Article
Biochemical Research Methods
Avantika Lal, Keli Liu, Robert Tibshirani, Arend Sidow, Daniele Ramazzotti
Summary: The study introduces a novel framework, SparseSignatures, for extracting signatures from somatic point mutation data. Experimental results on simulated data demonstrate that SparseSignatures outperforms current state-of-the-art methods in terms of accuracy. When applied to whole genome sequences of pancreatic and breast tumors, well-differentiated signatures linked to known mutagenic mechanisms and strongly associated with patient clinical features were discovered.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yameng Xu, Xinglong Wang, Chenyang Zhang, Xuan Zhou, Xianhao Xu, Luyao Han, Xueqin Lv, Yanfeng Liu, Song Liu, Jianghua Li, Guocheng Du, Jian Chen, Rodrigo Ledesma-Amaro, Long Liu
Summary: This study reports the engineering of Saccharomyces cerevisiae to produce rubusoside and rebaudiosides, which are considered as the next generation of sugar substitutes. Through a modular engineering approach, the authors were able to overcome several limitations and achieve high titers of these molecules. This research provides a sustainable and scalable solution for the production of diverse rebaudiosides.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Shan Li, Sridhar Hannenhalli, Ivan Ovcharenko
Summary: Using data from human and macaque embryonic neocortical H3K27ac, researchers identified approximately 4000 enhancer gains in humans, which appear to be caused by single-nucleotide essential mutations. These new enhancers play a role in embryonic brain development, increasing the expression of target genes in progenitor cells and interneurons involved in neural developmental processes. Essential mutations alter the activity of embryonic neocortex enhancers through changes in transcription factor binding and are associated with central nervous system disorders, suggesting their importance in human cognition.
Article
Biophysics
Kun Liu, Yunsen Zhang, Ke Liu, Yunqiu Zhao, Bei Gao, Xinyi Tao, Ming Zhao, Feng-Qing Wang, Dongzhi Wei
Summary: In this study, a de novo designed transcription factor (TF) named DLA was successfully developed for the construction of a biosensor for progesterone detection. The biosensor showed high sensitivity, a wide detection range, and rapid detection time. Furthermore, the strategy used in this study could be applied to develop various other biosensors.
BIOSENSORS & BIOELECTRONICS
(2022)
Review
Oncology
Coral Gonzalez-Martinez, Carmen Garrido-Navas, Miriam Alcaide-Lucena, Jose Antonio Lorente, Javier Lopez-Hidalgo, Francisco Gabriel Ortega, Maria Jose Serrano
Summary: miRNAs are important factors in cancer development and progression. This review aims to determine if metastasis in breast cancer is characterized by different miRNA signatures that can serve as specific biomarkers for each entity. After systematic search and review of literature from PubMed, Scopus, and Web of Science databases, a total of 30 records were included in this review. Results showed a genetic signature with 5 upregulated miRNAs in metastasis compared with early stages, with miR-23b and miR-200c exclusively present in relapse metastasis. A molecular signature for future studies is proposed as a complementary tool for diagnosis and characterization of metastasis in clinical trials.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2023)
Article
Multidisciplinary Sciences
Mingzhuo Li, Xianzhi He, Christophe La Hovary, Yue Zhu, Yilun Dong, Shibiao Liu, Hucheng Xing, Yajun Liu, Yucheng Jie, Dongming Ma, Seyit Yuzuak, De-Yu Xie
Summary: This study utilized transcription factors and cis-regulatory elements to design a De Novo regulation for altering plant secondary metabolism. Experimental and field trial results showed that this regulation method could effectively modify plant metabolites, indicating its potential application in plant engineering.
JOURNAL OF ADVANCED RESEARCH
(2022)
Article
Multidisciplinary Sciences
G. Ozan Bozdag, Seyed Alireza Zamani-Dahaj, Thomas C. Day, Penelope C. Kahn, Anthony J. Burnetti, Dung T. Lac, Kai Tong, Peter L. Conlin, Aishwarya H. Balwani, Eva L. Dyer, Peter J. Yunker, William C. Ratcliff
Summary: This study investigates the evolution of multicellular organisms using a long-term experiment with snowflake yeast as the model system. The results show that snowflake yeast evolved to be macroscopic in anaerobic conditions, while remaining microscopic in aerobic conditions. This research provides insights into how simple groups of cells overcome biophysical limitations through gradual multicellular evolution.
