Article
Engineering, Chemical
Angela Dedvukaj, Sofie Raemdonck, Ivo F. J. Vankelecom
Summary: Traditional polyamide thin-film composite membranes commonly used in nanofiltration and reverse osmosis tend to foul easily due to their rough surface. A new approach, spray-based interfacial polymerization, is introduced to address these issues. By using less chemicals and reducing waste production, this method is more time-efficient and environmentally friendly compared to conventional interfacial polymerization. It also overcomes the problems of non-wetted support pores and poor adhesion, while limiting hydrolysis reactions and improving the surface quality of the membranes.
JOURNAL OF MEMBRANE SCIENCE
(2023)
Article
Biochemical Research Methods
Vi Ngoc-Nha Tran, Alireza Shams, Sinan Ascioglu, Antal Martinecz, Jingyi Liang, Fabrizio Clarelli, Rafal Mostowy, Ted Cohen, Pia Abel zur Wiesch
Summary: This study extends a mechanistic binding-kinetic model and incorporates clinical drug concentration data to develop a web-based tool that allows non-quantitative scientists to create and visualize computational models of bacterial antibiotic target-binding. The vCOMBAT online tool is publicly available.
BMC BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Stefan R. Stefanov, Irmtraud M. Meyer
Summary: Researchers have developed a computational method called CYCLeR that accurately identifies the sequence and abundance of new and alternatively spliced circRNAs, while also estimating the abundance of known linear splicing isoforms. CYCLeR outperforms existing methods in terms of F score and transcript quantification in simulated data, and shows advantages compared to existing methods when analyzing long-read data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Gabriele Antonio Zingale, Alessia Distefano, Irene Pandino, Nunzio Tuccitto, Valentina Oliveri, Massimiliano Gaeta, Alessandro D'Urso, Alfio Arcoria, Giuseppe Grasso
Summary: In the field of conformational diseases, monitoring peptide and protein aggregation is crucial for understanding physiological pathways and pathological processes. A new experimental method based on the fluorescent properties of carbon dots upon protein binding is introduced to monitor protein aggregation. The proposed methodology allows for monitoring the initial stages of insulin aggregation under different experimental conditions without potential disturbances or molecular probes.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Automation & Control Systems
Bastien Toubhans, Philippe Lorong, Fabien Viprey, Guillaume Fromentin, Habib Karaouni
Summary: This research focuses on developing a general coupling approach to address the geometrical error caused by workpiece deflection when machining low-stiffness workpieces. Cutting forces are predicted using a mechanistic model and wear effects are expressed using cumulative removed volume. Workpiece stiffness is determined with a reduced model to significantly reduce computing time when machining large workpieces.
INTERNATIONAL JOURNAL OF ADVANCED MANUFACTURING TECHNOLOGY
(2021)
Review
Neurosciences
Daniel G. Blackmore, Daniel Razansky, Jurgen Gotz
Summary: Treating the brain with low-intensity focused ultrasound (FUS) elicits various responses in neurons, astroglia, and the extracellular matrix. Additionally, FUS combined with microbubbles can open the blood-brain barrier and enhance drug delivery. However, the lack of understanding of cellular specificity and the wide parameter space currently hinder the optimal application of FUS.
Article
Pharmacology & Pharmacy
Hira Zahoor, Kwanrutai Watchaputi, Janejira Hata, Wachirachai Pabuprapap, Apichart Suksamrarn, Lee Suan Chua, Nitnipa Soontorngun
Summary: There is a global demand for herbal extracts used in cosmetics, food, and health supplements. This study focuses on examining the antioxidant and anti-aging potential of flavonoids extracted from medicinal plants using Saccharomyces cerevisiae as a model organism. The results show that certain quercetin analogs can protect yeast cells against oxidative stress and extend the lifespan of wild-type S. cerevisiae.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Developmental Biology
Emmanuel Martin, Magali Suzanne
Summary: Live imaging of protein dynamics is crucial for cell and developmental biology research. Multicolor live imaging, however, remains challenging. The development of long Stokes shift red fluorescent proteins offers new possibilities to overcome this limitation. This article provides a detailed characterization of mBeRFP for in vivo live imaging and demonstrates its applications in Drosophila. It shows that mBeRFP can be combined with other fluorescent proteins without crosstalk and is suitable for quantitative analysis.
