Search

Objective: The objective of this study was to assess inflammatory cytologic alterations in the oral epithelium of patients on human immunodeficiency virus pre-exposure prophylaxis (PrEP)., Material and Methods: Epithelial cells from the buccal mucosa of 30 patients were collected by exfoliative cytology and were evaluated according to inflammatory cellular alterations: karyomegaly, bi- or multinucleation, karyopyknosis, karyorrhexis, perinuclear halo formation, metachromasia, cytoplasmic vacuolization, indistinct cytoplasmic border, keratinization, and atrophy. Epithelial cells were collected initially before PrEP onset (T1) and then after 30 days of PrEP use (T2). Two experienced cytopathologists independently analyzed the slides., Results: The nonparametric Wilcoxon test showed that there was a statistically significant increase in the number of cells with karyomegaly at T2 compared to T1 (P = .033). The other cellular alterations did not present with statistically significant differences between the 2 moments of evaluation (P > .05)., Conclusion: The increased number of oral epithelial cells with karyomegaly after 30 days of using PrEP suggests the presence of inflammatory alterations at this site., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Background: The oral mucosa is an important defense barrier to penetration of microorganisms. Thus, changes in the oral epithelium might indicate risk for infection in intensive care patients receiving mechanical ventilation., Objective: To evaluate the oral mucosa of intensive care patients who did or did not receive mechanical ventilation by using liquid-base exfoliative cytology., Methods: The sample consisted of 3 groups: 27 patients admitted to intensive care during a 7- to 14-day period who received mechanical ventilation, 29 patients admitted during the same period who did not receive mechanical ventilation, and 27 healthy patients who had no lesions in the mouth. For all 3 groups, samples were collected from the buccal mucosa by using cytology brushes. Smears were applied to glass slides before Papanicolaou staining and were codified for blind analyses by a cytopathologist. Kruskal-Wallis and Dunn tests were used to analyze the results., Results: Patients receiving mechanical ventilation had higher prevalence and intensity of karyomegaly, perinuclear halos, cell keratinization, deep cells, and leukocyte infiltrates than did patients in the other 2 groups ( P < .05). No significant differences were observed between the control group and the group who did not receive mechanical ventilation., Conclusions: Liquid-base exfoliative cytology can be used to detect preclinical alterations in the oral mucosa. Patients treated with mechanical ventilation are vulnerable to infections, and oral care may be valuable in their prognosis., (©2017 American Association of Critical-Care Nurses.)

Background: Minimotifs are short contiguous peptide sequences in proteins that have known functions. At its simplest level, the minimotif sequence is present in a source protein and has an activity relationship with a target, most of which are proteins. While many scientists routinely investigate new minimotif functions in proteins, the major web-based discovery tools have a high rate of false-positive prediction. Any new approach that reduces false-positives will be of great help to biologists., Methods and Findings: We have built three filters that use genetic interactions to reduce false-positive minimotif predictions. The basic filter identifies those minimotifs where the source/target protein pairs have a known genetic interaction. The HomoloGene genetic interaction filter extends these predictions to predicted genetic interactions of orthologous proteins and the node-based filter identifies those minimotifs where proteins that have a genetic interaction with the source or target have a genetic interaction. Each filter was evaluated with a test data set containing thousands of true and false-positives. Based on sensitivity and selectivity performance metrics, the basic filter had the best discrimination for true positives, whereas the node-based filter had the highest sensitivity. We have implemented these genetic interaction filters on the Minimotif Miner 2.3 website. The genetic interaction filter is particularly useful for improving predictions of posttranslational modifications such as phosphorylation and proteolytic cleavage sites., Conclusions: Genetic interaction data sets can be used to reduce false-positive minimotif predictions. Minimotif prediction in known genetic interactions can help to refine the mechanisms behind the functional connection between genes revealed by genetic experimentation and screens.

