Biophysical characterization dataset of native nicotinic acetylcholine receptor in lipid-like detergent complexes
Abstract not provided
Maldonado-Hernándezac, Rafael↗
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A lipase from Lacticaseibacillus rhamnosus IDCC 3201 with thermostability and pH resistance for use as a detergent additive
Lipases are important biocatalysts and ubiquitous in plants, animals, and microorganisms. The high growth rates of microorganisms with low production costs have enabled the wide application of microbial lipases in detergent, food, and cosmetic industries. Herein, a novel lipase from Lacticaseibacillus rhamnosus IDCC 3201 (Lac-Rh) was isolated and its activity analyzed under a range of reaction conditions to evaluate its potential industrial application. The isolated Lac-Rh showed a molecular weight of 24 kDa and a maximum activity of 3438.5 ± 1.8 U/mg protein at 60 °C and pH 8. Additionally, Lac-Rh retained activity in alkaline conditions and in 10% v/v concentrations of organic solvents, including glycerol and acetone. Interestingly, after pre-incubation in the presence of multiple commercial detergents, Lac-Rh maintained over 80% of its activity and the stains from cotton were successfully removed under a simulated laundry setting. Overall, the purified lipase from L. rhamnosus IDCC 3201 has potential for use as a detergent in industrial applications.
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Chain-length-controllable upcycling of polyolefins to sulfate detergents
Escalating global plastic pollution and the depletion of fossil-based resources underscore the urgent need for innovative end-of-life plastic management strategies in the context of a circular economy. Thermolysis is capable of upcycling end-of-life plastics to intermediate molecules suitable for downstream conversion to eventually high-value chemicals, but tuning the molar mass distribution of the products is challenging. Here, in this study, we report a temperature-gradient thermolysis strategy for the conversion of polyethylene and polypropylene into hydrocarbons with tunable molar mass distributions. The whole thermolysis process is catalyst- and hydrogen-free. The thermolysis of polyethylene and polyethylene/polypropylene mixtures with tailored temperature gradients generated oil with an average chain length of ~C 14 . The oil featured a high concentration of synthetically useful α-olefins. Computational fluid dynamics simulations revealed that regulating the reactor wall temperature was the key to tuning the hydrocarbon distributions. Subsequent oxidation of the obtained α-olefins by sulfuric acid and neutralization by potassium hydroxide afforded sulfate detergents with excellent foaming behaviour and emulsifying capacity and low critical micelle concentration. Overall, this work provides a viable approach to producing value-added chemicals from end-of-life plastics, improving the circularity of the anthropogenic carbon cycle.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Stable Picodisc Assemblies from Saposin Proteins and Branched Detergents
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Kurgan, Kathleen W.↗
Modification of Wool Fibers via Base/Cationic Detergent Pretreatment and Transglutaminase-mediated Reaction of Keratin
The surface modification of wool fibers is an important part of the textile industry to add functionality and stability to wool products. In this study, we developed a process utilizing a base/cationic surfactant solution pretreatment followed by an enzyme-mediated keratin crosslinking reaction to modify the wool fibers. Changes in water contact angle demonstrated the successful transformation of the hydrophobic wool surface to a more hydrophilic one after soaking in sodium carbonate solution containing hexadecyltrimethylammonium bromide (CTAB). The treated fabrics were further characterized by colorimetry and fluorescent spectrometry. Results showed that the pretreatment increased the yellowness of fabrics and caused some structural changes among certain amino acids, such as tryptophan and cystine. Keratin extracted from coarse wool fibers was further applied on pretreated fabrics through a microbial transglutaminase (mTGase) mediated reaction under mild conditions. Morphological characterization via SEM demonstrated the effective coverage of keratin on the scales of wool. The current method may provide an alternative processing protocol to modify wool fibers and improve the quality and performance of wool products.
