Article
Biotechnology & Applied Microbiology
Natsumi Maruoka, Takashi Makino, Jotaro Urabe
Summary: This study examined the gene expression of two genotypes of Daphnia pulex under high and low food levels, and found that only the JPN2 genotype produced resting eggs at low food levels. Sixteen candidate genes were identified that showed changes in expression before resting egg production. These genes may be involved in the regulation of resting egg production in Daphnia.
Article
Biochemical Research Methods
Nirmal Kumar Sampathkumar, Venkat Krishnan SundaramID, Prakroothi S. Danthi, Rasha Barakat, Shiden Solomon, Mrityunjoy Mondal, Ivo Carre, Tatiana El Jalkh, Aida Padilla-Ferrer, Julien Grenier, Charbel Massaad, Jacqueline C. Mitchell
Summary: The choice of reference genes heavily influences the assessment of differential gene expression by qPCR. Recent studies suggest using RNA-Seq to identify stable genes and statistical approaches to determine the best reference genes. However, this study demonstrates that the statistical approach to determine the best reference genes from commonly used candidates is more important than preselecting stable genes from RNA-Seq data.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Fisheries
Emilie Rojas, Loic Prosnier, Aurelie Pradeau, Nicolas Boyer, Vincent Medoc
Summary: Anthropogenic noise has the potential to alter community dynamics by modifying the strength of predation and nontrophic interactions. It remains unknown whether noise can modulate multiple-predator effects and indirectly alter per capita predation rates. Our study found that anthropogenic noise does not compromise foraging in the invasive P. parva, especially when considering the social context of foraging, such as the presence of conspecifics.
JOURNAL OF FISH BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Pauline Chatelain, Cecile Blanchard, Jeremy Astier, Agnes Klinguer, David Wendehenne, Sylvain Jeandroz, Claire Rosnoblet
Summary: Microalgae, especially the green alga Klebsormidium nitens, have recently gained attention as important biological models, particularly for studying the transition stages leading to terrestrial life colonization. This study identified optimal reference gene pairs for normalizing RT-qPCR data in K. nitens in response to abiotic stresses. The identified genes also served as marker genes in response to the three tested stresses.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Pramoda Kumar Sahoo, Sonali Parida, Subhadarshini Parida, Priyashree Parida, Anirban Paul
Summary: Argulosis is a economically significant freshwater fish ectoparasitic disease. Proper selection or normalization of reference genes is crucial for the accuracy of gene expression studies using real-time PCR. This study evaluated seven candidate reference genes and conducted comprehensive gene expression analysis in rohu carp infected with Argulus siamensis. The results identified stable and unstable reference genes and showed the role of immune modulation process in governing infection.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Xiaoxing Yang, Guangxiang Tong, Le Dong, Ting Yan, Huan Xu, Guopan Tang, Yongquan Zhang, Kai Ma, Jiasheng Yin, Youyi Kuang
Summary: This study evaluated the stability of 10 commonly used candidate reference genes in taimen and identified RPS29 and RPL19 as the optimal reference genes for qRT-PCR analysis of gene expression in taimen.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Jing Tong, Manman Hu, Beibei Han, Yanhai Ji, Baoju Wang, Hao Liang, Mingchi Liu, Zhanhui Wu, Ning Liu
Summary: Chinese chive has unique flavor, nutrient, and medicinal values, and investigating its molecular mechanism on flavor formation and metabolic pathways is crucial. This study identified GLY1 and SKP1 as the most stable reference genes for normalization, highlighting the importance of validating reference gene stability before use. Using at least two reference genes for normalization can provide more accurate results, with the combination of GLY1 and SKP1 showing reliable normalization results in qRT-PCR experiments.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Hua Cao, Han Li, Lin Lu, Yulu Ji, Lulin Ma, Shenchong Li
Summary: This study selected and evaluated the suitability of ten candidate RGs for normalizing leaf color-related genes' expression levels via qRT-PCR. The stability rankings analysis disclosed that EF1 alpha exhibited the highest stability and was chosen as the most reliable reference gene. The results offer key genetic resources for the functional characterization of leaf color-related genes and will pave the way for molecular dissection of leaf color mutations in D. officinale.
