Article
Medical Laboratory Technology
Timothy Blewett, Justin Rhoades, Ruolin Liu, Kan Xiong, Sainetra Sridhar, Andjela Crnjac, Ju Cheng, Aleigha R. Lawless, Dennie T. Frederick, Keith T. Flaherty, Gerassimos Mike Makrigiorgos, Viktor A. Adalsteinsson
Summary: MAESTRO-Pool is a highly sensitive method for detecting MRD and specifically targets patient-specific tumor mutations in cfDNA. The new MRD caller allows for testing more mutations and cfDNA molecules, thereby improving the ability to detect MRD in blood.
CLINICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Ronghua Yu, Shengda Wang, Yue Zhu, Qianyu Li, Jiangan You, Jian Qiu, Yanhui Wang, Jie Liu, Tao Tang
Summary: This article presents a simple material genome approach for high-throughput screening of intrinsic fire-safe and processable polycarbonates. Two optimized chemical structures were successfully predicted and synthesized, providing an efficient guide in the design and synthesis of highly fire-safe polymers.
JOURNAL OF MATERIALS CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Chun Qian, Qingshu Zheng, Jie Chen, Bo Tu, Tao Tu
Summary: Solid main-chain NHC-rhodium(i) polymers prepared by coordination assembly show high catalytic activity in the hydroaminomethylation of olefins, with significantly improved yields and linear selectivity. The catalyst also exhibits broad substrate scope and excellent recyclability, making it suitable for the synthesis of various pharmaceuticals.
Article
Multidisciplinary Sciences
Yao Wang, Tao Qi, Jingtong Liu, Yuan Yang, Ziwen Wang, Ying Wang, Tianyi Wang, Miaomiao Li, Mingqing Li, Daru Lu, Alex Chia Yu Chang, Li Yang, Song Gao, Yongming Wang, Feng Lan
Summary: The CRISPR-Cas system can treat autosomal dominant diseases by disrupting mutant alleles through nonhomologous end joining (NHEJ). However, current CRISPR-Cas systems cannot differentiate many single-nucleotide mutations from wild-type alleles. We identified Cas12j-8 as an ideal genome editor with comparable activity to AsCas12a and Un1Cas12f1. Cas12j-8 is a highly specific nuclease sensitive to single-nucleotide mismatches in the protospacer adjacent motif (PAM)-proximal region. It enables allele-specific disruption of genes with single-nucleotide polymorphisms (SNPs) and has potential therapeutic applications.
Article
Chemistry, Medicinal
Zhihong Liu, Dane Huang, Shuangjia Zheng, Ying Song, Bingdong Liu, Jingyuan Sun, Zhangming Niu, Qiong Gu, Jun Xu, Liwei Xie
Summary: The pre-trained self-attentive message passing neural network (P-SAMPNN) model was developed based on anti-osteoclastogenesis dataset for virtual screening. The model outperformed other baseline models and resulted in the identification of two nanomolar-level inhibitors against osteoclastogenesis with a new scaffold. Subsequent studies showed that these compounds significantly suppressed the expression of specific genes.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Mohammad Hajjar, Nicholas Chim, Chao Liu, Piet Herdewijn, John C. Chaput
Summary: In this study, researchers used X-ray crystallography to investigate the recognition of pTNA nucleotides by polymerases. The findings reveal that the polymerase mediates base pairing between pTNA and DNA, providing new insights into the enzymatic synthesis of XNAs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Physical
Joseph M. Dennis, Dmitry Yu Zubarev
Summary: This study successfully combines computational design and experimental evaluation to create three new polyimides with high glass transition temperatures, using competitive learning algorithms and supervised self-organizing maps. The predicted and measured values of the T-g for these polyimides are in close agreement, demonstrating the effectiveness of the proposed computational design strategy.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Multidisciplinary
Huixia Xuan, Qingbao Guan, Luzhi Zhang, Zhengwei You
Summary: This study developed swimming devices with rapid fabrication, intelligent transportation, and self-healing capabilities based on photoheating thermoplastics. Customized through 3D printing, the devices demonstrated versatile motion modes and high propulsive force. This design principle will inspire the development of thermoplastics in an exciting field.
