DOCSLIB.ORG

Databases and Identification D

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Databases and Identification D SESSION III – DATABASES “Databases and Identification” Prof. Jacques Vervoort BRAMA training for technicians – Module I, Rome For more information see http://fiehnlab.ucdavis.edu To be a master of spectra you need to be a master of structures in the first place. 765 100 OH N NH O O 50 N 807 747 O 705 O N O HO O O O 676 723 604 265 353 395 455 513 538 636 0 260 310 360 410 460 510 560 610 660 710 760 810 (nist_msms) Vincristine Complex MS data interpretations only possible with software MS data obtained by hyphenated techniques (GC-MS, LC-MS) Mass spectral database search and structure search routinely are used Mass spectrometers deliver multidimensional data 2 BRAMA training for technicians – Module I, Rome Be prepared – visualize your structures Try Marvin Space via Webstart 3 BRAMA training for technicians – Module I, Rome Organic Chemistry Reminder Molecular Formula C3H7F 47 100 F 50 61 27 41 13 19 33 59 0 4 10BRAMA20 training30 40 for50 technicians60 70 – Module I, Rome (mainlib) Propane, 2-fluoro- Be prepared - StereoIsomers How many stereoisomers can you expect from glucose ( KEGG )? O OH HO HO OH OH Glucose 5 BRAMAExample training calculated for technicians with MarvinView – Module I, Rome(via JAVA Webstart ) Be prepared – Tautomers How many tautomers can you expect? Important for mass spectral interpretations. O CH 3 H3C O Methyl acetate Example calculated with MarvinView Start via WebStart 6 BRAMA training for technicians – Module I, Rome Be prepared – Resonance (electron shifts) What are possible resonant structures? Important for mass spectral interpretation (electron impact, electrospray) OH Phenol Example calculated with MarvinView Start via WebStart 7 BRAMA training for technicians – Module I, Rome Structure search – know what could be possible How many compounds (isomer structures) are found in public databases? http://www.chemspider.com/ 8 BRAMA training for technicians – Module I, Rome H3 H3 Chemical Structure Handling C C H O H3 C O C C H H 3 O 3 C C H H Moronic Acid - CID: 489941 Most common structure formats you need to know: 3 3 SMILES /SMARTS - Simplified Molecular Input Line Entry Specification SDF /MOL - Structure Data File InChI /InChIkey - IUPAC In ternational Ch emical Identifier PDB - Protein Data Bank CML - Chemical Markup Language Some problems: • Data format needs to be based on Open Standard (problem with SMILES, ok with CML) • Stereo and aromatic bond information needs to be saved (ok with SDF) • Format needs to be small in space for millions of compounds (ok with SMILES) • SMILES notation needs to be unique (problem with SMILES) • Structure representation should be portable and based on Open Standard (ok with CML) 9 BRAMA training for technicians – Module I, Rome Chemical Structure Identifiers CH 3 N N O Structure Identifiers are needed for uniquely identifying structures Important for searching chemical structures in text and databases N N CH 3 H C 3 O Structure Name – IUPAC name or common name 1,3,7-trimethylpurine-2,6-dione CAS RN – Chemical Abstracts identifier 58-08-2 PubChem ID – PubChem Compound ID CID: 2519 InChIKey – Short representation of InChI InChiKey= RYYVLZVUVIJVGH -UHFFFAOYAW InChI – IUPAC In ternational Ch emical Identifier InChI=1/C8H10N4O2/c1-10-4-9-6- 5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3 10 BRAMA training for technicians – Module I, Rome SMILES structure format Positive: Good for storing structures in single line Fast text based search possible; human readable Negative: Many different SMILES codes exist SMILES for same structure can be different (canonical or unique SMILES needed) CH 3 C N N O HC N N CC CH 3 H C 3 O CCC InChI=1/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3 CCCC All those SMILES codes represent caffeine [c]1([n+]([CH3])[c]([c]2([c]([n+]1[CH3])[n][cH][n+]2[CH3]))[O-])[O-] CCCCO CN1C(=O)N(C)C(=O)C(N(C)C=N2)=C12 Cn1cnc2n(C)c(=O)n(C)c(=O)c12 Cn1cnc2c1c(=O)n(C)c(=O)n2C CCCCN N1(C)C(=O)N(C)C2=C(C1=O)N(C)C=N2 O=C1C2=C(N=CN2C)N(C(=O)N1C)C CN1C=NC2=C1C(=O)N(C)C(=O)N2C Caffeine SMILES Source InChiI FAQ 11 BRAMA training for technicians – Module I, Rome SDF/MOL