@book{sheppard_2021, title={Introduction to Brewing and Fermentation Science}, ISBN={9789811225314 9789811225321}, url={http://dx.doi.org/10.1142/11966}, DOI={10.1142/11966}, publisher={WORLD SCIENTIFIC}, author={Sheppard, John D}, year={2021}, month={Feb} }
 @article{madden_epps_fukami_irwin_sheppard_sorger_dunn_2018, title={The ecology of insect–yeast relationships and its relevance to human industry}, volume={285}, ISSN={0962-8452 1471-2954}, url={http://dx.doi.org/10.1098/rspb.2017.2733}, DOI={10.1098/rspb.2017.2733}, abstractNote={Many species of yeast are integral to human society. They produce many of our foods, beverages and industrial chemicals, challenge us as pathogens, and provide models for the study of our own biology. However, few species are regularly studied and much of their ecology remains unclear, hindering the development of knowledge that is needed to improve the relationships between humans and yeasts. There is increasing evidence that insects are an essential component of ascomycetous yeast ecology. We propose a ‘dispersal–encounter hypothesis' whereby yeasts are dispersed by insects between ephemeral, spatially disparate sugar resources, and insects, in turn, obtain the benefits of an honest signal from yeasts for the sugar resources. We review the relationship between yeasts and insects through three main examples: social wasps, social bees and beetles, with some additional examples from fruit flies. Ultimately, we suggest that over the next decades, consideration of these ecological and evolutionary relationships between insects and yeasts will allow prediction of where new yeast diversity is most likely to be discovered, particularly yeasts with traits of interest to human industry.}, number={1875}, journal={Proceedings of the Royal Society B: Biological Sciences}, publisher={The Royal Society}, author={Madden, Anne A. and Epps, Mary Jane and Fukami, Tadashi and Irwin, Rebecca E. and Sheppard, John and Sorger, D. Magdalena and Dunn, Robert R.}, year={2018}, month={Mar}, pages={20172733} }
 @article{vann_layfield_sheppard_2017, title={The application of near-infrared spectroscopy in beer fermentation for online monitoring of critical process parameters and their integration into a novel feedforward control strategy}, volume={123}, ISSN={["2050-0416"]}, DOI={10.1002/jib.440}, abstractNote={Traditional methods used in the analysis of fermentation media suffer from a number of limitations. The search for more rapid and efficient methods has led to the development and application of near-infrared spectroscopy. Near-infrared spectroscopy has been applied successfully in a variety of industrial processes: agricultural, food, chemical and pharmaceutical, generally in the areas of raw material quality control but also including intermediate and finished product testing. The present research explores its potential for online fermentation monitoring of total cell count (TCC), specific gravity (SG), free amino nitrogen (FAN) and percentage alcohol by volume (% v v−1) in a 300 L pilot-scale validation batch. Models that were generated from three calibration batches for each of these constituents exhibited overall favourable standard error of cross validation (SECV) and fit of predicted vs actual cross validated results (SECV, R2): SG (0.00072, 0.995), ethanol (0.17% v v−1, 0.990), FAN (16.5 mg L−1, 0.886) and TCC (1.24 × 106 cells mL−1, 0.640). The data that was most relevant to cell metabolism was determined to be sugar consumption rate, ethanol production rate, yield of ethanol and fermentation lag time. These ‘critical performance parameters’ were incorporated into a novel feed-forward control strategy where yeast pitching rate was modified based on values of the critical performance parameters from the previous batch. Use of this feed-forward strategy demonstrated how brewers can utilize near-infrared monitoring for quality assurance through early detection of shifts in fermentation performance. Copyright © 2017 The Institute of Brewing & Distilling}, number={3}, journal={JOURNAL OF THE INSTITUTE OF BREWING}, author={Vann, Lucas and Layfield, Johnathon B. and Sheppard, John D.}, year={2017}, month={Jul}, pages={347–360} }
 @article{vann_sheppard_2017, title={Use of near-infrared spectroscopy (NIRs) in the biopharmaceutical industry for real-time determination of critical process parameters and integration of advanced feedback control strategies using MIDUS control}, volume={44}, ISSN={["1476-5535"]}, DOI={10.1007/s10295-017-1984-2}, abstractNote={Abstract}, number={12}, journal={JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY}, author={Vann, Lucas and Sheppard, John}, year={2017}, month={Dec}, pages={1589–1603} }