Article
Astronomy & Astrophysics
Maria Cristina Fortuna, Henk Hoekstra, Benjamin Joachimi, Harry Johnston, Nora Elisa Chisari, Christos Georgiou, Constance Mahony
Summary: This study investigates the impact of different galaxy samples on cosmic shear studies using the halo model formalism, accounting for varied IA features and redshift dependencies. The model includes luminosity and signal radial dependencies, and uses realistic mocks to validate predictions. Results indicate that uncertainties in predicting IA signal largely stem from fainter galaxies.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
R. Prabakaran, Puneet Rawat, Sandeep Kumar, M. Michael Gromiha
Summary: This study focuses on predicting aggregation-nucleating regions in peptides and proteins, developing an effective tool ANuPP. By analyzing atomic-level features, a better understanding of the aggregation mechanism is gained, providing important insights for protein aggregation research.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Neurosciences
Joshua Barry, Allison Peng, Michael S. Levine, Carlos Cepeda
Summary: Huntington's disease is a fatal neurodegenerative disorder that affects striatal and cortical neurons, leading to synapse loss and cell death. Perturbed calcium (Ca2+) homeostasis plays a crucial role in the disease, and imaging techniques can monitor neuronal activity and Ca2+ dynamics.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Energy & Fuels
Petronilla Fragiacomo, Giuseppe Lucarelli, Matteo Genovese, Gaetano Florio
Summary: This article presents a novel and implemented optimization routine for combined cooling, heat, and power generation analysis. The routine is able to optimize energy systems with various technologies and has been validated through energy efficiency curves and unit cost analysis.
INTERNATIONAL JOURNAL OF ENERGY RESEARCH
(2022)
Article
Surgery
Tarek Ismail, David E. Kurlander, Z-Hye Lee, Alexander Lunger, John W. W. Shuck, Rene D. D. Largo, Edward I. I. Chang
Summary: The medial femoral condyle flap has been well-documented for reconstruction of small bone defects in the extremities. Limited case reports have shown its use in complex head and neck defects. This study presents a series of complex craniofacial defects that were successfully reconstructed using medial femoral condyle flaps, aiming to raise awareness among microsurgeons about this flap and its potential use.
PLASTIC AND RECONSTRUCTIVE SURGERY
(2023)
Review
Biochemical Research Methods
Sonja Schmid, Cees Dekker
Summary: Proteins are essential for cellular functions, but observing their functional cycle involving conformational changes and interactions is challenging. Single-molecule techniques like FRET and force spectroscopies provide insights but have limitations. Electrical nanopore detection offers a wide range of timescales relevant for protein dynamics and may provide new solutions for studying protein function at the molecular level.
BIOCHEMISTRY: ONE MOLECULE AT A TIME
(2021)
Article
Biophysics
Dan D. Erdmann-Pham, Wonjun Son, Khanh Dao Duc, Yun S. Song
Summary: The software package EGGTART quantifies and visualizes the dynamics of a generalized version of the TASEP with extended particle size and heterogeneous jump rates, providing key information such as particle density, flux, and phase diagram. It is based on analytic formulas derived from the hydrodynamic limit of the process, making it a valuable tool for biophysicists studying general transport processes and gene expression.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Dave M. Beal, Emma L. Bastow, Gemma L. Staniforth, Tobias von der Haar, Robert B. Freedman, Mick F. Tuite
