A chemical study of yoghurt produced under isostatic pressure during storage.

Yoghurt fermented under sub-lethal high pressure (10, 20, 30 and 40 MPa at 43 °C), and afterward placed under refrigeration (4 °C for 23 days) was studied and compared with yoghurt fermented at atmospheric pressure (0.1 MPa). For a deeper analysis, metabolite fingerprinting by nuclear magnetic resonance (NMR), sugars and organic acids assessment by high performance liquid chromatography (HPLC), total fatty acids (TFA) determination and quantification by gas chromatography with a flame ionization detector (GC-FID) were performed. Metabolomic analyses revealed that only 2,3-butanediol, acetoin, diacetyl and formate vary with the increase of pressure and probable relation with pressure influenced diacetyl reductase, acetoin reductase and acetolactate decarboxylase. Yoghurts fermented at 40 MPa had the lowest content in lactose (39.7 % of total sugar reduction) and the less content in TFA (56.1 %). Further research is of interest to understand more about fermentation processes under sub-lethal high pressure.

Chitosan Film as a Replacement for Conventional Sulphur Dioxide Treatment of White Wines: A 1H NMR Metabolomic Study.

Chitosan-genipin (Ch-Ge) films have been proposed for the replacement of sulfur dioxide (SO2) in white wines preservation to circumvent the adverse health consequences caused by SO2 intake. To assess the effects of different-sized Ch-Ge films (25 and 100 cm2) on wine composition compared to SO2-treated and untreated wines, nuclear magnetic resonance metabolomics was applied. Relative to SO2, 100 cm2 films induced significant changes in the levels of organic acids, sugars, amino acids, 5-hydroxymethylfurfural, among other compounds, while 25 cm2 films appeared to induce only small variations. The observed metabolite variations were proposed to arise from the mitigation of fermentative processes, electrostatic interactions between acids and the positively charged films and the promotion of Maillard and Strecker reactions. Qualitative sensory analysis showed that wines maintained overall appropriate sensory characteristics, with 100 cm2 film treated wines showing slightly higher attributes. Based on these results, the possibility of using Ch-Ge films as a replacement for SO2 treatment is discussed.

The role of NAD metabolism in neuronal differentiation.

BACKGROUND: Nicotinamide adenine dinucleotide (NAD) metabolism is involved in redox and non-redox reactions that regulate several processes including differentiation of cells of different origins. Here, the role of NAD metabolism in neuronal differentiation, which remains elusive so far, was investigated. MATERIAL AND METHODS: A protein-protein interaction network between neurotrophin signaling and NAD metabolic pathways was built. Expression of NAD biosynthetic enzymes in SH-SY5Y cells during retinoic acid (RA)/brain derived neurotrophic factor (BDNF) differentiation, was evaluated. The effects of NAD biosynthetic enzymes QPRT and NAPRT inhibition in neurite outgrowth, cell viability, NAD availability and histone deacetylase (HDAC) activity, were analyzed in RA- and BDNF-differentiated cells. RESULTS: Bioinformatics analysis revealed the interaction between NAD biosynthetic enzyme NMNAT1 and NTRK2, a receptor activated by RA/BDNF sequential treatment. Differences were found in the expression of NAD biosynthetic enzymes during neuronal differentiation, namely, increased QPRT gene expression along the course of RA/BDNF treatment and NAPRT protein expression after a 5-day treatment with RA. QPRT inhibition in BDNF-differentiated SH-SY5Y cells resulted in less neuritic length per cell, decreased expression of the neuronal marker ß-III Tubulin and also decreased NAD+ levels and HDAC activity. NAPRT inhibition had no effect in neuritic length per cell, NAD+ levels and HDAC activity. Of note, NAD supplementation along with RA, but not with BDNF, resulted in considerable cell death. CONCLUSIONS: Taken together, our results show the involvement of NAD metabolism in neuronal differentiation, specifically, the importance of QPRT-mediated NAD biosynthesis in BDNF-associated SH-SY5Y differentiation and suggest additional roles for NAPRT beyond NAD production in RA-differentiated cells.

The Long-Term Culture of Human Fibroblasts Reveals a Spectroscopic Signature of Senescence.

