Article
Biochemistry & Molecular Biology
Taylor B. Dolberg, Anthony T. Meger, Jonathan D. Boucher, William K. Corcoran, Elizabeth E. Schauer, Alexis N. Prybutok, Srivatsan Raman, Joshua N. Leonard
Summary: Splitting bioactive proteins into conditionally reconstituting fragments is powerful, but split proteins often exhibit high propensity to reconstitute, limiting their utility. This new technology, based on computational design strategy and experimental evaluation of mutants, can effectively address split protein design challenges.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Oana N. Antonescu, Andreas Rasmussen, Nicole A. M. Damm, Ditte F. Heidemann, Roman Popov, Alexander Nesterov-Mueller, Kristoffer E. Johansson, Jakob R. Winther
Summary: A novel platform for functional analysis of leave-one-out split fluorescent proteins (LOO-FPs) was established and validated, with over 12,000 variants of β-strand split fragment screened using high-density peptide microarrays. The effects of peptide length and different linkers on solid support, as well as amino acid substitutions on each position, were studied. Results indicate that the signal intensity on the peptide microarray faithfully reflects the binding affinity between split fragments, with a 9-fold higher affinity peptide identified.
Article
Virology
Jieshi Yu, Chen Huang, Zhao Wang, Radhey S. Kaushik, Zizhang Sheng, Feng Li, Dan Wang
Summary: In this study, a method to measure and identify the interaction of ZIKV capsid proteins was developed, and peptides that can inhibit the multimerization of ZIKV capsid were identified. This study is of great importance for the future discovery of ZIKV assembly inhibitors.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Virology
Tucker Hansen, Jodie Baris, Min Zhao, Richard E. Sutton
Summary: This study developed both cell-intact and cell-free systems that can reliably, rapidly, and reproducibly quantify Rev-Rev interaction. The results of mutant Revs tested in the cell-based assay correlated strongly with the results of a functional Rev trans-complementation infectivity assay. These assays may be useful in screening and identifying compounds that inhibit Rev function on a high throughput basis.
Article
Materials Science, Multidisciplinary
Yu He, Xin Li, Jiong Yang, Weimin Li, Gang Li, Tingjun Wu, Wenjie Yu, Lei Zhu
Summary: Current-induced spin polarization or electric-field-controlled energy splitting has potential applications in spintronic devices such as spin-orbit torque devices and spin transistors. In this study, a high-throughput workflow using the three-point-spin-texture method was designed to screen for materials with large spin-split energy. A total of 440 Rashba, 411 Dresselhaus, and 469 Zeeman-type candidate materials were identified. The spin-split energies of KSnSb, TaSi2, and PtN2 were found to be 0.19 eV, 0.82 eV, and 0.55 eV, respectively. This work expands the materials database for spintronic devices and facilitates further experimental research.
RESULTS IN PHYSICS
(2023)
Article
Plant Sciences
Kazusato Oikawa, Keiko Midorikawa, Yutaka Kodama, Keiji Numata
Summary: Organelles contribute to plant growth through their movements and interactions. In this study, a high-throughput method was developed to quantitatively evaluate the interactions between peroxisomes and chloroplasts in living plant cells using distance transformation algorithm and high-resolution 3D fluorescent images. The results showed that the distance between peroxisomes and chloroplasts was shorter in the light conditions.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Chemistry, Analytical
Parisa Ghanavatian, Hossein Salehi-Sedeh, Farangis Ataei, Saman Hosseinkhani
Summary: Different programed cell death (PCD) modalities involve protein-protein interactions in large complexes. Tumor necrosis factor alpha (TNF alpha) stimulated assembly of receptor-interacting protein kinase 1 (RIPK1)/Fas-associated death domain (FADD) interaction forms Ripoptosome complex that may cause either apoptosis or necroptosis. This reporter assay might be used to evaluate basic aspects of this interaction as well as for screening of necroptosis and apoptosis targeting drugs with potential therapeutic application.
