Article
Ecology
Mark A. Anthony, Thomas W. Crowther, Sietse van der Linde, Laura M. Suz, Martin Bidartondo, Filipa Cox, Marcus Schaub, Pasi Rautio, Marco Ferretti, Lars Vesterdal, Bruno De Vos, Mike Dettwiler, Nadine Eickenscheidt, Andreas Schmitz, Henning Meesenburg, Henning Andreae, Frank Jacob, Hans-Peter Dietrich, Peter Waldner, Arthur Gessler, Beat Frey, Oliver Schramm, Pim van den Bulk, Arjan Hensen, Colin Averill
Summary: This study investigates the effects of ectomycorrhizal fungi (EMF) on tree growth and finds that the composition of EMF is strongly correlated with tree growth rate. The study also suggests that the proportion of nitrogen acquisition genes and exploration types of EMF communities play a role in determining tree growth.
Article
Plant Sciences
Jiali Li, Chaofeng Li, Momi Tsuruta, Norihisa Matsushita, Susumu Goto, Zhenguo Shen, Daisuke Tsugama, Shijie Zhang, Chunlan Lian
Summary: Ectomycorrhizal fungi, including Cenococcum geophilum, play an important role in improving the salt tolerance of host plants. This study investigated the mechanisms of salt tolerance in different isolates of C. geophilum through in vitro mycelial growth experiments and analysis of ion concentrations and pH. RNA-sequencing and qRT-PCR analysis identified differentially expressed genes involved in transmembrane transport and oxidoreductase activity pathways. The study also found that salt-sensitive isolates exhibited more active accumulation and scavenging of reactive oxygen species compared to salt-tolerant isolates.
Review
Biochemistry & Molecular Biology
Muhammad Naeem, Zeeshan Ali, Anzal Khan, Sami-Ul-Allah, Hassan Javed Chaudhary, Javeria Ashraf, Faheem Shahzad Baloch
Summary: Rice, as a crucial food crop for half of the world population, has a small genome size and its whole sequenced genome has proven to be valuable for genome research. The sequenced rice genome provides insights into molecular biology, transcriptomics, and genetic variability, which are essential for improving yield, quality, and stress resistance in rice crop.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Microbiology
Yuyu Shi, Tianyi Yan, Chao Yuan, Chaofeng Li, Christopher Rensing, Yahua Chen, Rongzhang Xie, Taoxiang Zhang, Chunlan Lian
Summary: This study investigated the physiological and molecular responses of different strains of Cenococcum geophilum to cadmium exposure. It was found that cadmium inhibited the growth of all strains but had a lesser effect on tolerant strains, which may be due to lower cadmium content and higher activity of antioxidant enzymes. Transcriptomic analysis identified differentially expressed genes related to ion transport, compound metabolism, and redox pathways. These findings provide valuable insights into the cadmium tolerance mechanism of ectomycorrhizal fungi.
Review
Plant Sciences
Anamika Verma, Nowsheen Shameem, Hanuman Singh Jatav, Eetela Sathyanarayana, Javid A. Parray, Peter Poczai, R. Z. Sayyed
Summary: The concept of agricultural sustainability considers higher food production, socio-economic well-being, and environmental conservation. However, global warming-led climatic changes have negative consequences on agriculture, generating abiotic stresses for plants. By incorporating fungal endophytes, plants can endure these abnormal conditions, reinforcing stress resilience and promoting crop improvement and soil improvement, thus enabling climate-resilient aided sustainable agriculture.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Rehana Kausar, Xin Wang, Setsuko Komatsu
Summary: Food security is a major challenge in the world due to environmental stress and technological advancements impacting crop yield and quality. Proteomic analysis plays a key role in precise crop breeding and stress response mechanisms. Understanding cellular responses helps in predicting signaling pathways and protein interactions in crops.
Article
Plant Sciences
Su-Ee Lau, Teen-Lee Pua, Noor Baity Saidi, Janna Ong-Abdullah, Dhilia Udie Lamasudin, Boon Chin Tan
Summary: This study investigated the morphological and protein responses of banana plants to drought stress and post-drought recovery. The results showed that drought significantly reduced various growth parameters and induced oxidative stress in the banana plants. However, these effects were reversible after recovery from drought stress. Analysis of the proteome identified differentially abundant proteins related to various metabolic and biological processes.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Microbiology
Tianyi Yan, Panpan Zhang, Wenbo Pang, Xiaohui Zhang, Chunlan Lian, Taoxiang Zhang
Summary: The study reveals that C. geophilum exhibits different physiological and molecular responses to high temperature stress. Tolerant isolates show a more significant growth promotion effect, higher antioxidant enzyme activity, and greater succinate secretion, while sensitive isolates show higher oxalic acid secretion.
