Article
Agronomy
Pei-Hong Zhang, Xue-Jie Zhang, Ting-Wei Tang, Heng-Liang Hu, Ning-Ning Bai, Da-Wei Zhang, Shuan Meng, Jia-Shi Peng
Summary: In this study, three genes (BnMT2-22a, BnMT2-22b, and BnMT3b) responsible for Cd accumulation and tolerance in oilseed rape were isolated. Expression of these genes in yeast showed enhanced tolerance to Cd and Cu, but had no effect on Mn and Zn tolerance. These genes may contribute to Cd detoxification through cytosolic chelation.
Article
Plant Sciences
Alba Rodriguez-Parra, Jesus Picazo-Aragones, Francisco Balao
Summary: This study evaluated the stability of 13 candidate genes as reference genes in leaf and petal tissues in Dianthus broteri. The results found that the most stable candidate genes in leaf tissue were TIP41, TIF5A, PP2A, and SAMDC, while the most suitable reference genes in petal tissue were H3.1, TIP41, TIF5A, and ACT7. Therefore, TIP41 and TIF5A are suggested as the best reference genes for comparing different ploidy levels in both tissues of D. broteri.
Article
Biochemistry & Molecular Biology
Alice Nevone, Francesca Lattarulo, Monica Russo, Giada Panno, Paolo Milani, Marco Basset, Maria Antonietta Avanzini, Giampaolo Merlini, Giovanni Palladini, Mario Nuvolone
Summary: In the next-generation sequencing era, RT-qPCR remains widely used for quantifying nucleic acids due to its popularity, versatility, and cost-effectiveness. However, accurate measurement of transcriptional levels requires appropriate reference genes for normalization. Here, we present a strategy that utilizes publicly available transcriptomic datasets to select suitable reference genes for specific clinical or experimental settings and includes a pipeline for RT-qPCR assay design and validation. We demonstrated the efficacy of this strategy by identifying and validating reference genes for transcriptional studies of bone-marrow plasma cells in AL amyloidosis patients. This strategy can be applied to other settings with publicly available transcriptomic datasets.
Article
Environmental Sciences
Bingjian Cui, Chuncheng Liu, Chao Hu, Shengxian Liang
Summary: This study explores the physiological and gene expression characteristics of perennial ryegrass under cadmium (Cd) stress. High concentrations of Cd significantly inhibit the growth of ryegrass, while lower concentrations have minor effects. The activity levels of antioxidant enzymes increase in Cd-treated ryegrass leaves. The transcriptomic analysis identifies 1103 differentially expressed genes (DEGs) and reveals significant changes in molecular regulatory pathways.
Article
Fisheries
Shuaijie Sun, Zhitong Wang, Dongdong Yuan, Mengke Ni, Huifen Xu, Wanliang Wang, Chi Zhang, Meiqun Chen, Lamu ZhaXi, Jianshe Zhou, Ming Li
Summary: This study used RT-qPCR technology to investigate the expression of eight candidate genes in different tissues, developmental stages, and under bacterial stress in Salmo trutta. The stability of these genes was ranked using comprehensive analysis software. The results showed that the expression of the hprt1 gene was relatively stable under different conditions.
AQUACULTURE REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Monica Nordberg, Gunnar F. Nordberg
Summary: This review summarizes the adverse effects of cadmium on human and animal health and emphasizes the importance of preventive measures. It specifically focuses on the role of metallothionein (MT) in cadmium toxicology and highlights the binding of cadmium to MT and the importance of the Cd/Zn ratio in kidney toxicity. The review calls for the application of these findings in risk assessment and preventive measures against cadmium exposures.
Article
Environmental Sciences
Ju Mu, Yu Wang, Miao Wang, Dayi Zhang, Mingying Liu
Summary: This study constructed a mouse model exposed to poly-propylene microplastics (PP-MPs) to evaluate the bioaccumulation of PP-MPs in the kidney and explore potential reference genes using RT-qPCR. The stability and reliability of 19 candidate reference genes were assessed using four algorithms, and the top five most stable genes were determined (Cox4i1, Rps3, Rps9, Rps18, and Gapdh). Three genes associated with different biochemical processes were chosen to verify the identified reference genes, showing different expression profiles and emphasizing the importance of selecting reliable reference genes.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Plant Sciences
Maria Noelia Ulrich, Esteban Muniz-Padilla, Alejandra Corach, Esteban Hopp, Daniela Tosto
Summary: This study evaluated the stability of different reference genes of glyphosate-resistant S. halepense, finding that PP2A and ARI8 were the most stable genes. The results provide valuable information for gene expression analysis under glyphosate stress and will facilitate resistance mechanism studies in this weed species.