Article
Multidisciplinary Sciences
Tania Martin-Perez, Martina Koehsler, Julia Walochnik
Summary: This study evaluated the expression and stability of six commonly used housekeeping genes in N. gruberi and found significant variations in the stability of reference genes depending on the algorithms and experimental conditions. The geNorm, NormFinder, and RefFinder analysis identified ACT and G6PD as the most stable reference genes, while BestKeeper analysis identified 18S and TBP as the most stable reference genes. Additionally, normalizing the expression of the HSP90 gene with the most stable reference genes resulted in reliable gene expression, while using unstable reference genes led to unreliable results. This study has important implications for gene expression studies in N. gruberi.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Saqib Rahman, Zhenzhen Zhao, Muhammad Umair Sial, Yanning Zhang, Hongyun Jiang
Summary: This study confirmed the stability of Actin and 18S as reference genes for normalizing the expression of target genes in Myzus persicae under different conditions. Both genes were effective in normalizing the expression levels of target genes under insecticide treatment and starvation. However, Actin was more stable than 18S at the developmental stages of M. persicae.
Article
Multidisciplinary Sciences
Yongshun Zhou, Fanze Meng, Kai Han, Kaiyue Zhang, Jianfeng Gao, Fulong Chen
Summary: This study evaluated the expression stability of 9 endogenous reference genes of Chlorella sp. TLD 6B, a microalgae growing in the Taklamakan Desert, Xinjiang of China, under four abiotic stresses (drought, salt, cold and heat). The results showed that 18S, GTP, IDH and CYP were the most stable endogenous reference genes under different stress conditions, and UBC and 18S were the most suitable endogenous reference gene combinations for all samples. Using these reliable endogenous reference genes ensures more accurate RT-qPCR quantification, facilitating functional genomics studies of desert Chlorella and the mining of resistance genes.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Changan Ma, Xiaojie Liu, Di Zuo
Summary: This study cloned three subunits of AMPK in Daphnia pulex and found that the proteins encoded by these genes have conserved functional domains. The results provide basic information on how three types of AMPK in aquatic organisms respond to environmental contaminants.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Horticulture
Chenjie Zhang, Chengwei Song, Linfeng Chen, Huili Ma, Yabing Zhang, Dalong Guo, Lili Guo, Xiaogai Hou
Summary: The aim of this study was to identify suitable reference genes for normalizing the expression levels of miRNA in different developmental stages and tissues. Five algorithms were used for stability analysis, and the results identified mtr-MIR160b-p3 and gma-miR394a-5p as the most stable miRNAs during bud development in early-flowering tree peony 'Feng dan', while PC-5p-19095 was the most stable during bud development in late-flowering tree peony 'Lian he'. Additionally, mtr-miR159a was found to be the most stable miRNA during flower development stages of different tree peony varieties.
Article
Infectious Diseases
Tae Kwon Kim, Jessica Waldman, Freddy Ibanez-Carrasco, Lucas Tirloni, Camila Waltero, Christiano Calixo, Gloria R. Braz, Albert Mulenga, Itabajara da Silva Vaz, Carlos Logullo
Summary: This study identified and selected stable reference genes in the R. microplus genome and evaluated their expression stability during embryogenesis. Results showed that Rpl4, Elf1a, and GAPDH are suitable internal controls for normalizing qPCR during R. microplus embryogenesis.
TICKS AND TICK-BORNE DISEASES
(2023)
Article
Multidisciplinary Sciences
Long Ma, Ting Jiang, Xiangya Liu, Haijun Xiao, Yingchuan Peng, Wanna Zhang
Summary: This study evaluated the expression stabilities of eight candidate reference genes under different conditions and recommended the optimal suites of reference genes for tissue expression analysis, developmental stages, thermal stress, and pesticide exposure. The findings of this work would facilitate molecular studies of the brassica leaf beetle Phaedon brassicae.
Article
Ecology
Martina Weiss, Hannah Weigand, Florian Leese
Summary: The study revealed that despite the presence of numerous small in-stream barriers, most species can overcome these obstacles to prevent population fragmentation. However, populations of all species remain highly isolated within a few kilometers, indicating the existence of contemporary dispersal barriers.
