Article
Biochemistry & Molecular Biology
Hansaim Lim, Fatma Cankara, Chung -Jung Tsai, Ozlem Keskin, Ruth Nussinov, Attila Gursoy
Summary: This review discusses recent advancements in computational methods for predicting microbial effects on human cells, with a focus on protein-protein interactions. Traditional methods, as well as more recent deep learning methods, are categorized and potential solutions to challenges in structure-based approaches are discussed. The review provides a brief guide to the current status and future directions in the field.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yunxia Wang, Ziqi Pan, Minjie Mou, Weiqi Xia, Hongning Zhang, Hanyu Zhang, Jin Liu, Lingyan Zheng, Yongchao Luo, Hanqi Zheng, Xinyuan Yu, Xichen Lian, Zhenyu Zeng, Zhaorong Li, Bing Zhang, Mingyue Zheng, Honglin Li, Tingjun Hou, Feng Zhu
Summary: In this study, a task-specific encoding algorithm for RNAs and RNA-associated interactions was developed, which realized comprehensive RNA feature encoding by introducing novel features and enabled task-specific integration of interacting partners using convolutional autoencoder-directed feature embedding.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Chenqian Tang, Xin Chen, Yunfei Deng, Liyang Geng, Jianhui Ma, Xueyan Wei
Summary: This study analyzed the chloroplast genomes of Sorbus s.s. plants to investigate their phylogenetic relationships. The results showed that Sorbus s.s. is monophyletic, while Sorbus s.l. is polyphyletic. The current subgenus and section classifications were found to be problematic. The conserved genome structure of Sorbus s.s. can be used for population genetics, species delimitation, and phylogenetic studies, while hypervariable regions and repeat sequences are promising molecular markers.
Article
Chemistry, Medicinal
Octav Caldararu, Tom L. Blundell, Kasper P. Kepp
Summary: In this study, a simple multilinear regression model named SimBa is used for protein stability prediction, considering only solvent accessibility, volume difference, and polarity difference caused by mutation. The results show that this straightforward model performs comparably to more complex methods, indicating a hard limit in numerical accuracy and trend accuracy. New features are required to improve accuracy beyond this limit.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Oxana (Sachenkova) Lundstrom, Max Adriaan Verbiest, Feifei Xia, Helyaneh Ziaei Jam, Inti Zlobec, Maria Anisimova, Melissa Gymrek
Summary: Short tandem repeats (STRs), consisting of repeated one to six nucleotide motifs, have been shown to influence various traits in humans. However, the study of STRs has been limited due to technical challenges. Recent advancements in genome-wide analysis tools have enabled large-scale analysis of STR variations in populations.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Arturo Becerra, Israel Munoz-Velasco, Abelardo Aguilar-Camara, Wolfgang Cottom-Salas, Adrian Cruz-Gonzalez, Alberto Vazquez-Salazar, Ricardo Hernandez-Morales, Rodrigo Jacome, Jose Alberto Campillo-Balderas, Antonio Lazcano
Summary: Low complexity regions (LCRs) are protein sequences formed by compositionally biased residues. Four extremely conserved LCRs were found in the spike protein of several SARS-CoV-2 variants. These LCRs, especially in the Delta variant, may play a role in the rapid spread of the virus.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Mir Asif Iquebal, Sarika Jaiswal, Vineet Kumar Mishra, Rahul Singh Jasrotia, Ulavappa B. Angadi, Bhim Pratap Singh, Ajit Kumar Passari, Purbajyoti Deka, Ratna Prabha, Dhananjaya P. Singh, Vijai Kumar Gupta, Rukam Singh Tomar, Harinder Singh Oberoi, Anil Rai, Dinesh Kumar
Summary: Identification and diversity analysis of fungi pose great challenges, as traditional methods have limitations in differentiating between all groups and cryptic species. This study introduces a novel whole genome sequence-based microsatellite database, FungSatDB, containing >19M loci from >1900 fungal species/strains. Evaluation of genotyping efficacy through both in silico and in vitro PCR demonstrates successful differentiation of fungal species from eight countries across four continents. This database has the potential to accelerate fungal genomic research in various fields.
