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1.
Emily Eva Holmes Maria Jung Sebastian Meller Annette Leisse Verena Sailer Julie Zech Martina Mengdehl Leif-Alexander Garbe Barbara Uhl Glen Kristiansen Dimo Dietrich 《PloS one》2014,9(4)
DNA methylation analyses usually require a preceding bisulfite conversion of the DNA. The choice of an appropriate kit for a specific application should be based on the specific performance requirements with regard to the respective sample material. In this study, the performance of nine kits was evaluated: EpiTect Fast FFPE Bisulfite Kit, EpiTect Bisulfite Kit, EpiTect Fast DNA Bisulfite Kit (Qiagen), EZ DNA Methylation-Gold Kit, EZ DNA Methylation-Direct Kit, EZ DNA Methylation-Lightning Kit (Zymo Research), innuCONVERT Bisulfite All-In-One Kit, innuCONVERT Bisulfite Basic Kit, innuCONVERT Bisulfite Body Fluids Kit (Analytik Jena). The kit performance was compared with regard to DNA yield, DNA degradation, DNA purity, conversion efficiency, stability and handling using qPCR, UV, clone sequencing, HPLC, and agarose gel electrophoresis. All kits yielded highly pure DNA suitable for PCR analyses without PCR inhibition. Significantly higher yields were obtained when using the EZ DNA Methylation-Gold Kit and the innuCONVERT Bisulfite kits. Conversion efficiency ranged from 98.7% (EpiTect Bisulfite Kit) to 99.9% (EZ DNA Methylation-Direct Kit). The inappropriate conversion of methylated cytosines to thymines varied between 0.9% (innuCONVERT Bisulfite kits) and 2.7% (EZ DNA Methylation-Direct Kit). Time-to-result ranged from 131 min (innuCONVERT kits) to 402 min (EpiTect Bisulfite Kit). Hands-on-time was between 66 min (EZ DNA Methylation-Lightning Kit) and 104 min (EpiTect Fast FFPE and Fast DNA Bisulfite kits). Highest yields from formalin-fixed and paraffin-embedded (FFPE) tissue sections without prior extraction were obtained using the innuCONVERT Bisulfite All-In-One Kit while the EZ DNA Methylation-Direct Kit yielded DNA with only low PCR-amplifiability. The innuCONVERT Bisulfite All-In-One Kit exhibited the highest versatility regarding different input sample materials (extracted DNA, tissue, FFPE tissue, cell lines, urine sediment, and cellular fractions of bronchial aspirates, pleural effusions, ascites). The innuCONVERT Bisulfite Body Fluids Kit allowed for the analysis of 3 ml plasma, serum, ascites, pleural effusions and urine. 相似文献
2.
The aim of this report has been to present results concerning analytical quality controls of Hg analysis of fish and sediment, analyses of Fe, Ca, total-P, K, pH, alkalinity, conductivity, colour and hardness (Ca + Mg) of lake water samples. Despite the fact that these are standard parameters in many regular water control programs, there are major differences in the reliability with which these parameters can be determined. The focus here is on an overall inter-laboratory comparison between the parameters. Six laboratories have been involved in the analysis. Selected results: pH gives the lowest (average) relative standard deviation (error), about 2 %; conductivity gives an error of about 5–7 %; alkalinity yields an average error of as much as 13–25 %, which is the largest among the parameters studied here; colour also gives a high error, 9–15 %; hardness gives a relative standard deviation of about 6–7 %. Of the other parameters (i. e., Hg, Fe, Ca and P), Hg gives the best reliability and Fe and P the lowest. To have knowledge of the reliability of the analytical data is of paramount importance in most control programs and research projects. 相似文献
3.
