Early Life Relict Feature in Peptide Mass Distribution

Molecular mass of a biomolecule is characterized in mass spectroscopy by the monoisitopic mass M~mono~ and the average isotopic mass M~av~. We found that peptide masses mapped on a plane made by two parameters derived from M~mono~ and M~av~ form a peculiar global feature in form of a band-gap 5-7 ppm wide stretching across the whole peptide galaxy, with a narrow (FWHM 0.2 ppm) line in the centre. The a priori probability of such a feature to emerge by chance is less than 1:100. Peptides contributing to the central line have elemental compositions following the rules S=0; Z = (2C - N - H)/2 =0, which nine out of 20 amino acid residues satisfy. The relative abundances of amino acids in the peptides contributing to the central line correlate with the consensus order of emergence of these amino acids, with ancient amino acids being overrepresented in on-line peptides. Thus the central line is a relic of ancient life, and likely a signature of its emergence in abiotic synthesis. The linear correlation between M~av~ and M~mono~ reduces the complexity of polypeptide molecules, which may have increased the rate of their abiotic production. This, in turn may have influenced the selection of these amino acid residues for terrestrial life. Assuming the line feature is not spurious, life has emerged from elements with isotopic abundances very close to terrestrial levels, which rules out most of the Galaxy

Early life relict feature in peptide mass distribution

The molecular mass of a biomolecule is characterized by the monoisitopic mass Mmono and the average isotopic mass Mav. We found that tryptic peptide masses mapped on a plane made by two parameters derived from Mmono and Mav form a peculiar feature in the form of a 'band gap' stretching across the whole 'peptide galaxy', with a narrow line in the centre. The purpose of this study was to investigate possible reasons for the emergence of such a feature, provided it is not a random occurrence. The a priori probability of such a feature to emerge by chance was found to be less than 1:100. Peptides contributing to the central line have elemental compositions following the rules S = 0; Z = C - (N + H)/2 = 0, which nine out of 20 amino acid residues satisfy. The relative abundances of amino acids in the peptides contributing to the central line correlate with the consensus order of emergence of these amino acids, with ancient amino acids being overrepresented in on-Line peptides. Since linear correlation between Mav and Mmono reduces the complexity of polypeptide molecules, and the turnover rate of less complex molecules should be faster in non-equilibrium abiotic synthesis, we hypothesize that the line could be a signature of abiotic production of primordial biopolymers. The linear dependence between the average isotopic masses and monoisotopic masses may have influenced the selection of amino acid residues for terrestrial life. © 2010 Versita Warsaw and Springer-Verlag Berlin Heidelberg.link_to_subscribed_fulltex

Nano-LC-orbitrap MS/MS-based quantitative proteomics and transpcriptomics for uncovering the mechanisms of action of rosemary bioactives in colon cancer: a new foodomics approach

Resumen del trabajo presentado al 43rd Annual North American Meeting of the Federation of Analytical Chemistry and Spectroscopy Societies: "Great Scientific Exchange", celebrado en Minneapolis, Minnesota (USA) del 18 al 23 de septiembre de 2016.Recently, Foodomics has demonstrated to be a useful strategy to cover the identification of a wide range of molecular changes induced by rosemary compounds in in vitro cell models. Comprehensive transcriptomic and metabolomic analyses helped on identifying global changes induced by rosemary polyphenols on different cancer cell lines. In this work, a proteomics strategy based on nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) using an Orbitrap high-resolution mass spectrometer together with stable isotope dimethyl labeling (DML) is applied to quantitatively examine relative changes in the protein fraction of human colon cancer cells treated with different concentrations of rosemary polyphenols (carnosic acid, carnosol, and a polyphenol-enriched rosemary extract) over the time. This proteomics approach provided extra confirmation for microarray data and new valuable data that allows gaining more insight into the biological processes orchestrating the response of HT-29 cells to rosemary polyphenols exposure. In addition, the causal analytic tool, UR analysis, based on IPA algorithm and Ingenuity Knowledge Base, helped on elucidating the upstream regulatory molecules and associated mechanism to the observed protein changes. Furthermore, examination of our data revealed that each rosemary polyphenol affects protein homeostasis by different mechanisms. Carnosic acid treatment induced the expression of proteins involved in the unfolded protein response in a concentration dependent manner reflecting accumulation of misfolded proteins in the endoplasmic reticulum (ER), whereas carnosol directly inhibits chymotrypsin-like activity of the 20S proteasome. The presented unbiased proteome-wide approach has shown to be a powerful tool that reveals differences in the mechanisms of action of two related bioactive diterpenes against colon cancer cells proliferation.Peer Reviewe

