bluuebunny/crossref_metadata_2025 huggingface dataset:
The UNSIN project: exploring the molecular physiology of sins
Authors: Naji Faysal , Salci Lauren , Hoit Graeme , Rangachari P. K.
Published: March 2012

Although active learning works, promoting it in large undergraduate science classes is difficult. Here, three students (F. Naji, L. Salci, and G. Hoit) join their teacher (P. K. Rangachari) in describing one such attempt. Two cohorts in a first-year undergraduate biology course explored the molecular underpinnings of human misbehavior. Students were divided into 18 groups and randomly allotted to deal with one of the four deadly sins: sloth, gluttony, lust, and wrath. Students were expected to read primary sources to devise molecular ways to counter these sins. Group progress was monitored over the 12-wk period by the preceptor (P. K. Rangachari) at scheduled intervals. A single randomly selected student was questioned about the work done, and future directions were provided by the preceptor. At the end of the term, randomly selected students defended their group's approaches to the entire class. A final written report was graded. The following multiple target molecules were considered for each sin: gluttony (cholecystokinin, ghrelin, GABA, leptin, peptide YY, neuropeptide Y, and the melanocortin 4 receptor); sloth (dopamine, glutamate, GABA, and orexin); wrath (serotonin, GABA, glutamate, and corticotropin-releasing hormone receptor 2); and lust (prolactin, testosterone, oxytocin, dopamine, and estrogen). Students noted that the project provided a valuable learning experience, and the random selection approach gave students a greater sense of responsibility to their group. The project helped students hone their skills at searching, synthesizing, sharing, and presenting information, fostered group interactions, and provided a solid knowledge base for subsequent courses.
Effect of uniform versus expanding retrieval practice on the recall of physiology information
Authors: Dobson John L.
Published: March 2012

The purpose of this study was to compare the retention of selected physiology concepts throughout 30 days of two different uniform schedules of retrieval and two different expanding schedules of retrieval. Participants ( n = 250) first read and reread 30 immunology and reproductive physiology concepts and were then repeatedly assessed, without feedback, according to one of the following four randomly assigned schedules: 1) immediately after learning and again 9 and 19 days later [uniform ( days 1, 10, and 20)]; 2) 7, 14, and 21 days after learning [uniform ( days 8, 15, and 22)]; 3) immediately after learning and again 5 and 15 days later [expanding ( days 1, 6, and 16)]; and 4) 1, 6, and 16 days after learning [expanding ( days 2, 7, and 17)]. All participants completed a final assessment 29 days after learning the physiology concepts. Mean final assessment scores ± SE for the uniform ( days 1, 10, and 20), uniform ( days 8, 15, and 22), expanding ( days 1, 6, and 16), and expanding ( days 2, 7, and 17) groups were 36.15 ± 1.97, 32.31 ± 1.87, 45.80 ± 2.56, and 39.71 ± 2.48, respectively. There were no differences in final assessment scores between the two expanding retrieval groups, but expanding ( days 1, 6, and 16) group scores were significantly higher than those in both uniform retrieval groups (ANOVA, F = 6.52, P = 0.00). Also, the combined mean of the two expanding retrieval conditions (42.57 ± 1.80) was significantly higher ( F = 14.09, P = 0.00) than the combined mean of the two uniform retrieval conditions (34.10 ± 1.36). The results indicate that participants benefited more from expanding retrieval practice, particularly when the first assessment was administered immediately after learning.
Identification of minor products obtained during radiolysis of tributylphosphate (TBP)
Authors: Lesage Denis , Virelizier Henri , Jankowski Christophe K. , Tabet Jean Claude
Published: March 2012

The structure identification of the fraction of minor products obtained during radiolysis of tributylphosphate (TBP), the solvent used in reprocessing of nuclear fuel, is reported. These results were realised from the distillation residue of the EDIT loop. The primary radiolysis formed TBP radical dimerises and is transformed under oxidative nitric acid conditions into several butyl chains substituted hydroxy or nitro phosphates as well as alkylated TBP. The butyl chain hydroxylated phosphate is leading to ketones, ethers and O‐ester derivatives. The structures were determined by tandem mass spectrometry (MS–MS) and isotopic labelling techniques as well as by ion filiation and isotopic exchange studies. The analytical method developed consisted of the use of the integrated GC–MS, or GC–MS–MS, isotopic labelling technique. The combination of these techniques enabled to identify and to semi‐quantify most of highly functionalised TBP without their prior separation from the post radiolysis mixtures.
FTIR and 1H‐NMR studies of chiral (S)‐(‐)‐2‐methylbutyl 4′‐(4″‐hexyloxy‐, (S)‐(‐)‐2‐methylbutyl 4′‐(4″‐(d13)‐hexyloxy‒, (S)‐(‐)‐2‐methylbutyl 4′‐(4″‐octyloxy‐ and (S)‐(‐)‐2‐methylbutyl 4′‐(4″‐(d17)‐octyloxyphenyl)benzoates
Authors: Yeap Guan-Yeow , Takanishi Yoichi , Takezoe Hideo
Published: March 2012

Four organic chiral compounds (S)‐(‐)‐2‐methylbutyl 4′‐(4″‐hexyloxy‐, (S)‐(‐)‐2‐methylbutyl 4′‐(4″‐(d13)‐ hexyloxy‐, (S)‐(‐)‐2‐methylbutyl 4′‐(4″‐octyloxy‐ and (S)‐(‐)‐2‐methylbutyl 4′‐(4″‐(d17)‐octyloxy‐phenyl)benzoates were synthesized via generalized methods and characterized by elemental analysis, FTIR and 1H NMR. A noticeable difference between the compounds which possess hydrogenated achiral substituent with the deuterated counterparts as exemplified from the FTIR spectra has been suggested for the first time to result from the afinity of the latter compounds towards hydroxylation induced by potassium bromide.
Electron ionization mass spectrometry of difurfuryl diamines
Authors: Lesimple Alain , Le Bigot Yves , Delmas Michel , Banoub Joseph
Published: March 2012

