Scope and limitations of the simple 13C-n.m.r. method of structural analysis of carbohydrates: glucodisaccharides

The scope and limitations of the SIMPLE n.m.r. method (secondary isotope multiplet n.m.r. spectroscopy of partially labelled entities) has been investigated for a series of glucodisaccharies. ¹³C-SIMPLE n.m.r. measurements have been made on solutions of (1→1)- (α,α-trehalose), (1→2)- (sophorose and kojibiose), (1→3)- (laminaribiose), and (1→6)-linked (gentiobiose and isomaltose) glucodisaccharides in (CD₃)₂SO and the results combined with those previously published for (1→4)-linked analogues (maltose and cellobiose). Each linkage (and substitution) type gives rise to a unique pattern of ¹³C isotopomers which, in principle, may be used for complete assignment of the spectra and structural analysis of the molecule. The glucodisaccharides are difficult to analyse, compared with other disaccharides, because the presence of two glucose moieties leads to degeneracies of a few isotopic multiplets which cannot be differentiated by the magnitudes of the isotope effects. Assignments in aqueous solutions were obtained by using the DIS (differential isotope shift) n.m.r. method in conjunction with the results from SIMPLE n.m.r. In practice, nearly all of the signals can be assigned unequivocally and the remaining signals are choices between two possible assignments.     

Synthesis of peptides containing α,β-didehydroamino acids. Scope and limitations

Summary α, β-Didehydroamino acids, which are key components of both natural andde novo peptides, are frequently encountered in naturally occurring peptides — mostly of microbial and fungal origin and/or from marine organisms. Herein, we report on a reappraisal of the use of the water-soluble carbodiimide/CuCl method for the preparation of this kind of peptide in both solution and solid-phase modes and describe some side reactions encountered during the process. Abbreviations: Alloc, allyloxycarbonyl; Barlos resin, 2-chlorotrityl chloride resin, Boc,tert-butoxycarbonyl; Boc₂O, di-tert-butyl dicarbonate; Bzl, benzyl; DABCO, 1,4-diazabicyclo[2.2.2]octane; DAST, (diethylamino)sulfur trifluoride; DBU, 1,8-diazabicyclo[5.4.0]undec-7-ene; DDAAs, α, β-didehydroarnino acids; DEAD, diethyl azodicarboxylate; Dha, Didehydroalanine, (Z)-Dhb, Z-Didebydroaminobutyric acid; (Z)-Dhp, Z-Didehydrophenylalanine; DSC, disuccinimidyl carbonate; DDP, α, β-didehydropeptides; EDC, WSC, 3-(3′-dimethylaminopropyl)-1-ethylearbodiimide; Fmoc, fiuorenylmethoxycarbonyl; HATU, N-{(dimethylamino)-1H-1,2,3-triazolo[4,5-b]pyridino-1-ylmethylene}-N-methylmethanaminium hexafluorophosphate; HOAt, 1-hydroxy-7-azabenzotriazole; (β-OH)Phe, phenylserine or β-hydroxyphenylalanine; Ph₃P, triphenylphosphine; PyAOP, (7-azabenzotriazol-1-yloxy)-tris(pyrrolidino)phosphonium hexafluorophosphate; TEA, triethylamine; TFA, trifluoroacetic acid. Amino acid symbols denote thel-configuration unless stated otherwise. All solvent ratios are volume/volume unless stated otherwise.     

Fine needle aspiration cytodiagnosis of Hodgkin's disease and its subtypes. I. Scope and limitations

The fine needle aspiration (FNA) smears and paraffin-embedded sections from 89 cases with a cytologic and histologic diagnosis of Hodgkin's disease (HD) and 27 cases with minor or major cytohistologic discrepancies were reviewed. The accuracy of the initial cytologic study was found to be 91.8% for diagnosing HD and 58.1% for classifying its subtypes. Following review, 87 of the 89 agreement cases remained classified as HD. Of the 27 cases with initial cytohistologic discrepancies, 12 were classified as HD and 10 were categorized as lymphocytic or non-Hodgkin's lymphoma by both cytology and histology upon review. Following review, the accuracy of FNA cytology for the diagnosis of HD improved to 98.0%, with 71.4% correct subtyping. The greatest limitation of cytologic subtyping was in cases of nodular sclerotic HD: only 3 of 17 cases could be subtyped even after review. The cytomorphologic features of the HD subtypes are described, and the difficulties encountered in the cytodiagnosis of HD are discussed at length. The results of this study indicate that FNA cytology is a useful tool not only for the diagnosis of HD, but also for its subtyping.     

