Review
Spectroscopy
Giuseppe Paglia, Andrew J. Smith, Giuseppe Astarita
Summary: Researchers are utilizing ion mobility mass spectrometry (IM-MS) for metabolomics and lipidomics applications, which offers advantages such as measuring collision cross-section values, improving peak capacity and signal-to-noise ratio, and coupling with various fragmentation modes. These advancements provide a more robust tool for identification, quantification, and structural characterization in the field.
MASS SPECTROMETRY REVIEWS
(2022)
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
Food Science & Technology
Anastasios Tsoungos, Violeta Pemaj, Aleksandra Slavko, John Kapolos, Marina Papadelli, Konstantinos Papadimitriou
Summary: This review explores recent advances in table olive research through omics and meta-omics approaches, offering insights into the genomic, metagenomic, and metabolomic analysis of the microbial community in table olives. These methods hold the promise of groundbreaking advances in table olive processing technology.
Review
Plant Sciences
Deepmala Sehgal, Priyanka Dhakate, Heena Ambreen, Khasim Hussain Baji Shaik, Nagenahalli Dharmegowda Rathan, Nayanahalli Munireddy Anusha, Rupesh Deshmukh, Prashant Vikram
Summary: Plant omics has played a crucial role in discovering new genes and biomolecules that can improve crops, and has made significant progress in wheat research on both qualitative and quantitative traits. Combining various omics approaches has led to advances in gene discovery, pathway investigation, and understanding stress responses and yields. The development of a Wheat Omics database further aids functional genomics studies in wheat.
Article
Chemistry, Medicinal
Carlos Sanchez-Arcos, Debora Paris, Valerio Mazzella, Mirko Mutalipassi, Maria Costantini, Maria Cristina Buia, Eric von Elert, Adele Cutignano, Valerio Zupo
Summary: This study investigated the metabolic profiles of the macroalga Ulva prolifera under acidified and normal conditions using a multi-omics approach. The results showed that U. prolifera grows faster in acidified environments, with metabolic pathways being modulated and lipid biosynthesis being remodeled. These findings have implications for both the marine ecosystem and potential nutraceutical applications.
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
Chemistry, Analytical
Zengyu Wang, Baohong Liu, Ling Lin, Liang Qiao
Summary: Mitochondria are highly dynamic organelles involved in various cellular processes. Dysfunction of mitochondria is associated with multiple disorders, including neurodegenerative diseases, cardiovascular pathology, aging, and cancer. Significant advancements have been made in mitochondrial biology through the combination of high-throughput omics technologies and biochemical separation techniques. This review focuses on mass spectrometry-based mitochondrial proteomics, metabolomics, and multi-omics integration, as well as the development of machine learning tools for comprehensive and unprecedented insight into mitochondrial uncharted territory.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Kholoud Y. Abushawish, Sameh S. M. Soliman, Alexander D. Giddey, Hamza M. Al-Hroub, Muath Mousa, Karem H. Alzoubi, Waseem El-Huneidi, Eman Abu-Gharbieh, Sara M. Elgendy, Yasser Bustanji, Nelson C. Soares, Mohammad H. Semreen
Summary: This study investigated the proteomic and metabolomics alterations associated with sorafenib resistance in hepatocellular carcinoma cells. The findings identified potential biomarkers for sorafenib-resistant HCC and provided insights into their role in chemotherapeutic drug resistance, cancer progression, and aggressiveness.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Plant Sciences
Federico Scossa, Saleh Alseekh, Alisdair R. Fernie
Summary: Our agricultural systems are facing the urgent challenge of feeding a growing global population, requiring a better understanding of plant genetic and phenotypic diversity. Recent advances in plant genomics, combined with molecular profiling approaches such as genomics, transcriptomics, and metabolomics, offer insights into the complex architecture of agricultural traits and guide crop breeding strategies.
JOURNAL OF PLANT PHYSIOLOGY
(2021)
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
Biochemistry & Molecular Biology
Qiaolifan Aerqin, Zuo-Teng Wang, Kai-Min Wu, Xiao-Yu He, Qiang Dong, Jin-Tai Yu
Summary: This review summarizes the progress made in the discovery of reliable Alzheimer's disease (AD) biomarkers using genomics, transcriptomics, proteomics, and metabolomics. The importance of these biomarkers in the diagnosis and treatment of AD is discussed.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Oncology
Nasrin Gholami, Amin Haghparast, Iraj Alipourfard, Majid Nazari
Summary: Recent advances in omics technology have revolutionized the study of molecular changes underlying complex human diseases like cancer. The integration of multi-omic data has enabled integrated systems-level approaches, transforming medicine and biology. Multivariate signatures play a crucial role in cancer detection, screening, patient classification, treatment response assessment, and biomarker identification.