The low complexity of minimotif patterns results in a high false-positive prediction rate, hampering protein function prediction. A multi-filter algorithm, trained and tested on a linear regression model, support vector machine model, and neural network model, using a large dataset of verified minimotifs, vastly improves minimotif prediction accuracy while generating few false positives. An optimal threshold for the best accuracy reaches an overall accuracy above 90%, while a stringent threshold for the best specificity generates less than 1% false positives or even no false positives and still produces more than 90% true positives for the linear regression and neural network models. The minimotif multi-filter with its excellent accuracy represents the state-of-the-art in minimotif prediction and is expected to be very useful to biologists investigating protein function and how missense mutations cause disease.

Minimotif Miner (MnM available at http://minimotifminer.org or http://mnm.engr.uconn.edu) is an online database for identifying new minimotifs in protein queries. Minimotifs are short contiguous peptide sequences that have a known function in at least one protein. Here we report the third release of the MnM database which has now grown 60-fold to approximately 300,000 minimotifs. Since short minimotifs are by their nature not very complex we also summarize a new set of false-positive filters and linear regression scoring that vastly enhance minimotif prediction accuracy on a test data set. This online database can be used to predict new functions in proteins and causes of disease.

Protein-protein interactions are important to understanding cell functions; however, our theoretical understanding is limited. There is a general discontinuity between the well-accepted physical and chemical forces that drive protein-protein interactions and the large collections of identified protein-protein interactions in various databases. Minimotifs are short functional peptide sequences that provide a basis to bridge this gap in knowledge. However, there is no systematic way to study minimotifs in the context of protein-protein interactions or vice versa. Here we have engineered a set of algorithms that can be used to identify minimotifs in known protein-protein interactions and implemented this for use by scientists in Minimotif Miner. By globally testing these algorithms on verified data and on 100 individual proteins as test cases, we demonstrate the utility of these new computation tools. This tool also can be used to reduce false-positive predictions in the discovery of novel minimotifs. The statistical significance of these algorithms is demonstrated by an ROC analysis (P = 0.001)., (Copyright © 2010 Wiley-Liss, Inc.)

Background: Minimotifs are short contiguous peptide sequences in proteins that are known to have a function in at least one other protein. One of the principal limitations in minimotif prediction is that false positives limit the usefulness of this approach. As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions., Methodology/principal Findings: Certain domains and minimotifs are known to be strongly associated with a known cellular process or molecular function. Therefore, we hypothesized that by restricting minimotif predictions to those where the minimotif containing protein and target protein have a related cellular or molecular function, the prediction is more likely to be accurate. This filter was implemented in Minimotif Miner using function annotations from the Gene Ontology. We have also combined two filters that are based on entirely different principles and this combined filter has a better predictability than the individual components., Conclusions/significance: Testing these functional filters on known and random minimotifs has revealed that they are capable of separating true motifs from false positives. In particular, for the cellular function filter, the percentage of known minimotifs that are not removed by the filter is approximately 4.6 times that of random minimotifs. For the molecular function filter this ratio is approximately 2.9. These results, together with the comparison with the published frequency score filter, strongly suggest that the new filters differentiate true motifs from random background with good confidence. A combination of the function filters and the frequency score filter performs better than these two individual filters.

A nanosecond transient absorption spectroscopy study of flavone performed with a 248 nm pump radiation has been investigated with the support of a chemometric treatment: SIMPLISMA. The experimental spectra obtained in various solvent with a pump-probe delay lower than about 2 micros are in quite good concordance with those already presented in the literature. Nevertheless after about 10 micros, the spectrum pattern significantly evolves as a function of time particularly for the methanolic solution. A qualitative analysis together with a SIMPLISMA chemometric treatment of the experimental data allowed to elucidate and characterise two interdependent transient species in the alcoholic medium: the lowest T1 triplet state of flavone and the ketyl radical forming by H-abstraction reaction from the solvent. In cyclohexane and acetonitrile, the same species seem to be produced in the studied time-scale but the radical form is generated with variable quantum yield depending on the solvent polarity. The pure spectrum and the photochemical kinetics of each reaction intermediate could have been determined with the help of the second derivative SIMPLISMA calculation procedure.

