Article
Microbiology
Georgia Doing, Alexandra J. J. Lee, Samuel L. Neff, Taylor Reiter, Jacob D. Holt, Bruce A. Stanton, Casey S. Greene, Deborah A. Hogan
Summary: In this study, thousands of Pseudomonas aeruginosa RNA sequencing gene expression profiles were reanalyzed to create a powerful tool for hypothesis generation and testing. Raw sequence data were uniformly processed and validated using the Salmon pseudoaligner. Filtering criteria were developed to exclude samples with aberrant gene expression and normalization steps greatly improved gene expression correlations. The resulting compendia and algorithm for incorporating new data provide useful tools for P. aeruginosa RNA-seq analysis.
Article
Multidisciplinary Sciences
Hung X. Nguyen, Tianyu Wu, Daniel Needs, Hengtao Zhang, Robin M. Perelli, Sophia DeLuca, Rachel Yang, Michael Tian, Andrew P. Landstrom, Craig Henriquez, Nenad Bursac
Summary: This study demonstrates that introducing engineered prokaryotic voltage-gated sodium channels (BacNav) can enhance excitability and conduction in cardiomyocytes, potentially providing a new approach for treating cardiac arrhythmias. The use of small-sized, codon-optimized BacNav channels significantly improves excitability and conduction in rat and human cardiomyocytes, as well as adult cardiac tissues from different species. Additionally, the expression of BacNav reduces the occurrence of conduction block and reentrant arrhythmias in fibrotic cardiac cultures, without causing any adverse effects on cardiac electrophysiology in mice.
NATURE COMMUNICATIONS
(2022)
Review
Immunology
Fernando Baquero, Claudia Saralegui, Daniel Marcos-Mencia, Luna Ballestero, Sergio Vano-Galvan, Oscar M. Moreno-Arrones, Rosa del Campo
Summary: The epidermis plays a crucial role in interacting with commensal bacteria to maintain skin health. Through chemical and immunological interactions with bacteria, the epidermis maintains bacterial homeostasis and has antibacterial responses to eliminate pathogens. Hands, particularly fingers, are the primary platform for bacterial transmission.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
E. Eduardo Antunez, Clare S. Mahon, Ziqiu Tong, Nicolas H. Voelcker, Markus Muellner
Summary: The study focuses on developing thermally reversible biosensors for detecting Escherichia coli heat-labile enterotoxin (LTB), with the ability to accurately recognize LTB content and bacteria, emphasizing low cost, portability, and sensitivity. The biosensors can detect sub-micromolar concentrations of LTB in solution with label-free format, and exhibit temperature-mediated catch-and-release behavior, showing potential for selective protein capture, multiple readouts, and sensor regeneration over consecutive cycles of use.
Article
Automation & Control Systems
Yuyang Chen, Chao Zhang, Zhonghao Wu, Jiangran Zhao, Bo Yang, Jia Huang, Qingquan Luo, Linhui Wang, Kai Xu
Summary: The study highlights the importance of developing flexible and precise surgical robotic systems for minimally invasive surgery, and proposes a modular surgical robotic platform that can handle different types of procedures with potential adaptability. Further research involving larger animal studies and clinical trials is needed to verify the true potentials of the proposed system.
IEEE-ASME TRANSACTIONS ON MECHATRONICS
(2022)
Article
Automation & Control Systems
Yuyang Chen, Chao Zhang, Zhonghao Wu, Jiangran Zhao, Bo Yang, Jia Huang, Qingquan Luo, Linhui Wang, Kai Xu
Summary: Numerous surgical robotic systems have been developed to improve dexterity, precision, and ergonomics in minimally invasive surgery. A modular surgical robotic platform has been proposed to handle multiport, singleport, and hybrid-port procedures, with a focus on achieving suitable invasiveness with minimal skin incisions.
IEEE-ASME TRANSACTIONS ON MECHATRONICS
(2022)
Article
Health Care Sciences & Services
Kevin Y. X. Wang, Gulietta M. Pupo, Varsha Tembe, Ellis Patrick, Dario Strbenac, Sarah-Jane Schramm, John F. Thompson, Richard A. Scolyer, Samuel Muller, Garth Tarr, Graham J. Mann, Jean Y. H. Yang
Summary: In the era of precision medicine, molecular signatures from advanced omics technologies have the potential to guide clinical decisions. However, current approaches are often limited by location-specificity, which hampers the transferability of molecular signatures. To address this issue, the researchers developed a penalised regression model called Cross-Platform Omics Prediction (CPOP), which can predict patient outcomes in a platform-independent manner across time and experiments. CPOP improves upon traditional prediction frameworks by selecting ratio-based features with similar estimated effect sizes. The model demonstrated stable performance across datasets of similar biology, reducing the impact of technical noise generated by omics platforms. The researchers evaluated CPOP using melanoma transcriptomics data and showed its potential in a clinical screening framework for precision medicine. The model's generalization was further demonstrated with ovarian cancer and inflammatory bowel disease studies.
