from molecular biology to synthetic biology, what’s new? · •design team use big data and...
TRANSCRIPT
From Molecular Biology to Synthetic Biology whatrsquos new Sandra Taylor Senior Research Technician BSc (Hons) Mphil Rsci MIScT
sandrataylormanchesteracuk (0161) 306 5131
bull 1987 - First lab job veterinary tests Bacteriology post mortems blood urine faeces tests etc
Small beginnings in Norwich after my first degree
Plant Molecular Genetics 1988 to 1998 ndash the lab grew from 6 to 16 people and several
papers were published on the way that flowering is controlled
1998 to 2001 Biochemistry Division School of Biological Sciences Manchester University ndash I supported 6 research groups sharing expertise
Topics from cell division (in toads) to asthma (in horses and people) and cultured human cells
Career Break from 2001 to 2007
bull Starting again after 6 years was a challenge but I soon got back up to speed Technical roles are very varied never boring a bit like being a Mum
2007 to present
bull I spent 7 years in the Michael Smith Building (Life Sciences) ndash various roles (cell culture cloning yeast two-hybrid)
bull In 2014 I moved to the MIB ndash more ChemistryBiochemistry focussed
Nano-scale 3D printing
Micro-titre plates with 96 384 or even 1536 sample wells ndash technology is being developed to ldquowriterdquo strings of DNA into these tiny wells using
3D nano-printing technology
Present Challenges Supporting SYNBIOCHEM
bull New subject(s) and equipment to learn about
bull The new SYMBIOCHEM team is 10 people and 4 robots
bull IT technology means writing electronic lab notebooks instead of paper ones
bull The new team is multidisciplinary so lots to learn but good fun
bull This is now the age of writing DNA as opposed to just reading it
Publications (please note publications I contributed prior to 2006 were under my maiden name of Doyle)
Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARAEndofin with HD-PTP (2017) Deepankar Gahloth Colin Levy Louise Walker Lydia Wunderley A Paul Mould Sandra Taylor Philip Woodman and Lydia Tabernero Strucutre 25(7)p1011ndash1024 Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine a Nonribosomal Peptide Building Block (2015) Veronica Diez Mark Loznik Sandra Taylor Michael Winn Nicholas J W Rattray Helen Podmore Jason Micklefield Royston Goodacre Marnix H Medema Ulrike Muller Roel Bovenberg Dick B Janssen and Eriko Takano ACS Synthetic Biology - Ali N Zhang L Taylor S Mironov A Urbeacute S Woodman P (2013) Recruitment of UBPY and ESCRT Exchange Drive HD-PTP-Dependent Sorting of EGFR to the MVB Curr Biol 23(6)453-61 UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting - Flavia Stefani Ling Zhang Sandra Taylor Johanna Donovan Sara Rollinson Aurelie Doyotte Kim Brownhill Janis Bennion Stuart Pickering-Brown Philip Woodman (2011) UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting Curr Biol 21(14)1245-50 - Addinall SG Mayr PS Doyle S Sheehan JK Woodman PW and Allan VJ (2001) Phosphorylation by cdc2-CyclinB1 kinase releases cytoplasmic dynein from membranes J Biol Chem 276 15939-15944 - Schultz E Carpenter R Doyle S and Coen E (2001) The gene finbriata interacts non-cell autonomously with floral regulatory genes The Plant Journal 25(5) 499-507 - McSteen PCM Vincent CA Doyle S Carpenter R and Coen ES (1999) Control of floral homeotic gene expression and organ morphogenesis in Antirhinum Development 125 2359-2369 - Ingram GC Doyle S Carpenter R Schultz EA Simon R and Coen ES (1997) Dual role for fimbriata in regulating floral homeotic genes and cell division in Antirhinum EMBO J 16 6521-6534 - Carpenter R Copsey L Vincent C Doyle S Magrath R and Coen E (1995) Control of flower development and phyllotaxy by meristem identity genes in Antirhinum The Plant Cell 7 2001-2011 - Simon R Carpenter R Doyle S and Coen ES (1994) Fimbriata controls flower development by mediating between mertistem and organ identity genes Cell 78 99-107 - Hudson A Carpenter R Doyle S and Coen ES (1993) Olive a key gene required for chlorophyll biosynthesis in Antirhinum majus EMBO J 12 3711-3719 - Luo D Coen ES Doyle S and Carpenter R (1991) Pigmentation mutants produced by transposon mutagenesis in Antirhinum majus Plant J 1 59-69 - Coen ES Romero JM Doyle S Elliott R Murphy G and Carpenter R (1990) Floricaula a homoetic gene required for flower development in Antirhinum majus Cell 63 1311-1322 Published Abstract Davies L Gkourtza A Symeou C Lynch J Taylor S Demonacos C and M Krstic-Demonacos (2009) Endocrine Abstracts 19 Society for Endocrinology BES 2009 -
Six Synthetic Biology Centres across the UK
bull Centre for Synthetic Biology and Innovation in London
bull Synthetic Biology Research Centre in Nottingham
bull BrisSynBio in Bristol
bull The UK Centre for Mammalian Synthetic Biology in Edinburgh
bull Warwick Integrative Synthetic Biology Centre
bull SYNBIOCHEM in Manchester (speciality and fine chemicals)
DESIGN-BUILD-TEST (What is SYNBIOCHEM)
Current research themes
bull Terpenoids
bull Alkaloids
bull Flavanoids
bull Technologyplatform development
Our semi-automated laboratory
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
bull 1987 - First lab job veterinary tests Bacteriology post mortems blood urine faeces tests etc
Small beginnings in Norwich after my first degree
Plant Molecular Genetics 1988 to 1998 ndash the lab grew from 6 to 16 people and several
papers were published on the way that flowering is controlled
1998 to 2001 Biochemistry Division School of Biological Sciences Manchester University ndash I supported 6 research groups sharing expertise
Topics from cell division (in toads) to asthma (in horses and people) and cultured human cells
