecular hybrids with messenger ribonucleic acid (RNA) from both uninduced and ultraviolet-induced cultures of E. coli 15 TAU, but did not hybridize with E. coli ribosomal RNA. The molecular weight of coliphage 15 DNA was determined by constant velocity sucrose density gradient centrifugation to be about 33 × 106 daltons. PMID:4909911

  20. Isolation and Characterization of Supercoiled Circular Deoxyribonucleic Acid from Beta-Hemolytic Strains of Escherichia coli

    PubMed Central

    Goebel, Werner; Schrempf, Hildgund

    1971-01-01

    Covalently closed circular deoxyribonucleic acid (DNA) molecules were isolated by cesium chloride centrifugation in the presence of ethidium bromide from a naturally occurring beta-hemolytic Escherichia coli strain (SC52). The open circular forms have contour lengths of 2.25 ± 0.1 μm, 24.0 ± 0.3 μm, and 29.5 ± 0.5 μm. The beta-hemolytic character of E. coli SC52 can be transferred by conjugation to a nonhemolytic recipient strain. Analysis of the supercoiled DNA of the hemolytic recipient demonstrated that the two large supercoiled DNA molecules of E. coli SC52 are transferred during this event, too. A beta-hemolytic laboratory E. coli strain and several of its derivatives have been shown to contain at least one circular DNA molecule, slightly larger in size than those isolated from E. coli SC52 and its conjugant. The possible significance of these DNA molecules for hemolysin production and transfer is discussed. Images PMID:4929855

  1. Formation of an 8-hydroxyguanine moiety in deoxyribonucleic acid on gamma-irradiation in aqueous solution

    SciTech Connect

    Dizdaroglu, M.

    1985-07-30

    Isolation and characterization of a novel radiation-induced product, i.e., the 8-hydroxyguanine residue, produced in deoxyribonucleic acid (DNA), 2'-deoxyguanosine, and 2'-deoxyguanosine 5'-monophosphate by gamma-irradiation in aqueous solution, are described. For this purpose, gamma-irradiated DNA was first hydrolyzed with a mixture of four enzymes, i.e., DNase I, spleen and snake venom exonucleases, and alkaline phosphatase. Analysis of the resulting mixture by capillary gas chromatography-mass spectrometry after trimethylsilylation revealed the presence of a product, which was identified as 8-hydroxy-2'-deoxyguanosine on the basis of the typical fragment ions of its trimethylsilyl (Me3Si) derivative. This product was then isolated by using reversed-phase high-performance liquid chromatography. The UV and proton nuclear magnetic resonance spectra taken from the isolated product confirmed the structure suggested by the mass spectrum of its Me3Si derivative. The yield of 8-hydroxyguanine was also measured. Its mechanism of formation is believed to involve OH radical addition to the C-8 position of guanine followed by oxidation of the radical adduct.

  2. Automated Quantification of the Impact of Defects on the Mechanical Behavior of Deoxyribonucleic acid Origami Nanoplates.

    PubMed

    Liang, Bowen; Nagarajan, Anand; Hudoba, Michael W; Alvarez, Ricardo; Castro, Carlos E; Soghrati, Soheil

    2017-04-01

    Deoxyribonucleic acid (DNA) origami is a method for the bottom-up self-assembly of complex nanostructures for applications, such as biosensing, drug delivery, nanopore technologies, and nanomechanical devices. Effective design of such nanostructures requires a good understanding of their mechanical behavior. While a number of studies have focused on the mechanical properties of DNA origami structures, considering defects arising from molecular self-assembly is largely unexplored. In this paper, we present an automated computational framework to analyze the impact of such defects on the structural integrity of a model DNA origami nanoplate. The proposed computational approach relies on a noniterative conforming to interface-structured adaptive mesh refinement (CISAMR) algorithm, which enables the automated transformation of a binary image of the nanoplate into a high fidelity finite element model. We implement this technique to quantify the impact of defects on the mechanical behavior of the nanoplate by performing multiple simulations taking into account varying numbers and spatial arrangements of missing DNA strands. The analyses are carried out for two types of loading: uniform tensile displacement applied on all the DNA strands and asymmetric tensile displacement applied to strands at diagonal corners of the nanoplate.

  3. Size, Composition, and Structure of the Deoxyribonucleic Acid of Herpes Simplex Virus Subtypes 1 and 2

    PubMed Central

    Kieff, Elliott D.; Bachenheimer, Steven L.; Roizman, Bernard

    1971-01-01

    Studies of the size, composition, and structure of the deoxyribonucleic acid (DNA) of the F and G prototypes of herpes simplex virus (HSV) subtypes 1 and 2 (HSV-1 and HSV-2) showed the following. (i) As previously reported by Good-heart et al. HSV-1 and HSV-2 DNA have a buoyant density of 1.726 and 1.728 g/cm3, corresponding to 67 and 69 guanine ± cytosine moles per cent, respectively. The difference in guanine plus cytosine content of the DNA species was confirmed by the finding of a 1 C difference in Tm. (ii) The DNA from purified virus on cocentrifugation with T4 DNA in neutral sucrose density gradients sedimented at 55S, corresponding to 99 ± 5 million daltons in molecular weight. HSV-1 and HSV-2 DNA could not be differentiated with respect to size. (iii) Cosedimentation of alkali-denatured DNA from purified virus with T4 DNA on alkaline sucrose density gradients consistently yielded several bands of single-stranded HSV DNA ranging from fragments 7 × 106 daltons to intact strands 48 × 106 daltons in molecular weight. PMID:4329966

  4. Effects of intradermally administered plasmid deoxyribonucleic acid on ovine popliteal lymph node morphology.

    PubMed

    Uwiera, R R; Rankin, R; Adams, G P; Pontarollo, R; van Drunen Littel-van den Hurk, S; Middleton, D M; Babiuk, L A; Griebel, P J

    2001-02-01

    In the last decade it has become apparent that bacterial deoxyribonucleic acid (DNA) is recognized as a "danger signal" by the mammalian immune system. To investigate this interaction, sheep were injected intradermally two centimeters distal to the lateral prominence of the fibular head with 400 microg of purified plasmid DNA. Over a 28-day period ultrasound measurements indicated a progressive increase in size of both plasmid and saline (controls) treated popliteal lymph nodes and at Day 30 macroscopic and histological measurements of the lymph nodes were determined. Compared with the contralateral control lymph nodes, plasmid exposed lymph nodes were heavier (2.8 +/- 0.1g vs. 2.0 +/- 0.6 g) and displayed prominent histological changes in the cortex and medulla. Average medullary cord thickness (114.2 +/- 25.2 microm) and the average distance across medullary sinuses (64.4 +/- 2.5 microm) were significantly greater after plasmid exposure relative to contralateral controls (62.7 +/- 14.9 microm and 36.5 +/- 1.0 microm, respectively). Total number of germinal centers (71.4 +/- 17.7) and the total area of germinal centers (4.0 +/- 1.3 mm(2)) within the cortex of popliteal lymph nodes exposed to plasmid were also significantly greater than the controls (40.4 +/- 11.4 and 1.6 +/- 0.5 mm(2), respectively). Our results demonstrate that a single exposure to plasmid DNA has long term effects on regional lymph node weight and morphology.

  5. Gating of single-layer graphene with single-stranded deoxyribonucleic acids.

    PubMed

    Lin, Jian; Teweldebrhan, Desalegne; Ashraf, Khalid; Liu, Guanxiong; Jing, Xiaoye; Yan, Zhong; Li, Rong; Ozkan, Mihri; Lake, Roger K; Balandin, Alexander A; Ozkan, Cengiz S

    2010-05-21

    Patterning of biomolecules on graphene layers could provide new avenues to modulate their electrical properties for novel electronic devices. Single-stranded deoxyribonucleic acids (ssDNAs) are found to act as negative-potential gating agents that increase the hole density in single-layer graphene. Current-voltage measurements of the hybrid ssDNA/graphene system indicate a shift in the Dirac point and "intrinsic" conductance after ssDNA is patterned. The effect of ssDNA is to increase the hole density in the graphene layer, which is calculated to be on the order of 1.8 x 10(12) cm(-2). This increased density is consistent with the Raman frequency shifts in the G-peak and 2D band positions and the corresponding changes in the G-peak full width at half maximum. Ab initio calculations using density functional theory rule out significant charge transfer or modification of the graphene band structure in the presence of ssDNA fragments.

  6. Feasibility for quantitative determination of deoxyribonucleic acid by using near-infrared diffuse reflectance spectroscopy.

    PubMed

    Yang, Yafei; Tu, Jiarun; Cai, Wensheng; Shao, Xueguang

    2012-09-15

    A method for quantitative determination of fish sperm deoxyribonucleic acid (fsDNA) in solutions was developed by using adsorption preconcentration and near-infrared diffuse reflectance spectroscopy (NIRDRS). A high capacity adsorbent of amino-modified silica particle (AMSP) was prepared for preconcentration of fsDNA in solutions. Under the optimized conditions, the adsorption rate can be above 90% within 3 min. After adsorbing the DNA onto the adsorbent, near-infrared (NIR) spectra in diffuse reflectance mode were measured and partial least squares (PLS) model was established for fast quantitative prediction. The results show that the correlation coefficient (R) between the predicted and the reference concentration is 0.9894 and the recoveries are in the range of 92.9-123.4% for the validation samples in the concentration range of 3.00-29.38 mg L(-1). Therefore, the feasibility for quantitative analysis of DNA in solutions by NIRDRS is proved. This may provide an alternative way for fast determination of DNA in solutions.

  7. Repair of Single-Strand Deoxyribonucleic Acid Breaks in Ultraviolet Light-Irradiated Haemophilus influenzae

    PubMed Central

    Kantor, George J.; Barnhart, B. J.

    1973-01-01

    The wild-type strain and mutants of Haemophilus influenzae, sensitive or resistant to ultraviolet light (UV) as defined by colony-forming ability, were examined for their ability to perform the incision and rejoining steps of the deoxyribonucleic acid (DNA) dark repair process. Although UV-induced pyrimidine dimers are excised by the wild-type Rd and a resistant mutant BC200, the expected single-strand DNA breaks could not be detected on alkaline sucrose gradients. Repair of the gap resulting from excision must be rapid when experimental conditions described by us are employed. Single-strand DNA breaks were not detected in a UV-irradiated sensitive mutant (BC100) incapable of excising pyrimidine dimers, indicating that this mutant may be defective in a dimer-recognizing endonuclease. No single-strand DNA breaks were detected in a lysogen BC100(HP1c1) irradiated with a UV dose large enough to induce phage development in 80% of the cells. PMID:4540247

  8. Mutants of Escherichia coli with Cold-Sensitive Deoxyribonucleic Acid Synthesis

    PubMed Central

    Waskell, Lucy; Glaser, Donald A.

    1974-01-01

    Ten cold-sensitive mutants defective in deoxyribonucleic acid (DNA) synthesis at 20 C have been identified among 218 cold-sensitive mutants isolated from a mutagenized population of Escherichia coli K-12. Four of the ten mutant alleles, dna-339 dna-340, dna-341, and dna-342, cotransduce with serB+ and hence may be dnaC mutants. Two of these, dna-340 and dna-341, are recessive to their wild-type allele. The gene product of their wild-type allele is trans acting. Complementation tests have demonstrated that dna-340 and dna-341 are in the same cistron. The mapping of the remaining six mutations is in progress. In an attempt to determine whether LW4 and LW21 were initiator mutants, cultures of these strains were starved of an essential amino acid at 37 C and then incubated at 15 C with the essential amino acid. The amount of DNA synthesis observed under these circumstances was insignificant. These data are consistent with the idea that LW4 and LW21 are initiator mutants. However, attempts to integratively suppress LW4 and LW21 with F′ factors were unsuccessful. To resolve the question of whether or not LW4 and LW21 are initiator mutants, more specific tests and criteria are required. Cultures of LW4 and LW21 were toluene treated and used to measure in vitro DNA synthesis. If the cells were incubated either at 15 or 20 C before toluene treatment, they were capable of markedly less DNA synthesis than if preincubation had not occurred. The amount of in vitro DNA synthesis is directly proportional to the amount of DNA synthesis occurring during preincubation in vivo; i.e., more DNA synthesis is observed at 20 than at 15 C. The fact that the cold-sensitive mutants are unable to synthesize DNA when supplied with deoxyribonucleoside triphosphates, DNA precursors, is evidence they are not defective in precursor synthesis. PMID:4597994

  9. Deoxyribonucleic acid modified poly(dimethylsiloxane) microfluidic channels for the enhancement of microchip electrophoresis.

    PubMed

    Liang, Ruping; Hu, Pengfei; Gan, Guihua; Qiu, Jianding

    2009-03-15

    In this paper, deoxyribonucleic acid (DNA) was employed to construct a functional film on the PDMS microfluidic channel surface and apply to perform electrophoresis coupled with electrochemical detection. The functional film was formed by sequentially immobilizing chitosan and DNA to the PDMS microfluidic channel surface using the layer-by-layer assembly. The polysaccharide backbone of chitosan can be strongly adsorbed onto the hydrophobic PDMS surface through electrostatic interaction in the acidic media, meanwhile, chitosan contains one protonatable functional moiety resulting in a strong electrostatic interactions between the surface amine group of chitosan and the charged phosphate backbone of DNA at low pH, which generates a hydrophilic microchannel surface and reveals perfect resistance to nonspecific adsorption of analytes. Aminophenol isomers (p-, o-, and m-aminophenol) served as a separation model to evaluate the effect of the functional PDMS microfluidic chips. The results clearly showed that these analytes were efficiently separated within 60s in a 3.7 cm long separation channel and successfully detected on the modified microchip coupled with in-channel amperometric detection mode at a single carbon fiber electrode. The theoretical plate numbers were 74,021, 92,658 and 60,552 Nm(-1) at the separation voltage of 900 V with the detection limits of 1.6, 4.7 and 2.5 microM (S/N=3) for p-, o-, and m-aminophenol, respectively. In addition, this report offered an effective means for preparing hydrophilic and biocompatible PDMS microchannel surface, which would facilitate the use of microfluidic devices for more widespread applications.

  10. Report of the blind trial of the Cetus Amplitype HLA DQ alpha forensic deoxyribonucleic acid (DNA) amplification and typing kit.

    PubMed

    Walsh, P S; Fildes, N; Louie, A S; Higuchi, R

    1991-09-01

    The AmpliType HLA DQ alpha forensic DNA amplification and typing kit is designed for the qualitative analysis of the human leukocyte antigen (HLA) DQ alpha alleles present in deoxyribonucleic acid (DNA) extracted from forensic samples. The AmpliType kit is the first forensic DNA typing product based on the GeneAmp polymerase chain reaction (PCR) process. The kit was evaluated by five forensic science laboratories (test sites) to assess their ability to perform DNA typing using PCR on sample types typically encountered by forensic laboratories. None of the DNA-containing samples was mistyped. Of the 180 DNA-containing samples analyzed, results were reported for 178 (98.9%). Of the 178 samples with results, all were correctly typed. Two sites did not report a result for one sample each. Four of the five laboratories experienced no significant levels of contamination in the DNA-containing samples. At the one site with the highest number of DNA-containing samples with contamination, the typing results were not compromised. This site was able to correct the contamination problem through simple procedural changes and stricter attention to sterile technique. Blank controls were important to monitor contamination. In conclusion, the trial demonstrated that forensic science laboratories are capable of setting up a PCR-based DNA typing laboratory and successfully using the AmpliType HLA DQ alpha forensic DNA amplification and typing kit to analyze forensic samples.

  11. Fabrication of a deoxyribonucleic acid polymer ridge waveguide electro-optic modulator by nanoimprint lithography

    NASA Astrophysics Data System (ADS)

    Fehrman Cory, Emily Marie

    The purpose of this dissertation is to develop the nanoimprint lithography (NIL) technique for direct patterning of the deoxyribonucleic acid biopolymer DNA-CTMA. The Mach Zehnder modulator was chosen as the test device to demonstrate the NIL patterning technique for DNA-CTMA as well as the unique optical and electrical properties of the DNA-CTMA as a cladding material for poled electro-optic polymers. Towards this goal, a DNA-CTMA clad inverted ridge waveguide is demonstrated at 633 nm and 1550 nm, the structure of which is patterned directly in the DNA-CTMA cladding by NIL. Additionally, EO modulation is demonstrated in a slab waveguide structure with DNA-CTMA cladding and SEO110 EO polymer core. Marine-derived deoxyribonucleic acid biopolymer (DNA-CTMA) is a green, nontoxic, low cost optical polymer material derived from waste products of the salmon fishing industry. It exhibits low optical loss at 1550 nm, forms a thin flexible film, is compatible with existing poled polymer technologies, increases the poling efficiency when used as a low resistivity cladding layer, and is thermally stable to 200 oC. Due to chemical incompatibility with the photoresists and the associated solvents, NIL has been developed for patterning the DNA biopolymer cladding to form an inverted ridge waveguide for the basis of the Mach Zehnder modulator. While DNA-CTMA presents significant advantages over other commonly used cladding materials for the 1550 nm wavelength range, one of the commonly used bands for optical communications, the mechanical properties and environmental susceptibility of the material poses significant fabrication challenges. A study of the effects of optical and mechanical effects of environmental humidity exposure are presented for the DNA-CTMA and SEO110 polymers used in the inverted ridge waveguide. While the soft, flexible nature of the DNA-CTMA is desirable for certain applications, this presents a challenge in producing a clean polished window for optical

  12. The effect of deoxyribonucleic acid extraction methods from lymphoid tissue on the purity, content, and amplifying ability

    PubMed Central

    Ayatollahi, Hossein; Sadeghian, Mohammad Hadi; Keramati, Mohammad Reza; Ayatollahi, Ali; Shajiei, Arezoo; Sheikhi, Maryam; Bakhshi, Samane

    2016-01-01

    Background: Nowadays, definitive diagnosis of numerous diseases is based on the genetic and molecular findings. Therefore, preparation of fundamental materials for these evaluations is necessary. Deoxyribonucleic acid (DNA) is the first material for the molecular pathology and genetic analysis, and better results need more pure DNA. Furthermore, higher concentration of achieved DNA causes better results and higher amplifying ability for subsequent steps. We aim to evaluate five DNA extraction methods to compare DNA intimacy including purity, concentration, and amplifying ability with each other. Materials and Methods: The lymphoid tissue DNA was extracted from formalin-fixed, paraffin embedded (FFPE) tissue through five different methods including phenol-chloroform as the reference method, DNA isolation kit (QIAamp DNA FFPE Tissue Kit, Qiagen, Germany), proteinase K and xylol extraction and heat alkaline plus mineral oil extraction as authorship innovative method. Finally, polymerase chain reaction (PCR) and real-time PCR method were assessed to compare each following method consider to DNA purity and its concentration. Results: Among five different applied methods, the highest mean of DNA purity was related to heat alkaline method. Moreover, the highest mean of DNA concentration was related to heat alkaline plus mineral oil. Furthermore, the best result in quantitative PCR was in proteinase K method that had the lowest cycle threshold averages among the other extraction methods. Conclusion: We concluded that our innovative method for DNA extraction (heat alkaline plus mineral oil) achieved high DNA purity and concentration. PMID:27630381

  13. Fate of Donor Deoxyribonucleic Acid in a Highly Transformation-Deficient Strain of Haemophilus influenzae

    PubMed Central

    Kooistra, Jan; Venema, Gerard

    1974-01-01

    A transformation-deficient strain of Haemophilus influenzae (efficiency of transformation 104-fold less than that of the wild type), designated TD24, was isolated by selection for sensitivity to mitomycin C. In its properties the mutant was equivalent to recA type mutants of Escherichia coli. The TD24 mutation was linked with the str-r marker (about 30%) and only weakly linked with the nov-r2.5 marker. The uptake of donor deoxyribonucleic acid (DNA) was normal in the TD24 strain, but no molecules with recombinant-type activity (molecules carrying both the donor and the resident marker) were formed. In the mutant the intracellular presynaptic fate of the donor DNA was the same as that in the transformation-proficient (wild-type) strain, and the radioactive label of the donor DNA associated covalently with the recipient chromosome in about the same quantity as in the wild type. However, many fewer donor atoms were associated with segments of the mutant's recipient chromosome as compared with segments of the wild-type chromosome. In the mutant the association was accompanied by complete loss of donor marker activity. The lack of donor marker activity of the donor-recipient complex of DNA isolated from the mutant was not due to lack of uptake of the complex by the second recipient and its inability to associate with the second recipient's chromosome. Because the number of donor-atom-carrying resident molecules was higher than could be accounted for by the lengths of presynaptic donor molecules, we favor the idea that the association of donor DNA atoms with the mutant chromosome results from local DNA synthesis rather than from dispersive integration of donor DNA by recombination. PMID:4546806

  14. Thymineless Death in Escherichia coli: Deoxyribonucleic Acid Replication and the Immune State

    PubMed Central

    Cummings, Donald J.; Kusy, Alvin R.

    1970-01-01

    Thymineless death (TLD) and nalidixic acid (NA) inactivation were studied in multiple auxotrophic strains of Escherichia coli B and B/r. As expected, it was found that both E. coli B and B/r exhibited an “immune state,” i.e., a fraction of the population survived inactivation to both TLD and NA. With glucose as a carbon source in minimal medium, 0.1 to 0.3% of strain B and 0.2 to 0.5% of strain B/r survived inactivation; with acetate as the carbon source, the surviving fractions were increased to 1 to 2% and 5 to 7%, respectively. These immune fractions could be increased in magnitude by preincubation in minimal media containing thymine. Systematic analysis of the particular supplements necessary for the immune state indicated that the absence of the required amino acids was essential for the maximal expression of immunity. However, immunity was not abolished in acetate medium even in the presence of the required supplements. Further studies on the replication of deoxyribonucleic acid (DNA) during preincubation indicated that the degree of immunity did not necessarily correlate with the completion of a round of DNA replication. This finding was supported by examining the immune state in synchronous populations. In both glucose and acetate medium, there was no significant change in the degree of immunity to inactivation within the cell cycles of E. coli B and B/r. We concluded that some other event, possibly inhibition of protein synthesis, was necessary in determining the degree of the immune state. DNA replication was investigated after TLD and NA inactivation, and, as expected, it was found that both events led to premature initiation of replication. The only differences observed in the effects of these two processes on DNA synthesis were the following. (i) NA-induced replication was less sensitive to chloramphenicol than was TLD. (ii) TLD-induced replication was unaffected by pretreatment of the cells with mitomycin C, but this pretreatment prevented the

  15. Isolation and properties of highly purified Halobacterium cutirubrum deoxyribonucleic acid-dependent ribonucleic acid polumerase

    PubMed Central

    Louis, B. Gregory; Fitt, P. S.

    1972-01-01

    1. The subunits α and β of Halobacterium cutirubrum DNA-dependent RNA polymerase have been purified to electrophoretic homogeneity. Both have mol.wt. 18000 and they are required in equimolar amounts for optimum activity. 2. The instability of the complete enzyme, αβ, in the absence of salt is due to the rapid inactivation of the β subunit in these conditions. 3. Nearest-neighbour analysis of the product formed on poly[d(A-T)] as template shows that the enzyme copies the latter accurately. 4. The enzyme initiates new chains with purine nucleoside triphosphates exclusively. 5. The product obtained in the standard assay conditions contains some high mol.wt. (>16S) material, but consists primarily of short chains, of average length 70–80 nucleotide units. 6. The template specificity of the complete enzyme has been studied at high and low ionic strength. Its extreme dependence on salt concentration is unrelated to the gross overall base composition of the DNA used. 7. T7 DNA is transcribed asymmetrically and the enzyme selectively copies the T7 `early' genes. 8. Preliminary amino acid analyses of α and β subunits show that their overall content of acidic, basic and neutral amino acids does not differ appreciably from that of Escherichia coli RNA polymerase. PMID:5073755

  16. Initiation of Deoxyribonucleic Acid Replication in Germinating Spores of Bacillus subtilis 168 Carrying the dnaB(Ts)134 Mutation

    PubMed Central

    Callister, Heather; Mesurier, Sue Le; Wake, R. G.

    1977-01-01

    The nature of the deoxyribonucleic acid synthesis reported by others to occur at 45°C in germinating spores of the temperature-sensitive deoxyribonucleic acid initiation mutant of Bacillus subtilis 168, TsB134, has been investigated. Density transfer experiments, using 5-bromouracil, show that a normal round of replication can occur in a significant fraction of the spore population under such conditions. No repair synthesis is detectable. The possibility raised by this finding, that initiation of the first round of replication during spore outgrowth is unique in that its initiation is determined prior to germination, has been investigated by comparing the behavior of germinating spores of isogenic strains of B. subtilis 168, one carrying and the other without the dnaB (Ts)134 mutation. It is shown that deoxyribonucleic acid synthesis in the Ts strain is very sensitive to temperature in the vicinity of 45°C. At a slightly higher temperature, 49°C, initiation of the first round of replication in the Ts strain is completely (greater than 96%) blocked, but it proceeds normally in the Ts+ strain. Thus, it is concluded that, after the germination of a spore, the action of the dnaB134 gene product is an obligatory requirement for initiation of the first round of replication. The initiation of replication that can occur in spores of the original TsB134 strain germinating at 45°C is presumably due to incomplete inactivation of the dnaB134 gene product under such conditions. PMID:405369

  17. Calcium-requiring step in the uptake of deoxyribonucleic acid molecules through the surface of competent pneumococci.

    PubMed Central

    Seto, H; Tomasz, A

    1976-01-01

    The conversion of surface-adsorbed deoxyribonucleic acid (DNA) molecules to a state in which they are inaccessible to exogenous deoxyribonuclease requires specifically calcium ions; magnesium ions cannot replace calcium ions. Virtually maximal levels of nuclease-resistant DNA binding and genetic transformation can be obtained in media free from magnesium and containing only calcium ions. It is suggested that the calcium-requiring process is the transport of DNA molecules across the plasma membrane. Magnesium ions stimulate both the loss of surface-adsorbed DNA to the medium and the extracellular degradation of DNA. PMID:7544

  18. Mapping of colicin E2 and colicin E3 plasmid deoxyribonucleic acid EcoR-1-sensitive sites.

    PubMed

    Inselburg, J; Johns, V

    1975-01-01

    Colicin plasmids E2 and E3 (Col E2 and Col E3) deoxyribonucleic acid (DNA) has been shown to contain, respectively, two and three EcoR1 restriction endonuclease-sensitive sites. This was determined by measuring the DNA fragments generated after EcoR1 endonuclease treatment by agarose gel electrophoresis and electron microscopy. The structure of heteroduplex Col E2-col E3 DNA molecules formed from EcoR1-generated fragments permitted a localization of the EcoR1-sensitive sites on the plasmid chromosomes.

  19. Isolation and Characterization of a Mutant of Salmonella typhimurium Deficient in a Major Deoxyribonucleic Acid Polymerase Activity

    PubMed Central

    Whitfield, Harvey J.; Levine, Gary

    1973-01-01

    A mutant of Salmonella typhimurium strain LT2 that is deficient in a major deoxyribonucleic acid (DNA) polymerase activity has been isolated and characterized. This mutant resembles the pol mutants of E. coli in that it has low DNA polymerase activity and it is sensitive to methyl methane sulfonate as well as ultraviolet irradiation. Revertants selected for methyl methane sulfonate resistance are no longer sensitive to ultraviolet irradiation and contain normal DNA polymerase levels. No direct role in replication can be ascribed to this polymerase activity since cells grow well in its absence. In addition, the LT2 plasmid has been shown to exist in the mutant strain. PMID:4355486

  20. Identification of a Herbal Powder by Deoxyribonucleic Acid Barcoding and Structural Analyses

    PubMed Central

    Sheth, Bhavisha P.; Thaker, Vrinda S.

    2015-01-01

    Background: Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same. Objective: To identify a herbal powder obtained from a herbalist in the local vicinity of Rajkot, Gujarat, using deoxyribonucleic acid (DNA) barcoding and molecular tools. Materials and Methods: The DNA was extracted from a herbal powder and selected Cassia species, followed by the polymerase chain reaction (PCR) and sequencing of the rbcL barcode locus. Thereafter the sequences were subjected to National Center for Biotechnology Information (NCBI) basic local alignment search tool (BLAST) analysis, followed by the protein three-dimension structure determination of the rbcL protein from the herbal powder and Cassia species namely Cassia fistula, Cassia tora and Cassia javanica (sequences obtained in the present study), Cassia Roxburghii, and Cassia abbreviata (sequences retrieved from Genbank). Further, the multiple and pairwise structural alignment were carried out in order to identify the herbal powder. Results: The nucleotide sequences obtained from the selected species of Cassia were submitted to Genbank (Accession No. JX141397, JX141405, JX141420). The NCBI BLAST analysis of the rbcL protein from the herbal powder showed an equal sequence similarity (with reference to different parameters like E value, maximum identity, total score, query coverage) to C. javanica and C. roxburghii. In order to solve the ambiguities of the BLAST result, a protein structural approach was implemented. The protein homology models obtained in the present study were submitted to the protein model database (PM0079748-PM0079753). The pairwise structural alignment of the herbal powder (as template) and C. javanica and C. roxburghii (as targets individually) revealed a close similarity of the herbal powder with C. javanica. Conclusion: A strategy as used here, incorporating the integrated use of DNA

  1. Identification of a Herbal Powder by Deoxyribonucleic Acid Barcoding and Structural Analyses.

    PubMed

    Sheth, Bhavisha P; Thaker, Vrinda S

    2015-10-01

    Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same. To identify a herbal powder obtained from a herbalist in the local vicinity of Rajkot, Gujarat, using deoxyribonucleic acid (DNA) barcoding and molecular tools. The DNA was extracted from a herbal powder and selected Cassia species, followed by the polymerase chain reaction (PCR) and sequencing of the rbcL barcode locus. Thereafter the sequences were subjected to National Center for Biotechnology Information (NCBI) basic local alignment search tool (BLAST) analysis, followed by the protein three-dimension structure determination of the rbcL protein from the herbal powder and Cassia species namely Cassia fistula, Cassia tora and Cassia javanica (sequences obtained in the present study), Cassia Roxburghii, and Cassia abbreviata (sequences retrieved from Genbank). Further, the multiple and pairwise structural alignment were carried out in order to identify the herbal powder. The nucleotide sequences obtained from the selected species of Cassia were submitted to Genbank (Accession No. JX141397, JX141405, JX141420). The NCBI BLAST analysis of the rbcL protein from the herbal powder showed an equal sequence similarity (with reference to different parameters like E value, maximum identity, total score, query coverage) to C. javanica and C. roxburghii. In order to solve the ambiguities of the BLAST result, a protein structural approach was implemented. The protein homology models obtained in the present study were submitted to the protein model database (PM0079748-PM0079753). The pairwise structural alignment of the herbal powder (as template) and C. javanica and C. roxburghii (as targets individually) revealed a close similarity of the herbal powder with C. javanica. A strategy as used here, incorporating the integrated use of DNA barcoding and protein structural analyses could be adopted, as a novel

  2. Detection of deoxyribonucleic acid (DNA) targets using polymerase chain reaction (PCR) and paper surface-enhanced Raman spectroscopy (SERS) chromatography.

    PubMed

    Hoppmann, Eric P; Yu, Wei W; White, Ian M

    2014-01-01

    Surface-enhanced Raman spectroscopy (SERS) enables multiplex detection of analytes using simple, portable equipment consisting of a single excitation source and detector. Thus, in theory, SERS is ideally suited to replace fluorescence in assays that screen for numerous deoxyribonucleic acid (DNA) targets, but in practice, SERS-based assays have suffered from complexity and elaborate processing steps. Here, we report an assay in which a simple inkjet-fabricated plasmonic paper device enables SERS-based detection of multiple DNA targets within a single polymerase chain reaction (PCR). In prior work, we demonstrated the principles of chromatographic separation and SERS-based detection on inkjet-fabricated plasmonic paper. The present work extends that capability for post-PCR gene sequence detection. In this design, hydrolysis DNA probes with 5' Raman labels are utilized; if the target is present, the probe is hydrolyzed during PCR, freeing the reporter. After applying the PCR sample to a paper SERS device, an on-device chromatographic separation and concentration is conducted to discriminate between hydrolyzed and intact probes. SERS is then used to detect the reporter released by the hydrolyzed probes. This simple separation and detection on paper eliminates the need for complex sample processing steps. In this work, we simultaneously detect the methicillin-resistant Staphylococcus aureus genes mecA and femB to illustrate the concept. We envision that this approach could contribute to the development of multiplex DNA diagnostic tests enabling screening for several target sequences within a single reaction, which is necessary for cases in which sample volume and resources are limited.

  3. Association of mitochondrial deoxyribonucleic acid mutation with polymorphism in CYP2E1 gene in oral carcinogenesis

    PubMed Central

    Pandey, Rahul; Mehrotra, Divya; Catapano, Carlo; Choubey, Vimal; Sarin, Rajiv; Mahdi, Abbas Ali; Singh, Stuti

    2012-01-01

    Background Oral carcinogenesis is a complex process affected by genetic as well as environmental factors. CYP2E1 gene is involved in metabolism of number of compounds and carcinogens. Its normal functioning is required for homeostasis of free radical. Mitochondrial deoxyribonucleic acid (mtDNA) is 10–100 times more susceptible to damage than nuclear DNA. Mitochondrial DNA large scale deletions are well documented in oral cancer. However, the relationship between CYP2E1 gene polymorphisms and mtDNA damage is still not documented in literature. Materials and Methods Case–control study involving 50 subjects was carried out. Deoxyribonucleic acid extraction was done from study subject tissue samples. Restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR) amplification was done to confirm CYP2E1 gene polymorphisms. The PCR amplification was done for mtDNA 4977 bp deletion. Statistical analysis was carried out using SPSS version 11.5 with χ2 tests. Results c1c1 and DD polymorphisms are prevalent in North Indian population having oral cancer. These polymorphisms are significantly associated with mtDNA 4977 bp deletion. Conclusion Mitochondrial DNA damage induced by wild CYP2E1 forms and imperfect DNA repair in mtDNA may act synergistically to greatly enhance oral cancer risk. PMID:25756024

  4. Suppression of lex Mutations Affecting Deoxyribonucleic Acid Repair in Escherichia coli K-12 by Closely Linked Thermosensitive Mutations

    PubMed Central

    Mount, David W.; Walker, Anita C.; Kosel, C.

    1973-01-01

    A major class of ultraviolet (UV)-resistant derivatives of lex− strains of Escherichia coli K-12 grows normally at 30 C but at 42.5 C fails to produce colonies on complete or minimal agar. At 42.5 C these thermosensitive strains form filaments without septa, due to an apparent defect in cell division. Deoxyribonucleic acid degradation in UV-irradiated cultures of the thermosensitive strains is slow, in contrast to the rapid degradation in UV-irradiated cultures of the parental lex− strains. The thermosensitive mutations (tsl) are tightly linked (less than 0.04 min on the E. coli K-12 linkage map) to the site of the lex mutation in the parental strain and could lie within the same gene. The tsl+/tsl− heterozygotes grow at 42.5 C and are UV resistant when grown at 30 or 42.5 C. The tsl mutations are, therefore, recessive in contrast to lex mutations, which are dominant. It appears likely that the tsl mutations alter the diffusible product that gives rise to the Lex− mutant phenotype. This product appears to be necessary for deoxyribonucleic acid repair and cell division. PMID:4583257

  5. Alkylation by propylene oxide of deoxyribonucleic acid, adenine, guanosine and deoxyguanylic acid

    PubMed Central

    Lawley, P. D.; Jarman, M.

    1972-01-01

    1. Propylene oxide reacts with DNA in aqueous buffer solution at about neutral pH to yield two principal products, identified as 7-(2-hydroxypropyl)guanine and 3-(2-hydroxypropyl)adenine, which hydrolyse out of the alkylated DNA at neutral pH values at 37°C. 2. These products were obtained in quantity by reactions between propylene oxide and guanosine or adenine respectively. 3. The reactions between propylene oxide and adenine in acetic acid were parallel to those between dimethyl sulphate and adenine in neutral aqueous solution; the alkylated positions in adenine in order of decreasing reactivity were N-3, N-1 and N-9. A method for separating these alkyladenines is described. 4. Deoxyguanylic acid sodium salt was alkylated at N-7 by propylene oxide in neutral aqueous solution. 5. The nature of the side chain in the principal alkylation products was established by mass spectrometry, and the nature of the products is consistent with their formation by the bimolecular reaction mechanism. PMID:5073240

  6. Kinetics for exchange of imino protons in deoxyribonucleic acid, ribonucleic acid, and hybrid oligonucleotide helices

    SciTech Connect

    Pardi, A.; Tinoco, I. Jr.

    1982-09-14

    The lifetimes for opening of individual base pairs in a DNA (dCA/sub 5/G + dCT/sub 5/G), an RNA (rCA/sub 5/G + rCU/sub 5/G), and a hybrid DNA-RNA (rCA/sub 5/G + dCT/sub 5/G) helix have been measured by proton nuclear magnetic resonance. The lifetimes were obtained by saturation recovery experiments performed on the hydrogen-bonding imino protons of the Watson-Crick base pairs. In these oligonucleotide helices the observed relaxation rates were dominated by exchange with water, with the magnetic spin-lattice relaxation time of the imino protons possibly being important only at the lowest temperatures in the DNA helix. It was shown that three interior base pairs in the DNA heptamer dCA/sub 5/G + dCT/sub 5/G were in the open-limited region, which means that these imino protons exchange every time the base pair opens. The lifetimes of the terminal G-C base pairs in the DNA helix are much shorter than the interior A-T base pairs. The pH dependence of the terminal base pairs indicated that the ends of the helix open and close many times before exchange of the imino protons with water takes place. The temperature dependence of the lifetimes of the interior A-T imino protons in the DNA helix showed that these protons exchange only when the double helix was dissociated into single strands. Thus, these lifetimes measure the rate for dissociation of the double helix. The activation energy for this process was found to be 47 kcal/mol. Comparison of the lifetimes of the interior protons in the DNA, RNA, and hybrid helices showed that the rates of dissociation of the RNA and hybrid helices are very similar at 5/sup 0/ C, whereas the rate for the DNA helix was approximately 1 order of magnitude smaller than that for the other two helices.

  7. Evaluation of deoxyribonucleic acid (DNA) isolated from human bloodstains exposed to ultraviolet light, heat, humidity, and soil contamination

    SciTech Connect

    McNally, L.; Shaler, R.C.; Baird, M.; Balazs, I.; De Forest, P.; Kobilinsky, L. )

    1989-09-01

    This study was designed to analyze the effects of common environmental insults on the ability to obtain deoxyribonucleic acid (DNA) restriction fragment-length polymorphisms (RFLP) patterns from laboratory prepared specimens. The environmental conditions studied include the exposure of dried bloodstains to varying amounts of relative humidity (0, 33, 67, and 98%), heat (37{degree}C), and ultraviolet light for periods of up to five days. In addition, the effect of drying over a four-day period in whole blood collected with and without ethylenediaminetetraacetate (EDTA) was examined. The results of the study showed that, under the conditions studied, the integrity of DNA is not altered such that false RFLP patterns are obtained. The only effect observed was that the overall RFLP pattern becomes weaker, but individual RFLP fragments are neither created nor destroyed.

  8. Loss of Photoreversibility of Damage to Deoxyribonucleic Acid Replication in Ultraviolet-Irradiated Escherichia coli B/r thy trp

    PubMed Central

    Doudney, C. O.

    1974-01-01

    Loss of photoreversibility (LOP) of the ultraviolet (UV) damage which prevents reinitiation of deoxyribonucleic acid (DNA) replication occurred with incubation of Escherichia coli B/r thy trp cultures after UV doses of 240, 320, and 400 ergs/mm2. LOP occurred at the time of reinitiation of DNA replication in the cultures (i.e., after postirradiation lag periods of 45 min or more). Neither the absence of thymine nor the absence of tryptophan prevented LOP of the damage to DNA replication, suggesting that neither DNA replication nor protein synthesis is necessary for the process. These findings suggest that attempted initiation of DNA replication results in transformation of pyrimidine damage into permanent damage to chromosome structure at the reinitiation site. PMID:4607425

  9. Properties of bacteriophage T4 mutants defective in gene 30 (deoxyribonucleic acid ligase) and the rII gene.

    PubMed

    Karam, J D; Barker, B

    1971-02-01

    In Escherichia coli K-12 strains infected with phage T4 which is defective in gene 30 [deoxyribonucleic acid (DNA) ligase] and in the rII gene (product unknown), near normal levels of DNA and viable phage were produced. Growth of such T4 ligase-rII double mutants was less efficient in E. coli B strains which show the "rapidlysis" phenotype of rII mutations. In pulse-chase experiments coupled with temperature shifts and with inhibition of DNA synthesis, it was observed that DNA synthesized by gene 30-defective phage is more susceptible to breakdown in vivo when the phage is carrying a wild-type rII gene. Breakdown was delayed or inhibited by continued DNA synthesis. Mutations of the rII gene decreased but did not completely abolish the breakdown. T4 ligase-rII double mutants had normal sensitivity to ultraviolet irradiation.

  10. DNA Tetrominoes: The Construction of DNA Nanostructures Using Self-Organised Heterogeneous Deoxyribonucleic Acids Shapes

    PubMed Central

    Ong, Hui San; Rahim, Mohd Syafiq; Firdaus-Raih, Mohd; Ramlan, Effirul Ikhwan

    2015-01-01

    The unique programmability of nucleic acids offers alternative in constructing excitable and functional nanostructures. This work introduces an autonomous protocol to construct DNA Tetris shapes (L-Shape, B-Shape, T-Shape and I-Shape) using modular DNA blocks. The protocol exploits the rich number of sequence combinations available from the nucleic acid alphabets, thus allowing for diversity to be applied in designing various DNA nanostructures. Instead of a deterministic set of sequences corresponding to a particular design, the protocol promotes a large pool of DNA shapes that can assemble to conform to any desired structures. By utilising evolutionary programming in the design stage, DNA blocks are subjected to processes such as sequence insertion, deletion and base shifting in order to enrich the diversity of the resulting shapes based on a set of cascading filters. The optimisation algorithm allows mutation to be exerted indefinitely on the candidate sequences until these sequences complied with all the four fitness criteria. Generated candidates from the protocol are in agreement with the filter cascades and thermodynamic simulation. Further validation using gel electrophoresis indicated the formation of the designed shapes. Thus, supporting the plausibility of constructing DNA nanostructures in a more hierarchical, modular, and interchangeable manner. PMID:26258940

  11. Isolation and characterization of deoxyribonucleic acid from tissue of the woolly mammoth, Mammuthus primigenius.

    PubMed

    Johnson, P H; Olson, C B; Goodman, M

    1985-01-01

    DNA was isolated from tissue samples of several mammoth specimens, radiocarbon dated between 10,000 and 53,000 years old. The DNA was purified by chromatography on hydroxyapatite at 60 degrees C and was characterized as a heterogeneous population of fragments ranging in size from 3000 to 200 base pairs. Thermal denaturation analysis demonstrated that approximately 25% of the DNA had a base composition similar to Asian elephant DNA calculated as 36% G + C. Preliminary analysis by nucleic acid hybridization indicated that only a small fraction of DNA isolated from mammoth tissue (2-5%) was homologous to DNA of Asian elephant, a close living relative of the mammoth. Our results provide the first definitive isolation and characterization of DNA from ancient tissue and suggest a purification strategy that will lead to preparations of DNA from mammoth tissue significantly enriched in elephant-related DNA sequences.

  12. A homogeneous hemin/G-quadruplex DNAzyme based turn-on chemiluminescence aptasensor for interferon-gamma detection via in-situ assembly of luminol functionalized gold nanoparticles, deoxyribonucleic acid, interferon-gamma and hemin.

    PubMed

    Jiang, Jie; He, Yi; Yu, Xiuxia; Zhao, Jinyang; Cui, Hua

    2013-08-12

    A homogeneous hemin/G-quadruplex DNAzyme (HGDNAzyme) based turn-on chemiluminescence aptasensor for interferon-gamma (IFN-γ) detection is developed, via dynamic in-situ assembly of luminol functionalized gold nanoparticles (lum-AuNPs), DNA, IFN-γ and hemin. The G-quadruplex oligomer of the HGDNAzyme was split into two halves, which was connected with the complementary sequence of P1 (IFN-γ-binding aptamer) to form the oligonucleotide P2. P2 hybridized with IFN-γ-binding aptamer and meanwhile assembled onto lum-AuNPs through biotin-streptavidin specific interaction. When IFN-γ was recognized by aptamer, P2 was released into the solution. The two lateral portions of P2 combined with hemin to yield the catalytic hemin/G-quadruplex DNAzyme, which amplified the luminol oxidation for a turn-on chemiluminescence signaling. Based on this strategy, the homogeneous aptasensor enables the facile detection of IFN-γ in a range of 0.5-100 nM. Moreover, the aptasensor showed high sensitivity (0.4 nM) and satisfactory specificity, pointing to great potential applications in clinical analysis. Copyright © 2013. Published by Elsevier B.V.

  13. Effect of elevated temperature on extended enzyme synthesis induced by bacteriophage T4 amber mutants unable to synthesize deoxyribonucleic acid.

    PubMed

    Goz, B

    1971-03-01

    The extended synthesis of early enzymes by the deoxyribonucleic acid-negative amber mutants of bacteriophage T4 after infection of the nonpermissive host Escherichia coli B was prevented by incubating the infected cells at 44 C. This effect did not occur if the incubation temperature was 43 C or less or if the cells were grown and infected in broth rather than minimal medium (C medium). Once early enzyme synthesis had ceased at 44 C, lowering the incubation temperature to 37 C did not occasion resumption of synthesis. Experiments with chloramphenicol at 44 C indicated that increased degradation of early enzymes is an unlikely explanation for the effect. Examination of pulse-labeled ribonucleic acid and polysomes made at 37 and 44 C in infected cells revealed some differences, but at present there is no obvious way in which these differences may be related to the effect on enzyme formation. There was no discernible difference between the ribosomal ribonucleic acid and ribosomes at the two temperatures, nor was there a difference in the cell-free amino acid-incorporating systems isolated from cells infected at the two temperatures as judged by polyuridylic stimulation of phenylalanine incorporation. Incubation of cells infected with T4amN82 at 44 C with protein synthesis blocked by 5-methyltryptophan for 15 min did not prevent the typical pattern of enzyme synthesis at 44 C when the block was reversed by excess l-tryptophan. The relation of this and other observations relative to the effect at 44 C on the synthesis of early enzymes is discussed.

  14. Heritable and cancer risks of exposures to anticancer drugs: inter-species comparisons of covalent deoxyribonucleic acid-binding agents.

    PubMed

    Vogel, E W; Barbin, A; Nivard, M J; Stack, H F; Waters, M D; Lohman, P H

    1998-05-25

    In the past years, several methodologies were developed for potency ranking of genotoxic carcinogens and germ cell mutagens. In this paper, we analyzed six sub-classes of covalent deoxyribonucleic acid (DNA) binding antineoplastic drugs comprising a total of 37 chemicals and, in addition, four alkyl-epoxides, using four approaches for the ranking of genotoxic agents on a potency scale: the EPA/IARC genetic activity profile (GAP) database, the ICPEMC agent score system, and the analysis of qualitative and quantitative structure-activity and activity-activity relationships (SARs, AARs) between types of DNA modifications and genotoxic endpoints. Considerations of SARs and AARs focused entirely on in vivo data for mutagenicity in male germ cells (mouse, Drosophila), carcinogenicity (TD50s) and acute toxicity (LD50s) in rodents, whereas the former two approaches combined the entire database on in vivo and in vitro mutagenicity tests. The analysis shows that the understanding and prediction of rank positions of individual genotoxic agents requires information on their mechanism of action. Based on SARs and AARs, the covalent DNA binding antineoplastic drugs can be divided into three categories. Category 1 comprises mono-functional alkylating agents that primarily react with N7 and N3 moieties of purines in DNA. Efficient DNA repair is the major protective mechanism for their low and often not measurable genotoxic effects in repair-competent germ cells, and the need of high exposure doses for tumor induction in rodents. Due to cell type related differences in the efficiency of DNA repair, a strong target cell specificity in various species regarding the potency of these agents for adverse effects is found. Three of the four evaluation systems rank category 1 agents lower than those of the other two categories. Category 2 type mutagens produce O-alkyl adducts in DNA in addition to N-alkyl adducts. In general, certain O-alkyl DNA adducts appear to be slowly repaired, or

  15. Production of cells without deoxyribonucleic acid during thymidine starvation of lexA- cultures of Escherichia coli K-12.

    PubMed Central

    Howe, W E; Mount, D W

    1975-01-01

    When thymidine-requiring lexA- strains were starved for thymidine, the kinetics of survival were similar to those of a nearly isogenic lexA+ strain. The size distribution of cells in the lexA- and lexA+ cultures were, however, quite different. Whereas most of the cells in the starved lexA+ cultures grew into long filamentous forms (longer than 4.0 mum), many of the lexA- cells were found to have a normal rod shape (4.0 mum or shorter). It was shown that lexA- cells undergo more divisions during thymidine starvation than lexA+ cells. Furthermore, using an autoradiographic method to analyze deoxyribonucleic acid (DNA) distribution in the starved cells, we demonstrated that cells without DNA are produced in both normal and starved lexA- cultures at a much higher frequency than in lexA+ cultures. Some of these cells may be produced by breakdown of DNA, but we favor the hypothesis that they result from an abnormal cell division process. Since lexA mutations are dominant, we conclude that a diffusible product decreases the synthesis or activity of an inhibitor of cell division in lexA- strains when DNA synthesis is blocked by thymidine starvation. Images PMID:1104571

  16. Strong, but Age-Dependent, Protection Elicited by a Deoxyribonucleic Acid/Modified Vaccinia Ankara Simian Immunodeficiency Virus Vaccine.

    PubMed

    Chamcha, Venkateswarlu; Kannanganat, Sunil; Gangadhara, Sailaja; Nabi, Rafiq; Kozlowski, Pamela A; Montefiori, David C; LaBranche, Celia C; Wrammert, Jens; Keele, Brandon F; Balachandran, Harikrishnan; Sahu, Sujata; Lifton, Michelle; Santra, Sampa; Basu, Rahul; Moss, Bernard; Robinson, Harriet L; Amara, Rama Rao

    2016-01-01

    Background.  In this study, we analyzed the protective efficacy of a simian immunodeficiency virus (SIV) macaque 239 (SIVmac239) analogue of the clinically tested GOVX-B11 deoxyribonucleic acid (DNA)/modified vaccinia Ankara (MVA) human immunodeficiency virus vaccine. Methods.  The tested vaccine used a DNA immunogen mutated to mimic the human vaccine and a regimen with DNA deliveries at weeks 0 and 8 and MVA deliveries at weeks 16 and 32. Twelve weekly rectal challenges with 0.3 animal infectious doses of SIV sootey mangabey E660 (SIVsmE660) were administered starting at 6 months after the last immunization. Results.  Over the first 6 rectal exposures to SIVsmE660, <10-year-old tripartite motif-containing protein 5 (TRIM5)α-permissive rhesus macaques showed an 80% reduction in per-exposure risk of infection as opposed to a 46% reduction in animals over 10 years old; and, over the 12 challenges, they showed a 72% as opposed to a 10% reduction. Analyses of elicited immune responses suggested that higher antibody responses in the younger animals had played a role in protection. Conclusions.  The simian analogue of the GOVX-B11 HIV provided strong protection against repeated rectal challenges in young adult macaques.

  17. Detection of Low Level Microwave Radiation Induced Deoxyribonucleic Acid Damage Vis-à-vis Genotoxicity in Brain of Fischer Rats

    PubMed Central

    Deshmukh, Pravin Suryakantrao; Megha, Kanu; Banerjee, Basu Dev; Ahmed, Rafat Sultana; Chandna, Sudhir; Abegaonkar, Mahesh Pandurang; Tripathi, Ashok Kumar

    2013-01-01

    Background: Non-ionizing radiofrequency radiation has been increasingly used in industry, commerce, medicine and especially in mobile phone technology and has become a matter of serious concern in present time. Objective: The present study was designed to investigate the possible deoxyribonucleic acid (DNA) damaging effects of low-level microwave radiation in brain of Fischer rats. Materials and Methods: Experiments were performed on male Fischer rats exposed to microwave radiation for 30 days at three different frequencies: 900, 1800 and 2450 MHz. Animals were divided into 4 groups: Group I (Sham exposed): Animals not exposed to microwave radiation but kept under same conditions as that of other groups, Group II: Animals exposed to microwave radiation at frequency 900 MHz at specific absorption rate (SAR) 5.953 × 10−4 W/kg, Group III: Animals exposed to 1800 MHz at SAR 5.835 × 10−4 W/kg and Group IV: Animals exposed to 2450 MHz at SAR 6.672 × 10−4 W/kg. At the end of the exposure period animals were sacrificed immediately and DNA damage in brain tissue was assessed using alkaline comet assay. Results: In the present study, we demonstrated DNA damaging effects of low level microwave radiation in brain. Conclusion: We concluded that low SAR microwave radiation exposure at these frequencies may induce DNA strand breaks in brain tissue. PMID:23833433

  18. N-methylimidazolium modified magnetic particles as adsorbents for solid phase extraction of genomic deoxyribonucleic acid from genetically modified soybeans.

