Review
Biology
Heena Satam, Kandarp Joshi, Upasana Mangrolia, Sanober Waghoo, Gulnaz Zaidi, Shravani Rawool, Ritesh P. Thakare, Shahid Banday, Alok K. Mishra, Gautam Das, Sunil K. Malonia
Summary: Next-generation sequencing (NGS) is a powerful tool that can sequence millions of DNA fragments simultaneously, providing detailed information about genomes, genetic variations, gene activity, and changes in gene behavior. Recent advancements have focused on improving sequencing speed and accuracy, reducing costs, and enhancing data analysis. These advancements have great potential for advancing genomics research and improving our understanding of diseases and personalized healthcare.
Review
Chemistry, Analytical
Ting Wang, Wang Ziwei, Bai Linlin, Zhang Xingcai, Jia Feng, Cheng Qian, Wang Yongming, Rui Wang
Summary: Accurate diagnosis of human diseases is crucial and traditional molecular detection methods have limitations. The rapidly evolving CRISPR/Cas systems have revolutionized molecular diagnostics by providing a low-cost, versatile, and powerful toolbox. This review introduces the working principle of the CRISPR toolbox and various detection methods for both infectious and non-infectious diseases, with a focus on single nucleotide polymorphism detection. Challenges and future breakthrough applications in CRISPR molecular diagnostics are also discussed.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Lukasz Fulawka, Aleksandra Kuzan
Summary: This review presents the possibilities of molecular diagnostics available in Poland in 2022, including the samples useful for confirming SARS-CoV-2 infection, the methods used, the safeguards to prevent false-negative and false-positive results, and the products for diagnostic laboratories to choose from. It also discusses the diagnostic problems associated with virus mutation.
Article
Microbiology
Simone J. C. F. M. Moorlag, Jordy P. M. Coolen, Bart van den Bosch, Elisabeth Hui-Mei Jin, Jochem B. B. Buil, Heiman F. L. Wertheim, Willem J. G. Melchers
Summary: The study evaluates the clinical utility of a novel method called 16S RC-PCR for the identification of bacterial species. It shows that this method is more sensitive and accurate compared to the traditional 16S Sanger sequencing method, leading to improved clinical outcomes and patient care.
MICROBIOLOGY SPECTRUM
(2023)
Review
Chemistry, Analytical
Houman Kholafazad-Kordasht, Mohammad Hasanzadeh, Farzad Seidi
Summary: Smartphone-based immunosensing techniques have emerged as efficient, compact, and cost-effective devices for on-site screening and therapy management, offering semi-automated user interfaces and real-time monitoring capabilities. With high computational power and wireless data transferability, smartphones are poised to advance precision medicine towards personalized healthcare.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Miriam Sarkis, Andrea Bernardi, Nilay Shah, Maria M. Papathanasiou
Summary: This paper discusses the market outlook for Advanced Therapy Medicinal Products (ATMPs) and the application of mathematical models in this field, emphasizing the importance of process, techno-economic, and supply chain modeling, and discussing the prospects for Process Systems Engineering.
CURRENT OPINION IN CHEMICAL ENGINEERING
(2021)
Article
Oncology
Anahita Sehgal, Jose S. Pulido, Arman Mashayekhi, Tatyana Milman, Gabor Gy Deak
Summary: Diagnosing vitreoretinal lymphoma is highly challenging due to the common occurrence of false negative results. This study retrospectively analyzed the sensitivity of various diagnostic methods and found that MyD88 mutation analysis caused by a hotspot mutation in MyD88 exhibited the highest sensitivity and lowest coefficient of variation.
Article
Immunology
William F. Wright, Patricia J. Simner, Karen C. Carroll, Paul G. Auwaerter
Summary: Despite the continued prevalence of infectious diseases as the main cause of fever of unknown origin, advancements in molecular technologies offer hope in transforming the investigation of this condition by potentially replacing traditional microbial identification methods.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Public, Environmental & Occupational Health
Corey R. Hart, Patrick M. McLendon, Rajesh R. Naik
Summary: In this article, the global response to the COVID-19 pandemic is described, including the tracking of the virus and the development of new molecular testing technologies. The successes and failures observed in the pandemic are also discussed in relation to improving future pandemic responses.
Article
Public, Environmental & Occupational Health
Magdalena Ruskova, Maria Buckova, Adam Achs, Andrea Puskarova, Jer-Horng Wu, Tomas Kuchta, Zdeno Subr, Domenico Pangallo
Summary: This study selected an effective sample preparation procedure and combined it with a newly developed improved RT-PCR to detect viruses in wastewater samples. A model viral system was constructed using gene editing technology to evaluate the effectiveness of four viral RNA concentration/extraction methods. The research found that for wastewater samples with low viral loads, the OSN-qRT-PCR detection method performed the best and had the highest sensitivity.
INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH
(2022)
Article
Medicine, Legal
Haoliang Fan, Lingxiang Wang, Changhui Liu, Xiaoyu Lu, Xuding Xu, Kai Ru, Pingming Qiu, Chao Liu, Shao-Qing Wen
Summary: A novel MPS-based panel of 133-plex forensic STR markers was developed and comprehensively validated with a large number of profiles, demonstrating a high concordance rate between MPS-based and CE-based genotypes.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2022)
Article
Public, Environmental & Occupational Health
Amal Chihi, Lee O'Brien Andersen, Karim Aoun, Aida Bouratbine, Christen Rune Stensvold
Summary: Comprehensive detection and differentiation of intestinal protists can be achieved using next-generation sequencing of eukaryotic nuclear ribosomal genes. This study demonstrated the high sensitivity of metabarcoding for the detection and differentiation of intestinal eukaryotic protists at the species and subtype level.
