On the complexity of deriving position specific score matrices from positive and negative sequences

Position-specific score matrices (PSSMs) have been applied to various problems in computational molecular biology. In this paper, we study the following problem: given positive examples (sequences) and negative examples (sequences), find a PSSM which correctly discriminates between positive and negative examples. We prove that this problem is solved in polynomial time if the size of a PSSM is bounded by a constant. On the other hand, we prove that this problem is NP-hard if the size is not bounded. We also prove hardness results for deriving multiple PSSMs and related problems.     

A new HF-resistant tandem spray chamber for improved determination of trace elements and Pb isotopes using inductively coupled plasma-mass spectrometry

The use of a new HF-resistant tandem spray chamber arrangement consisting of a cyclonic spray chamber and a Scott-type spray chamber made from PFA and PEEK provides a straightforward approach for improving the performance of inductively coupled-mass spectrometry (ICP-MS). The characteristics of the tandem spray chamber were critically evaluated against a PEEK cyclonic and a PFA Scott-type spray chamber, respectively. Sensitivity across the entire mass range was increased by about three times compared to the conventional setup utilizing only one spray chamber. Precision of the results, especially at low signal intensities, improved by 160% and 31% compared to the cyclonic and Scott-type spray chamber, respectively. Using the tandem spray chamber, the oxide formation rate was lowered by about 50%. Signals as low as 30 counts could be determined under routine measurement conditions with a RSD of 2.4% thus allowing to precisely quantify small concentration differences at the ng l^− 1 concentration level. The excellent precision (0.02–0.07%) of ²⁰⁶Pb / ²⁰⁷Pb and ²⁰⁶Pb / ²⁰⁸Pb ratios determined in pore water samples was rather limited by the instrumental capabilities of the single collector ICP-MS instrument than by the performance of the tandem spray chamber.     

壳聚糖溶液pH对载细胞海藻酸钠-壳聚糖微胶囊性能的影响

以激光共聚焦扫描显微镜为研究手段, 原位直观地考察了在不同pH条件下聚电解质膜的络合程度和蛋白扩散情况. 通过分析pH值对微胶囊膜性能的影响规律, 并结合不同种类细胞对环境pH的敏感特性, 确定了制备细胞培养用海藻酸钠-壳聚糖微胶囊的最佳pH值. 结果表明, 当壳聚糖溶液的pH值由3.50增加到6.50, 微胶囊膜的络合深度呈现高-低-高的趋势, 而微胶囊膜的膨胀性能呈现低-高-低的趋势, 模型蛋白通过微囊膜的扩散呈现低-高-低的趋势, 拐点均出现在pH=4.00和5.50处. 结合动物细胞及微生物细胞对环境pH耐受能力的考察, 确定制备微囊化动物细胞时, 微胶囊成膜反应溶液的最佳pH值为5.50; 制备微囊化大肠杆菌时, 反应溶液的最佳pH值为5.00; 制备微囊化酵母菌时, 反应溶液的最佳pH值为4.50.     

Novel bifluorene based conjugated systems: synthesis and properties

A series of novel bifluorene based systems was synthesised by a convergent approach by means of a Suzuki cross-coupling between 7,7′-bis-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-9,9,9′,9′-tetraoctyl-2,2′-bifluorene and suitable aryl-bromides. All the oligomers have been characterized by ¹H, ¹³C NMR, FT-IR, UV-vis, PL spectroscopy and mass analyses. In particular, it has been demonstrated that the presence of strong electron donor (amines) or withdrawing (carboxylic esters) groups causes a bathochromic shift of the optical properties with respect to those of unsubstituted molecules. The effects of these functional groups on the HOMO-LUMO energy levels were investigated by cyclic voltammetry. Remarkably, the LUMO energy level of 7,7′-bis-[5′-carbodecaoxy-2,2′-bithiophen-5-yl]-9,9,9′,9′-tetraoctyl-2,2′-bifluorene (−3.07 eV) is strongly influenced by the presence of the ester functional group.     

Towards the synthesis of insulated oligoynes: A ring-closing-metathesis approach to molecular encapsulation

Masked hexayne 18 was prepared in 11 steps from commercially available reagents. The four butenyl substituents contained within the two arylsilane residues in 18 have been used in a double ring-closing-metathesis operation in an attempt to encapsulate the π-conjugated framework. When 18 was treated with Grubbs’ 1st generation metathesis catalyst however, double ring-closing metathesis provided macrocycle 19 as the major product in good yield. Reasons why the macrocycle in 19 crowns, rather than encapsulates, the π-conjugated framework are discussed.     