Aging is a complex process which leads to progressive loss of fitness/capability/ability, increasing susceptibility to disease and, ultimately, death. Regardless of the organism, there are some features common to aging, namely, the loss of proteostasis and cell senescence. Mammalian cell lines have been used as models to study the aging process, in particular, cell senescence. Thus, the aim of this study was to characterize the senescence-associated metabolic profile of a long-term culture of human fibroblasts using Fourier Transform Infrared and Nuclear Magnetic Resonance spectroscopy. We sub-cultivated fibroblasts from a newborn donor from passage 4 to passage 17 and the results showed deep changes in the spectroscopic profile of cells over time. Late passage cells were characterized by a decrease in the length of fatty acid chains, triglycerides and cholesterol and an increase in lipid unsaturation. We also found an increase in the content of intermolecular ß-sheets, possibly indicating an increase in protein aggregation levels in cells of later passages. Metabolic profiling by NMR showed increased levels of extracellular lactate, phosphocholine and glycine in cells at later passages. This study suggests that spectroscopy approaches can be successfully used to study changes concomitant with cell senescence and validate the use of human fibroblasts as a model to monitor the aging process.

Endo- and Exometabolome Crosstalk in Mesenchymal Stem Cells Undergoing Osteogenic Differentiation.

This paper describes, for the first time to our knowledge, a lipidome and exometabolome characterization of osteogenic differentiation for human adipose tissue stem cells (hAMSCs) using nuclear magnetic resonance (NMR) spectroscopy. The holistic nature of NMR enabled the time-course evolution of cholesterol, mono- and polyunsaturated fatty acids (including ω-6 and ω-3 fatty acids), several phospholipids (phosphatidylcholine, phosphatidylethanolamine, sphingomyelins, and plasmalogens), and mono- and triglycerides to be followed. Lipid changes occurred almost exclusively between days 1 and 7, followed by a tendency for lipidome stabilization after day 7. On average, phospholipids and longer and more unsaturated fatty acids increased up to day 7, probably related to plasma membrane fluidity. Articulation of lipidome changes with previously reported polar endometabolome profiling and with exometabolome changes reported here in the same cells, enabled important correlations to be established during hAMSC osteogenic differentiation. Our results supported hypotheses related to the dynamics of membrane remodelling, anti-oxidative mechanisms, protein synthesis, and energy metabolism. Importantly, the observation of specific up-taken or excreted metabolites paves the way for the identification of potential osteoinductive metabolites useful for optimized osteogenic protocols.

NMR Metabolomics Assessment of Osteogenic Differentiation of Adipose-Tissue-Derived Mesenchymal Stem Cells.

This Article presents, for the first time to our knowledge, an untargeted nuclear magnetic resonance (NMR) metabolomic characterization of the polar intracellular metabolic adaptations of human adipose-derived mesenchymal stem cells during osteogenic differentiation. The use of mesenchymal stem cells (MSCs) for bone regeneration is a promising alternative to conventional bone grafts, and untargeted metabolomics may unveil novel metabolic information on the osteogenic differentiation of MSCs, allowing their behavior to be understood and monitored/guided toward effective therapies. Our results unveiled statistically relevant changes in the levels of just over 30 identified metabolites, illustrating a highly dynamic process with significant variations throughout the whole 21-day period of osteogenic differentiation, mainly involving amino acid metabolism and protein synthesis; energy metabolism and the roles of glycolysis, the tricarboxylic acid cycle, and oxidative phosphorylation; cell membrane metabolism; nucleotide metabolism (including the specific involvement of O-glycosylation intermediates and NAD+); and metabolic players in protective antioxidative mechanisms (such as glutathione and specific amino acids). Different metabolic stages are proposed and are supported by putative biochemical explanations for the metabolite changes observed. This work lays the groundwork for the use of untargeted NMR metabolomics to find potential metabolic markers of osteogenic differentiation efficacy.

FTIR Spectroscopy as a Tool to Study Age-Related Changes in Cardiac and Skeletal Muscle of Female C57BL/6J Mice.