Article
Multidisciplinary Sciences
Dolma Michellod, Tanja Bien, Daniel Birgel, Marlene Violette, Manuel Kleiner, Sarah Fearn, Caroline Zeidler, Harald R. Gruber-Vodicka, Nicole Dubilier, Manuel Liebeke
Summary: Using various techniques, such as metabolite imaging and enzyme assays, we have discovered that gutless marine annelids synthesize the plant sterol sitosterol, which is commonly found in plants. This synthesis is facilitated by a noncanonical C-24 sterol methyltransferase, an enzyme that is essential for sitosterol synthesis in plants but not widely known in most animals. Our phylogenetic analyses also indicate that this enzyme is present in representatives of at least five animal phyla, suggesting that the synthesis of plant-like sterols is more common in animals than previously believed.
Article
Plant Sciences
Sang-Ho Kang, Woo-Haeng Lee, Joon-Soo Sim, Niha Thaku, Saemin Chang, Jong-Pil Hong, Tae-Jin Oh
Summary: Through RNA-Seq and Iso-Seq analysis, a transcriptomic analysis of S. occidentalis was performed, identifying genes related to the anthraquinone biosynthesis pathway and transcription factor families. Tissue-specific differential expression analysis and measurement of anthraquinone levels revealed the relationship between gene expression and anthraquinone accumulation, as well as the differences in anthraquinones produced by S. occidentalis and S. tora.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Satoko Miyatake, Mitsuhiro Kato, Takuma Kumamoto, Tomonori Hirose, Eriko Koshimizu, Takaaki Matsui, Hideyuki Takeuchi, Hiroshi Doi, Keisuke Hamada, Mitsuko Nakashima, Kazunori Sasaki, Akio Yamashita, Atsushi Takata, Kohei Hamanaka, Mai Satoh, Takabumi Miyama, Yuri Sonoda, Momoko Sasazuki, Hiroyuki Torisu, Toshiro Hara, Yasunari Sakai, Yushi Noguchi, Mazumi Miura, Yoko Nishimura, Kazuyuki Nakamura, Hideyuki Asai, Nodoka Hinokuma, Fuyuki Miya, Tatsuhiko Tsunoda, Masami Togawa, Yukihiro Ikeda, Nobusuke Kimura, Kaoru Amemiya, Asako Horino, Masataka Fukuoka, Hiroko Ikeda, Goni Merhav, Nina Ekhilevitch, Masaki Miura, Takeshi Mizuguchi, Noriko Miyake, Atsushi Suzuki, Shouichi Ohga, Hirotomo Saitsu, Hidehisa Takahashi, Fumiaki Tanaka, Kazuhiro Ogata, Chiaki Ohtaka-Maruyama, Naomichi Matsumoto
Summary: The study identified de novo ATP1A3 variants causing a severe form of polymicrogyria with epilepsy and developmental delay, distinct from traditional clinical features of AHC, RDP, or CAPOS. This suggests a previously unidentified category of polymicrogyria associated with ATP1A3 abnormalities.
Article
Multidisciplinary Sciences
Alysha K. Lee, Jeremy H. Wei, Paula V. Welander
Summary: The marine myxobacterium Enhygromyxa Salina can produce cholesterol and undergo further modifications, similar to eukaryotes. However, complete demethylation at the C-4 position is achieved through unique bacterial proteins.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Eirini Lionaki, Ilias Gkikas, Ioanna Daskalaki, Maria-Konstantina Ioannidi, Maria Klapa, Nektarios Tavernarakis
Summary: Inhibition of mitochondrial protein import reduces mitochondrial abundance and extends lifespan in Caenorhabditis elegans. This effect is mediated by activation of glycolysis and de novo serine biosynthesis. The study also shows that mitochondrial chaperone induction is not essential for lifespan extension.
NATURE COMMUNICATIONS
(2022)
Article
Clinical Neurology
Maria Ilenia De Bartolo, Giorgio Vivacqua, Daniele Belvisi, Romina Mancinelli, Andrea Fabbrini, Nicoletta Manzo, Matteo Costanzo, Giorgio Leodori, Antonella Conte, Giovanni Fabbrini, Sergio Morini, Alfredo Berardelli
Summary: This study aimed to investigate molecular biomarkers of a-synuclein and tau aggregation, autophagy, and inflammation in the saliva of de novo Parkinson's disease (PD) patients and their potential diagnostic power. The results showed that oligomeric a-synuclein, total-tau, MAP-LC3beta, and TNFalpha levels were significantly higher in PD patients compared to healthy subjects. The combination of salivary biomarkers targeting different molecular pathways, including oligomeric a-synuclein and MAP-LC3beta, showed accurate diagnostic performance.
