Applied Biochemistry and Microbiology最新文献

{"title":"Research Progress in the Biodegradation of Lignin (Review)","authors":"J. Li,&nbsp;X. Wu,&nbsp;J. Ru,&nbsp;X. Li,&nbsp;X. Wang,&nbsp;Z. Su,&nbsp;M. Xu","doi":"10.1134/S0003683825601623","DOIUrl":"10.1134/S0003683825601623","url":null,"abstract":"<p>China is rich in lignocellulosic resources from agricultural waste. However, for a long time, the utilization rate of lignocellulosic resources has been relatively low, which has led to problems such as resource waste and environmental pollution. Lignocellulose is usually composed of cellulose, hemicellulose and lignin. Among them, some enzymatic hydrolysis products of lignin have an inhibitory effect on enzymes and microorganisms. In addition, its structure hinders the contact between cellulase or hemicellulase and their substrates, thus, affecting the degradation of cellulose and hemicellulose. Although the biodegradation of lignin has the advantages of environmental friendliness and low energy consumption, it still faces problems such as the lack of efficient degrading bacteria and degrading enzymes, and the poor stability of most natural degrading enzymes. This manuscript introduces the diverse structures of lignin and various methods for analyzing lignin structure, reviews the recent research progress and the advantages of biological methods for lignin degradation, enumerates the main microbial groups with lignin-degrading ability and the main characteristics of various lignin-degrading enzymes. Moreover, it summarizes the current challenges and future development prospects of lignin biodegradation, hoping to provide certain scientific references for in-depth research in this field.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"62 1","pages":"17 - 28"},"PeriodicalIF":1.1,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147341257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation, Characterization, Partial Purification and Plasmid Curing Analysis of Bacteriocin of Pediococcus acidilactici KX688798 Isolated from Fermented Vigna radiate","authors":"M. Shukla,&nbsp;M. Patadiya,&nbsp;S. Gupte","doi":"10.1134/S0003683824606061","DOIUrl":"10.1134/S0003683824606061","url":null,"abstract":"<p>In recent years, consumers have grown increasingly concerned about the health risks associated with chemical preservation in food. At the same time, the food industry faces demand for effective ways to extend shelf life and reduce spoilage, driving interest in natural preservatives and alternative preservation techniques. The present investigations were taken up to isolate bacteriocin producers from various sources. Among 28 isolates, SM1 culture, which was isolated from fermented <i>Vigna radiata</i>, was found effective against a wide range of both Gram-positive and Gram-negative pathogens. Additionally, SM1 was characterized as a Gram-positive, non-motile, catalase-negative coccus. The 16S rRNA gene sequence analysis identified the isolate SM1 as <i>Pediococcus acidilactici</i>. Among the tested media, SM1 exhibited the highest production of cell-free neutral supernatant (CFNS) in Tryptone Glucose Yeast extract (TGY) medium. The CFNS exhibited antimicrobial activity starting in the early logarithmic phase, which continued until the conclusion of the exponential growth phase. The CFNS titer was measured at 106 ± 0.02 AU/mL. It demonstrated stability a wide temperature range (4–121°C) and maintained its activity within a pH range from 4.0 to 8.0. Furthermore, upon 5 min exposure towards UV light, the residual activity observed was 85.71 ± 0.01%. The highest residual activity was observed when treated with n-butyl alcohol and 1% Triton X-100. Ammonium sulphate precipitation was achieved at 65%. Further, desalting of precipitated sample was carried out using a dialysis membrane with 2–5 kDa cut-off. The plasmid profile of bacteriocin-producing organisms was analyzed for the study of plasmid-oriented bacteriocin properties. The curing rate of 2.3% was observed during the analysis.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"62 1","pages":"123 - 136"},"PeriodicalIF":1.1,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147341294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of a Thermostable Endoglucanase Involved in Cellulose Degradation from a Newly Isolated Bacillus subtilis SCUEC7 Strain","authors":"T. Feng,&nbsp;M. Yu,&nbsp;Z. Wu,&nbsp;Z. Feng,&nbsp;J. Zhang,&nbsp;M. Wang,&nbsp;Z. Yu,&nbsp;Y. Yang,&nbsp;Y. Xu,&nbsp;X. Zhang,&nbsp;X. Rao,&nbsp;X. Li","doi":"10.1134/S0003683825600320","DOIUrl":"10.1134/S0003683825600320","url":null,"abstract":"<p>With the aim of screening highly efficient cellulose-degrading microorganisms and enhancing the efficiency of cellulose degradation, a strain with a high ability to degrade cellulose was isolated from bovine rumen fluid, which was classified and named as <i>Bacillus subtilis</i> SCUEC7 strain