NPJ DIGITAL MEDICINE
(2022)
Article
Biology
Steven M. Foltz, Casey S. Greene, Jaclyn N. Taroni
Summary: By employing supervised and unsupervised machine learning evaluations, we identified the best normalization methods, including quantile and Training Distribution Matching normalization, for combining microarray and RNA-seq data. Nonparanormal normalization and z-scores were also found to be appropriate for certain applications. Our study demonstrates the possibility of effective cross-platform normalization using existing methods for machine learning applications.
COMMUNICATIONS BIOLOGY
(2023)
Article
Engineering, Electrical & Electronic
Mei Feng, Yanlei Gong, Xingze Jin, Zhiwu Han, Ji Zhao, Yan Li
Summary: This study proposes a new type of manual training platform for single-port minimally invasive surgery. It imitates the structure of a human arm and allows for the cooperative operation of multiple surgical instruments under a single incision. The effectiveness and reliability of the platform have been validated through a series of experiments.
Article
Surgery
Emily K. Funk, Philip Weissbrod, Santiago Horgan, Ryan K. Orosco, Joseph A. Califano
Summary: The study investigated a novel minimally invasive surgical platform for procedures in the oropharynx, hypopharynx, and larynx. The preliminary results showed that a wide range of procedures in these areas could be performed successfully using this platform. Further research is needed to evaluate its applicability in a clinical setting.
SURGICAL ENDOSCOPY AND OTHER INTERVENTIONAL TECHNIQUES
(2021)
Review
Biochemistry & Molecular Biology
Nicolas Borisov, Anton Buzdin
Summary: The emergence of high throughput gene expression methods has led to the development of quantitative transcriptomics, but also raised the question of comparing expression profiles obtained from different equipment, protocols, and/or experiments. Various methods have been proposed to address this issue, but there is no gold standard for unifying this type of Big Data. Recent developments have shown that platform/protocol/batch bias can be efficiently reduced, allowing for the transformation of gene expression profiles into a universal format that supports multiple inter-comparisons at a reasonable cost. This paves the way for the universal indexing of RNA sequencing and microarray hybridization profiles.
Article
Chemistry, Organic
James T. Brewster II, Samuel D. Randall, John Kowalski, Cole Cruz, Richard Shoemaker, Eugene Tarlton, Ronald J. Hinklin
Summary: Photoredox-transition metal dual catalysis is an important platform for constructing sp3-rich chemical matter, which is significant for medicinal chemistry programs. By cross-coupling commercially available or easily prepared compounds, novel saturated heterocyclic scaffolds can be obtained, providing opportunities for diversification.
Article
Multidisciplinary Sciences
Jonathan Nadjiri, Tobias Geith, Tobias Waggershauser, Stephan Forster, Philipp Paprottka
Summary: The main risk factor for adverse outcomes after radiographically guided port implantation at the forearm is the type of the implanted port system, while age is a risk factor for late complications.
Article
Engineering, Biomedical
Bruno Gil, Henry Ip, Panagiotis Kassanos, Benny Lo, Guang-Zhong Yang, Salzitsa Anastasova
Summary: Totally implanted access ports (TIAP) are widely used for long term central venous access in oncology patients. This paper proposes a smart TIAP device that can detect infection and monitor biomarkers in body fluids to provide vital information about the patient's health and potential port infection.
MATERIALS TODAY BIO
(2022)
Article
Biochemistry & Molecular Biology
Maria Claudia Villegas Kcam, Annette J. Tsong, James Chappell
Summary: CRISPR-Cas activator systems have the potential to selectively activate target genes, but face limitations in bacteria due to strict distance-dependent target binding requirements. By utilizing rational protein engineering, a new CRISPRa platform has been developed with increased modularity and targeting flexibility. This approach allows for easy customization and expanded target range through harnessing engineered Cas proteins.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Dries Decap, Louise de Schaetzen van Brienen, Maarten Larmuseau, Pascal Costanza, Charlotte Herzeel, Roel Wuyts, Kathleen Marchal, Jan Fostier
Summary: Halvade Somatic is a somatic variant calling pipeline that leverages Big Data processing platforms, enabling the processing of large volumes of sequencing data in a short amount of time with reliable and scalable performance.
