Article
Acoustics
Domenico De Salvio, Dario D'Orazio
Summary: This study assesses the acoustic environment quality of two historical university lecture halls before and after renovation by measuring student activity and speech levels. The results show that acoustic treatments and the redesign of the public address system using line arrays can make the environment quieter and improve the signal-to-noise ratio.
Article
Multidisciplinary Sciences
Fin J. Milder, Mandy Jongeneelen, Tina Ritschel, Pascale Bouchier, Ilona J. M. Bisschop, Martijn de Man, Daniel Veldman, Lam Le, Baerbel Kaufmann, Mark J. G. Bakkers, Jarek Juraszek, Boerries Brandenburg, Johannes P. M. Langedijk
Summary: This study stabilized influenza hemagglutinin (HA) by substituting three residues and revealed the mechanism by which these substitutions maintain the protein's structure. The findings advance our understanding of pH sensitivity in HA and propose a repair and stabilization approach that can improve the development and efficacy of influenza vaccines.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Nan-Nan Yu, Wirinthip Ketya, Eun-Ha Choi, Gyungsoon Park
Summary: This study evaluated the potential of a non-thermal atmospheric pressure plasma jet to improve cellulolytic enzyme production efficiency. The results showed that plasma treatment significantly increased the activity and protein concentration of cellulolytic enzymes. Furthermore, plasma treatment promoted the transcription and secretion of cellulolytic enzymes by enhancing the intracellular levels of NO and Ca2+.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Jian Yang, Yunzhu Xiao, Yu Liu, Ru Li, Lijuan Long
Summary: The recruitment and rapid evolution of promiscuous catalysis led to a new efficient biocatalyst for organophosphrus remediation, with a 10,000-fold increase in methyl-parathion hydrolysis and broadened substrate specificity. Structural, kinetic, and computational comparisons identified the molecular basis for the enhanced catalysis and revealed how the mutations reshaped the substrate pocket for better access to catalytic machinery.
CATALYSIS SCIENCE & TECHNOLOGY
(2021)
Article
Microbiology
Hengyi Li, Changsheng Zhang, Xi Chen, Hantian You, Luhua Lai
Summary: Researchers have developed an engineered Escherichia coli strain expressing a redesigned ribose-binding protein (RBP) that can effectively sense cadmium ions and regulate bacterial chemotaxis towards cadmium. The redesigned RBP, CdRBP1, binds to cadmium ions with high selectivity and could potentially be used in synthetic biology and environmental studies.
Review
Chemistry, Multidisciplinary
Yinglu Cui, Jinyuan Sun, Bian Wu
Summary: The increasing demands for enzymes in biotechnological applications have led to the use of computational methods in enzyme redesign. Model-based and data-driven approaches offer opportunities to achieve ambitious enzyme engineering goals in the future.
TRENDS IN CHEMISTRY
(2022)
Article
Mathematics
Marta Benkova, Dagmar Bednarova, Gabriela Bogdanovska, Marcela Pavlickova
Summary: College students have concerns about mastering the Statistics course. Scientific articles suggest that active learning methodologies can greatly improve their involvement and overall assessment results. This study is inspired by a modified Mathematics course and presents student results from both affected courses over the past 12 years. The Statistics course combines traditional teaching with active learning elements, following requests from stakeholders. The results are based on a survey of course graduates, online teaching experiences during the COVID-19 pandemic, and the introduction of active learning elements, highlighting both risks and opportunities in teaching the Statistics course.
Article
Agricultural Engineering
Shashi Kant Bhatia, Narisetty Vivek, Vinod Kumar, Neha Chandel, Meenu Thakur, Dinesh Kumar, Yung-Hun Yang, Arivalagan Pugazendhi, Gopalakrishnan Kumar
Summary: Metagenomics and directed evolution technologies have revolutionized the search for novel enzymes and improvement of existing enzymes. Despite advancements, maintaining enzyme activity during catalysis remains a challenge that researchers are working to overcome.
BIORESOURCE TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Dae-yeol Ye, Myung Hyun Noh, Jo Hyun Moon, Alfonsina Milito, Minsun Kim, Jeong Wook Lee, Jae-Seong Yang, Gyoo Yeol Jung
Summary: Unlike eukaryotic systems, bacterial hosts lack a membranous system, which is a limitation for efficient metabolic engineering. In this study, a kinetic compartmentalization strategy was used to increase substrate availability from competitive reactions for the efficient production of itaconate in E. coli.
