Article
Immunology
Jie Pan, Saineng Hu, Xuanyao Ren, Hao Hu, Xiaoying Deng, Bo Yu, Inma Cobos, Xiaofan Chen, Wei Zhang
Summary: This study is the first to explore circRNA profiles and circRNA-miRNA-mRNA networks in different B-cell developmental stages of mouse bone marrow, which contribute to further research on their mechanism in B-cell development and differentiation.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Mathematical & Computational Biology
Jiang Xie, Yiting Yin, Fuzhang Yang, Jiamin Sun, Jiao Wang
Summary: This study proposes a new method integrating prior information to construct gene regulatory networks for investigating multiple NSC differentiation paths. 12 common differentially expressed genes among the five NSC differentiation paths were found, with one common regulatory pattern (Gsk3b_App_Cdk5) shared by all paths.
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Jian-Fei Kuang, Chao-Jie Wu, Yu-Fan Guo, Dirk Walther, Wei Shan, Jian-Ye Chen, Lin Chen, Wang-Jin Lu
Summary: This study conducted temporal gene expression analyses to investigate the gene regulatory network involved in banana fruit ripening, identifying 25 transcription factors as prime candidates to regulate the ripening process by modulating different ripening-related pathways. This provides a basis for targeted manipulation of fruit ripening to achieve higher banana yield and reduced losses in commercialization.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Taro Harada, Itsuku Horiguchi, Sayaka Ueyama, Ai Murai, Chie Tsuzuki
Summary: This study illustrates the effects of sucrose treatment and hypoxic treatment on starch content, enzyme activities, and gene expression in carnation petals. The findings reveal how sugar metabolism in carnation petals is regulated in response to environmental cues, with modulation of activities and gene expression of a set of sucrolytic enzymes.
Article
Genetics & Heredity
David C. Walker, Zachary R. Lozier, Ran Bi, Pulkit Kanodia, W. Allen Miller, Peng Liu
Summary: Translational efficiency change is an important mechanism for regulating protein synthesis. A hierarchical Bayesian generalized linear mixed effects model is proposed and a software tool called riboVI is provided to analyze Ribo-seq data more efficiently and accurately. The tool outperforms existing methods in terms of identifying differentially translated genes and controlling false discovery rate.
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Konstantinos J. Bogias, Stephen M. Pederson, Shalem Leemaqz, Melanie D. Smith, Dale McAninch, Tanja Jankovic-Karasoulos, Dylan McCullough, Qianhui Wan, Tina Bianco-Miotto, James Breen, Claire T. Roberts
Summary: This study profiles transcript expression profiles in human placental tissue samples and finds that early placental development is mainly regulated by differential transcript expression (DTE) rather than differential gene expression (DGE). Transcript usage is likely a regulatory mechanism in early placentation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Chenggang Wang, Mengyun Zhang, Jiajie Zhou, Xun Gao, Shidong Zhu, Lingyun Yuan, Xilin Hou, Tongkun Liu, Guohu Chen, Xiaoyan Tang, Guolei Shan, Jinfeng Hou
Summary: The study revealed that starch and sucrose metabolism, as well as glutathione metabolism, may play roles in response to cold stress in Wucai, while the activation of alpha-linolenic acid metabolism may promote the synthesis of methyl jasmonate (MeJA) to enhance cold tolerance. These findings provide insights into the molecular mechanisms underlying cold tolerance in Wucai.
Article
Forestry
Jiabao Ye, Ke Yang, Yuting Li, Feng Xu, Shuiyuan Cheng, Weiwei Zhang, Yongling Liao, Xiaoyan Yang, Lina Wang, Qijian Wang
Summary: In this study, the transcriptomic analysis of different organs of G. biloba revealed the TTL regulatory network. Weighted gene co-expression network analysis and Cytoscape visualization identified transcription factors, structural genes, and CYP450 involved in TTL accumulation. This study provides molecular evidence for revealing the comprehensive regulatory network involved in TTL metabolism in G. biloba.