ANNALS OF NEUROLOGY
(2023)
Article
Materials Science, Multidisciplinary
Dong Zhang, Yijing Tang, Jintao Yang, Yijing Gao, Chunxin Ma, Lingbin Che, Jianguo Wang, Jiang Wu, Jie Zheng
Summary: Zwitterionic materials and allochroic materials offer distinct properties and functions for different applications. The development of zwitterionic, allochroic materials remains challenging. In this study, water-soluble and allochroic polymers of pVPES were designed and synthesized, which can self-polymerize into different architectures or co-polymerize with other functional polymers to become different smart devices. The pVPES-based hydrogel patches not only accelerated wound healing but also distinguished different types of wounds through color changes.
Review
Cardiac & Cardiovascular Systems
Josephine Harrington, Jonathan P. Piccini, John H. Alexander, Christopher B. Granger, Manesh R. Patel
Summary: FXIa inhibitors have the potential to improve precision in anticoagulation by primarily targeting thrombus formation while sparing clotting and hemostasis. Observational data and small phase 2 trials have shown promising results in terms of bleeding, safety, and prevention of venous thromboembolism. Larger clinical trials are needed to determine the role of FXIa inhibitors in different patient populations.
JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jonathan J. Chen, Lyndsey N. Schmucker, Donald P. Visco
CHEMICAL BIOLOGY & DRUG DESIGN
(2019)
Article
Biology
Jonathan J. Chen, Lyndsey N. Schmucker, Donald P. Visco
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2019)
Article
Biochemical Research Methods
Amir Pandi, Ioana Grigoras, Olivier Borkowski, Jean-Loup Faulon
ACS SYNTHETIC BIOLOGY
(2019)
Review
Biochemical Research Methods
Mathilde Koch, Amir Pandi, Olivier Borkowski, A. C. Batista, Jean-Loup Faulon
CURRENT OPINION IN BIOTECHNOLOGY
(2019)
Article
Multidisciplinary Sciences
Amir Pandi, Mathilde Koch, Peter L. Voyvodic, Paul Soudier, Jerome Bonnet, Manish Kushwaha, Jean-Loup Faulon
NATURE COMMUNICATIONS
(2019)
Article
Biochemical Research Methods
Mathilde Koch, Thomas Duigou, Jean-Loup Faulon
ACS SYNTHETIC BIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Sara Castano-Cerezo, Mathieu Fournie, Philippe Urban, Jean-Loup Faulon, Gilles Truan
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2020)
Article
Multidisciplinary Sciences
Olivier Borkowski, Mathilde Koch, Agnes Zettor, Amir Pandi, Angelo Cardoso Batista, Paul Soudier, Jean-Loup Faulon
NATURE COMMUNICATIONS
(2020)
Article
Materials Science, Multidisciplinary
A. Mohamed, D. P. Visco, D. M. Bastidas
Summary: The study shows that organic compounds with pi-electrons have better performance in inhibiting the corrosion of carbon steel reinforcements, with the pi-bond electrons playing a crucial role in the adsorption process.
Article
Biochemical Research Methods
Angelo Cardoso Batista, Antoine Levrier, Paul Soudier, Peter L. Voyvodic, Tatjana Achmedov, Tristan Reif-Trauttmansdor, Angelique DeVisch, Martin Cohen-Gonsaud, Jean-Loup Faulon, Chase L. Beisel, Jerome Bonnet, Manish Kushwaha
Summary: This study presents a simple, efficient, and cost-effective solution for using linear DNA templates in cell-free systems by deleting the exonuclease gene cluster from Escherichia coli. The research highlights the importance of tailoring buffer composition for the optimal experimental setup, and suggests that similar strategies can be applied to other species in cell-free synthetic biology.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Paul Soudier, Ana Zuniga, Thomas Duigou, Peter L. Voyvodic, Kenza Bazi-Kabbaj, Manish Kushwaha, Julie A. Vendrell, Jerome Solassol, Jerome Bonnet, Jean-Loup Faulon
Summary: This study reports the engineering of PeroxiHUB, a sensing platform centered around H2O2, that supports cell-free detection of different metabolites. The PeroxiHUB platform utilizes enzymatic transducers to convert metabolites of interest into H2O2, allowing for rapid reprogramming of sensor specificity. This platform has the potential to detect a wide range of metabolites in a modular and scalable fashion.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ahmed P. Mohamed, Donald M. Visco Jr, David Bastidas
Summary: Sodium succinate has been evaluated as an organic corrosion inhibitor for carbon steel rebars in simulated concrete pore solution. It showed strong inhibition performance by forming a protective film on the rebar surface. The inhibitor is classified as a mixed-type inhibitor and is able to displace water molecules and complex with ferrous ions, creating an adsorption film. Various surface characterizations and quantum chemical calculations have provided evidence for the adsorption of sodium succinate.