36 MATERIALS SCIENCE↗
FLC Notable Technology Award Oleo-Furan Surfactant
It’s a well-kept secret that laundry detergents are harmful to the environment. The important chemical in laundry detergent, called a surfactant. Surfactants are the workhorses of laundry detergent and soaps, and they're attracted to things like grease on your hands and dirt in your clothes to wash them away. Surfactants are used in everything from shampoo, hand soap, laundry detergent, and cosmetics. Many current surfactants are made from petroleum feedstock. These petroleum-derived building blocks come with a big carbon footprint. As the need for greener feedstock alternatives for synthesizing surfactants became obvious, manufacturers turned to natural oils, such as palm kernel and coconut oil. However, these oils are costly, particularly in areas where they are not domestically produced, and using them for surfactant synthesis competes with the food supply chain. Surfactants deactivate and do not work in hard water. Hard water is common - 85% of the U.S. water supply is considered hard because of the presence of small metal ions. These metal ions cover the surfactants making them useless. To solve this problem, many manufacturers add chemicals called chelators to bind the metal ions and make the water less hard, enhancing the effectiveness of the laundry detergent. However, this solution leads to more problems, including increased cost of detergent production and a large output of environmentally harmful chemicals. There remains a strong need for effective laundry detergents that do not negatively impact the environment and are available to consumers at an affordable cost. The American Cleaning Institute (ACI), a surfactant manufacturer organizing body, is emphasizing commitment to developing bio-renewable alternatives to current surfactants in laundry detergents. That’s why chemists at SIRONIX Renewables partnered with Los Alamos National Laboratory to further develop Oleo-furan surfactants (OFS). OFS are a new class of non-toxic, non-irritating surfactants for laundry detergent. It is the only surfactant that performs effectively in cold and hard water without chelators to bind the metal ions in hard water. OFS can be produced readily from sustainable, bio-derived molecules. They are multi-functional molecules - performing the role of a surfactant and a chelator in one - and are completely bio-degradable. OFS does not rely on petroleum feedstock and is synthesized from non-food, bio-renewable cellulosic feedstock. OFS solves each of the pertinent problems facing detergents and our environment today.
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CHARMM-GUI Bicelle Builder : An Extension of Membrane Builder for Modeling and Simulation of Bicelle Systems
Membrane mimetics, such as detergent micelles, nanodiscs, and amphipol complexes, which can provide membrane-like environments while retaining small and soluble features, have been utilized to study membrane proteins. A bicelle, composed of varying lipids and detergents, is a useful membrane mimetic because the lipid-to-detergent ratio, the q-value, can be adjusted to alter the properties of the aggregate, including the thickness and size of the bicelle. However, building a bicelle model for modeling and simulation studies requires nontrivial efforts, even for experts. We introduce CHARMM-GUI Bicelle Builder, a web-based platform that can generate various all-atom bicelle systems via a graphical user interface with all available lipids and detergents in Membrane Builder. To illustrate and validate Bicelle Builder with practical systems, we have modeled and simulated pure bicelles consisting of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids with 1,2-dihexanoyl-sn-glycero-3-phosphocholine (C6DHPC) detergents and protein–bicelle complexes, composed of DMPC with C6DHPC, foscholine-10 (FOS10), and lysophosphatidylcholine-12 (LPC12) detergents. Our simulation results indicate that Bicelle Builder can generate reliable and robust bicelle models with and without proteins that retain DMPC bilayer characteristics. Bicelle Builder is expected to help researchers better understand not only bicelles themselves but also atomistic-level structures of protein–bicelle complexes that are often difficult to access through experimental approaches.
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Rapid preparation of nanodiscs for biophysical studies
Nanodiscs, which are disc-shaped entities that contain a central lipid bilayer encased by an annulus of amphipathic helices, have emerged as a leading native-like membrane mimic. The current approach for the formation of nanodiscs involves the creation of a mixed-micellar solution containing membrane scaffold protein, lipid, and detergent followed by a time consuming process (3–12 h) of dialysis and/or incubation with sorptive beads to remove the detergent molecules from the sample. In contrast, the methodology described herein provides a facile and rapid procedure for the preparation of nanodiscs in a matter of minutes (<15 min) using Sephadex® G-25 resin to remove the detergent from the sample. A panoply of biophysical techniques including analytical ultracentrifugation, dynamic light scattering, gel filtration chromatography, circular dichroism spectroscopy, and cryogenic electron microscopy were employed to unequivocally confirm that aggregates formed by this method are indeed nanodiscs. We believe that this method will be attractive for time-sensitive and high-throughput experiments.
