Article
Agriculture, Multidisciplinary
Xiaomeng Fu, Kunqiang Hong, Haibin Wang, Chuanbo Zhang, Wenyu Lu
Summary: Enone oxidoreductase from Naumovozyma dairenensis CBS 421 was used for HEMF production for the first time, and the mutant NDEOT183W,K290W obtained through semirational protein engineering increased HEMF yield by 75.2%. The engineered strain BM4 produced the highest HEMF yield in 132 h.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Mrinal Sharma, Prranshu Yadav, Ankita Doshi, Hemang D. Brahmbhatt, C. Ratna Prabha
Summary: The study examined the effects of six double mutants derived from the ubiquitin mutant UbEP42 on cell functions, finding that the double mutation L50P-I61T had the most detrimental impact. Overall, these double mutations made cells more sensitive, and the negative effects under certain conditions could be compensated for by each other.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biotechnology & Applied Microbiology
Minakshi Mukherjee, Rachael Hageman Blair, Zhen Q. Wang
Summary: The production of terpenoids from engineered microbes plays a significant role in providing essential medicines, sustainable materials, and renewable fuels. The study focuses on the individual contribution of non-rate-limiting enzymes in the mevalonate pathway to the overall pathway flux and final terpenoid yield. It identifies the mevalonate kinase as the critical enzyme influencing product titer. Additionally, a platform strain is created by targeting the mevalonate pathway to both the cytosol and peroxisomes, resulting in significantly improved terpenoid production.
METABOLIC ENGINEERING
(2022)
Article
Agriculture, Multidisciplinary
Junhua Wang, Linghuan Zhu, Youran Li, Sha Xu, Wei Jiang, Chaojuan Liang, Yakun Fang, Alex Chu, Liang Zhang, Zhongyang Ding, Guiyang Shi
Summary: By using a GGPP synthase with stronger catalytic ability and increasing the metabolic flux of the MVA pathway and the supply of IPP, the production of GGOH in Saccharomyces cerevisiae was significantly enhanced. These strategies can also be applied to enhance the production of other terpenoids in the future.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Water Resources
Mohaddeseh Zahmatkesh Anbarani, Afsaneh Esmaeili Nasrabadi, Ziaeddin Bonyadi
Summary: The aim of this study was to evaluate the efficiency of S. cerevisiae in removing PS from aqueous solutions. BBD was used to determine the optimal removal conditions. The maximum PS removal efficiency was 98.81% under optimized conditions. Based on the results, it can be concluded that S. cerevisiae can be used as a natural and environmentally friendly biocoagulant to remove PS.
APPLIED WATER SCIENCE
(2023)
Article
Food Science & Technology
Jitka Laurent, Nore Struyf, An Bautil, Albina Bakeeva, Mikolaj Chmielarz, Marika Lyly, Beatriz Herrera-Malaver, Volkmar Passoth, Kevin J. Verstrepen, Christophe M. Courtin
Summary: A diet low in FODMAPs can help reduce symptoms in patients with irritable bowel syndrome, but avoiding cereal grain products may lead to nutritional deficiencies. Developing low-FODMAP, high-fiber cereal grain products using K. marxianus in bread production can effectively reduce fructan levels and maintain fructan and fructose levels below the threshold for low-FODMAP products.
FOOD AND BIOPROCESS TECHNOLOGY
(2021)
Article
Genetics & Heredity
Raquel Sorribes-Dauden, Maria Teresa Martinez-Pastor, Sergi Puig
Summary: Iron is essential for eukaryotic organisms, and its deficiency can lead to anemia. Yeast cells use the Ccc1 transporter to detoxify and store excess iron. Deletion of the Nt domain of Ccc1 can increase iron accumulation in cells.
