Article
Biotechnology & Applied Microbiology
Pavel Sinitcyn, Hamid Hamzeiy, Favio Salinas Soto, Daniel Itzhak, Frank McCarthy, Christoph Wichmann, Martin Steger, Uli Ohmayer, Ute Distler, Stephanie Kaspar-Schoenefeld, Nikita Prianichnikov, Sule Yilmaz, Jan Daniel Rudolph, Stefan Tenzer, Yasset Perez-Riverol, Nagarjuna Nagaraj, Sean J. Humphrey, Jurgen Cox
Summary: MaxDIA is a software platform specifically designed for analyzing DIA proteomics data within the MaxQuant environment, achieving deep proteome coverage and improved protein quantification accuracy. It provides accurate FDR estimates for hypothesis-free analysis of DIA samples.
NATURE BIOTECHNOLOGY
(2021)
Article
Nanoscience & Nanotechnology
Jie Zheng, Han Xu, Bingzhi Li, Muhammad Sohail, Jingjing Bi, Fuming Zhang, Robert J. Linhardt, He Huang, Xing Zhang
Summary: Based on the Modular-Enzymes Assembly by Spatial Segregation (MASS) strategy, a universal immobilization platform was developed to assemble multiple glycoenzymes in compartmentalized MOF particles, reducing interference and cross-inhibitions. Different glycans, including glycosyl donor, disaccharides, oligosaccharides, and polysaccharides with cofactor regeneration, were efficiently prepared. This robust multienzyme immobilization platform has industrial potential for enzymatic synthesis of more complex glycans.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Computer Science, Artificial Intelligence
Alvaro Belmonte, Amelia Zafra, Eva Gibaja
Summary: The MIML library is a Java software tool for developing, testing, and comparing classification algorithms for MIML learning. It includes 43 algorithms, provides specific data management and partitioning formats, supports various evaluation methods, and allows algorithms to be executed through xml configuration files.
Article
Chemistry, Physical
Christoph Bannwarth, Todd J. Martinez
Summary: The article presents an approach to unify ab initio and semiempirical electronic structure code paths. By separating the wavefunction ansatz and the matrix representations of operators, the Hamiltonian can refer to either an ab initio or semiempirical treatment. The authors built a semiempirical integral library and interfaced it to the GPU-accelerated electronic structure code TeraChem. This approach enables the combination of semiempirical Hamiltonians with the full functionality of the ab initio electronic structure code.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Jan Bierlmeier, Miguel Alvaro-Benito, Maren Scheffler, Kristina Sturm, Luisa Rehkopf, Christian Freund, Dirk Schwarzer
Summary: Sortase-mediated ligation is a powerful tool in protein chemistry for connecting peptides. By using switchable sortase substrates, multi-fragment SML can be achieved, expanding its applications in protein research.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Zhonggui Fang, Yige Wu, Yinyin Su, Juan Yi, Sicong Liu, Zheng Wang
Summary: This study proposes a novel soft robot design based on the body structure of earthworms and the compliance of soft robots. A cross-linked actuator coordination mechanism is used to achieve simultaneous multi-functional movements. The robot can perform grabbing, manipulation, and locomotion, and is able to transport multiple objects in unstructured environments. The experimental validation demonstrates the effectiveness of the cross-linked actuator coordination concept in soft robot design.
SCIENTIFIC REPORTS
(2023)
Article
Computer Science, Hardware & Architecture
Cristian C. Erazo-Agredo, Luis Diez, Ramon Aguero, Mario Garza-Fabre, Javier Rubio-Loyola
Summary: This paper presents the design and implementation of an experimental architecture that enables the actual separation of protocol layers into different nodes, allowing for experimentation with multiple functional split configurations. The validation results demonstrate the feasibility of the proposed implementation, which meets the latency requirements in all configurations.
Article
Chemistry, Physical
Moritz Voss, Robin Kung, Takahiro Hayashi, Magdalena Jonczyk, Michael Niklaus, Hans Iding, Dennis Wetzl, Rebecca Buller
Summary: This study presents a multi-faceted screening procedure to capture ketoreductase (KRED) diversity from different sources. By establishing a library containing 51 KRED enzymes, it was found that 29 of them had never been described before, with 18 exhibiting anti-Prelog preference. Additionally, analysis of the library's catalytic activity towards a diverse ketone substrate set revealed broad substrate scope and complementing enantio-preference of the individual KREDs.