    PubMed

    Deng, Manchen; Jiang, Cheng; Jia, Li

    2013-04-10

    N-Methylimidazolium modified magnetic particles (MIm-MPs) were prepared and applied in the solid phase extraction of genomic deoxyribonucleic acid (DNA) from genetically modified soybeans. The adsorption of MIm-MPs for DNA mainly resulted from the strong electrostatic interaction between the positively charged MPs and the negatively charged DNA. The elution of DNA from MPs-DNA conjugates using phosphate buffer resulted from the stronger electrostatic interaction of phosphate ions with MPs than DNA. In the extraction procedure, no harmful reagents (e.g. phenol, chloroform and isopropanol, etc.) used, high yield (10.4 μg DNA per 30 mg sample) and high quality (A260/A280=1.82) of DNA can be realized. The as-prepared DNA was used as template for duplex-polymerase chain reaction (PCR) and the PCR products were analyzed by a sieving capillary electrophoresis method. Quick and high quality extraction of DNA template, and fast and high resolution detection of duplex PCR products can be realized using the developed method. No toxic reagents are used throughout the method.

  19. Greater Vulnerability of the Infecting Viral Strand of Replicative-Form Deoxyribonucleic Acid of Bacteriophage φX174

    PubMed Central

    Datta, B.; Poddar, R. K.

    1970-01-01

    Four types of φX-infected cells of Escherichia coli CR, a thymine-requiring strain of E. coli C, were prepared in which the parental replicative-form deoxyribonucleic acid (RF DNA) was labeled with same specific amounts of bromouracil in (i) both strands, (ii) only the infecting viral strand, (iii) only the complementary strand, and (iv) neither strand. The sensitivity of each type of infected cell toward irradiation by ultraviolet light, visible light, and X rays was measured. The results indicate that a certain amount of radiation damage in the infecting viral strand of the parental RF was more inhibitory to the production of progeny phage than when the damage was in the complementary strand. Similar conclusions were also drawn from “suicide” experiments of the phage-infected complexes containing 32P of the same specific activity on either strand of the parental RF DNA. The results suggest that the beta decay occurring in the infecting viral strand was more effective in inactivating the plaque-forming ability of the complex. PMID:4921725

  20. Coordinate Variation in Lengths of Deoxyribonucleic Acid Molecules and Head Lengths in Morphological Variants of Bacteriophage T4

    PubMed Central

    Mosig, Gisela; Carnighan, Janet Renshaw; Bibring, Jane Baxandall; Cole, Robert; Bock, Hans-Georg Otto; Bock, Susan

    1972-01-01

    We have investigated three classes of small bacteriophage T4 particles which differ from normal T4 particles in length of their deoxyribonucleic acid (DNA), in head length, in protein content, and in density. The different particles contain DNA molecules measuring 0.90, 0.77, or 0.67, respectively, of the normal T4 length. An additional class of viable particles contains DNA molecules of 1.1 unit length. These discrete differences in DNA length correspond to discrete differences in length (but not width) of the respective heads and are roughly proportional to the resulting differences in head volumes. The measured relative dimensions of the different heads fit best the relative dimensions predicted by a quasi-icosahedral model in which the smallest T4 head corresponds to an icosahedron with a triangulation number T = 21. The mid-portion of this structure is thought to be elongated by adding successive rows of gene 23 protein hexamers, the normal T4 head having three added rows. Different mutants produce small particles of the three classes in varying proportions, but no mutant produces exclusively particles of a single class. Particles of each class, with indistinguishable DNA content, show additional minor differences in protein content, as measured by differences in buoyant density and in the relative ratio of 32P to 35S. Images PMID:5025493

  1. Initiation points for cellular deoxyribonucleic acid replication in human lymphoid cells converted by Epstein-Barr virus

    SciTech Connect

    Oppenheim, A.; Shlomai, Z.; Ben-Bassat, H.

    1981-08-01

    Replicon size was estimated in two Epstein-Barr virus (EBV)-negative human lymphoma lines, BJAB and Ramos, and four EBV-positive lines derived from the former ones by infection (conversion) with two viral strains, B95-8 and P3HR-1. Logarithmic cultures were pulse-labeled with (/sup -3/H)thymidine, and the deoxyribonucleic acid was spread on microscopic slides and autoradiographed by the method of Huberman and Riggs. Three of the four EBV-converted cell lines, BJAB/B95-8, Ra/B95-8, and Ra/HRIK, were found to have significantly shorter replicons (41, 21, 54% shorter, respectively), i.e., more initiation points, than their EBV-negative parents. BJAB/HRIK had replicons which were only slightly shorter (11%) than those of BJAB. However, analysis of track length demonstrated that extensive track fusion occurred during the labeling of BJAB/HRIK, implying that its true average replicon size is shorter than the observed value. The results indicate that in analogy to simian virus 40, EBV activates new initiation points for cellular DNA replication in EBV-transformed cells.

  2. Improving the Flame Retardant Efficiency of Layer by Layer Coatings Containing Deoxyribonucleic Acid by Post-Diffusion of Hydrotalcite Nanoparticles

    PubMed Central

    Carosio, Federico; Alongi, Jenny; Paravidino, Chiara; Frache, Alberto

    2017-01-01

    This work deals with the use of hydrotalcite nanoparticle post-diffusion in layer by layer (LbL) coatings with the aim of improving their flame retardant action on cotton. The selected LbL components, which encompass polydiallyldimethylammonium chloride and deoxyribonucleic acid, aim at the deposition of an intumescent coating. Infrared spectra pointed out a super-linear growth of the investigated assembly, indicating the ability to deposit thick coatings while maintaining a relatively low deposition number. A post-diffusion process, performed by exposing the LbL-treated fabrics to two different concentrations of hydrotalcite water suspensions (0.1 or 1 wt %), was carried out to improve the fireproofing efficiency of these coatings. Coatings treated with the lowest concentration suspension partially swelled as a consequence of their structural rearrangements while the use of the highest concentration led to nanoparticle aggregates. Horizontal flame spread tests were used for assessing the achieved flame retardant properties. The post-diffusion performed at the lowest hydrotalcite concentration lowers the minimum number of Bi-Layers required for obtaining cotton self-extinguishment while samples treated with the highest concentration showed detrimental effects on the performances of treated fabrics. This behavior is ascribed to the effects of hydrotalcite particles on the intumescence of LbL coatings, as evidenced by the morphological analyses of post-combustion residues. PMID:28773071

  3. Inhibition of Thymidine Kinase Activity and Deoxyribonucleic Acid Synthesis in L Cells Infected with the Meningopneumonitis Agent

    PubMed Central

    Lin, Hsiu-San

    1968-01-01

    The activities of enzymes related to deoxyribonucleic acid (DNA) synthesis were studied in uninfected L cells and in L cells infected with Chlamydia psittaci (strain meningopneumonitis). The meningopneumonitis agent multiplied normally but failed to induce the synthesis of thymidine kinase in LM (TK−) cells which contain no thymidine kinase in the uninfected state. It was concluded that this microorganism has no thymidine kinase of its own and that it does not depend on the functioning of the host enzyme for synthesizing its DNA. Exposure of clone 5b L cells to the meningopneumonitis agent was followed by a decline in their thymidine kinase activity to nearly zero levels, whereas the levels of uridine kinase and thymidylate synthetase remained unchanged. Inhibition of thymidine kinase activity in L cells occurred soon after infection and required new protein synthesis by the meningopneumonitis agent. This inhibition occurred before inhibition of host DNA synthesis, but it was not an essential prelude to the latter inhibition. On the basis of this and previous investigations and in light of present knowledge of the mammalian cell cycle, it was postulated that the meningopneumonitis agent inhibits macromolecular synthesis in L cells by preventing the initiation of a new cell cycle. PMID:5724972

  4. Use of a Single-Strand Specific Nuclease for Analysis of Bacterial and Plasmid Deoxyribonucleic Acid Homo- and Heteroduplexes

    PubMed Central

    Crosa, Jorge H.; Brenner, Don J.; Falkow, Stanley

    1973-01-01

    Bacterial and plasmid homo- and heteroduplexes have been analyzed with a single-strand specific endonuclease, S1, of Aspergillus oryzae. Under appropriate assay conditions, there was a high degree of correlation between the degree of deoxyribonucleic acid (DNA)-DNA homoduplex formation assessed by the S1 endonuclease and by hydroxyapatite (HA). Heteroduplexes which contain extensive regions of polynucleotide sequences in common are similarly recognized by the S1 endonuclease and HA. In instances where there is little or imperfect complementarity between heterologous DNA strands, the S1 endonuclease and the HA method give slightly different estimates. From DNA duplex thermal stability experiments assayed with the S1 endonuclease, there is preliminary evidence that well-matched sequences identified by the enzyme are not similarly recognized by HA. The assay of homo- and heteroduplexes with the S1 endonuclease permits an accurate, reproducible and rapid determination of polynucleotide sequence relationships and may be seriously considered as a method of choice for survey work and for investigations which require a large number of DNA-DNA hybridization assays. PMID:4728274

  5. Rapid concentration of deoxyribonucleic acid via Joule heating induced temperature gradient focusing in poly-dimethylsiloxane microfluidic channel.

    PubMed

    Ge, Zhengwei; Wang, Wei; Yang, Chun

    2015-02-09

    This paper reports rapid microfluidic electrokinetic concentration of deoxyribonucleic acid (DNA) with the Joule heating induced temperature gradient focusing (TGF) by using our proposed combined AC and DC electric field technique. A peak of 480-fold concentration enhancement of DNA sample is achieved within 40s in a simple poly-dimethylsiloxane (PDMS) microfluidic channel of a sudden expansion in cross-section. Compared to a sole DC field, the introduction of an AC field can reduce DC field induced back-pressure and produce sufficient Joule heating effects, resulting in higher concentration enhancement. Within such microfluidic channel structure, negative charged DNA analytes can be concentrated at a location where the DNA electrophoretic motion is balanced with the bulk flow driven by DC electroosmosis under an appropriate temperature gradient field. A numerical model accounting for a combined AC and DC field and back-pressure driven flow effects is developed to describe the complex Joule heating induced TGF processes. The experimental observation of DNA concentration phenomena can be explained by the numerical model.

  6. Strong, but Age-Dependent, Protection Elicited by a Deoxyribonucleic Acid/Modified Vaccinia Ankara Simian Immunodeficiency Virus Vaccine

    PubMed Central

    Chamcha, Venkateswarlu; Kannanganat, Sunil; Gangadhara, Sailaja; Nabi, Rafiq; Kozlowski, Pamela A.; Montefiori, David C.; LaBranche, Celia C.; Wrammert, Jens; Keele, Brandon F.; Balachandran, Harikrishnan; Sahu, Sujata; Lifton, Michelle; Santra, Sampa; Basu, Rahul; Moss, Bernard; Robinson, Harriet L.; Amara, Rama Rao

    2016-01-01

    Background. In this study, we analyzed the protective efficacy of a simian immunodeficiency virus (SIV) macaque 239 (SIVmac239) analogue of the clinically tested GOVX-B11 deoxyribonucleic acid (DNA)/modified vaccinia Ankara (MVA) human immunodeficiency virus vaccine. Methods. The tested vaccine used a DNA immunogen mutated to mimic the human vaccine and a regimen with DNA deliveries at weeks 0 and 8 and MVA deliveries at weeks 16 and 32. Twelve weekly rectal challenges with 0.3 animal infectious doses of SIV sootey mangabey E660 (SIVsmE660) were administered starting at 6 months after the last immunization. Results. Over the first 6 rectal exposures to SIVsmE660, <10-year-old tripartite motif-containing protein 5 (TRIM5)α-permissive rhesus macaques showed an 80% reduction in per-exposure risk of infection as opposed to a 46% reduction in animals over 10 years old; and, over the 12 challenges, they showed a 72% as opposed to a 10% reduction. Analyses of elicited immune responses suggested that higher antibody responses in the younger animals had played a role in protection. Conclusions. The simian analogue of the GOVX-B11 HIV provided strong protection against repeated rectal challenges in young adult macaques. PMID:27006959

  7. Assessment of the deoxyribonucleic acid damage caused by occupational exposure to chemical compounds in Isfahan Polyacryl Company

    PubMed Central

    Etebari, Mahmoud; Jafarian-Dehkordi, Abbas; Kahookar, Ahmad; Moradi, Shahla

    2014-01-01

    Background: Chemical pollutants found in industrial environments can cause chronic genotoxicity in vulnerable individuals during the long-term exposure. The primary purpose of the present study was to assess the deoxyribonucleic acid (DNA) damage caused by occupational exposure to industrial chemicals and secondary purpose is to investigate the effect of possible risk factors of genotoxicity. Materials and Methods: The blood samples of the workers of Isfahan Polyacryl Company were evaluated in terms of genotoxicity using the comet assay method. The percentage of DNA in the tail and tail moment were measured and DNA damage was evaluated. Furthermore, the effect of age, smoking, duration of working in the company and working in two parts of the company on the degree of vulnerability to genotoxicity was assessed. Results: The amount of DNA damage in the target group (the production line workers) was significantly higher than the control group (the staffs), 3.87 versus 1.52 as tail moment, (P < 0.0001). DNA damage was significantly higher in smoker groups compared with non-smoker target group and control group, 4.18 versus 3.07 and 1.52 respectively as tail moment, (P < 0.0001). Furthermore, it was higher in person working in two different parts of the company compared to those work in one part and control group, 4.63 versus 3.74 and 1.52 respectively as tail moment, (P < 0.0001). Conclusion: Occupational exposure to Polyacryl caused DNA damage. Smoking and working in two parts of the company may have a significant role in DNA damage. PMID:25197297

  8. Transformation of Bacillus subtilis in alpha-amylase productivity by deoxyribonucleic acid from B. subtilis var. amylosacchariticus.

    PubMed

    Yoneda, Y; Yamane, K; Yamaguchi, K; Nagata, Y; Maruo, B

    1974-12-01

    Deoxyribonucleic acid (DNA) of Bacillus subtilis var. amylosacchariticus showed almost the same ability as B. subtilis Marburg to induce transfer of several genetic markers in DNA-mediated transformation. DNA-DNA hybridization data also showed an intimate relationship between the two strains. Genetic elements involved in the production of extracellular alpha-amylase (EC 3.2.1.1.) in B. subtilis var. amylosacchariticus were studied by using DNA-mediated transformation. Two Marburg derivatives, NA20(amyR2) and NA20-22(amyR1), produced about 50 and 10 U of alpha-amylase per mg of cells, respectively, whereas B. subtilis var. amylosacchariticus produced as much as 150 U of the enzyme per mg of cells. When B. subtilis var. amylosacchariticus was crossed with strain NA20-22 as recipient, transformants that acquired high alpha-amylase productivity (about 50 U/mg of cells) were obtained. Genetic analysis revealed that a regulator gene (amyR) for alpha-amylase synthesis was found in B. subtilis var. amylosacchariticus, as in the case of B. natto 1212 (amyR2) and B. subtilis Marburg (amyR1). The allele was designated amyR3; it is phenotypically indistinguishable from amyR2, but is readily distinguishable from amyR1. The presence of amyR3 was not sufficient for an organism to render production of an exceptional amount of alpha-amylase. Extra-high alpha-amylase producers could be obtained by crossing B. subtilis var. amylosacchariticus as donor with strain NA20 as recipient. The transformants produced the same or even greater amounts of the enzyme than the donor strain. Results suggest the presence of another gene that is involved in the production of the exceptional amount of alpha-amylase.

  9. Molecular mechanisms of pyrimidine dimer excision in Saccharomyces cerevisiae: incision of ultraviolet-irradiated deoxyribonucleic acid in vivo

    SciTech Connect

    Reynolds, R.J.; Friedberg, E.C.

    1981-05-01

    A group of genetically related ultraviolet (uv)-sensitive mutants of Saccharomyces cerevisiae has been examined in terms of their survival after exposure to uv radiation, their ability to carry out excision repair or pyrimidine dimers as measured by the loss of sites (pyrimidine dimers) sensitive to a dimer-specific enzyme probe, and in terms of their ability to effect incision of their deoxyribonucleic acid (DNA) during post-uv incubation in vivo (as measured by the detection of single-strand breaks in nuclear DNA). In addition to a haploid RAD/sup +/ strain (S288C), 11 different mutants representing six RAD loci (RAD1, RAD2, RAD3, RAD4, RAD14, and RAD18) were examined. Quantitative analysis of excision repair capacity, as determined by the loss of sites in DNA sensitive to an enzyme preparation from M. luteus which is specific for pyrimidine dimers, revealed a profound defect in this parameter in all but three of the strains examined. The rad14-1 mutant showed reduced but significant residual capacity to remove enzyme-sensitive sites as did the rad2-4 mutant. The latter was the only one of three different rad2 alleles examined which was leaky in this respect. The uv-sensitive strain carrying the mutant allele rad18-1 exhibited normal loss of enzyme-sensitive sites consistent with its assignment to the RAD6 rather than the RAD3 epistatic group. All strains having mutant alleles of the RAD1, RAD2, RAD3, RAD4, and RAD14 loci showed no detectable incubation-dependent strand breaks in nuclear DNA after exposure to uv radiation. These experiments suggest that the RAD1, RAD2, RAD3, RAD4 (and probably RAD14) genes are all required for the incision of uv-irradiated DNA during pyrimidine dimer excision in vivo.

  10. Assessment of the deoxyribonucleic acid damage caused by occupational exposure to chemical compounds in Isfahan Polyacryl Company.

    PubMed

    Etebari, Mahmoud; Jafarian-Dehkordi, Abbas; Kahookar, Ahmad; Moradi, Shahla

    2014-06-01

    Chemical pollutants found in industrial environments can cause chronic genotoxicity in vulnerable individuals during the long-term exposure. The primary purpose of the present study was to assess the deoxyribonucleic acid (DNA) damage caused by occupational exposure to industrial chemicals and secondary purpose is to investigate the effect of possible risk factors of genotoxicity. The blood samples of the workers of Isfahan Polyacryl Company were evaluated in terms of genotoxicity using the comet assay method. The percentage of DNA in the tail and tail moment were measured and DNA damage was evaluated. Furthermore, the effect of age, smoking, duration of working in the company and working in two parts of the company on the degree of vulnerability to genotoxicity was assessed. The amount of DNA damage in the target group (the production line workers) was significantly higher than the control group (the staffs), 3.87 versus 1.52 as tail moment, (P < 0.0001). DNA damage was significantly higher in smoker groups compared with non-smoker target group and control group, 4.18 versus 3.07 and 1.52 respectively as tail moment, (P < 0.0001). Furthermore, it was higher in person working in two different parts of the company compared to those work in one part and control group, 4.63 versus 3.74 and 1.52 respectively as tail moment, (P < 0.0001). Occupational exposure to Polyacryl caused DNA damage. Smoking and working in two parts of the company may have a significant role in DNA damage.

  11. Structural studies of A-form sodium deoxyribonucleic acid: phosphorus-31 nuclear magnetic resonance of oriented fibers.

    PubMed

    Nall, B T; Rothwell, W P; Waugh, J S; Rupprecht, A

    1981-03-31

    A highly oriented sample of A-form sodium deoxyribonucleic acid (DNA) has been investigated by using proton-enhanced 31P nuclear magnetic resonance (NMR). Proton-decoupled spectra taken with different angles between the magnetic field direction and the fiber direction are compared to theoretical spectra which are calculated by assuming the following: (1) the orientation of the phosphate groups in the fiber is given by the A-form DNA coordinates suggested by Arnott & Hukins [Arnott, S., & Hukins, D. W. L. (1972) Biochem. Biophys. Res. Commun. 47, 1504-1509]; (2) the DNA phosphate groups may be considered stationary on the NMR time scale; (3) the relevant features of the spectra are determined solely by chemical shift anisotropy of the phosphorus atoms. The experimental and calculated spectra are in excellent agreement and support the validity of the above assumptions contrary to conclusions drawn in another investigation [Shindo, H., Wooton, J. B., Pheiffer, B. H., & Zimmerman, S. B. (1980) Biochemistry 19, 518-526]. In particular, we find no evidence to support the notion of a highly irregular phosphodiester backbone. Comparison of observed and simulated spectra allows the determination of the orientation of the 31P chemical shielding tensor relative to the bonding framework of the phosphodiester group. The orientation agrees with that expected from NMR studies of phosphodiester model compounds [Kohler, S. J., & Klein, M. P. (1976) Biochemistry 15, 967-973; Herzfeld, J., Griffin, R. G., & Haberkorn, R. A. (1978) Biochemistry 17, 2711-2718] and X-ray diffraction of oriented fibers [Arnott, S., & Hukins, D. W. L. (1972) Biochem. Biophys. Res. Commun. 47, 1504-1509].

  12. Deoxyribonucleic acid repair in Bacillus subtilis: development of competent cells into a tester for carcinogens

    SciTech Connect

    Yasbin, R.E.; Miehl, R.

    1980-04-01

    The development of competent transformed Bacillus subtilis into a tester system for carcinogens is described. Precocious or noninduced activation of SOS functions occurs in competent cells. Thus, lower doses or concentrations of SOS inducing agents are needed to cause cell death due to indigenous prophage activation and lysis of bacteria. The two known defective prophages in B. subtilis enhance the sensitivity of competent cells to the carcinogens ultraviolet light, mitomycin C, and methyl methanesulfonate. However, these same cells have no enhanced sensitivity for the non-carcinogenic ethyl methanesulfonate or for nalidixic acid. Therefore, competent B. subtilis appears to be a sensitive tester for carcinogens.

  13. Effect of Ethylene on Cell Division and Deoxyribonucleic Acid Synthesis in Pisum sativum1

    PubMed Central

    Apelbaum, Akiva; Burg, Stanley P.

    1972-01-01

    Ethylene and supraoptimal levels of 2,4-dichlorophenoxyacetic acid inhibit the growth of the apical hook region of etiolated Pisum sativum (var. Alaska) seedlings by stopping almost all cell divisions. Cells are prevented from entering prophase. The hormones also retard cell division in intact root tips and completely stop the process in lateral buds. The latter inhibition is reversed partially by benzyl adenine. In root tips and the stem plumular and subhook regions, ethylene inhibits DNA synthesis. The magnitude of this inhibition is correlated with the degree of repression of cell division in meristematic tissue, suggesting that the effect on cell division results from a lack of DNA synthesis. Ethylene inhibits cell division within a few hours with a dose-response curve similar to that for most other actions of the gas. Experiments with seedlings grown under hypobaric conditions suggest that the gas naturally controls plumular expansion and cell division in the apical region. Images PMID:16658105

  14. The Chinese hamster Alu-equivalent sequence: a conserved highly repetitious, interspersed deoxyribonucleic acid sequence in mammals has a structure suggestive of a transposable element.

    PubMed Central

    Haynes, S R; Toomey, T P; Leinwand, L; Jelinek, W R

    1981-01-01

    A consensus sequence has been determined for a major interspersed deoxyribonucleic acid repeat in the genome of Chinese hamster ovary cells (CHO cells). This sequence is extensively homologous to (i) the human Alu sequence (P. L. Deininger et al., J. Mol. Biol., in press), (ii) the mouse B1 interspersed repetitious sequence (Krayev et al., Nucleic Acids Res. 8:1201-1215, 1980) (iii) an interspersed repetitious sequence from African green monkey deoxyribonucleic acid (Dhruva et al., Proc. Natl. Acad. Sci. U.S.A. 77:4514-4518, 1980) and (iv) the CHO and mouse 4.5S ribonucleic acid (this report; F. Harada and N. Kato, Nucleic Acids Res. 8:1273-1285, 1980). Because the CHO consensus sequence shows significant homology to the human Alu sequence it is termed the CHO Alu-equivalent sequence. A conserved structure surrounding CHO Alu-equivalent family members can be recognized. It is similar to that surrounding the human Alu and the mouse B1 sequences, and is represented as follows: direct repeat-CHO-Alu-A-rich sequence-direct repeat. A composite interspersed repetitious sequence has been identified. Its structure is represented as follows: direct repeat-residue 47 to 107 of CHO-Alu-non-Alu repetitious sequence-A-rich sequence-direct repeat. Because the Alu flanking sequences resemble those that flank known transposable elements, we think it likely that the Alu sequence dispersed throughout the mammalian genome by transposition. Images PMID:9279371

  15. Deoxyribonuclease I generates single-stranded gaps in chromatin deoxyribonucleic acid.

    PubMed

    Riley, D E

    1980-06-24

    Production of 10-base multiple DNA ladder fragments during DNase I digestion of chromatin is explained by a model which does not involve site-specific nicking by the DNase I. This model was tested because it explains why 10-base (actually 10.4 base) multiple-related fragments are paradoxically generated by both endonucleolytic (DNase I) and exonucleolytic (exonuclease III) mechanisms. This new model also explains the phenomenon of substantial single-stranded DNA production during DNase I digestion of chromatin. The latter phenomenon has been widely observed but is not explained by previous models. The single-stranded gap model to be presented makes testable predictions. Primarily, these are that DNase I produces single-stranded gaps in chromatin DNA and that the termini of 10-base multiple ladder fragments are separated by single-stranded gaps. Single-stranded gap production by DNase I was confirmed by a number of methods. Sensitivity of ladder band components (from DNase I but not staphylococcal nuclease digests) to S1 nuclease suggested that the ladder fragments themselves may compose a significant portion of these gaps. Separation of ladder fragment termini by single-stranded gaps was verified by demonstrating both resistance to the nick-specific NAD+-dependent ligase and sensitivity to T4 ligase which can ligate across gaps. Many single-stranded gaps, occurring both individually and clusters, were observed by electron microscopy using either cytochrome c labeling (where the gaps) are thinner than duplex) or gene 32 protein labeling (gaps thicker than duplex). Gap sizes were estimated by protecting them with gene 32 protein and digesting away unprotected duplexes. By this method, gap sizes fall into a ladder distribution (from 10 or 20 bases up to 120 bases), which, at least in the region of the shorter sizes, clearly indicates the sizes of single-stranded gaps formed in chromatin by DNase I.

  16. Inhibition of Hsp27 Radiosensitizes Head-and-Neck Cancer by Modulating Deoxyribonucleic Acid Repair

    SciTech Connect

    Guttmann, David M.; Hart, Lori; Du, Kevin; Seletsky, Andrew; Koumenis, Constantinos

    2013-09-01

    Purpose: To present a novel method of tumor radiosensitization through Hsp27 knockdown using locked nucleic acid (LNA) and to investigate the role of Hsp27 in DNA double strand break (DSB) repair. Methods and Materials: Clonogenic survival assays, immunoblotting, the proximity ligation assay, and γH2AX foci analysis were conducted in SQ20B and FaDu human head-and-neck cancer cell lines treated with Hsp27 LNA and Hsp27 short hairpin RNA (shRNA). Additionally, nude mice with FaDu flank tumors were treated with fractionated radiation therapy after pretreatment with Hsp27 LNA and monitored for tumor growth. Results: Hsp27 LNA and Hsp27 shRNA radiosensitized head-and-neck cancer cell lines in an Hsp27-dependent manner. Ataxia-Telangectasia Mutated-mediated DNA repair signaling was impaired in irradiated cells with Hsp27 knockdown. ATM kinase inhibition abrogated the radiosensitizing effect of Hsp27. Furthermore, Hsp27 LNA and shRNA both attenuated DNA repair kinetics after radiation, and Hsp27 was found to colocalize with ATM in both untreated and irradiated cells. Last, combined radiation and Hsp27 LNA treatment in tumor xenografts in nude mice suppressed tumor growth compared with either treatment alone. Conclusions: These results support a radiosensitizing property of Hsp27 LNA in vitro and in vivo, implicate Hsp27 in double strand break repair, and suggest that Hsp27 LNA might eventually serve as an effective clinical agent in the radiotherapy of head-and-neck cancer.

  17. Dynamical features of deoxyribonucleic acid and configuration transition in the transcription process

    NASA Astrophysics Data System (ADS)

    Pang, Xiao-feng; Feng, Yuan Ping; Zhang, Huai-wu; Assad, S. M.

    2006-10-01

    Biological functions and genetic features of DNA, such as duplication, transcription and gene expression, are mainly determined by its structure, but depend also on the temperature and features of solution, such as salt concentration. We study the influence of temperature and salt concentration on the conformation changes and transcription of DNA by using a new dynamical model. This new model admits three degrees of freedom per base-pair: two displacement variables related to the vibrations of hydrogen atom in the hydrogen bonds and base (nucleotide), respectively, and an angular variable related to the rotation of base. The important role of motion of hydrogen atom in the hydrogen bonds is specially stressed in this model. This is helpful to reveal the mechanism of transcription of DNA. According to their properties of motion, we first give the Hamiltonian of the system, corresponding equations of motion and their soliton-solutions. The solitons are the excitation states formed by the displacements of hydrogen atoms and bases and the rotations of bases, arising from the energy absorbed by DNA, in the systems, respectively. By applying the transfer integral method we obtain the thermodynamic properties (e.g. free energy and entropy) of the thermal excitation state of DNA at the biological temperature in this model. According to the properties of these thermodynamic functions obtained we study the mechanism and processes of melting and transcription of DNA with the aid of the transforms of energy carried by the soliton in such a case. We further give the properties of the transcription of DNA with the help of the average value of the mean square of displacement of hydrogen atom, and the values of subcritical temperature and force of the phase transition are also found. Finally, we conclude that the transcription of DNA not only depends directly on the properties of its structure and of energy absorbed by it, but also is influenced by the temperature and salt

  18. Chromatographic isolation of the functionally active MutS protein covalently linked to deoxyribonucleic acid.

    PubMed

    Monakhova, Mayya; Ryazanova, Alexandra; Hentschel, Andreas; Viryasov, Mikhail; Oretskaya, Tatiana; Friedhoff, Peter; Kubareva, Elena

    2015-04-10

    DNA metabolism is based on formation of different DNA-protein complexes which can adopt various conformations. To characterize functioning of such complexes, one needs a solution-based technique which allows fixing a complex in a certain transient conformation. The crosslinking approach is a popular tool for such studies. However, it is under debate if the protein components retain their natural activities in the resulting crosslinked complexes. In the present work we demonstrate the possibility of obtaining pure DNA conjugate with functionally active protein using as example MutS protein from Escherichia coli mismatch repair system. A conjugate of a chemically modified mismatch-containing DNA duplex with MutS is fixed by thiol-disulfide exchange reaction. To perform a reliable test of the protein activity in the conjugate, such conjugate must be thoroughly separated from the uncrosslinked protein and DNA prior to the test. In the present work, we employ anion exchange chromatography for this purpose for the first time and demonstrate this technique to be optimal for the conjugate purification. The activity test is a FRET-based detection of DNA unbending. We show experimentally that MutS in the conjugate retains its ability to unbend DNA in response to ATP addition and find out for the first time that the DNA unbending rate increases with increasing ATP concentration. Since the crosslinked complexes contain active MutS protein, they can be used in further experiments to investigate MutS interactions with other proteins of the mismatch repair system.

  19. Charge transfer in deoxyribonucleic acid (DNA): Static disorder, dynamic fluctuations and complex kinetic

    NASA Astrophysics Data System (ADS)

    Edirisinghe Pathirannehelage, Neranjan S.

    The fact that loosely bonded DNA bases could tolerate large structural fluctuations, form a dissipative environment for a charge traveling through the DNA. Nonlinear stochastic nature of structural fluctuations facilitates rich charge dynamics in DNA. We study the complex charge dynamics by solving a nonlinear, stochastic, coupled system of differential equations. Charge transfer between donor and acceptor in DNA occurs via different mechanisms depending on the distance between donor and acceptor. It changes from tunneling regime to a polaron assisted hopping regime depending on the donor-acceptor separation. Also we found that charge transport strongly depends on the feasibility of polaron formation. Hence it has complex dependence on temperature and charge-vibrations coupling strength. Mismatched base pairs, such as different conformations of the G·A mispair, cause only minor structural changes in the host DNA molecule, thereby making mispair recognition an arduous task. Electron transport in DNA that depends strongly on the hopping transfer integrals between the nearest base pairs, which in turn are affected by the presence of a mispair, might be an attractive approach in this regard. I report here on our investigations, via the I-V characteristics, of the effect of a mispair on the electrical properties of homogeneous and generic DNA molecules. The I-V characteristics of DNA were studied numerically within the double-stranded tight-binding model. The parameters of the tight-binding model, such as the transfer integrals and on-site energies, are determined from first-principles calculations. The changes in electrical current through the DNA chain due to the presence of a mispair depend on the conformation of the G·A mispair and are appreciable for DNA consisting of up to 90 base pairs. For homogeneous DNA sequences the current through DNA is suppressed and the strongest suppression is realized for the G(anti)·A(syn) conformation of the G·A mispair. For

  20. No activation of new initiation points for deoxyribonucleic acid replication in BALB/c 3T3 cells transformed by Kirsten sarcoma virus

    SciTech Connect

    Oppenheim, A.; Horowitz, A.T.

    1981-08-01

    BALB/c 3T3 cells were transformed by Kirsten sarcoma virus, and five clones were isolated in soft agar. Average replicon sizes of the transformed cell lines were stimated by the method of fiber-autoradiography and found to be the same size as the nontransformed 3T3 cells, analyzed in parallel. The results indicate that, unlike simian virus 40 and Epstein-Barr virus, Kirsten sarcoma virus does not activate new initiation points for cellular deoxyribonucleic acid replication in murine sarcome virus-transformed BALB/c 3T3 cells.

  1. Validation and application of an assay for deoxyribonucleic acid to estimate concentrations of bull sperm.

    PubMed

    Fenton, S E; Ax, R L; Cowan, C M; Coyle, T; Gilbert, G R; Lenz, R W

    1990-11-01

    Spectrophotometers are used for estimating sperm concentrations from raw ejaculates in semen processing laboratories. Unfortunately, these instruments have a limited detection spectrum and do not permit accurate quantification of sperm numbers in highly diluted or concentrated samples. The objectives of this study were to validate a DNA assay for quantification of sperm numbers in extended or undiluted semen samples and to determine precision of the assay. The principle of the assay is based upon a fluorescent dye that binds to adenine-thymine base pairs in double-stranded DNA. Semen samples and calf thymus DNA standards were sonicated in 2 M NaCl buffer with 1 mM EDTA. The DNA content of samples was compared to standards of calf thymus DNA using fluorometry. Sensitivity of the assay was determined to be 1.4 x 10(5) sperm cells. Concentrations of sperm estimated from DNA assay values did not differ from flow cytometric cell counts. Assays were performed in three different laboratories, using different equipment, to assess the assay's repeatability. Estimates of sperm concentrations determined by the DNA assay were similar, regardless of location and source of equipment used to perform the assays. This assay fulfills statistical criteria for being sensitive, accurate, and repeatable, and it can be employed in laboratories processing semen for artificial insemination as a tool for spectrophotometer calibration, a check for straw filling accuracy, or to quantify sperm numbers in extended, packaged semen.

  2. Development of a small gantry robotic workcell for deoxyribonucleic acid (DNA) filter array construction

    SciTech Connect

    Beugelsdijk, T.J.; Hollen, R.M.; Snider, K.T.

    1990-01-01

    At Los Alamos National Laboratory, we have constructed a primary cosmid library of human chromosome 16. This library consists of an 11-fold representation of the chromosome and is arrayed in microtiter plate format. A need has arisen in the large scale physical mapping of this chromosome, to array spots of DNA from each of these colonies onto filter media for hybridization studies. We are currently developing a small gantry robot-based workcell to array small spots of DNA in an interleaved format. This allows for the construction of a high spot density format filter array. This paper will discuss the features incorporated into this workcell for the handling of thousands of colonies and their automatic tracking and positioning onto the filter. 7 refs., 3 figs., 1 tab.

  3. Characterization of deoxyribonucleic acid from cells infected with Aleutian disease virus

    SciTech Connect

    Hahn, E.C.; Ramos, L.; Kenyon, A.J.

    1983-07-01

    Viral DNA was extracted from Crandell feline kidney (CRFK) cells infected with Aleutian disease virus (ADV) and labeled with (/sup 3/H)thymidine. The sedimentation coefficient in alkaline sucrose gradients was 16S corresponding to a molecular weight of 1.5 X 10(6). The buoyant densities of DNA from infected and control cells were determined by isopyknic sedimentation in CsCl and NaI gradients. Two additional peaks of (/sup 3/H)DNA were found in infected cells, but not in control cell extracts. Fractionation of this DNA on hydroxylapatite indicated that the new peaks represented a single-stranded component, density 1.728 g/cm3, and a double-stranded component, presumed to be a viral replicative intermediate, density 1.718 g/cm3. The target antigen formation in CRFK cells was measured by gamma-irradiation of ADV and assayed for focus formation. The calculated size of ADV based on these measurements was 1.1 X 10(6). The H-1 parvovirus also was shown to have a size of 1.5 X 10(6) daltons for both antigen and plaque formation. The data indicated similarities existed between ADV and other autonomously replicating parvoviruses in most properties, except that less-than-unit length genome of ADV may be transcribed.

  4. A self-assembled deoxyribonucleic acid concatemer for sensitive detection of single nucleotide polymorphism.

    PubMed

    Wu, Wei; Chen, Junhua; Fang, Zhiyuan; Ge, Chenchen; Xiang, Zhicheng; Ouyang, Chuanyan; Lie, Puchang; Xiao, Zhuo; Yu, Luxin; Wang, Lin; Zeng, Lingwen

    2013-12-04

    Polymerase-free and label-free strategies for DNA detection have shown excellent sensitivity and specificity in various biological samples. Herein, we propose a method for single nucleotide polymorphism (SNP) detection by using self-assembled DNA concatemers. Capture probes, bound to magnetic beads, can joint mediator probes by T4 DNA ligase in the presence of target DNA that is complementary to the capture probe and mediator probe. The mediator probes trigger self-assembly of two auxiliary probes on magnetic beads to form DNA concatemers. Separated by a magnetic rack, the double-stranded concatemers on beads can recruit a great amount of SYBR Green I and eventually result in amplified fluorescent signals. In comparison with reported methods for SNP detection, the concatemer-based approach has significant advantages of low background, simplicity, and ultrasensitivity, making it as a convenient platform for clinical applications. As a proof of concept, BRAF(T1799A) oncogene mutation, a SNP involved in diverse human cancers, was used as a model target. The developed approach using a fluorescent intercalator can detect as low as 0.1 fM target BRAF(T1799A) DNA, which is better than those previously published methods for SNP detection. This method is robust and can be used directly to measure the BRAF(T1799A) DNA in complex human serum with excellent recovery (94-103%). It is expected that this assay principle can be directed toward other SNP genes by simply changing the mediator probe and auxiliary probes. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Subnucleosomes and their relationships to the arrangement of histone binding sites along nucleosome deoxyribonucleic acid

    SciTech Connect

    Nelson, D.A.; Mencke, A.J.; Chambers, S.A.; Oosterhof, D.K.; Rill, R.L.

    1982-01-01

    Micrococcal nuclease cleaves within nucleosomes at sites spaced about 10.4 base pairs (bp) apart. Cleavages at sites equivalent to 30-35 bp from the ends of 146-bp cores cause spontaneous loss of an H2a-H2b pair associated with 30-40 bp length DNA. Cleavages at certain other sites do not affect the nucleosome integrity unless a solvent perturbant such as urea is added. Chromatin moderately digested with micrococcal nuclease, when fractionated by sedimentation or electrophoresis in the presence of 3 M urea, yielded four previously unobserved subnucleosomes with the following histone/DNA compositions: (H3)/sub 2/(H4)/sub 2/(H2a)(H2b)/95-115 bp; (H3)(H4)/70-80 bp DNA; (H2a)(H2b)/50-60 bp DNA; and (H1)/60-70 bp DNA. All but the latter subnucleosome were also obtained upon DNase I digestion of purified nucleosome cores labeled on the 5' ends with /sup 32/P. Only subnucleosomes that retained H2a and H2b also retained labeled ends. These results show that H2a and H2b are paired on the terminal 30-40 bp of core DNA, as suggested from analyses of histone-DNA cross-link products by Mirzabekov and coworkers. Considerations of the orgins and compositions of subnucleosomes and of cross-linking data suggest an expanded model for the locations of histone binding sites along nucleosome core DNA. The principal features of this model are (i) strong electrostatic binding sites of H2a and H2b occur at positions approximately 20-30 bp from the core ends, (ii) strong electrostatic binding sites of H3 and H4 occur primarily on the central 40 bp of core DNA, (iii) strong nonelectrostatic, urea-sensitive binding sites of H3 and H4 occur at positions approximately 30-50 bp from the core ends, and (iv) urea-sensitive binding sites of H2a or H2b may occur on the terminal 10-20 bp of core DNA.

  6. Comparison of the Deoxyribonucleic Acid Molecular Weights and Homologies of Plasmids Conferring Linked Resistance to Streptomycin and Sulfonamides

    PubMed Central

    Barth, Peter T.; Grinter, Nigel J.

    1974-01-01

    Bacterial strains showing linked resistance to streptomycin (Sm) and sulfonamides (Su) were chosen representing a wide taxonomic and geographical range. Their SmSu resistances were transferred to Escherichia coli K-12 and then plasmid deoxyribonucleic acid (DNA) was isolated by ethidium bromide CsCl centrifugation. The plasmid DNA was examined by electron microscopy and analyzed by sedimentation through 5 to 20% neutral sucrose gradients. Plasmid DNA from strains having transmissible SmSu resistance consisted of two or three molecular species, one of which had a molecular mass of about 5.7 Mdal (106 daltons), the others varying between 20 to 60 Mdal. By using transformation or F′ mobilization, we isolated the SmSu-resistance determinant from any fellow resident plasmids in each strain and again isolated the plasmid DNA. Cosedimentation of each of these with a differently labeled reference plasmid DNA (R300B) showed 9 out of 12 of the plasmids to have a molecular mass not significantly different from the reference (5.7 Mdal); two others were 6.3 and 9.2 Mdal, but PB165 consisted of three plasmids of 7.4, 14.7, and 21.4 Mdal. Three separate isolations of the SmSu determinant from PB165 gave the same three plasmids, which we conclude may be monomer, dimer, and trimer, respectively. DNA-DNA hybridizations at 75 C demonstrated 80 to 93% homology between reference R300B DNA and each isolated SmSu plasmid DNA, except for the 9.2-Mdal plasmid which had 45% homology and PB165 which had 35%. All the SmSu plasmids were present as multiple copies (about 10) per chromosome. The conjugative plasmid of R300 (present as 1.3 copies per chromosome) has been shown to have negligible effect on the number of copies of its accompanying SmSu plasmid R300B. We conclude that the SmSu plasmids are closely related and probably have a common evolutionary origin. Images PMID:4616941

  7. Isolation and characterization of the specialized transducing bacteriophages phi80dargF and lambdah80cI857 dargF: specific cleavage of arginine transducing deoxyribonucleic acid by the endonucleases EcoRI and SmaR.

    PubMed Central

    James, P M; Sens, D; Natter, W; Moore, S K; James, E

    1976-01-01

    The directed transposition of argF to the tonB locus of the Escherichia coli chromosome and the subsequent isolation of the specialized transducing phage phi80dargF is described. The structure of this phage has been has been determined. A hybrid lambdah80cI857dargF phage has been constructed. Deoxyribonucleic acid isolated from these and their parent bacteriophages has been specifically cleaved by the endonucleases EcoRI and SmaR; the unique deoxyribonucleic acid fragments thus obtained have been resolved and analyzed by electrophoresis in agarose gel. Images PMID:770435

  8. Babesia gibsoni: detection in blood smears and formalin-fixed, paraffin-embedded tissues using deoxyribonucleic acid in situ hybridization analysis.

    PubMed

    Yamasaki, Masahiro; Kobayashi, Yusuke; Nakamura, Kensuke; Sasaki, Noboru; Murakami, Masahiro; Rajapakshage, Bandula Kumara Wickramasekara; Ohta, Hiroshi; Yamato, Osamu; Maede, Yoshimitsu; Takiguchi, Mitsuyoshi

    2011-01-01

    In this study, we attempted to detect Babesia gibsoni in blood smears and formalin-fixed, paraffin-embedded tissues obtained from B. gibsoni-infected dogs using in situ hybridization. Using a digoxigenin-conjugated deoxyribonucleic acid (DNA) probe, both intraerythrocytic and exoerythrocytic parasites in the culture could be specifically stained in blood smears fixed with 4% phosphate-buffered paraformaldehyde. This indicated that genomic DNA extracted from the parasites could be detected using in situ hybridization. Moreover, the parasite could be specifically stained in paraffin-embedded spleen, lymph node, and kidney sections using in situ hybridization. Infected erythrocytes in blood vessels in the spleen and kidney, hemosiderin-laden macrophages in the spleen, and phagocytized erythrocytes, which seemed to be infected with the parasites, in lymph nodes were also specifically stained. This suggests that in situ hybridization can be utilized to investigate both the life cycle of B. gibsoni and the pathological condition of canine babesiosis.

  9. Aminosulfhydryl and Aminodisulfide Compounds Enhance Binding of the Glucocorticoid Receptor Complex to Deoxyribonucleic Acid-Coated Cellulose and to Chromatin

    DTIC Science & Technology

    1993-01-01

    glucocorticoid receptor [21]. Diaminosulfhydryl chloroacetic acid was obtained from the Fisher compounds are more active at enhancing GRC Scientific...phase consisting of 0. I M BASE containing 25mM KCI and 3 mM chloroacetic acid and 5mM d/-10-camphorsul- MgCI2, pH 7.6 at 0 0C) was added to each tube...Enhance Binding of the Glucocorticoid Receptor Complex to Deoxy- ribonucleic Acid -Coated Cellulose and to Chromatin 4. AUThOR(S)’ J.M. Karle, R. Olmeda and

  10. Evaluation of deoxyribonucleic acid toxicity induced by the radiopharmaceutical 99mTechnetium-Methylenediphosphonic acid and by stannous chloride in Wistar rats.

    PubMed

    Mattos, José Carlos Pelielo De; Matos, Vanessa Coutinho de; Rodrigues, Michelle Pinheiro; Oliveira, Marcia Betânia Nunes de; Dantas, Flavio José S; Santos-Filho, Sebastião David; Bernardo-Filho, Mario; Caldeira-de-Araujo, Adriano

    2012-11-01

    Radiopharmaceuticals are employed in patient diagnostics and disease treatments. Concerning the diagnosis aspect, technetium-99m (99mTc) is utilized to label radiopharmaceuticals for single photon computed emission tomography (SPECT) due to its physical and chemical characteristics. 99mTc fixation on pharmaceuticals depends on a reducing agent, stannous chloride (SnCl(2)) being the most widely-utilized. The genotoxic, clastogenic and anegenic properties of the 99mTc-MDP(methylene diphosphonate used for bone SPECT) and SnCl(2) were evaluated in Wistar rat blood cells using the Comet assay and micronucleus test. The experimental approach was to endovenously administer NaCl 0.9% (negative control), cyclophosphamide 50 mg/kg b.w. (positive control), SnCl(2) 500 μg/mL or 99mTc-MDP to animals and blood samples taken immediately before the injection, 3, and 24 h after (in the Comet assay) and 36 h after, for micronucleus test. The data showed that both SnCl(2) and 99mTc-MDP-induced deoxyribonucleic acid (DNA) strand breaks in rat total blood cells, suggesting genotoxic potential. The 99mTc-MDP was not able to induce a significant DNA strand breaks increase in in vivo assays. Taken together, the data presented here points to the formation of a complex between SnCl(2) in the radiopharmaceutical 99mTc-MDP, responsible for the decrease in cell damage, compared to both isolated chemical agents. These findings are important for the practice of nuclear medicine.

  11. Viral and Host Deoxyribonucleic Acid Synthesis in Shope Fibroma Virus-infected Cells as Studied by Means of High-Resolution Autoradiography

    PubMed Central

    Scherrer, Raoul

    1968-01-01

    Incorporation of 3H-thymidine by BSC-1 cells infected with Shope fibroma virus was studied by means of high-resolution electron microscopic radioautography. One-hour pulses with the radioactive precursor were given at various times after infection, during a one-step growth cycle of the virus. In the cytoplasm of infected cells, reacted grains occurred over foci of viroplasm; these foci are believed to represent the true sites of viral deoxyribonucleic acid (DNA) replication. Shope fibroma virus DNA synthesis began before 3 hr postinfection, reached a maximum at 8 to 9 hr, and then declined rapidly. It was demonstrated that the decline in 3H-thymidine uptake is correlated with the onset of viral morphogenesis. In comparison with the noninfected culture, the nuclear labeling, which reflects host DNA metabolism, was slightly reduced by 4 hr postinfection. Inhibition became more marked as infection progressed, and host DNA synthesis was almost completely suppressed in late stages of viral development. Images PMID:4986482

  12. Physiological Modifications in the Production and Repair of Methyl Methane Sulfonate-Induced Breaks in the Deoxyribonucleic Acid of Escherichia coli K-12

    PubMed Central

    Scudiero, Dominic A.; Friesen, Benjamin S.; Baptist, Jeremy E.

    1973-01-01

    The medium in which Rec+ strains of Escherichia coli K-12 are grown affected their sensitivity to treatment with methyl methane sulfonate (MMS). Rec+ cells grown to the stationary phase in glucose-enriched nutrient broth (GNB) were more resistant to MMS than cells grown in nutrient broth (NB). The repair of MMS-induced breaks (or alkali-labile bonds) in the deoxyribonucleic acid (DNA) from E. coli K-12 strains AB1157, AB1886 uvrA6, and SR111 recA13 recB21 grown in GNB and NB media was examined by means of alkaline sucrose gradient centrifugation. It appeared that essentially all of the repair of breaks that occurred, as evidenced by an increase in “molecular weight,” took place within 10 min after treatment with MMS under our conditions. Cell survival was highest in cells for which the size of the DNA after the post-treatment incubation was the largest. The largest DNA after post-treatment incubation was found in Rec+ cells grown in GNB medium. The results suggest that these cells may have an enhanced capacity for repairing breaks in DNA. PMID:4349030

  13. Carcinogenic damage to deoxyribonucleic acid is induced by near-infrared laser pulses in multiphoton microscopy via combination of two- and three-photon absorption

    NASA Astrophysics Data System (ADS)

    Nadiarnykh, Oleg; Thomas, Giju; Van Voskuilen, Johan; Sterenborg, Henricus J. C. M.; Gerritsen, Hans C.

    2012-11-01

    Nonlinear optical imaging modalities (multiphoton excited fluorescence, second and third harmonic generation) applied in vivo are increasingly promising for clinical diagnostics and the monitoring of cancer and other disorders, as they can probe tissue with high diffraction-limited resolution at near-infrared (IR) wavelengths. However, high peak intensity of femtosecond laser pulses required for two-photon processes causes formation of cyclobutane-pyrimidine-dimers (CPDs) in cellular deoxyribonucleic acid (DNA) similar to damage from exposure to solar ultraviolet (UV) light. Inaccurate repair of subsequent mutations increases the risk of carcinogenesis. In this study, we investigate CPD damage that results in Chinese hamster ovary cells in vitro from imaging them with two-photon excited autofluorescence. The CPD levels are quantified by immunofluorescent staining. We further evaluate the extent of CPD damage with respect to varied wavelength, pulse width at focal plane, and pixel dwell time as compared with more pronounced damage from UV sources. While CPD damage has been expected to result from three-photon absorption, our results reveal that CPDs are induced by competing two- and three-photon absorption processes, where the former accesses UVA absorption band. This finding is independently confirmed by nonlinear dependencies of damage on laser power, wavelength, and pulse width.

  14. Role of Streptococcus sanguis (strain Wicky) cell surface-located deoxyribonucleic acid-binding factor in transformation of a homologous strain.

    PubMed Central

    Cegłowski, P; Kawczyński, M; Dobrzański, W T

    1981-01-01

    In a previous report we demonstrated the presence of a factor binding deoxyribonucleic acid (DNA) in vitro (BF) in cell leakage fluids from transformable Streptococcus sanguis strains Wicky, Challis, and Blackburn. BF originating from strain Wicky was purified to homogeneity, and its properties are described. In this work, it was found that BF occurs at the surface of Wicky cells in two forms, loosely bound (LB-BF) and strongly bound to the cell envelope. It was demonstrated that LB-BF formed fast-sedimenting complexes with exogenous DNA at the surface of Wicky cells. About 10-fold-more DNA became associated as a fast-sedimenting complex in competent than in incompetent cells. Thus, LB-BF is a cell receptor for exogenous DNA. However, the comparison of the effects of some agents on the transformation yield and the formation of LB-BF-DNA complexes, showed that the influence of these agents on both observed phenomena is not parallel and may be even opposite. These results are interpreted to mean that the LB-BF-DNA complexes do not take part in transformation. The problem of participation of BF strongly bound with the cell membrane fraction remains to be elucidated. Images PMID:6894295

  15. Development of a chamber system for rapid, high yield and cost-effective purification of deoxyribonucleic acid fragments from agarose gel.

    PubMed

    Eslami, Gilda; Salehi, Rasoul

    2014-01-01

    There are several methods commonly practicing for deoxyribonucleic acid (DNA) purification from agarose gel. In most laboratories, especially in developing countries, present methods for recovering of DNA fragments from the gel are mostly involved organic solvents. However, manual purification using organic solvents are toxic, labor intensive, time consuming and prone to contamination owing to several handling steps. The above mentioned burdens as well as cost and long time to import them, especially in developing countries, prompted us to design and develop a chamber system for rapid, non-toxic, cost-effective and user friendly device for polymerase chain reaction (PCR) products purification from agarose gel. The device was made from plexiglass plates. After amplification of two fragments of 250 and 850 bp, PCR products were electrophoresed. Subsequently, the desired bands were excised and purified with three method: HiPer Mini chamber, phenol extraction method and spin column procedure. To assess the suitability of the purified DNAs, restriction digestion was applied. Results showed that the yield of recovered DNA in our method was above 95%, whereas the yields obtained with conventional phenol extraction and spin column methods were around 60%. In conclusion, the current method for DNA elution is quick, inexpensive and robust and it does not require the use of toxic organic solvents. In addition, the purified DNA was well has suited for further manipulations such as restriction digestion, ligation, cloning, sequencing and hybridization.

