Content and Structure - la nuvola tv · PDF fileamplification success Species Product ITS...
Transcript of Content and Structure - la nuvola tv · PDF fileamplification success Species Product ITS...
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Content and Structure :� Quality of Herbal Materials, Biodiversity, Factors affecting Quality,
Adulterations� Quality Assessment and Control� Quality Assurance Systems: GAP, GCP, ISSC-MAP, HACCP, GMP
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Genetic Identity and PhytochemicalQuality of Plants and BotanicalsCh. FRANZ and J. NOVAK, Vetmeduni Vienna
�Tools in phytochemistry: chromatographic methods (TLC/HPTLC, GLC, GC-MS, HPLC, HPLC-MS, etc.)
� In-vitro methods as e.g. antioxidantactivity
�Tools in molecular biology/genetics: RAPD, PCR, HRM, new generationsequencing…
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DNA-based Identification in Everyday Life
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From Plant Raw Materials to Final Products:
C. Schmiderer, J. Ruzicka, B. Lukas, J. Novak, Ch. F ranzInstitute for Animal Nutrition and Functional Plant CompoundsUniversity of Veterinary Medicine, A-1210 Vienna, Austria
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Processed Materials / Final Products
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Tissue
Isolation of genomic DNA
Amplification of markergenes with PCR
DNA sequence
Cycle sequencing PCR and automatic DNA-sequencing
Molecular Plant Taxonomy Today
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Identification approach for admixturesPCR: Finding the needle in a haystack easily!
http://nl.ijs.si/et/talks/esslli02/metadata_files/Haystack-FINALb.jpg
forward primer
reverse primer
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DNA based identification systems for plants and PFS
Species investigated :�Calendula officinalis�Ginkgo biloba�Matricaria recutita (adulteration with Anthemis sp.)�Plantago lanceolata�Plantago ovata�Valeriana officinalis�and others
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Extraction
• releasing DNA• purifying DNA from compounds interacting with
subsequent PCR
Amplification
• producing multiple copies of a specific part of the DNA
• PCR
Sequencing
• ‚classical‘ Sanger (cycle) sequencing• next generation sequencing
Analysis & Interpretation
• data correction• alignment• bioinformatic approaches (phylogeny, etc.)
„DNA -Barcoding “
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„DNA -Barcoding “
Database
� Taxon 1 ATG CAT GGG CTT TAA GGC CT
� Taxon 2 ATG CAT GGT CTA GAA GGC CT
� Taxon 3 ATG CAA GGT CTA GAA GGT CT
� Taxon 4 ATG CAT GGT CTA TAA GGT CT
� Taxon 5 ATG CAA GGG CTT TAA GGT CT
� Unknown sample ATG CAA GGT CTA GAA GGT CT
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Intra- vs. Interspecific Variability
individuum 1individuum 2individuum 3individuum 4individuum 5
C T T A T T C T C T T A T C A C A A G T C T T G T. . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . N. . - - - - - - - - . . . . . . . . - - - - . . .. . - - - - - - - - . . . . . . . . - - - - . . .. . - - - - - - - - . . . . . . . . . . . . . . .. . - - - - - - - - . . . . . . . . . . . . . . .. . - - - - - - - - . . . . . . . . - - - - . . .
Species 1
Species 2
consensus sequence
intraspecific variation����interspecific variation����
individuum 1individuum 2individuum 3individuum 4individuum 5
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Identification of Passiflora incarnata by Sequencing and a Phylogenetic Tree
Neighbour-Joining tree based on ITS sequences
Sequence of Passiflora incarnata
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Routine Assays
� Hybridization-based methods� dynamic allele-specific hybridization, molecular beacons, SNP
microarrays� Enzyme-based methods
� restriction fragment length polymorphism, PCR-based methods (e.g. �ARMS (amplification refractory mutation system) ), flapendonuclease, primer extension, 5’- nuclease, oligonucleotide ligation assay
� Other post-amplification methods based on physical properties of DNA� Single strand conformation polymorphism, temperature gradient gel
electrophoresis, denaturing high performance liquid chromatography, high-resolution melting of the entire amplicon , use of DNA mismatch-binding proteins, SNPlex
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ARMS-Assay
C T T A T T C T C T T A T C A C A A G T C T T G T. . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . N. . - - - - - - - - . . . . . . . . - - - - . . .. . - - - - - - - - . . . . . . . . - - - - . . .. . - - - - - - - - . . . . . . . . . . . . . . .. . - - - - - - - - . . . . . . . . . . . . . . .. . - - - - - - - - . . . . . . . . - - - - . . .
