Review
Plant Sciences
Susmita Sett, Ashish Prasad, Manoj Prasad
Summary: Viruses are acellular pathogens that cause severe infections in plants, resulting in worldwide crop losses every year. Understanding the defense mechanisms of plants against viruses is crucial for devising proper management strategies. Plant resistance genes can regulate defense against viruses by eliciting a hypersensitive response and activating necrotic cell death, thereby stopping the spread of the disease.
TRENDS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Junhao Zhuge, Xiang Zhou, Lifeng Zhou, Jiafu Hu, Kai Guo
Summary: This study developed the Plant Parasitic Nematodes Database (PPND), a platform that provides genomic, transcriptomic, protein, and functional annotation data for plant parasitic nematode research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Zhiyuan Ji, Wei Guo, Xifeng Chen, Chunlian Wang, Kaijun Zhao
Summary: Executor (E) genes are a new type of plant resistance genes that activate expression and trigger hypersensitive response (HR) in plants by trapping TALEs released by pathogens. Utilizing E gene resistance plays a significant role in disease resistance breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Xinyu Dong, Kejun Zhao, Qi Wang, Xingcai Wu, Yuanqin Huang, Xue Wu, Tianhan Zhang, Yawen Dong, Yangyang Gao, Panfeng Chen, Yingwei Liu, Dongyu Chen, Shuang Wang, Xiaoyan Yang, Jing Yang, Yong Wang, Zhenran Gao, Xian Wu, Qingrong Bai, Shaobo Li, Gefei Hao
Summary: Plant disease is a significant problem that can cause massive yield loss. Smart diagnosing diseases using plant phenomics and sufficient image information is crucial for recovering most of the yield loss. However, incompatibilities in image data formats and descriptions provided by different communities limit multidisciplinary research exploration. To overcome this, the Plant Phenomics Analysis of Disease (PlantPAD) platform is developed, which contains extensive image data, well-annotated information, and pre-trained deep-learning models for accurate plant disease diagnosis. PlantPAD supports various applications across disciplines and aims to facilitate multidisciplinary research to combat plant diseases.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Engineering, Environmental
Shuyao Zhu, Bingqing Yang, Yuqian Jia, Feiyu Yu, Zhiqiang Wang, Yuan Liu
Summary: This study aimed to explore the impact of different disinfectants on the horizontal transfer of antibiotic resistance genes (ARGs) and their underlying mechanisms. The results showed that quaternary ammonium salt, organic halogen, alcohol, and guanidine disinfectants significantly facilitated the conjugative transfer, while heavy metals, peroxides, and phenols displayed an inhibitory effect. Furthermore, guanidine disinfectants promoted conjugation through increased cell membrane permeability, over-production of reactive oxygen species (ROS), enhanced SOS response, and altered expression of conjugative transfer-related genes. Moreover, guanidine disinfectants also promoted bacterial energy metabolism and flagellum motility. These findings highlight the potential risks caused by the massive use of guanidine disinfectants, especially during the COVID-19 pandemic.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Zhen Chen, Pei Zhao, Chen Li, Fuyi Li, Dongxu Xiang, Yong-Zi Chen, Tatsuya Akutsu, Roger J. Daly, Geoffrey Webb, Quanzhi Zhao, Lukasz Kurgan, Jiangning Song
Summary: iLearnPlus is the first machine-learning platform with graphical- and web-based interfaces for analysis and predictions using nucleic acid and protein sequences, providing a comprehensive set of algorithms and automating sequence-based feature extraction and analysis. It caters to experienced bioinformaticians and biologists with no programming background, showcasing its capabilities through case studies on lncRNA prediction and crotonylation site prediction.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Yujie Mao, Xiaohui Liu, Na Zhang, Zhi Wang, Maozhen Han
Summary: Antibiotic resistance genes (ARGs) are emerging pollutants found in various environments, and identifying these genes has become a growing concern. In this study, a non-redundant antibiotic resistance genes database (NRD) was constructed by consolidating sequences from existing databases. The advantages of NRD in detecting potential ARGs were demonstrated through comparisons with other databases using metagenome datasets.
Article
Multidisciplinary Sciences
Diego Simon, Omar Borsani, Carla Valeria Filippi
Summary: This study presents the use of Random Forest (RF) for predicting disease resistance (DR) proteins in plants. The reduced-dimension (RD) RFPDR model shows high sensitivity and specificity, and is robust to data imbalance. This approach provides valuable information for DR protein prediction, complementing existing strategies.
Article
Plant Sciences
Wenyuan Yan, Yinqiao Jian, Shaoguang Duan, Xiao Guo, Jun Hu, Xiaohui Yang, Guangcun Li
Summary: Hormones play a crucial role in plant disease resistance and defense. This study analyzed transcriptome data of a late blight-resistant potato genotype treated with ethylene, jasmonate, salicylic acid, and Phytophthora infestans to assess the ET/JA/SA regulatory network's role in disease resistance and predict resistant genes. The findings suggest that differentially expressed genes overlapped significantly in all treatments, and specific genes for disease interaction were expressed differently in the CN152 treatment. The study reveals the potential for inducing resistance genes through alternative splicing and highlights the synergistic effect of JA and ET pathways.