Electron impact mass spectrometry (ei‐ms) has aided the structural characterization of a novel series of synthetic difuranic diamines and permitted the comparison with a previous study employing electrospray ionization mass spectrometry. As expected, the molecular radical ion was inexistant in this series of compounds and the fragmentation routes of the molecular radical ion were governed either by homolytic cleavage of the radical R or by heterolytic loss of NH3 to give their respective base peaks.
Electron impact mass spectrometry of some 3‐[3‐(4‐aryl)‐1,2,4‐oxadiazole‐5‐yl] acyl arylaldehyde hydrazone derivatives
Authors: Leite Lúcia Fernanda C. C. , Barreiro Eliezer J. , Ramos Mozart N. , Silva João Bosco P. , Galdino Suely L. , Pitta Ivan R.
Published: March 2012

This report describes the results of a study of the electron impact mass spectrometry behaviour of 20 new compounds of a series of 3‐[3‐(4‐aryl)‐1,2,4‐oxadiazole‐5‐yl] acyl arylaldehyde hydrazone derivatives. The most relevant possible fragmentation patterns of this class of compounds under electron impact are outlined.
REGRAS: an auxiliary program for pattern recognition and substructure elucidation of monoterpenes
Authors: Ferreira Marcelo J. P. , Rodrigues Gilberto V. , Brant AntÔnio J. C. , Emerenciano Vicente P.
Published: March 2012

The main purpose of this paper is to present a procedure that utilizes 13C NMR for pattern recognition and substructure elucidation of monoterpenes. By this reason, a novel version of the REGRAS program was developed for the specialist SISTEMAT system. This program carries out an analysis of the 13C NMR data from a given compound and, from characteristic chemical shift ranges, recognizes the substructures and the skeleton present in a compound. At the end of this procedure, the program displays as analysis results the likely skeletons and substructures of the substance in question. The REGRAS program was tested on skeleton elucidation of 30 monoterpenes from the most varied skeleton types, exhibiting excellent results in skeleton and substructure prediction processes.
Enhancement of Eu3+ emission in solution by bulky chelating ligands and deuterium substitution
Authors: Zaitoun Mohammed A.
Published: March 2012

Binding the europium ion with a bulky chelating ligand provides one strategy for minimizing the quenching effects of water on the luminescence of the ion. 1,4,8,11‐tetraazacyclotetradecane‐1,4,8,11‐tetraaceticacid tetrahydrochloride (TTT) was used as a chelating agent to isolate Eu3+ from hydroxyl deactivation in water. A large enhancement in the Eu3+ emission was observed for the chelated Eu3+ compared to the unchelated. Absorption and emission spectra are reported together with lifetime measurements. The latter were used to study concentration quenching and quenching by water.
Comparison of the Photochemical Reaction of Photoactive Yellow Protein in Crystal with Reaction in Solution 1
Authors: Mano Eriko , Kamikubo Hironari , Imamoto Yasushi , Kataoka Mikio
Published: March 2012

Photoactive yellow protein (PYP) is a photoreceptor protein for the negative phototaxis of Ectothiorhodospira halophila. The crystal structures of several photo‒intermediates have been revealed by X‐ray crystallography. In the crystal structure of the active intermediate, PYPM, no significant structural changes were observed except for the vicinity of the chromophore. On the contrary, spectroscopic studies with solution condition demonstrated that global structural changes occur during the photo‒cycle. In order to reveal the origin of the discrepancies, we measured the reaction kinetics upon illumination under crystal condition and to compare them with those observed under solution condition. The reactive portion decreases with the increase of crystallinity. The rate constant of PYPM decay also decreases with the increase of crystallinity. These results suggest two possibilities: (1) PYP in crystal does not react by the illumination; (2) the photoreaction rate is highly accelerated in crystal. Consequently, the photoreaction in crystal is considered to be highly influenced by the force constraint from crystalline lattice.
β‒hairpin polypeptides by design and selection
Authors: Skelton Nicholas J. , Blandl Tamas , Russell Stephen J. , Starovasnik Melissa A. , Cochran Andrea G.
Published: March 2012

We have developed polypeptide scaffolds that readily adopt a β‒hairpin conformation (a pair of antiparallel strands connected by a turn) in solution. The study of such peptides allows us to understand the factors that govern stability and folding of these motifs in proteins, and permits mimicry of functionally important regions of proteins. Spectroscopic and biophysical methods have been used to characterize the conformational preferences and stability of these peptides, with a strong emphasis on using restraints generated from 1H NMR spectroscopy to determine their three‒dimensional structure. By optimization of inter‒strand interactions, we have developed highly stable disulfide‒cyclized and linear β‒hairpin peptides. In particular, tryptophan residues at non‒hydrogen bonded strand sites (NHB) are highly stabilizing. A variety of turn types have been presented from these scaffolds, suggesting that they might generally be useful in turn presentation. Interestingly, β‒hairpin peptides (containing a disulfide and a NHB tryptophan) have recently been discovered as antagonists of protein–protein interactions from naïve peptide libraries displayed on phage. Comparison of one such β‒hairpin peptide with an α‒helical peptide of very similar sequence provides further insight into the role that residue type and context play in determining polypeptide conformation.
Fibre‐Optic IR‐Spectroscopy for Biomedical Diagnostics
Authors: Bindig Uwe , Gersonde Ingo , Meinke Martina , Becker Yukiyo , Müller Gerhard
Published: March 2012