Studying aging is important to further understand the molecular mechanisms underlying this physiological process and, ideally, to identify a panel of aging biomarkers. Animals, in particular mice, are often used in aging studies, since they mimic important features of human aging, age quickly, and are easy to manipulate. The present work describes the use of Fourier Transform Infrared (FTIR) spectroscopy to identify an age-related spectroscopic profile of the cardiac and skeletal muscle tissues of C57BL/6J female mice. We acquired ATR-FTIR spectra of cardiac and skeletal muscle at four different ages: 6; 12; 17 and 24 months (10 samples at each age) and analyzed the data using multivariate statistical tools (PCA and PLS) and peak intensity analyses. The results suggest deep changes in protein secondary structure in 24-month-old mice compared to both tissues in 6-month-old mice. Oligomeric structures decreased with age in both tissues, while intermolecular ß-sheet structures increased with aging in cardiac muscle but not in skeletal muscle. Despite FTIR spectroscopy being unable to identify the proteins responsible for these conformational changes, this study gives insights into the potential of FTIR to monitor the aging process and identify an age-specific spectroscopic signature.

The Potential of Metabolomics in the Diagnosis of Thyroid Cancer.

Thyroid cancer is the most common endocrine system malignancy. However, there is still a lack of reliable and specific markers for the detection and staging of this disease. Fine needle aspiration biopsy is the current gold standard for diagnosis of thyroid cancer, but drawbacks to this technique include indeterminate results or an inability to discriminate different carcinomas, thereby requiring additional surgical procedures to obtain a final diagnosis. It is, therefore, necessary to seek more reliable markers to complement and improve current methods. "Omics" approaches have gained much attention in the last decade in the field of biomarker discovery for diagnostic and prognostic characterisation of various pathophysiological conditions. Metabolomics, in particular, has the potential to identify molecular markers of thyroid cancer and identify novel metabolic profiles of the disease, which can, in turn, help in the classification of pathological conditions and lead to a more personalised therapy, assisting in the diagnosis and in the prediction of cancer behaviour. This review considers the current results in thyroid cancer biomarker research with a focus on metabolomics.

Monitoring plasma protein aggregation during aging using conformation-specific antibodies and FTIR spectroscopy.

The loss of proteostasis during aging has been well described using different models, however little is known with respect to protein aggregation levels in biofluids with aging. Therefore, the aim of this study was to assess the pattern of age-related protein aggregation in human plasma using two distinct approaches: analysis with conformation-specific antibodies and FTIR spectroscopy. The latter has been widely used in biomedical research to study protein conformational changes in health and disease. Samples from a primary care based-cohort from the Aveiro region, Portugal, were used for slot-blot analyses followed by immunodetection with conformation-specific antibodies and for the acquisition of FTIR spectra. Immunoblot analyses revealed an age-dependent evolution of the protein conformational profile in human plasma, towards a decrease in prefibrillar oligomers and an increase in fibrillar structures. This finding was also supported by PLS-R multivariate analysis of FTIR data, where a positive correlation between the age of the donors and secondary structure of plasma proteins could be observed. Samples from younger donors are characterized by antiparallel ß-sheet-containing structures while intermolecular ß-sheets characterized older samples. Exclusion of age-associated co-morbidities improved the correlation between protein conformational profiles and aging. The results reveal structural changes in human plasma proteins from middle to old age, confirming the age-associated changes in protein aggregation, and support the applicability of FTIR as a reliable approach to study proteostasis during aging.

Host-defense peptides AC12, DK16 and RC11 with immunomodulatory activity isolated from Hypsiboas raniceps skin secretion.

Inflammation is a natural defense mechanism of the immune system; however, when unregulated, it can lead to chronic illness. Glucocorticoids are the most commonly used agents to effectively treat inflammatory conditions, including autoimmune diseases, however these substances can trigger a number of side effects. Thus, viable alternatives to the use of these drugs would be advantageous. In this study, we have analyzed the anti-inflammatory profile of three synthetic peptides first identified in skin secretion of the tree frog Hypsiboas raniceps. Structural characterization was performed using NMR spectroscopy and Mass Spectrometry, and the peptides were tested in vitro in RAW 264.7 cells and in vivo in Balb/c mice for their functional properties. The samples did not show a significant antimicrobial profile. NMR spectroscopy indicated that AC12 (ACFLTRLGTYVC) has a disulfide bond between C2 and C11 and a ß-sheet-turn-ß-sheet conformation in aqueous solution. This peptide showed no cytotoxic effect in mammalian cells and it was the most effective in reducing anti-inflammatory markers, such as NO, TNF-α and IL-12. Peptide DK16 (DKERPICSNTFRGRKC) demonstrated anti-inflammatory properties in vitro, while RC11 (RCFRRRGKLTC) significantly altered the cell viability in RAW 264.7 but was shown to be safe in Balb/c erythrocytes. Our results indicate that, of the three peptides studied, AC12 is the most efficient in reducing anti-inflammatory markers, and it could be a potential agent for the treatment of inflammatory diseases.

