Article
Microbiology
Sanqiang Gong, Jiayuan Liang, Xujie Jin, Lijia Xu, Meixia Zhao, Kefu Yu
Summary: This study investigated the microbiome of cold-water coral (CWC) species using metabarcoding, tissue section observation, and metatranscriptomes. The results revealed the diversity of bacteria and Symbiodiniaceae cells in CWC tissues, as well as the transcription levels of different genes. It showed that Symbiodiniaceae may have a symbiotic or parasitic relationship with CWC, and bacteria play important roles in carbon, nitrogen, and sulfur cycles in CWC.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Sanqiang Gong, Jiayuan Liang, Xujie Jin, Lijia Xu, Meixia Zhao, Kefu Yu
Summary: Recent deep-ocean exploration has revealed the presence of various cold-water coral ecosystems worldwide, but the molecular-level association between microbiomes and these corals remains unclear. This study utilized metabarcoding, tissue section observation, and metatranscriptomes to investigate the microbiome of cold-water coral species and found that these corals host diverse bacteria and symbiotic algae cells.
MICROBIOLOGY SPECTRUM
(2023)
Article
Chemistry, Multidisciplinary
Daniel Wangpraseurt, Yazhi Sun, Shangting You, Sing-Teng Chua, Samantha K. Noel, Helena F. Willard, David B. Berry, Alexander M. Clifford, Sydney Plummer, Yi Xiang, Henry H. Hwang, Jaap Kaandorp, Julia M. Diaz, Todd C. La Jeunesse, Mathieu Pernice, Silvia Vignolini, Martin Tresguerres, Shaochen Chen
Summary: This study uses 3D bioprinting technology to construct biomimetic coral microhabitats, replicating the biological processes involved in coral-algal symbiosis and providing a potential method for manufacturing synthetic designer corals.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Multidisciplinary Sciences
Jordan A. Gault, Bastian Bentlage, Danwei Huang, Alexander M. Kerr
Summary: Most lineages of reef-building corals are highly stable for their photosymbiosis trait, with almost no instances of loss, but in some clades this trait is more labile. This provides a framework for further studies on the factors shaping the evolutionary fate of photosymbiosis in reef-building corals.
Article
Microbiology
Minjie Hu, Yun Bai, Xiaobin Zheng, Yixian Zheng
Summary: In this study, the mechanism of endosymbiosis between coral and dinoflagellates was characterized using RNAi and single-cell RNA-seq. The researchers identified a host endosymbiotic cell marker called LePin, which binds to algae to initiate phagocytosis and modulate coral immune response. The evolutionary conservation of LePin among marine anthozoans suggests its general role in coral-algal recognition.
NATURE MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Evelyn Abbott, Groves Dixon, Mikhail Matz
Summary: The study found that changes in the abundance of different symbiont genera within coral hosts can affect the gene expression of symbionts, particularly impacting expression of photosynthesis components and proteins related to cell movement. When both genera are represented in comparable proportions within the host, the mixed symbiosis state may lead to more intense competition but does not result in increased stress for the host. After heat treatment, corals with mixed symbiosis showed the lowest stress signatures compared to corals dominated by either Cladocopium or Durusdinium.
Review
Microbiology
Amin R. Mohamed, Michael A. Ochsenkuehn, Ahmed M. Kazlak, Ahmed Moustafa, Shady A. Amin
Summary: Understanding the complex interactions between corals and their associated microbiome is essential for coral resilience in a warming ocean. Recent research focuses on manipulating the coral microbiome to enhance their ability to withstand stress. The potential mechanisms through which microbiota communicate with and modify host responses, as well as the power of omics tools in studying corals, are highlighted.
FEMS MICROBIOLOGY REVIEWS
(2023)
Article
Environmental Sciences
Elizabeth Ann Lenz, Lucy A. Bartlett, Anastasios Stathakopoulos, Ilsa B. Kuffner
Summary: This study evaluated the physiological characteristics of Porites astreoides corals at different geographic locations and seasons in the Florida Keys reef tract, finding significant differences in bleaching severity among sites and highlighting the better adaptation of colonies at the Dry Tortugas site to high temperature events. The results contribute to the selection of candidate sites for adaptive coral management strategies.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Multidisciplinary Sciences
Christopher P. Jury, Brian M. Boeing, Henry Trapido-Rosenthal, Ruth D. Gates, Robert J. Toonen
Summary: This study reveals that increased production of nitric oxide by algal symbionts is a more important driver of coral bleaching under acute thermal stress, compared to symbiont dysfunction.