Article
Biotechnology & Applied Microbiology
Venugopalan D. Nair, Mital Vasoya, Vishnu Nair, Gregory R. Smith, Hanna Pincas, Yongchao Ge, Collin M. Douglas, Karyn A. Esser, Stuart C. Sealfon
Summary: Chromatin accessibility influences gene expression, with tissue-specific differentially accessible regions predominantly located in intergenic and intron regions, related to differentially expressed genes enriched in distinct biological processes in each tissue. Enriched motifs in differentially accessible regions may predict binding sites for tissue-specific transcription factors, regulating the expression of target genes.
Article
Biochemistry & Molecular Biology
Karlis Pleiko, Kristina Posnograjeva, Maarja Haugas, Paarn Paiste, Allan Tobi, Kaarel Kurm, Una Riekstina, Tambet Teesalu
Summary: In vivo phage display is commonly used for identification of specific homing peptides, but current methods lack the ability to assess the distribution of specific peptide phages across tissues during screening. By applying bioinformatics tools for RNA sequencing to analyze high-throughput sequencing data, researchers were able to estimate the representation of individual peptides during biopanning in vivo, leading to the identification of novel lung- and brain-specific homing peptides. This approach offers a more efficient and reproducible method for in vivo peptide phage biopanning.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Saet-Byul Kim, Lisa Van den Broeck, Shailesh Karre, Hoseong Choi, Shawn A. Christensen, Guan-Feng Wang, Yeonhwa Jo, Won Kyong Cho, Peter Balint-Kurti
Summary: This study identified differentially expressed genes and metabolites associated with susceptibility and Rp1-D-mediated resistance in maize infected with Puccinia sorghi. The presence of Rp1-D gene in maize plants triggered defense responses and upregulation of specific metabolic pathways, providing insights into the mechanisms underlying resistance to common rust. Transcriptional and metabolic analyses revealed both common and specific responses to infection, with key transcription factors identified as potential signaling hubs in the resistance-specific response.
MOLECULAR PLANT PATHOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Tiantian Sun, Cong Xiao, Zhuliang Yang, Jixian Deng, Xiurong Yang
Summary: The avian eggshell is formed in the uterus, and changes in uterine function can affect eggshell quality. This study identified key genes and pathways involved in uterine functional maintenance in chickens through RNA sequencing and bioinformatics analysis. The differentially expressed genes were found to be enriched in the extracellular matrix and collagen-related pathways, and candidate genes for uterine functional maintenance were identified.
Article
Horticulture
Ryo Nishijima, Alvin Sanjaya, Harue Shinoyama, Yusuke Kazama
Summary: This study investigated the touch stimulus response in flower buds of Dianthus hybrida. The RNA-seq analysis revealed the upregulation and downregulation of certain genes upon touch treatment. Genes encoding protein kinases were significantly abundant among the upregulated genes, suggesting the importance of protein phosphorylation in touch stimulus response. The findings also showed that phosphorelay signaling is a common mechanism for touch stimulus response in both flowers and leaves, although with different players.
Article
Biochemistry & Molecular Biology
Pedro L. Baldoni, Yunshun Chen, Soroor Hediyeh-zadeh, Yang Liao, Xueyi Dong, Matthew E. Ritchie, Wei Shi, Gordon K. Smyth
Summary: Differential expression analysis of RNA-seq is commonly used in bioinformatics. However, transcript-level quantifications are more uncertain due to the ambiguity of sequence reads. To address this issue, a new method is proposed to estimate the overdispersion caused by read-to-transcript ambiguity and generate scaled transcript counts, which improves the efficiency and accuracy of differential analysis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Qijun Xu, Shunmou Huang, Ganggang Guo, Chunbao Yang, Mu Wang, Xingquan Zeng, Yulin Wang
Summary: In this study, the regulatory element landscape of hulless barley under abiotic stresses was investigated using various technologies. Lowly methylated regions (LMRs) and enhancer-gene pairs were identified, and a transcription factor regulatory network was inferred. The study highlighted the importance of epigenetic regulation in adaptation to complex environments.
