Article
Computer Science, Information Systems
Ehsan Elahi, Ana Iglesias, Jorge Morato
Summary: This research evaluates the impact of non-text images on webpage readability and proposes an automatic methodology to calculate the relevance of non-text images. Through user studies, it is found that relevant non-text images enhance the readability of web pages.
Article
Multidisciplinary Sciences
Johann H. Martinez, Sergi Romero, Jose J. Ramasco, Ernesto Estrada
Summary: The study investigates the international waste trade network from 2001 to 2019, identifying countries at risk of improper waste handling. Chemical tracers are utilized to determine the environmental impact of waste in these countries. The research reveals that most hazardous waste is traded among developed nations, but there is a disproportionate asymmetry in the flow from developed to developing countries. By using a dynamic model, the study simulates the propagation of waste stress through the network and its impact on countries. It identifies 28 countries with a low Environmental Performance Index that are at high risk of waste congestion and improper handling of hazardous waste. Evidence of pollution caused by heavy metals, volatile organic compounds, and persistent organic pollutants is found in several of these countries due to improper waste handling.
NATURE COMMUNICATIONS
(2022)
Review
Oncology
Maria Pia Campagna, Alexandre Xavier, Jeannette Lechner-Scott, Vicky Maltby, Rodney J. Scott, Helmut Butzkueven, Vilija G. Jokubaitis, Rodney A. Lea
Summary: The interaction between genetic and environmental factors drives the development of complex diseases, with the role of the epigenome in disease pathophysiology gaining attention. Epigenome-wide association studies (EWASes) investigating the association between phenotype and epigenetic variants, particularly DNA methylation, have increased in number in recent years due to advancements in technology. Studies focusing on methylation data in blood samples have been recommended as a cost-effective approach, with novel areas of EWAS analysis expanding to include longitudinal study designs and statistical deconvolution for identifying cell-specific differential methylation.
CLINICAL EPIGENETICS
(2021)
Article
Ecology
Patrick Lavelle, Jerome Mathieu, Alister Spain, George Brown, Carlos Fragoso, Emmanuel Lapied, Adriana De Aquino, Isabelle Barois, Edmundo Barrios, Maria Eleusa Barros, Jose Camilo Bedano, Eric Blanchart, Mark Caulfield, Yamileth Chagueza, Jun Dai, Thibaud Decaens, Anahi Dominguez, Yamileth Dominguez, Alexander Feijoo, Patricia Folgarait, Steven J. Fonte, Norma Gorosito, Esperanza Huerta, Juan Jose Jimenez, Courtland Kelly, Gladys Loranger, Robelio Marchao, Raphael Marichal, Catarina Praxedes, Leonardo Rodriguez, Guillaume Rousseau, Laurent Rousseau, Nuria Ruiz, Catalina Sanabria, Juan Carlos Suarez, Jerome Ebagnerin Tondoh, Anne De Valenca, Steven J. Vanek, Joel Vasquez, Elena Velasquez, Emily Webster, Chi Zhang
Summary: Soil macroinvertebrate communities respond to climatic, soil, and land-cover conditions. Different taxa are distributed under a wide range of geographical and environmental conditions, and agricultural practices have an impact on their abundance.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2022)
Article
Biochemistry & Molecular Biology
Shuo Han, Zhiyin Jiao, Meng-Xue Niu, Xiao Yu, Mengbo Huang, Chao Liu, Hou-Ling Wang, Yangyan Zhou, Wei Mao, Xiaofei Wang, Weilun Yin, Xinli Xia
Summary: Studies on GASA genes in Populus trichocarpa and Populus euphratica revealed that these genes are mainly expressed in young tissues and organs, and are involved in plant hormone responses and drought stress responses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Nicole Raad, Hannes Luidalepp, Michel Fasnacht, Norbert Polacek
Summary: This study suggests that bacteria may utilize small non-protein coding RNAs to maintain dormancy status during non-proliferating state, showing enriched sRNAs in the stationary growth phase and their origin from various genomic regions. Experimental validation of growth phase-dependent expression of these sRNAs provides important clues for understanding bacterial stationary phase biology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Environmental Sciences
Anqi Wang, Qiang Ma, Biao Gong, Long Sun, Francis-Kojo Afrim, Renjie Sun, Tongkun He, Hui Huang, Jingyuan Zhu, Guoyu Zhou, Yue Ba
Summary: The study revealed that long-term fluoride exposure can affect the methylation pattern of genomic DNA, leading to increased susceptibility of certain genes (such as NNAT and CALCA) to fluoride exposure, which may impact the healthy development of school-age children.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Biotechnology & Applied Microbiology
Chen Sisi, Deng Jieru, Cheng Peidong, Zhang Zhaolong, Wang Yihang, Chen Shuwen, Tang Yan, Wang Tianyu, Yang Guiyan
Summary: This study investigated the stress response mechanism of walnut trees by analyzing the PP2C genes in walnut trees. The results showed that JrPP2C genes exhibited diversity in response to stress and ABA treatment, indicating their potential roles in plant response to multiple stimuli and involvement in ABA-dependent signaling pathway.
