Review
Plant Sciences
Umer Mahmood, Xiaodong Li, Yonghai Fan, Wei Chang, Yue Niu, Jiana Li, Cunmin Qu, Kun Lu
Summary: Crop production is facing challenges from increasing food demand and climate change. Advances in omics techniques and machine learning algorithms can accelerate crop breeding to cope with these challenges. Plant breeding and genetic engineering can develop nutrient sufficient and climate-resilient crops.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Horticulture
Sandra Hilario, Micael F. M. Goncalves
Summary: The genus Diaporthe includes important plant pathogens, endophytes, and saprobes, with a wide distribution in tropical and temperate regions. The accurate detection and identification of plant pathogens using multi-omics approaches can unravel molecular mechanisms involved in infection processes and provide insight into pathogen-endophyte interactions. The published data in this literature review contribute significantly to the understanding of the importance of omics in fungal-plant interactions, paving the way for new strategies to control plant pathologies, utilize endophytes, and investigate fungal pathogenicity in the genus Diaporthe.
Review
Oncology
Zijian Zou, Wei Sun, Yu Xu, Wanlin Liu, Jingqin Zhong, Xinyi Lin, Yong Chen
Summary: Sarcomas are rare mesenchymal neoplasms with unique genetic characteristics, and their diagnosis relies heavily on pathological examination. Advanced treatments and multi-omics approaches have shown promise in improving outcomes and understanding sarcomas, but further research is needed to optimize their clinical application.
FRONTIERS IN ONCOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Alexander Arsov, Kaloyan Petrov, Penka Petrova
Summary: This article discusses the potential of microbial production of butanol as a new fuel and the challenge of butanol toxicity to microbes. Modern omics approaches have made significant progress in addressing the issue of low butanol tolerance, but a strain capable of both synthesis and tolerance at commercializable concentrations has yet to be discovered or produced.
BIOTECHNOLOGY ADVANCES
(2021)
Review
Food Science & Technology
Karolinny Cristiny de Oliveira Vieira, Hevelin Regiane Augusto da Silva, Isabela Poletto Masselli Rocha, Emmanuel Barboza, Lizziane Kretli Winkelstroter Eller
Summary: Outbreaks and deaths related to Foodborne Diseases (FBD) are constantly occurring worldwide, largely due to consumption of contaminated foodstuffs with pathogens. This review discusses the main omic techniques applied in foodborne pathogens and their potential in ensuring food safety. Omics have been shown to integrate variables that contribute to food safety and improve consumer health, costs, and product quality.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Review
Agronomy
Tiziana Maria Sirangelo, Richard Andrew Ludlow, Tatiana Chenet, Luisa Pasti, Natasha Damiana Spadafora
Summary: Biomass is a crucial source of renewable energy that reduces our reliance on fossil fuels. Understanding the biochemical and molecular processes behind biomass production is essential. This review focuses on cell wall biosynthesis and degradation mechanisms, highlighting multi-omics research and gene editing approaches as potential solutions for efficient biomass production and the development of bioproducts.
Review
Cell Biology
Jia-Chen Liu, Shan-Shan Dong, Hui Shen, Dan-Yue Yang, Bin-Bin Chen, Xue-Ying Ma, Yi-Ran Peng, Hong-Mei Xiao, Hong-Wen Deng
Summary: Sarcopenia is a systemic disease characterized by muscle dysfunction, with its genetic architecture and molecular mechanisms still largely unclear. Recent advancements in multi-omics studies offer new insights into the pathogenesis of sarcopenia and may lead to new clinical applications.
AGEING RESEARCH REVIEWS
(2022)
Review
Plant Sciences
Xiangyu Xu, Cassio Flavio Fonseca de Lima, Lam Dai Vu, Ive De Smet
Summary: Changes in weather patterns, drought risks, and rising global temperature negatively impact crop growth and productivity. Plants are exposed to multiple stresses simultaneously, but most studies focus on individual stress conditions. This mini-review focuses on the combination of drought and heat, summarizing current research results, identifying knowledge gaps, and suggesting potential future focus areas.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Pharmacology & Pharmacy
Mengyuan Kan, Blanca E. Himes
Summary: Glucocorticoid drugs are widely used in the treatment of diseases, but there is still much to learn about their cell type-specific mechanisms and why patients respond differently. Recent studies have used genomics, transcriptomics, and other omics approaches to address these questions, but there are still knowledge gaps to be filled related to glucocorticoid action mechanisms.
