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Fermentation

Fermenataion is a metabolic process in which an organism converts a carbohydrate, such as starch or a sugar, into an alcohol or an acid.
This process is commonly used in the production of food and beverages, as well as in the generation of biofuels.
Fermentation involves the breakdown of complex organic compounds into simpler substances, often through the action of enzymes or microorganisms like yeast or bacteria.
It plays a crucial role in diverse industries, from brewing and winemaking to the production of dairy products, pickles, and pharmaceuticals.
Understanding the principles and optimization of fermentation processes is essential for researchers and industry professionals seeking to enhance efficiency, productivity, and the development of novel fermentation-based applications.

Most cited protocols related to «Fermentation»

Since its inception two decades ago, yeast genomics has been built around the single reference genome of S288C. The original idea was the production of a single consensus representative S. cerevisiae genome against which all other yeast sequences could be measured. The reference genome serves as the scaffold on which to hang other genomic sequences, and the foundation on which to build different types of genomic datasets. Whereas the first genome took years to complete, through the efforts of the large international consortium described, the sequences of dozens of genomes have been determined in the past several years (Engel and Cherry 2013 ). As sequencing has become more widespread, less novel, and, above all, less expensive, decoding entire genomes has become less daunting. New genomes now take only days to sequence to full and deep coverage and are assembled quickly, by individuals or small groups, through comparison to the reference, which is an invaluable guide for the annotation of newly sequenced genomes.
It is becoming increasingly clear that the genome of a species can contain a great deal of complexity and diversity. A reference genome can vary significantly from that of any individual strain or isolate and therefore serves as the anchor from which to explore the diversity of allele and gene complements and to explore how these differences contribute to metabolic and phenotypic variation. In the pharmaceutical industry, knowledge of the yeast reference genome helps drive the development of strains tailored to specific purposes, such as the production of biofuels, chemicals, and therapeutic drugs (Runguphan and Keasling 2013 ). In the beverage industry, it aids in the fermentation of beers, wines, and sakes with specific attributes, such as desired flavor profiles or reduced alcohol (Engel and Cherry 2013 ). We have seen the advantage afforded the yeast and genetics communities because of the early availability of an S. cerevisiae reference genome. The great facilitation of scientific discoveries and breakthroughs is without question (Botstein and Fink 2011 (link)).
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Publication 2013
Acquired Immunodeficiency Syndrome Alleles Beer Beverages Biofuels Complement System Proteins Ethanol Fermentation Flavor Enhancers Genes Genome Pharmaceutical Preparations Prunus cerasus Saccharomyces cerevisiae Strains Therapeutics Vision Wine
The American Type Culture Collection (ATCC) provided the genomic DNA used to clone Acel_2062 (ATCC Number: ATCC 43068). Protein production and crystallization of the Acel_2062 protein was carried out by standard JCSG protocols
[8 (link)]. Clones were generated using the Polymerase Incomplete Primer Extension (PIPE) cloning method