Isogenic Escherichia coli strains carrying single DNA-repair mutations were compared for their capacity for (i) the repair of X-ray-induced DNA double-strand breaks (DSB) as measured using neutral sucrose gradients; (ii) medium-dependent resistance, i.e., a recA-dependent X-ray survival phenomenon that correlates closely with the capacity for repairing DSB; and (iii) the growth medium-dependent, recA-dependent repair of X-ray-induced DNA single-strand breaks (SSB) as measured using alkaline sucrose gradients (about 80% of these SSB are actually parts of DSB). These three capacities were measured to quantitate more accurately the involvement of the various genes in the repair of DSB over a wide dose range. The mutations tested were grouped into five classes according to their effect on the repair of X-ray-induced DSB: (I) the recA, recB, recC, and lexA mutants were completely deficient; (II) the radB and recN mutants were about 90% deficient; (III) the recF and recJ mutants were about 70% deficient; (IV) the radA and uvrD mutants were about 30% deficient; and (V) the umuC mutant resembled the wild-type strains in its capacity for the repair of DSB. 相似文献
4.
The unitary conductances and permeability sequences of the rat connexin40 (rCx40) gap junction channels to seven monovalent cations and anions were studied in rCx40-transfected neuroblastoma 2A (N2A) cell pairs using the dual whole cell recording technique. Chloride salt cation substitutions (115 mM principal salt) resulted in the following junctional maximal single channel current-voltage relationship slope conductances (γj in pS): CsCl (153), RbCl (148), KCl (142), NaCl (115), LiCl (86), TMACl (71), TEACl (63). Reversible block of the rCx40 channel was observed with TBA. Potassium anion salt γj are: Kglutamate (160), Kacetate (160), Kaspartate (158), KNO3 (157), KF (148), KCl (142), and KBr (132). Ion selectivity was verified by measuring reversal potentials for current in rCx40 gap junction channels with asymmetric salt solutions in the two electrodes and using the Goldman-Hodgkin-Katz equation to calculate relative permeabilities. The permeabilities relative to Li+ are: Cs+ (1.38), Rb+ (1.32), K+ (1.31), Na+ (1.16), TMA+ (0.53), TEA+ (0.45), TBA+ (0.03), Cl− (0.19), glutamate− (0.04), and NO3− (0.14), assuming that the monovalent anions permeate the channel by forming ion pairs with permeant monovalent cations within the pore thereby causing proportionate decreases in the channel conductance. This hypothesis can account for why the predicted increasing conductances with increasing ion mobilities in an essentially aqueous channel were not observed for anions in the rCx40 channel. The rCx40 effective channel radius is estimated to be 6.6 Å from a theoretical fit of the relationship of relative permeability and cation radius. 相似文献
5.
Acute and chronic toxicity tests for malathion, diazinon, copper (Cu), mercury (Hg), lead (Pb), zinc (Zn), nickel (Ni), and
iron (Fe) were conducted. Mortalities ofBarilius vagra andCyprinus carpio (common carp) were variable but LC50-96 hr were similar for pesticides. AdultB. vagra seem to be more sensitive to malathion than juvenile carp. Both juvenile carp and adultB. vagra were extremely sensitive to diazinon. Long-term exposure to pesticides modified morphology and behavior. The LC50-96 values
for Cu, Hg, and Pb were 0.3, 0.16, and 0.44, respectively, for smaller fish and 1.0, 0.77, and 1.33, respectively, for larger
fish. Replicate LC50 values for Zn, Ni, and Fe were somewhat variable, and for these metals, the size of the fish seemed to
affect response because LC50 values increased as fish size increased. Cooper, Pb, Zn, and Fe residues following exposure to
sublethal concentrations of these metals for 15 d were significantly greater in whole juvenile common carp than in controls. 相似文献
6.
DAVID R. SMITH 《Systematic Entomology》1988,13(2):205-261
Abstract Eight families of Symphyta for the Western Hemisphere south of the United States are reviewed: Xyelidae (one genus, two species), Pamphiliidae (one genus, four species), Cimbicidae (five genera, nine species), Diprionidae (three genera, thirteen species), Xiphydriidae (four genera, seventeen species), Siricidae (six genera, nine species), Orussidae (five genera, twelve species), and Cephidae (one genus, one species). New taxa are Acantholyda nigrostigmata (Pamphiliidae); Zadiprionfalsus, Neodiprion bicolor, N.equalis, N.omosus (Diprionidae); Derecyrta circularis, Steirocephala lateralba (Xiphydriidae); Sirotremex, S.flammeus (Siricidae); and Ophrynopus depressatus, O.plaumanni (Orussidae). Lopesiana is a new name for Lopesia Conde (Cimbicidae). Three new combinations and six new synonyms are proposed. The Xyelidae, Pamphiliidae, Diprionidae, Siricidae and Cephidae are primarily northern groups with southern extensions into Mexico, Central America and/or Cuba. The Cimbicidae, Xiphydriidae and Orussidae are more generally distributed throughout the neotropics. Keys to families, genera and species are provided. 相似文献
7.
