Review
Biochemistry & Molecular Biology
Adriana Volna, Martin Bartas, Petr Pecinka, Vladimir Spunda, Jiri Cerven
Summary: This paper reviews the current understanding of miRNAs in spring barley, discussing their roles in plant development, homeostasis, and immune processes, and proposing future research directions and unresolved questions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Environmental Sciences
Li Shi, Lingfang Feng, Yan Tong, Junlin Jia, Tao Li, Jing Wang, Zhaoqiang Jiang, Min Yu, Hailing Xia, Qi Jin, Xiyi Jiang, Yongran Cheng, Li Ju, Jiaqi Liu, Quan Zhang, Jianlin Lou
Summary: The study identified differentially expressed miRNAs in the DNA damage response induced by Cr (VI) exposure, indicating potential roles of several miRNAs in cell apoptosis and DDR.
ENVIRONMENT INTERNATIONAL
(2021)
Article
Multidisciplinary Sciences
Audrey Jalabert, Laura Reininger, Emmanuelle Berger, Yohann Coute, Emmanuelle Meugnier, Alexis Forterre, Elizabeth Errazuriz-Cerda, Alain Geloen, Myriam Aouadi, Karim Bouzakri, Jennifer Rieusset, Sophie Rome
Summary: The study revealed differences in the lipid, protein, and miRNA composition of skeletal muscle-released extracellular vesicles between atrophic insulin-resistant mice and wild-type mice, indicating a role of the ELVs in lipid metabolism and fatty acid oxidation.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Shizhe Yu, Haoren Wang, Lingpeng Yang, Yingxue Yan, Qiang Cai, Duo Ma, Long Jiang, Zehai Gao, Zhiyong Yu, Zongping Xia
Summary: The comprehensive study of the spatial-cellular anatomy of the human liver is crucial for understanding the cellular origins of liver disease. In this study, spatial transcriptomics were conducted on normal human liver tissue sections, providing detailed transcriptional information on liver zonation. A total of 6581 high-quality spots from normal livers were analyzed, mainly consisting of hepatocytes, which were classified into four sub-groups. These data serve as a reliable reference for studying the spatial heterogeneity of liver lobules.
Article
Multidisciplinary Sciences
Samina Shabbir, Prerona Boruah, Lingli Xie, Muhammad Fakhar-e-Alam Kulyar, Mohsin Nawaz, Salsabeel Yousuf, Tianyi Liu, Farhat Jabeen, Xiangyang Miao
Summary: Genome-wide sequencing of lncRNAs and mRNAs in ovaries of Hu sheep at different ages revealed key genes and regulatory pathways associated with ovarian development, follicular development, and steroid hormone biosynthesis. Identified genes were found to play vital roles in the final stages of follicles and ovary development in Hu sheep.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Ling Jin, Min Li, Hao Wang, Zhongnan Yin, Li Chen, Yang Zhou, Yongzheng Han, Qinghua Cui, Yuan Zhou, Lixiang Xue
Summary: This study found that differences in circulating miRNAs between arteries and veins increase in hypertension, suggesting that arterial miRNA deregulation may be associated with cardiovascular diseases. Compared to venous miRNAs, arterial miRNAs show a more prominent disease association in arterial blood vessels.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Stephanie M. Zimmerman, Robin Fropf, Bridget R. Kulasekara, Maddy Griswold, Oliver Appelbe, Arya Bahrami, Rich Boykin, Derek L. Buhr, Kit Fuhrman, Margaret L. Hoang, Quoc Huynh, Lesley Isgur, Andrew Klock, Alecksandr Kutchma, Alexa E. Lasley, Yan Liang, Jill McKay-Fleisch, Jeffrey S. Nelson, Karen Nguyen, Erin Piazza, Aric Rininger, Daniel R. Zollinger, Michael Rhodes, Joseph M. Beechem
Summary: Emerging spatial profiling technology allows high-plex molecular profiling in biological tissues while preserving the spatial and morphological context of gene expression. By expanding the chemistry for the Digital Spatial Profiling platform, researchers have successfully quantified whole transcriptomes in human and mouse tissues, enabling applications in cancer research, molecular pathology, and developmental biology.
Article
Plant Sciences
Jianlei Shi, Wenshan Zai, Zili Xiong, Kelei Wang, Deju Shui, Zan'ge Jing
Summary: This study used sRNA sequencing to investigate the role of miRNAs in regulating resistance to Ralstonia solanacearum infection in tomatoes. The researchers identified differentially expressed miRNAs and their target genes, which were annotated to be involved in plant-pathogen interactions, plant hormone signal transduction, defense responses, and other metabolic processes. These findings contribute to the understanding of the potential molecular mechanisms of Rs infection in different tomato genotypes and enrich the tomato miRNA repository.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Review
Plant Sciences
Harriet Middleton, Etienne Yergeau, Cecile Monard, Jean-Philippe Combier, Abdelhak El Amrani
Summary: Through coevolution, plants and microbes co-shape the plant microbiota, with miRNAs playing a crucial role as key mediators.