The use of microscopy is a valuable means of gaining vital information for medical diagnostics. Due to a number of recent technological developments advances have been made in IR microscopy and in particular, rapid detection methods. Microscopic examination methods usually involve sampling followed by a method of sample purification or preparation. The advantages of the IR analytical method are that it is based on a direct, non‒destructive measurement of sample material and that the resulting IR spectra provide extensive and specific information about the sample composition and structure. The course of a disease can lead to either formation or loss of organic compounds in metabolism as well as changes within the biological matrix. Corresponding changes can also be expected in the IR‒signature in view to the grading of alteration. Our preliminary IR microscopic investigations compared diseased and healthy tissue samples individually and basic information was obtained about the tissue specific spectral signature, taking account of biological variance. Human tissue samples taken from the colon were used for these studies. Given the number of endoscopic applications used in minimally invasive medicine, we hope to establish the IR fibre based procedure as an optical biopsy method for tissue diagnostics. The aqueous environment as well as the IR radiation source, signal detection and the flexible wave guide type will be a limiting factor for an IR system. The hygiene requirements are particularly high for a fibre based system to be used for in vivo applications.

First experiments were used to check the transmission of the IR microspectroscopic data. Fibre supported measurements were made in ATR and remission. High powered IR laser diodes were tested in subsequent trials for application in biomedicine. First results are presented on the way to an IR‐endo‐spectroscopic system.
Applications of Fourier transform infrared spectroscopy, Fourier transform infrared microscopy and near‐infrared spectroscopy to cancer research
Authors: Yano Kazuyuki , Sakamoto Yasushi , Hirosawa Narumi , Tonooka Shouko , Katayama Hiroo , Kumaido Kuniyoshi , Satomi Akira
Published: March 2012

Glycogen levels in human lung and colorectal cancerous tissues were measured by the Fourier transform (FT‐IR) spectroscopic method. Reliability of this method was confirmed by chemical analyses of the same tissues used for the FT‐IR spectroscopic measurements, suggesting that this spectroscopic method has a high specificity and sensitivity in discriminating human cancerous tissues from noncancerous tissues. The glycogen levels in the tissues were compared with the clinical, histological and histopathological factors of the cancer, demonstrating that glycogen is a critical factor in understanding the biological nature of neoplastic diseases. Furthermore, direct measurement of a very small amount of tissue by a FT‐IR microscope suggested that it could be used as a diagnostic instrument for various tissue samples obtained via a fine needle biopsy procedure. The progressive alterations in rat mammary gland tumors were investigated by a near‐infrared (NIR) spectrometer with a fiber optic probe. A lipid band due to the first overtone of n‐alkane was used to quantitatively evaluate malignant changes in the tumors. NIR spectroscopy may offer the potential for non‒invasive, in vivo diagnosis of human cancers.
Comparison of affinity ranking and immunochemical key data as measure for molecular antibody evolution
Authors: Kramer Karl , Rau Doris , Hock Bertold
Published: March 2012

The evolutionary optimization of antibody binding propertiesin vitro opens new perspectives for immunochemistry, since the affinity and selectivity of a given antibody molecule can be tailored to meet the requirements of the envisaged analytical application. An efficient strategy for molecular antibody evolution is described that combines randomized point mutations and sequential recombination of variable antibody gene repertoires employing a group‐selective library. This strategy enabled significant improvements in the binding of the model analyte atrazine that were monitored by both, kinetic measurements by the optical sensor BIAcore 2000TM and immunochemical key data obtained by enzyme‐linked immunosorbent assay (ELISA). The KD of the template antibody IPR‐7 was improved by a factor of 17 from 1.27×10–8 M to 7.46×10–10 M for the optimized variant IPR‐83. The enhanced KD is well in line with the 15 fold lowered IC50 of the atrazine ELISA, which was shifted from 13.6 µg/l for IPR‐7 to 0.9 µg/l for IPR‐83. Once the analytical properties of antibody fragments are optimized, antibody functionality can be tailored for specific technical demands, e.g. the directed immobilization on microchip surfaces. As an example, the variable region encoding genes of the scFv variants were subcloned into the Fab fragment expression vector pASK99, in order to reconstitute the antigen binding site of native antibody molecules. The expressed Fab fragments provide a C‐terminal affinity tag for functionalized sensor surfaces. Again, the evaluation by ELISA as well as by BIAcore revealed a consistent ratio of analyte binding enhancement for the engineered Fab fragments.
Using cryoprobes to decrease acquisition times of triple‐resonance experiments used for protein resonance assignments
Authors: Goger Michael J. , McDonnell James M. , Cowburn David
Published: March 2012

In most structural biology NMR laboratories, instrument time is a limiting factor in the number of structural projects a laboratory is able to support. In the post‐genomic era we can expect the number of structural targets to markedly increase. Here we address to what degree recently introduced cryoprobes, which are 3–4 times as sensitive as conventional probes, can alleviate this problem. To evaluate this approach, a set of triple‐resonance experiments for protein assignments were acquired with a cryoprobe. We show that, with the cryoprobe, high quality triple‐resonance data can be obtained within as 4 hours/experiment. These results show that a full set of data for protein assignments can now be practically collected in 1–2 days.
Tracking Chemical Changes in a Live Cell: Biomedical Applications of SR‐FTIR Spectromicroscopy
Authors: Holman Hoi-Ying N. , Martin Michael C. , McKinney Wayne R.
Published: March 2012

