Article
Biochemistry & Molecular Biology
Matteo Bisardi, Juan Rodriguez-Rivas, Francesco Zamponi, Martin Weigt
Summary: The study proposes stochastic models of experimental protein evolution based on reconstructed data-driven fitness landscapes, predicting important features of experimentally evolved sequence libraries. It showcases the potential of the approach in determining protein structure from epistasis signals in experimental sequence libraries, offering a quantitative explanation for outcomes of recent experiments and enabling forecasts for future evolution experiments.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Shun-ichi Tanaka, Minami Tsutaki, Seira Yamamoto, Hayate Mizutani, Ryo Kurahashi, Azumi Hirata, Kazufumi Takano
Summary: The study investigated random mutations in both conserved and non-conserved sites of two thermostable proteins. The results indicated that some conserved sites showed resistance to mutation, while some non-conserved sites lost enzymatic activity at high temperatures.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biology
Austin H. Patton, Emilie J. Richards, Katelyn J. Gould, Logan K. Buie, Christopher H. Martin
Summary: This study investigates the complex relationship between fitness and genotype or phenotype using the adaptive radiation of pupfishes as a model system. By analyzing genomic data and conducting field experiments, the researchers identify single nucleotide polymorphisms associated with fitness and construct genotypic fitness networks. They find that introgression and de novo mutations can alter the shape of the fitness landscape and facilitate the evolution of novelty.
Article
Physics, Fluids & Plasmas
Anna Frishman, Tobias Grafke
Summary: The transition to turbulence in pipes is characterized by a coexistence of laminar and turbulent states. At the lower end of the transition, localized turbulent pulses, called puffs, can be excited. Puffs can decay when rare fluctuations drive them close to an edge state lying at the phase-space boundary with laminar flow. At higher Reynolds numbers, homogeneous turbulence dominates over laminar flow. This study completes the landscape of localized states and suggests the existence of an antipuff and a related edge state called gap-edge, which mirror the puff and edge state. The observations of laminar gaps forming within homogeneous turbulence can be identified as antipuffs nucleating and decaying through the gap edge. The study also discusses alternative bifurcation diagrams that may be relevant for wall-bounded flows other than straight pipes.
Article
Multidisciplinary Sciences
Jennifer M. G. Shelton, Johanna Rhodes, Christopher B. Uzzell, Samuel Hemmings, Amelie P. Brackin, Thomas R. Sewell, Asmaa Alghamdi, Paul S. Dyer, Mark Fraser, Andrew M. Borman, Elizabeth M. Johnson, Frederic B. Piel, Andrew C. Singer, Matthew C. Fisher
Summary: Using a citizen science approach, researchers found that at least 40% of azole-resistant A. Fumigatus infections are acquired from environmental exposures. The study also revealed that hotspots and coldspots of aerosolized azole-resistant spores were not stable between seasons. The ubiquity of this measured exposure highlights the importance of determining sources of azole-resistant A. fumigatus to reduce treatment failure in patients with aspergillosis.
Article
Chemistry, Medicinal
Niklas E. Siedhoff, Alexander-Maurice Illig, Ulrich Schwaneberg, Mehdi D. Davari
Summary: Data-driven strategies in protein engineering are gaining attention, with PyPEF framework combining machine learning and statistical physics techniques to efficiently predict protein sequence fitness and improve screening efficiency.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Multidisciplinary Sciences
Wei Wei, Daniel J. Gaffney, Patrick F. Chinnery
Summary: Analysis of mtDNA in a large number of iPSC lines reveals that iPSC-specific mutations affect a higher proportion of mtDNA molecules, favoring non-synonymous protein-coding and tRNA variants. Additionally, stable heteroplasmy in mtDNA variants during cell differentiation influences mitochondrial metabolism and cell differentiation.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Samuel O'Donnell, Jia-Xing Yue, Omar Abou Saada, Nicolas Agier, Claudia Caradec, Thomas Cokelaer, Matteo De Chiara, Stephane Delmas, Fabien Dutreux, Teo Fournier, Anne Friedrich, Etienne Kornobis, Jing Li, Zepu Miao, Lorenzo Tattini, Joseph Schacherer, Gianni Liti, Gilles Fischer
Summary: A reference assembly panel (ScRAP) of 142 strains was generated to study the genetic diversity of Saccharomyces cerevisiae. The study revealed the presence of structural variants in these genomes, which can impact gene expression and genome evolution.