Article
Immunology
Francesca Soutter, Dirk Werling, Matthew Nolan, Tatiana Kuster, Elizabeth Attree, Virginia Marugan-Hernandez, Sungwon Kim, Fiona M. Tomley, Damer P. Blake
Summary: A cheap and easy-to-produce oral vaccine has been developed using Saccharomyces cerevisiae yeast expressing Eimeria tenella antigens. The vaccine effectively reduces the replication of Eimeria tenella and improves the growth of chickens, making it an important tool for controlling coccidiosis in chickens, particularly in low- and middle-income countries.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Juste Rozene, Inga Morkvenaite-Vilkonciene, Ingrida Bruzaite, Antanas Zinovicius, Arunas Ramanavicius
Summary: The efficiency of microbial fuel cells (MFCs) relies on the charge transfer capability from microbes to anodes, with redox mediators playing a crucial role. This study looked at the influence of 2-methyl-1,4-naphthoquinone (menadione (MD)) on yeast cells and found that baker's yeast cells were more resistant to dissolved MD. The maximal calculated power output of a designed baker's yeast-based MFC cell anode was 0.408 mW/m(2) at 24 mV.
Article
Microbiology
Bazile Ravoityte, Juliana Luksa, Ralf Erik Wellinger, Saulius Serva, Elena Serviene
Summary: This study analyzed the impact of L-A virus on gene expression in yeast hosts using high-throughput RNA sequencing data. It was found that the presence of L-A virus resulted in moderate alterations in gene expression, particularly in genes involved in ribosome biogenesis. Additionally, the transcriptional responses to L-A maintenance were similar to those induced by stress or nutrient availability. The study also identified yeast transcriptional regulators that modulate the levels of L-A dsRNA in cells.
Review
Biotechnology & Applied Microbiology
R. Sahaya Glingston, Jyoti Yadav, Jitika Rajpoot, Neha Joshi, Shirisha Nagotu
Summary: Yeast has been proven to be a valuable model system for studying viral infection and expression of viral proteins, advancing our understanding of important viruses. Through high-throughput analysis, genetic manipulation, and its compact genome, yeast provides insights into various aspects related to virus replication.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Chemistry, Applied
Sofia F. Reis, Susana Messias, Rita Bastos, Vitor J. Martins, Viviana G. Correia, Benedita A. Pinheiro, Lisete M. Silva, Angelina S. Palma, Manuel A. Coimbra, Elisabete Coelho
Summary: Brewing practice involves reusing the same yeast for subsequent fermentations. The yeast used for Lager beer (Saccharomyces pastorianus) is widely reused without changes in fermentation performance. However, the yeast used for Ale beer (Saccharomyces cerevisiae) is either partially or not reused due to poor performance. The study found that cells modulate their wall polysaccharides to increase cell wall strength.
CARBOHYDRATE POLYMERS
(2023)
Article
Plant Sciences
Bruna B. F. Cal, Luana B. N. Araujo, Brenno M. Nunes, Claudia R. da Silva, Marcia B. N. Oliveira, Bianka O. Soares, Alvaro A. C. Leitao, Marcelo de Padula, Debora Nascimento, Douglas S. A. Chaves, Rachel F. Gagliardi, Flavio J. S. Dantas
Summary: The ethanolic extract of Petiveria alliacea L. showed cytotoxic and mutagenic effects on Saccharomyces cerevisiae, possibly mediated by oxidative lesions.
Article
Biotechnology & Applied Microbiology
Cristobal A. Onetto, Anthony R. Borneman, Simon A. Schmidt
Summary: Interactions between non-Saccharomyces yeast species and Saccharomyces cerevisiae can impact fermentation performance, with strain selection playing a key role in optimizing fermentation outcomes when using non-Saccharomyces species.
FERMENTATION-BASEL
(2021)
Article
Biotechnology & Applied Microbiology
N. Grijalva-Vallejos, K. Krogerus, J. Nikulin, F. Magalhaes, A. Aranda, E. Matallana, B. Gibson
Summary: Research on yeasts isolated from traditional chichas shows potential for their application in beer production. Yeast strains from Ecuador exhibited varying fermentation performance under different conditions, with one strain showing particular promise for commercial use.
Review
Dentistry, Oral Surgery & Medicine
Taihiko Yamaguchi, Saki Mikami, Masana Maeda, Taishi Saito, Toshinori Nakajima, Wataru Yachida, Akihito Gotouda
Summary: This article reviews the current state of portable/wearable EMG devices for assessment of bruxism. The results show that ultra-miniaturized wearable EMG devices with performance equivalent to conventional devices have been developed and used during sleep and in the daytime, with a high level of diagnostic accuracy for sleep bruxism. However, a definite cut-off value for awake bruxism has not been established.