Synchrotron radiation‐based Fourier transform infrared (SR‐FTIR) spectromicroscopy is a newly emerging bioanalytical and imaging tool. This unique technique provides mid‒infrared (IR) spectra, hence chemical information, with high signal‐to‐noise at spatial resolutions as fine as 3 to 10 microns. Thus it enables researchers to locate, identify, and track specific chemical events within an individual living mammalian cell. Mid‐IR photons are too low in energy (0.05−0.5 eV) to either break bonds or to cause ionization. In this review, we show that the synchrotron IR beam has no detectable effects on the short‐ and long‐term viability, reproductive integrity, cell‐cycle progression, and mitochondrial metabolism in living human cells, and produces only minimal sample heating (<0.5°C). We will then present several examples demonstrating the application potentials of SR‐FTIR spectromicroscopy in biomedical research. These will include monitoring living cells progressing through the cell cycle, including death, and cells reacting to dilute concentrations of toxins.
Using UV‐Vis. Linear Dichroism to Study the Orientation of Molecular Probes and Biomolecules in Lipidic Membranes
Authors: Castanho M. A. R. B. , Lopes S. , Fernandes M.
Published: March 2012

Linear dichroism methodologies are based on the different interaction of molecules with linearly polarized light depending on their orientation. Theoretical predictions are used to conclude on the orientation of selected molecules relative to their neighbours (usually an organized matrix). In the specific case of linear dichroism methodologies applied to data obtained from UV‐Vis. spectroscopic techniques, the orientational distribution function of the chromophores′ electronic transition moment can be calculated and converted to the molecular axis distribution function. In this paper, the orientation of molecular probes and biomolecules in model systems of biomembranes (lipidic matrixes) is explored and illustrated using common membrane probes (trans‐parinaric acid, a cyanine and laurdan) and polyene antibiotics (Amphotericin B and Nystatin). The emphasis is on the technique and methodologies themselves, rather than the scientific impact of the attained distributions. The main addressed items are: (1) How to adapt a common UV‐Vis. spectrophotometer and spectrofluorimeter to perform linear dicrhoism experiments?, (2) Sample preparation, and (3) Data analysis (including artefacts corrections).
In situ FTIR Assessment of Desiccation‐Tolerant Tissues
Authors: Wolkers Willem F. , Hoekstra Folkert A.
Published: March 2012

This essay shows how Fourier transform infrared (FTIR) microspectroscopy can be applied to study thermodynamic parameters and conformation of endogenous biomolecules in desiccation‐tolerant biological tissues. Desiccation tolerance is the remarkable ability of some organisms to survive complete dehydration. Seed and pollen of higher plants are well known examples of desiccation‐tolerant tissues. FTIR studies on the overall protein secondary structure indicate that during the acquisition of desiccation tolerance, plant embryos exhibit proportional increases in α‐helical structures and that µ‐sheet structures dominate upon drying of desiccation sensitive‐embryos. During ageing of pollen and seeds, the overall protein secondary structure remains stable, whereas drastic changes in the thermotropic response of membranes occur, which coincide with a complete loss of viability. Properties of the cytoplasmic glassy matrix in desiccation‐tolerant plant organs can be studied by monitoring the position of the OH‐stretching vibration band of endogenous carbohydrates and proteins as a function of temperature. By applying these FTIR techniques to maturation‐defective mutant seeds of Arabidopsis thaliana we were able to establish a correlation between macromolecular stability and desiccation tolerance. Taken together, in situ FTIR studies can give unique information on conformation and stability of endogenous biomolecules in desiccation‐tolerant tissues.
Automated Peak Harvesting of MALDI–MS spectra for high throughput proteomics
Authors: Breen E. J. , Holstein W. L. , Hopwood F. G. , Smith P. E. , Thomas M. L. , Wilkins M. R.
Published: March 2012

High throughput proteomics is realized not only by the use of automated hardware but also by the application of efficient, automated software routines to complex data. In this paper, we present the recent developments of our software tool Peak Harvester for the automatic harvesting of monoisotopic peaks from MALDI‐TOF mass spectra of peptides. Peak Harvester uses advanced mathematical morphology to convert mass spectra into stick representations. Poisson modeling of theoretical isotopic distributions is then applied to derive the monoisotopic peptide mass from an isotopically resolved group of peaks. The accuracy of Peak Harvester is demonstrated via the analysis of peptide spectra from low concentrations of bovine serum albumin blotted onto PVDF membranes and of tryptic digested platelet proteins derived from human blood following two‐dimensional gel electrophoresis. The results demonstrate the power of this software as it can accurately assign monoisotopic masses, including those from overlapping isotopic distributions, and picks masses as accurately as an experienced human operator. We have further developed Peak Harvester to include peak harvesting from MALDI‐TOF Post Source Decay (PSD) experiments. Here we demonstrate the versatility of the software by both the analysis of PSD data from 2DE and the analysis of peptide mass spectra collected directly from tryptic digests on a PVDF membrane.
A structural analysis of heparin‒like glycosaminoglycans using MALDI‒TOF mass spectrometry
Authors: Kett Warren C. , Coombe Deirdre R.
Published: March 2012

