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
Virology
Serdal Arslan, Mehmet Bakir, Burcu Bayyurt, Eylem Aydemir, Kenan Kinaci, Aynur Engin
Summary: This study investigated the lncRNA gene expression profiles in CCHF using microarray for the first time. Several lncRNAs were found to be significantly regulated in both case and fatal case groups. These lncRNAs could be considered as important therapeutic targets for further studies on CCHF.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Plant Sciences
Qizhang Wang, Chunqian Guo, Shipeng Yang, Qiwen Zhong, Jie Tian
Summary: The aim of this study was to identify suitable reference genes for gene expression analysis during different growth conditions in garlic. Nine candidate reference genes were selected using garlic transcriptome sequence data and their expression levels were evaluated in specific tissues under drought and cold stress. Several statistical methods were used to assess the stability of the reference gene expression levels. The most stable reference genes were identified, and their reliability was confirmed by evaluating the expression of a stress-responsive gene. This study provides a theoretical reference for gene expression analysis in garlic under stress conditions.
Article
Genetics & Heredity
Guoqing Li, Jun Zhang, Dechen Liu, Qiong Wei, Hui Wang, Yingqi Lv, Zheng Ye, Gaifang Liu, Ling Li
Summary: This study aimed to identify novel biomarkers and mechanisms for diabetic nephropathy (DN) disease progression through weighted gene co-expression network analysis. Four potential RNA regulatory pathways were proposed, and IL6, CXCL8, MMP9, and ATF3 were identified as markers for early diagnosis of DN. Insights into the disease development mechanisms in DN at the transcriptome level were provided.
FRONTIERS IN GENETICS
(2021)
Article
Agriculture, Multidisciplinary
Yao-ke Duan, Rong Han, Yan Su, Ai-ying Wang, Shuang Li, Hao Sun, Hai-jun Gong
Summary: Tomato is a model plant for fruit development and stress response research, with gene expression analysis frequently conducted through techniques like qPCR. This study identified new reference genes in tomato by mining transcriptome sequencing data, evaluating their stability under different treatments. The results showed that the stability of reference genes varied under different conditions, with most genes recommended as preferred reference genes.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Immunology
Thomas J. Colgan, Peter A. Moran, Louise C. Archer, Robert Wynne, Stephen A. Hutton, Philip McGinnity, Thomas E. Reed
Summary: Vertebrates have evolved a complex immune system for identifying and responding to pathogens, but sex differences may affect immune gene expression. Past whole genome duplication events may have provided novel immune innovations for salmonids.
FRONTIERS IN IMMUNOLOGY
(2021)
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
Plant Sciences
Qian Zhang, Wen Zhou, Bin Li, Lin Li, Meng Fu, Li Zhou, Xiaoding Yu, Donghao Wang, Zhezhi Wang
Summary: By analyzing the genome of Hypericum perforatum, 101 ERF genes were identified and a systematic bioinformatic analysis was conducted, leading to the classification of HpERFs into 11 subfamilies. Most HpERFs were found to participate in plant biological processes, with cis-elements related to gene transcription regulation, stress response, and plant development. This study provides a theoretical basis for further research on stress-related ERFs in H. perforatum.
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
Genetics & Heredity
Yanli Liu, Chengcheng Zhang, Nunung Harijati, Ying Diao, Erxi Liu, Zhongli Hu
Summary: In this study, eight candidate internal reference genes were screened and detected using the Konjac transcriptome database of our laboratory and common internal reference genes in plants. They include 25S ribosomal RNA gene, 18S ribosomal RNA gene, actin gene, glyceraldehyde-3-phosphate dehydrogenase gene, ubiquitin gene, beta-tubulin gene, eukaryotic elongation factor 1-alpha gene, and eukaryotic translation initiation factor 4 beta-1 gene. The results from GeNorm, Normfinder, and BestKeeper were comprehensively analyzed. Stable expression levels were observed for 25S rRNA, 18S rRNA, and ACT during reproductive periods, eEF-1 alpha and eIF-4 alpha during nutritional periods, and eEF-1 alpha, UBQ, and ACT during different leaf developmental periods. These identified and stable internal reference genes will serve as a basis for future molecular biology-related studies of Konjac.