Article
Biochemistry & Molecular Biology
Peng Zhao, Siyu Zhou, Panpan Xu, Haoxiang Su, Yelin Han, Jie Dong, Hongtao Sui, Xin Li, Yongfeng Hu, Zhiqiang Wu, Bo Liu, Ting Zhang, Fan Yang
Summary: Rhinovirus (RV) is a common causative agent of both upper and lower respiratory diseases, and its genetic diversity is crucial for epidemiological surveillance and investigation of respiratory diseases. This study introduces RVdb, a comprehensive and high-quality RV data resource, which can be used to analyze the genetic characteristics of RVs and support the work of virologists and epidemiologists.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Food Science & Technology
Wioleta Chajecka-Wierzchowska, Urszula Zarzecka, Anna Zadernowska
Summary: This study found resistance of Enterococcus strains isolated from plant-derived food to various antibiotics, particularly aminoglycosides. The resistance was mainly attributed to different genes, with nearly half of the isolates carrying a conjugative transposon.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Genetics & Heredity
Antonio Di Maria, Salvatore Alaimo, Lorenzo Bellomo, Fabrizio Billeci, Paolo Ferragina, Alfredo Ferro, Alfredo Pulvirenti
Summary: The inference of novel knowledge and new hypotheses from current literature analysis is crucial for making new scientific discoveries. The BioTAGME system in bio-medicine combines an entity-annotation framework with a network-based inference methodology to create an extensive Knowledge Graph.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Andolfo Giuseppe, Ercolano Maria Raffaella
Summary: This study characterized the MLO gene family in 11 Lamiaceae species and identified 74 putative PM susceptibility genes. The results showed highly conserved motifs and a general high level of purifying selection. This study provides a theoretical basis for further research on PM susceptibility.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Jun-Jie Zheng, Po-Wen Wang, Tzu-Wen Huang, Yao-Jong Yang, Hua-Sheng Chiu, Pavel Sumazin, Ting-Wen Chen
Summary: Microbiota analyses play a crucial role in health and science, but the available tools require programming skills and statistical knowledge. MOCHI, a GUI tool for microbiota amplicon sequencing analysis, can help practitioners with real-time analysis and data visualization.
Review
Plant Sciences
Qianru Li, Limei Xian, Linxi Yuan, Zhiqing Lin, Xiaoren Chen, Jianjun Wang, Tao Li
Summary: The applications of selenium (Se) in biomedicine, agriculture, and environmental health have attracted significant research interest. While Se is essential for humans and animals, it also plays important roles in improving plant resistance to various stresses. This review focuses on recent findings regarding the effects and mechanisms of Se on plant fungal diseases and insect pests.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Infectious Diseases
Maria Paz Ventero, Oscar Moreno-Perez, Carmen Molina-Pardines, Andreu Paytuvi-Gallart, Vicente Boix, Isabel Escribano, Irene Galan, Pilar Gonzalez-delaAleja, Mario Lopez-Perez, Rosario Sanchez-Martinez, Esperanza Merino, Juan Carlos Rodriguez
Summary: This study analyzed the diversity and taxonomic composition of the nasopharyngeal microbiota, and found that higher diversity and the presence of certain genera may serve as early biomarkers for favorable clinical outcomes in hospitalized COVID-19 patients.
JOURNAL OF INFECTION
(2022)
Article
Biochemistry & Molecular Biology
Joan Calle Garcia, Anna Guadagno, Andreu Paytuvi-Gallart, Alfonso Saera-Vila, Ciro Gianmaria Amoroso, Daniela D'Esposito, Giuseppe Andolfo, Riccardo Aiese Cigliano, Walter Sanseverino, Maria Raffaella Ercolano
Summary: The PRGdb database has been significantly expanded and upgraded, providing more data and tools, with a new section dedicated to collecting plant resistance transcriptomic experimental data. Additionally, the DRAGO3 tool has been improved in accuracy and sensitivity, leading to more reliable predictions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Marco Di Marsico, Andreu Paytuvi Gallart, Walter Sanseverino, Riccardo Aiese Cigliano
Summary: The GreeNC database is a key reference database for studying plant lncRNAs, with the most recent update adding annotation for a large number of species and applying sequence clustering to provide additional information. The current version of the database can be accessed at the provided link.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Veterinary Sciences
Leyna Diaz, Gemma Castella, M. Rosa Bragulat, Andreu Paytuvi-Gallart, Walter Sanseverino, F. Javier Cabanes
Summary: This study assessed and quantified the presence of Malassezia yeast in canine pododermatitis using various methods, and found that the amount of Malassezia yeast was higher in samples before treatment.