T L Yaksh S R Michener J E Bailey G J Harty D L Lucas D K Nelson D R Roddy V L Go 《Peptides》1988,9(2):357-372
Levels of substance P (sP), peptide-histidine-isoleucine (PHI), vasoactive intestinal polypeptide (VIP), cholecystokinin (CCK), neurotensin (NT), bombesin (BOM) and methionine-enkephalin (Met-Enk) like immunoreactivity were measured in cat, dog, primate and sloth cervical, thoracic, lumbar and sacral dorsal and ventral horns and dorsal root ganglia. The levels of peptides in the cat sacral cord and the principal peaks of immunoreactivity on a 10-60% acetonitrile gradient on a C18 reverse phase high performance liquid chromatography (HPLC) were sP (sP1-11: 369 ng/g), PHI (PHI: 271 ng/g), VIP (VIP1-28: 210 ng/g), Met-Enk (Met1-5 and extended forms: 257 ng/g), BOM (BOM1-10 and GRP1-27: 20 ng/g), CCK (CCK-8: 15 ng/g) and NT (NT1-13: 10 ng/g). Consideration of the rostrocaudal levels revealed an approximately even distribution with the exception of VIP and PHI which showed sacral/cervical ratios of 79 and 63. For sP, Met-Enk and BOM dorsal/ventral ratios were greater than 1 at all spinal levels. For VIP, PHI and CCK these ratios were greater than 1 only in the sacral cord. Dorsal root ganglion (DRG) levels of sP, VIP, PHI were readily measurable in single ganglia and covaried with the respective levels in the dorsal cord. Pooled samples of spinal ganglia and the trigeminal ganglia revealed that the relative levels of peptide immunoreactivity were: sP (25 ng/g); VIP (26 ng/g); PHI (28 ng/g); Met-Enk (6 ng/g); CCK (2 ng/g); NT (1 ng/g); and BOM (1 ng/g). 相似文献
8.
Nodes in networks are often of different types, and in this sense networks are differentiated. Here we examine the relationship between network differentiation and network size in networks under economic or natural selective pressure, such as electronic circuits (networks of electronic components), Legos (networks of Lego pieces), businesses (networks of employees), universities (networks of faculty), organisms (networks of cells), ant colonies (networks of ants), and nervous systems (networks of neurons). For each of these we find that (i) differentiation increases with network size, and (ii) the relationship is consistent with a power law. These results are explained by a hypothesis that, because nodes are costly to build and maintain in such "selected networks", network size is optimized, and from this the power-law relationship may be derived. The scaling exponent depends on the particular kind of network, and is determined by the degree to which nodes are used in a combinatorial fashion to carry out network-level functions. We find that networks under natural selection (organisms, ant colonies, and nervous systems) have much higher combinatorial abilities than the networks for which human ingenuity is involved (electronic circuits, Legos, businesses, and universities). A distinct but related optimization hypothesis may be used to explain scaling of differentiation in competitive networks (networks where the nodes themselves, rather than the entire network, are under selective pressure) such as ecosystems (networks of organisms). 相似文献
9.
