Impact of Phyllosilicates on Amino Acid Formation Under Asteroidal Conditions V
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A Chemical Engineering Perspective on the Origins of Life
Processes 2015, 3, 309-338; doi:10.3390/pr3020309 processesOPEN ACCESS ISSN 2227-9717 www.mdpi.com/journal/processes Article A Chemical Engineering Perspective on the Origins of Life Martha A. Grover *, Christine Y. He, Ming-Chien Hsieh and Sheng-Sheng Yu School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Dr. NW, Atlanta, GA 30032, USA; E-Mails: [email protected] (C.Y.H.); [email protected] (M.-C.H.); [email protected] (S.-S.Y.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-404-894-2878 or +1-404-894-2866. Academic Editor: Michael Henson Received: 29 January 2015 / Accepted: 19 April 2015 / Published: 5 May 2015 Abstract: Atoms and molecules assemble into materials, with the material structure determining the properties and ultimate function. Human-made materials and systems have achieved great complexity, such as the integrated circuit and the modern airplane. However, they still do not rival the adaptivity and robustness of biological systems. Understanding the reaction and assembly of molecules on the early Earth is a scientific grand challenge, and also can elucidate the design principles underlying biological materials and systems. This research requires understanding of chemical reactions, thermodynamics, fluid mechanics, heat and mass transfer, optimization, and control. Thus, the discipline of chemical engineering can play a central role in advancing the field. In this paper, an overview of research in the origins field is given, with particular emphasis on the origin of biopolymers and the role of chemical engineering phenomena. A case study is presented to highlight the importance of the environment and its coupling to the chemistry. -
Microbial and Chemical Analysis of Non-Saccharomyces Yeasts from Chambourcin Hybrid Grapes for Potential Use in Winemaking
fermentation Article Microbial and Chemical Analysis of Non-Saccharomyces Yeasts from Chambourcin Hybrid Grapes for Potential Use in Winemaking Chun Tang Feng, Xue Du and Josephine Wee * Department of Food Science, The Pennsylvania State University, Rodney A. Erickson Food Science Building, State College, PA 16803, USA; [email protected] (C.T.F.); [email protected] (X.D.) * Correspondence: [email protected]; Tel.: +1-814-863-2956 Abstract: Native microorganisms present on grapes can influence final wine quality. Chambourcin is the most abundant hybrid grape grown in Pennsylvania and is more resistant to cold temperatures and fungal diseases compared to Vitis vinifera. Here, non-Saccharomyces yeasts were isolated from spontaneously fermenting Chambourcin must from three regional vineyards. Using cultured-based methods and ITS sequencing, Hanseniaspora and Pichia spp. were the most dominant genus out of 29 fungal species identified. Five strains of Hanseniaspora uvarum, H. opuntiae, Pichia kluyveri, P. kudriavzevii, and Aureobasidium pullulans were characterized for the ability to tolerate sulfite and ethanol. Hanseniaspora opuntiae PSWCC64 and P. kudriavzevii PSWCC102 can tolerate 8–10% ethanol and were able to utilize 60–80% sugars during fermentation. Laboratory scale fermentations of candidate strain into sterile Chambourcin juice allowed for analyzing compounds associated with wine flavor. Nine nonvolatile compounds were conserved in inoculated fermentations. In contrast, Hanseniaspora strains PSWCC64 and PSWCC70 were positively correlated with 2-heptanol and ionone associated to fruity and floral odor and P. kudriazevii PSWCC102 was positively correlated with a Citation: Feng, C.T.; Du, X.; Wee, J. Microbial and Chemical Analysis of group of esters and acetals associated to fruity and herbaceous aroma. -
Prebiotic Chemistry: Geochemical Context and Reaction Screening
Life 2013, 3, 331-345; doi:10.3390/life3020331 OPEN ACCESS life ISSN 2075-1729 www.mdpi.com/journal/life Article Prebiotic Chemistry: Geochemical Context and Reaction Screening Henderson James Cleaves II Earth Life Science Institute, Tokyo Institute of Technology, Institute for Advanced Study, Princeton, NJ 08540, USA; E-Mail: [email protected] Received: 12 April 2013; in revised form: 17 April 2013 / Accepted: 18 April 2013 / Published: 29 April 2013 Abstract: The origin of life on Earth is widely believed to have required the reactions of organic compounds and their self- and/or environmental organization. What those compounds were remains open to debate, as do the environment in and process or processes by which they became organized. Prebiotic chemistry is the systematic organized study of these phenomena. It is difficult to study poorly defined phenomena, and research has focused on producing compounds and structures familiar to contemporary biochemistry, which may or may not have been crucial for the origin of life. Given our ignorance, it may be instructive to explore the extreme regions of known and future investigations of prebiotic chemistry, where reactions fail, that will relate them to or exclude them from plausible environments where they could occur. Come critical parameters which most deserve investigation are discussed. Keywords: chemical evolution; prebiotic organic reactions-prebiotic reactions in the aqueous phase; prebiotic reactions in the solid state; energy sources on the primitive Earth; mineral catalysis 1. Introduction Prebiotic chemistry is the study of how organic compounds formed and self-organized for the origin of life on Earth and elsewhere [1]. -