Article
Biochemical Research Methods
Dries Van Daele, Bram Weytjens, Luc De Raedt, Kathleen Marchal
Summary: This study introduces a logic programming framework called OMEN, which effectively combines gene-specific driver properties and gene-set properties to improve the specificity of driver gene detection. It robustly identifies driver genes and modules as proxies of driver pathways.
Article
Agronomy
Taher Mohasseli, Razgar Seyed Rahmani, Reza Darvishzadeh, Sara Dezhsetan, Kathleen Marchal
Summary: Understanding the molecular effects of salinity stress is essential for improving salt tolerance in Zea mays. This study combined phenotyping and transcript profiling to investigate genotype-specific differences in salt tolerance. The analysis identified unique transcripts and enriched processes related to salt tolerance in the tolerant genotype, suggesting that more efficient potassium uptake and different calcium ion response contribute to better ionic hemostasis and salt tolerance in this genotype.
CEREAL RESEARCH COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Razgar Seyed Rahmani, Dries Decap, Jan Fostier, Kathleen Marchal
Summary: This study used a motif discovery algorithm to identify novel motifs in maize, and found that some of these motifs were functional and associated with transcription factor binding sites and open chromatin.
Article
Plant Sciences
Yue Zhang, Xingyu Yang, Yves Van de Peer, Jinming Chen, Kathleen Marchal, Tao Shi
Summary: This study reveals the relative contributions of alternative splicing and gene duplication to the functional diversity of genes in lotus. Alternative splicing events have rapidly evolved between orthologs and lineage-specific splice variants play a role in gene functional changes during species divergence. Single-copy genes contain more isoforms with a higher conservation of alternative splicing events across species and more complex tissue-dependent expression patterns. In contrast, isoforms of whole-genome duplicates are less conserved and display a less conserved tissue bias, suggesting their contribution to subfunctionalization. Through comparative analysis of isoform expression networks, orthologous genes with conserved tissue bias in isoform expression across species are identified, indicating a strong selection pressure for maintaining a stable expression pattern of these isoforms.
Review
Biochemistry & Molecular Biology
Marlies Boeren, Pieter Meysman, Kris Laukens, Peter Ponsaerts, Benson Ogunjimi, Peter Delputte
Summary: Herpesviruses manipulate immune recognition by T cells through hijacking the MHC I and MHC II antigen presentation pathways. The MHC immune evasion strategies of herpes simplex virus-1 (HSV-1) and varicella-zoster virus (VZV) are illustrated. MHC-T cell interactions in HSV-1 and VZV-infected neural ganglia are described, with CD8+ T cells playing a major role in controlling neuronal HSV-1 infection and CD4+ T cells being important in controlling VZV infection. Autologous human stem-cell-derived in vitro models provide valuable tools for studying these neuroimmune interactions.
TRENDS IN MICROBIOLOGY
(2023)
Article
Food Science & Technology
Florence E. Buytaers, Bavo Verhaegen, Mathieu Gand, Jolien D'aes, Kevin Vanneste, Nancy H. C. Roosens, Kathleen Marchal, Sarah Denayer, Sigrid C. J. De Keersmaecker
Summary: This proof-of-concept study explores the feasibility of using metagenomics to obtain whole genome sequences of norovirus from contaminated food and perform strain level characterization, as well as relate to human cases. The study compares different sequencing methods and demonstrates that shotgun metagenomics is effective for phylogenetic analysis while hybrid capture is suitable for lower contamination. The study also shows the potential of shotgun metagenomics to detect multiple viruses in food samples.
Article
Virology
Marlies Boeren, Elise Van Breedam, Tamariche Buyle-Huybrecht, Marielle Lebrun, Pieter Meysman, Catherine Sadzot-Delvaux, Viggo F. Van Tendeloo, Geert Mortier, Kris Laukens, Benson Ogunjimi, Peter Ponsaerts, Peter Delputte
Summary: This study developed a compartmentalized hiPSC-derived neuronal culture model to mimic natural VZV infection route. The study found that hiPSC-neurons do not mount an effective antiviral response following VZV infection, unlike Sendai virus infection. The cells do not upregulate interferon-stimulated genes and do not produce interferon-alpha. However, exogenous interferon-alpha effectively limits VZV spread in the neuronal cells and promotes upregulation of ISGs.
Article
Biotechnology & Applied Microbiology
Arne Claeys, Peter Merseburger, Jasper Staut, Kathleen Marchal, Jimmy van den Eynden
Summary: This study evaluated the performance of 13 HLA genotyping tools on Whole Exome Sequencing (WES) and RNA sequencing data. The results showed that Optitype and arcasHLA had the highest accuracies for MHC-I genotyping on WES and RNA sequencing data respectively, while HLA-HD was the most accurate tool for MHC-II genotyping on both data types. Therefore, depending on the available data type and computational resources, we recommend using Optitype and HLA-HD for MHC-I and MHC-II genotyping.
