Review
Oncology
Udo Heinemann, Yvette Roske
Summary: The cold-shock domain is a conserved protein domain with a simple architecture but complex biological functions, found from bacteria to humans, that can bind both DNA and RNA through non-specific molecular interactions. The structural properties of cold-shock domains allow them to function in transcription regulation, RNA splicing, translation, stability, and sequestration, primarily through promiscuous DNA and RNA binding.
Article
Biotechnology & Applied Microbiology
Thomas E. Speltz, Zeyu Qiao, Colin S. Swenson, Xianghang Shangguan, John S. Coukos, Christopher W. Lee, Deborah M. Thomas, Jesse Santana, Sean W. Fanning, Geoffrey L. Greene, Raymond E. Moellering
Summary: Synthetic transcriptional repressors (STRs) derived from the bHLH domain of MAX have been developed using a chemical strategy. These STRs can bind to MYC/MAX consensus E-box motif with high affinity, show specificity comparable to or better than full-length TFs, compete with MYC/MAX protein for DNA binding, and inhibit MYC-dependent expression and cell proliferation. Co-crystallization and structure determination confirm that STRs retain the DNA recognition capability similar to full-length bHLH TFs. Furthermore, STRs derived from alternative bHLH-TFs can also be designed, enabling the development of highly specific mimetics targeting different gene regulatory elements.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Gamze Ayaz, Gizem Turan, Cagla Ece Olgun, Gizem Kars, Burcu Karakaya, Kerim Yavuz, Oyku Deniz Demiralay, Tolga Can, Mesut Muyan, Pelin Yasar
Summary: CXXC5 interacts with proteins as a scaffold to potentially modulate gene expressions.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Xavier B. Tao, Sarah LaFrance, Yifei Xing, Alberto A. Nava, Hector Garcia Martin, Jay D. Keasling, Tyler W. H. Backman
Summary: Megasynthase enzymes, such as PKSs and NRPSs, play a crucial role in microbial chemical warfare by evolving rapidly to produce novel chemicals. ClusterCAD 2.0 is an improved tool for designing and testing engineered PKS variants, expanding the chemical space accessible to enzymes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Emma Persson, Erik L. L. Sonnhammer
Summary: InParanoid 9 database, an important bioinformatics tool for inferring protein function and evolutionary analysis, provides ortholog predictions for protein domains and full-length proteins in 640 species. This version is a major upgrade of the InParanoid database, covering more species and allowing operation at the domain level.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Castrense Savojardo, Giulia Babbi, Pier Luigi Martelli, Rita Casadio
Summary: Human genome resequencing projects provide detailed data on single-nucleotide variations in protein-coding regions, many of which are linked to genetic diseases. However, understanding the molecular mechanisms behind these diseases is still limited. This study aims to identify Pfam domains statistically associated with disease-related variations, using 2,513 human protein sequences and 22,763 disease-related variations. The study finds that Pfam models can serve as specific markers to bridge genes, diseases, and disease classes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biology
Bo-wen Liu, Xiang-yun Wang, Jin-ling Cao, Lu-lu Chen, Yi-lei Wang, Bing-qian Zhao, Jia Zhou, Zhi-fa Shen
Summary: TDP-43 contributes to the suppression of apoptosis in hepatocellular carcinoma (HCC) by facilitating lipid metabolism. It enhances the mRNA stability of ABHD2, promoting the production of fatty acids and ROS, which suppress apoptosis. The findings suggest that TDP-43/ABHD2 could be potential targets for precise treatment of HCC.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jacob M. Wurlitzer, Aleksa Stanisic, Sebastian Ziethe, Paul M. Jordan, Kerstin Guenther, Oliver Werz, Hajo Kries, Markus Gressler
Summary: This study identified and characterized the nonribosomal peptide synthetase (NRPS) MalA in early diverging fungi, which catalyzes the biosynthesis of the surface-active biosurfactants malpinins. Specificity-based precursor-directed biosynthesis resulted in the production of 20 new congeners, and the study demonstrated the importance of fungi as a source of chemically tractable compounds for pharmaceutical applications.
Article
Biochemistry & Molecular Biology
Shuze Wang, Mary P. Lee, Scott Jones, Jie Liu, Joerg Waldhaus
Summary: This study utilized single-cell omics approach to investigate the spatial formation of a lineage-specific regulatory landscape in hair cells, predicting cell type-specific functions of transcription factors and reconstructing gene regulatory networks. By clustering target genes, related transcription factors and their developmental functions were inferred. The study also revealed that gradual changes in the chromatin accessibility landscape lag behind the transcriptional identity of hair cells along the longitudinal axis of the organ.
Article
Genetics & Heredity
Sanjeet Kumar Mahtha, Ravi Kiran Purama, Gitanjali Yadav
Summary: The study comprehensively explores the START domain containing proteins in the rice pangenome, revealing their high conservation and critical functional roles across 10 rice genomes. It also demonstrates diversity in terms of sub-functionalization and duplication within the family, with strong negative selection pressures during rice domestication. The findings highlight the importance of START proteins in plant growth and reproductive development, advancing our understanding of their diversity and evolution.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Nir Hananya, Xuanjia Ye, Shany Koren, Tom W. Muir, Barbara Imperiali
Summary: Studying dynamic biological processes requires approaches compatible with short lifetimes of biochemical transactions. A genetically encoded system involving a fusion protein and cell-permeable probes allows mapping of protein neighborhoods using visible light. Different labeling pathways are revealed depending on the nature of the exogenous probe employed. This photoproximity labeling system in combination with quantitative proteomics provides snapshots of protein territories with high temporal and spatial resolution, and has broad applications in the biomedical field.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Ling Hu, Yi Qiao, Jingyu Liu, Chao Zheng, Xiaofeng Wang, Peng Sun, Yucheng Gu, Wen Liu
Summary: Thioamitides are a family of RiPP natural products with potential in anticancer drug development, featuring a unique hdmHis residue. The enzymatic process for His functionalization relies on specific enzymes and precursor peptide sequences, without the need for prior peptide thioamidation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Construction & Building Technology
Zhihui Lang, Hui Liu, Na Meng, Haining Wang, Han Wang, Fanyu Kong
Summary: The research revealed that China has the highest number of publications in the field of fire safety studies, with the University of Science and Technology of China having the highest number of publications among relevant institutions. The core paths in fire safety studies include building and tunnel fire safety, combustion behavior-simulation analysis, and flame-retardant material paths, with recent hot research areas being building and tunnel fires, forest fires, and materials science engineering.