Species 1
other species
consensus sequence
species specific primer
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Identification of Matricaria recutita and Anthemis spp.
Alignment excerpt; empty columns symbolize cut out sequence parts15
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MARMS Multiple ARMS (amplification refractorymutation system )Combining multiple PCR reactions in one tube
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MARMS for Matricaria recutita and Anthemis spp.
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MARMS for Matricaria recutita and Anthemis spp.
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MARMS discrimination:Matricaria recutita, Anthemis spp. and other Asteraceae
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Detection of adulterations of Valeriana officinalis with other Valeriana species bymultiplex PCR
Specific marker for the genus Valeriana
Specific for the species V. officinalis
Principle of multiplex PCR
Lanes (from the left): 1 and 13…molecular ladder2,4,5,6,12…V. officinalis3,7,10,11…species of Valeriana other than V. officinalis7,8…other species (not from the genus Valeriana)
Novak, J. et al.., unpubl.) 20
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Detection of adulterations ofValeriana officinalis with otherValeriana species by multiplex PCR
Specific for the genus Valeriana
Specific for the species V. officinalis
Lanes (from the left): 1 and 13…molecular ladder2,4,5,6,12…V. officinalis3,7,10,11…species of Valeriana other than V. officinalis7,8…other species (not from the genus Valeriana)
� Samples� 1…V. officinalis� 2…Valeriana sp.*
� 3…V. officinalis� 4…V. officinalis� 5…V. officinalis� 6…Valeriana sp. *
� 7…unknown adulteration� 8…unknown adulteration� 9…Valeriana sp. *
� 10…Valeriana sp. *
� 11…Valeriana officinalis*…another Valeriana species, but not V. officinalis
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HRM (High Resolution Melting)
http://www.gene-quantification.de
Invitrogen
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Identification of Matricaria recutitaDiscrimination of Anthemis spp. and other Asteraceae species by high resolution melting curve analysis ( HRM)
Matricaria recutita can be distinguished from M. discoidea by a second primer combination
PlantLIBRA PlantLIBRA PlantLIBRA PlantLIBRA
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High Resolution Melting Curves(HRM) of Calendula sp. DNA
Novak, J. et al.., unpubl.)24
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Detection of admixtures of Digitalis spp. in Plantago lanceolata
1) Plantago lanceolata (pure)2) 10% Digitalis3) 30% Digitalis4) 50% Digitalis5) 70% Digitalis6) 90% Digitalis7) Digitalis lanata (pure)NTC – non template control
Multiplex-PCR with primers specific for Plantago, P. lanceolata and Digitalis
High resolution melting curve analysis with primers specific for P. lanceolata and Digitalis
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DNA – Methods applicable at:
�Family, Genus and Species level (inter-and intraspecific)
�Population level
�Chemotype level
�but also in the authentification of intermediate and final products
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From Herbal Materials to Final Products
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fresh plant material
drug
drugconc.
oilmacerate
mother tincture
pressjuice
powder
oilmacerate
spissumextract
siccumextract
tea cuttings
crushing
pressingextraction
drying
cutting
grinding cutting
fluid extracttincture
extraction
dryinggrinding
drying
Processing of Herbal Materials to PFS / HMPs
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DNA Degradation
�DNA degradation is a process by which DNA breaks down into smaller fragments.
�Factors promoting DNA degradation:• physical shearing• boiling• nucleases• freezing• acid treatment• alkali treatment• UV exposure 29
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DNA-Extraction of Sage (Salvia officinalis)
1
10
100
'fresh' material Salviaeofficinalis folium;
pharmacy
TeekanneFixSalbei
AlnaturaSalbeitee
DN
A-c
onc.