  16. Cell cytotoxicity and serum albumin binding capacity of the morin-Cu(ii) complex and its effect on deoxyribonucleic acid.

    PubMed

    Roy, Atanu Singha; Samanta, Sintu Kumar; Ghosh, Pooja; Tripathy, Debi Ranjan; Ghosh, Sudip Kumar; Dasgupta, Swagata

    2016-08-16

    The dietary components, flavonoids, are important for their anti-oxidant properties and the ability to act as metal ion chelators. The characterization of the morin-Cu(ii) complex is executed using elemental analysis, FTIR and mass spectroscopy. DNA cleaving and cell cytotoxicity properties followed by serum albumin binding have been investigated in this report. The morin-Cu(ii) complex was found to cleave plasmid pBR322 DNA via an oxidative pathway as revealed by agarose gel based assay performed in the presence of some scavengers and reactive oxygen species. The breaking of the deoxyribose ring of calf thymus DNA (ct-DNA) was also confirmed by the formation of thiobarbituric acid reacting species (TBARS) between thiobarbituric acid and malonaldehyde. The morin-Cu(ii) complex is able to inhibit the growth of human HeLa cells. Fluorescence studies revealed that the morin-Cu(ii) complex can quench the intrinsic fluorescence of serum albumins (SAs) via a static quenching method. The binding constants were found to be in the order of 10(5) M(-1) and observed to increase with temperature. Both ΔH° and ΔS° are positive for the binding of the morin-Cu(ii) complex with serum albumins which indicated the presence of hydrophobic forces. Site-selectivity studies reveal that the morin-Cu(ii) complex binds to both site 1 (subdomain IIA) and site 2 (subdomain IIIA) of human serum albumin (HSA) and bovine serum albumin (BSA). Circular dichroism (CD) studies showed the structural perturbation of SAs during binding with the morin-Cu(ii) complex. The results from binding studies confirmed that after complexation with the Cu(ii) ion, morin alters its mode of interaction with SAs which could have differential implications on its other biological and pharmaceutical properties.

  17. Binding and elution behavior of small deoxyribonucleic acid fragments on a strong anion-exchanger multimodal chromatography resin.

    PubMed

    Matos, Tiago; Queiroz, João A; Bülow, Leif

    2013-08-09

    The separation behavior of small single-stranded from double-stranded DNA molecules has been determined on a multimodal (mixed-mode) chromatography system. The resin used is a strong anion exchanger which also modulates hydrophobic recognition. The intrinsic differences between single- and double-stranded DNAs concerning charge, hydrophobicity and three-dimensional structure render this form of MMC suitable for separation of the different nucleic acid molecules. All DNAs tested bound strongly to the resin and they could be eluted with increasing NaCl concentrations. Each homopolymeric ssDNA sample resulted in a base-specific elution pattern when using a linear NaCl gradient. The elution order was poly(dA)

  18. Prediction of drug cytotoxicity in 9L rat brain tumor by using flow cytometry with a deoxyribonucleic acid-binding dye.

    PubMed

    Iwadate, Y; Fujimoto, S; Sueyoshi, K; Namba, H; Tagawa, M; Yamaura, A

    1997-04-01

    Flow cytometry (FCM) with a deoxyribonucleic acid (DNA)-binding dye, propidium iodide, provides a rapid and quantitative method to detect apoptotic cell death. This technique was used to examine the sensitivity of tumor cells to anticancer agents, as a novel test of chemosensitivity in vitro. The in vitro chemosensitivity of 9L gliosarcoma cells to a panel of anticancer agents (cisplatin, nimustine, adriamycin, cyclophosphamide, vincristine, 5-fluorouracil, and methotrexate) was investigated by both FCM, yielding DNA histograms, and a microtiter tetrazolium test, measuring cellular metabolism. Clinically achievable concentrations of the agents were used for the analysis of DNA histograms and proliferation of 9L cells in vitro. Rats intracranially inoculated with 9L cells were treated with the agents, and tumor masses were visually monitored by using magnetic resonance imaging with gadolinium-diethylenetriaminepentaacetic acid enhancement. The cytotoxic effect of anticancer agents examined by the microtiter tetrazolium test correlated with a decreased G0/G1 peak in the DNA histograms. Serial FCM analysis showed that the decrease in the G0/G1 peak was subsequently accompanied by increased hypodiploid areas, suggesting DNA fragmentation induced by the agents. The in vitro chemosensitivity test and cell proliferation examination showed that all agents except cisplatin were effective. Growth retardation of inoculated brain tumors and prolonged survival of inoculated rats were observed with treatment with the anticancer agents, except cisplatin. The present study shows that FCM analysis with a DNA-binding dye can detect DNA damage induced by anticancer agents, and it suggests that this technique is a novel method to test chemosensitivity in vitro.

  19. Peptide purification, complementary deoxyribonucleic acid (DNA) and genomic DNA cloning, and functional characterization of ghrelin in rainbow trout.

    PubMed

    Kaiya, Hiroyuki; Kojima, Masayasu; Hosoda, Hiroshi; Moriyama, Shunsuke; Takahashi, Akiyoshi; Kawauchi, Hiroshi; Kangawa, Kenji

    2003-12-01

    We have identified ghrelin from the stomach of rainbow trout. Four isoforms of ghrelin peptide were isolated: the C-terminal amidated type of rainbow trout ghrelin (rt ghrelin) composed of 24 amino acids (GSSFLSPSQKPQVRQGKGKPPRV-amide) is a basic form; des-VRQ-rt ghrelin, which deleted three amino acids (V13R14Q15) from rt ghrelin; and further two types of rt ghrelin that retained the glycine residue at the C terminus, rt ghrelin-Gly, and des-VRQ-rt ghrelin-Gly. The third serine residue was modified by octanoic acid, decanoic acid, or the unsaturated form of those fatty acids. In agreement with the isolated peptides, two cDNAs of different lengths were isolated. The rt ghrelin gene has five exons and four introns, and two different mRNA molecules are predicted to be produced by alternative splicing of the gene. A high level of ghrelin mRNA expression was detected in the stomach, and moderate levels were detected in the brain, hypothalamus, and intestinal tracts. Des-VRQ-rt ghrelin stimulated the release of GH in the rat in vivo. Furthermore, des-VRQ-rt ghrelin stimulated the release of GH, but not the release of prolactin and somatolactin in rainbow trout in vivo and in vitro. These results indicate that ghrelin is a novel GH secretagogue in rainbow trout that may affect somatic growth or osmoregulation through GH. Because ghrelin is expressed in various tissues other than stomach, it may play important role(s) in cellular function as a local regulator.

  20. Modification and restriction of T-even bacteriophages. In vitro degradation of deoxyribonucleic acid containing 5-hydroxymethylctosine.

    PubMed

    Fleischman, R A; Cambell, J L; Richardson, C C

    1976-03-25

    Using the single-stranded circular DNA of bacteriophage fd as template, double-stranded circular DNA has been prepared in vitro with either 5-hydroxymethylcytosine ([hmdC]DNA) or cytosine ([dC]DNA) in the product strand. Extracts prepared from Escherichia coli cells restrictive to T-even phage containing nonglucosylated DNA degrade [hmdC]DNA to acid-soluble material in vitro, but do not degrade [dC]dna. In contrast, extracts prepared from E. coli K12 rglA- rglB-, a strain permissive to T-even phage containing nonglucosylated DNA, do not degrade [hmdC]DNA or [dC]DNA. In addition, glucosylation of the [hmdC]DNA renders it resistant to degradation by extracts from restrictive strains. The conversion of [hmdC]DNA to acid-soluble material in vitro consists of an HmCyt-specific endonucleolytic cleavage requiring the presence of the RglB gene product to form a linear molecule, followed by a non-HmCyt-specific hydrolysis of the linear DNA to acid-soluble fragments, catalyzed in part by exonuclease V. The RglB protein present in extracts of E. coli K12 rglA- rglB+ has been purified 200-fold by complementation with extracts from E. coli K12 rglA- rglB-. The purified RglB protein does not contain detectable HmCyt-specific endonuclease or exonuclease activity. In vitro endonucleolytic cleavage of [hmdC]DNA thus requires additional factors present in cell extracts.

  1. Induction of human choriogonadotropin in HeLa-cell cultures by aliphatic monocarboxylates and inhibitors of deoxyribonucleic acid synthesis

    PubMed Central

    Ghosh, Nimai K.; Rukenstein, Adriana; Cox, Rody P.

    1977-01-01

    The ectopic production of the glycopeptide hormone human placental choriogonadotropin by HeLa65 cells was measured by radioimmunoassay with antiserum against the β-subunit of choriogonadotropin and with the 125I-labelled β-subunit as a tracer antigen. Choriogonadotropin synthesis was markedly (500-fold) stimulated by sodium butyrate. Kinetic studies and the use of an inhibitor of protein synthesis, cycloheximide, indicated that protein synthesis was required for this induction. Investigation of the efficiency of 22 aliphatic short-chain fatty acids and derivatives in causing increased choriogonadotropin synthesis by HeLa cells showed stringent structural requirements. Induction of choriogonadotropin synthesis in HeLa cells was not restricted to butyrate. Other aliphatic acids (propionate, isobutyrate, valerate and hexanoate) were also capable of inducing choriogonadotropin synthesis at 10–50% of the efficiency of butyrate. Hydroxy derivatives of monocarboxylate inducers, related mono- and di-carboxylic acids, alcohols, amines, ketones, esters and sulphoxide were ineffective in increasing choriogonadotropin production by HeLa cells. A saturated C4 straight-chain acid without substituent hydroxyl groups but with a methyl group at one end and a carboxyl moiety at the other appeared to be most efficient in activating choriogonadotropin production. A second clonal line of HeLa cells, HeLa71, showed a higher constitutive synthesis of choriogonadotropin than HeLa65 cells, which was also markedly increased by butyrate. Butyrate and other aliphatic monocarboxylate inducers of choriogonadotropin synthesis inhibited HeLa-cell growth and DNA synthesis. This inhibition of DNA replication may be related to the mechanism of choriogonadotropin synthesis, since two well-characterized anti-neoplastic inhibitors of DNA synthesis, hydroxyurea and 1-β-d-arabinofuranosylcytosine, also stimulated a 300-fold increase in choriogonadotropin synthesis in HeLa cells and were synergistic

  2. Formation and rejoining of deoxyribonucleic acid double-strand breaks induced in isolated cell nuclei by antineoplastic intercalating agents.

    PubMed

    Pommier, Y; Schwartz, R E; Kohn, K W; Zwelling, L A

    1984-07-03

    The biochemical characteristics of the formation and disappearance of intercalator-induced DNA double-strand breaks (DSB) were studied in nuclei from mouse leukemia L1210 cells by using filter elution methodology [Bradley, M. O., & Kohn, K.W. (1979) Nucleic Acids Res. 7, 793-804]. The three intercalators used were 4'-(9-acridinylamino)-methanesulfon-m-anisidide (m-AMSA), 5-iminodaunorubicin (5-ID), and ellipticine. These compounds differ in that they produced predominantly DNA single-strand breaks (SSB) (m-AMSA) or predominantly DNA double-strand breaks (ellipticine) or a mixture of both SSB and DSB (5-ID) in whole cells. In isolated nuclei, each intercalator produced DSB at a frequency comparable to that which is produced in whole cells. Moreover, these DNA breaks reversed within 30 min after drug removal. It thus appeared that neither ATP nor other nucleotides were necessary for intercalator-dependent DNA nicking-closing reactions. The formation of the intercalator-induced DSB was reduced at ice temperature. Break formation was also reduced in the absence of magnesium, at a pH above 6.4 and at NaCl concentrations above 200 mM. In the presence of ATP and ATP analogues, the intercalator-induced cleavage was enhanced. These results suggest that the intercalator-induced DSB are enzymatically mediated and that the enzymes involved in these reactions can catalyze DNA double-strand cleavage and rejoining in the absence of ATP, although the occupancy of an ATP binding site might convert the enzyme to a form more reactive to intercalators. Three inhibitors of DNA topoisomerase II--novobiocin, nalidixic acid, and norfloxacin--reduced the formation of DNA strand breaks.(ABSTRACT TRUNCATED AT 250 WORDS)

  3. Effects of retinoids on iodine metabolism, thyroid peroxidase gene expression, and deoxyribonucleic acid synthesis in porcine thyroid cells in culture.

    PubMed

    Arai, M; Tsushima, T; Isozaki, O; Shizume, K; Emoto, N; Demura, H; Miyakawa, M; Onoda, N

    1991-12-01

    Effects of retinoids on DNA synthesis, iodine metabolism, and thyroid peroxidase messenger RNA levels were studied in cultured porcine thyroid cells. Retinol (10(-8)-10(-5) M) alone did not affect DNA synthesis but potentiated that induced by epidermal growth factor or insulin-like growth factor-I without changes in the number or affinity of receptors for the growth factors, suggesting that retinol stimulates postreceptor events responsible for DNA synthesis. Retinol was an inhibitor of TSH-stimulated iodine metabolism. Iodide uptake and release of organified iodine stimulated by TSH or forskolin were inhibited dose dependently by treatment with retinol. The inhibition was detected at 10(-8) M and was approximately 50% at 10(-6) M. The potency of retinoic acid was comparable to that of retinol. The inhibitory effect of retinol was detected after treatments of thyroid cells for 24 h, and the maximal effect occurred after 48 h incubation. The cAMP accumulation in cultures treated with TSH plus retinol was lower than that of control cultures treated with TSH alone. However, iodide uptake stimulated by 8-bromo-cAMP was also inhibited by retinoids. Retinol reduced TSH- or 8-bromo-cAMP-stimulated gene expression of thyroid peroxidase. Thus, the data suggest that retinoids inhibit TSH-stimulated iodine metabolism by reducing cAMP accumulation and also by acting on the steps subsequent to cAMP production.

  4. Postreplication repair of deoxyribonucleic acid and daughter strand exchange in Uvr/sup -/ mutants of Bacillus subtilis

    SciTech Connect

    Dodson, L.A.; Hadden, C.T.

    1980-11-01

    The fate of pyrimidine dimers in deoxyribonuclei acid (DNA) newly synthesized by Bacillus subtilis after ultraviolet irradiation was monitored by use of a damage-specific endonuclease that introduces single-strand breaks adjacent to nearly all of the dimer sites. Two Uvr/sup -/ strains, one defective in the initiation of dimer excision and the other defective in a function required for efficient dimer excision, were found to be similar to their wild-type parent in the kinetics and extent of converting low-molecular-weight DNA newly synthesized after ultraviolet irradiation to high molecular weight. In the Uvr/sup -/ strains large molecules of newly synthesized DNA remained susceptible to nicking by the damage-specific endonuclease even after extended incubation in growth medium, whereas the enzyme-sensitive sites were rapidly removed from both preexisting and newly synthesized DNA in Uvr/sup +/ cells. Our results support the hypothesis that postreplication repair in bacteria includes recombination between dimer-containing parental DNA strands and newly synthesized strands.

  5. Methylation changes in mature sperm deoxyribonucleic acid from oligozoospermic men: assessment of genetic variants and assisted reproductive technology outcome.

    PubMed

    Montjean, Debbie; Ravel, Célia; Benkhalifa, Moncef; Cohen-Bacrie, Paul; Berthaut, Isabelle; Bashamboo, Anu; McElreavey, Kenneth

    2013-11-01

    To characterize a potential genetic cause for methylation errors described in oligozoospermia. Analysis of PEG1/MEST-DMR and H19-DMR methylation level in sperm, in parallel with the study of several genes on the Y chromosome, DNMT3A, and DNMT3L. Clinical outcome was also looked at regarding PEG1/MEST-DMR and H19-DMR methylation level in sperm. Research and diagnostic laboratories. One hundred nineteen normospermic and 175 oligozoospermic men consulting for couple infertility. We studied PEG1/MEST-DMR and H19-DMR methylation profiles in 294 men. We searched for Y chromosome gene aberrations and for mutations in both DNMT3A and DNMT3L genes in men showing epimutations. Assisted reproductive technology (ART) outcomes were also investigated. Sperm samples were collected from 294 volunteers for genomic DNA isolation that was used to study methylation profiles in imprinted loci and Y chromosome SMCY, DNMT3A, and DNMT3L genes. Pregnancy rate was also studied after ART treatment using sperm showing epimutations. Epimutations in H19-DMR and PEG1/MEST-DMR were found in 20% and 3% of oligozoospermic men, respectively. We identified an amino acid change in DNMT3A in one case and in DNMT3L in eight men with altered methylation profiles. No mutations were detected in SMCY or in selected Y chromsome genes. No correlation between ART outcome and epimutations was found. We observed epimethylations in spermatozoa of oligozoospermic individuals, but no association was found with genetic variants or in the ART outcome. Copyright © 2013 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  6. The effect of feeding with a tryptophan-free amino acid mixture on rat liver magnesium ion-activated deoxyribonucleic acid-dependent ribonucleic acid polymerase

    PubMed Central

    Henderson, A. R.

    1970-01-01

    1. The Widnell & Tata (1966) assay method for Mg2+-activated DNA-dependent RNA polymerase was used for initial-velocity determinations of rat liver nuclear RNA polymerase. One unit (U) of RNA polymerase was defined as that amount of enzyme required for 1 mmol of [3H]GMP incorporation/min at 37°C. 2. Colony fed rats were found to have a mean RNA polymerase activity of 65.9μU/mg of DNA and 18h-starved rats had a mean activity of 53.2μU/mg of DNA. Longer periods of starvation did not significantly decrease RNA polymerase activity further. 3. Rats that had been starved for 18h were used for all feeding experiments. Complete and tryptophan-deficient amino acid mixtures were given by stomach tube and the animals were killed 15–120min later. The response of RNA polymerase to the feeding with the complete amino acid mixture was rapid and almost linear over the first hour of feeding, resulting in a doubling of activity. The activity was still elevated above the starvation value at 120min after feeding. The tryptophan-deficient amino acid mixture produced a much less vigorous response about 45min after the feeding, and the activity had returned to the starvation value by 120min after the feeding. 4. The response of RNA polymerase to the feeding with the complete amino acid mixture was shown to occur within a period of less than 5min to about 10min after the feeding. 5. Pretreatment of the animals with puromycin or cycloheximide was found to abolish the 15min RNA polymerase response to the feeding with the complete amino acid mixture, but the activity of the controls was unaffected. 6. The characteristics of the RNA polymerase from 18h-starved animals and animals fed with the complete or incomplete amino acid mixtures for 1h were examined. The effects of Mg2+ ions, pH, actinomycin D and nucleoside triphosphate omissions were determined. The [Mg2+]– and pH–activity profiles of the RNA polymerase from the animal fed with the complete mixture appeared to differ from

  7. Immobilization mechanisms of deoxyribonucleic acid (DNA) to hafnium dioxide (HfO2) surfaces for biosensing applications.

    PubMed

    Fahrenkopf, Nicholas M; Rice, P Zachary; Bergkvist, Magnus; Deskins, N Aaron; Cady, Nathaniel C

    2012-10-24

    Immobilization of biomolecular probes to the sensing substrate is a critical step for biosensor fabrication. In this work we investigated the phosphate-dependent, oriented immobilization of DNA to hafnium dioxide surfaces for biosensing applications. Phosphate-dependent immobilization was confirmed on a wide range of hafnium oxide surfaces; however, a second interaction mode was observed on monoclinic hafnium dioxide. On the basis of previous materials studies on these films, DNA immobilization studies, and density functional theory (DFT) modeling, we propose that this secondary interaction is between the exposed nucleobases of single stranded DNA and the surface. The lattice spacing of monoclinic hafnium dioxide matches the base-to-base pitch of DNA. Monoclinic hafnium dioxide is advantageous for nanoelectronic applications, yet because of this secondary DNA immobilization mechanism, it could impede DNA hybridization or cause nonspecific surface intereactions. Nonetheless, DNA immobilization on polycrystalline and amorphous hafnium dioxide is predominately mediated by the terminal phosphate in an oriented manner which is desirable for biosensing applications.

  8. Developing an electrochemical deoxyribonucleic acid (DNA) biosensor on the basis of human interleukine-2 gene using an electroactive label.

    PubMed

    Pournaghi-Azar, M H; Hejazi, M S; Alipour, E

    2006-06-16

    Development of an electrochemical DNA biosensor based on a human interleukine-2 (IL-2) gene probe, using a pencil graphite electrode (PGE) as transducer and methylene blue (MB) as electroactive label is described. The sensor relies on the immobilization of a 20-mer single stranded oligonucleotide probe (hIL-2) related to the IL-2 gene on the electrode. The hybridization between the probe and its complementary sequence (chIL-2) as the target was studied by square wave voltammetry (SWV) of MB accumulated on the PGE. In this approach the extent of hybridization is evaluated on the basis of the difference between SWV signals of MB accumulated on the probe-PGE and MB accumulated on the probe-target-PGE. Some hybridization experiments with non-complementary oligonucleotides were carried out to assess whether the suggested DNA sensor responds selectively to the target. Some experimental variables affecting the performance of the biosensor including: polishing of PGE, its electrochemical activation conditions (i.e., activation potential and activation time) and probe immobilization conditions on the electrodes (i.e., immobilization potential and time) were investigated and the optimum values of 1.80 V and 300 s for PGE activation, and -0.5 V and 400s for the probe immobilization on the electrode were suggested.

  9. A Two-Dimensional Deoxyribonucleic Acid (DNA) Matrix Based Biomolecular Computing and Memory Architecture

    DTIC Science & Technology

    2009-02-01

    decoded. On the aqueous side, binding proteins specific to each modification are used to selectively isolate DNA fragments and this selectivity is...used to do computation. As there are millions of molecules with corresponding binding proteins , this approach has the potential to yield unlimited...are used to selectively isolate DNA fragments by binding proteins specific to the label of interest. An implementation strategy for using these

  10. Molecular cloning of otoconin-22 complementary deoxyribonucleic acid in the bullfrog endolymphatic sac: effect of calcitonin on otoconin-22 messenger ribonucleic acid levels.

    PubMed

    Yaoi, Yuichi; Suzuki, Masakazu; Tomura, Hideaki; Sasayama, Yuichi; Kikuyama, Sakae; Tanaka, Shigeyasu

    2003-08-01

    Anuran amphibians have a special organ called the endolymphatic sac (ELS), containing many calcium carbonate crystals, which is believed to have a calcium storage function. The major protein of aragonitic otoconia, otoconin-22, which is considered to be involved in the formation of calcium carbonate crystals, has been purified from the saccule of the Xenopus inner ear. In this study, we cloned a cDNA encoding otoconin-22 from the cDNA library constructed for the paravertebral lime sac (PVLS) of the bullfrog, Rana catesbeiana, and sequenced it. The bullfrog otoconin-22 encoded a protein consisting of 147 amino acids, including a signal peptide of 20 amino acids. The protein had cysteine residues identical in a number and position to those conserved among the secretory phospholipase A(2) family. The mRNA of bullfrog otoconin-22 was expressed in the ELS, including the PVLS and inner ear. This study also revealed the presence of calcitonin receptor-like protein in the ELS, with the putative seven-transmembrane domains of the G protein-coupled receptors. The ultimobranchialectomy induced a prominent decrease in the otoconin-22 mRNA levels of the bullfrog PVLS. Supplementation of the ultimobranchialectomized bullfrogs with synthetic salmon calcitonin elicited a significant increase in the mRNA levels of the sac. These findings suggest that calcitonin secreted from the ultimobranchial gland, regulates expression of bullfrog otoconin-22 mRNA via calcitonin receptor-like protein on the ELS, thereby stimulating the formation of calcium carbonate crystals in the lumen of the ELS.

  11. Early effects of oestradiol-17β on the chromatin and activity of the deoxyribonucleic acid-dependent ribonucleic acid polymerases (I and II) of the rat uterus

    PubMed Central

    Glasser, S. R.; Chytil, F.; Spelsberg, T. C.

    1972-01-01

    Oestradiol-17β (1.0μg) was injected intravenously into ovariectomized rats. The earliest detectable hormonal response in isolated uterine nuclei was an increase (10–15min) in RNA polymerase II activity (DNA-like RNA synthesis), which reached a peak at 30min and then decreased to control values (by 1–2h) before displaying a second increase over control activity from 2 to 12h. The next response to oestradiol-17β was an increase (30–60min) in polymerase I activity (rRNA synthesis) and template capacity of the chromatin. The concentrations of acidic chromatin proteins did not begin to increase until 1h after injection of oestradiol-17β and histone concentrations showed no significant changes during the 8h period after administration. The early (15min) increase in RNA synthesis in `high-salt conditions' can be completely eliminated by α-amanitin, an inhibitor of the RNA polymerase II. The exact nature of this early increase in endogenous polymerase II activity remains to be determined, e.g. whether it is caused by the increased availability of transcribable DNA of the chromatin or via direct hormonal activation of the enzyme per se. PMID:4656807

  12. Methylated purines in the deoxyribonucleic acid of various Syrian-golden-hamster tissues after administration of a hepatocarcinogenic dose of dimethylnitrosamine.

    PubMed Central

    Margison, G P; Margison, J M; Montesano, R

    1976-01-01

    1. DNA was extracted from livers, kidneys and lungs of Syrian golden hamsters at various times (up to 96h) after injection of a hepatocarcinogenic dose of [14C]dimethylnitrosamine. Purine bases were released from the DNA by mild acid hydrolysis and separated by Sephadex G-10 chromatography. 2. At 7h after dimethylnitrosamine administration liver DNA was alkylated to the greatest extent, followed by that of lung and kidney, the values for which were 8 and 3% respectively of those for liver. 3. The O6-methylguanine/7-methylguanine ratios were initially the same in all three organs and in the liver DNA of rats under similar conditions of dose. 4. O6-Methylguanine was the most persistent alkylated purine in all three hamster tissues. There was evidence for excision of 7-methyl-guanine, the highest activity for this being present in the liver. 5. Detectable amounts of the minor products 3-methyladenine, 1-methyladenine, 3-methylguanine and 7-methyladenine were present in most hamster tissues, and their individual rates of loss from liver DNA were determined. 6. Ring-labelling of the normal purines in DNA was highest in the liver, followed closely by the lung (80% of that in liver) whereas the kidney had very low incorporation (3% of that in liver). 7. The results are discussed with respect to the hepatotoxicity of dimethylnitrosamine, the miscoding potential of the various alkylation products and the induction of liver tumours in hamsters. PMID:985411

  13. Bilateral lesions of suprachiasmatic nuclei affect circadian rhythms in (/sup 3/H)-thymidine incorporation into deoxyribonucleic acid in mouse intestinal tract, mitotic index of corneal epithelium, and serum corticosterone

    SciTech Connect

    Scheving, L.E.; Tsai, T.H.; Powell, E.W.; Pasley, J.N.; Halberg, F.; Dunn, J.

    1983-03-01

    Investigations into the role of the suprachiasmatic nuclei (SCN) in the coordination of circadian rhythms have presented differing results. Several reports have shown that ablation of the suprachiasmatic nuclei (SCNA) alters the phase and amplitude of rhythms but does not abolish them. The present study investigates the effect of SCNA on the rhythms in cell proliferation in various regions of the intestinal tract as measured by the incorporation of (/sup 3/H)-thymidine into deoxyribonucleic acid, in the mitotic activity of the corneal epithelium, and in serum corticosterone levels. The study involved mice with verified lesions of the SCN (six to 13 mice per time point) and control groups of both sham-operated and unoperated mice (seven of each per time point). The mice were killed in groups that represented seven time points over a single 24 hr span (3 hr intervals with the 0800 hr sampled both at start and end of the series). The tissues examined were the tongue, esophagus, gastric stomach, and colon for DNA synthesis, the corneal epithelium for mitotic index, and blood serum for corticosterone level. The most consistent result of SCNA was a phase advance in the rhythms in cell proliferation in the tongue, esophagus, gastric stomach, colon, and corneal epithelium. A reduction in rhythm amplitude occurred in the tongue, esophagus, and corneal epithelium; however, there was an amplitude increase for the stomach, colon, and serum corticosterone. The mesor (rhythm-adjusted mean) was increased by SCNA in all tissues except the corneal epithelium. These findings further support the role of the suprachiasmatic nuclear area in the control of rhythms in cell proliferation and corticosterone production, by acting as a ''phase-resetter'' and as a modulator of rhythm amplitude.

  14. Deoxyribonucleic acid directed metallization of platinum nanoparticles on graphite nanofibers as a durable oxygen reduction catalyst for polymer electrolyte fuel cells

    NASA Astrophysics Data System (ADS)

    Peera, S. Gouse; Sahu, A. K.; Arunchander, A.; Nath, Krishna; Bhat, S. D.

    2015-11-01

    Effective surface functionalization to the hydrophobic graphite nanofibers (GNF) is performed with the biomolecule, namely deoxy-ribo-nucleic-acid (DNA) via π-π interactions. Pt nanoparticles are impregnated on GNF-DNA composite by ethylene glycol reduction method (Pt/GNF-DNA) and its effect on electro catalytic activity for oxygen reduction reaction (ORR) is systemically studied. Excellent dispersion of Pt nanoparticles over GNF-DNA surfaces with no evidence on particle aggregation is a remarkable achievement in this study. This result in higher electro chemical surface area of the catalyst, enhanced ORR behavior with significant enhancement in mass activity. The catalyst is validated in H2-O2 polymer electrolyte fuel cell (PEFC) and a peak power density of 675 mW cm-2 is achieved at a load current density of 1320 mA cm-2 with a minimal catalyst loading of 0.1 mg cm-2 at a cell temperature of 70 °C and 2 bar absolute pressure. Repeated potential cycling up to 10000 cycles in acidic media is also performed for this catalyst and found excellent stability with only 60 mV drop in the ORR half wave potential. The superior behavior of Pt/GNF-DNA catalyst is credited to the robust fibrous structure of GNF and its effective surface functionalization process via π-π interaction.

  15. Absence of mutations in parathyroid hormone (PTH)/PTH-related protein receptor complementary deoxyribonucleic acid in patients with pseudohypoparathyroidism type Ib.

    PubMed

    Fukumoto, S; Suzawa, M; Takeuchi, Y; Kodama, Y; Nakayama, K; Ogata, E; Matsumoto, T; Fujita, T

    1996-07-01

    To clarify the mechanism of resistance to PTH in patients with pseudohypoparathyroidism (PHP) type Ib, the complementary DNA (cDNA) for PTH/PTH-related protein (PTHrP) receptor was analyzed in skin fibroblasts from three patients with PHP Ib and compared with those from a patient with PHP Ia and a normal subject. We have divided the full coding region of PTH/PTHrP receptor cDNA into five parts and amplified the cDNA by reverse transcription-coupled PCR. There was no difference in the size of PCR products among these patients and the normal control. Single strand conformation polymorphism analysis of the PCR products also showed no aberrant bands in PHP Ib patients. Furthermore, no mutation in PTH/PTHrP receptor cDNA was found by direct sequencing of the PCR products from these patients. These results demonstrate that there is no mutation in PTH/PTHrP receptor cDNA from skin fibroblasts at least in the examined patients with PHP Ib. In addition, the expression of PTH/PTHrP receptor messenger ribonucleic acid was reduced in two patients but was increased in one patient with PHP Ib, suggesting that a reduction in PTH/PTHrP receptor expression cannot explain the resistance to PTH in all patients with PHP Ib. Elucidation of the pathogenesis of PHP Ib may require examination of tissue-specific abnormality in the PTH signal transduction system in the kidney.

  16. Existing and emerging detection technologies for DNA (Deoxyribonucleic Acid) finger printing, sequencing, bio- and analytical chips: a multidisciplinary development unifying molecular biology, chemical and electronics engineering.

    PubMed

    Kumar Khanna, Vinod

    2007-01-01

    The current status and research trends of detection techniques for DNA-based analysis such as DNA finger printing, sequencing, biochips and allied fields are examined. An overview of main detectors is presented vis-à-vis these DNA operations. The biochip method is explained, the role of micro- and nanoelectronic technologies in biochip realization is highlighted, various optical and electrical detection principles employed in biochips are indicated, and the operational mechanisms of these detection devices are described. Although a diversity of biochips for diagnostic and therapeutic applications has been demonstrated in research laboratories worldwide, only some of these chips have entered the clinical market, and more chips are awaiting commercialization. The necessity of tagging is eliminated in refractive-index change based devices, but the basic flaw of indirect nature of most detection methodologies can only be overcome by generic and/or reagentless DNA sensors such as the conductance-based approach and the DNA-single electron transistor (DNA-SET) structure. Devices of the electrical detection-based category are expected to pave the pathway for the next-generation DNA chips. The review provides a comprehensive coverage of the detection technologies for DNA finger printing, sequencing and related techniques, encompassing a variety of methods from the primitive art to the state-of-the-art scenario as well as promising methods for the future.

  17. Methylation of free-floating deoxyribonucleic acid fragments in the bronchoalveolar lavage fluid of dogs with chronic bronchitis exposed to environmental tobacco smoke.

    PubMed

    Yamaya, Yoshiki; Sugiya, Hiroshi; Watari, Toshihiro

    2015-01-01

    The etiology of canine chronic bronchitis (CB) is not completely understood, although exposure to environmental tobacco smoke (ETS) affects the airway inflammatory responses in some dogs with CB. The mechanism by which this occurs is unknown. We investigated the concentrations and methylation rates of free-floating DNA fragments in bronchoalveolar lavage fluid (BALF) from dogs with chronic bronchitis. Based on serum cotinine levels, dogs with CB were divided into 2 groups: dogs that either had or had not been exposed to ETS. Our results demonstrated that the total nucleated cell and macrophage numbers increased in BALF of ETS-exposed dogs with CB. There were no significant differences in DNA concentrations and methylation rates in BALF between the 2 groups. However, 3 out of 8 dogs exposed to ETS had high DNA methylation rates in their BALF samples. Our results suggest that ETS exposure leads to epigenetic modifications of cellular components in BALF in dogs diagnosed with CB.

  18. Magnetic Resonance Imaging-Detected Tumor Residue after Intensity-Modulated Radiation Therapy and its Association with Post-Radiation Plasma Epstein-Barr Virus Deoxyribonucleic Acid in Nasopharyngeal Carcinoma

    PubMed Central

    Lv, Jia-Wei; Zhou, Guan-Qun; Li, Jia-Xiang; Tang, Ling-Long; Mao, Yan-Ping; Lin, Ai-Hua; Ma, Jun; Sun, Ying

    2017-01-01

    Purpose: To evaluate the prognostic value of magnetic resonance imaging (MRI)-detected tumor residue after intensity-modulated radiation therapy (IMRT) and its association with post-treatment plasma Epstein-Barr virus deoxyribonucleic acid (EBV DNA) in nasopharyngeal carcinoma (NPC). Methods and materials: A prospective database of patients with histologically-proven NPC was used to retrospectively analyze 664 cases. Pre- and post-treatment MRI scans were independently reviewed by two senior radiologists who were blinded to clinical findings. Factors significantly associated with MRI-detected tumor residue were identified and included in the following multivariate logistic regression model. Residual risk model were established. Receiver operating characteristic (ROC) identify the optimal cut-off risk score for tumor residue. Results: MRI-detected residual tumor at three months after IMRT was associated with poor prognosis. The 5-year survival rates for the non-residual and residual groups were: OS (93.8% vs. 76.6%, P<0.001), PFS (84.7% vs. 67.9%, P=0.006), LRFS (93.4% vs. 80.4%, P=0.002), and DMFS (90.3% vs. 87.9%, P=0.305), respectively. Three-month post-treatment EBV DNA was significantly associated with tumor residue (P<0.001). A residual risk score model was established, consisting of T and N categories and post-treatment EBV DNA. ROC identified 22.74 as the optimal cut-off risk score for tumor residue. High-risk score was independently associated with poor treatment outcomes. Conclusions: MRI-detected tumor residue was an independent adverse prognostic factor in NPC; and significantly associated with three-month post-treatment EBV DNA. As limited resources in some endemic areas prevent patients from undergoing routine post-treatment imaging, our study identifies a selection risk-model, providing a cost-effective reference for the selection of follow-up strategies and clinical decision-making. PMID:28382149

  19. Effects of direct radiation on deoxyribonucleic acid

    NASA Astrophysics Data System (ADS)

    Cullis, P. M.; Symons, M. C. R.

    It is argued that effects of ionizing radiation on DNA in cell nuclei may frequently be direct in the sense that many electron-gain and electron-loss centres become localised within the DNA molecules. The water of solvation that would also be present in the cell is presumed to pass on holes and electrons prior to the formation of OH· radicals and solvated electrons since these are not detected by ESR of in vitro model systems. Furthermore, a case is made that this direct damage may be particularly significant in that the cationic and anionic centres (G + and T - according to ESR results) are thought to be formed close enough together to lead, ultimately, to double strand breaks. Evidence that both G + and T - can lead to strand breaks is discussed. The presence of histone proteins modifies the yields of G + and T - to a significant extent. The effects of various additives are discussed. Oxygen has been shown by ESR spectroscopy to scavenge electrons in competition with DNA and also to react to form RO 2· radicals that are located on the DNA. It has been shown that this is accompanied by a significant enhancement of strand breaks. Nitroimidazoles act as efficient electron scavengers, their anions being clearly detected by ESR studies. The yield of T - is consequently reduced and that of the protonated form, TH·, falls to zero. However, the initial yields of G + are not greatly affected. This results in a reduction in the yield of single strand breaks and a proportionately greater decrease in the yield of double-strand breaks due to scavenging of only one of the radical centres. The origin of this is discussed in terms of a proposal for the mechanism of double-strand-break formation. Thus, at the molecular level these drugs protect the DNA against strand sission, in marked contrast with their radiosensitisation in vivo, particularly of hypoxic cells. Other additives studied include hydrogen peroxide and iodoacetamide. The studies on hydrogen peroxide have allowed us to assess the role of OH· radicals under the conditions used for ESR studies. Iodoacetamide gives ·CH 2CONH 2 radicals which are detected by ESR and, on annealing, these apparently attack the DNA to give species thought to be sugar radicals. This is associated with a significant increase in the yields of strand breaks. The ESR features assigned to sugar radicals have been shown to decay at temperatures below which the DNA radicals G + and T - are normally lost. This provides a good explanation of our failure to detect sugar radical intermediates by ESR spectroscopy on annealing samples in the absence of additives.

  20. Interactions of carcinogens with DNA (deoxyribonucleic acid)

    SciTech Connect

    Broyde, S.; Shapiro, R.

    1989-10-01

    The principal goal of this research has been the determination of the conformational changes produced in DNA by the covalent binding of a carcinogenic aromatic amine, and the correlation of these changes with the mutations and carcinogenic effects initiated by the same substances. To this end, we have devised new synthetic methods for the preparation of oligonucleotides modified by derivatives af 4-aminobiphenyl and aniline. We have also performed potential energy minimization studies on the above substances and on single and double stranded DNA fragments bearing the above amines as well as acetylaminofluorene, aminofluorene, aminopyrene and the antibiotic mitomycin. Our computations have been carried out on DOE supercomputers using our program, DUPLEX. We have defined a number of novel structures for these modified DNAs, including Hoogsteen, wedge'' (see below) denatured, cross-linked and intercalated forms. Some suggestions have been made about the relation of these forms to mutagenesis. 7 refs.

  1. DNA-Based Chiral Composites with Enhancement of Chirooptic and NLO Effects for NIMS Applications

    DTIC Science & Technology

    2008-11-24

    A. Miniewicz, A. Kochalska, J. Mysliwiec, A. Samoc, M. Samoc, and J. G. Grote, Deoxyribonucleic acid-based photochromic material for fast dynamic holography, Appl. Phys. Lett. 91, 041118-1/041118-3 (2007).

  2. Bio Organic-Semiconductor Field-Effect Transistor (BioFET) Based on Deoxyribonucleic Acid (DNA) Gate Dielectric

    DTIC Science & Technology

    2010-03-31

    ADDRESS(ES) Johannes Kepler University of Linz Altenbergerstr. 69 Linz A-4040 Austria 8. PERFORMING ORGANIZATION REPORT NUMBER N/A 9...Niyazi Serdar Sariciftci Experimental studies done by: Philipp Stadler and Dr. Birendra Singh Linz, Oktober 2009 Johannes Kepler Universität A...Organic Solar Cells (LIOS) at the Johannes Kepler University in Linz, Austria (Prof. Sariciftci). This process using CTMA enhances solubility and

  3. Acid-Base Homeostasis

    PubMed Central

    Nakhoul, Nazih; Hering-Smith, Kathleen S.

    2015-01-01

    Acid-base homeostasis and pH regulation are critical for both normal physiology and cell metabolism and function. The importance of this regulation is evidenced by a variety of physiologic derangements that occur when plasma pH is either high or low. The kidneys have the predominant role in regulating the systemic bicarbonate concentration and hence, the metabolic component of acid-base balance. This function of the kidneys has two components: reabsorption of virtually all of the filtered HCO3− and production of new bicarbonate to replace that consumed by normal or pathologic acids. This production or generation of new HCO3− is done by net acid excretion. Under normal conditions, approximately one-third to one-half of net acid excretion by the kidneys is in the form of titratable acid. The other one-half to two-thirds is the excretion of ammonium. The capacity to excrete ammonium under conditions of acid loads is quantitatively much greater than the capacity to increase titratable acid. Multiple, often redundant pathways and processes exist to regulate these renal functions. Derangements in acid-base homeostasis, however, are common in clinical medicine and can often be related to the systems involved in acid-base transport in the kidneys. PMID:26597304

  4. Acid-Base Homeostasis.

    PubMed

    Hamm, L Lee; Nakhoul, Nazih; Hering-Smith, Kathleen S

    2015-12-07

    Acid-base homeostasis and pH regulation are critical for both normal physiology and cell metabolism and function. The importance of this regulation is evidenced by a variety of physiologic derangements that occur when plasma pH is either high or low. The kidneys have the predominant role in regulating the systemic bicarbonate concentration and hence, the metabolic component of acid-base balance. This function of the kidneys has two components: reabsorption of virtually all of the filtered HCO3(-) and production of new bicarbonate to replace that consumed by normal or pathologic acids. This production or generation of new HCO3(-) is done by net acid excretion. Under normal conditions, approximately one-third to one-half of net acid excretion by the kidneys is in the form of titratable acid. The other one-half to two-thirds is the excretion of ammonium. The capacity to excrete ammonium under conditions of acid loads is quantitatively much greater than the capacity to increase titratable acid. Multiple, often redundant pathways and processes exist to regulate these renal functions. Derangements in acid-base homeostasis, however, are common in clinical medicine and can often be related to the systems involved in acid-base transport in the kidneys. Copyright © 2015 by the American Society of Nephrology.

  5. Understanding Acid Base Disorders.

    PubMed

    Gomez, Hernando; Kellum, John A

    2015-10-01

    The concentration of hydrogen ions is regulated in biologic solutions. There are currently 3 recognized approaches to assess changes in acid base status. First is the traditional Henderson-Hasselbalch approach, also called the physiologic approach, which uses the relationship between HCO3(-) and Pco2; the second is the standard base excess approach based on the Van Slyke equation. The third approach is the quantitative or Stewart approach, which uses the strong ion difference and the total weak acids. This article explores the origins of the current concepts framing the existing methods to analyze acid base balance. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Characterization of the chicken follicle-stimulating hormone receptor (cFSH-R) complementary deoxyribonucleic acid, and expression of cFSH-R messenger ribonucleic acid in the ovary.

    PubMed

    You, S; Bridgham, J T; Foster, D N; Johnson, A L

    1996-11-01

    Studies were conducted to characterize the chicken (c) FSH receptor (R) cDNA, and to evaluate expression of cFSH-R mRNA in the hen ovary at known stages during follicle development. A total of 2.5 kb of nucleic acid sequence including the complete cFSH-R coding region was isolated by a combination of the reverse-transcription polymerase chain reaction and 5'- and 3'-rapid amplification of cDNA ends techniques. Overall, the nucleic acid sequence homology of the cFSH-R cDNA coding region is 71.8% and 72.2% compared to the rat and bovine FSH-R, respectively, while the deduced amino acid sequence identity for the receptor protein (693 amino acids) is 71.9% and 72.4%, respectively. By comparison, the cFSH-R nucleic acid and amino acid sequences are 60.1% and 49.4% identical to the respective cLH-R sequences. Northern blot analysis detected a single 4.3-kb cFSH-R mRNA transcript, which was selectively expressed in ovarian (granulosa, theca, and stromal) tissues, but not the oviduct, adrenal, liver, muscle, or brain. As the follicle developed from the prehierarchical (6- to 8-mm diameter) to the largest preovulatory (F1 follicle) stage, cFSH-R mRNA levels progressively declined within both the granulosa and theca layers (p < 0.05). Moreover, cFSH-R mRNA levels were lower in whole atretic than in morphologically normal 3- to 5-mm follicles (p = 0.0015). The pattern of cFSH-R mRNA expression within the granulosa layer during follicle development was notably different from that of the recently reported cLH-R, in that cLH-R mRNA levels increase to become readily detectable coincident with dramatically increased steroidogenic capacity during the last few days before ovulation of the follicle. On the other hand, highest levels of cFSH-R mRNA in 6- to 8-mm (prehierarchical) follicles were consistent with a role for the cFSH-R in maintaining the viability of prehierarchical follicles and in initiating granulosa cell differentiation at the time when follicles are selected into the

  7. [Stewart's acid-base approach].

    PubMed

    Funk, Georg-Christian

    2007-01-01

    In addition to paCO(2), Stewart's acid base model takes into account the influence of albumin, inorganic phosphate, electrolytes and lactate on acid-base equilibrium. It allows a comprehensive and quantitative analysis of acid-base disorders. Particularly simultaneous and mixed metabolic acid-base disorders, which are common in critically ill patients, can be assessed. Stewart's approach is therefore a valuable tool in addition to the customary acid-base approach based on bicarbonate or base excess. However, some chemical aspects of Stewart's approach remain controversial.

  8. RESTORATION OF NORMAL GLUTAMIC ACID TRANSPORT IN VITAMIN B6-DEFICIENT LACTOBACILLUS PLANTARUM BY ACETATE, AMMONIUM, AND VITAMIN B6,

    DTIC Science & Technology

    GLUTAMIC ACID, * LACTOBACILLUS , VITAMIN B COMPLEX, METABOLIC DISEASES, VITAMIN B COMPLEX, ACETATES, AMMONIUM COMPOUNDS, CHLORAMPHENICOL, DEOXYRIBONUCLEIC ACIDS, AMINO ACIDS, PENICILLINS, CELL WALL, SYNTHESIS, OSMOSIS.

  9. Contribution of light scattering to the circular dichroism of deoxyribonucleic acid films, deoxyribonucleic acid-polylysine complexes, and deoxyribonucleic acid particles in ethanolic buffers

    SciTech Connect

    Maestre, M.F.; Reich, C.

    1980-01-01

    The contribution of scattering to the circular dichroism (CD) of DNA films with twisted structures, DNA-polylysine complexes, and condensed DNA aggregates in ethanolic buffers of defined salt concentrations has been studied by the use of novel measuring techniques. These techniques include fluorscat cuvettes, fluorescence-detected circular dichroism (FDCD) methods, backscattering capturing devices, and beam-mounted goniometer detectors. The result of the experimental measurement is that DNA films can be made which have very large ellipticities or CD at sharp specific wavelengths. The sign of these ellipticities is related to the handedness of the twists, with a right-handed twist producing large positive rotations and a left-handed one producing negative rotations. The film shows nodal angles at which the interaction with light is minimal. The scattering patterns of both films, DNA-polylysine particles and DNA-EtOH condensates, show that the main interaction is light scattering produced by a resonance phenomenon similar to that produced in cholestric liquid crystals and twisted-nematic liquid crystals. It is proposed that the so-called psi-type CD spectrum is a manifestation of a side-by-side packing of DNA molecules with a long-range twisting order whose helical parameters match the helical parameter of circularly polarized light at specific resonance or critical wavelengths. Application of the Bragg law for cholesteric liquid crystals gives the periodicity of the long-range ordered structures. 9 figures.

  10. Methylation of deoxyribonucleic acid in cultured mammalian cells by N-methyl-N′-nitro-N-nitrosoguanidine. The influence of cellular thiol concentrations on the extent of methylation and the 6-oxygen atom of guanine as a site of methylation

    PubMed Central

    Lawley, P. D.; Thatcher, Carolyn J.

    1970-01-01

    1. In neutral aqueous solution N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) yields salts of nitrocyanamide as u.v.-absorbing products. With cysteine, as found independently by Schulz & McCalla (1969), the principal product is 2-nitràminothiazoline-4-carboxylic acid. Both these reactions liberate the methylating species; thiols enhance the rate markedly at neutral pH values. An alternative reaction with thiols gives cystine, presumably via the unstable S-nitrosocysteine. 2. Thiols (glutathione or N-acetylcysteine) in vitro at about the concentration found in mammalian cells enhance the rate of methylation of DNA markedly over that in neutral solution. 3. Treatment of cultured mammalian cells with MNNG results in rapid methylation of nucleic acids, the extent being greater the higher the thiol content of the cells. Rodent embryo cells are more extensively methylated than mouse L-cells of the same thiol content. Cellular thiol concentrations are decreased by MNNG. Proteins are less methylated by MNNG than are nucleic acids. 4. Methylation of cells by dimethyl sulphate does not depend on cellular thiol content and protein is not less methylated than nucleic acids. Methylation by MNNG may therefore be thiol-stimulated in cells. 5. Both in vitro and in cells about 7% of the methylation of DNA by MNNG occurs at the 6-oxygen atom of guanine. The major products 7-methylguanine and 3-methyladenine are given by both MNNG and dimethyl sulphate, but dimethyl sulphate does not yield O6-methylguanine. Possible reaction mechanisms to account for this difference between these methylating agents and its possible significance as a determinant of their biological effects are discussed. PMID:5435496

  11. EFFECT OF LYSERGIC ACID DIETHYLAMIDE ON Escherichia coli, STRAIN B/r(lambda).

    DTIC Science & Technology

    LYSERGIC ACIDS , *ESCHERICHIA COLI), GROWTH(PHYSIOLOGY), CHROMOSOMES, DAMAGE, DOSAGE, PURINE ALKALOIDS, ULTRAVIOLET RADIATION, DEOXYRIBONUCLEIC ACIDS , INHIBITION, HALLUCINOGENS, CHEMICAL WARFARE AGENTS, BIOASSAY

  12. First-principles study of physisorption of nucleic acid bases on small-diameter carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Gowtham, S.; Scheicher, Ralph H.; Pandey, Ravindra; Karna, Shashi P.; Ahuja, Rajeev

    2008-03-01

    We report the results of our first-principles study based on density functional theory on the interaction of the nucleic acid base molecules adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U), with a single-walled carbon nanotube (CNT). Specifically, the focus is on the physisorption of base molecules on the outer wall of a (5, 0) metallic CNT possessing one of the smallest diameters possible. Compared to the case for CNTs with large diameters, the physisorption energy is found to be reduced in the high-curvature case. The base molecules exhibit significantly different interaction strengths and the calculated binding energies follow the hierarchy G>A>T>C>U, which appears to be independent of the tube curvature. The stabilizing factor in the interaction between the base molecule and CNT is dominated by the molecular polarizability that allows a weakly attractive dispersion force to be induced between them. The present study provides an improved understanding of the role of the base sequence in deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) in their interactions with carbon nanotubes of varying diameters.

  13. Effects of corn silage derived from a genetically modified variety containing two transgenes on feed intake, milk production, and composition, and the absence of detectable transgenic deoxyribonucleic acid in milk in Holstein dairy cows.

    PubMed

    Calsamiglia, S; Hernandez, B; Hartnell, G F; Phipps, R

    2007-10-01

    The objectives were to compare the chemical composition, nutritive value, feed intake, milk production and composition, and presence in milk of transgenic DNA and the encoded protein Cry1Ab when corn silages containing 2 transgenes (2GM: herbicide tolerance: mepsps and insect resistance: cry1Ab) were fed as part of a standard total mixed ration (TMR) compared with a near isogenic corn silage (C) to 8 multiparous lactating Holstein dairy cows in a single reversal design study. Cows were fed a TMR ration ad libitum and milked twice daily. Diets contained [dry matter (DM) basis] 45% corn silage, 10% alfalfa hay, and 45% concentrate (1.66 Mcal of net energy for lactation/kg of DM, 15.8% crude protein, 35% neutral detergent fiber, and 4.1% fat). Each period was 28-d long. During the last 4 d of each period, feed intake and milk production data were recorded and milk samples taken for compositional analysis, including the presence of transgenic DNA and Cry1Ab protein. There was no significant difference in the chemical composition between C and 2GM silages, and both were within the expected range (37.6% DM, 1.51 Mcal of net energy for lactation/kg, 8.6% crude protein, 40% neutral detergent fiber, 19.6% acid detergent fiber, pH 3.76, and 62% in vitro DM digestibility). Cows fed the 2GM silage produced milk with slightly higher protein (3.09 vs. 3.00%), lactose (4.83 vs. 4.72%) and solids-not-fat (8.60 vs. 8.40%) compared with C. However, the yield (kg/d) of milk (36.5), 3.5% fat-corrected milk (34.4), fat (1.151), protein (1.106), lactose (1.738), and solids-not-fat (3.094), somatic cell count (log10: 2.11), change in body weight (+7.8 kg), and condition score (+0.09) were not affected by type of silage, indicating no overall production difference. All milk samples were negative for the presence of transgenic DNA from either trait or the Cry1Ab protein. Results indicate that the 2GM silage modified with 2 transgenes did not affect nutrient composition of the silages and

  14. Evidence that growth hormone stimulates milk synthesis by direct action on the mammary gland and that prolactin exerts effects on milk secretion by maintenance of mammary deoxyribonucleic acid content and tight junction status.