59 BASIC BIOLOGICAL SCIENCES↗
Small angle neutron scattering and lipidomic analysis of a native, trimeric PSI-SMALP from a thermophilic cyanobacteria
The use of styrene-maleic acid copolymers (SMAs) to produce membrane protein-containing nanodiscs without the initial detergent isolation has gained significant interest over the last decade. We have previously shown that a Photosystem I SMALP from the thermophilic cyanobacterium, Thermosynechococcus elongatus (PSI-SMALP), has much more rapid energy transfer and charge separation in vitro than detergent isolated PSI complexes. In this study, we have utilized small-angle neutron scattering (SANS) to better understand the geometry of these SMALPs. These techniques allow us to investigate the size and shape of these particles in their fully solvated state. Further, the particle's proteolipid core and detergent shell or copolymer belt can be interrogated separately using contrast variation, a capability unique to SANS. Here we report the dimensions of the Thermosynechococcus elongatus PSI-SMALP containing a PSI trimer. At ~1.5 MDa, PSI-SMALP is the largest SMALP to be isolated; our lipidomic analysis indicates it contains ~1300 lipids/per trimeric particle, >40-fold more than the PSI-DDM particle and > 100 fold more than identified in the 1JB0 crystal structure. Interestingly, the lipid composition to the PSI trimer in the PSI-SMALP differs significantly from bulk thylakoid composition, being enriched ~50 % in the anionic sulfolipid, SQDG. Finally, utilizing the contrast match point for the SMA 1440 copolymer, we also can observe the ~1 nm SMA copolymer belt surrounding this SMALP for the first time, consistent with most models of SMA organization.
59 BASIC BIOLOGICAL SCIENCES↗
High-throughput cell-free screening of eukaryotic membrane protein expression in lipidic mimetics
Membrane proteins play essential roles in cellular function and metabolism. Nonetheless, biophysical and structural studies of membrane proteins are impeded by the difficulty of their expression in and purification from heterologous cell-based systems. As an alternative to these cell-based systems, cell-free protein synthesis has proven to be an exquisite method for screening membrane protein targets in a variety of lipidic mimetics. Here we report a high-throughput screening workflow and applied it to screen 61eukaryotic membrane protein targets. For each target, we tested its expression in lipidic mimetics: two detergents, two liposomes, and two nanodiscs. We show that 35 membrane proteins (57%) can be expressed in a soluble fraction in at least one of the mimetics with the two detergents performing significantly better than nanodiscs and liposomes, in that order. Using the established cell-free workflow, we studied the production and biophysical assays for mitochondrial pyruvate carrier (MPC) complexes. Our studies show that the complexes produced in cell-free are functional competent in complex formation and substrate binding. Our results highlight the utility of using cell-free systems for screening and production of eukaryotic membrane proteins.
59 BASIC BIOLOGICAL SCIENCES↗
Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform
Top-down proteomics is a powerful tool for characterizing genetic variations and post-translational modifications at intact protein level. That being said, one significant technical gap of top-down proteomics is the inability to analyze low amount of biological samples, which limits its access to isolated rare cells, fine-needle aspiration biopsies, and tissue substructures. Herein, we developed an ultrasensitive top-down platform by incorporating a microfluidic sample preparation system, termed nanoPOTS (Nanodroplet Processing in One pot for Trace Samples), into a top-down proteomics workflow. A unique combination of a nonionic detergent dodecyl-ß-D-maltopyranoside (DDM) with urea as protein extraction buffer significantly improved both protein extraction efficiency and sample recovery. We hypothesize that the DDM detergent improves protein recovery by efficiently reducing non-specific adsorption of intact proteins on container surfaces, while urea serves as a strong denaturant to disrupt noncovalent complexes and release intact proteins for downstream analysis. The nanoPOTS-based top-down platform reproducibly and quantitatively identified ~170 to ~620 proteoforms from ~70 to ~770 HeLa cells containing ~10 to ~115 ng of total protein. A variety of post-translational modifications including acetylation, myristoylation, and iron binding were identified using only less than 800 cells. We anticipate the nanoPOTS top-down proteomics platform will be broadly applicable in biomedical researches, particularly where clinical specimens are not available in amounts amenable to standard workflows.