Article
Computer Science, Information Systems
Zhiping Tan, Kangshun Li, Yi Wang
Summary: This paper proposes a differential evolution algorithm with an adaptive mutation operator based on fitness landscape (FLDE), which uses machine learning to choose the optimal mutation strategy. Experimental results show that the FLDE algorithm is highly competitive with five other DE algorithms.
INFORMATION SCIENCES
(2021)
Article
Multidisciplinary Sciences
Christoffer Norn, Basile I. M. Wicky, David Juergens, Sirui Liu, David Kim, Doug Tischer, Brian Koepnick, Ivan Anishchenko, Foldit Players, David Baker, Sergey Ovchinnikov
Summary: The protein design problem aims to find an appropriate amino acid sequence for a desired protein structure, with optimization over all possible sequences and structures using protein structure prediction and backpropagation. The trRosetta model is more effective than Rosetta single-point energy estimations, and combining trRosetta and Rosetta models can result in more funneled energy landscapes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Computer Science, Information Systems
Xinyu Zhou, Junyan Song, Shuixiu Wu, Mingwen Wang
Summary: As an effective optimization tool, the artificial bee colony (ABC) algorithm has gained attention but still lacks satisfactory performance. In order to address this, a novel ABC variant called FLABC is proposed, which considers the structural features of problems and incorporates online fitness landscape analysis. FLABC adapts the search to the fitness landscape by identifying landscape features and employing distinct solution search equations. It also includes dynamic multiple subpopulations and a modified scout bee phase. Experimental results demonstrate that FLABC has competitive performance, particularly on functions with rugged fitness landscapes. (c) 2022 Elsevier Inc. All rights reserved.
INFORMATION SCIENCES
(2023)
Article
Biology
Gonzalez Louisa Somermeyer, Aubin Fleiss, Alexander S. Mishin, Nina G. Bozhanova, Anna A. Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina Putintseva, Karen S. Sarkisyan, Fyodor A. Kondrashov
Summary: Studies on protein fitness landscapes help predict functional proteins, but the lack of systematic data on proteins with defined evolutionary relationships limits the generalization of these findings. We studied the fitness peaks of four orthologous fluorescent proteins and found that some peaks were sharp while others were flat.
Article
Multidisciplinary Sciences
Yunan Luo, Guangde Jiang, Tianhao Yu, Yang Liu, Lam Vo, Hantian Ding, Yufeng Su, Wesley Wei Qian, Huimin Zhao, Jian Peng
Summary: ECNet is a deep-learning algorithm that utilizes evolutionary contexts to predict functional fitness for protein engineering with high accuracy. It can guide the engineering of variants with improved resistance successfully.
NATURE COMMUNICATIONS
(2021)
Article
Ecology
J. Z. Chen, D. M. Fowler, N. Tokuriki
Summary: Fitness landscapes are important concepts in evolutionary biochemistry, but measurements of phenotype-fitness landscapes in proteins are limited. In this study, we quantified the single mutational effects on fitness and phenotype of VIM-2 beta-lactamase across a range of ampicillin concentrations and constructed a phenotype-fitness landscape. Our findings suggest that the evolution of VIM-2 can be predicted based on the selection environment, providing new quantitative knowledge on the evolution of beta-lactamases and proteins in general.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Jorge Fernandez-de-Cossio-Diaz, Guido Uguzzoni, Andrea Pagnani
Summary: A computational method is developed to study the relationship between genotype and fitness, trained on sequencing samples from multiple rounds of screening experiments and tested on large-scale mutational scans. The inferred fitness landscape is robust and exhibits high generalization power.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Satoshi Sano, Tetsuyuki Takemoto, Akira Ogihara, Kengo Suzuki, Takehiro Masumura, Shigeru Satoh, Kazufumi Takano, Yutaka Mimura, Shigeto Morita
Article
Biotechnology & Applied Microbiology
Akari Nishigaki, Mihoko Maruyama, Munenori Numata, Chisako Kanzaki, Shun-Ichi Tanaka, Hiroshi Y. Yoshikawa, Masayuki Imanishi, Masashi Yoshimura, Yusuke Mori, Kazufumi Takano
ENGINEERING IN LIFE SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Chikashi Ota, Shun-ichi Tanaka, Kazufumi Takano
Summary: The main factor of ANS-protein binding is found to be the microenvironment at the binding site, which restricts the attached ANS molecule, rather than diffusion-limited association.