The Role of Ligand Packing Frustration in Body-Centered Cubic (bcc) Superlattices of Colloidal Nanocrystals.

This paper addresses the assembly of body centered-cubic (bcc) superlattices of organic ligand-coated nanocrystals. First, examples of bcc superlattices of dodecanethiol-capped Au nanocrystals and oleic acid-capped PbS and PbSe nanocrystals are presented and examined by transmission electron microscopy (TEM) and grazing incidence small-angle X-ray scattering (GISAXS). These superlattices tend to orient on their densest (110) superlattice planes and exhibit a significant amount of {112} twinning. The same nanocrystals deposit as monolayers with hexagonal packing, and these thin films can coexist with thicker bcc superlattice layers, even though there is no hexagonal plane in a bcc lattice. Both the preference of bcc in bulk films over the denser face-centered cubic (fcc) superlattice structure and the transition to hexagonal monolayers can be rationalized in terms of packing frustration of the ligands. A model is presented to calculate the difference in entropy associated with capping ligand packing frustration in bcc and fcc superlattices.

Role of Halides in the Ordered Structure Transitions of Heated Gold Nanocrystal Superlattices.

Dodecanethiol-capped gold (Au) nanocrystal superlattices can undergo a surprisingly diverse series of ordered structure transitions when heated (Goodfellow, B. W.; Rasch, M. R.; Hessel, C. M.; Patel, R. N.; Smilgies, D.-M.; Korgel, B. A. Nano Lett. 2013, 13, 5710-5714). These are the result of highly uniform changes in nanocrystal size, which subsequently force a spontaneous rearrangement of superlattice structure. Here, we show that halide-containing surfactants play an essential role in these transitions. In the absence of any halide-containing surfactant, superlattices of dodecanethiol-capped (1.9-nm-diameter) Au nanocrystals do not change size until reaching about 190-205 °C, at which point the gold cores coalesce. In the presence of halide-containing surfactant, such as tetraoctylphosphonium bromide (TOPB) or tetraoctylammounium bromide (TOAB), the nanocrystals ripen at much lower temperature and superlattices undergo various ordered structure transitions upon heating. Chloride- and iodide-containing surfactants induce similar behavior, destabilizing the Au-thiol bond and reducing the thermal stability of the nanocrystals.

NMR metabolomics of human lung tumours reveals distinct metabolic signatures for adenocarcinoma and squamous cell carcinoma.

Lung tumour subtyping, particularly the distinction between adenocarcinoma (AdC) and squamous cell carcinoma (SqCC), is a critical diagnostic requirement. In this work, the metabolic signatures of lung carcinomas were investigated through (1)H NMR metabolomics, with a view to provide additional criteria for improved diagnosis and treatment planning. High Resolution Magic Angle Spinning Nuclear Magnetic Resonance (NMR) spectroscopy was used to analyse matched tumour and adjacent control tissues from 56 patients undergoing surgical excision of primary lung carcinomas. Multivariate modeling allowed tumour and control tissues to be discriminated with high accuracy (97% classification rate), mainly due to significant differences in the levels of 13 metabolites. Notably, the magnitude of those differences were clearly distinct for AdC and SqCC: major alterations in AdC were related to phospholipid metabolism (increased phosphocholine, glycerophosphocholine and phosphoethanolamine, together with decreased acetate) and protein catabolism (increased peptide moieties), whereas SqCC had stronger glycolytic and glutaminolytic profiles (negatively correlated variations in glucose and lactate and positively correlated increases in glutamate and alanine). Other tumour metabolic features were increased creatine, glutathione, taurine and uridine nucleotides, the first two being especially prominent in SqCC and the latter in AdC. Furthermore, multivariate analysis of AdC and SqCC profiles allowed their discrimination with a 94% classification rate, thus showing great potential for aiding lung tumours subtyping. Overall, this study has provided new, clear evidence of distinct metabolic signatures for lung AdC and SqCC, which can potentially impact on diagnosis and provide important leads for future research on novel therapeutic targets or imaging tracers.