structure format Positive: established standard format; good for storing structures safely can store 3D structure; can store metadata (boiling points, toxicity, mass spectra) Negative: large file size, need compression OpenBabel02240823422D 1 0 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 M END $$$$ OpenBabel02240823422D 2 1 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 1 2 1 0 0 0 M END $$$$ OpenBabel02240823422D Creator 3 2 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 Coordinates for 3D 0.0000 0.0000 0.0000 C 0 0 0 0 0 1 2 1 0 0 0 2 3 1 0 0 0 Connection of atoms M END $$$$ 12 BRAMA training for technicians – Module I, Rome Molecules and mass spectra Close relationship between molecular structure and mass spectra Molecular structure is reflected in mass spectral features (peaks, peak heights and peak combinations) Mass spectra reflect a state of gas phase ion physics and chemistry (rearrangements, fragmentations, bond cleavages) 130 130 130 100 100 100 73 73 Si N Si 73 NH O Si N Si 50 50 50 59 145 45 58 45 114 59 147 29 84 100 145 29 86 100 114 46 91 105 160 0 0 0 20 40 60 80 100 120 140 160 20 40 60 80 100 120 140 160 20 40 60 80 100 120 140 160 (mainlib) tert-Butylaminotrimethylsilane (mainlib) N,N-Diethyl-1,1,1-trimethylsilylamine (replib) Silanamine, N,1,1,1-tetramethyl-N-[1-methyl-2-phenyl-2-[(trimethylsilyl)oxy]ethyl]-, [S-(R*,R*)]- 13 BRAMAElectron impact training (70 eV) for mass technicians spectra; Source: NIST0– Module5 I, Rome Molecules and mass spectra Similar structures may or may have not similar mass spectra 130 100 Si N 73 O 50 Si 59 147 47 91 105 114 163 179 188 204 220 294 0 65 163 206 59 91 102 132 280 147 179 Si N O 44 50 Si 100 73 116 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 Silanamine, N,1,1,1-tetramethyl-N-[1-methyl-2-phenyl-2-[(trimethylsilyl)oxy]ethyl]-, [S-(R*,R*)]-N-Methylphenylethanolamine, bis(trimethylsilyl)- Electron impact (70 eV) mass spectra; Source: NIST05; Created using structure similarity search in NIST MS Search program 14 BRAMA training for technicians – Module I, Rome Molecules and mass spectra Similar mass spectra may or may have not similar structures 43 100 55 70 83 97 50 29 111 27 125 196 15 65 140 154 168 0 32 153 139 168 196 27 125 111 29 50 97 41 69 83 100 55 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 1-Tetradecene Cyclotetradecane Electron impact (70 eV) mass spectra; Source: NIST05; Created using spectral similarity search in NIST MS Search program 15 BRAMA training for technicians – Module I, Rome Mass spectral databases I Name Spectra count Type NIST05 200,000 electron impact spectra (EI 70 eV) Wiley 8 400,000 electron impact spectra (EI 70 eV) Palisade 600K 600,000 electron impact spectra (EI 70 eV) NIST MS/MS 5,200 MS/MS (ESI, +/-, 30-100V CID) MassFrontier 7,000 MS n, ESI, (Spectral Tree Library ) Important is data quality Annotation with CAS and Structure and Formula Link to literature or publication useful Currently no large ESI,APPI,APCI libraries available (free or commercial) 16 BRAMA training for technicians – Module I, Rome Mass spectral databases II 272 Smaller specialized libraries 100 Cl Cl Pfleger Maurer Weber (Drugs) MS+RI, 70eV Cl Cl Cl Cl Cl MassFinder (Volatiles) MS+RI, 70eV 50 237 Cl Cl RIZA DB (Toxicants) MS+RI, 70eV Cl Cl Cl 332 Golm DB (primary Metabolites) MS+RI, 70eV 404 0 230 250 270 290 310 330 350 370 390 410 430 450 Fiehnlib (primary Metabolites) MS+RI, 70eV (riza_web) |RI|2583|KEY|1596|CAS|2385-85-5|FRML|Empty|CMPD|Mirex| MassBank (Metabolites) ESI, MS n , accurate masses AAFS (Drugs, Forensic,Toxicology), MS+RI, 70eV ChemicalSoft (Drugs), MS/MS, MS E _____________________________________________________________ In case of electron impact (EI) same GC-Column (DB-5, RTX-5, DB-1, OV-1) and temperature program must be used for matching retention indices In case of ESI, APPI spectra (LC-MS) same mass spectrometer design and setup should be used (triple-quad, ion-trap, TOF, Q-TOF), collision energy 17 BRAMA training for technicians – Module I, Rome Searching Molecules on PubChem 18 million compound DB (++) 18 GotoBRAMA PubChem training for technicians Structure – Module Search I, Rome CAS SciFinder • 33 million molecules and 60 million peptides/proteins • largest reaction DB (14 million reactions) and literature DB • substructure and similarity search of structures • a must for chemists and biochemists/biologists • no bulk download, no good Import/ Export, no Link outs 19 BRAMA training for technicians – Module I, Rome Structure search in SciFinder Retrieved 4000 papers (refine search only MS and MALDI) 20 BRAMA training for technicians – Module I, Rome Atomic Mass Correct unit is [ u] – unified atomic mass unit or [ Da ] Dalton see SI units 1 u = 1 Da = 1/12 th of mass of carbon 12 C = 1.66053886 x 10 -27 kg C6Cl6: C6 Cl6 p(gss, s/p:40) Chrg 0 R: 1000 Res.Pwr..
