Review
Chemistry, Multidisciplinary
Sijie Zhou, Yi Wu, Ze-Xiong Xie, Bin Jia, Ying-Jin Yuan
Summary: Directed genome evolution uses recent technological advances in genome writing and editing to simulate natural evolution in the lab, generating desired phenotypes. Structural rearrangement techniques help create diverse genotypes and accelerate the evolution of phenotypic traits.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Biotechnology & Applied Microbiology
Francesca V. Gambacorta, Joshua J. Dietrich, Justin J. Baerwald, Stephanie J. Brown, Yun Su, Brian F. Pfleger
Summary: This study aimed to identify an isobutanol pathway cassette that can support the growth of a non-ethanol producing S. cerevisiae. By screening a combinatorial library of pathway enzymes, the researchers isolated a cassette that was able to produce 364 mg/L isobutanol under aerobic conditions. This approach shows promise for rewiring the metabolism of S. cerevisiae to produce other fermentation products.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Claudio Avila, Carlo Cassani, Thierry Kogej, Javier Mazuela, Sunil Sarda, Adam D. Clayton, Michael Kossenjans, Clive P. Green, Richard A. Bourne
Summary: This work proposes a stopped-flow synthesis as an alternative method for small molecule pharmaceutical discovery. By integrating a stopped-flow reactor into a high-throughput continuous platform, the success rate of synthesizing smaller libraries is significantly improved. The experimental datasets are used to train a neural network model, which shows good predictive performance when tested against external data.
Article
Biotechnology & Applied Microbiology
Hung Li, Nam Ngoc Pham, Claire R. Shen, Chin-Wei Chang, Yi Tu, Yi-Hao Chang, Jui Tu, Mai Thanh Thi Nguyen, Yu-Chen Hu
Summary: In this study, a combinatorial CRISPR interference (CRISPRi) library strategy was used to enhance cyanobacterial 2,3-butanediol (2,3-BDO) production by regulating specific genes. The results showed that inhibiting certain genes can increase 2,3-BDO synthesis, with fbp and pdh suppression having a more significant effect. This method opens up new possibilities for metabolic engineering of cyanobacteria.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Physical
Yutaka Saito, Misaki Oikawa, Takumi Sato, Hikaru Nakazawa, Tomoyuki Ito, Tomoshi Kameda, Koji Tsuda, Mitsuo Umetsu
Summary: The study shows that machine learning is a useful tool in designing proteins with desired functions in protein engineering. Depending on the presence or absence of highly positive variants in the training data, machine learning-guided directed evolution can lead to improved variants in different regions of sequence space.
Review
Biochemistry & Molecular Biology
Saurabh Rajendra Nirantar
Summary: Enzymes play a crucial role in biotransformations, however, they often need to be engineered for better performance in biotechnological applications. Researchers have developed a variety of wet-lab methods over the years to achieve this goal, which are examined in this review.
Review
Biotechnology & Applied Microbiology
Haoran Yu, Shuang Ma, Yiwen Li, Paul A. Dalby
Summary: Directed evolution is a powerful strategy to engineer protein properties, and hot spot prediction is crucial for producing smart libraries. Selection of hot spots based on sequence and structure allows for efficient generation of proteins with desired properties.
BIOTECHNOLOGY ADVANCES
(2022)
Review
Biochemistry & Molecular Biology
Cristina Cheng, Mi Zhou, Qiwen Su, Alexandra Steigmeyer, Jia Niu
Summary: The generation of a library of variant genes is necessary for directed evolution, and efficient library diversification in living cells is essential for in vivo technologies. Recent advancements in using genome editors allow for precise mutagenesis focused on specific genes, higher mutational density, and reduced occurrence of cheater mutations.
CELL CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Physical
A. Usha Vijayakumar, N. Aloni, V. Thazhe Veettil, G. Rahamim, S. S. Hardisty, M. Zysler, S. Tirosh, D. Zitoun
Summary: This study systematically investigates the performance of a ternary Ni-Fe-Co oxide gradient library for the oxygen evolution reaction (OER). The combinatorial approach used in this study allows for a faster and more reliable investigation compared to the traditional step by step approach. The results provide a foundation for exploring other mixed-metal oxide combinations.
ACS APPLIED ENERGY MATERIALS
(2022)
Review
Biotechnology & Applied Microbiology
Andrew Currin, Steven Parker, Christopher J. Robinson, Eriko Takano, Nigel S. Scrutton, Rainer Breitling
Summary: The ability to engineer biological systems is crucial in biotechnology and synthetic biology. Generating genetic diversity is essential to explore variations in phenotype, and recent advancements in DNA synthesis technology have enhanced our ability to create variant libraries. This review focuses on approaches to create diversity from enzyme level to entire pathways in vitro, emphasizing the creation of combinatorial libraries for significant improvements in function.