ANTIOXIDANTS & REDOX SIGNALING
(2019)
Article
Biochemistry & Molecular Biology
Jianling Xie, Viviane de Souza Alves, Tobias von der Haar, Louise O'Keefe, Roman Lenchine, Kirk B. Jensen, Rui Liu, Mark J. Coldwell, Xuemin Wang, Christopher G. Proud
Article
Biochemistry & Molecular Biology
Keerthi T. Chathoth, Nicolae Radu Zabet
Editorial Material
Plant Sciences
Valentina Fiorilli, Marco Catoni, Luisa Lanfranco, Nicolae Radu Zabet
FRONTIERS IN PLANT SCIENCE
(2020)
Article
Biochemical Research Methods
Drahomira Faktorova, R. Ellen R. Nisbet, Jose A. Fernandez Robledo, Elena Casacuberta, Lisa Sudek, Andrew E. Allen, Manuel Ares, Cristina Areste, Cecilia Balestreri, Adrian C. Barbrook, Patrick Beardslee, Sara Bender, David S. Booth, Francois-Yves Bouget, Chris Bowler, Susana A. Breglia, Colin Brownlee, Gertraud Burger, Heriberto Cerutti, Rachele Cesaroni, Miguel A. Chiurillo, Thomas Clemente, Duncan B. Coles, Jackie L. Collier, Elizabeth C. Cooney, Kathryn Coyne, Roberto Docampo, Christopher L. Dupont, Virginia Edgcomb, Elin Einarsson, Pia A. Elustondo, Fernan Federici, Veronica Freire-Beneitez, Nastasia J. Freyria, Kodai Fukuda, Paulo A. Garcia, Peter R. Girguis, Fatma Gomaa, Sebastian G. Gornik, Jian Guo, Vladimir Hampl, Yutaka Hanawa, Esteban R. Haro-Contreras, Elisabeth Hehenberger, Andrea Highfield, Yoshihisa Hirakawa, Amanda Hopes, Christopher J. Howe, Ian Hu, Jorge Ibanez, Nicholas A. T. Irwin, Yuu Ishii, Natalia Ewa Janowicz, Adam C. Jones, Ambar Kachale, Konomi Fujimura-Kamada, Binnypreet Kaur, Jonathan Z. Kaye, Eleanna Kazana, Patrick J. Keeling, Nicole King, Lawrence A. Klobutcher, Noelia Lander, Imen Lassadi, Zhuhong Li, Senjie Lin, Jean-Claude Lozano, Fulei Luan, Shinichiro Maruyama, Tamara Matute, Cristina Miceli, Jun Minagawa, Mark Moosburner, Sebastian R. Najle, Deepak Nanjappa, Isabel C. Nimmo, Luke Noble, Anna M. G. Novak Vanclova, Mariusz Nowacki, Isaac Nunez, Arnab Pain, Angela Piersanti, Sandra Pucciarelli, Jan Pyrih, Joshua S. Rest, Mariana Rius, Deborah Robertson, Albane Ruaud, Inaki Ruiz-Trillo, Monika A. Sigg, Pamela A. Silver, Claudio H. Slamovits, G. Jason Smith, Brittany N. Sprecher, Rowena Stern, Estienne C. Swart, Anastasios D. Tsaousis, Lev Tsypin, Aaron Turkewitz, Jernej Turnsek, Matus Valach, Valerie Verge, Peter von Dassow, Tobias von der Haar, Ross F. Waller, Lu Wang, Xiaoxue Wen, Glen Wheeler, April Woods, Huan Zhang, Thomas Mock, Alexandra Z. Worden, Julius Lukes
Article
Cell Biology
Victoria Eugenia Martinez-Miguel, Celia Lujan, Tristan Espie-Caullet, Daniel Martinez-Martinez, Saul Moore, Cassandra Backes, Suam Gonzalez, Evgeniy R. Galimov, Andre E. X. Brown, Mario Halic, Kazunori Tomita, Charalampos Rallis, Tobias von der Haar, Filipe Cabreiro, Ivana Bjedov
Summary: The loss of proteostasis is a fundamental process driving aging, and the accuracy of translation significantly affects proteostasis. A rare amino acid substitution found in certain hyperthermophilic archaea, when introduced into other organisms, improves translation accuracy, heat shock resistance, and longevity. Anti-aging drugs such as rapamycin, Torin1, and trametinib reduce translation errors and extend organismal longevity, particularly in mutants with high translation accuracy due to this unique substitution in the RPS23 protein.