Article
Forestry
Zhaoli Chen, Xiaogang Bai, Xiangyang Li, Bingshan Zeng, Bing Hu
Summary: The study evaluated the expression stability of ten candidate genes in Acacia melanoxylon using five different algorithms. The results showed that certain genes maintained stable expression under different conditions, which provides a reference for further gene expression analysis in this species.
Article
Plant Sciences
Leandro Francisco de Oliveira, Amanda Rusiska Piovezani, Dimitre A. Ivanov, Leonardo Yoshida, Eny Iochevet Segal Floh, Massuo Jorge Kato
Summary: This study identified stable reference genes for gene expression analysis in four Piper species and provided a list of recommended gene pairs for each species. These findings will facilitate further transcriptomic and functional gene research.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Chaofan Jiang, Lin Zhou, Qingchen Zhao, Mengke Wang, Sirui Shen, Te Zhao, Kaidi Cui, Leiming He
Summary: This study validated the expression stability of seven candidate reference genes in Sclerotium rolfsii under different conditions and recommended suitable reference gene combinations for RT-qPCR normalization. The results showed that using one or two reference genes to normalize the expression of target genes in S. rolfsii did not significantly differ.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Juan Zhao, Cheng Wang, Lin Zhang, Aiai Lei, Linjie Wang, Lili Niu, Siyuan Zhan, Jiazhong Guo, Jiaxue Cao, Li Li, Hongping Zhang, Tao Zhong
Summary: The rumen is essential for the absorption of energy substrate in ruminants, and understanding the gene expression profiles is crucial for exploring the regulatory mechanisms of rumen development in goats. This study identified 16 candidate reference genes from transcriptome sequencing of goat rumen tissues, and demonstrated that RPS4X and RPS6 were the most stable reference genes for quantifying gene expression in rumen tissues via RT-qPCR analysis.
Article
Virology
Cristina Ceriani, Gabrielle S. Streeter, Kena J. Lemu, Katherine S. James, Simon Ghofrani, Brigitte Allard, Bonnie E. Shook-Sa, David M. Margolis, Nancie M. Archin
Summary: The study evaluated the stability of reference genes (RGs) after latency-reversing agent (LRA) exposure and found that TBP, UBE2D2, and RPL27A were the most stable RGs, while GAPDH showed the most variability. Using unstable RGs significantly impacted the accuracy of host gene and HIV gene expression data.
JOURNAL OF VIROLOGY
(2021)
Article
Environmental Sciences
Yue Liu, Chengfei Yang, Le Sun, Aoming Wang, Xinhui Lan, Wei Xu, Yan Liang, Sanyuan Ma, Qingyou Xia
Summary: Heavy metal pollution is a major global issue affecting ecosystems. Silkworms are poisoned by heavy metals and a new metallothionein has been identified as a potential factor in improving heavy metal tolerance. Transcriptome sequencing revealed the toxicological mechanism of cadmium and a transgenic silkworm strain overexpressing metallothionein showed enhanced larval viability under cadmium exposure.
Article
Physiology
Wei Na, Yuxiang Wang, Pengfei Gong, Xinyang Zhang, Ke Zhang, Hui Zhang, Ning Wang, Hui Li
Summary: The study utilized the GeNorm algorithm to analyze the expression stability of 14 candidate reference genes in the abdominal adipose tissue of broilers, finding that TBP and HMBS genes exhibited the highest stability at each stage.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Evolutionary Biology
Armando J. Cruz-Laufer, Antoine Pariselle, Michiel W. P. Jorissen, Fidel Muterezi Bukinga, Anwar Al Assadi, Maarten Van Steenberge, Stephan Koblmuller, Christian Sturmbauer, Karen Smeets, Tine Huyse, Tom Artois, Maarten P. M. Vanhove
Summary: A study on parasites infecting cichlid fishes reveals the importance of discrete characters in characterizing species groups and the potential bias caused by discrete characters in masking phylogenetic signals. The study provides insights into the effects of explosive speciation on species interactions and calls for a revaluation of characters used in species characterizations.
Article
Parasitology
Nikol Kmentova, Armando J. Cruz-Laufer, Antoine Pariselle, Karen Smeets, Tom Artois, Maarten P. M. Vanhove
Summary: In this study, a meta-analysis of the phylogenetic relationships of Dactylogyridae was conducted, including representatives of all genera with available molecular data. The research revealed the limitations of using morphological characters for genus-level classification, as well as the biases in taxonomic and citation practices. The study also highlighted the need for a comprehensive and unbiased approach to analyze DNA sequences for a better understanding of the evolutionary and biogeographical patterns in Dactylogyridae.