 @article{bergen_cyr_strasser_blanchette_sheppard_jardim_2016, title={alpha,beta-Dicarbonyl reduction is mediated by the Saccharomyces Old Yellow Enzyme}, volume={16}, ISSN={["1567-1364"]}, DOI={10.1093/femsyr/fow059}, abstractNote={The undesirable flavor compounds diacetyl and 2,3-pentanedione are vicinal diketones (VDKs) formed by extracellular oxidative decarboxylation of intermediate metabolites of the isoleucine, leucine and valine (ILV) biosynthetic pathway. These VDKs are taken up by Saccharomyces and enzymatically converted to acetoin and 3-hydroxy-2-pentanone, respectively. Purification of a highly enriched diacetyl reductase fraction from Saccharomyces cerevisiae in conjunction with mass spectrometry identified Old Yellow Enzyme (Oye) as an enzyme capable of catalyzing VDK reduction. Kinetic analysis of recombinant Oye1p, Oye2p and Oye3p isoforms confirmed that all three isoforms reduced diacetyl and 2,3-pentanedione in an NADPH-dependent reaction. Transcriptomic analysis of S. cerevisiae (ale) and S. pastorianus (lager) yeast during industrial fermentations showed that the transcripts for OYE1, OYE2, arabinose dehydrogenase (ARA1), α-acetolactate synthase (ILV2) and α-acetohydroxyacid reductoisomerase (ILV5) were differentially regulated in a manner that correlated with changes in extracellular levels of VDKs. These studies provide insights into the mechanism for reducing VDKs and decreasing maturation times of beer which are of commercial importance.}, number={5}, journal={FEMS YEAST RESEARCH}, author={Bergen, Barry and Cyr, Normand and Strasser, Rona and Blanchette, Maxime and Sheppard, John D. and Jardim, Armando}, year={2016}, month={Aug} }
 @article{layfield_vann_sheppard_2014, title={A Novel Method of Inducing and Retaining Cell Cycle Synchronization in Cultures of Saccharomyces cerevisiae}, volume={72}, ISSN={["1943-7854"]}, DOI={10.1094/asbcj-2014-0324-02}, abstractNote={In conventional fermentation, at any one time, individual yeast cells are randomly distributed with respect to the stage of their growth and division cycle. The observed metabolic performance is, therefore, the result of an average of the entire population. In contrast, a synchronous population is characterized by cells that are aligned with respect to their metabolic processes, traversing the cell cycle and dividing mostly in unison. In this study, a novel method for inducing and retaining cell cycle synchronization in yeast cultures (diploid and polyploid-type) was developed using a simple and natural phased expansion method, in which the volume of the culture was increased step-wise at time periods equal to the cell doubling time. Results indicate that this method was effective in producing yeast cultures with a high degree of synchrony, verified by cell counts and fluorescent cytometry. When stored in relatively small volumes at −80°C in glycerol, the cultures maintained their synchrony upon thawing. Experiments were also conducted at the lab-scale to assess the potential use of synchronous cultures in brewing applications. The incorporation of phased seed expansion and periodic feeding of the yeast culture provided increased metabolic uniformity within the population and reduced variability in fermentation performance.}, number={2}, journal={JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS}, author={Layfield, J. Blake and Vann, Lucas R. and Sheppard, John D.}, year={2014}, pages={102–109} }
 @article{layfield_phister_sheppard_2011, title={Characterization of Hybrid Strains of Saccharomyces pastorianus for Desiccation Tolerance}, volume={69}, ISSN={["1943-7854"]}, DOI={10.1094/asbcj-2011-0301-01}, abstractNote={This study examines the impact of desiccation on the viability and fermentation performance of multiple strains of Saccharomyces pastorianus. S. pastorianus is a hybrid resulting from a cross between S. cerevisiae and S. bayanus. It has been proposed that S. pastorianus can be categorized into two distinct types: S. pastorianus-Saaz type, which has lost a significant amount of the genomic content contained within S. cerevisiae, and S. pastorianus-Frohberg type, which has retained almost all of the genomic content of S. cerevisiae. Both types of S. pastorianus, along with S. cerevisiae and S. bayanus strains, were desiccated by spray-drying and then rehydrated before assessing the extent of the damage to the cells. The viability of rehydrated cultures was determined using microscopic enumeration, capacitance, and plating. Fermentation performance was tested by inoculating equal amounts of viable rehydrated cells into brewer's wort and monitoring changes in cell count, carbohydrate utilization, and alcohol concentration until completion. The findings suggest that S. pastorianus-Frohberg type is less tolerant to desiccation than either S. cerevisiae or S. pastorianus-Saaz type. Selection of the correct type of S. pastorianus for use in active dry yeast could reduce the possibility of contamination or extended lag phases leading to stuck fermentations.}, number={2}, journal={JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS}, author={Layfield, J. Blake and Phister, Trevor G. and Sheppard, John D.}, year={2011}, pages={108–115} }
