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Recent evidence suggests that genetic and epigenetic mechanisms might be associated with acquired resistance to cancer therapies. The aim of this study was to assess the association of genome-wide genetic and epigenetic alterations with the response to anti-HER2 agents in HER2-positive breast cancer patients. PubMed was screened for articles published until March 2021 on observational studies investigating the association of genome-wide genetic and epigenetic alterations, measured in breast cancer tissues or blood, with the response to targeted treatment in HER2-positive breast cancer patients. Sixteen studies were included in the review along with ours, in which we compared the genome-wide DNA methylation pattern in breast tumor tissues of patients who acquired resistance to treatment (case group, n = 6) to that of patients who did not develop resistance (control group, n = 6). Among genes identified as differentially methylated between the breast cancer tissue of cases and controls, one of them, PRKACA, was also reported as differentially expressed in two studies included in the review. Although included studies were heterogeneous in terms of methodology and study population, our review suggests that genes of the PI3K pathway may play an important role in developing resistance to anti-HER2 agents in breast cancer patients. Genome-wide genetic and epigenetic alterations measured in breast cancer tissue or blood might be promising markers of resistance to anti-HER2 agents in HER2-positive breast cancer patients. Further studies are needed to confirm these data.

Background We identified two families with Paget's disease of bone (PDB) linked to the p.Pro392Leu mutation within the SQSTM1 gene displaying a possible digenism. This study aimed at identifying this second genetic variant cosegregating with the p.Pro392Leu mutation and at characterizing its impact on the clinical and cellular phenotypes of PDB. Methods Whole exome sequencing was performed in one patient per family and two healthy controls. We compared clinical characteristics of PDB in 14 relatives from the two families. The osteoclastic phenotype was compared in in vitro differentiated osteoclasts from 31 participants carrying the DOCK6 and/or SQSTM1 variants. Tridimensional models of SQSTM1 and DOCK6 proteins were generated to evaluate the impact of these variants on their stability and flexibility. Statistical analyses were performed with Graphpad prism. Results Whole-exome sequencing allowed us to identify the p.Val45Ile missense variant in the DOCK6 gene in patients. In both families, the mean age at PDB diagnosis was delayed in pagetic patients carrier of the p.Val45Ile variant alone compared to those carrying the p.Pro392Leu mutation alone (67 vs. 44 years, P = 0.03). Although both p.Val45Ile and p.Pro392Leu variants gave rise to a pagetic phenotype of osteoclast versus healthy controls, the p.Val45Ile variant was found to attenuate the severity of the osteoclastic phenotype of PDB caused by the p.Pro392Leu mutation when both variants were present. The DOCK6 mRNA expression was higher in carriers of the p.Val45Ile variant than in pagetic patients without any mutations and healthy controls. Structural bioinformatics analyses suggested that the p.Pro392Leu mutation might rigidify the UBA domain and thus decrease its possible intramolecular interaction with a novel domain, the serum response factor–transcription factor (SRF-TF)-like domain, whereas the p.Val45Ile variant may decrease SRF-TF-like activity. Conclusion The p.Val45Ile variant may attenuate the severity of the clinical phenotype of PDB in patient carriers of both variants. In vitro, the rare variant of the DOCK6 may have a modifier effect on the p.Pro392Leu mutation, possibly via its effect on the SRF-TF-like.

Spring floods have generated colossal damages to residential areas in the Province of Quebec, Canada, in 2017 and 2019. Government authorities need accurate modelling of the impact of theoretical floods in order to prioritize pre-disaster mitigation projects to reduce vulnerability. They also need accurate modelling of forecasted floods in order to direct emergency responses. We present a governmental-academic collaboration that aims at modelling flood impact for both theoretical and forecasted flooding events over all populated river reaches of meridional Quebec. The project, funded by the ministère de la Sécurité publique du Québec (Quebec ministry in charge of public security), consists in developing a diagnostic tool and methods to assess the risk and impacts of flooding. Tools under development are intended to be used primarily by policy makers. The project relies on water level data based on the hydrological regimes of nearly 25,000 km of rivers, on high-precision digital terrain models, and on a detailed database of building footprints and characterizations. It also relies on 24h and 48h forecasts of maximum flow for the subject rivers. The developed tools integrate large data sets and heterogeneous data sources and produce insightful metrics on the physical extent and costs of floods and on their impact on the population. The software also provides precise information about each building affected by rising water, including an estimated cost of the damages and impact on inhabitants.

