Article
Multidisciplinary Sciences
Unai Baroja, Inazio Garin, Nerea Vallejo, Amaia Caro, Carlos Ibanez, Andrea Basso, Urtzi Goiti
Summary: This study developed and evaluated two species-specific PCR assays to detect and quantify DNA of a major forest pest, Thaumetopoea pityocampa, in bat faeces. The quantitative experiment results showed that the qPCR assay accurately estimated the DNA abundance of T. pityocampa. The framework of this study can be used as a model to design similar assays for other species of interest.
SCIENTIFIC REPORTS
(2022)
Article
Food Science & Technology
Bettina Pancza, Miklos Szathmary, Istvan Gyurjan, Barbara Bankuti, Zoltan Tudos, Susan Szathmary, Laszlo Stipkovits, Zsofia Sipos-Kozma, Balazs Asvanyi, Laszlo Varga, Kalman Szenthe, Ferenc Banati
Summary: This study identified an efficient, rapid, simple, and cost-effective method for pretreating raw milk samples to produce PCR-ready DNA for microbial detection. The in-house procedure involving Triton X-100 based pretreatment and an inhibitor removal resin was shown to be superior in terms of DNA yield, sensitivity, ease of handling, time efficiency, and cost per sample.
Article
Microbiology
Johnson Edwards, Carmen Hoffbeck, Annie G. West, An Pas, Michael W. Taylor
Summary: This study evaluated the impact of two DNA preservation methods (95% ethanol and RNAlater) and five extraction approaches on the avian gut microbiota. Systematic testing revealed differences in extraction efficacy, but minimal influence on 16S rRNA gene-based microbiota profiles. The chosen preservation and extraction method was effective across phylogenetically and ecologically diverse avian species, providing an important foundation for ongoing research.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Microbiology
Ryanne Oldham, Michael Held
Summary: It is important for breweries of all sizes to monitor the microbiome of their process to prevent financial losses caused by microbial contamination. Lactic acid bacteria (LAB) are the main beer-spoiling microbes (BSMs) and can enter the viable but nonculturable (VBNC) state, making them invisible to traditional detection methods. Real-time quantitative polymerase chain reaction (qPCR), specifically SYBR Green qPCR, is the most suitable method for BSM detection in craft breweries due to its affordability, speed, specificity, sensitivity, quantification, and reliability.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biology
Schuyler D. Smith, Jinlyung Choi, Nicole Ricker, Fan Yang, Shannon Hinsa-Leasure, Michelle L. Soupir, Heather K. Allen, Adina Howe
Summary: The study presents a high-throughput sequencing method called DARTE-QM for screening antibiotic resistance genes in environmental DNA samples. It demonstrates the effectiveness of this method in soil, manure, and livestock fecal samples, as well as a synthetic mock-community reference.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Sanghwa Jeong, Eduardo Gonzalez-Grandio, Nicole Navarro, Rebecca L. Pinals, Francis Ledesma, Darwin Yang, Markita P. Landry
Summary: The global SARS-CoV-2 pandemic has driven a surge in demand for rapid and efficient viral infection diagnostic tests, leading to a shortage in diagnostic test consumables. A new method using carbon nanotubes and ssDNA sequences has been developed to achieve high-yield extraction of viral nucleic acids, with a 100% extraction yield of target SARS-CoV-2 RNA. This method allows direct extraction of nucleic acids from human saliva, bypassing the need for further biofluid purification and commercial extraction kits.
Article
Fisheries
Jenna L. Alexander, Shelagh K. Malham, David Smyth, Julie Webb, David Fidler, Philippa Bayford, James McDonald, Lewis Le Vay
Summary: Accurate identification of mussel larvae is crucial for improving the tracking and predictive capabilities of seed supply hydrodynamic models.
Article
Chemistry, Applied
Christopher David Viljoen, Chantelle Booysen, Sandhya Sreenisvasan Tantuan
Summary: Detecting species using DNA extracted from processed foods is important for food authenticity testing. It can be challenging to extract DNA from processed foods, and determining the concentration and purity of extracted DNA using spectrophotometry is considered essential. However, the impact of chemical residue from the processed food matrix on spectrophotometry readings has not been investigated.