Article
Biochemistry & Molecular Biology
Darren Taylor, Robert Lowe, Claude Philippe, Kevin C. L. Cheng, Olivia A. Grant, Nicolae Radu Zabet, Gael Cristofari, Miguel R. Branco
Summary: This study presents a novel approach for generating locus-specific protein-DNA binding profiles at interspersed repeats, uncovering previously unappreciated variations in the epigenetic profiles of young TE loci in mouse and human cells. Insights gained using this method will be valuable for understanding the molecular determinants of TE regulation and their impact on the genome.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Keerthi T. Chathoth, Liudmila A. Mikheeva, Gilles Crevel, Jareth C. Wolfe, Ioni Hunter, Saskia Beckett-Doyle, Sue Cotterill, Hongsheng Dai, Andrew Harrison, Nicolae Radu Zabet
Summary: This study uncovers a novel functional role for architectural proteins at TAD borders in Drosophila and establishes a link between TAD reorganization and subsequent changes in gene expression.
Article
Oncology
Sara Badodi, Nicola Pomella, Yau Mun Lim, Sebastian Brandner, Gillian Morrison, Steven M. Pollard, Xinyu Zhang, Nicolae Radu Zabet, Silvia Marino
Summary: This study identifies the therapeutic potential of a combination treatment with BMI1 and MAPK/ERK inhibitors in BMI1(High);CHD7(Low) MB cells, and elucidates the role of the CHD7-BMI1-MAPK regulatory axis in the pathogenesis of MB.
Article
Oncology
Olivia A. Grant, Yucheng Wang, Meena Kumari, Nicolae Radu Zabet, Leonard Schalkwyk
Summary: This study analyzed for the first time the autosomal sex differences in DNA methylation using human whole blood samples. The researchers identified and validated 396 sex-associated differentially methylated CpG sites, with the majority being female-biased CpGs. They also discovered 266 significant sex-associated differentially methylated regions overlapping genes, including novel genes.
CLINICAL EPIGENETICS
(2022)
Article
Biochemical Research Methods
Itunu G. Osuntoki, Andrew Harrison, Hongsheng Dai, Yanchun Bao, Nicolae Radu Zabet
Summary: Motivation: Several computational and statistical methods have been developed to analyze Hi-C data, but most of them do not consider the dependency in the data. Results: In this study, we present a novel statistical method called ZipHiC, which uses a hidden Markov random field model and Approximate Bayesian Computation to detect enriched contacts in Hi-C data. ZipHiC outperforms existing tools, provides insights into biases in Hi-C data, and identifies functional biological roles. Additionally, it corrects biases in micro-C datasets compared to similar Hi-C experiments.
Article
Biochemistry & Molecular Biology
Fabio Hedayioglu, Emma J. Mead, Patrick B. F. O'Connor, Matas Skiotys, Owen J. Sansom, Giovanna R. Mallucci, Anne E. Willis, Pavel Baranov, C. Mark Smales, Tobias von der Haar
Summary: The study validates two experimental tools for assessing ribosome binding to mRNAs, highlighting the usefulness of polysome profile reconstructions in evaluating dataset quality.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Romana T. Pop, Alessandra Pisante, Dorka Nagy, Patrick C. N. Martin, Liudmila A. Mikheeva, Ateequllah Hayat, Gabriella Ficz, Nicolae Radu Zabet
Summary: Transcription factors (TFs) are proteins that regulate gene expression by specifically binding to DNA regulatory regions. This study used ChIP-seq data and an explainable statistical model called ChIPanalyser to investigate the binding mechanism of hundreds of TFs. The results showed that approximately one third of TFs are predicted to bind the genome in a DNA accessibility independent manner, including TFs that can open chromatin and TFs with similar binding motifs. The study demonstrated the high accuracy of ChIPanalyser in predicting the binding of TFs and revealed the ability of many TFs to bind dense chromatin.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Jareth C. Wolfe, Liudmila A. Mikheeva, Hani Hagras, Nicolae Radu Zabet
Summary: By using machine learning and explainable artificial intelligence model, the location of known enhancers in Drosophila can be predicted accurately, providing insight into the underlying histone modifications code. A large set of putative enhancers with similar epigenetic signature as known enhancers were identified, showing intermediate enrichment of mediator and cohesin complexes. 10-15% of predicted enhancers display characteristics similar to super enhancers observed in other species.
Article
Biochemistry & Molecular Biology
Patrick C. N. Martin, Nicolae Radu Zabet
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2020)