Complex formation between aluminium and quercetin (Q) in methanol was studied by the combined use of spectroscopic measurements and quantum chemical calculations. Quercetin presents in its structure three possible chelating sites in competition. UV-visible spectroscopy has showed the successive formation of two complexes of stoichiometry Al(III):Q of 1:2 and 2:1, respectively. The first site involved in the complex formation process is the 3-hydroxychromone and the second one is the ortho-dihydroxyl group. Semiempirical treatment, using the AM1 hamiltonian, permitted calculation of the structural modifications engendered by the ligand through chelation of one then two aluminium ions. The electronic and vibrational spectra have been calculated with the same method in order to compare them to the experimental spectra and so confirm the involved chelating sites. The simulated electronic spectra obtained from the complex models are in good agreement with the experimental UV-visible absorption spectra. In the same way the vibrational spectra of the complexes validate the proposed complex formation mechanism. The pH influence on the complexes stoichiometry and on the preferentially occupied chelating sites has been also investigated.

Complex formation between aluminium chloride and 3'4'-dihydroxyflavone (3'4'diOHF) in methanol has been studied by UV-visible and Raman spectroscopies combined with quantum chemical calculations. Job's method of continuous variation and the molar ratio method were applied to ascertain the stoichiometry composition of the chelate in pure methanol. A 1:1 complex was indicated by both the methods. Geometry optimizations of free and complexed molecules by AMI and DFT methods show that structural modifications of the ligand, induced by complexation, are minor, and are localized on the chelating site. The good agreement between experimental and theoretical electronic spectra of both 3'4'diOHF and complex confirm the structural models. The great similarities between Raman spectra of the free and complexed form constitute an another proof of the absence of pronounced electronic and geometric changes, and notably demonstrate that the quinoidal form induced by the deprotonation of the two hydroxyl groups does not participate in the 3'4'diOHF complex structure. Whereas no complexation occurs in acidic medium, complexes of high stoichiometry are formed in alkaline medium. (Al(3'4'diOHF)2)- and (Al(3'4'diOHF)3)3- species are observed in methanol in the presence of sodium acetate or sodium methanoate.

The FT-infrared and Raman microscopy spectra of the 2',6'-dimethoxyflavone and its 1:1 complex with formic acid in solid state have been recorded and analysed. Some vibrational components appear as specific to the cis-rotamer of formic acid in the crystalline sample, especially the CH group stretching vibration feature. The broad and intense infrared absorption observed in the range 3400-1900 cm(-1) and assigned to the hydrogen bonded OH group stretching vibration exhibits the characteristic ABC structure of strong hydrogen bonded complexes. This ABC pattern corroborates previous X-ray crystallographic data showing that cis-formic acid is strongly hydrogen bonded to the flavonic compound. The inclusion complex is quite unstable and the infrared spectrum clearly shows that formic acid disappears after a period of a few months. In order to get some information on the stability criterions of the intermolecular hydrogen bonded complex, semiempirical AM1 calculations have been investigated. The comparison of the calculated heats of complexation (deltacH) for chelates involving the cis- and trans-conformers of formic acid suggests that the reaction of hydrogen bonding complexation with the cis-rotamer is surely favoured.

3-Hydroxyflavone (3HF), which is the simplest molecule of the flavonol class, possesses chelating properties towards Al(III). Spectrophotometric methods have shown that the 3HF molecule forms an Al(3HF)2 complex in pure methanol. The structure of this complex, obtained by quantum semi-empirical AM1 method, indicated that complexed 3HF adopts a pyronium form. Structural and electronic modifications induced by chelation are illustrated by the important frequency shifts observed between free and complexed 3HF FT-Raman spectra and by the chemical shifts variations in the 13C NMR spectra of the two species. Complexes with the same stoichiometry were formed when AcO- or MeO- are present in the medium. However, in acidic medium the chelate composition is Al2(3HF).