Article
Biochemistry & Molecular Biology
Hyukjun Choi, Soomin Eom, Han-ul Kim, Yoonji Bae, Hyun Suk Jung, Sebyung Kang
Summary: Genetically engineered encapsulin protein cage nanoparticles were designed as modular nanoplatforms by introducing split-C-intein and SpyTag on the interior and exterior surfaces, respectively, allowing for dual functionalization of the interior space and exterior surface. This approach has the potential for developing novel protein-based nanostructured devices and nanomedical tools.
Article
Pharmacology & Pharmacy
Abdin Shakirin Mohamad Norpi, Muhammad Luqman Nordin, Nuraziemah Ahmad, Haliza Katas, Abdullah Al-Hadi Ahmad Fuaad, Asif Sukri, Nirmal Marasini, Fazren Azmi
Summary: Two variants of nanoparticle-based vaccines against group A streptococcus (GAS) were developed in this study. The vaccines, composed of encapsulated KLH protein and lipidated M-protein derived B cell peptide epitope, showed high antigen-specific antibody titres and opsonic activity against GAS strains in immunized mice.
ASIAN JOURNAL OF PHARMACEUTICAL SCIENCES
(2022)
Article
Engineering, Electrical & Electronic
Gang Zhang, Lei Wang, Zhongjun Jiang
Summary: To address the disadvantages of small transmission rate and poor Bit Error Rate (BER) of M-ary differential chaos shift keying, an expanded capacity orthogonal noise suppression multi-level Differential Chaotic Shift Keying (DCSK) communication system is proposed. An improved orthogonal chaotic signal generator is designed at the transmitter of the system. It can generate four sets of orthogonal chaos-based signals, which can greatly increase the communication capacity. The system utilizes a particle swarm algorithm to optimize each parameter and has a lower BER and better integrated utility compared to other systems.
JOURNAL OF ELECTRONICS & INFORMATION TECHNOLOGY
(2023)
Review
Chemistry, Analytical
Behide Saltepe, Lei Wang, Baojun Wang
Summary: Wastewater surveillance is an important tool for understanding community health by tracking biomarkers such as pollutants and pathogens in wastewater. Advances in synthetic biology have facilitated the development of portable biosensing platforms for rapid and low-cost monitoring of water contaminants and health-related biomarkers.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Editorial Material
Biotechnology & Applied Microbiology
Shimshon Belkin, Baojun Wang
MICROBIAL BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Eunice A. Ferreira, Catarina C. Pacheco, Joao S. Rodrigues, Filipe Pinto, Pedro Lamosa, David Fuente, Javier Urchueguia, Paula Tamagnini
Summary: This study successfully produced glycine betaine using the cyanobacterium Synechocystis sp. PCC 6803 as a chassis, through the construction of synthetic devices in mutant strains.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Analytical
Sheng-Yan Chen, Yan Zhang, Renjie Li, Baojun Wang, Bang-Ce Ye
Summary: This study improves the performance of whole-cell biosensors for arsenic contamination by optimizing the promoter design. The arsenic-responsive system from Escherichia coli is used as the sensing element, and a genetic circuit is constructed to characterize the refactored promoters. A novel promoter with maximal repression efficiency and optimal fold change is discovered, and high sensitivity fluorescence and colorimetric sensors are developed for quantifying arsenic levels in groundwater.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Yang Liu, Filipe Pinto, Xinyi Wan, Zhugen Yang, Shuguang Peng, Mengxi Li, Jonathan M. Cooper, Zhen Xie, Christopher E. French, Baojun Wang
Summary: This study reveals the programmability of crRNA-tracrRNA hybridization in type II CRISPR systems. By reprogramming the crRNA-tracrRNA interactions, the researchers demonstrate the design of orthogonal cellular computing devices and the hijacking of endogenous small RNAs/mRNAs as crRNAs. Furthermore, they demonstrate the use of re-engineered gRNA pairings as RNA sensors for monitoring gene transcription or detecting SARS-CoV-2 RNA.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Shuyao Li, Jing Xiao, Tianzheng Sun, Fangjian Yu, Kaihang Zhang, Yuantao Feng, Chenchao Xu, Baojun Wang, Lei Cheng
Summary: This study developed a microbial experimental system that allows for rapidly generating microbial consortia with programmable ecological interactions. By using engineered microbial consortia, the researchers showed different population dynamics under different initial inoculation conditions and controlled the transitions between exploitation, competition, and synergy by tuning the engineered modules. Mathematical models were derived to quantitatively capture the experimentally observed population dynamics of these synthetic microbial consortia.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Ella Lucille Thornton, Sarah Maria Paterson, Zoe Gidden, Mathew H. Horrocks, Nadanai Laohakunakorn, Lynne Regan
