Τρίτη 1 Δεκεμβρίου 2020

Bioaugmentation of Nitrifying Microorganisms to Increase the Efficiency of the Oxidation of Nitrogen Compounds during Wastewater Biofiltration

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Abstract

The efficiency of the bioaugmentation of nitrifying bacteria into biofilm microbiocenosis with 30 days of continuous biofiltration of a solution of municipal model wastewater has been assessed. The laboratory setup consisted of two parallel operating biofilters. Cultures of ammonium-oxidizing and nitrite-oxidizing bacteria of the Nitrobacter genus were sequentially introduced into one of them after the initial period. It was established that the bioaugmentation of ammonium-oxidizing bacteria into the biofilm microbiocenosis led to an increase in the efficiency of the removal of ammonium nitrogen by an average of 1.6 times as compared to the control biofilter. The subsequent bioaugmentation of nitrite-oxidizing bacteria caused an increase in the amount of nitrates in purified water by an average of two times. The bioaugmentation of nitrifying bacteria in the biofilm microbiocenosis intensified the nitrification process. The quantitative and qualita tive identification of microorganisms via fluorescence in situ hybridization showed an increased number of nitrifying microorganisms in the biofilm of the experimental biofilter and a correlation between this characteristic and the biotransformation of nitrogen compounds, which confirms the efficiency of the introduction of microorganisms into the biofilm.

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Laminin 521 Modulates the Сytotoxic Effect of 5-Fluorouracil on HT29 Colorectal Cancer Cells

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The cytotoxic effect of 5-fluorouracil (5FU) and regorafenib (RF), drugs with different mechanisms of action used to treat colorectal cancer, on an HT29 cell line cultured on plastic or laminin 521 (LM-521) has been studied. It is first shown that LM-521 can increase the sensitivity of tumor cells to 5FU. A possible mechanism of the observed effect of LM-521 on the HT29 cell viability is proposed based on transcriptome and proteome analysis. The interaction of β1-containing integrins on the cell surface with LM-521 can activate the FAK/PI3K/Akt signaling pathways and promote phosphorylation of the YAP transcription coactivator and its binding to the complex with the 14-3-3σ protein. The formation of this complex leads to YAP retention in the cytoplasm and prevents its transport to the nucleus and the activation of antiapoptotic gene transcription.

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Expression of the NADPH + -Dependent Formate-Dehydrogenase Gene from Pseudomona s Increases Lysine Production in Corynebacterium glutamicum

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The psefdh_D221Q gene encodes a mutant formate dehydrogenase from Pseudomonas (P-seFDG_D221Q), which catalyzes formate oxidation with the simultaneous formation of NADPH. It is expressed in cells of lysine-producing Corynebacterium glutamicum strains. The psefdh_D221Q gene was introduced into C. glutamicum strains as part of an autonomous plasmid or was integrated into the chromosome with the simultaneous inactivation of the host formate-dehydrogenase genes. It was shown that the C. glutamicum strains with NADP+-dependent formate dehydrogenase have an increased level of L-lysine synthesis in the presence of formate if their own formate dehydrogenase is inactivated.

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In Vitro System for the Detection of Prostate Cancer Markers via Loop-Mediated Isothermal Amplification

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Loop-mediated isothermal amplification (LAMP) of nucleic acids enables the detection of amplification products 10–20 min after the beginning of the reaction. An intraoperative method for the detection of metastases in lymph nodes based on LAMP, one-step nucleic acid amplification (OSNA), allows the rapid detection of the epithelial-specific marker gene KRT19 in lymph nodes. The standard protocol for OSNA was developed more than 10 years ago to detect breast cancer metastases in lymph nodes. Since then, a new version of the key enzyme involved in the reaction (Bst-polymerase) was obtained, but its use in OSNA has remained unexplored. Moreover, the time has come to apply OSNA to the detection of other cancer types, in particular, prostate cancer. The first step is to create an in vitro system that allows LAMP to be carried out on prostate-cancer cell lines. In this work, the LAMP protocol was developed for the new Bst 3.0 polymerase with optim ized dNTP concentrations and without reverse transcriptase, and cell lines were selected (DU-145 for prostate cancer and Molt-4 for negative control). As a result, a new, in vitro system for the LAMP-based detection of prostate cancer with the marker gene KRT19 was developed.