Formose Reaction Controlled by a Copolymer of N,N-Dimethylacrylamide and 4-Vinylphenylboronic Acid
polymers Article Formose Reaction Controlled by a Copolymer of N,N-Dimethylacrylamide and 4-Vinylphenylboronic Acid Tomohiro Michitaka, Toru Imai and Akihito Hashidzume * ID Department of Macromolecular Science, Graduate School of Science, Osaka University, Osaka 560-0043, Japan; [email protected] (T.M.); [email protected] (T.I.) * Correspondence: [email protected]; Tel.: +81-6-6850-8174 Received: 8 October 2017; Accepted: 24 October 2017; Published: 25 October 2017 Abstract: The formose reaction is an oligomerization of formaldehyde under basic conditions, which produces a complicated mixture of monosaccharides and sugar alcohols. Selective formation of useful monosaccharides by the formose reaction has been an important challenge. In this study, we have investigated the formose reaction controlled by N,N-dimethylacrylamide/4-vinylphenylboronic acid copolymer (pDMA/VBA) and phenylboronic acid (PBA) because boronic acid compounds form esters with polyols, e.g., monosaccharides and sugar alcohols. We obtained time–conversion data in the presence of these boronic acid compounds, and characterized the products by liquid chromatography-mass spectroscopy and NMR measurements. pDMA/VBA and PBA decelerated the formose reaction because of the formation of boronic acid esters with products. It is noteworthy that the formose reaction in the presence of pDMA/VBA and PBA formed favorably six- and seven-carbon branched monosaccharides and sugar alcohols. Keywords: formose reaction; boronic acid compounds; N,N-dimethylacrylamide/4-vinylphenyl boronic acid copolymer; phenylboronic acid; monosaccharides; sugar alcohols 1. Introduction Carbohydrates are ubiquitous in our life and very important biological materials [1,2]. Carbohydrates can be divided into three categories based on their molecular weight; (1) low molecular weight saccharides, e.g., monosaccharides and disaccharides, (2) oligosaccharides, and (3) polysaccharides. -
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars Jakob L Andersen1,4, Christoph Flamm2*, Daniel Merkle1* and Peter F Stadler2,3,4,5,6,7
Andersen et al. Journal of Systems Chemistry 2013, 4:4 http://www.jsystchem.com/content/4/1/4 RESEARCH ARTICLE Open Access Inferring chemical reaction patterns using rule composition in graph grammars Jakob L Andersen1,4, Christoph Flamm2*, Daniel Merkle1* and Peter F Stadler2,3,4,5,6,7 Abstract Background: Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach to modeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like merging, splitting, and isomerisation of molecules. It is often convenient, in particular in the analysis of larger systems, to summarize several subsequent reactions into a single composite chemical reaction. Results: We introduce a generic approach for composing graph grammar rules to define a chemically useful rule compositions. We iteratively apply these rule compositions to elementary transformations in order to automatically infer complex transformation patterns. As an application we automatically derive the overall reaction pattern of the Formose cycle, namely two carbonyl groups that can react with a bound glycolaldehyde to a second glycolaldehyde. Rule composition also can be used to study polymerization reactions as well as more complicated iterative reaction schemes. Terpenes and the polyketides, for instance, form two naturally occurring classes of compounds of utmost pharmaceutical interest that can be understood as “generalized polymers” consisting of five-carbon (isoprene) and two-carbon units, respectively. Conclusion: The framework of graph transformations provides a valuable set of tools to generate and investigate large networks of chemical networks. Within this formalism, rule composition is a canonical technique to obtain coarse-grained representations that reflect, in a natural way, “effective” reactions that are obtained by lumping together specific combinations of elementary reactions. -
Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Harvard University - DASH Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. Citation Rappoport, Dmitrij, Cooper J. Galvin, Dmitry Zubarev, and Alán Aspuru-Guzik. 2014. “Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.” Journal of Chemical Theory and Computation 10 (3) (March 11): 897–907. Published Version doi:10.1021/ct401004r Accessed February 19, 2015 5:14:37 PM EST Citable Link http://nrs.harvard.edu/urn-3:HUL.InstRepos:12697373 Terms of Use This article was downloaded from Harvard University's DASH repository, and is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#OAP (Article begins on next page) Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry Dmitrij Rappoport,∗,† Cooper J Galvin,‡ Dmitry Yu. Zubarev,† and Alán Aspuru-Guzik∗,† Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA, and Pomona College, 333 North College Way, Claremont, CA 91711, USA E-mail: [email protected]; [email protected] Abstract While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for mod- eling complex structures and large-scale chemical systems. Here we present heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in metabolism and prebiotic chemistry. -
The Power of Crowding for the Origins of Life
Orig Life Evol Biosph (2014) 44:307–311 DOI 10.1007/s11084-014-9382-5 ORIGIN OF LIFE The Power of Crowding for the Origins of Life Helen Greenwood Hansma Received: 2 October 2014 /Accepted: 2 October 2014 / Published online: 14 January 2015 # Springer Science+Business Media Dordrecht 2015 Abstract Molecular crowding increases the likelihood that life as we know it would emerge. In confined spaces, diffusion distances are shorter, and chemical reactions produce fewer and more regular products. Crowding will occur in the spaces between Muscovite mica sheets, which has many advantages as a site for life’s origins. Keywords Muscovite mica . Molecular crowding . Origin of life . Mechanochemistry. Abiogenesis . Chemical confinement effects . Chirality. Protocells Cells are crowded. Protein molecules in cells are typically so close to each other that there is room for only one protein molecule between them (Phillips, Kondev et al. 2008). This is nothing like a dilute ‘prebiotic soup.’ Therefore, by analogy with living cells, the origins of life were probably also crowded. Molecular Confinement Effects Many chemical reactions are limited by the time needed for reactants to diffuse to each other. Shorter distances speed up these reactions. Molecular complementarity is another principle of life in which pairs or groups of molecules form specific interactions (Root-Bernstein 2012). Current examples are: enzymes & substrates & cofactors; nucleic acid base pairs; antigens & antibodies; nucleic acid - protein interactions. Molecular complementarity is likely to have been involved at life’s origins and also benefits from crowding. Mineral surfaces are a likely place for life’s origins and for formation of polymeric molecules (Orgel 1998). -
4 Carbohydrates
Basic classes of biomolecules • Aminoacids • Lipids • Carbohydrates (sugars) • Nucleobases • Nucleosides (sugar+nucleobase) Nucleotides - components Phosphates and the prebiotic synthesis of oligonucleotides Activated ribonucleotides in the potentially prebiotic assembly of RNA. Potential P–O bond forming polymerization chemistry is indicated by the curved arrows. Phosphorylation reagents DAP M. A. Pasek, et al. Angew. Chem. Int. Ed. 2008, 47, 7918-7920 A. Eschenmoser, et al. Orig. Life Evol. Biosph. 1999, 29, 333-354 Phosphorylation reagents DAP M. A. Pasek, et al. Angew. Chem. Int. Ed. 2008, 47, 7918-7920 A. Eschenmoser, et al. Orig. Life Evol. Biosph. 1999, 29, 333-354 Phosphorylation of sugars A. Eschenmoser, et al. Angew. Chem. Int. Ed. 2000, 39, 2281-2285 Phosphorylation of sugars A. Eschenmoser, et al. Angew. Chem. Int. Ed. 2000, 39, 2281-2285 Nucleosides - nucleobases + sugars Carbohydrates Formose reaction Alexander Butlerov (1828-1886) St. Petersburg, Kazan, Russia The reaction begins with two formaldehyde molecules condensing to make glycolaldehyde 1 which further reacts in an aldol reaction with another equivalent of formaldehyde to make glyceraldehyde 2. An aldose-ketose isomerization of 2 forms dihydroxyacetone 3 which can Ronald Breslow (1931-) react with 1 to form ribulose 4, and through another isomerization ribose 5. Molecule 3 also Columbia University, USA can react with formaldehyde to produce tetrulose 6 and then aldoltetrose 7. Molecule 7 can split into 2 in a retro-aldol reaction. Formaldehyde condensation Aldol -
Gravitational Influence on Human Living Systems and the Evolution Of
molecules Review Gravitational Influence on Human Living Systems and the Evolution of Species on Earth Konstantinos Adamopoulos 1 , Dimitrios Koutsouris 1 , Apostolos Zaravinos 2,* and George I. Lambrou 1,3,* 1 School of Electrical and Computer Engineering, Biomedical Engineering Laboratory, National Technical University of Athens, Heroon Polytechneiou 9, Zografou, 15780 Athens, Greece; [email protected] (K.A.); [email protected] (D.K.) 2 Department of Life Sciences, School of Sciences, European University Cyprus, 1516 Nicosia, Cyprus 3 First Department of Pediatrics, Choremeio Research Laboratory, National and Kapodistrian University of Athens, Thivon & Levadeias 8, Goudi, 11527 Athens, Greece * Correspondence: [email protected] (A.Z.); [email protected] (G.I.L.); Tel.: +357-22713043 (A.Z.); +30-210-7467427 (G.I.L.) Abstract: Gravity constituted the only constant environmental parameter, during the evolutionary period