Article
Biotechnology & Applied Microbiology
Valerio Napolioni, Fortunato Bianconi, Rossella Potenza, Francesco M. Carpi, Vienna Ludovini, Matteo Picciolini, Francesca R. Tofanetti, Antonello Bufalari, Stefano Pallotti, Camilla Poggi, Marco Anile, Niccolo Daddi, Federico Venuta, Francesco Puma, Jacopo Vannucci
Summary: The study in a swine model showed changes in lung tissue structure and identified 553 differentially expressed genes post-experimental pneumonectomy. Gene network analysis indicated a dysregulation in gene inter-connections, with a predominance of macrophage-specific genes among the differentially expressed genes. Enrichment analysis highlighted genes related to apoptotic signaling pathway, response to insulin, and negative regulators of DDX58/IFIH1 signaling in the gene expression patterns.
Article
Multidisciplinary Sciences
Jun Seo Ha, Hyundoo Jeong
Summary: Recent advances in single-cell sequencing techniques have allowed for gene expression profiling at the individual cell level, accelerating biomedical research for complex disease treatment. In this study, we introduce a novel single-cell clustering algorithm, GRACE, which employs ensemble similarity learning and graph autoencoders to accurately classify cells. Through evaluations using real-world single-cell sequencing datasets, we demonstrate that GRACE achieves high assessment metric scores and yields accurate single-cell clustering results.
Article
Fisheries
Sara Zaldivar-Lopez, Juber Herrera-Uribe, Rocio Bautista, Angeles Jimenez, Angela Moreno, M. Gonzalo Claros, Juan J. Garrido
Summary: Salmonella infection induces transcriptional and phosphorylation changes in neutrophils, leading to increased neutrophil survival, decreased immune response, and impaired intracellular vesicle transport. These changes are mediated by overexpression of virulence factors and affect JAK/STAT, toll-like receptor, MAPK, interferons I and II signaling pathways. The results also suggest that Salmonella inhibits proinflammatory cytokine receptor genes, activates p53 signaling and NFκB-proteasome pathways, and downregulates the expression of STAT1 and STAT2. These findings provide insights into the pathogenesis of Salmonella Typhimurium infection.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Cristina Zamora-Ballesteros, Jorge Martin-Garcia, Aroa Suarez-Vega, Julio Javier Diez
Summary: This study conducted the first comprehensive genome-wide analysis of P. radiata lncRNAs, revealing their important regulatory role in response to Fusarium circinatum infection and potential involvement in regulating defense mechanisms such as cell wall reinforcement.
Article
Neurosciences
Abdellah Tebani, Jelena Jotanovic, Neda Hekmati, Asa Sivertsson, Olafur Gudjonsson, Britt Eden Engstrom, Johan Wikstrom, Mathias Uhlen, Olivera Casar-Borota, Fredrik Ponten
Summary: The study extended the classification of PitNETs based on global transcriptomics landscape, identifying three main clusters of PitNETs aligned with the main pituitary TFs expression patterns. The analysis enabled further identification of specific genes and expression patterns that could distinguish different classes of PitNETs. The transcriptomic analysis revealed potentially targetable tumor-driving genes with previously unknown role in pituitary tumorigenesis.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2021)
Review
Plant Sciences
Ce Chen, Yining Ge, Lingli Lu
Summary: Single-cell and spatial transcriptomics have shifted researchers' focus from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into transcriptomes at the single-cell level, while spatial transcriptomes help preserve spatial information. Though these two omics technologies are mature and helpful, further research is needed to ensure their widespread applicability in plant studies.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Yaowen Chang, Wenxia Sun, Alastair I. H. Murchie, Dongrong Chen
Summary: This study identified over 200 Kanamycin B binding RNAs in Escherichia coli through transcriptome-profiling analysis. Functional classification analysis revealed a diverse range of cellular functions for these RNAs. In vitro experiments confirmed the binding of Kanamycin B to small RNA fragments and small mRNA.