We have developed a new method for the identification of bacterial species causing Urinary Tract Infections. The first training step used DIA analysis on multiple replicates of bacterial inoculates to define a peptide signature by machine learning classifiers. In a second identification step, the signature is monitored by targeted proteomics on unknown samples. This fast, culture-free and accurate method paves the way of the development of new diagnostic approaches limiting the emergence of antimicrobial resistances., Graphical Abstract Highlights Fast and culture-free method for the identification of the 15 bacterial species causing UTIs. Combination of DIA analysis and machine learning algorithms to define a peptide signature. High accuracy, good linearity and reproducibility, sensitivity below standard threshold. Transferability to other laboratories and other mass spectrometers., Fast identification of microbial species in clinical samples is essential to provide an appropriate antibiotherapy to the patient and reduce the prescription of broad-spectrum antimicrobials leading to antibioresistances. MALDI-TOF-MS technology has become a tool of choice for microbial identification but has several drawbacks: it requires a long step of bacterial culture before analysis (≥24 h), has a low specificity and is not quantitative. We developed a new strategy for identifying bacterial species in urine using specific LC-MS/MS peptidic signatures. In the first training step, libraries of peptides are obtained on pure bacterial colonies in DDA mode, their detection in urine is then verified in DIA mode, followed by the use of machine learning classifiers (NaiveBayes, BayesNet and Hoeffding tree) to define a peptidic signature to distinguish each bacterial species from the others. Then, in the second step, this signature is monitored in unknown urine samples using targeted proteomics. This method, allowing bacterial identification in less than 4 h, has been applied to fifteen species representing 84% of all Urinary Tract Infections. More than 31,000 peptides in 190 samples were quantified by DIA and classified by machine learning to determine an 82 peptides signature and build a prediction model. This signature was validated for its use in routine using Parallel Reaction Monitoring on two different instruments. Linearity and reproducibility of the method were demonstrated as well as its accuracy on donor specimens. Within 4h and without bacterial culture, our method was able to predict the predominant bacteria infecting a sample in 97% of cases and 100% above the standard threshold. This work demonstrates the efficiency of our method for the rapid and specific identification of the bacterial species causing UTI and could be extended in the future to other biological specimens and to bacteria having specific virulence or resistance factors.

The identification of microbial species in biological samples is essential to many applications in health, food safety and environment. MALDI-TOF MS technology has become a tool of choice for microbial identification but it has several drawbacks including: it requires a long step of bacterial culture prior to analysis (24h), it has a low specificity and is not quantitative. We have developed a new strategy for identifying bacterial species in biological samples using specific LC-MS/MS peptidic signatures. In the first training step, deep proteome coverage of bacteria of interest is obtained in Data Independent Acquisition (DIA) mode, followed by the use of machine learning to define the peptides the most susceptible to distinguish each bacterial species from the others. Then, in the second step, this peptidic signature is monitored in biological samples using targeted proteomics. This method, which allows the bacterial identification from clinical specimens in less than 4h, has been applied to fifteen species representing 84% of all Urinary Tract Infections (UTI). More than 31000 peptides in 200 samples have been quantified by DIA and analyzed by machine learning to determine an 82 peptides signature and build prediction models able to classify the fifteen bacterial species. This peptidic signature was validated for its use in routine conditions using Parallel Reaction Monitoring on a capillary flow chromatography coupled to a Thermo Scientific™ Q Exactive HF-X instrument. Linearity and reproducibility of the method were demonstrated as well as its accuracy on donor specimens. Within 4h and without bacterial culture, our method was able to predict the predominant bacteria infecting a sample in 97% of cases and 100% above the 1×105 CFU/mL threshold commonly used by clinical laboratories. This work demonstrates the efficiency of our method for the rapid and specific identification of the bacterial species causing UTI and could be extended in the future to other biological specimens and to bacteria having specific virulence or resistance factors.

