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ACS Omega Jun 2024This study investigates the commercial viability of repurposing fruit waste for enzyme production, specifically focusing on the invertase enzyme derived from . By...
This study investigates the commercial viability of repurposing fruit waste for enzyme production, specifically focusing on the invertase enzyme derived from . By utilizing fruit pulp that incorporates mulberry, carob, Figure, and grape pulp as a nutrient source, it is observed that the culture medium containing carob pulp exhibits the highest invertase activity. Specifically, the invertase activity in this medium is approximately 2.5 times greater (12.90 U/mg protein) than that observed in the peptone medium (5.98 U/mg protein). The extract undergoes several purification steps, including ultrafiltration, ammonium sulfate precipitation, dialysis, and ion-exchange chromatography (purification ratio: 12.11 times, yield: 26.93%). The purified enzyme is immobilized using alginate beads, improving pH and thermal stability. The immobilized enzyme exhibits optimal activity between pH 3.50 and pH 7.00, thereby broadening the enzyme's high-activity pH range. The thermal stability of the immobilized invertase enzyme is significantly improved, especially at 65 °C. Activity studies in the presence of metal ions and certain chemicals have been conducted. The immobilized enzyme's activity increases by approximately 40% in the presence of Ca and Mg, and the immobilized enzyme maintains its activity in the presence of detergents such as SDS, Tween-20, and organic solvents like ethanol and methanol. The potential for the reuse of immobilized invertase was investigated under standard assay conditions. After 20 cycles, the immobilized enzyme was found to retain 80% of its initial activity. Overall, the study establishes the commercial potential of fruit pulp, typically discarded in fruit juice production, as a valuable source for obtaining an invertase enzyme. Furthermore, this study also aims to develop a suitable purification process for invertase in the fruit juice industry. By harnessing fruit waste and implementing innovative enzyme production strategies, industries can enhance their efficiency, reduce their environmental footprint, and optimize resource utilization.
PubMed: 38911758
DOI: 10.1021/acsomega.4c01732 -
Biophysical Journal Jun 2024The ATP-binding cassette (ABC) transporter P-glycoprotein (P-gp) is a multidrug efflux pump that is overexpressed in a variety of cancers and associated with the drug...
The ATP-binding cassette (ABC) transporter P-glycoprotein (P-gp) is a multidrug efflux pump that is overexpressed in a variety of cancers and associated with the drug resistance phenomenon. P-gp structures were previously determined in detergent and in nanodiscs, in which different transmembrane helix conformations were found, "straight" and "kinked", respectively, indicating a possible role of the lipid environment on the P-gp structural ensemble. Here, we investigate the dynamic conformational ensembles and protein-lipid interactions of two human P-gp inward-open conformers, straight and kinked, employing all-atom molecular dynamics simulations in asymmetric multicomponent lipid bilayers that mimic the highly specialized hepatocyte membrane in which P-gp is expressed. The two conformers are found to differ in terms of the accessibility of the substrate cavity. The MD simulations show how cholesterol and different lipid species wedge, snorkel, and partially enter within the cavity of the straight P-gp conformer solved in detergent. However, the access to the cavity of kinked P-gp conformer solved in nanodiscs is restricted. Furthermore, the volume and dynamic fluctuations of the substrate cavity largely differ between the two P-gp structures, and are modulated by the presence (or absence) of cholesterol in the membrane and/or of ATP. From the mechanistic perspective, the findings indicate that the straight conformer likely precedes the kinked conformer in the functional working cycle of P-gp, with the latter conformation representing a post substrate-bound state. The inaccessibility of the main transmembrane cavity in the kinked conformer might be crucial in preventing substrate disengagement and transport withdrawal. Remarkably, in our unbiased MD simulations, one transmembrane helix (TM10) of the straight conformer underwent a spontaneous conformational transition to a kinked conformation, underlining the relevance of both conformations in a native phospholipid environment and revealing structural descriptors defining the transition between two P-gp conformers.
PubMed: 38909280
DOI: 10.1016/j.bpj.2024.06.020 -
Biodegradation Jun 2024The microbial fuel cell (MFC) is considered a modern technology used for treating wastewater and recovering electrical energy. In this study, a new dual technology...