JOURNAL OF FOOD COMPOSITION AND ANALYSIS
(2022)
Article
Microbiology
Barbara J. Bucher, Gillian Muchaamba, Tim Kamber, Philipp A. Kronenberg, Kubanychbek K. Abdykerimov, Myktybek Isaev, Peter Deplazes, Cristian A. Alvarez Rojas
Summary: The study focuses on detecting Echinococcus multilocularis in infected canids and the environment, proposing two cost-effective and efficient DNA extraction methods for field studies in low-income countries for the prevalence study of E. multilocularis.
Article
Engineering, Marine
Raquel Lopez-Nunez, Emilio Cortes Melendreras, Francisca Gimenez Casalduero, Patricia Prado, Federico Lopez-Moya, Luis Vicente Lopez-Llorca
Summary: Pinna nobilis, the largest bivalve endemic to the Mediterranean, has recently become critically endangered along the Spanish Mediterranean coast. Coinfections caused by Haplosporidium pinnae and bacterial pathogens are believed to be the main cause of mortality. In this study, non-invasive sampling using faecal DNA analysis was used to detect and quantify Haplosporidium pinnae in P. nobilis, providing a potential new method for epidemiology and recovery assessment studies.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Article
Medicine, Legal
Isis Thornton, Claire Cartozzo, D'Arcy Mays, Baneshwar Singh, Tal Simmons
Summary: This study assessed the impact of long-term submersion, aquatic environment, bone type, and DNA extraction method on DNA quality and quantity in bones collected from aquatic environments. The results showed a significant decline in DNA quality with increasing submersion time, and no difference in DNA quantity between bone types, DNA extraction methods, or locations. Overall, DNA can be extracted from waterlogged bone to generate an STR profile up to 4000 years.
JOURNAL OF FORENSIC SCIENCES
(2021)
Article
Agronomy
Craig Billington, Jenelle Schmidt, Robyn Mundle, Elmar J. Prenner, Liping Pang
Summary: We have developed new synthetic DNA tracers for tracking water contamination. Accurate quantitation of initial DNA tracer concentrations is crucial for successful downstream detections. We compared three portable analytical techniques (Nanodrop, Qubit, and OptiQ) and found that Qubit and OptiQ were more sensitive at detecting lower concentrations of DNA tracers.
AGROSYSTEMS GEOSCIENCES & ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Rosana Wiscovitch-Russo, Harinder Singh, Lauren M. Oldfield, Alexey Fedulov, Norberto Gonzalez-Juarbe
Summary: This study compares different sample pre-treatment and extraction methods to find a standardized method for DNA extraction that can increase DNA yield and sequencing coverage of low microbial biomass frozen samples while minimizing environmental contamination.
Article
Chemistry, Multidisciplinary
Weina Liu, Simone Giaveri, Daniel Ortiz, Francesco Stellacci
Summary: Nature has the ability to recycle its components for self-sustenance, such as the digestion of proteins into amino acids by living organisms and subsequent synthesis of new proteins. Recent research has shown that protein recycling can also be achieved outside living organisms. This study demonstrates the production of dNTPs from calf DNA through enzymatic phosphorylation, which can be further utilized for PCR and DNA diagnosis. This approach provides an efficient, convenient, and environmentally friendly method for producing dNTPs and DNA in accordance with the circular economy paradigm.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Agriculture, Dairy & Animal Science
Carlo Pinna, Carla Giuditta Vecchiato, Costanza Delsante, Monica Grandi, Giacomo Biagi
Summary: This study investigated the impact of different sampling points on the abundance of microbial populations and metabolites within canine stool. Inner stool subsamples had higher concentrations of bacterial metabolites but not microbial populations, suggesting subsampling may not represent the microbiota and metabolome uniformly. Complete homogenisation of stool prior to analysis is recommended for studying the canine gut microbiome.
Article
Pediatrics
Amina El Amouri, Kato Delva, Aurelie Foulon, Charlotte Vande Moortel, Koen Van Hoeck, Griet Glorieux, Wim Van Biesen, Johan Vande Walle, Ann Raes, Evelien Snauwaert, Sunny Eloot
Summary: Dietary potassium and fiber intake are closely related but not associated with circulating potassium levels in pediatric CKD.