Load more

Recommended publications
  • Suspect and Target Screening of Natural Toxins in the Ter River Catchment Area in NE Spain and Prioritisation by Their Toxicity
    toxins Article Suspect and Target Screening of Natural Toxins in the Ter River Catchment Area in NE Spain and Prioritisation by Their Toxicity Massimo Picardo 1 , Oscar Núñez 2,3 and Marinella Farré 1,* 1 Department of Environmental Chemistry, IDAEA-CSIC, 08034 Barcelona, Spain; [email protected] 2 Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, 08034 Barcelona, Spain; [email protected] 3 Serra Húnter Professor, Generalitat de Catalunya, 08034 Barcelona, Spain * Correspondence: [email protected] Received: 5 October 2020; Accepted: 26 November 2020; Published: 28 November 2020 Abstract: This study presents the application of a suspect screening approach to screen a wide range of natural toxins, including mycotoxins, bacterial toxins, and plant toxins, in surface waters. The method is based on a generic solid-phase extraction procedure, using three sorbent phases in two cartridges that are connected in series, hence covering a wide range of polarities, followed by liquid chromatography coupled to high-resolution mass spectrometry. The acquisition was performed in the full-scan and data-dependent modes while working under positive and negative ionisation conditions. This method was applied in order to assess the natural toxins in the Ter River water reservoirs, which are used to produce drinking water for Barcelona city (Spain). The study was carried out during a period of seven months, covering the expected prior, during, and post-peak blooming periods of the natural toxins. Fifty-three (53) compounds were tentatively identified, and nine of these were confirmed and quantified. Phytotoxins were identified as the most frequent group of natural toxins in the water, particularly the alkaloids group.
    [Show full text]
  • Alpha-Tomatine Content in Tomato and Tomato Products Determined By
    J. Agric. Food Chem. 1995, 43, 1507-151 1 1507 a-Tomatine Content in Tomato and Tomato Products Determined by HPLC with Pulsed Amperometric Detection Mendel Friedman* and Carol E. Levin Food Safety and Health Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 800 Buchanan Street, Albany, California 94710 Tomato plants (Lycopersicon esculentum) synthesize the glycoalkaloid a-tomatine, possibly as a defense against insects and other pests. As part of an effort to improve the safety of plant foods, the usefulness of a new HPLC pulsed amperometric detection (PAD) method for the direct analysis of a-tomatine in different parts of the tomato plant; in store-bought and field-grown, including transgenic, tomatoes; in a variety of commercial and home-processed tomato products; and in eggplant and tomatillos was evaluated. The method was found to be useful for analysis of a variety of products including high-tomatine calyxes, flowers, leaves, roots, and stems of the tomato plant (14-130 mg/100 g of fresh weight), low-tomatine red tomatoes (0.03-0.08 mg/100 g), intermediate- tomatine tomatoes (0.1-0.8 mg/100 g), and high-tomatine fresh and processed green, including pickled and fried, tomatoes (0.9-55 mg/100 g). No experimental difficulties were encountered with extraction and analysis of tomatine in complex foods such as tomato juice, ketchup, salsa, sauce, and sun-dried tomatoes. Microwaving and frying did not significantly affect tomatine levels of tomato foods. The tomatine content of fresh market and transgenic delayed-ripening varieties was not different from the range ordinarily seen in tomato.
