Article
Biochemical Research Methods
Mihai Lefter, Jonathan K. Vis, Martijn Vermaat, Johan T. den Dunnen, Peter E. M. Taschner, Jeroen F. J. Laros
Summary: The Human Genome Variation Society provides guidelines on accurately describing genetic variants, with the Mutalyzer tool suite being able to automatically apply these guidelines for users to check and correct their descriptions. Mutalyzer has successfully processed over 133 million descriptions, with around 50% being reported as correct and able to automatically correct descriptions for approximately 7% of cases.
Article
Multidisciplinary Sciences
Hong-Wen Tang, Kerstin Spirohn, Yanhui Hu, Tong Hao, Istvan A. Kovacs, Yue Gao, Richard Binari, Donghui Yang-Zhou, Kenneth H. Wan, Joel S. Bader, Dawit Balcha, Wenting Bian, Benjamin W. Booth, Atina G. Cote, Steffi de Rouck, Alice Desbuleux, Kah Yong Goh, Dae-Kyum Kim, Jennifer J. Knapp, Wen Xing Lee, Irma Lemmens, Cathleen Li, Mian Li, Roujia Li, Hyobin Julianne Lim, Yifang Liu, Katja Luck, Dylan Markey, Carl Pollis, Sudharshan Rangarajan, Jonathan Rodiger, Sadie Schlabach, Yun Shen, Dayag Sheykhkarimli, Bridget TeeKing, Frederick P. Roth, Jan Tavernier, Michael A. Calderwood, David E. Hill, Susan E. Celniker, Marc Vidal, Norbert Perrimon, Stephanie E. Mohr
Summary: This study uses advanced methods to identify protein-protein interactions in Drosophila, generating widely useful physical and data resources for the identification of new components in pathways, complexes, and processes. The generation of reference maps of interactome networks provides a protein-centric approach to discover new components in existing pathways, complexes, and processes, which is helpful for genetic studies. The results include the FlyBi dataset and the DroRI reference interaction network, which provide a foundation for building new hypotheses about protein networks and function.
NATURE COMMUNICATIONS
(2023)
Article
Physics, Multidisciplinary
F. P. An, W. D. Bai, A. B. Balantekin, M. Bishai, S. Blyth, G. F. Cao, J. Cao, J. F. Chang, Y. Chang, H. S. Chen, H. Y. Chen, S. M. Chen, Y. Chen, Y. X. Chen, J. Cheng, Z. K. Cheng, J. J. Cherwinka, M. C. Chu, J. P. Cummings, O. Dalager, F. S. Deng, Y. Y. Ding, M. Diwan, T. Dohnal, D. Dolzhikov, J. Dove, D. A. Dwyer, J. P. Gallo, M. Gonchar, G. H. Gong, H. Gong, W. Q. Gu, J. Y. Guo, L. Guo, X. H. Guo, Y. H. Guo, Z. Guo, R. W. Hackenburg, S. Hans, M. He, K. M. Heeger, Y. K. Heng, Y. K. Hor, Y. B. Hsiung, B. Z. Hu, J. R. Hu, T. Hu, Z. J. Hu, H. X. Huang, J. H. Huang, X. T. Huang, Y. B. Huang, P. Huber, D. E. Jaffe, K. L. Jen, X. L. Ji, X. P. Ji, R. A. Johnson, D. Jones, L. Kang, S. H. Kettell, S. Kohn, M. Kramer, T. J. Langford, J. Lee, J. H. C. Lee, R. T. Lei, R. Leitner, J. K. C. Leung, F. Li, H. L. Li, J. J. Li, Q. J. Li, R. H. Li, S. Li, S. C. Li, W. D. Li, X. N. Li, X. Q. Li, Y. F. Li, Z. B. Li, H. Liang, C. J. Lin, G. L. Lin, S. Lin, J. J. Ling, J. M. Link, L. Littenberg, B. R. Littlejohn, J. C. Liu, J. L. Liu, J. X. Liu, C. Lu, H. Q. Lu, K. B. Luk, B. Z. Ma, X. B. Ma, X. Y. Ma, Y. Q. Ma, R. C. Mandujano, C. Marshall, K. T. McDonald, R. D. McKeown, Y. Meng, J. Napolitano, D. Naumov, E. Naumova, T. M. T. Nguyen, J. P. Ochoa-Ricoux, A. Olshevskiy, H-R Pan, J. Park, S. Patton, J. C. Peng, C. S. J. Pun, F. Z. Qi, M. Qi, X. Qian, N. Raper, J. Ren, C. Morales Reveco, R. Rosero, B. Roskovec, X. C. Ruan, H. Steiner, J. L. Sun, T. Tmej, K. Treskov, W-H