Article
Genetics & Heredity
Tianxin Zhao, Zelin Wang
Summary: GraphBio is an online web application for visualizing omics data, offering 15 popular visualization analysis methods. Experimental biologists can easily perform popular visualization analysis without programming skills. GraphBio is freely available and provides publication-ready figures.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Ruijie Ren, Xiang-e Sun, Lin Hu
Summary: This study proposes a method of using front-end technology and separating front-end and back-end to build an application hosting platform, which solves the problems in MATLAB Web application deployment, improves user experience, and provides new ideas for hosting and sharing.
SCIENTIFIC REPORTS
(2022)
Review
Chemistry, Physical
Cesar Zuniga Loyola, Soledad Ureta-Zanartu, Jose H. Zagal, F. Tasca
Summary: Electrochemistry and electrochemical experiments are powerful tools for obtaining information about the thermodynamics and kinetics of electrochemical reactions. In this work, the study of the oxygen reduction reaction (ORR) is explored to clarify the significance and utility of obtaining volcano-type correlations to compare and identify the most active catalysts. This research is important for understanding the interactions between catalysts and reactants in energy conversion devices.
CURRENT OPINION IN ELECTROCHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Shubhajit Das, Roland C. Turnell-Ritson, Paul J. Dyson, Clemence Corminboeuf
Summary: Despite recent progress in the chemistry of frustrated Lewis pairs (FLPs), direct FLP-catalyzed hydrogenation of CO2 remains elusive. The authors propose a mapping method to link the chemical composition of FLPs with their activity in catalytic hydrogenation of CO2, and they experimentally validate a combination with high catalytic turnover.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemical Research Methods
Eszter Csibra, Guy-Bart Stan
Summary: With the increasing demand for automation of biological assays, the range of measurement types implemented by multiwell plate readers has expanded. However, most plate readers export data in formats without metadata, which requires specific parser functions for analysis. To address this issue, we have developed an interactive web application called Parsley, which allows users to parse plate reader data easily without the need for software installation or coding.
Article
Construction & Building Technology
Ghaith A. Abureden, Walid M. Hasan, Ayman N. Ababneh
Summary: The study found that additively manufactured corrugated web beams have higher load carrying capacity compared to traditionally manufactured ones, performing very closely to finite element analysis results. Additive manufacturing technology shows potential in reducing safety factors and overall costs in structural systems.
JOURNAL OF CONSTRUCTIONAL STEEL RESEARCH
(2021)
Article
Biochemical Research Methods
Jessica L. Burnett, Renee Dale, Chung-Yi Hou, Gabriela Palomo-Munoz, Kaitlin Stack Whitney, Steve Aulenbach, Robert Sky Bristol, Denis Valle, Tristan P. Wellman
Summary: The use of scientific web applications in biological and environmental sciences has grown exponentially, but researchers often lack training in creating such tools. While rolling out SWApps may be simple and quick, ensuring their usefulness, usability, and sustainability is a challenge. These 10 rules provide a foundation for researchers with little to no experience in web application design and development.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Computer Science, Information Systems
Fiona Fylan, Beth Fylan
Summary: The study found that people support sharing health and social care data but have concerns about its use for research or service planning, particularly related to identification, security limitations, and care rationing. Results from surveys and co-creation groups indicate that participants believe GPs and hospital doctors and nurses should have access to their records and that records should be used for planning services, maintaining health, and finding cures.
INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS
(2021)
Article
Chemistry, Physical
Yian Wang, Minhua Shao
Summary: In this study, theoretical screening was performed on transition metal-N-4-doped graphene (TM-N-4/C) as active and selective electrocatalysts for electrochemical nitrate reduction reaction (NO3RR). The study explored detailed reaction mechanisms and activity origins, and found that Cu- and Pt-N-4/C showed high activity for NO3RR via NH3 and N-2 formation pathways, respectively, attributed to optimal NO and N adsorptions. Moreover, Re- and Pt-N-4/C exhibited high selectivity towards NH3 and N-2 formations, respectively. This work provides theoretical insights for the rational design of TM-N-4/C catalysts for NO3RR and offers opportunities for efficient nitrate removal and ammonia synthesis strategies.
Article
Communication
Nick Mathews, Valerie Belair-Gagnon, Seth C. Lewis
Summary: In this study, qualitative interview responses from US news consumers were examined to understand why people choose not to share news online. The findings suggest that non-sharers perceive news as toxic and potentially damaging to their reputations and relationships. Not sharing news serves as a protective mechanism for identity maintenance, although it brings concerns about voice suppression.