Career Break from 2001 to 2007
bull Starting again after 6 years was a challenge but I soon got back up to speed Technical roles are very varied never boring a bit like being a Mum
2007 to present
bull I spent 7 years in the Michael Smith Building (Life Sciences) ndash various roles (cell culture cloning yeast two-hybrid)
bull In 2014 I moved to the MIB ndash more ChemistryBiochemistry focussed
Nano-scale 3D printing
Micro-titre plates with 96 384 or even 1536 sample wells ndash technology is being developed to ldquowriterdquo strings of DNA into these tiny wells using
3D nano-printing technology
Present Challenges Supporting SYNBIOCHEM
bull New subject(s) and equipment to learn about
bull The new SYMBIOCHEM team is 10 people and 4 robots
bull IT technology means writing electronic lab notebooks instead of paper ones
bull The new team is multidisciplinary so lots to learn but good fun
bull This is now the age of writing DNA as opposed to just reading it
Publications (please note publications I contributed prior to 2006 were under my maiden name of Doyle)
Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARAEndofin with HD-PTP (2017) Deepankar Gahloth Colin Levy Louise Walker Lydia Wunderley A Paul Mould Sandra Taylor Philip Woodman and Lydia Tabernero Strucutre 25(7)p1011ndash1024 Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine a Nonribosomal Peptide Building Block (2015) Veronica Diez Mark Loznik Sandra Taylor Michael Winn Nicholas J W Rattray Helen Podmore Jason Micklefield Royston Goodacre Marnix H Medema Ulrike Muller Roel Bovenberg Dick B Janssen and Eriko Takano ACS Synthetic Biology - Ali N Zhang L Taylor S Mironov A Urbeacute S Woodman P (2013) Recruitment of UBPY and ESCRT Exchange Drive HD-PTP-Dependent Sorting of EGFR to the MVB Curr Biol 23(6)453-61 UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting - Flavia Stefani Ling Zhang Sandra Taylor Johanna Donovan Sara Rollinson Aurelie Doyotte Kim Brownhill Janis Bennion Stuart Pickering-Brown Philip Woodman (2011) UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting Curr Biol 21(14)1245-50 - Addinall SG Mayr PS Doyle S Sheehan JK Woodman PW and Allan VJ (2001) Phosphorylation by cdc2-CyclinB1 kinase releases cytoplasmic dynein from membranes J Biol Chem 276 15939-15944 - Schultz E Carpenter R Doyle S and Coen E (2001) The gene finbriata interacts non-cell autonomously with floral regulatory genes The Plant Journal 25(5) 499-507 - McSteen PCM Vincent CA Doyle S Carpenter R and Coen ES (1999) Control of floral homeotic gene expression and organ morphogenesis in Antirhinum Development 125 2359-2369 - Ingram GC Doyle S Carpenter R Schultz EA Simon R and Coen ES (1997) Dual role for fimbriata in regulating floral homeotic genes and cell division in Antirhinum EMBO J 16 6521-6534 - Carpenter R Copsey L Vincent C Doyle S Magrath R and Coen E (1995) Control of flower development and phyllotaxy by meristem identity genes in Antirhinum The Plant Cell 7 2001-2011 - Simon R Carpenter R Doyle S and Coen ES (1994) Fimbriata controls flower development by mediating between mertistem and organ identity genes Cell 78 99-107 - Hudson A Carpenter R Doyle S and Coen ES (1993) Olive a key gene required for chlorophyll biosynthesis in Antirhinum majus EMBO J 12 3711-3719 - Luo D Coen ES Doyle S and Carpenter R (1991) Pigmentation mutants produced by transposon mutagenesis in Antirhinum majus Plant J 1 59-69 - Coen ES Romero JM Doyle S Elliott R Murphy G and Carpenter R (1990) Floricaula a homoetic gene required for flower development in Antirhinum majus Cell 63 1311-1322 Published Abstract Davies L Gkourtza A Symeou C Lynch J Taylor S Demonacos C and M Krstic-Demonacos (2009) Endocrine Abstracts 19 Society for Endocrinology BES 2009 -
Six Synthetic Biology Centres across the UK
bull Centre for Synthetic Biology and Innovation in London
bull Synthetic Biology Research Centre in Nottingham
bull BrisSynBio in Bristol
bull The UK Centre for Mammalian Synthetic Biology in Edinburgh
bull Warwick Integrative Synthetic Biology Centre
bull SYNBIOCHEM in Manchester (speciality and fine chemicals)
DESIGN-BUILD-TEST (What is SYNBIOCHEM)
Current research themes
bull Terpenoids
bull Alkaloids
bull Flavanoids
bull Technologyplatform development
Our semi-automated laboratory
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Plant Molecular Genetics 1988 to 1998 ndash the lab grew from 6 to 16 people and several
papers were published on the way that flowering is controlled
1998 to 2001 Biochemistry Division School of Biological Sciences Manchester University ndash I supported 6 research groups sharing expertise
Topics from cell division (in toads) to asthma (in horses and people) and cultured human cells
Career Break from 2001 to 2007
bull Starting again after 6 years was a challenge but I soon got back up to speed Technical roles are very varied never boring a bit like being a Mum
2007 to present
bull I spent 7 years in the Michael Smith Building (Life Sciences) ndash various roles (cell culture cloning yeast two-hybrid)
bull In 2014 I moved to the MIB ndash more ChemistryBiochemistry focussed
Nano-scale 3D printing
Micro-titre plates with 96 384 or even 1536 sample wells ndash technology is being developed to ldquowriterdquo strings of DNA into these tiny wells using
3D nano-printing technology
Present Challenges Supporting SYNBIOCHEM
bull New subject(s) and equipment to learn about
bull The new SYMBIOCHEM team is 10 people and 4 robots
bull IT technology means writing electronic lab notebooks instead of paper ones
bull The new team is multidisciplinary so lots to learn but good fun