Article
Environmental Sciences
Edgar A. Lopez-Landavery, Clara E. Galindo-Sanchez, Laura L. Lopez-Galindo, Nancy Ramirez-alvarez, Anaid Saavedra-Flores, Gerardo Amador-Cano, Claudia Ventura-Lopez, Pablo San Martin-Del Angel, Rosa I. Hernandez-Herrera
Summary: The Gulf of Mexico is a vital crude oil reserve, with the oyster Crassostrea virginica being an ideal species to study the effects of oil spills on marine invertebrates. This study measured the concentrations of polycyclic aromatic hydrocarbons (PAHs) and aliphatic hydrocarbons (AHs) in sediment, water, and tissues of C. virginica in eight oyster productive areas in the Gulf of Mexico. Significant differences in gene expression related to xenobiotic detoxification were observed between lagoons, with Las Enramadas showing the highest expression levels. This study validates the use of molecular markers to assess the impact of hydrocarbons on oysters in the Southern Gulf of Mexico.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Agronomy
Ester Sales, Eva Miedes, Luis Marques
Summary: This study aimed to investigate temperature-induced expression changes in genes underlying quantitative trait loci associated with low temperature germinability in rice. It was found that a wide region on chromosome 3 was related to increased seedling growth rate in certain families. Additionally, variation in the LTG phenotype was consistently associated with changes in expression patterns of five genes in the tagged regions on rice chromosome 3.
Article
Genetics & Heredity
Joyshikh Sonowal, Chhabi Lal Patel, Kapil Dev, Rohit Singh, N. Barkathullah, Waseem Akram Malla, Ravi Kumar Gandham, Ravi Kant Agarwal, Deepak Kumar, Shikha Saxena, E. Kalaiselvan, Amitesh Dubey, Krishna Bharali, Raja Ishaq Nabi Khan, B. P. Mishra, Bina Mishra
Summary: Virus infection alters host gene expression, so it is important to find stable reference genes for normalization. In this study, seven housekeeping genes were assessed for their expression stability in Sheeppox virus infected lamb testis cells. Several genes showed good stability at different time points, with B2M being the most stable reference gene in the control and overall infected groups.
Article
Fisheries
Joanna Szczygiel, Teresa Kaminska-Gibas, Jules Petit, Patrycja Jurecka, Geert Wiegertjes, Ilgiz Irnazarow
Summary: The study ranked the expression stability of duplicated genes in different tissues of common carp and found that 40s, b2m, ef1 alpha, and actb genes showed the most stable expression across all physiological conditions, while gapdh, odc1, and g6pd genes demonstrated lower stability. Functional divergence between duplicated genes was observed, emphasizing the importance of considering this aspect in selecting reference genes in polyploid species.
FISH & SHELLFISH IMMUNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Thomas Krause, Elena Jolkver, Paul Mc Kevitt, Michael Kramer, Matthias Hemmje
Summary: Genetics is becoming increasingly important in medical diagnostics, however, the requirements for laboratory diagnostics are constantly changing and the existing software cannot keep up with the latest developments. A systematic requirements engineering process is essential to ensure the quality of the final product, but currently, there is no well-defined software development procedure.
BIOENGINEERING-BASEL
(2022)
Article
Ecology
Kyle W. Wellband, John W. Heath, Daniel D. Heath
Article
Biochemistry & Molecular Biology
Shelby D. Toews, Kyle W. Wellband, Brian Dixon, Daniel D. Heath
Article
Biochemistry & Molecular Biology
Kyle Wellband, Claire Merot, Tommi Linnansaari, J. A. K. Elliott, R. Allen Curry, Louis Bernatchez
Article
Genetics & Heredity
Jenna Jones, Kyle Wellband, Barbara Zielinski, Daniel D. Heath
G3-GENES GENOMES GENETICS
(2019)
Article
Fisheries
Christina A. D. Semeniuk, Pauline M. Capelle, Mitchel G. E. Dender, Robert Devlin, Brian Dixon, Jane Drown, John Heath, Russell Hepburn, Dennis M. Higgs, Kevyn Janisse, Sarah J. Lehnert, Oliver P. Love, Jessica Mayrand, Megan Mickle, Trevor E. Pitcher, Bryan Neff, Shawna L. Semple, Jennifer L. Smith, Shelby Toews, Kyle Wellband, Clare J. Venney, Daniel Heath
Article
Ecology
Clare J. Venney, Kyle W. Wellband, Daniel D. Heath
Summary: Genetic architecture and phenotypic plasticity are important factors when studying trait variation and its interaction with environmental factors. DNA methylation shows plasticity and gene-specific effects in different rearing environments, indicating developmental stage-specific influences of environmental factors on DNA methylation. Understanding genetic and environmental influences on methylation is crucial for future studies on acclimation and adaptation mechanisms.