Article
Biochemical Research Methods
Yunze Liu, Gang Li
Summary: Researchers have developed an R package and a web server called Genekitr to assist biologists in exploring large gene sets. Genekitr includes four modules: gene information retrieval, ID conversion, enrichment analysis, and publication-ready plotting. This tool makes bioinformatics tasks accessible to non-programming scientists.
BMC BIOINFORMATICS
(2023)
Article
Microbiology
Felicita Mabel Dure, Melise Chaves Silveira, Claudio Marcos Rocha-de-Souza, Robson Souza Leao, Ivson Cassiano de Oliveira Santos, Rodolpho Mattos Albano, Elizabeth Andrade Marques, Ana Paula D'Alincourt Carvalho-Assef, Fabricio Alves Barbosa da Silva
Summary: With the recent advancements in NGS technologies, genome sequencing is generating vast amounts of data with valuable biological information. Understanding genomes and their functions in a biologically meaningful way is a challenge that needs to be addressed, especially in the context of global antimicrobial resistance. In order to properly analyze the rapidly accumulating genomic data, there is a need for new, user-friendly and comprehensive analytical tools. This article proposes a web application called CABGen, which provides an easy-to-use and scalable environment for storing, organizing, analyzing, and interpreting bioinformatics data.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Fidele Ntie-Kang, Kiran K. Telukunta, Serge A. T. Fobofou, Victor Chukwudi Osamor, Samuel A. Egieyeh, Marilia Valli, Yannick Djoumbou-Feunang, Maria Sorokina, Conrad Stork, Neann Mathai, Paul Zierep, Ana L. Chavez-Hernandez, Miquel Duran-Frigola, Smith B. Babiaka, Romuald Tematio Fouedjou, Donatus B. Eni, Simeon Akame, Augustine B. Arreyetta-Bawak, Oyere T. Ebob, Jonathan A. Metuge, Boris D. Bekono, Mustafa A. Isa, Raphael Onuku, Daniel M. Shadrack, Thommas M. Musyoka, Vaishali M. Patil, Justin J. J. van der Hooft, Vanderlan da Silva Bolzani, Jose L. Medina-Franco, Johannes Kirchmair, Tilmann Weber, Ozlem Tastan Bishop, Marnix H. Medema, Ludger A. Wessjohann, Jutta Ludwig-Mueller
Summary: The online open-access workshop CAiSMD discussed the potential applications of computational methodologies in the search for secondary metabolites, with invited speakers from academia and industry across five continents. The workshop included keynote lectures, oral presentations, round table discussions, and hands-on sessions, fostering interaction among participants.