VETERINARY RESEARCH COMMUNICATIONS
(2023)
Article
Agriculture, Dairy & Animal Science
Giorgia Gioacchini, Sara Filippi, Rossella Debernardis, Luca Marisaldi, Riccardo Aiese Cigliano, Oliana Carnevali
Summary: This study aimed to evaluate the cross-talk among metabolism, stress response, immune system and reproduction in immature and mature female swordfish. Transcriptomic and histological analysis revealed that mature females have compromised detoxification capacity and immune system, indicating higher susceptibility to environmental stress and pollutants during the reproductive season.
Article
Biochemistry & Molecular Biology
Ciro Gianmaria Amoroso, Daniela D'Esposito, Riccardo Aiese Cigliano, Maria Raffaella Ercolano
Summary: This study analyzed and compared the transcriptomic responses of resistant and susceptible tomato genotypes to multiple biotic and abiotic stresses. Many genes involved in defense mechanisms were identified, including those encoding for TFs, phytohormones, and participating in signaling and cell wall metabolic processes. A total of 1474 DEGs were commonly found between biotic and abiotic stress, with 67 DEGs involved in response to at least four different stresses. The detected genes responsive to multiple stress could be further studied and utilized to enhance plant tolerance through biotechnological approaches.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Andrology
Celia Corral-Vazquez, Joan Blanco, Riccardo Aiese Cigliano, Sarrate Zaida, Francesca Vidal, Ester Anton
Summary: The study used Next Generation Sequencing (NGS) to characterize the viral and bacterial RNA cargo of human sperm cells from healthy fertile donors. RNA-seq raw data from 12 sperm samples were aligned to microbiome databases and analyzed using GAIA software. The results showed common microbiome patterns among the samples and identified viruses and bacteria that make up the human sperm microbiome.
SYSTEMS BIOLOGY IN REPRODUCTIVE MEDICINE
(2023)
Article
Agriculture, Dairy & Animal Science
Anna Maria Sutera, Francesca Arfuso, Giuseppe Tardiolo, Valentina Riggio, Francesco Fazio, Riccardo Aiese Cigliano, Andreu Paytuvi, Giuseppe Piccione, Alessandro Zumbo
Summary: This study investigated the potential impact of a co-feed liquid whey-integrated diet on the fecal microbiota of crossbred pigs. The results showed that the supplementation with liquid whey affected the diversity and abundance of the bacterial community in the pig's feces. Furthermore, the correlation analysis suggested that the identified differentially abundant genera were associated with the physiological parameters of the pigs.
Article
Agriculture, Dairy & Animal Science
Giuseppe Tardiolo, Orazio Romeo, Alessandro Zumbo, Marco Di Marsico, Anna Maria Sutera, Riccardo Aiese Cigliano, Andreu Paytuvi, Enrico D'Alessandro
Summary: Liquid feeding is an alternative method in swine production that utilizes low-cost liquid by-products to reduce environmental impact. The study investigated the fecal microbiota of the Nero Siciliano pig breed fed a liquid whey-supplemented diet. The results showed changes in the abundance of certain bacterial genera, indicating a potential effect of the diet on the microbial community.
Article
Biochemistry & Molecular Biology
Giovanni Sarnelli, Alessandro Del Re, Marcella Pesce, Jie Lu, Giovanni Esposito, Walter Sanseverino, Chiara Corpetti, Silvia Basili Franzin, Luisa Seguella, Irene Palenca, Sara Rurgo, Fatima Domenica Elisa De Palma, Aurora Zilli, Giuseppe Esposito
Summary: Researchers proposed an engineered Escherichia coli strain with SARS-CoV-2 spike protein to elicit potent mucosal immunity. The intragastrically administered, engineered EcN demonstrated the ability to produce specific systemic and mucosal immunoglobulins against SARS-CoV-2 spike protein in mice, indicating its potential as an oral vaccine against COVID-19. The vaccine is safe, inexpensive, and capable of stimulating the production of both systemic and mucosal anti-SARS-CoV-2 spike protein antibodies.
Article
Plant Sciences
Simone Landi, Paola Punzo, Roberta Nurcato, Rossella Albrizio, Walter Sanseverino, Riccardo Aiese Cigliano, Pasquale Giorio, Florinda Fratianni, Giorgia Batelli, Sergio Esposito, Stefania Grillo
Summary: 'Corbarino' (COR) and 'Lucariello' (LUC) are Mediterranean long shelf-life tomato landraces that produce high-quality fruits under low water input cultivation. Understanding their unique drought stress tolerance at morpho-physiological and molecular levels may be crucial for their utilization in breeding programs.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Davide Borroni, Andreu Paytuvi-Gallart, Walter Sanseverino, Carmen Gomez-Huertas, Paola Bonci, Vito Romano, Giuseppe Giannaccare, Miguel Rechichi, Alessandro Meduri, Giovanni William Oliverio, Carlos Rocha-de-Lossada
Summary: This study aims to explore and characterize healthy eye microbiota. By analyzing samples from healthy subjects, it was found that healthy eye microbiota has low diversity with Staphylococcus as the predominant genus. A better understanding of healthy eye microbiota has the potential to improve disease diagnosis and personalized treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
