D B Archer

Summary

Affiliation: University of Nottingham
Country: UK

Publications

  1. pmc Population heterogeneity and dynamics in starter culture and lag phase adaptation of the spoilage yeast Zygosaccharomyces bailii to weak acid preservatives
    Malcolm Stratford
    School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom Mologic Ltd, Bedford Technology Park, Thurleigh, Bedford, MK44 2YP, United Kingdom Electronic address
    Int J Food Microbiol 181:40-7. 2014
  2. pmc Extreme resistance to weak-acid preservatives in the spoilage yeast Zygosaccharomyces bailii
    Malcolm Stratford
    School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
    Int J Food Microbiol 166:126-34. 2013
  3. ncbi request reprint The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger
    Jolanda M van Munster
    School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK Electronic address
    Fungal Genet Biol 72:34-47. 2014
  4. pmc Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger
    Laure Ries
    School of Biology, University of Nottingham, Nottingham NG7 2RD, UK
    BMC Genomics 14:541. 2013
  5. pmc Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing
    Stéphane Delmas
    School of Biology, University of Nottingham, Nottingham, United Kingdom
    PLoS Genet 8:e1002875. 2012
  6. pmc Native-state stability determines the extent of degradation relative to secretion of protein variants from Pichia pastoris
    Graham Whyteside
    School of Biology, University of Nottingham, Nottingham, United Kingdom
    PLoS ONE 6:e22692. 2011
  7. pmc Genome-wide expression analysis upon constitutive activation of the HacA bZIP transcription factor in Aspergillus niger reveals a coordinated cellular response to counteract ER stress
    Neuza Dsp Carvalho
    Institute of Biology Leiden, Leiden University, Molecular Microbiology and Biotechnology, BE Leiden, The Netherlands
    BMC Genomics 13:350. 2012
  8. pmc Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing
    Michaela Novodvorska
    School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
    BMC Genomics 14:246. 2013
  9. pmc Genomic analysis of the secretion stress response in the enzyme-producing cell factory Aspergillus niger
    Thomas Guillemette
    School of Biology, University of Nottingham, University Park, Nottingham, UK
    BMC Genomics 8:158. 2007
  10. pmc Decarboxylation of sorbic acid by spoilage yeasts is associated with the PAD1 gene
    Malcolm Stratford
    School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
    Appl Environ Microbiol 73:6534-42. 2007

Detail Information

Publications49

  1. pmc Population heterogeneity and dynamics in starter culture and lag phase adaptation of the spoilage yeast Zygosaccharomyces bailii to weak acid preservatives
    Malcolm Stratford
    School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom Mologic Ltd, Bedford Technology Park, Thurleigh, Bedford, MK44 2YP, United Kingdom Electronic address
    Int J Food Microbiol 181:40-7. 2014
    ..bailii to sorbic acid. Furthermore, the significance of phenotypic diversity and heterogeneity in microbial populations is discussed more broadly with potential relevance to bacterial "persisters", natural selection and evolution...
  2. pmc Extreme resistance to weak-acid preservatives in the spoilage yeast Zygosaccharomyces bailii
    Malcolm Stratford
    School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
    Int J Food Microbiol 166:126-34. 2013
    ..This reduces the level of accumulation of any weak acid in the cytoplasm, thus conferring resistance to all weak acids, but not to other inhibitors. ..
  3. ncbi request reprint The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger
    Jolanda M van Munster
    School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK Electronic address
    Fungal Genet Biol 72:34-47. 2014
    ..Analysis of the enzymatic activity and the reaction products, indicates that these proteins are enzymes that can degrade various plant polysaccharides to generate both known, as well as potentially new, inducers of CAZymes. ..
  4. pmc Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger
    Laure Ries
    School of Biology, University of Nottingham, Nottingham NG7 2RD, UK
    BMC Genomics 14:541. 2013
    ..The global induction of genes in response to exposure of T. reesei to wheat straw was explored using RNA-seq and compared to published RNA-seq data and model of how A. niger senses and responds to wheat straw...