[ng/
µl]
(Quiagen DNeasy Plant Mini Kit; ng/µl)
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amplification successSpecies Product ITS psbA-trnHValerianae radix Reference HM ���� ����
Pharmacy HMP ���� ����
Doskar PFS ���� ����
Ginseng radix pharmacy HMP ���� ����
Aurita PFS ���� ����
Doskar PFS ���� ����
Menthae folium Reference HM ���� ����
pharmacy HMP ���� ����
Alnatura Herbal tea ���� ����
Teekanne Herbal tea ���� ����
Salviae folium Reference HM ���� ����
pharmacy HMP ���� ����
Alnatura Herbal tea ���� ����
Teekanne Herbal tea ���� ����
(Schmiderer, Lukas, Novak, ZAG 18:65-72, 2013)
PCR-Successin different HM, HMP and PFS Products
HM: Herbal Material, HMP: Herbal Medicinal Product,PFS: Plant Food Supplement
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amplification successSpecies Product ITS psbA-trnHValerianae radix Reference HM ���� ����
Pharmacy HMP ���� ����
Doskar PFS ���� ����
Ginseng radix pharmacy HM ���� ����
Aurita PFS ���� ����
Doskar PFS ���� ����
Menthae folium Reference HM ���� ����
pharmacy HMP ���� ����
Alnatura Herbal tea ���� ����
Teekanne Herbal tea ���� ����
Salviae folium Reference HM ���� ����
pharmacy HMP ���� ����
Alnatura Herbal tea ���� ����
Teekanne Herbal tea ���� ����
(Schmiderer, Lukas, Novak, ZAG 18:65-72, 2013)
PCR-Successin Different Drugs and Products
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amplification successSpecies Product ITS psbA-trnHMatricariae flos Reference HM ���� ����
Pharmacy HMP ���� ����
Alnatura Herbal tea ���� ����
Teekanne Herbal tea ���� ����
Foeniculi fructus Reference HM ���� ����
Pharmacy HMP ���� ����
Alnatura Herbal tea ���� ����
Teekanne Herbal tea ���� ����
Juniperi pseudo-fructus Pharmacy HM ���� ����
Fuchs Spice ���� ����
Kotanyi Spice ���� ����
Salicis cortex Reference HM ���� ����
Pharmacy HMP ���� ����
Cinnamomi cortex Pharmacy HMP ���� ����
Alnatura PFS ���� ����
Kotanyi Spice ���� ����
(Schmiderer, Lukas, Novak, ZAG 18:65-72, 2013)
PCR-Successin Different Drugs and Products
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DNA-based identification of an ethanolic extract„Echinacea sp. – spissum extract“
130 140 150 160 170 180
TTAAAGGGCTTGTGCTGTTATGCCCCGTCA-TTGGTGTGCATAGT-GTGCGTTGCTTCTTT plant extract..............................-..............-............... Echinacea purpurea..............................-............C.-............... Echinacea paradoxa..............................-............C.-..-............ Echinacea pallida..............................A............C.-............... Echinacea atrorubens..............................A............C.-............... Echinacea simulata..............................-............C.-............... Echinacea tennesseensisA.G...T..CC...T.........NN..T.-GC.......-..T.-.CA...GTG..... Rudbeckia fulgida var. fulgida..G...T..CC.....A...C...NN..TT-GC.......G-.T.-..A...G.A...... Rudbeckia subtomentosa.........CC.....A........-....-CC.......G.GT.-......G........ Sanvitalia fruticosaA.G...T..CC...T.............T.-GC.......G..T.-.CA...GTG...... Rudbeckia missouriensis.-G...T..CA..-......C.......T--GC.......G..TA-..A...G....TC. Rudbeckia heliopsidis....G.-.........T.G.C......CTT-GC.......GA.T.T.C....G........ Oblivia mikanioides......A.........A.G.C.......TT-GC.......GA.T.-..A..CGAA...... Idiopappus quitensis
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DNA-based identification of a tincture and fluid extract of chamomile
Novak et al.: DNA-Based Authentication of Plant Extracts. Food Research International 40: 388-392, 2007.
10 20 30 40 50 60
G A T TG C A G A A T CC C G T G A A CC A T C G A G TT T T T G A A CG C A A G T T GC G C C C G A AG C C T T T T GG C C G
. . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . .
. . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . .
A . . .. . . . . . . .. . . . . . . .. . . . . . . .C . . . . . . .. . . . . . . .. . . . . . . .. . . A . . A .. . . .
70 80 90 100 110 120
A G G GC A C G T C T GC C T G G G C GT C A C G C A TC G C G T C G CC C C C A - - -- - - - - - - -- - - A C A A AC T A T
. . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . - - -- - - - - - - -- - - . . . . .. . . .
. . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . - - -- - - - - - - -- - - . . . . .. . . .
. . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . C C G CC C T C C G T GC G C . . . G CG C C C
130 140 150 160 170 180 190
G T T GG G G G - - - -- - - - C G G AT A T T G G T CT C C C G T G CT T A T G G - -- C G T G G T TG G C C A A A AT A G G
. . . .. . . . - - - -- - - - . . . .. . . . . . . .. . . . . . . .. . . . . . - -- . . . . . . .. . . . . . . .. . . .
. . . .. . . . - - - -- - - - . . . .. . . . . . . .. . . . . . . .. . . . . . - -- . . . . . . .. . . . . . . .. . . .
. . . .. . . . A G G GG G G G . . . .. . . . . . C .. . . . . . . .. C C . C . G CG . . C . . C .. . . . C . . .. G C .