on the basis of the morphological observation, physiological and biochemical characteristics and 16S rDNA sequence analysis. However, the mechanism for cellulose degradation in this strain remains unclear, therefore, the function and biological properties of the <i>ba7gA</i> gene in the strain SCUEC7 were analyzed. The <i>ba7gA</i> gene was cloned by PCR with total DNA of <i>B. subtilis</i> SCUEC7 as template and used to construct the recombinant plasmid pET28a(+)-<i>ba7gA,</i> and expressed in <i>Escherichia coli</i> BL21(DE3). The overexpression of the Ba7gA protein was detected by SDS-PAGE analysis, and the effects of temperature, pH, and metal ions on the biological activities of the Ba7gA protein were studied. The endoglucanase gene <i>ba7gA</i>, which is composed of 1482 bp and encodes 493 amino acids, was cloned and sequenced from this strain. The Ba7gA protein contains two primary functional domains: the GH5 family catalytic domain and the CBM3 family cellulose-binding domain, and exhibited a molecular weight of approximately 54.5 kDa by SDS-PAGE, in agreement with a molecular weight of 54.53 kDa based on the amino acid sequence. The optimal reaction conditions for the biological activities of Ba7gA protein with CMC-Na as the substrate were determined to be 60°C and pH 6.0. Meanwhile, Fe²⁺, Mg²⁺, Mn²⁺, Ca²⁺, and Ni²⁺ enhanced its biological activity, whereas Cu²⁺, Na⁺, K⁺, Zn²⁺, Fe³⁺, and Li⁺ exhibited inhibitory effects. The suitable storage conditions for the Ba7gA protein were 0°C and pH 6.0. Using CMC-Na as the substrate, the <i>K</i>_M and <i>V</i>_max of the Ba7gA protein were 2.35 mM and 54.56 U/mg, respectively. These properties highlight the potential application of the Ba7gA protein from <i>B. subtilis</i> SCUEC7 strain as an endocellulase in the pretreatment of biomass.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"62 1","pages":"39 - 49"},"PeriodicalIF":1.1,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147341252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Response Mechanism of Lactobacillus plantarum under Simulated Digestion Based on Proteomics and Metabolomics Analysis","authors":"L. Zhao,&nbsp;Z. Cheng,&nbsp;Y. Ling,&nbsp;Y. Wu,&nbsp;M. Zhang,&nbsp;H. Yang,&nbsp;Z. Li","doi":"10.1134/S0003683825600034","DOIUrl":"10.1134/S0003683825600034","url":null,"abstract":"<p>Proteomics and a metabolomics strategy were used to investigate the probiotic properties of <i>Lactobacillus plantarum</i> BW2013 under simulated in vitro digestion. Thirty seven significant differential proteins including 6-phosphogluconate dehydrogenase, pyruvate kinase, F0F1 ATP synthase, ABC-type transporters, ribosomal and universal stress proteins and 40 significant differential metabolites, such as indole-3-lactic acid, Pro, trans-cinnamic acid, betaine, citric acid, D-fructose, and γ-aminobutyric acid were identified and characterized. The association analysis indicated that most upregulated proteins and metabolites are involved primarily in stress response, regulation of intestinal flora and accumulation of beneficial substances relating to carbohydrate and energy metabolic pathways, amino acid metabolism pathways, nucleotide metabolism pathways, overall/universal stress response. The results provide new insights into the response mechanism of <i>L. plantarum</i> BW2013 under the simulated digestion conditions, facilitating the exploitation of its potential application in probiotic products.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"62 1","pages":"50 - 59"},"PeriodicalIF":1.1,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147341256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differences in 2,6-Dimethoxy-1,4-benzoquinone Reduction Systems between Brown-rot and White-rot Fungi","authors":"R. Mori,&nbsp;Y. Yoshida,&nbsp;H. Suzuki,&nbsp;M. Kato,&nbsp;M. Shimizu","doi":"10.1134/S0003683825600939","DOIUrl":"10.1134/S0003683825600939","url":null,"abstract":"<p>Brown-rot fungi decompose polysaccharides such as cellulose and hemicellulose through mechanisms that do not involve extracellular polysaccharide-degrading enzymes. Instead, oxidative degradation occurs via the Fenton reaction, which requires hydroquinone as an extracellular electron donor. However, the mechanisms by which brown-rot fungi generate and transport hydroquinones remains unclear. This study aimed to investigate the quinone reduction systems in the brown-rot fungus <i>Tyromyces palustris</i> and compare it with that in the white-rot fungus <i>Pleurotus ostreatus</i>. Using fungal protoplasts, we found that <i>T. palustris</i> rapidly reduced 2,6-dimethoxy-1,4-benzoquinone (2,6-DMBQ) to 1,4-dihydroxy-2,6-dimethoxybenzene (2,6-DMHQ), and 2,6-DMHQ, which accumulated exclusively in the extracellular fraction. In contrast, <i>P. ostreatus</i> exhibited lower reduction activity, with 2,6-DMBQ and 2,6-DMHQ retained within the intracellular compartments. The addition of the uncoupling reagent carbonyl cyanide <i>m</i>-chlorophenylhydrazone (CCCP), which disrupts the pH gradient across the plasma membrane, had little effect on extracellular 2,6-DMHQ formation in <i>T. palustris</i> but significantly inhibited 2,6-DMBQ reduction in <i>P. ostreatus</i>. These findings suggest that brown-rot fungi employ a plasma membrane-bound enzyme with an outward-facing quinone-reducing site, enabling the extracellular supply of hydroquinone to facilitate the Fenton reaction. Understanding this mechanism enhances our knowledge of fungal biodegradation and may have applications in biotechnological processes involving lignocellulose degradation.