TRENDS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Ferhat Alkan, Oscar G. Wilkins, Santiago Hernandez-Perez, Sofia Ramalho, Joana Silva, Jernej Ule, William J. Faller
Summary: Recent studies have identified multiple mechanisms that contribute to the heterogeneity in ribosomal composition, and have developed a new method, called dripARF, to study this phenomenon. This method uses Ribosome Profiling (Ribo-seq) data to detect differential protein incorporation into the ribosome by combining "waste" rRNA fragment data with the known 3D structure of the human ribosome. The results indicate that ribosome heterogeneity can be detected in Ribo-seq data, providing a new tool to study this phenomenon.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Muhammad Zahid Hussain, Muhammad Shahbaz Haris, Muhammad Rizwan, Nida Sarosh Ashraf, Maryam Arshad, Ishrat Mahjabeen
Summary: This study investigates the role of exosomal miRNAs in the pathogenesis of rheumatoid arthritis (RA). It finds that certain miRNAs are downregulated in RA patients and are negatively correlated with increased oxidative stress and histone deacetylation.
Article
Multidisciplinary Sciences
Michael Rohr, Jordan Beardsley, Sai Preethi Nakkina, Xiang Zhu, Jihad Aljabban, Dexter Hadley, Deborah Altomare
Summary: The study developed a meta-dataset comprising healthy, adenoma, and CRC tissue samples from multiple independent studies, providing a robust platform for investigating colorectal adenoma formation and malignant transformation through integrated analysis and functional validation.
Article
Biochemical Research Methods
Sachin Bhatt, Prithvi Singh, Archana Sharma, Arpita Rai, Ravins Dohare, Shweta Sankhwar, Akash Sharma, Mansoor Ali Syed
Summary: This study investigates the molecular mechanism of HCC progression and identifies key genes, miRNAs, and transcription factors associated with HCC development.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Adam Ustaszewski, Julia Paczkowska, Joanna Janiszewska, Stephan H. Bernhart, Julia Bein, Nuria Russinol, Martin-Leo Hansmann, Vicente Chapaprieta, Jose I. Martin-Subero, Reiner Siebert, Sylvia Hartmann, Maciej Giefing
Summary: This study identified potential novel oncomiRs in classic Hodgkin Lymphoma (cHL) cell lines, including two miRNAs expressed together with the TENM2 gene. The open chromatin and hypomethylation of TENM2 gene in cHL cell lines suggest an epigenetic mechanism for the aberrant expression of both the TENM2 gene and the novel miRNA. Although no typical cHL-related ontologies were found, several interesting candidate genes involved in lymphopoiesis were identified.
Article
Multidisciplinary Sciences
Reza Mirzazadeh, Zaneta Andrusivova, Ludvig Larsson, Phillip T. Newton, Leire Alonso Galicia, Xesus M. Abalo, Mahtab Avijgan, Linda Kvastad, Alexandre Denadai-Souza, Nathalie Stakenborg, Alexandra B. Firsova, Alia Shamikh, Aleksandra Jurek, Niklas Schultz, Monica Nister, Christos Samakovlis, Guy Boeckxstaens, Joakim Lundeberg
Summary: Spatially resolved transcriptomics allows genome-wide mRNA expression profiling within tissue sections. The RNA quality is crucial for methods targeting mRNA polyA tails, and the high cost of current spatial transcriptomics assays requires careful sample screening. In this study, the authors introduce a workflow called RRST for mRNA recovery from fresh frozen specimens with moderate to low RNA quality, and demonstrate its robustness on different tissue types.
NATURE COMMUNICATIONS
(2023)
Article
Environmental Sciences
Fei Yu, Lita Yi, Xiaoyu Mao, Qi Song, Helena Korpelainen, Meihua Liu
Summary: Cd toxicity and simulated N deposition have different effects on male, female, and hermaphrodite mulberry seedlings, with females showing lower tolerance to Cd stress. N deposition can help alleviate the negative effects of Cd on leaves and reduce sexual differences in the seedlings. Cd tolerance in mulberry seedlings may be improved through different ways with the help of N deposition.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Plant Sciences
Lei Yu, Zongdi Huang, Zhijun Li, Helena Korpelainen, Chunyang Li
Summary: This study investigated the nutrient resorption patterns in females and males of Populus euphratica and identified sexual dimorphism in leaf nutrient resorption. The different nutrient resorption strategies were related to leaf economics, with males possessing a conservation strategy and females resorbing more phosphorus for reproductive investment. Understanding these sex-specific nutrient resorption strategies is important for studying plant nutrient balance and adaptation strategies under climate change.
