New biotechnology最新文献

{"title":"New strategy for bioplastic and exopolysaccharides production: Enrichment of field microbiomes with cyanobacteria","authors":"Beatriz Altamira-Algarra ,&nbsp;Estel Rueda ,&nbsp;Artai Lage ,&nbsp;David San León ,&nbsp;Juan F. Martínez-Blanch ,&nbsp;Juan Nogales ,&nbsp;Joan García ,&nbsp;Eva Gonzalez-Flo","doi":"10.1016/j.nbt.2023.10.008","DOIUrl":"10.1016/j.nbt.2023.10.008","url":null,"abstract":"<div><p>Seven photosynthethic microbiomes were collected from field environmental samples to test their potential in polyhydroxybutyrate (PHB) and exopolysaccharides (EPS) production, both alternatives to chemical-based polymers. Microscope observations together with microbial sequence analysis revealed the microbiome enrichment in cyanobacteria after culture growth under phosphorus limitation. PHB and EPS production were studied under three culture factors (phototrophy, mixotrophy and heterotrophy) by evaluating and optimizing the effect of three parameters (organic and inorganic carbon and days under light:dark cycles) by Box-Behnken design. Results showed that optimal conditions for both biopolymers synthesis were microbiome-dependent; however, the addition of organic carbon boosted PHB production in all the tested microbiomes, producing up to 14 %_dcw PHB with the addition of 1.2 g acetate·L⁻¹ and seven days under light:dark photoperiods. The highest EPS production was 59 mg·L⁻¹ with the addition of 1.2 g acetate·L⁻¹ and four days under light:dark photoperiods. The methodology used is suitable for enriching microbiomes in cyanobacteria, and for testing the best conditions for bioproduct synthesis for further scale up.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678423000560/pdfft?md5=0e4bccaa66a1a608161698c0b862379f&pid=1-s2.0-S1871678423000560-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49680324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electrochemical H2O2 - stat mode as reaction concept to improve the process performance of an unspecific peroxygenase","authors":"Giovanni V. Sayoga ,&nbsp;Victoria S. Bueschler ,&nbsp;Hubert Beisch ,&nbsp;Tyll Utesch ,&nbsp;Dirk Holtmann ,&nbsp;Bodo Fiedler ,&nbsp;Daniel Ohde ,&nbsp;Andreas Liese","doi":"10.1016/j.nbt.2023.10.007","DOIUrl":"https://doi.org/10.1016/j.nbt.2023.10.007","url":null,"abstract":"<div><p>The electroenzymatic hydroxylation of 4-ethylbenzoic acid catalyzed by the recombinant unspecific peroxygenase from the fungus <em>Agrocybe aegerita</em> (r<em>Aae</em>UPO) was performed in a gas diffusion electrode (GDE)-based system. Enzyme stability and productivity are significantly affected by the way the co-substrate hydrogen peroxide (H₂O₂) is supplied. In this study, two <em>in-situ</em> electrogeneration modes of H₂O₂ were established and compared. Experiments under galvanostatic conditions (constant productivity of H₂O₂) were conducted at current densities spanning from 0.8 mA cm⁻² to 6.4 mA cm⁻². For comparison, experiments under H₂O₂-stat mode (constant H₂O₂ concentration) were performed. Here, four H₂O₂ concentrations between 0.06 mM and 0.28 mM were tested. A maximum H₂O₂ productivity of 5.5 µM min⁻¹ cm⁻² and productivity of 10.5 g L⁻¹ d⁻¹ were achieved under the galvanostatic condition at 6.4 mA cm⁻². Meanwhile, the highest total turnover number (TTN) of 710,000 mol mol⁻¹ and turnover frequency (TOF) of 87.5 s⁻¹ were obtained under the H₂O₂-stat mode at concentration limits of 0.15 mM and 0.28 mM, respectively. The most favorable outcome in terms of maximum achievable TTN, TOF and productivity was found under the H₂O₂-stat mode at concentration limit of 0.2 mM. Here, a TTN of 655,000 mol mol⁻¹, a TOF of 80.3 s⁻¹ and a productivity of 6.1 g L⁻¹ d⁻¹ were achieved. The electrochemical H₂O₂-stat mode not only offers a promising alternative reaction concept to the well-established galvanostatic mode but also enhances the process performance of unspecific peroxygenases.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49705523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Personalized 3D printed scaffolds: The ethical aspects","authors":"Manon van Daal ,&nbsp;Anne-Floor J. de Kanter ,&nbsp;Annelien L. Bredenoord ,&nbsp;Nienke de Graeff","doi":"10.1016/j.nbt.2023.10.006","DOIUrl":"10.1016/j.nbt.2023.10.006","url":null,"abstract":"<div><p>Personalized 3D printed scaffolds are a new generation of implants for tissue engineering and regenerative medicine purposes. Scaffolds support cell growth, providing an artificial extracellular matrix for tissue repair and regeneration and can biodegrade once cells have assumed their physiological and structural roles. The ethical challenges and opportunities of these implants should be mapped in parallel with the life cycle of the scaffold to assist their development and implementation in a responsible, safe, and ethically sound manner. This article provides an overview of these relevant ethical aspects. We identified nine themes which were linked to three stages of the life cycle of the scaffold: the development process, clinical