ADVANCED FUNCTIONAL MATERIALS
(2021)
Article
Medicine, Research & Experimental
Carlye Frisch, William W. Kostes, Brooke Galyon, Brycelyn Whitman, Stefan J. Tekel, Kylie Standage-Beier, Gayathri Srinivasan, Xiao Wang, David A. Brafman
Summary: Prime editing technologies allow precise genome editing with improved efficiency compared to CRISPR nuclease-based methods. However, current methods for identifying and isolating prime-edited cell populations are inefficient. In this study, we developed a fluorescence-based system called PINE-TREE for real-time enrichment of prime-edited cell populations and demonstrated its broad utility for efficient editing at various genomic loci, including difficult-to-edit human pluripotent stem cell lines.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Microbiology
Zhenwu Luo, Alexander V. Alekseyenko, Elizabeth Ogunrinde, Min Li, Quan-Zhen Li, Lei Huang, Betty P. Tsao, Diane L. Kamen, Jim C. Oates, Zihai Li, Gary S. Gilkeson, Wei Jiang
Summary: Blood microbiome research is crucial for studying microbial-host interactions and immune perturbations. A quality-filtering strategy has been developed to analyze plasma microbiome and identify pathogenesis-associated bacteria in individuals with different health conditions. Identified bacteria were further verified for their pathogenic activities in vitro.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Genetics & Heredity
Jing Ge, Le P. Ngo, Simran Kaushal, Ian J. Tay, Elina Thadhani, Jennifer E. Kay, Patrizia Mazzucato, Danielle N. Chow, Jessica L. Fessler, David M. Weingeist, Robert W. Sobol, Leona D. Samson, Scott R. Floyd, Bevin P. Engelward
Summary: DNA damage is directly linked to aging, cancer, and other diseases, and cells have evolved highly conserved DNA repair pathways to counteract its deleterious effects. The CometChip platform offers increased throughput and sensitivity for parallel analysis of multiple DNA repair activities, expanding the utility of the comet assay for precise, high-throughput assessment of repair deficiencies in different pathways.
Article
Nanoscience & Nanotechnology
Lingxuan Kong, Hanqi Wen, Yifei Luo, Xiaodong Chen, Xing Sheng, Yuxin Liu, Peng Chen
Summary: This paper introduces a dual-conductive and stiffness-morphing microneedle patch (DSMNP) for high-fidelity electrophysiological recordings with reduced tissue damage. The DSMNP can absorb electrolyte and provide a stable interface, and has been proven to have various applications in plant physiology research and smart agriculture.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Biochemical Research Methods
Cheng Ye, Bryan Thornlow, Angie Hinrichs, Alexander Kramer, Cade Mirchandani, Devika Torvi, Robert Lanfear, Russell Corbett-Detig, Yatish Turakhia
Summary: matOptimize is a fast and memory-efficient tool for optimizing phylogenetic trees, offering significant improvements in runtime and memory usage compared to existing methods. It addresses the pressing need for maintaining and optimizing large-scale phylogenetic trees during the COVID-19 pandemic.
Article
Chemistry, Multidisciplinary
Zhiyong Wang, Xiangkun Jia, Panpan Zhang, Yannan Liu, Haoyuan Qi, Peng Zhang, Ute Kaiser, Sebastian Reineke, Renhao Dong, Xinliang Feng
Summary: The high-performance ECDs with a fully crystalline viologen-immobilized 2D polymer thin film demonstrate rapid switching speed, high coloration efficiency, and low energy consumption. By vertically integrating the V2DP ECDs with transparent solar cells, transmission-tunable, self-sustainable EC window prototypes were successfully fabricated.
ADVANCED MATERIALS
(2022)
Article
Chemistry, Medicinal
Ningning Yao, Zhiping Jia, Yongbin Tian, Shuzeng Hou, Xiaoxiao Yang, Jihong Han, Yajun Duan, Chenzhong Liao, Yi Kong, Zhouling Xie
Summary: In this study, novel selective FXIa inhibitors were identified through structure-based drug design strategies, which have extra interactions with the S2 subsite of FXIa. Compound 35 displayed good inhibitory activity against FXIa and high selectivity over PKal and other serine proteases. In vivo experiments showed that 35 exhibited significant antithrombotic activity without increasing bleeding risk and toxicity in mice, suggesting it as a promising candidate for further research.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Review
Chemistry, Multidisciplinary
Bar Israeli, Livne Vaserman, Miriam Amiram
ISRAEL JOURNAL OF CHEMISTRY
(2020)
Article
Multidisciplinary Sciences
Felipe Garcia Quiroz, Nan K. Li, Stefan Roberts, Patrick Weber, Michael Dzuricky, Isaac Weitzhandler, Yaroslava G. Yingling, Ashutosh Chilkoti
Article
Multidisciplinary Sciences
Felipe Garcia Quiroz, Vincent F. Fiore, John Levorse, Lisa Polak, Ellen Wong, H. Amalia Pasolli, Elaine Fuchs
Article
Multidisciplinary Sciences
Vincent F. Fiore, Matej Krajnc, Felipe Garcia Quiroz, John Levorse, H. Amalia Pasolli, Stanislav Y. Shvartsman, Elaine Fuchs
Correction
Multidisciplinary Sciences
Vincent F. Fiore, Matej Krajnc, Felipe Garcia Quiroz, John Levorse, H. Amalia Pasolli, Stanislav Y. Shvartsman, Elaine Fuchs
Article
Biochemistry & Molecular Biology
Katharina Laass, Felipe Garcia Quiroz, Johannes Hunold, Stefan Roberts, Ashutosh Chilkoti, Dariush Hinderberger
Summary: The study reveals the hydration dynamics in phase-separating IDPs, showing that side-chain rehydration forms a dynamic water shield that affects solubility. This water shell strength is a sequence feature of IDPs, encoding for the stability of their phase-separated assemblies. The complexity of nanoscopic water-IDP interactions dictates their rich phase separation behavior.