CANCER CELL INTERNATIONAL
(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
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
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)
Article
Energy & Fuels
Maria Hasnain, Zainul Abideen, Shagufta Naz, Ute Roessner, Neelma Munir
Summary: The study investigates the use of microwave irradiation for simultaneous in situ transesterification and extraction of algae lipids to enhance biodiesel production. Results show that microwave technique significantly improves biodiesel yield, with potential optimization in catalyst concentration and reaction time. The study highlights Ulothrix sp. as the most efficient feedstock for biodiesel production.
BIOMASS CONVERSION AND BIOREFINERY
(2023)
Article
Biochemistry & Molecular Biology
Gemma L. Sadler, Katherine N. Lewis, Vinod K. Narayana, David P. De Souza, Joel Mason, Catriona McLean, David G. Gonsalvez, Bradley J. Turner, Samantha K. Barton
Summary: This study found dysregulated lipid levels and corresponding enzyme expression in the white matter of ALS patients, likely leading to changes in myelin composition and affecting motor neuron function. This highlights the potential critical role of oligodendrocytes in the pathogenesis of ALS.
Article
Biotechnology & Applied Microbiology
Wenying Zhang, Cong Tan, Haifei Hu, Rui Pan, Yuhui Xiao, Kai Ouyang, Gaofeng Zhou, Yong Jia, Xiao-Qi Zhang, Camilla Beate Hill, Penghao Wang, Brett Chapman, Yong Han, Le Xu, Yanhao Xu, Tefera Angessa, Hao Luo, Sharon Westcott, Darshan Sharma, Eviatar Nevo, Roberto A. Barrero, Matthew Bellgard, Tianhua He, Xiaohai Tian, Chengdao Li
Summary: Divergent selection in different environments leads to functional genomic divergence. This study examined the genomic differentiation and gene expression patterns in two populations of wild barley under abiotic stress. The researchers identified structural variants and single nucleotide polymorphisms (SNPs) that may be associated with well-differentiated phenotypes and local adaptation. The findings provide new insights into the genomic basis of local adaptation and have implications for the genetic improvement of cultivated barley.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Janice W. -Y. Mui, David P. De Souza, Eleanor C. Saunders, Malcolm J. McConville, Spencer J. Williams
Summary: The microbial degradation of sulfoquinovose through sulfoglycolysis allows the utilization of its carbon content and contributes to the biomineralization of its sulfur.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Oncology
Gio Fidelito, David P. De Souza, Birunthi Niranjan, William De Nardo, Shivakumar Keerthikumar, Kristin Brown, Renea A. Taylor, Matthew J. Watt
Summary: Cancer cells undergo metabolic reprogramming to meet increased bioenergetic demands. Glucose, glutamine, and fatty acid oxidation were upregulated in malignant PDXs compared with benign PDXs. Fatty acid uptake and oxidation are targetable metabolic dependencies in human prostate cancer.
MOLECULAR CANCER RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ziheng Zhou, Cong Tan, Matthew Hoi Kin Chau, Xiaosen Jiang, Ziyuan Ke, Xiaoyan Chen, Ye Cao, Yvonne K. Kwok, Matthew Bellgard, Tak Yeung Leung, Kwong Wai Choy, Zirui Dong
Summary: In this study, we curated and analyzed sequencing data from multiple developmental periods of humans and various model organisms, providing insights into gene expression, chromatin accessibility, and gene-gene regulation interactions. The findings contribute to our understanding of the roles of genes in tissue/organ development and disease mechanisms.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Orthopedics
X. Wu, C. Liyanage, M. Plan, T. Stark, T. McCubbin, R. A. Barrero, J. Batra, R. Crawford, Y. Xiao, I. Prasadam
Summary: This study aims to identify the changes in energy metabolism in osteoarthritis (OA) cartilage. Metabolomics, proteomics, and transcriptomics analyses were conducted to investigate the global alterations in OA metabolism. The results showed increased lactate production and decreased mitochondrial respiratory rates in OA chondrocytes. This study provides a basis for targeting metabolism as a therapeutic approach for OA.
