Bioengineered最新文献

{"title":"Advancements in genetic engineering for enhanced Polyhydroxyalkanoates (PHA) production: a comprehensive review of metabolic pathway manipulation and gene deletion strategies.","authors":"Raghavendra Paduvari, Divyashree Mysore Somashekara","doi":"10.1080/21655979.2025.2458363","DOIUrl":"10.1080/21655979.2025.2458363","url":null,"abstract":"<p><p>Polyhydroxyalkanoates (PHA) are bioplastics produced by few bacteria as intracellular lipid inclusions under excess carbon source and nutrient-deprived conditions. These polymers are biodegradable and resemble petroleum-based plastics. The rising environmental concerns have increased the demand for PHA, but the low yield in wild-type bacterial strains limits large-scale production. An improvement in the PHA production can be achieved by genetically engineering the wild-type bacterial strains by removing competitive pathways that divert the metabolites away from PHA biosynthesis, cloning strong promotors to overexpress the genes involved in PHA biosynthesis and constructing non-native metabolic pathways that feed the metabolites for PHA production. The desired monomers in the PHA polymers were obtained by elimination of genes involved in PHA biosynthetic pathway. The chain length degradation specific-gene deletion of β-oxidation pathway resulted in the accumulation of PHA monomers having high carbon chain length. A controlled accumulation of monomers in the PHA polymer was achieved by constructing novel pathways in the bacteria and deleting native genes of competitive pathways from the genome of non-PHA producers. The present review attempts to showcase the novel genetic modification approaches conducted so far to enhance the PHA production with a special focus on metabolic pathway gene deletion in various bacteria.</p>","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":"16 1","pages":"2458363"},"PeriodicalIF":4.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fractionation of waste-derived volatile fatty acids by multi-stage adsorption using activated charcoal and Diaion HP-20 resin.","authors":"Negar Basereh, Steven Wainaina, Amir Mahboubi, Mohammad J Taherzadeh","doi":"10.1080/21655979.2025.2458366","DOIUrl":"10.1080/21655979.2025.2458366","url":null,"abstract":"<p><p>Substituting waste-derived Volatile Fatty Acids (VFAs) with their conventionally applied fossil-derived counterparts in a spectrum of industrial applications necessitates its proper fractionation into individual acids. This study explored a multi-stage batch adsorption approach for fractionating acidogenic fermentation VFAs effluents from food waste (FW) and chicken manure (CKM) using Diaion HP-20 and activated charcoal. Initial screening at different washing conditions and pH (3.5 and 6.5) revealed the unwashed granular-activated charcoal (GAC-Unwashed) and milli-Q water-washed Diaion (DI-MQ Washed) as the most promising candidates for VFA fractionation of a synthetic VFA mixture at 4 gL^-1. At pH 3.5 (<math><mo><</mo><mi>p</mi><mrow><msub><mi>K</mi><mi>a</mi></msub></mrow></math>), GAC-Unwashed adsorbed 2-6 carbon atom VFAs completely, while DI-MQ Washed exhibited minimal adsorption of acetic acid (AA) (8%), favoring caproic (CA) and valeric acids (VA) (<math><mo>></mo></math>97%). While at pH 6.5 <math><mo>(</mo><mo>></mo><mi>p</mi><mrow><msub><mi>K</mi><mi>a</mi></msub></mrow></math>), GAC-Unwashed selectively targeted VA (79%) and CA (100%). Fractionating VFAs from FW and CKM were conducted in a two-stage adsorption process with optimal results being achieved using GAC-Unwashed at FW initial pH (5.3) and DI-MQ Washed at pH below CKM <math><mi>p</mi><mrow><msub><mi>K</mi><mi>a</mi></msub></mrow></math> (3.5), respectively. The first adsorption stage primarily adsorbed higher molecular weight (MW) VFAs (FW:99.1% CA, CKM:72.9% butyric acid (BA)) with a minor quantity of lower ones (FW:56.5% BA, CKM:29.3% propionic acid (PA)), leaving AA intact. Subsequent stages aimed to isolate AA by adsorbing the remaining low MW VFA (FW:58.9% BA, CKM:27.8% PA, 70% BA) other than AA, indicating effluent fractionation while preserving and purifying AA. Applied selective multi-stage adsorption approach offers a promising method to broaden waste-derived VFA applications.</p>","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":"16 1","pages":"2458366"},"PeriodicalIF":4.