  5. pmc Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing
    Stéphane Delmas
    School of Biology, University of Nottingham, Nottingham, United Kingdom
    PLoS Genet 8:e1002875. 2012
    ..We also showed that antisense transcripts are abundant and that their expression can be regulated by growth conditions...
  6. pmc Native-state stability determines the extent of degradation relative to secretion of protein variants from Pichia pastoris
    Graham Whyteside
    School of Biology, University of Nottingham, Nottingham, United Kingdom
    PLoS ONE 6:e22692. 2011
    ..We discuss the secretion of proteins in relation to lysozyme amyloidosis, in particular, and optimised protein secretion, in general...
  7. pmc Genome-wide expression analysis upon constitutive activation of the HacA bZIP transcription factor in Aspergillus niger reveals a coordinated cellular response to counteract ER stress
    Neuza Dsp Carvalho
    Institute of Biology Leiden, Leiden University, Molecular Microbiology and Biotechnology, BE Leiden, The Netherlands
    BMC Genomics 13:350. 2012
    ..The impact of constitutive HacA activity during exponential growth was explored in bioreactor controlled cultures using transcriptomic analysis to identify affected genes and processes...
  8. pmc Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing
    Michaela Novodvorska
    School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
    BMC Genomics 14:246. 2013
    ..niger conidia using both next generation RNA-sequencing and GeneChips. The metabolism of storage compounds during conidial germination was also examined and compared to the transcript levels from associated genes...
  9. pmc Genomic analysis of the secretion stress response in the enzyme-producing cell factory Aspergillus niger
    Thomas Guillemette
    School of Biology, University of Nottingham, University Park, Nottingham, UK
    BMC Genomics 8:158. 2007
    ..This study aims at uncovering transcriptional and translational responses occurring in A. niger exposed to secretion stress...
  10. pmc Decarboxylation of sorbic acid by spoilage yeasts is associated with the PAD1 gene
    Malcolm Stratford
    School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
    Appl Environ Microbiol 73:6534-42. 2007
    ....
  11. ncbi request reprint Filamentous fungi as microbial cell factories for food use
    D B Archer
    School of Life and Environmental Sciences, University of Nottingham, University Park, NG7 2RD, Nottingham, UK
    Curr Opin Biotechnol 11:478-83. 2000
    ....
  12. ncbi request reprint Filamentous fungi for production of food additives and processing aids
    David B Archer
    School of Biology, University of Nottingham, University Park, NG7 2RD, Nottingham, UK
    Adv Biochem Eng Biotechnol 111:99-147. 2008
    ..In this review chapter we focus on the use of fungi in the production of food additives but take a largely pre-genomic, albeit a mainly molecular, view of the topic...
  13. ncbi request reprint From genomics to post-genomics in Aspergillus
    David B Archer
    School of Biology, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
    Curr Opin Microbiol 7:499-504. 2004
    ..Advances in our understanding of the fundamental biology of the Aspergilli, together with applications within the biotechnology and medical fields, are anticipated...
  14. pmc The weak-acid preservative sorbic acid is decarboxylated and detoxified by a phenylacrylic acid decarboxylase, PadA1, in the spoilage mold Aspergillus niger
    Andrew Plumridge
    School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
    Appl Environ Microbiol 74:550-2. 2008
    ..A. niger DeltapadA1 mutants are unable to decarboxylate sorbic and cinnamic acids, and the MIC of sorbic acid required to inhibit spore germination was reduced by approximately 50% in DeltapadA1 mutants...
  15. ncbi request reprint The decarboxylation of the weak-acid preservative, sorbic acid, is encoded by linked genes in Aspergillus spp
    Andrew Plumridge
    School of Biology, University Park, University of Nottingham, Nottingham NG7 2RD, UK
    Fungal Genet Biol 47:683-92. 2010
    ..This cluster is absent from the genomes of A. fumigatus and A. clavatus and, as a consequence, neither species is capable of decarboxylating sorbic acid...