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Ligand modulation of the conformational dynamics of the A 2A adenosine receptor revealed by single-molecule fluorescence
G protein-coupled receptors (GPCRs) are the largest class of transmembrane proteins, making them an important target for therapeutics. Activation of these receptors is modulated by orthosteric ligands, which stabilize one or several states within a complex conformational ensemble. The intra- and inter-state dynamics, however, is not well documented. Here, we used single-molecule fluorescence to measure ligand-modulated conformational dynamics of the adenosine A 2A receptor (A 2A R) on nanosecond to millisecond timescales. Experiments were performed on detergent-purified A 2R in either the ligand-free (apo) state, or when bound to an inverse, partial or full agonist ligand. Single-molecule Förster resonance energy transfer (smFRET) was performed on detergent-solubilized A 2A R to resolve active and inactive states via the separation between transmembrane (TM) helices 4 and 6. The ligand-dependent changes of the smFRET distributions are consistent with conformational selection and with inter-state exchange lifetimes ≥ 3 ms. Local conformational dynamics around residue 229 6.31 on TM6 was measured using fluorescence correlation spectroscopy (FCS), which captures dynamic quenching due to photoinduced electron transfer (PET) between a covalently-attached dye and proximal aromatic residues. Global analysis of PET-FCS data revealed fast (150–350 ns), intermediate (50–60 μs) and slow (200–300 μs) conformational dynamics in A 2A R, with lifetimes and amplitudes modulated by ligands and a G-protein mimetic (mini-G s ). Most notably, the agonist binding and the coupling to mini-G s accelerates and increases the relative contribution of the sub-microsecond phase. Molecular dynamics simulations identified three tyrosine residues (Y112, Y288 7.53 , and Y290 7.55 ) as being responsible for the dynamic quenching observed by PET-FCS and revealed associated helical motions around residue 229 6.31 on TM6. As a result, this study provides a quantitative description of conformational dynamics in A 2A R and supports the idea that ligands bias not only GPCR conformations but also the dynamics within and between distinct conformational states of the receptor.
59 BASIC BIOLOGICAL SCIENCES↗
Cryo-ET of Toxoplasma parasites gives subnanometer insight into tubulin-based structures
Tubulin is a conserved protein that polymerizes into different forms of filamentous structures in Toxoplasma gondii, an obligate intracellular parasite in the phylum Apicomplexa. Two key tubulin-containing cytoskeletal components are subpellicular microtubules (SPMTs) and conoid fibrils (CFs). The SPMTs help maintain shape and gliding motility, while the CFs are implicated in invasion. Here, we use cryogenic electron tomography to determine the molecular structures of the SPMTs and CFs in vitrified intact and detergent-extracted parasites. Subvolume densities from detergent-extracted parasites yielded averaged density maps at subnanometer resolutions, and these were related back to their architecture in situ. An intralumenal spiral lines the interior of the 13-protofilament SPMTs, revealing a preferred orientation of these microtubules relative to the parasite’s long axis. Each CF is composed of nine tubulin protofilaments that display a comma-shaped cross-section, plus additional associated components. Conoid protrusion, a crucial step in invasion, is associated with an altered pitch of each CF. The use of basic building blocks of protofilaments and different accessory proteins in one organism illustrates the versatility of tubulin to form two distinct types of assemblies, SPMTs and CFs.
59 BASIC BIOLOGICAL SCIENCES↗
Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants
The serotonin transporter (SERT) is a member of the SLC6 neurotransmitter transporter family that mediates serotonin reuptake at presynaptic nerve terminals. SERT is the target of both therapeutic antidepressant drugs and psychostimulant substances such as cocaine and methamphetamines, which are small molecules that perturb normal serotonergic transmission by interfering with serotonin transport. Despite decades of studies, important functional aspects of SERT such as the oligomerization state of native SERT and its interactions with potential proteins remain unresolved. Here, we develop methods to isolate SERT from porcine brain (pSERT) using a mild, nonionic detergent, utilize fluorescence-detection size-exclusion chromatography to investigate its oligomerization state and interactions with other proteins, and employ single-particle cryo-electron microscopy to elucidate the structures of pSERT in complexes with methamphetamine or cocaine, providing structural insights into psychostimulant recognition and accompanying pSERT conformations. Methamphetamine and cocaine both bind to the central site, stabilizing the transporter in an outward open conformation. We also identify densities attributable to multiple cholesterol or cholesteryl hemisuccinate (CHS) molecules, as well as to a detergent molecule bound to the pSERT allosteric site. Under our conditions of isolation, we find that pSERT is best described as a monomeric entity, isolated without interacting proteins, and is ensconced by multiple cholesterol or CHS molecules.