Article
Biodiversity Conservation
Shuwen Jia, Zhongjie Wu, Yuanchao Li, Yi Wang, Zefu Cai, Jie Shen, Daoru Wang, Shiquan Chen
Summary: Coral reefs in the South China Sea have been severely degraded by global climate change, human activities, and environmental pollution. Platygyra daedalea, a stress-resistant coral species, is widely distributed and dominant in certain regions. This study shows that environmental factors strongly influence the genetic diversity of P. daedalea and the composition of Symbiodiniaceae types.
ECOLOGICAL INDICATORS
(2023)
Article
Biology
Yunqing Liu, Xin Liao, Tingyu Han, Ao Su, Zhuojun Guo, Na Lu, Chunpeng He, Zuhong Lu
Summary: This study obtained relatively complete transcriptome data of Montipora foliosa through PacBio Sequel II sequencing technology, providing valuable resources for the study of coral symbiosis. Analysis of symbiosis-related genes' function and isoforms was conducted, shedding light on the mechanisms behind coral-zooxanthellae symbiosis.
Article
Environmental Sciences
Jessica L. Bergman, Tayla Shaw, Suhelen Egan, Tracy D. Ainsworth
Summary: With advancements in sequencing techniques, there has been a rapid increase in studies on the microbiome in coral health and response to environmental change. However, methodological variations in DNA extraction protocols and tissue sampling can impact downstream analyses of microbial communities. Different studies have focused on whole organisms or specific microhabitats within coral, leading to variations in microbial data generated.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Tuo Shi, Gaofeng Niu, Hagit Kvitt, Xinqing Zheng, Qiaoyun Qin, Danye Sun, Zhiliang Ji, Dan Tchernov
Summary: Symbiodiniaceae, a type of typical endosymbionts, play a crucial role in mediating coral responses to environmental changes as photosynthetic dinoflagellates. Analysis of the ITS2 sequences can determine the diversity of Symbiodiniaceae, but caution is needed to avoid confusion with adjacent rRNA sequences. A database has been established containing a large number of definitive genotype and secondary structure Symbiodiniaceae ITS2 sequences, providing an important reference for further research.
MOLECULAR ECOLOGY RESOURCES
(2021)
Editorial Material
Oncology
Zsolt Megyesfalvi, Simon Heeke, Benjamin J. Drapkin, Anna Solta, Ildiko Kovacs, Kristiina Boettiger, Lilla Horvath, Busra Ernhofer, Janos Fillinger, Ferenc Renyi-Vamos, Clemens Aigner, Karin Schelch, Christian Lang, Gyorgy Marko-Varga, Carl M. Gay, Lauren A. Byers, Benjamin B. Morris, John Heymach, Peter Van Loo, Fred R. Hirsch, Balazs Dome
Summary: The integration of rapid autopsies and preclinical models into SCLC research is advocated as a comprehensive strategy with the potential to revolutionize current treatment paradigms.
Review
Environmental Sciences
Gabriel Ferreira, Elena Bollati, Michael Kuhl
Summary: Corals are capable of synthesizing various pigments that give them their characteristic colors. These pigments, mostly green fluorescent protein-like pigments, cover almost the entire visible spectrum and can fluoresce from cyan to red. The role of these host pigments in coral biology is not fully understood, but they have the ability to modify the light exposure of photosymbionts, potentially helping the holobiont adapt to different environmental conditions. Mechanisms such as energy transfer between pigments and tissue plasticity may play a role in photoprotection or photoenhancement. This review discusses the current knowledge and challenges in investigating the link between host pigments and symbiont photosynthesis in reef-building corals.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Marine & Freshwater Biology
Kristen T. Brown, Gal Eyal, Sophie G. Dove, Katie L. Barott
Summary: Increasing ocean temperatures pose a threat to coral reefs worldwide, and corals in habitats with high thermal variability are believed to be more resilient to climate-induced heat stress. This study used long-term ecological observations and temperature data to examine how temperature dynamics in different reef habitats changed during a marine heatwave and its impact on coral community survival. The findings showed that thermally variable habitats experienced greater heat stress and subsequent declines in hard coral cover compared to stable sites. Interestingly, habitats with greater seawater exchange with the open ocean provided the most protection to corals during severe marine heatwaves.