Mass spectrometry (MS) techniques have spear‒headed the field of proteomics. Recently, MS has been used to structurally analyse carbohydrates. The heparin/heparan sulfate‒like glycosaminoglycans (HLGAGs) present a special set of difficulties for structural analysis because they are highly sulfated and heterogeneous. We have used a matrix‒assisted laser desorption/ionization time of flight mass spectrometry (MALDI‒MS) technique in which heparin fragments are non‒covalently bound to basic peptides of a known mass, so as to limit in‒source desulfation and hence afford an accurate mass. We examined a range of different sized fragments with varying degrees of sulfation. The potential of combining the MALDI‒MS technique with enzymatic digestion to obtain saccharide sequence information on heparin fragments was explored. A disaccharide analysis greatly assists in determining a sequence from MALDI‒MS data. Enzymatic digestion followed by MALDI‒MS allows structural data on heparin fragments too large for direct MALDI‒MS to be obtained. We demonstrate that synthetic sulfated oligosaccharides can also be analysed by MALDI‒MS. There are advantages and limitations with this methodology, but until superior MS techniques become readily accessible to biomedical scientists the MALDI‒MS method provides a means to structurally analyse HLGAG fragments that have therapeutic potential because of their ability to bind to and functionally regulate a host of clinically important proteins.
Ruthenium trisbipyridine as a candidate for gas‐phase spectroscopic studies in a Fourier transform mass spectrometer
Authors: Scott Jill R. , Ham Jason E. , Durham Bill , Tremblay Paul L.
Published: March 2012

Metal polypyridines are excellent candidates for gas‐phase optical experiments where their intrinsic properties can be studied without complications due to the presence of solvent. The fluorescence lifetimes of [Ru(bpy)3]1+ trapped in an optical detection cell within a Fourier transform mass spectrometer were obtained using matrix‐assisted laser desorption/ionization to generate the ions with either 2,5‐dihydroxybenzoic acid (DHB) or sinapinic acid (SA) as matrix. All transients acquired, whether using DHB or SA for ion generation, were best described as approximately exponential decays. The rate constant for transients derived using DHB as matrix was 4×107 s−1, while the rate constant using SA was 1×107 s−1. Some suggestions of multiple exponential decay were evident although limited by the quality of the signals. Photodissociation experiments revealed that [Ru(bpy)3]1+ generated using DHB can decompose to [Ru(bpy)2]1+, whereas ions generated using SA showed no decomposition. Comparison of the mass spectra with the fluorescence lifetimes illustrates the promise of incorporating optical detection with trapped ion mass spectrometry techniques.
Cell apoptosis specific marker found by Fourier Transform Infrared Spectroscopy
Authors: Gaudenzi Silvia , Pozzi Deleana , Toro Paolo , Silvestri Ida , Morrone Stefania , Castellano Agostina Congiu
Published: March 2012

We used Fourier Transform Infrared Spectroscopy (FTIR) combined with flow cytometry to study the apoptosis and necrosis processes in Jurkat, a lymphocyte cell line. The apoptosis was induced in the cells by a chemical agent, the actinomycin D, while the necrosis was induced lowering the pH value to 4.2. The apoptotic events were analysed by flow cytometry (using annexin V and propidium iodide) and contemporary monitored by FTIR spectroscopy at different times after the treatment. This comparison allowed us to find in the IR spectrum, between 3000 cm−1 and 2800 cm−1, a “marker band” of the apoptosis corresponding to the exposure of phosphatidylserine on the outer leaflet of the membrane. A marker of a specific cellular process obtained by using a non‒destructive technique such as FTIR spectroscopy, has a great significance in the diagnostic medicine providing a tool for detecting pathologies in vivo.
Probing the role of metal ions on reversible peptide–protein interactions by NMR
Authors: D′Amelio Nicola , Gaggelli Elena , Gaggelli Nicola , Mancini Francesca , Molteni Elena , Valensin Daniela , Valensin Gianni
Published: March 2012

This work provides evidence that paramagnetic lanthanide ions constitute ideal probes suitable for investigations of metal effects upon peptide–receptor interactions with the use of NMR methods. Cerium(III) is herein used for assessing metal effects upon the interaction between angiotensin II and a fragment from the AT1A receptor. Angiotensin II forms a complex with cerium(III) in water while the fCT300–320 receptor fragment is poorly affected by cerium(III). However, the addition of the fragment displaces cerium(III) from the complex, thus directly demonstrating the higher affinity of angiotensin II for the receptor and probing the peptide residues involved in receptor binding.
FT‐IR studies of sickle hemoglobin interaction with phosphatidylserine
Authors: Ouyang Hao , Moore David J. , Sills Richard H. , Mendelsohn Richard
Published: March 2012

The interaction of dilauroylphosphatidylserine (DLPS) vesicles with both normal human hemoglobin (HbA) and hemoglobin from patients with sickle cell disease (HbS) has been investigated with FTIR spectroscopy. Changes in the conformational order of the phospholipid chains were directly monitored via the acyl chain CH2 symmetric stretching mode frequencies. The hemoglobin oxygenation state was simultaneously monitored via the S−H stretching contour. The current study reveals that under oxygenated conditions, DLPS shows little interaction with either HbA or HbS. In contrast, deoxyHbS interacted with DLPS by abolishing the gel−liquid crystal phase transition.
An NMR‐based metabolomic approach to the analysis of the effects of xenobiotics on endogenous metabolite levels in plants
Authors: Bailey Nigel J. C. , Oven Matjaz , Holmes Elaine , Zenk Meinhart H. , Nicholson Jeremy K.
Published: March 2012

High field 1H NMR spectroscopy has been employed to obtain, in conjunction with chemometric analysis, information regarding fluctuations in endogenous metabolic profiles for Crotalaria cobalticola plant cells following exposure to cobalt chloride.

