Review
Biochemistry & Molecular Biology
Mughair Abdul Aziz, Miloofer Sabeem, Sangeeta Kutty Mullath, Faical Brini, Khaled Masmoudi
Summary: Plants have evolved defense mechanisms in response to environmental stresses, including overexpressing stress-responsive genes, among them genes encoding intrinsically disordered proteins (IDPs) like group II LEA proteins. These proteins play vital roles in protecting plant integrity by preventing crystallization of cellular components prior to various stresses, with studies on their distribution, structure, and genomic diversification providing insights into their role in plant stress tolerance mechanisms.
Article
Multidisciplinary Sciences
Masato Suzuki, Koki Kamiya
Summary: Lipid vesicles are used to study life's origin and artificial cell construction, but micro-sized protein vesicles are difficult to form. This study successfully generated cell-sized asymmetric phospholipid-amphiphilic protein (oleosin) vesicles that can reconstitute membrane proteins and undergo growth and fission. The vesicles consist of a lipid membrane on the outer leaflet and an oleosin membrane on the inner leaflet, and their growth and fission mechanisms were elucidated by feeding phospholipid micelles. These vesicles have the advantages of both lipid and protein layers, potentially advancing our understanding of biochemistry and synthetic biology.
Article
Plant Sciences
Kristyna Kundratova, Martin Bartas, Petr Pecinka, Ondrej Hejna, Andrea Rychla, Vladislav Curn, Jiri Cerven
Summary: This study conducted transcriptomic and proteomic analysis on the non-model plant species Papaver somniferum under drought stress, identifying key genes and proteins related to drought resistance for potential breeding of drought-resistant varieties in the future.
Article
Horticulture
Lin Ouyang, Leen Leus, Ellen De Keyser, Marie-Christine Van Labeke
Summary: Low temperatures and short photoperiods are the main environmental factors that trigger cold acclimation in roses, with different effects on different genotypes.
SCIENTIA HORTICULTURAE
(2022)
Article
Plant Sciences
Gergana Mihailova, Nikolai K. Christov, Eva Sarvari, Adam Solti, Richard Hembrom, Katalin Solymosi, Aron Keresztes, Maya Velitchkova, Antoaneta Popova, Lyudmila Simova-Stoilova, Elena Todorovska, Katya Georgieva
Summary: Haberlea rhodopensis is a unique desiccation-tolerant angiosperm that survives winter frost. This study reveals the structural alterations and organization of photosynthetic apparatus during recovery after drought- and freezing-induced desiccation, suggesting similar dynamics in remodeling and restoration. The findings also indicate the importance of certain proteins in maintaining cellular integrity and enhancing electron flow.
Article
Biochemistry & Molecular Biology
Yuan-Cheng Meng, Hua-Feng Zhang, Xiao-Xiao Pan, Nan Chen, Hui-Fang Hu, Saeed ul Haq, Abid Khan, Ru-Gang Chen
Summary: CaDHN3 plays an important role in salt and drought stress tolerance by enhancing antioxidant enzyme activities, reducing oxidative contents, and relative electrolyte leakage in plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Jorge Villegas-Camas, Karina Verdel-Aranda, Joel Lara-Reyna, Aida Martinez-Hernandez
Summary: By analyzing transcriptomic data, this study investigated the LEAPs genes in A. tequilana and identified three structurally different AteqLEAPs. Among them, AteqLEA_5Bs play a significant protective role in fully photosynthetic leaves, while AteqDHNs protect tissues in differentiation and storage organs.
BOTANICAL SCIENCES
(2022)
Article
Horticulture
Yudou Cheng, Jingang He, Yunxiao Feng, Jiangli Zhao, Junfeng Guan
Summary: This study identified and characterized specific genes PbDHNs in 'Huangguan' pear fruit and found that low temperature treatment can alleviate chilling injury. These findings are important for improving pear fruit quality and cold storage techniques.
Article
Biochemistry & Molecular Biology
Isam Fattash, Zachary Deitch, Relindis Njah, Nelson Osuagwu, Vera Mageney, Robert C. Wilson, Jahn Davik, Muath Alsheikh, Stephen Randall
Summary: Analyzing cold-responsive genes in Fragaria vesca reveals differences in transcription levels among genotypes, with FvCBF1E and FvADH showing strong cold up-regulation. These differences in gene expression may contribute to variations in cold tolerance among different strawberry cultivars.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Margaret A. Smith, Steffen P. Graether
Summary: Dehydrins are intrinsically disordered proteins with various structural motifs. They are widely present in plants and play a role in improving plant's desiccation tolerance. Dehydrins are involved in protecting membranes, proteins, and DNA from abiotic stresses, although the molecular mechanisms behind these actions are not fully understood.