of living matter on Earth. However, whether gravity has affected the evolution of species, and its impact is still ongoing. The topic has not been investigated in depth, as this would require frequent and long-term experimentations in space or an environment of altered gravity. In addition, each organism should be studied throughout numerous generations to determine the profound biological changes in evolution. Here, we review the significant abnormalities presented in the cardiovascular, immune, vestibular and musculoskeletal systems, due to altered gravity conditions. We also review the impact that gravity played in the anatomy of snakes and amphibians, during their evolution. Overall, it appears that gravity does not only curve the space–time continuum but the biological Citation: Adamopoulos, K.; continuum, as well. Koutsouris, D.; Zaravinos, A.; Lambrou, G.I. -
Openchrom: a Cross-Platform Open Source Software for the Mass Spectrometric Analysis of Chromatographic Data Philip Wenig*, Juergen Odermatt
Wenig and Odermatt BMC Bioinformatics 2010, 11:405 http://www.biomedcentral.com/1471-2105/11/405 SOFTWARE Open Access OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data Philip Wenig*, Juergen Odermatt Abstract Background: Today, data evaluation has become a bottleneck in chromatographic science. Analytical instruments equipped with automated samplers yield large amounts of measurement data, which needs to be verified and analyzed. Since nearly every GC/MS instrument vendor offers its own data format and software tools, the consequences are problems with data exchange and a lack of comparability between the analytical results. To challenge this situation a number of either commercial or non-profit software applications have been developed. These applications provide functionalities to import and analyze several data formats but have shortcomings in terms of the transparency of the implemented analytical algorithms and/or are restricted to a specific computer platform. Results: This work describes a native approach to handle chromatographic data files. The approach can be extended in its functionality such as facilities to detect baselines, to detect, integrate and identify peaks and to compare mass spectra, as well as the ability to internationalize the application. Additionally, filters can be applied on the chromatographic data to enhance its quality, for example to remove background and noise. Extended operations like do, undo and redo are supported. Conclusions: OpenChrom is a software application to edit and analyze mass spectrometric chromatographic data. It is extensible in many different ways, depending on the demands of the users or the analytical procedures and algorithms. It offers a customizable graphical user interface. -
(GC–GC/MS and GC/MS) Workflows
G Model CHROMA-358514; No. of Pages 10 ARTICLE IN PRESS Journal of Chromatography A, xxx (2017) xxx–xxx Contents lists available at ScienceDirect Journal of Chromatography A j ournal homepage: www.elsevier.com/locate/chroma Full length article Optimizing targeted/untargeted metabolomics by automating gas chromatography/mass spectrometry (GC–GC/MS and GC/MS) workflows a,∗ a b b Albert Robbat Jr. , Nicole Kfoury , Eugene Baydakov , Yuriy Gankin a Department of Chemistry, Tufts University, 200 Boston Ave, Suite G700, Medford, MA, 02155, United States b EPAM Systems, 41 University Drive, Newtown, PA 18940, United States a r t i c l e i n f o a b s t r a c t Article history: New database building and MS subtraction algorithms have been developed for automated, sequential Received 26 January 2017 two-dimensional gas chromatography/mass spectrometry (GC–GC/MS). This paper reports the first use Received in revised form 20 April 2017 of a database building tool, with full mass spectrum subtraction, that does not rely on high resolution Accepted 5 May 2017 MS data. The software was used to automatically inspect GC–GC/MS data of high elevation tea from Available online xxx Yunnan, China, to build a database of 350 target compounds. The database was then used with spectral deconvolution to identify 285 compounds by GC/MS of the same tea. Targeted analysis of low elevation Keywords: tea by GC/MS resulted in the detection of 275 compounds. Non-targeted analysis, using MS subtraction, Annotated database building yielded an additional eight metabolites, unique to low elevation tea. -
Sardine Roe As a Source of Lipids to Produce Liposomes Marta Guedes, Ana Rita Costa-Pinto, Virgínia Gonçalves, Joana Moreira- Silva, Maria Tiritan, Rui L
Subscriber access provided by UNIV OF NEBRASKA - LINCOLN Controlled Release and Delivery Systems Sardine roe as a source of lipids to produce liposomes Marta Guedes, Ana Rita Costa-Pinto, Virgínia Gonçalves, Joana Moreira- Silva, Maria Tiritan, Rui L. Reis, Helena Ferreira, and Nuno M. Neves ACS Biomater. Sci. Eng., Just Accepted Manuscript • DOI: 10.1021/ acsbiomaterials.9b01462 • Publication Date (Web): 07 Jan 2020 Downloaded from pubs.acs.org on January 10, 2020 Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.