    PubMed

    Flint, D J; Gardner, M

    1994-09-01

    lactation by inducing PRL and GH deficiency for 48 h and then attempted to reinitiate it by administering GH either systemically or by local oil-based implants into the mammary gland. Oil-based GH implants were as effective in stimulating milk secretion in the treated (but not contralateral, control) gland as was systemic GH treatment. Thus, GH does act directly on the mammary gland to stimulate milk synthesis, although this does not rule out the possibility that GH acts by stimulating local production of IGF-I.(ABSTRACT TRUNCATED AT 400 WORDS)

  15. Molecular mechanisms in alkylation mutagenesis. Induced reversion of bacteriophage T4rII AP72 by ethyl methanesulphonate in relation to extent and mode of ethylation of purines in bacteriophage deoxyribonucleic acid.

    PubMed Central

    Lawley, P D; Martin, C N

    1975-01-01

    Survival and reversion to T4r+ of bacteriophage T4rII AP72 after treatment with ethyl methanesulphonate at 37 degrees or 45 degrees C were studied in relation to the extent and mode of alkylation of purines in DNA of ethylated bacteriophage. A single-burst technique was used for reversion assay. Survival was lower at 45 degrees C than at 37 degrees C at a given extent of ethylation of bacteriophage DNA, confirming that events subsequent to ethylation, probably depurinations, are the main cause of decreased survival. Reversion was positively correlated (approximately linearly except at low extents at 37 degrees C) with ethylation of bacteriophage DNA, showing that ethylation itself causes mutation. Following the concept that reversion results from G-C leads to A-T transition at a single site (Krieg, 1963a,b) and the suggestion that O6-alkylation of guanine generates the miscoding base (Loveless, 1969), it was calculated that about one-third of induced O6-ethylguanines at this site would miscode to induce mutation. PMID:172067

  16. A new point mutation in the deoxyribonuclic acid-binding domain of the vitamine D receptor in a kindred with hereditary 1,25-dihydroxyvitamin d-resistant rickets

    SciTech Connect

    Yagi, Hideki; Miyake, Hiroshi; Nagashima, Kanji; Kuroume, Takayoshi ); Ozone, K.; Pike, J.W. )

    1993-02-01

    Hereditary 1,25-dihydroxyvitamin D [1,25-(OH)[sub 2]D]-resistant rickets (HVDRR) is a rare disorder characterized by rickets, alopecia, hypocalcemia, secondary hyperparathyroidism, and normal or elevated serum 1,25-dihydroxyvitamin D levels. The authors describe a patient with typical clinical characteristics of HVDRR, except that elevated levels of serum phosphorus were present coincident with increased levels of serum intact PTH. The patient was treated with high dose calcium infusion after an ineffective treatment with 1[alpha]-hydroxyvitamin D[sub 3]; serum calcium and phosphorus as well as intact PTH and alkaline phosphatase levels were normalized. Evaluation of phytohemagglutinin-activated lymphocytes derived from this patient revealed that 1,25-(OH)[sub 2]D[sub 3] was unable to inhibit thymidine incooperation, a result that contrast with the capacity of 1,25-(OH)[sub 2]D[sub 3] to inhibit uptake into normal activated lymphocytes. 1,25-(OH)[sub 2]D[sub 3] did not induce human osteocalcin promoter activity after transfection of this DNA linked to a reporter gene into patient cells. Cointroduction of a human vitamin D receptor (VDR) cDNA expression vector with the reporter plasmid, however, restored the hormone response. Evaluation of extracts from the patient cells for VDR DNA binding revealed a defect in DNA binding. Analysis of genomic DNA from the patient's cells by PCR confirmed the presence of a point mutation in exon 2 of the VDR. This exon directs synthesis of a portion of the DNA-binding domain of the receptor. We conclude that the genetic basis for 1,25-(OH)[sub 2]D[sub 3] resistance in this kindred with VDR-positive HVDRR is due to a single base mutation in the VDR that leads to production of a receptor unable to interact appropriately with DNA. 20 refs., 3 figs., 1 tab.

  17. [Acid-base balance disorders

    PubMed

    Piva, J P; Garcia, P C; Martha, V F

    1999-11-01

    OBJECTIVE: Review the theoretical bases on the maintenance of the acid-basic balance, the pathophysiology of the disturbances and its therapeutics in the child.METHODS: References were obtained from computerized searches on the National Library of Medicine (Medline), recent review articles and personal files.RESULTS: Acid-basic disturbances are frequently found in critical ill children. Their pathophysiology and main causes are a complex and multifactorial process. The management depends on precocious diagnosis and of the understanding of the base cause. The treatment should be adjusted for each disturbance and its base cause. Frequently it requests an aggressive correction and continuous monitoring.CONCLUSIONS: The knowledge of the physiology of the acid-basic balance as well as the understanding of the pathophysiology of the main disturbances associated to the clinical situations represent a challenge for the pediatrician. The management of acid-basic balance demands appropriate and careful intervention.

  18. Unscheduled deoxyribonucleic acid (DNA) synthesis assays for toxicological studies. May 1977-March 1990 (A Bibliography from the NTIS data base). Report for May 1977-March 1990

    SciTech Connect

    Not Available

    1990-04-01

    This bibliography contains citations concerning the unscheduled DNA synthesis (UDS) assay for toxicological studies. UDS assays provide very sensitive measures of damage to DNA by detecting induction of DNA synthesis in non-S-phase cells. UDS toxicological studies analyzing gamma radiation, drugs, pesticides, nerve gas, jet engine fuels, ultraviolet light, chlorated organic compounds, and aromatic compounds are discussed. UDS studies using both human and animal tissue cultures are described. (Contains 57 citations fully indexed and including a title list.)

  19. Technical note: High fidelity of whole-genome amplified sheep (Ovis aries) deoxyribonucleic acid using a high-density single nucleotide polymorphism array-based genotyping platform.

    PubMed

    Magee, D A; Park, S D E; Scraggs, E; Murphy, A M; Doherty, M L; Kijas, J W; MacHugh, D E

    2010-10-01

    Advances in high-throughput genotyping technologies have afforded researchers the opportunity to study ever-increasing numbers of SNP in animal genomes. However, many studies encounter difficulties in obtaining sufficient quantities of high-quality DNA for such analyses, particularly when the source biological material is limited or degraded. The recent development of in vitro whole-genome amplification approaches has permitted researchers to circumvent these challenges by increasing the amount of usable DNA in normally small-quantity samples. Here, we assess the performance of whole-genome amplification products generated from ovine genomic DNA using a high-throughput SNP genotyping platform, the newly developed Illumina ovineSNP50 BeadChip. Our results demonstrate a high genotype call rate for conventional genomic DNA and whole-genome amplified genomic DNA. The data also reveal an exceptionally high concordance rate ( > or = 99%) between the genotypes generated from whole-genome amplified products and their conventional genomic DNA counterparts. This study supports the use of whole-genome amplification as a viable solution for the analysis of high-density SNP genotypic data using compromised or limited starting material.

  20. Method Optimization of Deoxyribonucleic Acid (DNA) Thin Films for Biotronics

    DTIC Science & Technology

    2011-09-01

    Added to the Spin-coater ......................................................................4 3.3 Comparison of Spin - Coating Speed and Sample...precipitate after centrifugation. ..............................3 Figure 3. Diagram of spin - coating method. First, the DNA-CTMA solution was pipetted onto... spin - coating speeds. ...................................................................................................................6 Figure 5

  1. KINETOPLAST DEOXYRIBONUCLEIC ACID OF THE HEMOFLAGELLATE TRYPANOSOMA LEWISI

    PubMed Central

    Renger, Hartmut C.; Wolstenholme, David R.

    1970-01-01

    Cesium chloride centrifugation of DNA extracted from cells of blood strain Trypanosoma lewisi revealed a main band, ρ = 1.707, a light satellite, ρ = 1.699, and a heavy satellite, ρ = 1.721. Culture strain T. lewisi DNA comprised only a main band, ρ = 1.711, and a light satellite, ρ = 1.699. DNA isolated from DNase-treated kinetoplast fractions of both the blood and culture strains consisted of only the light satellite DNA. Electron microscope examination of rotary shadowed preparations of lysates revealed that DNA from kinetoplast fractions was mainly in the form of single 0.4 µ circular molecules and large masses of 0.4 µ interlocked circles with which longer, often noncircular molecules were associated. The 0.4 µ circular molecules were mainly in the covalently closed form: they showed a high degree of resistance to thermal denaturation which was lost following sonication; and they banded at a greater density than linear DNA in cesium chloride-ethidium bromide gradients. Interpretation of the large masses of DNA as comprising interlocked covalently closed 0.4 µ circles was supported by the findings that they banded with single circular molecules in cesium chloride-ethidium bromide gradients, and following breakage of some circles by mild sonication, they disappeared and were replaced by molecules made up of low numbers of apparently interlocked 0.4 µ circles. When culture strain cells were grown in the presence of either ethidium bromide or acriflavin, there was a loss of stainable kinetoplast DNA in cytological preparations. There was a parallel loss of light satellite and of circular molecules from DNA extracted from these cells. PMID:5497546

  2. Concordance among sperm deoxyribonucleic acid integrity assays and semen parameters.

    PubMed

    Stahl, Peter J; Cogan, Chava; Mehta, Akanksha; Bolyakov, Alex; Paduch, Darius A; Goldstein, Marc

    2015-07-01

    To assess the concordance of sperm chromatin structure assay (SCSA) results, epifluorescence TUNEL assay results, and standard semen parameters. Prospective, observational study. Tertiary referral andrology clinic. A total of 212 men evaluated for subfertility by a single physician. Clinical history, physical examination, semen analysis, SCSA, and TUNEL assay. Spearman's rank correlation coefficients (r) between SCSA DNA fragmentation index (DFI), percentage TUNEL-positive sperm, and semen analysis parameters. There was a positive correlation between SCSA DFI and TUNEL (r = 0.31), but the strength of this correlation was weaker than has previously been reported. The discordance rate between SCSA and TUNEL in classifying patients as normal or abnormal was 86 of 212 (40.6%). The SCSA DFI was moderately negatively correlated with sperm concentration and motility. The TUNEL results were unrelated to standard semen parameters. The SCSA DFI and percentage TUNEL-positive sperm are moderately correlated measures of sperm DNA integrity but yield different results in a large percentage of patients. The DFI is well-correlated with semen analysis parameters, whereas TUNEL is not. These data indicate that the SCSA and TUNEL assay measure different aspects of sperm DNA integrity and should not be used interchangeably. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  3. Application of deoxyribonucleic acid barcoding in Lauraceae plants.

    PubMed

    Liu, Zhen; Chen, Shi-Lin; Song, Jing-Yuan; Zhang, Shou-Jun; Chen, Ke-Li

    2012-01-01

    This study aims to determine the candidate markers that can be used as DNA barcode in the Lauraceae family. Polymerase chain reaction amplification, sequencing efficiency, differential intra- and interspecific divergences, DNA barcoding gap, and identification efficiency were used to evaluate the four different DNA sequences of psbA-trnH, matK, rbcL, and ITS2. We tested the discrimination ability of psbA-trnH in 68 plant samples belonging to 42 species from 11 distinct genera and found that the rate of successful identification with the psbA-trnH was 82.4% at the species level. However, the correct identification of matK and rbcL were only 30.9% and 25.0%, respectively, using BLAST1. The PCR amplification efficiency of the ITS2 region was poor; thus, ITS2 was not included in subsequent experiments. To verify the capacity of the identification of psbA-trnH in more samples, 175 samples belonging to 117 species from the experimental data and from the GenBank database of the Lauraceae family were tested. Using the BLAST1 method, the identification efficiency were 84.0% and 92.3% at the species and genus level, respectively. Therefore, psbA-trnH is confirmed as a useful marker for differentiating closely related species within Lauraceae.

  4. Application of deoxyribonucleic acid barcoding in Lauraceae plants

    PubMed Central

    Liu, Zhen; Chen, Shi-Lin; Song, Jing-Yuan; Zhang, Shou-Jun; Chen, Ke-Li

    2012-01-01

    Background: This study aims to determine the candidate markers that can be used as DNA barcode in the Lauraceae family. Material and Methods: Polymerase chain reaction amplification, sequencing efficiency, differential intra- and interspecific divergences, DNA barcoding gap, and identification efficiency were used to evaluate the four different DNA sequences of psbA-trnH, matK, rbcL, and ITS2. We tested the discrimination ability of psbA-trnH in 68 plant samples belonging to 42 species from 11 distinct genera and found that the rate of successful identification with the psbA-trnH was 82.4% at the species level. However, the correct identification of matK and rbcL were only 30.9% and 25.0%, respectively, using BLAST1. The PCR amplification efficiency of the ITS2 region was poor; thus, ITS2 was not included in subsequent experiments. To verify the capacity of the identification of psbA-trnH in more samples, 175 samples belonging to 117 species from the experimental data and from the GenBank database of the Lauraceae family were tested. Results: Using the BLAST1 method, the identification efficiency were 84.0% and 92.3% at the species and genus level, respectively. Conclusion: Therefore, psbA-trnH is confirmed as a useful marker for differentiating closely related species within Lauraceae. PMID:22438656

  5. Deoxyribonucleic acid (DNA)-Ni-nanostrands composites for EMI shielding

    NASA Astrophysics Data System (ADS)

    Ouchen, Fahima; Wilson, Benjamin G.; Yaney, Perry P.; Salour, Michael M.; Grote, James G.

    2016-09-01

    In this study, we demonstrated the use of DNA-CTMA (DC) in combination with Nickel Nanostrands (NiNs) for application in Electromagnetic Interference (EMI) shielding. The addition of NiNs fillers to DC led to films with higher shielding effectiveness (SE) than when Silver nanoparticles were used. An enhanced EMI shielding effectiveness (SE) was also achieved by the fabrication of the DC-NiNs shielding film structure in a layered architecture. Very thin layer of Guanine ( 60 nm) were inserted between layers of DNA-NiNs ( 100um each) to total a thickness of 500um of the shielding film. An increase of the SE by 6-8 dB for the layered structure as compared to the bulk thick film with NiNs loadings up to 10 wt%. At higher loadings (>10 wt. %), a significant physical degradation of the films was observed for all films regardless of the thickness or the process of fabrication.

  6. Studies on the sonic degradation of deoxyribonucleic acid.

    PubMed

    FREIFELDER, D; DAVISON, P F

    1962-05-01

    T7 DNA was partially degraded by x-rays, DNAase, and sonic irradiation. The molecular weight distributions were calculated from sedimentation velocity studies on the resulting preparations. Comparison with the theoretical curve derived by Montroll and Simha showed that the first two degradative methods act grossly at random, whereas sonication is a non-random process resulting in the preferential halving of the DNA molecules in solution.

  7. Studies on the Sonic Degradation of Deoxyribonucleic Acid

    PubMed Central

    Freifelder, David; Davison, Peter F.

    1962-01-01

    T7 DNA was partially degraded by x-rays, DNAase, and sonic irradiation. The molecular weight distributions were calculated from sedimentation velocity studies on the resulting preparations. Comparison with the theoretical curve derived by Montroll and Simha showed that the first two degradative methods act grossly at random, whereas sonication is a non-random process resulting in the preferential halving of the DNA molecules in solution. PMID:13894963

  8. [The immunotropic properties of the deoxyribonucleic acid from Salmonidae milt].

    PubMed

    Besednova, N N; Kas'ianenko, Iu I; Epshteĭn, L M; Gazha, A K

    1999-01-01

    The study of the immunotropic action of DNA from salmon milt showed that it increased the antiinfectious resistance of mice to Escherichia coli and Salmonella enteritidis, stimulated the antibody response to the thymus-dependent corpuscular antigen (sheep erythrocytes), increased the production of the antibody forming cells (AFC) in the murine spleen and intensified the absorptive and digestive activities of the cells of the mononuclear phagocytes. The immunotropic properties of the DNA permitted to broaden the DNA application spectrum with its supplementing by immunodeficiency of various genesis and diseases with phagocytic protection mechanisms. It is quite possible that the salmon milt DNA be used as a food additive.

  9. Deoxyribonucleic acid polymerase III of Escherichia coli. Purification and properties.

    PubMed

    Livingston, D M; Hinkle, D C; Richardson, C C

    1975-01-25

    DNA polymerase III has been purified 4,500-fold from the Escherichis coli mutant, HMS83, which lacks DNA polymerases I and II. When subjected to disc gel electrophoresis, the most purified fraction exhibits a single major protein band from which enzymatic activity may be recovered. Polyacrylamide gel electrophoresis under denaturing conditions produces two protein bands with molecular weights of 140,000 and 40,000. The sedimentation coefficient of the enzyme is 7.0 S, and the Stokes radius is 62 A. Taken together these tow parameters indicate a native molecular weight of 180,000. Purified DNA polymerase III catalyzes the polymerization of nucleotides into DNA when provided with both a DNA template and a complementary primer strand. The newly synthesized DNA is covalently attached to the 3' terminus of the primer strand. Because the extent of polymerization is only 10 to 100 nucleotides, the best substrates are native DNA molecules with small single-stranded regions. The most purified enzyme preparation is devoid of endonuclease activities. In addition to the two exonuclease activities described in the accompanying paper, purified polymerase III also catalyzes pyrophosphorolysis and the exchange of pyrophosphate into deoxynucleoside triphosphates. DNA polymerase III has also been isolated from wild type E. coli containing the other two known DNA polymerases. Futhermore, the enzyme purified from three different polC mutants exhibits altered polymerase III activity, confirming that polC is the structural gene for DNA polymerase III (Gefter, M., Hirota, Y., Kornberb, T., Wechsler, J., and Barnoux, C. (1971) Proc. Natl. Acad. Sci. U. S. A. 68, 3150-3153).

  10. Simple acid-base tutorial.

    PubMed

    Ayers, Phil; Dixon, Carman

    2012-01-01

    The nutrition support practitioner is confronted with numerous metabolic abnormalities in the daily care of patients. An understanding of the basic principles of acid-base balance, along with the ability to recognize common causes of the various disorders, enhances the clinician's ability to provide specialized nutrition support. The basic metabolic and respiratory disorders, along with common causes, are reviewed in this tutorial.

  11. Self-assembled monolayer for toxicant detection using nucleic acid sensor based on surface plasmon resonance technique.

    PubMed

    Solanki, Pratima R; Prabhakar, Nirmal; Pandey, M K; Malhotra, B D

    2008-10-01

    Double stranded calf thymus deoxyribonucleic acid (dsCT-DNA) has been covalently immobilized onto self-assembled monolayer (SAM) of beta-merceptoethanol (MCE) on gold substrates via N-ethyl-N'-(3-dimethylaminopropyl) carbodiimide and N-hydroxysuccinimide chemistry for fabrication of the surface plasmon resonance (SPR) based biosensing device. The dsCT-DNA-MCE-SAM/Au bioelectrode has been characterized using electrochemical impedance spectroscopy, cyclic voltammetry, contact angle measurements and atomic force microscopy, respectively. This biosensing device has been utilized for detection of cypermethrin (0.0005 ppm) using electrochemical and SPR techniques, respectively. The mechanism of interaction of cypermethrin with dsCT-DNA immobilized onto MCE-SAM has been proposed.

  12. Nucleic acid based molecular devices.

    PubMed

    Krishnan, Yamuna; Simmel, Friedrich C

    2011-03-28

    In biology, nucleic acids are carriers of molecular information: DNA's base sequence stores and imparts genetic instructions, while RNA's sequence plays the role of a messenger and a regulator of gene expression. As biopolymers, nucleic acids also have exciting physicochemical properties, which can be rationally influenced by the base sequence in myriad ways. Consequently, in recent years nucleic acids have also become important building blocks for bottom-up nanotechnology: as molecules for the self-assembly of molecular nanostructures and also as a material for building machinelike nanodevices. In this Review we will cover the most important developments in this growing field of nucleic acid nanodevices. We also provide an overview of the biochemical and biophysical background of this field and the major "historical" influences that shaped its development. Particular emphasis is laid on DNA molecular motors, molecular robotics, molecular information processing, and applications of nucleic acid nanodevices in biology. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Nucleic acid based logical systems.

    PubMed

    Han, Da; Kang, Huaizhi; Zhang, Tao; Wu, Cuichen; Zhou, Cuisong; You, Mingxu; Chen, Zhuo; Zhang, Xiaobing; Tan, Weihong

    2014-05-12

    Researchers increasingly visualize a significant role for artificial biochemical logical systems in biological engineering, much like digital logic circuits in electrical engineering. Those logical systems could be utilized as a type of servomechanism to control nanodevices in vitro, monitor chemical reactions in situ, or regulate gene expression in vivo. Nucleic acids (NA), as carriers of genetic information with well-regulated and predictable structures, are promising materials for the design and engineering of biochemical circuits. A number of logical devices based on nucleic acids (NA) have been designed to handle various processes for technological or biotechnological purposes. This article focuses on the most recent and important developments in NA-based logical devices and their evolution from in vitro, through cellular, even towards in vivo biological applications.

  14. Use of an Acid-Base Table.

    ERIC Educational Resources Information Center

    Willis, Grover; And Others

    1986-01-01

    Identifies several ways in which an acid-base table can provide students with information about chemical reactions. Cites examples of the chart's use and includes a table which indicates the strengths of some common acids and bases. (ML)

  15. In vivo selection of CVI988 based vaccine, pCVI988-699-2: characterization of its efficacy and safety

    USDA-ARS?s Scientific Manuscript database

    In order to increase the efficacy of current vaccines, we have constructed a bacterial artificial chromosome (BAC),id-based infectious clone of CVI 988 (Rispens) of low passage (p23), using deoxyribonucleic acid (DNA) provided from Merial, Inc., and obtained from the Central Veterinary Institute, Le...

  16. The Acid-Base Titration of a Very Weak Acid: Boric Acid

    ERIC Educational Resources Information Center

    Celeste, M.; Azevedo, C.; Cavaleiro, Ana M. V.

    2012-01-01

    A laboratory experiment based on the titration of boric acid with strong base in the presence of d-mannitol is described. Boric acid is a very weak acid and direct titration with NaOH is not possible. An auxiliary reagent that contributes to the release of protons in a known stoichiometry facilitates the acid-base titration. Students obtain the…

  17. The Acid-Base Titration of a Very Weak Acid: Boric Acid

    ERIC Educational Resources Information Center

    Celeste, M.; Azevedo, C.; Cavaleiro, Ana M. V.

    2012-01-01

    A laboratory experiment based on the titration of boric acid with strong base in the presence of d-mannitol is described. Boric acid is a very weak acid and direct titration with NaOH is not possible. An auxiliary reagent that contributes to the release of protons in a known stoichiometry facilitates the acid-base titration. Students obtain the…

  18. The ABC's of Acid-Base Balance

    PubMed Central

    Sacks, Gordon S.

    2004-01-01

    A step-wise systematic approach can be used to determine the etiology and proper management of acid-base disorders. The objectives of this article are to: (1) discuss the physiologic processes involved in acid-base disturbances, (2) identify primary and secondary acid-base disturbances based upon arterial blood gas and laboratory measurements, (3) utilize the anion gap for diagnostic purposes, and (4) outline a stepwise approach for interpretation and treatment of acid-base disorders. Case studies are used to illustrate the application of the discussed systematic approach. PMID:23118702

  19. Phosphonic acid based exchange resins

    DOEpatents

    Horwitz, E.P.; Alexandratos, S.D.; Gatrone, R.C.; Chiarizia, R.

    1995-09-12

    An ion exchange resin is described for extracting metal ions from a liquid waste stream. An ion exchange resin is prepared by copolymerizing a vinylidene diphosphonic acid with styrene, acrylonitrile and divinylbenzene. 10 figs.

  20. Nucleic Acid-Based Nanoconstructs

    Cancer.gov

    Focuses on the design, synthesis, characterization, and development of spherical nucleic acid constructs as effective nanotherapeutic, single-entity agents for the treatment of glioblastoma multiforme and prostate cancers.

  1. Phosphonic acid based exchange resins

    DOEpatents

    Horwitz, E. Philip; Alexandratos, Spiro D.; Gatrone, Ralph C.; Chiarizia, Ronato

    1995-01-01

    An ion exchange resin for extracting metal ions from a liquid waste stream. An ion exchange resin is prepared by copolymerizing a vinylidene diphosphonic acid with styrene, acrylonitrile and divinylbenzene.

  2. The Conjugate Acid-Base Chart.

    ERIC Educational Resources Information Center

    Treptow, Richard S.

    1986-01-01

    Discusses the difficulties that beginning chemistry students have in understanding acid-base chemistry. Describes the use of conjugate acid-base charts in helping students visualize the conjugate relationship. Addresses chart construction, metal ions, buffers and pH titrations, and the organic functional groups and nonaqueous solvents. (TW)

  3. The Kidney and Acid-Base Regulation

    ERIC Educational Resources Information Center

    Koeppen, Bruce M.

    2009-01-01

    Since the topic of the role of the kidneys in the regulation of acid base balance was last reviewed from a teaching perspective (Koeppen BM. Renal regulation of acid-base balance. Adv Physiol Educ 20: 132-141, 1998), our understanding of the specific membrane transporters involved in H+, HCO , and NH transport, and especially how these…

  4. The Conjugate Acid-Base Chart.

    ERIC Educational Resources Information Center

    Treptow, Richard S.

    1986-01-01

    Discusses the difficulties that beginning chemistry students have in understanding acid-base chemistry. Describes the use of conjugate acid-base charts in helping students visualize the conjugate relationship. Addresses chart construction, metal ions, buffers and pH titrations, and the organic functional groups and nonaqueous solvents. (TW)

  5. Students' Alternate Conceptions on Acids and Bases

    ERIC Educational Resources Information Center

    Pan, Hanqing; Henriques, Laura

    2015-01-01

    Knowing what students bring to the classroom can and should influence how we teach them. This study is a review of the literature associated with secondary and postsecondary students' ideas about acids and bases. It was found that there are six types of alternate ideas about acids and bases that students hold. These are: macroscopic properties of…

  6. The Kidney and Acid-Base Regulation

    ERIC Educational Resources Information Center

    Koeppen, Bruce M.

    2009-01-01

    Since the topic of the role of the kidneys in the regulation of acid base balance was last reviewed from a teaching perspective (Koeppen BM. Renal regulation of acid-base balance. Adv Physiol Educ 20: 132-141, 1998), our understanding of the specific membrane transporters involved in H+, HCO , and NH transport, and especially how these…

  7. Students' Alternate Conceptions on Acids and Bases

    ERIC Educational Resources Information Center

    Pan, Hanqing; Henriques, Laura

    2015-01-01

    Knowing what students bring to the classroom can and should influence how we teach them. This study is a review of the literature associated with secondary and postsecondary students' ideas about acids and bases. It was found that there are six types of alternate ideas about acids and bases that students hold. These are: macroscopic properties of…

  8. Sequential injection redox or acid-base titration for determination of ascorbic acid or acetic acid.

    PubMed

    Lenghor, Narong; Jakmunee, Jaroon; Vilen, Michael; Sara, Rolf; Christian, Gary D; Grudpan, Kate

    2002-12-06

    Two sequential injection titration systems with spectrophotometric detection have been developed. The first system for determination of ascorbic acid was based on redox reaction between ascorbic acid and permanganate in an acidic medium and lead to a decrease in color intensity of permanganate, monitored at 525 nm. A linear dependence of peak area obtained with ascorbic acid concentration up to 1200 mg l(-1) was achieved. The relative standard deviation for 11 replicate determinations of 400 mg l(-1) ascorbic acid was 2.9%. The second system, for acetic acid determination, was based on acid-base titration of acetic acid with sodium hydroxide using phenolphthalein as an indicator. The decrease in color intensity of the indicator was proportional to the acid content. A linear calibration graph in the range of 2-8% w v(-1) of acetic acid with a relative standard deviation of 4.8% (5.0% w v(-1) acetic acid, n=11) was obtained. Sample throughputs of 60 h(-1) were achieved for both systems. The systems were successfully applied for the assays of ascorbic acid in vitamin C tablets and acetic acid content in vinegars, respectively.

  9. Acid and base degraded products of ketorolac.

    PubMed

    Salaris, Margherita; Nieddu, Maria; Rubattu, Nicola; Testa, Cecilia; Luongo, Elvira; Rimoli, Maria Grazia; Boatto, Gianpiero

    2010-06-05

    The stability of ketorolac tromethamine was investigated in acid (0.5M HCl) and alkaline conditions (0.5M NaOH), using the same procedure reported by Devarajan et al. [2]. The acid and base degradation products were identified by liquid chromatography-mass spectrometry (LC-MS).

  10. Solid Acid Based Fuel Cells

    DTIC Science & Technology

    2007-11-02

    superprotonic solid acids with elements such as P, As, Si and Ge, which have greater affinities to oxygen , we anticipate that the reduction reaction will be...bulk material consisted of an apatite phase (hexagonal symmetry) of variable composition, LixLa10-x(SiO4)6O3-x, with excess lithium residing in the...in Tables 1 and 2, indicate that this compound is a rather conventional apatite with fixed stoichiometry, LiLa9(SiO4)6O2 (x = 1). Such a result is

  11. Disorders of acid-base balance.

    PubMed

    Kellum, John A

    2007-11-01

    Intensivists spend much of their time managing problems related to fluids, electrolytes, and blood pH. Recent advances in the understanding of acid-base physiology have resulted from the application of basic physical-chemical principles of aqueous solutions to blood plasma. All changes in blood pH, in health and in disease, occur through changes in three variables: carbon dioxide, relative electrolyte concentrations, and total weak acid concentrations. However, while this quantitative approach has enjoyed widespread use among researchers, clinicians are reluctant to employ it. Recent advances have brought a measure of parity between the newer and the older, descriptive approach to acid-base physiology. Case-based review of the literature. Both quantitative and traditional approaches can be easily combined to result in a powerful tool for bedside acid-base analysis.

  12. Whole body acid-base modeling revisited.

    PubMed

    Ring, Troels; Nielsen, Søren

    2017-04-01

    The textbook account of whole body acid-base balance in terms of endogenous acid production, renal net acid excretion, and gastrointestinal alkali absorption, which is the only comprehensive model around, has never been applied in clinical practice or been formally validated. To improve understanding of acid-base modeling, we managed to write up this conventional model as an expression solely on urine chemistry. Renal net acid excretion and endogenous acid production were already formulated in terms of urine chemistry, and we could from the literature also see gastrointestinal alkali absorption in terms of urine excretions. With a few assumptions it was possible to see that this expression of net acid balance was arithmetically identical to minus urine charge, whereby under the development of acidosis, urine was predicted to acquire a net negative charge. The literature already mentions unexplained negative urine charges so we scrutinized a series of seminal papers and confirmed empirically the theoretical prediction that observed urine charge did acquire negative charge as acidosis developed. Hence, we can conclude that the conventional model is problematic since it predicts what is physiologically impossible. Therefore, we need a new model for whole body acid-base balance, which does not have impossible implications. Furthermore, new experimental studies are needed to account for charge imbalance in urine under development of acidosis.

  13. Acid-base disorders: learning the basics.

    PubMed

    Ayers, Phil; Dixon, Carman; Mays, Andrew

    2015-02-01

    Nutrition support practitioners should be confident in their ability to recognize and treat various metabolic and respiratory disorders encountered in daily practice. A clinician's comprehension of the underlying physiologic processes and/or exogenous causes that occur during acid-base disorders is essential when making therapeutic decisions regarding fluids, parenteral nutrition, and electrolyte management. This invited review will discuss basic metabolic and respiratory disorders while briefly addressing mixed acid-base disorders. © 2014 American Society for Parenteral and Enteral Nutrition.

  14. Synthesis of new kojic acid based unnatural α-amino acid derivatives.

    PubMed

    Balakrishna, C; Payili, Nagaraju; Yennam, Satyanarayana; Devi, P Uma; Behera, Manoranjan

    2015-11-01

    An efficient method for the preparation of kojic acid based α-amino acid derivatives by alkylation of glycinate schiff base with bromokojic acids have been described. Using this method, mono as well as di alkylated kojic acid-amino acid conjugates have been prepared. This is the first synthesis of C-linked kojic acid-amino acid conjugate where kojic acid is directly linked to amino acid through a C-C bond.

  15. DNA-nucleobases: Gate Dielectric/Passivation Layer for Flexible GFET-based Sensor Applications (Postprint)

    DTIC Science & Technology

    2015-09-24

    AFRL-RX-WP-JA-2016-0271 DNA -NUCLEOBASES: GATE DIELECTRIC/ PASSIVATION LAYER FOR FLEXIBLE GFET-BASED SENSOR APPLICATIONS (POSTPRINT...TITLE AND SUBTITLE DNA -NUCLEOBASES: GATE DIELECTRIC/ PASSIVATION LAYER FOR FLEXIBLE GFET-BASED SENSOR APPLICATIONS (POSTPRINT) 5a. CONTRACT...deposition of the gate dielectric layer used for making transistor devices. The approach was introducing a thin film of deoxyribonucleic acid ( DNA

  16. Determinants of plasma acid-base balance.

    PubMed

    Kellum, John A

    2005-04-01

    An advanced understanding of acid-base physiology is central to the practice of critical care medicine. Intensivists spend much of their time managing problems that are related to fluids, electrolytes, and blood pH. Recent advances in the understanding of acid-base physiology occurred as the result of the application of basic physical-chemical principles of aqueous solutions to blood plasma. This analysis revealed three independent variables that regulate pH in blood plasma: carbon dioxide, relative electrolyte concentrations, and total weak acid concentrations. All changes in blood pH, in health and in disease, occur through changes in these three variables. This article reviews the physical-chemical approach to acid-base balance and considers clinical implications for these findings.

  17. A Direct, Biomass-Based Synthesis of Benzoic Acid: Formic Acid-Mediated Deoxygenation of the Glucose-Derived Materials Quinic Acid and Shikimic Acid

    SciTech Connect

    Arceo, Elena; Ellman, Jonathan; Bergman, Robert

    2010-05-03

    An alternative biomass-based route to benzoic acid from the renewable starting materials quinic acid and shikimic acid is described. Benzoic acid is obtained selectively using a highly efficient, one-step formic acid-mediated deoxygenation method.

  18. [Kidney, Fluid, and Acid-Base Balance].

    PubMed

    Shioji, Naohiro; Hayashi, Masao; Morimatsu, Hiroshi

    2016-05-01

    Kidneys play an important role to maintain human homeostasis. They contribute to maintain body fluid, electrolytes, and acid-base balance. Especially in fluid control, we, physicians can intervene body fluid balance using fluid resuscitation and diuretics. In recent years, one type of fluid resuscitation, hydroxyl ethyl starch has been extensively studied in the field of intensive care. Although their effects on fluid resuscitation are reasonable, serious complications such as kidney injury requiring renal replacement therapy occur frequently. Now we have to pay more attention to this important complication. Another topic of fluid management is tolvaptan, a selective vasopressin-2 receptor antagonist Recent randomized trial suggested that tolvaptan has a similar supportive effect for fluid control and more cost effective compared to carperitide. In recent years, Stewart approach is recognized as one important tool to assess acid-base balance in critically ill patients. This approach has great value, especially to understand metabolic components in acid-base balance. Even for assessing the effects of kidneys on acid-base balance, this approach gives us interesting insight. We should appropriately use this new approach to treat acid-base abnormality in critically ill patients.

  19. Acid-base balance in heart failure.

    PubMed

    Frangiosa, A; De Santo, L S; Anastasio, P; De Santo, N G

    2006-01-01

    In end-stage heart failure, various acid-base disorders can be discovered due to the renal loss of hydrogen ions and hydrogen ion movements into cells, the reduction of the effective circulating volume, hypoxemia and renal failure. This justifies the occurrence of metabolic alkalosis, metabolic acidosis, respiratory alkalosis, as well as respiratory acidosis alone or in combination. Several studies have been published on the acid-base state in heart failure. In a 1951 study, Squires et al analyzed the distribution of body fluid in congestive heart failure by taking into consideration the abnormalities in serum electrolyte concentration and in acid-base equilibrium. A recent study by Milionis et al, analyzed 86 patients with congestive heart failure receiving conventional treatment; the majority of these patients exhibited hypokalemia, hyponatremia, hypocalcemia and hypophosphatemia. Disorders in acid-base balance were noted in 37.2% of patients. In a recent study, 70 patients with severe congestive heart failure before heart transplantation showed high-normal pH, slightly reduced pCO 2 and a slight loss of hydrogen ions. After heart transplantation, stability of blood pH and hydrogen ion concentrations was found. In contrast, bicarbonate and pCO 2 increased significantly. The data led us to formulate the diagnosis of a mixed acid-base disorder that includes respiratory alkalosis and metabolic alkalosis before heart transplantation. In heart failure, the presence of acid-base imbalance associated with the activation of mechanisms that lead to salt and water retention reveals evidence concerning the pivotal role of the kidney in determining the outcome of these patients.

  20. Novel materials based on DNA-CTMA and lanthanide (Ce(3+) , Pr(3+) ).

    PubMed

    Lazar, Cosmina Andreea; Kajzar, François; Mihaly, Maria; Rogozea, Adina Elena; Petcu, Adina Roxana; Olteanu, Nicoleta Liliana; Rau, Ileana

    2016-09-01

    New, deoxyribonucleic acid (DNA) based compounds, functionalized with hexadecyltrimethylammonium chloride (CTMA) and lanthanide hydroxide nanoparticles were synthesized. The spectral measurements suggest that between the DNA-CTMA complex and the lanthanide (III) ions a chemical interaction takes place. The obtained materials exhibit an improved fluorescence efficiency, showing a potential interest for application in photonics, and more particularly, in light emitting devices. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 613-617, 2016. © 2016 Wiley Periodicals, Inc.

  1. Reagentless Measurement of Aminoglycoside Antibiotics in Blood Serum via an Electrochemical, Ribonucleic Acid Aptamer-Based Biosensor

    PubMed Central

    Rowe, Aaron A.; Miller, Erin A.; Plaxco, Kevin W.

    2011-01-01

    Biosensors built using ribonucleic acid (RNA) aptamers show promise as tools for point-of-care medical diagnostics, but they remain vulnerable to nuclease degradation when deployed in clinical samples. To explore methods for protecting RNA-based biosensors from such degradation we have constructed and characterized an electrochemical, aptamer-based sensor for the detection of aminoglycosidic antibiotics. We find that while this sensor achieves low micromolar detection limits and subminute equilibration times when challenged in buffer, it deteriorates rapidly when immersed directly in blood serum. In order to circumvent this problem, we have developed and tested sensors employing modified versions of the same aptamer. Our first effort to this end entailed the methylation of all of the 2′-hydroxyl groups outside of the aptamer’s antibiotic binding pocket. However, while devices employing this modified aptamer are as sensitive as those employing an unmodified parent, the modification fails to confer greater stability when the sensor is challenged directly in blood serum. As a second potentially naive alternative, we replaced the RNA bases in the aptamer with their more degradation-resistant deoxyribonucleic acid (DNA) equivalents. Surprisingly and unlike control DNA-stem loops employing other sequences, this DNA aptamer retains the ability to bind aminoglycosides, albeit with poorer affinity than the parent RNA aptamer. Unfortunately, however, while sensors fabricated using this DNA aptamer are stable in blood serum, its lower affinity pushes their detection limits above the therapeutically relevant range. Finally, we find that ultrafiltration through a low-molecular-weight-cutoff spin column rapidly and efficiently removes the relevant nucleases from serum samples spiked with gentamicin, allowing the convenient detection of this aminoglycoside at clinically relevant concentrations using the original RNA-based sensor. PMID:20687587

  2. Molecular hybridization between rat liver deoxyribonucleic acid and complementary ribonucleic acid

    PubMed Central

    Melli, Marialuisa; Bishop, J. O.

    1970-01-01

    RNA (cRNA) was synthesized in vitro on a template of rat liver DNA and its hybridization with rat liver DNA was studied by using the nitrocellulose-filter method. Sonication of the DNA diminished its apparent capacity to hybridize with RNA by about 50%. This is not due to cross-linkage of DNA molecules, because it could be shown that less than 2% of the sonicated DNA was cross-linked. The effect is due instead to the small size of the sonicated DNA molecules. Below a single-stranded molecular weight of 5×105 the DNA showed a progressive loss of capacity to hybridize with decrease in molecular weight. Evidence is presented suggesting that the apparently diminished capacity of the DNA to hybridize is due to loss of hybridized DNA from the membrane filters. When cRNA at concentrations of up to 25μg/ml is annealed with sonicated total DNA, an apparent hybridization saturation value is found at which about 2.5% of the DNA is hybridized with RNA. Increasing the cRNA concentration tenfold brought about the hybridization of a second component of the DNA approximately equal in amount to the first. The renaturation of rat liver DNA was studied by measuring the fall in the extinction at 260nm and two different components of renaturation were observed within the reiterated fraction of DNA. By hybridizing cRNA with different fractions of rat DNA the two components of the hybridization curve are shown to correspond to the two components of the renaturation curve. The conclusion is drawn that at a cRNA concentration of 250μg/ml most of the reiterated fraction of rat liver DNA is hybridized after annealing for 16h under standard conditions (0.30m-sodium chloride–30mm-sodium citrate at 65°C). Even with such a high cRNA concentration little or no hybridization of the slowly renaturing DNA fraction occurs. It is suggested that the most highly reiterated DNA component is poorly transcribed in vitro. PMID:5493851

  3. Fatty Acid Composition of Unicellular Strains of Blue-Green Algae1

    PubMed Central

    Kenyon, C. N.

    1972-01-01

    The fatty acids of 34 strains of unicellular blue-green algae provisionally assigned to the genera Synechococcus, Aphanocapsa, Gloeocapsa, Microcystis, and Chlorogloea by Stanier et al. have been chemically characterized. The strains analyzed can be divided into a series of compositional groups based upon the highest degree of unsaturation of the major cellular fatty acids. Twenty strains fall into the group characterized by one trienoic fatty acid isomer (α-linolenic acid), and seven strains fall into a group characterized by another trienoic acid isomer (γ-linolenic acid). These groups in many cases correlate well with groupings based upon other phenotypic characters of the strains, e.g., deoxyribonucleic acid base composition. The assignment of a strain to a compositional group is not altered when the strain is grown under a variety of different culture conditions. All strains contain glycolipids with the properties of mono- and digalactosyldiglycerides. PMID:4621688

  4. Fermented probiotic beverages based on acid whey.

    PubMed

    Skryplonek, Katarzyna; Jasińska, Małgorzata

    2015-01-01

    Production of fermented probiotic beverages can be a good method for acid whey usage. The obtained products combine a high nutritional value of whey with health benefits claimed for probiotic bacteria. The aim of the study was to define quality properties of beverages based on fresh acid whey and milk with addition of buttermilk powder or sweet whey powder. Samples were inoculated with two strains of commercial probiotic cultures: Lactobacillus acidophilus La-5 or Bifidobacterium animalis Bb-12. After fermentation, samples were stored at refrigerated conditions. After 1, 4, 7, 14 and 21 days sensory characteristics, hardness, acetaldehyde content, titratable acidity, pH acidity and count of bacteria cells were evaluated. Throughout all storage period, the number of bacteria was higher than 8 log cfu/ml in the all samples. Beverages with La-5 strain had higher hardness and acidity, whilst samples with Bb-12 contained more acetaldehyde. Samples with buttermilk powder had better sensory properties than with sweet whey powder. Obtained products made of acid whey combined with milk and fortified with buttermilk powder or sweet whey powder, are good medium for growth and survival of examined probiotic bacteria strains. The level of bacteria was sufficient to provide health benefits to consumers.

  5. Jigsaw Cooperative Learning: Acid-Base Theories

    ERIC Educational Resources Information Center

    Tarhan, Leman; Sesen, Burcin Acar

    2012-01-01

    This study focused on investigating the effectiveness of jigsaw cooperative learning instruction on first-year undergraduates' understanding of acid-base theories. Undergraduates' opinions about jigsaw cooperative learning instruction were also investigated. The participants of this study were 38 first-year undergraduates in chemistry education…

  6. Separation of Acids, Bases, and Neutral Compounds

    NASA Astrophysics Data System (ADS)

    Fujita, Megumi; Mah, Helen M.; Sgarbi, Paulo W. M.; Lall, Manjinder S.; Ly, Tai Wei; Browne, Lois M.

    2003-01-01

    Separation of Acids, Bases, and Neutral Compounds requires the following software, which is available for free download from the Internet: Netscape Navigator, version 4.75 or higher, or Microsoft Internet Explorer, version 5.0 or higher; Chime plug-in, version compatible with your OS and browser (available from MDL); and Flash player, version 5 or higher (available from Macromedia).

  7. Jigsaw Cooperative Learning: Acid-Base Theories

    ERIC Educational Resources Information Center

    Tarhan, Leman; Sesen, Burcin Acar

    2012-01-01

    This study focused on investigating the effectiveness of jigsaw cooperative learning instruction on first-year undergraduates' understanding of acid-base theories. Undergraduates' opinions about jigsaw cooperative learning instruction were also investigated. The participants of this study were 38 first-year undergraduates in chemistry education…

  8. Linear Titration Curves of Acids and Bases.

    PubMed

    Joseph, N R

    1959-05-29

    The Henderson-Hasselbalch equation, by a simple transformation, becomes pH - pK = pA - pB, where pA and pB are the negative logarithms of acid and base concentrations. Sigmoid titration curves then reduce to straight lines; titration curves of polyelectrolytes, to families of straight lines. The method is applied to the titration of the dipeptide glycyl aminotricarballylic acid, with four titrable groups. Results are expressed as Cartesian and d'Ocagne nomograms. The latter is of a general form applicable to polyelectrolytes of any degree of complexity.

  9. Prebiotic synthesis of carboxylic acids, amino acids and nucleic acid bases from formamide under photochemical conditions⋆

    NASA Astrophysics Data System (ADS)

    Botta, Lorenzo; Mattia Bizzarri, Bruno; Piccinino, Davide; Fornaro, Teresa; Robert Brucato, John; Saladino, Raffaele

    2017-07-01

    The photochemical transformation of formamide in the presence of a mixture of TiO2 and ZnO metal oxides as catalysts afforded a large panel of molecules of biological relevance, including carboxylic acids, amino acids and nucleic acid bases. The reaction was less effective when performed in the presence of only one mineral, highlighting the role of synergic effects between the photoactive catalysts. Taken together, these results suggest that the synthesis of chemical precursors for both the genetic and the metabolic apparatuses might have occurred in a simple environment, consisting of formamide, photoactive metal oxides and UV-radiation.

  10. The first proton sponge-based amino acids: synthesis, acid-base properties and some reactivity.

    PubMed

    Ozeryanskii, Valery A; Gorbacheva, Anastasia Yu; Pozharskii, Alexander F; Vlasenko, Marina P; Tereznikov, Alexander Yu; Chernov'yants, Margarita S

    2015-08-21

    The first hybrid base constructed from 1,8-bis(dimethylamino)naphthalene (proton sponge or DMAN) and glycine, N-methyl-N-(8-dimethylamino-1-naphthyl)aminoacetic acid, was synthesised in high yield and its hydrobromide was structurally characterised and used to determine the acid-base properties via potentiometric titration. It was found that the basic strength of the DMAN-glycine base (pKa = 11.57, H2O) is on the level of amidine amino acids like arginine and creatine and its structure, zwitterionic vs. neutral, based on the spectroscopic (IR, NMR, mass) and theoretical (DFT) approaches has a strong preference to the zwitterionic form. Unlike glycine, the DMAN-glycine zwitterion is N-chiral and is hydrolytically cleaved with the loss of glycolic acid on heating in DMSO. This reaction together with the mild decarboxylative conversion of proton sponge-based amino acids into 2,3-dihydroperimidinium salts under air-oxygen was monitored with the help of the DMAN-alanine amino acid. The newly devised amino acids are unique as they combine fluorescence, strongly basic and redox-active properties.

  11. Chem I Supplement: Emphasis on Acids and Bases

    ERIC Educational Resources Information Center

    Journal of Chemical Education Staff

    1977-01-01

    Provides supplementary notes on acids and bases suitable for secondary school chemistry instruction, including acidity in solid and natural waters, acidity balance in body chemistry, acid and basic foods, pH values of common fluids, examples of drugs, and commercial preparation of nitric acid. (SL)

  12. Quantum interference in DNA bases probed by graphene nanoribbons

    NASA Astrophysics Data System (ADS)

    Jeong, Heejeong; Seul Kim, Han; Lee, Sung-Hoon; Lee, Dongho; Hoon Kim, Yong; Huh, Nam

    2013-07-01

    Based on first-principles nonequilibrium Green's function calculations, we demonstrate quantum interference (QI) effects on the tunneling conductance of deoxyribonucleic acid bases placed between zigzag graphene nanoribbon electrodes. With the analogy of QI in hydrocarbon ring structures, we hypothesize that QI can be well preserved in the π-π coupling between the carbon-based electrode and a single DNA base. We demonstrate indications of QI, such as destructively interfered anti-resonance or Fano-resonance, that affect the variation of tunneling conductance depending on the orientation of a base. We find that guanine, with a 10-fold higher transverse conductance, can be singled out from the other bases.

  13. Complexity in Acid-Base Titrations: Multimer Formation Between Phosphoric Acids and Imines.

    PubMed

    Malm, Christian; Kim, Heejae; Wagner, Manfred; Hunger, Johannes

    2017-08-10

    Solutions of Brønsted acids with bases in aprotic solvents are not only common model systems to study the fundamentals of proton transfer pathways but are also highly relevant to Brønsted acid catalysis. Despite their importance the light nature of the proton makes characterization of acid-base aggregates challenging. Here, we track such acid-base interactions over a broad range of relative compositions between diphenyl phosphoric acid and the base quinaldine in dichloromethane, by using a combination of dielectric relaxation and NMR spectroscopy. In contrast to what one would expect for an acid-base titration, we find strong deviations from quantitative proton transfer from the acid to the base. Even for an excess of the base, multimers consisting of one base and at least two acid molecules are formed, in addition to the occurrence of proton transfer from the acid to the base and simultaneous formation of ion pairs. For equimolar mixtures such multimers constitute about one third of all intermolecular aggregates. Quantitative analysis of our results shows that the acid-base association constant is only around six times larger than that for the acid binding to an acid-base dimer, that is, to an already protonated base. Our findings have implications for the interpretation of previous studies of reactive intermediates in organocatalysis and provide a rationale for previously observed nonlinear effects in phosphoric acid catalysis. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  14. Investigating Students' Reasoning about Acid-Base Reactions

    ERIC Educational Resources Information Center

    Cooper, Melanie M.; Kouyoumdjian, Hovig; Underwood, Sonia M.

    2016-01-01

    Acid-base chemistry is central to a wide range of reactions. If students are able to understand how and why acid-base reactions occur, it should provide a basis for reasoning about a host of other reactions. Here, we report the development of a method to characterize student reasoning about acid-base reactions based on their description of…

  15. Investigating Students' Reasoning about Acid-Base Reactions

    ERIC Educational Resources Information Center

    Cooper, Melanie M.; Kouyoumdjian, Hovig; Underwood, Sonia M.

    2016-01-01

    Acid-base chemistry is central to a wide range of reactions. If students are able to understand how and why acid-base reactions occur, it should provide a basis for reasoning about a host of other reactions. Here, we report the development of a method to characterize student reasoning about acid-base reactions based on their description of…

  16. The Bronsted-Lowery Acid-Base Concept.

    ERIC Educational Resources Information Center

    Kauffman, George B.

    1988-01-01

    Gives the background history of the simultaneous discovery of acid-base relationships by Johannes Bronsted and Thomas Lowry. Provides a brief biographical sketch of each. Discusses their concept of acids and bases in some detail. (CW)

  17. An Introductory Laboratory Exercise for Acids and Bases.

    ERIC Educational Resources Information Center

    Miller, Richard; Silberman, Robert

    1986-01-01

    Discusses an acid-base neutralization exercise requiring groups of students to determine: (1) combinations of solutions giving neutralization; (2) grouping solutions as acids or bases; and (3) ranking groups in order of concentration. (JM)

  18. An Introductory Laboratory Exercise for Acids and Bases.

    ERIC Educational Resources Information Center

    Miller, Richard; Silberman, Robert

    1986-01-01

    Discusses an acid-base neutralization exercise requiring groups of students to determine: (1) combinations of solutions giving neutralization; (2) grouping solutions as acids or bases; and (3) ranking groups in order of concentration. (JM)

  19. The Bronsted-Lowery Acid-Base Concept.

    ERIC Educational Resources Information Center

    Kauffman, George B.