bull This is now the age of writing DNA as opposed to just reading it
Publications (please note publications I contributed prior to 2006 were under my maiden name of Doyle)
Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARAEndofin with HD-PTP (2017) Deepankar Gahloth Colin Levy Louise Walker Lydia Wunderley A Paul Mould Sandra Taylor Philip Woodman and Lydia Tabernero Strucutre 25(7)p1011ndash1024 Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine a Nonribosomal Peptide Building Block (2015) Veronica Diez Mark Loznik Sandra Taylor Michael Winn Nicholas J W Rattray Helen Podmore Jason Micklefield Royston Goodacre Marnix H Medema Ulrike Muller Roel Bovenberg Dick B Janssen and Eriko Takano ACS Synthetic Biology - Ali N Zhang L Taylor S Mironov A Urbeacute S Woodman P (2013) Recruitment of UBPY and ESCRT Exchange Drive HD-PTP-Dependent Sorting of EGFR to the MVB Curr Biol 23(6)453-61 UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting - Flavia Stefani Ling Zhang Sandra Taylor Johanna Donovan Sara Rollinson Aurelie Doyotte Kim Brownhill Janis Bennion Stuart Pickering-Brown Philip Woodman (2011) UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting Curr Biol 21(14)1245-50 - Addinall SG Mayr PS Doyle S Sheehan JK Woodman PW and Allan VJ (2001) Phosphorylation by cdc2-CyclinB1 kinase releases cytoplasmic dynein from membranes J Biol Chem 276 15939-15944 - Schultz E Carpenter R Doyle S and Coen E (2001) The gene finbriata interacts non-cell autonomously with floral regulatory genes The Plant Journal 25(5) 499-507 - McSteen PCM Vincent CA Doyle S Carpenter R and Coen ES (1999) Control of floral homeotic gene expression and organ morphogenesis in Antirhinum Development 125 2359-2369 - Ingram GC Doyle S Carpenter R Schultz EA Simon R and Coen ES (1997) Dual role for fimbriata in regulating floral homeotic genes and cell division in Antirhinum EMBO J 16 6521-6534 - Carpenter R Copsey L Vincent C Doyle S Magrath R and Coen E (1995) Control of flower development and phyllotaxy by meristem identity genes in Antirhinum The Plant Cell 7 2001-2011 - Simon R Carpenter R Doyle S and Coen ES (1994) Fimbriata controls flower development by mediating between mertistem and organ identity genes Cell 78 99-107 - Hudson A Carpenter R Doyle S and Coen ES (1993) Olive a key gene required for chlorophyll biosynthesis in Antirhinum majus EMBO J 12 3711-3719 - Luo D Coen ES Doyle S and Carpenter R (1991) Pigmentation mutants produced by transposon mutagenesis in Antirhinum majus Plant J 1 59-69 - Coen ES Romero JM Doyle S Elliott R Murphy G and Carpenter R (1990) Floricaula a homoetic gene required for flower development in Antirhinum majus Cell 63 1311-1322 Published Abstract Davies L Gkourtza A Symeou C Lynch J Taylor S Demonacos C and M Krstic-Demonacos (2009) Endocrine Abstracts 19 Society for Endocrinology BES 2009 -
Six Synthetic Biology Centres across the UK
bull Centre for Synthetic Biology and Innovation in London
bull Synthetic Biology Research Centre in Nottingham
bull BrisSynBio in Bristol
bull The UK Centre for Mammalian Synthetic Biology in Edinburgh
bull Warwick Integrative Synthetic Biology Centre
bull SYNBIOCHEM in Manchester (speciality and fine chemicals)
DESIGN-BUILD-TEST (What is SYNBIOCHEM)
Current research themes
bull Terpenoids
bull Alkaloids
bull Flavanoids
bull Technologyplatform development
Our semi-automated laboratory
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
1998 to 2001 Biochemistry Division School of Biological Sciences Manchester University ndash I supported 6 research groups sharing expertise
Topics from cell division (in toads) to asthma (in horses and people) and cultured human cells
Career Break from 2001 to 2007
bull Starting again after 6 years was a challenge but I soon got back up to speed Technical roles are very varied never boring a bit like being a Mum
2007 to present
bull I spent 7 years in the Michael Smith Building (Life Sciences) ndash various roles (cell culture cloning yeast two-hybrid)
bull In 2014 I moved to the MIB ndash more ChemistryBiochemistry focussed
Nano-scale 3D printing
Micro-titre plates with 96 384 or even 1536 sample wells ndash technology is being developed to ldquowriterdquo strings of DNA into these tiny wells using
3D nano-printing technology
Present Challenges Supporting SYNBIOCHEM
bull New subject(s) and equipment to learn about
bull The new SYMBIOCHEM team is 10 people and 4 robots
bull IT technology means writing electronic lab notebooks instead of paper ones
bull The new team is multidisciplinary so lots to learn but good fun
bull This is now the age of writing DNA as opposed to just reading it
Publications (please note publications I contributed prior to 2006 were under my maiden name of Doyle)
Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARAEndofin with HD-PTP (2017) Deepankar Gahloth Colin Levy Louise Walker Lydia Wunderley A Paul Mould Sandra Taylor Philip Woodman and Lydia Tabernero Strucutre 25(7)p1011ndash1024 Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine a Nonribosomal Peptide Building Block (2015) Veronica Diez Mark Loznik Sandra Taylor Michael Winn Nicholas J W Rattray Helen Podmore Jason Micklefield Royston Goodacre Marnix H Medema Ulrike Muller Roel Bovenberg Dick B Janssen and Eriko Takano ACS Synthetic Biology - Ali N Zhang L Taylor S Mironov A Urbeacute S Woodman P (2013) Recruitment of UBPY and ESCRT Exchange Drive HD-PTP-Dependent Sorting of EGFR to the MVB Curr Biol 23(6)453-61 UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting - Flavia Stefani Ling Zhang Sandra Taylor Johanna Donovan Sara Rollinson Aurelie Doyotte Kim Brownhill