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Fermentation, Volume 1, Issue 1 (December 2015) – 9 articles , Pages 1-126

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Article
Antisense-RNA-Mediated Gene Downregulation in Clostridium pasteurianum
Fermentation 2015, 1(1), 113-126; https://doi.org/10.3390/fermentation1010113 - 09 Dec 2015
Cited by 9 | Viewed by 3221
Abstract
Clostridium pasteurianum is receiving growing attention for its unique metabolic properties, particularly its ability to convert waste glycerol and glycerol-rich byproducts into butanol, a prospective biofuel. Genetic tool development and whole genome sequencing have recently been investigated to advance the genetic tractability of [...] Read more.
Clostridium pasteurianum is receiving growing attention for its unique metabolic properties, particularly its ability to convert waste glycerol and glycerol-rich byproducts into butanol, a prospective biofuel. Genetic tool development and whole genome sequencing have recently been investigated to advance the genetic tractability of this potential industrial host. Nevertheless, methodologies for tuning gene expression through plasmid-borne expression and chromosomal gene downregulation are still absent. Here we demonstrate plasmid-borne heterologous gene expression and gene knockdown using antisense RNA in C. pasteurianum. We first employed a common thermophilic β-galactosidase (lacZ) gene reporter system from Thermoanaerobacterium thermosulfurogenes to characterize two promoters involved in the central fermentative metabolism of C. pasteurianum. Due to a higher level of constitutive lacZ expression compared to the ferredoxin gene (fdx) promoter, the thiolase (thl) promoter was selected to drive expression of asRNA. Expression of a lacZ asRNA resulted in 52%–58% downregulation of β-galactosidase activity compared to the control strain throughout the duration of culture growth. Subsequent implementation of our asRNA approach for downregulation of the native hydrogenase I gene (hydA) in C. pasteurianum resulted in altered end product distribution, characterized by an increase in production of reduced metabolites, particularly butyrate (40% increase) and ethanol (25% increase). Knockdown of hydA was also accompanied by increased acetate formation and lower levels of 1,3-propanediol, signifying a dramatic shift in cellular metabolism in response to inhibition of the hydrogenase enzyme. The methodologies described herein for plasmid-based heterologous gene expression and antisense-RNA-mediated gene knockdown should promote rational metabolic engineering of C. pasteurianum for enhanced production of butanol as a prospective biofuel. Full article
(This article belongs to the Special Issue Metabolic Engineering)
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Article
Development of Novel Textile Bioreactor for Anaerobic Utilization of Flocculating Yeast for Ethanol Production
Fermentation 2015, 1(1), 98-112; https://doi.org/10.3390/fermentation1010098 - 23 Nov 2015
Cited by 3 | Viewed by 3605
Abstract
Process development, cheaper bioreactor cost, and faster fermentation rate can aid in reducing the cost of fermentation. In this article, these ideas were combined in developing a previously introduced textile bioreactor for ethanol production. The bioreactor was developed to utilize flocculating yeast for [...] Read more.
Process development, cheaper bioreactor cost, and faster fermentation rate can aid in reducing the cost of fermentation. In this article, these ideas were combined in developing a previously introduced textile bioreactor for ethanol production. The bioreactor was developed to utilize flocculating yeast for ethanol production under anaerobic conditions. A mixing system, which works without aerators, spargers, or impellers, but utilizes the liquid content in the bioreactor for suspending the flocculating yeast to form a fluidized bed, was developed and examined. It could be used with dilution rates greater than 1.0 h1 with less possibility of washout. The flow conditions required to begin and maintain a fluidized bed were determined. Fermentation experiments with flow rate and utilization of the mixing system as process variables were carried out. The results showed enhanced mass transfer as evidenced by faster fermentation rates on experiments with complete sucrose utilization after 36 h, even at 30 times lesser flow rate. Full article
(This article belongs to the Special Issue Yeast Biotechnology)
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Article
Modeling the Growth of Lactococcus lactis NCIM 2114 under Differently Aerated and Agitated Conditions in Broth Medium
Fermentation 2015, 1(1), 86-97; https://doi.org/10.3390/fermentation1010086 - 29 Oct 2015
Cited by 5 | Viewed by 2840
Abstract
The study of growth of Lactococcus lactis NCIM 2114, a nisin producer, was modeled using continuously generated concentration data for growth in fermenter. The sigmoidal growth functions, Logistic, Gompertz, and Richards were used to fit the data. A nonlinear regression method was [...] Read more.