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11801348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Photoregulation of the biosynthetic activity of fungus <i>Inonotus obliquus</i> using colloidal solutions of biogenic metal nanoparticles and low-intensity laser radiation.","authors":"Oksana Mykchaylova, Anatoliy Negriyko, Nadiia Matvieieva, Kostiantyn Lopatko, Natalia Poyedinok","doi":"10.1080/21655979.2025.2458371","DOIUrl":"10.1080/21655979.2025.2458371","url":null,"abstract":"<p><p>This article presents new data on the integrated use of colloidal solutions of nanoparticles and low-intensity laser radiation on the biosynthetic activity of the medicinal mushroom <i>Inonotus obliquus in vitro</i>. Traditional mycological methods, colloidal solutions of biogenic metals, and unique photobiological methods have also been used. It was found that colloidal solutions of nanoparticles of all metals used increased the growth characteristics of <i>I. obliquus</i> (55-60%), while irradiation of the fungal inoculum with laser light in a medium with nanoparticles reduced the growth activity of <i>I. obliquus</i> mycelia by 12.3-35.4%. Silver nanoparticles (AgNPs) in a nutrient medium suppressed the biosynthesis of extracellular polysaccharides, whereas laser irradiation in the same medium increased the synthesis of intracellular polysaccharides by 9.7 times. Magnesium nanoparticles (MgNPs) and iron nanoparticles (FeNPs) inhibited the synthesis of intracellular polysaccharides in the mycelial mass of <i>I. obliquus</i>. At the same time, laser irradiation of the inoculum with MgNPs, on the contrary, induced a sharp increase in the amount of polysaccharides in the culture liquid (20 times). Treatment of the inoculum in a medium with nanoparticles with a laser caused an intensification of the synthesis of flavonoids in the mycelial mass and an increase in the synthesis of melanin pigments (25-140%). The results obtained suggest the possibility of the complex use of colloidal solutions of Fe, Ag, and Mg nanoparticles and low-intensity laser radiation as environmentally friendly factors for regulating biosynthetic activity in the biotechnology of cultivating the valuable medicinal mushroom <i>I. obliquus</i>.</p>","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":"16 1","pages":"2458371"},"PeriodicalIF":4.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11776471/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbial dysbiosis associated to diarrheic irritable bowel syndrome can be efficiently simulated in the Mucosal ARtificial COLon (M-ARCOL).","authors":"Ophélie Uriot, Charlotte Deschamps, Julien Scanzi, Morgane Brun, Nicolas Kerckhove, Christian Dualé, Elora Fournier, Claude Durif, Sylvain Denis, Michel Dapoigny, Philippe Langella, Monique Alric, Lucie Etienne-Mesmin, Blanquet-Diot Stéphanie","doi":"10.1080/21655979.2025.2458362","DOIUrl":"10.1080/21655979.2025.2458362","url":null,"abstract":"<p><p>Irritable bowel syndrome (IBS) is a common chronic gastrointestinal disorder, with diarrhea-predominant IBS (IBS-D) as the most frequent subtype. The implication of gut microbiota in the disease's etiology is not fully understood. <i>In vitro</i> gut systems can offer a great alternative to <i>in vivo</i> assays in preclinical studies, but no model reproducing IBS-related dysbiotic microbiota has been developed. Thanks to a large literature review, a new Mucosal ARtifical COLon (M-ARCOL) adapted to IBS-D physicochemical and nutritional conditions was set-up. To validate the model and further exploit its potential in a mechanistic study, <i>in vitro</i> fermentations were performed using bioreactors inoculated with stools from healthy individuals (<i>n</i> = 4) or IBS-D patients (<i>n</i> = 4), when the M-ARCOL was set-up under healthy or IBS-D conditions. Setting IBS-D parameters in M-ARCOL inoculated with IBS-D stools maintained the key microbial features associated to the disease <i>in vivo</i>, validating the new system. In particular, compared to the healthy control, the IBS-D model was characterized by a decreased bacterial diversity, together with a lower abundance of <i>Rikenellaceae</i> and <i>Prevotellaceae</i>, but a higher level of <i>Proteobacteria</i> and <i>Akkermansiaceae</i>. Of interest, applying IBS-D parameters to healthy stools was not sufficient to trigger IBS-D dysbiosis and applying healthy parameters to IBS-D stools was not enough to restore microbial balance. This validated IBS-D colonic model can be used as a robust <i>in vitro</i> platform for studies focusing on gut microbes in the absence of the host, as well as for testing food and microbiota-related interventions aimed at personalized restoration of gut microbiota eubiosis.