Native analysis of plasma-derived clotting factor VIII concentrates: "sponge effect" and contaminants

In the present study, we analysed two commercially available plasma-derived FVIII preparations, Beriate and Emoclot, through native gel-based approaches (CN-PAGE). The rationale behind this study was to assess whether protein complexes from plasma resisted the aggressive manufacturing processes. A preliminary analysis of plasma complexes was performed focusing on the molecular weight range between 45 kDa and 1 MDa. As a result, we could evidence in both preparations the presence of complexes, which resisted the cryoprecipitation, chromatographic and heat treatment processing steps. These complexes behaved in a "sponge-effect"-like fashion through the enrichment of otherwise less abundant contaminants. The use of an alternative electrophoretic approach such as CN-PAGE allowed us to confirm 2DE-based observations and expand the list of non-FVIII proteins which contaminate the preparations.     

Recombinant clotting factor VIII concentrates: Heterogeneity and high‐purity evaluation

Factor VIII is an important glycoprotein involved in hemostasis. Insertion of expression vectors containing either the full‐length cDNA sequence of human factor VIII (FLrFVIII) or B‐domain deleted (BDDrFVIII) into mammalian cell lines results in the production of recombinant factor VIII (rFVIII) for therapeutic usage. Three commercially available rFVIII concentrates (Advate^®, Helixate NexGen^® and Refacto^®), either FLrFVIII or BDDrFVIII, were investigated by 1‐ and 2‐DE and MS. The objective of this study was to compare the heterogeneity and the high purity of both rFVIII preparations before and after thrombin digestion. In particular, the 2‐D gel was optimized to better highlight the presence of contaminants and many unexpected proteins. Recombinant strategies consisting of insertion of expression vectors containing BDDrFVIII and FLrFVIII resulted in homogeneous and heterogeneous protein products, respectively, the latter consisting in a heterogeneous mixture of various B‐domain‐truncated forms of the molecule. Thrombin digestion of all the three rFVIII gave similar final products, plus one unexpected fragment of A2 domain missing 11 amino acids. Regarding the contaminants, Helixate NexGen^® showed the presence of impurities, such as Hsp70 kDa, haptoglobin and proapolipoprotein; Refacto^® showed glutathione S‐transferase and β‐lactamase, whereas Advate^® apparently did not contain any contaminants. The proteomic approach will contribute to improving the quality assurance and manufacturing processes of rFVIII concentrates. In this view, the 2‐DE is mandatory for revealing the presence of contaminants.     

Proteomic characterization of plasma‐derived clotting factor VIII–von Willebrand factor concentrates

Proteomic methods were used to identify the levels of impurities in three commercial plasma‐derived clotting factor VIII‐von Willebrand factor (FVIII/VWF) concentrates. In all three concentrates, significant amounts of other plasma proteins were found. In Octanate and Haemoctin, two concentrates developed in the 1990s, the major impurities identified were inter‐α inhibitor proteins, fibrinogen and fibronectin. These two concentrates were also found to contain additional components such as clotting factor II (prothrombin) that are known activators of FVIII. In Wilate, a recently developed FVIII/VWF concentrate, the amount of these impurities was significantly reduced. Batch‐to‐batch variations and differences between three investigated products were detected using iTRAQ, an isotope labeling technique for comparative MS, demonstrating the potential value of this technique for quality control analysis. The importance of thorough proteomic investigations of therapeutic FVIII/VWF preparations from human plasma is also discussed.     