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"62 1","pages":"137 - 143"},"PeriodicalIF":1.1,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147341376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cooperative Roles of Trehalose and Heat Shock Proteins in the Response of Saccharomyces cerevisiae to Ethanol Stress","authors":"F. Cui,&nbsp;Z. Chen,&nbsp;Y. Ji,&nbsp;H. Li","doi":"10.1134/S0003683825602082","DOIUrl":"10.1134/S0003683825602082","url":null,"abstract":"<p>During the fermentation process, the growth and metabolism of <i>Saccharomyces cerevisiae</i> cells are often inhibited by the accumulated ethanol. The accumulation of trehalose, heat shock proteins (HSPs) and other protectants can respectively improve the ethanol tolerance of <i>S. cerevisiae</i>. In this study, the transcriptional level changes of genes involved in metabolisms of trehalose and HSPs in <i>S. cerevisiae</i> cells cultured at various concentrations of ethanol (i.e., 0, 5, 10, and 15% vol/vol) were determined by quantitative real-time polymerase chain reaction. The <i>S. cerevisiae</i> cells in ethanol-treated groups had higher expressions of genes which are responsible for encoding enzymes that are involved in the synthesis of trehalose (i.e., <i>TPS1</i>, <i>TPS2</i>, <i>TPS3</i>, and <i>TSL1</i>) and the HSPs synthetic genes than cells in control group. Moreover, a positive correlation was observed between the genes involved in the synthesis of trehalose and HSPs. On the contrary, except for <i>NTH1</i>, the expressions of genes involved in the degradation of trehalose decreased under ethanol stress. Given the similar expression patterns of genes involved in synthesis of trehalose and HSPs induced by ethanol and respective protective effects on cells against ethanol stress, trehalose might cooperate with HSPs to confer ethanol tolerance to <i>S. cerevisiae</i>.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"62 1","pages":"116 - 122"},"PeriodicalIF":1.1,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147341292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of Plasmid pLD3 of Enterococcus hirae LD3 Isolated from a Popular Indian Fermented Food, Dosa","authors":"I. Kumari,&nbsp;S. K. Tiwari","doi":"10.1134/S0003683825603555","DOIUrl":"10.1134/S0003683825603555","url":null,"abstract":"<p><i>Enterococcus hirae</i> LD3 was previously characterized for the production of bacteriocin with potential probiotic property. In this study, we have analysed the plasmid profile of <i>E. hirae</i> LD3 and its characterization using curing methods and gene sequencing. This bacterium was found to be resistant to gentamycin, kanamycin and streptomycin whereas sensitive to ampicillin, chloramphenicol, erythromycin and tetracycline. <i>E. hirae</i> LD3 showed the presence of a single plasmid, pLD3 with 33.3% GC content with molecular weight 28.69 kb. The plasmid sequence revealed the presence of stress response gene, <i>rli28</i>; multidrug efflux pump gene, <i>emeA</i> and kanamycin and gentamicin resistant gene, <i>aph(2')-IIIa.</i> The plasmid was cured using acriflavine, ethidium bromide and SDS. The plasmid-cured strain LD3 became sensitive to kanamycin and exhibited drastic reduction in the bacteriocin activity, 20–40 AU/mL compared to 160 AU/mL in wild-type strain LD3. Thus, <i>E. hirae</i> LD3 contains a plasmid with low GC content which is linked with antibiotic resistance.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"62 1","pages":"70 - 77"},"PeriodicalIF":1.1,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147341254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Research on the Development and Application of Antimicrobial Food Coatings to Maintain Quality and Increase the Shelf Life of Poultry Meat","authors":"L. G. Stoyanova,&nbsp;M. A. Dibirasulaev,&nbsp;D. M. Dibirasulaev,&nbsp;L. B. Umiralieva,&nbsp;M. Kh. Iskakov,&nbsp;I. D. Filatov","doi":"10.1134/S0003683825700164","DOIUrl":"10.1134/S0003683825700164","url":null,"abstract":"<p>Preserving the quality, improving safety, and extending the shelf life of food products are priority directions of healthy nutrition development. To prolong the shelf life of products, the technology of refrigerated processing and maintenance