testing, and the implementation process. The described ethical issues are related to good research and clinical practices, such as privacy issues concerning digitalization, first-in-human trials, responsibility and commercialization. At the same time, this article also creates awareness for underexplored ethical issues, such as irreversibility, embodiment and the ontological status of these scaffolds. Moreover, it exemplifies how to include gender in the ethical assessment of new technologies. These issues are important for responsible development and implementation of personalized 3D printed scaffolds and in need of more attention within the additive manufacturing and tissue engineering field. Moreover, the insights of this review reveal unresolved qualitative empirical and normative questions that could further deepen the understanding and co-creation of the ethical implications of this new generation of implants.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41237117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Open (non-sterile) cultivations of Debaryomyces hansenii for recombinant protein production combining industrial side-streams with high salt content","authors":"Mònica Estrada ,&nbsp;Clara Navarrete ,&nbsp;Sønke Møller ,&nbsp;Manuel Quirós ,&nbsp;José L. Martínez","doi":"10.1016/j.nbt.2023.10.005","DOIUrl":"10.1016/j.nbt.2023.10.005","url":null,"abstract":"<div><p>The halotolerant non-conventional yeast <em>Debaryomyces hansenii</em> can grow in media containing high concentrations of salt (up to 4 M), metabolize alternative carbon sources than glucose, such as lactose or glycerol, and withstand a wide range of temperatures and pH. These inherent capabilities allow this yeast to grow in harsh environments and use alternative feedstock than traditional commercial media. For example, <em>D. hansenii</em> could be a potential cell factory for revalorizing industrial salty by-products, using them as a substrate for producing new valuable bioproducts, boosting a circular economy. In this work, three different salty by-products derived from the dairy and biopharmaceutical industry have been tested as a possible feedstock for <em>D. hansenii</em>’s growth. The yeast was not only able to grow efficiently in all of them but also to produce a recombinant protein (Yellow Fluorescent Protein, used as a model) without altering its performance. Moreover, open cultivations at different laboratory scales (1.5 mL and 1 L) were performed under non-sterile conditions and without adding fresh water or any nutritional supplement to the cultivation, making the process cheaper and more sustainable.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41237116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Site-specific antibody masking enables conditional activation with different stimuli","authors":"Roberta Lucchi,&nbsp;Maria C. Lucana,&nbsp;Montserrat Escobar-Rosales,&nbsp;Cristina Díaz-Perlas,&nbsp;Benjamí Oller-Salvia","doi":"10.1016/j.nbt.2023.10.004","DOIUrl":"10.1016/j.nbt.2023.10.004","url":null,"abstract":"<div><p>Antibody therapeutics show great potential to treat a variety of diseases. Often, the dose that can be safely administered is limited by side effects that arise from the interaction with the target outside the diseased tissue. Conditionally-active antibodies provide an additional layer of selectivity to improve safety. Distinct external stimuli or internal cues enable different control strategies and applications. However, current antibody masking strategies have low transferability across stimuli. Here we propose a versatile approach to conditionally mask antibody derivatives and its application to a single chain variable fragment (scFv) against a receptor expressed on cancer stem cells in several tumours. Our strategy relies on the site-specific conjugation of a polymer to an engineered cysteine residue through a chemically-synthesised linker that can be cleaved in response to the target stimulus. We show that the masking efficiency depends on the conjugation site and the size of the mask. An optimised mask decreases antigen binding by up to 20-fold and affinity can be fully recovered upon activation by exposure to light at 365 nm or by incubation with matrix metalloproteinases overexpressed in solid tumours. This approach opens up the possibility to rapidly engineer antibodies activatable with any internal or external stimulus.