    1988-01-01

    Gives the background history of the simultaneous discovery of acid-base relationships by Johannes Bronsted and Thomas Lowry. Provides a brief biographical sketch of each. Discusses their concept of acids and bases in some detail. (CW)

  20. Coronavirus phylogeny based on triplets of nucleic acids bases

    NASA Astrophysics Data System (ADS)

    Liao, Bo; Liu, Yanshu; Li, Renfa; Zhu, Wen

    2006-04-01

    We considered the fully overlapping triplets of nucleotide bases and proposed a 2D graphical representation of protein sequences consisting of 20 amino acids and a stop code. Based on this 2D graphical representation, we outlined a new approach to analyze the phylogenetic relationships of coronaviruses by constructing a covariance matrix. The evolutionary distances are obtained through measuring the differences among the two-dimensional curves.

  1. Mathematical modeling of acid-base physiology.

    PubMed

    Occhipinti, Rossana; Boron, Walter F

    2015-01-01

    pH is one of the most important parameters in life, influencing virtually every biological process at the cellular, tissue, and whole-body level. Thus, for cells, it is critical to regulate intracellular pH (pHi) and, for multicellular organisms, to regulate extracellular pH (pHo). pHi regulation depends on the opposing actions of plasma-membrane transporters that tend to increase pHi, and others that tend to decrease pHi. In addition, passive fluxes of uncharged species (e.g., CO2, NH3) and charged species (e.g., HCO3(-), [Formula: see text] ) perturb pHi. These movements not only influence one another, but also perturb the equilibria of a multitude of intracellular and extracellular buffers. Thus, even at the level of a single cell, perturbations in acid-base reactions, diffusion, and transport are so complex that it is impossible to understand them without a quantitative model. Here we summarize some mathematical models developed to shed light onto the complex interconnected events triggered by acids-base movements. We then describe a mathematical model of a spherical cells-which to our knowledge is the first one capable of handling a multitude of buffer reactions-that our team has recently developed to simulate changes in pHi and pHo caused by movements of acid-base equivalents across the plasma membrane of a Xenopus oocyte. Finally, we extend our work to a consideration of the effects of simultaneous CO2 and HCO3(-) influx into a cell, and envision how future models might extend to other cell types (e.g., erythrocytes) or tissues (e.g., renal proximal-tubule epithelium) important for whole-body pH homeostasis. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Mathematical modeling of acid-base physiology

    PubMed Central

    Occhipinti, Rossana; Boron, Walter F.

    2015-01-01

    pH is one of the most important parameters in life, influencing virtually every biological process at the cellular, tissue, and whole-body level. Thus, for cells, it is critical to regulate intracellular pH (pHi) and, for multicellular organisms, to regulate extracellular pH (pHo). pHi regulation depends on the opposing actions of plasma-membrane transporters that tend to increase pHi, and others that tend to decrease pHi. In addition, passive fluxes of uncharged species (e.g., CO2, NH3) and charged species (e.g., HCO3− , NH4+) perturb pHi. These movements not only influence one another, but also perturb the equilibria of a multitude of intracellular and extracellular buffers. Thus, even at the level of a single cell, perturbations in acid-base reactions, diffusion, and transport are so complex that it is impossible to understand them without a quantitative model. Here we summarize some mathematical models developed to shed light onto the complex interconnected events triggered by acids-base movements. We then describe a mathematical model of a spherical cell–which to our knowledge is the first one capable of handling a multitude of buffer reaction–that our team has recently developed to simulate changes in pHi and pHo caused by movements of acid-base equivalents across the plasma membrane of a Xenopus oocyte. Finally, we extend our work to a consideration of the effects of simultaneous CO2 and HCO3− influx into a cell, and envision how future models might extend to other cell types (e.g., erythrocytes) or tissues (e.g., renal proximal-tubule epithelium) important for whole-body pH homeostasis. PMID:25617697

  3. Bipolar Membranes for Acid Base Flow Batteries

    NASA Astrophysics Data System (ADS)

    Anthamatten, Mitchell; Roddecha, Supacharee; Jorne, Jacob; Coughlan, Anna

    2011-03-01

    Rechargeable batteries can provide grid-scale electricity storage to match power generation with consumption and promote renewable energy sources. Flow batteries offer modular and flexible design, low cost per kWh and high efficiencies. A novel flow battery concept will be presented based on acid-base neutralization where protons (H+) and hydroxyl (OH-) ions react electrochemically to produce water. The large free energy of this highly reversible reaction can be stored chemically, and, upon discharge, can be harvested as usable electricity. The acid-base flow battery concept avoids the use of a sluggish oxygen electrode and utilizes the highly reversible hydrogen electrode, thus eliminating the need for expensive noble metal catalysts. The proposed flow battery is a hybrid of a battery and a fuel cell---hydrogen gas storing chemical energy is produced at one electrode and is immediately consumed at the other electrode. The two electrodes are exposed to low and high pH solutions, and these solutions are separated by a hybrid membrane containing a hybrid cation and anion exchange membrane (CEM/AEM). Membrane design will be discussed, along with ion-transport data for synthesized membranes.

  4. Photocurable bioadhesive based on lactic acid.

    PubMed

    Marques, D S; Santos, J M C; Ferreira, P; Correia, T R; Correia, I J; Gil, M H; Baptista, C M S G

    2016-01-01

    Novel photocurable and low molecular weight oligomers based on l-lactic acid with proven interest to be used as bioadhesive were successfully manufactured. Preparation of lactic acid oligomers with methacrylic end functionalizations was carried out in the absence of catalyst or solvents by self-esterification in two reaction steps: telechelic lactic acid oligomerization with OH end groups and further functionalization with methacrylic anhydride. The final adhesive composition was achieved by the addition of a reported biocompatible photoinitiator (Irgacure® 2959). Preliminary in vitro biodegradability was investigated by hydrolytic degradation in PBS (pH=7.4) at 37 °C. The adhesion performance was evaluated using glued aminated substrates (gelatine pieces) subjected to pull-to-break test. Surface energy measured by contact angles is lower than the reported values of the skin and blood. The absence of cytoxicity was evaluated using human fibroblasts. A notable antimicrobial behaviour was observed using two bacterial models (Staphylococcus aureus and Escherichia coli). The cured material exhibited a strong thrombogenic character when placed in contact with blood, which can be predicted as a haemostatic effect for bleeding control. This novel material was subjected to an extensive characterization showing great potential for bioadhesive or other biomedical applications where biodegradable and biocompatible photocurable materials are required.

  5. Nuclear Fraction of Bacillus subtilis as a Template for Ribonucleic Acid Synthesis

    PubMed Central

    Mizuno, S.; Whiteley, H. R.

    1968-01-01

    A “nuclear fraction” prepared from Bacillus subtilis was a more efficient template than purified deoxyribonucleic acid for the synthesis of ribonucleic acid by exogenously added ribonucleic acid polymerase isolated from B. subtilis. The initial rate of synthesis with the nuclear fraction was higher and synthesis continued for several hours, yielding an amount of ribonucleic acid greater than the amount of deoxyribonucleic acid used as the template. The product was heterogenous in size, with a large portion exceeding 23S. When purified deoxyribonucleic acid was the template, a more limited synthesis was observed with a predominantly 7S product. However, the ribonucleic acids produced in vitro from these templates were very similar to each other and to in vivo synthesized ribonucleic acid as determined by the competition of ribonucleic acid from whole cells in the annealing of in vitro synthesized ribonucleic acids to deoxyribonucleic acid. Treatment of the nuclear fraction with heat (60 C for 15 min) or trypsin reduced the capacity of the nuclear fraction to synthesize ribonucleic acid to the level observed with purified deoxyribonucleic acid. PMID:4296512

  6. Using Willie's Acid-Base Box for Blood Gas Analysis

    ERIC Educational Resources Information Center

    Dietz, John R.

    2011-01-01

    In this article, the author describes a method developed by Dr. William T. Lipscomb for teaching blood gas analysis of acid-base status and provides three examples using Willie's acid-base box. Willie's acid-base box is constructed using three of the parameters of standard arterial blood gas analysis: (1) pH; (2) bicarbonate; and (3) CO[subscript…

  7. Assessing College Students' Understanding of Acid Base Chemistry Concepts

    ERIC Educational Resources Information Center

    Wan, Yanjun Jean

    2014-01-01

    Typically most college curricula include three acid base models: Arrhenius', Bronsted-Lowry's, and Lewis'. Although Lewis' acid base model is generally thought to be the most sophisticated among these three models, and can be further applied in reaction mechanisms, most general chemistry curricula either do not include Lewis' acid base model, or…

  8. Teaching Acid/Base Physiology in the Laboratory

    ERIC Educational Resources Information Center

    Friis, Ulla G.; Plovsing, Ronni; Hansen, Klaus; Laursen, Bent G.; Wallstedt, Birgitta

    2010-01-01

    Acid/base homeostasis is one of the most difficult subdisciplines of physiology for medical students to master. A different approach, where theory and practice are linked, might help students develop a deeper understanding of acid/base homeostasis. We therefore set out to develop a laboratory exercise in acid/base physiology that would provide…

  9. Teaching Acid/Base Physiology in the Laboratory

    ERIC Educational Resources Information Center

    Friis, Ulla G.; Plovsing, Ronni; Hansen, Klaus; Laursen, Bent G.; Wallstedt, Birgitta

    2010-01-01

    Acid/base homeostasis is one of the most difficult subdisciplines of physiology for medical students to master. A different approach, where theory and practice are linked, might help students develop a deeper understanding of acid/base homeostasis. We therefore set out to develop a laboratory exercise in acid/base physiology that would provide…

  10. A clinical approach to acid-base conundrums.

    PubMed

    Garrubba, Carl; Truscott, Judy

    2016-04-01

    Acid-base disorders can provide essential clues to underlying patient conditions. This article provides a simple, practical approach to identifying simple acid-base disorders and their compensatory mechanisms. Using this stepwise approach, clinicians can quickly identify and appropriately treat acid-base disorders.

  11. Using Willie's Acid-Base Box for Blood Gas Analysis

    ERIC Educational Resources Information Center

    Dietz, John R.

    2011-01-01

    In this article, the author describes a method developed by Dr. William T. Lipscomb for teaching blood gas analysis of acid-base status and provides three examples using Willie's acid-base box. Willie's acid-base box is constructed using three of the parameters of standard arterial blood gas analysis: (1) pH; (2) bicarbonate; and (3) CO[subscript…

  12. Oleic acid-based gemini surfactants with carboxylic acid headgroups.

    PubMed

    Sakai, Kenichi; Umemoto, Naoki; Matsuda, Wataru; Takamatsu, Yuichiro; Matsumoto, Mutsuyoshi; Sakai, Hideki; Abe, Masahiko

    2011-01-01

    Anionic gemini surfactants with carboxylic acid headgroups have been synthesized from oleic acid. The hydrocarbon chain is covalently bound to the terminal carbonyl group of oleic acid via an ester bond, and the carboxylic acid headgroups are introduced to the cis double bond of oleic acid via disuccinyl units. The surfactants exhibit pH-dependent protonation-deprotonation behavior in aqueous solutions. In alkaline solutions (pH 9 in the presence of 10 mmol dm(-3) NaCl as the background electrolyte), the surfactants can lower the surface tension as well as form molecular assemblies, even in the region of low surfactant concentrations. Under acidic (pH 3) or neutral (pH 6-7) conditions, the surfactants are intrinsically insoluble in aqueous media and form a monolayer at the air/water interface. In this study, we have investigated physicochemical properties such as the function of the hydrocarbon chain length by means of static surface tension, pyrene fluorescence, dynamic light scattering, surface pressure-area isotherms, and infrared external reflection measurements.

  13. Identifying a base in a nucleic acid

    DOEpatents

    Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

    2005-02-08

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  14. Acid-base chemistry and aluminum transport in an acidic watershed and pond in New Hampshire

    Treesearch

    Scott W. Bailey; Charles T. Driscoll; James W. Hornbeck

    1995-01-01

    Cone Pond is one of the few acidic, clear-water ponds in the White Mountains of New Hampshire, a region dominated by high inputs of strong acids from atmospheric deposition and low base content of bedrock. Monitoring was conducted for 13 months to compare and contrast the acid-base chemistry of the terrestrial and aquatic portions of the watershed. Variations in Al...

  15. Polarity based fractionation of fulvic acids.

    PubMed

    Li, Aimin; Hu, Jundong; Li, Wenhui; Zhang, Wei; Wang, Xuejun

    2009-11-01

    Fulvic acids from the soil of Peking University (PF) and a Nordic river (NF) were separated into well defined sub-fractions using sequential elution techniques based on eluent polarity. The chemical properties of the fractions including: PF1 and NF1 (eluted by 0.01 M HCl), PF2 and NF2 (eluted by 0.01 M HCl+20% methanol), PF3 and NF3 (eluted by 0.01 M HCl+40% methanol), and PF4 and NF4 (eluted by 100% methanol), were characterized using UV-Visible spectroscopy, elemental analysis and (13)C NMR. The results showed that the UV absorptions of the elution peaks at 280 nm (A280) increased from PF2 to PF4 and NF2 to NF4. No elution peaks were observed for PF1 and NF1. The carbon contents increased from 43.34% to 51.90% and 43.06% to 53.26% while the oxygen contents decreased from 46.39% to 36.76% and 49.76% to 40.03% for PF1-PF4 and NF1-NF4, respectively. As a polarity indicator, the (O+N)/C ratio for PF1-PF4 and NF1-NF4 decreased from 0.88 to 0.62 and 0.89 to 0.58, respectively. The aromatic carbon content increased from PF1 to PF4 and NF1 to NF4, suggesting an increase of the hydrophobicity of these fractions. The polarity was positively related to the ratio of UV absorption at 250 nm and 365 nm (E2/E3), and negatively related to the aromaticity. A high positive relationship between the aromaticity and E2/E3 of fulvic acid fractions was also obtained. The use of an eluent with a decreasing polarity allowed to providing simpler fractions of soil and aquatic fulvic acids.

  16. History of nutrition and acid-base physiology.

    PubMed

    Manz, F

    2001-10-01

    In the 17th century the notion of nutrition and diet changed in northern European countries. First chemical experiments fostered the idea that salts resulted from a union of acids and bases. Digestion was no more regarded as a process of cooking but a succession of fermentations controlled by a balanced production of acids and alkali. Life seemed to depend on the equilibrium of acids and alkalis. In the 19th century food was systematically analysed for the content of energy and macronutrients and first scientifically based nutritional standards were formulated. The preferred use of processed food from the new food industry resulted in epidemics of nutritional disorders. Acidosis seemed to be a plausible pathogenic factor. Practitioners (S Ishizuka, H Hay, FX Mayr) formulated holistic doctrines integrating the concept of balance of acids and bases and recommending food with an excess of alkali. New micromethods to determine the concentration of electrolytes and blood acid-base status promoted physiological and clinical research into acid-base metabolism in the 1960s. In the new physiologically based terminology of systemic acid-base status, the relationship between blood acid-base status and net acid intake or excretion was, however, incorrectly simplified. In the 1970s metabolic acidosis was observed in patients on chemically defined diets and parenteral nutrition. Based on the data of comprehensive acid-base balance studies, calculation models were used to estimate renal net acid excretion from nutrient intake and to predict the potential renal acid load of single foods. Extrapolating current trends to the future, one can say that acid-base physiology will probably remain a challenge in nutrition and functional medicine over the next few years. The challenge will include new concepts for the manipulation of nutritional acid load in sports, dietetics and preventive medicine as well as new definitions of the upper intake level of potential renal acid load in

  17. Tridentate Lewis-acids based on triphenylsilane.

    PubMed

    Tomaschautzky, Janek; Neumann, Beate; Stammler, Hans-Georg; Mix, Andreas; Mitzel, Norbert W

    2017-01-31

    Several derivatives of the propeller-shaped ortho-substituted triphenylsilanes, carrying metal- or silicon-based acceptor groups, are reported. They were synthesized starting from tris(2-bromophenyl)fluorosilane, tris(2-vinylphenyl)fluorosilane and tris(2-ethynylphenyl)fluorosilane to generate a scope of Lewis-acidic molecules with different cavities. An improved synthetic protocol for donor-free tris(2-lithiophenyl)silanes is described. First attempts in host-guest chemistry to probe the binding between a threefold alane-functionalised ortho-substituted triphenylsilane and a tridentate Lewis-basic guest molecule are presented. The synthesis and a first molecular structure determination in the crystalline state of a bismasilatriptycene is reported.

  18. Striking similarities are exhibited by two small Epstein-Barr virus-encoded ribonucleic acids and the adenovirus-associated ribonucleic acids VAI and VAII

    SciTech Connect

    Rosa, M.D.; Gottlieb, E.; Lerner, M.R.; Steitz, J.A.

    1981-09-01

    The nucleotide sequence of the region of the Epstein-Barr virus genome that specified two small ribonucleic acids (RNAs), EBER 1 and EBER 2, has been determined. Both of these RNAs are encoded by the right-hand 1,000 base pairs of the EcoRI J fragment of EBV deoxyribonucleic acid. EBER 1 is 166 (167) nucleotides long and EBER 2 is 172 +- 1 nucleotides long; the heterogeneity resides at the 3' termini. The EBER genes are separated by 161 base pairs and are transcribed from the same deoxyribonucleic acid strand. In vitro, both EBER genes can be transcribed by RNA polymerase III; sequences homologous to previously identified RNA polymerase III intragenic transcription control regions are present. Striking similarities are therefore apparent both between the EBERs and the two adenovirus-associated RNAs, VAI and VAII, and between the regions of the two viral genomes that specify these small RNAs. We have shown that VAII RNA as well as VAI RNA and the EBERs exist in ribonucleoprotein complexes which are precipitable by anti-La antibodies associated with systemic lupus erythematosus. Finally the authors have demonstrated that the binding of protein(s) from uninfected cells confers antigenicity on each of the four virus-encoded small RNAs.

  19. Acid-base bifunctional catalytic surfaces for nucleophilic addition reactions.

    PubMed

    Motokura, Ken; Tada, Mizuki; Iwasawa, Yasuhiro

    2008-09-01

    This article illustrates the modification of oxide surfaces with organic amine functional groups to create acid-base bifunctional catalysts, summarizing our previous reports and also presenting new data. Immobilization of organic amines as bases on inorganic solid-acid surfaces afforded highly active acid-base bifunctional catalysts, which enabled various organic transformations including C--C coupling reactions, though these reactions did not proceed with either the homogeneous amine precursors or the acidic supports alone. Spectroscopic characterization, such as by solid-state MAS NMR and FTIR, revealed not only the interactions between acidic and basic sites but also bifunctional catalytic reaction mechanisms.

  20. Thermochemical comparisons of homogeneous and heterogeneous acids and bases. 1. Sulfonic acid solutions and resins as prototype Broensted acids

    SciTech Connect

    Arnett, E.M.; Haaksma, R.A.; Chawla, B.; Healy, M.H.

    1986-08-06

    Heats of ionization by thermometric titration for a series of bases (or acids) can be used to compare solid acids (or bases) with liquid analogues bearing the same functionalities in homogeneous solutions. The method is demonstrated for Broensted acids by reacting a series of substituted nitrogen bases with solutions of p-toluenesulfonic acid (PTSA) in acetonitrile and with suspensions of the microporous polymeric arylsulfonic acid resin-Dowex 50W-X8 in the same solvent. Under well-controlled anhydrous conditions there is a good correlation (r = 0.992) between the heats of reaction of the bases with the homogeneous and heterogeneous acid systems, but the homogeneous system gives a more exothermic interaction by 3-4 kcal mol/sup -1/ for a series of 29 substituted pyrimidines, anilines, and some other amines. This difference may be attributed to homohydrogen bonding interactions between excess acid and sulfonate anion sites which are more restricted geometrically in the resin than in solution. Other factors which affect the enthalpy change for the acid-base interaction are the acid/base ratio, the water content of the sulfonic acid, the solvent, and the resin structure (e.g., microporous vs. macroporous). Steric hindrance in the base does not differentiate solid from homogeneous acid. In addition to the use of titration calorimetry, heats of immersion are reported for the Dowex-arylsulfonic acid resins and the Nafion-perfluorinated sulfonic acid resin in a series of basic liquids. The results are compared with each other and with those from a previous study of several varieties of coal.

  1. Base pairing and base mis-pairing in nucleic acids

    NASA Technical Reports Server (NTRS)

    Wang, A. H. J.; Rich, A.

    1986-01-01

    In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

  2. Base pairing and base mis-pairing in nucleic acids

    NASA Technical Reports Server (NTRS)

    Wang, A. H. J.; Rich, A.

    1986-01-01

    In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

  3. Identification of Biological Warfare (BW) Threat Agents Using Deoxyribonucleic Acid (DNA) Microarrays

    DTIC Science & Technology

    2005-02-01

    Escherichia coli 0157:H7 and the non-virulent K-12 strain. By assaying for the presence of: 1) unique sequences at various levels of the phylogenetic tree , 2...the phylogenetic tree , 2) virulence genes, 3) antibiotic resistance genes, 4) virulence plasmid sequences and 5) ribosomal genes, we are in a unique...demonstrating species-level discrimination between Bacillus anthracis, vaccinia virus and Yersinia pestis and strain-level discrimination between

  4. Superimposed Code Theoretic Analysis of Deoxyribonucleic Acid (DNA) Codes and DNA Computing

    DTIC Science & Technology

    2010-01-01

    hybridization that occurs between a DNA strand and its Watson - Crick complement can be used to perform mathematical computation. This research addresses how the...are 5′→3′ and strands with strikethrough are 3′→5′. A dsDNA duplex formed between a strand and its reverse complement is called a Watson - Crick (WC...3’ 5’ 3’ 5’TACGCGACTTTC3’ 5’GAAAGTCGCGTA3’ ATCAAACGATGC GCATCGTTTGAT Watson Crick (WC) Duplexes TACGCGACTTTC

  5. Photoluminescence and Lasing from Deoxyribonucleic Acid Thin Films Doped With Sulforhodamine

    DTIC Science & Technology

    2007-03-20

    daltons. A sonication process16 was utilized to reduce the DNA MW to 150–200 kDa. For comparison to DNA, we have also used poly( methyl methacrylate ) (PMMA...29, 2729– (1990). 18. M. D. Rahn and T . A. King, “Comparison of laser performance of dye molecules in sol–gel, polycom, ormosil, and poly( methyl ...CTMA and PMMA thin films, solid DNA–CTMA and SRh powder were mixed and dissolved in butanol solution with different weight ratios. PMMA granules and

  6. Assisted reproductive technology alters deoxyribonucleic acid methylation profiles in bloodspots of newborn infants.

    PubMed

    Estill, Molly S; Bolnick, Jay M; Waterland, Robert A; Bolnick, Alan D; Diamond, Michael P; Krawetz, Stephen A

    2016-09-01

    To evaluate the effect of infertility and intracytoplasmic sperm injection (ICSI) on DNA methylation of offspring. Microarray analysis of DNA methylation in archived neonatal bloodspots of in vitro fertilization (IVF)/ICSI-conceived children compared with controls born to fertile and infertile parents. Academic research laboratory. Neonatal blood spots of 137 newborns conceived spontaneously, through intrauterine insemination (IUI), or through ICSI using fresh or cryopreserved (frozen) embryo transfer. None. The Illumina Infinium HumanMethylation450k BeadChip assay determined genome-wide DNA methylation. Methylation differences between conception groups were detected using a Bioconductor package, ChAMP, in conjunction with Adjacent Site Clustering (A-clustering). The methylation profiles of assisted reproductive technology and IUI newborns were dramatically different from those of naturally (in vivo) conceived newborns. Interestingly, the profiles of ICSI-frozen (FET) and IUI infants were strikingly similar, suggesting that cryopreservation may temper some of the epigenetic aberrations induced by IVF or ICSI. The DNA methylation changes associated with IVF/ICSI culture conditions and/or parental infertility were detected at metastable epialleles, suggesting a lasting impact on a child's epigenome. Both infertility and ICSI alter DNA methylation at specific genomic loci, an effect that is mitigated to some extent by FET. The impact of assisted reproductive technology and/or fertility status on metastable epialleles in humans was uncovered. This study provides an expanded set of loci for future investigations on IVF populations. Copyright © 2016 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  7. Excretion of Deoxyribonucleic Acid by Lymphocytes Stimulated with Phytohemagglutinin or Antigen

    PubMed Central

    Rogers, John C.; Boldt, David; Kornfeld, Stuart; Skinner, Sister Ann; Valeri, C. Robert

    1972-01-01

    When human lymphocytes are cultured in the presence of phytomitogens, 70-90% of the cells undergo blast transformation and synthesize DNA. However, less than 40% of these lymphocytes actually undergo mitosis while 35-90% of the newly synthesized DNA is excreted into the media. The release of DNA by the cells is selective since experiments with [14C]uridine indicate that RNA is not lost into the culture media. DNA excretion occurs under many culture conditions. The excreted DNA has an estimated molecular weight of 3 to 12 × 106 as determined by gel filtration on Sepharose 2B. It forms a single sharp peak at a density of 1.055 g/cm3 when examined by sucrose density gradient centrifugation, suggesting that the DNA is complexed to protein or lipid. PMID:4505646

  8. DNA (deoxyribonucleic acid) synthesis following microinjection of heterologous sperm and somatic cell nuclei into hamster oocytes

    SciTech Connect

    Naish, S.J.; Perreault, S.D.; Zirkin, B.R.

    1987-01-01

    The authors investigated the ability of the hamster oocyte to initiate DNA synthesis in nuclei differing in basic protein content. DNA synthesis was studied by autoradiography in oocytes that had been incubated in /sup 3/H-thymidine after being parthenogenetically activated by sham microinjection, or microinjected with hamster, mouse, rabbit, or fish sperm nuclei, or hamster hepatocyte nuclei. Within 6 hr of sham or nucleus microinjection, nuclei of each type underwent transformation into pronuclei and synthesized DNA. These results demonstrated that the hamster egg can access and utilize its own and each type of template provided, whether homologous or heterologous. However, pronuclei derived from hamster sperm nuclei were more likely to be synthesizing DNA at 6 hr than pronuclei derived from sperm nuclei of other species. The authors conclude that the mechanisms employed by the hamster oocyte to transform hamster sperm nuclei into pronuclei and to effect DNA synthesis in these nuclei are not specific for the hamster sperm nucleus. Nevertheless, these mechanisms apparently operate more efficiently when the hamster sperm nucleus, rather than a heterologous sperm nucleus, is present.

  9. A modular microfluidic system for deoxyribonucleic acid identification by short tandem repeat analysis.

    PubMed

    Reedy, Carmen R; Hagan, Kristin A; Marchiarullo, Daniel J; Dewald, Alison H; Barron, Annalise; Bienvenue, Joan M; Landers, James P

    2011-02-21

    Microfluidic technology has been utilized in the development of a modular system for DNA identification through STR (short tandem repeat) analysis, reducing the total analysis time from the ∼6 h required with conventional approaches to less than 3h. Results demonstrate the utilization of microfluidic devices for the purification, amplification, separation and detection of 9 loci associated with a commercially-available miniSTR amplification kit commonly used in the forensic community. First, DNA from buccal swabs purified in a microdevice was proven amplifiable for the 9 miniSTR loci via infrared (IR)-mediated PCR (polymerase chain reaction) on a microdevice. Microchip electrophoresis (ME) was then demonstrated as an effective method for the separation and detection of the chip-purified and chip-amplified DNA with results equivalent to those obtained using conventional separation methods on an ABI 310 Genetic Analyzer. The 3-chip system presented here demonstrates development of a modular, microfluidic system for STR analysis, allowing for user-discretion as to how to proceed after each process during the analysis of forensic casework samples. Copyright © 2010 Elsevier B.V. All rights reserved.

  10. Pellet pestle homogenization of agarose gel slices at 45 degrees C for deoxyribonucleic acid extraction.

    PubMed

    Kurien, B T; Kaufman, K M; Harley, J B; Scofield, R H

    2001-09-15

    A simple method for extracting DNA from agarose gel slices is described. The extraction is rapid and does not involve harsh chemicals or sophisticated equipment. The method involves homogenization of the excised gel slice (in Tris-EDTA buffer), containing the DNA fragment of interest, at 45 degrees C in a microcentrifuge tube with a Kontes pellet pestle for 1 min. The "homogenate" is then centrifuged for 30 s and the supernatant is saved. The "homogenized" agarose is extracted one more time and the supernatant obtained is combined with the previous supernatant. The DNA extracted using this method lent itself to restriction enzyme analysis, ligation, transformation, and expression of functional protein in bacteria. This method was found to be applicable with 0.8, 1.0, and 2.0% agarose gels. DNA fragments varying from 23 to 0.4 kb were extracted using this procedure and a yield ranging from 40 to 90% was obtained. The yield was higher for fragments 2.0 kb and higher (70-90%). This range of efficiency was maintained when the starting material was kept between 10 and 300 ng. The heat step was found to be critical since homogenization at room temperature failed to yield any DNA. Extracting DNA with our method elicited an increased yield (up to twofold) compared with that extracted with a commercial kit. Also, the number of transformants obtained using the DNA extracted with our method was at least twice that obtained using the DNA extracted with the commercial kit.

  11. Transfecting deoxyribonucleic acid of Bacillus bacteriophage phi 29 that is protease sensitive.

    PubMed

    Hirokawa, H

    1972-06-01

    The transfecting activity of Bacillus phage varphi29 DNA, extracted either by sodium lauroyl sarcosine-phenol or by 2 M perchlorate, was destroyed by treatment with proteolytic enzymes, although these enzymes did not effect transfecting DNAs of SPP1, SPO1, and SP50. These facts suggest that a protein is associated with transfective varphi29 DNA. Stabilization of protease-resistance during transfection appeared earlier than that of DNaseresistance, indicating that the protein associated with varphi29 DNA is necessary for initiation of the incorporation of DNA molecules into competent cells. The physical nature of varphi29 DNA before and after the trypsin treatment was investigated by sucrose and CsCl density gradient centrifugations. The trypsin treatment did not alter the sedimentation rate of the unit varphi29 DNA; however, it did convert the sedimentation rate of the aggregated material in the untreated DNA to that of the unit varphi29 DNA. The density of the trypsinized DNA was 0.009 g/cm(3) greater than that of the untreated DNA. The possible location of the protein on the DNA is discussed.

  12. Aberrant expression and localization of deoxyribonucleic acid methyltransferase 3B in endometriotic stromal cells.

    PubMed

    Dyson, Matthew T; Kakinuma, Toshiyuki; Pavone, Mary Ellen; Monsivais, Diana; Navarro, Antonia; Malpani, Saurabh S; Ono, Masanori; Bulun, Serdar E

    2015-10-01

    To define the expression and function of DNA methyltransferases (DNMTs) in response to decidualizing stimuli in endometriotic cells compared with healthy endometrial stroma. Basic science. University research center. Premenopausal women with or without endometriosis. Primary cultures of stromal cells from healthy endometrium (E-IUM) or endometriomas (E-OSIS) were subjected to in vitro decidualization (IVD) using 1 μM medroxyprogesterone acetate, 35 nM 17β-estradiol, and 0.05 mM 8-Br-cAMP. Expression of DNMT1, DNMT3A, and DNMT3B in E-IUM and E-OSIS were assessed by quantitative real-time polymerase chain reaction and immunoblotting. Recruitment of DNMT3B to the promoters of steroidogenic factor 1 (SF-1) and estrogen receptor α (ESR1) was examined by chromatin immunoprecipitation. IVD treatment reduced DNMT3B messenger RNA (74%) and protein levels (81%) only in E-IUM; DNMT1 and DNMT3A were unchanged in both cell types. Significantly more DNMT3B bound to the SF-1 promoter in E-IUM compared with E-OSIS, and IVD treatment reduced binding in E-IUM to levels similar to those in E-OSIS. Enrichment of DNMT3B across 3 ESR1 promoters was reduced in E-IUM after IVD, although the more-distal promoter showed increased DNMT3B enrichment in E-OSIS after IVD. The inability to downregulate DNMT3B expression in E-OSIS may contribute to an aberrant epigenetic fingerprint that misdirects gene expression in endometriosis and contributes to its altered response to steroid hormones. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  13. Transfection of Streptococcus sanguis by phage deoxyribonucleic acid isolated from Streptococcus mutans.

    PubMed

    Higuchi, M; Rhee, G H; Araya, S; Higuchi, M

    1977-03-01

    Streptococcus sanguis ATCC 10556 cells were infected with free phage DNA of S, mutans strain PK 1. Two transformants were isolated which made colonies with large mucoid forms on mitis-salivarius agar. Both transformants had an increased ability to synthesize insoluble glucan and showed an adhesive nature on glass surfaces. These characteristics of the transformants bear a resemblance to S. mutans. These transformants had many physiological characteristics by which they could be recognized as S. sanguis. However, they resembled S. salivarius in forming a large amount of soluble fructan. Furthermore, the transformant cells did not produce ammonia from arginine, whereas their parent cells did.

  14. Partial Characterization of Small Plasmid Deoxyribonucleic Acid Present in ’ Neisseria Meningitidis’,

    DTIC Science & Technology

    1981-05-01

    could account for the patterns of recent epidemics of meningococcal meningitis in Brazil and Finland. In those outbreaks, there was a rapid increase...strains of this organism. Such studies will further help in the diagnosis, treatment and control of meningococcal meningitis. UNCLASSIFIED ._7 7--Li;A...been pre- viously shown to be highly virulent in a mouse model of meningococcal septicemia (Holbein, B.E., Infect. Immun., in press). As some virulence

  15. Assisted reproductive technology alters deoxyribonucleic acid methylation profiles in bloodspots of newborn infants

    USDA-ARS?s Scientific Manuscript database

    To evaluate the effect of infertility and intracytoplasmic sperm injection (ICSI) on DNA methylation of offspring. Microarray analysis of DNA methylation in archived neonatal bloodspots of in vitro fertilization (IVF)/ICSI-conceived children compared with controls born to fertile and infertile paren...

  16. Nonuniform backbone conformation of deoxyribonucleic acid indicated by phosphorus-31 nuclear magnetic resonance chemical shift anisotropy.

    PubMed

    Shindo, H; Wooten, J B; Pheiffer, B H; Zimmerman, S B

    1980-02-05

    31P nuclear magnetic resonance of highly oriented DNA fibers has been observed for three different conformations, namely, the A, B, and C forms of DNA. At a parallel orientation of the fiber axis with respect to the magnetic field, DNA fibers in both the A and B forms exhibit a single, abnormally broad resonance; in contrast, fibers in the C form show almost the full span of the chemical shift anisotropy (170 ppm). The spectra of the fibers oriented perpendicular indicate that the DNA molecules undergo a considerable rotational motion about the helical axis, with a rate of greater than 2 x 10(3) s-1 for the B-form DNA. Theoretical considerations indicate that the 31P chemical shift data for the B-form DNA fibers are consistent with the atomic coordinates of the phosphodiester group proposed by Langridge et al. [Langridge, R., Wilson, H. R. Hooper, C. W., Wilkins, M. H. F., & Hamilton, L. D. (1960) J. Mol. Biol. 2, 19--37] but not with the corresponding coordinates proposed by Arnott and Hukins [Arnott, S., & Hukins, D. W. L. (1972) Biochem. Biophys. Res. Coomun. 47, 1504--1509], and also lead to the conclusion that the phosphodiester orientation must vary significantly along the DNA molecule. The latter result suggests that DNA has significant variations in its backbone conformation along the molecule.

  17. Plasma Epstein–Barr Viral Deoxyribonucleic Acid Predicts Worse Outcomes in Pediatric Nonmetastatic Nasopharyngeal Carcinoma Patients

    PubMed Central

    Shen, Ting; Tang, Lin-Quan; Gu, Wei-Guang; Luo, Dong-Hua; Chen, Qiu-Yan; Li, Pei-Jing; Mai, Dong-Mei; Mai, Hai-Qiang; Mo, Hao-Yuan

    2015-01-01

    Abstract To evaluate the clinical significance of pretreatment levels of plasma Epstein–Barr virus DNA (pEBV DNA) on prognoses in pediatric nasopharyngeal carcinoma (NPC) patients. Eighty-nine patients aged 21 years old or younger with nonmetastatic NPC were evaluated to determine the effect of pEBV DNA levels on progression-free survival (PFS), distant metastasis-free survival (DMFS), and overall survival (OS). Survival probabilities in patient groups that were segregated by clinical stage or pEBV DNA load (low or high) were compared. The median pretreatment concentrations of pEBV DNA were 3440 copies/mL in 35 patients with stage III disease and 14,900 copies/mL in 50 patients with stage IV disease (P = 0.059). The median concentration of pEBV DNA was 34,500 copies/mL in 17 patients with relapse, which was higher than the concentration in 72 patients without relapse, who had a median level of 4985 copies/mL (P = 0.057). Further study showed that pretreatment pEBV DNA load was an independent prognostic indicator in pediatric NPC patients. High pEBV DNA was associated with adverse clinical outcomes, including PFS [3-year PFS rate = 80.5% versus 95.8%, hazard ratio (HR) = 5.00, 95% confidence interval (CI) = 1.00–25.00; P = 0.050], DMFS (3-year DMFS rate = 80.5% versus 95.8%, HR = 5.20, 95% CI = 1.04–26.00; P = 0.045), and OS (3-year OS rate = 82.9% versus 95.8%, HR = 5.41, 95% CI = 1.08–27.22; P = 0.040). Pretreatment pEBV DNA load was an independent prognostic indicator for PFS, DMFS, and OS in pediatric patients with NPC. Prospective studies, however, are needed to validate these results. PMID:26683909

  18. [Preparation of deoxyribonucleic acid (DNA) form salmon milt by the phenol method].

    PubMed

    Gracheva, S F; Bakhvalov, O V; Levagina, G M

    1978-01-01

    The paper presents a modification of the Kirby method for the DNA preparation from salmon milt. The modified procedure includes ethanol pretreatment and subsequent homogenization in 0.01 M. Trylon B. The paper describes the conditions for DNA purification through alkaline treatment and renaturation at 66 degrees C. The modified method can be used to obtain two preparations of DNA viscous solution in water (DNA homogenate), employed as a raw material in the preparation of 5-deoxyribonucleotides, and a dry preparation.

  19. Quantitation of pyrimidine dimer contents of nonradioactive deoxyribonucleic acid by electrophoresis in alkaline agarose gels

    SciTech Connect

    Sutherland, B.M.; Shih, A.G.

    1983-02-15

    We have developed a method of quantitating the pyrimidine dimer content of nonradioactive DNAs. DNA samples are treated with the UV-endonuclease from Micrococcus luteus and then separated according to molecular weight by electrophoresis on alkaline agarose gels. From their migration relative to known molecular weight standards, their median molecular weight and thus the number of dimers per DNA molecule in each sample can be calculated. Results of action spectra for dimer formation in T7 bacteriophage measured by this method agree well with action spectra for T7 killing. In addition, the method gives dimer yields in good agreement with those obtained by others using alkaline sucrose gradient sedimentation.

  20. Studies on the interaction of the food colorant tartrazine with double stranded deoxyribonucleic acid.

    PubMed

    Basu, Anirban; Suresh Kumar, Gopinatha

    2016-05-01

    Interaction of the food additive tartrazine with double-stranded DNA was studied by spectroscopic and calorimetric techniques. Absorbance studies revealed that tartrazine exhibited hypochromism in the presence of DNA without any bathochromic effects. Minor groove displacement assay of DAPI and Hoechst 33258 suggested that tartrazine binds in the minor groove of DNA. The complexation was predominantly entropy driven with a smaller but favorable enthalpic contribution to the standard molar Gibbs energy. The equilibrium constant was evaluated to be (3.68 ± .08) × 10(4) M(-1) at 298.15 K. The negative standard molar heat capacity value along with an enthalpy-entropy compensation phenomenon proposed the involvement of dominant hydrophobic forces in the binding process. Tartrazine enhanced the thermal stability of DNA by 7.53 K under saturation conditions.

  1. Detection of toxins in single molecule level using deoxyribonucleic acid aptamers

    USDA-ARS?s Scientific Manuscript database

    Toxins in foodstuffs are always a threat to food safety Among many toxins related to food, ricin (category B toxin) from castor beans has been mentioned in some poisoning cases happened. Atomic Force Microscopy (AFM) is a widely used nanotechnology to detect biospecies in vitro and in situ. The AFM...

  2. The Simulation and Analysis of an Evolutionary Model of Deoxyribonucleic Acid (DNA).

    DTIC Science & Technology

    1983-09-01

    Armstrong, Robert A. and Michael E. Gilpin. "Evolution in a Time-Varying Environment," Scienge: 591-592, 11 February 1977. 6. Arnheim, Normal and Charles...Hecht, and William C. Steere. New York NY: Appleton Century-Crofts, 1970. 62. and Etan Markowitz. "An Improved Method for Determining Codon...Methods," Markoy Chains and Monte Carla Calclations in 2olvmer Science, Edited by George G. Lowry. New York NY: Marcel Dekker, Inc., 1970. 64. Fogel

  3. Deoxyribonucleic acid strand breaks caused by ozone and nitrogen dioxide in rat lung cells

    SciTech Connect

    Bermudez, E.

    1991-01-01

    Toxic effects of O{sub 3} and NO{sub 2}, the major oxidants of photochemical smog, are mediated in part by free radical mechanisms. The present study was undertaken to determine if an exposure to O{sub 3} PIUS NO{sub 2} would cause a damage to lung cellular DNA. Three-month old male Sprague-Dawley rats, free of specific pathogens, were exposed to either 1.2 ppm NO{sub 2} or 0.3 ppm O{sub 3} alone, or a combination of the two oxidants continuously for 3 days. The oxidant effects were substantiated by determining total and differential cell counts, lactate dehydrogenase activity and total soluble protein in bronchoalveolar lavage. DNA damage was measured as single-strand breaks (SSB) by alkaline elution assay. The activation of poly (ADP-ribose) synthetase activity was used as an indicator of DNA repair. The results showed that, relative to control, NO{sub 2} exposure at 1.2 ppm did not cause any significant change in the parameters studied. Exposure to 0.3 PPM O{sub 3} and combined exposure to O{sub 3} and NO{sub 2} caused significant changes in all the parameters studied except cell viability. The changes for the combined exposure were synergistic for some of the parameters such as the number of polymorphonuclear neutrophil (PMN), the percentage of PMNs and pulmonary alveolar macrophage (PAM), and activity of poly(ADPR) synthetase. For the other parameters the increase was additive relative to the effects of O{sub 3} or NO{sub 2} alone. Exposure to O{sub 3} and NO{sub 2} increased the frequency of DNA-SSB in lung cells. This damage induced DNA repair process as shown by an increase in the poly(ADPR) synthetase activity which was synergistic with the combined exposure.

  4. Absence of chlamydial deoxyribonucleic acid from testicular and epididymal samples from men with obstructive azoospermia.

    PubMed

    Sripada, Sreebala; Amezaga, Maria Rosario; Hamilton, Mark; McKenzie, Hamish; Templeton, Allan; Bhattacharya, Siladitya

    2010-02-01

    To identify Chlamydia trachomatis DNA by polymerase chain reaction in the upper genital tract of men with obstructive azoospermia compared with men seeking vasectomy reversal. Case-control study. Tertiary referral center, Aberdeen Royal Infirmary, Aberdeen, United Kingdom. Cases were men with idiopathic obstructive azoospermia, and controls were men with azoospermia secondary to vasectomy. Chlamydia trachomatis-specific DNA test by polymerase chain reaction on testicular and epididymal biopsy samples, as well as epididymal aspirate. Presence of Chlamydia trachomatis DNA. We did not detect the presence of Chlamydia trachomatis-specific DNA by polymerase chain reaction in the epididymis or testis of 36 asymptomatic men with obstructive azoospermia (14 cases, 22 controls). Our hypothesis that unrecognized, asymptomatic chlamydial infection will lead to complete bilateral obstruction of the male genital tract remains unproven. Copyright 2010 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  5. [Epigenetic heredity (deoxyribonucleic acid methylation): Clinical context in neurodegenerative disorders and ATXN2 gene].

    PubMed

    Laffita-Mesa, José Miguel; Bauer, Peter

    2014-10-21

    Epigenetics is the group of changes in the phenotype which are related with the process independently of the primary DNA sequence. These changes are intimately related with changes in the gene expression level and its profile across the body. These are mediated by histone tail modifications, DNA methylation, micro-RNAs, with chromatin remodeling remaining as the foundation of epigenetic changes. DNA methylation involves the covalent addition of methyl group to cytosine of the DNA, which is mediated by methyltransferases enzymes. DNA methylation regulates gene expression by repressing transcription, while de-methylation activates gene transcription. Several human diseases are related with the epigenetic process: cancer, Alzheimer disease, stroke, Parkinson disease, and diabetes. We present here the basis of epigenetic inheritance and show the pathogenic mechanisms relating epigenetics in human diseases, specifically with regard to neurodegeneration. We discuss current concepts aimed at understanding the contribution of epigenetics to human neurodegenerative diseases. We also discuss recent findings obtained in our and other centers regarding the ATXN2 gene that causes spinocerebellar ataxia 2 and amyotrophic lateral sclerosis. Epigenetics play a pivotal role in the pathogenesis of human diseases and in several neurodegenerative disorders, and this knowledge will illuminate the pathways in the diagnostic and therapeutic field, which ultimately will be translated into the clinic context of neurodegenerative diseases. Copyright © 2013 Elsevier España, S.L.U. All rights reserved.

  6. Determination of mammalian deoxyribonucleic acid (DNA) in commercial vegetarian and vegan diets for dogs and cats.

    PubMed

    Kanakubo, K; Fascetti, A J; Larsen, J A

    2017-02-01

    The determination of undeclared ingredients in pet food using different analytical methods has been reported in recent years, raising concerns regarding adequate quality control, dietary efficacy and the potential for purposeful adulteration. The objective of this study was to determine the presence or absence of mammalian DNA using multiplex polymerase chain reaction (PCR) on diets marketed as vegetarian or vegan for dogs and cats. The diets were tested in duplicate; two samples were purchased approximately 3 to 4 months apart with different lot numbers. Multiplex PCR-targeted mitochondrial DNA with two species-specific primers was used to amplify and sequence two sections of the cytochrome b gene for each of the 11 mammalian species. Half of the diets assessed (7/14) were positive for one or more undeclared mammalian DNA source (bovine, porcine, or ovine), and the result was repeatable for one or more species in six diets. While most of the detected DNA was found at both time points, in some cases, the result was positive only at one time point, suggesting the presence may have been due to unintentional cross-contact with animal-sourced ingredients. DNA from feline, cervine, canine, caprine, equine, murine (mouse and rat) and leporine was not identified in any samples. However, evidence of mammalian DNA does not confirm adulteration by the manufacturer nor elucidate its clinical significance when consumed by animals that may benefit from a vegetarian or vegan diet.

  7. Comprehensive preimplantation genetic screening and sperm deoxyribonucleic acid fragmentation from three males carrying balanced chromosome rearrangements.

    PubMed

    Ramos, Laia; Daina, Gemma; Del Rey, Javier; Ribas-Maynou, Jordi; Fernández-Encinas, Alba; Martinez-Passarell, Olga; Boada, Montserrat; Benet, Jordi; Navarro, Joaquima

    2015-09-01

    To assess whether preimplantation genetic screening can successfully identify cytogenetically normal embryos in couples carrying balanced chromosome rearrangements in addition to increased sperm DNA fragmentation. Comprehensive preimplantation genetic screening was performed on three couples carrying chromosome rearrangements. Sperm DNA fragmentation was assessed for each patient. Academic center. One couple with the male partner carrying a chromosome 2 pericentric inversion and two couples with the male partners carrying a Robertsonian translocation (13:14 and 14:21, respectively). A single blastomere from each of the 18 cleavage-stage embryos obtained was analysed by metaphase comparative genomic hybridization. Single- and double-strand sperm DNA fragmentation was determined by the alkaline and neutral Comet assays. Single- and double-strand sperm DNA fragmentation values and incidence of chromosome imbalances in the blastomeres were analyzed. The obtained values of single-strand sperm DNA fragmentation were between 47% and 59%, and the double-strand sperm DNA fragmentation values were between 43% and 54%. No euploid embryos were observed in the couple showing the highest single-strand sperm DNA fragmentation. However, euploid embryos were observed in the other two couples: embryo transfer was performed, and pregnancy was achieved by the couple showing the lowest sperm DNA fragmentation values. Preimplantation genetic screening enables the detection of euploid embryos in couples affected by balanced chromosome rearrangements and increased sperm DNA fragmentation. Even though sperm DNA fragmentation may potentially have clinical consequences on fertility, comprehensive preimplantation genetic screening allows for the identification and transfer of euploid embryos. Copyright © 2015. Published by Elsevier Inc.

  8. Renal regulation of acid-base balance.

    PubMed

    Yucha, Carolyn

    2004-01-01

    Because maintaining a normal body pH is essential to the efficient functioning of many physiologic processes, the body has a number of mechanisms that prevent pH fluctuations. Some of these prevent minute-to-minute pH fluctuations over the course of the day, whereas others maintain pH balance from day to day. The kidney plays a key role in both processes. The renal process of bicarbonate reclamation prevents the loss of bicarbonate in the urine and, thus, maintains plasma levels of one substrate that is instrumental to preventing minute-to-minute pH fluctuations. The other renal process, bicarbonate regeneration, replenishes the body's supply of bicarbonate and, thus, maintains pH balance on a day-to-day basis. This article will discuss basic principles of acid-base physiology, the mechanisms that prevent fluctuations in body pH, and the renal processes involved in maintaining a homeostatic pH environment.

  9. Polymer gel dosimeter based on itaconic acid.

    PubMed

    Mattea, Facundo; Chacón, David; Vedelago, José; Valente, Mauro; Strumia, Miriam C

    2015-11-01

    A new polymeric dosimeter based on itaconic acid and N, N'-methylenebisacrylamide was studied. The preparation method, compositions of monomer and crosslinking agent and the presence of oxygen in the dosimetric system were analyzed. The resulting materials were irradiated with an X-ray tube at 158cGy/min, 226cGymin and 298cGy/min with doses up to 1000Gy. The dosimeters presented a linear response in the dose range 75-1000Gy, sensitivities of 0.037 1/Gyat 298cGy/min and an increase in the sensitivity with lower dose rates. One of the most relevant outcomes in this study was obtaining different monomer to crosslinker inclusion in the formed gel for the dosimeters where oxygen was purged during the preparation method. This effect has not been reported in other typical dosimeters and could be attributed to the large differences in the reactivity among these species. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. History of medical understanding and misunderstanding of Acid base balance.

    PubMed

    Aiken, Christopher Geoffrey Alexander

    2013-09-01

    To establish how controversies in understanding acid base balance arose, the literature on acid base balance was reviewed from 1909, when Henderson described how the neutral reaction of blood is determined by carbonic and organic acids being in equilibrium with an excess of mineral bases over mineral acids. From 1914 to 1930, Van Slyke and others established our acid base principles. They recognised that carbonic acid converts into bicarbonate all non-volatile mineral bases not bound by mineral acids and determined therefore that bicarbonate represents the alkaline reserve of the body and should be a physiological constant. They showed that standard bicarbonate is a good measure of acidosis caused by increased production or decreased elimination of organic acids. However, they recognised that bicarbonate improved low plasma bicarbonate but not high urine acid excretion in diabetic ketoacidosis, and that increasing pCO2 caused chloride to shift into cells raising plasma titratable alkali. Both indicate that minerals influence pH. In 1945 Darrow showed that hyperchloraemic metabolic acidosis in preterm infants fed milk with 5.7 mmol of chloride and 2.0 mmol of sodium per 100 kcal was caused by retention of chloride in excess of sodium. Similar findings were made but not recognised in later studies of metabolic acidosis in preterm infants. Shohl in 1921 and Kildeberg in 1978 presented the theory that carbonic and organic acids are neutralised by mineral base, where mineral base is the excess of mineral cations over anions and organic acid is the difference between mineral base, bicarbonate and protein anion. The degree of metabolic acidosis measured as base excess is determined by deviation in both mineral base and organic acid from normal.

  11. History of Medical Understanding and Misunderstanding of Acid Base Balance

    PubMed Central

    Aiken, Christopher Geoffrey Alexander

    2013-01-01

    To establish how controversies in understanding acid base balance arose, the literature on acid base balance was reviewed from 1909, when Henderson described how the neutral reaction of blood is determined by carbonic and organic acids being in equilibrium with an excess of mineral bases over mineral acids. From 1914 to 1930, Van Slyke and others established our acid base principles. They recognised that carbonic acid converts into bicarbonate all non-volatile mineral bases not bound by mineral acids and determined therefore that bicarbonate represents the alkaline reserve of the body and should be a physiological constant. They showed that standard bicarbonate is a good measure of acidosis caused by increased production or decreased elimination of organic acids. However, they recognised that bicarbonate improved low plasma bicarbonate but not high urine acid excretion in diabetic ketoacidosis, and that increasing pCO2 caused chloride to shift into cells raising plasma titratable alkali. Both indicate that minerals influence pH. In 1945 Darrow showed that hyperchloraemic metabolic acidosis in preterm infants fed milk with 5.7 mmol of chloride and 2.0 mmol of sodium per 100 kcal was caused by retention of chloride in excess of sodium. Similar findings were made but not recognised in later studies of metabolic acidosis in preterm infants. Shohl in 1921 and Kildeberg in 1978 presented the theory that carbonic and organic acids are neutralised by mineral base, where mineral base is the excess of mineral cations over anions and organic acid is the difference between mineral base, bicarbonate and protein anion. The degree of metabolic acidosis measured as base excess is determined by deviation in both mineral base and organic acid from normal. PMID:24179938

  12. Weak vs Strong Acids and Bases: The Football Analogy

    NASA Astrophysics Data System (ADS)

    Silverstein, Todd P.