CRANIO-THE JOURNAL OF CRANIOMANDIBULAR & SLEEP PRACTICE
(2023)
Editorial Material
Biotechnology & Applied Microbiology
Jens Nielsen
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Chemistry, Physical
Feiran Li, Le Yuan, Hongzhong Lu, Gang Li, Yu Chen, Martin K. M. Engqvist, Eduard J. Kerkhoven, Jens Nielsen
Summary: The turnover numbers (k(cat)) of enzymes are crucial for understanding cellular metabolism and physiological diversity. In this study, a deep learning approach (DLKcat) was developed to predict k(cat) values for metabolic enzymes using only substrate structures and protein sequences. The predicted k(cat) values showed good performance in a genome-scale analysis of more than 300 yeast species, and were able to explain phenotypic differences.
Article
Biochemistry & Molecular Biology
Feiran Li, Yu Chen, Mihail Anton, Jens Nielsen
Summary: Enzyme parameters are crucial for understanding, modeling, and engineering cells. Experimental measurements only cover a small portion of enzyme-compound pairs, and even less in non-model organisms. Artificial intelligence techniques have accelerated the exploration of enzyme properties by predicting them in a high-throughput manner. GotEnzymes is a comprehensive database that provides predicted enzyme parameters using AI approaches, allowing for interactive web exploration and programmatic access.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Gang Li, Filip Buric, Jan Zrimec, Sandra Viknander, Jens Nielsen, Aleksej Zelezniak, Martin K. M. Engqvist
Summary: Temperature is a crucial factor in shaping the evolution of organisms, and understanding the thermal determinants of protein sequences is significant for various biological applications. Through a deep neural network model called DeepET, we learned temperature-related protein representations that capture the structural properties affecting thermal stability. Our DeepET model outperforms classical regression models when predicting enzyme optimal catalytic temperatures and protein melting temperatures using a transfer learning approach.
Editorial Material
Biotechnology & Applied Microbiology
Gen Zou, Jens B. Nielsen, Yongjun Wei
Summary: Recent advances in synthetic biology have revolutionized mushroom farming by shifting the focus from traditional cultivation to comprehensive applications using cutting-edge biotechnologies. Promising applications in this field include precision breeding, exploration of biosynthetic gene clusters, development of mushroom chassis cells, and construction of cell factories for high-value products.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Peishun Li, Boyang Ji, Hao Luo, Daniel Sundh, Mattias Lorentzon, Jens Nielsen
Summary: Recent studies have demonstrated the beneficial effects of probiotic supplementation on bone metabolism, specifically showing that Lactobacillus reuteri ATCC PTA 6475 supplementation can reduce bone loss in older women with low bone mineral density. Secondary analysis of good responders and poor responders in a randomized controlled trial revealed that good responders had higher gene richness of gut microbiota and improved inflammatory state after 12 months of daily supplementation.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Multidisciplinary Sciences
Johan Gustafsson, Mihail Anton, Fariba Roshanzamir, Rebecka Jornsten, Eduard J. Kerkhoven, Jonathan L. Robinson, Jens Nielsen
Summary: Single-cell RNA sequencing combined with genome-scale metabolic models has the potential to unravel metabolism differences across cell types and cell states. This study develops a method for generating cell-type-specific models and evaluates the impact of RNA-Seq normalization methods on model topology. The approach successfully detects unique metabolic profiles and cancer-associated differences.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Le Yuan, Hongzhong Lu, Feiran Li, Jens Nielsen, Eduard J. Kerkhoven
Summary: In this study, a computational toolbox called HGTphyloDetect was developed, which combines high-throughput analysis with phylogenetic inference to accurately identify horizontal gene transfer (HGT) events and illustrate the transmission pathway among evolutionarily distant or closely related species. The HGTphyloDetect toolbox is user-friendly, capable of detecting HGT events with high efficiency and low false discovery rate.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Min Chen, Tingting Xie, Huan Li, Yingping Zhuang, Jianye Xia, Jens Nielsen
Summary: Supply and regulation of Gibbs free energy and precursors in cellular metabolism are essential for cellular function. In this study, we used multi-omics data under different conditions to investigate the regulation of central carbon metabolism (CCM) in yeast. We identified a metabolism-specific CCM flux regulation mechanism, which is affected by posttranslational modification and allosteric regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Analytical
Ivana Bardino Novosel, Anina Ritterband-Rosenbaum, Georgios Zampoukis, Jens Bo Nielsen, Jakob Lorentzen
Summary: This study developed and trained an image-based Convolutional Neural Network (CNN) to recognize specific movement classifiers relevant to individuals with cerebral palsy (CP). Monitoring and quantifying movement behavior in CP patients using multiple wearable sensors and CNN is of great value for improving their health outcomes.