Article
Multidisciplinary Sciences
Leon Faure, Bastien Mollet, Wolfram Liebermeister, Jean-Loup Faulon
Summary: Constraint-based metabolic models have been used to predict microorganism phenotype, but accurate predictions require labor-intensive measurements. We propose hybrid neural-mechanistic models as a machine learning architecture to improve phenotype predictions. Our models outperform constraint-based models with smaller training set sizes, offering a time and resource-saving approach in systems biology and biological engineering projects.
NATURE COMMUNICATIONS
(2023)
Article
Education & Educational Research
Kristin L. K. Koskey, Nidaa Makki, Wondimu Ahmed, Nicholas G. Garafolo, Donald P. Visco
SCHOOL SCIENCE AND MATHEMATICS
(2020)
Article
Biochemical Research Methods
Mark S. Dunstan, Christopher J. Robinson, Adrian J. Jervis, Cunyu Yan, Pablo Carbonell, Katherine A. Hollywood, Andrew Currin, Neil Swainston, Rosalind Le Feuvre, Jason Micklefield, Jean-Loup Faulon, Rainer Breitling, Nicholas Turner, Eriko Takano, Nigel S. Scrutton
Article
Biochemical Research Methods
Nousheen Parvaiz, Asma Abro, Syed Sikander Azam
Summary: Protein Tyrosine Phosphatase 1B (PTP1B) is a negative regulator of insulin signaling pathways and has potential as a medicinal target. This study explores the binding and conformational orientation of zinc(II) complexes in PTP1B using advanced computational methods. The findings suggest that zinc(II) complexes can bind to important residues in the enzyme and inhibit its activity.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Hira Zubair, Muhamed Salim Akhter, Muhammad Waqas, Mariam Ishtiaq, Ijaz Ahmed Bhatti, Javed Iqbal, Ahmed M. Skawky, Rasheed Ahmad Khera
Summary: Improving open-circuit voltage is crucial for enhancing the overall efficiency of organic solar cells. This study successfully improved the open-circuit voltage by modulating the molecular structure and proposed a promising design concept for acceptor molecules that may contribute to the development of advanced organic solar cells.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Jerica Wilson, Bahrad A. Sokhansanj, Wei Chuen Chong, Rohan Chandraghatgi, Gail L. Rosen, Hai-Feng Ji
Summary: Fragment-based drug design is a computer-aided drug discovery method, however, it has limitations in processing time and success rate. In this study, a new method called Fragment Databases from Screened Ligands Drug Design (FDSL-DD) was proposed, which intelligently incorporates fragment characteristics into the drug design process to improve the binding affinity between drugs and protein targets.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
M. Chamani, G. H. Farrahi
Summary: This paper employs the Generalized Particle (GP) method to simulate nanoindentation and nanoscratching, showing that this method maintains consistent atomic properties across different scales and achieves results consistent with full atomic simulations.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Paola Vottero, Elena Carlotta Olivetti, Lucia Chiara D'Agostino, Luca Di Grazia, Enrico Vezzetti, Maral Aminpour, Jacek Adam Tuszynski, Federica Marcolin
Summary: This study aims to characterize the spike protein of the SARS-CoV-2 virus and investigate its interaction with the ACE2 receptor using a geometric analysis. The 3D depth maps of the proteins are filtered using a specific convolutional filter to obtain geometric features. Geometric descriptors and a Support Vector Machine classifier are used for feature extraction and classification, revealing the geometrical reasons for the higher contagiousness of the Omicron variant compared to other variants.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Diana Margarita Mojica-Munoz, Karla Lizbeth Macias-Sanchez, Estefania Odemaris Juarez-Hernandez, Aurora Rodriguez-Alvarez, Jean-Michel Grevy, Armando Diaz-Valle, Mauricio Carrillo-Tripp, Jose Marcos Falcon-Gonzalez
Summary: By employing molecular dynamics simulations, we investigated the molecular mechanisms underlying the plasticization of starch. Our study revealed that chain size affects the solubility of starch, temperature influences its diffusivity and elastic properties, and oleic acid shows potential as an alternative plasticizer. Blending glycerol or oleic acid with water enhances the elasticity of starch.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Sandip Kumar Baidya, Suvankar Banerjee, Balaram Ghosh, Tarun Jha, Nilanjan Adhikari
Summary: This study utilized classification-based QSAR techniques and fragment-based data mining to analyze different MMP-9 inhibitors, revealing the importance of certain molecular fragments in MMP-9 inhibition. These findings have implications for the development of effective MMP-9 inhibitors in the future.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Farid Faraji Chanzab, Saber Mohammadi, Fatemeh Alemi Mahmoudi