Article
Oncology
Marija Pizurica, Maarten Larmuseau, Kim Van der Eecken, Louise de Schaetzen van Brienen, Francisco Carrillo-Perez, Simon Isphording, Nicolaas Lumen, Jo Van Dorpe, Piet Ost, Sofie Verbeke, Olivier Gevaert, Kathleen Marchal
Summary: Deep learning models predicting TP53 mutations from whole slide images of prostate cancer capture histologic phenotypes associated with stromal composition, lymph node metastasis, and biochemical recurrence, indicating their potential as in silico prognostic biomarkers.
Article
Multidisciplinary Sciences
Wim L. Cuypers, Pieter Meysman, Francois-Xavier Weill, Rene S. Hendriksen, Getenet Beyene, John Wain, Satheesh Nair, Marie A. Chattaway, Blanca M. Perez-Sepulveda, Pieter-Jan Ceyssens, Tessa de Block, Winnie W. Y. Lee, Maria Pardos de la Gandara, Christian Kornschober, Jacob Moran-Gilad, Kees T. Veldman, Martin Cormican, Mia Torpdahl, Patricia I. Fields, Tomas Cerny, Liselotte Hardy, Bieke Tack, Kate C. Mellor, Nicholas Thomson, Gordon Dougan, Stijn Deborggraeve, Jan Jacobs, Kris Laukens, Sandra Van Puyvelde
Summary: This study provides a genomic overview of the population structure and antimicrobial resistance of Salmonella enterica serovar Concord. The researchers found that S. Concord is distributed among three Salmonella super-lineages and exhibits different levels of antimicrobial resistance and geographical distribution among different lineages.
NATURE COMMUNICATIONS
(2023)
Article
Immunology
Katrien Skorobogatov, Marianne Foiselle, Jean-Romain Richard, Wahid Boukouaci, Ching-Lien Wu, Sophie Raynal, Christel Carbonne, Kris Laukens, Pieter Meysman, Violette Coppens, Philippe le Corvoisier, Caroline Barau, Livia De Picker, Manuel Morrens, Ryad Tamouza, Marion Leboyer
Summary: The study investigated the impact of serum kynurenine metabolite levels on diagnosis, clinical state, symptom severity, and clinical course in SCZ and BD patients. Lower levels of kynurenine metabolites were found in all patients compared to healthy controls. Hospitalized patients had significantly lower levels than stabilized outpatients, and specific metabolites were associated with psychotic symptoms and illness duration.
BRAIN, BEHAVIOR, & IMMUNITY - HEALTH
(2023)
Article
Biotechnology & Applied Microbiology
Luka Svet, Ilse Parijs, Simon Isphording, Bram Lories, Kathleen Marchal, Hans P. Steenackers
Summary: The development of antimicrobial resistance in dense and diverse biofilm communities is different from that in free-living bacteria. In duo-species biofilms, the competition between brewery isolates enhanced antimicrobial tolerance and resistance development in Pseudomonas rhodesiae. The acquired resistance phenotype depends on complex interactions between low-frequency mutations in the genetic background of the strains.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Immunology
Alexandra Vujkovic, My Ha, Tessa de Block, Lida van Petersen, Isabel Brosius, Caroline Theunissen, Sabrina H. van Ierssel, Esther Bartholomeus, Wim Adriaensen, Guido Vanham, George Elias, Pierre Van Damme, Viggo Van Tendeloo, Philippe Beutels, Maartje van Frankenhuijsen, Erika Vlieghe, Benson Ogunjimi, Kris Laukens, Pieter Meysman, Koen Vercauteren
Summary: This study demonstrates that annotating TCR sequences of activated CD8+ T cells can be used to diagnose acute viral infections and differentiate them from historical exposures.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Biochemical Research Methods
Pieter-Paul Strybol, Maarten Larmuseau, Louise de Schaetzen van Brienen, Tim Van den Bulcke, Kathleen Marchal
Summary: We present deep link prediction (DLP), a method for the interpretation of loss-of-function screens. Our approach uses representation-based link prediction to reprioritize phenotypic readouts by integrating screening experiments with gene-gene interaction networks. DLP-DeepWalk outperforms other methods in recovering cell-specific dependencies, achieving an average precision well above 90% across 7 different cancer types and on both RNAi and CRISPR data. The genes ranked highest by DLP-DeepWalk are more enriched in drug targets compared to the ranking based on original screening scores.
CELL REPORTS METHODS
(2022)