Article
Allergy
Jochen Behrends, Christian Schwager, Martina Hein, Thomas Scholzen, Skadi Kull, Uta Jappe
Summary: This study successfully established a highly specific, high-throughput, and automated basophil activation test (BAT) through a novel gating strategy, optimized storage conditions, and automated measurement, demonstrating efficient detection of allergies.
Article
Plant Sciences
Pavel Vitamvas, Ilja Tom Prasil, Jan Vitamvas, Miroslav Klima
Summary: The study aimed to investigate the impact of different temperature treatments on the accumulation of cold-regulated dehydrins and dry weight content in five wheat cultivars. Results showed a correlation between lower growth temperatures, higher levels of frost tolerance, dry weight content, and dehydrin accumulation in all cultivars. Highly frost-tolerant wheat cultivars accumulated higher levels of WCS120 proteins at certain temperatures, allowing for differentiation between differently frost-tolerant cultivars.
Article
Biochemical Research Methods
F. William Townes, Barbara E. E. Engelhardt
Summary: Nonnegative matrix factorization (NMF) is a widely used method for analyzing high-dimensional count data, but it lacks the ability to incorporate known structure between observations. We present a new model called nonnegative spatial factorization (NSF) that addresses this limitation and achieves better accuracy and prediction performance than existing methods on spatial transcriptomics datasets. We also propose a hybrid extension of NSF that combines spatial and nonspatial components to quantify spatial importance. A TensorFlow implementation of NSF is available for researchers to use.
Article
Multidisciplinary Sciences
Haoyang Li, Juexiao Zhou, Zhongxiao Li, Siyuan Chen, Xingyu Liao, Bin Zhang, Ruochi Zhang, Yu Wang, Shiwei Sun, Xin Gao
Summary: Spatial transcriptomics technologies are utilized to analyze transcriptomes while preserving spatial information, providing high-resolution characterization of transcriptional patterns and tissue architecture reconstruction. Cellular heterogeneity plays a crucial role in deciphering spatial patterns of cell types, and various related methods have been proposed. In this study, we benchmarked 18 existing methods for cellular deconvolution using 50 real-world and simulated datasets, evaluating their accuracy, robustness, and usability. CARD, Cell2location, and Tangram showed the best performance for the cellular deconvolution task. Additionally, we provide decision-tree-style guidelines and recommendations for method selection and their additional features, facilitating users in choosing the optimal method for their specific needs. This comprehensive evaluation of 18 state-of-the-art methods for cellular deconvolution in spatial transcriptomics and the accompanying decision-tree-style guidelines and recommendations are valuable resources for researchers in this field.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Linhua Wang, Mirjana Maletic-Savatic, Zhandong Liu
Summary: Spatially resolved transcriptomics is a new technique for mapping transcriptional information within tissues. In this study, the authors present MIST, a computational tool that detects molecular regions and denoises missing gene expression values using region-specific imputation.
NATURE COMMUNICATIONS
(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
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
Microbiology
Ahto Agan, Halvor Solheim, Kalev Adamson, Ari Mikko Hietala, Leho Tedersoo, Rein Drenkhan
Summary: The relationship between the ecological success of needle pathogens of forest trees and species richness of co-inhabiting endophytic fungi is complex and influenced by various factors such as season, needle age, and specific fungal species composition. The abundance of the most dangerous foliar pathogen of pine, Dothistroma septosporum, is affected by overall fungal richness and specific fungal species composition in Estonia and Norway. The colonization threshold for needle shed in Pinus sylvestris may be breached earlier in Estonia than in Norway, with Lophodermium conigenum playing a significant role in affecting fungal species richness in pine needles.
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
Plant Sciences
Nina Elisabeth Nagy, Hans Ragnar Norli, Monica Fongen, Runa Berg Ostby, Inger M. Heldal, Jahn Davik, Ari M. Hietala
Summary: Lignan impregnation in wood protects against oxidative degradation by fungi, and traumatic resin canals may play important roles in the synthesis and translocation of defense compounds in response to xylem pathogens.
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)