Article
Biochemistry & Molecular Biology
Shun-ichi Tanaka, Minami Tsutaki, Seira Yamamoto, Hayate Mizutani, Ryo Kurahashi, Azumi Hirata, Kazufumi Takano
Summary: The study investigated random mutations in both conserved and non-conserved sites of two thermostable proteins. The results indicated that some conserved sites showed resistance to mutation, while some non-conserved sites lost enzymatic activity at high temperatures.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Crystallography
Yuka Tsuri, Nana Inaoka, Mihoko Maruyama, Katsuo Tsukamoto, Hiroaki Adachi, Hiroshi Y. Yoshikawa, Kazufumi Takano, Masayuki Imanishi, Masashi Yoshimura, Yusuke Mori
Summary: This study investigated the crystallization of acetaminophen form II using ultrasonic irradiation with a polyethylene (PE) ball or a teflon (PTFE) ball. It was found that the nucleation probability of form II was enhanced by a PTFE ball under ultrasonic irradiation, with the key parameter being the amount of gases entrapped on the plastic ball's surface. Additionally, the wettability of the solvent on the solid surface played a crucial role in dictating the amount of entrapped gases and ultimately affecting the crystallization process.
JOURNAL OF CRYSTAL GROWTH
(2021)
Article
Crystallography
Akari Nishigaki, Mihoko Maruyama, Shun-ichi Tanaka, Hiroshi Y. Yoshikawa, Masayuki Imanishi, Masashi Yoshimura, Yusuke Mori, Kazufumi Takano
Summary: The study found that the crystals of form II grown in agarose gel have higher stability and dissolve more slowly. However, the stability of trihydrate crystals in the gel is reduced due to a fine morphology.
Article
Crystallography
Akari Nishigaki, Mihoko Maruyama, Shun-ichi Tanaka, Hiroshi Y. Yoshikawa, Masayuki Imanishi, Masashi Yoshimura, Yusuke Mori, Kazufumi Takano
Summary: The report highlights the effectiveness of cavitation bubbles generated by femtosecond laser and ultrasonic irradiations in controlling polymorph crystallization, as well as the generation of cavitation bubbles by dropping a vial. The study demonstrates the crystallization of acetaminophen by drop impact and confirms the potency of the air-liquid interface in metastable phase formation. The phenomenon of crystallization by drop impact is considered a new development in the field.
Article
Biochemistry & Molecular Biology
Rafida Razali, Fikran Aranda Fahrudin, Vijay Kumar Subbiah, Kazufumi Takano, Cahyo Budiman
Summary: This study successfully expressed a small-sized bromelain from MD2 pineapple and purified 14 mg of pure product. The bromelain showed optimal activity at 50 degrees C and pH 8.0, modulated by divalent ions, and exhibited the ability to scavenge DPPH.
Article
Biochemistry & Molecular Biology
Satoshi Murakami, Hiroaki Adachi, Hiroyoshi Matsumura, Kazufumi Takano, Tsuyoshi Inoue, Yusuke Mori
Summary: In this study, shadowgraph was used to monitor the migration and separation of proteins in polyacrylamide gels in real time without staining. This method provides instant protein profiles in the early stage of electrophoresis, saving time and reducing waste.
JOURNAL OF BIOCHEMISTRY
(2023)
Article
Crystallography
Mihoko Maruyama, Hiroshi Y. Yoshikawa, Kazufumi Takano, Masashi Yoshimura, Yusuke Mori
Summary: Polymorphism is crucial in organic solid-state chemistry, and the control of crystal polymorphism involves nucleation, crystal growth, and phase transition. Understanding the phase transition from metastable to stable phase is essential.
JOURNAL OF CRYSTAL GROWTH
(2023)
Article
Chemistry, Multidisciplinary
Chikashi Ota, Hikari Suzuki, Shun-ichi Tanaka, Kazufumi Takano
Summary: This study investigates the molecular mechanism of ligand-protein interactions with flexible binding sites using RNase HI and ANS as a model system. The results show that the crowding effect in a crowded environment leads to the binding of ANS molecules to additional binding sites, resulting in a change in the fluorescence behavior. The fluorescence vibronic structure analysis provides detailed information on the structure of ANS and the binding sites, suggesting a potential mechanism for the dispersion of binding pathways.
