Article
Mathematical & Computational Biology
Daniel Brunnsaker, Gabriel K. Reder, Nikul K. Soni, Otto I. Savolainen, Alexander H. Gower, Ievgeniia A. Tiukova, Ross D. King
Summary: In this study, constrained dynamical flux balance analysis (dFBA) was used to select ten regulatory deletant strains. These strains were then analyzed using untargeted metabolomics to understand their role in metabolic reconfiguration. The results showed that metabolomics can provide insights into cellular transformations and the biological consequences of gene deletion. The study also demonstrated that untargeted metabolomics is a useful tool for guiding high-throughput model improvement and is well-suited for automated approaches.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Paul Cachera, Helen Olsson, Hilde Coumou, Mads L. Jensen, Benjamin J. Sanchez, Tomas Strucko, Marcel van den Broek, Jean-Marc Daran, Michael K. Jensen, Nikolaus Sonnenschein, Michael Lisby, Uffe H. Mortensen
Summary: CRI-SPA allows simple and rapid transfer of chromosomal genetic features between different strains of Saccharomyces cerevisiae. It is highly efficient and reproducible, and even allows marker-free transfer of genetic features. The simplicity, speed, and reliability of CRI-SPA make it a versatile tool for studying biological processes at a systems level.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Yingying Wang, Zhen Zhu, Ke Liu, Qin Xiao, Yangye Geng, Feng Xu, Shuiping Ouyang, Ke Zheng, Yimin Fan, Nan Jin, Xiangwei Zhao, Mario A. Marchisio, Dejing Pan, Qing-An Huang
Summary: In this study, a high-throughput microfluidic chip for diploid yeast long-term culturing, optical inspection, and cell-aging analysis was developed. The chip features delicate microstructures to ensure cell stability and alleviate stress. Using this chip, the researchers were able to track the replicative lifespan and budding time interval of diploid yeast cells and observe cell desynchronization during aging.
JOURNAL OF NANOBIOTECHNOLOGY
(2022)
Article
Biology
Brooke D. Huisman, Zheng Dai, David K. Gifford, Michael E. Birnbaum, Satyajit Rath
Summary: T cells play a crucial role in adaptive immune response by recognizing peptide antigens presented on cell surfaces by MHC proteins. A yeast display-based platform has been developed to assess the binding of user-defined peptides in a high-throughput manner. The approach was used to evaluate the binding of SARS-CoV-2 and dengue virus peptides to human class II MHCs, revealing both consistent and experimentally validated computational false positives and false negatives. This approach can complement current datasets and predictions, providing insights into viral conservation and MHC binding.
Article
Biotechnology & Applied Microbiology
Steven A. van der Hoek, Matej Rusnak, Guokun Wang, Lyubomir Dimitrov Stanchev, Luana de Fatima Alves, Mathew M. Jessop-Fabre, Kalaivani Paramasivan, Irene Hjorth Jacobsen, Nikolaus Sonnenschein, Jose L. Martinez, Behrooz Darbani, Douglas B. Kell, Irina Borodina
Summary: Ergothioneine is a rare sulfur-containing amino acid with potent antioxidant properties. Engineered yeast strains can be used to produce high levels of ergothioneine using glucose as the carbon source. Metabolic engineering and medium optimization are effective strategies to improve ergothioneine production.
METABOLIC ENGINEERING
(2022)
Article
Microbiology
Ludimila Dias Almeida, Ali Salim Faraj Silva, Daniel Calixto Mota, Adrielle Ayumi Vasconcelos, Antonio Pedro Camargo, Gabriel Silva Pires, Monique Furlan, Helena Martins Ribeiro da Cunha Freire, Angelica Hollunder Klippel, Suelen Fernandes Silva, Cleslei Fernando Zanelli, Marcelo Falsarella Carazzolle, Stephen G. Oliver, Elizabeth Bilsland
Summary: By utilizing a library of double transporter deletion strains, potential drug import and export routes can be rapidly identified, aiding in determining the necessary chemical groups for transport via specific carriers. This information can lead to the development of drugs with optimal absorption and reduced likelihood of resistance.
