The Z-Conformation of Poly(dA-dT) · Poly(dA-dT) in Solution as Studied by Ultraviolet Resonance Raman Spectroscopy

Abstract

Poly(dA-dT) poly(dA-dT) structures in aqueous solutions with high NaCl concentrations and in the presence of Ni²⁺ ions have been studied with resonance Raman spectroscopy (RRS). In low water activity the effects of added 95 mM NiCl₂ in solution stabilize the syn geometry of the purines and reorganize the water distribution via local interactions of Ni-water charged complexes with the adenine N7 position. It is shown that RRS provides good marker bands for a left-handed helix: i) a purine ring breathing mode around 630 cm″^?1coupled to the deoxyribose vibration in the syn geometry, ii) a 1300-1340 cm^?1 region characterizing local chemical interactions of the Ni²⁺ ions with the adenien N7 position, iii) lines at about 1483-and 1582 cm^?1 correlated to the anti/syn reorientation of the adenine residues on B-Z structure transition, iv) marker bands of the thymidine carbonyl group couplings at 1680-and 1733 cm^?1 due to the disposition of the thymidine residues in the Z helix specific geometry. Hence poly(dA-dT) poly(dA-dT) can adopt a Z form in solution. The Z form observed in alternate purine-pyrimidine sequences does not require G-C base pairs.     

Estimation of Cellobiohydrolase I Activity by Numerical Differentiation of Dynamic Ultraviolet Spectroscopy

1,4-β-D-glucan cellobiohydrolase I (CBH I),p-nitrophenyl β-D-cellobioside,p-nitrophenol andcellobiose show distinct ultraviolet spectra,allowing the design of an assay to track the dynamic process ofp-nitrophenyl β-D-cellobioside hydrolysis by CBH I.Based on the linear relationship between p-nitrophenolformation in the hydrolysate and its first derivative absorption Curve of AUC340_400_(nm)(area under the curve),a new sensitive assay for the determination of CBH I activity was developed.The dynamic parameters ofcatalysis reaction,such as Vm and k_(cat),can all be derived from this result.The influence of β-glucosidase andendoglucanase in crude enzyme sample on the assay was discussed in detail.This approach is useful foraccurate determination of the activity of CBHs.     

A novel and efficient ligand-based virtual screening approach using the HWZ scoring function and an enhanced shape-density model

In this work, we extend our previous ligand shape-based virtual screening approach by using the scoring function Hamza–Wei–Zhan (HWZ) score and an enhanced molecular shape-density model for the ligands. The performance of the method has been tested against the 40 targets in the Database of Useful Decoys and compared with the performance of our previous HWZ score method. The virtual screening results using the novel ligand shape-based approach demonstrated a favorable improvement (area under the receiver operator characteristics curve AUC?=?.89?±?.02) and effectiveness (hit rate HR^1%?=?53.0%?±?6.3 and HR^10%?=?71.1%?±?4.9). The comparison of the overall performance of our ligand shape-based method with the highest ligand shape-based virtual screening approach using the data fusion of multi queries showed that our strategy takes into account deeper the chemical information of the set of active ligands. Furthermore, the results indicated that our method are suitable for virtual screening and yields superior prediction accuracy than the other study derived from the data fusion using five queries. Therefore, our novel ligand shape-based screening method constitutes a robust and efficient approach to the 3D similarity screening of small compounds and open the door to a whole new approach to drug design by implementing the method in the structure-based virtual screening.     