Tse, C. E. Tull, B. Viren, V. Vorobel, C. H. Wang, J. Wang, M. Wang, N. Y. Wang, R. G. Wang, W. Wang, X. Wang, Y. Wang, Y. F. Wang, Z. Wang, Z. Wang, Z. M. Wang, H. Y. Wei, L. H. Wei, L. J. Wen, K. Whisnant, C. G. White, H. L. H. Wong, E. Worcester, D. R. Wu, Q. Wu, W. J. Wu, D. M. Xia, Z. Q. Xie, Z. Z. Xing, H. K. Xu, J. L. Xu, T. Xu, T. Xue, C. G. Yang, L. Yang, Y. Z. Yang, H. F. Yao, M. Ye, M. Yeh, B. L. Young, H. Z. Yu, Z. Y. Yu, B. B. Yue, V Zavadskyi, S. Zeng, Y. Zeng, L. Zhan, C. Zhang, F. Y. Zhang, H. H. Zhang, J. L. Zhang, J. W. Zhang, Q. M. Zhang, S. Q. Zhang, X. T. Zhang, Y. M. Zhang, Y. X. Zhang, Y. Y. Zhang, Z. J. Zhang, Z. P. Zhang, Z. Y. Zhang, J. Zhao, R. Z. Zhao, L. Zhou, H. L. Zhuang, J. H. Zou
Summary: This study reports the first measurement of high-energy reactor antineutrinos at Daya Bay, with a successful separation of 2500 signal events from background using a multivariate analysis method. The existence of antineutrinos with energies above 10 MeV is confirmed and a 29% deficit in antineutrino flux in the energy region of 8-11 MeV is observed. This result provides a data-based reference for other experiments to further investigate the production of antineutrinos in commercial reactors.
PHYSICAL REVIEW LETTERS
(2022)
Article
Physics, Multidisciplinary
Javier Mazzitelli, Pier Francesco Monni, Paolo Nason, Emanuele Re, Marius Wiesemann, Giulia Zanderighi
Summary: Studying the production of top-quark pairs in hadronic collisions is crucial for understanding the properties of the heaviest quark observed in nature, with Monte Carlo simulations being heavily relied upon and challenged by experimental measurements. This work presents the first matched computation of top-quark pair production at next-to-next-to-leading order in QCD with all-order radiative corrections using parton-shower simulations, marking an important step towards simulating other hadronic processes with color charges in the final state.
PHYSICAL REVIEW LETTERS
(2021)
Article
Multidisciplinary Sciences
Ellen S. Cameron, Philip J. Schmidt, Benjamin J-M Tremblay, Monica B. Emelko, Kirsten M. Muller
Summary: Amplicon sequencing revolutionizes the study of environmental DNA samples, providing a rapid and sensitive technique for microbial community analysis. Rarefaction, while statistically controversial, remains prevalent in practice for normalizing library sizes for diversity analysis. Repeated rarefying proposed as a tool to proportionately represent all observed sequences and characterize random variation in diversity analysis.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Andrew E. Short, Dowan Kim, Prasaad T. Milner, Corey J. Wilson
Summary: This study presents a technology that uses repurposed parts of Transcriptional Programming to regulate recombinase function and facilitate synthetic memory in the living system. The interception synthetic memory allows programmable loss-of-function and gain-of-function, as well as nested Boolean logical operations. It offers a 5-fold increase in memory capacity compared to previous generations and is 10 times faster. This memory technology complements decision-making via Transcriptional Programming and can be used in developing intelligent synthetic biological systems.
NATURE COMMUNICATIONS
(2023)
Article
Engineering, Environmental
Zexin Tao, Xiaojuan Lin, Yao Liu, Feng Ji, Suting Wang, Ping Xiong, Li Zhang, Qing Xu, Aiqiang Xu, Ning Cui
Summary: This study collected sewage samples from Jinan, China from 2018 to 2019, and analyzed classic and novel HAstVs using real-time quantitative PCR and next generation sequencing. The results showed that sewage contains a high diversity of astroviruses, and there are multiple co-circulating lineages within each local HAstV genotype.