Article
Materials Science, Multidisciplinary
Morteza Aghaee, Arun Akkala, Zulfi Alam, Rizwan Ali, Alejandro Alcaraz Ramirez, Mariusz Andrzejczuk, Andrey E. Antipov, Pavel Aseev, Mikhail Astafev, Bela Bauer, Jonathan Becker, Srini Boddapati, Frenk Boekhout, Jouri Bommer, Tom Bosma, Leo Bourdet, Samuel Boutin, Philippe Caroff, Lucas Casparis, Maja Cassidy, Sohail Chatoor, Anna Wulf Christensen, Noah Clay, William S. Cole, Fabiano Corsetti, Ajuan Cui, Paschalis Dalampiras, Anand Dokania, Gijs de Lange, Michiel de Moor, Juan Carlos Estrada Saldana, Saeed Fallahi, Zahra Heidarnia Fathabad, John Gamble, Geoff Gardner, Deshan Govender, Flavio Griggio, Ruben Grigoryan, Sergei Gronin, Jan Gukelberger, Esben Bork Hansen, Sebastian Heedt, Jesus Herranz Zamorano, Samantha Ho, Ulrik Laurens Holgaard, Henrik Ingerslev, Linda Johansson, Jeffrey Jones, Ray Kallaher, Farhad Karimi, Torsten Karzig, Cameron King, Maren Elisabeth Kloster, Christina Knapp, Dariusz Kocon, Jonne Koski, Pasi Kostamo, Peter Krogstrup, Mahesh Kumar, Tom Laeven, Thorvald Larsen, Kongyi Li, Tyler Lindemann, Julie Love, Roman Lutchyn, Morten Hannibal Madsen, Michael Manfra, Signe Markussen, Esteban Martinez, Robert McNeil, Elvedin Memisevic, Trevor Morgan, Andrew Mullally, Chetan Nayak, Jens Nielsen, William Hvidtfelt Padkaer Nielsen, Bas Nijholt, Anne Nurmohamed, Eoin OFarrell, Keita Otani, Sebastian Pauka, Karl Petersson, Luca Petit, Dmitry I. Pikulin, Frank Preiss, Marina Quintero-Perez, Mohana Rajpalke, Katrine Rasmussen, Davydas Razmadze, Outi Reentila, David Reilly, Richard Rouse, Ivan Sadovskyy, Lauri Sainiemi, Sydney Schreppler, Vadim Sidorkin, Amrita Singh, Shilpi Singh, Sarat Sinha, Patrick Sohr, Tomas Stankevic, Lieuwe Stek, Henri Suominen, Judith Suter, Vicky Svidenko, Sam Teicher, Mine Temuerhan, Nivetha Thiyagarajah, Raj Tholapi, Mason Thomas, Emily Toomey, Shivendra Upadhyay, Ivan Urban, Saulius Vaitiekenas, Kevin Van Hoogdalem, David Van Woerkom, Dmitrii V. Viazmitinov, Dominik Vogel, Steven Waddy, John Watson, Joseph Weston, Georg W. Winkler, Chung Kai Yang, Sean Yau, Daniel Yi, Emrah Yucelen, Alex Webster, Ruichen Zhao
Summary: In this study, measurements and simulations of semiconductor-superconductor heterostructure devices were conducted to observe topological superconductivity and Majorana zero modes. The devices were optimized to ensure robustness against nonuniformity and disorder. Experimental results indicate the presence of a topological superconducting phase, which is a prerequisite for experiments involving Majorana zero modes fusion and braiding.
Article
Biotechnology & Applied Microbiology
Tingting Xie, Min Chen, Jens Nielsen, Jianye Xia
Summary: The article investigates the previously unreported Crabtree effect under dynamic conditions and finds that citric acid shuttles play an important role in supporting the accumulation of alpha-ketoglutarate during the Crabtree effect.
FEMS YEAST RESEARCH
(2022)