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41207173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pilot-scale production of mcl-PHA by Pseudomonas citronellolis using acetic acid as the sole carbon source","authors":"Milos Kacanski ,&nbsp;Franz Stelzer ,&nbsp;Meg Walsh ,&nbsp;Shane Kenny ,&nbsp;Kevin O’Connor ,&nbsp;Markus Neureiter","doi":"10.1016/j.nbt.2023.10.003","DOIUrl":"10.1016/j.nbt.2023.10.003","url":null,"abstract":"<div><p>Medium-chain-length polyhydroxyalkanoates (mcl-PHA) are biobased materials with promising properties for environmentally friendly applications. Due to high production costs, which are related to the cost of the carbon sources combined with conversion insufficiencies, currently only small quantities are produced. This results in a lack of reliable data on properties and application potential for the variety of polymers from different types of production strains. This study investigated the potential for the production of mcl-PHA from volatile fatty acids (VFA) at a larger scale, given their potential as low-cost and sustainable raw material within a carboxylate-platform based biorefinery. <em>Pseudomonas citronellolis</em> (DSMZ 50332) was chosen as the production strain, and acetic acid was selected as the main carbon and energy source. Nitrogen was limited to trigger polymer production, and a fed-batch process using a pH-stat feeding regime with concentrated acid was established. We report successful production, extraction, and characterization of mcl PHA, obtaining a total of 1.76 kg from two 500-litre scale fermentations. The produced polymer was identified as a copolymer of 3-hydroxydecanoate (60.7%), 3-hydroxyoctanoate (37.3%), and 3-hydroxyhexanoate (2.0%) with a weight average molecular weight (M_w) of 536 kDa. NMR analysis indicates the presence of unsaturated side chains, which may offer additional possibilities for modification. The results confirm that there is a potential to produce significant amounts of mcl-PHA with interesting rubber-like properties from waste-derived VFA.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41207172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microalgae harvesting for wastewater treatment and resources recovery: A review","authors":"Etiele Greque de Morais ,&nbsp;Igor Carvalho Fontes Sampaio ,&nbsp;Eva Gonzalez-Flo ,&nbsp;Ivet Ferrer ,&nbsp;Enrica Uggetti ,&nbsp;Joan García","doi":"10.1016/j.nbt.2023.10.002","DOIUrl":"10.1016/j.nbt.2023.10.002","url":null,"abstract":"<div><p>Microalgae-based wastewater treatment has been conceived to obtain reclaimed water and produce microalgal biomass for bio-based products and biofuels generation. However, microalgal biomass harvesting is challenging and expensive, hence one of the main bottlenecks for full-scale implementation. Finding an integrated approach that covers concepts of engineering, green chemistry and the application of microbial anabolism driven towards the harvesting processes, is mandatory for the widespread establishment of full-scale microalgae wastewater treatment plants. By using nature-based substances and applying concepts of chemical functionalization in already established harvesting methods, the costs of harvesting processes could be reduced while preventing microalgae biomass contamination. Moreover, microalgae produced during wastewater treatment have unique culture characteristics, such as the consortia, which are primarily composed of microalgae and bacteria, that should be accounted for prior to downstream processing. The aim of this review is to examine recent advances in microalgal biomass harvesting and recovery in wastewater treatment systems, considering the impact of consortia variability. The costs of available harvesting technologies, such as coagulation/flocculation, coupled to sedimentation and differential air flotation, are provided. Additionally, promising technologies are discussed, including autoflocculation, bioflocculation, new filtration materials, nanotechnology, microfluidic and magnetic methods.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41207171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Droplet digital PCR: A comprehensive tool for genetic analysis and prediction of bispecific antibody assembly during cell line development","authors":"Daniel Heinzelmann,&nbsp;Benjamin Lindner,&nbsp;Benjamin Renner,&nbsp;Simon Fischer,&nbsp;Patrick Schulz,&nbsp;Moritz Schmidt","doi":"10.1016/j.nbt.2023.10.001","DOIUrl":"10.1016/j.nbt.2023.10.001","url":null,"abstract":"<div><p>Molecular biological methods have emerged as inevitable tools to accompany the process of cell line development for the generation of stable and highly productive manufacturing cell lines in the biopharmaceutical industry. PCR-based methods are especially useful for screening and characterization of cell lines due to their low cost, scalability, precision and propensity for multidimensional read-outs. In this study, the diverse applications of droplet digital PCR (ddPCR) as a molecular biological tool for cell line development are demonstrated. Specifically, it is shown that ddPCR can be used to enable precise, sensitive and reproducible absolute quantification of genomically integrated transgene copies during cell line development and cell bank characterization. Additionally, an amplitude multiplexing approach is applied to simultaneously run multiple assays on different genetic targets in a single reaction and advance clonal screening by measuring gene expression profiles to predict the assembly and homogeneity of difficult-to-express (DTE) proteins. The implementation of ddPCR-based assays during cell line development allows for early screening at a transcriptional level, particularly for complex, multidomain proteins, where balanced polypeptide chain ratios are of primary importance. Moreover, it is demonstrated that ddPCR-based genomic characterization improves the robustness, efficiency and comparability of absolute transgene copy number quantification, an essential genetic parameter that must be demonstrated to regulatory authorities during clinical trial and market authorization application submissions to support genetic stability and consistency of the selected cell substrate.