Article
Biochemical Research Methods
Masaki Tagashira
Summary: Aligning and folding RNA homologs has been a fundamental framework in RNA science, but learning sufficient scoring parameters for simultaneous AF (SAF) remains an undeveloped subject due to the high computational cost of evaluation. In this study, we developed ConsTrain, a gradient-based machine learning method, to obtain rich SAF scoring parameters. We also implemented ConsAlign, a SAF tool composed of ConsTrain's learned scoring parameters. Through transfer learning and ensemble modeling, ConsAlign demonstrated competitive AF prediction quality among current AF tools while maintaining comparable running time.
Article
Plant Sciences
Bao Li, Qian Yang, Lulu Yang, Xing Zhou, Lichao Deng, Liang Qu, Dengli Guo, Rongkui Hui, Yiming Guo, Xinhong Liu, Tonghua Wang, Lianyi Fan, Mei Li, Mingli Yan
Summary: This study presents a gap-free assembly of the oilseed rape genome using a combination of sequencing technologies, revealing important genes related to flowering regulation. The high-quality genome assembly provides a valuable genetic resource for functional genomic studies and breeding of oilseed rape.
HORTICULTURE RESEARCH
(2023)
Article
Multidisciplinary Sciences
Huseyin Tombuloglu, Hussein Sabit, Hamoud Al-Khallaf, Juma H. Kabanja, Moneerah Alsaeed, Najat Al-Saleh, Ebtesam Al-Suhaimi
Summary: This study describes a fast and accurate multiplex SARS-CoV-2 RT-PCR detection method that can simultaneously detect viral genes and a human gene, with high sensitivity and specificity. It can be used as a diagnostic tool for SARS-CoV-2 in medical institutions and for research purposes.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Michael Menzel, Sabine Hurka, Stefan Glasenhardt, Andreas Gogol-Doering
Summary: In this study, a novel approach is presented for reliably identifying transcription factor-binding motifs in ChIP-Seq data without peak detection. By evaluating sequencing reads distributions around k-mers in the genome, binding motifs that are not detected in traditional pipelines can be identified.
Article
Multidisciplinary Sciences
Taeheon Lee, Sangseon Lee, Minji Kang, Sun Kim
Summary: This study introduces DeepHier, a deep learning model that learns representations of GPCR family hierarchy from protein sequences with a unified single model. A novel loss term based on metric learning is used to incorporate hierarchical relations between proteins, successfully capturing the hierarchical relationships between sequences.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Chance Meers, Hoang C. Le, Sanjana R. Pesari, Florian T. Hoffmann, Matt W. G. Walker, Jeanine Gezelle, Stephen Tang, Samuel H. Sternberg
Summary: This study reveals the importance of RNA-guided DNA cleavage in the retention and spread of transposable elements.
Article
Multidisciplinary Sciences
Sizhen Li, He Zhang, Liang Zhang, Kaibo Liu, Boxiang Liu, David H. Mathews, Liang Huang
Summary: Emergence of COVID-19 variants challenges the effectiveness of current vaccines and tests, emphasizing the need to identify conserved structures in the SARS-CoV-2 genome. Existing algorithms for predicting these structures are limited by their scalability and inability to capture long-range interactions critical for RNA functions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Sizhen Li, He Zhang, Liang Zhang, Kaibo Liu, Boxiang Liu, David H. Mathews, Liang Huang
Summary: In response to the evolving COVID-19 variants, researchers have developed LinearTurboFold, an algorithm that can linearly fold RNA homologs, enabling unprecedented global structural analysis on SARS-CoV-2. Surprisingly, LinearTurboFold not only closely predicts experimentally-guided models for local structures, but also captures end-to-end pairs between 5' and 3' UTRs that match with experimental work, identifying undiscovered conserved structures and regions as potential targets for designing efficient and mutation-insensitive drugs and genetic tools. LinearTurboFold is a versatile technique applicable to other RNA viruses and genome studies, proving to be a valuable tool in combatting current and future pandemics.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Swapnil C. Devarkar, Michael Vetick, Shravani Balaji, Ivan B. Lomakin, Luojia Yang, Danni Jin, Wendy V. Gilbert, Sidi Chen, Yong Xiong
Summary: Research has found that MERS-CoV Nsp1 directly interacts with the 40S ribosomal subunit to restrict host gene expression through translation inhibition. The extensive interactions between MERS-CoV Nsp1 and the mRNA entry channel of the 40S ribosomal subunit are critical for its translation inhibition function, and this mechanism is strikingly similar to SARS-CoV and SARS-CoV-2 Nsp1.