The microbial fuel cell (MFC) is considered a modern technology used for treating wastewater and recovering electrical energy. In this study, a new dual technology combining MFC and a specialized biofilter was used. The anodic materials in the system were crushed graphite, either without coating (UFB-MFC) or coated with nanomaterials (nano-UFB-MFC). This biofilter served as a barrier to retain and remove turbidity and suspended solids, while also facilitating the role of bacteria in the removal of organic pollutants, phosphates, nitrates, sulfates, oil and greases. The results demonstrated that both systems exhibited high efficiency in treating kitchen wastewater, specifically greywater and dishwashing wastewater with high detergent concentrations. The removal efficiencies of COD, oil and grease, suspended solids, turbidity, nitrates, sulfates, and phosphates in first UFB-MFC were found to be 88, 95, 89, 86, 87, 75, and 94%, respectively, and in Nano-UFB-MFC were 86, 99, 95, 91, 81, 88, and 95%, respectively, with a high efficiency in recovering bioenergy reaching a value of 1.8 and 1.5 A m, respectively. The results of this study demonstrate the potential for developing MFC and utilizing it as a domestic system to mitigate pollution risks before discharging wastewater into the sewer network.
PubMed: 38909143
DOI: 10.1007/s10532-024-10087-0 -
Acta Biomaterialia Jun 2024The use of decellularized extracellular matrix products in tissue regeneration is quite alluring yet practically challenging due to the limitations of its availability,...
The use of decellularized extracellular matrix products in tissue regeneration is quite alluring yet practically challenging due to the limitations of its availability, harsh processing techniques, and host rejection. Scaffolds obtained by either incorporating extracellular matrix (ECM) material or coating the surface can resolve these challenges to some extent. However, these scaffolds lack the complex 3D network formed by proteins and growth factors observed in natural ECM. This study introduces an approach utilizing 3D nanofiber scaffolds decorated with dECM to enhance cellular responses and promote tissue regeneration. Notably, the dECM can be customized according to specific cellular requirements, offering a tailored environment for enhanced therapeutic outcomes. Two types of 3D expanded scaffolds, namely radially aligned scaffolds (RAS) and laterally expanded scaffolds (LES) fabricated by the gas-foaming expansion were utilized. To demonstrate the proof-of-concept, human dermal fibroblasts (HDFs) seeded on these scaffolds for up to 8 weeks, resulted in uniform and highly aligned cells which deposited ECM on the scaffolds. These cellular components were then removed from the scaffolds through decellularization (e.g., SDS treatment and freeze-thaw cycles). The dECM-decorated 3D expanded nanofiber scaffolds can direct and support cell alignment and proliferation along the underlying fibers upon recellularization. An in vitro inflammation assay indicates that dECM-decorated LES induces a lower immune response than dECM-decorated RAS. Further, subcutaneous implantation of dECM-decorated RAS and LES shows higher cell infiltration and angiogenesis within 7 and 14 days than RAS and LES without dECM decoration. Taken together, dECM-decorated 3D expanded nanofiber scaffolds hold great potential in tissue regeneration and tissue modeling. STATEMENT OF SIGNIFICANCE: Decellularized ECM scaffolds have attained widespread attention in biomedical applications due to their intricate 3D framework of proteins and growth factors. Mimicking such a complicated architecture is a clinical challenge. In this study, we developed natural ECM-decorated 3D electrospun nanofiber scaffolds with controlled alignments to mimic human tissue. Fibroblasts were cultured on these scaffolds for 8 weeks to deposit natural ECM and decellularized by either freeze-thawing or detergent to obtain decellularized ECM scaffolds. These scaffolds were tested in both in-vitro and in-vivo conditions. They displayed higher cellular attributes with lower immune response making them a good grafting tool in tissue regeneration.
PubMed: 38908416
DOI: 10.1016/j.actbio.2024.06.020 -
Methods in Molecular Biology (Clifton,... 2024With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk cells. However, such bulk measurement obscures...
With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk cells. However, such bulk measurement obscures cell-to-cell heterogeneity, precluding proteome profiling of single cells and small numbers of cells of interest. To address this issue, in the recent 5 years, there has been a surge of small sample preparation methods developed for robust and effective collection and processing of single cells and small numbers of cells for in-depth MS-based proteome profiling. Based on their broad accessibility, they can be categorized into two types: methods based on specific devices and those based on standard PCR tubes or multi-well plates. In this chapter, we describe the detailed protocol of our recently developed, easily adoptable, Surfactant-assisted One-Pot (SOP) sample preparation coupled with MS method termed SOP-MS for label-free single-cell and nanoscale proteomics. SOP-MS capitalizes on the combination of an MS-compatible surfactant, n-dodecyl-β-D-maltoside (DDM), and standard low-bind PCR tube or multi-well plate for "all-in-one" one-pot sample preparation without sample transfer. With its robust and convenient features, SOP-MS can be readily implemented in any MS laboratory for single-cell and nanoscale proteomics. With further improvements in MS detection sensitivity and sample throughput, we believe that SOP-MS could open an avenue for single-cell proteomics with broad applicability in biological and biomedical research.
