Article
Chemistry, Analytical
Yinghui Feng, Qi Liu, Xinyi Zhao, Miao Chen, Xiaotong Sun, Hexiang Li, Xiaoqing Chen
Summary: In this study, a framework nucleic acid (FNA)-based nonenzymatic spatial-confinement amplifier was developed for rapid and reliable intracellular miRNA imaging. By encapsulating the localized catalytic hairpin assembly (L-CHA) reactor in the inner cavity of the FNA and utilizing the spatial-confinement effect, the reaction rate was accelerated and the dynamic performance was improved.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Yongsong Zhou, Wei Cui, Buling Wu, Bofeng Zhu
Summary: A 6-dye multiplex Y-chromosomal short tandem repeat (Y-STR) panel named Y34plex was constructed to increase discrimination capacity and reduce adventitious match probability, combining 25 Y-chromosomal markers and nine highly polymorphic Y-STR loci. A validation study showed that Y34plex has high discrimination power and applicability for forensic investigations.
Article
Genetics & Heredity
Yuguo Huang, Haijun Zhang, Yifan Wei, Yueyan Cao, Qiang Zhu, Xi Li, Tiantian Shan, Xuan Dai, Ji Zhang
Summary: This study developed a multiplex PCDR system and tested it in forensic low-template DNA analysis using MPS technology. The findings showed that the PCDR-MPS workflow is an effective approach for obtaining complete STR profiles.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Biochemical Research Methods
Qiang Zhu, Haoyu Wang, Yueyan Cao, Yuguo Huang, Yuhan Hu, Yijun Zhou, Yifan Wei, Xi Li, Tingyun Hou, Yuting Wang, Panyin Shu, Feng Song, Ji Zhang
Summary: This study constructed a microfluidic water-in-oil droplet PCR system and analyzed the sensitivity, concordance, amplification efficiency of the droplet PCR, and influence factors. The droplet PCR showed high concordance with conventional bulk PCR and had high sensitivity, particularly in identifying minor contributors in mixed DNA samples. The study provides a basis for the wide application of droplet PCR in forensic science.
Article
Anthropology
Hui Xu, Ming Zhao, Shuyan Mei, Yunying Zhang, Meiming Cai, Fanzhang Lei, Bofeng Zhu
Summary: The study assessed Y-STR genetic information of Han male subjects from Shaanxi, China, revealing high genetic polymorphisms. Genetic relationship comparisons with other Chinese populations were conducted, highlighting significant genetic differences and similarities.
ANNALS OF HUMAN BIOLOGY
(2022)
Article
Genetics & Heredity
Olivier Tytgat, Sonja Skevin, Dieter Deforce, Filip Van Nieuwerburgh
Summary: Nanopore sequencing for forensic purposes, combined with advanced basecallers and analysis methods, resulted in significantly improved STR genotyping accuracy compared to previous studies, while also achieving high accuracy in iso-allele detection.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2022)
Article
Multidisciplinary Sciences
Ruoxu Li, Ning Su, Xiaodong Ren, Xiange Sun, Wenman Li, Yuwei Li, Jin Li, Chen Chen, Hong Wang, Weiping Lu, Shaoli Deng, Qing Huang
Summary: This study developed a centrifugal microfluidics-based multiplex RT-RPA assay for rapid detection of SARS-CoV-2. The microfluidic chip could simultaneously detect three target genes and one reference gene, with high sensitivity and specificity. It has the potential to be used for point-of-care testing and detection of emerging SARS-CoV-2 variants.
Article
Immunology
Yonglu Wang, Ziqiang He, Patigul Ablimit, Shunshi Ji, Dong Jin
Summary: In this study, a multiplex MCDA-LFB assay was developed for rapid and convenient identification of virulent S. sonnei within 30 minutes, without the need for expensive lab equipment.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Chemistry, Analytical
Xing Yang, Jingjin Zhao, Li Hou, Ivan Yu Sakharov, Jianniao Tian, Shulin Zhao
Summary: Based on the microchip electrophoresis chemiluminescence detection platform, an ultrasensitive method was developed for the detection of microRNA-141 by using a triple-cycle cascade chemiluminescence signal amplification strategy. This method showed excellent specificity and a very low detection limit for miRNA-141 assay. It has important applications in clinical diagnostics and biomedical research of miRNAs.
