Multivariate analysis of extremely large ToFSIMS imaging datasets by a rapid PCA method

Principal component analysis (PCA) and other multivariate analysis methods have been used increasingly to analyse and understand depth profiles in X‐ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES) and secondary ion mass spectrometry (SIMS). These methods have proved equally useful in fundamental studies as in applied work where speed of interpretation is very valuable. Until now these methods have been difficult to apply to very large datasets such as spectra associated with 2D images or 3D depth‐profiles. Existing algorithms for computing PCA matrices have been either too slow or demanded more memory than is available on desktop PCs. This often forces analysts to ‘bin’ spectra on much more coarse a grid than they would like, perhaps even to unity mass bins even though much higher resolution is available, or select only part of an image for PCA analysis, even though PCA of the full data would be preferred. We apply the new ‘random vectors’ method of singular value decomposition proposed by Halko and co‐authors to time‐of‐flight (ToF)SIMS data for the first time. This increases the speed of calculation by a factor of several hundred, making PCA of these datasets practical on desktop PCs for the first time. For large images or 3D depth profiles we have implemented a version of this algorithm which minimises memory needs, so that even datasets too large to store in memory can be processed into PCA results on an ordinary PC with a few gigabytes of memory in a few hours. We present results from ToFSIMS imaging of a citrate crystal and a basalt rock sample, the largest of which is 134GB in file size corresponding to 67 111 mass values at each of 512 × 512 pixels. This was processed into 100 PCA components in six hours on a conventional Windows desktop PC. © 2015 The Authors. Surface and Interface Analysis published by John Wiley & Sons Ltd.     

Mesoporous Silica Nanoparticles Decorated with Carbosilane Dendrons as New Non‐viral Oligonucleotide Delivery Carriers

A novel nanosystem based on mesoporous silica nanoparticles covered with carbosilane dendrons grafted on the external surface of the nanoparticles is reported. This system is able to transport single‐stranded oligonucleotide into cells, avoiding an electrostatic repulsion between the cell membrane and the negatively charged nucleic acids thanks to the cationic charge provided by the dendron coating under physiological conditions. Moreover, the presence of the highly ordered pore network inside the silica matrix would make possible to allocate other therapeutic agents within the mesopores with the aim of achieving a double delivery. First, carbosilane dendrons of second and third generation possessing ammonium or tertiary amine groups as peripheral functional groups were prepared. Hence, different strategies were tested in order to obtain their suitable grafting on the outer surface of the nanoparticles. As nucleic acid model, a single‐stranded DNA oligonucleotide tagged with a fluorescent Cy3 moiety was used to evaluate the DNA adsorption capacity. The hybrid material functionalised with the third generation of a neutral dendron showed excellent DNA binding properties. Finally, the cytotoxicity as well as the capability to deliver DNA into cells, was tested in vitro by using a human osteoblast‐like cell line, achieving good levels of internalisation of the vector DNA/carbosilane dendron‐functionalised material without affecting the cellular viability.     

Adding a Structural Context to the Deprotometalation and Trans‐Metal Trapping Chemistry of Phenyl‐Substituted Benzotriazole

Organometallic bases are becoming increasingly complex, because mixing components can lead to bases superior to single‐component bases. To better understand this superiority, it is useful to study metalated intermediate structures prior to quenching. This study is on 1‐phenyl‐1H‐benzotriazole, which was previously deprotonated by an in situ ZnCl₂ ? TMEDA/LiTMP (TMEDA=N,N,N′,N′‐tetramethylethylenediamine; TMP=2,2,6,6‐tetramethylpiperidide) mixture and then iodinated. Herein, reaction with LiTMP exposes the deficiency of the single‐component base as the crystalline product obtained was [{4‐R‐1‐(2‐lithiophenyl)‐1H‐benzotriazole ? 3THF}₂], [R=2‐C₆H₄(Ph)NLi], in which ring opening of benzotriazole and N₂ extrusion had occurred. Supporting lithiation by adding iBu₂Al(TMP) induces trans‐metal trapping, in which C?Li bonds transform into C?Al bonds to stabilise the metalated intermediate. X‐ray diffraction studies revealed homodimeric [(4‐R′‐1‐phenyl‐1H‐benzotriazole)₂], [R′=(iBu)₂Al(μ‐TMP)Li], and its heterodimeric isomer [(4‐R′‐1‐phenyl‐1H‐benzotriazole){2‐R′‐1‐phenyl‐1H‐benzotriazole}], whose structure and slow conformational dynamics were probed by solution NMR spectroscopy.     

New Features in the Lipid A Structure of <Emphasis Type="Italic">Brucella suis</Emphasis> and <Emphasis Type="Italic">Brucella abortus</Emphasis> Lipopolysaccharide

Brucellaceae are Gram-negative bacteria that cause brucellosis, one of the most distributed worldwide zoonosis, transmitted to humans by contact with either infected animals or their products. The lipopolysaccharide exposed on the cell surface has been intensively studied and is considered a major virulence factor of Brucella. In the last years, structural studies allowed the determination of new structures in the core oligosaccharide and the O-antigen of this lipopolysaccharide. In this work, we have reinvestigated the lipid A structure isolated from B. suis and B. abortus lipopolysaccharides. A detailed study by MALDI-TOF mass spectrometry in the positive and negative ion modes of the lipid A moieties purified from both species was performed. Interestingly, a new feature was detected: the presence of a pyrophosphorylethanolamine residue substituting the backbone. LID-MS/MS analysis of some of the detected ions allowed assurance that the Lipid A structure composed by the diGlcN3N disaccharide, mainly hexa-acylated and penta-acylated, bearing one phosphate and one pyrophosphorylethanolamine residue.