Article
Biochemical Research Methods
Lorenzo Favilli, Corey M. Griffith, Emma L. Schymanski, Carole L. Linster
Summary: Identifying metabolites in model organisms is critical for understanding biology. Stable isotope labelling is a useful strategy for distinguishing biologically relevant features from background signals. Researchers developed a high-throughput metabolomics approach using stable isotope labelling, resulting in the successful annotation of 198 metabolites.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Engineering, Chemical
Wei-Yang Wang, Shi-Hua Wu, Yuan-Han Xie, Miao Zhong, Man-Li Wei, Ze-Yang Li, Xiu-Feng Long, Fu-Xing Niu
Summary: This study successfully established a Saccharomyces cerevisiae mutant library capable of tolerating high sucrose concentration, leading to increased ethanol yield and improved sucrose utilization efficiency.
Review
Biotechnology & Applied Microbiology
P. W. J. Labuschagne, B. Divol
Summary: Thiamine is crucial for yeast growth and the production of flavor compounds during alcoholic fermentation, with its concentration affecting fermentation kinetics and wine sensory properties. Its utilization and metabolism in Saccharomyces cerevisiae are influenced by various factors, making it important to optimize thiamine concentrations for industrial yeast applications.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
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
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.
Review
Biochemistry & Molecular Biology
Laura Vanderwaeren, Ruveyda Dok, Karin Voordeckers, Sandra Nuyts, Kevin J. Verstrepen
Summary: Yeast is an important enzyme source for bread and beer production and is an ideal model organism for studying eukaryotic cell biology and genetics. This review discusses the characteristics that make yeast such a widely used model organism, with a focus on the DNA damage response pathway as an example of its contribution to elucidating highly conserved biological processes. Differences in the DNA damage response of yeast and humans are also highlighted, along with the challenges of using yeast as a model system.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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
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.
Article
Plant Sciences
Patrick Z. Ellsworth, Max J. Feldman, Ivan Baxter, Asaph B. Cousins
Review
Plant Sciences
Ivan Baxter
CURRENT OPINION IN PLANT BIOLOGY
(2020)
Article
Plant Sciences
Lauren Whitt, Felipe Klein Ricachenevsky, Greg Ziegler Ziegler, Stephan Clemens, Elsbeth Walker, Frans J. M. Maathuis, Philip Kear, Ivan Baxter
Article
Biochemistry & Molecular Biology
David M. Goad, Ivan Baxter, Elizabeth A. Kellogg, Kenneth M. Olsen
Summary: The different ecotypes of seashore paspalum have varying adaptive strategies, likely influenced by clonal propagation, ploidy variation, and interspecific hybridization. The coarse-textured ecotype appears to be a hybrid of fine-textured seashore paspalum and another Paspalum species, while triploid genotypes show variation in subgenome composition that may be associated with local ocean salinity levels and play a role in local adaptation.
Article
Plant Sciences
Parthiban Thathapalli Prakash, Darshi Banan, Rachel E. Paul, Maximilian J. Feldman, Dan Xie, Luke Freyfogle, Ivan Baxter, Andrew D. B. Leakey
Summary: Mechanistic modeling suggests that reducing stomatal conductance can enhance water use efficiency in C-4 crops. Genetic variation in stomatal density and canopy temperature was evaluated in Setaria, a C-4 genus. Multiple QTL were identified for stomatal density and canopy temperature, indicating a common genetic architecture between stomatal patterning and WUE.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Plant Sciences
Joanna Friesner, Adan Colon-Carmona, Alexandra M. Schnoes, Anna Stepanova, Grace Alex Mason, Gustavo C. Macintosh, Hemayat Ullah, Ivan Baxter, Judy Callis, Kimberly Sierra-Cajas, Kiona Elliott, Elizabeth S. Haswell, Maria Elena Zavala, Mary Wildermuth, Mary Williams, Mentewab Ayalew, Natalie Henkhaus, Nathanael Prunet, Peggy G. Lemaux, Ramin Yadegari, Rick Amasino, Roger Hangarter, Roger Innes, Siobhan Brady, Terri Long, Terry Woodford-Thomas, Victoria May, Ying Sun, Jose R. Dinneny
Summary: Population growth and climate change will impact food security and the environment, calling for a diverse community of plant science professionals to be trained. Engaging students and the public in the wonder of plants and science requires efforts utilizing technology and new funding models. This symposium aimed to re-envision how outreach programs are funded, evaluated, acknowledged, and shared within the plant science community, with the goal of generating a roadmap for future efforts.