    [Show full text]
  • Fall TNP Herbals.Pptx
    8/18/14 Introduc?on to Objecves Herbal Medicine ● Discuss history and role of psychedelic herbs Part II: Psychedelics, in medicine and illness. Legal Highs, and ● List herbs used as emerging legal and illicit Herbal Poisons drugs of abuse. ● Associate main plant and fungal families with Jason Schoneman RN, MS, AGCNS-BC representave poisonous compounds. The University of Texas at Aus?n ● Discuss clinical management of main toxic Schultes et al., 1992 compounds. Psychedelics Sacraments: spiritual tools or sacred medicine by non-Western cultures vs. Dangerous drugs of abuse vs. Research and clinical tools for mental and physical http://waynesword.palomar.edu/ww0703.htm disorders History History ● Shamanic divinaon ○ S;mulus for spirituality/religion http://orderofthesacredspiral.blogspot.com/2012/06/t- mckenna-on-psilocybin.html http://www.cosmicelk.net/Chukchidirections.htm 1 8/18/14 History History http://www.10zenmonkeys.com/2007/01/10/hallucinogenic- weapons-the-other-chemical-warfare/ http://rebloggy.com/post/love-music-hippie-psychedelic- woodstock http://fineartamerica.com/featured/misterio-profundo-pablo- amaringo.html History ● Psychotherapy ○ 20th century: un;l 1971 ● Recreaonal ○ S;mulus of U.S. cultural revolu;on http://qsciences.digi-info-broker.com http://www.uspharmacist.com/content/d/feature/c/38031/ http://en.wikipedia.org/nervous_system 2 8/18/14 Main Groups Main Groups Tryptamines LSD, Psilocybin, DMT, Ibogaine Other Ayahuasca, Fly agaric Phenethylamines MDMA, Mescaline, Myristicin Pseudo-hallucinogen Cannabis Dissociative
    [Show full text]
  • Environmental Health Human Health
    Environmental Health Human Health Health & Environmental Solutions Network Christopher Vakas – 17 October 2017 Environmental Health Risk Management (EHRM) Health & Environmental Solutions Network Recycled drinking water Health & Environmental Solutions Network Health & Environmental Solutions Network Intrusive noise – how much is to much • Traffic • Rail • Aircraft • Air conditioners • Pool pumps • Compressors • Loud music • Power tools • Concerts Health & Environmental Solutions Network Clandestine drug labs • The drug “cooks” don’t care • Chemicals destroy property • Drugs destroy lives • Are dangerous • Volatile organic compounds • Weapons • Aggressive people Health & Environmental Solutions Network To produce 1 kg of methamphetamine in excess of 30 kg of toxic waste is produced Health & Environmental Solutions Network Food safety – Heat Stable Toxins • Seafood toxins – Saxitoxin and its derivatives • Green Potatoes – Solanine • Staphylococcal & Streptococcal – Enterotoxin • Clostridium Botulinum - Botulinum • FSS 3.2.2 Clause 7 Food Processing • How long is too long for foods that are yet to undergo a pathogen control step? • (2) A food business must, when processing potentially hazardous food that is not undergoing a pathogen control step, ensure that the time the food remains at temperatures that permit the growth of infectious or toxigenic micro-organisms in the food is minimised. Health & Environmental Solutions Network Seafood Toxins • collectively referred to as paralytic shellfish toxins (PSTs), • paralytic shellfish poisoning (PSP), • amnesic shellfish poisoning (ASP), • diarrheic shellfish poisoning (DSP), • ciguatera shellfish poisoning (CFP), • azaspiracid shellfish poisoning (AZP) • Responsible for 750 to 7500 death annually, from up to 0.5 M cased reported • Saxitoxin is one of the most potent neurotoxins • Ciguatoxin CTXs are tasteless, colourless, odourless, heat and acid stable, and stable for at least six months at commercial freezing temperatures.