The study of growth of Lactococcus lactis NCIM 2114, a nisin producer, was modeled using continuously generated concentration data for growth in fermenter. The sigmoidal growth functions, Logistic, Gompertz, and Richards were used to fit the data. A nonlinear regression method was used to fit the data and estimate growth parameter values of L. lactis, using Marquardt algorithm with Statistical Software SPSS, version 20. Bacterial growth data from the exponential phase of the bacteria’s growth was analyzed. An F test showed that the Gompertz and Logistic functions were acceptable 92% and 67% of times respectively in the batch fermenter runs where this particular application was used to derive the lag time, growth rates, and time to maximum growth rates of L. lactis. The maximal specific growth rate ranged between 0.23 h−1 to 0.30 h−1 and the lag time lasted up to a maximum of 1.63 h depending upon aeration conditions provided to the organism. This study will help to estimate specific growth rates and lag time of L. lactis under different growth conditions. Predicted values can be accurately determined. Full article
(This article belongs to the Special Issue Beneficial Fermentation Microbes and Their Functional Compounds)
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Brief Report
The Application of an On-Line Optical Sensor to Measure Biomass of a Filamentous Bioprocess
Fermentation 2015, 1(1), 79-85; https://doi.org/10.3390/fermentation1010079 - 24 Sep 2015
Cited by 2 | Viewed by 2407
Abstract
Monitoring of all critical process parameters in bioprocess engineering is essential. Sensors have been previously developed for specific parameters such as on-line temperature, pH or stirring control and data logging. However, biomass monitoring needs further development. All current non-invasive technology, such as Near [...] Read more.
Monitoring of all critical process parameters in bioprocess engineering is essential. Sensors have been previously developed for specific parameters such as on-line temperature, pH or stirring control and data logging. However, biomass monitoring needs further development. All current non-invasive technology, such as Near Infra-Red, is limited on biomass measurement of animal and insect cells. Biomass monitoring of industrial bioprocesses of filamentous microorganisms still requires sample removal from the vessel, which could potentially compromise sterility. This study has focused on the application of a non-invasive optical sensor in the on-line monitoring of the biomass of the filamentous microorganism Streptomyces coelicolor A3 (2). Raw output data from the biomass monitor were directly compared to data from the sensors measuring dissolved oxygen levels and off gas evolution and the results successfully demonstrate that the optical sensor is sensitive in identifying different levels of biomass. Therefore, it is possible to use the simple output data to provide real time information on biomass levels of filamentous microorganisms, a very powerful tool in bioprocess engineering. Full article
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Review
Microfluidic Bioreactors for Cellular Microarrays
Fermentation 2015, 1(1), 38-78; https://doi.org/10.3390/fermentation1010038 - 07 Aug 2015
Cited by 10 | Viewed by 4302
Abstract
Living cell microarrays have been combined with microfluidic bioreactors, which provide multiple advantages for multiplex dynamic analyses and high-throughput screening. In the last decade, many developments in this new field have been introduced. The technology has evolved from fixed cell analysis towards living [...] Read more.
Living cell microarrays have been combined with microfluidic bioreactors, which provide multiple advantages for multiplex dynamic analyses and high-throughput screening. In the last decade, many developments in this new field have been introduced. The technology has evolved from fixed cell analysis towards living single-cell dynamic systems’ biology and high content analyses. The aim of this review is to provide an updated overview of the developments of living cellular microarrays in microfluidic bioreactors. Cell arrays in microfluidic bioreactors constructed with adherent mammalian cells are compared to non-adherent cells (mainly microbial cells). An overview is given on the design and construction of these microfluidic devices with a particular focus on cell patterning techniques. Cell patterning on adhesive micropatterns using techniques such as microcontact printing, microfluidic patterning, dip-pen nanolithography and polymer pen lithography as well as photo-patterning and laser-patterning strategies are discussed. Additionally, developments in mechanical cell patterning methods and robotic cell printing are reviewed. Two-dimensional (2D) as well as recently developed 3D cell arraying are discussed. Finally, cell array microfluidic setups and operation for single-cell types versus cell population variants are illustrated and compared on the basis of some illustrative examples in the field of drug screening, cytotoxicity evaluation, and basic cellular and microbiology research. Full article
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Article
Activity of Lactobacillus brevis Alcohol Dehydrogenase on Primary and Secondary Alcohol Biofuel Precursors
Fermentation 2015, 1(1), 24-37; https://doi.org/10.3390/fermentation1010024 - 05 Aug 2015
Cited by 6 | Viewed by 3656
Abstract
The R-specific alcohol dehydrogenase (ADH) from Lactobacillus brevis LB19 (LbADH) was studied with respect to its ability to reduce a series of 3- through 5-carbon 2-alkanones and aldehydes of relevance as biofuel precursors. Although active on all substrates tested, Lb [...] Read more.