NEW MEDIA & SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Kerry A. Mullan, Liesl M. Bramberger, Prithvi Raj Munday, Gabriel Goncalves, Jerico Revote, Nicole A. Mifsud, Patricia T. Illing, Alison Anderson, Patrick Kwan, Anthony W. Purcell, Chen Li
Summary: ggVolcanoR is an R-based Shiny application that allows customizable generation and visualization of volcano plots, correlation plots, upset plots, and heatmaps for differential expression datasets. It provides practical options for analyzing and comparing dysregulated genes/proteins across multiple datasets, and offers a downloadable list of filtered dysregulated expression data for downstream pathway analysis. The source code is available on GitHub and a webserver is freely accessible for academic purposes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Computer Science, Information Systems
Pei-Hung Liao, William Chu
Summary: With the rise of patients with osteoporosis-induced fractures, this study designed a web-based app for pain relief instructions, with the goal of easing pain and improving bodily functions. The observational study divided patients into experimental and control groups, using pain surveys and health surveys to collect data. The results showed significant effects in relieving back pain for the experimental group.
MULTIMEDIA TOOLS AND APPLICATIONS
(2023)
Article
Engineering, Chemical
Heng Liu, Hao Zheng, Zhenhe Jia, Binghui Zhou, Yan Liu, Xuelu Chen, Yajun Feng, Li Wei, Weijie Yang, Hao Li
Summary: This article introduces CatMath, an online platform for generating catalytic volcano activity models, and provides functions for analyzing catalyst activity and electrocatalytic surface states.
FRONTIERS OF CHEMICAL SCIENCE AND ENGINEERING
(2023)
Article
Nutrition & Dietetics
Alessandro Rangel Carolino Sales Silva, Cliona Ni Mhurchu, Lucilene Rezende Anastacio
Summary: This study compares the effectiveness of front-of-pack nutrition labeling (FoPNL) systems in Brazil and Mexico in relation to consumer purchasing decisions for dairy products. The results show that the Mexican FoPNL system performs better in facilitating consumer decision-making and quick purchase decisions.
FRONTIERS IN NUTRITION
(2022)
Article
Biochemical Research Methods
Patrick Adelberger, Klaus Eckelt, Markus J. Bauer, Marc Streit, Christian Haslinger, Thomas Zichner
Summary: A main task in computational cancer analysis is to identify patient subgroups based on metadata attributes or genomic markers, and the web-based cohort analysis tool Coral is designed to support this task by allowing users to interactively create, refine, and compare cohorts. Coral also visualizes the evolution of cohorts and provides intuitive access to prevalence information, as well as the ability to store, share, and reproduce findings. It is pre-loaded with data from over 128,000 samples from various cancer research projects.
Article
Biochemistry & Molecular Biology
Joachim Goedhart
Article
Chemistry, Multidisciplinary
Anna Pietraszewska-Bogiel, Linda Joosen, Anna O. Chertkova, Joachim Goedhart
Article
Cell Biology
Joachim Goedhart
Summary: Plots and charts are important graphical tools for making data understandable to humans. The oversimplification of data by only plotting statistical summaries can conflict with transparent communication of results. The superplot is a proposed method to improve the communication of experimental design and results.
MOLECULAR BIOLOGY OF THE CELL
(2021)
Review
Cell Biology
Diana van den Heuvel, Yana van der Weegen, Daphne E. C. Boer, Tomoo Ogi, Martijn S. Luijsterburg
Summary: DNA lesions are a major obstacle during gene transcription by RNA polymerase II enzymes, but can be eliminated by the transcription-coupled DNA repair pathway. Recent advances suggest that RNAPII ubiquitylation activates TCR complex assembly during repair and promotes processing and degradation of RNAPII to prevent prolonged stalling, making the fate of stalled RNAPII a crucial link between TCR and associated human diseases.
TRENDS IN CELL BIOLOGY
(2021)
Article
Cell Biology
Eike K. Mahlandt, Janine J. G. Arts, Werner J. van der Meer, Franka H. van der Linden, Simon Tol, Jaap D. van Buul, Theodorus W. J. Gadella, Joachim Goedhart
Summary: This study investigated improved localization-based genetically encoded fluorescent biosensors for detecting endogenous Rho activity, demonstrating their broader application in visualizing Rho activity during various cellular processes. The enhanced avidity of the new biosensors for Rho activity leads to a better understanding of cellular processes regulated by Rho.