Article
Biochemistry & Molecular Biology
Yann Dorant, Hugo Cayuela, Kyle Wellband, Martin Laporte, Quentin Rougemont, Claire Merot, Eric Normandeau, Remy Rochette, Louis Bernatchez
Article
Microbiology
Camille Lavoie, Kyle Wellband, Alysse Perreault, Louis Bernatchez, Nicolas Derome
Summary: The study revealed that the gut microbiota composition of stocked and wild salmon from the same genetic population and environment depended on the early rearing environment, while the skin microbiota of stocked individuals converged towards that of wild individuals. Taxonomic composition and co-occurrence network analyses suggested an impairment of wild bacteria recruitment and higher instability for the gut microbiota of stocked parr. This study emphasized the long-term effect of early microbiota ontogeny in artificial rearing for natural population conservation programs, highlighting the need for implementing microbial ecology.
Article
Evolutionary Biology
Raphael Bouchard, Kyle Wellband, Laurie Lecomte, Louis Bernatchez, Julien April
Summary: Captive-breeding programs, although effective in mitigating biodiversity loss, can result in genetic and nongenetic changes that reduce the fitness of supplemented individuals. This study investigated the reproductive success and genetic diversity of Atlantic salmon stocked at the parr stage in Quebec, Canada. The findings suggest that parr-stage stocking leads to reduced reproductive success compared to wild salmon, but still improves relative reproductive success compared to other stocking practices. Additionally, the supplementation of captive-bred salmon significantly contributes to increasing genetic diversity.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Evolutionary Biology
Maeva Leitwein, Kyle Wellband, Hugo Cayuela, Jeremy Le Luyer, Kayla Mohns, Ruth Withler, Louis Bernatchez
Summary: Human activities and resource exploitation have led to a decline in wild salmonid populations. Conservation programs have been developed to supplement wild populations, but studies have shown reduced fitness of hatchery-born fish compared to wild fish. This study uses RNA sequencing and Whole Genome Bisulfite Sequencing to investigate gene expression differences between hatchery and wild-born Coho salmon. The results suggest that early-life hatchery-rearing environment-induced gene expression differentiation is maintained until the fish return to their natal river. The study highlights the importance of considering both the epigenome and transcriptome in large-scale supplementation programs.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Clare J. Venney, Kyle W. Wellband, Eric Normandeau, Carolyne Houle, Dany Garant, Celine Audet, Louis Bernatchez
Summary: This study investigates the effects of parental and offspring temperatures on DNA methylation in brook charr. The results show that parental maturation temperature has a significant impact on offspring methylation, while offspring rearing temperature has a minimal effect. The intergenerational inheritance of DNA methylation could facilitate adaptation to a warming environment.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Fisheries
Raphael Bouchard, Kyle Wellband, Laurie Lecomte, Louis Bernatchez, Julien April
Summary: This study compared the reproductive success of caught-and-released Atlantic salmon to non-caught salmon and found that the reproductive success of caught-and-released females was lower. The temperature at release did not affect the reproductive success of released fish, but warmer temperatures made fish less likely to enter a trap.
FISHERIES MANAGEMENT AND ECOLOGY
(2022)
Article
Fisheries
Carlo A. Biagi, Rosalind A. Leggatt, Dionne Sakhrani, Mike Wetklo, Wendy E. Vandersteen, Kris A. Christensen, Eric B. Rondeau, Breanna M. Watson, Kyle W. Wellband, Ben F. Koop, Ruth E. Withler, Robert H. Devlin
Summary: Doubled haploid gynogens are individuals with two identical maternal chromosome sets and no paternal genetic contributions. They are useful in whole-genome sequence assembly to eliminate allelic variation. This study successfully determined the timing for producing doubled haploid gynogens in multiple salmonid species and assessed their survival rate and genotypes.
NORTH AMERICAN JOURNAL OF AQUACULTURE
(2022)
Correction
Evolutionary Biology
Maeva Leitwein, Kyle Wellband, Hugo Cayuela, Jeremy Le Luyer, Kayla Mohns, Ruth Withler, Louis Bernatchez
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Kyle Wellband, David Roth, Tommi Linnansaari, R. Allen Curry, Louis Bernatchez
Summary: In teleost fishes like Atlantic Salmon, differential methylation in response to captivity during maturation leads to intergenerational phenotypic differences. This mechanism of transgenerational plasticity is mediated by late-life acquired DNA methylation.
G3-GENES GENOMES GENETICS
(2021)