New biotechnology最新文献

{"title":"Learning vs. understanding: When does artificial intelligence outperform process-based modeling in soil organic carbon prediction?","authors":"Luca G. Bernardini ,&nbsp;Christoph Rosinger ,&nbsp;Gernot Bodner ,&nbsp;Katharina M. Keiblinger ,&nbsp;Emma Izquierdo-Verdiguier ,&nbsp;Heide Spiegel ,&nbsp;Carl O. Retzlaff ,&nbsp;Andreas Holzinger","doi":"10.1016/j.nbt.2024.03.001","DOIUrl":"10.1016/j.nbt.2024.03.001","url":null,"abstract":"<div><p>In recent years, machine learning (ML) algorithms have gained substantial recognition for ecological modeling across various temporal and spatial scales. However, little evaluation has been conducted for the prediction of soil organic carbon (SOC) on small data sets commonly inherent to long-term soil ecological research. In this context, the performance of ML algorithms for SOC prediction has never been tested against traditional process-based modeling approaches. Here, we compare ML algorithms, calibrated and uncalibrated process-based models as well as multiple ensembles on their performance in predicting SOC using data from five long-term experimental sites (comprising 256 independent data points) in Austria. Using all available data, the ML-based approaches using Random forest and Support vector machines with a polynomial kernel were superior to all process-based models. However, the ML algorithms performed similar or worse when the number of training samples was reduced or when a leave-one-site-out cross validation was applied. This emphasizes that the performance of ML algorithms is strongly dependent on the data-size related quality of learning information following the well-known curse of dimensionality phenomenon, while the accuracy of process-based models significantly relies on proper calibration and combination of different modeling approaches. Our study thus suggests a superiority of ML-based SOC prediction at scales where larger datasets are available, while process-based models are superior tools when targeting the exploration of underlying biophysical and biochemical mechanisms of SOC dynamics in soils. Therefore, we recommend applying ensembles of ML algorithms with process-based models to combine advantages inherent to both approaches.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"81 ","pages":"Pages 20-31"},"PeriodicalIF":5.4,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000086/pdfft?md5=63bda49e4bb9729283361b81ea4e3f0f&pid=1-s2.0-S1871678424000086-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140094397","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":"The origins and success of the EFB Journal New Biotechnology under the leadership of Mike Taussig","authors":"Jeffrey A. Cole","doi":"10.1016/j.nbt.2024.02.005","DOIUrl":"10.1016/j.nbt.2024.02.005","url":null,"abstract":"","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"81 ","pages":"Page 32"},"PeriodicalIF":5.4,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000074/pdfft?md5=06577845d9491c43f552f115ea3b00a2&pid=1-s2.0-S1871678424000074-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140012997","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":"XPORT ENTRAP: A droplet microfluidic platform for enhanced DNA transfer between microbial species","authors":"Jose A. Wippold ,&nbsp;Monica Chu ,&nbsp;Rebecca Renberg ,&nbsp;Yuwen Li ,&nbsp;Bryn Adams ,&nbsp;Arum Han","doi":"10.1016/j.nbt.2024.02.003","DOIUrl":"10.1016/j.nbt.2024.02.003","url":null,"abstract":"<div><p>A significant hurdle for the widespread implementation and use of synthetic biology is the challenge of highly efficient introduction of DNA into microorganisms. This is especially a barrier for the utilization of non-model organisms and/or novel chassis species for a variety of applications, ranging from molecular biology to biotechnology and biomanufacturing applications. Common approaches to episomal and chromosomal gene editing, which employ techniques such as chemical competence and electroporation, are typically only amenable to a small subset of microbial species while leaving the vast majority of microorganisms in nature genetically inaccessible. To address this challenge, we have employed the previously described B. subtilis broad-host conjugation strain, XPORT, which was modularly designed for loading DNA cargo and conjugating such DNA into recalcitrant microbes. In this current work, we have leveraged and adapted the XPORT strain for use in a droplet microfluidic platform to enable increased efficiency of conjugation-based DNA transfer. The system named DNA ENTRAP (DNA ENhanced TRAnsfer Platform) utilizes cell-encapsulated water-in-oil emulsion droplets as pico-liter-volume bioreactors that allows controlled contacts between the donor and receiver cells within the emulsion bioreactor. This allowed enhanced XPORT-mediated genetic transfer over the current benchtop XPORT process, demonstrated using two different Bacillus subtilis strains (donor and receiver), as well as increased throughput (e.g., number of successfully conjugated cells) due to the automated assay steps inherent to microfluidic lab-on-a-chip systems. DNA ENTRAP paves the way for a streamlined automation of culturing and XPORT-mediated genetic transfer processes as well as future high-throughput cell engineering and screening applications.