Semiempirical AM1 calculations have been carried out for beta-carotene and the three xanthophylls (zeaxanthin, canthaxanthin, and astaxanthin) containing oxygen functions (hydroxy/keto groups) found in the majority of natural pigment. The fully optimized geometries correspond well with the X-ray structures of beta-carotene and canthaxanthin and indicate that substitutions on the terminal rings have a minimal effect on the conformation of the chromophore. Twisting along the polyenic chain results from steric interaction involving methyl substituents, and a Ci point group can be proposed for the four investigated carotenoids. AM1 calculated excitation energies for the strongly allowed excited states can be compared to with the experimental absorption band in the visible region, considering solvent effect. Resonance Raman (RR) and Fourier transform (FT) Raman spectra of natural astaxanthin as well as astaxanthins specifically 13C labeled at the positions 12,12'; 13,13'; 14,14'; 15,15'; 15, and 20,20' were recorded. Furthermore the RR and FT Raman spectra of the asymmetric carotenoid 20-norastaxanthin are presented. The data reveal a substantial amount of information about the coupling between the different vibrations, and enabled an extensive experimental verification of the theoretical normal-coordinate analysis previously performed on polyenic molecules [J Raman Spectrosc 1983, 14, 310-321; Advances in Infrared and Raman Spectroscopy, Vol. 12, 1985, pp. 115-178; Spectrochim Acta 1996, 53, 381-392; Biochim Biophys Acta 1994, 1185, 188-196]. The results make up a very interesting dataset which allowed the interpretation and/or observation of several, hitherto never observed or not well understood, effects in the Raman spectra of the differently labeled astaxanthins.

Resonance Raman spectroscopy and quantum chemical calculations were used to investigate the molecular origin of the large redshift assumed by the electronic absorption spectrum of astaxanthin in alpha-crustacyanin, the major blue carotenoprotein from the carapace of the lobster, Homarus gammarus. Resonance Raman spectra of alpha-crustacyanin reconstituted with specifically 13C-labeled astaxanthins at the positions 15, 15,15', 14,14', 13,13', 12,12', or 20,20' were recorded. This approach enabled us to obtain information about the effect of the ligand-protein interactions on the geometry of the astaxanthin chromophore in the ground electronic state. The magnitude of the downshifts of the C==C stretching modes for each labeled compound indicate that the main perturbation on the central part of the polyene chain is not homogeneous. In addition, changes in the 1250-1400 cm(-1) spectral range indicate that the geometry of the astaxanthin polyene chain is moderately changed upon binding to the protein. Semiempirical quantum chemical modeling studies (Austin method 1) show that the geometry change cannot be solely responsible for the bathochromic shift from 480 to 632 nm of protein-bound astaxanthin. The calculations are consistent with a polarization mechanism that involves the protonation or another interaction with a positive ionic species of comparable magnitude with both ketofunctionalities of the astaxanthin-chromophore and support the changes observed in the resonance Raman and visible absorption spectra. The results are in good agreement with the conclusions that were drawn on the basis of a study of the charge densities in the chromophore in alpha-crustacyanin by solid-state NMR spectroscopy. From the results the dramatic bathochromic shift can be explained not only from a change in the ground electronic state conformation but also from an interaction in the excited electronic state that significantly decreases the energy of the pi-antibonding C==O orbitals and the HOMO-LUMO gap.

Selective isotope enrichment, 13C magic angle spinning (MAS) NMR, and semiempirical quantum chemical modeling, have been used to analyze ligand-protein interactions associated with the bathochromic shift of astaxanthin in alpha-crustacyanin, the blue carotenoprotein complex from the carapace of the lobster Homarus gammarus. Spectra of alpha-crustacyanin were obtained after reconstitution with astaxanthins labeled with 13C at positions 4,4', 12,12', 13,13', or 20,20'. The data reveal substantial downfield shifts of 4.9 and 7.0 ppm at positions 12 and 12' in the complex, respectively. In contrast, at the 13 and 13' positions, small upfield shifts of 1.9 ppm were observed upon binding to the protein. These data are in line with previously obtained results for positions 14,14' (3.9 and 6.8 ppm downfield) and 15,15' (0.6 ppm upfield) and confirm the unequal perturbation of both halves after binding of the chromophore. However, these results also show that the main perturbation is of symmetrical origin, since the chemical shift differences exhibit a similar pattern in both halves of the astaxanthin molecule. A small downfield shift of 2.4 ppm was detected for the 4 and 4' positions. Finally, the 20,20' methyl groups are shifted 0.4 ppm upfield by the protein. The full data set provides convincing evidence that charge polarization is of importance for the bathochromic shift. The NMR shifts are compared with calculated charge densities for astaxanthin subjected to variations in protonation states of the ring-functional groups, as models of ligand-protein interactions. Taking into account the color shift and other available optical data, the current model for the mechanisms of interaction with the protein was refined. The results point toward a mechanism in which the astaxanthin is charged and subject to strong electrostatic polarizations originating from both keto groups, most likely a double protonation.