PHARMACOLOGY & THERAPEUTICS
(2021)
Review
Plant Sciences
Yamshi Arif, Priyanka Singh, Andrzej Bajguz, Pravej Alam, Shamsul Hayat
Summary: This review discusses the crucial role of silicon in plant development and stress responses, highlighting its interactions with plant hormones and antioxidants, as well as its application in 'omic approaches. Furthermore, it emphasizes the need for further research on the role of silicon during abiotic stress in plants for a better understanding at a broader level.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Microbiology
Dana L. Carper, Manasa R. Appidi, Sameer Mudbhari, Him K. Shrestha, Robert L. Hettich, Paul E. Abraham
Summary: Microorganisms play a crucial role in plant sustainability and productivity. Recent research on plant holobiont theory and microbial invasion ecology has revolutionized our understanding of plant-microbe interactions. Omic technologies, such as genomics, transcriptomics, proteomics, and metabolomics, have greatly advanced our knowledge in this field, although there are still limitations to overcome.
Review
Biotechnology & Applied Microbiology
Ranjna Sirohi, Jaemin Joun, Hong Ii Choi, Vivek Kumar Gaur, Sang Jun Sim
Summary: This article discusses the potential of microalgae as an energy feedstock and the efforts to increase microalgae productivity using various omics techniques, with a particular focus on the application of genome sequencing and metabolic engineering in this field.
MICROBIAL CELL FACTORIES
(2021)
Review
Fisheries
Thao V. Nguyen, Andrea C. Alfaro, Craig Mundy, Jillian Petersen, Norman L. C. Ragg
Summary: The steady increase in global abalone aquaculture production has led to growing interest in applying new technologies, such as omics approaches, for abalone research. Omics techniques like genomics, transcriptomics, proteomics, and metabolomics are revealing key molecules and pathways in biological processes and identifying potential biomarkers. Integration of multiple omics approaches shows great potential in overcoming challenges and limitations to improve abalone production.
Review
Biochemistry & Molecular Biology
Theodore Alexandrov, Julio Saez-Rodriguez, Sinem K. Saka
Summary: Spatial omics is a rapidly growing field that integrates imaging and omics to obtain spatially resolved information. It has opened up new opportunities and challenges for method developers and provides a new window into spatial biology.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Review
Microbiology
Jonathon L. Baker
Summary: Research on the oral microbiome using omics approaches is crucial for improving human health and quality of life. This review provides a comprehensive perspective on the current state-of-the-art tools available for analyzing and studying the oral microbiome.
FEMS MICROBIOLOGY REVIEWS
(2023)
Article
Plant Sciences
Qiang Guo, Jiwan Han, Cui Li, Xincun Hou, Chunqiao Zhao, Qinghai Wang, Juying Wu, Luis A. J. Mur
Summary: In this study, we investigated the mechanisms of osmotic adjustment and ROS homeostasis in Karelinia caspia under salt stress using multi-omic approaches. Our results showed that salt treatment had no physical effect on K. caspia, but led to the accumulation of primary/secondary metabolites and changes in metabolic pathways. Transcriptomic analysis identified differentially expressed genes closely related to these metabolite changes. We also observed important changes, including shifts in carbohydrate metabolism and enhanced chlorogenic acid/vitamin E biosynthesis, which contributed to maintaining osmotic balance and scavenging ROS.
PHYSIOLOGIA PLANTARUM
(2022)
Editorial Material
Plant Sciences
Aiswarya Girija, Habte Jifar, Chris Jones, Rattan Yadav, John Doonan, Luis A. J. Mur
Summary: This article introduces tef, a highly nutritious gluten-free Ethiopian cereal, and highlights the factors that affect its productivity. With the recent availability of tef genome sequences, there is a need to harness its benefits to improve food security.
TRENDS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Robert Hasterok, Pilar Catalan, Samuel P. Hazen, Anne C. Roulin, John P. Vogel, Kai Wang, Luis A. J. Mur
Summary: It has been 20 years since Brachypodium distachyon was suggested as a model grass species, and the research has now expanded to the entire genus. Extensive genome sequencing and cytomolecular studies have provided important resources for understanding population diversity and various aspects of plant biology. Brachypodium is not only relevant to the biofuel industry, but also serves as an intriguing model plant for studying climate change and combinatorial stress.