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Kinetics of Lime Pretreatment of Sugarcane Bagasse to Enhance Enzymatic Hydrolysis

The objective of this work was to determine the optimum conditions of sugarcane bagasse pretreatment with lime to increase the enzymatic hydrolysis of the polysaccharide component and to study the delignification kinetics. The first stage was an evaluation of the influence of temperature, reaction time, and lime concentration in the pretreatment performance measured as glucose release after hydrolysis using a 2³ central composite design and response surface methodology. The maximum glucose yield was 228.45 mg/g raw biomass, corresponding to 409.9 mg/g raw biomass of total reducing sugars, with the pretreatment performed at 90°C, for 90 h, and with a lime loading of 0.4 g/g dry biomass. The enzymes loading was 5.0 FPU/dry pretreated biomass of cellulase and 1.0 CBU/dry pretreated biomass of β-glucosidase. Kinetic data of the pretreatment were evaluated at different temperatures (60°C, 70°C, 80°C, and 90°C), and a kinetic model for bagasse delignification with lime as a function of temperature was determined. Bagasse composition (cellulose, hemicellulose, and lignin) was measured, and the study has shown that 50% of the original material was solubilized, lignin and hemicellulose were selectively removed, but cellulose was not affected by lime pretreatment in mild temperatures (60–90°C). The delignification was highly dependent on temperature and duration of pretreatment.     

Cloning, Sequencing, and Identification Using Proteomic Tools of a Protease from Bromelia hieronymi Mez

Fruits of Bromelia hieronymi, a tropical South American plant, possess a high content of peptidases with potential biotechnological uses. Total RNA was extracted from unripe fruits and peptidase cDNA was obtained by 3'RACE-PCR. The consensus sequence of the cysteine peptidase cDNA contained 875 bp, the 690 first ones codifying for a hypothetical polypeptide chain of the mature peptidase, named Bh-CP1 (molecular mass 24.773 kDa, pI 8.6, extinction molar coefficient 58,705 M(-1) cm(-1)). Bh-CP1 sequence shows a high percentage of identity with those of other cysteine plant proteases. The presence of highly preserved residues is observed, like those forming the catalytic site (Gln19, Cys25, His159, and Asn175, papain numbering), as well as other six Cys residues, involved in the formation of disulfide bounds. Molecular modeling results suggest the enzyme belongs to the α?+?β class of proteins, with two disulfide bridges (Cys23-Cys63 and Cys57-Cys96) in the α domain, while the β domain is stabilized by another disulfide bridge (Cys153-Cys203). Additionally, peptide mass fingerprints (PMFs) of the three peptidases previously isolated from B. hieronymi fruits (namely hieronymain I, II, and III) were performed and compared with the theoretical fingerprint of PMF of Bh-CP1, showing a partial matching between the in silico-translated protein and hieronymain II.     

Sulfonamide carbazole receptors for anion recognition

Carbazole-based receptors functionalized with two sulfonamide groups have been synthesized and their properties as anion receptors have been evaluated. The receptor with bis(trifluoromethyl)aniline groups has shown a very high affinity for halide ions, especially remarkable as only two hydrogen bonds are formed in the complexes. (1)H NMR and fluorescence titrations have been carried out and binding constants up to 7.9 × 10(6) M(-1) have been reached. X-ray structures have been obtained and a modelling study has shown the possible reasons for the large affinity of these compounds for halide anions.     

Canonical geometrically ruled surfaces

We prove the existence of canonical scrolls; that is, scrolls playing the role of canonical curves. First of all, they provide the geometrical version of Riemann Roch Theorem: any special scroll is the projection of a canonical scroll and they allow to understand the classification of special scrolls in P^N. Canonical scrolls correspond to the projective model of canonical geometrically ruled surfaces over a smooth curve. We also prove that the generic canonical scroll is projectively normal except in the hyperelliptic case and for very particular cases in the nonhyperelliptic situation. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Kinetics and structural studies of the atmospheric corrosion of carbon steels in Panama

The corrosion of a carbon steel was studied in different atmospheres at sites in the Republic of Panama. The weight loss (corrosion penetration) suffered by the carbon steel is related to time by a bilogarithmic law. Mössbauer spectroscopy indicated the rust was composed of non-stoichiometric magnetite (Fe_3-xO₄), maghemite (γ-Fe₂O₃), goethite (α-FeOOH) of intermediate particle size, lepidocrocite (γ-FeOOH) and superparamagnetic particles. Magnetite formation is related to the alternating dry--wet cycles. Goethite is related to corrosion penetration by a saturation type of behavior, following a Langmuir type of relationship. Goethite in rust protects steel against further atmospheric corrosion.     

C-H...O hydrogen bonds in cyclohexenone reveal the spectroscopic behavior of Csp3-H and Csp2-H donors.

C-H...O hydrogen bonds in liquid 2-cyclohexen-1-one are studied to assess the vibrational spectroscopic behavior of the Csp2-H and Csp3-H donors. The presence of a pseudo-isosbestic point in the vC = O region supports the assignment of the two observed bands to two species in equilibrium, considered to be the free and 1:1 associated forms. The values of deltaH degrees =-18.5 +/- 0.6 kJmol(-1) and deltaS degrees = -76 +/- 2 J K(-1) mol(-1) for the dimerization through C-H...O hydrogen bonds were obtained from the dimerization constant at different temperatures. The concentration-dependent intensity of the vCH2 band profile is ascribed to the presence of a blue-shifted band from the hydrogen-bonded Csp3-H group. However, the most surprising result is the absence of concentration- or temperature-dependent intensities in the bands assigned to the stretching modes of the Csp2-H donors.