    2000-07-01

    An important topic in any introductory chemistry course is that of acids and bases. Students generally have no trouble learning the Brønsted-Lowry definition of an acid as a proton donor and a base as a proton acceptor. Problems often arise, however, when chemistry teachers attempt to explain the difference between weak and strong acids, and between weak and strong bases. For acids in aqueous solution, discussing complete in contrast to partial ionization works well for those with a strong grasp of the equilibrium concept, but for many students it does not seem to do the trick. Partial ionization may not evoke much in the mind of a "visual learner". Accordingly, I have developed a football analogy for acids and bases in which acids are compared to quarterbacks, whose job is to get rid of the ball (H+). A strong acid, like an excellent quarterback, delivers the ball effectively; a weak acid, like a poor quarterback, is often left holding the ball. Furthermore, bases may be likened to wide receivers, whose job is to catch and hold onto the ball (H+). A strong base, like an excellent wide receiver, holds onto the ball; a weak base, like a poor receiver, often drops the ball. The concept of throwing and catching a ball is easy to visualize and the analogy to acids and bases can help even students unfamiliar with the mores of the gridiron to comprehend the mores of aqueous protons.

  13. Acid-Base Pairs in Lewis Acidic Zeolites Promote Direct Aldol Reactions by Soft Enolization.

    PubMed

    Lewis, Jennifer D; Van de Vyver, Stijn; Román-Leshkov, Yuriy

    2015-08-17

    Hf-, Sn-, and Zr-Beta zeolites catalyze the cross-aldol condensation of aromatic aldehydes with acetone under mild reaction conditions with near quantitative yields. NMR studies with isotopically labeled molecules confirm that acid-base pairs in the Si-O-M framework ensemble promote soft enolization through α-proton abstraction. The Lewis acidic zeolites maintain activity in the presence of water and, unlike traditional base catalysts, in acidic solutions.

  14. Determination of acidity constants of acid-base indicators by second-derivative spectrophotometry

    NASA Astrophysics Data System (ADS)

    Kara, Derya; Alkan, Mahir

    2000-12-01

    A method for calculation of acid-base dissociation constants of monoprotic weak organic acids whose acid and base species have overlapping spectra from absorptiometric and pH measurements is described. It has been shown that the second-derivative spectrophotometry can effectively be used for determining the dissociation constants, when dissociation constants obtained for methyl orange and bromothymol blue were compared with the values given in the literature.

  15. Acid-base status of biological fluids: amount of acid, kind of acid, anion-cation difference, and buffer value.

    PubMed

    Kildeberg, P

    1983-04-01

    A formal concept of amount of substance of 'acid' and 'base' is proposed which is based upon the change in extent of protolytic equilibria in an arbitrary reference state for the components of the system concerned and equally consistent with the Brønsted-Lowry terminology, the older medical 'anion-cation' terminology, and the operational principle of titration. It is shown how this concept allows formulations of the 'acid-base status' of biological fluids in accordance with various types of physiological, biochemical, or clinical problems. Finally, a general expression for buffer value is presented which is valid for any acid, base, or ampholyte at any pH.

  16. Chip-based sequencing nucleic acids

    DOEpatents

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  17. Assessment of acid-base balance. Stewart's approach.

    PubMed

    Fores-Novales, B; Diez-Fores, P; Aguilera-Celorrio, L J

    2016-04-01

    The study of acid-base equilibrium, its regulation and its interpretation have been a source of debate since the beginning of 20th century. Most accepted and commonly used analyses are based on pH, a notion first introduced by Sorensen in 1909, and on the Henderson-Hasselbalch equation (1916). Since then new concepts have been development in order to complete and make easier the understanding of acid-base disorders. In the early 1980's Peter Stewart brought the traditional interpretation of acid-base disturbances into question and proposed a new method. This innovative approach seems more suitable for studying acid-base abnormalities in critically ill patients. The aim of this paper is to update acid-base concepts, methods, limitations and applications.

  18. Phosphonic acid based ion exchange resins

    DOEpatents

    Horwitz, E. Philip; Alexandratos, Spiro D.; Gatrone, Ralph C.; Chiarizia, Ronato

    1996-01-01

    An ion exchange resin for extracting metal ions from a liquid waste stream. An ion exchange resin is prepared by copolymerizing a vinylidene diphosphonic acid with styrene, acrylonitrile and divinylbenzene.

  19. Phosphonic acid based ion exchange resins

    DOEpatents

    Horwitz, E. Philip; Alexandratos, Spiro D.; Gatrone, Ralph C.; Chiarizia, Ronato

    1994-01-01

    An ion exchange resin for extracting metal ions from a liquid waste stream. An ion exchange resin is prepared by copolymerizing a vinylidene disphosphonic acid with styrene, acrylonitrile and divinylbenzene.

  20. Phosphonic acid based ion exchange resins

    DOEpatents

    Horwitz, E.P.; Alexandratos, S.D.; Gatrone, R.C.; Chiarizia, R.

    1994-01-25

    An ion exchange resin is described for extracting metal ions from a liquid waste stream. An ion exchange resin is prepared by copolymerizing a vinylidene diphosphonic acid with styrene, acrylonitrile and divinylbenzene. 9 figures.

  1. Phosphonic acid based ion exchange resins

    DOEpatents

    Horwitz, E.P.; Alexandratos, S.D.; Gatrone, R.C.; Chiarizia, R.

    1996-07-23

    An ion exchange resin is described for extracting metal ions from a liquid waste stream. An ion exchange resin is prepared by copolymerizing a vinylidene diphosphonic acid with styrene, acrylonitrile and divinylbenzene. 10 figs.

  2. Calcium-based Lewis acid catalysts.

    PubMed

    Begouin, Jeanne-Marie; Niggemann, Meike

    2013-06-17

    Recently, Lewis acidic calcium salts bearing weakly coordinating anions such as Ca(NTf₂)₂, Ca(OTf)₂, CaF₂ and Ca[OCH(CF₃)₂]₂ have been discovered as catalysts for the transformation of alcohols, olefins and carbonyl compounds. High stability towards air and moisture, selectivity and high reactivity under mild reaction conditions render these catalysts a sustainable and mild alternative to transition metals, rare-earth metals or strong Brønsted acids.

  3. Advances in nucleic acid-based detection methods.

    PubMed Central

    Wolcott, M J

    1992-01-01

    Laboratory techniques based on nucleic acid methods have increased in popularity over the last decade with clinical microbiologists and other laboratory scientists who are concerned with the diagnosis of infectious agents. This increase in popularity is a result primarily of advances made in nucleic acid amplification and detection techniques. Polymerase chain reaction, the original nucleic acid amplification technique, changed the way many people viewed and used nucleic acid techniques in clinical settings. After the potential of polymerase chain reaction became apparent, other methods of nucleic acid amplification and detection were developed. These alternative nucleic acid amplification methods may become serious contenders for application to routine laboratory analyses. This review presents some background information on nucleic acid analyses that might be used in clinical and anatomical laboratories and describes some recent advances in the amplification and detection of nucleic acids. PMID:1423216

  4. The Roles of Acids and Bases in Enzyme Catalysis

    ERIC Educational Resources Information Center

    Weiss, Hilton M.

    2007-01-01

    Many organic reactions are catalyzed by strong acids or bases that protonate or deprotonate neutral reactants leading to reactive cations or anions that proceed to products. In enzyme reactions, only weak acids and bases are available to hydrogen bond to reactants and to transfer protons in response to developing charges. Understanding this…

  5. Acid-base properties of titanium-antimony oxides catalysts

    SciTech Connect

    Zenkovets, G.A.; Paukshtis, E.A.; Tarasova, D.V.; Yurchenko, E.N.

    1982-06-01

    The acid-base properties of titanium-antimony oxide catalysts were studied by the methods of back titration and ir spectroscopy. The interrelationship between the acid-base and catalytic properties in the oxidative ammonolysis of propylene was discussed. 3 figures, 1 table.

  6. A Closer Look at Acid-Base Olfactory Titrations

    ERIC Educational Resources Information Center

    Neppel, Kerry; Oliver-Hoyo, Maria T.; Queen, Connie; Reed, Nicole

    2005-01-01

    Olfactory titrations using raw onions and eugenol as acid-base indicators are reported. An in-depth investigation on olfactory titrations is presented to include requirements for potential olfactory indicators and protocols for using garlic, onions, and vanillin as acid-base olfactory indicators are tested.

  7. Luminol as a fluorescent acid-base indicator.

    PubMed

    Erdey, L; Buzás, I; Vigh, K

    1966-03-01

    The acid and base dissociation constants of luminol are determined at various ionic strengths. The transition interval occurs at pH 7.7-9.0, therefore luminol is a fluorescent indicator for the titration of strong and weak acids and strong bases. Its value as an indicator is established by titrating milk, red wine and cherry juice.

  8. A Closer Look at Acid-Base Olfactory Titrations

    ERIC Educational Resources Information Center

    Neppel, Kerry; Oliver-Hoyo, Maria T.; Queen, Connie; Reed, Nicole

    2005-01-01

    Olfactory titrations using raw onions and eugenol as acid-base indicators are reported. An in-depth investigation on olfactory titrations is presented to include requirements for potential olfactory indicators and protocols for using garlic, onions, and vanillin as acid-base olfactory indicators are tested.

  9. What is the Ultimate Goal in Acid-Base Regulation?

    ERIC Educational Resources Information Center

    Balakrishnan, Selvakumar; Gopalakrishnan, Maya; Alagesan, Murali; Prakash, E. Sankaranarayanan

    2007-01-01

    It is common to see chapters on acid-base physiology state that the goal of acid-base regulatory mechanisms is to maintain the pH of arterial plasma and not arterial PCO [subscript 2] (Pa[subscript CO[subscript 2

  10. The Roles of Acids and Bases in Enzyme Catalysis

    ERIC Educational Resources Information Center

    Weiss, Hilton M.

    2007-01-01

    Many organic reactions are catalyzed by strong acids or bases that protonate or deprotonate neutral reactants leading to reactive cations or anions that proceed to products. In enzyme reactions, only weak acids and bases are available to hydrogen bond to reactants and to transfer protons in response to developing charges. Understanding this…

  11. What is the Ultimate Goal in Acid-Base Regulation?

    ERIC Educational Resources Information Center

    Balakrishnan, Selvakumar; Gopalakrishnan, Maya; Alagesan, Murali; Prakash, E. Sankaranarayanan

    2007-01-01

    It is common to see chapters on acid-base physiology state that the goal of acid-base regulatory mechanisms is to maintain the pH of arterial plasma and not arterial PCO [subscript 2] (Pa[subscript CO[subscript 2

  12. Proton defect solvation and dynamics in aqueous acid and base.

    PubMed

    Kale, Seyit; Herzfeld, Judith

    2012-10-29

    Easy come, easy go: LEWIS, a new model of reactive and polarizable water that enables the simulation of a statistically reliable number of proton hopping events in aqueous acid and base at concentrations of practical interest, is used to evaluate proton transfer intermediates in aqueous acid and base (picture, left and right, respectively).

  13. Disorders of Acid-Base Balance: New Perspectives.

    PubMed

    Seifter, Julian L; Chang, Hsin-Yun

    2017-01-01

    Disorders of acid-base involve the complex interplay of many organ systems including brain, lungs, kidney, and liver. Compensations for acid-base disturbances within the brain are more complete, while limitations of compensations are more apparent for most systemic disorders. However, some of the limitations on compensations are necessary to survival, in that preservation of oxygenation, energy balance, cognition, electrolyte, and fluid balance are connected mechanistically. This review aims to give new and comprehensive perspective on understanding acid-base balance and identifying associated disorders. All metabolic acid-base disorders can be approached in the context of the relative losses or gains of electrolytes or a change in the anion gap in body fluids. Acid-base and electrolyte balance are connected not only at the cellular level but also in daily clinical practice. Urine chemistry is essential to understanding electrolyte excretion and renal compensations. Many constructs are helpful to understand acid-base, but these models are not mutually exclusive. Electroneutrality and the close interconnection between electrolyte and acid-base balance are important concepts to apply in acid-base diagnoses. All models have complexity and shortcuts that can help in practice. There is no reason to dismiss any of the present constructs, and there is benefit in a combined approach.

  14. A Modern Approach to Acid-Base Chemistry

    ERIC Educational Resources Information Center

    Drago, Russell S.

    1974-01-01

    Summarizes current status of our knowledge about acid-base interactions, including Lewis considerations, experimental design, data about donor-acceptor systems, common misconceptions, and hard-soft acid-base model. Indicates that there is the possibility of developing unifying concepts for chemical reactions of inorganic compounds. (CC)

  15. Connecting Acids and Bases with Encapsulation... and Chemistry with Nanotechnology

    ERIC Educational Resources Information Center

    Criswell, Brett

    2007-01-01

    The features and the development of various new acids and bases activity sets that combines chemistry with nanotechnology are being described. These sets lead to the generation of many nanotechnology-based pharmaceuticals for the treatment of various diseases.

  16. Connecting Acids and Bases with Encapsulation... and Chemistry with Nanotechnology

    ERIC Educational Resources Information Center

    Criswell, Brett

    2007-01-01

    The features and the development of various new acids and bases activity sets that combines chemistry with nanotechnology are being described. These sets lead to the generation of many nanotechnology-based pharmaceuticals for the treatment of various diseases.

  17. Partitioning of acidic, basic and neutral amino acids into imidazolium-based ionic liquids.

    PubMed

    Absalan, Ghodratollah; Akhond, Morteza; Sheikhian, Leila

    2010-06-01

    In this paper, partitioning behaviors of typical neutral (Alanine), acidic (Glutamic acid) and basic (Lysine) amino acids into imidazolium-based ionic liquids [C(4)mim][PF(6)], [C(6)mim][PF(6)], [C(8)mim][PF(6)], [C(6)mim][BF(4)] and [C(8)mim][BF(4)] as extracting solvents were examined. [C(6)mim][BF(4)] showed the best efficiency for partitioning of amino acids. The partition coefficients of amino acids in ionic liquids were found to depend strongly on pH of the aqueous solution, amino acid and ionic liquid chemical structures. Different chemical forms of amino acids in aqueous solutions were pH dependent, so the pH value of the aqueous phase was a determining factor for extraction of amino acids into ionic liquid phase. Both water content of ionic liquids and charge densities of their anionic and cationic parts were important factors for partitioning of cationic and anionic forms of amino acids into ionic liquid phase. Extracted amino acids were back extracted into phosphate buffer solutions adjusted on appropriate pH values. The results showed that ionic liquids could be used as suitable modifiers on the stationary phase of an HPLC column for efficient separation of acidic, basic, and neutral amino acids.

  18. A Computer-Based Simulation of an Acid-Base Titration

    ERIC Educational Resources Information Center

    Boblick, John M.

    1971-01-01

    Reviews the advantages of computer simulated environments for experiments, referring in particular to acid-base titrations. Includes pre-lab instructions and a sample computer printout of a student's use of an acid-base simulation. Ten references. (PR)

  19. Quantification of Lewis acid induced Brønsted acidity of protogenic Lewis bases.

    PubMed

    Lathem, A Paige; Heiden, Zachariah M

    2017-05-09

    Proton transfer promoted by the coordination of protogenic Lewis bases to a Lewis acid is a critical step in catalytic transformations. Although the acidification of water upon coordination to a Lewis acid has been known for decades, no attempts have been made to correlate the Brønsted acidity of the coordinated water molecule with Lewis acid strength. To probe this effect, the pKa's (estimated error of 1.3 pKa units) in acetonitrile of ten protogenic Lewis bases coordinated to seven Lewis acids containing Lewis acidities varying 70 kcal mol(-1), were computed. To quantify Lewis acid strength, the ability to transfer a hydride (hydride donor ability) from the respective main group hydride was used. Coordination of a Lewis acid to water increased the acidity of the bound water molecule between 20 and 50 pKa units. A linear correlation exhibiting a 2.6 pKa unit change of the Lewis acid-water adduct per ten kcal mol(-1) change in hydride donor ability of the respective main group hydride was obtained. For the ten protogenic Lewis bases studied, the coordinated protogenic Lewis bases were acidified between 10 and 50 pKa units. On average, a ten kcal mol(-1) change in hydride donor ability of the respective main group hydride resulted in about a 2.8 pKa unit change in the Brønsted acidity of the Lewis acid-Lewis base adducts. Since attempts to computationally investigate the pKa of main group dihydrogen complexes were unsuccessful, experimental determination of the first reported pKa of a main group dihydrogen complex is described. The pKa of H2-B(C6F5)3 was determined to be 5.8 ± 0.2 in acetonitrile.

  20. Ammonia Transporters and Their Role in Acid-Base Balance.

    PubMed

    Weiner, I David; Verlander, Jill W

    2017-04-01

    Acid-base homeostasis is critical to maintenance of normal health. Renal ammonia excretion is the quantitatively predominant component of renal net acid excretion, both under basal conditions and in response to acid-base disturbances. Although titratable acid excretion also contributes to renal net acid excretion, the quantitative contribution of titratable acid excretion is less than that of ammonia under basal conditions and is only a minor component of the adaptive response to acid-base disturbances. In contrast to other urinary solutes, ammonia is produced in the kidney and then is selectively transported either into the urine or the renal vein. The proportion of ammonia that the kidney produces that is excreted in the urine varies dramatically in response to physiological stimuli, and only urinary ammonia excretion contributes to acid-base homeostasis. As a result, selective and regulated renal ammonia transport by renal epithelial cells is central to acid-base homeostasis. Both molecular forms of ammonia, NH3 and NH4(+), are transported by specific proteins, and regulation of these transport processes determines the eventual fate of the ammonia produced. In this review, we discuss these issues, and then discuss in detail the specific proteins involved in renal epithelial cell ammonia transport. Copyright © 2017 the American Physiological Society.

  1. Nucleic acid duplexes incorporating a dissociable covalent base pair

    NASA Technical Reports Server (NTRS)

    Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    1999-01-01

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

  2. Nucleic acid duplexes incorporating a dissociable covalent base pair

    NASA Technical Reports Server (NTRS)

    Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    1999-01-01

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

  3. Nucleic Acid Duplexes Incorporating a Dissociable Covalent Base Pair

    NASA Astrophysics Data System (ADS)

    Gao, Kui; Orgel, Leslie E.

    1999-12-01

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

  4. [Acid-base imbalance in acute obstructive uropathies].

    PubMed

    Belyĭ, L E

    2007-01-01

    The aim of this study was to evaluate impairment of acid-base balance (ABB) in acute obstructive uropathies. Evaluation of acid-base balance was performed by pH, partial carbon dioxide pressure, plasma bicarbonate concentration, buffer bases, basis excess, hydrogen ion concentration. An automatic gas analyzer was used, plasma anion gap was calculated. Characteristic ABB alterations in different acute obstructive uropathies were detected. Acidotic shifts in acute obstruction of the upper urinary tracts and its inflammatory complications were assessed pathophysiologically. A comparative study of pathological acid-base disorders in acute supra- and infravesical obstructive uropathies was performed.

  5. General base-general acid catalysis by terpenoid cyclases.

    PubMed

    Pemberton, Travis A; Christianson, David W

    2016-07-01

    Terpenoid cyclases catalyze the most complex reactions in biology, in that more than half of the substrate carbon atoms often undergo changes in bonding during the course of a multistep cyclization cascade that proceeds through multiple carbocation intermediates. Many cyclization mechanisms require stereospecific deprotonation and reprotonation steps, and most cyclization cascades are terminated by deprotonation to yield an olefin product. The first bacterial terpenoid cyclase to yield a crystal structure was pentalenene synthase from Streptomyces exfoliatus UC5319. This cyclase generates the hydrocarbon precursor of the pentalenolactone family of antibiotics. The structures of pentalenene synthase and other terpenoid cyclases reveal predominantly nonpolar active sites typically lacking amino acid side chains capable of serving general base-general acid functions. What chemical species, then, enables the Brønsted acid-base chemistry required in the catalytic mechanisms of these enzymes? The most likely candidate for such general base-general acid chemistry is the co-product inorganic pyrophosphate. Here, we briefly review biological and nonbiological systems in which phosphate and its derivatives serve general base and general acid functions in catalysis. These examples highlight the fact that the Brønsted acid-base activities of phosphate derivatives are comparable to the Brønsted acid-base activities of amino acid side chains.

  6. Acid-base properties of 2-phenethyldithiocarbamoylacetic acid, an antitumor agent

    NASA Astrophysics Data System (ADS)

    Novozhilova, N. E.; Kutina, N. N.; Petukhova, O. A.; Kharitonov, Yu. Ya.

    2013-07-01

    The acid-base properties of the 2-phenethyldithiocarbamoylacetic acid (PET) substance belonging to the class of isothiocyanates and capable of inhibiting the development of tumors on many experimental models were studied. The acidity and hydrolysis constants of the PET substance in ethanol, acetone, aqueous ethanol, and aqueous acetone solutions were determined from the data of potentiometric (pH-metric) titration of ethanol and acetone solutions of PET with aqueous solidum hydroxide at room temperature.

  7. Bio-based production of methacrylic acid

    USDA-ARS?s Scientific Manuscript database

    Methacrylic acid (MAA) is an important industrial chemical commodity, with annual production exceeding 3 million metric tons and a market value surpassing $9 billion. The primary use of MAA is the conversion to ester derivatives, which are further converted into numerous useful polymers. Despite the...

  8. Molecular Dipole Osmosis Based on Induced Charge Electro-Osmosis

    NASA Astrophysics Data System (ADS)

    Sugioka, Hideyuki

    2016-09-01

    We propose a novel mechanism of producing a large nonlinear electrokinetic vortex flow around a nonconductive polar molecule in an electrolyte. That is, a large nonlinear electrokinetic slip velocity is derived by considering a local giant permittivity due to a molecular electric dipole moment with induced-charge electro-osmosis (ICEO). Different from the conventional ICEO theory, our theory predicts that a nonconductive biomaterial, such as a base of a deoxyribonucleic acid (DNA) molecule, has a significantly high ICEO flow velocity because of its large local permittivity. We consider that our findings will contribute markedly to promising biomedical applications.

  9. Reactive Distillation for Esterification of Bio-based Organic Acids

    SciTech Connect

    Fields, Nathan; Miller, Dennis J.; Asthana, Navinchandra S.; Kolah, Aspi K.; Vu, Dung; Lira, Carl T.

    2008-09-23

    The following is the final report of the three year research program to convert organic acids to their ethyl esters using reactive distillation. This report details the complete technical activities of research completed at Michigan State University for the period of October 1, 2003 to September 30, 2006, covering both reactive distillation research and development and the underlying thermodynamic and kinetic data required for successful and rigorous design of reactive distillation esterification processes. Specifically, this project has led to the development of economical, technically viable processes for ethyl lactate, triethyl citrate and diethyl succinate production, and on a larger scale has added to the overall body of knowledge on applying fermentation based organic acids as platform chemicals in the emerging biorefinery. Organic acid esters constitute an attractive class of biorenewable chemicals that are made from corn or other renewable biomass carbohydrate feedstocks and replace analogous petroleum-based compounds, thus lessening U.S. dependence on foreign petroleum and enhancing overall biorefinery viability through production of value-added chemicals in parallel with biofuels production. Further, many of these ester products are candidates for fuel (particularly biodiesel) components, and thus will serve dual roles as both industrial chemicals and fuel enhancers in the emerging bioeconomy. The technical report from MSU is organized around the ethyl esters of four important biorenewables-based acids: lactic acid, citric acid, succinic acid, and propionic acid. Literature background on esterification and reactive distillation has been provided in Section One. Work on lactic acid is covered in Sections Two through Five, citric acid esterification in Sections Six and Seven, succinic acid in Section Eight, and propionic acid in Section Nine. Section Ten covers modeling of ester and organic acid vapor pressure properties using the SPEAD (Step Potential

  10. Assessing Acid-Base Status: Physiologic Versus Physicochemical Approach.

    PubMed

    Adrogué, Horacio J; Madias, Nicolaos E

    2016-11-01

    The physiologic approach has long been used in assessing acid-base status. This approach considers acids as hydrogen ion donors and bases as hydrogen ion acceptors and the acid-base status of the organism as reflecting the interaction of net hydrogen ion balance with body buffers. In the physiologic approach, the carbonic acid/bicarbonate buffer pair is used for assessing acid-base status and blood pH is determined by carbonic acid (ie, Paco2) and serum bicarbonate levels. More recently, the physicochemical approach was introduced, which has gained popularity, particularly among intensivists and anesthesiologists. This approach posits that the acid-base status of body fluids is determined by changes in the dissociation of water that are driven by the interplay of 3 independent variables: the sum of strong (fully dissociated) cation concentrations minus the sum of strong anion concentrations (strong ion difference); the total concentration of weak acids; and Paco2. These 3 independent variables mechanistically determine both hydrogen ion concentration and bicarbonate concentration of body fluids, which are considered as dependent variables. Our experience indicates that the average practitioner is familiar with only one of these approaches and knows very little, if any, about the other approach. In the present Acid-Base and Electrolyte Teaching Case, we attempt to bridge this knowledge gap by contrasting the physiologic and physicochemical approaches to assessing acid-base status. We first outline the essential features, advantages, and limitations of each of the 2 approaches and then apply each approach to the same patient presentation. We conclude with our view about the optimal approach. Copyright © 2016 National Kidney Foundation, Inc. All rights reserved.

  11. Polymerization of amino acids containing nucleotide bases

    NASA Technical Reports Server (NTRS)

    Ben Cheikh, Azzouz; Orgel, Leslie E.

    1990-01-01

    The nucleoamino acids 1-(3'-amino,3'-carboxypropyl)uracil (3) and 9-(3'-amino,3'-carboxypropyl)adenine (4) have been prepared as (L)-en-antiomers and as racemic mixtures. When 3 or 4 is suspended in water and treated with N,N'-carbon-yldiimidazole, peptides are formed in good yield. The products formed from the (L)-enantiomers are hydrolyzed to the monomeric amino acids by pronase. Attempts to improve the efficiency of these oligomerizations by including a polyuridylate template in the reaction mixture were not successful. Similarly, oligomers derived from the (L)-enantiomer of 3 did not act as templates to facilitate the oligomerization of 4.

  12. Polymerization of amino acids containing nucleotide bases

    NASA Technical Reports Server (NTRS)

    Ben Cheikh, Azzouz; Orgel, Leslie E.

    1990-01-01

    The nucleoamino acids 1-(3'-amino,3'-carboxypropyl)uracil (3) and 9-(3'-amino,3'-carboxypropyl)adenine (4) have been prepared as (L)-en-antiomers and as racemic mixtures. When 3 or 4 is suspended in water and treated with N,N'-carbon-yldiimidazole, peptides are formed in good yield. The products formed from the (L)-enantiomers are hydrolyzed to the monomeric amino acids by pronase. Attempts to improve the efficiency of these oligomerizations by including a polyuridylate template in the reaction mixture were not successful. Similarly, oligomers derived from the (L)-enantiomer of 3 did not act as templates to facilitate the oligomerization of 4.

  13. Carbon-based strong solid acid for cornstarch hydrolysis

    SciTech Connect

    Nata, Iryanti Fatyasari; Irawan, Chairul; Mardina, Primata; Lee, Cheng-Kang

    2015-10-15

    Highly sulfonated carbonaceous spheres with diameter of 100–500 nm can be generated by hydrothermal carbonization of glucose in the presence of hydroxyethylsulfonic acid and acrylic acid at 180 °C for 4 h. The acidity of the prepared carbonaceous sphere C4-SO{sub 3}H can reach 2.10 mmol/g. It was used as a solid acid catalyst for the hydrolysis of cornstarch. Total reducing sugar (TRS) concentration of 19.91 mg/mL could be obtained by hydrolyzing 20 mg/mL cornstarch at 150 °C for 6 h using C4-SO{sub 3}H as solid acid catalyst. The solid acid catalyst demonstrated good stability that only 9% decrease in TRS concentration was observed after five repeat uses. The as-prepared carbon-based solid acid catalyst can be an environmentally benign replacement for homogeneous catalyst. - Highlights: • Carbon solid acid was successfully prepared by one-step hydrothermal carbonization. • The acrylic acid as monomer was effectively reduce the diameter size of particle. • The solid acid catalyst show good catalytic performance of starch hydrolysis. • The solid acid catalyst is not significantly deteriorated after repeated use.

  14. Nucleic Acid-Based Nanodevices in Biological Imaging.

    PubMed

    Chakraborty, Kasturi; Veetil, Aneesh T; Jaffrey, Samie R; Krishnan, Yamuna

    2016-06-02

    The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid-based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid-based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand.

  15. Nucleic Acid--Based Nanodevices in Biological Imaging

    PubMed Central

    Chakraborty, Kasturi; Veetil, Aneesh T.

    2017-01-01

    The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid--based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid--based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand. PMID:27294440

  16. Acid-base properties of adhesive dental polymers.

    PubMed

    Morra, M

    1993-11-01

    The surface energetics of three resins (polymethylmethacrylate, polyhydroxyethylmethacrylate, and Bis-GMA/triethyleneglycoldimethacrylate) commonly used in adhesive interactions with tooth hard tissues were evaluated according to the Fowkes acid-base theory of interfacial interactions. From the measurement of the contact angle of test acidic and basic liquids on the sample surfaces, the acid-base contribution to the work of adhesion was evaluated. Results show that polyhydroxyethylmethacrylate is a comparatively strong Lewis base, a finding that can explain the important role played by this material in the formulation of dentin adhesive.

  17. Respiratory Acid-Base Disorders in the Critical Care Unit.

    PubMed

    Hopper, Kate

    2017-03-01

    The incidence of respiratory acid-base abnormalities in the critical care unit (CCU) is unknown, although respiratory alkalosis is suspected to be common in this population. Abnormal carbon dioxide tension can have many physiologic effects, and changes in Pco2 may have a significant impact on outcome. Monitoring Pco2 in CCU patients is an important aspect of critical patient assessment, and identification of respiratory acid-base abnormalities can be valuable as a diagnostic tool. Treatment of respiratory acid-base disorders is largely focused on resolution of the primary disease, although mechanical ventilation may be indicated in cases with severe respiratory acidosis. Published by Elsevier Inc.

  18. Differential titration of bases in glacial acetic acid.

    PubMed

    Castellano, T; Medwick, T; Shinkai, J H; Bailey, L

    1981-01-01

    A study of bases in acetic acid and their differential titration was carried out. The overall basicity constants for 20 bases were measured in acetic acid, and the differential titration of five binary mixtures of variable delta pKb values in acetic acid was followed using a glass electrode-modified calomel electrode system. Agreement with literature values was good. A leveling diagram was constructed that indicated that bases stronger than aqueous pKb 10 are leveled to an acetous pKb 5.69, whereas weaker bases are not leveled but instead exhibit their own intrinsic basicity, with the acetous pKb to aqueous pKb values being linearly related (slope 1.18, correlation coefficient 0.962). A minimum acetous delta pKb of four units is required for the satisfactory differential titration of two bases in acetic acid.

  19. The acid-base titration of montmorillonite

    NASA Astrophysics Data System (ADS)

    Bourg, I. C.; Sposito, G.; Bourg, A. C.

    2003-12-01

    Proton binding to clay minerals plays an important role in the chemical reactivity of soils (e.g., acidification, retention of nutrients or pollutants). If should also affect the performance of clay barriers for waste disposal. The surface acidity of clay minerals is commonly modelled empirically by assuming generic amphoteric surface sites (>SOH) on a flat surface, with fitted site densities and acidity constant. Current advances in experimental methods (notably spectroscopy) are rapidly improving our understanding of the structure and reactivity of the surface of clay minerals (arrangement of the particles, nature of the reactive surface sites, adsorption mechanisms). These developments are motivated by the difficulty of modelling the surface chemistry of mineral surfaces at the macro-scale (e.g., adsorption or titration) without a detailed (molecular-scale) picture of the mechanisms, and should be progressively incorporated into surface complexation models. In this view, we have combined recent estimates of montmorillonite surface properties (surface site density and structure, edge surface area, surface electrostatic potential) with surface site acidities obtained from the titration of alpha-Al2O3 and SiO2, and a novel method of accounting for the unknown initial net proton surface charge of the solid. The model predictions were compared to experimental titrations of SWy-1 montmorillonite and purified MX-80 bentonite in 0.1-0.5 mol/L NaClO4 and 0.005-0.5 mol/L NaNO3 background electrolytes, respectively. Most of the experimental data were appropriately described by the model after we adjusted a single parameter (silanol sites on the surface of montmorillonite were made to be slightly more acidic than those of silica). At low ionic strength and acidic pH the model underestimated the buffering capacity of the montmorillonite, perhaps due to clay swelling or to the interlayer adsorption of dissolved aluminum. The agreement between our model and the experimental

  20. Nucleic acid based fluorescent sensor for mercury detection

    DOEpatents

    Lu, Yi; Liu, Juewen

    2013-02-05

    A nucleic acid enzyme comprises an oligonucleotide containing thymine bases. The nucleic acid enzyme is dependent on both Hg.sup.2+and a second ion as cofactors, to produce a product from a substrate. The substrate comprises a ribonucleotide, a deoxyribonucleotide, or both.

  1. Boronic acid-tethered amphiphilic hyaluronic acid derivative-based nanoassemblies for tumor targeting and penetration.

    PubMed

    Jeong, Jae Young; Hong, Eun-Hye; Lee, Song Yi; Lee, Jae-Young; Song, Jae-Hyoung; Ko, Seung-Hak; Shim, Jae-Seong; Choe, Sunghwa; Kim, Dae-Duk; Ko, Hyun-Jeong; Cho, Hyun-Jong

    2017-02-16

    (3-Aminomethylphenyl)boronic acid (AMPB)-installed hyaluronic acid-ceramide (HACE)-based nanoparticles (NPs), including manassantin B (MB), were fabricated for tumor-targeted delivery. The amine group of AMPB was conjugated to the carboxylic acid group of hyaluronic acid (HA) via amide bond formation, and synthesis was confirmed by spectroscopic methods. HACE-AMPB/MB NPs with a 239-nm mean diameter, narrow size distribution, negative zeta potential, and >90% drug encapsulation efficiency were fabricated. Exposed AMPB in the outer surface of HACE-AMPB NPs (in the aqueous environment) may react with sialic acid of cancer cells. The improved cellular accumulation efficiency, in vitro antitumor efficacy, and tumor penetration efficiency of HACE-AMPB/MB NPs, compared with HACE/MB NPs, in MDA-MB-231 cells (CD44 receptor-positive human breast adenocarcinoma cells) may be based on the CD44 receptor-mediated endocytosis and phenylboronic acid-sialic acid interaction. Enhanced in vivo tumor targetability, infiltration efficiency, and antitumor efficacies of HACE-AMPB NPs, compared with HACE NPs, were observed in a MDA-MB-231 tumor-xenografted mouse model. In addition to passive tumor targeting (based on an enhanced permeability and retention effect) and active tumor targeting (interaction between HA and CD44 receptor), the phenylboronic acid-sialic acid interaction can play important roles in augmented tumor targeting and penetration of HACE-AMPB NPs. STATEMENT OF SIGNIFICANCE: (3-Aminomethylphenyl)boronic acid (AMPB)-tethered hyaluronic acid-ceramide (HACE)-based nanoparticles (NPs), including manassantin B (MB), were fabricated and their tumor targeting and penetration efficiencies were assessed in MDA-MB-231 (CD44 receptor-positive human adenocarcinoma) tumor models. MB, which exhibited antitumor efficacies via the inhibition of angiogenesis and hypoxia inducible factor (HIF)-1, was entrapped in HACE-AMPB NPs in this study. Phenylboronic acid located in the outer surface

  2. Acid-base titration curves for acids with very small ratios of successive dissociation constants.

    PubMed

    Campbell, B H; Meites, L

    1974-02-01

    The shapes of the potentiometric acid-base titration curves obtained in the neutralizations of polyfunctional acids or bases for which each successive dissociation constant is smaller than the following one are examined. In the region 0 < < 1 (where is the fraction of the equivalent volume of reagent that has been added) the slope of the titration curve decreases as the number j of acidic or basic sites increases. The difference between the pH-values at = 0.75 and = 0.25 has (1 j)log 9 as the lower limit of its maximum value.

  3. Renal acidification responses to respiratory acid-base disorders.

    PubMed

    Madias, Nicolaos E

    2010-01-01

    Respiratory acid-base disorders are those abnormalities in acid-base equilibrium that are expressed as primary changes in the arterial carbon dioxide tension (PaCO2). An increase in PaCO2 (hypercapnia) acidifies body fluids and initiates the acid-base disturbance known as respiratory acidosis. By contrast, a decrease in PaCO2 (hypocapnia) alkalinizes body fluids and initiates the acid-base disturbance known as respiratory alkalosis. The impact on systemic acidity of these primary changes in PaCO2 is ameliorated by secondary, directional changes in plasma [HCO3¯] that occur in 2 stages. Acutely, hypercapnia or hypocapnia yields relatively small changes in plasma [HCO3¯] that originate virtually exclusively from titration of the body's nonbicarbonate buffers. During sustained hypercapnia or hypocapnia, much larger changes in plasma [HCO3¯] occur that reflect adjustments in renal acidification mechanisms. Consequently, the deviation of systemic acidity from normal is smaller in the chronic forms of these disorders. Here we provide an overview of the renal acidification responses to respiratory acid-base disorders. We also identify gaps in knowledge that require further research.

  4. An Olfactory Indicator for Acid-Base Titrations.

    ERIC Educational Resources Information Center

    Flair, Mark N.; Setzer, William N.

    1990-01-01

    The use of an olfactory acid-base indicator in titrations for visually impaired students is discussed. Potential olfactory indicators include eugenol, thymol, vanillin, and thiophenol. Titrations performed with each indicator with eugenol proved to be successful. (KR)

  5. Teaching acid/base physiology in the laboratory.

    PubMed

    Friis, Ulla G; Plovsing, Ronni; Hansen, Klaus; Laursen, Bent G; Wallstedt, Birgitta

    2010-12-01

    Acid/base homeostasis is one of the most difficult subdisciplines of physiology for medical students to master. A different approach, where theory and practice are linked, might help students develop a deeper understanding of acid/base homeostasis. We therefore set out to develop a laboratory exercise in acid/base physiology that would provide students with unambiguous and reproducible data that clearly would illustrate the theory in practice. The laboratory exercise was developed to include both metabolic acidosis and respiratory alkalosis. Data were collected from 56 groups of medical students that had participated in this laboratory exercise. The acquired data showed very consistent and solid findings after the development of both metabolic acidosis and respiratory alkalosis. All results were consistent with the appropriate diagnosis of the acid/base disorder. Not one single group failed to obtain data that were compatible with the diagnosis; it was only the degree of acidosis/alkalosis and compensation that varied.

  6. Acid-base and potassium disorders in liver disease.

    PubMed

    Ahya, Shubhada N; José Soler, Maria; Levitsky, Josh; Batlle, Daniel

    2006-11-01

    Acid-base and potassium disorders occur frequently in the setting of liver disease. As the liver's metabolic function worsens, particularly in the setting of renal dysfunction, hemodynamic compromise, and hepatic encephalopathy, acid-base disorders ensue. The most common acid-base disorder is respiratory alkalosis. Metabolic acidosis alone or in combination with respiratory alkalosis also is common. Acid-base disorders in patients with liver disease are complex. The urine anion gap may help to distinguish between chronic respiratory alkalosis and hyperchloremic metabolic acidosis when a blood gas is not available. A negative urine anion gap helps to rule out chronic respiratory alkalosis. In this disorder a positive urine anion gap is expected owing to suppressed urinary acidification. Distal renal tubular acidosis occurs in autoimmune liver disease such as primary biliary cirrhosis, but often is a functional defect from impaired distal sodium delivery. Potassium disorders are often the result of the therapies used to treat advanced liver disease.

  7. Biologist's Toolbox. Acid-base Balance: An Educational Computer Game.

    ERIC Educational Resources Information Center

    Boyle, Joseph, III; Robinson, Gloria

    1987-01-01

    Describes a microcomputer program that can be used in teaching the basic physiological aspects of acid-base (AB) balance. Explains how its game format and graphic approach can be applied in diagnostic and therapeutic exercises. (ML)

  8. Towards lactic acid bacteria-based biorefineries.

    PubMed

    Mazzoli, Roberto; Bosco, Francesca; Mizrahi, Itzhak; Bayer, Edward A; Pessione, Enrica

    2014-11-15

    Lactic acid bacteria (LAB) have long been used in industrial applications mainly as starters for food fermentation or as biocontrol agents or as probiotics. However, LAB possess several characteristics that render them among the most promising candidates for use in future biorefineries in converting plant-derived biomass-either from dedicated crops or from municipal/industrial solid wastes-into biofuels and high value-added products. Lactic acid, their main fermentation product, is an attractive building block extensively used by the chemical industry, owing to the potential for production of polylactides as biodegradable and biocompatible plastic alternative to polymers derived from petrochemicals. LA is but one of many high-value compounds which can be produced by LAB fermentation, which also include biofuels such as ethanol and butanol, biodegradable plastic polymers, exopolysaccharides, antimicrobial agents, health-promoting substances and nutraceuticals. Furthermore, several LAB strains have ascertained probiotic properties, and their biomass can be considered a high-value product. The present contribution aims to provide an extensive overview of the main industrial applications of LAB and future perspectives concerning their utilization in biorefineries. Strategies will be described in detail for developing LAB strains with broader substrate metabolic capacity for fermentation of cheaper biomass.

  9. Synthesis and antimicrobial activities of new higher amino acid Schiff base derivatives of 6-aminopenicillanic acid and 7-aminocephalosporanic acid

    NASA Astrophysics Data System (ADS)

    Özdemir (nee Güngör), Özlem; Gürkan, Perihan; Özçelik, Berrin; Oyardı, Özlem

    2016-02-01

    Novel β-lactam derivatives (1c-3c) (1d-3d) were produced by using 6-aminopenicillanic acid (6-APA), 7-aminocephalosporanic acid (7-ACA) and the higher amino acid Schiff bases. The synthesized compounds were characterized by elemental analysis, IR, 1H/13C NMR and UV-vis spectra. Antibacterial activities of all the higher amino acid Schiff bases (1a-3a) (1b-3b) and β-lactam derivatives were screened against three gram negative bacteria (Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Acinetobacter baumannii RSKK 02026), three gram positive bacteria (Staphylococcus aureus ATCC 25923, Enterococcus faecalis ATCC 07005, Bacillus subtilis ATCC 6633) and their drug-resistant isolates by using broth microdilution method. Two fungi (Candida albicans and Candida krusei) were used for antifungal activity.

  10. Acid-base homeostasis in the human system

    NASA Technical Reports Server (NTRS)

    White, R. J.

    1974-01-01

    Acid-base regulation is a cooperative phenomena in vivo with body fluids, extracellular and intracellular buffers, lungs, and kidneys all playing important roles. The present account is much too brief to be considered a review of present knowledge of these regulatory systems, and should be viewed, instead, as a guide to the elements necessary to construct a simple model of the mutual interactions of the acid-base regulatory systems of the body.

  11. TRANSFUSIONS—Hazardous Acid-Base Changes with Citrated Blood

    PubMed Central

    Pedro, Jovita M. San; Iwai, Seizo; Hattori, Mitsuo; Leigh, M. Digby

    1962-01-01

    In a study of the acid-base changes in the blood of rabbits during and following transfusions of citrated blood and of heparinized blood, it was observed that, with citrated blood, pH decreased and carbon dioxide tensions rose. With heparinized blood, the acid-base balance was maintained within normal limits following transfusions. The potential hazards of rapid massive citrated blood transfusions in the anesthetized patient during operation must be kept in mind. PMID:14496706

  12. Synthesis of polyacrylic-acid-based thermochromic polymers

    NASA Astrophysics Data System (ADS)

    Srivastava, Jyoti; Alam, Sarfaraz; Mathur, G. N.

    2003-10-01

    Smart materials respond to environmental stimuli with particular changes in some variables (for example temperature, pressure and electric field etc), for that reason they are often called responsive materials. In the present work, we have synthesized thermochromic polymer based on poly acrylic acid cobalt chloride (CoCl2) and phosphoric acid (H3PO4) that visually and reversibly changes color in the temperature range (70 - 130°C). These thermochromic materials can be used as visual sensors of temperature. Thermochromic polymers are based on polyacrylic acid and CoCl2 complex.

  13. Acid Base Titrations in Nonaqueous Solvents and Solvent Mixtures

    NASA Astrophysics Data System (ADS)

    Barcza, Lajos; Buvári-Barcza, Ágnes

    2003-07-01

    The acid base determination of different substances by nonaqueous titrations is highly preferred in pharmaceutical analyses since the method is quantitative, exact, and reproducible. The modern interpretation of the reactions in nonaqueous solvents started in the last century, but several inconsistencies and unsolved problems can be found in the literature. The acid base theories of Brønsted Lowry and Lewis as well as the so-called solvent theory are outlined first, then the promoting (and leveling) and the differentiating effects are discussed on the basis of the hydrogen-bond concept. Emphasis is put on the properties of formic acid and acetic anhydride since their importance is increasing.

  14. A clinical approach to paediatric acid-base disorders.

    PubMed

    Carmody, J Bryan; Norwood, Victoria F

    2012-03-01

    Acid-base disorders are common in pediatric patients. We present a simple methodology for assessing both simple and complex acid-base disorders that is applicable to patients of all ages, and focus specifically on the usefulness of this approach in the pediatric patient. The application of four simple rules in sequence will define even the most complicated acid-base disturbance. However, because acid-base disorders are manifestations of systemic disorders, the primary value of characterizing them is that each generates a unique differential diagnosis. For each of the cardinal acid base disorders, the common and clinically-relevant causes in pediatric patients are explored. Additional diagnostic tools (including the serum anion gap, the delta-delta, the alveolar-arterial gradient, urine anion gap, and urine chloride), certain easily-recalled mnemonics, and empiric rules of thumb are also useful in specific situations. The treatment of acid-base disturbances is also considered, though treatment is generally best directed at the underlying disorder.

  15. Tailoring peritoneal dialysis fluid for optimal acid-base targets.

    PubMed

    Feriani, Mariano

    2009-01-01

    Mild derangements of acid-base status are common features in peritoneal dialysis patients, metabolic acidosis being the most frequent alteration. One of the main tasks of dialysis is to correct these derangements and the target is the normalization of the acid-base parameters since they affect several organs and functions. Since factors affecting acid-base homeostasis are intrinsic characteristics of the individual patient (metabolic acid production, distribution space for bicarbonate, dialytic prescription, etc.), it is not surprising that only relatively few patients achieve the normal range. Only a certain modulation of buffer infusion by using different buffer concentrations in the dialysis fluid may ensure a good correction in a large percentage of patients.

  16. HF acid blends based on formation conditions eliminate precipitation problems

    SciTech Connect

    Gdanski, R.; Shuchart, C.

    1997-03-01

    Formulating HCl-HF acid blends based on the mineralogy and temperature of a formation can increase the success of hydrofluoric acid (HF) treatments. Sodium and potassium in the structures of formation minerals can cause precipitation and matrix plugging problems during acidizing. Slight modifications of the acid blend used in the treatment can help eliminate fluosilicate precipitation. Researchers recently conducted tests to determine how acid blends react in different formations under varying temperatures. The results of the tests indicate that the minimum HCl:HF ratio in an acid blend is 6-to-1, and the optimum ratio is 9-to-1. Regular mud acid (12% HCl-3% HF) has been used successfully for years to enhance production in sandstone formations. By the 1980s, operators began to vary the concentration of HF and HCl acids to solve excessive sanding problems in sandstone. The paper discusses treatment problems, formation characteristics, alumino-silicate scaling, research results, brine compatibility, optimum treatment, and acid volume guidelines.

  17. An Acid-Base Chemistry Example: Conversion of Nicotine

    NASA Astrophysics Data System (ADS)

    Summerfield, John H.

    1999-10-01

    The current government interest in nicotine conversion by cigarette companies provides an example of acid-base chemistry that can be explained to students in the second semester of general chemistry. In particular, the conversion by ammonia of the +1 form of nicotine to the easier-to-assimilate free-base form illustrates the effect of pH on acid-base equilibrium. The part played by ammonia in tobacco smoke is analogous to what takes place when cocaine is "free-based".

  18. Effect of acute acid loading on acid-base and calcium metabolism.

    PubMed

    Osther, Palle J

    2006-01-01

    To investigate the acid-base and calcium metabolic responses to acute non-carbonic acid loading in idiopathic calcium stone-formers and healthy males using a quantitative organ physiological approach. Five-h ammonium chloride loading studies were performed in 12 male recurrent idiopathic calcium stone-formers and 12 matched healthy men using a randomized, placebo-controlled, cross-over design. Arterialized capillary blood, serum and urine were collected hourly for measurement of electrolytes, ionized calcium, magnesium, phosphate, parathyroid hormone and acid-base status. Concentrations of non-metabolizable base (NB) and acid (NA) were calculated from measured concentrations of non-metabolizable ions. The extracellular acid-base status in the stone-formers during basal conditions and acid loading was comparable to the levels in the healthy controls. The stone-formers tended to have lower renal excretion rates of NA during acid loading; however, for a given degree of non-carbonic acidosis, controls and stone-formers excreted approximately the same amount of NA in the urine, suggesting that the capacity of tubular regeneration of NB was comparable in the two groups. Acid loading resulted in significantly increased concentrations of ionized calcium in serum in both controls and stone-formers. The increase in serum ionized calcium in response to acid loading was, however, significantly higher in the calcium stone-formers than in the healthy individuals. Acid loading resulted in massive calciuria in both groups, with significantly higher urinary calcium excretion rates in the stone-formers compared to the healthy subjects. Renal excretion rates of NA correlated significantly with renal calcium excretion rates in both groups. However, the stone-formers excreted significantly more calcium in the urine at a given rate of renal NA excretion. The hypercalciuric and hypercalcaemic responses to loading with non-carbonic acid are more pronounced in recurrent idiopathic calcium

  19. Disturbed acid-base transport: an emerging cause of hypertension

    PubMed Central

    Boedtkjer, Ebbe; Aalkjaer, Christian

    2013-01-01

    Genome-wide association studies and physiological investigations have linked alterations in acid-base transporters to hypertension. Accordingly, Na+-coupled HCO−3-transporters, Na+/H+-exchangers, and anion-exchangers have emerged as putative mechanistic components in blood pressure disturbances. Even though hypertension has been studied extensively over the last several decades, the cause of the high blood pressure has in most cases not been identified. Renal, cardiovascular, and neuronal dysfunctions all seem to play a role in hypertension development but their relative importance and mutual interdependency are still being debated. Multiple functional and structural alterations have been described in patients and animals with hypertension but it is typically unclear whether they are causes or consequences of hypertension or represent mechanistically unrelated associations. Perturbed blood pressure regulation has been demonstrated in several animal models with disrupted expression of acid-base transporters; and reciprocally, disturbed acid-base transport function has been described in hypertensive individuals. In addition to regulating intracellular and extracellular pH, Na+-coupled HCO−3-transport, Na+/H+-exchange, and anion-exchange also contribute to water and electrolyte balance in cells and systemically. Since acid-base transporters are widely expressed, alterations in transport activities likely affect multiple cell and organ functions, and it is a significant challenge to determine the mechanisms linking perturbed acid-base transport function to hypertension. It is the purpose of this review to evaluate the current evidence for involvement of acid-base transporters in hypertension development and discuss the cellular and integrative mechanisms, which may link changes in acid-base transport to blood pressure disturbances. PMID:24399970

  20. Study of acid-base equilibria of fleroxacin.

    PubMed

    Popović, G; Milovanović, L; Kapetanović, V

    1998-12-01

    The acid-base equilibria of fleroxacin were studied by means of potentiometry and spectrophotometry. It was established that fleroxacin undergoes a complex acid-base equilibrium due to its zwitterionic nature and two proton-binding sites of similar acidity. The stoichiometric equilibrium constants were determined at 25 degrees C and constant ionic strength 0.1 M (NaCl). The acidity constants pK1 = 5.59 +/- 0.01 and pK2 = 8.08 +/- 0.04 were found by potentiometry, and pK1 = 5.61 +/- 0.03 and pK2 = 8.11 +/- 0.06 by spectrophotometry. The distribution diagram of the corresponding ionic species is given.

  1. Poly (ricinoleic acid) based novel thermosetting elastomer.

    PubMed

    Ebata, Hiroki; Yasuda, Mayumi; Toshima, Kazunobu; Matsumura, Shuichi

    2008-01-01

    A novel bio-based thermosetting elastomer was prepared by the lipase-catalyzed polymerization of methyl ricinoleate with subsequent vulcanization. Some mechanical properties of the cured carbon black-filled polyricinoleate compounds were evaluated as a thermosetting elastomer. It was found that the carbon black-filled polyricinoleate compounds were readily cured by sulfur curatives to produce a thermosetting elastomer that formed a rubber-like sheet with a smooth and non-sticky surface. The curing behaviors and mechanical properties were dependent on both the molecular weight of the polyricinoleate and the amount of the sulfur curatives. Cured compounds consisting of polyricinoleate with a molecular weight of 100,800 showed good mechanical properties, such as a hardness of 48 A based on the durometer A measurements, a tensile strength at break of 6.91 MPa and an elongation at break of 350%.