Nano-liquid chromatography-orbitrap ms-based quantitative proteomics reveals differences between the mechanisms of action of carnosic acid and carnosol in colon cancer cells

Carnosic acid (CA) and carnosol (CS) are two structurally related diterpenes present in rosemary herb (Rosmarinus officinalis). Although several studies have demonstrated that both diterpenes can scavenge free radicals and interfere in cellular processes such as cell proliferation, they may not necessarily exert the same effects at the molecular level. In this work, a shotgun proteomics study based on stable isotope dimethyl labeling (DML) and nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) has been performed to identify the relative changes in proteins and to gain some light on the specific molecular targets and mechanisms of action of CA and CS in HT-29 colon cancer cells. Protein profiles revealed that CA and CS induce different Nrf2-mediated response. Furthermore, examination of our data revealed that each diterpene affects protein homeostasis by different mechanisms. CA treatment induces the expression of proteins involved in the unfolded protein response in a concentration dependent manner reflecting ER stress, whereas CS directly inhibits chymotrypsin-like activity of the 20S proteasome. In conclusion, the unbiased proteomics-wide method applied in the present study has demonstrated to be a powerful tool to reveal differences on the mechanisms of action of two related bioactive compounds in the same biological model.This work was supported by the project AGL2014-53609-P (Ministerio de Economía y Competitividad, Spain) and S2013/ABI-2728 (Comunidad de Madrid). A.V. thanks the Ministerio de Economía y Competitividad for his FPI pre-doctoral fellowship (BES-2012-057014). The Swedish Research Council (2011-4423 and 2015-4870; J.B.) is acknowledged for financial support.Peer Reviewe

N-Terminal Tagging Strategy for De Novo Sequencing of Short Peptides by ESI-MS/MS and MALDI-MS/MS

The major portion of skin secretory peptidome of the European Tree frog Hyla arborea consists of short peptides from tryptophyllin family. It is known that b-ions of these peptides undergo head-to-tail cyclization, forming a ring that can open, resulting in several linear forms. As a result, the spectrum contains multiple ion series, thus complicating de novo sequencing. This was observed in the Q-TOF spectrum of one of the tryptophyllins isolated from Hyla arborea; the sequence FLPFFP-NH2 was established by Edman degradation and counter-synthesis. Though no rearrangements were observed in FTICR-MS and MALDI-TOF/TOF spectra, both of them were not suitable for mass-spectrometry sequencing due to the low sequence coverage. To obtain full amino acid sequence by mass spectrometry, three chemical modifications to N-terminal amino moiety were applied. They include acetylation and sulfobenzoylation of N-amino group and its transformation to 2,4,6-trimethylpyridinium by interaction with 2,4,6-trimethylpyrillium tetrafluoroborate. All three reagents block scrambling and provide spectra better than the intact peptide. Unfortunately, all of them also readily react with lysine side chain. Hence, all investigated procedures can be used to improve sequencing of short peptides, while acetylation is the recommended one. It shows excellent results, and it is plain and simple to perform. This is the procedure of choice for MS-sequencing of short peptides by manual or automatic algorithms