PARASITE EPIDEMIOLOGY AND CONTROL
(2022)
Article
Oncology
Charlotte Derpoorter, Ruben Van Paemel, Katrien Vandemeulebroecke, Jolien Vanhooren, Bram De Wilde, Genevieve Laureys, Tim Lammens
Summary: Survival rates for pediatric cancer have increased, but the cause still remains largely unknown. Genetic susceptibility plays a role in some cases, but there are likely other hereditary factors. Whole genome sequencing has identified coding and non-coding variants associated with familial cancer predisposition.
PEDIATRIC HEMATOLOGY AND ONCOLOGY
(2023)
Article
Chemistry, Medicinal
Muhammad Rishfi, Simon Krols, Fien Martens, Sarah-Lee Bekaert, Ellen Sanders, Aline Eggermont, Fanny De Vloed, Joshua Robert Goulding, Martijn Risseeuw, Jan Molenaar, Bram De Wilde, Serge Van Calenbergh, Kaat Durinck
Summary: We conducted a structure-activity relationship (SAR) study of MK-5108-derived PROTACs against AURKA in neuroblastoma. SK2188 showed the most potent AURKA degradation and excellent binding and degradation selectivity. It induced MYCN degradation, replication stress/DNA damage, and apoptosis in neuroblastoma cells.
EUROPEAN JOURNAL OF MEDICINAL 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
Immunology
Kai Ling Liang, Juliette Roels, Marieke Lavaert, Tom Putteman, Lena Boehme, Laurentijn Tilleman, Imke Velghe, Valentina Pegoretti, Inge van de Walle, Stephanie Sontag, Jolien Vandewalle, Bart Vandekerckhove, Georges Leclercq, Pieter Van Vlierberghe, Claude Libert, Filip Van Nieuwerburgh, Roman Fischer, Roland E. Kontermann, Klaus Pfizenmaier, Gina Doody, Martin Zenke, Tom Taghon
Summary: The interaction between thymocytes and thymic stromal cells is crucial for T cell development. This study demonstrates that intrathymic development of dendritic cells (DCs) plays a role in supporting early stages of human T cell development. The transcription factor IRF8 and transmembrane TNF are involved in this process. Selective targeting of TNFR2 has the potential to enhance the generation of T cell precursors for clinical applications.
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
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
Virology
Thomas-Wolf Verdonckt, Anton Bilsen, Filip Van Nieuwerburgh, Loes De Troij, Dulce Santos, Jozef Vanden Broeck
Summary: Insect cell expression systems are used in the medical industry for vaccine development against diseases like COVID-19. The study focuses on the characterization of a specific virus called Bombyx mori latent virus (BmLV) and its pathogenicity. The results demonstrate that a variant of BmLV causes acute infections and strong cytopathic effects in cell lines and animal models. The study also examines the RNAi-based immune response in the cell line and animal models, shedding light on the genomic diversity of BmLV.
Article
Agriculture, Dairy & Animal Science
Evy Beckers, Sofie F. M. Bhatti, Mario Van Poucke, Ingeborgh Polis, Frederic Farnir, Filip Van Nieuwerburgh, Paul Mandigers, Luc Van Ham, Luc Peelman, Bart J. G. Broeckx
Summary: A significant percentage of Dutch partridge dogs suffer from epileptic seizures, but little is known about the genetic cause. This study identified a risk locus for idiopathic epilepsy on chromosome 12 and a variant in the CCDC85A gene that increases the risk of disease in homozygous variant dogs. Further research is needed to determine the usefulness of these findings in breeding decisions.
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
Immunology
Leen Hermans, Sofie Denaeghel, Robert J. J. Jansens, Steffi De Pelsmaeker, Filip Van Nieuwerburgh, Dieter Deforce, Everardo Hegewisch-Solloa, Emily M. Mace, Eric Cox, Bert Devriendt, Herman W. Favoreel
Summary: Two subsets of NK cells are found in the pig liver, one resembling human lrNK cells and the other resembling conventional CD8a(high) NK cells in peripheral blood. The transcriptome analysis reveals that CD8a(dim) lrNK cells exhibit an immature and anti-inflammatory phenotype, while the CD8a(high) NK cells in the liver have an intermediate phenotype expressing liver residency-associated transcripts.
FRONTIERS IN IMMUNOLOGY
(2023)
Meeting Abstract
Allergy
Sharon Van Nevel, Tim Meese, Gabriele Holtappels, Natalie De Ruyck, Stijn Vanhee, Nan Zhang, Filip Van Nieuwerburgh, Claus Bachert
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jose Manuel Salvador Lopez, Lea Vidal, Michelle Patricia Adiutama, Filip Van Nieuwerburgh, Dieter Deforce, Jean-Marc Nicaud, Inge Noelle Adrienne Van Bogaert
Summary: Comparative transcriptomics was conducted to identify proteins involved in fatty acid export through the cell wall in an engineered fatty acid secreting Yarrowia lipolytica yeast. The study revealed that the deletion of the faa1 gene led to the accumulation and secretion of free fatty acids (FFAs). By comparing the transcriptome of the mutant with a wildtype-like strain, several upregulated genes were identified, including cell wall proteins and proteins with unknown functions. However, none of these proteins had a clear role in FFA export.
FEMS YEAST RESEARCH
(2023)