Evaluation of antioxidants: Scope, limitations and relevance of assays

Peroxidation of lipids, particularly polyunsaturated fatty acid residues (PUFA) of phospholipids and cholesterol esters, is a process of marked implications: it shortens the shelf-life of food and drugs, it causes fragmentation of DNA, it damages cellular membranes and it promotes the genesis of many human diseases. Much effort is therefore devoted to a search for "potent antioxidants", both synthetic and from natural sources, mostly plants. This, in turn, requires a reliable, simple, preferably high throughput assay of the activity of alleged antioxidants. The most commonly used assays are based on measurements of the total antioxidant capacity (TAC) of a solution, as evaluated either by determining the rate of oxidation of the antioxidant or by measuring the protection of an easily determined indicator against oxidation by the antioxidants. The commonly used assays utilized for ranking antioxidants share three common problems: (i) They usually evaluate the effects of those antioxidants that quench free radicals, which constitute only a part of the body's antioxidative network, in which enzymes play the central role. (ii) Both the capacity and potency of antioxidants, as obtained by various methods, do not necessarily correlate with each other. (iii) Most estimates are based on methods conducted in solution and are therefore not necessarily relevant to processes that occur at the lipid-water interfaces in both membranes and micro emulsions (e.g. lipoproteins). Given this "state of art", many researchers, including us, try to develop a method based on the formation of hydroperoxides (LOOH) upon peroxidation of PUFA in lipoproteins or in model membranes, such as liposomes. In these systems, as well as in lipoproteins, the most apparent effect of antioxidants is prolongation of the lag time preceding the propagation of a free radical chain reaction. In fact, under certain conditions both water soluble antioxidants (e.g. vitamin C and urate) and the lipid soluble antioxidant tocopherol (vitamin E), promote or even induce peroxidation. Based on the published data, including our results, we conclude that terms such as 'antioxidative capacity' or 'antioxidative potency' are context-dependent. Furthermore, criteria of the efficacy of antioxidants based on oxidation in solution are not necessarily relevant to the effects of antioxidants on peroxidation in biological systems or model lipid assemblies, because the latter processes occur at water/lipid interfaces. We think that evaluation of antioxidants requires kinetic studies of the biomarker used and that the most relevant characteristic of 'oxidative stress' in the biological context is the kinetics of ex vivo peroxidation of lipids. We therefore propose studying the kinetics of lipid-peroxidation in the absence of the studied antioxidant and in its presence at different antioxidant concentrations. These protocols mean that antioxidants are assayed by methods commonly used to evaluate oxidative stress. The advantage of such evaluation is that it enables quantization of the antioxidants' efficacy in a model of relevance to biological systems. In view of the sensitivity of the lag time preceding peroxidation, we propose studying how much antioxidant is required to double the lag observed prior to rapid peroxidation. The latter quantity (C(2lag)) can be used to express the strength of antioxidants in the relevant system (e.g. LDL, serum or liposomes).     

Scope and limitations of rotating-frame nuclear Overhauser enhancement spectroscopy applied to oligosaccharides

Two-dimensional rotating-frame nuclear Overhauser enhancement spectroscopy has been applied to milk oligosaccharides containing the blood-group determinants Lea, Led, or Leb. The results indicate a large number of dipolar interactions that are consistent with the preferred conformations described for these blood-group determinants. Despite careful experimental conditions, coherent transfer processes are not suppressed completely, allowing only a qualitative evaluation of the nuclear Overhauser data. The 1H- and 13C-n.m.r. spectra are assigned by comparison with literature data and by application of two-dimensional 13C-1H shift-correlation spectroscopy.     

Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations

Background  

Structure-based computational methods are needed to help identify and characterize protein-protein complexes and their function. For individual proteins, the most successful technique is homology modelling. We investigate a simple extension of this technique to protein-protein complexes. We consider a large set of complexes of known structures, involving pairs of single-domain proteins. The complexes are compared with each other to establish their sequence and structural similarities and the relation between the two. Compared to earlier studies, a simpler dataset, a simpler structural alignment procedure, and an additional energy criterion are used. Next, we compare the Xray structures to models obtained by threading the native sequence onto other, homologous complexes. An elementary requirement for a successful energy function is to rank the native structure above any threaded structure. We use the DFIRE _β energy function, whose quality and complexity are typical of the models used today. Finally, we compare near-native models to distinctly non-native models.     

Scope and limitations of imidazolium-based ionic liquids as room temperature glycosylation promoters

The scope and limitations of imidazolium-based ionic liquids as room temperature glycosylation promoters have been studied. Herein, we report the effects of modifying the structure of the imidazolium cation and how important the choice of counter ion becomes on model glycosylation reactions of thioglycosides at room temperature in the presence of N-iodosuccinimide (NIS).     