[9 (link)]. The gene encoding Acel_2062 (GenBank: YP_873820[GenBank:YP_873820]; UniProtKB: A0LWM4[UniProtKB:A0LWM4]) was synthesized with codons optimized for Escherichia coli expression (Codon Devices, Cambridge, MA) and cloned into plasmid pSpeedET, which encodes an expression and purification tag followed by a tobacco etch virus (TEV) protease cleavage site (MGSDKIHHHHHHENLYFQ/G) at the amino terminus of the full-length protein. Escherichia coli GeneHogs (Invitrogen) competent cells were transformed and dispensed on selective LB-agar plates. The cloning junctions were confirmed by DNA sequencing. Expression was performed in a selenomethionine-containing medium at 37°C. Selenomethionine was incorporated via inhibition of methionine biosynthesis
[10 (link)], which does not require a methionine auxotrophic strain. At the end of fermentation, lysozyme was added to the culture to a final concentration of 250 μg/ml, and the cells were harvested and frozen. After one freeze/thaw cycle the cells were homogenized in lysis buffer [50 mM HEPES, 50 mM NaCl, 10 mM imidazole, 1 mM Tris(2-carboxyethyl)phosphine-HCl (TCEP), pH 8.0] and passed through a Microfluidizer (Microfluidics). The lysate was clarified by centrifugation at 32,500 x g for 30 minutes and loaded onto a nickel-chelating resin (GE Healthcare) pre-equilibrated with lysis buffer, the resin was washed with wash buffer [50 mM HEPES, 300 mM NaCl, 40 mM imidazole, 10% (v/v) glycerol, 1 mM TCEP, pH 8.0], and the protein was eluted with elution buffer [20 mM HEPES, 300 mM imidazole, 10% (v/v) glycerol, 1 mM TCEP, pH 8.0]. The eluate was buffer exchanged with TEV buffer [20 mM HEPES, 200 mM NaCl, 40 mM imidazole, 1 mM TCEP, pH 8.0] using a PD-10 column (GE Healthcare), and incubated with 1 mg of TEV protease per 15 mg of eluted protein for 2 hours at 20°–25°C followed by overnight at 4°C. The protease-treated eluate was passed over nickel-chelating resin (GE Healthcare) pre-equilibrated with HEPES crystallization buffer [20 mM HEPES, 200 mM NaCl, 40 mM imidazole, 1 mM TCEP, pH 8.0] and the resin was washed with the same buffer. The flow-through and wash fractions were combined and concentrated to 15.6 mg/ml by centrifugal ultrafiltration (Millipore) for crystallization trials.
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Publication 2014
Agar Anabolism Buffers Cells Centrifugation Codon Crystallization Cytokinesis Escherichia coli Fermentation Freezing G-substrate Genes Genome Glycerin GTP-Binding Proteins HEPES imidazole Medical Devices Methionine Muramidase Nickel Oligonucleotide Primers Peptide Hydrolases phosphine Plasmids Proteins Psychological Inhibition Resins, Plant Selenomethionine Sodium Chloride Strains TEV protease Tobacco etch virus tris(2-carboxyethyl)phosphine Tromethamine Ultrafiltration
The integrated plant was modeled assuming a 1G raw material loading of 360,000 tons dry grain per year and a 2G raw material loading of 180,000 tons dry wheat straw per year. These raw material loadings correspond to an estimated annual ethanol production of 200,000 m3, assuming C6 fermentation only. In some of the simulated cases, C5 fermentation was also considered, which increased the annual ethanol production to approximately 230,000 m3. It was assumed that the plant was in operation 8000 h per year, and could be managed by 28 people. One 1G case and six integrated 1G + 2G cases were modeled. In the integrated cases, ethanol, DDGS, and biogas production from the C5 sugars were investigated, as well as biogas upgrading to vehicle fuel quality. A sensitivity analysis was also performed for the six integrated cases to assess variations in the biogas yield which increased the investigated configurations to another six supplementary cases.
An overview of the process is shown in Fig. 11, and further details are provided in Section “Case description” below.