Article
Energy & Fuels
Yu Liu, Wei Liu, Yiwen Shen, Xin Zhao, Shan Gao
Summary: This paper proposes a practical solution to address the simultaneous action problems in real time load monitoring, utilizing an adaptive-window detection approach and a deep dictionary learning model to handle overlapping operations effectively, leading to improved monitoring performance.
Article
Multidisciplinary Sciences
Suresh Pokhrel, Kun Huang, Sebastien Belanger, Junpeng Zhan, Jeffrey L. Caplan, Elena M. Kramer, Blake C. Meyers
Summary: Plant small RNAs play an important role in regulating gene expression and maintaining genome integrity. Reproductive phasiRNAs are key elements in plant development, present in various plant species and playing a crucial role in the development of floral reproductive organs.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Andreas Grigorjew, Artur Gynter, Fernando H. C. Dias, Benjamin Buchfink, Hajk-Georg Drost, Alexandru I. Tomescu
Summary: Sequence alignments are crucial in life science research, but current focus on optimal alignments neglects information from suboptimal solutions. We propose using multiple suboptimal solutions to explore the biodiversity of the protein universe. To achieve this, we introduce pairwise alignment-safety to identify robustly shared amino acid positions. We have developed a software library called EMERALD for alignment-safety inference and applied it to 400k sequences from the SwissProt database.
Article
Genetics & Heredity
Charles J. Underwood, Kitty Vijverberg, Diana Rigola, Shunsuke Okamoto, Carla Oplaat, Rik H. M. Op den Camp, Tatyana Radoeva, Stephen E. Schauer, Joke Fierens, Kim Jansen, Sandra Mansveld, Marco Busscher, Wei Xiong, Erwin Datema, Koen Nijbroek, Evert-Jan Blom, Ross Bicknell, Andrew Catanach, Sylvia Erasmuson, Christopher Winefield, Arjen J. van Tunen, Marcel Prins, M. Eric Schranz, Peter J. van Dijk
Summary: The PAR gene in dandelion triggers embryo development without fertilization, a rare phenomenon in flowering plants. This gene is inserted with a MITE transposon in the promoter region, and its expression is able to induce embryogenesis in the absence of fertilization.
Article
Biochemistry & Molecular Biology
Yupeng Wang, Zhikang Hu, Ning Ye, Hengfu Yin
Summary: Long-read transcriptome sequencing is designed to sequence full-length RNA molecules, useful for identifying alternative splice isoforms. IsoSplitter is a versatile tool developed for reverse-tracing and validating AS gene split sites, showing high accuracy and efficiency in handling different transcriptomes.
Article
Multidisciplinary Sciences
Nick Wytinck, Dylan J. Ziegler, Philip L. Walker, Daniel S. Sullivan, Kirsten T. Biggar, Deirdre Khan, Solihu K. Sakariyahu, Olivia Wilkins, Steve Whyard, Mark F. Belmonte
Summary: This study demonstrates the effectiveness of Host Induced Gene Silencing (HIGS) in protecting Brassica napus from Sclerotinia sclerotiorum infection. Through molecular and anatomical analyses, it was found that HIGS protected plants showed significant changes in the expression of defense-related genes and the formation of structural barriers to restrict the pathogen.
Article
Biochemical Research Methods
Michael Uhl, Dominik Rabsch, Florian Eggenhofer, Rolf Backofen
Summary: This article introduces Peakhood, the first tool that utilizes CLIP-seq peak regions, CLIP-seq read information, and genomic annotations to determine the context for each peak region and determine the most probable splice variant, resulting in a comprehensive collection of transcript context binding sites.
Article
Biochemical Research Methods
Peter F. Stadler, Sebastian Will
Summary: This study introduces the concept of bi-alignments, which can be used to align sequence and structure similarity simultaneously. Using affine cost bi-alignments, efficient alignments of large proteins can be computed.