Article
Biology
Giacomo Paonessa, Giulia Siciliano, Rita Graziani, Cristiana Lalli, Ottavia Cecchetti, Cristina Alli, Roberto La Valle, Alessia Petrocchi, Alessio Sferrazza, Monica Bisbocci, Mario Falchi, Carlo Toniatti, Alberto Bresciani, Pietro Alano
Summary: High-throughput screening and validation assays have identified potential antimalarial drugs that can kill both sexual and asexual blood stages of Plasmodium falciparum, thus blocking parasite transmission through mosquitoes.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Hau B. Nguyen, Thomas C. Terwilliger, Geoffrey S. Waldo
Summary: Research has shown the utility of split fluorescent proteins for large scale protein labeling in cells, but efficient split fluorescent proteins that do not cross-react are needed for multiplexing experiments. The newly proposed split ccGFP from C. californica complements up to threefold faster compared to the original A. victoria split GFP, enabling multiplexed labeling with existing A. victoria split YFP and CFP.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Kathryn E. Luker, Gary D. Luker
Summary: This study reveals the regulation of PKM2 and cellular metabolism by CXCL12 signaling through CXCR4 and ACKR3, leading to the dissociation of PKM2 from beta-arrestin 2 and a shift in its oligomerization state.
Article
Cell Biology
Yilin He, Jiayang Gao, Mengqian Luo, Caiji Gao, Youshun Lin, Hiu Yan Wong, Yong Cui, Xiaohong Zhuang, Liwen Jiang
Summary: This study identified and characterized two Arabidopsis SNAREs, AT4G15780/VAMP724 and AT1G04760/VAMP726, involved in plant autophagy. Phenotypic analysis showed that mutants of VAMP724 and VAMP726 are sensitive to nutrient-starved conditions. Further experiments demonstrated that VAMP724 and VAMP726 regulate autophagosome formation likely working together with ATG9 in Arabidopsis.
Article
Biochemistry & Molecular Biology
Katja F. Hellendahl, Maryke Fehlau, Sebastian Hans, Peter Neubauer, Anke Kurreck
Summary: The study introduces a luciferase-based assay for the detection of NK activity, which was validated in a 96-well plate format. The high-throughput assay showed comparable results to HPLC analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Siddhant Chaturvedi, Neha Thakur, Shahirina Khan, Mithilesh Kumar Sardar, Alka Jangra, Siddharth Tiwari
Summary: In this study, the banana cultivar Nendran was found to have the highest concentration of ascorbic acid (AsA). Five genes related to AsA synthesis were identified from the banana genome database, and three of them were shown to significantly enhance AsA levels in plant leaves through overexpression in Arabidopsis thaliana. The findings of this study have important implications for the development of AsA-rich plants, particularly in developing countries where staple foods are crucial.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Multidisciplinary
Emily R. Ruskowitz, Brizzia G. Munoz-Robles, Alder C. Strange, Carson H. Butcher, Sebastian Kurniawan, Jeremy R. Filteau, Cole A. DeForest
Summary: Proteins play a crucial role in regulating various biological processes, and new techniques are needed to effectively control protein activity in living systems and biomaterials to study cell signaling and guide biological fate. This study presents a generalizable strategy for activating protein function with precise spatiotemporal control. By using a genetically encoded and light-activated SpyLigation (LASL), bioactive proteins can be reassembled from non-functional fragments with the help of cytocompatible light. The researchers demonstrate protein activation and subcellular localization control in solution, biomaterials, and living mammalian cells. These photoclick-based optogenetic approaches are expected to greatly contribute to understanding and directing complex cellular fates in both time and three-dimensional space.
Review
Chemistry, Multidisciplinary
Romany J. McLure, Sheena E. Radford, David J. Brockwell
Summary: Directed evolution is a powerful tool for engineering new functions in biomolecules and gaining insights into protein behavior. It accelerates the process of natural evolution through multiple rounds of gene diversification and selection.