Janis Bennion Stuart Pickering-Brown Philip Woodman (2011) UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting Curr Biol 21(14)1245-50 - Addinall SG Mayr PS Doyle S Sheehan JK Woodman PW and Allan VJ (2001) Phosphorylation by cdc2-CyclinB1 kinase releases cytoplasmic dynein from membranes J Biol Chem 276 15939-15944 - Schultz E Carpenter R Doyle S and Coen E (2001) The gene finbriata interacts non-cell autonomously with floral regulatory genes The Plant Journal 25(5) 499-507 - McSteen PCM Vincent CA Doyle S Carpenter R and Coen ES (1999) Control of floral homeotic gene expression and organ morphogenesis in Antirhinum Development 125 2359-2369 - Ingram GC Doyle S Carpenter R Schultz EA Simon R and Coen ES (1997) Dual role for fimbriata in regulating floral homeotic genes and cell division in Antirhinum EMBO J 16 6521-6534 - Carpenter R Copsey L Vincent C Doyle S Magrath R and Coen E (1995) Control of flower development and phyllotaxy by meristem identity genes in Antirhinum The Plant Cell 7 2001-2011 - Simon R Carpenter R Doyle S and Coen ES (1994) Fimbriata controls flower development by mediating between mertistem and organ identity genes Cell 78 99-107 - Hudson A Carpenter R Doyle S and Coen ES (1993) Olive a key gene required for chlorophyll biosynthesis in Antirhinum majus EMBO J 12 3711-3719 - Luo D Coen ES Doyle S and Carpenter R (1991) Pigmentation mutants produced by transposon mutagenesis in Antirhinum majus Plant J 1 59-69 - Coen ES Romero JM Doyle S Elliott R Murphy G and Carpenter R (1990) Floricaula a homoetic gene required for flower development in Antirhinum majus Cell 63 1311-1322 Published Abstract Davies L Gkourtza A Symeou C Lynch J Taylor S Demonacos C and M Krstic-Demonacos (2009) Endocrine Abstracts 19 Society for Endocrinology BES 2009 -
Six Synthetic Biology Centres across the UK
bull Centre for Synthetic Biology and Innovation in London
bull Synthetic Biology Research Centre in Nottingham
bull BrisSynBio in Bristol
bull The UK Centre for Mammalian Synthetic Biology in Edinburgh
bull Warwick Integrative Synthetic Biology Centre
bull SYNBIOCHEM in Manchester (speciality and fine chemicals)
DESIGN-BUILD-TEST (What is SYNBIOCHEM)
Current research themes
bull Terpenoids
bull Alkaloids
bull Flavanoids
bull Technologyplatform development
Our semi-automated laboratory
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Career Break from 2001 to 2007
bull Starting again after 6 years was a challenge but I soon got back up to speed Technical roles are very varied never boring a bit like being a Mum
2007 to present
bull I spent 7 years in the Michael Smith Building (Life Sciences) ndash various roles (cell culture cloning yeast two-hybrid)
bull In 2014 I moved to the MIB ndash more ChemistryBiochemistry focussed
Nano-scale 3D printing
Micro-titre plates with 96 384 or even 1536 sample wells ndash technology is being developed to ldquowriterdquo strings of DNA into these tiny wells using
3D nano-printing technology
Present Challenges Supporting SYNBIOCHEM
bull New subject(s) and equipment to learn about
bull The new SYMBIOCHEM team is 10 people and 4 robots
bull IT technology means writing electronic lab notebooks instead of paper ones
bull The new team is multidisciplinary so lots to learn but good fun
bull This is now the age of writing DNA as opposed to just reading it
Publications (please note publications I contributed prior to 2006 were under my maiden name of Doyle)
Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARAEndofin with HD-PTP (2017) Deepankar Gahloth Colin Levy Louise Walker Lydia Wunderley A Paul Mould Sandra Taylor Philip Woodman and Lydia Tabernero Strucutre 25(7)p1011ndash1024 Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine a Nonribosomal Peptide Building Block (2015) Veronica Diez Mark Loznik Sandra Taylor Michael Winn Nicholas J W Rattray Helen Podmore Jason Micklefield Royston Goodacre Marnix H Medema Ulrike Muller Roel Bovenberg Dick B Janssen and Eriko Takano ACS Synthetic Biology - Ali N Zhang L Taylor S Mironov A Urbeacute S Woodman P (2013) Recruitment of UBPY and ESCRT Exchange Drive HD-PTP-Dependent Sorting of EGFR to the MVB Curr Biol 23(6)453-61 UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting - Flavia Stefani Ling Zhang Sandra Taylor Johanna Donovan Sara Rollinson Aurelie Doyotte Kim Brownhill Janis Bennion Stuart Pickering-Brown Philip Woodman (2011) UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting Curr Biol 21(14)1245-50 - Addinall SG Mayr PS Doyle S Sheehan JK Woodman PW and Allan VJ (2001) Phosphorylation by cdc2-CyclinB1 kinase releases cytoplasmic dynein from membranes J Biol Chem 276 15939-15944 - Schultz E Carpenter R Doyle S and Coen E (2001) The gene finbriata interacts non-cell autonomously with floral regulatory genes The Plant Journal 25(5) 499-507 - McSteen PCM Vincent CA Doyle S Carpenter R and Coen ES (1999) Control of floral homeotic gene expression and organ morphogenesis in Antirhinum Development 125 2359-2369 - Ingram GC Doyle S Carpenter R Schultz EA Simon R and Coen ES (1997) Dual role for fimbriata in regulating floral homeotic genes and cell division in Antirhinum EMBO J 16 6521-6534 - Carpenter R Copsey L Vincent C Doyle S Magrath R and Coen E (1995) Control of flower development and phyllotaxy by meristem identity genes in Antirhinum The Plant Cell 7 2001-2011 - Simon R Carpenter R Doyle S and Coen ES (1994) Fimbriata controls flower development by mediating between mertistem and organ identity genes Cell 78 99-107 - Hudson A Carpenter R Doyle S and Coen ES (1993) Olive a key gene required for chlorophyll biosynthesis in Antirhinum majus EMBO J 12 3711-3719 - Luo D Coen ES Doyle S and Carpenter R (1991) Pigmentation mutants produced by transposon mutagenesis in Antirhinum majus Plant J 1 59-69 - Coen ES Romero JM Doyle S Elliott R Murphy G and Carpenter R (1990) Floricaula a homoetic gene required for flower development in Antirhinum majus Cell 63 1311-1322 Published Abstract Davies L Gkourtza A Symeou C Lynch J Taylor S Demonacos C and M Krstic-Demonacos (2009) Endocrine Abstracts 19 Society for Endocrinology BES 2009 -
