From NMR chemical shifts to amino acid types: Investigation of the predictive power carried by nuclei

An approach to automatic prediction of the amino acid type from NMR chemical shift values of its nuclei is presented here, in the frame of a model to calculate the probability of an amino acid type given the set of chemical shifts. The method relies on systematic use of all chemical shift values contained in the BioMagResBank (BMRB). Two programs were designed, one (BMRB stats) for extracting statistical chemical shift parameters from the BMRB and another one (RESCUE2) for computing the probabilities of each amino acid type, given a set of chemical shifts. The Bayesian prediction scheme presented here is compared to other methods already proposed: PROTYP RESCUE and PLATON and is found to be more sensitive and more specific. Using this scheme, we tested various sets of nuclei. The two nuclei carrying the most information are C(beta) and H(beta), in agreement with observations made in Grzesiek and Bax, 1993. Based on four nuclei: H(beta), C(beta), C(alpha) and C', it is possible to increase correct predictions to a rate of more than 75%. Taking into account the correlations between the nuclei chemical shifts has only a slight impact on the percentage of correct predictions: indeed, the largest correlation coefficients display similar features on all amino acids.     

Gram-staining characterisation of activated sludge filamentous bacteria by automated colour analysis

An automated image analysis method has been developed for the monitoring of the Gram-staining characteristics of filamentous bacteria in activated sludge. The binary method of pixel classification agreed with manual estimation (level of correlation of 0.9 for Gram-positive bacteria). Its robustness has been assessed by repeatability tests. Population shifts in terms of Gram-staining characteristics have been monitored in laboratory-scale experiments with two feeding schedules using this technique.Revisions requested 22 September 2004; Revisions received 11 October 2004     

CVT-4325: a potent fatty acid oxidation inhibitor with favorable oral bioavailability

New inhibitors of palmitoyl-CoA oxidation are based on the introduction of nitrogen heterocycles in the ‘Western Portion’ of the molecule. SAR studies led to the discovery of CVT-4325 (shown), a potent FOXi (IC₅₀ = 380 nM rat mitochondria) with favorable PK properties (F = 93%, t_1/2 = 13.6 h, dog).     

脑组织核因子-κB激活对实验性变态反应性脑脊髓炎的作用

为探讨脑组织核因子－κB（NF－κB）对实验性变态反应性脑脊髓炎（EAE）的作用,分别用凝胶电泳迁移分析和NF－κB p65免疫组化方法测定了CFA－GPSCH诱导大鼠EAE1、7、14和21d时脑组织NF－κB活性和蛋白表达的动态变化,并观察了这些变化与EAE症状之间的关系。结果表明;对照组大鼠脑组织仅有少量NF－κB蛋白表达,其活性也很低;诱导EAE后,伴随着大鼠EAE症状及脑组织病理损伤的出现和进行性加重,其NF－κB活性和蛋白表达量逐渐增高;在免疫后14d达到高峰,NF－κB阳性细胞主要位于脉络丛、穹隆下器、血管“套袖样”病灶的周围,与EAE病变部位一致,此时大鼠EAE发病率最高、病情最重、体重减轻最显著、脑组织病理改变也最明显;21h脑组织NF－κB活性和蛋白表达量逐渐下降,大鼠EAE症状也逐渐恢复。应用NF－κB特异性抑制剂PDTC以抑制脑内组织NF－κB活性和蛋白表达量逐渐下降,大鼠EAE症状也逐渐恢复。应用NF－κB特异性抑制剂PDTC以抑制脑内NF－κB蛋白表达后,大鼠EAE症状和脑组织损伤明显减轻,说明脑组织NF－κB的动态变化与EAE症状及脑组织损伤程度密切相关。结论：脑组织NF－κB的激活对EAE的发病起着关键的作用,应用NF－κB抑制剂可能是防治该病的有效方法之一。     

Sequential radiation of unrelated organisms: the gall fly Eurosta solidaginis and the tumbling flower beetle Mordellistena convicta

Host shifts and the formation of insect-host races are likely common processes in the speciation of herbivorous insects. The interactions of goldenrods Solidago (Compositae), the gall fly Eurosta solidaginis (Diptera: Tephritidae) and the beetle Mordellistena convicta (Coleoptera: Mordellidae) provide behavioural, ecological and genetic evidence of host races that may represent incipient species forming via sympatric speciation. We summarize evidence for Eurosta host races and show that M. convicta has radiated from goldenrod stems to Eurosta galls to form host-part races and, having exploited the galler's host shift, has begun to differentiate into host races within galls. Thus, host-race formation has occurred in two interacting, but unrelated organisms representing two trophic levels, resulting in 'sequential radiation' (escalation of biodiversity up the trophic system). Distributions of host races and their behavioural isolating mechanisms suggest sympatric differentiation. Such differentiation suggests host-race formation and subsequent speciation may be an important source of biodiversity.     

Rice HMGB1 protein recognizes DNA structures and bends DNA efficiently

We analyzed the DNA-binding and DNA-bending properties of recombinant HMGB1 proteins based on a rice HMGB1 cDNA. Electrophoretic mobility shift assay demonstrated that rice HMGB1 can bind synthetic four-way junction (4H) DNA and DNA minicircles efficiently but the binding to 4H can be completed out by HMGA and histone H1. Conformational changes were detected by circular dichroism analysis with 4H DNA bound to various concentrations of HMGB1 or its truncated forms. T4 ligase-mediated circularization assays with short DNA fragments of 123 bp showed that the protein is capable of increasing DNA flexibility. The 123-bp DNA formed closed circular monomers efficiently in its presence, similar to that in an earlier study on maize HMG. Additionally, our results show for the first time that the basic N-terminal domain enhances the affinity of the plant HMGB1 protein for 4H DNA, while the acidic C-terminal domain has the converse effects.     

Structure of an elastin-mimetic polypeptide by solid-state NMR chemical shift analysis

The conformation of an elastin-mimetic recombinant protein, [(VPGVG)4(VPGKG)]39, is investigated using solid-state NMR spectroscopy. The protein is extensively labeled with 13C and 15N, and two-dimensional 13C-13C and 15N-13C correlation experiments were carried out to resolve and assign the isotropic chemical shifts of the various sites. The Pro 15N, 13Calpha, and 13Cbeta isotropic shifts, and the Gly-3 Calpha isotropic and anisotropic chemical shifts support the predominance of type-II beta-turn structure at the Pro-Gly pair but reject a type-I beta-turn. The Val-1 preceding Pro adopts mostly beta-sheet torsion angles, while the Val-4 chemical shifts are intermediate between those of helix and sheet. The protein exhibits a significant conformational distribution, shown by the broad line widths of the 15N and 13C spectra. The average chemical shifts of the solid protein are similar to the values in solution, suggesting that the low-hydration polypeptide maintains the same conformation as in solution. The ability to measure these conformational restraints by solid-state NMR opens the possibility of determining the detailed structure of this class of fibrous proteins through torsion angles and distances.