Such ‘metabolomic’ type data analysis is often confounded by experimental, environmental or genetic factors that are not correlated to the classifications of interest and serve only to complicate the extraction of meaningful answers from a dataset. This work demonstrates the application of data filtering to remove extraneous data that result from spectrometer variation rather than being correlated with the classes of interest. Samples were analysed from Crotalaria cobalticola suspension cell culture following exposure to cobalt chloride using 2 spectrometers. Removal of confounding data due to spectrometer variation resulted in clear separation between control and dosed classes. It was then possible to use the model to determine key changes in biochemical status caused as a result of exposure to cobalt. Branched chain amino acids, succinate and secondary metabolite precursors phenylalanine and tyrosine were all higher in the control samples, whilst choline, glutamate, alanine and lactate were higher in the dosed samples.
Subcellular localisation of cholesterol and phosphocholine with pattern‐recognition‐imaging‐TOF‐SIMS
Authors: Malmberg Per , Nygren Håkan , Sjövall Peter , Lausmaa Jukka
Published: March 2012

Molecular ions of cholesterol, and its fragments, and phosphocholine fragments of phospholipids, were localized in single cells with a resolution of <1 μm. This is the first example of subcellular localisation of membrane lipids with pattern‐recognition, imaging time‐of‐flight secondary ion mass spectrometry (PRITS) here utilized for identification and subcellular localisation of cholesterol and phosphocholine in PMN leukocytes. Cell imprints were produced by transferring the cell constituents of freeze‐dried cells to a silver foil, and the silver surface was analyzed by TOF‐SIMS. TOF‐SIMS spectra were recorded by scanning the primary ion beam over the analysis area and acquiring a positive mass spectrum of the ions leaving the surface. Data were collected at either high mass resolution m/Δm > 7000 or high lateral resolution. High mass resolution spectra were recorded on reference samples of pure cholesterol and phosphatidylcholine. Characteristic fragment peaks and the silver cationised quasimolecular ion [M+Ag]+ were selected as a pattern for the identification of the lipids in TOF‐SIMS images of surface‐adhering leukocytes. The localisation of membrane lipids showed lateral heterogeneity over the cell surface.
The fragmentation pathways of azaspiracids elucidated using positive nanospray hybrid quadrupole time‐of‐flight (QqTOF) mass spectrometry
Authors: Hamilton Brett , Díaz Sierra Mónica , Lehane Mary , Furey Ambrose , James Kevin J.
Published: March 2012

The azaspiracids, AZA1, AZA2 and AZA3, are the predominant shellfish toxins responsible for the human toxic syndrome, azaspiracid poisoning. Collision induced dissociation (CID) mass spectra were generated for azaspiracids using nano‐electrospray ionisation (ESI) with a hybrid quadrupole time‐of‐flight (QqTOF) mass spectrometer in positive mode. Six main backbone fragmentations of the polyether skeleton of azaspiracids were observed as well as multiple neutral losses of water molecules from the parent and product ions. The characteristic charge‐remote fragmentation of the carbon skeleton of azaspiracids produced nitrogenous ions. The three azaspiracids differ from one another by 14 Da due to methylation in the A‐ and E‐rings. Three fragmentation pathways, involving cleavage of the E‐ring, C27–C28 and G‐ring, gave ions that were common to all azaspiracids. Another three fragmentations involving the A‐ring, C‐ring and C19–C20, were useful for distinguishing between azaspiracid analogues. Multiple tandem ion‒trap mass spectrometry (MSn) was used to confirm the fragmentation pathways.
Preparation and in vitro/in vivo characterisation of a melt pelletised paracetamol/stearic acid sustained release delivery system
Authors: Grassi Mario , Voinovich Dario , Grabnar Iztok , Franceschinis Erica , Perissutti Beatrice , Filipovic-Grcic Jelena
Published: March 2012

The potential of a sustained release formulation for paracetamol produced by melt pelletisation was investigated. After the production of the pellets, based on the combination of stearic acid as a melting binder and anhydrous lactose as a filler, the 3000–2000 μm size fraction was selected in the light of the promising in vitro dissolution results for further characterisations, including scanning electron microscopy (SEM), X‐ray photoelectron spectroscopy (XPS), specific surface area and true density determination. Hence the release mechanism was analysed with the help of an appropriate mathematical model. The mathematical model was built on the hypotheses that drug diffusion and solid drug dissolution in the release environment are the key phenomena affecting drug release kinetics. Bioavailability of the developed formulation was evaluated in an in vivo study in eight subjects.
Affinity studies of hypocrellin B and mono‐cysteine substituted hypocrellin B with CT‐DNA using spectroscopic methods
Authors: Wei Shaohua , Zhou Jiahong , Feng Yuying , Huang Deyin , Wang Xuesong , Zhang Baowen , Shen Jian
Published: March 2012

The interaction of anticancer drug hypocrellin B (HB) and mono‐cysteine substituted hypocrellin B (MCHB) with calf thymus deoxyribonucleic acid (CT‐DNA) has been investigated using spectral methods. The results of UV–visible spectra showed that the HB and MCHB can intercalate into the base‐stacking domain of the CT‐DNA double helix. Further studies based on fluorescence spectroscopy and circular dichroism (CD) spectroscopy also supported the intercalation mechanism.
Detection of biocolloids in aquatic media by Nano‐Particle Analyzer
Authors: Bundschuh T. , Wagner T. , Eberhagen I. , Hambsch B. , KÖster R.
Published: March 2012