Topics: Proteomics; Surface-Active Agents; Single-Cell Analysis; Humans; Mass Spectrometry; Proteome; Nanotechnology; Glucosides
PubMed: 38907149
DOI: 10.1007/978-1-0716-3934-4_8 -
Journal of Proteomics Jun 2024Trypanosoma evansi, the causative agent of surra, is the most prevalent pathogenic salivarian trypanosome and affects the majority of domesticated and wild animals in...
Trypanosoma evansi, the causative agent of surra, is the most prevalent pathogenic salivarian trypanosome and affects the majority of domesticated and wild animals in endemic regions. This work aimed to analyze detergent-solubilized T. evansi proteins and identify potential diagnostic biomarkers for surra. Triton X-114-extracted membrane-enriched proteins (MEP) of T. evansi bloodstream forms were analyzed using a gel-free technique (LC-ESI-MS/MS). 247 proteins were identified following the MS analysis of three biological and technical replicates. Two of these proteins were predicted to have a GPI-anchor, 100 (40%) were predicted to have transmembrane domains, and 166 (67%) were predicted to be membrane-bound based on at least one of six features: location (WolfPSORT, DeepLoc-2.0, Protcomp-9.0), transmembrane, GPI, and gene ontology. It was predicted that 76 (30%) of proteins had membrane evidence. Typical membrane proteins for each organelle were identified, among them ISG families (64, 65, and 75 kDa), flagellar calcium-binding protein, 24 kDa calflagin, syntaxins and oligosaccharyltransferase some of which had previously been studied in other trypanosomatids. T. evansi lacks singletons and exclusive orthologous groups, whereas three distinct epitopes have been identified. Data are available via ProteomeXchange with identifier PXD040594. SIGNIFICANCE: Trypanosoma evansi is a highly prevalent parasite that induces a pathological condition known as "surra" in various species of ungulates across five continents. The infection gives rise to symptoms that are not pathognomonic, thereby posing challenges in its diagnosis and leading to substantial economic losses in the livestock industry. A significant challenge arises from the absence of a diagnostic test capable of distinguishing between Trypanosoma equiperdum and T. evansi, both of which are implicated in equine diseases. Therefore, there is a pressing need to conduct research on the biochemistry of the parasite in order to identify proteins that could potentially serve as targets for differential diagnosis or therapeutic interventions.
PubMed: 38906247
DOI: 10.1016/j.jprot.2024.105231 -
Biomaterials Science Jun 2024Nanostructured 7-9-residue cyclic and unstructured lipopeptide-based facial detergents have been engineered to stabilize the model integral membrane protein,...
Nanostructured 7-9-residue cyclic and unstructured lipopeptide-based facial detergents have been engineered to stabilize the model integral membrane protein, bacteriorhodopsin. Formation of a cylindrical-type micelle assembly induced by facial amphipathic lipopeptides resembles a biological membrane more effectively than conventional micelles. The hydrophobic face of this cylindrical-type micelle provides extended stability to the membrane protein and the hydrophilic surface interacts with an aqueous environment. In our present study, we have demonstrated experimentally and computationally that lipopeptide-based facial detergents having an unstructured or β-turn conformation can stabilize membrane proteins. However, constrained peptide detergents can provide enhanced stability to bacteriorhodopsin. In this study, we have computationally examined the structural stability of bacteriorhodopsin in the presence of helical, beta-strand, and cyclic unstructured peptide detergents, and conventional detergent-like peptides. Our study demonstrates that optimal membranomimetics (detergents) for stabilizing a specific membrane protein can be screened based on the following criteria: (i) hydrodynamic radii of the self-assembled peptide detergents, (ii) stability assay of detergent-encased membrane proteins, (iii) percentage covered area of detergent-encased membrane proteins obtained computationally and (iv) protein-detergent interaction energy.