NATURE COMMUNICATIONS
(2022)
Article
Agricultural Engineering
Jixiang Liu, Shilei Wang, Zhi Wang, Caihong Shen, Dong Liu, Xiaojuan Shen, Longfei Weng, Yun He, Simin Wang, Jiaxin Wang, Wei Zhuang, Yafan Cai, Jingliang Xu, Hanjie Ying
Summary: This study synthesized a microbial consortium to produce efficient crude enzyme for the hydrolysis of Chinese distillers' grains (CDGs). The hydrolysis damaged the lignocellulose and decreased its crystallinity. Through two pathways, the true protein content of CDGs significantly increased, with the second pathway demonstrating higher economic benefits.
BIORESOURCE TECHNOLOGY
(2023)
Review
Chemistry, Multidisciplinary
Chenyan Lv, Xiaorong Zhang, Yu Liu, Tuo Zhang, Hai Chen, Jiachen Zang, Bowen Zheng, Guanghua Zhao
Summary: Compartmentalization is a key feature of living systems, where artificial protein nanocages are being designed and constructed with advancements to serve as crucial components and carriers in the fields of nanomaterials, electrochemistry, and drug delivery.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Maria Luisa Romero, Hector Garcia Seisdedos, Beatriz Ibarra-Molero
Summary: The stabilization of natural proteins has been a long-standing goal in protein engineering. This study focused on optimizing the stability of thioredoxin by removing buried charged residues in the active site without sacrificing catalytic activity. By substituting a buried and functional group with a charged-to-hydrophobic substitution, the stability of the protein was significantly increased, although the catalytic activity was abolished. A combinatorial library of variants targeting surface residues adjacent to the active site was then designed to simulate the catalytic role of the buried ionizable group. More than 50% of the variants restored the catalytic activity to some extent. The study revealed that a single point mutation at the protein surface is sufficient to fully restore catalytic activity without sacrificing thermostability. With this method, one of the highest thermal stabilities reported for a protein with a natural occurring fold (137 degrees C) was achieved. The engineered variant also preserved catalytic activity both in vitro and in vivo.
Article
Computer Science, Software Engineering
Amina Mustansir, Khurram Shahzad, Muhammad Kamran Malik
Summary: This study proposes a NLP-based approach to identify redesign suggestions for business process redesign from end-user feedback in natural language text. The approach includes annotation guidelines for generating computational resources and is demonstrated to be effective through experiments with real-world business processes and end-user feedback.
AUTOMATED SOFTWARE ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Guangbo Yan, Xia Li, Jun Yang, Zhongchen Li, Jia Hou, Ben Rao, Yong Hu, Lixin Ma, Yaping Wang
Summary: The study successfully synthesized ATP and SAM using engineered multidomain scaffold proteins to lower production costs and achieve efficient conversion through multi-enzyme catalysis. Complex 1 and complex 2 were utilized to increase ATP and SAM production, respectively.
Article
Chemistry, Physical
Elizabeth A. Osifalujo, Bailey N. Rutkowski, Louis R. Satterwhite, Phillip C. Betts, Angel K. Nkosi, Jordan T. Froese
Summary: Dioxygenase variants with expanded substrate scopes have been developed through rational enzyme engineering, overcoming the limitations of Rieske dioxygenases in terms of substrate scopes and selectivity. These catalysts have facilitated the production of novel and valuable chiral metabolites.
