journal
https://read.qxmd.com/read/38531507/complete-genome-sequence-and-transcriptome-response-to-vitamin-c-supplementation-of-novacetimonas-hansenii-si1-producer-of-highly-stretchable-cellulose
#1
JOURNAL ARTICLE
Małgorzata Ryngajłło, Izabela Cielecka, Maurycy Daroch
Novacetimonas hansenii SI1, previously known as Komagataeibacter hansenii, produces bacterial nanocellulose (BNC) with unique ability to stretch. The addition of vitamin C in the culture medium increases the porosity of the membranes and their stretchability making them highly moldable. To better understand the genetic background of this strain, we obtained its complete genome sequence using a hybrid sequencing and assembly strategy. We described the functional regions in the genome which are important for the synthesis of BNC and acetan-like II polymer...
March 24, 2024: New Biotechnology
https://read.qxmd.com/read/38521182/food-and-human-health-applications-of-edible-mushroom-by-products
#2
REVIEW
Pablo Navarro-Simarro, Lourdes Gómez-Gómez, Oussama Ahrazem, Ángela Rubio-Moraga
Mushroom waste can account for up to 50% of the total mushroom mass. Spent mushroom substrate, misshapen mushrooms, and mushroom stems are examples of mushroom byproducts. In ancient cultures, fungi were prized for their medicinal properties. Aqueous extracts containing high levels of β-glucans as functional components capable of providing prebiotic polysaccharides and improved texture to foods have been widely used and new methods have been tested to improve extraction yields. Similarly, the addition of insoluble polysaccharides controls the glycemic index, counteracting the effects of increasingly high-calorie diets...
March 21, 2024: New Biotechnology
https://read.qxmd.com/read/38493996/full-length-article-for-submission-to-new-biotechnology-a-monodispersed-metal-complexing-peptide-based-polymer-for-mass-cytometry-enabling-spectral-applications
#3
JOURNAL ARTICLE
J Verhoeff, S van Asten, L Kuijper, M van den Braber, Erika Amstalden, Rob Haselberg, H Kalay, J J Garcia Vallejo
We report the synthesis of a novel class of metal-complexing peptide-based polymers, which we name HyperMAPs (Hyper-loaded MetAl-complexed Polymers). The controlled solid-phase synthesis of HyperMAPs' scaffold peptide provides our polymer with a well-defined molecular structure that allows for an accurate on-design assembly of a wide variety of metals. The peptide-scaffold features a handle for direct conjugation to antibodies or any other biomolecules by means of a thiol-maleimide-click or aldehyde-oxime reaction, a fluorogenic moiety for biomolecule conjugation tracking, and a well-defined number of functional groups for direct incorporation of metal-chelator complexes...
March 15, 2024: New Biotechnology
https://read.qxmd.com/read/38462171/learning-vs-understanding-when-does-artificial-intelligence-outperform-process-based-modeling-in-soil-organic-carbon-prediction
#4
JOURNAL ARTICLE
Luca G Bernardini, Christoph Rosinger, Gernot Bodner, Katharina M Keiblinger, Emma Izquierdo-Verdiguier, Heide Spiegel, Carl O Retzlaff, Andreas Holzinger
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...
March 8, 2024: New Biotechnology
https://read.qxmd.com/read/38428808/the-origins-and-success-of-the-efb-journal-new-biotechnology-under-the-leadership-of-mike-taussig
#5
EDITORIAL
Jeff Cole
No abstract text is available yet for this article.
February 28, 2024: New Biotechnology
https://read.qxmd.com/read/38408724/xport-entrap-a-droplet-microfluidic-platform-for-enhanced-dna-transfer-between-microbial-species
#6
JOURNAL ARTICLE
Jose A Wippold, Monica Chu, Rebecca Renberg, Yuwen Li, Bryn Adams, Arum Han
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...
February 24, 2024: New Biotechnology
https://read.qxmd.com/read/38401749/continuous-h-b-e-fermentation-by-clostridium-carboxidivorans-co-vs-syngas
#7
JOURNAL ARTICLE
F Lanzillo, S Pisacane, M Capilla, F Raganati, M E Russo, P Salatino, A Marzocchella
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 Clostridia, ferment syngas, converting CO or CO2 + H2 into Hexanol, Butanol and Ethanol (H-B-E fermentation). This work reports of Clostridium carboxidivorans 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...
February 22, 2024: New Biotechnology
https://read.qxmd.com/read/38367910/earth-extinguishing-anthropogenic-risks-through-harmonization
#8
REVIEW
Tae Seok Moon
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...