 @article{tam_matsumoto_sheppard_2008, title={A Kinetic Model for Suspended and Attached Growth of a Defined Mixed Culture}, volume={21}, ISSN={8756-7938}, url={http://dx.doi.org/10.1021/bp0500720}, DOI={10.1021/bp0500720}, abstractNote={Kinetic experiments were carried out in a semicontinuous wastewater treatment process called self‐cycling fermentation (SCF) using a defined mixed culture and various concentrations of synthetic brewery wastewater. The same consortium, which had been previously identified as Acinetobacter sp., Enterobacter sp., and Candida sp., were used in these experiments. The overall rate of substrate removal was attributable to both suspended microbes and the biofilm that formed during the treatment process. A rate expression was developed for the SCF system for a range of synthetic wastewaters containing glucose and various initial concentrations of ethanol and maltose. The data indicated that substrate removal by the suspended cells was directly related to the biomass concentration. However, substrate removal by the biofilm was apparently not affected by the biofilm thickness and was a function of substrate concentration only.}, number={3}, journal={Biotechnology Progress}, publisher={Wiley}, author={Tam, Kawai and Matsumoto, Mark R. and Sheppard, John D.}, year={2008}, month={Sep}, pages={720–727} }
 @article{tam_yang_matsumoto_crowley_sheppard_2008, title={Comparison of PCR-DGGE and Selective Plating Methods for Monitoring the Dynamics of a Mixed Culture Population in Synthetic Brewery Wastewater}, volume={21}, ISSN={8756-7938}, url={http://dx.doi.org/10.1021/bp050107w}, DOI={10.1021/bp050107w}, abstractNote={Enrichment of an activated sludge inoculum in synthetic brewery wastewater, which included glucose, maltose, and ethanol, was conducted in batch experiments to identify the dominant microbes present, to determine methodologies capable of monitoring the mixed culture population dynamics, and to determine the consortiumapos;s substrate degradation behavior. These results and methodologies were subsequently used in the determination of the population dynamics of suspended and attached microorganisms in a sequencing batch system in the second part of this research work. The three‐membered microbial community comprised two bacterial and one fungal species that were identified as Acinetobacter sp., Enterobacter sp., and Candida sp. PCR‐DGGE and plating on selective media were used to track the population dynamics of the consortium during the degradation of different substrates in synthetic wastewater containing glucose, maltose, and ethanol. Enterobacter sp. could degrade glucose and maltose but not ethanol, whereas Acinetobacter and Candida could degrade all three carbon sources. In buffered batch mixed culture experiments, Enterobacter was the predominant bacterium until the sugar concentrations decreased to levels that enabled Acinetobacter and Candida to degrade ethanol. PCR‐DGGE was effective for detecting the dominant species, but culture‐based methods were more accurate for monitoring the population dynamics of these microorganisms during growth in the wastewater medium.}, number={3}, journal={Biotechnology Progress}, publisher={Wiley}, author={Tam, Kawai and Yang, Ching-Hong and Matsumoto, Mark R. and Crowley, David E. and Sheppard, John D.}, year={2008}, month={Sep}, pages={712–719} }
 @article{blanchette_bergen_sheppard_2007, title={Development of a LC/MS method for analysis of total vicinal diketones in beer}, volume={65}, ISSN={["1943-7854"]}, DOI={10.1094/ASBC-J-2007-0403-01}, number={2}, journal={JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS}, author={Blanchette, Maxime and Bergen, Barry and Sheppard, John D.}, year={2007}, pages={70–76} }
 @article{sheppard_cooper_2007, title={The effects of a biosurfactant on oxygen transfer in a cyclone column reactor}, volume={48}, ISSN={0268-2575 1097-4660}, url={http://dx.doi.org/10.1002/jctb.280480308}, DOI={10.1002/jctb.280480308}, abstractNote={Abstract}, number={3}, journal={Journal of Chemical Technology & Biotechnology}, publisher={Wiley}, author={Sheppard, John D. and Cooper, David G.}, year={2007}, month={Apr}, pages={325–336} }
 @article{cyr_blanchette_price_sheppard_2007, title={Vicinal diketone production and amino acid uptake by two active dry lager yeasts during beer fermentation}, volume={65}, DOI={10.1094/asbcj-2007-0515-01}, abstractNote={Amino acid consumption and vicinal diketone (VDK) production of two different strains of commercially available active dry lager yeasts (ADLYs) were compared with freshly propagated cultures of the corresponding yeast strains. Rehydrated dry yeasts and freshly propagated yeasts were pitched in all-malt wort and allowed to ferment at 14°C. Dry yeast strains took 15–26 hr longer to attenuate the wort to final gravity and 24–48 hr longer to significantly reduce wort amino acid content. A new indicator was introduced as a means to quantitatively characterize VDK production and reduction profiles. This indicator effectively demonstrated a large discrepancy in the diacetyl profile between the fresh and dry cultures: fermentations made with dried yeasts resulted in 1.5–7 times higher diacetyl indices. With one of the dry strains, diacetyl concentrations remained over the taste threshold value after 7 days of fermentation. These differences could be linked to a reduced ability of the rehydrated mother cells to absorb wort constituents caused by cell membrane damage occurring during the ADLY production process. Overall, dry yeasts resulted in a reduced level of performance compared with freshly propagated cultures, suggesting that the direct utilization of ADLY as an inoculum for beer fermentation at the industrial scale is not recommended.}, number={3}, journal={Journal of the American Society of Brewing Chemists}, author={Cyr, N. and Blanchette, M. and Price, S. P. and Sheppard, J. D.}, year={2007}, pages={138–144} }