59 BASIC BIOLOGICAL SCIENCES↗
Effects of antibacterial peptide-producing Bacillus subtilis, gallic acid, and cellulase on fermentation quality and bacterial community of whole-plant corn silage
In the current study, we assessed the effects of antibacterial peptide-producing Bacillus subtilis (BS), gallic acid (GA) and cellulase (CL) on the fermentation quality and bacterial community of various varieties of whole-plant corn silage. Three different varieties of whole-plant corn (Yuqing386, Enxiai298, and Nonghe35) were treated with 0.02% BS (fresh material basis), 0.2% GA (fresh material basis) and 0.02% CL (fresh material basis), after which 45 days of anaerobic fermentation were conducted. With the exception of its low dry matter content, the results showed that Yuqing386’s crude protein, water-soluble carbohydrate, and lactic acid contents were significantly higher than those of the other two corn varieties. However, its acid detergent fiber and cellulose contents were significantly lower than those of the other two corn varieties. Among the three corn variety silages, Yuqing386 had the highest relative abundance of Lactobacillus at the genus level and the biggest relative abundance of Firmicutes at the phylum level. In addition, the three additives markedly enhanced the quantity of dry matter and crude protein as compared to the control group. The application of GA considerably decreased the level of neutral detergent fiber while significantly increasing the content of lactic acid and water-soluble carbohydrates. Even though all additives enhanced the structure of the bacterial community following silage, the GA group experienced the greatest enhancement. On a phylum and genus level, the GA group contains the highest relative abundance of Firmicutes and Lactobacillus , respectively. Overall, of the three corn varieties, Yuqing386 provides the best silage qualities. GA has the biggest impact among the additions employed in this experiment to enhance the nutritional preservation and fermentation quality of whole-plant corn silage.
Zhang, Zhiheng↗
Identification of pleiotropic loci mediating structural and non-structural carbohydrate accumulation within the sorghum bioenergy association panel using high-throughput markers
Molecular characterization of diverse germplasm can contribute to breeding programs by increasing genetic gain for sorghum [ Sorghum bicolor (L.) Moench] improvement. Identifying novel marker-trait associations and candidate genes enriches the existing genomic resources and can improve bioenergy-related traits using genomic-assisted breeding. In the current scenario, identifying the genetic loci underlying biomass and carbon partitioning is vital for ongoing efforts to maximize each carbon sink’s yield for bioenergy production. Here, we have processed a high-density genomic marker (22 466 550) data based on whole-genome sequencing (WGS) using a set of 365 accessions from the bioenergy association panel (BAP), which includes ~19.7 million (19 744 726) single nucleotide polymorphism (SNPs) and 2.7 million (~2 721 824) insertion deletions (indels). A set of high-quality filtered SNP (~5.48 million) derived markers facilitated the assessment of population structure, genetic diversity, and genome-wide association studies (GWAS) for various traits related to biomass and its composition using the BAP. The phenotypic traits for GWAS included seed color (SC), plant height (PH), days to harvest (DTH), fresh weight (FW), dry weight (DW), brix content % (BRX), neutral detergent fiber (NDF), acid detergent fiber (ADF), non-fibrous carbohydrate (NFC), and lignin content. Several novel loci and candidate genes were identified for bioenergy-related traits, and some well-characterized genes for plant height ( Dw1 and Dw2 ) and the YELLOW SEED1 locus ( Y1 ) were validated. We further performed a multi-variate adaptive shrinkage analysis to identify pleiotropic QTL, which resulted in several shared marker-trait associations among bioenergy and compositional traits. Significant marker-trait associations with pleiotropic effects can be used to develop molecular markers for trait improvement using a marker-assisted breeding approach. Significant nucleotide diversity and heterozygosity were observed between photoperiod-sensitive and insensitive individuals of the panel. This diverse bioenergy panel with genomic resources will provide an excellent opportunity for further genetic studies, including selecting parental lines for superior hybrid development to improve biomass-related traits in sorghum.