Article
Genetics & Heredity
Matheus Baseggio, Matthew Murray, Di Wu, Gregory Ziegler, Nicholas Kaczmar, James Chamness, John P. Hamilton, C. Robin Buell, Olena K. Vatamaniuk, Edward S. Buckler, Margaret E. Smith, Ivan Baxter, William F. Tracy, Michael A. Gore
Summary: The study found a probable pleiotropic association of zinc and iron concentrations with the gene nas5 in sweet corn kernels, and highlighted the potential role of heavy metal ATPase3 (hma3) in cadmium accumulation in seeds. Low cadmium selection was shown not to affect zinc levels in fresh kernels.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Crystal A. Sorgini, Lucas M. Roberts, Madsen Sullivan, Asaph B. Cousins, Ivan Baxter, Anthony J. Studer
Summary: Leaf stable carbon isotope composition (δ C-13) is a potential tool for breeders, but the underlying mechanisms in C-4 plants are not clear. Significant QTL for leaf δ C-13 were identified in maize, including one region containing an Erecta-like gene known to regulate transpiration efficiency and leaf δ C-13 in Arabidopsis. Data shows no relationship between δ C-13 and specific leaf area (SLA), with only a weak correlation between molybdenum and δ C-13 detected.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
David M. Goad, Elizabeth A. Kellogg, Ivan Baxter, Kenneth M. Olsen
Summary: Most plant species, including crops, struggle in salt-affected soils due to high sodium levels disrupting water and nutrient uptake. Halophytes have evolved adaptations to overcome these challenges, offering insights into salt tolerance mechanisms and genes transferable to crops. Differences in ion accumulation between populations of halophytic species may reflect locally adapted responses to salt stress.
G3-GENES GENOMES GENETICS
(2021)
Editorial Material
Plant Sciences
Ivan R. Baxter
Editorial Material
Multidisciplinary Sciences
Rocio Deanna, Bethann Garramon Merkle, Kwok Pan Chun, Deborah Navarro-Rosenblatt, Ivan Baxter, Nora Oleas, Alejandro Bortolus, Patricia Geesink, Luisa Diele-Viegas, Valeria Aschero, Maria Jose de Leone, Sonia Oliferuk, Rui Zuo, Andrea Cosacov, Mariana Grossi, Sandra Knapp, Alicia Lopez-Mendez, Elina Welchen, Pamela Ribone, Gabriela Auge
Summary: Mentor relationships are crucial for the retention, success, and well-being of women and underrepresented minority scientists in academia. A diverse network of mentors can support the achievement of long-term career goals, advancement, and retention of both mentors and mentees, thereby enhancing diversity, equity, and inclusion initiatives.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Ben F. Lucker, Joshua A. Temple, Nicolas L. Panchy, Urs F. Benning, Jacob D. Bibik, Peter G. Neofotis, Joseph C. Weissman, Ivan R. Baxter, Shin-Han Shiu, David M. Kramer
Summary: This study demonstrates an approach to produce hybrid algal strains with increased photosynthetic productivity through breeding and competition methods. The results indicate that the green alga Chlamydomonas reinhardtii has untapped directed evolution capacity that can be harnessed to improve photosynthetic efficiency and biomass production. By mapping selection-enriched genomic loci, further insights into the genetic and mechanistic basis of photosynthetic productivity can be obtained.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Editorial Material
Plant Sciences
Ivan Baxter
Article
Multidisciplinary Sciences
Takeshi Yoshihara, Nathan D. Miller, Fernando A. Rabanal, Hannah Myles, Il-Youp Kwak, Karl W. Broman, Boris Sadkhin, Ivan Baxter, Brian P. Dilkes, Matthew E. Hudson, Edgar P. Spalding
Summary: By conducting large-scale experiments on two plant species, we have discovered four naturally varying components of a conserved process in gravitropism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Meng Li, Sergio Perez-Limon, M. Rosario Ramirez-Flores, Benjamin Barrales-Gamez, Marco Antonio Meraz-Mercado, Gregory Ziegler, Ivan Baxter, Victor Olalde-Portugal, Ruairidh J. H. Sawers
Summary: This study evaluated the effect of symbiotic relationships on the concentration of 20 mineral elements in the leaves and grain of maize. The compatibility of AMF was associated with differences in element concentrations, suggesting genotypic variations in the impact of AMF on plant nutrition.