at reduced temperature is used, which allows us to increase the shelf life of products and reduce their weight loss. However, chilled meat has a limited shelf life. One of the effective ways to preserve quality and reduce weight loss during chilled storage is the treatment of the product surface with protective food film–forming compositions (FFC) based on surface-active and antimicrobial substances. Studies were conducted to evaluate the effectiveness of lactic acid of different concentrations (0.5–2.0%) and bacteriocin nisin (0.025%) in the composition of FFC-10 on the reduction of total contamination and pathogen contamination of broiler chicken half-carcasses during chilled storage. The values of active acidity and redox potential in solutions of different composition of FFC-10 on the growth and development of potential contaminants of food raw materials were determined. By means of microscopy changes in the integrity of the structure of FFC-10 during storage were studied. The obtained data will allow us to optimize the use of protective film–forming compositions for creation of biotechnology of poultry processing in order to preserve the quality and increase the shelf life of poultry meat during chilled storage.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"61 7","pages":"1389 - 1398"},"PeriodicalIF":1.1,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145698432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A State-of-the-Art Digital PCR Platform","authors":"Yu. L. Lebedeva,&nbsp;E. A. Cherkashin,&nbsp;V. G. Akimkin","doi":"10.1134/S0003683825700188","DOIUrl":"10.1134/S0003683825700188","url":null,"abstract":"<p>The traditional quantitative real-time polymerase chain reaction is the gold standard among molecular diagnostic methods and is used both for the identification of pathogens of various diseases, and for genotyping and standardization of the NGS library. The digital polymerase chain reaction technology is an upgraded version of the polymerase chain reaction, and over the past five years has proven to be more sensitive, specific, and accurate. This article provides an overview of the modern digital polymerase chain reaction platform and their comparative analysis. Special features, uses, and possible applications are selected.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"61 7","pages":"1423 - 1442"},"PeriodicalIF":1.1,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145698614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Placenta-on-a-Chip Microfluidic Model: Optimization of Perfusion Conditions","authors":"S. Yu. Paul,&nbsp;Yu. A. Safronova,&nbsp;O. E. Chebotareva,&nbsp;I. A. Khaustov,&nbsp;A. E. Karimova,&nbsp;D. V. Kolesov,&nbsp;P. A. Vishnyakova,&nbsp;J. A. Makarova,&nbsp;E. N. Knyazev","doi":"10.1134/S0003683825700140","DOIUrl":"10.1134/S0003683825700140","url":null,"abstract":"<p>The design and development of a placenta-on-a-chip model is of great importance for various fields of cell biology, especially in studies of the molecular mechanisms of disease pathogenesis and the action of potential drugs. Currently, milling technique is most commonly used to fabricate microfluidic devices from thermoplastics. However, this technology leads to the formation of undesirable surface roughness, which promotes the formation of air bubbles and reduces the optical transparency of the polymer. In this regard, the problem of improving the technology of chip manufacturing and operation seems to be very important. We have analyzed various methods of surface modification of polycarbonate and further optimizing the circuit. It was shown that vapor polishing treatment with JINHF solution (JINHF, China) effectively removed roughness from the surface of the polycarbonate chip. The selected surface treatment method significantly reduced the roughness of the internal channels, which facilitated the filling of the chip without forming areas with stubborn air bubbles. During the optimization process, two “passive” methods for eliminating bubbles from the microfluidic system were explored, namely vertical positioning of the chip and creating air bubble traps inside the chip. These methods were compared with the “active” bubble removal by connecting an Elveflow trap (Elveflow Elvesys, France) with a vacuum pump to the chip. The method of vertical positioning of the organ-on-a-chip during cultivation proved to be more effective in removing air bubbles than built-in and external traps. The developed variant of the microfluidic device with the contour configuration that showed the best result was tested on the process of long-term cultivation of BeWo b30 and EA.hy926 cells as models of placenta-on-chip in dynamics.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"61 7","pages":"1369 - 1378"},"PeriodicalIF":1.1,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145698795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}