CATALYSIS SCIENCE & TECHNOLOGY
(2023)
Article
Biochemical Research Methods
Tobias Marschall, Manja Marz, Thomas Abeel, Louis Dijkstra, Bas E. Dutilh, Ali Ghaffaari, Paul Kersey, Wigard P. Kloosterman, Veli Makinen, Adam M. Novak, Benedict Paten, David Porubsky, Eric Rivals, Can Alkan, Jasmijn A. Baaijens, Paul I. W. De Bakker, Valentina Boeva, Raoul J. P. Bonnal, Francesca Chiaromonte, Rayan Chikhi, Francesca D. Ciccarelli, Robin Cijvat, Erwin Datema, Cornelia M. Van Duijn, Evan E. Eichler, Corinna Ernst, Eleazar Eskin, Erik Garrison, Mohammed El-Kebir, Gunnar W. Klau, Jan O. Korbel, Eric-Wubbo Lameijer, Benjamin Langmead, Marcel Martin, Paul Medvedev, John C. Mu, Pieter Neerincx, Klaasjan Ouwens, Pierre Peterlongo, Nadia Pisanti, Sven Rahmann, Ben Raphael, Knut Reinert, Dick de Ridder, Jeroen de Ridder, Matthias Schlesner, Ole Schulz-Trieglaff, Ashley D. Sanders, Siavash Sheikhizadeh, Carl Shneider, Sandra Smit, Daniel Valenzuela, Jiayin Wang, Lodewyk Wessels, Ying Zhang, Victor Guryev, Fabio Vandin, Kai Ye, Alexander Schonhuth
BRIEFINGS IN BIOINFORMATICS
(2018)
Article
Biochemistry & Molecular Biology
Florien A. Gorter, Martijn F. L. Derks, Joost van den Heuvel, Mark G. M. Aarts, Bas J. Zwaan, Dick de Ridder, J. Arjan G. M. de Visser
MOLECULAR BIOLOGY AND EVOLUTION
(2017)
Article
Plant Sciences
Harm Nijveen, Wilco Ligterink, Joost J. B. Keurentjes, Olivier Loudet, Jiao Long, Mark G. Sterken, Pjotr Prins, Henk W. Hilhorst, Dick de Ridder, Jan E. Kammenga, Basten L. Snoek
Article
Biochemical Research Methods
Ehsan Motazedi, Dick de Ridder, Richard Finkers, Samantha Baldwin, Susan Thomson, Katrina Monaghan, Chris Maliepaard
Article
Plant Sciences
Sander Y. A. Rodenburg, Michael F. Seidl, Dick De Ridder, Francine Govers
MOLECULAR PLANT PATHOLOGY
(2018)
Article
Plant Sciences
Sevgin Demirci, Sander A. Peters, Dick de Ridder, Aalt D. J. van Dijk
Article
Biochemical Research Methods
Siavash Sheikhizadeh Anari, Dick de Ridder, M. Eric Schranz, Sandra Smit
BMC BIOINFORMATICS
(2018)
Article
Biochemistry & Molecular Biology
Richard Janissen, Mathia M. A. Arens, Natalia N. Vtyurina, Zaida Rivai, Nicholas D. Sunday, Behrouz Eslami-Mossallam, Alexey A. Gritsenko, Liedewij Laan, Dick de Ridder, Irina Artsimovitch, Nynke H. Dekker, Elio A. Abbondanzieri, Anne S. Meyer
Editorial Material
Biotechnology & Applied Microbiology
Dick de Ridder
MICROBIAL BIOTECHNOLOGY
(2019)
Article
Biochemical Research Methods
Miguel Correa Marrero, Richard G. H. Immink, Dick de Ridder, Aalt D. J. van Dijk
Article
Biochemical Research Methods
Christian Gross, Dick de Ridder, Marcel Reinders
BMC BIOINFORMATICS
(2018)
Article
Biotechnology & Applied Microbiology
Sven Warris, Elio Schijlen, Henri van de Geest, Rahulsimham Vegesna, Thamara Hesselink, Bas te Lintel Hekkert, Gabino Sanchez Perez, Paul Medvedev, Kateryna D. Makova, Dick de Ridder
Article
Biochemical Research Methods
Ehsan Motazedi, Richard Finkers, Chris Maliepaard, Dick de Ridder
BRIEFINGS IN BIOINFORMATICS
(2018)
Article
Agriculture, Dairy & Animal Science
Martijn F. L. Derks, Hendrik-Jan Megens, Mirte Bosse, Jeroen Visscher, Katrijn Peeters, Marco C. A. M. Bink, Addie Vereijken, Christian Gross, Dick de Ridder, Marcel J. T. Reinders, Martien A. M. Groenen
GENETICS SELECTION EVOLUTION
(2018)
Article
Microbiology
Irma M. H. van Rijswijck, Martijn F. L. Derks, Tjakko Abee, Dick de Ridder, Eddy J. Smid
GENOME ANNOUNCEMENTS
(2017)