ECOLOGY AND EVOLUTION
(2022)
Article
Biochemical Research Methods
Dominik Buchner, Till-Hendrik Macher, Florian Leese
Summary: DNA metabarcoding is a new approach to assess and monitor global biodiversity. APSCALE, a data processing pipeline, meets the requirements of being platform independent, easy to use, fast, and compliant with data protection regulations. It handles common tasks of sequence data processing and provides both command line and GUI versions.
Review
Biodiversity Conservation
Anke Schneeweiss, Noel P. D. Juvigny-Khenafou, Stephen Osakpolor, Andreas Scharmueller, Sebastian Scheu, Verena C. Schreiner, Roman Ashauer, Beate Escher, Florian Leese, Ralf B. Schaefer
Summary: The increasing production, use and emission of synthetic chemicals into the environment is a major driver of global change. Recent advances in biomolecular and computational methods show promise for improving our capacity to predict the effects of these chemicals. However, the complexity of the chemicals, limited knowledge on exposure patterns and effects, and the lack of data covering different levels of biological organization pose challenges to prediction.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Evolutionary Biology
Ximo Mengual, Christoph Mayer, Trevor O. Burt, Kevin M. Moran, Lars Dietz, Gaby Nottebrock, Thomas Pauli, Andrew D. Young, Marie Brasseur, Sandra Kukowka, Scott Kelso, Claudia Etzbauer, Sander Bot, Martin Hauser, Kurt Jordaens, Gil F. G. Miranda, Gunilla Stahls, Wouter van Steenis, Ralph S. Peters, Jeffrey H. Skevington
Summary: Flower flies, as one of the most species-rich dipteran families, play important roles in pollination, biological control, organic matter recycling, and nutrient redistribution. This study used a high-throughput sequencing approach to capture and enrich phylogenetically and evolutionarily informative exonic regions. A new bait kit (SYRPHIDAE1.0) was developed to target specific loci in flower fly species, and the analyses based on amino acid and nucleotide data sets supported the common origin of certain subfamilies and the divergence of predatory flower flies.
SYSTEMATIC ENTOMOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Marie V. Brasseur, Arne J. Beermann, Vasco Elbrecht, Daniel Grabner, Bianca Peinert-Voss, Romana Salis, Martina Weiss, Christoph Mayer, Florian Leese
Summary: This study used transcriptome-wide sequencing data to quantify the effects of multiple anthropogenic stressors on gene expression in the freshwater amphipod Gammarus fossarum. The results showed that stressor exposure led to the suppression of genes involved in metabolic and energy consuming cellular processes. The strongest transcriptional response was induced by increased salinity, which contradicted the observed abundance patterns. The interactions between stressors were mainly antagonistic.
Article
Evolutionary Biology
Kamil Hupalo, Denis Copilas-Ciocianu, Florian Leese, Martina Weiss
Article
Ecology
Lars Dietz, Jonas Eberle, Christoph Mayer, Sandra Kukowka, Claudia Bohacz, Hannes Baur, Marianne Espeland, Bernhard A. A. Huber, Carl Hutter, Ximo Mengual, Ralph S. S. Peters, Miguel Vences, Thomas Wesener, Keith Willmott, Bernhard Misof, Oliver Niehuis, Dirk Ahrens
Summary: Species recognition is crucial for science and society, and molecular methods have become popular for animal species identification. In this study, genomic data from nine animal lineages were used to explore the use of metazoan-level universal single-copy orthologs (metazoan USCOs) for species delimitation. The results showed that USCOs outperformed classical mitochondrial DNA barcoding in distinguishing closely related species and accurately assigning samples to different taxonomic levels.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Environmental Sciences
Marie V. V. Brasseur, Jan Martini, Olivia Wilfling, Remo Wuethrich, Emil Birnstiel, Rebecca Oester, Vera M. A. Zizka, Gabriel Singer, Florian Leese, Simon Vitecek
Summary: Reliable biodiversity data are crucial for environmental research and management. DNA metabarcoding has accelerated biodiversity data generation. However, in the process of metabarcoding, specimens are usually destroyed, precluding later specimen-based analyses.