Summary: A comprehensive study using molecular dynamics technique was conducted to investigate the behavior of PAP molecules in a n-heptane/toluene solution and the role of SWCNTs, both bare and functionalized with carboxyl groups, in the aggregation of PAP molecules. The study found that the CNTs hindered the association of PAP molecules through steric hindrance and adsorption mechanisms. The presence of carboxyl groups on the CNTs improved the stability and adsorption of PAP molecules. The results have implications for future research on controlling asphaltene precipitation in the oil industry.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Ramin Bairami Habashi, Mohammad Najafi, Reza Zarghami
Summary: A vigorous Monte Carlo strategy was developed to simulate the copolymerization of ethylene and 1-butene using a dual-site metallocene catalyst. The results showed that the second catalyst site had higher activity than the first site, with ethylene and 1-butene consumption rates five times higher and hydrogen transfer rates three times faster. The molar percentage of 1-butene in the copolymers synthesized from the second site was around 12%, while in the copolymers from the first site it was around 2%. Increasing the 1-butene concentration led to an increase in overall molecular weight, while increasing the hydrogen concentration resulted in a decrease in molecular weight. The ratio of ethylene to 1-butene affected the melt index and the weight fraction of crystals, with higher ratios leading to smaller melt indexes and higher weight fractions of crystals. Increasing the temperature caused changes in molecular weight, bimodal molecular weight distribution, crystal thickness and weight fraction, and density of HDPE.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Yufan Lu, Xingmin Guo, Shuya Liu
Summary: This paper investigates how to control the nontrivial topological structures of DNA nanocages by adjusting the number of ssDNA strands. A new algorithm and program are developed to calculate the component number of polyhedral links, filling the gap in computer programs on this aspect. The study provides a complete list of topological structures with different component numbers for DNA octahedrons assembled from one or more ssDNA strands.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Peng Cui, Shideng Yuan, Heng Zhang, Shiling Yuan
Summary: Understanding the mechanisms of viscosity enhancement in crude oil phases is crucial for optimizing extraction and transportation processes. This study employed molecular dynamics simulations to investigate the behavior and viscosification mechanism of asphaltene molecules in complex oil phases. The research suggests that electrostatic interactions and interactions between asphaltene and crude oil molecules contribute to the enhanced viscosity. The findings provide insight into the viscosity enhancement mechanisms in crude oil phases.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Kun Lv, Jin Zhang, Xiaohua Liu, Yuqiao Zhou, Kai Liu
Summary: In this paper, the authors propose a robust method for evaluating the interactions between chiral catalysts and substrates using computer simulations. The method involves constructing 3D models from point cloud data, filtering out non-interacting points, determining interacting points, and accurately calculating interacted volumes. Experimental results demonstrate the effectiveness of the method in removing non-interacting points and calculating interacted volumes with low errors.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Crisciele Fontana, Joao Luiz de Meirelles, Hugo Verli
Summary: By using the GROMOS force field and molecular simulations, this study assessed the dynamics of STA-analogs in aqueous solution and their interaction with water, expanding the knowledge of the conformational space of these ligands and providing potential implications for understanding conformational selection during complexation.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Wei Zhao, Wenjie Zou, Fengyang Liu, Fang Zhou, N. Emre Altun
Summary: The effect of grafting rate on the water solubility of chitosan-grafted polyacrylamide (Chi-gPAM) was investigated using molecular dynamics simulations. The results showed that the intramolecular hydrogen bonding of Chi-gPAM played a dominant role in its water solubility. Additionally, the interaction between Chi-gPAM and water increased with grafting rate.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Nassima Bachir, Samir Kenouche, Jorge I. Martinez-Araya
Summary: This study investigates the local chemical reactivity of FOX-7 and explores the interaction between the compound and different metals. The findings suggest that the stability and charge transfers of the compound are influenced by the metal involved, and the interaction between Metallocene Methyl Cations and the compound shows potential for neutralization.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)