采用广义加法模型整合数字高程模型和遥感数据进行植被分布预测

为了采用广义加法模型整合数字高程模型和遥感数据进行植被分布的预测, 并探索耦合环境变量和遥感数据作为预测变量是否能够有效地提高植被分布预测的精度, 选择海拔、坡度、至黄河最近距离、至海岸线最近距离, 以及从SPOT5遥感影像中提取的光谱变量作为预测变量, 采用广义加法模型整合环境变量和光谱变量, 建立植被分布预测模型。研究设置3种建模情景(以环境变量作为预测变量, 以光谱变量作为预测变量, 综合使用环境变量与光谱变量作为预测变量)对黄河三角洲的优势植被类型的分布进行了预测, 并对预测结果采用偏差分析、受试者工作特征曲线和野外采样点对比等3种方法进行了验证。结果表明: (1)基于广义加法模型的植被分布预测方法具有一定的实用性, 可以较为准确地预测植被的分布; 盖度较高的植被类型预测精度较高, 盖度较低的植被类型预测精度较低, 植物群落结构的特点是出现这些差异的主要原因; 综合使用环境变量和光谱变量作为预测变量的模型, 预测精度高于单独以环境变量或者光谱变量作为预测变量的模型。(2)环境变量、光谱变量大多被选入模型, 二者均对植被分布预测有重要的作用; 同一预测变量在不同植被类型的预测模型中的贡献不同, 这与植被的光谱、环境特征差异有关; 同一预测变量在不同的建模情景下对模型的贡献不同, 环境变量与光谱变量的耦合效应可能是导致预测变量对模型的贡献出现变化的原因。     

Modeling the activity burst in the initial phase of cellulose hydrolysis by the processive cellobiohydrolase Cel7A

The hydrolysis of cellulose by processive cellulases, such as exocellulase TrCel7A from Trichoderma reesei, is typically characterized by an initial burst of high activity followed by a slowdown, often leading to incomplete hydrolysis of the substrate. The origins of these limitations to cellulose hydrolysis are not yet fully understood. Here, we propose a new model for the initial phase of cellulose hydrolysis by processive cellulases, incorporating a bound but inactive enzyme state. The model, based on ordinary differential equations, accurately reproduces the activity burst and the subsequent slowdown of the cellulose hydrolysis and describes the experimental data equally well or better than the previously suggested model. We also derive steady-state expressions that can be used to describe the pseudo-steady state reached after the initial activity burst. Importantly, we show that the new model predicts the existence of an optimal enzyme-substrate affinity at which the pseudo-steady state hydrolysis rate is maximized. The model further allows the calculation of glucose production rate from the first cut in the processive run and reproduces the second activity burst commonly observed upon new enzyme addition. These results are expected to be applicable also to other processive enzymes.     

Quantitative determination of carbamazepine and carbamazepine-10,11-epoxide in rat brain areas by multiple ion detection mass fragmentography.

A specific and sensitive method is described for the simultaneous determination of carbamazepineand carbamazepine-10,11-epoxide in biological specimens by combined gas chromatography-mass spectrometry. Cytenamide is used as the internal standard for quantitation. Kinetics of the distribution of the drug and its metabolite in plasma and in different areas of rat brain are reported. Determinations are possible at the nanogram level.     

Bacterial Genome Partitioning: N-Terminal Domain of IncC Protein Encoded by Broad-Host-Range Plasmid RK2 Modulates Oligomerisation and DNA Binding

ParA Walker ATPases form part of the machinery that promotes better-than-random segregation of bacterial genomes. ParA proteins normally occur in one of two forms, differing by their N-terminal domain (NTD) of approximately 100 aa, which is generally associated with site-specific DNA binding. Unusually, and for as yet unknown reasons, parA (incC) of IncP-1 plasmids is translated from alternative start codons producing two forms, IncC1 (364 aa) and IncC2 (259 aa), whose ratio varies between hosts. IncC2 could be detected as an oligomeric form containing dimers, tetramers and octamers, but the N-terminal extension present in IncC1 favours nucleotide-stimulated dimerisation as well as high-affinity and ATP-dependent non-specific DNA binding. The IncC1 NTD does not dimerise or bind DNA alone, but it does bind IncC2 in the presence of nucleotides. Mixing IncC1 and IncC2 improved polymerisation and DNA binding. Thus, the NTD may modulate the polymerisation interface, facilitating polymerisation/depolymerisation and DNA binding, to promote the cycle that drives partitioning.     

A New Estimation Method for Noncompartmental Pharmacokinetic Analysis

The mathematical tools of Hilbert space theory and Gauß quadrature are used to derive a new method of curve fitting and calculation of statistical moments of the concentration-time curve.     

Development of a hazard map for oak wilt disease in Japan

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