Following healthy pregnancy by NMR metabolomics of plasma and correlation to urine.

This work presents the first NMR metabolomics study of maternal plasma during pregnancy, including correlation between plasma and urine metabolites. The expected decrease in circulating amino acids early in pregnancy was confirmed with six amino acids being identified as required by the fetus in larger extents. Newly observed changes in citrate, lactate, and dimethyl sulfone suggested early adjustments in energy and gut microflora metabolisms. Alterations in creatine levels were also noted, in addition to creatinine variations reflecting alterations in glomerular filtration rate. Regarding plasma macromolecules, HDL and LDL+VLDL levels were confirmed to increase throughout pregnancy, although at different rates and accompanied by increases in fatty acid chain length and degree of unsaturation. Correlation studies suggested (a) an inverse relationship between lipoproteins (HDL and LDL+VLDL) and albumin, with a possible direct correlation to excreted (unassigned) pregnancy markers resonating at δ 0.55 and δ 0.63, (b) a direct link between LDL+VLDL and N-acetyl-glycoproteins, together with excreted marker at δ 0.55, and (c) correlation of plasma albumin with particular circulating and excreted metabolites. These results have unveiled specific lipoprotein/protein metabolic aspects of pregnancy with impact on the excreted metabolome and, therefore, provide an interesting lead for the further understanding of pregnancy metabolism.

Ordered structure rearrangements in heated gold nanocrystal superlattices.

Small-angle X-ray scattering (SAXS) data reveal that superlattices of organic ligand-stabilized gold (Au) nanocrystals can undergo a series of ordered structure transitions at elevated temperature. An example is presented of a body-centered cubic superlattice that evolves into a hexagonal close-packed structure, followed by the formation of binary simple cubic AB13 and hexagonal AB5 superlattices. Ultimately the superlattice decomposes at high temperature to bicontinuous domains of coalesced Au and intervening hydrocarbon. Transmission electron microscopy revealed that the ordered structure transformations result from partial ligand desorption and controlled Au nanocrystal growth during heating, which forces changes in superlattice symmetry. These observations suggest some similarity between organic ligand-coated nanocrystals and microphase-segregated diblock copolymers, where thermally induced nanophase-segregation of Au and organic ligand influences the ordered arrangements in the superlattice.

Second trimester maternal urine for the diagnosis of trisomy 21 and prediction of poor pregnancy outcomes.

Given the recognized lack of prenatal clinical methods for the early diagnosis of preterm delivery, intrauterine growth restriction, preeclampsia and gestational diabetes mellitus, and the continuing need for optimized diagnosis methods for specific chromosomal disorders (e.g., trisomy 21) and fetal malformations, this work sought specific metabolic signatures of these conditions in second trimester maternal urine, using (1)H Nuclear Magnetic Resonance ((1)H NMR) metabolomics. Several variable importance to the projection (VIP)- and b-coefficient-based variable selection methods were tested, both individually and through their intersection, and the resulting data sets were analyzed by partial least-squares discriminant analysis (PLS-DA) and submitted to Monte Carlo cross validation (MCCV) and permutation tests to evaluate model predictive power. The NMR data subsets produced significantly improved PLS-DA models for all conditions except for pre-premature rupture of membranes. Specific urinary metabolic signatures were unveiled for central nervous system malformations, trisomy 21, preterm delivery, gestational diabetes, intrauterine growth restriction and preeclampsia, and biochemical interpretations were proposed. This work demonstrated, for the first time, the value of maternal urine profiling as a complementary means of prenatal diagnostics and early prediction of several poor pregnancy outcomes.

Influence of composition on the performance of sintered Cu(In,Ga)Se2 nanocrystal thin-film photovoltaic devices.