  2. Amino acid profile of milk-based infant formulas.

    PubMed

    Viadel, B; Alegriá, A; Farré, R; Abellán, P; Romero, F

    2000-09-01

    The protein content and amino acid profile of three milk-based infant formulas, two of which were powdered (adapted and follow-on) and the third liquid, were determined to check their compliance with the EU directive and to evaluate whether or not they fulfil an infant's nutritional needs. To obtain the amino acid profile proteins were subjected to acid hydrolysis, prior to which the sulfur-containing amino acids were oxidized with performic acid. The amino acids were derivatized with phenylisothiocyanate (PITC) and then determined by ion-pair reverse phase high performance liquid chromatography (HPLC) In the case of tryptophan a basic hydrolysis was applied and there was no need of derivatization. The protein contents of the analysed formulas were in the ranges established by the EU directive for these products and the amino acid contents were in the ranges reported by other authors for these types of formulas. In all cases the tryptophan content determined the value of the chemical score, which was always lower than 80% of the reference protein but in the ranges reported by other authors. The analysed adapted infant formula provides amino acids in amounts higher than the established nutritional requirements.

  3. Nanopore-based sequencing and detection of nucleic acids.

    PubMed

    Ying, Yi-Lun; Zhang, Junji; Gao, Rui; Long, Yi-Tao

    2013-12-09

    Nanopore-based techniques, which mimic the functions of natural ion channels, have attracted increasing attention as unique methods for single-molecule detection. The technology allows the real-time, selective, high-throughput analysis of nucleic acids through both biological and solid-state nanopores. In this Minireview, the background and latest progress in nanopore-based sequencing and detection of nucleic acids are summarized, and light is shed on a novel platform for nanopore-based detection. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Soil Studies: Applying Acid-Base Chemistry to Environmental Analysis.

    ERIC Educational Resources Information Center

    West, Donna M.; Sterling, Donna R.

    2001-01-01

    Laboratory activities for chemistry students focus attention on the use of acid-base chemistry to examine environmental conditions. After using standard laboratory procedures to analyze soil and rainwater samples, students use web-based resources to interpret their findings. Uses CBL probes and graphing calculators to gather and analyze data and…

  5. High School Students' Concepts of Acids and Bases.

    ERIC Educational Resources Information Center

    Ross, Bertram H. B.

    An investigation of Ontario high school students' understanding of acids and bases with quantitative and qualitative methods revealed misconceptions. A concept map, based on the objectives of the Chemistry Curriculum Guideline, generated multiple-choice items and interview questions. The multiple-choice test was administered to 34 grade 12…

  6. Soil Studies: Applying Acid-Base Chemistry to Environmental Analysis.

    ERIC Educational Resources Information Center

    West, Donna M.; Sterling, Donna R.

    2001-01-01

    Laboratory activities for chemistry students focus attention on the use of acid-base chemistry to examine environmental conditions. After using standard laboratory procedures to analyze soil and rainwater samples, students use web-based resources to interpret their findings. Uses CBL probes and graphing calculators to gather and analyze data and…

  7. Hard and soft acids and bases: atoms and atomic ions.

    PubMed

    Reed, James L

    2008-07-07

    The structural origin of hard-soft behavior in atomic acids and bases has been explored using a simple orbital model. The Pearson principle of hard and soft acids and bases has been taken to be the defining statement about hard-soft behavior and as a definition of chemical hardness. There are a number of conditions that are imposed on any candidate structure and associated property by the Pearson principle, which have been exploited. The Pearson principle itself has been used to generate a thermodynamically based scale of relative hardness and softness for acids and bases (operational chemical hardness), and a modified Slater model has been used to discern the electronic origin of hard-soft behavior. Whereas chemical hardness is a chemical property of an acid or base and the operational chemical hardness is an experimental measure of it, the absolute hardness is a physical property of an atom or molecule. A critical examination of chemical hardness, which has been based on a more rigorous application of the Pearson principle and the availability of quantitative measures of chemical hardness, suggests that the origin of hard-soft behavior for both acids and bases resides in the relaxation of the electrons not undergoing transfer during the acid-base interaction. Furthermore, the results suggest that the absolute hardness should not be taken as synonymous with chemical hardness but that the relationship is somewhat more complex. Finally, this work provides additional groundwork for a better understanding of chemical hardness that will inform the understanding of hardness in molecules.

  8. Ionic liquid supported acid/base-catalyzed production of biodiesel.

    PubMed

    Lapis, Alexandre A M; de Oliveira, Luciane F; Neto, Brenno A D; Dupont, Jairton

    2008-01-01

    The transesterification (alcoholysis) reaction was successfully applied to synthesize biodiesel from vegetable oils using imidazolium-based ionic liquids under multiphase acidic and basic conditions. Under basic conditions, the combination of the ionic liquid 1-n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BMINTf2), alcohols, and K2CO3 (40 mol %) results in the production of biodiesel from soybean oil in high yields (>98%) and purity. H2SO4 immobilized in BMINTf2 efficiently promotes the transesterification reaction of soybean oil and various primary and secondary alcohols. In this multiphase process the acid is almost completely retained in the ionic liquid phase, while the biodiesel forms a separate phase. The recovered ionic liquid containing the acid could be reused at least six times without any significant loss in the biodiesel yield or selectivity. In both catalytic processes (acid and base), the reactions proceed as typical multiphasic systems in which the formed biodiesel accumulates as the upper phase and the glycerol by-product is selectively captured by the alcohol-ionic liquid-acid/base phase. Classical ionic liquids such as 1-n-butyl-3-methylimidazolium tetrafluoroborate and hexafluorophosphate are not stable under these acidic or basic conditions and decompose.

  9. A computational study of ultrafast acid dissociation and acid-base neutralization reactions. I. The model

    NASA Astrophysics Data System (ADS)

    Maurer, Patrick; Thomas, Vibin; Rivard, Ugo; Iftimie, Radu

    2010-07-01

    Ultrafast, time-resolved investigations of acid-base neutralization reactions have recently been performed using systems containing the photoacid 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS) and various Brønsted bases. Two conflicting neutralization mechanisms have been formulated by Mohammed et al. [Science 310, 83 (2005)] and Siwick et al. [J. Am. Chem. Soc. 129, 13412 (2007)] for the same acid-base system. Herein an ab initio molecular dynamics based computational model is formulated, which is able to investigate the validity of the proposed mechanisms in the general context of ground-state acid-base neutralization reactions. Our approach consists of using 2,4,6-tricyanophenol (exp. pKa≅1) as a model for excited-state HPTS∗ (pKa≅1.4) and carboxylate ions for the accepting base. We employ our recently proposed dipole-field/quantum mechanics (QM) treatment [P. Maurer and R. Iftimie, J. Chem. Phys. 132, 074112 (2010)] of the proton donor and acceptor molecules. This approach allows one to tune the free energy of neutralization to any desired value as well as model initial nonequilibrium hydration effects caused by a sudden increase in acidity, making it possible to achieve a more realistic comparison with experimental data than could be obtained via a full-QM treatment of the entire system. It is demonstrated that the dipole-field/QM model reproduces correctly key properties of the 2,4,6-tricyanophenol acid molecule including gas-phase proton dissociation energies and dipole moments, and condensed-phase hydration structure and pKa values.

  10. A computational study of ultrafast acid dissociation and acid-base neutralization reactions. I. The model.

    PubMed

    Maurer, Patrick; Thomas, Vibin; Rivard, Ugo; Iftimie, Radu

    2010-07-28

    Ultrafast, time-resolved investigations of acid-base neutralization reactions have recently been performed using systems containing the photoacid 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS) and various Bronsted bases. Two conflicting neutralization mechanisms have been formulated by Mohammed et al. [Science 310, 83 (2005)] and Siwick et al. [J. Am. Chem. Soc. 129, 13412 (2007)] for the same acid-base system. Herein an ab initio molecular dynamics based computational model is formulated, which is able to investigate the validity of the proposed mechanisms in the general context of ground-state acid-base neutralization reactions. Our approach consists of using 2,4,6-tricyanophenol (exp. pKa congruent with 1) as a model for excited-state HPTS( *) (pKa congruent with 1.4) and carboxylate ions for the accepting base. We employ our recently proposed dipole-field/quantum mechanics (QM) treatment [P. Maurer and R. Iftimie, J. Chem. Phys. 132, 074112 (2010)] of the proton donor and acceptor molecules. This approach allows one to tune the free energy of neutralization to any desired value as well as model initial nonequilibrium hydration effects caused by a sudden increase in acidity, making it possible to achieve a more realistic comparison with experimental data than could be obtained via a full-QM treatment of the entire system. It is demonstrated that the dipole-field/QM model reproduces correctly key properties of the 2,4,6-tricyanophenol acid molecule including gas-phase proton dissociation energies and dipole moments, and condensed-phase hydration structure and pKa values.

  11. Acid-base properties of humic and fulvic acids formed during composting.

    PubMed

    Plaza, César; Senesi, Nicola; Polo, Alfredo; Brunetti, Gennaro

    2005-09-15

    The soil acid-base buffering capacity and the biological availability, mobilization, and transport of macro- and micronutrients, toxic metal ions, and xenobiotic organic cations in soil are strongly influenced by the acid-base properties of humic substances, of which humic and fulvic acids are the major fractions. For these reasons, the proton binding behavior of the humic acid-like (HA) and fulvic acid-like (FA) fractions contained in a compost are believed to be instrumental in its successful performance in soil. In this work, the acid-base properties of the HAs and FAs isolated from a mixture of the sludge residue obtained from olive oil mill wastewater (OMW) evaporated in an open-air pond and tree cuttings (TC) at different stages of composting were investigated by a current potentiometric titration method and the nonideal competitive adsorption (NICA)-Donnan model. The NICA-Donnan model provided an excellent description of the acid-base titration data, and pointed out substantial differences in site density and proton-binding affinity between the HAs and FAs examined. With respect to FAs, HAs were characterized by a smaller content of carboxylic- and phenolic-type groups and their larger affinities for proton binding. Further, HAs featured a greater heterogeneity in carboxylic-type groups than FAs. The composting process increased the content and decreased the proton affinity of carboxylic- and phenolic-type groups of HAs and FAs, and increased the heterogeneity of phenolic-type groups of HAs. As a whole, these effects indicated that the composting process could produce HA and FA fractions with greater cation binding capacities. These results suggest that composting of organic materials improves their agronomic and environmental value by increasing their potential to retain and exchange macro- and micronutrients, and to reduce the bioavailability of organic and inorganic pollutants.

  12. Synthesis and characterization of boric acid mediated metal-organic frameworks based on trimesic acid and terephthalic acid

    NASA Astrophysics Data System (ADS)

    Ozer, Demet; Köse, Dursun A.; Şahin, Onur; Oztas, Nursen Altuntas

    2017-08-01

    The new metal-organic framework materials based on boric acid reported herein. Sodium and boron containing metal-organic frameworks were synthesized by one-pot self-assembly reaction in the presence of trimesic acid and terephthalic acid in water/ethanol solution. Boric acid is a relatively cheap boron source and boric acid mediated metal-organic framework prepared mild conditions compared to the other boron source based metal-organic framework. The synthesized compounds were characterized by FT-IR, p-XRD, TGA/DTA, elemental analysis, 13C-MAS NMR, 11B-NMR and single crystal measurements. The molecular formulas of compounds were estimated as C18H33B2Na5O28 and C8H24B2Na2O17 according to the structural analysis. The obtained complexes were thermally stable. Surface properties of inorganic polymer complexes were investigated by BET analyses and hydrogen storage properties of compound were also calculated.

  13. Acid-base patterns in acute severe asthma.

    PubMed

    Raimondi, Guillermo A; Gonzalez, Silvia; Zaltsman, Jorge; Menga, Guillermo; Adrogué, Horacio J

    2013-12-01

    Acid-base status in acute severe asthma (ASA) remains undefined; some studies report complete absence of metabolic acidosis, whereas others describe it as present in one fourth of patients or more. Conclusion discrepancies would therefore appear to derive from differences in assessment methodology. Only a systematic approach centering on patient clinical findings can correctly establish true acid-base disorder prevalence levels. This study examines acid-base patterns in ASA (314 patients), taking into account both natural history of disease and treatment, in patients free of other diseases altering acid-base status. Data were collected from patients admitted for ASA without prior history of chronic bronchitis, emphysema, kidney or liver disease, heart failure, uncontrolled diabetes mellitus or gastrointestinal illness. Informed consent was obtained for all patients, after study protocol approval by the Institutional Review Board. Arterial blood gases, plasma electrolytes, lactate levels, and FEV(1) were measured on arrival. Severe airway obstruction was found with FEV(1) values of 25.6 ± 10.0%, substantial hypoxemia (PaO(2) 66.1 ± 11.9 mmHg) and increased A-a O(2) gradient (39.3 ± 12.3 mmHg) breathing room air. While respiratory alkalosis occurred in patients with better preservation of FEV1, respiratory acidosis was observed with more severe airway obstruction, as was increased lactate in the majority of patients, independent of PaO(2) and PaCO(2) levels. Predominant acid-base patterns observed in ASA in this patient population included primary hypocapnia, or less frequently, primary hypercapnia. Lactic acidosis occurred in 11% of patients and presented consistently as a mixed acid-base disorder. These findings suggest lactic acidosis results from the combined effects of both ASA and medication-related sympathetic effects.

  14. Acid-Base Titration of (S)-Aspartic Acid: A Circular Dichroism Spectrophotometry Experiment

    NASA Astrophysics Data System (ADS)

    Cavaleiro, Ana M. V.; Pedrosa de Jesus, Júlio D.

    2000-09-01

    The magnitude of the circular dichroism of (S)-aspartic acid in aqueous solutions at a fixed wavelength varies with the addition of strong base. This laboratory experiment consists of the circular dichroism spectrophotometric acid-base titration of (S)-aspartic acid in dilute aqueous solutions, and the use of the resulting data to determine the ionization constant of the protonated amino group. The work familiarizes students with circular dichroism and illustrates the possibility of performing titrations using a less usual instrumental method of following the course of a reaction. It shows the use of a chiroptical property in the determination of the concentration in solution of an optically active molecule, and exemplifies the use of a spectrophotometric titration in the determination of an ionization constant.

  15. Relativistic effects on acidities and basicities of Brønsted acids and bases containing gold.

    PubMed

    Koppel, Ilmar A; Burk, Peeter; Kasemets, Kalev; Koppel, Ivar

    2013-11-07

    It is usually believed that relativistic effects as described by the Dirac-Schrödinger equation (relative to the classical or time-independent Schrödinger equation) are of little importance in chemistry. A closer look, however, reveals that some important and widely known properties (e.g., gold is yellow, mercury is liquid at room temperature) stem from relativistic effects. So far the influence of relativistic effects on the acid-base properties has been mostly ignored. Here we show that at least for compounds of gold such omission is completely erroneous and would lead to too high basicity and too low acidity values with errors in the range of 25-55 kcal mol(-1) (or 20 to 44 powers of ten in pK(a) units) in the gas-phase. These findings have important implications for the design of new superstrong acids and bases, and for the understanding of gold-catalysed reactions.

  16. Simultaneous spectrophotometric determination of benzoic acid, sorbic acid, and ascorbic acid using a net analyte signal-based method.

    PubMed

    Naseri, Abdolhossein; Ghorbani-Kalhor, Ebrahim; Vallipour, Javad; Jafari, Samira; Shahverdizadeh, Gholam Hossein; Asadpour-Zeynali, Karim

    2009-01-01

    The net analyte preprocessing/classical least-squares (NAP/CLS) method is a simple chemometric method that has been used for the simultaneous spectrophotometric determination of benzoic acid, sorbic acid, and ascorbic acid. The obtained results indicated that the performances of the NAP/CLS and partial least-squares methods were almost identical. The net analyte signal (NAS) concept was also used to calculate multivariate analytical figures of merit, such as LOD, selectivity, and sensitivity. Wavelength selection was applied based on the concept of NAS regression, and improved the method performance in samples containing nonmodeled interferences. The method afforded recoveries in the range of 98-105%. The proposed method was successfully applied to determination of the analytes in an Iranian soft drink.

  17. Nucleic acid-based nanoengineering: novel structures for biomedical applications

    PubMed Central

    Li, Hanying; LaBean, Thomas H.; Leong, Kam W.

    2011-01-01

    Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson–Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine. PMID:23050076

  18. Crystal and molecular structure of eight organic acid-base adducts from 2-methylquinoline and different acids

    NASA Astrophysics Data System (ADS)

    Zhang, Jing; Jin, Shouwen; Tao, Lin; Liu, Bin; Wang, Daqi

    2014-08-01

    Eight supramolecular complexes with 2-methylquinoline and acidic components as 4-aminobenzoic acid, 2-aminobenzoic acid, salicylic acid, 5-chlorosalicylic acid, 3,5-dinitrosalicylic acid, malic acid, sebacic acid, and 1,5-naphthalenedisulfonic acid were synthesized and characterized by X-ray crystallography, IR, mp, and elemental analysis. All of the complexes are organic salts except compound 2. All supramolecular architectures of 1-8 involve extensive classical hydrogen bonds as well as other noncovalent interactions. The results presented herein indicate that the strength and directionality of the classical hydrogen bonds (ionic or neutral) between acidic components and 2-methylquinoline are sufficient to bring about the formation of binary organic acid-base adducts. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. These weak interactions combined, the complexes 1-8 displayed 2D-3D framework structure.

  19. Design of cinnamaldehyde amino acid Schiff base compounds based on the quantitative structure–activity relationship

    Treesearch

    Hui Wang; Mingyue Jiang; Shujun Li; Chung-Yun Hse; Chunde Jin; Fangli Sun; Zhuo Li

    2017-01-01

    Cinnamaldehyde amino acid Schiff base (CAAS) is a new class of safe, bioactive compounds which could be developed as potential antifungal agents for fungal infections. To design new cinnamaldehyde amino acid Schiff base compounds with high bioactivity, the quantitative structure–activity relationships (QSARs) for CAAS compounds against Aspergillus niger (A. niger) and...

  20. Elucidating the hard/soft acid/base principle: a perspective based on half-reactions.

    PubMed

    Ayers, Paul W; Parr, Robert G; Pearson, Ralph G

    2006-05-21

    A comprehensive analysis is presented for the acid-base double-exchange reaction as well as the associated acid-displacement and base-displacement "half-reactions" with the goal of elucidating the meaning of the hard/soft acid/base (HSAB) principle and the conditions for its validity. When electron-transfer effects are important and other effects are negligible, the HSAB principle is driven by the surpassing stability of the soft acid/soft base product. When electrostatic effects dominate the reactivity, the HSAB principle is driven by the surpassing stability of the hard acid/hard base product. Because electron-transfer effects favor soft/soft interactions, while electrostatic effects favor hard/hard interactions, acid-base exchange reactions may be used to determine whether a reagent's reactivity is dominated by electron-transfer or by electrostatic effects. Because electron-transfer and electrostatic considerations separately favor the HSAB principle whenever the electronic chemical potentials of the acids and bases involved in the reaction are similar, our analysis provides strong support for the HSAB principle. The electronic chemical potential measures the intrinsic strength of acids and bases.

  1. Acid-base metabolism: implications for kidney stones formation.

    PubMed

    Hess, Bernhard

    2006-04-01

    The physiology and pathophysiology of renal H+ ion excretion and urinary buffer systems are reviewed. The main focus is on the two major conditions related to acid-base metabolism that cause kidney stone formation, i.e., distal renal tubular acidosis (dRTA) and abnormally low urine pH with subsequent uric acid stone formation. Both the entities can be seen on the background of disturbances of the major urinary buffer system, NH3+ <--> NH4+. On the one hand, reduced distal tubular secretion of H+ ions results in an abnormally high urinary pH and either incomplete or complete dRTA. On the other hand, reduced production/availability of NH4+ is the cause of an abnormally low urinary pH, which predisposes to uric acid stone formation. Most recent research indicates that the latter abnormality may be a renal manifestation of the increasingly prevalent metabolic syndrome. Despite opposite deviations from normal urinary pH values, both the dRTA and uric acid stone formation due to low urinary pH require the same treatment, i.e., alkali. In the dRTA, alkali is needed for improving the body's buffer capacity, whereas the goal of alkali treatment in uric acid stone formers is to increase the urinary pH to 6.2-6.8 in order to minimize uric acid crystallization.

  2. Current chemical concepts of acids and bases and their application to anionic ("acid") and cationic ("basic") dyes.

    PubMed

    Puchtler, H; Meloan, S N; Spencer, M

    1985-01-01

    In biomedical studies, dyes are divided into "acid" and "basic" dyes. This classification cannot be reconciled with current chemical definitions of acids and bases. Brönsted-Lowry acids are compounds that can donate protons; bases are proton acceptors. The definition of acids and bases is independent of the electric charge, i.e. acids and bases can be neutral, anionic or cationic. Reactions between acids and bases result in formation of new acid-base pairs. Lewis acids and bases do not depend on a particular element, but are characterized by their electronic configurations. Lewis bases are electron donors; Lewis acids are electron acceptors. This classification is also unrelated to the electric charge. Lewis acids and bases interact by formation of coordinate covalent bonds. In histochemistry and histology, dyes containing -SO3-, -COO- and/or -O- groups are classified as "acid" dyes. However, such compounds are electron pair donors and hence Brönsted-Lowry and Lewis anionic bases. Dyes carrying a positive charge are termed "basic" dyes. Chemically, many cationic dyes are Lewis acids because they can add a base, e.g. OH-, acetate, halides. The hypothesis that transformation of -NH2 into ammonium groups imparts "basic" properties to dyes is untenable; ammonium groups are proton donors and hence acids. Furthermore, conversion of an amino into an ammonium group blocks a lone electron pair and the color of the dye changes drastically, e.g. from violet to green and yellow. It appears therefore highly unlikely that ammonium groups are responsible for binding of cationic ("basic") dyes. In histochemistry, it is usually not of critical importance whether anionic or cationic dyes are chemically acids or bases.(ABSTRACT TRUNCATED AT 250 WORDS)

  3. Dynamic Buffer Capacity in Acid-Base Systems.

    PubMed

    Michałowska-Kaczmarczyk, Anna M; Michałowski, Tadeusz

    The generalized concept of 'dynamic' buffer capacity βV is related to electrolytic systems of different complexity where acid-base equilibria are involved. The resulting formulas are presented in a uniform and consistent form. The detailed calculations are related to two Britton-Robinson buffers, taken as examples.

  4. Students' Understanding of Acids/Bases in Organic Chemistry Contexts

    ERIC Educational Resources Information Center

    Cartrette, David P.; Mayo, Provi M.

    2011-01-01

    Understanding key foundational principles is vital to learning chemistry across different contexts. One such foundational principle is the acid/base behavior of molecules. In the general chemistry sequence, the Bronsted-Lowry theory is stressed, because it lends itself well to studying equilibrium and kinetics. However, the Lewis theory of…

  5. Using Spreadsheets to Produce Acid-Base Titration Curves.

    ERIC Educational Resources Information Center

    Cawley, Martin James; Parkinson, John

    1995-01-01

    Describes two spreadsheets for producing acid-base titration curves, one uses relatively simple cell formulae that can be written into the spreadsheet by inexperienced students and the second uses more complex formulae that are best written by the teacher. (JRH)

  6. Linear titration plots for polyfunctional weak acids and bases.

    PubMed

    Midgley, D; McCallum, C

    1976-04-01

    Procedures are derived for obtaining the equivalence volumes in the potentiometric titrations of polyfunctional weak acids and weak bases by a linear titration plot method. The effect of errors in the equilibrium constants on the accuracy is considered. A Fortran program is available to do the calculations.

  7. Acid-Base Disorders--A Computer Simulation.

    ERIC Educational Resources Information Center

    Maude, David L.

    1985-01-01

    Describes and lists a program for Apple Pascal Version 1.1 which investigates the behavior of the bicarbonate-carbon dioxide buffer system in acid-base disorders. Designed specifically for the preclinical medical student, the program has proven easy to use and enables students to use blood gas parameters to arrive at diagnoses. (DH)

  8. Turkish Prospective Chemistry Teachers' Alternative Conceptions about Acids and Bases

    ERIC Educational Resources Information Center

    Boz, Yezdan

    2009-01-01

    The purpose of this study was to obtain prospective chemistry teachers' conceptions about acids and bases concepts. Thirty-eight prospective chemistry teachers were the participants. Data were collected by means of an open-ended questionnaire and semi-structured interviews. Analysis of data indicated that most prospective teachers did not have…

  9. Evolution of Acid-Base Concept (1917-1984).

    ERIC Educational Resources Information Center

    Gamble, James L., Jr.

    1984-01-01

    Evaluates the accuracy and usefulness of a simpler rationale for teaching acid-base physiology as compared to more complex approaches frequently taught in physiology courses. Also reviews problems of terminology, giving emphasis to the significant effects that the choice of words can have on students' concepts. (JN)

  10. Turkish Prospective Chemistry Teachers' Alternative Conceptions about Acids and Bases

    ERIC Educational Resources Information Center

    Boz, Yezdan

    2009-01-01

    The purpose of this study was to obtain prospective chemistry teachers' conceptions about acids and bases concepts. Thirty-eight prospective chemistry teachers were the participants. Data were collected by means of an open-ended questionnaire and semi-structured interviews. Analysis of data indicated that most prospective teachers did not have…

  11. Students' Understanding of Acids/Bases in Organic Chemistry Contexts

    ERIC Educational Resources Information Center

    Cartrette, David P.; Mayo, Provi M.

    2011-01-01

    Understanding key foundational principles is vital to learning chemistry across different contexts. One such foundational principle is the acid/base behavior of molecules. In the general chemistry sequence, the Bronsted-Lowry theory is stressed, because it lends itself well to studying equilibrium and kinetics. However, the Lewis theory of…

  12. An approach to complex acid-base problems

    PubMed Central

    Herd, Anthony M.

    2005-01-01

    OBJECTIVE To review rules and formulas for solving even the most complex acid-base problems. SOURCES OF INFORMATION MEDLINE was searched from January 1966 to December 2003. The search was limited to English-language review articles involving human subjects. Nine relevant review papers were found and provide the background. As this information is well established and widely accepted, it is not judged for strength of evidence, as is standard practice. MAIN MESSAGE An understanding of the body’s responses to acidemia or alkalemia can be gained through a set of four rules and two formulas that can be used to interpret almost any acid-base problems. Physicians should, however, remember the “golden rule” of acid-base interpretation: always look at a patient’s clinical condition. CONCLUSION Physicians practising in acute care settings commonly encounter acid-base disturbances. While some of these are relatively simple and easy to interpret, some are more complex. Even complex cases can be resolved using the four rules and two formulas. PMID:15751566

  13. Acid-Base Disorders--A Computer Simulation.

    ERIC Educational Resources Information Center

    Maude, David L.

    1985-01-01

    Describes and lists a program for Apple Pascal Version 1.1 which investigates the behavior of the bicarbonate-carbon dioxide buffer system in acid-base disorders. Designed specifically for the preclinical medical student, the program has proven easy to use and enables students to use blood gas parameters to arrive at diagnoses. (DH)

  14. Hard and soft acids and bases: small molecules.

    PubMed

    Reed, James L

    2009-08-03

    The operational chemical hardness has been determined for the hydride, chloride, and fluoride derivatives of the anionic atomic bases of the second period. Of interest is the identification of the structure and associated processes that give rise to hard-soft behavior in small molecules. The Pearson Principle of Hard and Soft Acids and Bases has been taken to be the defining statement about hard-soft behavior and as a definition of chemical hardness. Similar to the case for atoms, the molecule's responding electrons have been identified as the structure giving rise to hard-soft behavior, and a relaxation described by a modified Slater model has been identified as the associated process. The responding electrons are the molecule's valence electrons that are not undergoing electron transfer in an acid-base interaction. However, it has been demonstrated that chemical hardness is a local property, and only those responding electrons that are associated with the base's binding atom directly impact chemical hardness.

  15. Plasmonics-based SERS nanobiosensor for homogeneous nucleic acid detection.

    PubMed

    Wang, Hsin-Neng; Fales, Andrew M; Vo-Dinh, Tuan

    2015-05-01

    Developing a simple and efficient nucleic acid detection technology is essential for clinical diagnostics. Here, we describe a new conceptually simple and selective "turn on" plasmonics-based nanobiosensor, which integrates non-enzymatic DNA strand-displacement hybridization for specific nucleic acid target identification with surface-enhanced Raman scattering (SERS) detection. This SERS nanobiosensor is a target label-free, and rapid nanoparticle-based biosensing system using a homogeneous assay format that offers a simple and efficient tool for nucleic acid diagnostics. Our results showed that the nanobiosensor provided a limit of detection of ~0.1nM (200amol) in the current bioassay system, and exhibited high specificity for single nucleotide mismatch discrimination. Surface-enhanced Raman scattering (SERS) is a sensitive technique that enhances Raman scattering by molecules adsorbed on rough metal surfaces. The enhancement means that the technique may even detect single molecules. In this article, the authors describe a simple and efficient nucleic acid detection technology using SERS, with "OFF-to-ON" signal switch upon nucleic acid target identification and capture, which provides high sensitivity and specificity for single nucleotide mismatch discrimination. This new technology will be most welcomed in clinical diagnostics. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Enzymes for fatty acid-based hydrocarbon biosynthesis.

    PubMed

    Herman, Nicolaus A; Zhang, Wenjun

    2016-12-01

    Surging energy consumption and environmental concerns have stimulated interest in the production of chemicals and fuels through sustainable and renewable approaches. Fatty acid-based hydrocarbons, such as alkanes and alkenes, are of particular interest to directly replace fossil fuels. Towards this effort, understanding of hydrocarbon-producing enzymes is the first indispensable step to bio-production of hydrocarbons. Here, we review recent advances in the discovery and mechanistic study of enzymes capable of converting fatty acid precursors into hydrocarbons, and provide perspectives on the future of this rapidly growing field. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Acid-base transport in pancreas—new challenges

    PubMed Central

    Novak, Ivana; Haanes, Kristian A.; Wang, Jing

    2013-01-01

    Along the gastrointestinal tract a number of epithelia contribute with acid or basic secretions in order to aid digestive processes. The stomach and pancreas are the most extreme examples of acid (H+) and base (HCO−3) transporters, respectively. Nevertheless, they share the same challenges of transporting acid and bases across epithelia and effectively regulating their intracellular pH. In this review, we will make use of comparative physiology to enlighten the cellular mechanisms of pancreatic HCO−3 and fluid secretion, which is still challenging physiologists. Some of the novel transporters to consider in pancreas are the proton pumps (H+-K+-ATPases), as well as the calcium-activated K+ and Cl− channels, such as KCa3.1 and TMEM16A/ANO1. Local regulators, such as purinergic signaling, fine-tune, and coordinate pancreatic secretion. Lastly, we speculate whether dys-regulation of acid-base transport contributes to pancreatic diseases including cystic fibrosis, pancreatitis, and cancer. PMID:24391597

  18. Coulometric titration of bases in acetic acid and acetonitrile media.

    PubMed

    Vajgand, V J; Mihajlović, R

    1969-09-01

    The working conditions and the results for coulometric titration of milligram amounts of some bases in 0.1M sodium perchlorate in a mixture of acetic acid and acetic anhydride (1:6), are given. Determinations were made both by coulometric back-titration or direct titration at the platinum anode. Back-titration was done in the catholyte, by coulometric titration of the excess of added perchloric acid. The titration end-point was detected photometrically with Crystal Violet as indicator. The direct titration of bases was done at the platinum anode, in the same electrolyte, to which hydroquinone was added as anode depolarizer and as the source of hydrogen ions, Malachite Green being used as indicator. Similarly, bases can be determined in acetonitrile if sodium perchlorate, hydroquinone and Malachite Green are added to the solvent. Errors are below 1 %, and the precision is satisfactory.

  19. Food composition and acid-base balance: alimentary alkali depletion and acid load in herbivores.

    PubMed

    Kiwull-Schöne, Heidrun; Kiwull, Peter; Manz, Friedrich; Kalhoff, Hermann

    2008-02-01

    Alkali-enriched diets are recommended for humans to diminish the net acid load of their usual diet. In contrast, herbivores have to deal with a high dietary alkali impact on acid-base balance. Here we explore the role of nutritional alkali in experimentally induced chronic metabolic acidosis. Data were collected from healthy male adult rabbits kept in metabolism cages to obtain 24-h urine and arterial blood samples. Randomized groups consumed rabbit diets ad libitum, providing sufficient energy but variable alkali load. One subgroup (n = 10) received high-alkali food and approximately 15 mEq/kg ammonium chloride (NH4Cl) with its drinking water for 5 d. Another group (n = 14) was fed low-alkali food for 5 d and given approximately 4 mEq/kg NH4Cl daily for the last 2 d. The wide range of alimentary acid-base load was significantly reflected by renal base excretion, but normal acid-base conditions were maintained in the arterial blood. In rabbits fed a high-alkali diet, the excreted alkaline urine (pH(u) > 8.0) typically contained a large amount of precipitated carbonate, whereas in rabbits fed a low-alkali diet, both pH(u) and precipitate decreased considerably. During high-alkali feeding, application of NH4Cl likewise decreased pH(u), but arterial pH was still maintained with no indication of metabolic acidosis. During low-alkali feeding, a comparably small amount of added NH4Cl further lowered pH(u) and was accompanied by a significant systemic metabolic acidosis. We conclude that exhausted renal base-saving function by dietary alkali depletion is a prerequisite for growing susceptibility to NH4Cl-induced chronic metabolic acidosis in the herbivore rabbit.

  20. Acid-base titrations by stepwise addition of equal volumes of titrant with special reference to automatic titrations-II Theory of titration of mixtures of acids, polyprotic acids, acids in mixture with weak bases, and ampholytes.

    PubMed

    Pehrsson, L; Ingman, F; Johansson, S

    A general method for evaluating titration data for mixtures of acids and for acids in mixture with weak bases is presented. Procedures are given that do not require absolute [H]-data, i.e., relative [H]-data may be used. In most cases a very rough calibration of the electrode system is enough. Further, for simple systems, very approximate values of the stability constants are sufficient. As examples, the titration of the following are treated in some detail: a mixture of two acids, a diprotic acid, an acid in presence of its conjugate base, and an ampholyte.

  1. Effects of dietary strong acid anion challenge on regulation of acid-base balance in sheep.

    PubMed

    Las, J E; Odongo, N E; Lindinger, M I; AlZahal, O; Shoveller, A K; Matthews, J C; McBride, B W

    2007-09-01

    The acid-base status of the extracellular fluid is directly affected by the concentrations of strong basic cations and strong acid anions that are absorbed into the bloodstream from the diet. The objective of this study was to develop and characterize a model for dietary acid challenge in sheep by decreasing the dietary cation-anion difference (DCAD) using NutriChlor (HCl-treated canola meal), an anionic feed supplement. Ten fully fleeced sheep (Rideau-Arcott, 54.3 +/- 6.7 kg of BW) were fed either a control supplement [200 g/d of canola meal, DCAD = 184 mEq/kg of DM, calculated as (Na+ + K+) - (Cl- + S2-)] or an anionic supplement (AS; 200 g/d of NutriChlor, DCAD = -206 mEq/kg of DM) offered twice daily at 0700 and 1100 in a randomized complete block design. The sheep were individually housed and limit-fed a basal diet of dehydrated alfalfa pellets (22% CP and 1.2 Mcal of NE(g)/kg, DM basis) at 1.1 kg of DM/d offered twice daily at 1000 and 1300. Two days before the beginning of the experiment, the sheep were fitted with vinyl catheters (0.86-mm i.d., 1.32-mm o.d.) in the left jugular vein to facilitate blood sampling. Blood and urine samples were obtained daily from 1100 to 1130 on d 1 through 9 and at 0700, 1000, 1300, 1600, and 1900 on d 10. Blood was analyzed for hematocrit, plasma pH, gases, strong ions, and total protein. Urine samples were analyzed for pH. The AS induced a nonrespiratory acid-base disturbance associated with lower (P < 0.05) plasma pH (7.47 vs. 7.39), lower (P < 0.05) urine pH (8.13 vs. 6.09), and lower (P < 0.05) strong ion difference (42.5 vs. 39.5). The AS reduced (P < 0.05) the concentration of plasma glucose, base excess, and bicarbonate and increased (P < 0.05) the concentration of K+ and Cl-. Lowering DCAD increased (P < 0.05) Ca2+ concentrations in plasma by 13%. In conclusion, this dietary model successfully induced a significant acid-base disturbance in sheep. Although the acidifying effects of negative DCAD in the diet may have

  2. Hard and soft acids and bases: structure and process.

    PubMed

    Reed, James L

    2012-07-05

    Under investigation is the structure and process that gives rise to hard-soft behavior in simple anionic atomic bases. That for simple atomic bases the chemical hardness is expected to be the only extrinsic component of acid-base strength, has been substantiated in the current study. A thermochemically based operational scale of chemical hardness was used to identify the structure within anionic atomic bases that is responsible for chemical hardness. The base's responding electrons have been identified as the structure, and the relaxation that occurs during charge transfer has been identified as the process giving rise to hard-soft behavior. This is in contrast the commonly accepted explanations that attribute hard-soft behavior to varying degrees of electrostatic and covalent contributions to the acid-base interaction. The ability of the atomic ion's responding electrons to cause hard-soft behavior has been assessed by examining the correlation of the estimated relaxation energies of the responding electrons with the operational chemical hardness. It has been demonstrated that the responding electrons are able to give rise to hard-soft behavior in simple anionic bases.

  3. Bio-based production of organic acids with Corynebacterium glutamicum.

    PubMed

    Wieschalka, Stefan; Blombach, Bastian; Bott, Michael; Eikmanns, Bernhard J

    2013-03-01

    The shortage of oil resources, the steadily rising oil prices and the impact of its use on the environment evokes an increasing political, industrial and technical interest for development of safe and efficient processes for the production of chemicals from renewable biomass. Thus, microbial fermentation of renewable feedstocks found its way in white biotechnology, complementing more and more traditional crude oil-based chemical processes. Rational strain design of appropriate microorganisms has become possible due to steadily increasing knowledge on metabolism and pathway regulation of industrially relevant organisms and, aside from process engineering and optimization, has an outstanding impact on improving the performance of such hosts. Corynebacterium glutamicum is well known as workhorse for the industrial production of numerous amino acids. However, recent studies also explored the usefulness of this organism for the production of several organic acids and great efforts have been made for improvement of the performance. This review summarizes the current knowledge and recent achievements on metabolic engineering approaches to tailor C. glutamicum for the bio-based production of organic acids. We focus here on the fermentative production of pyruvate, L- and D-lactate, 2-ketoisovalerate, 2-ketoglutarate, and succinate. These organic acids represent a class of compounds with manifold application ranges, e.g. in pharmaceutical and cosmetics industry, as food additives, and economically very interesting, as precursors for a variety of bulk chemicals and commercially important polymers.

  4. Acid-Base Balance in Uremic Rats with Vascular Calcification

    PubMed Central

    Peralta-Ramírez, Alan; Raya, Ana Isabel; Pineda, Carmen; Rodríguez, Mariano; Aguilera-Tejero, Escolástico; López, Ignacio

    2014-01-01

    Background/Aims Vascular calcification (VC), a major complication in humans and animals with chronic kidney disease (CKD), is influenced by changes in acid-base balance. The purpose of this study was to describe the acid-base balance in uremic rats with VC and to correlate the parameters that define acid-base equilibrium with VC. Methods Twenty-two rats with CKD induced by 5/6 nephrectomy (5/6 Nx) and 10 nonuremic control rats were studied. Results The 5/6 Nx rats showed extensive VC as evidenced by a high aortic calcium (9.2 ± 1.7 mg/g of tissue) and phosphorus (20.6 ± 4.9 mg/g of tissue) content. Uremic rats had an increased pH level (7.57 ± 0.03) as a consequence of both respiratory (PaCO2 = 28.4 ± 2.1 mm Hg) and, to a lesser degree, metabolic (base excess = 4.1 ± 1 mmol/l) derangements. A high positive correlation between both anion gap (AG) and strong ion difference (SID) with aortic calcium (AG: r = 0.604, p = 0.02; SID: r = 0.647, p = 0.01) and with aortic phosphorus (AG: r = 0.684, p = 0.007; SID: r = 0.785, p = 0.01) was detected. Conclusions In an experimental model of uremic rats, VC showed high positive correlation with AG and SID. PMID:25177336

  5. Acid-base balance in uremic rats with vascular calcification.

    PubMed

    Peralta-Ramírez, Alan; Raya, Ana Isabel; Pineda, Carmen; Rodríguez, Mariano; Aguilera-Tejero, Escolástico; López, Ignacio

    2014-01-01

    Vascular calcification (VC), a major complication in humans and animals with chronic kidney disease (CKD), is influenced by changes in acid-base balance. The purpose of this study was to describe the acid-base balance in uremic rats with VC and to correlate the parameters that define acid-base equilibrium with VC. Twenty-two rats with CKD induced by 5/6 nephrectomy (5/6 Nx) and 10 nonuremic control rats were studied. The 5/6 Nx rats showed extensive VC as evidenced by a high aortic calcium (9.2 ± 1.7 mg/g of tissue) and phosphorus (20.6 ± 4.9 mg/g of tissue) content. Uremic rats had an increased pH level (7.57 ± 0.03) as a consequence of both respiratory (PaCO2 = 28.4 ± 2.1 mm Hg) and, to a lesser degree, metabolic (base excess = 4.1 ± 1 mmol/l) derangements. A high positive correlation between both anion gap (AG) and strong ion difference (SID) with aortic calcium (AG: r = 0.604, p = 0.02; SID: r = 0.647, p = 0.01) and with aortic phosphorus (AG: r = 0.684, p = 0.007; SID: r = 0.785, p = 0.01) was detected. In an experimental model of uremic rats, VC showed high positive correlation with AG and SID.

  6. Acid-base properties of Baltic Sea dissolved organic matter

    NASA Astrophysics Data System (ADS)

    Hammer, Karoline; Schneider, Bernd; Kuliński, Karol; Schulz-Bull, Detlef E.

    2017-09-01

    Calculations related to the marine CO2 system that are based on alkalinity data may be strongly biased if the contributions of organic compounds are ignored. In coastal seas, concentrations of dissolved organic matter (DOM) are frequently high and alkalinity from inorganic compounds is low. In this study, based on measurements of total alkalinity, total CO2, and pH, we determined the organic alkalinity, Aorg, in water from the central Baltic Sea. The maximum Aorg measured in the surface mixed layer during the spring bloom was > 50 μmol/kg-SW but the Aorg decreased with depth and approached zero below the permanent halocline. This behavior could be attributed to the decreased pH of deeper water layers. The data were used to calculate the bulk dissociation constant, KDOM, for marine DOM and the fraction f of dissolved organic carbon (DOC) that acts as a carrier for acid-base functional groups. The p KDOM (7.27) agreed well with the value (7.34) previously estimated in a preliminary study of organic alkalinity in the Baltic Sea. The fraction of carbon atoms carrying acid-base groups was 17% and was somewhat higher than previously reported (12%). Spike experiments performed using artificial seawater and three different humic/fulvic substances tested whether the acid-base properties of these substances explain the results of our field study. Specifically, Aorg was determined at different concentrations (DOC) of the added humic/fulvic substances. The relationship between Aorg and the DOC concentrations indicated that humic/fulvic substances are more acidic (p KDOM < 6.5) than the bulk DOC natural occurring in the Baltic Sea.

  7. Developing nucleic acid-based electrical detection systems

    PubMed Central

    Gabig-Ciminska, Magdalena

    2006-01-01

    Development of nucleic acid-based detection systems is the main focus of many research groups and high technology companies. The enormous work done in this field is particularly due to the broad versatility and variety of these sensing devices. From optical to electrical systems, from label-dependent to label-free approaches, from single to multi-analyte and array formats, this wide range of possibilities makes the research field very diversified and competitive. New challenges and requirements for an ideal detector suitable for nucleic acid analysis include high sensitivity and high specificity protocol that can be completed in a relatively short time offering at the same time low detection limit. Moreover, systems that can be miniaturized and automated present a significant advantage over conventional technology, especially if detection is needed in the field. Electrical system technology for nucleic acid-based detection is an enabling mode for making miniaturized to micro- and nanometer scale bio-monitoring devices via the fusion of modern micro- and nanofabrication technology and molecular biotechnology. The electrical biosensors that rely on the conversion of the Watson-Crick base-pair recognition event into a useful electrical signal are advancing rapidly, and recently are receiving much attention as a valuable tool for microbial pathogen detection. Pathogens may pose a serious threat to humans, animal and plants, thus their detection and analysis is a significant element of public health. Although different conventional methods for detection of pathogenic microorganisms and their toxins exist and are currently being applied, improvements of molecular-based detection methodologies have changed these traditional detection techniques and introduced a new era of rapid, miniaturized and automated electrical chip detection technologies into pathogen identification sector. In this review some developments and current directions in nucleic acid-based electrical

  8. Bimodal proton transfer in acid-base reactions in water

    SciTech Connect

    Rini, Matteo; Pines, Dina; Magnes, Ben-Zion; Pines, Ehud; Nibbering, Erik T.J.

    2004-11-15

    We investigate one of the fundamental reactions in solutions, the neutralization of an acid by a base. We use a photoacid, 8-hydroxy-1,3,6-trisulfonate-pyrene (HPTS; pyranine), which upon photoexcitation reacts with acetate under transfer of a deuteron (solvent: deuterated water). We analyze in detail the resulting bimodal reaction dynamics between the photoacid and the base, the first report on which was recently published [M. Rini, B.-Z. Magnes, E. Pines, and E. T. J. Nibbering, Science 301, 349 (2003)]. We have ascribed the bimodal proton-transfer dynamics to contributions from preformed hydrogen bonding complexes and from initially uncomplexed acid and base. We report on the observation of an additional (6 ps)-1 contribution to the reaction rate constant. As before, we analyze the slower part of the reaction within the framework of the diffusion model and the fastest part by a static, sub-150 fs reaction rate. Adding the second static term considerably improves the overall modeling of the experimental results. It also allows to connect experimentally the diffusion controlled bimolecular reaction models as defined by Eigen-Weller and by Collins-Kimball [D. Shoup and A. Szabo, Biophys. J. 40, 33 (1982)]. Our findings are in agreement with a three-stage mechanism for liquid phase intermolecular proton transfer: mutual diffusion of acid and base to form a 'loose' encounter complex, followed by reorganization of the solvent shells and by 'tightening' of the acid-base encounter complex. These rearrangements last a few picoseconds and enable a prompt proton transfer along the reaction coordinate, which occurs faster than our time resolution of 150 fs. Alternative models for the explanation of the slower 'on-contact' reaction time of the loose encounter complex in terms of proton transmission through a von Grotthuss mechanism are also discussed.

  9. The physiological assessment of acid-base balance.

    PubMed

    Howorth, P J

    1975-04-01

    Acid-base terminology including the sue of SI units is reviewed. The historical reasons why nomograms have been particularly used in acid-base work are discussed. The theoretical basis of the Henderson-Hasselbalch equation is considered. It is emphasized that the solubility of CO2 in plasma and the apparent first dissociation constant of carbonic acid are not chemical constants when applied to media of uncertain and varying composition such as blood plasma. The use of the Henderson-Hasselbalch equation in making hypothermia corrections for PCO2 is discussed. The Astrup system for the in vitro determination of blood gases and derived parameters is described and the theoretical weakness of the base excess concept stressed. A more clinically-oriented approach to the assessment of acid-base problems is presented. Measurement of blood [H+] and PCO2 are considered to be primary data which should be recorded on a chart with in vivo CO2-titration lines (see below). Clinical information and results of other laboratory investigations such as plasma bicarbonate, PO2,P50 are then to be considered together with the primary data. In order to interpret this combined information it is essential to take into account the known ventilatory response to metabolic acidosis and alkalosis, and the renal response to respiratory acidosis and alkalosis. The use is recommended of a chart showing the whole-body CO2-titration points obtained when patients with different initial levels of non-respiratory [H+] are ventilated. A number of examples are given of the use of this [H+] and PCO2 in vivo chart in the interpretation of acid-base data. The aetiology, prognosis and treatment of metabolic alkalosis is briefly reviewed. Treatment with intravenous acid is recommended for established cases. Attention is drawn to the possibility of iatrogenic production of metabolic alkalosis. Caution is expressed over the use of intravenous alkali in all but the severest cases of metabolic acidosis. The role of

  10. Acid and base stress and transcriptomic responses in Bacillus subtilis.

    PubMed

    Wilks, Jessica C; Kitko, Ryan D; Cleeton, Sarah H; Lee, Grace E; Ugwu, Chinagozi S; Jones, Brian D; BonDurant, Sandra S; Slonczewski, Joan L

    2009-02-01

    Acid and base environmental stress responses were investigated in Bacillus subtilis. B. subtilis AG174 cultures in buffered potassium-modified Luria broth were switched from pH 8.5 to pH 6.0 and recovered growth rapidly, whereas cultures switched from pH 6.0 to pH 8.5 showed a long lag time. Log-phase cultures at pH 6.0 survived 60 to 100% at pH 4.5, whereas cells grown at pH 7.0 survived <15%. Cells grown at pH 9.0 survived 40 to 100% at pH 10, whereas cells grown at pH 7.0 survived <5%. Thus, growth in a moderate acid or base induced adaptation to a more extreme acid or base, respectively. Expression indices from Affymetrix chip hybridization were obtained for 4,095 protein-encoding open reading frames of B. subtilis grown at external pH 6, pH 7, and pH 9. Growth at pH 6 upregulated acetoin production (alsDS), dehydrogenases (adhA, ald, fdhD, and gabD), and decarboxylases (psd and speA). Acid upregulated malate metabolism (maeN), metal export (czcDO and cadA), oxidative stress (catalase katA; OYE family namA), and the SigX extracytoplasmic stress regulon. Growth at pH 9 upregulated arginine catabolism (roc), which generates organic acids, glutamate synthase (gltAB), polyamine acetylation and transport (blt), the K(+)/H(+) antiporter (yhaTU), and cytochrome oxidoreductases (cyd, ctaACE, and qcrC). The SigH, SigL, and SigW regulons were upregulated at high pH. Overall, greater genetic adaptation was seen at pH 9 than at pH 6, which may explain the lag time required for growth shift to high pH. Low external pH favored dehydrogenases and decarboxylases that may consume acids and generate basic amines, whereas high external pH favored catabolism-generating acids.

  11. Acid-base properties of bentonite rocks with different origins.

    PubMed

    Nagy, Noémi M; Kónya, József

    2006-03-01

    Five bentonite samples (35-47% montmorillonite) from a Sarmatian sediment series with bentonite sites around Sajóbábony (Hungary) is studied. Some of these samples were tuffogenic bentonite (sedimentary), the others were bentonitized tuff with volcano sedimentary origin. The acid-base properties of the edge sites were studied by potentiometric titrations and surface complexation modeling. It was found that the number and the ratio of silanol and aluminol sites as well as the intrinsic stability constants are different for the sedimentary bentonite and bentonitized tuff. The characteristic properties of the edges sites depend on the origins. The acid-base properties are compared to other commercial and standard bentonites.

  12. Synthesis and characterization of copolyanhydrides of carbohydrate-based galactaric acid and adipic acid.

    PubMed

    Mehtiö, Tuomas; Nurmi, Leena; Rämö, Virpi; Mikkonen, Hannu; Harlin, Ali

    2015-01-30

    A series of copolyanhydrides, consisting of 2,3,4,5-tetra-O-acetylgalactaric acid (AGA) and adipic acid (AA) as monomer units, was polymerized. Synthesis of AGA monomer consisted of two steps. First, O-acetylation of galactaric acid secondary hydroxyl groups was performed using acetic anhydride as a reagent. Acetic anhydride was then further used as a reagent in the synthesis of diacetyl mixed anhydride of AGA. Polymerizations were conducted as bulk condensation polymerization at 150 °C. Thermal properties of the copolymers varied depending on monomer composition. Increase in the AGA content had a clear increasing effect on the Tg. A similar increasing effect was observed in Tm. The degree of crystallinity decreased as AGA content increased. There was a slightly lowering tendency in the molecular weights of the obtained polymers when the AGA content in the polymerization mixtures increased. The described synthesis route shows that bio-based aldaric acid monomers are potential candidates for the adjustment of thermal properties of polyanhydrides.

  13. Acid-base thermochemistry of gaseous aliphatic α-aminoacids.

    PubMed

    Bouchoux, Guy; Huang, Sihua; Inda, Bhawani Singh

    2011-01-14

    Acid-base thermochemistry of isolated aliphatic amino acids (denoted AAA): glycine, alanine, valine, leucine, isoleucine and proline has been examined theoretically by quantum chemical computations at the G3MP2B3 level. Conformational analysis on neutral, protonated and deprotonated species has been used to identify the lowest energy conformers and to estimate the population of conformers expected to be present at thermal equilibrium at 298 K. Comparison of the G3MP2B3 theoretical proton affinities, PA, and ΔH(acid) with experimental results is shown to be correct if experimental thermochemistry is re-evaluated and adapted to the most recent acidity-basicity scales. From this point of view, a set of evaluated proton affinities of 887, 902, 915, 916, 919 and 941 kJ mol(-1), and a set of evaluated ΔH(acid) of 1433, 1430, 1423, 1423, 1422 and 1426 kJ mol(-1), is proposed for glycine, alanine, valine, leucine, isoleucine and proline, respectively. Correlations with structural parameters (Taft's σ(α) polarizability parameter and molecular size) suggest that polarizability of the side chain is the major origin of the increase in PA and decrease in ΔH(acid) along the homologous series glycine, alanine, valine and leucine/isoleucine. Heats of formation of gaseous species AAA, AAAH(+) and [AAA-H](-) were computed at the G3MP2B3 level. The present study provides previously unavailable Δ(f)H°(298) for the ionized species AAAH(+) and [AAA-H](-). Comparison with Benson's estimate, and correlation with molecular size, show that several experimental Δ(f)H°(298) values of neutral or gaseous AAA might be erroneous.