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41143660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biostimulation effect of different amendments on Cr(VI) recovering microbial community","authors":"Marina Tumolo ,&nbsp;Domenico De Paola ,&nbsp;Vito Felice Uricchio ,&nbsp;Valeria Ancona","doi":"10.1016/j.nbt.2023.09.007","DOIUrl":"10.1016/j.nbt.2023.09.007","url":null,"abstract":"<div><p>The present study used Cr(VI)-polluted microcosms amended with lactate or yeast extract, and nonamended microcosms as control, to investigate how a native bacterial community varied in response to the treatment and during the pollutant removal. Results suggested that providing electron donors resulted in a proliferation of a few bacterial species, with the consequent decrease in observed species richness and evenness, and was a driving force for the bacterial compositional shift. Lactate promoted, in the first instance, the enrichment of fermentative bacteria belonging to Chromobacteriaceae, including Paludibacterium, and Micrococcaceae as observed after 4 days. When the rate of Cr(VI) removal was maximum in microcosms amended with lactate, the most represented taxa were Pseudarcicella and Azospirillum. Using yeast extract as a carbon source and electron donor led instead to the significant enrichment of Shewanella, followed by Vogesella and Acinetobacter on the 4th day, corresponding to 90% of Cr(VI) removed from the system. After the complete Cr(VI) removal, achieved in 7 days in the presence of yeast extract, α-diversity was notably increased. The amendment-specific turnover of the enriched bacterial taxa resulted in a different kinetic of pollutant removal. In particular, yeast extract promoted the quickest Cr(VI) reduction, while lactate supported a slower, but also considerable, pollutant removal from water. Since it is reasonable to assume that a macroscopic effect, such as the observed Cr(VI) removal, involved the overrepresented taxa, deepening the knowledge of the native bacterial community and its changes were used to hypothesize the possible microbial pathways involved.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41139394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Shedding light on the black box of a neural network used to detect prostate cancer in whole slide images by occlusion-based explainability","authors":"Matej Gallo ,&nbsp;Vojtěch Krajňanský ,&nbsp;Rudolf Nenutil ,&nbsp;Petr Holub ,&nbsp;Tomáš Brázdil","doi":"10.1016/j.nbt.2023.09.008","DOIUrl":"10.1016/j.nbt.2023.09.008","url":null,"abstract":"<div><p>Diagnostic histopathology faces increasing demands due to aging populations and expanding healthcare programs. Semi-automated diagnostic systems employing deep learning methods are one approach to alleviate this pressure. The learning models for histopathology are inherently complex and opaque from the user's perspective. Hence different methods have been developed to interpret their behavior. However, relatively limited attention has been devoted to the connection between interpretation methods and the knowledge of experienced pathologists. The main contribution of this paper is a method for comparing morphological patterns used by expert pathologists to detect cancer with the patterns identified as important for inference of learning models. Given the patch-based nature of processing large-scale histopathological imaging, we have been able to show statistically that the VGG16 model could utilize all the structures that are observable by the pathologist, given the patch size and scan resolution. The results show that the neural network approach to recognizing prostatic cancer is similar to that of a pathologist at medium optical resolution. The saliency maps identified several prevailing histomorphological features characterizing carcinoma, e.g., single-layered epithelium, small lumina, and hyperchromatic nuclei with halo. A convincing finding was the recognition of their mimickers in non-neoplastic tissue. The method can also identify differences, i.e., standard patterns not used by the learning models and new patterns not yet used by pathologists. Saliency maps provide added value for automated digital pathology to analyze and fine-tune deep learning systems and improve trust in computer-based decisions.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2023-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41125847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}