Article
Chemistry, Multidisciplinary
Mihoko Maruyama, Yutaro Tanaka, Koichi Momma, Yoshihiro Furukawa, Hiroshi Y. Yoshikawa, Rie Tajiri, Masanori Nakamura, Kazumi Taguchi, Shuzo Hamamoto, Ryosuke Ando, Katsuo Tsukamoto, Kazufumi Takano, Masayuki Imanishi, Shigeyoshi Usami, Kenjiro Kohri, Atsushi Okada, Takahiro Yasui, Masashi Yoshimura, Yusuke Mori
Summary: In this study, the researchers investigated the phase transition of calcium oxalate kidney stones and found direct evidence of the solution-mediated phase transition from calcium oxalate dihydrate (COD) to calcium oxalate monohydrate (COM). They examined the crystal phases, crystal textures, and protein distributions within thin sections of the stones. The results showed that the mosaic-like COM crystals are secondary structures formed by the phase transition, while the COD single crystals and concentrically laminated COM are primary structures.
CRYSTAL GROWTH & DESIGN
(2023)
Article
Multidisciplinary Sciences
Mihoko Maruyama, Koichi P. Sawada, Yutaro Tanaka, Atsushi Okada, Koichi Momma, Masanori Nakamura, Ryota Mori, Yoshihiro Furukawa, Yuki Sugiura, Rie Tajiri, Kazumi Taguchi, Shuzo Hamamoto, Ryosuke Ando, Katsuo Tsukamoto, Kazufumi Takano, Masayuki Imanishi, Masashi Yoshimura, Takahiro Yasui, Yusuke Mori
Summary: We conducted a study to quantitatively analyze calcium oxalate (CaOx) kidney stones at the micrometer level, with a focus on the identification of calcium oxalate monohydrate (COM) and dihydrate (COD). We used Fourier transform infrared (FTIR) spectroscopy, powder X-ray diffraction (PXRD), and microfocus X-ray computed tomography measurements (microfocus X-ray CT) to compare their results. By analyzing the FTIR spectrum at the 780 cm(-1) peak, we successfully achieved a reliable analysis of the COM/COD ratio. This quantitative analysis method provides valuable information on the composition and formation processes of kidney stones.
Article
Chemistry, Physical
Chikashi Ota, Tomoya Konishi, Shun-ichi Tanaka, Kazufumi Takano
Summary: Protein-ligand interactions are important in crowded cellular environments. This study investigates the use of ANS-ICD to analyze local conformational changes at binding sites. The results show distinct changes in the ANS-ICD spectra, indicating its potential for analyzing internal protein conformation. Temperature-dependent measurements reveal different denaturation pathways in crowded and diluted environments.
Article
Chemistry, Multidisciplinary
Akari Nishi, Hikaru Matsui, Azumi Hirata, Atsushi Mukaiyama, Shun-ichi Tanaka, Takuya Yoshizawa, Hiroyoshi Matsumura, Ryota Nomura, Kazuhiko Nakano, Kazufumi Takano
Summary: In this study, the researchers focused on the structure and activity of collagen-binding proteins from Streptococcus mutans. They found that the N1 and N2 domains as well as the linker region are important for collagen binding. Understanding these mechanisms could potentially lead to the development of CBD inhibitors for infective endocarditis caused by S. mutans.
CHEMISTRY-SWITZERLAND
(2023)
Article
Biotechnology & Applied Microbiology
Thore Bach Thomsen, Tobias S. Radmer, Anne S. Meyer
Summary: Plastic pollution, particularly from PET, is a significant environmental challenge. This study investigates the enzyme kinetics of PET degradation and finds that the degree of crystallinity (X-C) has a substantial impact on the enzymatic reaction rate. The mobile amorphous fraction (X-MAF) is a better descriptor for the rate of enzymatic degradation. The longer lag phase observed with increased X-C is proposed to be due to increased substrate entanglement density and unproductive enzyme binding to the crystalline regions of PET.