TUNNELLING AND UNDERGROUND SPACE TECHNOLOGY
(2021)
Article
Geography, Physical
Valentin T. Bickel, Lukas Mandrake, Gary Doran
Summary: Rockfalls, small-scale mass wasting events found across the solar system, are valuable sources of information about planetary activities. Using multi-domain training for automated rockfall mapping on different planets, such as the Moon and Mars, can improve detection performance significantly. This approach not only enhances performance in known domains like Mars, but also shows greater effectiveness in completely unknown domains, highlighting its importance in machine learning-enabled planetary science discovery.
ISPRS JOURNAL OF PHOTOGRAMMETRY AND REMOTE SENSING
(2021)
Article
Plant Sciences
Huiming Huang, Liangguang Yue, Fayu Deng, Xiaoyu Wang, Ning Wang, Hu Chen, Huayue Li
Summary: The integration of NMR-metabolomic and genomic analyses allows for enhanced identification of structural properties and biosynthetic information in natural products. In this study, NMR-based metabolomic profiling and genome mining were employed to isolate and determine the structures of two new natural products from Streptomyces sp. S063. The cytotoxicity evaluation demonstrated moderate growth inhibition against several human cancer cells.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Chemistry, Multidisciplinary
Jaekyun Jeon, Xin Qiao, Ivan Hung, Alok K. Mitra, Ambroise Desfosses, Daniel Huang, Peter L. Gor'kov, Rebecca C. Craven, Richard L. Kingston, Zhehong Gan, Fangqiang Zhu, Bo Chen
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2017)
Article
Multidisciplinary Sciences
Soumeya A. Jaballah, Graham D. Bailey, Ambroise Desfosses, Jaekyung Hyun, Alok K. Mitra, Richard L. Kingston
SCIENTIFIC REPORTS
(2017)
Article
Virology
Melissa N. Webby, Matthew P. Sullivan, Kavestri M. Yegambaram, Mazdak Radjainia, Jeremy R. Keown, Richard L. Kingston
Article
Biophysics
N. Herr, M. N. Webby, E. M. M. Bulloch, M. Schmitz, R. L. Kingston
BIOMOLECULAR NMR ASSIGNMENTS
(2019)
Article
Biochemistry & Molecular Biology
Ghader Bashiri, Laura V. Nigon, Ehab N. M. Jirgis, Ngoc Anh Thu Ho, Tamsyn Stanborough, Stephanie S. Dawes, Edward N. Baker, Esther M. M. Bulloch, Jodie M. Johnston
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biochemical Research Methods
Jordan Douglas, Richard Kingston, Alexei J. Drummond
PLOS COMPUTATIONAL BIOLOGY
(2020)
Review
Virology
Jordan Douglas, Alexei J. Drummond, Richard L. Kingston
Summary: The phosphoprotein gene of paramyxoviruses encodes multiple protein products, with the P protein being essential and V protein sometimes encoded by default, requiring guanosines to be inserted to encode P.
Article
Virology
Melissa N. Webby, Nicole Herr, Esther M. M. Bulloch, Michael Schmitz, Jeremy R. Keown, David C. Goldstone, Richard L. Kingston
Summary: The paramyxoviral phosphoprotein plays a crucial role in RNA synthesis, with a stable structure and dynamic linker, facilitating interactions between the polymerase and genomic RNA. The protein's C-terminal region exhibits a gradual disorder-to-order transition at the interface between the structured binding domain and disordered linker.
Correction
Biochemical Research Methods
J. Douglas, R. Kingston, A. J. Drummond
PLOS COMPUTATIONAL BIOLOGY
(2021)
Meeting Abstract
Biochemistry & Molecular Biology
Melissa Webby, Richard Kingston, Nicole Herr, Jeremy Keown, Michael Schmitz, Esther Bulloch
Article
Biophysics
Milka Doktorova, Frederick A. Heberle, Richard L. Kingston, George Khelashvili, Michel A. Cuendet, Yi Wen, John Katsaras, Gerald W. Feigenson, Volker M. Vogt, Robert A. Dick
BIOPHYSICAL JOURNAL
(2017)
Review
Biochemistry & Molecular Biology
Andrew C. Hausrath, Richard L. Kingston
CELLULAR AND MOLECULAR LIFE SCIENCES
(2017)
Article
Chemistry, Multidisciplinary
Matthew P. Sullivan, Michael Groessl, Samuel M. Meier, Richard L. Kingston, David C. Goldstone, Christian G. Hartinger
CHEMICAL COMMUNICATIONS
(2017)
Review
Virology
Jordan Douglas, Alexei J. Drummond, Richard L. Kingston
Summary: The phosphoprotein gene of paramyxoviruses encodes multiple protein products, with P, V, and W proteins generated by transcriptional slippage. Non-templated guanosine nucleosides are inserted to encode P, with variations in the editing process and evolutionary history observed between viruses. The physical mechanisms of cotranscriptional editing via slippage of the viral RNA polymerase are also reviewed.
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)