Article
Food Science & Technology
Lei Zhao, Dong Zhang, Yang Liu, Yi-Nan Zhang, Dong-Qing Meng, Qiong Xu, Jiang Zhong, Qiu-Yue Jiang, Yu Zhao, Shi-Jie Wang
Summary: This study identified a strain-specific locus within the holA gene for Lacticaseibacillus rhamnosus X253 using comparative genomics and single nucleotide polymorphisms (SNPs). The developed quantitative PCR assay showed high sensitivity, repeatability, and reproducibility, and accurately enumerated L. rhamnosus X253 in various dairy product samples.
Article
Microbiology
Bingqian Zhou, Guangpu Yang, Zhe Hu, Kewei Chen, Wei Guo, Xiaojun Wang, Cheng Du
Summary: A new qPCR method was developed to detect T. haneyi infection in horses, showing high specificity and sensitivity. Its accuracy was further validated by comparison with the traditional nested PCR method.
Article
Multidisciplinary Sciences
Monika Beinhauerova, Martina Beinhauerova, Sarah McCallum, Eric Seller, Matteo Ricchi, Rory O'Brien, Beatrice Blanchard, Iva Slane, Vladimir Babak, Petr Kralik
Summary: The study aimed to prepare an international MAP reference standard prototype to promote clinical data comparability, selecting a lyophilised fecal suspension as the most suitable form of the standard. After stability testing, the lyophilisation matrix with 10% skimmed milk was chosen for its best recovery and stability.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Masataka Aoki, Yasuyuki Takemura, Shuji Kawakami, Wilasinee Yoochatchaval, P. Thao Tran, Noriko Tomioka, Yoshitaka Ebie, Kazuaki Syutsubo
Summary: This study investigates the abundance and reduction rates of pathogenic bacteria in wastewater treatment facilities and reveals correlations between water quality parameters and the abundance of these bacteria. The findings provide valuable insights for the development and appropriate management of wastewater treatment facilities to produce safe water.
Article
Infectious Diseases
Jackson Alves da Silva Queiroz, Rita de Cassia Pontello Rampazzo, Ediva Basilio da Silva Filho, Gabriella Sgorlon Oliveira, Suyane da Costa Oliveira, Luan Felipo Botelho Souza, Soraya dos Santos Pereira, Moreno Magalhaes de Souza Rodrigues, Adriana Cristina Salvador Maia, Cicileia Correia da Silva, Aline Linhares Ferreira de Melo Mendonca, Celina Aparecida Bertoni Lugtenburg, Francisco de Assis Araujo Aguiar, Rosiane de Souza Soares Rodrigues, Caio Henrique Nemeth Santos, Alice Paula Di Sabatino Guimaraes, Fernando Rodrigues Maximo, Alcione de Oliveira dos Santos, Marco Aurelio Krieger, Juan Miguel Villalobos Salcedo, Deusilene Souza Vieira Dall'Acqua
Summary: This study aimed to develop a high-precision quantitative one-step RT-qPCR reaction that can quantify as few as 2.5 copies per reaction, showing 100% agreement with a qualitative RT-qPCR assay. The assay successfully quantified viral load in patients and accurately diagnosed negative cases in a population of 244 selected patients.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Microbiology
Shuaijie Li, Kui Guo, Xuefeng Wang, Yuezhi Lin, Jinhui Wang, Yaoxin Wang, Cheng Du, Zhe Hu, Xiaojun Wang
Summary: A tat-gag-based real-time quantitative PCR (TG-qPCR) was developed as an effective tool for early diagnosis of clinical Equine Infectious Anemia (EIA) disease. The TG-qPCR showed high specificity, sensitivity, and reproducibility, and had better inclusivity compared to the traditional qPCR method.
MICROBIOLOGY SPECTRUM
(2023)
Article
Veterinary Sciences
Hyun Jin Hwang, Yun Seong Choi, Kyungyoung Song, Maciej Frant, Jeong Hee Kim
Summary: A fast and quantitative molecular detection method of African swine fever virus (ASFV) is presented in this study. The method can detect all genotypes of ASFV based on the major capsid protein p72, with high sensitivity and specificity.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Food Science & Technology
David A. Vargas, Gabriela K. Betancourt-Barszcz, Daniela R. Chavez-Velado, Angelica Sanchez, Rossy Bueno Lopez, Marcos X. Sanchez-Plata
Summary: A bio-mapping study was conducted in a South American country to establish a microbiological baseline in commercial broiler processing facilities. The study found significant differences in total viable counts and Enterobacteriaceae counts between different stages of the processing line, as well as variations in Salmonella and Campylobacter counts.