Article
Biochemistry & Molecular Biology
Dagan Hadar, Sigal Gelkop, Livne Vaserman, Miriam Amiram
Summary: The evolution of Methanocaldococcus jannaschii tyrosyl-tRNA synthetase has led to increased production of green fluorescent protein containing specific unnatural amino acids, enabling efficient fluorescent labeling of proteins in bacteria. This method allows for high-yield expression of elastin-like polypeptides with multiple unnatural amino acids, creating potential applications in protein and biomaterial conjugates.
Article
Chemistry, Multidisciplinary
Bar Israeli, Daniela S. Strugach, Sigal Gelkop, Shir Weber, Dor S. Gozlan, Miriam Amiram
Summary: This study demonstrates the successful incorporation of multiple light-responsive uAAs in elastin-like polypeptides, enabling reversible phase transitions and the creation of self-assembled nanostructures. The evolved translation machinery can be used for the design of other families of protein-based biomaterials with customized and tunable light-responsive behavior.
ADVANCED FUNCTIONAL MATERIALS
(2021)
Article
Multidisciplinary Sciences
Koen Vanderschuren, Pol Arranz-Gibert, Minsoo Khang, Dagan Hadar, Alice Gaudin, Fan Yang, Ewa Folta-Stogniew, W. Mark Saltzman, Miriam Amiram, Farren J. Isaacs
Summary: The use of biologics in disease treatment has been increasing due to their specificity, low toxicity, and limited side effects. However, peptide- and protein-based drugs have limitations in terms of short half-lives and immunogenicity. To address these challenges, researchers have used a genomically recoded organism to produce synthetic biopolymers with programmable binding affinity and tunable half-lives. This work provides a proof of concept for extending and regulating the half-life of protein or peptide therapeutics.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biotechnology & Applied Microbiology
Osher Gueta, Ortal Sheinenzon, Rotem Azulay, Hadas Shalit, Daniela S. Strugach, Dagan Hadar, Sigal Gelkop, Anat Milo, Miriam Amiram
Summary: The incorporation of non-canonical amino acids using engineered aminoacyl-tRNA synthetases allows for the expansion of the chemical repertoire of proteins. This study identified high-performance aaRS variants that enable efficient multi-site incorporation of different aromatic ncAAs. It also demonstrated the impact of aromatic ncAAs on the properties and functions of protein-based polymers, providing insight for the design of new polymers with improved properties.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Pharmacology & Pharmacy
Osher Gueta, Miriam Amiram
Summary: Expanding the chemical repertoire of protein-based polymers allows the production of sequence-defined biopolymers with diverse chemical properties. Various techniques, such as chemical and enzymatic treatments and the incorporation of unnatural amino acids, can be used to install different chemical groups, enabling the design of customized protein-based drug delivery systems.
ADVANCED DRUG DELIVERY REVIEWS
(2022)
News Item
Oncology
Kelsey P. Kubelick, Felipe Garcia Quiroz
Summary: A recent study has revealed the connection between PD-L1 upregulation on cancer cells and IRF1-KAT8 transactivation hubs at PD-L1 loci. Targeting these hubs therapeutically could enhance anti-tumor immunity.
Article
Biochemical Research Methods
Daniela S. Strugach, Dagan Hadar, Miriam Amiram
Summary: This study found a photoswitch with suitable light-responsive properties that can be incorporated into proteins, enabling light-responsive behavior. The method allows for multisite incorporation of the photoswitch at the polypeptide level, providing a general approach for designing proteins and polymers with robust light-responsive behavior.
ACS SYNTHETIC BIOLOGY
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Felipe G. Quiroz
Review
Engineering, Biomedical
Dagan Hadar, Daniela S. Strugach, Miriam Amiram
Summary: This review discusses recent progress in the production and application of recombinant PBP-conjugates, including various approaches for protein conjugation or crosslinking, and demonstrates the utility of this approach in imparting new properties and functions onto PBPs composed of elastin, resilin, silk, or collagen-based sequences.
ADVANCED NANOBIOMED RESEARCH
(2022)