Article
Fisheries
Hao Li, Yuehong Zhao, Xiaoli Zhang, Hui Zhao, Weiwei Li, Qun Wang
Summary: In this study, the transcriptional response of Eriocheir sinensis to different forms of Dscam ICDs was investigated. The results showed that different forms of Dscam ICDs can affect key immune, metabolic, and cell proliferation-regulated genes and pathways.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ashley Mae Conard, Nathaniel Goodman, Yanhui Hu, Norbert Perrimon, Ritambhara Singh, Charles Lawrence, Erica Larschan
Summary: TIMEOR is the first web-based and adaptive time-series multi-omics pipeline method that infers the relationship between gene regulatory events across time, addressing the critical need for determining causal regulatory mechanism networks. It integrates time-series RNA-seq, motif analysis, protein-DNA binding data, and protein-protein interaction networks.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Environmental Sciences
Graciela Lopez-Soop, Trine Husoy, Marcin Wlodzimierz Wojewodzic, Hege Hjertholm, Anastasia Spyropoulou, Effrosyni S. Katsanou, Petros Batakis, Katerina Kyriakopoulou, Kyriaki Machera, Hubert Dirven, Birgitte Lindeman, Nur Duale
Summary: Exposure to phthalates is common in Europe, and their effects on the human transcriptome are largely unknown. A study conducted on blood samples from the Norwegian EuroMix cohort revealed that phthalate exposure led to differential gene expression, with DINCH showing the highest number of differentially expressed genes. Gene ontology analysis indicated that the differentially expressed genes were mainly associated with cellular metabolism, while phthalate metabolites MnBP and DINCH showed enrichment in immunological function pathways. The study also found associations between phthalates and genes involved in the PPAR signaling pathway. Overall, DINCH had similar effects on gene expression as phthalates, despite being considered a substitute for them.
ENVIRONMENTAL RESEARCH
(2023)
Article
Microbiology
Marcela Legue, Blanca Aguila, Andrea Calixto
Summary: Communication with bacteria have significant impact on the life history traits of hosts, with bacteria capable of promoting phenotypic and behavioral changes in nematodes. The study reveals a pathogen-induced diapause formation (PIDF) strategy in nematodes exposed to pathogens, which is recalled transgenerationally. Interspecies RNA interactions are explored during PIDF conditions through transcriptomic data analysis, shedding light on potential mechanisms of RNA-mediated interactions.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Environmental Sciences
Benjamin N. Daniels, Cassidy L. Andrasz, Nicholas Zarate, Andy Lee, Cataixa Lopez, Paul Anderson, Robert J. Toonen, Mark R. Christie, Crow White, Jean M. Davidson
Summary: Understanding the genomic characteristics of non-model organisms is crucial for bridging the gap between ecology and evolution. This study successfully assembled the genome and transcriptome sequences of the non-model organism Kellet's whelk for the first time. The robust reference genome and transcriptome provide valuable resources for enhancing our understanding of its ecology, evolution, and mechanisms of range expansion.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Engineering, Environmental
Sahar Daer, Joseph E. Goodwill, Kaoru Ikuma
Summary: Disinfection mechanisms vary by disinfectant, with monochloramine potentially inducing viable but non-culturable state through reduced protein synthesis and metabolism, while ferrate does not have this effect. Both disinfectants upregulate oxidative stress response genes, with monochloramine showing slower disinfection kinetics compared to ferrate.
Article
Medicine, General & Internal
Maria Tio-Coma, Szymon M. Kielbasa, Susan J. F. van den Eeden, Hailiang Mei, Johan Chandra Roy, Jacco Wallinga, Marufa Khatun, Sontosh Soren, Abu Sufian Chowdhury, Khorshed Alam, Anouk van Hooij, Jan Hendrik Richardus, Annemieke Geluk
Summary: The study identified a prospective transcriptional risk signature in blood that can predict the development of leprosy 4 to 61 months before clinical diagnosis. Using a machine learning approach, a leprosy signature was identified and validation showed potential value in confirming leprosy risk.
Article
Plant Sciences
Haiye Luan, Changyu Chen, Ju Yang, Hailong Qiao, Hongtao Li, Shufeng Li, Junyi Zheng, Huiquan Shen, Xiao Xu, Jun Wang
Summary: Waterlogging is a major factor affecting the yield and quality of barley. This study used genome-wide association study and transcriptome analysis to identify SNPs and differentially expressed genes associated with waterlogging tolerance in barley. Several candidate genes were found to have a role in enhancing waterlogging tolerance, which has implications for breeding waterlogging-tolerant barley varieties.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Immunology
Estefania Rodriguez-Garcia, Nerea Zabaleta, Irene Gil-Farina, Manuela Gonzalez-Aparicio, Maite Echeverz, Heike Bahre, Cristina Solano, Inigo Lasa, Gloria Gonzalez-Aseguinolaza, Mirja Hommel
Summary: Several bacterial diguanylate cyclases, particularly AdrA from Salmonella Enteritidis, have been identified as potent inducers of a STING-mediated IFN response. Using mouse models, it was shown that AdrA can reduce viremia in hepatitis B virus-transgenic and adenovirus-associated virus-HBV mice. The antiviral activity of AdrA relies on the presence of STING, type I IFN, and TNF-alpha, which act synergistically in combating viral infections.