Schematic overview of the 1G + 2G process and alternative configurations

Simulations were performed with the flow sheeting program Aspen Plus (version 8.2 from Aspen Technology Inc., Massachusetts, USA). Data for biomass components such as cellulose and lignin were retrieved from the National Renewable Energy Laboratory (NREL) database developed for biofuel components [28 ]. The NRTL-HOC property method was used for all units except in the heat and power production steam cycle, where STEAMNBS was used. The simulation models were further developments of previous work by Wingren et al. [29 (link), 30 (link)], Sassner and Zacchi [31 (link)] and Joelsson et al. [32 ]. Heat integration was implemented as described previously [32 ] using Aspen Energy Analyzer (version 8.2). The results from Aspen Plus were implemented in APEA, and were used together with vendors’ quotations to evaluate the capital and operational costs. Further details on the Aspen Plus modeling can be found in a previous publication [33 (link)].
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Publication 2016
Biofuels Biogas Cellulose Cereals Ethanol Fermentation Hypersensitivity Lignin Plants Steam Sugars Triticum aestivum
Chemically defined substances should be described by generic name, chemical name according to the International Union of Pure and Applied Chemistry (IUPAC) nomenclature, other generic international names and abbreviations and the Chemical Abstract Service (CAS) number and the European Inventory of Existing Commercial chemical Substances number (EINECS), European Community number and European Enzyme Commission number if available. The structural and molecular formula, the openSMILES notation and the molecular weight must be included. Where relevant, the isomeric forms should be given. Information on structurally related substances should be included, when appropriate.
For chemically defined compounds used as flavourings, the EU Flavour Information System (FLAVIS) number in connection with relevant chemical group should be included.
For additives of plant origin, the characterisation should include the scientific name of the plant of origin and its botanical classification (family, genus, species, if appropriate subspecies). The parts of the plant used to obtain the active substance(s) (e.g. leaves, flowers, seeds, fruits, tubers, roots) should be indicated. The identification criteria and other relevant aspects of the plants should be indicated. For complex mixtures of many compounds obtained by an extraction process, it is recommended to follow the relevant terminology such as essential oil, absolute, tincture, extract and related terms widely used for botanically defined flavouring products to describe the extraction process. Reasonable efforts should be made to identify and quantify all components of the mixture. One or more marker compounds should be selected, which will allow the additive to be identified in the different studies. Information on the variability in composition of comparable products should be provided. This could be done by reference to published literature.
For natural products of non‐plant origin, an equivalent approach to the above may be used.
Additives in which not all constituents can be identified should be characterised by the constituent(s) contributing to its activity. One or more marker compounds should be selected which will allow the additive to be identified in the different studies.
For clays' data on elemental and mineralogical composition as well as information on the structure should be provided by appropriate methods (e.g. atomic absorption spectrophotometry, X‐ray diffraction, differential thermal analysis).
For enzyme and enzyme preparations, the number and systematic name proposed by the International Union of Biochemistry (IUB) in the most recent edition of ‘Enzyme Nomenclature’ should be given for each declared activity. For activities not yet included, a systematic name consistent with the IUB rules of nomenclature shall be used. Trivial names are acceptable provided that they are unambiguous and used consistently throughout the dossier, and they can be clearly related to the systematic name and IUB number at their first mention.
When the active substance(s)/agent(s) is/are supplied by a third party, the requirements/specifications (e.g. purity and impurities with safety relevance) set by the applicant should be provided.
For chemical substances produced by fermentation, the microbial origin should also be described (see Section 2.2.1.2).
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Publication 2017
Clay Complex Mixtures Differential Thermal Analysis Enzymes Europeans Fermentation Flowers Fruit Generic Drugs Genes, Plant Isomerism Oils, Volatile Plant Embryos Plant Proteins Plant Roots Plants Plant Tubers Safety Spectrophotometry, Atomic Absorption X-Ray Diffraction
The isolates included in this project were carefully selected to be representative of the S. cerevisiae whole species. All the isolate details, including ecological and geographical origins, providers and references, are listed in Supplementary Table 1. We maximized the isolate ecological origins by including both human-associated environments such as wine and sake fermentation, brewing and dairy products, as well as natural environments such as soil, insects, tree exudate and fruit. Geographical origins are also highly diverse and have a worldwide distribution (Supplementary Table 1). In addition to the 918 isolates provided by research laboratories and yeast collections, we included 93 strains sequenced in previous studies6 (link)–8 (link), to give a total of 1,011 samples analysed in this study. We sought to keep the isolates in their natural state before sequencing to provide a global picture of the ploidy and level of heterozogosity. However, among the 918 selected isolates, 124 were non-natural haploid with the HO gene deleted and the 93 external isolates were genetically manipulated and made homozygous before sequencing.
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Publication 2018
Dairy Products Exudate Fermentation Fruit Homo sapiens Homozygote Insecta Natural Childbirth Strains Trees Wine Yeast, Dried

Most recents protocols related to «Fermentation»

Example 9

NEBT7EL-pA06238 was grown on LB with 50 μg/ml kanamycin. A 600 ml culture of TBkan50 was inoculated with NEBT7EL-pA06238 and incubated overnight at 37° C. at 200 rpm. The next morning, a 10 L fermentor was prepared with 9.5 L of TB and then inoculated with 500 ml of the overnight culture. The culture was grown at 37° C. The pH was maintained at 6.2 with NaOH and the dO2 was maintained ≥20%. After 2 hours of growth, the temperature was dropped to 25° C. The culture was grown for an additional 1 hour with the OD600 around 7. IPTG was added to a final concentration of 1 mM and CoCl2 was added to 25 μM. Additional CoCl2 was added 1 and 2 hours after induction to bring the final concentration to 300 μM. The cells were grown for 20 hours at which point the fermentor was chilled to 10° C. and the cells were harvested by centrifugation. The cell pellet was stored at −80° C. until use.

The cell pellet from the fermentation was lysed by stirring in buffer with lysozyme and DNAse. Cell debris was removed by centrifugation and the supernatant was filtered through a 0.45 micron filter. Filtered supernatant was incubated with Ni-NTA agarose resin and then enzyme was eluted with imidazole. Purified FC4E pA06238 was immobilized onto 5.25 grams of ECR8204F resin using the standard published protocol from Purolite.

The immobilized enzyme was loaded into a 11×300 mm glass fixed bed reactor and run for approximately 200 h at constant temperature (60° C.) with a constant feed composition of 30 wt % fructose+70 wt % aqueous buffer solution (20 mM KPO4, 50 mM NaCl, 300 uM CoCl2). Feed rate was held constant at 140 uL/min throughout the run. The fixed bed reaction reached a maximal conversion of approximately 30% tagatose and had a half-life of −50 hours (FIG. 15).