ALGORITHMS FOR MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Simon Bray, Tim Dudgeon, Rachael Skyner, Rolf Backofen, Bjorn Gruning, Frank von Delft
Summary: Several workflows for protein-ligand docking and free energy calculation in Galaxy, a workflow management system, are presented. These workflows incorporate widely used open-source tools such as rDock and GROMACS, and can be executed either through Galaxy's graphical interface or the command line on public infrastructure. The utility of these workflows is demonstrated by conducting a high-throughput virtual screening of approximately 50000 compounds against the SARS-CoV-2 main protease, a system of extensive study in the past year.
JOURNAL OF CHEMINFORMATICS
(2022)
Article
Microbiology
Chunyu Liao, Sahil Sharma, Sarah L. Svensson, Anuja Kibe, Zasha Weinberg, Omer S. Alkhnbashi, Thorsten Bischler, Rolf Backofen, Neva Caliskan, Cynthia M. Sharma, Chase L. Beisel
Summary: CRISPR-Cas systems store foreign DNA fragments as immunological recordings to combat infections. The newest spacers stored in the system are prioritized for immune defense and this process involves the interaction between the leader region and the conserved repeats bordering the newest spacer, leading to accelerated crRNA processing.
NATURE MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Alexander Mitrofanov, Marcus Ziemann, Omer S. Alkhnbashi, Wolfgang R. Hess, Rolf Backofen
Summary: This study introduces a new pipeline, CRISPRtracrRNA, for screening and evaluating tracrRNA candidates in genomes. The pipeline combines evidence from different components of the Cas9-sgRNA complex. It also utilizes a newly developed structural model to simulate the structure of tracrRNA. Additionally, evidence is provided through the detection of repeat sequences, terminator signals, and RNA-RNA interactions.
Article
Multidisciplinary Sciences
Dominika Grzejda, Jana Mach, Johanna Aurelia Schweizer, Barbara Hummel, Andrew Mischa Rezansoff, Florian Eggenhofer, Amol Panhale, Maria-Eleni Lalioti, Nina Cabezas Wallscheid, Rolf Backofen, Johannes Felsenberg, Valerie Hilgers
Summary: This study identifies a long noncoding RNA, mimi, as a scaffold for large neuronal granules in the adult nervous system. Neuronal ELAV-like proteins directly bind mimi and mediate granule assembly, while Staufen maintains condensate integrity. mimi granules contain mRNAs and proteins involved in synaptic processes, and their loss impairs nervous system maturity and neuropeptide-mediated signaling, leading to neurodegeneration.
Article
Instruments & Instrumentation
Minho Kwon, Aaron Holman, Quan Gan, Chun-Wei Liu, Matthew Molinelli, Ian Stevenson, Sebastian Will
Summary: We present a design and characterization of a cold atom source for strontium (Sr) using a two-dimensional magneto-optical trap (MOT) that is loaded directly from the atom jet of a dispenser. The atom flux of the source is characterized by measuring the loading rate of a three-dimensional MOT, which reaches loading rates of up to 10^8 atoms per second. This compact and low-power consumption setup addresses the challenge of reducing complexity in cold beam sources for Sr, making it important for applications in optical atomic clocks, quantum simulation, and computing devices based on ultracold Sr.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2023)
Article
Astronomy & Astrophysics
Jiayi Sun, Adam K. Leroy, Eve C. Ostriker, Sharon Meidt, Erik Rosolowsky, Eva Schinnerer, Christine D. Wilson, Dyas Utomo, Francesco Belfiore, Guillermo A. Blanc, Eric Emsellem, Christopher Faesi, Brent Groves, Annie Hughes, Eric W. Koch, Kathryn Kreckel, Daizhong Liu, Hsi-An Pan, Jerome Pety, Miguel Querejeta, Alessandro Razza, Toshiki Saito, Amy Sardone, Antonio Usero, Thomas G. Williams, Frank Bigiel, Alberto D. Bolatto, Melanie Chevance, Daniel A. Dale, Jindra Gensior, Simon C. O. Glover, Kathryn Grasha, Jonathan D. Henshaw, Maria J. Jimenez-Donaire, Ralf S. Klessen, J. M. Diederik Kruijssen, Eric J. Murphy, Lukas Neumann, Yu-Hsuan Teng, David A. Thilker
Summary: We measured the empirical relationships between local star formation rate and properties of the star-forming molecular gas in 80 nearby galaxies. These relationships, known as star formation laws, aim to predict the local SFR surface density using different combinations of molecular gas surface density, galactic orbital time, molecular cloud free fall time, and interstellar medium dynamical equilibrium pressure. Our results show that these relationships have intrinsic scatter and the slope of the molecular Kennicutt-Schmidt relation remains roughly constant across different environments. The other relationships show variations in their slopes, suggesting systematic changes in star formation efficiency and pressure-to-SFR surface density ratio.