Review
Plant Sciences
Mahmoud F. Seleiman, Nasser Al-Suhaibani, Nawab Ali, Mohammad Akmal, Majed Alotaibi, Yahya Refay, Turgay Dindaroglu, Hafiz Haleem Abdul-Wajid, Martin Leonardo Battaglia
Summary: Drought stress is a significant environmental factor affecting plant growth, with plants developing complex resistance and adaptation mechanisms to improve tolerance. Plants adopt strategies such as altering stomatal conductance, enhancing photosynthetic efficiency, and adjusting root to shoot ratio dynamics to cope with water deficit.
Article
Ecology
Yexu Zheng, Chao Yuan, Norihisa Matsushita, Chunlan Lian, Qifang Geng
Summary: This study used a model to simulate the distribution pattern of C. geophilum and found that the mean temperature of the coldest quarter and annual precipitation are key environmental factors influencing its distribution. The future suitable habitat for C. geophilum is projected to shift northward with global warming.
ECOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Jacek Olchowik, Marzena Suchocka, Pawel Jankowski, Tadeusz Malewski, Dorota Hilszczanska
Summary: The linden tree is popular in central and northwest European countries, including Poland, for landscaping and urban environments. Ectomycorrhizal fungi form symbiotic relationships with urban tree species, protecting them from heavy metals and salinity. A study in Gdask, Poland found that Cenococcum geophilum was the most abundant ectomycorrhizal fungal species among urban linden trees of varying degrees of damage.
Review
Plant Sciences
Xin Wang, Setsuko Komatsu
Summary: Climate change poses a threat to soybean production through reduced seed yield and quality. This review summarizes the morphophysiological changes in soybeans under abiotic stress and discusses cellular metabolisms and regulatory mechanisms in response to organellar stress using subcellular proteomics. The communication pathways involving reactive oxygen species scavenging, molecular chaperones, and phytohormone signals among subcellular compartments are highlighted. Given the complexity of climate change and plant limitations in coping with multiple abiotic stresses, a generic response involving calcium and abscisic acid signals in subcellular organelles is proposed. This review provides an overview of subcellular proteomics research on stressed soybeans and discusses the future potential of subcellular proteomics in enhancing climate-tolerant crops.
Review
Plant Sciences
Hina Arya, Mohan B. Singh, Prem L. Bhalla
Summary: Drought poses a significant threat to soybean production, but through research on drought tolerance mechanisms and genetic engineering, drought-tolerant soybean cultivars have been developed to ensure sustainable soybean production.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agronomy
Saba Kavian, Mehdi Zarei, Ali Niazi, Reza Ghasemi-Fasaei, Amir Ghaffar Shahriari, Tibor Janda
Summary: The present experiment aimed to analyze the impact of inoculation with Bacillus paralicheniformis and Trichoderma asperellum on the growth and antioxidant response modulation of maize under drought and Cadmium stresses. The results showed that inoculation significantly increased leaf dry biomass and leaf area, and reduced the accumulation of malondialdehyde in maize leaves. Additionally, inoculation increased the activities of superoxide dismutase and peroxidase in the roots, and minimized Cd accumulation in the leaves.
Article
Plant Sciences
Olga Patricia Ponce, Yerisf Torres, Ankush Prashar, Robin Buell, Roberto Lozano, Gisella Orjeda, Lindsey Compton
Summary: Potato, a drought-sensitive crop, is facing threats to its global sustainable production due to changes in water availability. This study compared the responses of two Andigenum varieties with contrasting drought tolerance at early and late time points of drought stress exposure. The results showed widespread differences in the response of the two varieties, with the tolerant variety exhibiting faster upregulation of ABA-related genes and stronger cell wall reinforcement and remodeling in both leaves and roots. These findings provide insights into the molecular bases of drought tolerance mechanisms and have implications for improving drought resistance and yield stability in modern potato cultivars.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
M. Estela Del Castillo Busto, Susana Cuello-Nunez, Christian Ward-Deitrich, Tim Morley, Heidi Goenaga-Infante
Summary: This study introduces a novel speciation strategy for determining the main Cu-species in human serum, utilizing anion-exchange high-performance liquid chromatography coupled to inductively coupled plasma mass spectrometry (HPLC-ICP-MS) and a label-free protein quantification approach. The methodology was characterized in terms of selectivity, sensitivity, precision, and robustness, with protein recovery assessed by comparison with species-specific isotope dilution (ID).