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"81 ","pages":"Pages 10-19"},"PeriodicalIF":5.4,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000050/pdfft?md5=867a11eebe725573f887c953217efece&pid=1-s2.0-S1871678424000050-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139972840","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":"Continuous H-B-E fermentation by Clostridium carboxidivorans: CO vs syngas","authors":"F. Lanzillo ,&nbsp;S. Pisacane ,&nbsp;M. Capilla ,&nbsp;F. Raganati ,&nbsp;M.E. Russo ,&nbsp;P. Salatino ,&nbsp;A. Marzocchella","doi":"10.1016/j.nbt.2024.02.004","DOIUrl":"10.1016/j.nbt.2024.02.004","url":null,"abstract":"<div><p>Leveraging renewable carbon-based resources for energy and chemical production is a promising approach to decrease reliance on fossil fuels. This entails a thermo/biotechnological procedure wherein bacteria, notably <em>Clostridia</em>, ferment syngas, converting CO or CO₂ + H₂ into Hexanol, Butanol and Ethanol (H-B-E fermentation). This work reports of <em>Clostridium carboxidivorans</em> performance in a stirred tank reactor continuously operated with respect to the gas and the cell/liquid phases. The primary objective was to assess acid and solvent production at pH 5.6 by feeding pure CO or synthetic syngas under gas flow differential conditions. Fermentation tests were conducted at four different dilution rates (D_L) of the fresh medium in the range 0.034–0.25 h⁻¹. The fermentation pathways of <em>C. carboxidivorans</em> were found to be nearly identical for both CO and syngas, with consistent growth and metabolite production at pH 5.6 within a range of dilution rates. Wash-out conditions were observed at a <strong>D</strong>_{<strong>L</strong>} of 0.25 h⁻¹ regardless of the carbon source. Ethanol was the predominant solvent produced, but a shift towards butanol production was observed with CO as the substrate and towards hexanol production with synthetic syngas. In particular, the maximum cell concentration (0.5 g_DM/L) was obtained with pure CO at D_L 0.05 h⁻¹; the highest solvent productivity (60 mg/L*h of total solvent) was obtained at D_L 0.17 h⁻¹ by using synthetic syngas as C-source. The findings highlight the importance of substrate composition and operating conditions in syngas fermentation processes. These insights contribute to the optimization of syngas fermentation processes for biofuel and <strong>chemical</strong> production.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"81 ","pages":"Pages 1-9"},"PeriodicalIF":5.4,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000062/pdfft?md5=93196e9ded63aa1ac091dedd71228029&pid=1-s2.0-S1871678424000062-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139944348","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":"Earth: Extinguishing anthropogenic risks through harmonization","authors":"Tae Seok Moon","doi":"10.1016/j.nbt.2024.02.002","DOIUrl":"10.1016/j.nbt.2024.02.002","url":null,"abstract":"<div><p>Human diseases can kill one person at a time, but the COVID-19 pandemic showed massacres could be possible. The climate crisis could be even worse, potentially leading to a bigger number of deaths of the human species and all living systems on Earth. I urge us to change our human-focused mindset to solve many problems, including the climate crisis, which humans caused to the entire ecosystems due to our arrogance: humans own this world. In this perspective article, I propose four recommendations to address climate issues through paradigm change and safe and sustainable technologies.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"80 ","pages":"Pages 69-71"},"PeriodicalIF":5.4,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000049/pdfft?md5=3e424e2b9e6d6ad7bed94830f0bb922e&pid=1-s2.0-S1871678424000049-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139872948","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":"Deep mining of antibody phage-display selections using Oxford Nanopore Technologies and Dual Unique Molecular Identifiers","authors":"Oscar Mejias-Gomez ,&nbsp;Marta Braghetto ,&nbsp;Morten Kielsgaard Dziegiel Sørensen ,&nbsp;Andreas Visbech Madsen ,&nbsp;Laura Salse Guiu ,&nbsp;Peter Kristensen ,&nbsp;Lasse Ebdrup Pedersen ,&nbsp;Steffen Goletz","doi":"10.1016/j.nbt.2024.02.001","DOIUrl":"https://doi.org/10.1016/j.nbt.2024.02.001","url":null,"abstract":"<div><p>Antibody