Article
Cell Biology
Diego Carlos Andrade Pereira, Rafael Goncalves Teixeira-Neto, Valeriana Valadares Lopes, Heber Paulino Pena, Gustavo Fontes Paz, Carlos Henrique Xavier Custodio, Vinicius Silva Belo, Antonio Augusto da Fonseca Junior, Eduardo Sergio da Silva
Summary: In this study, qPCR and ddPCR were used to quantify the parasite load in spleen samples from dogs infected with Leishmania (L.) infantum. The results showed 100% agreement between the two methods. These tools are important for the detection of L. infantum in dogs and humans, and ddPCR, as a new tool, can provide more in-depth information about parasitic loads and the pathogenesis of leishmaniasis.
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2023)
Article
Biology
Nathan Dumont-Leblond, Marc Veillette, Christine Racine, Philippe Joubert, Caroline Duchaine
Summary: The study validates a complete workflow for 16S rRNA gene amplicon sequencing in lung microbiota research. It demonstrates that the choice of DNA extraction kits significantly impacts bacterial composition in control groups, with extracted bacterial signatures in human tissues showing distinct differences from controls.
COMMUNICATIONS BIOLOGY
(2021)
Article
Veterinary Sciences
A-Tai Truong, Sedat Sevin, Seonmi Kim, Mi-Sun Yoo, Yun Sang Cho, Byoungsu Yoon
Summary: The study developed a rapid UR-qPCR method for quantifying N. ceranae in infected bees, which was more sensitive than traditional microscopic enumeration. The results showed that UR-qPCR could detect lower levels of N. ceranae in infected bees within 20 minutes, making it a promising tool for rapid detection of Nosema.
JOURNAL OF VETERINARY SCIENCE
(2021)
Article
Veterinary Sciences
Kunying Lv, Yiwei Zhang, Yixin Yang, Zheng Liu, Liang Deng
Summary: Equine piroplasmosis (EP) is a tick-borne blood protozoan disease caused by Theileria equi (T. equi), Babesia caballi (B. caballi) and Theileria haneyi. This study compared nested PCR (nPCR) and duplex real-time fluorescence quantitative PCR (qPCR) for the detection of T. equi and B. caballi. The results showed that nPCR had good sensitivity and specificity for detecting both parasites, while qPCR had low sensitivity but could readily distinguish between T. equi and B. caballi infections.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Salome R. Rieder, Marina P. Oliveira, Sereina Riniker, Philippe H. Hunenberger
Summary: This article introduces enu, a freely-downloadable, open-source, and standalone program written in C++ for enumerating constitutional isomers and stereoisomers of a molecular formula. The program uses graph theory to enumerate all the constitutional isomers based on their canonical adjacency matrix, and the stereoisomers based on the automorphism group of this matrix. The results are reported in XML format files with canonical SMILES strings. The program allows flexible specification of the molecule family of interest and is optimized for computational efficiency. The article describes the algorithms and implementations of enu and presents illustrative applications. The enu code is available on GitHub at https://github.com/csms-ethz/CombiFF.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Immunology
Abigail J. Porzucek, Abigale M. Proctor, Katharina E. Klinkhammer, Sarah R. Tritsch, Molly A. Robertson, Jonathan P. Bashor, Jack Villani, Jorge L. Sepulveda, Christopher N. Mores
Summary: During the 2022 monkeypox outbreak, limited testing and delayed results allowed for ongoing transmission of the virus. This research adapted and validated a qPCR assay for monkeypox detection, which showed high sensitivity and specificity. Broad implementation of this assay in research and public health laboratories can help increase diagnostic capacity amid the growing outbreak.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Chemistry, Analytical
Areti Strati, Martha Zavridou, Dimitrios Paraskevis, Gkikas Magiorkinis, Spyros Sapounas, Pagona Lagiou, Nikolaos S. Thomaidis, Evi S. Lianidou
Summary: A highly sensitive and specific five-plex one-step RT-ddPCR assay for SARS-CoV-2 detection was developed and analytically validated. The assay allows simultaneous absolute quantification of different regions of the viral nucleoprotein, as well as synthetic RNA and an endogenous RNA internal control. The assay showed excellent performance characteristics and higher sensitivity compared to a commercially available RT-qPCR kit.