This article contains raw and processed data related to research published in “Role of the polypeptide N-acetylgalactosaminyltransferase 3 in ovarian cancer progression: possible implications in abnormal mucin O-glycosylation” [1]. The data presented here was obtained with the application of a bioorthogonal chemical reporter strategy analyzing differential glycoprotein expression following the knock-down (KD) of the GALNT3 gene in the epithelial ovarian cancer (EOC) cell line A2780s. LC-MS/MS mass spectrometry analysis was then performed and the processed data related to the identified glycoproteins show that several hundred proteins are differentially expressed between control and GALNT3 KD A2780s cells. The obtained data also uncover numerous novel glycoproteins; some of which could represent new potential EOC biomarkers and/or therapeutic targets. Keywords: GALNT3, Glycosylation, Ac4GalNAz labeling, Label free quantification, NetOGlyc and NetNGlyc prediction analysis, Glycoproteomics

Hybrid materials based on one organic dye, the carminic acid, and montmorillonite have been prepared and characterized by a multi-technical approach. Aluminum and tin II cations were used in the experimental mixtures in order to have a chelating effect with the carminic acid. X-Ray diffraction patterns (XRD) did not highlight any intercalation of the organic molecule in the interlayer space, a result confirmed by transmission electron microscopy (TEM) micrographs. The fixation of the organic molecules on the phyllosilicates was then investigated by 13 C solid state nuclear magnetic resonance (NMR) and time resolved fluorescence spectroscopies. The spectra showed the role that the ketone and catechol functions of the dye played for its fixation and stressed on the decrease of its mobility when the lake pigment was formed. The role of the clay edges and/or surface was highlighted by this set of experimental data.

Exercise limitation comes from a close interaction between cardiovascular and skeletal muscle impairments. To better understand the implication of possible peripheral oxidative metabolism dysfunction, we studied the proteomic signature of skeletal muscle in pulmonary arterial hypertension (PAH). Eight idiopathic PAH patients and eight matched healthy sedentary subjects were evaluated for exercise capacity, skeletal muscle proteomic profile, metabolism, and mitochondrial function. Skeletal muscle proteins were extracted, and fractioned peptides were tagged using an iTRAQ protocol. Proteomic analyses have documented a total of 9 downregulated proteins in PAH skeletal muscles and 10 upregulated proteins compared to healthy subjects. Most of the downregulated proteins were related to mitochondrial structure and function. Focusing on skeletal muscle metabolism and mitochondrial health, PAH patients presented a decreased expression of oxidative enzymes (pyruvate dehydrogenase, p

Male factors account for 40% of infertility cases. The identification of differentially expressed proteins on spermatozoa from fertile and infertile men can help in the elucidation of the molecular basis of male infertility. The aim of this study was to compare sperm proteomes from 3 different groups: fertile men, normozoospermic men consulting for infertility, and normozoospermic men with an impaired capacity for fertilization (IVF-failure). We used differential proteomics with isobaric tags for relative and absolute quantitation (iTRAQ) labeling, and LC-MS analysis to identify proteins that are differentially expressed. A total of 348 unique proteins were identified and quantified. The analysis identified 33 proteins that were differentially expressed in the IVF-failure group vs the fertile group. Comparison of the infertile and fertile groups revealed that 18 proteins appeared to be differentially expressed. Four proteins were similarly altered in the IVF-failure and infertile groups: semenogelin 1 (SEMG1), prolactin-induced protein (PIP), glyceraldehyde-3-phosphate dehydrogenase (GAPDHS), and phosphoglycerate kinase 2 (PGK2). These protein markers were selected for validation using multiple reactions monitoring mass spectrometry (MRM-MS) and further confirmed by Western blot analysis. Overall, these results suggest that a panel of proteins may be used as biomarkers for future studies of infertility.

International audience; PURPOSE. Development of liver metastasis remains the most common cause of mortality in uveal melanoma (UM). A few cell lines cultured from primary UM tumors have been used widely to investigate the pathobiology of UM. However, the translation of basic knowledge to the clinic for the treatment of the metastatic disease has remained incremental at best. In this study, we examined whether the properties of UM cell lines at various passages were similar to their corresponding primary tumors. METHODS. Gene expression profiling by microarray was performed on UM primary tumors and derived cell lines cultured at varying passages. Expression of UM protein markers was monitored by immunohistochemical analyses and Western blotting. The in vivo tumorigenic properties of UM cultures were evaluated using athymic nude mice. RESULTS. Cell passaging severely reduced the expression of genes encoding markers typical of UM, including those of the prognostic gene signature. Marked differences between gene expression profiles of primary tumors and cell lines could be linked to the infiltrating immune and stromal cells in situ. In addition, the tumorigenic properties of UM cell lines also increased with cell passaging in culture as evaluated by their subcutaneous injection into athymic mice. CONCLUSIONS. Together, these findings demonstrate that the short-term UM primary cultures exhibit molecular features that resemble the respective surgical material and, thus, represent the best model for in vitro-assessed cancer treatments.