Six Synthetic Biology Centres across the UK
bull Centre for Synthetic Biology and Innovation in London
bull Synthetic Biology Research Centre in Nottingham
bull BrisSynBio in Bristol
bull The UK Centre for Mammalian Synthetic Biology in Edinburgh
bull Warwick Integrative Synthetic Biology Centre
bull SYNBIOCHEM in Manchester (speciality and fine chemicals)
DESIGN-BUILD-TEST (What is SYNBIOCHEM)
Current research themes
bull Terpenoids
bull Alkaloids
bull Flavanoids
bull Technologyplatform development
Our semi-automated laboratory
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
2007 to present
bull I spent 7 years in the Michael Smith Building (Life Sciences) ndash various roles (cell culture cloning yeast two-hybrid)
bull In 2014 I moved to the MIB ndash more ChemistryBiochemistry focussed
Nano-scale 3D printing
Micro-titre plates with 96 384 or even 1536 sample wells ndash technology is being developed to ldquowriterdquo strings of DNA into these tiny wells using
3D nano-printing technology
Present Challenges Supporting SYNBIOCHEM
bull New subject(s) and equipment to learn about
bull The new SYMBIOCHEM team is 10 people and 4 robots
bull IT technology means writing electronic lab notebooks instead of paper ones
bull The new team is multidisciplinary so lots to learn but good fun
bull This is now the age of writing DNA as opposed to just reading it
Publications (please note publications I contributed prior to 2006 were under my maiden name of Doyle)
Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARAEndofin with HD-PTP (2017) Deepankar Gahloth Colin Levy Louise Walker Lydia Wunderley A Paul Mould Sandra Taylor Philip Woodman and Lydia Tabernero Strucutre 25(7)p1011ndash1024 Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine a Nonribosomal Peptide Building Block (2015) Veronica Diez Mark Loznik Sandra Taylor Michael Winn Nicholas J W Rattray Helen Podmore Jason Micklefield Royston Goodacre Marnix H Medema Ulrike Muller Roel Bovenberg Dick B Janssen and Eriko Takano ACS Synthetic Biology - Ali N Zhang L Taylor S Mironov A Urbeacute S Woodman P (2013) Recruitment of UBPY and ESCRT Exchange Drive HD-PTP-Dependent Sorting of EGFR to the MVB Curr Biol 23(6)453-61 UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting - Flavia Stefani Ling Zhang Sandra Taylor Johanna Donovan Sara Rollinson Aurelie Doyotte Kim Brownhill Janis Bennion Stuart Pickering-Brown Philip Woodman (2011) UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting Curr Biol 21(14)1245-50 - Addinall SG Mayr PS Doyle S Sheehan JK Woodman PW and Allan VJ (2001) Phosphorylation by cdc2-CyclinB1 kinase releases cytoplasmic dynein from membranes J Biol Chem 276 15939-15944 - Schultz E Carpenter R Doyle S and Coen E (2001) The gene finbriata interacts non-cell autonomously with floral regulatory genes The Plant Journal 25(5) 499-507 - McSteen PCM Vincent CA Doyle S Carpenter R and Coen ES (1999) Control of floral homeotic gene expression and organ morphogenesis in Antirhinum Development 125 2359-2369 - Ingram GC Doyle S Carpenter R Schultz EA Simon R and Coen ES (1997) Dual role for fimbriata in regulating floral homeotic genes and cell division in Antirhinum EMBO J 16 6521-6534 - Carpenter R Copsey L Vincent C Doyle S Magrath R and Coen E (1995) Control of flower development and phyllotaxy by meristem identity genes in Antirhinum The Plant Cell 7 2001-2011 - Simon R Carpenter R Doyle S and Coen ES (1994) Fimbriata controls flower development by mediating between mertistem and organ identity genes Cell 78 99-107 - Hudson A Carpenter R Doyle S and Coen ES (1993) Olive a key gene required for chlorophyll biosynthesis in Antirhinum majus EMBO J 12 3711-3719 - Luo D Coen ES Doyle S and Carpenter R (1991) Pigmentation mutants produced by transposon mutagenesis in Antirhinum majus Plant J 1 59-69 - Coen ES Romero JM Doyle S Elliott R Murphy G and Carpenter R (1990) Floricaula a homoetic gene required for flower development in Antirhinum majus Cell 63 1311-1322 Published Abstract Davies L Gkourtza A Symeou C Lynch J Taylor S Demonacos C and M Krstic-Demonacos (2009) Endocrine Abstracts 19 Society for Endocrinology BES 2009 -
Six Synthetic Biology Centres across the UK
bull Centre for Synthetic Biology and Innovation in London
bull Synthetic Biology Research Centre in Nottingham
bull BrisSynBio in Bristol
bull The UK Centre for Mammalian Synthetic Biology in Edinburgh
bull Warwick Integrative Synthetic Biology Centre
bull SYNBIOCHEM in Manchester (speciality and fine chemicals)
DESIGN-BUILD-TEST (What is SYNBIOCHEM)
Current research themes
bull Terpenoids
bull Alkaloids
bull Flavanoids
bull Technologyplatform development
Our semi-automated laboratory
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Nano-scale 3D printing
Micro-titre plates with 96 384 or even 1536 sample wells ndash technology is being developed to ldquowriterdquo strings of DNA into these tiny wells using
3D nano-printing technology
Present Challenges Supporting SYNBIOCHEM
bull New subject(s) and equipment to learn about
bull The new SYMBIOCHEM team is 10 people and 4 robots
bull IT technology means writing electronic lab notebooks instead of paper ones