Article
Agriculture, Multidisciplinary
Ayisha Zia, Misbah Zahoor, Abdullah Abdullah, Asma Nisar, Neelam Batool, Amana Bibi, Kiran Saba, Ibrar Ahmed, Arzu Karatas, Ekrem Gurel, Mohammad Tahir Waheed
Summary: This study sequenced and analyzed the chloroplast genomes of two cultivars of broccoli, revealing highly similar genome structures and providing insights into gene encoding frequencies and repeat sequences. The findings will contribute to a better understanding of the chloroplast genomes of broccoli and serve as a resource for chloroplast genetic engineering.
TURKISH JOURNAL OF AGRICULTURE AND FORESTRY
(2022)
Article
Plant Sciences
Huahao Jiang, Muhammad Waseem, Yong Wang, Sana Basharat, Xia Zhang, Yun Li, Pingwu Liu
Summary: Sugarcane is an important agricultural crop used for sugar production and biofuel. The genetic complexity of sugarcane makes it a challenging crop to improve. This study developed SSR markers from sugarcane ESTs, which can be used for genetic characterization and breeding efforts. Functional annotation analysis showed that the markers cover molecular, cellular, and biological pathways.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Paul L. Babb, Matjaz Gregoric, Nicholas F. Lahens, David N. Nicholson, Cheryl Y. Hayashi, Linden Higgins, Matjaz Kuntner, Ingi Agnarsson, Benjamin F. Voight
Summary: By studying the genomes and transcriptomes of Darwin's bark spider, researchers have identified at least 31 potential silk protein genes and analyzed the gene expression in different silk glands. This study expands the knowledge of silk protein sequences and gene expression, contributing to a better understanding of the biophysical properties of silks.
Article
Plant Sciences
Yiwei Zhou, Xue Wei, Farhat Abbas, Yunyi Yu, Rangcai Yu, Yanping Fan
Summary: In this study, a large number of SSR markers were identified in the genome of Hedychium coronarium 'ZS', and genetic diversity analysis and genotype identification were conducted among different species, showing clear regional distribution characteristics. These new SSR markers will provide important references for genetic diversity analysis and breeding of Hedychium.
JOURNAL OF APPLIED RESEARCH ON MEDICINAL AND AROMATIC PLANTS
(2021)
Article
Plant Sciences
P. R. Shidhi, F. Nadiya, V. C. Biju, Sheethal Vijayan, Anu Sasi, C. L. Vipin, Akhil Janardhanan, S. Aswathy, Veena S. Rajan, Achuthsankar S. Nair
Summary: The study focused on annotating and characterizing the complete chloroplast genome of Evolvulus alsinoides, identifying mutational hotspots, and conducting phylogenetic analysis. The genome comparison with Solanales species revealed unique gene composition and sequence features in E. alsinoides. The findings suggest potential molecular markers for species identification and genetic divergence studies, and highlight the conservation and evolutionary dynamics of the chloroplast genome.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2021)
Article
Plant Sciences
Weijie Chen, Jingang Huang, Shiwei Chen, Lin Zhang, Jean-David Rochaix, Lianwei Peng, Qiang Xin
Summary: This study investigates the regulatory mechanisms of chloroplast development and biogenesis, discovering the crucial roles of CDB1 and CDB1L in chloroplast development and providing evidence for the similar function of CDB1L in angiosperms.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Ante Turudic, Zlatko Liber, Martina Grdisa, Jernej Jakse, Filip Varga, Zlatko Satovic
Summary: The development of next-generation sequencing technology and the increasing amount of sequencing data have made bioinformatic tools used in genome assembly important. In the final step of genome annotation, specialized tools are used to identify organelle genes and structural features, with most tools targeting chloroplast sequences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Zhi-Luo Deng, Philipp C. Munch, Rene Mreches, Alice C. McHardy
Summary: This article introduces a novel software called RiboDetector, based on a bi-directional long short-term memory neural network, which can rapidly and accurately identify ribosomal RNA (rRNA) sequences from different types of RNA. The software produces fewer misclassifications compared to current state-of-the-art methods and has the ability to detect novel rRNA sequences. Additionally, RiboDetector has a much faster processing speed than other methods.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Peter A. Thomas, Tomasz Leski, Nicola La Porta, Monika Dering, Grzegorz Iszkulo
Summary: Crataegus laevigata is a shade-tolerant shrub or small tree native to central and northern Europe, traditionally used in herbal medicine and as food. Its fruit is primarily dispersed by birds and it easily hybridizes with other species.