February 15, 2024: New Biotechnology
https://read.qxmd.com/read/38354946/deep-mining-of-antibody-phage-display-selections-using-oxford-nanopore-technologies-and-dual-unique-molecular-identifiers
#9
JOURNAL ARTICLE
Oscar Mejias-Gomez, Marta Braghetto, Morten Kielsgaard Dziegiel Sørensen, Andreas Visbech Madsen, Laura Salse Guiu, Peter Kristensen, Lasse Ebdrup Pedersen, Steffen Goletz
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...
February 12, 2024: New Biotechnology
https://read.qxmd.com/read/38302001/robust-and-resource-efficient-production-process-suitable-for-large-scale-production-of-baculovirus-through-high-cell-density-seed-train-and-optimized-infection-strategy
#10
JOURNAL ARTICLE
Lena Achleitner, Martina Winter, Patricia Pereira Aguilar, Nico Lingg, Alois Jungbauer, Miriam Klausberger, Peter Satzer
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%...
January 30, 2024: New Biotechnology
https://read.qxmd.com/read/38253287/from-food-waste-to-eco-friendly-functionalized-polymer-composites-investigation-of-orange-peels-as-active-filler
#11
JOURNAL ARTICLE
Elia Pagliarini, Carmen Minichiello, Laura Sisti, Grazia Totaro, Loredana Baffoni, Diana Di Gioia, Andrea Saccani
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-co-adipate) (PBSA), with orange peels up to 20wt%, to yield active polymer composites...
January 20, 2024: New Biotechnology
https://read.qxmd.com/read/38182076/protein-coding-regions-prediction-by-fusing-dna-shape-features
#12
JOURNAL ARTICLE
Miao Chen, Yangyang Li, Kun Zhang, Hao Liu
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...
January 3, 2024: New Biotechnology
https://read.qxmd.com/read/38176452/live-cell-pool-and-rare-cell-isolation-using-enrich-trovo-system
#13
JOURNAL ARTICLE
Stephen Rotatori, Yichong Zhang, Kirby Madden-Hennessey, Christina Mohammed, Chi-Han Yang, Jordan Urbani, Prem Shrestha, Joseph Pettinelli, Dong Wang, Xueqi Liu, Qi Zhao
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...
January 2, 2024: New Biotechnology
https://read.qxmd.com/read/38163476/novel-%C3%AE-galactosidase-activity-and-first-crystal-structure-of-glycoside-hydrolase-family-154
#14
JOURNAL ARTICLE
Lisanne Hameleers, Tjaard Pijning, Brandon B Gray, Régis Fauré, Edita Jurak
Polysaccharide Utilization Loci (PULs) are physically linked gene clusters conserved in the Gram-negative phylum of Bacteroidota and are valuable sources for Carbohydrate Active enZyme (CAZyme) discovery. This study focuses on BD-β-Gal, an enzyme encoded in a metagenomic PUL and member of the Glycoside Hydrolase family 154 (GH154). BD-β-Gal showed exo-β-galactosidase activity with regiopreference for hydrolyzing β-d-(1,6) glycosidic linkages. Notably, it exhibited a preference for d-glucopyranosyl (d-Glcp) over d-galactopyranosyl (d-Galp) and d-fructofuranosyl (d-Fruf) at the reducing end of the investigated disaccharides...
December 30, 2023: New Biotechnology
https://read.qxmd.com/read/38159596/co-culture-platform-for-tuning-of-cancer-receptor-density-allows-for-evaluation-of-bispecific-immune-cell-engagers
#15
JOURNAL ARTICLE
Aman Mebrahtu, Gustav Aniander, Alessandro Mega, Mona Moradi Barzadd, Niklas Berndt Thalén, Lindvi Gudmundsdotter, Eva Backström Rydin, Anna Sandegren, Fredrik Y Frejd, Johan Rockberg
Cancer immunotherapy, where a patient's immune system is harnessed to eradicate cancer cells selectively, is a leading strategy for cancer treatment. However, successes with immune checkpoint inhibitors (ICI) are hampered by reported systemic and organ-specific toxicities and by two-thirds of the patients being non-responders or subsequently acquiring resistance to approved ICIs. Hence substantial efforts are invested in discovering novel targeted immunotherapies aimed at reduced side-effects and improved potency...