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Ecology
Arun K. Bose, Andreas Rigling, Arthur Gessler, Frank Hagedorn, Ivano Brunner, Linda Feichtinger, Christof Bigler, Simon Egli, Sophia Etzold, Martin M. Gossner, Claudia Guidi, Mathieu Levesque, Katrin Meusburger, Martina Peter, Matthias Saurer, Daniel Scherrer, Patrick Schleppi, Leonie Schoenbeck, Michael E. Vogel, Georg Arx, Beat Wermelinger, Thomas Wohlgemuth, Roman Zweifel, Marcus Schaub
Summary: Climate change can have strong and rapid effects on ecosystems, but our understanding of how different traits and functions of individual trees and the overall ecosystem respond to these changes is still limited. By conducting an irrigation experiment in Switzerland over 15 years, we found that increased water availability had varying effects on different traits and functions. The responses of aboveground tree traits were faster and stronger compared to belowground tree traits. Overall, our results highlight the complex and dynamic nature of ecosystem responses to climate change.
ECOLOGICAL MONOGRAPHS
(2022)
Article
Forestry
Charalambos Neophytou, Katrin Heer, Pascal Milesi, Martina Peter, Tanja Pyhajarvi, Marjana Westergren, Christian Rellstab, Felix Gugerli
Summary: Rapid human-induced environmental changes like climate warming pose challenges for forest ecosystems, as their genetic adaptation may not keep up with the pace of change. Understanding adaptation to environmental change and its genetic mechanisms is crucial for sustainable forest support and management. The EvolTree conference brought together scientists to discuss the latest developments in forest evolutionary research, showcasing the application of genomics in studying demography, adaptation, and conservation in forests.
TREE GENETICS & GENOMES
(2022)
Article
Biochemical Research Methods
Firas Hamood, Florian P. Bayer, Mathias Wilhelm, Bernhard Kuster, Matthew The
Summary: Isobaric stable isotope labeling techniques like TMT have gained popularity in proteomics due to their ability to quantitate proteins accurately. However, combining multiple TMT experiments leads to an increase in missing values. To address this issue, the authors developed SIMSI-Transfer, a software tool that clusters similar MS2 spectra from multiple TMT experiments to transfer peptide identifications. Applying SIMSI-Transfer to published datasets led to a significant decrease in missing values and an increase in identified MS2 spectra with TMT quantifications.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Microbiology
Florian Staubli, Lea Imola, Benjamin Dauphin, Virginie Molinier, Stephanie Pfister, Yasmine Pinuela, Laura Schuerz, Ludger Sproll, Brian S. Steidinger, Uli Stobbe, Willy Tegel, Ulf Buentgen, Simon Egli, Martina Peter
Summary: In this study, the genetic patterns of three Burgundy truffle populations were analyzed, revealing distinct genetic structures between females and males. The genetic structures of root tips were also investigated, uncovering interesting phenomena such as the potential role of persistent mycelia as males and the growth of fruitbodies in a fairy ring formed by a large female individual.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Toxicology
John R. Foster, Kharmen Billimoria, M. Estela del Castillo Busto, Stanislav Strekopytov, Heidi Goenaga-Infante, Timothy J. Morley
Summary: This study investigated the effects of daily dosing of a molybdenum compound on rats and observed the accumulation of molybdenum in tissues. Although there was no tissue toxicity, prolonged exposure could potentially have adverse effects on cellular function, emphasizing the need for sensitive monitoring of tissue molybdenum levels to prevent toxicity.
JOURNAL OF APPLIED TOXICOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Polina Prokofeva, Stefanie Hoefer, Maximilian Hornisch, Miriam Abele, Bernhard Kuster, Guillaume Medard
Summary: Finding the targets of natural products is crucial in chemical biology and drug discovery, and understanding cofactor interactomes contributes to proteome functional annotation. In this study, a protocol for immobilizing natural products on beads was developed, and systematic affinity-based proteome profiling was performed. The study successfully identified multiple affinity targets of diverse natural products.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biodiversity Conservation
Brian S. Steidinger, Ulf Buentgen, Uli Stobbe, Willy Tegel, Ludger Sproll, Matthias Haeni, Barbara Moser, Istvan Bagi, Jose-Antonio Bonet, Marc Buee, Benjamin Dauphin, Fernando Martinez-Pena, Virginie Molinier, Roman Zweifel, Simon Egli, Martina Peter
Summary: Global warming is causing populations to exceed their physiological tolerance, leading to a decrease in fruitbody productivity of summer truffle. The study found that summer drought has a greater impact on fruitbody production of summer truffle than expected based on its species' climatic tolerance. The results suggest that there may be vulnerable populations of T. aestivum in Central Europe that are more sensitive to climate-driven declines.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Spectroscopy
Iria Rujido-Santos, M. Estela del Castillo Busto, Isabel Abad-Alvaro, Paloma Herbello-Hermelo, Pilar Bermejo-Barrera, Maria Carmen Barciela-Alonso, Heidi Goneaga-Infante, Antonio Moreda-Pineiro
Summary: Single particle inductively coupled plasma mass spectrometry (spICP-MS) is used to assess the concentration and size distribution of silver nanoparticles released from textiles. The releasing procedure using shaking and ultrapure water ensures the stability of silver nanoparticles. Filtration and centrifugation do not affect the concentration and size distribution of the silver nanoparticles. The method has low detection limits and good repeatability.