可降解自固化类骨磷灰石支架的研究

0引言一直以来,钙磷生物材料如羟基磷灰石(hy-droxyapatite,HA)由于其成份与骨的无机成份相似,具有良好的生物相容性,作为骨修复材料引起了人们广泛的兴趣。磷酸钙骨水泥是一类可在生理条件下自固化的非陶瓷型类HA人工骨材料,这种由磷酸钙骨水泥(calcium phosphate cement,CPC)转变而成的HA,与天然骨磷灰石有类似的组成结构,植入人体后可参与新陈代谢,促进骨组织生长[1,2]。一些研究显示,CPC具有成骨活性和生物降解性,在体内被吸收的同时可引导新骨的生成,从而可克服自体骨、磷酸三钙陶瓷因吸收降解过快造成的局部缺陷以及陶瓷型HA长…     

Alkanethiolate self-assembled monolayers as functional spacers to resist protein adsorption upon Au-coated nerve microelectrode

Alkanethiolate self-assembled monolayers (SAMs) of varied chain lengths were adsorbed upon Au-coated nerve microelectrodes and employed as protein-resistant spacers. The microelectrode spiraled as a cuff type can be used for restoring motor function via electrical stimulation on the peripheral nerve system; however, an increase of electrode impedance might occur during implantation. In this work, a thin-film SAMs treatment upon Au/polyimide (PI) surface of the microelectrode provided a hydrophobic characteristic, which retarded protein adsorption at the initial stage and subsequent pileup (or thickening) process. The protein-resistant effect exhibited comparable SAMs of different chain lengths adsorbed upon Au/PI surfaces. The increase of electrode impedance as a function of protein deposition time was mainly correlated with the addition of reactance that was associated with the pileup thickness of the deposited protein. Particularly, the SAMs-modified surface was capable to detach a significant portion of the accumulated protein from the protein-deposited SAMs/Au/PI, whereas the protein-deposited layers exhibited firm adhesion upon Au/PI surface. It is therefore very promising to apply thin-film SAMs adsorbed upon Au-coated surface for bioinvasive devices that have the need of functional electrical stimulations or sensing nerve signals during chronic implantation.     

predForm-Site: Formylation site prediction by incorporating multiple features and resolving data imbalance

Formylation is one of the newly discovered post-translational modifications in lysine residue which is responsible for different kinds of diseases. In this work, a novel predictor, named predForm-Site, has been developed to predict formylation sites with higher accuracy. We have integrated multiple sequence features for developing a more informative representation of formylation sites. Moreover, decision function of the underlying classifier have been optimized on skewed formylation dataset during prediction model training for prediction quality improvement. On the dataset used by LFPred and Formator predictor, predForm-Site achieved 99.5% sensitivity, 99.8% specificity and 99.8% overall accuracy with AUC of 0.999 in the jackknife test. In the independent test, it has also achieved more than 97% sensitivity and 99% specificity. Similarly, in benchmarking with recent method CKSAAP_FormSite, the proposed predictor significantly outperformed in all the measures, particularly sensitivity by around 20%, specificity by nearly 30% and overall accuracy by more than 22%. These experimental results show that the proposed predForm-Site can be used as a complementary tool for the fast exploration of formylation sites. For convenience of the scientific community, predForm-Site has been deployed as an online tool, accessible at http://103.99.176.239:8080/predForm-Site.     

Preparation and characterization of self-assembled nanoparticles based on glycol chitosan bearing adriamycin

An anthracycline drug, adriamycin, was chemically conjugated onto the backbone of glycol chitosan via an acid-labile cis-aconityl linkage. The physicochemical characteristics of the glycol chitosan–adriamycin (GC–ADR) conjugates were investigated by dynamic light scattering, atomic force microscopy, and fluorescence spectroscopy. The GC–ADR conjugates were capable of forming nano-sized self-aggregates in an aqueous medium, when the adriamycin content in the conjugate was in the range of 2.0–5.0 wt.%. The self-aggregates were spherical in shape, and had mean diameters of 238–304 nm, depending on the adriamycin content. The critical aggregation concentrations of the conjugates, estimated by the fluorescence quenching method, were as low as 1.0–2.5×10⁻² mg/ml. The size of self-aggregates was not affected by the polymer concentration in the range from 50 to 2,000 μg/ml, and was maintained up to 8 days in phosphate-buffered saline (pH 7.4), indicating high colloidal stability. The release of adriamycin from self-aggregates was significantly dependent on the pH of the medium due to the cis-aconityl linkage; e.g., the amount of adriamycin released for 4 days was 7.3±0.3% at pH 7, whereas it was 29.3±1.9% at pH 4. The cell viability results demonstrated that free adriamycin shows more potent cytotoxicity than the conjugates, primarily attributed to the sustained release of adriamycin from self-aggregates. In conclusion, the self-aggregates, formed by GC–ADR conjugates, might be useful for the site-specific delivery of adriamycin in a sustained manner.     

Quantum dot nanocrystals for in vivo molecular and cellular imaging

Semiconductor quantum dots (QD) are nanometer-sized crystals with unique photochemical and photophysical properties that are not available from either isolated molecules or bulk solids. In comparison with organic dyes and fluorescent proteins, QD are emerging as a new class of fluorescent labels with improved brightness, resistance against photobleaching and multicolor fluorescence emission. These properties could improve the sensitivity of biological detection and imaging by at least 10- to 100-fold. Further development in high-quality near-infrared-emitting QD should allow ultrasensitive and multicolor imaging of molecular targets in deep tissue and living animals. Here, we discuss recent developments in QD synthesis and bioconjugation, applications in molecular and cellular imaging as well as promising directions for future research.