A simple device for uniform inoculation of nutrient surfaces.

A simple and inexpensive device for uniform surface inoculation is described. Efficiency and uniformity of inoculation were estimated with agar plates exposed to a bacterial suspension, containing 10 different strains, atomized with a spray gun. The fine mist settled, after a fall of 106 cm, upon the agar surfaces at the bottom of a cylindrical chamber. No significant differences were observed with regard to uniformity of inoculation between nine plates.     

Scope and limitations of MALDI-TOF MS blood serum peptide profiling in cancer diagnostics

Serum samples (33 healthy women, 34 ovarian cancer, 28 colorectal cancer, 34 syphilis patients and 136 patients with various benign gynecological diseases) were analyzed by MALDI-TOF MS peptide profiling and respective predictive models were generated by genetic and supervised neural network algorithms. Classification models for pathology versus healthy control showed up to 100% sensitivity and specificity for all target diseases. However, the specificity dropped to unsatisfactory 25–40% in case of target versus nontarget disease diagnostics. Expansion of the control group to an artificial “nominal control” group by adding profiles of benign gynecological diseases considerably improved specificity of the models distinguishing ovarian cancer from healthy control and benign gynecological diseases. The suggested version of MALDI-TOF MS profiling of sera could be applied to differentiate between cancers and benign neoplasms of the same localization which is a challenging task for classical methods. To increase the specificity of diagnostic methods based on peptidome analysis of blood samples, it is necessary to identify sets of concrete peptide structures which qualitatively or quantitatively differ among patients with different diseases.     

Scope and limitations of in vivo brain dialysis: a comparison of its application to various neurotransmitter systems

Brain dialysis is rapidly becoming a routine research method with a wide range of applications. Since 1982 this sampling technique is frequently used as a method to study the in vivo release of endogenous neurotransmitters such as dopamine, noradrenaline, serotonin, acetylcholine and certain amino acids. In this review most of the studies that have appeared in this field, are evaluated. Special attention was given to the question whether the neurotransmitter content in the dialysate is related to neurotransmission. Criteria such as the presence of a high tissue/dialysate concentration ratio, the sensitivity of the transmitters to membrane active compounds and the occurrence of receptor-mediated effects, are discussed. It is concluded that dopamine, noradrenaline and acetylcholine found in the dialysate are directly derived from neurotransmission, whereas the overflow of excitatory amino acid neurotransmitters is related to neurogenic as well as to metabolic events.     

Rapid and simple quantification of bacterial cells by using a microfluidic device

This study investigated a microfluidic chip-based system (on-chip flow cytometry) for quantification of bacteria both in culture and in environmental samples. Bacterial numbers determined by this technique were similar to those obtained by direct microscopic count. The time required for this on-chip flow cytometry was only 30 min per 6 samples.     

Fabrication of glass micropipettes: a semi-automatic approach for trimming the pipette tip.

Micropipettes as research instruments are well established in cell biology, including blood rheology. However, the experimental results are, to some extent, dependent on the quality of the pipette itself; it is usually critical to have the desired pipette internal diameter and a perpendicular tip. Pipette fabrication is a two-step procedure involving: a) the pulling of the pipette from a glass capillary; b) the trimming of the pipette tip. A common method to trim and fracture the pipette tip is the use of a melted glass bead on a heated tungsten wire. Previous devices using this method were often associated with problems because the heated wire varied in length with temperature. As a result, the bead together with the attached pipette tip moved markedly and thus hampered the possibility to obtain a perpendicularly cut pipette tip. An improved design, based on the same principle with a melted glass bead, is thus suggested; it eliminates the problem with a moving glass bead and, in addition, allows semi-automatic pipette trimming by utilizing the heat-induced elongation/retraction of the heated wire to fracture the tip without requiring manual assistance. Furthermore, a simple pipette storing technique is suggested, based on standard laboratory utensils, in order to more easily handle fragile pipettes without risk of breakage.     

Galactose oxidase and alcohol oxidase: Scope and limitations for the enzymatic synthesis of aldehydes

The utility of both galactose oxidase and alcohol oxidase for alcohol-to-aldehyde oxidation has been investigated, from a synthetic point of view. The speed of reaction and degree of conversion has been measured for 29 different primary alcohols. The two oxidative enzymes show complementary synthetic use, i.e. galactose oxidase for galactose-derived polyols and alcohol oxidase for aliphatic mono- and diols. Alcohol oxidase has been successfully used in combination with the aldolase DERA in a two-step, one-pot reaction cascade.