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Patent 2024
ARID1A protein, human Buffers Cells Centrifugation Deoxyribonucleases Enzymes Enzymes, Immobilized Fermentation Fermentors Fructose imidazole Isopropyl Thiogalactoside Kanamycin Muramidase Resins, Plant Sepharose Sodium Chloride tagatose

Example 3

Astragalus membranaceus was crushed and sieved through 8 mesh to obtain Astragalus membranaceus powder. The Astragalus membranaceus powder was mixed evenly with distilled water with a weight ratio of 2.5:1, sterilized in a steam sterilization pot at 90° C. for 60 min, and then cooled to room temperature to obtain a solid medium of Astragalus membranaceus. Paecilomyces cicadae was evenly inoculated into the solid medium of Astragalus membranaceus with an inoculation amount of 20 wt % of Astragalus membranaceus. The inoculated medium was cultured at a constant temperature of 26° C. and a constant relative humidity of 80% for 24 days to obtain fermentation fungal substance of Astragalus membranaceus/Paecilomyces cicadae E (hereinafter referred to as “fungal substance E”).

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Patent 2024
Astragalus membranaceus Cordyceps cicadae Fermentation Humidity Powder Steam Sterilization Vaccination zymogen E

Example 1

Expression vectors are constructed with the promoter regions upstream of a gene for expression of a fusion protein or an enzyme, such as lipase. Vectors for protein expression may be constructed with the promoter placed immediately upstream of the translational start site of a gene encoding the protein. Thus, in some embodiments, these vectors can be used for transforming cells for protein expression in the absence of methanol. In some embodiments the cells are Komagataella cells.

Protein expression from the Komagataella cells may be assayed under fermentation conditions. It should be expected that the promoters described herein will drive protein expression independent of methanol (SEQ ID NO: 1-7).

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Patent 2024
Cells Cloning Vectors Enzymes Fermentation Gene Products, Protein Lipase Methanol Protein Biosynthesis Proteins

Example 1

Fermentation/Concentration

In some embodiments, whey permeate, concentrated permeate, and/or ultrafiltration permeate is pasteurized and then fermented with Lactic acid bacteria for 20 to 30 hours at 10-130° F. with injection of NH4(OH) to maintain pH at 5.5 to 5.6 during fermentation. The resulting fermented liquid is concentrated by mechanical vapor recompression (MVR) to achieve a solids content of about 58%-64%. The concentrated fermented liquid is then sent to a pH balance tank where it is injected with NH4(OH) to achieve a pH of about 6.5 to 6.7.

Crystallization

The concentrated fermented liquid is then sent to a plate heat exchanger (PHE) to bring the temperature of the liquid to about 130° F. The concentrated fermented liquid is then sent to a crystallization tank where the concentrated fermented liquid is agitated and allowed to cool to about 110° F. to 115° F., during which crystal formation occurs. In some embodiments, once the temperature of the concentrated fermented liquid reaches about 90° F. to 115° F. the concentrated fermented liquid is sent to a decanter centrifuge to separate the solid crystals from the liquid. Across 12 fermentation batches from production, the average yield of solid crystals was 1,744 lb.

Across multiple processing trials the following crystal yields were achieved:

Ratio (finished
FinishedFinishedFinishedcrystal/finished
StartingLiquidLiquidCrystalcrystal +
AmountAmountAmountAmountfinished
Trial(gallons)(gallons)(pounds)(pounds)liquid)
Standardn.a.47814828824454.8%
fermentation,
no seeding
Standardn.a.57405797421403.6%
fermentation,
no seeding
Standardn.a.47384785424484.9%
fermentation,
no seeding
Standardn.a.36533689522185.7%
fermentation,
no seeding
Standardn.a.66746740734704.9%
fermentation,
no seeding
Standardn.a.27162743211314.0%
fermentation,
no seeding

Example 2

Fermentation/Concentration

In some embodiments, whey permeate, concentrated permeate, and/or ultrafiltration permeate is pasteurized and then fermented with Lactic acid bacteria for 20 to 30 hours at 100-120° F. with injection of NH4(OH) to maintain pH at 5.5 to 5.6. The resulting fermented liquid is concentrated by mechanical vapor recompression (MVR) to achieve a solids content of about 61%-64%.

Crystallization

The concentrated fermented liquid is then sent directly to a crystallizer tank with continuous agitation. In this example, the liquid is not sent to pH balance tank or chiller plate heat exchanger. To achieve higher crystal yield, a 3000 (w/w) CaOH slurry is added to the concentrated fermented liquid in the crystallization tank to achieve a calcium concentration of 0.9-2.0% (w/w) in the combined mixture. The CaOH slurry is added to the concentrated fermented liquid in the crystallizer tank slowly to allow thorough mixing. The mixture is then allowed to stand in the crystallization tank for 6 to 18 hours, during which time the temperature is allowed to cool to about 90 to 115° F. and crystals are formed. Once the temperature of the concentrated fermented liquid reaches about 90 to 115° F. the concentrated fermented liquid is sent to a decanter to separate the solid crystals from the liquid.