Epithelial ovarian cancer (EOC) is a disease responsible for more deaths among women in the Western world than all other gynecologic malignancies. There is urgent need for new therapeutic targets and a better understanding of EOC initiation and progression. We have previously identified the polypeptide N-acetylgalactosaminyltransferase 3 ( GALNT3 ) gene, a member of the GalNAc-transferases (GalNAc-Ts) gene family, as hypomethylated and overexpressed in high-grade serous EOC tumors, compared to low malignant potential EOC tumors and normal ovarian tissues. This data also suggested for a role of GALNT3 in aberrant EOC glycosylation, possibly implicated in disease progression. To evaluate differential glycosylation in EOC caused by modulations in GALNT3 expression, we used a metabolic labeling strategy for enrichment and mass spectrometry-based characterization of glycoproteins following GALNT3 gene knockdown (KD) in A2780s EOC cells. A total of 589 differentially expressed glycoproteins were identified upon GALNT3 KD. Most identified proteins were involved in mechanisms of cellular metabolic functions, post-translational modifications, and some have been reported to be implicated in EOC etiology. The GALNT3 -dependent glycoproteins identified by this metabolic labeling approach support the oncogenic role of GALNT3 in EOC dissemination and may be pursued as novel EOC biomarkers and/or therapeutic targets. Biological significance Knowledge of the O-glycoproteome has been relatively elusive, and the functions of the individual polypeptide GalNAc-Ts have been poorly characterized. Alterations in GalNAc-Ts expression were shown to provide huge variability in the O-glycoproteome in various pathologies, including cancer. The application of a chemical biology approach for the metabolic labeling and subsequent characterization of O-glycoproteins in EOC using the Ac 4 GalNAz metabolite has provided a strategy allowing for proteomic discovery of GalNAc-Ts specific functions. Our study supports an essential role of one of the GalNAc-Ts — GALNT3, in EOC dissemination, including its implication in modulating PTMs and EOC metabolism. Our approach validates the use of the applied metabolic strategy to identify important functions of GalNAc-Ts in normal and pathological conditions.

Methylene is found in the repeat units of many polymers including proteins. In some cases it appears to be a useful reporter of variation in local environment whilst in other contexts average behaviour seems to dominate. In this paper we apply a particular 2DIR technique to a range of systems containing methylene groups, showing that mode frequencies, linewidths and splittings can be easily extracted even when the infrared absorption bands are too congested to allow reliable analysis. 2DIR spectra of polyethylene and several liquid alkanes are compared and it is shown for the case of l -arginine that the methylene scissor modes are split and that this can be resolved by tracking the 2DIR spectrum as a function of time. Calculations from first principles reveal that for most of the methylene modes studied, electrical anharmonicity is the dominant contributor to the 2DIR cross-peak intensity, with the mechanical anharmonicity making only a small contribution.

International audience; The existence of the ribose moiety in biomolecules poses two problems for prebiotic chemistry. First, the exclusive presence of the furanose isomer in RNA has to be accounted for since furanose is a minor form in solution and does not exist in crystals. Second, all D-ribose polymorphs are unstable in aqueous medium so that a stabilization mechanism has to be invoked. We observed that the adsorption on mineral surfaces as amorphous silica protects the sugar from degradation processes. Moreover, this silica surface, used as realistic chert model, is able to increase significantly the proportion of ribofuranose compared to ribopyranose forms. The interaction between surface and sugar was analyzed by C-13 NMR. Our results show a very significant chemical and thermal stabilization of the adsorbed sugar by a silica surface and an almost twofold increase of ribofuranose compared to ribose in solution.