SPECTROCHIMICA ACTA PART B-ATOMIC SPECTROSCOPY
(2022)
Article
Nutrition & Dietetics
Sarah Brajkovic, Nils Rugen, Carlos Agius, Nicola Berner, Stephan Eckert, Amirhossein Sakhteman, Claus Schwechheimer, Bernhard Kuster
Summary: Plants are crucial for sustainable global food supply, but the understanding of crop proteomes is limited. The presence of secondary metabolites in crop plants has hindered proteomic analyses, requiring individually optimized protein extraction protocols. In this study, a universal protein extraction protocol combined with an automated SP3 protocol and optimized micro-LC-MS/MS conditions was developed for high-quality proteomic analysis of crop plants. The workflow was successfully applied to analyze the proteomes of mature tomato fruits, demonstrating its robustness and potential for large-scale projects mapping crop tissue proteomes.
Review
Biochemistry & Molecular Biology
Benjamin Dauphin, Martina Peter
Summary: This article discusses the potential and current limitations of landscape genomics in investigating local adaptation in natural populations of ECM fungi.
TRENDS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Liping Liu, Jakob Trendel, Guojing Jiang, Yanhui Liu, Astrid Bruckmann, Bernhard Kuester, Stefanie Sprunck, Thomas Dresselhaus, Andrea Bleckmann
Summary: RNA binding proteins play multiple and essential roles in the regulation of gene expression in all living organisms. However, little is known about their function in reproductive processes in plants. Through RNA interactome capture experiments, 728 proteins associated with poly(A(+))-RNA were identified in the egg cells of Arabidopsis. These findings provide a valuable resource to study the function of RBPs in egg cell development, fertilization, and early embryogenesis.
BIOLOGICAL CHEMISTRY
(2023)
Article
Soil Science
Claudia Guidi, Marco M. Lehmann, Katrin Meusburger, Matthias Saurer, Valentina Vitali, Martina Peter, Ivano Brunner, Frank Hagedorn
Summary: The contribution of different sources (foliage, roots, and fungi) to soil organic matter (SOM) was investigated using stable hydrogen isotope ratios (82Hn). It was found that the 82Hn values varied among these sources, with foliar litter having the lowest values (-153%o), followed by fine roots (-118%o), and fungal mycelia (-81%o). Adding 2H-depleted water allowed for tracing new organic H and assessing SOM turnover. The results showed that foliar litter dominated the organic layers and coarse particulate organic matter (POM), while roots dominated fine POM. Fungal mycelia mainly contributed to mineral associated organic matter (MOM). The long-term 2H-labelling experiment indicated a higher turnover rate of organic H in coarse soil fractions compared to fine fractions.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Mathematical & Computational Biology
Klaudia Adamowicz, Lis Arend, Andreas Maier, Johannes R. Schmidt, Bernhard Kuster, Olga Tsoy, Olga Zolotareva, Jan Baumbach, Tanja Laske
Summary: Proteomics technologies are important for biomarker identification and disease mechanism research. However, leveraging publicly available proteomics data for these purposes is challenging due to the heterogeneity of data generated by different research groups using different organisms and assay systems. To address this issue, researchers have developed ProHarMeD, a tool that harmonizes and compares proteomics data from multiple studies and extracts disease mechanisms and drug repurposing candidates.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)
Article
Chemistry, Medicinal
Thomas Hanke, Sebastian Mathea, Julia Woortman, Eidarus Salah, Benedict-Tilman Berger, Anthony Tumber, Risa Kashima, Akiko Hata, Bernhard Kuster, Susanne Mueller, Stefan Knapp
Summary: In this study, three highly selective LIMK1/2 inhibitors were characterized, providing potential candidate drugs for the treatment of diseases associated with LIMK dysregulation.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)