bull The new team is multidisciplinary so lots to learn but good fun
bull This is now the age of writing DNA as opposed to just reading it
Publications (please note publications I contributed prior to 2006 were under my maiden name of Doyle)
Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARAEndofin with HD-PTP (2017) Deepankar Gahloth Colin Levy Louise Walker Lydia Wunderley A Paul Mould Sandra Taylor Philip Woodman and Lydia Tabernero Strucutre 25(7)p1011ndash1024 Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine a Nonribosomal Peptide Building Block (2015) Veronica Diez Mark Loznik Sandra Taylor Michael Winn Nicholas J W Rattray Helen Podmore Jason Micklefield Royston Goodacre Marnix H Medema Ulrike Muller Roel Bovenberg Dick B Janssen and Eriko Takano ACS Synthetic Biology - Ali N Zhang L Taylor S Mironov A Urbeacute S Woodman P (2013) Recruitment of UBPY and ESCRT Exchange Drive HD-PTP-Dependent Sorting of EGFR to the MVB Curr Biol 23(6)453-61 UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting - Flavia Stefani Ling Zhang Sandra Taylor Johanna Donovan Sara Rollinson Aurelie Doyotte Kim Brownhill Janis Bennion Stuart Pickering-Brown Philip Woodman (2011) UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting Curr Biol 21(14)1245-50 - Addinall SG Mayr PS Doyle S Sheehan JK Woodman PW and Allan VJ (2001) Phosphorylation by cdc2-CyclinB1 kinase releases cytoplasmic dynein from membranes J Biol Chem 276 15939-15944 - Schultz E Carpenter R Doyle S and Coen E (2001) The gene finbriata interacts non-cell autonomously with floral regulatory genes The Plant Journal 25(5) 499-507 - McSteen PCM Vincent CA Doyle S Carpenter R and Coen ES (1999) Control of floral homeotic gene expression and organ morphogenesis in Antirhinum Development 125 2359-2369 - Ingram GC Doyle S Carpenter R Schultz EA Simon R and Coen ES (1997) Dual role for fimbriata in regulating floral homeotic genes and cell division in Antirhinum EMBO J 16 6521-6534 - Carpenter R Copsey L Vincent C Doyle S Magrath R and Coen E (1995) Control of flower development and phyllotaxy by meristem identity genes in Antirhinum The Plant Cell 7 2001-2011 - Simon R Carpenter R Doyle S and Coen ES (1994) Fimbriata controls flower development by mediating between mertistem and organ identity genes Cell 78 99-107 - Hudson A Carpenter R Doyle S and Coen ES (1993) Olive a key gene required for chlorophyll biosynthesis in Antirhinum majus EMBO J 12 3711-3719 - Luo D Coen ES Doyle S and Carpenter R (1991) Pigmentation mutants produced by transposon mutagenesis in Antirhinum majus Plant J 1 59-69 - Coen ES Romero JM Doyle S Elliott R Murphy G and Carpenter R (1990) Floricaula a homoetic gene required for flower development in Antirhinum majus Cell 63 1311-1322 Published Abstract Davies L Gkourtza A Symeou C Lynch J Taylor S Demonacos C and M Krstic-Demonacos (2009) Endocrine Abstracts 19 Society for Endocrinology BES 2009 -
Six Synthetic Biology Centres across the UK
bull Centre for Synthetic Biology and Innovation in London
bull Synthetic Biology Research Centre in Nottingham
bull BrisSynBio in Bristol
bull The UK Centre for Mammalian Synthetic Biology in Edinburgh
bull Warwick Integrative Synthetic Biology Centre
bull SYNBIOCHEM in Manchester (speciality and fine chemicals)
DESIGN-BUILD-TEST (What is SYNBIOCHEM)
Current research themes
bull Terpenoids
bull Alkaloids
bull Flavanoids
bull Technologyplatform development
Our semi-automated laboratory
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Present Challenges Supporting SYNBIOCHEM
bull New subject(s) and equipment to learn about
bull The new SYMBIOCHEM team is 10 people and 4 robots
bull IT technology means writing electronic lab notebooks instead of paper ones
bull The new team is multidisciplinary so lots to learn but good fun
bull This is now the age of writing DNA as opposed to just reading it
Publications (please note publications I contributed prior to 2006 were under my maiden name of Doyle)
Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARAEndofin with HD-PTP (2017) Deepankar Gahloth Colin Levy Louise Walker Lydia Wunderley A Paul Mould Sandra Taylor Philip Woodman and Lydia Tabernero Strucutre 25(7)p1011ndash1024 Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine a Nonribosomal Peptide Building Block (2015) Veronica Diez Mark Loznik Sandra Taylor Michael Winn Nicholas J W Rattray Helen Podmore Jason Micklefield Royston Goodacre Marnix H Medema Ulrike Muller Roel Bovenberg Dick B Janssen and Eriko Takano ACS Synthetic Biology - Ali N Zhang L Taylor S Mironov A Urbeacute S Woodman P (2013) Recruitment of UBPY and ESCRT Exchange Drive HD-PTP-Dependent Sorting of EGFR to the MVB Curr Biol 23(6)453-61 UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting - Flavia Stefani Ling Zhang Sandra Taylor Johanna Donovan Sara Rollinson Aurelie Doyotte Kim Brownhill Janis Bennion Stuart Pickering-Brown Philip Woodman (2011) UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting Curr Biol 21(14)1245-50 - Addinall SG Mayr PS Doyle S Sheehan JK Woodman PW and Allan VJ (2001) Phosphorylation by cdc2-CyclinB1 kinase releases cytoplasmic dynein from membranes J Biol Chem 276 15939-15944 - Schultz E Carpenter R Doyle S and Coen E (2001) The gene finbriata interacts non-cell autonomously with floral regulatory genes The Plant Journal 25(5) 499-507 - McSteen PCM Vincent CA Doyle S Carpenter R and Coen ES (1999) Control of floral homeotic gene expression and organ morphogenesis in Antirhinum Development 125 2359-2369 - Ingram GC Doyle S Carpenter R Schultz EA Simon R and Coen ES (1997) Dual role for fimbriata in