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Forestry
Pengwei Zhang, Zhinuo Huang, Huicong Zhang, Haiwen Lu, Qimin Li, Juan Zhuo, Hantian Wei, Dan Hou, Xinchun Lin
Summary: This study identified six PeSERK genes in moso bamboo and classified them into four groups. These genes showed highly similar distribution of conserved domains and were found to have stress and hormone response elements on their promoters. PeSERK1 had higher expression in all tissues and stages of shoot development compared to PeSERK3. PeSERK3 had higher expression in leaf sheaths and might play a more vital role in drought stress response than PeSERK1. This study provides a theoretical basis for further understanding the SERK response to stress conditions in moso bamboo.
Article
Biochemistry & Molecular Biology
Daniel Walke, Kay Schallert, Prasanna Ramesh, Dirk Benndorf, Emanuel Lange, Udo Reichl, Robert Heyer
Summary: The taxonomic and functional characterization of microbial communities from diverse environments is increasingly important, with researchers using multi-omics methods to assign genes, transcripts, or proteins to biological pathways. The MPA_Pathway_Tool is a new web application that helps users create and map microbial community data onto specific pathways for better understanding of their functions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Henoke K. Shiferaw, Celine S. Hong, David N. Cooper, Jennifer J. Johnston, Leslie G. NISC, Leslie G. Biesecker
Summary: Polyadenylation is a crucial process for mRNA stabilization and export, with hexamers playing a key role. However, only a few disorders have been associated with hexamer variants, possibly due to lack of defined hexamers in molecular analysis. To address this, the study aimed to define functionally important hexamers genome-wide and identified predominant polyA sites and putative predominant hexamers. Variants in these predominant hexamers showed potential pathogenic impact and could be used for interrogating exome and genome data in human diseases.
HUMAN MOLECULAR GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Michael L. Samulevich, Rambon Shamilov, Brian J. Aneskievich
Summary: Intrinsically disordered proteins (IDPs) in keratinocytes, especially those associated with the cornified envelope, demonstrate high levels of intrinsic disorder and potential for liquid-liquid phase separation (LLPS).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Antonio Giaco, Paola De Giorgi, Giovanni Astuti, Lucia Varaldo, Llorenc Saez, Rodrigo Carballal, Miguel Serrano, Gabriele Casazza, Paolo Caputo, Gianluigi Bacchetta, Lorenzo Peruzzi
Summary: In this study, a traditional karyomorphological approach was used to investigate the cytotaxonomic relationships among the species of the Santolina chamaecyparissus complex. Chromosome number, total haploid length, and karyotype asymmetry indices were calculated for each species. The results showed that polyploids have a more asymmetric karyotype compared to diploids. Chromosome data were provided for S. benthamiana and S. vedranensis for the first time, and a new hexaploid cytotype was reported for S. villosa.
Article
Plant Sciences
Giulia Albani Rocchetti, Charles Davis, Giulia Caneva, Gianluigi Bacchetta, Giuseppe Fabrini, Giuseppe Fenu, Bruno Foggi, Gabriele Galasso, Domenico Gargano, Gianpietro Giusso del Galdo, Mauro Iberite, Sara Magrini, Alfred Mayer, Andrea Mondoni, Chiara Nepi, Simone Orsenigo, Lorenzo Peruzzi, Thomas Abeli
Summary: Herbaria could be valuable sources for recovering lost genetic variation and extinct plant species, with the potential for de-extinction through germinating viable diaspores or culturing tissues. Despite potential risks to historical specimens, there is a consensus in the scientific community to use herbarium specimens for resurrecting extinct plant species.
Article
Biology
Paola De Giorgi, Antonio Giaco, Giovanni Astuti, Luigi Minuto, Lucia Varaldo, Daniele De Luca, Alessandro De Rosa, Gianluigi Bacchetta, Marco Sarigu, Lorenzo Peruzzi
Summary: This study investigated the taxonomy of plant species Santolina, commonly known as lavender-cotton. It found that two putative species from Corsica and Sardinia are actually very similar and should be reclassified as a single species. The study highlights the importance of integrating different sources of information for reliable taxonomic hypotheses and contributes to our understanding of plant evolution in the Mediterranean Basin.