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Inactivation of Yarrowia lipolytica YlACL2 gene Coding Subunit of ATP Citrate Lyase Using CRISPR/Cas9 System

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In this study, YlACL2 was inactivated by two methods: traditional approach based on homologous recombination and uracil marker and markerless system using CRISPR/Cas9. The efficiency of YlACL2 inactivation using traditional approach was 4% (one ΔYlacl2 strain out of 24 tested transformants) whereas knockout efficiency using CRISPR/Cas9 system was 75% (18 ΔYlacl2 strains out of 24 tested transformants). YlACL2 null mutant strains were not able to utilize citrate as a single carbon source. Growth kinetics was investigated in the media with glucose and acetate as a single carbon source. The fact that ΔYlacl2 is able to grow in the minimal medium with glucose as a single carbon source provides evidence that there is an alternative source of acetyl-CoA on carbohydrate substrates in Y. lipolytica.

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Study of the Potential of the Reversal of the Fatty-Acid Beta-Oxidation Pathway for Stereoselective Biosynthesis of ( S )-1,3-Butanediol from Glucose by Recombinant Escherichia coli Strains

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The possible contribution of collateral enzymes to the formation of the key precursor metabolite, 3-hydroxybutyryl-CoA, has been evaluated in a recombinant Escherichia coli strain engineered for 1,3-butanediol biosynthesis from glucose via the inverted fatty-acid beta-oxidation pathway. Inactivation of the 3-hydroxyadipyl-CoA dehydrogenase gene, paaH, did not prevent 1,3-butanol biosynthesis during anaerobic glucose utilization by a strain with an intact, essential gene, fabG. This gene encodes 3-ketoacyl-ACP reductase, which can catalyze the conversion of acetoacetyl-CoA to (R)-3-hydroxybutyryl-CoA. The subsequent inactivation in the strain of the fadB gene, which encodes (S)-stereospecific 3-hydroxyacyl-CoA dehydrogenase of the fatty-acid beta oxidation led to the cessation of 1,3-butanediol synthesis. The respective diol was also not found among the products secreted by the strain possessing the intact fabG and paaH genes upon the individual deletion of the fadB gene. It was established that the collateral enzymes did not participate in the formation of 3-hydroxybutyryl-CoA in the studied strains, and the respective CoA derivative was synthesized solely by the (S)-specific enzyme of the fatty-acid beta-oxidation pathway. The results indicate that reversal of the fatty-acid beta oxidation pathway can ensure the enantioselective biosynthesis of the (S)-stereoisomer of 1,3-butanediol in engineered E. coli strains.

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Construction of Recombinant Producers of Enzyme Preparations for Feed Production with an Expression System Based on Penicillium verruculosum Fungus

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Producer strains have been created with an expression system based on the recipient strain Penicillium verruculosum 537 (ΔniaD) and the cellobiohydrolase-1 gene promoter. These strains made it possible to obtain new enzyme preparations (EPs) for feed production that were characterized by a high content of endodepolymerases (endo-β-1,4-glucanases and endo-β-1,4-xylanase), which degrade nonstarch polysaccharides (NSPs) of grain cereals used as a feed component. The proportion of endodepolymerases in the new EPs was 44–68% of the total protein content (as compared to 15% in the recipient-based preparation), whereas the percentage of exodepolymerases (cellobiohydrolases) fell to 8–26% as compared to 60% in the recipient strain-based product. The new EPs have a high specific activity of endodepolymerases, which was 1.8–4.6 times greater than that in the EP obtained from the recipient strain, and the specific activity of exodepolymer ases decreased by 2.0–3.7 times. The new EPs demonstrated endoglucanase and xylanase activities in a wide range of pH and temperature, including the physiological values of these parameters (pH 3.0 and 7.0, and t 37–38°C). They were characterized by high endodepolymerase stability under the action of digestive proteases (pepsin and trypsin). The EPs also retained their endoglucanase and xylanase activities during feed granulation (80°C). The xylanase contained in the new EPs was not affected by proteinaceous inhibitors from cereals. Experimental batches of EPs were made by the Agroferment enzyme-producing plant and were tested in broiler and piglet feeding. The addition of the new commercial EPs to the animals' diets increased their live weight, reduced feed and protein intake, and decreased the metabolic energy per unit of body weight, improving digestibility and assimilability of feed nutrients, especially raw fiber and NSP.

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Effects of Fibroblast Growth Factor-2 and Other Microsupplements on the Productivity of IgG- and IgA-Producing Cell Lines

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Several serum-free media have been developed and are successfully used at present for the cultivation of various recombinant eukaryotic cell lines. Therapeutic recombinant IgA antibodies have recently been increasingly used along with numerous IgG1 isotype antibodies. Therefore, it became necessary to improve the growth characteristics, metabolism, and productivity of cell cultures producing these antibodies. The stimulating effect of a complex supplement containing Zn salts and FGF-2 on cell cultivation on basal media, DMEM and IMDM, was revealed in this work. The addition of dextran sulfate sodium salt and iron citrate to the basal medium was accompanied by improved productivity of stable IgG- and IgA-producing cell lines, as well as the homogeneity and density of cell cultures, which is most important in IgA-antibody production.