  16. ncbi request reprint Comparison of modular and non-modular xylanases as carrier proteins for the efficient secretion of heterologous proteins from Penicillium funiculosum
    M J C Alcocer
    School of Life and Environmental Sciences, University of Nottingham, University Park, NG7 2RD, Nottingham
    Appl Microbiol Biotechnol 60:726-32. 2003
    ..funiculosum when expressed as an XYNA fusion but that the secreted GUS protein, cleaved in vivo from XYNA, is glycosylated and enzymatically inactive...
  17. ncbi request reprint Stability of recombinant 2 S albumin allergens in vitro
    G J Murtagh
    School of Life and Environmental Sciences, University of Nottingham, University Park, UK
    Biochem Soc Trans 30:913-5. 2002
    ....
  18. ncbi request reprint The major human structural IgE epitope of the Brazil nut allergen Ber e 1: a chimaeric and protein microarray approach
    Marcos J C Alcocer
    School of Biosciences, Division of Nutritional Biochemistry, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
    J Mol Biol 343:759-69. 2004
    ....
  19. ncbi request reprint The expression and processing of two recombinant 2S albumins from soybean (Glycine max) in the yeast Pichia pastoris
    Jing Lin
    School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, UK
    Biochim Biophys Acta 1698:203-12. 2004
    ..This internal processing provides useful information on the endoproteolytic activity in P. pastoris. We also show that, similar to many plant allergens, the 2S albumins from soybean are stable to heat and chemical treatments...
  20. ncbi request reprint Genomics reveals sexual secrets of Aspergillus
    Paul S Dyer
    School of Life and Environmental Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
    Microbiology 149:2301-3. 2003
  21. ncbi request reprint Auxotrophy for uridine increases the sensitivity of Aspergillus niger to weak-acid preservatives
    Petter Melin
    School of Biology, University of Nottingham, University Park, Nottingham, UK
    Microbiology 154:1251-7. 2008
    ..In conclusion, this study describes a previously unknown mechanism of action of weak acids against the filamentous fungus A. niger, which may fundamentally affect our understanding of the preservation of food against spoilage fungi...
  22. ncbi request reprint Inhibition of spoilage mould conidia by acetic acid and sorbic acid involves different modes of action, requiring modification of the classical weak-acid theory
    Malcolm Stratford
    School of Biology, University of Nottingham, University Park, Nottingham, United Kingdom
    Int J Food Microbiol 136:37-43. 2009
    ..It was concluded that while acetic acid inhibition of A. niger conidia was due to cytoplasmic acidification, inhibition by sorbic acid was not. A possible membrane-mediated mode of action of sorbic acid is discussed...
  23. ncbi request reprint Microwave radiation can alter protein conformation without bulk heating
    David I de Pomerai
    School of Life and Environmental Sciences, University of Nottingham, University Park, NG7 2RD, Nottingham, UK
    FEBS Lett 543:93-7. 2003
    ..We also show that heat-shock responses both to heat and microwaves are suppressed after RNA interference ablating heat-shock factor function...
  24. ncbi request reprint The disulphide mapping, folding and characterisation of recombinant Ber e 1, an allergenic protein, and SFA8, two sulphur-rich 2S plant albumins
    Marcos J C Alcocer
    School of Life and Environmental Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
    J Mol Biol 324:165-75. 2002
    ..The secreted production of these properly folded sulphur-rich plant albumins presents an opportunity to delineate the attributes that make an allergen and to facilitate the diagnosis and therapy of type I allergy...
  25. ncbi request reprint In vitro stability and immunoreactivity of the native and recombinant plant food 2S albumins Ber e 1 and SFA-8
    G J Murtagh
    School of Life and Environmental Sciences, University of Nottingham, University Park, Nottingham, UK
    Clin Exp Allergy 33:1147-52. 2003
    ....