regulating floral homeotic genes and cell division in Antirhinum EMBO J 16 6521-6534 - Carpenter R Copsey L Vincent C Doyle S Magrath R and Coen E (1995) Control of flower development and phyllotaxy by meristem identity genes in Antirhinum The Plant Cell 7 2001-2011 - Simon R Carpenter R Doyle S and Coen ES (1994) Fimbriata controls flower development by mediating between mertistem and organ identity genes Cell 78 99-107 - Hudson A Carpenter R Doyle S and Coen ES (1993) Olive a key gene required for chlorophyll biosynthesis in Antirhinum majus EMBO J 12 3711-3719 - Luo D Coen ES Doyle S and Carpenter R (1991) Pigmentation mutants produced by transposon mutagenesis in Antirhinum majus Plant J 1 59-69 - Coen ES Romero JM Doyle S Elliott R Murphy G and Carpenter R (1990) Floricaula a homoetic gene required for flower development in Antirhinum majus Cell 63 1311-1322 Published Abstract Davies L Gkourtza A Symeou C Lynch J Taylor S Demonacos C and M Krstic-Demonacos (2009) Endocrine Abstracts 19 Society for Endocrinology BES 2009 -
Six Synthetic Biology Centres across the UK
bull Centre for Synthetic Biology and Innovation in London
bull Synthetic Biology Research Centre in Nottingham
bull BrisSynBio in Bristol
bull The UK Centre for Mammalian Synthetic Biology in Edinburgh
bull Warwick Integrative Synthetic Biology Centre
bull SYNBIOCHEM in Manchester (speciality and fine chemicals)
DESIGN-BUILD-TEST (What is SYNBIOCHEM)
Current research themes
bull Terpenoids
bull Alkaloids
bull Flavanoids
bull Technologyplatform development
Our semi-automated laboratory
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Publications (please note publications I contributed prior to 2006 were under my maiden name of Doyle)
Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARAEndofin with HD-PTP (2017) Deepankar Gahloth Colin Levy Louise Walker Lydia Wunderley A Paul Mould Sandra Taylor Philip Woodman and Lydia Tabernero Strucutre 25(7)p1011ndash1024 Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine a Nonribosomal Peptide Building Block (2015) Veronica Diez Mark Loznik Sandra Taylor Michael Winn Nicholas J W Rattray Helen Podmore Jason Micklefield Royston Goodacre Marnix H Medema Ulrike Muller Roel Bovenberg Dick B Janssen and Eriko Takano ACS Synthetic Biology - Ali N Zhang L Taylor S Mironov A Urbeacute S Woodman P (2013) Recruitment of UBPY and ESCRT Exchange Drive HD-PTP-Dependent Sorting of EGFR to the MVB Curr Biol 23(6)453-61 UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting - Flavia Stefani Ling Zhang Sandra Taylor Johanna Donovan Sara Rollinson Aurelie Doyotte Kim Brownhill Janis Bennion Stuart Pickering-Brown Philip Woodman (2011) UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting Curr Biol 21(14)1245-50 - Addinall SG Mayr PS Doyle S Sheehan JK Woodman PW and Allan VJ (2001) Phosphorylation by cdc2-CyclinB1 kinase releases cytoplasmic dynein from membranes J Biol Chem 276 15939-15944 - Schultz E Carpenter R Doyle S and Coen E (2001) The gene finbriata interacts non-cell autonomously with floral regulatory genes The Plant Journal 25(5) 499-507 - McSteen PCM Vincent CA Doyle S Carpenter R and Coen ES (1999) Control of floral homeotic gene expression and organ morphogenesis in Antirhinum Development 125 2359-2369 - Ingram GC Doyle S Carpenter R Schultz EA Simon R and Coen ES (1997) Dual role for fimbriata in regulating floral homeotic genes and cell division in Antirhinum EMBO J 16 6521-6534 - Carpenter R Copsey L Vincent C Doyle S Magrath R and Coen E (1995) Control of flower development and phyllotaxy by meristem identity genes in Antirhinum The Plant Cell 7 2001-2011 - Simon R Carpenter R Doyle S and Coen ES (1994) Fimbriata controls flower development by mediating between mertistem and organ identity genes Cell 78 99-107 - Hudson A Carpenter R Doyle S and Coen ES (1993) Olive a key gene required for chlorophyll biosynthesis in Antirhinum majus EMBO J 12 3711-3719 - Luo D Coen ES Doyle S and Carpenter R (1991) Pigmentation mutants produced by transposon mutagenesis in Antirhinum majus Plant J 1 59-69 - Coen ES Romero JM Doyle S Elliott R Murphy G and Carpenter R (1990) Floricaula a homoetic gene required for flower development in Antirhinum majus Cell 63 1311-1322 Published Abstract Davies L Gkourtza A Symeou C Lynch J Taylor S Demonacos C and M Krstic-Demonacos (2009) Endocrine Abstracts 19 Society for Endocrinology BES 2009 -
Six Synthetic Biology Centres across the UK
bull Centre for Synthetic Biology and Innovation in London
bull Synthetic Biology Research Centre in Nottingham
bull BrisSynBio in Bristol
bull The UK Centre for Mammalian Synthetic Biology in Edinburgh
bull Warwick Integrative Synthetic Biology Centre
bull SYNBIOCHEM in Manchester (speciality and fine chemicals)
DESIGN-BUILD-TEST (What is SYNBIOCHEM)
Current research themes
bull Terpenoids
bull Alkaloids
bull Flavanoids
bull Technologyplatform development
Our semi-automated laboratory
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Six Synthetic Biology Centres across the UK
bull Centre for Synthetic Biology and Innovation in London
bull Synthetic Biology Research Centre in Nottingham
bull BrisSynBio in Bristol
bull The UK Centre for Mammalian Synthetic Biology in Edinburgh
bull Warwick Integrative Synthetic Biology Centre
bull SYNBIOCHEM in Manchester (speciality and fine chemicals)
DESIGN-BUILD-TEST (What is SYNBIOCHEM)
Current research themes
bull Terpenoids
bull Alkaloids
bull Flavanoids
bull Technologyplatform development
Our semi-automated laboratory
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
DESIGN-BUILD-TEST (What is SYNBIOCHEM)
Current research themes