JOURNAL OF ECOLOGY
(2021)
Article
Microbiology
Riccardo Rosselli, Nicola La Porta, Rosella Muresu, Piergiorgio Stevanato, Giuseppe Concheri, Andrea Squartini
Summary: Pangenome analysis reveals evolutionary instances and critical genome core conservation in Rhizobiales, with a core genome of 700 genes enriched in macromolecule metabolism and translation machinery, while membrane/periplasm-associated genes and transport domains are under-represented.
Article
Biochemical Research Methods
Stefania Di Lella, Nicola La Porta, Roberto Tognetti, Fabio Lombardi, Tiziana Nardin, Roberto Larcher
Summary: Silver fir is a valuable conifer species in Europe and is susceptible to root and butt rot caused by opportunistic pathogens. This study analyzed the changes in phenolic compounds during silver fir wood degradation by wood-decay fungi Armillaria ostoyae and Heterobasidion abietinum. The results showed a decrease in certain phenolic compounds with the accumulation of scopoletin, indicating a similar phenolic content at the end of wood degradation despite differences in fungal enzymatic pools.
PHYTOCHEMICAL ANALYSIS
(2022)
Article
Environmental Sciences
Federico Calamita, Hafiz Ali Imran, Loris Vescovo, Mohamed Lamine Mekhalfi, Nicola La Porta
Summary: This study investigates the potential of hyperspectral techniques to differentiate between fungi-infected and healthy grapevine plants, demonstrating significant differences in reflectance patterns in diseased, asymptomatic, and healthy plants. Machine learning algorithms, particularly Naive Bayes, were effective in distinguishing between different plant groups, with promising applications for non-invasive root rot disease diagnosis in woody plants. Further validation studies are needed to confirm the findings and explore the possibility of implementing hyperspectral data on UAVs for precision viticulture.
Article
Multidisciplinary Sciences
Elisabeth Poetzelsberger, Martin M. Gossner, Ludwig Beenken, Anna Gazda, Michal Petr, Tiina Ylioja, Nicola La Porta, Dimitrios N. Avtzis, Elodie Bay, Maarten De Groot, Rein Drenkhan, Mihai-Leonard Duduman, Rasmus Enderle, Margarita Georgieva, Ari M. Hietala, Bjoern Hoppe, Herve Jactel, Kristjan Jarni, Srdan Keren, Zsolt Keseru, Marcin Koprowski, Andrej Kormutak, Maria Josefa Lombardero, Aljona Lukjanova, Vitas Marozas, Edurad Mauri, Maria Cristina Monteverdi, Per Holm Nygaard, Nikica Ogris, Nicolai Olenici, Christophe Orazio, Bernhard Perny, Gloria Pinto, Michael Power, Radoslaw Puchalka, Hans Peter Ravn, Ignacio Sevillano, Sophie Stroheker, Paul Taylor, Panagiotis Tsopelas, Josef Urban, Kaljo Voolma, Marjana Westergren, Johanna Witzell, Olga Zborovska, Milica Zlatkovic
Summary: This study collected information on attacks on non-native tree species by both native and non-native species, identifying insects and fungi as the main biotic threats. The database compiled provides valuable insights for identifying attack patterns and drivers, as well as assessing health risks for tree planting. Additionally, it serves as a baseline for future impact analysis on non-native tree species.