    [Show full text]
  • Poisonous Plants in New Zealand
    THE NEW ZEALAND MEDICAL JOURNAL Journal of the New Zealand Medical Association Poisonous plants in New Zealand: a review of those that are most commonly enquired about to the National Poisons Centre Robin J Slaughter, D Michael G Beasley, Bruce S Lambie, Gerard T Wilkins, Leo J Schep Abstract Introduction New Zealand has a number of plants, both native and introduced, contact with which can lead to poisoning. The New Zealand National Poisons Centre (NZNPC) frequently receives enquiries regarding exposures to poisonous plants. Poisonous plants can cause harm following inadvertent ingestion, via skin contact, eye exposures or inhalation of sawdust or smoked plant matter. Aim The purpose of this article is to determine the 15 most common poisonous plant enquiries to the NZNPC and provide a review of current literature, discussing the symptoms that might arise upon exposure to these poisonous plants and the recommended medical management of such poisonings. Methods Call data from the NZNPC telephone collection databases regarding human plant exposures between 2003 and 2010 were analysed retrospectively. The most common plants causing human poisoning were selected as the basis for this review. An extensive literature review was also performed by systematically searching OVID MEDLINE, ISI Web of Science, Scopus and Google Scholar. Further information was obtained from book chapters, relevant news reports and web material. Results For the years 2003–2010 inclusive, a total of 256,969 enquiries were received by the NZNPC. Of these enquiries, 11,049
    [Show full text]
  • Food Borne Diseases
    204 Food Science 19 Food Borne Diseases While food is necessary for sustaining life, it could also be a cause of illness. There is a general misconception that if a food is ‘natural’, it must be ‘safe’. Unfortunately the fact that many toxins occur in natural plant foods, falsifies this naïve view. Most of these endogenous toxins are in plant foods and a few in animal foods. Toxins from Plants Solanine of potatoes is one of the best known plant toxins. It is a steroid which occurs in potatoes and other members of solanaceae family (e.g., aubergine) and the highly poisonous nightshades. Normally potatoes contain 2–15 mg per 100 g (fresh weight). When potatoes are exposed to light and turn green, the level of solanine can be as high as 100 mg per 100 g. It is mostly concentrated under the skin. Potato sprouts may contain even higher amounts. Solanine can cause abdominal pain and diarrhoea, if injested in large amounts. Solanine is an inhibitor of the enzyme acetyl choline esterase, which is a key component of the nervous system. Ingestion of solanine have been reported to lead to signs of neurological damage. As there is a general public awareness of the health hazards of eating green potatoes, the incidence of potato poisoning is low. Solanine is not lost during normal cooking as it is insoluble in water and is heat stable. Caffeine is a purine alkaloid. Theobromine is another important member of this group. These occur in tea, coffee, cocoa and cola beverages, which are regarded as stimulants.
    [Show full text]
  • Potential Terrorist Use of Nicotine and Solanine Toxins - 09/05/2003
    For Health Professionals Health Alerts Health Advisory #48 - Potential Terrorist Use of Nicotine and Solanine Toxins - 09/05/2003 Over the past several years, various reports have described a growing terrorist interest in the use of two plant toxins as potential mass poisoning agents. These kinds of poisons have been associated with training for limited-scope attacks, such as assassination. These poisons, nicotine and solanine, are naturally occurring toxins obtained from tobacco and potatoes, respectively. References to nicotine and solanine appear in numerous terrorist training manuals and documents seized in Afghanistan. There are no known instances of actual use of either poison by Islamic terrorist organizations; however, nicotine was used in a recent domestic criminal poisoning incident, resulting in the sickening of nearly 100 people in Michigan. The acute toxicity of nicotine is well documented as a result of a number of accidental poisonings. While comparatively less toxic than cyanide, botulinium toxin or ricin, both substances can be lethal in high doses or if medical treatment is significantly delayed. Both toxins occur naturally in established agricultural products making their availability and ease of chemical separation the key attractions for terrorists. The most likely technique for nicotine or solanine poisoning would be food, beverage, or water contamination; however, nicotine can also be absorbed through the skin and mouth and the digestive and respiratory tracts. Terrorist manuals detail simple instructions on how to produce both nicotine and solanine poisons. Nicotine is widely available, inexpensive, and uncomplicated--it can be produced using a basic knowledge of chemistry. Nicotine is a fast-acting poison, absorbed through the digestive and respiratory tracts, as well as through the skin and mouth.