We have determined and compared trace metals concentration in saliva taken from chemical warfare injures who were under the exposure of mustard gas and healthy subjects by means of inductively coupled plasma optical emission spectroscopy (ICP-OES) for the first time. The influence of preliminary operations on the accuracy of ICP-OES analysis, blood contamination, the number of restored teeth in the mouth, salivary flow rate, and daily variations in trace metals concentration in saliva were also considered. Unstimulated saliva was collected at 10:00–11:00 a.m. from 45 subjects in three equal groups. The first group was composed of 15 healthy subjects (group 1); the second group consisted of 15 subjects who, upon chemical warfare injuries, did not use Salbutamol spray, which they would have normally used on a regular basis (group 2); and the third group contained the same number of patients as the second group, but they had taken their regular medicine (Salbutamol spray; group 3). Our results showed that the concentration of Cu in saliva was significantly increased in the chemical warfare injures compared to healthy subjects, as follows: healthy subjects 15.3± 5.45(p.p.b.), patients (group 2) 45.77±13.65, and patients (Salbutamol spray; group 3) 29 ±8.51 (P <0.02). In contrast, zinc was significantly decreased in the patients, as follows: healthy subjects 37 ± 9.03(p.p.b.), patients (group 2) 12.2 ± 3.56, and patients (Salbutamol spray; group 3) 20.6 ±10.01 (P < 0.01). It is important to note that direct dilution of saliva samples with ultrapure nitric acid showed the optimum ICP-OES outputs. 相似文献
10.
Electron attachment rates and gas phase acidities for the canonical tautomers of the nucleobases and electron affinities for thymine, deprotonated thymine, and cytosine are reported The latter are from a new analysis of published photoelectron spectra. The values for deprotonated thymine are (all in eV) keto-N1-H, 3.327(5); enol-N3-H, 3.250(5), enol-C2OH, 3.120(5) enol-N1-H, 3.013(5), and enol-C4OH,3.123(5). The values for deprotonated cytosine, keto-N1-H, 3.184(5); trans-NH-H, 3.008(5); cis-NH-H, 3.039(5); and enol-N1-H, 2.750(5) and enol-O-H, 2.950(5). The gas phase acidities from these values are obtained from these values using experimental or theoretical calculations of bond dissociation energies. Kinetic and thermodynamic properties for thermal electron attachment to thymine are obtained from mass spectrometric data. We report an activation energy of 0.60 eV and electron affinity of thymine, 1.0(1) eV. 相似文献
11.
Anti-plasmodial action of de novo-designed, cationic, lysine-branched, amphipathic, helical peptides
ABSTRACT: BACKGROUND: A lack of vaccine and rampant drug resistance demands new anti-malarials. METHODS: In vitro blood stage anti-plasmodial properties of several de novo-designed, chemically synthesized, cationic, amphipathic, helical, antibiotic peptides were examined against Plasmodium falciparum using SYBR Green assay. Mechanistic details of anti-plasmodial action were examined by optical/fluorescence microscopy and FACS analysis. RESULTS: Unlike the monomeric decapeptides {(Ac-GXRKXHKXWA-NH2) (X = F,DeltaF) (Fm, DeltaFm IC50 >100 muM)}, the lysine-branched,dimeric versions showed far greater potency {IC50 (muM) Fd 1.5 , DeltaFd 1.39}. The more helical and proteolytically stable DeltaFd was studied for mechanistic details. DeltaFq, a K-K2 dendrimer of DeltaFm and (DeltaFm)2 a linear dimer of DeltaFm showed IC50 (muM) of 0.25 and 2.4 respectively. The healthy/infected red cell selectivity indices were >35 (DeltaFd), >20 (DeltaFm)2 and 10 (DeltaFq). FITC-DeltaFd showed rapid and selective accumulation in parasitized red cells. Overlaying DAPI and FITC florescence suggested that DeltaFd binds DNA. Trophozoites and schizonts incubated with DeltaFd (2.5 muM) egressed anomalously and Band-3 immunostaining revealed them not to be associated with RBC membrane. Prematurely egressed merozoites from peptide-treated cultures were found to be invasion incompetent. CONCLUSION: Good selectivity (>35), good resistance index (1.1) and low cytotoxicity indicate the promise of DeltaFd against malaria. 相似文献
12.