200 210 220 230 240 250
A G T CC C T T - C G AT G G A C G C AC G A A C T A GT G G T G G T CG T A A A A A CC - - - C T C GT T C T T T G TT T T G
. . . .. . . . - . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. - - - . . . .. . . . . . . .. . . .
. . . .. . . . - . . .. . . . . . . .. . . . . . . .. . . . . . . .. . . . . . . .. - - - . . . .. . . . . . . .. . . .
. T C .. T C G G . . .C T C . T . T CA C G . . A . .. . . . . . . T. A . C . . C T. A A T . . . .C G . G C C . .C G . .
Tin
ctur
e
Ref
eren
ce
Flu
idex
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t
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Passiflora incarnata drug and productsIdentification success using a simple standard approach
Denomination no. of samples success [%]Drugs (raw material) 36 36 [100%]
Liquids 7 0 [0%]Dry extract 1 0 [0%]Extract 1 0 [0%]Extractum ethanoleum 5 0 [0%]
Pills 37 21 [57%]Raw material 2 2 [100%]Dry extract 14 10 [71%]Extract 16 7 [44%]not specified 5 2 [40%]
Dry extracts (powder) 2 1 [50%]36
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Future PerspectivesPart 1: ‚Low Tech‘
� Victor M. Ugaz, A Pocket-Sized Convective PCR Thermocycler, Angewandte Chemie International Edition, doi: 10.1002/anie.200700306
� Open Source Biotechnology
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Future PerspectivesPart 2: ‚High Tech‘ – Lab-on-a-Chip
http://lab-on-chip.gene-quantification.info/ 38
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Future PerspectivesPart 2: ‚High Tech‘ – Lab-on-a-Chip
Microchip-based one step DNA extraction and real-time PCR in one chamber for rapid pathogen identificationJeong-Gun Lee, Kwang Ho Cheong, Nam Huh, Suhyeon Kim, Jeong-Woo Choib and Christopher KoaLab Chip, 2006, 6, 886–895
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Future PerspectivesPart 2: ‚High Tech‘ Next Generation Sequencing (NGS)
Method ‚Classical‘ Sanger-Sequencing
NGS - Illumina
Read length 600 - 1000 bp 50 – 300 bp
Sequences per run 96 Up to 3 billion
Price per 1 million bp 1700.-€ 0.07.-€
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Notopterygium/Hansenia Identity, Phylogenesis and Admixture Identification
Notopterygium incisumnew nomencl.: Hansenia
?
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Genetic Identity and PhytochemicalQuality of Plants and Botanicals
�Tools in phytochemistry: chromatographic methods (TLC/HPTLC, GLC, GC-MS, HPLC, HPLC-MS, etc.)
� In-vitro methods as e.g. antioxidantactivity
�Tools in molecular biology/genetics: RAPD, PCR, HRM, new generationsequencing…
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Kabelitz 2003
Atractylodis macrocephalae Rhizoma, TLC on flavonoid constituents, UV -light 366 nm
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HPTLC phytochemical profile of Camellia sinensisEC C EGCG ECG EGC CAF GT2 GT1 DGT BT DBT T GA Q K
EC=Epicatechin GT2=Green tea 2
C=Catechin GT1=Green tea 1
EGCG=Epigallocatechin-3-gallate DGT=Decaffeinated green tea
EGC=Epigallocatechin BT=Black tea
CAF=Caffeine DBT=Decaffeinated black tea
T=Theaflavin Q=Quercetin
GA=Gallic acid K=Kaemferol
HPTLC of tea samples after derivatization with Fast Blue
Salt B reagent
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� Analytical profiles for caffeine and catechin in Camellia sinensisproducts were obtained by gradient RP-HPLC/UV
� Analytical profiles for active amines (octopamine and synephrine) in PFS containing Citrus aurantium and other ingredients were performed using the same chromatographic conditions coupled with a fluorimetric detector
Figure 1 – Caffeine and catechin profile in green te a infusion
Figure 2 – Octopamine and synephrine in PFS containi ng Citrus aurantium
Phase A (v/v) Phase B (v/v)
Water 99.5% Acetonitrile 99.5%
Formic acid 0.5% Formic acid 0.5%
Phase A (v/v) Phase B (v/v)
SDS 0.288 g/L 100%
SDS 0.288 g/L 50%
Acetonitrile 50%
Partner: UMIL
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0
10
20
30
40
50
60
70
EC
ECG
EGC
ECCG
Caffeine
Green-Tea-ExtractsGreen-Tea-Extracts combined with
other botanical extracts
Variability in Caffeine ofGreen Tea containing PFS
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Rosmarinic acid in various Thymus vulgaris accessions and its contribution to theantioxidant activity
Waste: leaves after hydrodistillationChizzola et al. 2008, JAFC
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AU
-0,05