Article
Biochemistry & Molecular Biology
David Ochoa, Andrew Hercules, Miguel Carmona, Daniel Suveges, Jarrod Baker, Cinzia Malangone, Irene Lopez, Alfredo Miranda, Carlos Cruz-Castillo, Luca Fumis, Manuel Bernal-Llinares, Kirill Tsukanov, Helena Cornu, Konstantinos Tsirigos, Olesya Razuvayevskaya, Annalisa Buniello, Jeremy Schwartzentruber, Mohd Karim, Bruno Ariano, Ricardo Esteban Martinez Osorio, Javier Ferrer, Xiangyu Ge, Sandra Machlitt-Northen, Asier Gonzalez-Uriarte, Shyamasree Saha, Santosh Tirunagari, Chintan Mehta, Juan Maria Roldan-Romero, Stuart Horswell, Sarah Young, Maya Ghoussaini, DavidG Hulcoop, Ian Dunham, EllenM McDonagh
Summary: The Open Targets Platform is an open-source resource that facilitates drug target identification and prioritization using publicly available data. It has been redesigned and rebuilt to improve data integration, expand the ways users can explore the data, and enhance the user experience. The platform now includes enhanced gene-disease evidence, new features for assessing target safety and tractability, and machine learning applications for extracting knowledge from literature, clinical trials, and drug labels.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Ping Zhang, Min Wang, Tao Zhou, Daozhen Chen
Summary: SeqWiz is a state-of-the-art toolkit for constructing next-generation sequence databases and performing proteomic-centric sequence analyses. It introduces two derived data formats, SQPD and SET, which outperform traditional FASTA or PEFF formats in terms of time and resource consumption. SeqWiz also provides compatible functions for handling traditional text formats and can promote the implementation of complementary proteomics for precision proteomics.
BMC BIOINFORMATICS
(2023)
Article
Biodiversity Conservation
Weiwei Yu, Dian Zhang, Jianji Liao, Li Ma, Xiaofen Zhu, Wanting Zhang, Wenjia Hu, Zhiyuan Ma, Bin Chen
Summary: Coastal bays, as part of Earth's critical zone, have significant ecological and socioeconomic roles. This study developed an integrated ecosystem health assessment framework to determine critical indicators and establish reference benchmarks based on specific ecosystem services. The framework was applied to two typical coastal bays, revealing that Daya Bay was healthier than Jiaozhou Bay. The findings provide important information for prospective bay management.
ECOLOGICAL INDICATORS
(2022)
Article
Multidisciplinary Sciences
Sara Sanz Juste, Emily M. Okamoto, Christina Nguyen, Xuechun Feng, Victor Lopez Del Amo
Summary: One method for reducing the impact of vector-borne diseases is through the use of CRISPR-based gene drives. The authors present a proof-of-concept gene-drive system driven by Cas12a that can be regulated via temperature modulation, and also demonstrate the capability of building double gene drives by combining Cas9 and Cas12a.
NATURE COMMUNICATIONS
(2023)
Article
Physics, Multidisciplinary
F. P. An, W. D. Bai, A. B. Balantekin, M. Bishai, S. Blyth, G. F. Cao, J. Cao, J. F. Chang, Y. Chang, H. S. Chen, H. Y. Chen, S. M. Chen, Y. Chen, Y. X. Chen, Z. Y. Chen, J. Cheng, Z. K. Cheng, J. J. Cherwinka, M. C. Chu, J. P. Cummings, O. Dalager, F. S. Deng, Y. Y. Ding, X. Y. Ding, M. V. Diwan, T. Dohnal, D. Dolzhikov, J. Dove, H. Y. Duyang, D. A. Dwyer, J. P. Gallo, M. Gonchar, G. H. Gong, H. Gong, W. Q. Gu, J. Y. Guo, L. Guo, X. H. Guo, Y. H. Guo, Z. Guo, R. W. Hackenburg, Y. Han, S. Hans, M. He, K. M. Heeger, Y. K. Heng, Y. K. Hor, Y. B. Hsiung, B. Z. Hu, J. R. Hu, T. Hu, Z. J. Hu, H. X. Huang, J. H. Huang, X. T. Huang, Y. B. Huang, P. Huber, D. E. Jaffe, K. L. Jen, X. L. Ji, X. P. Ji, R. A. Johnson, D. Jones, L. Kang, S. H. Kettell, S. Kohn, M. Kramer, T. J. Langford, J. Lee, J. H. C. Lee, R. T. Lei, R. Leitner, J. K. C. Leung, F. Li, H. L. Li, J. J. Li, Q. J. Li, R. H. Li, S. Li, S. C. Li, W. D. Li, X. N. Li, X. Q. Li, Y. F. Li, Z. B. Li, H. Liang, C. J. Lin, G. L. Lin, S. Lin, J. J. Ling, J. M. Link, L. Littenberg, B. R. Littlejohn, J. C. Liu, J. L. Liu, J. X. Liu, C. Lu, H. Q. Lu, K. B. Luk, B. Z. Ma, X. B. Ma, X. Y. Ma, Y. Q. Ma, R. C. Mandujano, C. Marshall, K. T. McDonald, R. D. McKeown, Y. Meng, J. Napolitano, D. Naumov, E. Naumova, T. M. T. Nguyen, J. P. Ochoa-Ricoux, A. Olshevskiy, H. -R. Pan, J. Park, S. Patton, J. C. Peng, C. S. J. Pun, F. Z. Qi, M. Qi, X. Qian, N. Raper, J. Ren, C. Morales Reveco, R. Rosero, B. Roskovec, X. C. Ruan, B. Russell, H. Steiner, J. L. Sun, T. Tmej, K. Treskov, W. -H. Tse, C. E. Tull, B. Viren, V. Vorobel, C. H. Wang, J. Wang, M. Wang, N. Y. Wang, R. G. Wang, W. Wang, X. Wang, Y. Wang, Y. F. Wang, Z. Wang, Z. Wang, Z. M. Wang, H. Y. Wei, L. H. Wei, W. Wei, L. J. Wen, K. Whisnant, C. G. White, H. L. H. Wong, E. Worcester, D. R. Wu, Q. Wu, W. J. Wu, D. M. Xia, Z. Q. Xie, Z. Z. Xing, H. K. Xu, J. L. Xu, T. Xu, T. Xue, C. G. Yang, L. Yang, Y. Z. Yang, H. F. Yao, M. Ye, M. Yeh, B. L. Young, H. Z. Yu, Z. Y. Yu, B. B. Yue, V. Zavadskyi, S. Zeng, Y. Zeng, L. Zhan, C. Zhang, F. Y. Zhang, H. H. Zhang, J. L. Zhang, J. W. Zhang, Q. M. Zhang, S. Q. Zhang, X. T. Zhang, Y. M. Zhang, Y. X. Zhang, Y. Y. Zhang, Z. J. Zhang, Z. P. Zhang, Z. Y. Zhang, J. Zhao, R. Z. Zhao, L. Zhou, H. L. Zhuang, J. H. Zou
Summary: We present a new determination of the smallest neutrino mixing angle 013 and the mass-squared difference Delta m232 using a final sample of 5.55 x 106 inverse beta-decay (IBD) candidates with the final-state neutron captured on gadolinium. Compared to the previous Daya Bay results, selection of IBD candidates has been optimized, energy calibration refined, and treatment of back-grounds further improved. The resulting oscillation parameters are sin22013 = 0.0851 +/- 0.0024, Delta m232 = (2.466 +/- 0.060) x 10-3 eV2 for the normal mass ordering or Delta m232 = -(2.571 +/- 0.060) x 10-3 eV2 for the inverted mass ordering.
PHYSICAL REVIEW LETTERS
(2023)
Editorial Material
Biotechnology & Applied Microbiology
Jessica Rouge
Summary: The rapid deployment of mRNA vaccines against COVID-19 is possible due to early studies on RNA nanocarriers, specifically the study by Zimmermann et al. that demonstrated the efficacy of RNA nanocarriers in vivo. This study, along with others, eventually led to the development of Onpattro, the first FDA-approved RNA formulation.
TRENDS IN BIOTECHNOLOGY
(2023)
Review
Biochemical Research Methods
Jose M. Escandell, Daniel Am Pais, Sofia B. Carvalho, Karen Vincent, Patricia Gomes-Alves, Paula M. Alves
Summary: This article discusses the R&D needs and Chemistry, Manufacturing and Control (CMC) efforts required for the growing demand of recombinant adeno-associated (rAAV) vector-based gene therapy. The key aspects mentioned include scalability and productivity improvement, enhanced safety, and increased process understanding along with the development of orthogonal bioanalytics for identifying, monitoring, and controlling Critical Quality Attributes (CQAs) during bioprocessing.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Sebastian M. Castillo-Hair, Georg Seelig
Summary: Over the past two years, mRNA therapeutics and vaccines have rapidly made a transition from concept to real-world impact. While some aspects have been optimized for decades, the selection and design of noncoding sequences controlling translation efficiency have received less attention. Model-driven design is proposed as a promising alternative to provide unprecedented control over untranslated region function.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)