Article
Chemistry, Analytical
Michelle Buoso, Beatrice Campanella, Massimo Onor, Emanuela Pitzalis, Alessandro D'Ulivo
Summary: The use of BH intermediates as derivatization reagents significantly improves the tolerance to interference from transition metal ions in the generation of SbH3 and BiH3, and shows high tolerance in a wide range of acidity. The method has been successfully applied to the determination of Sb and Bi in complex samples, providing further understanding of the chemical behavior of borohydrides.
JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY
(2024)
Article
Chemistry, Analytical
Chao-Feng Li, Xuan-Ce Wang, Zhu-Yin Chu, Peng Peng
Summary: Thermal ionization mass spectrometry (TIMS) is the standard method for obtaining precise Sr-87/Sr-86 isotopic ratios. However, our developed hydrofluoric acid coprecipitation method offers a low-cost, rapid, simple, and high-throughput alternative for analyzing red wine samples, effectively eliminating isobaric interference and matrix element inhibition.
JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY
(2024)
Article
Chemistry, Analytical
Ivan B. Krstic, Bratislav M. Obradovic, Milorad M. Kuraica
Summary: This paper presents the spatio-temporal dynamics of a Grimm-type microsecond pulsed glow discharge (mu PGD) in argon at 6 mbar. The occurrence of a high current peak during the discharge ignition is analyzed and the importance of displacement current is emphasized. The development of electron excitation temperature for argon atoms and ions at various distances from the cathode is measured. The spatio-temporal evolution of selected spectral lines of argon and copper atoms and ions is analyzed during different phases of the discharge. The results suggest that the behavior of spectral line emissions differs between the pre-peak and afterglow periods, with different lines reaching maximum intensity during these phases. The appearance time and decay time of the afterpeak are shorter for ions than for atoms. These findings are explained in terms of three-body recombination processes and ion mobilities.
JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY
(2024)
Article
Chemistry, Analytical
Qiuyun Wang, Anmin Chen, Xun Gao
Summary: In this paper, the combination of Tesla coil discharge (TCD) and laser-induced breakdown spectroscopy (LIBS) was used to enhance the emission of Al atomic lines and AlO molecular bands. The optimized distance between the TCD tip and the sample surface was found to be 5 mm, and the optimal laser energy was 25.1 mJ. Furthermore, TCD-SELIBS showed lower limits of detection (LoDs) for Cr and Pb elements compared to surface enhanced LIBS (SELIBS). The combination of TCD and LIBS is a promising technology for high-sensitivity analysis of heavy metals in water, with the advantages of simplicity, low cost, ease of operation, industrialization, and commercialization.
JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY
(2024)
Article
Chemistry, Analytical
Yanwen Tang, Tingguang Lan, Jianfeng Gao, Zhongjie Bai, Xiaowen Huang, Junjie Han, Na Liu
Summary: Titanium is an important metal widely used in various industries. Ilmenite minerals are the main source of titanium metal and can be found in igneous and metamorphic rocks as well as different types of deposits. To accurately determine U-Pb ages of ilmenite, a new calibration method and appropriate reference materials are urgently needed. Laser ablation sector field inductively coupled plasma mass spectrometry has been used to minimize matrix effects and zircon 91500 has been identified as a suitable reference material for measuring the Pb/U ratio in ilmenite. The direct calibration method using zircon 91500 as an external standard has been found to be effective for in situ U-Pb dating of ilmenite samples under different ablation settings.
JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY
(2024)