Thinking inside the box: Novel linear scaling algorithm for Coulomb potential evaluation

Beginning with the Poisson equation, and expanding the electronic potential in terms of sine functions, the natural orbitals for describing the particle‐in‐a‐box problem, we find that simple analytic forms can be found for the evaluation of the Coulomb energy for both the interacting and non‐interacting system of N‐electrons in a box. This method is reminiscent of fast‐Fourier transform and scales linearly. To improve the usefulness of this result, we generalize the idea by considering a molecular system, embedded in a box, within which we determine the electrostatic potential, in the same manner as that described for our model systems. Within this general formalism, we consider both periodic and aperiodic recipes with specific application to systems described using Gaussian orbitals; although in principle the method is seen to be completely general. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Simple evaluation of Franck–Condon factors and non‐Condon effects in the Morse potential

The calculation of Franck–Condon factors between different 1‐D Morse potential eigenstates using a formula derived from the Wigner function is discussed. Our numerical calculations using a simple program written in Mathematica are compared with other calculations. We show that our results have a similar accuracy as those calculations performed with more sophisticated methods. We discuss the extension of our method to include non‐Condon effects in the calculation. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 88: 280–295, 2002     

用拓扑指数＆mT预测化合物在热导上的相对物质的量校正因子

在邻接矩阵的基础上,建立一种新的拓扑指数mT,mY=∑(δi·δj·δk…)0.5,其中0T=∑(δi)0.5,1Y=∑(δi·δj)0.5,并计算了10个系列142个分子的0T,1T值.发现mT与这些化合物的气相色谱相对物质的量校正因子有很好的相关性.相关系数均大于0.96,拓扑指数mT能较好地反映化合物的结构特征.     

Infrared spectra of CO in absorption and evaluation of radial functions for potential energy and electric dipolar moment

From quantum-chemical calculations of rotational g factor and new experimental measurements of strengths of lines in infrared spectra of vibration–rotational bands v′–0 in absorption, with 1≤v′≤4, of ¹²C¹⁶O, and from analysis of 16,947 frequencies and wave numbers assigned to pure rotational and vibration–rotational transitions within electronic ground state X ¹Σ⁺, including new measurements of band 4–0 of ¹²C¹⁶O, we evaluate radial functions for potential energy and electric dipolar moment, the latter both in polynomial form and as a rational function that has qualitatively correct behaviour under limiting conditions. Received: 8 November 2001 / Accepted: 5 February 2002 / Published online: 14 August 2002     

An explicit expression for the static structure factor for a multi-Yukawa fluid: the one-component case

By using the mean spherical approximation, we obtain an analytical expression for the static structure factor (SSF) for a monodisperse system of particles interacting through a potential given by a hard-sphere contribution and M Yukawa terms. This expression depends on scaling matrix Γ, which is determined by solving a set of nonlinear equations. Our theoretical results show that using three Yukawa terms in the closure relation greatly improves the accuracy when compared with hypernetted-chain closure and Monte Carlo simulation data, which display a secondary low-k peak in the SSF, due to the formation of an intermediate range order structure governed by a short-range attraction and a long-range repulsion. We discuss the appearance of such a peak in terms of the microstructure order given by the radial distribution function. Following the original proposal made by Waisman (Mol Phys. 1973; 25:45–48), we give an explicit expression that improves the structural properties of a hard-sphere system.     

Quantification of the velocity acceleration factor for colloidal transport in porous media using NMR

Nuclear magnetic resonance (NMR) techniques were used to quantify the transport of colloids through porous media. This was achieved via the application of chemically-resolved pulsed field gradient (PFG) methods, hence probing the displacement (probability distribution) propagators of both the colloidal and continuous liquid phase. A dilute decane-in-water emulsion was used with flow through a random glass sphere packing being considered. The acquired propagators allowed for quantification of both colloidal entrapment and the velocities of both the continuous phase and the flowing colloids. The flowing colloids were found to experience a velocity acceleration factor (VAF) increase of 1.08 relative to the continuous phase. This was found to be independent of displacement observation time or flowrate. It was speculated to be a consequence of radial exclusion due to the finite size of the colloids. Simulations of the colloidal transport were also performed using a lattice Boltzmann platform and a Lagrangian particle-tracking algorithm which incorporated colloidal radial exclusion. Reasonable agreement was observed between the simulation and the experimental data.     