This article deals with the theoretical, didactic and technological problems associated with developing a computer-aided learning environment for scientifi c modelling through the fusion of a computer-aided experiment system and a computer-aided simulation system. The most innovative aspect of this new environment resides in the possibility of comparing animated simulation and a video sequence through the direct layering of images. The main conclusions concern the use of this environment in the teaching of traditional mechanics in post-secondary education as well as the possibility of automated modelling of the learning process of students. Results show that the characteristics of this new software should be further studied especially as regards the time required to learn how to use modelling equipment, the improved thinking processes of students and the ability to induce and deduce., Cet article présente les considérations théoriques, didactiques et technologiques qui nous ont amené à entreprendre une recherche relative au développement d’un environnement informatisé d’apprentissage de la modélisation scientifique combinant un système d’expérimentation assistée par ordinateur et un système de simulation assistée par ordinateur. La fonctionnalité la plus originale de cet environnement permet de comparer une simulation animée et une séquence vidéo au moyen de la superposition directe des images. Les principaux résultats de cette recherche concernent l’utilisation de l’environnement développé dans le contexte de la formation à la mécanique classique au niveau de l’enseignement supérieur, et la possibilité de modélisation automatique des cheminements d’apprentissage des étudiants. Les propriétés de ce nouveau genre de logiciel, mises en évidence par notre recherche, mériteraient d’être étudiées plus en profondeur, surtout en ce qui concerne la rapidité d’apprentissage de la modélisation, l’enrichissement du raisonnement de l’étudiant et les sollicitations entre induction et déduction., Este artículo presenta las consideraciones teóricas, didácticas y tecnológicas que nos han llevado a emprender una investigación relativa al desarrollo de un entorno informatizado de aprendizaje de la modelización científi ca que combina un sistema de experimentación asistida por ordenador y un sistema de simulación asistida por ordenador. La funcionalidad más original de dicho entorno permite comparar una simulación animada y una secuencia de vídeo por medio de la superposición directa de las imágenes. Los principales resultados de esta investigación atañen a la utilización del contorno desarrollado en el contexto de la formación en mecanica clásica, al nivel de la enseñanza universitaria y a la posibilidad de modelización automática de los razonamientos de aprendizaje de los estudiantes. Las propiedades de este nuevo tipo de software, puestas en evidencia por nuestra investigación, merecerían ser estudiadas más profundamente, sobre todo en lo relativo a la rapidez de aprendizaje de la modelización, al enriquecimiento del razonamiento del estudiante y a las solicitaciones entre inducción y deducción., Riopel Martin, Raîche Gilles, Potvin Patrice, Fournier Frédéric, Nonnon Pierre. Une approche intégrée de la modélisation scientifique assistée par l'ordinateur. In: Aster, n°43, 2006. modélisation et simulation. pp. 57-79.

Femtosecond visible pulses at 800 nm are observed to induce permanent spectral changes in the CO internal stretch region of CO/Pt(1 1 1) at 300 K, using sum frequency generation vibrational spectroscopy. By contrast, IR femtosecond, and visible picosecond pulses do not induce any change. Defects, disordering, water coadsorption or laser induced CO dissociation can be ruled out to account for the observed changes, which seem to be due to the formation of a metastable structure. With this structure, the CO coverage seems to increase reversibly in equilibrium with gas phase CO, which normally occurs on various surfaces, but not on Pt(1 1 1). An unusually high frequency for linearly bonded CO at 300 K is obtained above ≈10 −7 mbar. More experimental work using other techniques is required to confirm the occurrence of a metastable structure and to characterize it. Nevertheless the available spectroscopic and structural data concerning CO on Pt(1 1 1) do not support an interpretation where the laser induced metastable structure would remain close to the regular c(4×2) structure.

Second harmonic non-linear susceptibilities of Pd(1 1 1) are derived at 800 nm fundamental wavelength from measurements of second harmonic generation (SHG) as a function of azimuth and input and output polarizations. By contrast to other metal surfaces and to other wavelengths, Pd(1 1 1) does not exhibit any anisotropy related to azimuth at 800 nm. SHG is also measured during CO adsorption at 1064 and 800 nm. Opposite trends are observed at the two wavelengths. The results are discussed in the light of previously reported experiments on Pd(1 1 1) at other wavelengths and on other metals. At 800 nm, free electrons and/or the Shockley surface state probably dominate the SHG response of Pd(1 1 1). CO chemisorption probably reduces the density of the d-band states probed at 1064 nm, and on the contrary enhances the density of the states probed at 800 nm.

The ability to detect molecular complexes and determine their geometries is crucial to our understanding of all biological phenomena, including protein structures and functions. We recently demonstrated that a novel 2DIR technique, EVV 2DIR spectroscopy, can be used for this purpose. In this paper, we evaluate the potential utility of the method for the analysis of protein composition, structure and function. In order to do this we apply computational tools to a group of selected biological systems, for which our calculated spectra all showed features that can in principle be detected with existing sensitivities. We also investigate the possibility of using our technique to detect and analyse hydrogen-bonded systems through a tyrosine–water model.