ENZYME AND MICROBIAL TECHNOLOGY
(2024)
Article
Biotechnology & Applied Microbiology
Purna Bahadur Poudel, Dipesh Dhakal, Jong Cheol Lee, Jae Kyung Sohng
Summary: Methylation plays important roles in various biological processes, and this study characterized the function of ThnM3 in regioselective modifications of 1,8-dihydroxynaphthalene.
ENZYME AND MICROBIAL TECHNOLOGY
(2024)
Article
Biotechnology & Applied Microbiology
Feng Song, Ivan Birukou, Mark Bednarcik, Scott Young
Summary: In this study, a highly sensitive and specific method using ultra performance liquid chromatography (UPLC) was developed to measure the enzymatic activity of APH4 in plants. The method exhibited good precision and accuracy, and was validated for use with samples from different sources.
ENZYME AND MICROBIAL TECHNOLOGY
(2024)
Article
Biotechnology & Applied Microbiology
Yuan Rao, Wei Zhuang, Jinle Liu, Ting Tang, Zhi Wang, Hanjie Ying
Summary: This study describes a mild and versatile strategy to immobilize glucose oxidase (GOD) on carboxyl-activated metal-organic framework (MOF) through DNA-directed immobilization technology. The immobilized GOD showed enhanced stability and catalytic activity, making it a potential candidate for applications in biocatalysis and biotechnology.
ENZYME AND MICROBIAL TECHNOLOGY
(2024)
Article
Biotechnology & Applied Microbiology
Julen Ordenana Manso, Martin B. Nielsen, Eva Balaguer Moya, Juliana P. Sandri, Celina K. Yamakawa, Solange I. Mussatto
Summary: This study focuses on the development of an enzymatic cocktail for the conversion of corn fiber into monosaccharides. The results reveal that the recalcitrance and unique chemical composition of corn fiber require a tailored enzymatic cocktail for degradation, and attention should also be given to the pretreatment step.
ENZYME AND MICROBIAL TECHNOLOGY
(2024)
Article
Biotechnology & Applied Microbiology
Cuixia Zhou, Guangcheng Yang, Panpan Meng, Weishuai Qin, Yanyan Li, Zhenxian Lin, Wei Hui, Huitu Zhang, Fuping Lu
Summary: Bacillus licheniformis 2709 is an important industrial producer of alkaline protease (AprE), and this study identified the UP elements of the aprE gene and demonstrated the lack of significant effect of CggR, FruR, and YhcZ transcription factors on aprE expression. Enhanced aprE expression and enzyme activity were achieved by deleting a negative regulatory factor binding site in the genome. These findings provide valuable insights into the high-level production of proteins in other Bacillus species.
ENZYME AND MICROBIAL TECHNOLOGY
(2024)
Article
Biotechnology & Applied Microbiology
Xinqi Xu, Tianheng Chen, Lian Xu, Juan Lin
Summary: In this study, laccase was immobilized on modified magnetic nanoparticles, improving the enzyme's thermostability and efficiency for polymerization of phenols.
ENZYME AND MICROBIAL TECHNOLOGY
(2024)
Article
Biotechnology & Applied Microbiology
Handan Ustukarci, Gul Ozyilmaz, Ali Tuncay Ozyilmaz
Summary: A biofilm layer called biofouling is formed over time by organic molecules and microorganisms on solid surfaces immersed in a liquid medium. This study focused on the antifouling performance of polyaniline (PANI) and investigated the immobilization of hydrolytic enzymes in PANI coatings. The results showed that the alpha-amylase-containing film exhibited the highest antifouling activity. Surface properties and biofilm composition were analyzed to support these findings.
ENZYME AND MICROBIAL TECHNOLOGY
(2024)
Article
Biotechnology & Applied Microbiology
Mariana Ortiz-Sanchez, Juan Camilo Solarte-Toro, Pablo Jose Inocencio-Garcia, Carlos Ariel Cardona Alzate
Summary: This study evaluated the sustainability of biorefineries using orange peel as a raw material. By applying the concept of biorefineries and experimental data, it was found that steam distillation and polyphenolic compound extraction can improve the process performance, resulting in higher yields of different products. The integrated utilization of orange peel in biorefineries showed a high sustainability index.
ENZYME AND MICROBIAL TECHNOLOGY
(2024)