PEDIATRIC NEPHROLOGY
(2022)
Article
Nutrition & Dietetics
Zarina Ebrahim, Sebastian Proost, Raul Yhossef Tito, Jeroen Raes, Griet Glorieux, Mohammed Rafique Moosa, Renee Blaauw
Summary: There is growing evidence that gut dysbiosis contributes to the progression of chronic kidney disease. This study found that ss-glucan prebiotic has a positive effect on kidney function, uremic toxins, and the gut microbiome in CKD participants.
Article
Nutrition & Dietetics
Zarina Ebrahim, Griet Glorieux, M. Rafique Moosa, Renee Blaauw
Summary: This study investigated the effect of simplified dietary advice on nutritional outcomes and adherence in chronic kidney disease (CKD) patients. The findings suggest that the simplified dietary advice can improve nutritional outcomes without compromising kidney function, especially in overweight and obese individuals. This highlights the importance and feasibility of simplified nutrition education in CKD.
SOUTH AFRICAN JOURNAL OF CLINICAL NUTRITION
(2022)
Review
Biochemistry & Molecular Biology
Mieke Steenbeke, Reinhart Speeckaert, Stephanie Desmedt, Griet Glorieux, Joris R. Delanghe, Marijn M. Speeckaert
Summary: Patients with chronic kidney disease (CKD) are more prone to oxidative stress and chronic inflammation, resulting in increased production and decreased clearance of advanced glycation end products (AGEs). AGEs may contribute to decreased kidney function and increased all-cause mortality in CKD patients. Interaction between AGEs and their cell-bound receptor RAGE activates nuclear factor kappa-B (NF-kappa B), leading to cell dysfunction and increased production of inflammatory cytokines. Alterations in the AGE-RAGE system are associated with the development of various chronic kidney diseases. Soluble RAGE (sRAGE) acts as a decoy receptor to inhibit membrane-bound RAGE activation and AGE-RAGE-related toxicity. The ratio of AGEs to sRAGE may be a useful tool for predicting the prognosis of kidney diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Nutrition & Dietetics
Mieke Steenbeke, Ignace De Decker, Sophie Marchand, Griet Glorieux, Wim Van Biesen, Bruno Lapauw, Joris R. Delanghe, Marijn M. Speeckaert
Summary: The study found that a diet restricted in AGE consumption for two months did not affect AGE content in the body or sRAGE concentration in the blood. The impact of blood glucose levels appears to be more significant than the consumption of dAGEs.
Article
Food Science & Technology
Raymond Vanholder, Sanjay K. Nigam, Stephane Burtey, Griet Glorieux
Summary: Uremic toxicity and its metabolic pathways have been extensively studied in the nephrological community. However, it is less considered that these pathways may also produce molecules with beneficial effects on the body. This study focuses on tryptophan-derived metabolites to discuss this dualism and proposes the remote sensing and signaling theory (RSST) as a broader context to understand this phenomenon.
Article
Health Care Sciences & Services
Francis Verbeke, Raymond Vanholder, Wim Van Biesen, Griet Glorieux
Summary: This study found a negative correlation between serum albumin and hemoglobin and the free levels of p-cresyl sulfate (pCS) and p-cresyl glucuronide (pCG). Lower concentrations of pCS and pCG were associated with higher levels of serum albumin and hemoglobin. Serum albumin was found to be a strong and independent predictor for adverse outcome.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Review
Urology & Nephrology
Hubert Krukowski, Sophie Valkenburg, Avra-Melina Madella, Johan Garssen, Jeroen van Bergenhenegouwen, Saskia Adriana Overbeek, Geert R. B. Huys, Jeroen Raes, Griet Glorieux
Summary: In recent years, there has been a growing interest in the association between gut microbiome dysbiosis and chronic kidney disease. However, previous studies have not adequately considered the confounding factors characteristic of the disease. Future research should focus on harmonization of relevant data, in-depth quantitative analysis, and functional exploration of the gut microbiome to guide personalized interventions for CKD. High-quality standards throughout the microbiome analysis workflow are crucial for reliable and reproducible results.