Thin-film photovoltaic devices (PVs) were prepared by selenization using oleylamine-capped Cu(In,Ga)Se2 (CIGS) nanocrystals sintered at a high temperature (>500 °C) under Se vapor. The device performance varied significantly with [Ga]/[In+Ga] content in the nanocrystals. The highest power conversion efficiency (PCE) observed in the devices studied was 5.1 % under air mass 1.5 global (AM 1.5 G) illumination, obtained with [Ga]/[In+Ga]=0.32. The variation in PCE with composition is partly a result of bandgap tuning and optimization, but the main influence of nanocrystal composition appeared to be on the quality of the sintered films. The [Cu]/[In+Ga] content was found to be strongly influenced by the [Ga]/[In+Ga] concentration, which appears to be correlated with the morphology of the sintered film. For this reason, only small changes in the [Ga]/[In+Ga] content resulted in significant variations in device efficiency.

Mid-infrared (MIR) metabolic fingerprinting of amniotic fluid: a possible avenue for early diagnosis of prenatal disorders?

This work describes a mid-infrared (MIR) metabolic profiling study of 2nd trimester amniotic fluid in relation to selected prenatal disorders, with results focusing on fetal malformations (FM), preterm delivery (PTD) and premature rupture of membranes (PROM), the latter two conditions occurring later in pregnancy. Partial least squares-discriminant analysis (PLS-DA) models were obtained for FM and pre-PTD subject groups, supported by Monte Carlo Cross Validation (MCCV), and identified specific MIR profile changes. For pre-PROM subjects, minor changes were noted. MIR interpretation was assisted by intra- (MIR/MIR) and inter- (MIR/NMR) domain statistical correlation analysis, the results unveiling possible biomarker MIR signatures for FM and pre-PTD subjects. Biofluid MIR metabolic profiling holds enticing possibilities as a low cost, easy to use, rapid method and the results presented have shown its sensitivity to clinically diagnosed conditions such as FM, and to the pre-clinical stages of PTD. Specific improvement needs are discussed, namely regarding sample numbers and experimental reproducibility.

Following healthy pregnancy by nuclear magnetic resonance (NMR) metabolic profiling of human urine.

In this work, untargeted NMR metabonomics was employed to evaluate the effects of pregnancy on the metabolite composition of maternal urine, thus establishing a control excretory trajectory for healthy pregnancies. Urine was collected for independent groups of healthy nonpregnant and pregnant women (in first, second, third trimesters) and multivariate analysis performed on the corresponding NMR spectra. Models were validated through Monte Carlo Cross Validation and permutation tests and metabolite correlations measured through Statistical Total Correlation Spectroscopy. The levels of 21 metabolites were found to change significantly throughout pregnancy, with variations observed for the first time to our knowledge for choline, creatinine, 4-deoxyerythronic acid, 4-deoxythreonic acid, furoylglycine, guanidoacetate, 3-hydroxybutyrate, and lactate. Results confirmed increased aminoaciduria across pregnancy and suggested (a) a particular involvement of isoleucine and threonine in lipid oxidation/ketone body synthesis, (b) a relation of excreted choline, taurine, and guanidoacetate to methionine metabolism and urea cycle regulation, and (c) a possible relationship of furoylglycine and creatinine to pregnancy, based on a tandem study of nonfasting confounding effects. Results demonstrate the usefulness of untargeted metabonomics in finding biomarker metabolic signatures for healthy pregnancies, against which disease-related deviations may be confronted in future studies, as a base for improved diagnostics and prediction.

Chloroform-enhanced incorporation of hydrophobic gold nanocrystals into dioleoylphosphatidylcholine (DOPC) vesicle membranes.

Vesicles of dioleoylphosphatidylcholine (DOPC) formed by extrusion (liposomes) with hydrophobic alkanethiol-capped Au nanocrystals were studied. Dodecanethiol-capped 1.8-nm-diameter Au nanocrystals accumulate in the lipid bilayer, but only when dried lipid-nanocrystal films were annealed with chloroform prior to hydration. Without chloroform annealing, the Au nanocrystals phase separate from DOPC and do not load into the liposomes. Au nanocrystals with slightly longer capping ligands of hexadecanethiol or with a larger diameter of 4.1 nm disrupted vesicle formation and created lipid assemblies with many internal lamellar attachments.