Sequence specificity in spermine-induced structural changes in CG-oligomers

The role of spermine in inducing A-DNA conformation in deoxyoligonucleotides has been studied using CCGG and GGCC as model sequences. It has been found that while CCGG adopts an alternating B-DNA conformation in low salt solution at low temperature, addition of spermine to this medium induces a B --greater than A transition. In contrast, the A-DNA-like structure of GGCC in low salt solution at low temperature does not change under the influence of spermine. This suggests a sequence-dependent behaviour of spermine. Further these results suggest that the A-DNA conformation observed in the crystals of d(iCCGG) and d(GGCC)2 might have been due to the presence of spermine in the crystallization cocktail.

Interruptions of (CG)n sequences by GG, TG and CA need not prevent B to Z transition in solution

Oligonucleotides containing alternating purines-pyrimidines with AT base pairs have been shown to exist in the Z-form preferably in solid state. We report that oligodeoxyribonucleotides with GG, TG and CA interruptions in their alternating CG sequences can undergo B to Z transition in solution in the absence of any chemical modification or topological constraint. The sequences, d(CGCGCGGCGCGC) and d(CGTGCGCACG) have been synthesised and shown to adopt Z- conformation in presence of millimolar concentrations of Ni2+ under low water activity conditions. Significance of GG, TG and CA interruptions in the B to Z transition is discussed.

Development of an LH receptor assay capable of measuring serum LH/CG in a wide variety of species

The development of a radioreceptor assay (RRA) that can measure serum LH in a variety of species and CG in sera and urine of pregnant women and monkeys is reported. Using sheep luteal membrane as the receptor source and I-125-labelled hLH/hCG as the tracer, dose-response (displacement) curves were obtained using hLH or hCG as standard. The addition of LH-free serum (200 mul per tube) had no affect on the standard displacement curve. The assay is simple, requires less than 90 min to complete and provides reproducible results. The sensitivity of the assay was 0.6 ng hLH per tube and the intra- and interassay variations were 9.6 and 9.8, respectively. Sera obtained from male and female bonnet monkeys (Macaca radiata) and monkey pituitary extract showed parallelism to the standard curve. The concentrations of LH measured correlated with the physiological status of the animals. Sera of rats, rabbits, hamsters, guinea-pigs, sheep and humans showed parallelism to the hLH standard curve indicating the viability of the RRA to measure serum LH of different species. Since the receptors recognize LH and CG, detection of pregnancy in monkeys and women was possible using this assay. The sensitivity of the assay for hCG was 8.7 miu per tube. This RRA could be a convenient alternative to the Leydig cell bioassay for obtaining the LH bioactivity profile of sera and biological fluids.

MILU-CG method and the numerical study on the flow around a rotating circular cylinder

A hybrid finite difference method and vortex method (HDV), which is based on domain decomposition and proposed by the authors (1992), is improved by using a modified incomplete LU decomposition conjugate gradient method (MILU-CG), and a high order implicit difference algorithm. The flow around a rotating circular cylinder at Reynolds number R-e = 1000, 200 and the angular to rectilinear speed ratio alpha is an element of (0.5, 3.25) is studied numerically. The long-time full developed features about the variations of the vortex patterns in the wake, and drag, lift forces on the cylinder are given. The calculated streamline contours agreed well with the experimental visualized flow pictures. The existence of critical states and the vortex patterns at the states are given for the first time. The maximum lift to drag force ratio can be obtained nearby the critical states.

MILU-CG方法和绕旋转圆柱流动的数值研究

本文采用以修正的不完全ＬＵ分解作预处理器的共轭梯度法（ＭＩＬＵ＿ＣＧ），结合高阶隐式差分格式，改进了作者（１９９２）提出的基于区域分解、有限差分法与涡法杂交的数值方法（ＨＤＶ）·系统地研究了雷诺数Ｒｅ＝１０００，２００，旋转速度比α∈（０５，３２５）范围内，绕旋转圆柱从突然起动到充分发展，长时间内尾流旋涡结构和阻力、升力系数的变化规律·计算所得流线与实验流场显示相比，完全吻合·首次揭示了临界状态时的旋涡结构特性，并指出最佳升阻比就在该状态附近得到

Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading.