Direct observation of the target cell for jasmonate-type leaf-closing factor: genus-specific binding of leaf-movement factors to the plant motor cell

We report the synthesis of the novel fluorescence-labeled jasmonate glycoside 2 based on β-d-glucopyranosyl 12-hydroxyjasmonate 1, which is a leaf-closing substance of Albizzia julibrissin Durazz. The fluorescence study using 2 revealed that the target cell for 1 is a motor cell. Probe 2 bound to the motor cells of two plants belonging to genus Albizzia. This result suggested that a receptor for 2, which is common among genus Albizzia would be involved in the nyctinastic leaf movement.     

Discriminant analysis in the presence of interferences: Combined application of target factor analysis and a Bayesian soft-classifier

A method is described for performing discriminant analysis in the presence of interfering background signal. The method is based on performing target factor analysis on a data set comprised of contributions from analyte(s) and interfering components. A library of data from representative analyte classes is tested for possible contributing factors by performing oblique rotations of the principal factors to obtain the best match, in a least-squares sense, between test and predicted vectors. The degree of match between the test and predicted vectors is measured by the Pearson correlation coefficient, r, and the distribution of r for each class is determined. A Bayesian soft classifier is used to calculate the posterior probability based on the distributions of r for each class, which assist the analyst in assessing the presence of one or more analytes. The method is demonstrated by analyses performed on spectra obtained by laser induced breakdown spectroscopy (LIBS). Single and multiple bullet jacketing transfers to steel and porcelain substrates were analyzed to identify the jacketing materials. Additionally, the metal surrounding bullet holes was analyzed to identify the class of bullet jacketing that passed through a stainless steel plate. Of 36 single sample transfers, the copper jacketed (CJ) and non-jacketed (NJ) class on porcelain had an average posterior probability of the metal deposited on the substrate of 1.0. Metal jacketed (MJ) bullet transfers to steel and porcelain were not detected as successfully. Multiple transfers of CJ/NJ and CJ/MJ on the two substrates resulted in posterior probabilities that reflected the presence of both jacketing materials. The MJ/NJ transfers gave posterior probabilities that reflected the presence of the NJ material, but the MJ component was mistaken for CJ on steel, while non-zero probabilities were obtained for both CJ and MJ on porcelain. Jacketing transfer from a bullet to steel as the projectile passed through the steel also proved difficult to analyze. Over 50% of the samples left insufficient transfer to be identified. Transfer from NJ and CJ jacketing was successfully identified by posterior probabilities greater than 0.8.     

In silico analysis of different signal peptides for the secretory production of recombinant human keratinocyte growth factor in Escherichia coli

BackgroundThe recombinant human truncated Keratinocyte growth factor (Palifermin) is the only FDA approved medicine for the treatment of oral mucositis. The Keratinocyte growth factor is a fairly unstable protein due to its high aggregation propensity and therefore its expression as a secretory protein may results in the production of a protein with more stability, higher solubility, better folding, enhanced biological activity, N-terminal authenticity and simplified downstream processing.ObjectiveThe aim of this study was in silico evaluation of 31 different secretory signal peptides to determine the best theoretical candidates for the secretory production of recombinant truncated human KGF in E. coli.MethodsThirty different prokaryotic signal peptides experimentally shown to be capable of recombinant protein secretion in E.coli, along with the native KGF signal peptide were selected for further investigations. The signal peptide sequences were retrieved from the UniProt database. The ability of SPs to act as a secretory leader peptide for rhKGF and the location of cleavage sites were predicted by SignalP 4.1. Physicochemical properties of the signal peptides, which may influence protein secretion, were analyzed by ProtParam and PROSOII. Furthermore, the mRNA secondary structure and Gibbs free energy profile of the selected SPs were analyzed in the fusion state with the rhKGF using Visual Gene Developer package.Results and ConclusionComputational analysis of the physicochemical properties affecting protein secretion identified Sec-B dependent OmpC, Bla, and StaI and SRP dependent TolB signal peptides as the best theoretical candidates for the secretory production of recombinant truncated human KGF in E.coli.     