  14. [Injuries caused by acids and bases - emergency treatment].

    PubMed

    Reifferscheid, Florian; Stuhr, Markus; Kaiser, Guido; Freudenberg, Matthias; Kerner, Thoralf

    2014-06-01

    Emergency medical care for injuries caused by acids and bases is challenging for rescue services. They have to deal with operational safety, detection of the toxic agent, emergency medical care of the patient and handling of the rescue mission. Because of the rareness of such situations experience and routine are largely missing. This article highlights some basic points for the therapy and provides support for such rescue missions. © Georg Thieme Verlag Stuttgart · New York.

  15. [Acid-base status in patients treated with peritoneal dialysis].

    PubMed

    Katalinić, Lea; Blaslov, Kristina; Pasini, Eva; Kes, Petar; Bašić-Jukić, Nikolina

    2014-04-01

    When compared to hemodialysis, peritoneal dialysis is very simple yet low cost method of renal replacement therapy. Series of studies have shown its superiority in preserving residual renal function, postponing uremic complications, maintaining the acid-base balance and achieving better post-transplant outcome in patients treated with this method. Despite obvious advantages, its role in the treatment of chronic kidney disease is still not as important as it should be. Metabolic acidosis is an inevitable complication associated with progressive loss of kidney function. Its impact on mineral and muscle metabolism, residual renal function, allograft function and anemia is very complex but can be successfully managed. The aim of our study was to evaluate the efficiency in preserving the acid-base balance in patients undergoing peritoneal dialysis at Zagreb University Hospital Center. Twenty-eight patients were enrolled in the study. The mean time spent on the treatment was 32.39 ± 43.43 months. Only lactate-buffered peritoneal dialysis fluids were used in the treatment. Acid-base balance was completely maintained in 73.07% of patients; 11.54% of patients were found in the state of mild metabolic acidosis, and the same percentage of patients were in the state of mild metabolic alkalosis. In one patient, mixed alkalosis with respiratory and metabolic component was present. The results of this study showed that acid-base balance could be maintained successfully in patients undergoing peritoneal dialysis, even only with lactate-buffered solutions included in the treatment, although they were continuously proclaimed as inferior in comparison with bicarbonate-buffered ones. In well educated and informed patients who carefully use this method, accompanied by the attentive and thorough care of their physicians, this method can provide quality continuous replacement of lost renal function as well as better quality of life.

  16. Diagnosis and treatment of simple acid-base disorders.

    PubMed

    Ayers, Phil; Warrington, Laurie

    2008-01-01

    The ability to diagnose and treat acid-base disorders is an important component in the practice of the nutrition support clinician. A complete understanding of the basic principles of metabolic and respiratory disorders allows the practitioner to formulate educated decisions regarding fluids, parenteral nutrition salts, and the management of electrolytes. This review will discuss the diagnosis and treatment of common metabolic and respiratory disorders encountered in nutrition support practice.

  17. Analysis of the mineral acid-base components of acid-neutralizing capacity in Adirondack Lakes

    NASA Astrophysics Data System (ADS)

    Munson, R. K.; Gherini, S. A.

    1993-04-01

    Mineral acids and bases influence pH largely through their effects on acid-neutralizing capacity (ANC). This influence becomes particularly significant as ANC approaches zero. Analysis of data collected by the Adirondack Lakes Survey Corporation (ALSC) from 1469 lakes throughout the Adirondack region indicates that variations in ANC in these lakes correlate well with base cation concentrations (CB), but not with the sum of mineral acid anion concentrations (CA). This is because (CA) is relatively constant across the Adirondacks, whereas CB varies widely. Processes that supply base cations to solution are ion-specific. Sodium and silica concentrations are well correlated, indicating a common source, mineral weathering. Calcium and magnesium also covary but do not correlate well with silica. This indicates that ion exchange is a significant source of these cations in the absence of carbonate minerals. Iron and manganese concentrations are elevated in the lower waters of some lakes due to reducing conditions. This leads to an ephemeral increase in CB and ANC. When the lakes mix and oxic conditions are restored, these ions largely precipitate from solution. Sulfate is the dominant mineral acid anion in ALSC lakes. Sulfate concentrations are lowest in seepage lakes, commonly about 40 μeq/L less than in drainage lakes. This is due in part to the longer hydraulic detention time in seepage lakes, which allows slow sulfate reduction reactions more time to decrease lake sulfate concentration. Nitrate typically influences ANC during events such as snowmelt. Chloride concentrations are generally low, except in lakes impacted by road salt.

  18. Fundamental studies into zirconium modified phosphonic acid based ionic membranes

    NASA Astrophysics Data System (ADS)

    Schlichting, Gregory Joseph

    The demand for a sustainable energy economy requires the development of new solid stare electrochemical energy conversion devices. Ionic membranes are the bases for most of these devices. Solid super acids based on zirconium phosphonates show great promise for development into these membranes. Copolymers of vinyl phosphonic acid with zirconium vinyl phosphonate have been synthesized via UV free radical polymerization from immiscible mixtures into amorphous, transparent, water stable, flexible membranes. Ion exchange capacities range from 6 to 10 meq/g corresponding to equivalent weights well below 200 g/mol. A 20wt% loading of the VZP co-monomer is XRD amorphous. It is shown that 1.5 of the 2 protons in the beginning acidic groups are dissociated in the 20wt% VZP loaded ionomer allowing these materials to have high proton conductivities, up to and exceeding 0.1 S cm^-1 at 80°C and 80%RH. Water uptake measurementsshow very little swelling of the material below 70%RH and ca. 1 water per proton at low RH. Proton conductivity under dry conditions, roughly 0.05 S cm-1 with a lambda < 1, indicates that the material conducts protons under limiting hydration conditions and strongly implicates transport by a pure Grotthuss mechanism. Through this work, it has been demonstrated that zirconium vinyl phosphonate can, in fact, be dispersed and incorporated into a polymer to create new, hybrid organic-inorganic ionomers. High conductivities over 0.15 S/cm have been shown for multiple formulations of these ionomers, which is approaching conductivities that are comparable to liquid and molten phosphoric and phosphonic acids. Phosphonic acid functionalization yielded high proton conductivities, however the increased ionic character rendered the ionomer vulnerable to attack from water. Annealing provides a rise in conductivity at 150 degrees Celsius, but shows decreases after heating to 175 degrees Celsius, where the ionomer is obviously starting to degrade.

  19. Synthesis of bio-based methacrylic acid by decarboxylation of itaconic acid and citric acid catalyzed by solid transition-metal catalysts.

    PubMed

    Le Nôtre, Jérôme; Witte-van Dijk, Susan C M; van Haveren, Jacco; Scott, Elinor L; Sanders, Johan P M

    2014-09-01

    Methacrylic acid, an important monomer for the plastics industry, was obtained in high selectivity (up to 84%) by the decarboxylation of itaconic acid using heterogeneous catalysts based on Pd, Pt and Ru. The reaction takes place in water at 200-250 °C without any external added pressure, conditions significantly milder than those described previously for the same conversion with better yield and selectivity. A comprehensive study of the reaction parameters has been performed, and the isolation of methacrylic acid was achieved in 50% yield. The decarboxylation procedure is also applicable to citric acid, a more widely available bio-based feedstock, and leads to the production of methacrylic acid in one pot in 41% selectivity. Aconitic acid, the intermediate compound in the pathway from citric acid to itaconic acid was also used successfully as a substrate.

  20. Direct Isolation of Purines and Pyrimidines from Nucleic Acids Using Sublimation

    NASA Technical Reports Server (NTRS)

    Glavin, Daniel P.; Schubert, Michael; Bada, Jeffrey L.

    2003-01-01

    A sublimation technique was developed to isolate purines and pyrimidines directly from lambda-deoxyribonucleic acid (lambda-DNA) and Escherichia coli cells. The sublimation of adenine, cytosine, guanine, and thymine from lambda-DNA was tested under reduced pressure (approx. 0.5 Torr) at temperatures of >150 C. With the exception of guanine, approximately 60 -75% of each base was sublimed directly from the lambda-DNA and recovered on a coldfinger of the sublimation apparatus after heating to 450 C. Several nucleobases including adenine, cytosine, thymine, and uracil were also recovered from E. coli bacteria after heating the cells to the same temperature, although some thermal decomposition of the bases also occurred. These results demonstrate the feasibility of using sublimation to isolate purines and pyrimidines from native E. coli DNA and RNA without any chemical treatment of the cells.

  1. Direct Isolation of Purines and Pyrimidines from Nucleic Acids Using Sublimation

    NASA Technical Reports Server (NTRS)

    Glavin, Daniel P.; Schubert, Michael; Bada, Jeffrey L.

    2003-01-01

    A sublimation technique was developed to isolate purines and pyrimidines directly from lambda-deoxyribonucleic acid (lambda-DNA) and Escherichia coli cells. The sublimation of adenine, cytosine, guanine, and thymine from lambda-DNA was tested under reduced pressure (approx. 0.5 Torr) at temperatures of >150 C. With the exception of guanine, approximately 60 -75% of each base was sublimed directly from the lambda-DNA and recovered on a coldfinger of the sublimation apparatus after heating to 450 C. Several nucleobases including adenine, cytosine, thymine, and uracil were also recovered from E. coli bacteria after heating the cells to the same temperature, although some thermal decomposition of the bases also occurred. These results demonstrate the feasibility of using sublimation to isolate purines and pyrimidines from native E. coli DNA and RNA without any chemical treatment of the cells.

  2. Influence of ions on aqueous acid-base reactions.

    PubMed

    Cox, M Jocelyn; Siwick, Bradley J; Bakker, Huib J

    2009-01-12

    We study the effects of bromide salts on the rate and mechanism of the aqueous proton/deuteron-transfer reaction between the photoacid 8-hydroxy-1,3,6-pyrenetrisulfonic acid (HPTS) and the base acetate. The proton/deuteron release is triggered by exciting HPTS with 400 nm femtosecond laser pulses. Probing the electronic and vibrational resonances of the photoacid, the conjugate photobase, the hydrated proton/deuteron and the accepting base with femtosecond visible and mid-infrared pulses monitors the proton transfer. Two reaction channels are identified: 1) direct long-range proton transfer over hydrogen-bonded water bridges that connect the acid and base and 2) acid dissociation to produce fully solvated protons followed by proton scavenging from solution by acetate. We observe that the addition of salt affects the long-range reaction pathway, and reduces both the rate at which protons are released to solution by HPTS and the rate at which solvated protons are scavenged from solution by acetate. We study the dependence of these effects on the nature and concentration of the dissolved salt.

  3. Food mineral composition and acid-base balance in rabbits.

    PubMed

    Kiwull-Schöne, Heidrun; Kalhoff, Hermann; Manz, Friedrich; Kiwull, Peter

    2005-12-01

    Alkali-rich diets are often recommended in human medicine to prevent the pathological consequences of nutritional acid load in conditions of impaired renal function. This study was undertaken in rabbits as common laboratory animals for basic medical research to explore the impact of high versus low dietary alkali intake on systemic acid-base balance and renal control in a typical herbivore. Male rabbits (2.3-4.8 kg) were kept in a metabolism cage. The 24h urine and arterial blood samples were analysed for acid-base data. The metabolic CO2 production was measured to calculate alveolar ventilation. Three randomized groups of animals were fed ad libitum with rabbit chow providing sufficient energy but variable alkali load, assessed by the ashes' cation-anion difference. The average daily nutritional alkali load (+/- SEM) was 67.1 +/- 2.2 mEq x kg(-1) (N = 58) in the group on high, 45.4 +/- 2.5 mEq x kg(-1) (N = 31) in the group on normal and 1.7 +/- 0.5 mEq x kg(-1) (N = 11) in the group on low alkali food. Respective mean arterial base excess values (BE) were 1.4 +/- 0.3 mM, 0.3 +/- 0.4 mM and 0.0 +/- 0.3 mM, being significantly higher on high alkali food (P < 0.05) than in the other groups. Arterial PCO2, alveolar ventilation and metabolic CO2 production were not significantly different between groups. On normal and high-alkali chow, an alkaline urine (pH(u) > 8.0) with 18-20 mmol x kg(-1) bicarbonate/carbonate was excreted daily, typically containing an insoluble precipitate of 35-60% carbonate. On low-alkali diet, the mean pH(u) decreased to 6.26 +/- 0.14, due to a strong reduction of daily excreted soluble bicarbonate and precipitated carbonate to 1.2 +/- 0.6 and 0.7 +/- 0.2 mmol x kg(-1), respectively. Thereby, nearly complete fractional base reabsorption of 97.8 +/- 0.7 % was reached. Herbivore nutritional alkali-load elicited large rates of renal base excretion including precipitates, to which the urinary tract of the rabbits appeared to be adapted. Dietary

  4. The normal acid-base status of mice.

    PubMed

    Iversen, Nina K; Malte, Hans; Baatrup, Erik; Wang, Tobias

    2012-03-15

    Rodent models are commonly used for various physiological studies including acid-base regulation. Despite the widespread use of especially genetic modified mice, little attention have been made to characterise the normal acid-base status in these animals in order to reveal proper control values. Furthermore, several studies report blood gas values obtained in anaesthetised animals. We, therefore, decided to characterise blood CO(2) binding characteristic of mouse blood in vitro and to characterise normal acid-base status in conscious BALBc mice. In vitro CO(2) dissociation curves, performed on whole blood equilibrated to various PCO₂ levels in rotating tonometers, revealed a typical mammalian pK' (pK'=7.816-0.234 × pH (r=0.34)) and a non-bicarbonate buffer capacity (16.1 ± 2.6 slyke). To measure arterial acid-base status, small blood samples were taken from undisturbed mice with indwelling catheters in the carotid artery. In these animals, pH was 7.391 ± 0.026, plasma [HCO(3)(-)] 18.4 ± 0.83 mM, PCO₂ 30.3 ± 2.1 mm Hg and lactate concentration 4.6 ± 0.7 mM. Our study, therefore, shows that mice have an arterial pH that resembles other mammals, although arterial PCO₂ tends to be lower than in larger mammals. However, pH from arterial blood sampled from mice anaesthetised with isoflurane was significantly lower (pH 7.239 ± 0.021), while plasma [HCO(3)(-)] was 18.5 ± 1.4 mM, PCO₂ 41.9 ± 2.9 mm Hg and lactate concentration 4.48 ± 0.67 mM. Furthermore, we measured metabolism and ventilation (V(E)) in order to determine the ventilation requirements (VE/VO₂) to answer whether small mammals tend to hyperventilate. We recommend, therefore, that studies on acid-base regulation in mice should be based on samples taken for indwelling catheters rather than cardiac puncture of terminally anaesthetised mice.

  5. Lewis base activation of Lewis acids: development of a Lewis base catalyzed selenolactonization.

    PubMed

    Denmark, Scott E; Collins, William R

    2007-09-13

    The concept of Lewis base activation of Lewis acids has been applied to the selenolactonization reaction. Through the use of substoichiometric amounts of Lewis bases with "soft" donor atoms (S, Se, P) significant rate enhancements over the background reaction are seen. Preliminary mechanistic investigations have revealed the resting state of the catalyst as well as the significance of a weak Brønsted acid promoter.

  6. [Nutrition, acid-base metabolism, cation-anion difference and total base balance in humans].

    PubMed

    Mioni, R; Sala, P; Mioni, G

    2008-01-01

    The relationship between dietary intake and acid-base metabolism has been investigated in the past by means of the inorganic cation-anion difference (C(+)(nm)-A(-)(nm)) method based on dietary ash-acidity titration after the oxidative combustion of food samples. Besides the inorganic components of TA (A(-)(nm)-C(+)(nm)), which are under renal control, there are also metabolizable components (A(-)(nm)-C(+)(nm)) of TA, which are under the control of the intermediate metabolism. The whole body base balance, NBb(W), is obtained only by the application of C(+)(nm)-A(-)(nm) to food, feces and urine, while the metabolizable component (A(-)(nm)-C(+)(nm)) is disregarded. A novel method has been subsequently suggested to calculate the net balance of fixed acid, made up by the difference between the input of net endogenous acid production: NEAP = SO(4)(2-)+A(-)(m)-(C(+)(nm)-A(-)(nm)), and the output of net acid excretion: NAE = TA + NH(4)(+) - HCO(3)(-). This approach has been criticized because 1) it includes metabolizable acids, whose production cannot be measured independently; 2) the specific control of metabolizable acid and base has been incorrectly attributed to the kidney; 3) the inclusion of A-m in the balance input generates an acid overload; 4) the object of measurement in making up a balance has to be the same, a condition not fulfilled as NEAP is different from NAE. Lastly, by rearranging the net balance of the acid equation, the balance of nonmetabolizable acid equation is obtained. Therefore, any discrepancy between these two equations is due to the inaccuracy in the urine measurement of metabolizable cations and/or anions.

  7. Acid Base Equilibrium in a Lipid/Water Gel

    NASA Astrophysics Data System (ADS)

    Streb, Kristina K.; Ilich, Predrag-Peter

    2003-12-01

    A new and original experiment in which partition of bromophenol blue dye between water and lipid/water gel causes a shift in the acid base equilibrium of the dye is described. The dye-absorbing material is a monoglyceride food additive of plant origin that mixes freely with water to form a stable cubic phase gel; the nascent gel absorbs the dye from aqueous solution and converts it to the acidic form. There are three concurrent processes taking place in the experiment: (a) formation of the lipid/water gel, (b) absorption of the dye by the gel, and (c) protonation of the dye in the lipid/water gel environment. As the aqueous solution of the dye is a deep purple-blue color at neutral pH and yellow at acidic pH the result of these processes is visually striking: the strongly green-yellow particles of lipid/water gel are suspended in purple-blue aqueous solution. The local acidity of the lipid/water gel is estimated by UV vis spectrophotometry. This experiment is an example of host-guest (lipid/water gel dye) interaction and is suitable for project-type biophysics, physical chemistry, or biochemistry labs. The experiment requires three, 3-hour lab sessions, two of which must not be separated by more than two days.

  8. Recent Developments in Peptide-Based Nucleic Acid Delivery

    PubMed Central

    Veldhoen, Sandra; Laufer, Sandra D.; Restle, Tobias

    2008-01-01

    Despite the fact that non-viral nucleic acid delivery systems are generally considered to be less efficient than viral vectors, they have gained much interest in recent years due to their superior safety profile compared to their viral counterpart. Among these synthetic vectors are cationic polymers, branched dendrimers, cationic liposomes and cell-penetrating peptides (CPPs). The latter represent an assortment of fairly unrelated sequences essentially characterised by a high content of basic amino acids and a length of 10–30 residues. CPPs are capable of mediating the cellular uptake of hydrophilic macromolecules like peptides and nucleic acids (e.g. siRNAs, aptamers and antisense-oligonucleotides), which are internalised by cells at a very low rate when applied alone. Up to now, numerous sequences have been reported to show cell-penetrating properties and many of them have been used to successfully transport a variety of different cargos into mammalian cells. In recent years, it has become apparent that endocytosis is a major route of internalisation even though the mechanisms underlying the cellular translocation of CPPs are poorly understood and still subject to controversial discussions. In this review, we will summarise the latest developments in peptide-based cellular delivery of nucleic acid cargos. We will discuss different mechanisms of entry, the intracellular fate of the cargo, correlation studies of uptake versus biological activity of the cargo as well as technical problems and pitfalls. PMID:19325804

  9. Acid-base chemistry of frustrated water at protein interfaces.

    PubMed

    Fernández, Ariel

    2016-01-01

    Water molecules at a protein interface are often frustrated in hydrogen-bonding opportunities due to subnanoscale confinement. As shown, this condition makes them behave as a general base that may titrate side-chain ammonium and guanidinium cations. Frustration-based chemistry is captured by a quantum mechanical treatment of proton transference and shown to remove same-charge uncompensated anticontacts at the interface found in the crystallographic record and in other spectroscopic information on the aqueous interface. Such observations are untenable within classical arguments, as hydronium is a stronger acid than ammonium or guanidinium. Frustration enables a directed Grotthuss mechanism for proton transference stabilizing same-charge anticontacts.

  10. Nutrition, acid-base status and growth in early childhood.

    PubMed

    Kalhoff, H; Manz, F

    2001-10-01

    Optimal growth is only possible in a well-balanced "inner milieu". Premature infants are especially vulnerable for disturbances of acid-base metabolism with a predisposition to metabolic acidosis due to a transient disproportion between age-related low renal capacity for net acid excretion (NAE) and an unphysiologically high actual renal NAE on nutrition with standard formulas. During a 50 month period, 452 low birth-weight infants were screened for spontaneous development of incipient late metabolic acidosis (ILMA), an early stage during the development of retention acidosis, characterized by maximum renal acid stimulation (MRAS, urine-pH < 5.4) on two consecutive days but still compensated systemic acid-base status. Compared with controls, patients with ILMA showed higher serum creatinine values, an increased urinary excretion of sodium, aldosterone and nitrogen, but only slightly lower blood pH (7.38 vs 7.41) and base excess (-2.8 vs. 0.2 mmol/l) with respiratory compensation (PCO2 35 vs 37 mm Hg). Patients with altogether 149 episodes of ILMA were subsequently randomly allocated to either treatment with NaHCO3 2 mmol/kg/d for 7 days or no special therapy in protocol I, or NaHCO3 vs NaCl each 2 mmol/kg/d for 7 days in protocol II. Patients of protocol I with persistent MRAS for 7 days showed lowest weight gain and a tendency for a further increase in urinary aldosterone and nitrogen excretion. NaCl supplementation (protocol II) seemed to promote weight gain without affecting either impaired mineralization or suboptimal nitrogen retention. Patients with alkali therapy under both protocols showed normal weight gain and normalization of hormonal stimulation, mineralization (protocol II) and nitrogen assimilation. Modification of the mineral content of a standard preterm formula decreased renal NAE to the low level seen on alimentation with human milk and reduced the incidence of ILMA in preterm and small-for-gestational-age infants to 1%. The data show that ILMA is

  11. Bench-to-bedside review: a brief history of clinical acid-base.

    PubMed

    Story, David A

    2004-08-01

    The history of assessing the acid-base equilibrium and associated disorders is intertwined with the evolution of the definition of an acid. In the 1950s clinical chemists combined the Henderson-Hasselbalch equation and the Bronsted-Lowry definition of an acid to produce the current bicarbonate ion-centred approach to metabolic acid-base disorders. Stewart repackaged pre-1950 ideas of acid-base in the late 1970s, including the Van Slyke definition of an acid. Stewart also used laws of physical chemistry to produce a new acid-base approach. This approach, using the strong ion difference (particularly the sodium chloride difference) and the concentration of weak acids (particularly albumin), pushes bicarbonate into a minor role as an acid-base indicator rather than as an important mechanism. The Stewart approach may offer new insights into acid-base disorders and therapies.

  12. Acid-base thermochemistry of gaseous oxygen and sulfur substituted amino acids (Ser, Thr, Cys, Met).

    PubMed

    Riffet, Vanessa; Frison, Gilles; Bouchoux, Guy

    2011-11-07

    Acid-base thermochemistry of isolated amino acids containing oxygen or sulfur in their side chain (serine, threonine, cysteine and methionine) have been examined by quantum chemical computations. Density functional theory (DFT) was used, with B3LYP, B97-D and M06-2X functionals using the 6-31+G(d,p) basis set for geometry optimizations and the larger 6-311++G(3df,2p) basis set for energy computations. Composite methods CBS-QB3, G3B3, G4MP2 and G4 were applied to large sets of neutral, protonated and deprotonated conformers. Conformational analysis of these species, based on chemical approach and AMOEBA force field calculations, has been used to identify the lowest energy conformers and to estimate the population of conformers expected to be present at thermal equilibrium at 298 K. It is observed that G4, G4MP2, G3B3, CBS-QB3 composite methods and M06-2X DFT lead to similar conformer energies. Thermochemical parameters have been computed using either the most stable conformers or equilibrium populations of conformers. Comparison of experimental and theoretical proton affinities and Δ(acid)H shows that the G4 method provides the better agreement with deviations of less than 1.5 kJ mol(-1). From this point of view, a set of evaluated thermochemical quantities for serine, threonine, cysteine and methionine may be proposed: PA = 912, 919, 903, 938; GB = 878, 886, 870, 899; Δ(acid)H = 1393, 1391, 1396, 1411; Δ(acid)G = 1363, 1362, 1367, 1382 kJ mol(-1). This study also confirms that a non-negligible ΔpS° is associated with protonation of methionine and that the most acidic hydrogen of cysteine in the gas phase is that of the SH group. In several instances new conformers were identified thus suggesting a re-examination of several IRMPD spectra. This journal is © the Owner Societies 2011

  13. A mathematical model of blood-interstitial acid-base balance: application to dilution acidosis and acid-base status.

    PubMed

    Wolf, Matthew B; Deland, Edward C

    2011-04-01

    We developed mathematical models that predict equilibrium distribution of water and electrolytes (proteins and simple ions), metabolites, and other species between plasma and erythrocyte fluids (blood) and interstitial fluid. The models use physicochemical principles of electroneutrality in a fluid compartment and osmotic equilibrium between compartments and transmembrane Donnan relationships for mobile species. Across the erythrocyte membrane, the significant mobile species Cl⁻ is assumed to reach electrochemical equilibrium, whereas Na(+) and K(+) distributions are away from equilibrium because of the Na(+)/K(+) pump, but movement from this steady state is restricted because of their effective short-term impermeability. Across the capillary membrane separating plasma and interstitial fluid, Na(+), K(+), Ca²(+), Mg²(+), Cl⁻, and H(+) are mobile and establish Donnan equilibrium distribution ratios. In each compartment, attainment of equilibrium by carbonates, phosphates, proteins, and metabolites is determined by their reactions with H(+). These relationships produce the recognized exchange of Cl(-) and bicarbonate across the erythrocyte membrane. The blood submodel was validated by its close predictions of in vitro experimental data, blood pH, pH-dependent ratio of H(+), Cl⁻, and HCO₃⁻ concentrations in erythrocytes to that in plasma, and blood hematocrit. The blood-interstitial model was validated against available in vivo laboratory data from humans with respiratory acid-base disorders. Model predictions were used to gain understanding of the important acid-base disorder caused by addition of saline solutions. Blood model results were used as a basis for estimating errors in base excess predictions in blood by the traditional approach of Siggaard-Andersen (acid-base status) and more recent approaches by others using measured blood pH and Pco₂ values. Blood-interstitial model predictions were also used as a basis for assessing prediction errors of

  14. Age estimation based on aspartic acid racemization in human sclera.

    PubMed

    Klumb, Karolin; Matzenauer, Christian; Reckert, Alexandra; Lehmann, Klaus; Ritz-Timme, Stefanie

    2016-01-01

    Age estimation based on racemization of aspartic acid residues (AAR) in permanent proteins has been established in forensic medicine for years. While dentine is the tissue of choice for this molecular method of age estimation, teeth are not always available which leads to the need to identify other suitable tissues. We examined the suitability of total tissue samples of human sclera for the estimation of age at death. Sixty-five samples of scleral tissue were analyzed. The samples were hydrolyzed and after derivatization, the extent of aspartic acid racemization was determined by gas chromatography. The degree of AAR increased with age. In samples from younger individuals, the correlation of age and D-aspartic acid content was closer than in samples from older individuals. The age-dependent racemization in total tissue samples proves that permanent or at least long-living proteins are present in scleral tissue. The correlation of AAR in human sclera and age at death is close enough to serve as basis for age estimation. However, the precision of age estimation by this method is lower than that of age estimation based on the analysis of dentine which is due to molecular inhomogeneities of total tissue samples of sclera. Nevertheless, the approach may serve as a valuable alternative or addition in exceptional cases.

  15. Acid-base catalysis of N-[(morpholine)methylene]daunorubicin.

    PubMed

    Krause, Anna; Jelińska, Anna; Cielecka-Piontek, Judyta; Klawitter, Maria; Zalewski, Przemysław; Oszczapowicz, Irena; Wąsowska, Małgorzata

    2012-08-01

    The stability of N-[(morpholine)methylene]-daunorubicin hydrochloride (MMD) was investigated in the pH range 0.44-13.54, at 313, 308, 303 and 298 K. The degradation of MMD as a result of hydrolysis is a pseudo-first-order reaction described by the following equation: ln c = ln c(0) - k(obs)• t. In the solutions of hydrochloric acid, sodium hydroxide, borate, acetate and phosphate buffers, k(obs) = k(pH) because general acid-base catalysis was not observed. Specific acid-base catalysis of MMD comprises the following reactions: hydrolysis of the protonated molecules of MMD catalyzed by hydrogen ions (k(1)) and spontaneous hydrolysis of MMD molecules other than the protonated ones (k(2)) under the influence of water. The total rate of the reaction is equal to the sum of partial reactions: k(pH) = k(1) • a(H)+ • f(1) + k(2) • f(2) where: k(1) is the second-order rate constant (mol(-1) l s(-1)) of the specific hydrogen ion-catalyzed degradation of the protonated molecules of MMD; k(2) is the pseudo-first-order rate constant (s(-1)) of the water-catalyzed degradation of MMD molecules other than the protonated ones, f(1) - f(2) are fractions of the compound. MMD is the most stable at approx. pH 2.5.

  16. A microarray-based method to perform nucleic acid selections.

    PubMed

    Aminova, Olga; Disney, Matthew D

    2010-01-01

    This method describes a microarray-based platform to perform nucleic acid selections. Chemical ligands to which a nucleic acid binder is desired are immobilized onto an agarose microarray surface; the array is then incubated with an RNA library. Bound RNA library members are harvested directly from the array surface via gel excision at the position on the array where a ligand was immobilized. The RNA is then amplified via RT-PCR, cloned, and sequenced. This method has the following advantages over traditional resin-based Systematic Evolution of Ligands by Exponential Enrichment (SELEX): (1) multiple selections can be completed in parallel on a single microarray surface; (2) kinetic biases in the selections are mitigated since all RNA binders are harvested from an array via gel excision; (3) the amount of chemical ligand needed to perform a selection is minimized; (4) selections do not require expensive resins or equipment; and (5) the matrix used for selections is inexpensive and easy to prepare. Although this protocol was demonstrated for RNA selections, it should be applicable for any nucleic acid selection.

  17. Renal regulation of acid-base equilibrium during chronic administration of mineral acid.

    PubMed Central

    De Sousa, R C; Harrington, J T; Ricanati, E S; Shelkrot, J W; Schwartz, W B

    1974-01-01

    load is the inability of the distal exchange mechanism to conserve the Na+ increment fully by means of H+ exchange. Escape of Na+ and K+ into the urine and the resulting stimulus to Na(+)-H+ exchange remove this constraint and are responsible for establishment of a new steady-state of acid-base equilibrium at plasma [HCO3-] levels significantly higher than those seen with HCl. The feeding of HCl in the presence of a normal salt intake led to a degree of metabolic acidosis not significantly different from that seen in dogs ingesting a low-salt diet. We suggest that the presence of dietary sodium at distal exchange sites did not enhance acid excretion because it is only after a loss of body sodium stores that sodium avidity is increased sufficiently to allow full removal of the acid load. The present findings indicate that the fundamental factors controlling acid excretion and bicarbonate reabsorption in metabolic acidosis are closely similar to those operative in metabolic alkalosis. PMID:11344560

  18. How Do Undergraduate Students Conceptualize Acid-Base Chemistry? Measurement of a Concept Progression

    ERIC Educational Resources Information Center

    Romine, William L.; Todd, Amber N.; Clark, Travis B.

    2016-01-01

    We developed and validated a new instrument, called "Measuring Concept progressions in Acid-Base chemistry" (MCAB) and used it to better understand the progression of undergraduate students' understandings about acid-base chemistry. Items were developed based on an existing learning progression for acid-base chemistry. We used the Rasch…

  19. How Do Undergraduate Students Conceptualize Acid-Base Chemistry? Measurement of a Concept Progression

    ERIC Educational Resources Information Center

    Romine, William L.; Todd, Amber N.; Clark, Travis B.

    2016-01-01

    We developed and validated a new instrument, called "Measuring Concept progressions in Acid-Base chemistry" (MCAB) and used it to better understand the progression of undergraduate students' understandings about acid-base chemistry. Items were developed based on an existing learning progression for acid-base chemistry. We used the Rasch…

  20. Reaction mechanisms of riboflavin triplet state with nucleic acid bases.

    PubMed

    Lin, Weizhen; Lu, Changyuan; Du, Fuqiang; Shao, Zhiyong; Han, Zhenhui; Tu, Tiecheng; Yao, Side; Lin, Nianyun

    2006-04-01

    ESR and laser flash photolysis studies have determined a reasonable order of reactivity of nucleotides with triplet riboflavin (3Rb*) for the first time. ESR detection of triplet state reactivity of Rb with nucleoside, polynucleotide and DNA has been obtained simultaneously. In addition, ESR spin elimination measurement of the reactivity of 3Rb* with nucleotides in good accord with laser flash photolysis determination of the corresponding rate constants offers a simple and reliable method to detect the reactivities of nucleic acids and its components with photoexcited flavins. Kinetic, ESR and thermodynamic studies have demonstrated that Rb should be a strong endogenous photosensitizer capable of oxidizing all nucleic acid bases, and preferentially two purine nucleotides with high rate constants.

  1. Urea biosensors based on PVC membrane containing palmitic acid.

    PubMed

    Karakuş, Emine; Pekyardimci, Sule; Esma, Kiliç

    2005-01-01

    A new urea biosensor was prepared by immobilizing urease with four different procedures on poly(vinylchloride) (PVC) ammonium membrane electrode containing palmitic acid by using nonactine as an ammonium-ionophore. The analytical characteristics were investigated and were compared those of the biosensor prepared by using carboxylated PVC. The effect of pH, buffer concentration, temperature, urease concentration, stirring rate and enzyme immobilization procedures on the response to urea of the enzyme electrode were investigated. The linear working range and sensitivity of the biosensor were also determined. The urea biosensor prepared by using the PVC membranes containing palmitic acid showed more effective performance than those of the carboxylated PVC based biosensors. Additionally, urea assay in serum was successfully carried out by using the standard addition method.

  2. Bio-based production of organic acids with Corynebacterium glutamicum

    PubMed Central

    Wieschalka, Stefan; Blombach, Bastian; Bott, Michael; Eikmanns, Bernhard J

    2013-01-01

    The shortage of oil resources, the steadily rising oil prices and the impact of its use on the environment evokes an increasing political, industrial and technical interest for development of safe and efficient processes for the production of chemicals from renewable biomass. Thus, microbial fermentation of renewable feedstocks found its way in white biotechnology, complementing more and more traditional crude oil-based chemical processes. Rational strain design of appropriate microorganisms has become possible due to steadily increasing knowledge on metabolism and pathway regulation of industrially relevant organisms and, aside from process engineering and optimization, has an outstanding impact on improving the performance of such hosts. Corynebacterium glutamicum is well known as workhorse for the industrial production of numerous amino acids. However, recent studies also explored the usefulness of this organism for the production of several organic acids and great efforts have been made for improvement of the performance. This review summarizes the current knowledge and recent achievements on metabolic engineering approaches to tailor C. glutamicum for the bio-based production of organic acids. We focus here on the fermentative production of pyruvate, l-and d-lactate, 2-ketoisovalerate, 2-ketoglutarate, and succinate. These organic acids represent a class of compounds with manifold application ranges, e.g. in pharmaceutical and cosmetics industry, as food additives, and economically very interesting, as precursors for a variety of bulk chemicals and commercially important polymers. Funding Information Work in the laboratories of the authors was supported by the Fachagentur Nachwachsende Rohstoffe (FNR) of the Bundesministerium für Ernährung, Landwirtschaft und Verbraucherschutz (BMELV; FNR Grants 220-095-08A and 220-095-08D; Bio-ProChemBB project, ERA-IB programme), by the Deutsche Bundesstiftung Umwelt (DBU Grant AZ13040/05) and the Evonik Degussa AG. PMID

  3. Superabsorbent biphasic system based on poly(lactic acid) and poly(acrylic acid)

    NASA Astrophysics Data System (ADS)

    Sartore, Luciana; Pandini, Stefano; Baldi, Francesco; Bignotti, Fabio

    2016-05-01

    In this research work, biocomposites based on crosslinked particles of poly(acrylic acid), commonly used as superabsorbent polymer (SAP), and poly-L-lactic acid (PLLA) were developed to elucidate the role of the filler (i.e., polymeric crosslinked particles) on the overall physico-mechanical behavior and to obtain superabsorbent thermoplastic products. Samples prepared by melt-blending of components in different ratios showed a biphasic system with a regular distribution of particles, with diameter ranging from 5 to 10 μm, within the PLLA polymeric matrix. The polymeric biphasic system, coded PLASA i.e. superabsorbent poly(lactic acid), showed excellent swelling properties, demonstrating that cross-linked particles retain their superabsorbent ability, as in their free counterparts, even if distributed in a thermoplastic polymeric matrix. The thermal characteristics of the biocomposites evidence enhanced thermal stability in comparison with neat PLLA and also mechanical properties are markedly modified by addition of crosslinked particles which induce regular stiffening effect. Furthermore, in aqueous environments the particles swell and are leached from PLLA matrix generating very high porosity. These new open-pore PLLA foams, produced in absence of organic solvents and chemical foaming agents, with good physico-mechanical properties appear very promising for several applications, for instance in tissue engineering for scaffold production.

  4. General analytical procedure for determination of acidity parameters of weak acids and bases.

    PubMed

    Pilarski, Bogusław; Kaliszan, Roman; Wyrzykowski, Dariusz; Młodzianowski, Janusz; Balińska, Agata

    2015-01-01

    The paper presents a new convenient, inexpensive, and reagent-saving general methodology for the determination of pK a values for components of the mixture of diverse chemical classes weak organic acids and bases in water solution, without the need to separate individual analytes. The data obtained from simple pH-metric microtitrations are numerically processed into reliable pK a values for each component of the mixture. Excellent agreement has been obtained between the determined pK a values and the reference literature data for compounds studied.

  5. General Analytical Procedure for Determination of Acidity Parameters of Weak Acids and Bases

    PubMed Central

    Pilarski, Bogusław; Kaliszan, Roman; Wyrzykowski, Dariusz; Młodzianowski, Janusz; Balińska, Agata

    2015-01-01

    The paper presents a new convenient, inexpensive, and reagent-saving general methodology for the determination of pK a values for components of the mixture of diverse chemical classes weak organic acids and bases in water solution, without the need to separate individual analytes. The data obtained from simple pH-metric microtitrations are numerically processed into reliable pK a values for each component of the mixture. Excellent agreement has been obtained between the determined pK a values and the reference literature data for compounds studied. PMID:25692072

  6. Equilibrium of acidifying and alkalinizing metabolic acid-base disorders in cirrhosis.

    PubMed

    Funk, Georg-Christian; Doberer, Daniel; Osterreicher, Christoph; Peck-Radosavljevic, Markus; Schmid, Monika; Schneeweiss, Bruno

    2005-06-01

    Conflicting results exist with regard to metabolic acid-base status in liver cirrhosis, when the classic concept of acid-base analysis is applied. The influence of the common disturbances of water, electrolytes and albumin on acid-base status in cirrhosis has not been studied. The aim of this study was to clarify acid-base status in cirrhotic patients by analyzing all parameters with possible impact on acid-base equilibrium. Fifty stable cirrhotic patients admitted to a university hospital. Arterial acid-base status was analyzed using the principles of physical chemistry and compared with 10 healthy controls. Apart from mild hypoalbuminemic alkalosis, acid-base state was normal in Child-Pugh A cirrhosis. Respiratory alkalosis was the net acid-base disorder in Child-Pugh B and C cirrhosis with a normal overall metabolic acid-base state (Base excess-1.0 (-3.6 to 1.6) vs 1.1 (-0.2 to 1.1) mmol/l, P = 0.136, compared with healthy controls, median (interquartile range)). Absence of an apparent metabolic acid-base disorder was based on an equilibrium of hypoalbuminemic alkalosis and of dilutional acidosis and hyperchloremic acidosis. A balance of offsetting acidifying and alkalinizing metabolic acid-base disorders leaves the net metabolic acid-base status unchanged in cirrhosis.

  7. Analytic calculation of physiological acid-base parameters in plasma.

    PubMed

    Wooten, E W

    1999-01-01

    Analytic expressions for plasma total titratable base, base excess (DeltaCB), strong-ion difference, change in strong-ion difference (DeltaSID), change in Van Slyke standard bicarbonate (DeltaVSSB), anion gap, and change in anion gap are derived as a function of pH, total buffer ion concentration, and conditional molar equilibrium constants. The behavior of these various parameters under respiratory and metabolic acid-base disturbances for constant and variable buffer ion concentrations is considered. For constant noncarbonate buffer concentrations, DeltaSID = DeltaCB = DeltaVSSB, whereas these equalities no longer hold under changes in noncarbonate buffer concentration. The equivalence is restored if the reference state is changed to include the new buffer concentrations.

  8. Functional nucleic-acid-based sensors for environmental monitoring.

    PubMed

    Sett, Arghya; Das, Suradip; Bora, Utpal

    2014-10-01

    Efforts to replace conventional chromatographic methods for environmental monitoring with cheaper and easy to use biosensors for precise detection and estimation of hazardous environmental toxicants, water or air borne pathogens as well as various other chemicals and biologics are gaining momentum. Out of the various types of biosensors classified according to their bio-recognition principle, nucleic-acid-based sensors have shown high potential in terms of cost, sensitivity, and specificity. The discovery of catalytic activities of RNA (ribozymes) and DNA (DNAzymes) which could be triggered by divalent metallic ions paved the way for their extensive use in detection of heavy metal contaminants in environment. This was followed with the invention of small oligonucleotide sequences called aptamers which can fold into specific 3D conformation under suitable conditions after binding to target molecules. Due to their high affinity, specificity, reusability, stability, and non-immunogenicity to vast array of targets like small and macromolecules from organic, inorganic, and biological origin, they can often be exploited as sensors in industrial waste management, pollution control, and environmental toxicology. Further, rational combination of the catalytic activity of DNAzymes and RNAzymes along with the sequence-specific binding ability of aptamers have given rise to the most advanced form of functional nucleic-acid-based sensors called aptazymes. Functional nucleic-acid-based sensors (FNASs) can be conjugated with fluorescent molecules, metallic nanoparticles, or quantum dots to aid in rapid detection of a variety of target molecules by target-induced structure switch (TISS) mode. Although intensive research is being carried out for further improvements of FNAs as sensors, challenges remain in integrating such bio-recognition element with advanced transduction platform to enable its use as a networked analytical system for tailor made analysis of environmental

  9. Determination of the Acid-Base Dissociation Constant of Acid-Degradable Hexamethylenetetramine by Capillary Zone Electrophoresis.

    PubMed

    Takayanagi, Toshio; Shimakami, Natsumi; Kurashina, Masashi; Mizuguchi, Hitoshi; Yabutani, Tomoki

    2016-01-01

    The acid-base equilibrium of hexamethylenetetramine (hexamine) was analyzed with its effective electrophoretic mobility by capillary zone electrophoresis. Although hexamine is degradable in a weakly acidic aqueous solution, and the degraded products of ammonia and formaldehyde can be formed, the effective electrophoretic mobility of hexamine was measured in the pH range between 2.8 and 6.9. An acid-base dissociation equilibrium of the protonated hexamine was analyzed based on the mobility change, and an acid dissociation constant of pKa = 4.93 ± 0.01 (mean ± standard error, ionic strength: 0.020 mol dm(-3)) was determined. The monoprotic acid-base equilibrium of hexamine was confirmed through comparisons of its electrophoretic mobility with the N-ethylquinolinium ion and with the monocationic N-ethyl derivative of hexamine, as well as a slope analysis of the dissociation equilibrium.

  10. Fatty acid based hyperbranched polymeric nanoparticles for hydrophobic drug delivery.

    PubMed

    Güç, Esra; Gündüz, Güngör; Gündüz, Ufuk

    2010-10-01

    In recent years nano-sized dendrimer/hyperbranched polymers gained importance in drug delivery applications. In this study, a novel fatty acid-based hyperbranched resin (HBR) was synthesized and used for tamoxifen (TAM) and idarubicin (IDA) delivery. The core of the HBR was dipentaerythritol, and the branching was provided by dimethylolpropionic acid. The molecule was terminated by ricinoleic acid. Chemical and structural characterization of the resin was carried out and then drug-loading experiments were performed. The loading efficiencies were found to be 73.3% for TAM and 74% for IDA. The Fourier transform infrared spectroscopy analysis showed that TAM physically bounded onto the resin whereas IDA interacted chemically. Controlled release in phosphate buffer was improved by Pseudomonas sp. lipase and sodium dodecyl sulfate. The release rates decreased with the increase of loading concentrations. The cytotoxicity analyses were carried out on MCF-7 breast cancer cells for both drug-free and drug-loaded HBR. Drug-free particles did not have significant toxicity. Drug-loaded nanoparticles caused higher levels of cell death than pure drugs.

  11. Liquid crystal based biosensors for bile acid detection

    NASA Astrophysics Data System (ADS)

    He, Sihui; Liang, Wenlang; Tanner, Colleen; Fang, Jiyu; Wu, Shin-Tson

    2013-03-01

    The concentration level of bile acids is a useful indicator for early diagnosis of liver diseases. The prevalent measurement method in detecting bile acids is the chromatography coupled with mass spectrometry, which is precise yet expensive. Here we present a biosensor platform based on liquid crystal (LC) films for the detection of cholic acid (CA). This platform has the advantage of low cost, label-free, solution phase detection and simple analysis. In this platform, LC film of 4-Cyano-4'-pentylbiphenyl (5CB) was hosted by a copper grid supported with a polyimide-coated glass substrate. By immersing into sodium dodecyl sulfate (SDS) solution, the LC film was coated with SDS which induced a homeotropic anchoring of 5CB. Addition of CA introduced competitive adsorption between CA and SDS at the interface, triggering a transition from homeotropic to homogeneous anchoring. The detection limit can be tuned by changing the pH value of the solution from 12uM to 170uM.

  12. A homogeneous nucleic acid hybridization assay based on strand displacement.

    PubMed Central

    Vary, C P

    1987-01-01

    A homogeneous nucleic acid hybridization assay which is conducted in solution and requires no separation steps is described. The assay is based on the concept of strand displacement. In the strand displacement assay, an RNA "signal strand" is hybridized within a larger DNA strand termed the "probe strand", which is, in turn, complementary to the target nucleic acid of interest. Hybridization of the target nucleic acid with the probe strand ultimately results in displacement of the RNA signal strand. Strand displacement, therefore, causes conversion of the RNA from double to single-stranded form. The single-strand specificity of polynucleotide phosphorylase (EC 2.7.7.8) allows discrimination between double-helical and single-stranded forms of the RNA signal strand. As displacement proceeds, free RNA signal strands are preferentially phosphorolyzed to component nucleoside diphosphates, including adenosine diphosphate. The latter nucleotide is converted to ATP by pyruvate kinase(EC 2.7.1.40). Luciferase catalyzed bioluminescence is employed to measure the ATP generated as a result of strand displacement. Images PMID:3309890

  13. Paediatric acid-base disorders: A case-based review of procedures and pitfalls

    PubMed Central

    Carmody, J Bryan; Norwood, Victoria F

    2013-01-01

    Acid-base disorders occur frequently in paediatric patients. Despite the perception that their analysis is complex and difficult, a straightforward set of rules is sufficient to interpret even the most complex disorders – provided certain pitfalls are avoided. Using a case-based approach, the present article reviews the fundamental concepts of acid-base analysis and highlights common mistakes and oversights. Specific topics include the proper identification of the primary disorder; distinguishing compensatory changes from additional primary disorders; use of the albumin-corrected anion gap to generate a differential diagnosis for patients with metabolic acidosis; screening for mixed disorders with the delta-delta formula; recognizing the limits of compensation; use of the anion gap to identify ‘hidden’ acidosis; and the importance of using information from the history and physical examination to identify the specific cause of a patient’s acid-base disturbance. PMID:24381489

  14. A fully automatic system for acid-base coulometric titrations

    PubMed Central

    Cladera, A.; Caro, A.; Estela, J. M.; Cerdà, V.

    1990-01-01

    An automatic system for acid-base titrations by electrogeneration of H+ and OH- ions, with potentiometric end-point detection, was developed. The system includes a PC-compatible computer for instrumental control, data acquisition and processing, which allows up to 13 samples to be analysed sequentially with no human intervention. The system performance was tested on the titration of standard solutions, which it carried out with low errors and RSD. It was subsequently applied to the analysis of various samples of environmental and nutritional interest, specifically waters, soft drinks and wines. PMID:18925283

  15. Acid-Base Homeostasis: Overview for Infusion Nurses.

    PubMed

    Masco, Natalie A

    2016-01-01

    Acid-base homeostasis is essential to normal function of the human body. Even slight alterations can significantly alter physiologic processes at the tissue and cellular levels. To optimally care for patients, nurses must be able to recognize signs and symptoms that indicate deviations from normal. Nurses who provide infusions to patients-whether in acute care, home care, or infusion center settings-have a responsibility to be able to recognize the laboratory value changes that occur with the imbalance and appreciate the treatment options, including intravenous infusions.

  16. Biofuncationalized microfiber Bragg grating for acid-based sensing

    NASA Astrophysics Data System (ADS)

    Ran, Yang; Huang, Yunyun; Shen, Xiang; Sun, Dandan; Wang, Xiuxin; Jin, Long; Li, Jie; Guan, Baiou

    2014-05-01

    We demonstrate an acid-based sensor from the biofuncationalized microfiber Bragg grating. By electrostatic selfassembly layer-by-layer technique, the film consisting of sodium alginate which has hygroscopic response to the potential of hydrogen is coated on the fiber surface. Consequently, the refractive index variation of the sensing film caused by water absorption can be measured by mFBG's higher order mode peak which can be translated into pH value information. The sensitivity of the sensor is received as high as 265pm/pH.

  17. DNA-Based Applications in Nanobiotechnology

    PubMed Central

    Abu-Salah, Khalid M.; Ansari, Anees A.; Alrokayan, Salman A.

    2010-01-01

    Biological molecules such as deoxyribonucleic acid (DNA) have shown great potential in fabrication and construction of nanostructures and devices. The very properties that make DNA so effective as genetic material also make it a very suitable molecule for programmed self-assembly. The use of DNA to assemble metals or semiconducting particles has been extended to construct metallic nanowires and functionalized nanotubes. This paper highlights some important aspects of conjugating the unique physical properties of dots or wires with the remarkable recognition capabilities of DNA which could lead to miniaturizing biological electronics and optical devices, including biosensors and probes. Attempts to use DNA-based nanocarriers for gene delivery are discussed. In addition, the ecological advantages and risks of nanotechnology including DNA-based nanobiotechnology are evaluated. PMID:20652049

  18. Predicting the Viscosity of Low VOC Vinyl Ester and Fatty Acid-Based Resins

    DTIC Science & Technology

    2005-12-01

    The sample was titrated with the perchloric acid / peracetic acid solution (Aldrich) until the indicator, 0.1% crystal violet in acetic acid (Aldrich...Predicting the Viscosity of Low VOC Vinyl Ester and Fatty Acid -Based Resins by John J. La Scala, Amutha Jeyarajasingam, Cherise Winston...Aberdeen Proving Ground, MD 21005-5069 ARL-TR-3681 December 2005 Predicting the Viscosity of Low VOC Vinyl Ester and Fatty Acid -Based

  19. 78 FR 36698 - Microbiology Devices; Reclassification of Nucleic Acid-Based Systems for Mycobacterium tuberculosis

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-19

    ... Nucleic Acid-Based Systems for Mycobacterium tuberculosis Complex in Respiratory Specimens AGENCY: Food...) is proposing to reclassify nucleic acid-based in vitro diagnostic devices for the detection of... Controls Guideline: Nucleic Acid-Based In Vitro Diagnostic Devices for the Detection of Mycobacterium...

  20. Soluble adenylyl cyclase is an acid-base sensor in epithelial base-secreting cells.

    PubMed

    Roa, Jinae N; Tresguerres, Martin

    2016-08-01

    Blood acid-base regulation by specialized epithelia, such as gills and kidney, requires the ability to sense blood acid-base status. Here, we developed primary cultures of ray (Urolophus halleri) gill cells to study mechanisms for acid-base sensing without the interference of whole animal hormonal regulation. Ray gills have abundant base-secreting cells, identified by their noticeable expression of vacuolar-type H(+)-ATPase (VHA), and also express the evolutionarily conserved acid-base sensor soluble adenylyl cyclase (sAC). Exposure of cultured cells to extracellular alkalosis (pH 8.0, 40 mM HCO3 (-)) triggered VHA translocation to the cell membrane, similar to previous reports in live animals experiencing blood alkalosis. VHA translocation was dependent on sAC, as it was blocked by the sAC-specific inhibitor KH7. Ray gill base-secreting cells also express transmembrane adenylyl cyclases (tmACs); however, tmAC inhibition by 2',5'-dideoxyadenosine did not prevent alkalosis-dependent VHA translocation, and tmAC activation by forskolin reduced the abundance of VHA at the cell membrane. This study demonstrates that sAC is a necessary and sufficient sensor of extracellular alkalosis in ray gill base-secreting cells. In addition, this study indicates that different sources of cAMP differentially modulate cell biology. Copyright © 2016 the American Physiological Society.