Article
Ecology
Marco D'Antraccoli, Gianni Bedini, Lorenzo Peruzzi
Summary: The vast amount of occurrence records available for biodiversity data analyses poses challenges in terms of reliability and interpretation. To address this, we developed an R package that incorporates spatial and temporal uncertainties, providing a map of floristic ignorance and a virtual floristic list for a study area. The method can handle large amounts of occurrence data and represents relative floristic ignorance in a computationally sustainable way. The approach integrates uncertainty into biodiversity analyses through methodological approaches and spatial representations. This workflow improves the accuracy of outputs.
ECOLOGICAL INFORMATICS
(2022)
Article
Plant Sciences
Marco D'Antraccoli, Gianni Bedini, Lorenzo Peruzzi
Summary: This study proposes a workflow that integrates various methods and tools to address the limitations of current floristic inventories, aiming to advance the field of floristics.
Article
Plant Sciences
Lijuan Liu, Giovanni Astuti, Andrea Coppi, Lorenzo Peruzzi
Summary: Hybridization and introgression have a significant impact on the taxonomically controversial genus Pulmonaria. The P. hirta complex shows complex systematic relationships and phenotypic differences in southern Europe, with molecular and morphological evidence of hybrid origin and gene flow between different clades. Despite some morphological differentiation, there are intermediate features between different morphs, indicating ongoing gene flow between these taxa.
Review
Forestry
Krassimir D. Naydenov, Michel K. Naydenov, Alexander Alexandrov, Todor Gurov, Veselka Gyuleva, Georgi Hinkov, Sofiya Ivanovska, Anatoly Tsarev, Biljana Nikolic, Venceslas Goudiaby, Christopher Carcaillet, Roman Volosyanchuk, Srdjan Bojovic, Kole Vasilevski, Vlado Matevski, Lorenzo Peruzzi, Andreas Christou, Despina Paitaridou, Irina Goia, Salim Kamary, Suleyman Gulcu, Cengiz Ture, Faruk Bogunic
Summary: Based on macrophylogeographic mtDNA empirical data, a scenario for the evolution and speciation of European black pine and Scotch pine, along with their subspecies and varieties, is proposed. INDEL variability in the Pinus mitochondrial genome is found to be relatively old and linked to historical continental fluctuations rather than climate change. Attention is given to the relationships between speciation models, migration patterns, and differences between central and peripheral populations for conservation and management biodiversity program recommendations.
EUROPEAN JOURNAL OF FOREST RESEARCH
(2023)
Article
Plant Sciences
Mauro Di Stasi, David Dolci, Lorenzo Peruzzi, Alessandra Braca, Marinella De Leo
Summary: This article reports the first complete phytochemical study of Stachys sylvatica aerial parts, including the isolation and characterization of 23 known compounds. The compounds were identified using various analytical techniques, including nuclear magnetic resonance spectroscopy and mass spectrometry. The study also tentatively identified an additional phenolic derivative and four carboxylic acids. The chemosystematic relationships between S. sylvatica and related species were highlighted.
Article
Biodiversity Conservation
Tiberio Fiaschi, Emanuele Fanfarillo, Simona Maccherini, Giovanni Bacaro, Gianmaria Bonari, Bruno Foggi, Lorenzo Peruzzi, Lorenzo Pinzani, Leonardo Rosati, Anna Scoppola, Daniele Viciani, Claudia Angiolini
Summary: Vascular plants are important indicators of environmental conditions. This study tested the effectiveness of the Floristic Quality Assessment (FQA) approach using the flora of a suburban riverscape in central Italy. The results showed that a minimum of five botanists can provide stable assessments. The study also found a positive correlation between plant diversity and anthropogenic disturbance.