December 28, 2023: New Biotechnology
https://read.qxmd.com/read/38158018/biorefinery-of-brewery-spent-grain-to-obtain-bioproducts-with-high-value-added-in-the-market
#16
JOURNAL ARTICLE
David Outeiriño, Iván Costa-Trigo, Aida Ochogavias, Ricardo Pinheiro de Souza Oliveira, Nelson Pérez Guerra, José Manuel Salgado, José Manuel Domínguez
The brewery industry is under economic and environmental pressure to minimize residual management costs, particularly brewery spent grain (BSG), which accounts for 80-85% (w/w) of the total by-products generated. BSG is a lignocellulosic material primarily composed of carbohydrates, proteins and lipids. Developing a biorefinery model for conversion of BSG into value-added products is a plausible idea. Previous work optimized the pretreatment of BSG with the ionic liquid [N1112OH ][Gly] and further release of fermentable sugar-containing solutions by enzymatic hydrolysis, using an enzymatic cocktail obtained by solid-state fermentation of BSG with Aspergillus brasiliensis CECT 2700 and Trichoderma reesei CECT 2414...
December 27, 2023: New Biotechnology
https://read.qxmd.com/read/38158017/post-translational-secretion-stress-regulation-in-bacillus-subtilis-is-controlled-by-intra-and-extracellular-proteases
#17
JOURNAL ARTICLE
Ayşegül Öktem, Dicky A Pranoto, Jan Maarten van Dijl
The Gram-positive bacterium Bacillus subtilis is a prolific producer of industrial enzymes that are effectively harvested from the fermentation broth. However, the high capacity of B. subtilis for protein secretion has so far not been exploited to the full due to particular bottlenecks, including product degradation by extracellular proteases and counterproductive secretion stress responses. To unlock the Bacillus secretion pathway for difficult-to-produce proteins, various cellular interventions have been explored, including genome engineering...
December 27, 2023: New Biotechnology
https://read.qxmd.com/read/38154615/inefficient-transcription-is-a-production-bottleneck-for-artificial-therapeutic-bite%C3%A2-proteins
#18
JOURNAL ARTICLE
Tobias Jerabek, Madina Burkhart, Selina Goetz, Benedikt Greck, Anika Menthe, Ruediger Neef, Kerstin Otte
Antibodies are potent biopharmaceuticals used to treat severe diseases, including cancers. During the past decade, more complex modalities have been developed including bispecific T-cell engager (BiTE®) molecules, e.g. by Amgen. However, non-natural and complex molecule formats often prove to be difficult-to-express (DTE), which is the case for BiTE® molecules. Due to the growing importance of multispecific modalities such as half-life extended (HLE) BiTE® and HLE dual-targeting bispecific T-cell engager (dBiTE) molecules, this artificial class of therapeutic proteins was investigated for molecular bottlenecks in stable production cell lines, by analyzing all relevant steps of recombinant protein production...
December 26, 2023: New Biotechnology
https://read.qxmd.com/read/38154614/in-pursuit-of-a-minimal-cho-genome-establishment-of-large-scale-genome-deletions
#19
JOURNAL ARTICLE
Tobias Jerabek, Linus Weiß, Hannah Fahrion, Nikolas Zeh, Nadja Raab, Benjamin Lindner, Simon Fischer, Kerstin Otte
Chinese hamster ovary (CHO) cells are the most commonly used mammalian cell line for the production of complex therapeutic glycoproteins. As CHO cells have evolved as part of a multicellular organism, they harbor many cellular functions irrelevant for their application as production hosts in industrial bioprocesses. Consequently, CHO cells have been the target for numerous genetic engineering efforts in the past, but a tailored host cell chassis holistically optimized for its specific task in a bioreactor is still missing...
December 26, 2023: New Biotechnology
https://read.qxmd.com/read/38145650/pre-analytical-properties-of-different-respiratory-viruses-for-pcr-based-detection-comparative-analysis-of-sampling-devices-and-sample-stabilization-solutions
#20
JOURNAL ARTICLE
Melina Hardt, Franziska Kaiser, Thorsten Voss, Uwe Oelmüller, Kurt Zatloukal
After the decline of the COVID-19 pandemic, health systems were challenged by the simultaneous prevalence of different respiratory viruses causing a wide overlap in symptoms. This increased the demand for multi-virus diagnostic tests which require suitable pre-analytical workflow solutions in order to receive valid diagnostic results. In this context, the effects of specimen storage duration and temperature on the RNA/DNA copy number stability of influenza A/B, RSV A/B, SARS-CoV-2 and adenovirus were examined for four commercially available transport swab systems and saliva collection devices...
December 23, 2023: New Biotechnology
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