Summary: rTANDEM is an R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. The package can run the multi-threaded algorithm on proteomic data files directly from R. It also provides functions to convert search parameters and results to/from R as well as functions to manipulate parameters and automate searches. An associated R package, shinyTANDEM, provides a web-based graphical interface to visualize and interpret the results. Together, those two packages form an entry point for a general MS/MS-based proteomic pipeline in R/Bioconductor. Availability and implementation: rTANDEM and shinyTANDEM are distributed in R/Bioconductor, http://bioconductor.org/packages/release/bioc/ . The packages are under open licenses (GPL-3 and Artistice-1.0). Contact: frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca Supplementary information: Supplementary data are available at Bioinformatics online.

In the last 10 years, several forms of two-dimensional infrared (2DIR) spectroscopy have been developed, such as IR pump−probe spectroscopy and photon-echo techniques. In this Account, we describe a doubly vibrationally enhanced four-wave mixing method, in which a third-order nonlinear signal is generated from the interaction of two independently tunable IR beams and an electron-polarizing visible beam at 790 nm. When the IR beams are independently in resonance with coupled vibrational transitions, the signal is enhanced and cross-peaks appear in the spectrum. This method is known as either DOVE (doubly vibrationally enhanced) four-wave mixing or EVV (electron−vibration−vibration) 2DIR spectroscopy. We begin by discussing the basis and properties of EVV 2DIR. We then discuss several biological and potential biomedical applications. These include protein identification and quantification, as well as the potential of this label-free spectroscopy for protein and peptide structural analysis. In proteomics, we...

Electrical interactions between molecular vibrations can be non-linear and thereby produce intermolecular coupling even in the absence of a chemical bond. We use this fact to detect the formation of an intermolecular complex using electron-vibration-vibration two-dimensional infrared spectroscopy (EVV 2DIR) and also to determine the distance and angle between the two molecular species.

In the last 10 years, several forms of two-dimensional infrared (2DIR) spectroscopy have been developed, such as IR pump-probe spectroscopy and photon-echo techniques. In this Account, we describe a doubly vibrationally enhanced four-wave mixing method, in which a third-order nonlinear signal is generated from the interaction of two independently tunable IR beams and an electron-polarizing visible beam at 790 nm. When the IR beams are independently in resonance with coupled vibrational transitions, the signal is enhanced and cross-peaks appear in the spectrum. This method is known as either DOVE (doubly vibrationally enhanced) four-wave mixing or EVV (electron-vibration-vibration) 2DIR spectroscopy. We begin by discussing the basis and properties of EVV 2DIR. We then discuss several biological and potential biomedical applications. These include protein identification and quantification, as well as the potential of this label-free spectroscopy for protein and peptide structural analysis. In proteomics, we also show how post-translational modifications in peptides (tyrosine phosphorylation) can be detected by EVV 2DIR spectroscopy. The feasibility of EVV 2DIR spectroscopy for tissue imaging is also evaluated. Preliminary results were obtained on a mouse kidney histological section that was stained with hematoxylin (a small organic molecule). We obtained images by setting the IR frequencies to a specific cross-peak (the strongest for hematoxylin was obtained from its analysis in isolation; a general CH(3) cross-peak for proteins was also used) and then spatially mapping as a function of the beam position relative to the sample. Protein and hematoxylin distribution in the tissue were measured and show differential contrast, which can be entirely explained by the different tissue structures and their functions. The possibility of triply resonant EVV 2DIR spectroscopy was investigated on the retinal chromophore at the centre of the photosynthetic protein bacteriorhodopsin (bR). By putting the visible third beam in resonance with an electronic transition, we were able to enhance the signal and increase the sensitivity of the method by several orders of magnitude. This increase in sensitivity is of great importance for biological applications, in which the number of proteins, metabolites, or drug molecules to be detected is low (typically pico- to femtomoles). Finally, we present theoretical investigations for using EVV 2DIR spectroscopy as a structural analysis tool for inter- and intramolecular interaction geometries.

The sum frequency generation (SFG) spectrum of ${\text{CH}}_{2}$ and ${\text{CH}}_{3}$ modes in the self-assembled monolayer of octadecanethiol is modeled in order to understand the reasons of the very low SFG intensity of ${\text{CH}}_{2}$ modes and to investigate quantitatively the two types of L-shaped conformations qualitatively suggested in the literature. ${\text{CH}}_{2}$ modes are assumed local in order to calculate easily the spectrum of any conformation, and ab initio molecular hyperpolarizabilities are used. It is found that the absence of ${\text{CH}}_{2}$ bands does not imply an all-trans conformation and vice versa. Several conformations are compatible with SFG, but only one of them can be arranged on Au(111) and completely agrees with x-ray diffraction. All conformational details of the L-shape molecules are obtained.