ANALYTICAL CHEMISTRY
(2022)
Article
Environmental Sciences
Cindy Ka Y. Law, Kankana Kundu, Luiza Bonin, Lorena Penacoba-Antona, Eduardo Bolea-Fernandez, Frank Vanhaecke, Korneel Rabaey, Abraham Esteve-Nunez, Bart De Gusseme, Nico Boon
Summary: In this study, biogenic palladium nanoparticles were used for the reductive transformation and/or dehalogenation of persistent micropollutants. The size of the nanoparticles and their catalytic activity could be controlled by adjusting the H-2 flow rate. The results showed that the nanoparticles with larger sizes exhibited higher catalytic activity and more efficient removal of micropollutants.
JOURNAL OF ENVIRONMENTAL SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Cindy Ka Y. Law, Eduardo Bolea-Fernandez, Tong Liu, Luiza Bonin, Elien Wallaert, Kim Verbeken, Bart De Gusseme, Frank Vanhaecke, Nico Boon
Summary: This study investigates the formation process of biogenic palladium nanoparticles using various techniques. The distribution of palladium over cells is strongly dependent on Pd2+ concentration, biomass, and partial H-2 pressure. Additionally, cell density and H-2 partial pressure significantly affect the size of the nanoparticles.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Engineering, Environmental
Kristel Mijnendonckx, Tom Rogiers, Francisco J. Gimenez del Rey, Mohamed L. Merroun, Adam Williamson, Md Muntasir Ali, Daniel Charlier, Natalie Leys, Nico Boon, Rob Van Houdt
Summary: Uranium contamination is a widespread issue caused by natural and human activities. However, the molecular mechanisms underlying uranium resistance in bacteria are still not well understood. This study investigated the resistance mechanisms of Cupriavidus metallidurans NA4 to toxic uranium concentrations. Through the increased expression of a specific small periplasmic protein, PrsQ2, the bacteria were able to form periplasmic uranium-phosphate precipitates, thus improving their resistance to uranium.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Biotechnology & Applied Microbiology
Wannes Van Holm, Rita Carvalho, Lize Delanghe, Tom Eilers, Naiera Zayed, Fabian Mermans, Kristel Bernaerts, Nico Boon, Ingmar Claes, Sarah Lebeer, Wim Teughels
Summary: Several oral diseases are caused by changes in the oral microbiome, and antibiotics are commonly used to treat them. However, due to antibiotic resistance, alternatives such as probiotics are being explored. This study compared the effects of different strains of Lactobacillus and Streptococcus salivarius on oral biofilms. It was found that certain Lactobacillus strains reduced the pathobiont A. actinomycetemcomitans, while S. salivarius strains were more effective against other pathobionts.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Construction & Building Technology
Xuejiao Zhu, Myrsini Sakarika, Ramon Ganigue, Kim Van Tittelboom, Yusuf Cagatay Ersan, Nico Boon, Nele De Belie
Summary: A sequential batch reactor (SBR) was used to produce a self-protected CaCO3-precipitating biomass powder (CPB) that can hydrolyze urea and reduce nitrate. The addition of CPB to mortar showed higher crack healing ratio compared to Bacillus sphaericus spores. CPB also revealed a corrosion inhibition effect equivalent to nitrite, making it a suitable bio-additive for crack closure and corrosion inhibition in cementitious composites.
CEMENT & CONCRETE COMPOSITES
(2023)
Article
Construction & Building Technology
Puput Risdanareni, Jianyun Wang, Nico Boon, Nele De Belie
Summary: A bacteria-based self-healing concrete was proposed for autonomous repair of micro-cracks, using vegetative cells of Bacillus sphaericus encapsulated in alkali activated lightweight aggregate (LWA) made from fly ash and Sidoarjo volcanic Mud (Lusi). The study showed that the healing performance of the bacteria decreased significantly when cracks were fabricated at a later age. Additionally, the fly ash-based LWA carrier exhibited excellent autogenous healing in young mortar.
CONSTRUCTION AND BUILDING MATERIALS
(2023)
Article
Dentistry, Oral Surgery & Medicine
N. Zayed, J. Ghesquiere, N. H. N. Kamarudin, K. Bernaerts, N. Boon, A. Braem, W. Van Holm, W. Teughels
Summary: Oral cryotherapy is a safe, simple, and low-cost treatment used in dentistry for oral lesions. However, its effect on oral biofilms was unknown. This study found that cryotherapy significantly reduced the biofilm load and had the potential to control the deterioration of oral biofilms by modifying their structure and composition.