PubMed: 38904161
DOI: 10.1039/d4bm00250d -
International Journal of Environmental... Jun 2024Sodium dodecylbenzene sulfonate (SDBS), a predominant component in detergents, requires an evaluation of its toxicological potential due to its hazardous environmental...
Sodium dodecylbenzene sulfonate (SDBS), a predominant component in detergents, requires an evaluation of its toxicological potential due to its hazardous environmental levels. Therefore, we evaluated the toxicological effects of SDBS on the liver and kidney of male . Therefore, we evaluated the toxicological effects of SDBS on the liver and kidney of male D. rerio. The fish were divided into three groups: 0.0 (control), 0.25, and 0.5 mg/L of SDBS with exposure for up to 96 hours. After exposure, histopathological, histochemical (hepatic glycogen content), and biochemical analyses (SOD and CAT enzyme analysis) were performed on both organs. The results showed significant histopathological effects, such as circulatory disturbances and progressive and regressive alterations, leading to an altered histopathological alteration index. SOD and CAT enzymes exhibited prominent changes. Thus, it became clear that the surfactant SDBS can cause serious hepatic and renal problems in fish, even with short-term exposure, necessitating more stringent control and regulation in the disposal of this surfactant.
PubMed: 38902975
DOI: 10.1080/09603123.2024.2369221 -
Insect Molecular Biology Jun 2024Bombyx mori cecropin A (Bmcecropin A) has antibacterial, antiviral, anti-filamentous fungal and tumour cell inhibition activities and is considered a potential...
Bombyx mori cecropin A (Bmcecropin A) has antibacterial, antiviral, anti-filamentous fungal and tumour cell inhibition activities and is considered a potential succedaneum for antibiotics. We clarified the antibacterial mechanism and structure-activity relationships and then directed the structure-activity optimization of Bmcecropin A. Firstly, we found Bmcecropin A shows a strong binding force and permeability to cell membranes like a detergent; Bmcecropin A could competitively bind to the cell membrane with the cell membrane-specific dye DiI, then damaged the membrane for the access of DiI into the cytoplasm and leading to the leakage of electrolyte and proteins. Secondly, we found Bmcopropin A could also bind to and degrade DNA; furthermore, DNA library polymerase chain reaction (PCR) results indicated that Bmcecropin A inhibited DNA replication by non-specific binding. In addition, we have identified C-terminus amidation and serine-lysine- glycine (SLG) amino acids of Bmcecropin A played critical roles in the membrane damage and DNA degradation. Based on the above results, we designed a mutant of Bmcecropin A (E to H, D to K, K to A), which showed higher antibacterial activity, thermostability and pH stability than ampicillin but no haemolytic activity. Finally, we speculated that Bmcecropin A damaged the cell membrane through a carpet model and drew the schematic diagram of its antibacterial mechanism, based on the antibacterial mechanism and the three-dimensional configuration. These findings yield insights into the mechanism of antimicrobial peptide-pathogen interaction and beneficial for the development of new antibiotics.
PubMed: 38898565
DOI: 10.1111/imb.12934 -
Biotechnology For Biofuels and... Jun 2024Lignocellulosic biomass is currently underutilized, but it offers promise as a resource for the generation of commercial end-products, such as biofuels, detergents, and...
Lignocellulosic biomass is currently underutilized, but it offers promise as a resource for the generation of commercial end-products, such as biofuels, detergents, and other oleochemicals. Rhodococcus opacus PD630 is an oleaginous, Gram-positive bacterium with an exceptional ability to utilize recalcitrant aromatic lignin breakdown products to produce lipid molecules such as triacylglycerols (TAGs), which are an important biofuel precursor. Lipid carbon storage molecules accumulate only under growth-limiting low nitrogen conditions, representing a significant challenge toward using bacterial biorefineries for fuel precursor production. In this work, we screened overexpression of 27 native transcriptional regulators for their abilities to improve lipid accumulation under nitrogen-rich conditions, resulting in three strains that accumulate increased lipids, unconstrained by nitrogen availability when grown in phenol or glucose. Transcriptomic analyses revealed that the best strain (#13) enhanced FA production via activation of the β-ketoadipate pathway. Gene deletion experiments confirm that lipid accumulation in nitrogen-replete conditions requires reprogramming of phenylalanine metabolism. By generating mutants decoupling carbon storage from low nitrogen environments, we move closer toward optimizing R. opacus for efficient bioproduction on lignocellulosic biomass.
PubMed: 38898475
DOI: 10.1186/s13068-024-02523-3