</p>","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":"16 1","pages":"2458362"},"PeriodicalIF":4.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel mannan-specific chimeric antigen receptor M-CAR redirects T cells to interact with <i>Candida</i> spp. hyphae and <i>Rhizopus oryzae</i> spores.","authors":"Júlia Garcia Guimarães, Gabriela Yamazaki de Campos, Michele Procópio Machado, Patrícia Kellen Martins Oliveira Brito, Thaila Fernanda Dos Reis, Gustavo Henrique Goldman, Patricia Vianna Bonini Palma, Thais Fernanda de Campos Fraga-Silva, Daniela Cardoso Umbelino Cavallin, James Venturini, Thiago Aparecido da Silva","doi":"10.1080/21655979.2025.2458786","DOIUrl":"10.1080/21655979.2025.2458786","url":null,"abstract":"<p><p>Invasive fungal infections (IFIs) are responsible for elevated rates of morbidity and mortality, causing around of 1.5 million deaths annually worldwide. One of the main causative agents of IFIs is <i>Candida albicans</i>, and non-albicans <i>Candida</i> species have emerged as a spreading global public health concernment. Furthermore, COVID-19 has contributed to a boost in the incidence of IFIs, such as mucormycosis, in which <i>Rhizopus oryzae</i> is the most prevalent causative agent. The effector host immune response against IFIs depends on the activity of T cells, which are susceptible to the regulatory effects triggered by fungal virulence factors. The fungal cell wall plays a crucial role as a virulence factor, and its remodeling compromises the development of a specific T-cell response. The redirection of Jurkat T cells to target <i>Candida</i> spp. by recognizing targets expressed on the fungal cell wall can be facilitated using chimeric antigen receptor (CAR) technology. This study generated an M-CAR that contains an scFv with specificity to α-1,6 mannose backbone of fungal mannan, and the expression of M-CAR on the surface of modified Jurkat cells triggered a strong activation against <i>Candida albicans</i> (hyphae form), <i>Candida tropicalis</i> (hyphae form), <i>Candida parapsilosis</i> (pseudohyphal form), and <i>Candida glabrata</i> (yeast form). Moreover, M-CAR Jurkat cells recognized <i>Rhizopus oryzae</i> spores, which induced high expression of cell activation markers. Thus, a novel Mannan-specific CAR enabled strong signal transduction in modified Jurkat cells in the presence of <i>Candida</i> spp. or <i>R. oryzae</i>.</p>","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":"16 1","pages":"2458786"},"PeriodicalIF":4.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792852/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143073625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing the effect of temperature drop on a stable anaerobic fermentation for volatile fatty acids production.","authors":"Manuel Joao Afecto Gonçalves, Cristina González-Fernández, Silvia Greses","doi":"10.1080/21655979.2025.2458369","DOIUrl":"10.1080/21655979.2025.2458369","url":null,"abstract":"<p><p>Anaerobic fermentation (AF) processes are sensitive to temperature fluctuations, which can influence the microbial activity and overall metabolic performances. Anaerobic reactors can face unforeseen temperature control failures, leading to instabilities in the process. The present study investigated the effect of two short-term temperature perturbations (down to 20°C and 15°C) on AF of food wastes (FWs). While 20°C did not exhibit a negative impact on AF performance maintaining the bioconversion yields over 40%, the reactor subjected to 15°C presented an acidogenic limitation, which decreased the bioconversion yields (36.4 ± 1.8%). As a result, 2.2 ± 0.5 g/L of succinic acid was accumulated in the reactor, being identified as a temperature failure indicator. Once the conditions were reestablished (operation temperature of 25ºC), the metabolic redundancies identified in the reactors allowed the AFs recovery to initial fermentation yields. 20°C was further tested as operational temperature resulting in stable bioconversion yield similar to the Control Reactor (43.2 ± 0.3%). These results showed the feasibility of conducting AF under low temperatures, indicating the potential of this technology to increase the cost-effectiveness of AF at psychrophilic conditions.