Article
Plant Sciences
Maria Salud Justamante, Mariem Mhimdi, Marta Molina-Perez, Alfonso Albacete, Maria Angeles Moreno, Ines Mataix, Jose Manuel Perez-Perez
Summary: Prunus species are important stone fruits in the Mediterranean region, and rootstocks with specific adaptations are needed. Adventitious root formation is a crucial mechanism for stress tolerance in Prunus sp. Through the evaluation of hardwood cuttings from different rootstocks, genotype-dependent responses in rooting were observed. A time-series study revealed dynamic changes in endogenous hormone homeostasis, which may explain the differences in rooting performance.
Article
Plant Sciences
Manuela Giraldo-Acosta, Cristina Martinez-Andujar, Purificacion A. Martinez-Melgarejo, Antonio Cano, Josefa Hernandez-Ruiz, Marino B. Arnao
Summary: Melatonin, a plant regulatory molecule, shows potential as a biostimulator and protector against abiotic and biotic stressors. In this study, the protective effect of melatonin on mungbean seedlings treated with copper oxychloride fungicide was investigated. Melatonin improved growth, protected photosynthetic pigments, reduced membrane damage, and affected the hormonal profile of the seedlings.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Plant Sciences
Abelardo Modrego, Taras Pasternak, Moutasem Omary, Alfonso Albacete, Antonio Cano, Jose Manuel Perez-Perez, Idan Efroni
Summary: The removal of the root system triggers the formation of new roots from the remaining shoot, a process primarily regulated by the phytohormone auxin. In this study, the tomato mutation rosette (ro) was found to have a deficiency in shoot-borne root formation and reduced auxin transport rates. The ro gene was identified as the tomato ortholog of BIG and UBR4/p600 genes, which are known to regulate auxin transport in Arabidopsis thaliana and calcium homeostasis in mammals. The study suggests that the RO/BIG protein maintains auxin flow by stabilizing the membrane localization of the auxin transporter PIN1, potentially through attenuating the inhibitory effect of calcium on cytoplasmic streaming.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Taras Pasternak, Klaus Palme, Jose Manuel Perez-Perez
Summary: Reactive oxygen species (ROS) play a dual role in plant biology, acting as important signal transduction molecules and as toxic byproducts of aerobic metabolism that accumulate in cells upon exposure to different stressors and lead to cell death. In this study, it was found that ROS is an important modulator of auxin distribution and response in plant roots. Genetic alterations in ROS balance led to defective auxin distribution and growth-related responses in roots.
Review
Engineering, Chemical
Antonio Cano, Ana B. Maestre, Josefa Hernandez-Ruiz, Marino B. Arnao
Summary: ABTS is a widely used compound for determining the total antioxidant capacity (TAC) of various samples. It can be used in different determination methodologies, such as automated photometric measures and liquid chromatographic separation. The ABTS/TAC method allows for the determination of both hydrophilic and lipophilic antioxidant activity, providing total antioxidant activity values. This review highlights the major achievements and applications of the ABTS/TAC method.
Review
Biochemistry & Molecular Biology
Marino B. Arnao, Manuela Giraldo-Acosta, Ana Castejon-Castillejo, Marta Losada-Loran, Pablo Sanchez-Herrerias, Amina El Mihyaoui, Antonio Cano, Josefa Hernandez-Ruiz
Summary: Melatonin dietary supplements are widely consumed, with developed countries as the largest consumers. Its use has expanded from treating sleep disorders to various other applications. The chemical industry currently meets the market's needs, but there is also interest in obtaining melatonin from plants and genetically modified microorganisms. This paper reviews the synthesis methods and compares the advantages of natural melatonin over chemically synthesized melatonin.
Article
Biochemistry & Molecular Biology
Amina El Mihyaoui, El Hadi Erbiai, Saoulajan Charfi, Eugenia Pinto, Maria Emilia Candela Castillo, Josefa Hernandez-Ruiz, Antonio Cano, Alain Badoc, Ahmed Lamarti, Joaquim C. G. Esteves da Silva, Marino B. B. Arnao
Summary: The study investigated the chemical composition and bioactivity of methanolic extracts from Cladanthus mixtus in northern Morocco for the first time. Phenolic and flavonoid contents were determined and the composition of the extracts was analyzed by GC-MS. The extracts showed antioxidant and antimicrobial activities, with higher phenolic and flavonoid contents in flower extracts. The extracts were most effective against Staphylococcus aureus and Trichophyton rubrum.