JOURNAL OF CELL SCIENCE
(2021)
Article
Cell Biology
Sergei Chavez-Abiega, Max L. B. Groenloh, Theodorus W. J. Gadella, Frank J. Bruggeman, Joachim Goedhart
Summary: This study reveals substantial cell-to-cell heterogeneity in kinase activity driven by GPCRs through imaging and analysis strategy.
JOURNAL OF CELL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Max L. B. Gronloh, Janine J. G. Arts, Sebastian Palacios Martinez, Amerens A. van Der Veen, Lanette Kempers, Abraham C. van Steen, Joris J. T. H. Roelofs, Martijn A. Nolte, Joachim Goedhart, Jaap D. van Buul
Summary: Using a photoconvertible probe, researchers traced and identified the original endothelial transmigration hotspots, and found that these hotspots function to limit vascular leakage during transmigration events. The distribution of ICAM-1 determines the location of the transmigration hotspot.
Article
Cell Biology
Gabriel Kreider-Letterman, Abel Castillo, Eike K. K. Mahlandt, Joachim Goedhart, Agustin Rabino, Silvia Goicoechea, Rafael Garcia-Mata
Summary: The study reveals that ARHGAP17, a Cdc42-specific RhoGAP, plays a crucial role in regulating the spatiotemporal activity of Cdc42 during invadopodia turnover. ARHGAP17 restricts the activity of Cdc42 to the core during invadopodia assembly, promoting invadopodia growth. During invadopodia disassembly, ARHGAP17 translocates from the invadopodia ring to the core and inactivates Cdc42, initiating invadopodia disassembly.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Cell Biology
Eike K. Mahlandt, Gabriel Kreider-Letterman, Anna O. Chertkova, Rafael Garcia-Mata, Joachim Goedhart
Summary: In this study, relocation sensor candidates for Rac and Cdc42 were identified and their efficiency was improved using a multi-domain approach. Optimized sensors for Cdc42 were found to have sufficient relocation efficiency and specificity. These findings enable the wider application of Rho GTPase relocation sensors and were showcased by the detection of local endogenous Cdc42 activity at assembling invadopodia. The characterization and optimization of relocation sensors will broaden their application and acceptance.
JOURNAL OF CELL SCIENCE
(2023)
Editorial Material
Biochemistry & Molecular Biology
George Yakoub, Martijn S. Luijsterburg
Summary: A recent study in Nature unveils the mechanism of how transcriptionally active RNA polymerase II clings to the genomic tightrope during replication, enabled by protein-protein interactions between the replication and transcription machineries.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Biology
Eike K. Mahlandt, Sebastian Palacios Martinez, Janine J. G. Arts, Simon Tol, Jaap D. van Buul, Joachim Goedhart
Summary: This study investigates the role of Rho GTPases in the vascular barrier of endothelial cells using optogenetics. The results show that by precisely controlling the activation of Rho GTPases, the strength of the vascular barrier can be precisely regulated in a VE-cadherin-independent manner through cell-cell overlap-dependent mechanism. Furthermore, optogenetic control over morphological features of endothelial cells, such as cell size and shape, is also demonstrated.
Article
Multidisciplinary Sciences
Daniel Salas-Lloret, Nicolette S. Jansen, Easa Nagamalleswari, Coen van der Meulen, Ekaterina Gracheva, Arnoud H. de Ru, H. Anne Marie Otte, Peter A. van Veelen, Andrea Pichler, Joachim Goedhart, Alfred C. O. Vertegaal, Roman Gonzalez-Prieto
Summary: Ubiquitin and ubiquitin-like conjugation cascades involve E1, E2, and E3 enzymes, with E3s providing substrate specificity. Through mass spectrometry-based approaches, more than 6500 SUMO2/3 target proteins have been identified. Using SUMO-activated target traps (SATTs), the substrates for eight different SUMO E3s were systematically identified, revealing E3 substrate preference. Quantitative proteomics and the Polar SATTs web-based tool were developed to measure substrate specificity and browse the dataset interactively. Overall, the study uncovers the E3-to-target wiring of 1388 SUMO substrates for different SUMO E3 ligases.
Correction
Multidisciplinary Sciences
Yana van der Weegen, Hadar Golan-Berman, Tycho E. T. Mevissen, Katja Apelt, Roman Gonzalez-Prieto, Joachim Goedhart, Elisheva E. Heilbrun, Alfred C. O. Vertegaal, Diana van den Heuvel, Johannes C. Walter, Sheera Adar, Martijn S. Luijsterburg
NATURE COMMUNICATIONS
(2020)