bull Terpenoids
bull Alkaloids
bull Flavanoids
bull Technologyplatform development
Our semi-automated laboratory
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Current research themes
bull Terpenoids
bull Alkaloids
bull Flavanoids
bull Technologyplatform development
Our semi-automated laboratory
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Our semi-automated laboratory
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
SYNBIOCHEMndasha SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell Andrew Currin Mark Dunstan Donal Fellows Adrian Jervis Nicholas JW Rattray Christopher J Robinson Neil Swainston Maria Vinaixa Alan Williams Cunyu Yan Perdita Barran Rainer Breitling George Guo-Qiang Chen Jean-Loup Faulon Carole Goble Royston Goodacre Douglas B Kell Rosalind Le Feuvre Jason Micklefield Nigel S Scrutton Philip Shapira Eriko Takano Nicholas J Turner Biochemical Society Transactions Jun 09 201644(3)675-677DOI 101042BST20160009 ldquoThe Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals The Centres integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals productionrdquo
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Scientometrics September 2017 Volume 112 Issue 3 pp 1439ndash1469
ldquoTracking the emergence of synthetic biologyrdquo Philip Shapira Seokbeom Kwon Jan Youtie
ldquoSynthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research innovation and policy interest in recent yearsrdquo
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Fragrances and flavours
Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages These can be produced naturally but sometimes there is more demand than can be supplied We will look at a range of natural ldquosmellsrdquo and ask how these can be used and whether there are any substitutes Part of our research is to look at novel ways to make in-demand fragrances
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
The search for novel materials
bull Materials (Basel) 2016 Jul 119(7) pii E560 doi 103390ma9070560
bull Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering
bull Hardy JG1 Torres-Rendon JG2 Leal-Egantildea A3 Walther A4 Schlaad H5 Coumllfen H6 Scheibel TR7 bull Author information bull Abstract bull Materials based on biodegradable polyesters such as poly(butylene terephthalate) (PBT) or
poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT) have potential application as pro-regenerative scaffolds for bone tissue engineering Herein the preparation of films composed of PBT or PBTAT and an engineered spider silk protein (eADF4(C16)) that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering
bull KEYWORDS bull biodegradable polymers biomaterials biomineralization bone tissue engineering recombinant
protein spider silk bull PMID 28773681 PMCID PMC5456849 DOI 103390ma9070560
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Menthol
Minty flavour cool sensation
Mentha avensis and mentha piperita
Used for over 2000 years in some parts of the world
Earliest reference in the West in 1771
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Novel ways to produce rare or novel compounds
bull Select a host organism to express the chosen enzyme pathway ndash Escherichia coli yeast etc
bull Design team use Big Data and algorithms to select good candidate pathways ndash varying elements like varying strength promoters ribosomal binding sites heterologous enzymes with useful function etc
bull Build team use automation to assemble and then express as many permutations as possible
bull Test team analyse the expressed compounds to identify what amount of target chemical was synthesised
bull Design team analyse results and re-run algorithms to come up with better designs which are then made and tested
bull Finally strain and media optimisation to maximise yields
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Advantages
bull Relatively cheap feed stocks (eg glucose and glycerol) bull Using relatively simple host organisms well
characterised defined media and growth conditions bull Able to test many permutations of pathways quickly to
optimise production bull Some chemical processes are expensive or difficult but
biological enzymes could do the same job bull Agriculture is crop dependent (time of year) and
weather dependent and for example vanilla is in higher demand than can be produced naturally
bull Biological enzyme promiscuity (substitution)
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Disadvantages
bull Co-factors and supplements may be expensive
bull Biological enzyme promiscuity
bull Metabolic pathways complex
bull May impact traditional agriculture
bull Chemical methods tried and tested
bull
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Automation and the Technician
bull As Robots and Artificial Intelligence are found increasingly frequently in Industry and the workplace how will this change the technical role
bull Advantages for large scale and repetitive tasks eg 96 format sequening PCR DNA assembly etc
bull Not so good for fine tuning protocol optimisation biological variation (eg colony picking)
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Acknowlegements bull Nick Weisse (Public outreach)
bull Helen Toogood (Design an enzyme)
bull Rob Meckin
bull Barbara Ribeiro
bull SYNBIOCHEM Directors Prof Nigel Scrutton Prof Eriko Takano and Prof Nick Turner
bull Director of Operations Dr Ros Le Feuvre
bull And my team
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung
Neil Swainston
Alan Williams
Maria Vinaixa
Andy Currin
Mark Dunstan
Adrian Jervis
Donal Fellows
Ros Le Feuvre
Cunyu Yan Nik Rattray
Kat Holloywood
Reynard Speiss Rehana Sung