Future orientation’s association with academic achievement

Šī pētījuma mērķis bija noskaidrot vai pastāv orientācijas uz nākotni saistība ar akadēmiskiem sasniegumiem. Pētījumā piedalījās 60 studējošie indivīdi (42 sievietes un 18 vīrieši), vecumā no 20 līdz 38 (vidējais vecums M=22,42). Lai mērītu dalībnieku orientāciju uz laiku tika izmantota Aleksandra Koļesova izstrādātā aptauja par nākotnes laika perspektīvu, kas balstās uz Seginer, Vermulst un Shoyer (2004) modeli. Lai noteiktu saistību starp orientāciju uz nākotni un akadēmiskiem sasniegumiem šī aptauja tika papildināta ar jautājumiem par indivīdu akadēmiskiem sasniegumiem. Pētījuma rezultāti paradīja, ka orientāciju uz nākotni ir saistīta ar akadēmiskiem sasniegumiem. Taču augstāka orientācija uz nākotni neprognozē augstākus akadēmiskos sasniegumus regresijas modelī.The aim of this study was to find whether there is relevance between future orientation and academic achievements. 60 students participated in the study (42 females and 18 male) aged 20 to 38 (average age M = 22.42). Future orientation was measured by a questionnaire developed by A. Koļesovs on the basis of the model of Seginer, Vermulst, and Shoyer (2004). In order to determine the relationship between future time orientation and academic achievements, this survey was supplemented with questions about academic achievements. The results of the study showed that future time orientation is related to academic achievement. However, higher future orientation does not predict higher academic achievements within a regression model

Comprehensive Proteomic Study of the Antiproliferative Activity of a Polyphenol-Enriched Rosemary Extract on Colon Cancer Cells Using Nanoliquid Chromatography–Orbitrap MS/MS

In this work, a proteomics strategy based on nanoliquid chromatography–tandem mass spectrometry (nano-LC–MS/MS) using an Orbitrap high-resolution mass spectrometer together with stable isotope dimethyl labeling (DML) is applied to quantitatively examine relative changes in the protein fraction of HT-29 human colon cancer cells treated with different concentrations of a polyphenol-enriched rosemary extract over the time. The major objective of this study was to gain insights into the antiproliferative mechanisms induced by rosemary polyphenols. Using this methodology, 1909 and 698 proteins were identified and quantified in cell extracts. The polyphenol-enriched rosemary extract treatment changed the expression of several proteins in a time- and concentration-dependent manner. Most of the altered proteins are implicated in the activation of Nrf2 transcription factor and the unfolded protein response. In conclusion, rosemary polyphenols induced proteomic changes that were related to the attenuation of aggresome formation and activation of autophagy to alleviate cellular stress

Signaling in Insulin-Secreting MIN6 Pseudoislets and Monolayer Cells.

Cell-cell interactions are of fundamental importance for cellular function. In islets of Langerhans, which control blood glucose levels by secreting insulin in response to the blood glucose concentration, the secretory response of intact islets is higher than that of insulin-producing beta-cells not arranged in the islet architecture. The objective was to define mechanisms by which cellular performance is enhanced when cells are arranged in three-dimensional space. The task was addressed by making a comprehensive analysis based on protein expression patterns generated from insulin-secreting MIN6 cells grown as islet-like clusters, so-called pseudoislets, and in monolayers. After culture, glucose-stimulated insulin secretion (GSIS) was measured from monolayers and pseudoislets. GSIS rose 6-fold in pseudoislets but only 3-fold in monolayers when the glucose concentration was increased from 2 to 20 mmol/L. Proteins from pseudoislets and monolayers were extracted and analyzed by liquid-chromatography mass spectrometry, and differentially expressed proteins were mapped onto KEGG pathways. Protein profiling identified 1576 proteins, which were common to pseudoislets and monolayers. When mapped onto KEGG pathways, 11 highly enriched pathways were identified. On the basis of differences in expression of proteins belonging to the pathways in pseudoislets and monolayers, predictions of differential pathway activation were performed. Mechanisms enhancing insulin secretory capacity of the beta-cell, when situated in the islet, include pathways regulating glucose metabolism, cell interaction, and translational regulation