The Nano‐Particle Analyzer (NPA) based on Laser‐Induced Breakdown Detection (LIBD) selectively generates and detects plasma events on colloids in aquatic media. Here, it is made use of the fact that the power density required for plasma generation decreases from the gaseous to the solid medium. At an adequate laser pulse energy, plasmas can thus be generated selectively on colloids. The detections of biocolloids by LIBD‐based NPA as described in this paper for the first time clearly reveal that the method is well suited for detecting not only non‐biological particulate matter in water, but also microorganisms in the transition range between solid and liquid matter. Consequently, the method can be used for online‐monitoring, for example of both the non‐biological and biological particulate content during the purification, transport and storage of drinking water. It is further possible to monitor online contamination of pure water or process chemicals by biological matter e.g. in biomedical industry.
FT‐IR spectra and vibrational spectroscopy of Andrographolide
Authors: Singh P. K. , Hasan Tanveer , Prasad Onkar , Sinha Leena , Raj Kanwal , Misra Neeraj
Published: March 2012

A complete normal coordinate analysis was performed for andrographolide in terms of the calculation by using Wilson′s G‐F matrix method and Urey Bradley force field. Normal coordinate analysis has been carried out to understand the dynamical behaviour of the bioactive labdane diterpenoid of the medicinally useful terrestrial plant Andrographis paniculata. The structural elucidation of a novel, biologically active natural product followed by its total synthesis lays the groundwork for investigations into its biological mechanism of action including putative cellular receptor isolation.
Application of SELDI‐TOF mass spectrometry in clinical evaluation of thrombotic thrombocytopenic purpura
Authors: Wu Haifeng M. , Cataland Spero R. , Bissell Michael , Jin Ming
Published: March 2012

Surface Enhanced Laser Desorption/Ionization Time Of Flight (SELDI‐TOF) mass spectrometry is characterized by integration of mass spectrometry with surface chemistry, which gives rise to rapid purification and subsequent determination of protein/peptide analytes. There are several surface matrices, named proteinChips, available for analyzing a particular analyte or a subset of biomolecules in biological samples. Each proteinChip has a unique surface property suitable for fractionation of a specific group of molecules. This article demonstrates the application of SELDI‐TOF for the analysis of a cleaved peptide (Mr 7739 daltons) from von Willebrand Factor by a metalloproteinase, ADAMTS13. Deficiency of ADAMTS13 is a known primary risk factor for the devastating hematological disorder, Thrombotic thrombocytopenic purpura (TTP). Rapid determination of ADAMTS13 activity helps clinicians tremendously in making the correct diagnosis and initiating timely therapy. Most patients with TTP are acquired cases who exhibit a production of autoimmune antibodies against ADAMTS13 protease. TTP′s clinical course is critically controlled by the autoantibody′s ability to inhibit ADAMTS13 function. Thus, a second SELDI‐TOF based test has been devised to measure ADAMTS13 autoantibody activity for the evaluation of TTP disease activity. In conclusion, the unique features of SELDI‐TOF which allow for the examination of the role of key proteases in disease processes have opened up new doors for the clinical application of mass spectrometer based techniques.
The potential of Raman microscopy and Raman imaging in plant research
Authors: Gierlinger Notburga , Schwanninger Manfred
Published: March 2012

To gain a better understanding on structure, chemical composition and properties of plant cells, tissues and organs several microscopic, chemical and physical methods have been applied during the last years. However, a knowledge gap exists about the location, quantity and structural arrangement of molecules in the native sample or what happens on the molecular level when samples are chemically or mechanically treated or how they respond to mechanical stress. These questions need to be answered to optimise utilization of plants in food industry and pharmacy and to understand structure‐function relationships of plant cells to learn from natures unique. Advances in combining microscopy with Raman spectroscopy have tackled this problem in a non‐invasive way and provide chemical and structural information in situ without any staining or complicated sample preparation. In this review the different Raman techniques (e.g. near infrared Fourier Transform Raman spectroscopy (NIR‐FT), resonance Raman spectroscopy, surface‐enhanced Raman spectroscopy) are briefly described before approaches in plant science are summarised. Investigations on structural cell wall components, valuable plant substances, metabolites and inorganic substances are included with emphasis on Raman imaging. The introduction of the NIR‐FT‐Raman technique led to many applications on green plant material by eliminating the problem of sample fluorescence. For mapping and imaging of whole plant organs (seeds, fruits, leaves) the lateral resolution (~10 μm) of the NIR‐FT technique is adequate, whereas for investigations on the lower hierarchical level of cells and cell walls the high resolution gained with a visible laser based system is needed. Examples on high resolution Raman imaging are given on wood cells, showing that changes in chemistry and orientation can be followed within and between different cell wall layers having dimensions smaller than 1 μm. In addition imaging the distribution of amorphous silica is shown on horsetail tissue, including an area scan from a cross section as well as a depth profiling within a silica rich knob of the outer stem wall.
Coleopteran Antimicrobial Peptides: Prospects for Clinical Applications
Authors: Ntwasa Monde , Goto Akira , Kurata Shoichiro
Published: March 2012

Antimicrobial peptides (AMPs) are activated in response to septic injury and have important roles in vertebrate and invertebrate immune systems. AMPs act directly against pathogens and have both wound healing and antitumor activities. Although coleopterans comprise the largest and most diverse order of eukaryotes and occupy an earlier branch thanDrosophilain the holometabolous lineage of insects, their immune system has not been studied extensively. Initial research reports, however, indicate that coleopterans possess unique immune response mechanisms, and studies of these novel mechanisms may help to further elucidate innate immunity. Recently, the complete genome sequence ofTriboliumwas published, boosting research on coleopteran immunity and leading to the identification ofTriboliumAMPs that are shared byDrosophilaand mammals, as well as other AMPs that are unique. AMPs have potential applicability in the development of vaccines. Here, we review coleopteran AMPs, their potential impact on clinical medicine, and the molecular basis of immune defense.
Novel Nonsymmetrically p-Benzyl-Substituted (Benz)imidazole N-Heterocyclic Carbene-Silver(I) Acetate Complexes: Synthesis and Biological Evaluation
Authors: Hackenberg Frauke , Deally Anthony , Lally Grainne , Malenke Sina , Müller-Bunz Helge , Paradisi Francesca , Patil Siddappa , Quaglia Daniela , Tacke Matthias
Published: March 2012