Design,synthesis and evaluation of novel dehydroabietic acid-dithiocarbamate hybrids as potential multi-targeted compounds for tumor cytotoxicity

In the present study, novel representatives of the important group of biologically-active, dehydroabietic acid-bearing dithiocarbamate moiety, were synthesized and characterized by ¹H NMR, ¹³C NMR, HR-MS. The in vitro antiproliferative activity evaluation (MTT) indicated that these compounds exhibited potent inhibitory activities in various cancer cell lines (HepG-2, MCF-7, HeLa, T-24, MGC-803). Particularly, compound III-b possessed extraordinary cytotoxicity with low micromolar IC₅₀ values ranging from 4.07 to 38.84 µM against tested cancer cell lines, while displayed weak cytotoxicity on two normal cell lines (LO-2 and HEK 293 T). Subsequently, the potential mechanisms of representative compound III-b were elementarily investigated by Transwell experiment, which showed III-b can inhibit cancer cells migration. Annexin-V/PI dual staining showed that the compound can induce HepG-2 cells apoptosis in a dose-dependent manner. Meanwhile this apoptosis may be related to the upregulated protein expression of cleaved-caspase 3, cleaved-caspase 9, Bax and downregulated of Bcl-2 indicated by Western Blot. Later study further confirmed that ROS levels in HepG-2 cells increased significantly with the rise of concentrations. In addition, through the network pharmacology data analyzing, the core targets and signaling pathways of compound III-b for treatment of liver neoplasms were forecasted. Molecular docking model showed that compound III-b had high affinity with hub targets (CASP3, EGFR, HSP90AA1, MAPK1, ERBB2, MDM2), suggesting that compound III-b might target the hub protein to modulate signaling activity. Taken together, these data indicated that dehydroabietic acid structural modification following the “Molecular hybridization” principle is a feasible way to discover the potential multi-targeted antitumor compounds.     

Evaluation of robustness to surface conditions of the target factor analysis method for determining the dielectric function from reflection electron energy loss spectra: Application to GaAs

Target factor analysis (TFA) of a series of angle‐resolved reflection electron energy loss spectra (REELS) was recently demonstrated to be a useful method to determine bulk energy loss functions (ELFs), which by the TFA are separated from the surface‐loss structures of REELS. The dielectric function is then readily derived by Kramers–Kronig analysis of the ELF. The advantage of the method compared with other methods, which are also based on the analysis of REELS, is that the condition of the outermost surface region is unimportant because the excitations that occur there are removed by the TFA and ideally a pure bulk component is determined. Our method is thus particularly useful for determining the ELF from compound materials that are hard to clean without modifying the outermost atomic layers. In this paper, the robustness of the method was studied by applying it to three GaAs samples with different surface compositions caused by different surface cleaning methods. The results showed that when electrons of energy 3000–4500 eV were used, the resulting bulk ELFs were essentially identical except for small differences for the sample that had the largest thickness of the modified surface layer. It is concluded that this is a useful method, provided that the thickness of the modified layer is kept to a minimum by using shallow angle sputtering and by using REELS electrons at a sufficiently high energy that a major part of the electron trajectories are at a depth larger than the thickness of the modified surface layer. Copyright © 2013 John Wiley & Sons, Ltd.     

Determination of rank by median absolute deviation (DRMAD): a simple method for determining the number of principal factors responsible for a data matrix

Median absolute deviation (MAD) is a well‐established statistical method for determining outliers. This simple statistic can be used to determine the number of principal factors responsible for a data matrix by direct application to the residual standard deviation (RSD) obtained from principal component analysis (PCA). Unlike many other popular methods the proposed method, called determination of rank by MAD (DRMAD), does not involve the use of pseudo degrees of freedom, pseudo F‐tests, extensive calibration tables, time‐consuming iterations, nor empirical procedures. The method does not require strict adherence to normal distributions of experimental uncertainties. The computations are direct, simple to use and extremely fast, ideally suitable for online data processing. The results obtained using various sets of chemical data previously reported in the chemical literature agree with the early work. Limitations of the method, determined from model data, are discussed. An algorithm, written in MATLAB format, is presented in the Appendix. Copyright © 2008 John Wiley & Sons, Ltd.     