Article
Chemistry, Analytical
Feifei Luo, Yuqi Lu, Xing Geng, Zhi Li, Ge Dai, Zhaohui Chu, Jingwen Zhang, Fan Zhang, Pingang He, Qingjiang Wang
Summary: A new dT-SDA strategy was proposed for detecting longer DNA, which generates numerous ssDNA products through the formation of defective T junction structures and cascade SDA cycling. This strategy consumes less time and has satisfactory sensitivity, making it suitable for effective bacterial screening and infection diagnosis.
ANALYTICAL CHEMISTRY
(2021)
Article
Biology
Luca Miglietta, Yuwen Chen, Zhi Luo, Ke Xu, Ning Ding, Tianyi Peng, Ahmad Moniri, Louis Kreitmann, Miguel Cacho-Soblechero, Alison Holmes, Pantelis Georgiou, Jesus Rodriguez-Manzano
Summary: This study introduces a simplified workflow called Smart-Plexer for developing multiplex PCR assays, which is applied to detect respiratory infection targets. The method combines empirical testing and computer simulation to achieve specific and sensitive identification of multiple analytes. The results demonstrate that optimized multiplex PCR assays, combined with data-driven methodology, can accurately classify the presence of seven common respiratory infection pathogens in a single test.
COMMUNICATIONS BIOLOGY
(2023)
Article
Genetics & Heredity
Courtney Patterson, Shayna Gray, Frank R. Wendt, Reena Roy
Summary: The study examined the inhibitory effects of copper and other metals on bloodstain deposition, as well as the efficiency of DNA profiling using different amplification methods. Direct amplification proved to be more effective in obtaining complete STR profiles compared to extraction methods, with copper composition showing limited impact on profile completeness.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Biophysics
Yuecan Zhao, Junzhu Xiang, Hao Cheng, Xiaojuan Liu, Feng Li
Summary: The development of a novel flexible photoelectrochemical biosensor for miRNA determination showed promising potential for ultrasensitive disease diagnosis. The biosensor exhibited excellent analytical performance, selectivity, stability, flexibility, and practical applicability, making it a valuable tool for bioassays and early disease detection.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Chemistry, Multidisciplinary
Cheryl S. Y. Yeap, Thanyarat Chaibun, Su Yin Lee, Bin Zhao, Yuan Jan, Chan La-o-vorakiat, Werasak Surareungchai, Shiping Song, Benchaporn Lertanantawong
Summary: The study presents a highly sensitive and selective multiplex assay utilizing an electrochemical DNA sensor and isothermal rolling circle amplification to detect and discriminate three common entero-pathogens in a single reaction. The assay has femtomolar sensitivity and is particularly useful for field- or resource-limited settings.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Ozlem Yaren, Jacquelyn McCarter, Andrew R. R. Morris, Kevin M. M. Bradley, Nilesh B. B. Karalkar, Daniel C. C. McLendon, Dongmin Kim, Bradley H. H. Eastmond, Nathan D. D. Burkett-Cadena, Barry W. W. Alto, Steven A. A. Benner
Summary: The recently reported DP-LAMP architecture has been proven to amplify viral RNA from SARS-CoV-2 with minimal sample processing. This molecular strategy allows for spatial separation and independent sequencing of target nucleic acids, making it an attractive option for the detection of arboviral RNA carried by mosquitoes in the field, when integrated with trap and sampling innovations.
ANALYTICAL CHEMISTRY
(2023)
Article
Respiratory System
Hannelore P. Van Eeckhoutte, Chantal Donovan, Richard Y. Kim, Thomas M. Conlon, Meshal Ansari, Haroon Khan, Ranjith Jayaraman, Nicole G. Hansbro, Yves Dondelinger, Tom Delanghe, Allison M. Beal, Brad Geddes, John Bertin, Tom Vanden Berghe, Joyceline De Volder, Tania Maes, Peter Vandenabeele, Bart M. Vanaudenaerde, Dieter Deforce, Sonja Skevin, Filip Van Nieuwerburgh, Fien M. Verhamme, Guy F. Joos, Sobia Idrees, Herbert B. Schiller, Ali Oender Yildirim, Alen Faiz, Mathieu J. M. Bertrand', Guy G. Brusselle, Philip M. Hansbro, Ken R. Bracke
Summary: RIPK1 plays a key role in COPD pathogenesis by mediating cell death and inflammation. Inhibition of RIPK1 kinase activity can alleviate airway inflammation and cell death caused by COPD, making it a potential therapeutic approach.