INTERNATIONAL JOURNAL FOR PARASITOLOGY
(2022)
Article
Public, Environmental & Occupational Health
Charlotte Cosemans, Nicolas Van Larebeke, Bram G. Janssen, Dries S. Martens, Willy Baeyens, Liesbeth Bruckers, Elly Den Hond, Dries Coertjens, Vera Nelen, Greet Schoeters, Hans-Wolfgang Hoppe, Esther Wolfs, Karen Smeets, Tim S. Nawrot, Michelle Plusquin
Summary: Glyphosate and its metabolite AMPA may be associated with biomarkers of biological aging, with AMPA exposure possibly being related to telomere biology.
INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH
(2022)
Article
Biochemistry & Molecular Biology
Mare Geraerts, Carl Vangestel, Tom Artois, Jorge Manuel de Oliveira Fernandes, Michiel W. P. Jorissen, Auguste Chocha Manda, Celestin Danadu Mizani, Karen Smeets, Jos Snoeks, Gontran Sonet, Yang Tingbao, Maarten Van Steenberge, Emmanuel Vreven, Soleil Lunkayilakio Wamuini, Maarten P. M. Vanhove, Tine Huyse
Summary: This study examines the genetic consequences of introducing Nile tilapia into the Congo Basin, finding evidence of genetic admixture with other tilapia species and the potential threat to the genetic integrity of native tilapias. The study also identifies genetic differentiation between Nile tilapia populations from different regions, suggesting independent introductions. The authors recommend avoiding further introductions of Nile tilapia in non-native regions and using native tilapias in future aquaculture efforts.
Article
Ecology
Armando J. Cruz-Laufer, Tom Artois, Stephan Koblmueller, Antoine Pariselle, Karen Smeets, Maarten Van Steenberge, Maarten P. M. Vanhove
Summary: This study explores the effects of adaptive radiation on community assembly in African cichlid fishes and their interactions with flatworm gill parasites. The results suggest that the hosts' evolutionary history determines the host repertoire of parasites, while ecological and evolutionary parameters predict host-parasite interactions. Additionally, adaptive radiation increases specialization and environmental stability in meta-communities.
Meeting Abstract
Toxicology
N. Saenen, M. Witters, F. Van Belleghem, K. Smeets
TOXICOLOGY LETTERS
(2022)
Meeting Abstract
Toxicology
M. Witters, N. Saenen, E. Browko, A. Bronckaers, K. Smeets
TOXICOLOGY LETTERS
(2022)
Article
Engineering, Environmental
Charlotte Cosemans, Congrong Wang, Dries S. Martens, Bram G. Janssen, Charlotte Vanpoucke, Wouter Lefebvre, Karen Smeets, Tim S. Nawrot, Michelle Plusquin
Summary: This study investigated the impact of prenatal air pollution on fetal cord-blood mtDNA mutations and found that prenatal NO2 exposure is associated with cord-blood mtDNA mutations, with two critical exposure windows in mid-to-late pregnancy. No significant associations were observed with prenatal PM2.5 exposure.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Biochemical Research Methods
Andrew Collins, Peter Moller, Goran Gajski, Sona Vodenkova, Abdulhadi Abdulwahed, Diana Anderson, Ezgi Eyluel Bankoglu, Stefano Bonassi, Elisa Boutet-Robinet, Gunnar Brunborg, Christy Chao, Marcus S. S. Cooke, Carla Costa, Solange Costa, Alok Dhawan, Joaquin de Lapuente, Cristian Del Bo, Julien Dubus, Maria Dusinska, Susan J. J. Duthie, Naouale El Yamani, Bevin Engelward, Isabel Gaivao, Lisa Giovannelli, Roger Godschalk, Sofia Guilherme, Kristine B. B. Gutzkow, Khaled Habas, Alba Hernandez, Oscar Herrero, Marina Isidori, Awadhesh N. N. Jha, Siegfried Knasmueller, Ingeborg M. M. Kooter, Gudrun Koppen, Marcin Kruszewski, Carina Ladeira, Blanca Laffon, Marcelo Larramendy, Ludovic Le Hegarat, Angelique Lewies, Anna Lewinska, Guillermo E. E. Liwszyc, Adela Lopez de Cerain, Mugimane Manjanatha, Ricard Marcos, Mirta Milic, Vanessa Moraes de Andrade, Massimo Moretti, Damian Muruzabal, Matjaz Novak, Rui Oliveira, Ann-Karin Olsen, Norah Owiti, Mario Pacheco, Alok K. K. Pandey, Stefan Pfuhler, Bertrand Pourrut, Kerstin Reisinger, Emilio Rojas, Elise Runden-Pran, Julen Sanz-Serrano, Sergey Shaposhnikov, Ville Sipinen, Karen Smeets, Helga Stopper, Joao Paulo Teixeira, Vanessa Valdiglesias, Mahara Valverde, Frederique van Acker, Frederik-Jan van Schooten, Marie Vasquez, Johannes F. F. Wentzel, Maciej Wnuk, Annelies Wouters, Bojana Zegura, Tomas Zikmund, Sabine A. S. Langie, Amaya Azqueta
Summary: The comet assay is a versatile method for detecting various types of DNA damage in individual eukaryotic cells. It has been widely used in research, industry, and regulatory agencies, and has been adopted as an in vivo test for genotoxicity. The present document provides consensus protocols for applying the comet assay to different cell types, species, and types of DNA damage.