Electron-vibration-vibration two-dimensional coherent spectroscopy, a variant of 2DIR, is shown to be a useful tool to differentiate a set of 10 proteins based on their amino acid content. Two-dimensional vibrational signatures of amino acid side chains are identified and the corresponding signal strengths used to quantify their levels by using a methyl vibrational feature as an internal reference. With the current apparatus, effective differentiation can be achieved in four to five minutes per protein, and our results suggest that this can be reduced to

We employ a particular form of two-dimensional infrared four-wave mixing (2DIR FWM) as a vibrational spectroscopic tool to quantify the amino acid content of a number of peptides. Vibrational features corresponding to ring modes of the aromatic groups of phenylalanine (Phe) and tyrosine (Tyr), as well as a methylene mode that is used as an internal reference, are identified. We show that the ratios of the integrated intensities, and the amplitudes, of the aromatic peaks of Phe and Tyr relative to the methylene integrated intensity, and amplitude, are proportional to the actual ratio of Phe and Tyr to CH2 in the samples within a precision of ±12.5%. This precision is shown to be sufficient to use this form of 2DIR spectroscopy as a possible proteins fingerprinting tool.

We show that it is possible to both directly measure and directly calculate Fermi resonance couplings in benzene. The measurement method used was a particular form of two-dimensional infrared spectroscopy (2D-IR) known as doubly vibrationally enhanced four wave mixing. By using different pulse orderings, vibrational cross peaks could be measured either purely at the frequencies of the base vibrational states or split by the coupling energy. This capability is a feature currently unique to this particular form of 2D-IR and can be helpful in the decongestion of complex spectra. Five cross peaks of the ring breathing mode nu13 with a range of combination bands were observed spanning a region of 1500-4550 cm(-1). The coupling energy was measured for two dominant states of the nu13+nu16 Fermi resonance tetrad. Dephasing rates were measured in the time domain for nu13 and the two (nu13+nu16) Fermi resonance states. The electronic and mechanical vibrational anharmonic coefficients were calculated to second and third orders, respectively, giving information on relative intensities of the cross peaks and enabling the Fermi resonance states of the combination band nu13+nu16 at 3050-3100 cm(-1) to be calculated. The excellent agreement between calculated and measured spectral intensities and line shapes suggests that assignment of spectral features from ab initio calculations is both viable and practicable for this form of spectroscopy.

This paper summarizes results from two educational research Ph.D. theses carried out in recent years at the "Laboratoire de Robotique Pedagogique" of the Universite de Montreal. Both theses focus on innovative educational software and technology for use in science laboratories. The first is the work of Riopel and concerns the combination of computer-simulated experimentation software and microcomputer-based laboratories to provide learners with complete computerized assistance in carrying out both inductive and deductive reasoning. The second, the work of Fournier, concerns a microcomputer- based laboratory environment that allows students to design and construct a measuring system from start to finish, in order to better understand the concepts of measurement and of physical variables. In both of these technological applications, the software is used to automatically record and identify learners' actions.

Insulin resistance (IR) is associated with increased production of triglyceride-rich lipoproteins of intestinal origin. In order to assess whether insulin resistance affects the proteins involved in lipid metabolism, we used two mass spectrometry based quantitative proteomics techniques to compare the intestinal proteome of 14 IR patients to that of 15 insulin sensitive (IS) control patients matched for age and waist circumference. A total of 3886 proteins were identified by the iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) mass spectrometry approach and 2290 by the SWATH-MS strategy (Serial Window Acquisition of Theoretical Spectra). Using these two methods, 208 common proteins were identified with a confidence corresponding to FDR < 1%, and quantified with p-value < 0.05. The quantification of those 208 proteins has a Pearson correlation coefficient (r2) of 0.728 across the two techniques. Gene Ontology analyses of the differentially expressed proteins revealed that annotations related to lipid metabolic process and oxidation reduction process are overly represented in the set of under-expressed proteins in IR subjects. Furthermore, both methods quantified proteins of relevance to IR. These data also showed that SWATH-MS is a promising and compelling alternative to iTRAQ for protein quantitation of complex mixtures.