JOURNAL OF IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Arancha Catalan-Moreno, Marta Cela, Pilar Menendez-Gil, Naiara Irurzun, Carlos J. Caballero, Isabelle Caldelari, Alejandro Toledo-Arana
Summary: The production of cold shock proteins CspB and CspC from Staphylococcus aureus is controlled by two paralogous RNA thermoswitches, which adopt alternative RNA structures at different temperatures, affecting the translation process. Simultaneous deletion of these genes or their RNA thermoswitches significantly decreases the growth rate of the bacteria at lower temperatures.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Pedro Dorado-Morales, M. Pilar Garcillan-Barcia, Inigo Lasa, Cristina Solano
Summary: Plasmids play a major role in the spread of antibiotic resistance genes among bacterial strains. This study demonstrates that the initial fitness cost of plasmids in Staphylococcus aureus can be alleviated over time through plasmid rearrangements mediated by insertion sequences, leading to the loss of antimicrobial resistance genes. The results suggest the potential benefits of reducing antibiotic use in both animal and clinical settings to prevent the spread of clinical multidrug resistance plasmids.
Review
Biotechnology & Applied Microbiology
Carmen Gomez-Arrebola, Cristina Solano, Inigo Lasa
Summary: Two-component systems (TCSs) are essential sensory systems in bacteria, involving a histidine kinase and a response regulator. In addition to phosphorylated state, unphosphorylated response regulators may also have regulatory functions. Recent studies have shown that unphosphorylated response regulators control critical bacterial processes, indicating the need to revisit the classical view on their activity.
INTERNATIONAL MICROBIOLOGY
(2021)
Article
Microbiology
Ariadna Fernandez-Calvet, Begona Euba, Celia Gil-Campillo, Arancha Catalan-Moreno, Javier Moleres, Sara Marti, Alexandra Merlos, Jeroen D. Langereis, Francisco Garcia-del Portillo, Lauren O. Bakaletz, Garth D. Ehrlich, Eric A. Porsch, Margarita Menendez, Joshua C. Mell, Alejandro Toledo-Arana, Junkal Garmendia
Summary: This study reveals the molecular mechanisms of NTHi pathoadaptation based on within-patient lifestyle switching controlled by phase variation. Adhesins such as HMW1A in NTHi display allelic variation, driving changes in epithelial invasion phenotype over time. This highlights the importance of bacterial adaptation in chronic infections and the role of genetic variants in shaping bacterial behavior.
Review
Infectious Diseases
Leticia Matilla-Cuenca, Alejandro Toledo-Arana, Jaione Valle
Summary: Amyloids play a significant role in bacterial biofilms, serving as potential targets for drug development to enhance therapeutic strategies against biofilm-related infections.
Article
Biochemistry & Molecular Biology
Laurene Bastet, Pilar Bustos-Sanmamed, Arancha Catalan-Moreno, Carlos J. Caballero, Sergio Cuesta, Leticia Matilla-Cuenca, Maite Villanueva, Jaione Valle, Inigo Lasa, Alejandro Toledo-Arana
Summary: This study reveals that a bacterial antisense RNA (lexA-asRNA) in Staphylococcus aureus is generated through a transcriptional read-through event. The read-through occurs on the intrinsic terminator of the sbrB gene, which is located downstream of the lexA gene. A natural mutation destabilizes the terminator structure and affects its efficiency, leading to the production of the antisense RNA. The expression of lexA-asRNA is linked to cellular stress and regulated by the stress transcription factor SigB. Comparative analysis also suggests strain-specific nucleotide polymorphisms within the terminator sequence.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Emma Desgranges, Laura Barrientos, Lucas Herrgott, Stefano Marzi, Alejandro Toledo-Arana, Karen Moreau, Francois Vandenesch, Pascale Romby, Isabelle Caldelari
Summary: The study focused on the sRNA RsaG derived from Staphylococcus aureus and its induction with uhpT when bacteria are internalized into host cells or in the presence of mucus-secreting cells. RsaG was found to control redox homeostasis and adjust metabolism by stabilizing, degrading, or repressing the translation of mRNA targets.