  26. pmc The weak acid preservative sorbic acid inhibits conidial germination and mycelial growth of Aspergillus niger through intracellular acidification
    Andrew Plumridge
    School of Biology, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
    Appl Environ Microbiol 70:3506-11. 2004
    ..The disruption of pH homeostasis by sorbic acid at concentrations below the MIC could account for the delay in spore germination and retardation of the onset of subsequent mycelial growth...
  27. ncbi request reprint The potential allergenicity of two 2S albumins from soybean (Glycine max): a protein microarray approach
    Jing Lin
    School of Biosciences, Division of Nutritional Sciences, University of Nottingham, Loughborough, Leicestershire, UK
    Int Arch Allergy Immunol 141:91-102. 2006
    ..The widespread distribution and stability to digestion of allergenic 2S albumins raise the question of why some members of this family present in important food sources, such as soybean, are not regarded as major allergens...
  28. ncbi request reprint Identification and characterisation of eroA and ervA, encoding two putative thiol oxidases from Aspergillus niger
    Anna R Harvey
    School of Biology, University of Nottingham, Nottingham, NG7 2RD, UK
    Gene 461:32-41. 2010
    ....
  29. ncbi request reprint Impact of the unfolded protein response upon genome-wide expression patterns, and the role of Hac1 in the polarized growth, of Candida albicans
    Tithira T Wimalasena
    School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, UK
    Fungal Genet Biol 45:1235-47. 2008
    ..albicans and in the expression of genes encoding cell surface proteins during ER stress, factors that are important in virulence of this fungal pathogen...
  30. ncbi request reprint Genetic differentiation of the Aspergillus section Flavi complex using AFLP fingerprints
    Dolores Montiel
    School of Life and Environmental Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
    Mycol Res 107:1427-34. 2003
    ..In addition, sequencing of ribosomal ITS regions and AFLP analysis suggested that some species annotations in public culture collections may be inaccurate...
  31. ncbi request reprint siRNA as a molecular tool for use in Aspergillus niger
    Sally E Barnes
    School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
    Biotechnol Lett 30:885-90. 2008
    ..The down-regulation was transient and was not carried over to conidiation. We concluded that gene silencing by siRNA provides a relatively quick method for analysis of gene function in A. niger...
  32. ncbi request reprint Mating type and the genetic basis of self-fertility in the model fungus Aspergillus nidulans
    Mathieu Paoletti
    School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
    Curr Biol 17:1384-9. 2007
    ..However, unlike heterothallic species, aspects of pheromone signaling appeared to be independent of MAT control...
  33. ncbi request reprint Transcript-specific translational regulation in the unfolded protein response of Saccharomyces cerevisiae
    Tom Payne
    School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, UK
    FEBS Lett 582:503-9. 2008
    ..Splicing of HAC1 mRNA is shown to be required for efficient ribosomal loading...
  34. ncbi request reprint Endoplasmic reticulum stress leads to the selective transcriptional downregulation of the glucoamylase gene in Aspergillus niger
    Hashem Al-Sheikh
    School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, UK
    Mol Microbiol 53:1731-42. 2004
    ..niger. Although the transcription of glaA was attenuated in that strain of A. niger, UPR was not evident, suggesting that the transcriptional downregulation mechanism is controlled differently from the UPR...
  35. pmc HacA-independent induction of chaperone-encoding gene bipA in Aspergillus niger strains overproducing membrane proteins
    Anoushka Davé
    School of Biology, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
    Appl Environ Microbiol 72:953-5. 2006
    ..Despite elevated bipA mRNA levels, no 5'-truncated hacA transcript was detected, raising the possibility of a hacA-independent induction of bipA mRNA under the stress of membrane protein overproduction in A. niger...
  36. ncbi request reprint Spore germination in Mortierella alpina is associated with a transient depletion of arachidonic acid and induction of fatty acid desaturase gene expression
    C Lounds
    School of Biology, University of Nottingham, University Park, Nottingham, UK
    Arch Microbiol 188:299-305. 2007
    ..We propose that ARA serves as a reserve supply of carbon and energy that is utilised during the early stages of spore germination in Mortierella alpina...