Interaction of CO adsorbed on Pt(111) with electrons and phonons is studied experimentally by means of a pump-probe experiment where CO is probed by IR + visible sum frequency generation under a pump laser intensity that allows photodesorption. Vibrational spectra of CO internal stretch are obtained as a function of pump-probe delay. A two-temperature and anharmonic coupling model is used to extract from the spectra the real time variations of CO peak frequency and dephasing time. The main conclusions are the following: (i) The CO stretch is perturbed by two low-frequency modes, assigned to frustrated rotation and frustrated translation. (ii) The frustrated rotation is directly coupled to electrons photoexcited in Pt(111) by the pump laser. (iii) There is no evidence of Pt-CO stretch excitation in the spectra. The implications for the photodesorption dynamics are discussed.

CO photodesorption from Pt(111) induced by femtosecond laser pulses is probed by IR+visible sum frequency generation (SFG). Steady state analysis of SFG spectra at varying CO pressure and laser fluence allows one to measure a approximately 5 orders of magnitude decrease of the photodesorption rate constant when CO coverage decreases from 0.37 to 0.07 monolayer. We ascribe this effect in the framework of the Menzel-Gomer-Redhead mechanism to electron delocalization in the CO layer. The lifetime of electronic excitation decreases when coverage decreases.

Photodesorption of adsorbed molecules resulting from electronic excitation of the substrate is an important problem. It allows studying how electrons are coupled to adsorbate degrees of freedom, which has a broad interest for surface chemistry in general. So far, photodesorption has been studied using femtosecond pulses by a two-pulse correlation approach. This allows determining whether it scales temporally with electronic excitation, or with substrate heating. A second method was employed recently, consisting of probing adsorbate vibrations with femtosecond temporal resolution using sum frequency generation (SFG). For CO/Ru(0001) (a case of phonon mediated photodesorption) a broadening and red-shift of CO internal stretch was observed. Data analysis reveals that frustrated rotation is excited at the fluences where photodesorption occurs. In this chapter, this method is applied to a system where photodesorption is believed to be mediated by electrons rather than by phonons. The results show that CO responds at a sub-ps time scale (

CO photodesorption from Pt(111) induced by femtosecond laser pulses is probed by IR+visible sum frequency generation (SFG). Steady state analysis of SFG spectra at varying CO pressure and laser fluence allows one to measure a approximately 5 orders of magnitude decrease of the photodesorption rate constant when CO coverage decreases from 0.37 to 0.07 monolayer. We ascribe this effect in the framework of the Menzel-Gomer-Redhead mechanism to electron delocalization in the CO layer. The lifetime of electronic excitation decreases when coverage decreases.

Aquatic ecosystems have formed the focus of several UNESCO research projects because of the impact on them of human activities such as intensification of agricultural activity, erosion and sedimentation due to irrigation projects, groundwater pollution and eutrophication. Interfaces, or ecotones, between terrestrial and aquatic ecosystems were found to have an essential role in the movement of water and materials throughout the landscape. Ecotones are zones where ecological processes are more intense and resources more diversified. They are also zones which react quickly to human influences and changes of environmental variables. This volume summarises the results presented at an international conference dedicated to the study of groundwater/surface water ecotones, with contributors of international scientific reputation representing the multidisciplinary viewpoints of hydrologists, biologists and ecologists. It addresses areas of active research in hydrology and biology, and is aimed towards researchers, water resource project managers and policy makers.

Adsorption of methyl chloride and coadsorption of CH3Cl and D2O on Pd(111) surfaces at T=100 K have been studied under ultrahigh-vacuum conditions using femtosecond sum frequency generation (SFG) spectroscopy in the spectral regions of CH and OD bands. On the bare Pd(111) substrate, the CH3Cl coverage dependence of the resonant SFG signal is consistent with a progressive molecular rearrangement starting at half saturation followed by the growth of two ordered monolayers in which the molecular axes are perpendicular to the surface. When CH3Cl is adsorbed on top of predeposited D2O on Pd(111), the SFG signals as a function of the CH3Cl exposure indicate that methyl chloride is adsorbed onto D2O through hydrogen bonding. On the contrary when the adsorption order is reversed the strong decrease of the CH3 signal as a function of the D2O exposure is explained by assuming that water molecules penetrate inside the CH3Cl layers, leading to the formation of disordered CH3Cl clusters. In all cases a nonresonant contribution due to molecular adsorption is observed and it shows a dependence upon surface structure and coverage significantly different from that of the resonant vibrational bands.