JOURNAL OF ECOLOGY
(2022)
Article
Plant Sciences
Lei Yu, Zongdi Huang, Shuanglei Tang, Helena Korpelainen, Chunyang Li
Summary: This study investigated the sexual dimorphism in Populus euphratica under drought, salinity, and combined stress. The results showed that male P. euphratica seedlings exhibited stronger resistance to stress and had protective structures, higher biomass, and enhanced physiological responses compared to females. The significant sex x drought x salinity interactions suggested that the sexual dimorphism depends on the severity of stress. These findings imply that future climate change with increased aridity and soil salinity may lead to more severe shifts in the sex ratio of P. euphratica forests.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Qingxue Guo, Jianhui Ye, Jianming Zeng, Liang Chen, Helena Korpelainen, Chunyang Li
Summary: Selenium acquisition from daily diet can reduce disease risk. The main source of dietary Se is the edible parts of crop plants, which is determined by Se bioavailability in soil. Recent research has focused on the biogeochemical cycle of Se driven by specific microorganisms, emphasizing the oxidizing process. Plant root exudates and rhizosphere microorganisms affect soil Se availability. Beneficial microorganisms, including endophytes, promote crop quality and improve crop tolerance to stresses. Understanding Se transformation along the plant-soil continuum is crucial for agriculture and human health.
HORTICULTURE RESEARCH
(2023)
Article
Plant Sciences
Lei Yu, Shuanglei Tang, Chengjin Guo, Helena Korpelainen, Chunyang Li
Summary: Soil salinity and alkalization in northwest China negatively impact plant growth and result in severe ecological problems. This study investigated the responses of male and female Populus euphratica seedlings to salinity, alkali, and their interaction. The results showed that male seedlings exhibited superior resistance and performed better than females under these stress conditions, with differences observed in growth, gas exchange, stomatal density, carbon isotope composition, soluble sugar and starch contents, Na+ accumulation and allocation, oxidative stress, and antioxidants.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Environmental Sciences
Miao Liu, Junhua Wang, Wenting Zhao, Helena Korpelainen, Chunyang Li
Summary: This study assesses the influence of nutrient availability on plant-soil feedback (PSF) and sexual competition in dioecious Populus cathayana. The results show that PSF reduces sexual competition at low nitrogen availability, and intersexual competition and nutrient limitation promote sexual coexistence.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Review
Biochemistry & Molecular Biology
Qingxue Guo, Yuanjing Zhu, Helena Korpelainen, Uelo Niinemets, Chunyang Li
Summary: Plant microbiota can be controlled by the sex of the host plant, with male plants forming more stable and resistant microbiota that help the host resist environmental stresses. Male and female plants can distinguish their own and different sex plants, and males can alleviate stress-induced damage in females. Understanding the role of sex in microbiota assembly is important for protecting female plants from unfavorable environments.
TRENDS IN MICROBIOLOGY
(2023)
Article
Plant Sciences
Zhichao Xia, Yue He, Helena Korpelainen, Ulo Niinemets, Chunyang Li
Summary: This study found that female roots release a greater amount and more diverse phenolic allelochemicals, resulting in growth inhibition of same-sex neighbors and deterioration of the soil microorganism community. When grown with males, female growth was consistently enhanced, especially in the roots. The presence of males also reduced phenolic accumulation in the soil, leading to a shift from allelopathic inhibition to chemical facilitation. These effects were enhanced by a favorable soil bacterial community and increased bacterial diversity, which induced changes in the orientation of female roots.
Review
Biology
Helena Korpelainen, Maria Pietilainen
Summary: We explored various traits that promote plant invasions, such as life history traits, genetic variation patterns, competitive and dispersal abilities, phenotypic plasticity, resistance, tolerance, and allelopathic interactions. External factors, including abiotic and biotic constraints, also play a significant role in invasion success. The introduction of invasive species is often associated with human activities, and their adaptation may not be reflected in their geographical distribution. However, repeated introductions and novel mutations can compensate for a lack of adaptation. As a case study, we used data from the Global Invasive Species Database to identify factors contributing to invasiveness, such as human-assisted dispersal, preference for disturbed habitats, and being used as ornamentals. We found that invasive species commonly have mixed reproduction systems, providing flexibility for spreading and establishment.
Article
Ecology
Zhichao Xia, Yue He, Jiahui Xu, Zuodong Zhu, Helena Korpelainen, Chunyang Li
Summary: This study investigated the responses of fine root traits and rhizosphere microbial communities to drought in Populus euphratica plants. The results showed that females increased specific root length (SRL) in response to drought, while males showed no changes in roots but had increased arbuscular mycorrhizal hyphal biomass and Gram-negative bacteria populations. Furthermore, the composition of fungal symbiotroph communities associated with male and female roots differed under drought conditions. These findings indicate that the responses of soil microbes to drought are influenced by plant sex and microbial group and are related to root trait adjustments.
SOIL ECOLOGY LETTERS
(2023)