0,00
0,05
0,10
0,15
0,20
0,25
Minutes5,00 10,00 15,00 20,00 25,00 30,00 35,00 40,00 45,00 50,00 55,00 60,00 65,00
P. lagopusA
U
0,00
0,02
0,04
0,06
0,08
0,10
0,12
0,14
0,16
0,18
0,20
0,22
nm200,00220,00240,00260,00280,00300,00320,00340,00360,00380,00400,00420,00440,00460,00480,00500,00520,00540,00560,00580,00
198,0
241,4
326,7
Chlorogenic acid
Species Origin IPK number
P. afra San Marino di Urbino, Italy IPK-PLA 16
P. albicans Gene Bank of IRA, Medenine, Tunisia IPK-PLA 19
P. arenaria Institute for breeding research Braunschweig, Germany IPK-PLA 40
P. cornuti Botanical garden University Bologna, Italy IPK-PLA 52
P. coronopus "Rühlemann" seed producing industry, Germany Rühl-Pla 18x
P. coronopus Madeira, Portugal IPK-PLA 55
P. coronopus seed producing industry, north Italy IPK-PLA 18
P. lagopus Botanical garden University Maputo, Mozambique IPK-PLA 50
P. lagopus France IPK-PLA 42
P. lanceolata wild collected Vienna, Austria
P. lanceolata Elverdamskroen, Denmark IPK-PLA 51
P. major wild collected Vienna, Austria
P. maritima Botanical garden Univ. Halle/Saale, Germany IPK-PLA 27
P. media wild collected Vienna, Austria
P. sempervirens Creissels, Aveyron, France IPK-PLA 64
P. subulata Pont-de-Montvert, Lozere, France IPK-PLA 65
DPPH- assayHPLC-DAD
Fast- GC-FID
Plantago sp.:Diversity of iridoids profile between species and plant parts resp.Diversity of the polyphenols profile and the antioxidant activity between species
Sponza, S. et al., unpubl.49
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Harpagophytum procumbensPhytochemical profiling of plant raw material (prov ided by PhytoLab)
Pla
nt s
ourc
e co
mpa
rison
Hotellings T2 Range comparison: >95% similarity but clear differences detected
Marker compounds identified by accurate mass detection
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Harpagophytum procumbensMethod development - Waters Acquity UPLC and Synapt HDMS
Standards profiles
MeOH/ACN based extraction
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Volatile profiles of Matricaria and Anthemis species(German Chamomile and confused species)
Matricaria recutita:Chamazulene, bisabololoxide A, dicyloethers
Matricaria matricarioides:dicycloethers
Matricaria trichophylla,M. disciforms, M. perforata:Polyacetylenes: Matricariaesters
Anthemis austriaca: chrysanthenylacetate
Anthemis altissima, A. arvensis and A. cotula: very low in volatiles, mainly common sesquiterpenoids (e .g. anthecotulide: allergenic!)
Species morphological similar: flower heads with wh ite ray florets and yellow disc florets
VUW-Bot52
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Misidentification / Adulteration!(Problem: PAs and Allergenic Compounds in Herbal In fusions
and………… PFS!)
Anthemis sp.
True Chamomile
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Calendula officinalis
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New varietywith high faradiol monoester content
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Influence of Processing
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Influence of the Solvent Ethanol-Water-Ratio on the Extraction of Bioactive Compoundsof Sage ( Salvia off.)
Durling 2006 Food Chemistry 101, 1417
TSS: Total soluble
Solids
TP: Total Phenolics
RA: Rosmarinic
acid
CT: Carnosol etc.
EO: Essential Oil
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Influence of Temperature on the Extractionof Phenolic Compounds in Sage ( Salvia off.)
Durling 2006 Food Chemistry 101, 1417
TSS: Total soluble
Solids
TP: Total Phenolics
RA: Rosmarinic
acid
CT: Carnosol etc.
EO: Essential Oil
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Conclusion and Prospects
Quality Assessment and Quality Assurance of PFS- Identity / Authenticity of the material (PCR,…)- Phytochemical Quality: from starting material to
final product (variation / range within species andbetween products!)
- Contaminations, Residues, Toxic Compounds- Quality Guidelines for herbal materials and
extracts used in PFS already elaborated in co-operation with European Botanical Forum/FSE
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Supply Chain Management requested !
� Good Agricultural and Wild Collection Practice (GACP)
� Good Manufacturing Practice (GMP)
� Identification / Authentication� Quality Control: Phytochemistry� Quality Control: Contaminations, Residues
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