phage-display technology identifies antibody-antigen interactions through multiple panning rounds, but traditional screening gives no information on enrichment or diversity throughout the process. This results in the loss of valuable binders. Next Generation Sequencing can overcome this problem. We introduce a high accuracy long-read sequencing method based on the recent Oxford Nanopore Technologies (ONT) Q20 + chemistry in combination with dual unique molecular identifiers (UMIs) and an optimized bioinformatic analysis pipeline to monitor the selections. We identified binders from two single-domain antibody libraries selected against a model protein. Traditional colony-picking was compared with our ONT-UMI method. ONT-UMI enabled monitoring of diversity and enrichment before and after each selection round. By combining phage antibody selections with ONT-UMIs, deep mining of output selections is possible. The approach provides an alternative to traditional screening, enabling diversity quantification after each selection round and rare binder recovery, even when the dominating binder was &gt; 99% abundant. Moreover, it can give insights on binding motifs for further affinity maturation and specificity optimizations. Our results demonstrate a platform for future data guided selection strategies.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"80 ","pages":"Pages 56-68"},"PeriodicalIF":5.4,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000037/pdfft?md5=1176b02afd77c461fb2499dc51641c5c&pid=1-s2.0-S1871678424000037-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139732750","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":"Robust and resource-efficient production process suitable for large-scale production of baculovirus through high cell density seed train and optimized infection strategy","authors":"Lena Achleitner ,&nbsp;Martina Winter ,&nbsp;Patricia Pereira Aguilar ,&nbsp;Nico Lingg ,&nbsp;Alois Jungbauer ,&nbsp;Miriam Klausberger ,&nbsp;Peter Satzer","doi":"10.1016/j.nbt.2024.01.002","DOIUrl":"10.1016/j.nbt.2024.01.002","url":null,"abstract":"<div><p>The aim of this study was the development of a scalable production process for high titer (10⁸ pfu/mL and above) recombinant baculovirus stocks with low cell line-derived impurities for the production of virus-like particles (VLP). To achieve this, we developed a high cell density (HCD) culture for low footprint cell proliferation, compared different infection strategies at multiplicity of infection (MOI) 0.05 and 0.005, different infection strategies and validated generally applicable harvest criteria of cell viability ≤ 80%. We also investigated online measurable parameters to observe the baculovirus production. The infection strategy employing a very low virus inoculum of MOI 0.005 and a 1:2 dilution with fresh medium one day after infection proved to be the most resource efficient. There, we achieved higher cell-specific titers and lower host cell protein concentrations at harvest than other tested infection strategies with the same MOI, while saving half of the virus stock for infecting the culture compared to other tested infection strategies. HCD culture by daily medium exchange was confirmed as suitable for seed train propagation, infection, and baculovirus production, equally efficient as the conventionally propagated seed train. Online measurable parameters for cell concentration and average cell diameter were found to be effective in monitoring the production process. The study concluded that a more efficient VLP production process in large scale can be achieved using this virus stock production strategy, which could also be extended to produce other proteins or extracellular vesicles with the baculovirus expression system.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"80 ","pages":"Pages 46-55"},"PeriodicalIF":5.4,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000025/pdfft?md5=1705bb421e3bf8a9906f1e1bc47fee2a&pid=1-s2.0-S1871678424000025-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139672260","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":"From food waste to eco-friendly functionalized polymer composites: Investigation of orange peels as active filler","authors":"Elia Pagliarini ,&nbsp;Carmen Minichiello ,&nbsp;Laura Sisti ,&nbsp;Grazia Totaro ,&nbsp;Loredana Baffoni ,&nbsp;Diana Di Gioia ,&nbsp;Andrea Saccani","doi":"10.1016/j.nbt.2024.01.001","DOIUrl":"10.1016/j.nbt.2024.01.001","url":null,"abstract":"<div><p>The development of eco-friendly polymer composites with multifunctional properties aligns with the goals of the circular economy agenda, which aims to minimize waste and promote the sustainable use of resources by closing the loop of product life cycles. Eco-friendly polymer composites play a crucial role in achieving these