BIOTECHNOLOGY ADVANCES
(2021)
Article
Microbiology
Longping Tse, Rita M. Meganck, Stephanie Dong, Lily E. Adams, Laura J. White, Michael L. Mallory, Ramesh Jadi, Aravinda M. de Silva, Ralph S. Baric
Summary: Mature DENVs that are the target for vaccine development were generated using multiple strategies and a reliable cell line was developed. The study provides reliable strategies and reagents for DENV antibody neutralization and vaccination immunity studies.
Article
Biochemical Research Methods
Kristen Van Gelder, Edmar R. Oliveira-Filho, Jorge Donato Garcia-Garcia, You Hu, Steven D. Bruner, Andrew D. Hanson
Summary: Sulfide-dependent THI4 thiazole synthases could potentially replace plant cysteine-dependent suicide THI4s due to their lower energy consumption. However, they are not suitable for aerobic conditions and have slow enzyme activity. By using directed evolution, seven beneficial single mutations were identified that improved aerotolerance and activity. This study demonstrates that sulfide-dependent THI4s can evolve and the yeast OrthoRep system can be used to adapt nonplant enzymes for better performance in plants.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Philipp Stephan, Chloe Langley, Daniela Winkler, Jerome Basquin, Lorenzo Caputi, Sarah E. E. O'Connor, Hajo Kries
Summary: Engineering of biosynthetic enzymes is used to synthesize antibiotics analogues. This study focuses on nonribosomal peptide synthetases (NRPSs) responsible for producing antimicrobial peptides. By directed evolution, the substrate specificity of an adenylation domain of a Pro-specific NRPS module was completely switched to a non-standard amino acid. This achievement was made through screening of mutant libraries and can be replicated with different substrates and NRPS modules. New possibilities for modifying NRPS specificity in a biosynthetically useful way are presented.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Biochemical Research Methods
Aitor Manteca, Alejandra Gadea, David Van Assche, Pauline Cossard, Melanie Gillard-Bocquet, Thomas Beneyton, C. Axel Innis, Jean-Christophe Baret
Summary: Optimizing the properties of biological molecules is crucial for various industrial and medical applications. Directed evolution is a powerful technique for modifying biomolecules by mimicking natural evolution. Droplet-based microfluidic systems offer a high-throughput solution for enhancing efficiency and overcoming screening limitations.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemical Research Methods
Jing Liang, Huibin Zhang, Yee Ling Tan, Huimin Zhao, Ee Lui Ang
Summary: Bacteriophages are a promising alternative to antibiotics in combating antimicrobial resistance. This study presents a strategy for generating large libraries of phage variants, allowing for engineering of phage specificity and improved qualities. The findings demonstrate the potential of directed evolution in enhancing phage therapy for therapeutic applications.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Computer Science, Information Systems
Zhao-Yue Zhang, Zi-Jie Sun, Yu-He Yang, Hao Lin
Summary: This study presents a support vector machine-based approach that incorporates mutual information algorithm and incremental feature selection strategy to improve the prediction performance of lncRNA subcellular localization.
FRONTIERS OF COMPUTER SCIENCE
(2022)
Article
Biochemical Research Methods
Zijie Sun, Qinlai Huang, Yuhe Yang, Shihao Li, Hao Lv, Yang Zhang, Hao Lin, Lin Ning
Summary: Many studies have shown the important roles of small nucleolar RNAs (snoRNAs) in the development of complex human diseases. However, traditional experimental approaches for uncovering associations between snoRNAs and diseases are costly and time-consuming. This study proposed a method called PSnoD, which achieved superior performance and computational efficiency in predicting snoRNA-disease associations.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Xiaoming Song, Nan Li, Yingchao Zhang, Yi Liang, Rong Zhou, Tong Yu, Shaoqin Shen, Shuyan Feng, Yu Zhang, Xiuqing Li, Hao Lin, Xiyin Wang
Summary: Through transcriptomics and genomics analysis, this study identified and analyzed the genes related to chlorophyll and carotenoid in celery and other species. The study found that transcription factors play a role in regulating the expression of these genes. Expansion of carotenoid-related genes was observed in celery, while no notable expansion was found in chlorophyll biosynthesis genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Zhao-Yue Zhang, Lin Ning, Xiucai Ye, Yu-He Yang, Yasunori Futamura, Tetsuya Sakurai, Hao Lin
Summary: The location of miRNAs in cells plays a crucial role in their regulatory function. Current prediction algorithms for miRNA subcellular localization have limitations. In this study, a new data partitioning strategy and deep learning algorithm were proposed to accurately predict miRNA subcellular localization and explore the underlying mechanisms through motif analysis. Additionally, a user-friendly web server was established for convenient use.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biology
Jianqiang Xiao, Mujiexin Liu, Qinlai Huang, Zijie Sun, Lin Ning, Junguo Duan, Siquan Zhu, Jian Huang, Hao Lin, Hui Yang
Summary: This study investigated the relationship between environmental, habits, parental vision, demographic factors and adolescent myopia by analyzing questionnaire data. Machine learning algorithms were used to classify the samples. The age variable and parental myopia status were found to be important risk factors, while measures taken by children and the distance between books and eyes during reading were identified as protective factors.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Zahoor Ahmed, Hasan Zulfiqar, Lixia Tang, Hao Lin
Summary: The study found that polar amino acids, short bond length, wide DHA angle, and aromatic amino acids play important roles in the thermostability of proteins through statistical analysis on pairs of thermophilic proteins and their non-thermophilic orthologous.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Guangrong Li, Qiheng Chen, Wenxi Jiang, Ahui Zhang, Ennian Yang, Zujun Yang
Summary: Using multi-color non-denaturing fluorescence in situ hybridization (ND-FISH), a novel disease-resistant wheat-Th. intermedium double substitution line X479 was identified. Through sequential ND-FISH with multiple probes, 15 types of wheat-Thinopyrum translocation chromosomes were developed and characterized. The wheat-4J(S)L translocation lines showed high levels of resistance to stripe rust prevalent races.