Article
Plant Sciences
Edeline Gagnon, Rebecca Hilgenhof, Andres Orejuela, Angela McDonnell, Gaurav Sablok, Xavier Aubriot, Leandro Giacomin, Yuri Gouvea, Thamyris Bragionis, Joao Renato Stehmann, Lynn Bohs, Steven Dodsworth, Christopher Martine, Peter Poczai, Sandra Knapp, Tiina Sarkinen
Summary: Gene tree discordance in Solanum, a large flowering plant genus, suggests incomplete lineage sorting caused by rapid diversification. Embracing uncertainty is crucial for understanding the evolution of large and rapidly radiating lineages.
AMERICAN JOURNAL OF BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Florian Mattenberger, Mario A. Fares, Christina Toft, Beatriz Sabater-Munoz
Summary: The cell central metabolism in yeast has been shaped by gene duplication events over evolutionary time, allowing for adaptation to different carbon sources. Transcriptional plasticity and functional divergence of duplicated genes in response to environmental challenges remain unresolved. By challenging yeast with lactic acid as the sole carbon source, growth adaptation to acidic stress was observed mainly through the repression of whole-genome duplicates involved in glycolysis and overexpression of ROS response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biodiversity Conservation
Filip Alimpic, Jelena Milovanovic, Remigiusz Pielech, Georgi Hinkov, Roland Jansson, Simon Dufour, Marcin Beza, Nebi Bilir, Luis Santos del Blanco, Gregor Bozic, Daniel Bruno, Pier Mario Chiarabaglio, Neli Doncheva, Yasar Selman Gultekin, Mladen Ivankovic, Mary Kelly-Quinn, Nicola La Porta, Marina Nonic, Eduardo Notivol, Eva Papastergiadou, Mirjana Sijacic-Nikolic, Lorenzo Vietto, Marc Villar, Petar Zhelev, Patricia Maria Rodriguez-Gonzalez
Summary: This study investigated the opinions of experts on the current status and conservation needs of genetic diversity of riparian tree species in Europe. The experts recognized that a combination of in situ and ex situ measures is the most appropriate option for conserving the genetic diversity of riparian tree species.
JOURNAL OF APPLIED ECOLOGY
(2022)
Article
Environmental Sciences
Patricia M. Rodriguez-Gonzalez, Eleni Abraham, Francisca Aguiar, Andrea Andreoli, Ligita Balezentiene, Naim Berisha, Ivan Bernez, Michael Bruen, Daniel Bruno, Carlo Camporeale, Andraz Carni, Mila Chilikova-Lubomirova, Dov Corenblit, Renata Custerevska, Tanya Doody, Judy England, Andre Evette, Robert Francis, Virginia Garofano-Gomez, Marta Gonzalez del Tanago, Yasar Selman Gultekin, Florian Guyard, Seppo Hellsten, Georgi Hinkov, Jiri Jakubinsky, Philippe Janssen, Roland Jansson, Jochem Kail, Emine Keles, Mary Kelly-Quinn, Anna Kidova, Timea Kiss, Mart Kulvik, Nicola La Porta, Marianne Laslier, Melissa Latella, Stefan Lorenz, Dejan Mandzukovski, Paraskevi Manolaki, Vanesa Martinez-Fernandez, David Merritt, Adrien Michez, Jelena Milovanovic, Tomasz Okruszko, Eva Papastergiadou, Ellis Penning, Remigiusz Pielech, Emilio Politti, Ana Portela, Tenna Riis, Zeljko Skvorc, Michal Slezak, Barbara Stammel, John Stella, Danijela Stesevic, Vladimir Stupar, Olga Tammeorg, Priit Tammeorg, Therese Moe Fosholt, Gorazd Urbanic, Marc Villar, Ioannis Vogiatzakis, Paul Vrchovsky, Rasoul Yousefpour, Peggy Zinke, Tzvetan Zlatanov, Simon Dufour
Summary: This article identifies and discusses 10 key challenges in riparian vegetation science and management improvement, providing guidance for future research in this field.