EUROPEAN RESPIRATORY JOURNAL
(2023)
Article
Genetics & Heredity
Tamara Jarayseh, Brecht Guillemyn, Hanna De Saffel, Jan Willem Bek, Delfien Syx, Sofie Symoens, Yannick Gansemans, Filip Nieuwerburgh, Sujatha Jagadeesh, Jayarekha Raja, Fransiska Malfait, Paul J. Coucke, Adelbert De Clercq, Andy Willaert
Summary: Bi-allelic mutations in TAPT1 gene lead to a wide range of phenotypes, from severe skeletal and congenital abnormalities to isolated early-onset cataract. A frameshift mutation in the TAPT1 gene was identified in a patient with bilateral early-onset cataract and skeletal abnormalities, expanding the phenotypic spectrum. A zebrafish model with TAPT1 gene knockout exhibited eye malformations, loss of vision, increased photokinetics, and hyperpigmentation, providing insights into the ultrastructural and molecular characteristics of TAPT1 mutations.
Article
Environmental Sciences
Xiangrong Chen, Mohamed F. Abdallah, Charlotte Grootaert, Filip Van Nieuwerburgh, Andreja Rajkovic
Summary: This study investigated the combined toxicity of Aflatoxin B1 (AFB1) and fumonisin B1 (FB1) on mitochondrial and glycolytic activity in HepG2 cells. The results showed that the co-exposure, especially at high doses, significantly inhibited mitochondrial respiration. Moreover, RNA transcriptome sequencing revealed differential expression of the p53 signaling pathway and downregulation of genes encoding for Complexes I, II, III, and IV.
ENVIRONMENT INTERNATIONAL
(2023)
Article
Biochemistry & Molecular Biology
Annelies Raes, Eline Wydooghe, Krishna Chaitanya Pavani, Osvaldo Bogado Pascottini, Katleen Van Steendam, Maarten Dhaenens, Annekatrien Boel, Sonia Heras, Bjorn Heindryckx, Luc Peelman, Dieter Deforce, Filip Van Nieuwerburgh, Geert Opsomer, Ann Van Soom, Katrien Smits
Summary: While animal models have shown that culturing embryos in groups improves blastocyst yield and quality, the identity of the responsible embryotrophins remains largely unknown. This study identified cathepsin-L as an important embryotrophin in bovine in vitro embryo production, and demonstrated that supplementation of cathepsin-L significantly improved blastocyst development and quality.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Daniel Angel-Velez, Tim Meese, Mohamed Hedia, Andrea Fernandez-Montoro, Tine De Coster, Osvaldo Bogado Pascottini, Filip Van Nieuwerburgh, Jan Govaere, Ann Van Soom, Krishna Pavani, Katrien Smits
Summary: In the last decade, in vitro embryo production has become an established clinical practice in horses. However, the blastocyst rates from vitrified equine oocytes remain low due to cryopreservation's negative effect on oocyte developmental potential. This study compared the transcriptome profiles of vitrified equine oocytes before and after in vitro maturation. The results showed that vitrification of in vitro matured oocytes had subtle advantages in terms of the mRNA profile, highlighting the potential for further improvements in equine oocyte vitrification efficiency.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Lore Billiet, Laurenz De Cock, Guillem Sanchez Sanchez, Rupert L. Mayer, Glenn Goetgeluk, Stijn De Munter, Melissa Pille, Joline Ingels, Hanne Jansen, Karin Weening, Eva Pascal, Killian Raes, Sarah Bonte, Tessa Kerre, Niels Vandamme, Ruth Seurinck, Jana Roels, Marieke Lavaert, Filip Van Nieuwerburgh, Georges Leclercq, Tom Taghon, Francis Impens, Bjorn Menten, David Vermijlen, Bart Vandekerckhove
Summary: Billiet et al. identify a well-defined but heterogeneous unconventional TCR alpha beta(+) lineage mainly confined to CD8(+) Helios(+) T cells, which represents the post-thymic progeny of CD10(+) PD-1(+) precursors in humans. These unconventional T cells (UTCs) in thymus and blood share a common developmental trajectory, characterized by hallmark transcription factors (ZNF683 and IKZF2) and a polycolonal TCR repertoire with autoreactive features. The UTC lineage can be identified in adult blood and intestinal tissues.