objectives. The present work focuses on the preparation of fully biobased blends obtained by melt mixing a bio-polyester, poly(butylene succinate-<em>co</em>-adipate) (PBSA), with orange peels up to 20 wt%, to yield active polymer composites. Orange peels, employed here as natural filler, are largely available from food wastes, they are rich in phenolic compounds and possess antioxidant activity as shown by the experimental tests carried out. The thermal stability of the formulated composites is almost unchanged by the filler addition, showing only a slight decrease of the crystallization temperatures and crystalline fraction within the composites. The mechanical properties of the compounds evidence an increase in the elastic modulus together with a decrease in the tensile strength, while the elongation at break remains almost constant. The incorporation of the natural filler enabled the integration of antioxidant and antibacterial properties, which were absent in the original pristine polymer.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"80 ","pages":"Pages 37-45"},"PeriodicalIF":5.4,"publicationDate":"2024-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000013/pdfft?md5=56721300de0dba00dd86b1b3289b01ee&pid=1-s2.0-S1871678424000013-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139515588","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":"Protein coding regions prediction by fusing DNA shape features","authors":"Miao Chen,&nbsp;Yangyang Li,&nbsp;Kun Zhang,&nbsp;Hao Liu","doi":"10.1016/j.nbt.2023.12.006","DOIUrl":"10.1016/j.nbt.2023.12.006","url":null,"abstract":"<div><p>Exons crucial for coding are often hidden within introns, and the two tend to vary greatly in length, which results in deep learning-based protein coding region prediction methods often performing poorly when applied to more structurally complex biological genomes. DNA shape information also plays a role in revealing the underlying logic of gene expression, yet current methods ignore the influence of DNA shape features when distinguishing coding and non-coding regions. We propose a method to predict protein-coding regions using the CNNS-BRNN model, which incorporates DNA shape features and improves the model's ability to distinguish between intronic and exonic features. We use a fusion coding technique that combines DNA shape features and traditional sequence features. Experiments show that this method outperforms the baseline method in metrics such as AUC and F1 by 2.3% and 5.3%, respectively, and the fusion coding method that introduces DNA shape features has a significant improvement in model performance.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"80 ","pages":"Pages 21-26"},"PeriodicalIF":5.4,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678423000742/pdfft?md5=3228719b72781fa5bb99d884c3fd3bc6&pid=1-s2.0-S1871678423000742-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139102928","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":"Live cell pool and rare cell isolation using Enrich TROVO system","authors":"Stephen Rotatori ,&nbsp;Yichong Zhang ,&nbsp;Kirby Madden-Hennessey,&nbsp;Christina Mohammed,&nbsp;Chi-han Yang,&nbsp;Jordan Urbani,&nbsp;Prem Shrestha,&nbsp;Joseph Pettinelli,&nbsp;Dong Wang,&nbsp;Xueqi Liu,&nbsp;Qi Zhao","doi":"10.1016/j.nbt.2023.12.013","DOIUrl":"10.1016/j.nbt.2023.12.013","url":null,"abstract":"<div><p>Although several technologies have been developed to isolate cells of interest from a heterogenous sample, clogging and impaired cell viability limit such isolation. We have developed the Enrich TROVO system as a novel, nonfluidic technology to sort live cells. The TROVO system combines imaging-based cell selection and photo-crosslinking of (gelatin methacrylate) gelMA-hydrogel to capture cells. After capture, cells are released by enzymatic digestion of the hydrogel and then retrieved for downstream analysis or further cell culturing. The system can capture cells with a recovery rate of 48% while maintaining 90% viability. Moreover, TROVO can enrich rare cells 506-fold with 93% efficiency using single step isolation from a 1:10⁴ cell mixture, and can also capture one target cell from 1 million cells, reaching an enrichment ratio of 9128. In addition, 100% purity and 49% recovery rate can be achieved by a following negative isolation process. Compared to existing technologies, the TROVO system is clog-resistant, highly biocompatible, and can process a wide range of sample sizes.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"80 ","pages":"Pages 12-20"},"PeriodicalIF":5.4,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S187167842300081X/pdfft?md5=a51ba68b6a02ba0f5b04a336976ddd7d&pid=1-s2.0-S187167842300081X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139098417","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}