ECOLOGICAL INDICATORS
(2023)
Article
Environmental Sciences
Vanessa Lozano, Mirko Di Febbraro, Giuseppe Brundu, Maria Laura Carranza, Alessandro Alessandrini, Nicola Maria Giuseppe Ardenghi, Elena Barni, Gianni Bedini, Laura Celesti-Grapow, Kevin Cianfaglione, Annalena Cogoni, Gianniantonio Domina, Simonetta Fascetti, Giulio Ferretti, Bruno Foggi, Mauro Iberite, Lorenzo Lastrucci, Lorenzo Lazzaro, Andrea Mainetti, Francesca Marinangeli, Chiara Montagnani, Carmelo Maria Musarella, Simone Orsenigo, Simonetta Peccenini, Lorenzo Peruzzi, Laura Poggio, Chiara Proietti, Filippo Prosser, Aldo Ranfa, Leonardo Rosati, Annalisa Santangelo, Alberto Selvaggi, Giovanni Spampinato, Adriano Stinca, Gabriella Vacca, Mariacristina Villani, Consolata Siniscalco
Summary: This study used a methodological framework to assess and analyze the invasion risk of 14 invasive alien plants of Union concern in Italy. The framework combined invasive Species Distribution Models based on propagule pressure, abiotic and biotic factors, and the local interpretable model-agnostic explanation analysis. The study found that the distribution of invasive alien plants in Italy is influenced by biogeographic regions, protected areas, abiotic factors, propagule pressure, and biotic filters.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Green & Sustainable Science & Technology
Marco D'Antraccoli, Nora Weiger, Leonardo Cocchi, Lorenzo Peruzzi
Summary: Botanical gardens are invaluable for cultivating, managing, studying, and preserving tree diversity. However, climate change poses a significant challenge for tree management and conservation, as it exposes trees to more adverse environmental conditions. This research assesses the impact of future climate change on the tree collection of Botanic Garden of Pisa, highlighting the potential consequences for tree cultivation and management. The study also explores the opportunities and challenges in managing urban green areas, focusing on botanical garden communities.
Article
Plant Sciences
Manuel Tiburtini, Gianluigi Bacchetta, Marco Sarigu, Salvatore Cambria, Paolo Caputo, Daniele De Luca, Gianniantonio Domina, Alessia Turini, Lorenzo Peruzzi
Summary: An integrative approach was used to resolve the complex taxonomy and systematics of the genus Armeria in Sardinia and Corsica. The study found that some taxa are no longer supported by new data, leading to a new taxonomic hypothesis that considers only five species endemic to the islands.
Editorial Material
Biology
Lorenzo Peruzzi
Article
Plant Sciences
Jacopo Franzoni, Giovanni Astuti, Gianluigi Bacchetta, Giulio Barone, Fabrizio Bartolucci, Liliana Bernardo, Angelino Carta, Fabio Conti, Gianniantonio Domina, Bozo Frajman, Gianpietro Giusso del Galdo, Duilio Iamonico, Mauro Iberite, Luigi Minuto, Marco Sarigu, Ana Terlevic, Alessia Turini, Lucia Varaldo, Daniel Volgger, Lorenzo Peruzzi
Summary: This study reevaluates the taxonomy of the Dianthus virgineus L. complex by examining the chromosome number and genome size of wild carnation populations in Italy and Morocco. The results indicate that the differentiation of these taxa is primarily associated with geographical distribution rather than morphological characteristics.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Biology
Jacopo Franzoni, Giovanni Astuti, Lorenzo Peruzzi
Summary: By studying the relationship between genetic divergence at neutral loci, phenotypic variation, and geographic and environmental distances, micro-evolutionary scenarios involving natural selection and neutral evolution can be analyzed. In this study, we examined the patterns of intraspecific genetic and phenotypic variation along an elevational gradient using Dianthus virgineus as a study system. We found a weak genetic structure related to geographic distance, but genetic drift was not the primary factor driving phenotypic traits. The high degree of phenotypic differentiation in relation to genetic divergence at neutral loci suggests that selection, possibly driven by changing conditions at different sites, may explain the observed patterns of variation.