  37. ncbi request reprint A third fatty acid delta9-desaturase from Mortierella alpina with a different substrate specificity to ole1p and ole2p
    Donald A MacKenzie
    Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
    Microbiology 148:1725-35. 2002
    ..Conversely, high levels of desaturase in the endoplasmic reticulum membrane of these yeast transformants may increase the availability of suitable monounsaturated substrates for fatty acid elongation...
  38. ncbi request reprint Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
    James E Galagan
    The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA
    Nature 438:1105-15. 2005
    ..These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation...
  39. ncbi request reprint Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
    William C Nierman
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Nature 438:1151-6. 2005
    ..The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus...
  40. ncbi request reprint Genome sequencing and analysis of Aspergillus oryzae
    Masayuki Machida
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology AIST, Higashi 1 1 1, Tsukuba, Ibaraki 305 8566, Japan
    Nature 438:1157-61. 2005
    ..Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation...
  41. ncbi request reprint The activity of barley alpha-amylase on starch granules is enhanced by fusion of a starch binding domain from Aspergillus niger glucoamylase
    Nathalie Juge
    Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK
    Biochim Biophys Acta 1764:275-84. 2006
    ..9 for rAMY1. Remarkably, at low concentration (2 nM), AMY1-SBD hydrolysed barley starch granules 15-fold faster than rAMY1, while higher amounts of AMY-SBD caused molecular overcrowding of the starch granule surface...
  42. ncbi request reprint Engineering a camelid antibody fragment that binds to the active site of human lysozyme and inhibits its conversion into amyloid fibrils
    Pak Ho Chan
    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
    Biochemistry 47:11041-54. 2008
    ..Moreover, this work further demonstrates the unique properties of camelid single-domain antibody fragments as structural probes for studying the mechanism of aggregation and as potential inhibitors of fibril formation...
  43. ncbi request reprint A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme
    Mireille Dumoulin
    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
    Nature 424:783-8. 2003
    ....
  44. ncbi request reprint Impact of the native-state stability of human lysozyme variants on protein secretion by Pichia pastoris
    Janet R Kumita
    Department of Chemistry, University of Cambridge, UK
    FEBS J 273:711-20. 2006
    ..These findings indicate that a complex interplay between reduced native-state stability, lower secretion levels, and protein aggregation propensity influences the types of mutation that give rise to familial forms of amyloid disease...
  45. ncbi request reprint Reduced global cooperativity is a common feature underlying the amyloidogenicity of pathogenic lysozyme mutations
    Mireille Dumoulin
    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
    J Mol Biol 346:773-88. 2005
    ....
  46. ncbi request reprint Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
    Herman J Pel
    DSM Food Specialties, PO Box 1, 2600 MA Delft, The Netherlands
    Nat Biotechnol 25:221-31. 2007
    ..niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis...
  47. ncbi request reprint Local cooperativity in the unfolding of an amyloidogenic variant of human lysozyme
    Denis Canet
    Oxford Centre for Molecular Sciences, New Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QH, UK
    Nat Struct Biol 9:308-15. 2002
    ....
  48. pmc Calnexin overexpression increases manganese peroxidase production in Aspergillus niger
    Ana Conesa
    Department of Applied Microbiology and Gene Technology, TNO Food and Nutrition Research Institute, 3700 AJ Zeist, The Netherlands
    Appl Environ Microbiol 68:846-51. 2002
    ..However, when additional heme was provided in the culture medium, calnexin overexpression had no synergistic effect on MnP production. The possible function of these two chaperones in MnP maturation and production is discussed...
  49. ncbi request reprint Rationalising lysozyme amyloidosis: insights from the structure and solution dynamics of T70N lysozyme
    Russell J K Johnson
    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
    J Mol Biol 352:823-36. 2005
    ....