ASTROPHYSICAL JOURNAL LETTERS
(2023)
Review
Cardiac & Cardiovascular Systems
Sabine Steffens, Katrin Schroeder, Martina Krueger, Christoph Maack, Katrin Streckfuss-Boemeke, Johannes Backs, Rolf Backofen, Bettina Baessler, Yvan Devaux, Ralf Gilsbach, Jordi Heijman, Jochen Knaus, Rafael Kramann, Dominik Linz, Allyson L. Lister, Henrike Maatz, Lars Maegdefessel, Manuel Mayr, Benjamin Meder, Sara Y. Nussbeck, Eva A. Rog-Zielinska, Marcel H. Schulz, Albert Sickmann, Goekhan Yigit, Peter Kohl
Summary: Sharing and documentation of cardiovascular research data are essential but challenges like lack of time, incentives, funding, standardization, and legal understanding exist. More tools, education, and training are needed for effective data sharing and an open science culture. Long-term effort is required for FAIR RDM.
CLINICAL RESEARCH IN CARDIOLOGY
(2023)
Article
Biology
Anup Kumar, Gianmauro Cuccuru, Bjoern Gruening, Rolf Backofen
Summary: An open-source, docker-based, and GPU-enabled JupyterLab infrastructure is developed that runs on the public compute infrastructure of Galaxy Europe. It enables rapid prototyping and development of end-to-end AI projects, including large-scale data training and remote AI model training execution.
Article
Biochemistry & Molecular Biology
Franziska Wimmer, Frank Englert, Katharina G. Wandera, Omer S. Alkhnbashi, Scott P. Collins, Rolf Backofen, Chase L. Beisel
Summary: This study investigates extensive self-targeting in the plant pathogen Xanthomonas albilineans by two CRISPR-Cas systems and identifies two Acrs proteins that inhibit the activity of Cas3, expanding the known suite of DNA degradation-inhibiting Acrs.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Sandra Fischer, Chiara Lichtenthaeler, Anastasiya Stepanenko, Florian Heyl, Daniel Maticzka, Katrin Kemmerer, Melina Klostermann, Rolf Backofen, Kathi Zarnack, Julia E. Weigand
Summary: HNRNPDL plays an important role in endothelial cell functions, and its knockdown affects cell proliferation, migration, and sprouting ability, possibly through regulating the expression of specific genes.
BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Thomas Schwarzl, Sudeep Sahadevan, Benjamin Lang, Milad Miladi, Rolf Backofen, Wolfgang Huber, Matthias W. Hentze, Gian Gaetano Tartaglia
Summary: Enhanced crosslinking and immunoprecipitation sequencing (eCLIP-seq) is a method for detecting RNA-binding protein binding sites. However, current analysis strategies have low replication and high false positive rates. DEWSeq, a R/Bioconductor package, improves the detection of binding regions by utilizing replicate information and size-matched input controls. It has been shown to significantly increase the number and quality of binding sites.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Joachim Wolff, Rolf Backofen, Bjoern Gruening
Summary: This study presents an algorithm for detecting chromatin loops using continuous negative binomial distributions and the HiCCUPS method, which has been integrated into the HiCExplorer software. The method achieves high detection rate and accuracy, and is the fastest CPU implementation currently available.
Article
Optics
Niccolo Bigagli, Daniel W. Savin, Sebastian Will
Summary: We present a scheme for laser cooling of C-12(2) and provide calculations for the branching ratios of cycling and repumping transitions. Our results show that C-2 cooling, using specific bands, is achievable under realistic experimental conditions. This work opens up possibilities for cooling molecules with carbon-carbon bonds and potentially enables quantum control of organic molecules.