Article
Toxicology
Beate I. Escher, Rolf Altenburger, Matthias Blueher, John K. Colbourne, Ralf Ebinghaus, Peter Fantke, Michaela Hein, Wolfgang Koeck, Klaus Kuemmerer, Sina Leipold, Xiaojing Li, Martin Scheringer, Stefan Scholz, Michael Schloter, Pia-Johanna Schweizer, Tamara Tal, Igor Tetko, Claudia Traidl-Hoffmann, Lukas Y. Wick, Kathrin Fenner
Summary: The assessment of persistence, bioaccumulation, and toxicity is crucial for ensuring chemical safety and is a cornerstone of the EU's chemicals regulation. Existing methods for PBT assessment are complex, inaccurate, and rely on animal testing. New-approach methodologies propose innovative hazard indicators, CTE and PTE, which can be measured using high throughput in vitro bioassays.
ARCHIVES OF TOXICOLOGY
(2023)
Article
Evolutionary Biology
Lars Dietz, Matthias Seidel, Jonas Eberle, Bernhard Misof, Thaynara L. L. Pacheco, Lars Podsiadlowski, Sasanka Ranasinghe, Nicole L. L. Gunter, Oliver Niehuis, Christoph Mayer, Dirk Ahrens
Summary: Scarab beetles (Scarabaeidae) are a diverse and ecologically important group of angiosperm-associated insects. Previous phylogenetic analyses have been unable to determine whether the two major lineages, dung beetles and phytophagous Pleurosticti, form a monophyletic group. Our study using transcriptomes and phylogenetic analyses of over 50 species of Scarabaeidae provides convincing support for the monophyly of Scarabaeidae and confirms the sister group relationship between dung beetles and phytophagous pleurostict scarabs.
SYSTEMATIC ENTOMOLOGY
(2023)
Article
Ecology
Marie V. Brasseur, Jonas J. Astrin, Matthias F. Geiger, Christoph Mayer
Summary: Researchers developed MitoGeneExtractor, an innovative tool that extracts mitochondrial protein coding genes from next-generation sequencing datasets. It uses multiple sequence alignments to accurately and quickly extract these genes. In a case study with bird genomic datasets, MitoGeneExtractor showed higher sensitivity and faster speed compared to existing methods.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Jessica M. Holsopple, Shannon R. Smoot, Ellen M. Popodi, John K. Colbourne, Joseph R. Shaw, Brain A. Oliver, Thomas C. Kaufman, Jason M. Tennessen
Summary: Human industries generate numerous chemicals, many of which have not been sufficiently studied for environmental safety or human health impacts. The current testing methods using mammals are expensive, laborious, and time-consuming, exacerbating the lack of chemical safety information. To address this, scientists and regulators are developing new approaches for chemical safety testing, including the use of invertebrate organisms, such as fruit flies, to understand common chemical modes of action across different species, including humans. In this study, a simple and affordable method using Drosophila melanogaster is described to assess chemical safety, which can also be adapted for genomic and metabolomic analyses.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2023)
Article
Environmental Sciences
Marie Brasseur, Florian Leese, Ralf B. Schafer, Verena C. Schreiner, Christoph Mayer
Summary: Pesticides are major stressors for freshwater species, disrupting their ecosystems and functions. The specific effects of the widely-used insecticide chlorantraniliprole on aquatic non-target taxa are poorly understood.
ENVIRONMENTAL POLLUTION
(2023)
Article
Biochemistry & Molecular Biology
Anurag Chaturvedi, Xiaojing Li, Vignesh Dhandapani, Hollie Marshall, Stephen Kissane, Maria Cuenca-Cambronero, Giovanni Asole, Ferriol Calvet, Marina Ruiz-Romero, Paolo Marangio, Roderic Guigo, Daria Rago, Leda Mirbahai, Niamh Eastwood, John K. Colbourne, Jiarui Zhou, Eamonn Mallon, Luisa Orsini
Summary: This study presents the first hologenome of Daphnia magna, including a chromosomal-level assembly of its genome and the draft assembly of its metagenome. Transcriptome sequencing and mapping expand the annotated gene set for this species and provide evidence for the potential role of gene-body DNA methylation and gut microbiota in genome evolution.
NUCLEIC ACIDS RESEARCH
(2023)