JOURNAL OF EXPERIMENTAL MEDICINE
(2023)
Article
Plant Sciences
Willem Desmedt, Maarten Ameye, Osvaldo Filipe, Evelien De Waele, Filip Van Nieuwerburgh, Dieter Deforce, Lieven Van Meulebroek, Lynn Vanhaecke, Tina Kyndt, Monica Hofte, Kris Audenaert
Summary: This study showed that Z-3-hexenyl acetate-induced resistance (Z-3-HAC-IR) in rice can effectively protect against rice blast, sheath blight, and brown spot diseases, while also increasing rice yield.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Multidisciplinary Sciences
A. S. Vermeersch, M. Ali, Y. Gansemans, F. Van Nieuwerburgh, P. Geldhof, R. Ducatelle, D. Deforce, J. Callens, G. Opsomer
Summary: This study is the first to explore the changes in gene expression in severe udder cleft dermatitis lesions (UCD) in Holstein-Friesian cows. RNA Seq-Technology was used to compare gene expression levels in UCD lesions and healthy udder skin, revealing significant differences in inflammatory pathways. Upregulated genes included chemokines CXCL2, CXCL5, CXCL8, and CCL11, as well as multifunctional molecules ADAM12 and SLPI, while downregulated genes were associated with keratins. Pathway analysis showed significant upregulation of inflammatory pathways such as chemokine signaling, cytokine receptor interaction, and IL-17 signaling. These findings suggest a dysregulated inflammatory response, disrupted skin barrier integrity, and impaired wound repair mechanism in severe UCD lesions.
Article
Agriculture, Dairy & Animal Science
Marielen de Souza, Venessa Eeckhaut, Evy Goossens, Richard Ducatelle, Filip Van Nieuwerburgh, Karl Poulsen, Ana Angelita Sampaio Baptista, Ana Paula Frederico Rodrigues Loureiro Bracarense, Filip Van Immerseel
Summary: Galactomannans in broiler feed can negatively impact zootechnical performance and gut microbiota composition. Mannanase supplementation can restore the gut microbiota and improve performance to normal levels.
Article
Biochemistry & Molecular Biology
Eva Gijbels, Kevin De Muynck, Bart Vanderborght, Tim Meese, Filip Van Nieuwerburgh, Aude Vanlander, Frederik Berrevoet, Bart Hendrikx, Anne Hoorens, Hans Van Vlierberghe, Mathieu Vinken, Lindsey Devisscher
Meeting Abstract
Nutrition & Dietetics
B. Boshuizen, L. Mare, C. De Meeus, L. Devisscher, C. Vidal Moreno de Vega, J. De Oliveira, G. Hosotani, Y. Gansemans, T. Meese, F. Van Nieuwerburgh, D. Deforce, C. Delesalle
PROCEEDINGS OF THE NUTRITION SOCIETY
(2023)
Article
Pharmacology & Pharmacy
Koen Deserranno, Laurentijn Tilleman, Kaat Rubben, Dieter Deforce, Filip Van Nieuwerburgh
Summary: Pharmacogenomics (PGx) studies the impact of genomic variation on drug response and allows personalized dosing. Current PGx testing methods cannot identify large structural variants and star-alleles. This study successfully enriched 1,036 PGx-relevant genes using Oxford Nanopore Technologies and demonstrated accurate variant and star-allele calling. It also showed that up to three samples can be multiplexed without significant decrease in variant calling performance.
FRONTIERS IN PHARMACOLOGY
(2023)