Across multiple processing trials the following crystal yields were achieved with a calcium concentration of 3.33% (non-seeded data from Example 1 is included for comparison):

Ratio (finished
FinishedFinishedFinishedcrystal/finished
StartingLiquidLiquidCrystalcrystal +
AmountAmountAmountAmountfinished
Trial(gallons)(gallons)(pounds)(pounds)liquid)
Seeded3000202620463755527.0%
w/1,000 lbs
Calcium
hydroxide
Seeded3000225022725952629.5%
w/1,000 lbs
Calcium
hydroxide
Seeded30003293332591061324.2%
w/1,000 lbs
Calcium
hydroxide
Seeded3000202120412506619.9%
w/1,000 lbs
Calcium
hydroxide
Seeded30002805283311323731.8%
w/1,000 lbs
Calcium
hydroxide
Seeded2000198320028532521.0%
w/1,000 lbs
Calcium
hydroxide
Standardn.a.47814828824454.8%
fermentation,
no seeding
Standardn.a.57405797421403.6%
fermentation,
no seeding
Standardn.a.47384785424484.9%
fermentation,
no seeding
Standardn.a.36533689522185.7%
fermentation,
no seeding
Standardn.a.66746740734704.9%
fermentation,
no seeding
Standardn.a.27162743211314.0%
fermentation,
no seeding

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Patent 2024
Calcium, Dietary Crystallization Fermentation Hydroxide, Calcium Lactobacillales Liquid Crystals TO 115 Ultrafiltration Whey

Example 4

Experiments were performed in 100 ml Kautex bottles. Model waste was mixed with water to a volume at 50 ml and at TS concentration of 7.5%. CBC and the selected blend (B.a protease:T.I pholip:A.a BG:CBC in ratio of 10:5:15:70) were added in amounts corresponding to 0%, 25%, 50%, 75%, 100% and 200% of the concentration that has been used as default during the previous experiments (2.4% enzymes protein/TS). Bottles were incubated on a Stuart Rotator SB3 and placed in a 50° C. oven for 24 hours.

A significant improvement in TS-solubilization was seen at all applied enzyme concentrations, when comparing the blend with CBC. The TS-solubilization at default settings (2.4% CBC/TS) was around 25%. This was obtained with only approximately 0.9% of the blend, which corresponds to a lowering in enzyme dosage of approximately 2.5 to 2.7 times (See FIG. 2). At the same time we found a clear increase in hydrolysis and fermentation products such as glucose, xylose, lactic acid (FIG. 3, and FIG. 5). This is a surprise since 15% of CBC (cellulase and xylanase activities) was replaced with the lipase and protease.

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Patent 2024
Cellulase Enzymes Fermentation Glucose Hydrolysis Lactic Acid Lipase Peptide Hydrolases Proteins Xylose

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More about "Fermentation"

Fermentation is a crucial metabolic process that has wide-ranging applications in various industries, from food and beverage production to biofuel generation and pharmaceutical development.
This microbial-driven transformation involves the breakdown of complex carbohydrates, such as starch or sugars, into simpler substances like alcohols or acids.
The fermentation process is facilitated by the action of enzymes and microorganisms, including yeast and bacteria.
It plays a vital role in diverse products, including beer, wine, dairy items, pickles, and even certain medicines.
Understanding the principles and optimization of fermentation processes is essential for researchers and industry professionals seeking to enhance efficiency, productivity, and the development of novel fermentation-based applications.
Techniques like SAS 9.4, MacConkey agar, HPLC, MRS broth, Whatman No. 1 filter paper, API 20E, No. 1 filter paper, Mannitol salt agar, Prism 8, and the MiSeq platform are commonly used in fermentation research and development to analyze, optimize, and characterize these complex microbial processes.
By leveraging the insights gained from these tools and methods, scientists and engineers can unlock new frontiers in fermentation-based innovation, driving progress in fields as diverse as food, biofuels, and pharmaceuticals.
PubCompare.ai, an AI-driven platform, revolutionizes fermentation research by enabling users to locate the best protocols from literature, preprints, and patents, and identify the optimal solutions for their specific needs.
This innovative tool empowers researchers to compare and optimize their fermentation processes, accelerating their discoveries and advancements in this dynamic and impactful field.