Article
Green & Sustainable Science & Technology
Paul Arevalo, Antonio Cano, Francisco Jurado
Summary: Sizing optimization and power smoothing in grid-connected renewable systems are important challenges. This article presents a novel methodology for a photovoltaic-hydrokinetic system, considering power fluctuations reduction using supercapacitors. The research shows that pattern search method can find the global optimum and the use of supercapacitors reduces power fluctuations and increases self-consumption significantly.
ENERGY FOR SUSTAINABLE DEVELOPMENT
(2023)
Article
Engineering, Chemical
Ana-Belen Maestre-Hernandez, Juan-Jose Vicente-Lopez, Francisca Perez-Llamas, Maria-Emilia Candela-Castillo, Maria-Teresa Garcia-Conesa, Maria-Jose Frutos, Antonio Cano, Josefa Hernandez-Ruiz, Marino B. Arnao
Summary: Saffron bio-residues, generated during the production of saffron spices, contain high amounts of phenolic and flavonoid compounds with strong antioxidant potential. Different extraction conditions were applied to obtain hydrophilic and lipophilic components, and the antioxidant activity of the bioactive compounds was analyzed using the ABTS method. The variability in pH and color must be considered when using bio-residues as additives in the pharmaceutical and food industries.
Review
Plant Sciences
Josefa Hernandez-Ruiz, Manuela Giraldo-Acosta, Amina El Mihyaoui, Antonio Cano, Marino B. Arnao
Summary: Melatonin is a versatile molecule with various physiological activities, acting as a hormone and antioxidant in animals, and a regulator and biomolecule in plants. It has shown potential as a biocontrol agent against virus diseases in crops.
Article
Plant Sciences
Taras Pasternak, Jose Manuel Perez-Perez, Benedetto Ruperti, Tatiana Aleksandrova, Klaus Palme
Summary: Arabidopsis thaliana research often relies on in vitro culture media for studying plant responses to various signals. This study describes an optimized and nutritionally balanced culture medium that enables the growth and propagation of A. thaliana mutants, even those lacking a root system. The use of this protocol can avoid bias in phenotypic characterization during stress experiments.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Plant Sciences
Taras Pasternak, Stefan Kircher, Klaus Palme, Jose Manuel Perez-Perez
Summary: Root development is regulated by sucrose and light. Carbohydrate starvation during skotomorphogenesis leads to compaction of nuclei in the root apical meristem, hindering cell cycle progression and causing irreversible root differentiation. Adding carbohydrates promotes seedling growth. Transferring carbohydrate-grown seedlings from light to dark promotes cell elongation and reduces root meristem size. Carbohydrates are essential for cell cycle activity and auxin-regulated response in the root apical meristem.
Article
Agronomy
Manuela Giraldo-Acosta, Domingo Ruiz-Cano, Antonio Cano, Josefa Hernandez-Ruiz, Marino B. Arnao
Summary: Melatonin has been found to be effective in post-harvest treatment of fruits and vegetables. This study demonstrates the effectiveness of melatonin treatments in extending the shelf life of broccolini during cold storage. Treatment with 50μM melatonin for 15 minutes appears to be the most effective in preserving the freshness and antioxidant properties of broccolini.
Article
Plant Sciences
Olha Yaroshko, Taras Pasternak, Eduardo Larriba, Jose Manuel Perez-Perez
Summary: This study analyzed the effect of different concentrations of zeatin and indole-3-acetic acid on the regeneration of cotyledon explants in tomato cultivars M82 and Micro-Tom. The best hormone combination produced shoot-like structures after 2-3 weeks, and leaf primordia were observed from these structures after about 3-4 weeks. Whole plantlets could be obtained between 4 and 6 weeks by transferring the regenerating micro-stems to a defined growth medium. This method has direct applications for plant transformation, gene editing techniques, and vegetative propagation of elite cultivars.