WILEY INTERDISCIPLINARY REVIEWS-WATER
(2022)
Review
Forestry
Paolo Baldi, Nicola La Porta
Summary: This article focuses on the effects of drought stress on trees and their adaptation strategies. Different tree species have different responses to drought stress, and the types of drought stress that trees can withstand throughout their life cycle vary. Future research can increase our understanding of drought resistance by expanding the range of species and genera studied and exploring gene expression in adult plants.
Review
Biodiversity Conservation
Thomas Wohlgemuth, Martin M. Gossner, Thomas Campagnaro, Helia Marchante, Marcela van Loo, Giorgio Vacchiano, Pilar Castro-Diez, Dorota Dobrowolska, Anna Gazda, Srdjan Keren, Zsolt Keseru, Marcin Koprowski, Nicola La Porta, Vitas Marozas, Per Holm Nygaard, Vilem Podrazsky, Radoslaw Puchalka, Orna Reisman-Berman, Lina Straigyte, Tiina Ylioja, Elisabeth Potzelsberger, Joaquim S. Silva
Summary: In the context of global change, the integration of non-native tree species in European forestry is a topic of increasing discussion. However, the ecological consequences of using or spreading non-native tree species in European forests are still uncertain. This study compiles data on the impacts of seven important non-native tree species on soil properties and diversity attributes in Europe, and summarizes their commonalities and differences. The results suggest that forest managers should be cautious in using non-native tree species, as they often have negative impacts on biodiversity and soil properties.
Correction
Forestry
Valeriu-Norocel Nicolescu, William L. Mason, Jean-Charles Bastien, Torsten Vor, Krasimira Petkova, Vilem Podrazsky, Martina Dodan, Sanja Peric, Nicola La Porta, Robert Brus, Sinisa Andrasev, Martin Slavik, Juraj Modransky, Michal Pastor, Karoly Redei, Branislav Cvjetkovic, Ahmet Sivacioglu, Vasyl Lavnyy, Cornelia Buzatu-Goanta, Gheorghe Mihailescu
JOURNAL OF FORESTRY RESEARCH
(2023)
Review
Forestry
Valeriu-Norocel Nicolescu, William L. Mason, Jean-Charles Bastien, Torsten Vor, Krasimira Petkova, Vilem Podrazsky, Martina Dodan, Sanja Peric, Nicola La Porta, Robert Brus, Sinisa Andrasev, Martin Slavik, Juraj Modransky, Michal Pastor, Karoly Redei, Branislav Cvjetkovic, Ahmet Sivacioglu, Vasyl Lavnyy, Cornelia Buzatu-Goanta, Gheorghe Mihailescu
Summary: Douglas-fir, introduced to Europe in 1827, has become a major afforestation species in Western Europe and one of the most widespread non-native tree species across the continent. It is valued for its commercial importance and its lower sensitivity to drought, making it a potential alternative to other tree species. The species grows in 35 countries on over 0.83 million ha, and its importance in Europe is expected to increase in the future.
JOURNAL OF FORESTRY RESEARCH
(2023)
Article
Green & Sustainable Science & Technology
Marina Zanardo, Matteo Giannattasio, Gaurav Sablok, Massimo Pindo, Nicola La Porta, Michele Lorenzetti, Carlo Noro, Piergiorgio Stevanato, Giuseppe Concheri, Andrea Squartini
Summary: Horn manure is a biodynamic agricultural product made from cow fecal material fermented in cow horns. In this study, the changes in bacterial and fungal communities during the maturation of horn manure were analyzed. The microbial community showed a significant shift from Firmicutes to Proteobacteria and later to Actinobacteria. The most abundant fungus in the starting fecal material belonged to the Onygenales order, suggesting a link between manure and horn degradation processes.
ENVIRONMENT DEVELOPMENT AND SUSTAINABILITY
(2023)