Review
Biochemistry & Molecular Biology
Ann Cuypers, Isabeau Vanbuel, Verena Iven, Kris Kunnen, Stephanie Vandionant, Michiel Huybrechts, Sophie Hendrix
Summary: Cadmium is a toxic compound that is harmful to human health and efforts are needed to remediate Cd-polluted soils. It is important to understand the molecular mechanisms underlying Cd stress responses in plants and develop strategies for economic validation of these soils.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Review
Plant Sciences
Verena Iven, Isabeau Vanbuel, Sophie Hendrix, Ann Cuypers
Summary: Cadmium uptake inhibits plant growth and disturbs physiological processes by affecting the cellular redox environment. Glutathione, an antioxidant, plays a role in redox homeostasis but can be depleted due to its involvement in Cd chelation. This triggers a signaling cascade involving the phytohormone ethylene, organellar stress signaling, and autophagy, leading to acclimation and plant tolerance to Cd stress.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Nelly D. D. Saenen, Margo S. S. Witters, Inneke Hantoro, Ines Tejeda, Anitha Ethirajan, Frank Van Belleghem, Karen Smeets
Summary: We investigated how the size and shape of microplastics (MPs) affect cellular health using a human epithelial colorectal adenocarcinoma cell line (Caco-2). We found that both spherical and fibre-/fragment-shaped MPs were taken up by the cells in a size-dependent manner. The uptake of 2 μm spheres led to differential expressions of redox-related genes and changes in mitochondrial parameters. Overall, all PS-MPs induced defensive responses in Caco-2 cells, with the 200 nm spheres having the most profound effects.
Article
Plant Sciences
Sophie Hendrix, Rossella Alfano, Michelle Plusquin, Ann Cuypers
Summary: Cadmium exposure has different effects on individual leaves in Arabidopsis thaliana, with the leaf emerged during Cd exposure showing the most similar response to the regulation of the DNA damage response and cell cycle progression observed in the entire rosette. This finding is important for interpreting rosette data in the context of plant development and response to Cd exposure.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Engineering, Environmental
J. Viaene, N. Peiren, D. Vandamme, A. Lataf, A. Cuypers, M. Jozefczak, B. Vandecasteele
Summary: This study evaluated the effects of biochar, clinoptilolite, and elemental sulfur on ammonia and greenhouse gas emissions during cattle slurry storage, as well as on the agronomic quality of the solid and liquid fractions. The results showed that the addition of biochar reduced ammonia emissions by 12% during the first 7 days of storage, and the combination of extra biochar, clinoptilolite, and elemental sulfur further decreased ammonia emissions by approximately 20%. The application of biochar-enriched solid fractions led to a short-term positive priming effect on carbon mineralization.
Article
Engineering, Environmental
A. Lataf, R. Carleer, J. Yperman, S. Schreurs, J. D'Haen, A. Cuypers, D. Vandamme
Summary: Fourteen biochars from seven biomass sources were tested for their long-term Cd2+ removal efficiency. Insect frass, spent peat, and chicken manure-derived biochars showed potential as Cd2+ adsorbents. The pyrolysis temperature played a crucial role in optimizing Cd2+ removal by insect frass and spent peat-derived biochars. The Cd2+ removal by chicken manure biochars, on the other hand, was not affected by the pyrolysis temperature. The kinetics of Cd2+ removal over the course of ten days revealed that insect frass biochar (450 degrees C) showed a gradual increase from 36 to 75 % Cd2+ removal, while chicken manure and spent peat-derived biochar (450 degrees C) already exhibited higher Cd2+ removal (72 - 89 %) after day 1. These findings highlight the importance of considering the long-term Cd2+ removal effect of certain biochars in future soil-based experiments.