Summary: This article presents a new method for surface capture of proteins in cell-free protein synthesis (CFPS), demonstrating the spontaneous self-assembly of protein BslA into functionalizable surfaces. The method allows for the covalent capture of proteins using Catcher/Tag technology. The simplicity and cost efficiency of this method suggest its potential applications in cell-free-based techniques.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yang W. Huan, Jidapha Fa-arun, Baojun Wang
Summary: The alternative tail fiber S' of Enterobacteria phage P1 can efficiently transduce genes into Shigella flexneri and Escherichia coli bacteria. At least one O-antigen unit is required for P1(S') transduction. Improved transduction efficiency of P1(S') facilitates the delivery of antimicrobial genes into Shigella flexneri.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Chemistry, Analytical
Yuwei Pan, Kang Mao, Qinxin Hui, Baojun Wang, Jonathan Cooper, Zhugen Yang
Summary: This paper critically reviews the recent development of paper-based analytical devices (PADs) for the diagnosis of infectious diseases and wastewater monitoring. PADs have attracted significant attention due to their rapid and low-cost nature, facilitating a better understanding of the transmission routes of infectious diseases within populations.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Jidapha Fa-arun, Yang Wei Huan, Elise Darmon, Baojun Wang
Summary: This study developed a bacteriophage P4 cosmid system for delivering Cas9 antimicrobial into clinically relevant human gut pathogens. The genetic engineering of the phage tail fiber improved the transduction efficiency of cosmid DNA and allowed recognition of a nonnative host. This research demonstrates the potential of the P4 cas9 cosmid system as a DNA sequence-specific antimicrobial against clinically relevant gut pathogenic bacteria.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
Yang W. Huan, Vincenzo Torraca, Russell Brown, Jidapha Fa-arun, Sydney L. Miles, Diego A. Oyarzun, Serge Mostowy, Baojun Wang
Summary: The discovery of CRISPR-Cas9 provides opportunities to selectively kill specific bacteria, but its delivery into bacterial cells is inefficient. In this study, the P1-derived phagemid is used to efficiently deliver the CRISPR-Cas9 chromosomal-targeting system into Escherichia coli and Shigella flexneri, achieving DNA sequence-specific killing of targeted bacterial cells. The P1 phage particles can also deliver cas9 phagemids into S. flexneri in vivo, reducing bacterial load and promoting host survival. This study demonstrates the potential of combining P1 phage-based delivery with the CRISPR system for efficient clearance of bacterial infection.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Microbiology
Yang Wei Huan, Russell Brown, Baojun Wang
Summary: Our study demonstrates that RepL expression and the lytic stage origin, oriL, are necessary for the lytic replication of bacteriophage P1. We found that a specific region in the repL gene sequence, AT2, plays a significant role in RepL-mediated DNA replication. Mutations in this region affect the RepL-mediated signal amplification, while mutations in IHF and DnaA binding sites have minimal effects. Furthermore, combining repL gene expression with a non-protein-coding copy of repL gene sequence (nc-repL) enhances the output of an arsenic biosensor. These findings provide insights into P1 oriL and suggest the potential of repL constructs in genetic biosensor modulation.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Pharmacology & Pharmacy
Xiyan Wang, Nan Zhou, Baojun Wang
Summary: Bacterial synthetic biology provides powerful tools for drug discovery, including bioinformatic tools, CRISPR tools, engineered transcriptional regulators, and synthetic biosensors. Reprogramming bacteriophages as living drugs is also a recent advancement in this field.
EXPERT OPINION ON DRUG DISCOVERY
(2023)
Review
Biochemistry & Molecular Biology
Yang Liu, Wei Liu, Baojun Wang
Summary: The programmability of the CRISPR system based on Watson-Crick base pairing is a valuable feature in engineering RNA sensors. Despite the existence of successful RNA sensing approaches, the continuous expansion of CRISPR family members indicates the promising potential of CRISPR-based RNA sensors for various new functions and applications.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)