Plants use siRNAs to target cytosine DNA methylation to both symmetrical CG and nonsymmetrical (CHG and CHH) sequence contexts. DNA methylation and siRNA clusters most frequently overlap with transposons in the Arabidopsis thaliana genome. However, a significant number of protein-coding genes also show promoter DNA methylation, and this can be used to silence their expression. Loss of the majority of non-CG DNA methylation in drm1 drm2 cmt3 triple mutants leads to developmental phenotypes. We identified the gene responsible for these phenotypes as SUPPRESSOR OF drm1 drm2 cmt3 (SDC), which encodes an F-box protein and possesses seven promoter tandem repeats. The SDC repeats show a unique silencing requirement for non-CG DNA methylation directed redundantly by histone methylation and siRNAs, and display spreading of siRNAs and methylation beyond the repeated region. In addition to revealing the complexity of DNA methylation control in A. thaliana, SDC has important implications for how plant genomes utilize gene silencing to repress endogenous genes.

RNAi, DRD1, and histone methylation actively target developmentally important Non-CG DNA methylation in Arabidopsis

Cytosine DNA methylation protects eukaryotic genomes by silencing transposons and harmful DNAs, but also regulates gene expression during normal development. Loss of CG methylation in the Arabidopsis thaliana met1 and ddm1 mutants causes varied and stochastic developmental defects that are often inherited independently of the original met1 or ddm1 mutation. Loss of non-CG methylation in plants with combined mutations in the DRM and CMT3 genes also causes a suite of developmental defects. We show here that the pleiotropic developmental defects of drm1 drm2 cmt3 triple mutant plants are fully recessive, and unlike phenotypes caused by met1 and ddm1, are not inherited independently of the drm and cmt3 mutations. Developmental phenotypes are also reversed when drm1 drm2 cmt3 plants are transformed with DRM2 or CMT3, implying that non-CG DNA methylation is efficiently re-established by sequence-specific signals. We provide evidence that these signals include RNA silencing though the 24-nucleotide short interfering RNA (siRNA) pathway as well as histone H3K9 methylation, both of which converge on the putative chromatin-remodeling protein DRD1. These signals act in at least three partially intersecting pathways that control the locus-specific patterning of non-CG methylation by the DRM2 and CMT3 methyltransferases. Our results suggest that non-CG DNA methylation that is inherited via a network of persistent targeting signals has been co-opted to regulate developmentally important genes. © 2006 Chan et al.

CG光学扫描全息术和FZP光学扫描全息术分辨率比较

于2010-11-23批量导入

Caractérisation moléculaire d’un récent modèle d’étude de la leucémie myéloïde aigüe à caryotype normal :la lignée cellulaire CG-SH

La leucémie myéloïde aigüe (LMA) est la forme de leucémie la plus fréquente chez l’adulte au Canada. Bien que de nombreux réarrangements chromosomiques récurrents aient été identifiés chez les patients LMA, près de la moitié des cas présentent un caryotype normal (LMA-CN). L’étude de la LMA-CN in vitro est rendue difficile par le fait que la survie des cellules primaires de patients est défectueuse sur le long terme et que les lignées cellulaires leucémiques ont un caryotype hautement anormal. En 2009, Munker et son équipe ont établi une nouvelle lignée cellulaire, CG-SH, ayant la particularité d’avoir un caryotype normal. L’objectif principal de ce projet d’étude est de caractériser plus en détail ce nouveau modèle d’étude. Nous avons identifié l’ensemble des variants génétiques présents dans CG-SH grâce au séquençage du génome entier. Les variants susceptibles de participer à la leucémogénèse ont été isolés, tels que des insertions détectées dans EZH2 et GATA2, et de nombreux variants faux-sens détectés dans des gènes pertinents pour la LMA. Nous avons montré que les cellules CG-SH sont sensibles à l’effet prolifératif d’une combinaison de cytokines, qui agissent sur le comportement des cellules en modifiant l’expression des gènes associés à la régulation de la prolifération, de l’apoptose et de la différentiation. De plus, les cytokines diminuent le taux de nécrose des cellules en culture sur le court terme. La présente étude a permis d’approfondir notre connaissance sur les caractéristiques moléculaires de la lignée cellulaire CG-SH, un nouveau modèle d’étude in vitro de la LMA-CN.