    [Show full text]
  • Food Safety I
    BMF 29 - Food Safety I Highly Purified Natural Toxins for Food Analysis Chiron has built up a strong track record of supplying new reference standards during the past 30 years of operation. We are proud to announce our extended offer of Highly Purified Natural Toxins for Food Analysis: Mycotoxins Plant toxins Marine toxins The basis of a good analytical method is the availability of appropriate standards of defined purity and concentration. Our mission is to market highly purified toxin calibrates in crystalline as well as standardized solutions for chemical analysis, including internal standards. Your benefits using our standards include: ◊ Fast turnover time due to excellent service. ◊ Guaranteed high and consistent quality. ◊ Sufficient capacity to serve the market, and bulk quantities available on request. ◊ Custom solutions on request. Reference materials (RM) play an important role as they build the link between measurement results in the laboratory and international recognized standards in the traceability chain. Our standards are made according to the general requirements of ISO 9001. In 2011 we started to implement ISO 17025 and ISO guides 30-35 . Other relevant food analysis literature: Food Safety I (BMF 29): Natural Toxins; Mycotoxins, Plant toxins and Marine toxins. Food Safety II (BMF 30): Food Contaminants. Food Safety III (BMF 31): Food Colours and Aroma. Allergens: BMF 47. Glycidyl fatty acid esters: BMF 56. Melamine: BMF 48. 3-Monochloropropanediol esters (3-MCPD esters): BMF 49. Plasticizers, Phthalates and Adipates: BMF 32 and BMF 50. PFCs (Perfluorinated compounds) including PFOS and PFOA: BMF 20. PCBs: BMF 14. PBDEs (flame retardants): BMF 15. Pesticides: BMF 33 and 34, and the Chiron catalogue 2008.
    [Show full text]
  • A High-Throughput Extraction and Analysis Method for Steroidal Glycoalkaloids in Tomato
    fpls-11-00767 June 19, 2020 Time: 15:23 # 1 METHODS published: 18 June 2020 doi: 10.3389/fpls.2020.00767 A High-Throughput Extraction and Analysis Method for Steroidal Glycoalkaloids in Tomato Michael P. Dzakovich1, Jordan L. Hartman1 and Jessica L. Cooperstone1,2* 1 Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States, 2 Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States Tomato steroidal glycoalkaloids (tSGAs) are a class of cholesterol-derived metabolites uniquely produced by the tomato clade. These compounds provide protection against biotic stress due to their fungicidal and insecticidal properties. Although commonly reported as being anti-nutritional, both in vitro as well as pre-clinical animal studies have indicated that some tSGAs may have a beneficial impact on human health. However, the paucity of quantitative extraction and analysis methods presents a major obstacle for determining the biological and nutritional functions of tSGAs. To address Edited by: this problem, we developed and validated the first comprehensive extraction and Heiko Rischer, VTT Technical Research Centre ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC- of Finland Ltd., Finland MS/MS) quantification method for tSGAs. Our extraction method allows for up to 16 Reviewed by: samples to be extracted simultaneously in 20 min with 93.0 ± 6.8 and 100.8 ± 13.1% José Juan Ordaz-Ortiz, Instituto Politécnico Nacional recovery rates for tomatidine and alpha-tomatine, respectively. Our UHPLC-MS/MS (CINVESTAV), Mexico method was able to chromatographically separate analytes derived from 18 tSGA peaks Elzbieta˙ Rytel, representing 9 different tSGA masses, as well as two internal standards, in 13 min.
    [Show full text]
  • Antioxidants in Potatoes: a Functional View on One of the Major Food Crops Worldwide
    molecules Review Antioxidants in Potatoes: A Functional View on One of the Major Food Crops Worldwide Hanjo Hellmann 1,* , Aymeric Goyer 2 and Duroy A. Navarre 3 1 School of Biological Sciences, Washington State University, Pullman, WA 99164, USA 2 Hermiston Agricultural Research and Extension Center, Department of Botany and Plant Pathology, Oregon State University, Hermiston, OR 97838, USA; [email protected] 3 USDA-ARS, Prosser, WA 99350, USA; [email protected] * Correspondence: [email protected] Abstract: With a growing world population, accelerating climate changes, and limited arable land, it is critical to focus on plant-based resources for sustainable food production. In addition, plants are a cornucopia for secondary metabolites, of which many have robust antioxidative capacities and are beneficial for human health. Potato is one of the major food crops worldwide, and is recognized by the United Nations as an excellent food source for an increasing world population. Potato tubers are rich in a plethora of antioxidants with an array of health-promoting effects. This review article provides a detailed overview about the biosynthesis, chemical and health-promoting properties of the most abundant antioxidants in potato tubers, including several vitamins, carotenoids and phenylpropanoids. The dietary contribution of diverse commercial and primitive cultivars are detailed and document that potato contributes much more than just complex carbohydrates to the diet. Finally, the review provides insights into the current and future potential of potato-based systems as tools and resources for healthy and sustainable food production. Citation: Hellmann, H.; Goyer, A.; Keywords: potato; antioxidant; vitamin; glycoalkaloids; patatin; phenolic antioxidants; nutrition; Navarre, D.A.