bioenergy association panel↗
Optimizing dietary rumen-degradable starch to rumen-degradable protein ratio improves lactation performance and nitrogen utilization efficiency in mid-lactating Holstein dairy cows
The dietary rumen-degradable starch (RDS) to rumen-degradable protein (RDP) ratio, denoted as the RDS-to-RDP ratio (SPR), has been proven to enhance in vitro rumen fermentation. However, the effects of dietary SPR in vivo remain largely unexplored. This study was conducted to investigate the effect of dietary SPR on lactation performance, nutrient digestibility, rumen fermentation patterns, blood indicators, and nitrogen (N) partitioning in mid-lactating Holstein cows. Seventy-two Holstein dairy cows were randomly assigned to three groups (24 head/group), balanced for (mean ± standard deviation) days in milk (116 ± 21.5), parity (2.1 ± 0.8), milk production (42 ± 2.1 kg/d), and body weight (705 ± 52.5 kg). The cows were fed diets with low (2.1, control), medium (2.3), or high (2.5) SPR, formulated to be isoenergetic, isonitrogenous, and iso-starch. The study consisted of a one-week adaptation phase followed by an eight-week experimental period. The results indicated that the high SPR group had a lower dry matter intake compared to the other groups ( p < 0.05). A quadratic increase in milk yield and feed efficiency was observed with increasing dietary SPR ( p < 0.05), peaking in the medium SPR group. The medium SPR group exhibited a lower milk somatic cell count and a higher blood total antioxidant capacity compared to other groups ( p < 0.05). With increasing dietary SPR, there was a quadratic improvement ( p < 0.05) in the total tract apparent digestibility of crude protein, ether extract, starch, neutral detergent fiber, and acid detergent fiber. Although no treatment effect was observed in rumen pH, the rumen total volatile fatty acids concentration and microbial crude protein synthesis increased quadratically ( p < 0.05) as dietary SPR increased. The molar proportion of propionate linearly increased ( p = 0.01), while branched-chain volatile fatty acids linearly decreased ( p = 0.01) with increasing dietary SPR. The low SPR group (control) exhibited higher concentration of milk urea N, rumen ammonia N, and blood urea N than other groups ( p < 0.05). Despite a linear decrease ( p < 0.05) in the proportion of urinary N to N intake, increasing dietary SPR led to a quadratic increase ( p = 0.01) in N utilization efficiency and a quadratic decrease ( p < 0.05) in the proportion of fecal N to N intake. In conclusion, optimizing dietary SPR has the potential to enhance lactation performance and N utilization efficiency. Based on our findings, a medium dietary SPR (with SPR = 2.3) is recommended for mid-lactating Holstein dairy cows. Nevertheless, further research on rumen microbial composition and metabolites is warranted to elucidate the underlying mechanisms of the observed effects.
Chen, Panliang↗
A novel sub-pilot-scale direct-contact ultrasonic dehydration technology for sustainable production of distillers dried grains (DDG)
DDG is a major source of protein, calcium, phosphorus, and sulfur is arguably the most important byproduct of the bioethanol industry with increasing demand over the past few years. Reducing energy consumption in the DDG production process and energy recovery from DDG is vital for sustainable bioethanol productions. In this paper, a novel direct-contact multi-frequency, multimode, and modulated (MMM) ultrasonic dryer (US) was developed for the first time and has been applied in dehydration of wet distillers' grain (WDG). Ultrasonic drying (US) was combined with a convective airflow (HA) at different temperatures of 25 (room temperature), 50 and 70 °C to evaluate the impact of US, HA, and US + HA on drying kinetics, activation energy, chemical compositions, microstructure, and color of DDG. Semi-empirical kinetic models were developed and evaluating drying performances showed that the application of ultrasound significantly enhanced the drying rate and decreased the drying time (by 46%), especially at low drying temperatures. The activation energy for moisture removal in the presence of ultrasound was about 50% of that without ultrasound. The final dried distillers' grains product processed by ultrasonic drying had a brighter color, a higher available protein, a higher digestible protein (the lowest acid detergent insoluble crude protein), and a better surface profile with no compromise on minerals and fiber contents.
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