Nonsymmetrically substituted N-heterocyclic carbene (NHC) precursors 1a–d and 3a–d were synthesised by first reacting 1H-(benz)imidazole with p-cyanobenzyl bromide to give 4-(1H-imidazole-1-ylmethyl)benzonitrile (1) and 4-(1H-benzimidazole-1-ylmethyl)benzonitrile (3) and afterwards introducing benzyl bromide, 1-(bromomethyl)-4-methylbenzene, 1-(bromomethyl)-4-methoxybenzene, and methyl 4-(bromomethyl)benzoate. The NHC-silver(I) acetate complexes (1-benzyl-3-(4-cyanobenzyl)-2,3-dihydro-1H-imidazole-2-ylidene) silver(I) acetate (2a), (1-(4-cyanobenzyl)-3-(4-methylbenzyl)-2,3-dihydro-1H-imidazole-2-ylidene) silver(I) acetate (2b), (1-(4-cyanobenzyl)-3-[4-(methoxycarbonyl)benzyl]-2,3-dihydro-1H-imidazole-2-ylidene) silver(I) acetate (2c), (1-benzyl-3-(4-cyanobenzyl)-2,3-dihydro-1H-benzimidazole-2-ylidene) silver(I) acetate (4a), (1-(4-cyanobenzyl)-3-(4-methylbenzyl)-2,3-dihydro-1H-benzimidazole-2-ylidene) silver(I) acetate (4b), (1-(4-cyanobenzyl)-3-(4-methoxybenzyl)-2,3-dihydro-1H-benzimidazole-2-ylidene) silver(I) acetate (4c), and (1-(4-cyanobenzyl)-3-[4-(methoxycarbonyl)benzyl]-2,3-dihydro-1H-benzimidazole-2-ylidene) silver(I) acetate (4d) were yielded by reacting these NHC precursors with silver(I) acetate. The silver(I) acetate complex 4b was characterised by single crystal X-ray diffraction. Preliminary in vitro antibacterial studies against the Gram-positive bacteria Staphylococcus aureus and the Gram-negative bacteria Escherichia coli, using the Kirby-Bauer disc diffusion method, were carried out on the seven NHC-silver(I) acetate complexes 2a–c and 4a–d. Also the IC50 values of these seven complexes were determined by an MTT-based assay against the human renal cancer cell line Caki-1. The complexes 2a–c and 4a–c revealed the following IC50 values, respectively, 25 (±1), 15 (±2), 5.4 (±0.8), 16 (±2), 7.1 (±1), 20 (±4), and 14 (±1) μM.
(+)-Z-Bisdehydrodoisynolic Acid Enhances Basal Metabolism and Fatty Acid Oxidation in Female Obese Zucker Rats
Authors: Banz William J. , Strader April D. , Ajuwon Kolapo M. , Hou Yuqing , Meyers Cal Y. , Davis Jeremy E.
Published: March 2012

We have previously reported that the synthetic estrogen, (+)-Z-bisdehydrodoisynolic Acid [(+)-Z-BDDA], attenuated weight gain and cardiovascular risk in obese rodents. To determine if these antiobesity effects were attributed to changes in basal metabolism, we assessed indirect calorimetry and metabolic profile in female obese Zucker (OZR) rats provided (+)-Z-BDDA (0.0002% food admixture) for 11 weeks. Similar to our previous findings, (+)-Z-BDDA reduced weight gain and improved lipid and glucose homeostasis in OZR rats. Furthermore, resting energy expenditure was increased by (+)-Z-BDDA, as evident by heat production and oxygen consumption. We also observed a marked reduction in respiratory quotient (RQ) along with a corresponding induction of hepatic AMPK in rodents provided (+)-Z-BDDA. Collectively, these findings indicate that (+)-Z-BDDA partially attenuated obesity and associated pathologies through increased resting energy expenditure and fatty acid utilization. Further investigation is required to fully elucidate the mechanisms involved as well as to determine the potential therapeutic implications for (+)-Z-BDDA on obesity and its related pathologies.
Using Different Approaches to Approximate a Pareto Front for a Multiobjective Evolutionary Algorithm: Optimal Thinning Regimes forEucalyptus fastigata
Authors: Chikumbo Oliver
Published: March 2012

A stand-level, multiobjective evolutionary algorithm (MOEA) for determining a set of efficient thinning regimes satisfying two objectives, that is, value production for sawlog harvesting and volume production for a pulpwood market, was successfully demonstrated for aEucalyptus fastigatatrial in Kaingaroa Forest, New Zealand. The MOEA approximated the set of efficient thinning regimes (with a discontinuous Pareto front) by employing a ranking scheme developed by Fonseca and Fleming (1993), which was a Pareto-based ranking (a.k.a Multiobjective Genetic Algorithm—MOGA). In this paper we solve the same problem using an improved version of a fitness sharing Pareto ranking algorithm (a.k.a Nondominated Sorting Genetic Algorithm—NSGA II) originally developed by Srinivas and Deb (1994) and examine the results. Our findings indicate that NSGA II approximates the entire Pareto front whereas MOGA only determines a subdomain of the Pareto points.