Hong Y. Wen Randall L. Davis Bing Shi Jau-Jiin Chen Lugen Chen Mallory Boylan Julian E. Spallholz 《Biological trace element research》1997,58(1-2):43-53
The bioavailability of selenium (Se) from veal, chicken, beef, pork, lamb, flounder, tuna, selenomethionine (SeMet), and sodium selenite was assessed in Se-deficient Fischer-344 rats. Se as veal, chicken, beef, pork, lamb, flounder, tuna, SeMet, and sodium selenite was added to torula yeast (TY) basal diets to comprise Se-inadequate (0.05 mg Se/kg) diets. Se as sodium selenite was added to a TY basal diet to comprise a Se-adequate (0.10 mg Se/kg), Se-control diet. The experimental diets were fed to weanling Fischer-344 rats that had been subjected to dietary Se depletion for 6 wk. After 9 wk of the dietary Se repletion, relative activity of liver glutathione peroxidase (GSHPx) from the different dietary groups compared with control rats (100%) was: flounder 106%, tuna 101%, pork 86%, sodium selenite 81%, SeMet 80%, beef 80%, chicken 77%, veal 77%, and lamb 58%. Se from flounder was the most efficient at restoring Se concentrations in the liver and skeletal muscle. Se from sodium selenite, SeMet, beef, veal, chicken, pork, lamb, and tuna was not dietarily sufficient to restore liver and muscle Se after 9 wk of recovery following a 6-wk period of Se depletion. 相似文献
13.
14.
High-pressure liquid chromatography and microcalorimetry have been used to study the thermodynamics of the hydrolysis reactions of a series of disaccharides. The enzymes used to bring about the hydrolyses were: beta-galactosidase for lactulose and 3-o-beta-D-galactopyranosyl-D-arabinose; beta-glucosidase for alpha-D-melibiose; beta-amylase for D-trehalose; isomaltase for palatinose; and alpha-glucosidase for D-turanose. The buffer used was sodium acetate (0.02-0.10 M and pH 4.44-5.65). For the following processes at 298.15 K: lactulose(aq) + H2O(liq) = D-galactose(aq) + D-fructose(aq), K0 = 128 +/- 10 and delta H0 = 2.21 +/- 0.10 kJ mol-1; alpha-D-melibiose(aq) + H2O(liq) = D-galactose(aq) + D-glucose(aq), K0 = 123 +/- 42 and delta H0 = -0.88 +/- 0.50 kJ mol-1; palatinose(aq) + H2O(liq) = D-glucose(aq) + D-fructose(aq), delta H0 = -4.44 +/- 1.1 kJ mol-1; D-trehalose(aq) + H2O(liq) = 2 D-glucose(aq), K0 = 119 +/- 10 and delta H0 = 4.73 +/- 0.41 kJ mol-1; D-turanose(aq) + H2O(liq) = D-glucose(aq) + D-fructose(aq), delta H0 = -2.68 +/- 0.75 kJ mol-1; and 3-o-beta-D-galactopyranosyl-D-arabinose(aq) + H2O(liq) = D-galactose(aq) + D- arabinose(aq),0H0 = 107 +/- 10 and delta H0 = 2.97 +/- 0.10 kJ mol-1.(ABSTRACT TRUNCATED AT 250 WORDS) 相似文献
15.
In order to compare the endocrine response of placental minces to luteinizing hormone releasing hormone (LHRH) and dibutyryl cAMP (dbcAMP) and to screen for effects of potential stimulatory and inhibitory substances, the simultaneous outputs of PGF2 alpha, 13, 14-dihydro-15-keto-prostaglandin F2 alpha (PGFM), progesterone, 17 beta-estradiol, and hCG were evaluated during a 4 hour incubation in 5 placentas. The output of hCG was highest for 12-week placentas, intermediate for a 16 week placenta, and lowest for term placentas. The output of 17 beta-estradiol by 12 and 16 week placentas in the presence of 30 microM dehydroepian-drosterone sulfate (DHEAS) was greater than that by term placentas. Progesterone output was apparently independent of gestational age although some variation between 12-week placentas was demonstrated. Output of PGF2 alpha was lower in 12 and 16-week placentas than in term placentas and that of PGFM was lower in 12-week placentas than in term placentas. LHRH (100 nM) produced stimulation of PGF2 alpha output (P less than .005) and a trend toward inhibition of progesterone output (which failed to achieve statistical significance) but no stimulation of hCG under these conditions. Stimulation of the outputs of hCG (P less than .005) and PGF2 alpha (P less than .001) and inhibition of that of progesterone (P less than .005) was produced by 20 mM dbcAMP. DHEAS inhibited output of progesterone (P less than .01) and PGF2 alpha (P less than .01). There were no effects of potassium, estrogens, progesterone, or prostaglandins on output of any measured substance. 相似文献
16.