TRENDS IN CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Marina Suekawa, Yukichi Fujikawa, Muneharu Esaka
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2018)
Article
Cell Biology
Misoon Park, Cornelia Krause, Matthias Karnahl, Ilka Reichardt, Farid El Kasmi, Ulrike Mayer, York-Dieter Stierhof, Ulrike Hiller, Georg Strompen, Martin Bayer, Marika Kientz, Masa H. Sato, Marc T. Nishimura, Jeffery L. Dangl, Anton A. Sanderfoot, Gerd Juergens
DEVELOPMENTAL CELL
(2018)
Article
Plant Sciences
Narender Kumar, Renee Dale, Daniel Kemboi, Elizabeth A. Zeringue, Naohiro Kato, John C. Larkin
Article
Multidisciplinary Sciences
Koh Yamada, Michiko Sasabe, Yukichi Fujikawa, Takuji Wada, Rumi Tominaga-Wada
Article
Biochemistry & Molecular Biology
Yukichi Fujikawa, Marina Suekawa, Satoshi Endo, Youjirou Fukami, Shoji Mano, Mikio Nishimura, Muneharu Esaka
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2019)
Article
Biochemical Research Methods
Takayuki Saitoh, Yasumitsu Seto, Yukichi Fujikawa, Noriaki Iijima
ANALYTICAL BIOCHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Renee Dale, Yuki Ohmuro-Matsuyama, Hiroshi Ueda, Naohiro Kato
Article
Plant Sciences
Kai Wang, Ruth W. Ndathe, Narender Kumar, Elizabeth A. Zeringue, Naohiro Kato, John C. Larkin
Article
Biotechnology & Applied Microbiology
Tsuyoshi Tanaka, Yoshiaki Maeda, Noraiza Suhaimi, Chiharu Tsuneoka, Tomomi Nonoyama, Tomoko Yoshino, Naohiro Kato, Kyle J. Lauersen
Summary: The study found the phenomenon of intron mediated enhancement (IME) in the oleaginous diatom, Fistulifera solaris, showing that inclusion of introns in heterologous sequences can significantly increase transgene expression, leading to enhanced resistance and selection.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2021)
Article
Cell Biology
Naohiro Kato, Gabela Nelson, Kyle J. Lauersen
Summary: Fatty acids play a crucial role in biological processes, but their metabolism in microalgae, particularly in Chlamydomonas reinhardtii, differs from animals and yeast. Recent studies on C. reinhardtii suggest that lipid turnover is mainly focused on recycling acyl chains within membranes rather than beta-oxidation for energy production. This preference for membrane turnover over beta-oxidation is highlighted through fluorescence microscopy analysis, which also reveals the detoxifying capability of the alga towards hydrogen peroxide produced during beta-oxidation.
Article
Multidisciplinary Sciences
Hee Jin Kim, Naohiro Kato, Ruth Ndathe, Gregory N. Thyssen, Don C. Jones, Harish H. Ratnayaka
Summary: The study found that under optimal temperature, the im mutant displayed similar photosynthetic performance as TM-1, but under high temperature stress, the im mutant reduced photosynthesis by disproportionately decreasing stomatal conductance. Transcriptomic analysis showed differences in expression of heat stress response genes between NIL leaves, suggesting that mitochondrial complex I activity is required for optimal photosynthetic performance and adaptation to high temperature stress.
Article
Plant Sciences
Ruth Ndathe, Renee Dale, Naohiro Kato
Summary: The ABA signaling pathway is crucial for plants to defend against drought stress. Recent research suggests that ABA alters the expression kinetics of over 6,500 genes through ABF-ABRE associations. This study constructed a model that highlights the importance of a single ABRE in the ABA gene regulatory network.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Cell Biology
Naohiro Kato, Clayton McCuiston, Kimberly A. Szuska, Kyle J. Lauersen, Gabela Nelson, Alexis Strain
Summary: Chlamydomonas reinhardtii preferentially sequesters lipid acyl chains as a means to rapidly rebuild its membranes. It has a complete set of peroxisome biogenesis factors and can simultaneously carry diverse populations of peroxisomes, modulating their contents based on light conditions. These results support the idea that lipid biosynthesis, rather than beta-oxidation, is the primary metabolic preference for fatty acids in the alga.
Article
Multidisciplinary Sciences
Gabela Nelson, Alexis Strain, Atsuko Isu, Alireza Rahnama, Ken-ichi Wakabayashi, Adam T. T. Melvin, Naohiro Kato
Summary: The mechanisms governing chemotaxis in Chlamydomonas reinhardtii are still poorly understood. In this study, a modified Petri dish assay revealed a novel mechanism for ammonium chemotaxis in Chlamydomonas. Light exposure enhanced the chemotactic response, but phototaxis-incompetent mutant strains still exhibited normal chemotaxis. Collective migration was observed during chemotaxis but not phototaxis. The AGG1 protein was found to suppress collective migration during chemotaxis.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Takayuki Kondo, Yukichi Fujikawa, Muneharu Esaka
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2017)