The R-specific alcohol dehydrogenase (ADH) from Lactobacillus brevis LB19 (LbADH) was studied with respect to its ability to reduce a series of 3- through 5-carbon 2-alkanones and aldehydes of relevance as biofuel precursors. Although active on all substrates tested, LbADH displays a marked preference for longer chain substrates. Interestingly, however, 2-alkanones were found to impose substrate inhibition towards LbADH, whereas aldehyde substrates rendered no such effect. Inhibition caused by 2-alkanones was furthermore found to intensify with increasing chain length. Despite demonstrating both primary and secondary ADH activities, a preliminary sequence analysis suggests that LbADH remains distinct from other, previously characterized primary-secondary ADHs. In addition to further characterizing the substrate range of this industrially important enzyme, this study suggests that LbADH has the potential to serve as a useful enzyme for the engineering of various novel alcohol biofuel pathways. Full article
(This article belongs to the Special Issue Metabolic Engineering)
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Article
Optimization of Phytase Production from Escherichia coli by Altering Solid-State Fermentation Conditions
Fermentation 2015, 1(1), 13-23; https://doi.org/10.3390/fermentation1010013 - 30 Jul 2015
Cited by 10 | Viewed by 4219
Abstract
Cultivation of Escherichia coli on wheat-bran substrate under various Solid-State Fermentation (SSF) conditions was evaluated for phytase yield along with the enzyme activity profile as a potential, low-cost alternative to submerged-liquid fermentation. The maximum phytase activity achieved by E. coli was 350 ± [...] Read more.
Cultivation of Escherichia coli on wheat-bran substrate under various Solid-State Fermentation (SSF) conditions was evaluated for phytase yield along with the enzyme activity profile as a potential, low-cost alternative to submerged-liquid fermentation. The maximum phytase activity achieved by E. coli was 350 ± 50 SPU of phytase activity per gram of bran, incubated for 96 h with a substrate bed moisture content of 70% (w/v) at 37 °C with a relative air humidity of 90%, and supplemented with 10% (w/w bran) Luria-Bertani broth powder which translates into a 300% increase in phytase activity compared with an un-supplemented culture. The greatest improvements in phytase yield were associated with nutrient supplementation and the optimization of initial substrate moisture content. E. coli production of phytase utilizing solid-state fermentation technology was shown to be feasible utilizing the low-cost agro-residue wheat bran as substrate. Furthermore, the effect of pH and temperature on phytase activity was monitored from pH 2.5 to pH 7.5, and for temperatures ranging from 20 °C to 70 °C. Optimal phytase activity was at pH 5.5 and 50 °C when produced under the SSF optimized conditions. Full article
(This article belongs to the Special Issue Beneficial Fermentation Microbes and Their Functional Compounds)
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Article
Evaluation of Zygosaccharomyces bailii to Metabolize Residual Sugar Present in Partially-Fermented Red Wines
Fermentation 2015, 1(1), 3-12; https://doi.org/10.3390/fermentation1010003 - 26 Mar 2015
Cited by 7 | Viewed by 3842
Abstract
An alternative approach to remove residual sugar from red wines using strains of Zygosaccharomyces bailli was studied. Fructose (40 or 60 g/L) and alcohol (13%, 15%, or 17% v/v) were added to a Cabernet Sauvignon wine before inoculation of Z. [...] Read more.
An alternative approach to remove residual sugar from red wines using strains of Zygosaccharomyces bailli was studied. Fructose (40 or 60 g/L) and alcohol (13%, 15%, or 17% v/v) were added to a Cabernet Sauvignon wine before inoculation of Z. bailii B2, B6, or W3, or Saccharomyces cerevisiae EC1118. Most yeasts maintained populations ≥106 cfu/mL up to 100 days—the exceptions being W3 and EC1118, which declined to ≤30 cfu/mL in 17% alcohol wines beyond day 75. Wines containing 40 g/L fructose and 13% alcohol achieved dryness (<2 g/L), except those inoculated with B6. At 15% alcohol, B6, W3, and EC1118 consumed large levels of fructose (>80% of the 40 g/L; >50% of the 60 g/L) but limited amounts from wines containing 17% alcohol. Volatile acidities were higher in wines inoculated with strains of Z. bailli compared to S. cerevisiae (0.88 and 0.75 g/L, respectively). Fructose utilization in a partially-fermented Syrah wine varied, with dryness achieved by EC1118 or a mixed culture of B2 and B6. While Z. bailii metabolized residual fructose in wines of varying alcohol content, the use of S. cerevisiae EC1118 was generally as effective and did not produce as much volatile acidity. Full article
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Editorial
Welcome to Fermentation: A New Multidisciplinary Open Access Journal
Fermentation 2015, 1(1), 1-2; https://doi.org/10.3390/fermentation1010001 - 24 Dec 2014
Viewed by 2672
Abstract
It is my great pleasure to welcome you to a new open access journal, Fermentation, which represents a multidisciplinary scope that meets the growing need for a high quality peer-reviewed international journal with easy access to all researchers globally. The journal aims [...] Read more.
It is my great pleasure to welcome you to a new open access journal, Fermentation, which represents a multidisciplinary scope that meets the growing need for a high quality peer-reviewed international journal with easy access to all researchers globally. The journal aims at a broad multidisciplinary readership, which includes both academia and industries, and covers broad areas of research, development and technological advances in all aspects of fermentation. Fully comprehensive in its scope, the journal coverage includes without being limited to: [...] Full article
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