How the interplay of different control mechanisms affects the initiator efficiency factor in controlled radical polymerization: An investigation using organometallic Mo-based catalysts

Compound CpMoI₂(iPr₂dad) (iPr₂dad = iPrNCHCHNiPr), obtained by halide exchange from CpMoCl₂(iPr₂dad) and NaI, has been isolated and characterized by EPR spectroscopy, cyclic voltammetry, and X-ray crystallography. Its action as a catalyst in atom transfer radical polymerization (ATRP) and as a spin trap in organometallic radical polymerization (OMRP) of styrene and methyl acrylate (MA) monomers has been investigated and compared with that of the dichloro analogue. Compound CpMoCl₂(iPr₂dad) catalyzes the ATRP of styrene and MA with low efficiency factors f (as low as 0.37 for MA and ethyl 2-chloropropionate as initiator), while it irreversibly traps the corresponding growing radical chains under OMRP conditions. On the other hand, compound CpMoI₂(iPr₂dad) has a greater ATRP catalytic activity than the dichloro analogue and yields f = 1 for MA and ethyl 2-iodopropionate as initiator. Under OMRP conditions, it does not irreversibly trap the growing radical chains. This comparison serves to illustrate the general principle that low initiator efficiency factors, sometimes observed in ATRP, may result from the interplay of the ATRP and OMRP mechanisms, when the latter ones involves an irreversible radical trapping process.     

Capillary electrophoresis for the detection of PMP22 gene duplication: study in Mexican patients

Charcot-Marie-Tooth (CMT) disease is the most common inherited disorder of the human peripheral nerve, with an estimated overall prevalence of 17-40/10 000 [1]. The typical phenotype presents peroneal muscular atrophy and pes cavus [2]. CMT is usually divided into two large types, about two-thirds of the patients have CMT type 1 (CMT1), that affects the layer of myelin (demyelination). In type 2 (CMT2) the nerve fibers are affected (axonal). CMT diseases have autosomal dominant, autosomal recessive, and X-linked inheritance [1]. The most frequent subtype is 1A (CMT1A) with autosomal dominant transmission, secondary in most cases to a tandem duplication of a 1.5 Mb DNA fragment on chromosome 17p11.2-p12 [4-7]. In this region, the codification of the peripheral myelin protein 22 (PMP22) takes place. The severity of the disease varies among patients, even within the same family, from almost no symptoms to severe foot-drop and sensory loss. The PMP22 gene has four exons and is regulated by two promoters located toward the extreme 5'. The origin of the duplication that causes the disease is an uneven exchange of the chromatids during the meiosis. This unequal recombination occurs between two regions that limit the PMP22 gene, described as REP places of 24 kb, proximal and distal [3, 4].     

LC-MS-based multi-omics analysis of brain tissue for the evaluation of the anti-ischemic stroke potential of Tribulus terrestris L. fruit extract in MCAO rats

This study aimed to investigate the chemical composition of Tribulus terrestris L. fruit (TT) extract named TT15 and its protective effect against ischemic stroke (IS) as well as corresponding mechanisms. The chemical composition of TT15 was analyzed by liquid chromatography-mass spectrometry (LC-MS), and the compound identification was conducted via searching the in-house database. The LC-MS-based multi-omics approach was applied to search the differential metabolites and differential proteins in rat brain tissue and to explore the biomarker and molecular mechanism of TT15 against middle cerebral artery occlusion (MCAO). A total of 20 compounds were identified from TT15, mainly including alkaloids, flavonoids, phenols, quinones, and esters. These 20 compounds significantly affected the metabolism of 44 metabolites and the expression of 51 proteins. Joint pathway analysis showed that these metabolites and proteins were mainly involved in the response to elevated platelet cytosolic Ca²⁺ and platelet activation, which inferred that TT15 may exert a protective effect against cerebral ischemic injury via regulating platelet function. This study provides useful information for further exploration of the mechanisms of TT extract against IS.