Article
Limnology
Tania M. M. Kenyon, Christopher Doropoulos, Kennedy Wolfe, Gregory E. E. Webb, Sophie Dove, Daniel Harris, Peter J. J. Mumby
Summary: This article reviews the dynamics of rubble beds on coral reefs, with a focus on the changes expected in the generation, mobilization, binding, and coral recruitment of rubble on future reefs. It predicts that major disturbances, such as storms and coral bleaching, will increase in intensity and frequency, leading to larger quantities of coral rubble. With smaller recovery windows and increased bioerosion, smaller and less complex rubble pieces will be generated more often. The time available for binding will be reduced, and changing ocean chemistry may affect the efficacy of binders. Ultimately, increased rubble cover will negatively impact coral recruitment into rubble beds.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Article
Plant Sciences
Mark C. C. Derbyshire, Jacob Marsh, Soodeh Tirnaz, Henry T. T. Nguyen, Jacqueline Batley, Philipp E. E. Bayer, David Edwards
Summary: This study analyzes the soybean pangenome to identify fatty acid biosynthesis genes and their sequence diversity. It finds possible instances of gene missing in wild soybean and identifies missense variants in fatty acid biosynthesis genes. The frequency of these variants has been significantly reduced during domestication.
Article
Environmental Sciences
Monica F. Danilevicz, Roberto Lujan Rocha, Jacqueline Batley, Philipp E. Bayer, Mohammed Bennamoun, David Edwards, Michael B. Ashworth
Summary: Narrow-leafed lupin is an important dryland crop, but it is challenging to control the closely related sandplain lupin, which reduces yield and quality. A segmentation model was trained using deep learning to detect sandplain lupins and differentiate them from narrow-leafed lupins under field conditions.
Article
Plant Sciences
Aldrin Y. Cantila, William J. W. Thomas, Nur Shuhadah Mohd Saad, Anita A. Severn-Ellis, Robyn Anderson, Philipp E. Bayer, David Edwards, Angela P. van de Wouw, Jacqueline Batley
Summary: Utilising resistance genes, such as LepR1, could help manage blackleg disease in canola and increase crop yield. A genome wide association study in canola revealed significant SNPs associated with LepR1 resistance, with the majority located on chromosome A02 and containing multiple resistance gene analogs. This research provides insights into blackleg resistance in canola and aids in the identification of functional LepR1 candidate genes.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Andrew Chen, Jiaman Sun, Guillaume Martin, Lesley-Ann Gray, Eva Hribova, Pavla Christelova, Nabila Yahiaoui, Steve Rounsley, Rebecca Lyons, Jacqueline Batley, Ning Chen, Sharon Hamill, Subash K. Rai, Lachlan Coin, Brigitte Uwimana, Angelique D'Hont, Jaroslav Dolezel, David Edwards, Rony Swennen, Elizabeth A. B. Aitken
Summary: In this study, the resistance to Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4) in Musa acuminata ssp. malaccensis was characterized. QTL-seq analysis of an F2 population segregating for resistance revealed a major QTL on the long arm of chromosome 3. This research provides a foundation for marker assisted selection in breeding programs and identification of resistance genes.
Article
Microbiology
Andrew Chen, Jiaman Sun, Altus Viljoen, Diane Mostert, Yucong Xie, Leroy Mangila, Sheryl Bothma, Rebecca Lyons, Eva Hribova, Pavla Christelova, Brigitte Uwimana, Delphine Amah, Stephen Pearce, Ning Chen, Jacqueline Batley, David Edwards, Jaroslav Dolezel, Peter Crisp, Allan F. Brown, Guillaume Martin, Nabila Yahiaoui, Angelique D'Hont, Lachlan Coin, Rony Swennen, Elizabeth A. B. Aitken
Summary: Fusarium wilt of banana is a destructive disease that has caused significant damage to banana production worldwide. In this study, the genetic basis of host resistance to the causal agent Fusarium oxysporum f. sp. Cubense (Foc) is dissected using two segregating populations. Marker loci and trait association analysis revealed a specific genetic interval associated with resistance on chromosome 3. The expression of pattern recognition receptors was found to be rapidly upregulated in resistant progenies, suggesting their involvement in resistance. The developed markers can aid breeding programs in selecting for resistance to Foc.