J. B. Sutherland J. P. Freeman A. J. Williams 《Applied microbiology and biotechnology》1998,49(4):445-449
Streptomyces viridosporus T7A (ATCC␣39115), during growth in tryptone/yeast extract broth, cometabolized five heterocyclic nitrogen-containing compounds.
The metabolites produced from the azaarenes were identified by high-performance liquid chromatography, UV/visible absorption
spectroscopy, and mass spectrometry. Isoquinoline was transformed to 1(2H)-isoquinolinone (14%), phenanthridine to 6(5H)-phenanthridinone (25%), phthalazine to 1(2H)-phthalazinone (46%), quinazoline to 2,4(1H,3H)-quinazolinedione (4%), and quinoxaline to 2(1H)-quinoxalinone (8%) and 1-methyl-2(1H)-quinoxalinone (12%).
Received: 29 July 1997 / Received revision: 19 November 1997 / Accepted: 29 November 1997 相似文献
17.
18.
Edward C.M. Chen John R. Wiley Edward S. Chen 《Nucleosides, nucleotides & nucleic acids》2013,32(5):506-524
Electron attachment rates and gas phase acidities for the canonical tautomers of the nucleobases and electron affinities for thymine, deprotonated thymine, and cytosine are reported The latter are from a new analysis of published photoelectron spectra. The values for deprotonated thymine are (all in eV) keto-N1-H, 3.327(5); enol-N3-H, 3.250(5), enol-C2OH, 3.120(5) enol-N1-H, 3.013(5), and enol-C4OH,3.123(5). The values for deprotonated cytosine, keto-N1-H, 3.184(5); trans-NH-H, 3.008(5); cis-NH-H, 3.039(5); and enol-N1-H, 2.750(5) and enol-O-H, 2.950(5). The gas phase acidities from these values are obtained from these values using experimental or theoretical calculations of bond dissociation energies. Kinetic and thermodynamic properties for thermal electron attachment to thymine are obtained from mass spectrometric data. We report an activation energy of 0.60 eV and electron affinity of thymine, 1.0(1) eV. 相似文献
19.
Norman D. Levine 《Journal of invertebrate pathology》1977,29(2):175-181
The genera and species in six families of the eugregarine suborder Aseptatorina Chakravarty, 1960, are reviewed and the presently accepted ones are listed: Aikinetocystidae Bhatia, 1930 (two genera and two species); Diplocystidae Bhatia, 1930 (one genus and eight species); Allantocystidae tocystidae Bhatia, 1930 (one genus and one species); Schaudinnellidae Poche, 1913 (one genus and one species); Ganymedidae Huxley, 1910 (one genus and one species); and Enterocystidae Codreanu, 1940 (one genus and eight species). A list of 22 synonyms and lapsi calami is also given. Species which might be of value in the biological control of disease vectors are indicated. 相似文献
20.
A new polynitro cage compound 2, 4, 6, 8, 10, 12, 13, 14, 15-nonanitro-2, 4, 6, 8, 10, 12, 13, 14, 15-nonaazaheptcyclo [5.5.1.1(3,11).1(5,9)] pentadecane (NNNAHP) was designed in the present work. Its molecular structure was optimized at the B3LYP/6-31 G(d,p) level of density functional theory (DFT) and crystal structure was predicted using the Compass and Dreiding force fields and refined by DFT GGA-RPBE method. The obtained crystal structure of NNNAHP belongs to the P-1 space group and the lattice parameters are a = 9.99 ?, b = 10.78 ?, c = 9.99 ?, α = 90.01°, β = 120.01°, γ = 90.00°, and Z = 2, respectively. Based on the optimized crystal structure, the band gap, density of state, thermodynamic properties, infrared spectrum, strain energy, detonation characteristics, and thermal stability were predicted. Calculation results show that NNNAHP has detonation properties close to those of CL-20 and is a high energy density compound with moderate stability. 相似文献