MOLECULAR MICROBIOLOGY
(2022)
Article
Microbiology
Pilar Menendez-Gil, Arancha Catalan-Moreno, Carlos J. Caballero, Alejandro Toledo-Arana
Summary: Iron acquisition and modulation are crucial for all living organisms. This study found that the ftnA 3'UTR is affected by RNase III and PNPase, and the half-life of ftnA mRNA is also influenced by both RNase III and ftnA 3'UTR. Additionally, the deletion of ftnA 3'UTR impairs S. aureus growth.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Liliana Morales-Laverde, Maite Echeverz, Margarita Trobos, Cristina Solano, Inigo Lasa
Summary: This study investigated the nucleotide-level survey of Staphylococcus aureus strains obtained from prosthetic joint infections (PJI) and wounds. The intergenic regions (IGRs) of the icaADBCR locus responsible for biofilm formation were highly conserved, and no PJI-specific SNPs were found. However, a SNP in the icaR coding region resulted in increased icaADBC operon transcription and PIA/PNAG production, as well as reduced virulence in a Galleria mellonella infection model.
Article
Biotechnology & Applied Microbiology
Leticia Matilla-Cuenca, Agustina Taglialegna, Carmen Gil, Alejandro Toledo-Arana, Inigo Lasa, Jaione Valle
Summary: Biofilm engineering is a controllable method to create living structures with programmable functionalities. This study uses facultative amyloid-like protein Bap to decorate the extracellular biofilm matrix or the bacterial cell surface with functional domains or proteins. By modulating pH, the localization of functional tags can be changed. A tool for trapping and covalently immobilizing molecules at bacterial cell surface or biofilm matrix is built based on Bap features. The cell wall of various Gram-positive bacteria can be functionalized through the addition of recombinant Bap-amyloid domain.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Food Science & Technology
Liliana Lai, Maite Villanueva, Ane Muruzabal-Galarza, Ana Beatriz Fernandez, Argine Unzue, Alejandro Toledo-Arana, Primitivo Caballero, Carlos J. Caballero
Summary: Aedes albopictus, a mosquito species from Southeast Asia, has rapidly spread to temperate regions, making them vulnerable to diseases like dengue, yellow fever, zika, and chikungunya. The mosquito has developed resistance to commonly used insecticides, necessitating the search for new toxins to control their population.
Article
Microbiology
Beatriz Rapun-Araiz, Ioritz Sorzabal-Bellido, Javier Asensio-Lopez, Maria Lazaro-Diez, Mikel Ariz, Carlos Sobejano de la Merced, Begona Euba, Ariadna Fernandez-Calvet, Ivan Cortes-Dominguez, Saioa Burgui, Alejandro Toledo-Arana, Carlos Ortiz-de-Solorzano, Junkal Garmendia
Summary: Standardized clinical procedures for antibiotic administration often fail to optimize treatment for respiratory pathogens due to polyclonal infections. This study presents a panel of plasmid tools for labeling and visualizing H. influenzae polyclonal infections, and demonstrates their usefulness in analyzing mixed biofilm growth, antibiotic efficacy, and bacterial co-infection dynamics.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Carmen Gomez-Arrebola, Sara B. Hernandez, Elizabeth J. Culp, Gerard D. Wright, Cristina Solano, Felipe Cava, Inigo Lasa
Summary: The overuse of antibiotics has led to the emergence of antimicrobial resistance, stimulating the search for novel antibiotics. This study investigates the role of the VraSR sensory system in Staphylococcus aureus susceptibility to Complestatin and Corbomycin, revealing the important role of spdC and sagB genes in antibiotic resistance.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Liliana Morales-Laverde, Margarita Trobos, Maite Echeverz, Cristina Solano, Inigo Lasa
Summary: The expression level of surface adhesins may modulate the propensity of Staphylococcus aureus strains to cause prosthetic joint infections. Strains from the same clonal complex display specific patterns of single-nucleotide polymorphisms (SNPs) in the regulatory region of genes encoding surface adhesins, resulting in specific profiles of surface protein expression for each clonal lineage. Some lineages show a higher colonization capacity and greater ability to form a biofilm on surfaces coated with plasma proteins.