OSTEOARTHRITIS AND CARTILAGE
(2023)
Article
Biochemical Research Methods
Selvam Paramasivan, Janna L. Morrison, Mitchell C. Lock, Jack R. T. Darby, Roberto A. Barrero, Paul C. Mills, Pawel Sadowski
Summary: Sequential window acquisition of all theoretical mass spectra-mass spectrometry, supported by advanced bioinformatics, provides a comprehensive framework for proteome analysis and biomarker discovery. However, the lack of a generic sample preparation platform for heterogeneous materials from different sources limits its broad application. We developed universal and fully automated workflows using a robotic sample preparation platform, enabling in-depth and reproducible proteome coverage of bovine and ovine specimens. The high correlation between sheep proteomics and transcriptomics datasets validates this development and suggests the potential for various clinical applications across different animal species and disease models.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Stefan Sanow, Weiqi Kuang, Gabriel Schaaf, Pitter Huesgen, Ulrich Schurr, Ute Roessner, Michelle Watt, Borjana Arsova
Summary: This review summarizes the molecular mechanisms behind Pseudomonas-driven plant growth promotion, focusing on improving plant performance and nitrogen content under limited nitrogen conditions. However, there are still many aspects of the Pseudomonas-plant interaction mechanisms that need further exploration.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2023)
Article
Oncology
Chameera Ekanayake Weeramange, Kai Dun Tang, Roberto A. Barrero, Gunter Hartel, Zhen Liu, Rahul Ladwa, Julian Langton-Lockton, Ian Frazer, Lizbeth Kenny, Sarju Vasani, Chamindie Punyadeera
Summary: This study found that salivary microRNAs could be used for early detection and prognosis of oropharyngeal cancer, specifically the HPV-associated fraction. A panel of nine microRNAs was identified to effectively distinguish HPV-positive oropharyngeal cancer from HPV-positive controls, and a panel of six microRNAs was identified to distinguish oropharyngeal cancer from controls regardless of HPV status. Additionally, downregulation of hsa-miR-7-5p was associated with poor overall survival of oropharyngeal cancer patients, and a panel of nine microRNAs was identified to predict overall survival.
Review
Agronomy
Sneha Gupta, Sibel Yildirim, Benjamin Andrikopoulos, Uta Wille, Ute Roessner
Summary: Optimizing nitrogen availability to plants is crucial for maximizing crop yield and quality. However, ensuring the appropriate supply of nitrogen to crops is challenging due to various pathways of nitrogen loss. The use of urease and nitrification inhibitors has emerged as a strategy to synchronize nitrogen availability with plant uptake and mitigate nitrogen loss.
Article
Agriculture, Multidisciplinary
Sibel C. Yildirim, Robert M. Walker, Ute Roessner, Uta Wille
Summary: This article presents a simple and cost-efficient colorimetric assay developed for the rapid evaluation of the efficiency of new synthetic nitrification inhibitors (NIs) to identify the most promising compounds for subsequent soil studies. The assay allows for simultaneous screening of multiple compounds' inhibitory activity with high reproducibility and can be manipulated to determine pH and temperature-dependent effects on NIs.
ACS AGRICULTURAL SCIENCE & TECHNOLOGY
(2023)
Letter
Plant Sciences
Michael Ogden, Sarah J. Whitcomb, Ghazanfar Abbas Khan, Ute Roessner, Rainer Hoefgen, Staffan Persson
Article
Agriculture, Multidisciplinary
Sibel C. Yildirim, Robert M. Walker, Ute Roessner, Uta Wille
Summary: Nitrification inhibitors, such as DMP and DCD, have been used in agriculture since the 1970s to modulate the conversion of nitrogen in soils. This study reveals for the first time the mechanism of inhibition, efficacy, and acute toxicity of DMP and DCD on Nitrosomonas europaea. The results show that both inhibitors target the enzyme AMO and act as uncompetitive inhibitors. DMP exhibits higher inhibitory efficiency and lower toxicity compared to DCD.
ACS AGRICULTURAL SCIENCE & TECHNOLOGY
(2023)