NATURE REVIEWS NEPHROLOGY
(2023)
Article
Urology & Nephrology
Joosep Paats, Annika Adoberg, Jurgen Arund, Annemieke Dhondt, Anders Fernstrom, Ivo Fridolin, Griet Glorieux, Emilio Gonzalez-Parra, Jana Holmar, Liisi Leis, Merike Luman, Vanessa Maria Perez-Gomez, Kristjan Pilt, Didier Sanchez-Ospina, Marten Segelmark, Fredrik Uhlin, Alberto Ortiz
Summary: This study assesses the feasibility of estimating the intradialytic serum time-averaged concentration (TAC) of different uraemic toxins from their concentration in spent dialysate that can be estimated non-invasively online with optical methods. The results show that the estimated serum TAC from spent dialysate concentrations is highly consistent with the TAC calculated from total removed solute and logarithmic mean concentrations of spent dialysate.
CLINICAL KIDNEY JOURNAL
(2023)
Article
Cardiac & Cardiovascular Systems
Griet Glorieux, Sanjay K. Nigam, Raymond Vanholder, Francis Verbeke
Summary: Homeostasis is crucial for maintaining health, especially in the context of the gut microbiota. The communication and exchange of metabolites, signaling molecules, and toxins between different organs and organisms play a critical role in maintaining homeostasis. Disruptions in the gut microbiota can lead to the accumulation of toxic metabolites, impacting the cardiovascular system and contributing to kidney dysfunction. Preserving gut homeostasis and barrier functions can potentially improve patient outcomes and quality of life in diseases such as cardiovascular and kidney disease.
CIRCULATION RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Sonnal Lohia, Agnieszka Latosinska, Jerome Zoidakis, Manousos Makridakis, Harald Mischak, Griet Glorieux, Antonia Vlahou, Vera Jankowski
Summary: Chronic kidney disease (CKD) affects 10% of the world's adult population, and the role of protein glycosylation in CKD progression is not well understood. This study aimed to identify urinary O-linked glycopeptides associated with CKD to better understand the molecular manifestations of CKD. Analysis of urine samples from CKD patients and healthy subjects revealed 17 O-linked glycopeptides from 7 proteins, primarily from Insulin-like growth factor-II (IGF2). Age was found to be positively correlated with certain glycopeptides, while eGFR showed a strong negative association with an IGF2 glycopeptide. Further experiments supported the hypothesis of altered IGF2 protein forms in CKD patients. Protease predictions also indicated the activation of cathepsin S in CKD, suggesting the need for further investigation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Medicinal
Mayra Alejandra Jaimes Campos, Ivan Andujar, Felix Keller, Gert Mayer, Peter Rossing, Jan A. Staessen, Christian Delles, Joachim Beige, Griet Glorieux, Andrew L. Clark, William Mullen, Joost P. Schanstra, Antonia Vlahou, Kasper Rossing, Karlheinz Peter, Alberto Ortiz, Archie Campbell, Frederik Persson, Agnieszka Latosinska, Harald Mischak, Justyna Siwy, Joachim Jankowski
Summary: In this study, we used urinary peptidomic classifiers to predict renal or cardiovascular events in a cohort of 5585 subjects. The results showed significant prediction of events for heart failure, coronary artery disease, and chronic kidney disease. We implemented in silico treatment to simulate changes in peptide abundance based on commonly used interventions, and the proteomic classifiers indicated the individual benefits of specific interventions on a personalized level.
Correction
Ophthalmology
Heleen Delbeke, Ingele Casteels, Marie Joossens
ASIA-PACIFIC JOURNAL OF OPHTHALMOLOGY
(2022)
Article
Microbiology
Frits van Charante, Anneleen Wieme, Petra Rigole, Evelien De Canck, Lisa Ostyn, Lucia Grassi, Dieter Deforce, Aurelie Crabbe, Peter Vandamme, Marie Joossens, Filip Van Nieuwerburgh, Pieter Depuydt, Tom Coenye
Summary: The biofilm on endotracheal tubes (ETs) in COVID-19 patients may pose a potential risk for secondary infections, with variations in biofilm composition and antimicrobial resistance.
Letter
Ophthalmology
Heleen Delbeke, Ingele Casteels, Marie Joossens
ASIA-PACIFIC JOURNAL OF OPHTHALMOLOGY
(2022)