The frequency shift observed when light is scattered by molecules is called Raman effect. Raman spectroscopy like infrared spectroscopy is a method of studying molecular vibrations. The two methods are complementary, they both give much informations about the structure of molecules and crystals, the nature of chemical bonds and intermolecular interactions. Infrared absorption is allowed if the vibration is accompanied by a variation of electric dipole moment, however Raman scattering will only be observed if a variation of molecular polarizability appears during the vibration. Symetry properties of molecules of crystals lead to the determination of the number of normal vibrational modes and their Raman or infrared activity. The discovery of Laser light source has permitted a great development of Raman instrumentation. Raman spectrometers can easily record the whole spectrum of molecular vibrations (0-4000 cm-1) of samples in solid, liquid or gazeous state. Very small quantities of material are required (several milligrams). Aqueous solutions are easily investigated. Owing to the easy exploration of the low frequency range by modern spectrometers, new areas are opened in the study of the solid state and polymeric chains. Resonance Raman effect allows the spectra of very dilute solutions to be obtained. With the development of rapid scanning systems and electro-optical spectrometers, study of transients species is now possible. Among the physical analysis methods, Raman spectroscopy is now more and more used, and this technic has already been successfully used in numerous biological and biochemical problems.

Yersinia enterocolitica 195A14J, a milk-isolated strain of biovar 1, produces a non-diffusible yellow pigment and forms star-shaped colonies when grown on egg-yolk agar at 28 degrees C. Solubility properties and in situ Raman spectrum of the pigment support evidence that it is not a carotenoid, although it contains a 9 (+/- 1) double-bond polyenic chain. Pigmentless variants, also star-shaped, appeared with a frequency of ca.10(-3) when bacteria were grown at 38 degrees C. Agarose gel electrophoresis of DNA extracted from the pigmented strain revealed the presence of a 42-kb plasmid which was lost in pigmentless variants.

Raman spectroscopy was used to study the interactions between bovine trypsin and a competitive inhibitor. For this purpose, a chromophoric substrate analogue, 4-amidino-4'-dimethylamine azobenzene, was synthesized. This compound competitively inhibits the enzyme with a 1:1 stoichiometry and an inhibition constant Ki of 2.3 muM at pH 6.08 and 15 degrees. Resonance Raman spectra in aqueous solution of free or enzyme-bound inhibitor were analyzed. The main spectral changes observed upon enzyme-inhibitor complex formation were changes in the relative intensities of four bands (1171, 1206, 1315, 1608 cm-1) while no large frequency shifts occurred. The binding of the inhibitor molecule to the enzyme did not induce a twisting of the phenyl groups around the N=N bond. Some modifications of the band widths are interpreted in terms of a restriction of rotational motions in the inhibitor molecule. The possible involvement of specific interactions between trypsin and the benzamidinium ion part of the inhibitor molecule is discussed.

Two reconstituted carotenoproteins have been studied by resonance Raman spectroscopy. They were prepared from the apoprotein of the Asterias rubens carotenoprotein, asteriarubin and either astaxanthin or 15,15'-didehydroastaxanthin. Spectral properties of dehydrocarotenoids are first discussed. The spectral properties of the complexes are compared to those of the free carotenoids and of other carotenoproteins containing astaxanthin, and possible protein-carotenoid interactions are discussed. Greater delocalisation of the pi-electron system in the central part of the polyene chain, and the role of lateral methyl groups in binding is emphasised.