Review
Biochemical Research Methods
Li Liu, Kaiyuan Han, Huimin Sun, Lu Han, Dong Gao, Qilemuge Xi, Lirong Zhang, Hao Lin
Summary: This review provides an overview of loop-calling tools for various 3C-based techniques. It categorizes and summarizes these tools, discusses background biases and denoising algorithms, and helps researchers select the most appropriate method for loop calling and downstream analysis. It is also useful for bioinformatics scientists aiming to develop new loop-calling algorithms.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Xiang Feng, Hongqi Zhang, Hao Lin, Haixia Long
Summary: In this study, a directed graph neural network called scDGAE was developed for scRNA-seq analysis, using graph autoencoders and graph attention network. The experiment results showed that the scDGAE model achieved promising performance in gene imputation and cell clustering prediction, and it can be applied to general scRNA-Seq analyses.
Article
Chemistry, Medicinal
Xiao-Wei Liu, Tian-Yu Shi, Dong Gao, Cai-Yi Ma, Hao Lin, Dan Yan, Ke-Jun Deng
Summary: Diabetes mellitus is a chronic metabolic disease that disrupts blood glucose homeostasis and leads to severe complications. The development of artificial intelligence has provided a powerful tool, iPADD, for accelerating the discovery of potential antidiabetic drugs. iPADD achieved high accuracy in drug prediction by using molecular fingerprints and machine learning algorithms.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Plant Sciences
Chengzhi Jiang, Xiaodan Liu, Zujun Yang, Guangrong Li
Summary: In this study, the researchers established the 42-chromosome karyotype of Elymus dahuricus using non-denaturing fluorescent in situ hybridization (ND-FISH) and Oligo-FISH painting methods. They also discovered a new type of intergenomic rearrangement between 2H and 5Y. Furthermore, the comparison of centromeric tandem repeats and immunostaining results suggested that centromere-associated sequences in H subgenomes were continuously changing during the process of polyploidization.
Article
Medicine, General & Internal
Wen Zhu, Shi-Shi Yuan, Jian Li, Cheng-Bing Huang, Hao Lin, Bo Liao
Summary: This study provides the first recognition framework for accurately identifying HBP based on machine learning. By using four sequence descriptors, HBP and non-HBP samples were represented by discrete numbers and input into SVM and RF algorithms for comparison. The SVM-based classifier was found to have the greatest potential for identifying HBP.
Review
Biochemistry & Molecular Biology
Hasan Zulfiqar, Zhiling Guo, Bakanina Kissanga Grace-Mercure, Zhao-Yue Zhang, Hui Gao, Hao Lin, Yun Wu
Summary: Hormone binding proteins (HBPs) belong to soluble carrier proteins that interact selectively and non-covalently with hormones, promoting growth hormone signaling in humans and other animals. The identification of HBPs is crucial for understanding these proteins and their applications in medical and commercial fields. Computational prediction methods, using sequence information and machine learning algorithms, have played a significant role in recognizing HBPs, offering a time-saving and cost-effective alternative to experimental methods.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biodiversity Conservation
Wenfei Liao, Hao Lin
Summary: Urbanisation has complex effects on the morphological traits of aquatic insect species, with different species exhibiting different strategies and abilities to cope with movement barriers caused by urbanisation.
INSECT CONSERVATION AND DIVERSITY
(2023)
Article
Biology
Jie Gao, Yongxian Feng, Yan Yang, Yuetong Shi, Junjie Liu, Hao Lin, Lirong Zhang
Summary: This study systematically identified and analyzed key CpG sites closely related to differential expression of genes in LUSC through a two-step correlation analysis method, and found that these sites and genes can serve as effective biomarkers for LUSC.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)