    [Show full text]
  • Review of the Inhibition of Biological Activities of Food-Related Selected Toxins by Natural Compounds
    Toxins 2013, 5, 743-775; doi:10.3390/toxins5040743 OPEN ACCESS toxins ISSN 2072-6651 www.mdpi.com/journal/toxins Review Review of the Inhibition of Biological Activities of Food-Related Selected Toxins by Natural Compounds Mendel Friedman 1,* and Reuven Rasooly 2 1 Produce Safety and Microbiology Research Unit, Agricultural Research Service, USDA, Albany, CA 94710, USA 2 Foodborne Contaminants Research Unit, Agricultural Research Service, USDA, Albany, CA 94710, USA; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-510-559-5615; Fax: +1-51-559-6162. Received: 27 March 2013; in revised form: 5 April 2013 / Accepted: 16 April 2013 / Published: 23 April 2013 Abstract: There is a need to develop food-compatible conditions to alter the structures of fungal, bacterial, and plant toxins, thus transforming toxins to nontoxic molecules. The term ‘chemical genetics’ has been used to describe this approach. This overview attempts to survey and consolidate the widely scattered literature on the inhibition by natural compounds and plant extracts of the biological (toxicological) activity of the following food-related toxins: aflatoxin B1, fumonisins, and ochratoxin A produced by fungi; cholera toxin produced by Vibrio cholerae bacteria; Shiga toxins produced by E. coli bacteria; staphylococcal enterotoxins produced by Staphylococcus aureus bacteria; ricin produced by seeds of the castor plant Ricinus communis; and the glycoalkaloid α-chaconine synthesized in potato tubers and leaves. The reduction of biological activity has been achieved by one or more of the following approaches: inhibition of the release of the toxin into the environment, especially food; an alteration of the structural integrity of the toxin molecules; changes in the optimum microenvironment, especially pH, for toxin activity; and protection against adverse effects of the toxins in cells, animals, and humans (chemoprevention).
    [Show full text]
  • 3. Forage Legumes and Fleshy Forage Plants
    3. Forage legumes and fleshy forage plants 1 Forage legumes Occurence: • Perennial or annual herbs of Fabaceae family used for their stem and leaves • Wild species on pastures • For forage: wild species and selected cultivars applied exclusively or mixed with cereals Importance: • Animal nutrition – Rich in protein and fiber – Rich in minerals: Ca and P – High content β-carotine • Pasture for honey bees • Root nodules Rhizobium species ability to fix athmospheic 2 N2 green manure Utilization • Grazing plants with decumbent stem (difficult to mow) see Grasslands • Hay : plants are mow in the beginning of flowering stage 3-4 times/year) – Avoid dried leaves fall off – Drying for 2-3 days to protect ß-carotine from degradation • Dried and grinded hay comressed into pellets and cakes • Ensilage: – Silage : higher CH content which support fermentation – Haylage : drying hay to increase CH content up to 40-45% in dry weight, then ensilage (often mixed with molasses and conserved by formic acid) 3 Antinutritive effects and compounds Bloating (distension) Freshly eaten forage legumes can be fermented easily in the intestines Water-soluble peptids of low molecular weights are released Rapid digestion by rumen microbes slime production frothy bloat (distension caused by foam and gases) Effects: low O2 levels in tissues and painful spasm Taut skin, death 4 5 Saponins Amphipathic glycosides (hydrophilic and lipophilic properties) – emulsifying effect • sapo (in Latin) means soap produce foam in the rumen • can enter into the lipid bilayer of membranes disintegrated membranes • red blood cells are affected haemolytic effect • low conversion rate from digestive tract • irritation of mucous membranes 6 Photosensitization (hypericosis) • Plants causing liver damage microbially produced metabolites of chlorophyll (phyotodynamic agents) immediate „sunburn” = dermatitis with wounds • If caused by Trifolium spp.
    [Show full text]