TRENDS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Li Zhang, Ruolin Wu, Luis A. J. Mur, Chenchen Guo, Xuan Zhao, Huizhen Meng, Di Yan, Xiuhong Zhang, Huirui Guan, Guodong Han, Bin Guo, Fangzheng Yue, Yahui Wei, Peng Zhao, Wei He
Summary: This study conducted whole genome sequencing of the most common locoweed in China and obtained a high-quality, chromosome-level reference genome. The toxicity of locoweed is related to the mycotoxin swainsonine produced by symbiotic endophytes. The genomes of Oxytropis ochrocephala and A. oxytropis were analyzed, and the genes involved in swainsonine biosynthesis were refined. The study also identified differentially expressed genes related to defense and secondary metabolism in the host.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Plant Sciences
Huirui Guan, Xin Liu, Yanping Fu, Xiaomin Han, Yanli Wang, Qing Li, Liang Guo, Luis A. J. Mur, Yahui Wei, Wei He
Summary: In this study, physiological and genetic analyses were conducted to show that A. oxytropis promotes growth and development in plants by regulating auxin, suggesting a possible role in benefiting its locoweed hosts independent of its toxin production.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Simon J. S. Cameron, Arwyn Edwards, Robert J. Lambert, Mike Stroud, Luis A. J. Mur
Summary: Understanding the impact of long-term physiological and environmental stress on the human microbiota and metabolome is crucial for the success of space flight. This study examines the microbiota and metabolome changes during prolonged stress through an analogy of the Transarctic Winter Traverse expedition. The results show significant alterations in bacterial load, diversity, and metabolite fingerprints in saliva, while only a single taxonomic unit in the Ruminococcaceae family is altered in stool samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Environmental Sciences
Amanda Pacholak, Joanna Zur-Pinska, Artur Pinski, Quynh Anh Nguyen, Marta Ligaj, Magdalena Luczak, Long D. Nghiem, Ewa Kaczorek
Summary: This study reports the long-term impact of two nitrofuran antibiotics on bacterial strains isolated from a wastewater treatment plant. After 12-month exposure, the bacteria showed significant changes in metabolic pathways and disrupted protein biosynthesis. The antibiotics also triggered mutagenic effects, affected metabolic activity, and facilitated oxidative stress within the cells. The results contribute to a better understanding of the potential risks and impacts of nitrofuran antibiotics in the environment.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Editorial Material
Plant Sciences
Artur Pinski, Meiliang Zhou, Alexander Betekhtin
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Prakash I. Gangashetty, Chandra Bhan Yadav, Mohammed Riyazaddin, Anilkumar Vermula, Peter Anabire Asungre, Ignatitius Angarawai, Luis A. J. Mur, Rattan S. Yadav
Summary: In this study, we identified three pearl millet hybrids (G3, G8, G13) that showed the highest stability and average performance among the five testing environments. These hybrids were selected based on their high concentration of digestible and resistant starch. The results indicate that these hybrids have great potential for cultivation in different environments.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Nutrition & Dietetics
Arwel W. Jones, Adrian Mironas, Luis A. J. Mur, Manfred Beckmann, Rhys Thatcher, Glen Davison
Summary: The study aimed to investigate the effects of vitamin D status on exercise-induced immune dysfunction. The results showed that deficiency in vitamin D led to a decrease in lymphocyte count and an increase in neutrophil:lymphocyte ratio. It also affected metabolomic profiles, including purine/pyrimidine catabolites, inflammatory markers, lactate, and tyrosine/adrenaline.
EUROPEAN JOURNAL OF NUTRITION
(2023)
Article
Plant Sciences
Messaoud B. Bensaci, Omrane Toumatia, Noureddine Bouras, Fatma Rahmania, Brian Douglas, Stephen Wade, Gareth W. Griffith, Luis A. J. Mur
Summary: This study isolated and identified Mauginiella scaettae as the causal agent of date palm inflorescence rot and confirmed it through Koch's postulates. The researchers further characterized the pathogen using molecular biology and microscopy techniques, discovering its infection process and pathways in date palm inflorescence. These findings provide new insights for the detection and management of this disease.
PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY
(2023)
Article
Plant Sciences
Bahareh Sadat Haddadi, Rui Fang, Aiswarya Girija, Divya Kattupalli, Emma Widdowson, Manfred Beckmann, Rattan Yadav, Luis A. J. Mur
Summary: Salinity-induced metabolite responses in tef seedlings showed differential accumulation of flavonoids and antioxidant metabolites in shoots and roots, which suggested an improved antioxidant capacity for salt adaptation. In this study, 19 tef varieties were screened for salt tolerance and investigated using metabolomic approaches. The results showed significant differences in germination rates and root pigmentation among the varieties under NaCl treatment. The salt-tolerant tef varieties accumulated flavonoid derivatives, sugars, and cell wall associated metabolites in their roots, demonstrating a mitigating response to salinity.
Article
Plant Sciences
Artur Pinski, Alexander Betekhtin
Summary: Fagopyrum tataricum is an exceptional crop known for its health benefits and gluten-free properties. Through optimized genetic transformation, the study demonstrates the feasibility of trait enhancement in F. tataricum.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Oncology
Vanessa G. P. Souza, Aisling Forder, Nikita Telkar, Greg L. Stewart, Robson F. Carvalho, Luis A. J. Mur, Wan L. Lam, Patricia P. Reis
Summary: This study investigates the molecular changes in brain metastases (BM) from lung adenocarcinoma (LUAD) patients using a comprehensive transcriptomic dataset. The research reveals an immunosuppressive tumor microenvironment in LUAD-BM and identifies key genes involved in the development of BM.
Meeting Abstract
Respiratory System
T. Kramaric, R. Paes de Araujo, K. Love, T. Asibey-Berko, S. Ghosh, K. E. Lewis, L. A. J. Mur