Guanine specific binding at a DNA junction formed by d[CG(5-BrU)ACG]2 with a topoisomerase poison in the presence of Co2+Ions†,‡

The structure of the duplex d[CG(5-BrU)ACG]2 bound to 9-bromophenazine-4-carboxamide has been solved through MAD phasing at 2.0 Å resolution. It shows an unexpected and previously unreported intercalation cavity stabilized by the drug and novel binding modes of Co2+ ions at certain guanine N7 sites. For the intercalation cavity the terminal cytosine is rotated to pair with the guanine of a symmetry-related duplex to create a pseudo-Holliday junction geometry, with two such cavities linked through the minor groove interactions of the N2/N3 guanine sites at an angle of 40°, creating a quadruplex-like structure. The mode of binding of the drug is shown to be disordered, with the major conformations showing the side chain bound to the N7 position of adjacent guanines. The other end of the duplex exhibits a terminal base fraying in the presence of Co2+ ions linking symmetry-related guanines, causing the helices to intertwine through the minor groove. The stabilization of the structure by the intercalating drug shows that this class of compound may bind to DNA junctions as well as duplex DNA or to strand-nicked DNA (‘hemi-intercalated'), as in the cleavable complex. This suggests a structural basis for the dual poisoning of topoisomerase I and II enzymes by this family of drugs.

Comparação entre metodologias de extração de HPAs em água utilizando um planejamento fatorial com quantificação no CG/EM

PAHs (Polycyclic Aromatic Hydrocarbons) are a group of organic substances which receive considerable attention because of the carcinogenic and mutagenic properties of some of them. It is therefore important to determine the PAHs in different environmental matrices. Several studies have shown the use of gas chromatography coupled to mass spectrometry as a technique for quantification of PAHs by presenting excellent detection limits. This study aimed to develop an analytical methodology for the determination of 16 PAHs listed by the USEPA, test two methods for extraction of PAHs in water from a 23 factorial design, quantify them through the analytical technique coupled to gas chromatography mass spectrometry (GC/MS) using the method developed, and finally apply the results in chemometrics. The sample was synthesized and subjected to tests of the 23 factorial design, which has the factors: the type of extraction technique (ultrasound and digester), the ratio solvent / sample (1:1 and 1:3) and the type of solvent (dichloromethane / hexane and acetone / dichloromethane). The responses of eight combinations of the factorial design were obtained from the quantification by external calibration in GC/MS. The quantification method was developed from an optimized adaptation of the USEPA Method 8270. We used the full scan mode as a way of acquiring the mass spectra of 16 PAHs. The time in which the samples were subjected to ultrasound was fixed at 10 min and held an investigation to establish the conditions of power and time in the digester. We had the best response in the investigation of the digester power of 100 watts and the time of six minutes. The factorial design of liquid-liquid extraction showed that the most representative factors were: the use of the digester as extraction technique, the ratio solvent / sample 1:1 and the use of a 1:1 mixture of dichloromethane / hexane as a solvent more suitable. These results showed that the 1:1 mixture of dichloromethane / hexane is an excellent mixture to recover the extraction of PAHs an aqueous sample using the microwave digester. The optimization of the method of separation, identification and quantification of PAHs in the GC/MS was valid for 16 PAHs present in each chromatogram of the samples

Composition of constitutive heterochromatin of Pseudonannolene strinatii Mauriès, 1974 (Diplopoda, Spirostreptida) analyzed by AT/CG specific fluorochromes.

Triple staining with fluorochromes (DA/DAPI/CMA) and C-banding were used to characterize the composition of Pseudonannolene strinatii heterochromatin. C-banding showed C+ bands of different labeling intensity on chromosomes 1 and 2 in some cells. Fluorochrome staining revealed DAPI+ regions corresponding to the C-banding pattern, indicating that the heterochromatin of this species is abundant in AT-rich sequences.

Detecção in silico e caracterização estrutural dos constituintes micromoleculares majoritários presentes no fungo endofitico Phomopsis stipata isolado de folhas de Styrax camporum Pohl (Styracaceae) usando CLAE-DAD/EMAR e CG-MS

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