</p>","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":"16 1","pages":"2458369"},"PeriodicalIF":4.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeted insertion of heterogenous DNA using Cas9-gRNA ribonucleoprotein-mediated gene editing in <i>Ganoderma lucidum</i>.","authors":"Hyerang Eom, Yeon-Jae Choi, Rutuja Nandre, Minseek Kim, Youn-Lee Oh, Sinil Kim, Takehito Nakazawa, Yoichi Honda, Hyeon-Su Ro","doi":"10.1080/21655979.2025.2458376","DOIUrl":"10.1080/21655979.2025.2458376","url":null,"abstract":"<p><p>Gene editing is emerging as a powerful tool for introducing novel functionalities in mushrooms. While CRISPR/Cas9-induced double-strand breaks (DSBs) typically rely on non-homologous end joining (NHEJ) for gene disruption, precise insertion of heterologous DNA in mushrooms is less explored. Here, we evaluated the efficacy of inserting donor DNAs (8-1008 bp) with or without homologous arms at Cas9-gRNA RNP-induced DSBs. Co-transformation of donor DNAs with RNP targeting the <i>pyrG</i> gene in <i>Ganoderma lucidum</i> yielded 184 transformants without homologous arms and 781 with 300-bp homologous arms (HR_donor DNAs). Restriction analysis and sequencing identified 122 hR_donor DNA transformants with complete donor DNA sequences, achieving 15.6% HDR efficiency (122/781), contrasting with 8 instances via NHEJ from the 184 transformants. These findings highlight the viability of HDR for precise genomic editing in mushrooms, enabling targeted modifications to enhance functionalities.</p>","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":"16 1","pages":"2458376"},"PeriodicalIF":4.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11781247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Statement of Retraction: Knockdown of long non-coding RNA AGAP2-AS1 suppresses the proliferation and metastasis of glioma by targeting microRNA-497-5p.","authors":"","doi":"10.1080/21655979.2024.2302648","DOIUrl":"10.1080/21655979.2024.2302648","url":null,"abstract":"","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":"15 1","pages":"2302648"},"PeriodicalIF":4.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139490490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Statement of Retraction: MYCN contributes to the sensitization of acute myelogenous leukemia cells to cisplatin by targeting SRY-box transcription factor 4.","authors":"","doi":"10.1080/21655979.2024.2302650","DOIUrl":"10.1080/21655979.2024.2302650","url":null,"abstract":"","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":"15 1","pages":"2302650"},"PeriodicalIF":4.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10841030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139650263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Retracted article: MYCN contributes to the sensitization of acute myelogenous leukemia cells to cisplatin by targeting SRY-box transcription factor 4.","authors":"Xianbao Huang, Ling Qi, Wei Lu, Ziye Li, Wuping Li, Fei Li","doi":"10.1080/21655979.2021.1997697","DOIUrl":"10.1080/21655979.2021.1997697","url":null,"abstract":"<p><p>Xianbao Huang, Ling Qi, Wei Lu, Ziye Li, Wuping Li and Fei Li. MYCN contributes to the sensitization of acute myelogenous leukemia cells to cisplatin by targeting SRY-box transcription factor 4. Bioengineered. 2021 Oct. doi: 10.1080/21655979.2021.1997697.Since publication, significant concerns have been raised about the compliance with ethical policies for human research and the integrity of the data reported in the article.When approached for an explanation, the authors provided some original data but were not able to provide all the necessary supporting information. As verifying the validity of published work is core to the scholarly record's integrity, we are retracting the article. All authors listed in this publication have been informed.We have been informed in our decision-making by our editorial policies and the COPE guidelines.The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as 'Retracted.'</p>","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":" ","pages":"1997697"},"PeriodicalIF":4.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10841026/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39565966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}