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Transcriptome Analysis of Signaling Pathways in Caco-2 Cells Involved in the Formation of Intestinal Villi

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Caco-2 cells are traditionally used to construct in vitro models of the intestinal barrier. One characteristic of the mature intestine is the presence of villi—connective tissue outgrowths covered with epithelial cells. It was recently shown that Caco-2 cells form structures resembling intestinal villi during prolonged cultivation. In this work, we showed via transcriptome analysis that the BMP and PDGF signaling cascades involved in the formation of villi in vivo are significantly altered during the differentiation of Caco-2 cells and, therefore, can participate in the formation of similar structures in vitro. In particular, we found a significant decrease in the expression of the BMP4, BMP7, and BMP8A genes in differentiated cells as compared to undifferentiated cells. We also first discovered periodic fluctuations in transepithelial resistance upon the differentiation of Caco-2 cells. The period of observed fluctuations indicates that they can occur as a result of cell proliferation during villus formation.

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Properties and Biotechnological Application of Mutant Derivatives of the Mini-Intein PRP8 from Penicillium chrysogenu m with Improved Control of C-Terminal Processing

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Mutant variants of mini-intein PRP8 from Penicillium chrysogenum (Int4b) with improved control of C-terminal processing are characterized. The studied variants can serve as the basis for the self-removal of polypeptide tags that can carry an affine label and optimize the process of the obtainment of target proteins and peptides in E. coli cells. They make it possible to synthesize target molecules composed of soluble and insoluble hybrid proteins (fusions), to conduct their affine purification and autocatalytic processing, and to obtain mature target products. The presented variants have a number of features as compared to the known prototypes. In particular, the mutant mini-intein Int4bPRO, which contains the L93P mutation, has temperature-dependent properties. It is able to produce target molecules composed of soluble fusions at a cultivation temperature below 30°C; however, it directs most synthesized fusions into insoluble intracellular aggregates after an increase in temperature to 37°C. The transition of Int4bPRO to an insoluble form is accompanied by the complete inactivation of C-terminal processing. Further application of the standard protein denaturation–renaturation procedures enables efficient reactivation of Int4bPRO and the processing of its fusions in vitro. Two other variants, Int4b56 and Int4b36, which contain the point mutation T62N or a combination of D144N and L146T mutations, respectively, have a reduced rate of C-terminal processing. Their use in E. coli cells allows optimization of the biosynthesis of biologically active target proteins and peptides composed of soluble fusions that are suitable for affine purification and subsequent intein-dependent processing without the use of protein denaturation–renaturation procedures.

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Clusterin ameliorates tau pathology in vivo by inhibiting fibril formation

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The molecular chaperone Clusterin (CLU) impacts the amyloid pathway in Alzheimer's disease (AD) but its role in tau pathology is unknown. We observed CLU co-localization with tau aggregates in AD and primary tauopathies and CLU levels were upregulated in response to tau accumulation. To further elucidate the effect of CLU on tau pathology, we utilized a gene delivery approach in CLU knock-out (CLU KO) mice to drive expression of tau bearing the P301L mutation. We found that loss of CLU was associated with exacerbated tau pathology and anxiety-like behaviors in our mouse model of tauopathy. Additionally, we found that CLU dramatically inhibited tau fibrilization using an in vitro assay. Together, these results demonstrate that CLU plays a major role in both amyloid and tau pathologies in AD.

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Cerebral organoids: emerging ex vivo humanoid models of glioblastoma

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Glioblastoma is an aggressive form of brain cancer that has seen only marginal improvements in its bleak survival outlook of 12–15 months over the last forty years. There is therefore an urgent need for the development of advanced drug screening platforms and systems that can better recapitulate glioblastoma's infiltrative biology, a process largely responsible for its relentless propensity for recurrence and progression. Recent advances in stem cell biology have allowed the generation of artificial tridimensional brain-like tissue termed cerebral organoids. In addition to their potential to model brain development, these reagents are providing much needed synthetic humanoid scaffolds to model glioblastoma's infiltrative capacity in a faithful and scalable manner. Here, we highlight and review the early breakthroughs in this growing field and discuss its potential future role for glioblastoma research.

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