Article
Plant Sciences
Muhammad Burhan Bootter, Jing Li, Wenxu Zhou, David Edwards, Jacqueline Batley
Summary: Phytosterols, natural compounds found in higher plants, play various roles in plant growth regulation and stress tolerance. They also influence the development and reproductive rate of herbivorous insects and agronomic traits in plants. This study analysed the phytosterol composition in Brassica napus cultivars and related wild species, revealing significant variability in the wild accessions' phytosterol profiles. Some wild accessions exhibited high levels of specific phytosterols, which could contribute to plant stress tolerance and insect resistance in crop breeding.
Review
Food Science & Technology
Ting Xiang Neik, Kadambot H. M. Siddique, Sean Mayes, David Edwards, Jacqueline Batley, Tafadzwanashe Mabhaudhi, Beng Kah Song, Festo Massawe
Summary: The recent Russia-Ukraine conflict has caused significant concerns about global food security, particularly for low-income countries reliant on grain imports. The conflict has led to restricted access to staple food crops and soaring food prices, impacting the livelihoods of many. This review emphasizes the importance of diversifying agrifood systems to enhance resilience in future food supply chains.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2023)
Article
Limnology
Robert A. B. Mason, William J. Skirving, Sophie G. Dove
Summary: Photoacclimation is a crucial process that allows photosymbiotic reef corals to thrive in varying light conditions. However, the timing of photoacclimation has not been well characterized. In this study, we investigated the time dynamics of photoacclimation in two coral taxa and found that the light environment within the coral tissue plays a role in the temporal response of photoacclimation.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Article
Agronomy
Aldrin Y. Cantila, William J. W. Thomas, Philipp E. Bayer, David Edwards, Jacqueline Batley
Summary: This study predicts and identifies the number and function of TM-CC genes in Brassicaceae plants, and suggests that they may play a significant role in disease resistance. It provides a valuable resource for the study of TM-CCs and their potential functional involvement in resistance.
Article
Plant Sciences
Cassandria G. Tay G. Fernandez, Philipp E. Bayer, Jakob Petereit, Rajeev Varshney, Jacqueline Batley, David Edwards
Summary: Many genome annotations contain false-positive gene models, which can lead to errors in phylogenetic and comparative studies. In this study, a method based on evolutionary conservation is proposed to predict gene models and identify potentially erroneous annotations. A set of 15,345 representative gene models from 12 legume assemblies is developed using this method, which can support genome annotations for other legumes.
Article
Remote Sensing
Wijayanti Nurul Khotimah, Mohammed Bennamoun, Farid Boussaid, Lian Xu, David Edwards, Ferdous Sohel
Summary: Transformers have been successful in computer vision tasks due to their ability to capture long-range feature dependencies. However, for hyperspectral data classification, capturing both short and long-range band dependencies is important. To address this, a convolution-transformer (conformer) based framework called MCE-ST is proposed. MCE-ST combines the strengths of transformers and CNNs by using a convolution-based tokenization method and a multiscale conformer encoder.
INTERNATIONAL JOURNAL OF APPLIED EARTH OBSERVATION AND GEOINFORMATION
(2023)
Article
Biotechnology & Applied Microbiology
Jian Wang, Wu Yang, Shaohong Zhang, Haifei Hu, Yuxuan Yuan, Jingfang Dong, Luo Chen, Yamei Ma, Tifeng Yang, Lian Zhou, Jiansong Chen, Bin Liu, Chengdao Li, David Edwards, Junliang Zhao
Summary: The researchers developed a novel strategy and analysis pipeline for constructing a plant pangenome and identifying the position information of genetic variants. They successfully constructed a high-quality rice pangenome and identified causal structural variations related to rice grain weight and plant height. This study provides valuable genomic resources for rice genomics research and improvement.
Review
Biotechnology & Applied Microbiology
Haifei Hu, Armin Scheben, Jian Wang, Fangping Li, Chengdao Li, David Edwards, Junliang Zhao
Summary: Inversions significantly impact plant adaptation and gene functions. This review highlights advancements in technology and methodology that allow a better understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants.
PLANT BIOTECHNOLOGY JOURNAL
(2023)