JOURNAL OF DENTAL RESEARCH
(2023)
Article
Engineering, Environmental
Paula Alejandra Lamprea Pineda, Kristof Demeestere, Manuel Toledo, Nico Boon, Herman Van Langenhove, Christophe Walgraeve
Summary: In this study, the removal of N,N-Dimethylformamide (DMF) was evaluated using a lab-scale biofilter for 472 days under mesophilic and thermophilic conditions. The biofilter achieved an average removal efficiency of 99.7% at ambient temperature with an inlet load of 297g DMF/m3 h and an EBRT of 10.7 s. However, a decrease in EBRT and an increase in temperature led to a decrease in removal efficiency. Microbial analysis revealed that the dominant bacteria were Rhizobiaceae and Alcaligenaceae, but their abundance decreased with increasing temperature. Overall, biofiltration showed promise for removing DMF from waste gas streams.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Environmental Sciences
Kankana Kundu, Josefien Van Landuyt, Valerie Mattelin, Bram Martin, Marijke Neyts, Koen Parmentier, Nico Boon
Summary: This study found that the microbiome in sediment near a World War I munition dumpsite in the Belgian part of the North Sea can degrade 2,4,6-trinitrotoluene (TNT). The degradation of TNT was enhanced by adding methanol and several enriched genera, such as Colwellia, Thalossospira, and Methylophaga, were identified as TNT-utilizing bacteria.
MARINE POLLUTION BULLETIN
(2023)
Article
Biotechnology & Applied Microbiology
Justien Ghesquiere, Kenneth Simoens, Erin Koos, Nico Boon, Wim Teughels, Kristel Bernaerts
Summary: This study established a drip flow biofilm reactor to mimic the natural environment of the oral cavity and successfully created a complex multispecies periodontal model similar to that of a healthy individual. Using this model, the researchers validated the multifaceted effects of L-arginine on the oral biofilm, including inhibiting the growth and incorporation of pathogenic species, reducing biofilm thickness and volume, and producing specific metabolic products. This drip flow reactor setup shows promising potential for studying the spatiotemporal behavior of a multispecies periodontal community.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Environmental Sciences
Miao Peng, Maaike Vercauteren, Charlotte Grootaert, Andreja Rajkovic, Nico Boon, Colin Janssen, Jana Asselman
Summary: This study investigated the cellular and bioenergetic effects of microplastics (MPs) on four types of human cell lines in different exposure scenarios. The results showed that even after a single intake, MPs had significant long-term impacts on cellular and mitochondrial functions, potentially leading to chronic stress and harmful effects.
ENVIRONMENTAL POLLUTION
(2023)
Article
Engineering, Electrical & Electronic
Chupao Lin, David Schaubroeck, Roel Baets, Nico Boon, Nicolas Le Thomas
Summary: We propose a photonic integrated circuit design that adds practicality and new functionalities to optical applications like optical microscopy. This design enables the generation of a far-field structured UV illumination pattern with a fringe period of 370 nm, a fringe visibility of 0.83, and a radiant intensity of 0.49 mW. By using single mode waveguides with low propagation losses, diffraction gratings, a beam splitter, a phase shifter, fluorescent gratings, and a collecting lens, the current PICs experimentally demonstrate the Moiré pattern at the heart of optical resolution enhancement and achieve a doubling of optical resolution in the direction of illumination.
IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS
(2023)
Article
Engineering, Environmental
Kevin Sabbe, Liese D'Haen, Nico Boon, Ramon Ganigu
Summary: As part of the circular bio-economy paradigm shift, waste management has shifted focus towards producing added-value compounds. The use of mixed culture bioprocesses for converting waste to platform chemicals has gained interest, but these processes often lack microbiological diversity and are prone to disturbances. To address this, flow cytometry was used to monitor a lactic acid chain elongation process for caproic acid production, allowing for qualitative and quantitative assessment. Specific community types were identified and correlated to functionality and genotypic diversity, and machine-learning algorithms showed high accuracy in predicting production rates.
Article
Engineering, Chemical
Cristina Garcia-Timermans, Bram Malfroot, Cameron Dierendonck, Zoe Mol, Thomas Pluym, Fien Waegenaar, Jan B. A. Arends, Kristof Demeestere, Christophe Walgraeve, Nico Boon, Bart De Gusseme
Summary: Researchers have developed a novel pilot plant design that mimics distribution networks to monitor changes in drinking water quality, such as taste and odor events and microbial regrowth. The pilot plant includes sensors and instrumentation, with three independent loops allowing simultaneous testing of three different conditions. Real-time measurements and biofilm sampling inside the pipes are feasible, making it suitable for studying various factors affecting DW quality in the distribution network.
Article
Environmental Sciences
Valentin Faust, Nico Boon, Ramon Ganigue, Siegfried E. Vlaeminck, Kai M. Udert
Summary: Nitrification in urine stabilization requires controlling pH within an appropriate range. A narrow pH control band increases microbial diversity and improves process robustness, but is more susceptible to external disturbances.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2023)
