969 results match your criteria investigations metabolomic

Can omics deliver temperature resilient ready-to-grow crops?

Crit Rev Biotechnol 2021 Apr 7:1-24. Epub 2021 Apr 7.

Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.

Plants are extensively well-thought-out as the main source for nourishing natural life on earth. In the natural environment, plants have to face several stresses, mainly heat stress (HS), chilling stress (CS) and freezing stress (FS) due to adverse climate fluctuations. These stresses are considered as a major threat for sustainable agriculture by hindering plant growth and development, causing damage, ultimately leading to yield losses worldwide and counteracting to achieve the goal of "zero hunger" proposed by the Food and Agricultural Organization (FAO) of the United Nations. Read More

View Article and Full-Text PDF

iTRAQ-based proteome profiling revealed the role of Phytochrome A in regulating primary metabolism in tomato seedling.

Sci Rep 2021 Apr 6;11(1):7540. Epub 2021 Apr 6.

Proteomics Lab, Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, 400076, India.

In plants, during growth and development, photoreceptors monitor fluctuations in their environment and adjust their metabolism as a strategy of surveillance. Phytochromes (Phys) play an essential role in plant growth and development, from germination to fruit development. FR-light (FR) insensitive mutant (fri) carries a recessive mutation in Phytochrome A and is characterized by the failure to de-etiolate in continuous FR. Read More

View Article and Full-Text PDF

Physarum polycephalum macroplasmodium exhibits countermeasures against TiO nanoparticle toxicity: A physiological, biochemical, transcriptional, and metabolic perspective.

Environ Pollut 2021 Mar 12;279:116936. Epub 2021 Mar 12.

Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China. Electronic address:

Concerns about the environmental and human health implications of TiO nanoparticles (nTiO) are growing with their increased use in consumer and industrial products. Investigations of the underlying molecular mechanisms of nTiO tolerance in organisms will assist in countering nTiO toxicity. In this study, the countermeasures exhibited by the slime mold Physarum polycephalum macroplasmodium against nTiO toxicity were investigated from a physiological, transcriptional, and metabolic perspective. Read More

View Article and Full-Text PDF

Physiological and molecular attributes contribute to high night temperature tolerance in cereals.

Plant Cell Environ 2021 Mar 25. Epub 2021 Mar 25.

Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany.

Asymmetric warming resulting in a faster increase in night compared to day temperatures affects crop yields negatively. Physiological characterization and agronomic findings have been complemented more recently by molecular biology approaches including transcriptomic, proteomic, metabolomic and lipidomic investigations in crops exposed to high night temperature (HNT) conditions. Nevertheless, the understanding of the underlying mechanisms causing yield decline under HNT is still limited. Read More

View Article and Full-Text PDF

Metabolomic and kinetic investigations on the electricity-aided production of butanol by strains.

Eng Life Sci 2021 Mar 6;21(3-4):181-195. Epub 2020 Dec 6.

Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany.

In this contribution, we studied the effect of electro-fermentation on the butanol production of strains by a targeted metabolomics approach. Two strains were examined: an electrocompetent wild type strain (R525) and a mutant strain (dhaB mutant) lacking formation of 1,3-propanediol (PDO). The dhaB-negative strain was able to grow on glycerol without formation of PDO, but displayed a high initial intracellular NADH/NAD ratio which was lowered subsequently by upregulation of the butanol production pathway. Read More

View Article and Full-Text PDF

Transcriptome sequencing and metabolite analysis reveal the toxic effects of nanoplastics on tilapia after exposure to polystyrene.

Environ Pollut 2021 May 3;277:116860. Epub 2021 Mar 3.

School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen, 518055, China. Electronic address:

Plastic particles, which are formed from routinely used plastics and their fragments, have become a new pollutant raising widespread concern about their potential effects. Several studies have been conducted to examine their toxicity, but the effects of nano-sized plastic fragments on freshwater organisms remain largely unclear and need to be further investigated. In this study, larval tilapia were first exposed to 100 nm polystyrene nanoparticles (PS-NPs, 20 mg/L) for seven days and then returned to freshwater without PS-NPs for another seven days in order to determine the toxic effects of PS-NPs at both transcriptomic and metabolomic levels. Read More

View Article and Full-Text PDF

Hypoxia promotes erythroid differentiation through the development of progenitors and proerythroblasts.

Exp Hematol 2021 Mar 3. Epub 2021 Mar 3.

Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ. Electronic address:

Oxygen is a critical noncellular component of the bone marrow microenvironment that plays an important role in the development of hematopoietic cell lineages. In this study, we investigated the impact of low oxygen (hypoxia) on ex vivo myeloerythroid differentiation of human cord blood-derived CD34 hematopoietic stem and progenitor cells. We characterized the culture conditions to demonstrate that low oxygen inhibits cell proliferation and causes a metabolic shift in the stem and progenitor populations. Read More

View Article and Full-Text PDF

Oral administration of elevates systemic antiaging and anticancer metabolites.

Aging (Albany NY) 2021 Mar 2;13(5):6375-6405. Epub 2021 Mar 2.

Gustave Roussy Comprehensive Cancer Institute, Villejuif, France.

The presence of (Akk) in the human gut is associated with good health, leanness and fitness. Mouse experimentation has demonstrated positive effects for Akk, which counteracts aging, mediates antiobesity and antidiabetic effects, dampens inflammation and improves anticancer immunosurveillance. Clinical trials have confirmed antidiabetic effects for Akk. Read More

View Article and Full-Text PDF

Gas chromatography-mass spectrometry based metabolomic approach to investigate the changes in goat milk yoghurt during storage.

Food Res Int 2021 Feb 29;140:110072. Epub 2020 Dec 29.

Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA. Electronic address:

The overall goal was to utilize a gas chromatography spectrometry based metabolomics approach to investigate the metabolite changes in goat milk yoghurt during storage. A total of 129 metabolites were identified in goat milk yoghurt during 28 days refrigerated storage. Among 129, 39 metabolites were differentially regulated (p < 0. Read More

View Article and Full-Text PDF
February 2021

Succinate dehydrogenase inhibitors: in silico flux analysis and in vivo metabolomics investigations show no severe metabolic consequences for rats and humans.

Food Chem Toxicol 2021 Apr 23;150:112085. Epub 2021 Feb 23.

BASF SE, Ludwigshafen, Germany. Electronic address:

Succinate dehydrogenase complex II inhibitors (SDHIs) are widely used fungicides since the 1960s. Recently, based on published in vitro cell viability data, potential health effects via disruption of the mitochondrial respiratory chain and tricarboxylic acid cycle have been postulated in mammalian species. As primary metabolic impact of SDH inhibition, an increase in succinate, and compensatory ATP production via glycolysis resulting in excess lactate levels was hypothesized. Read More

View Article and Full-Text PDF

Magnetic resonance spectroscopy for the study of cns malignancies.

Prog Nucl Magn Reson Spectrosc 2021 Feb 2;122:23-41. Epub 2020 Dec 2.

Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institute of Health, Bethesda, United States. Electronic address:

Despite intensive research, brain tumors are amongst the malignancies with the worst prognosis; therefore, a prompt diagnosis and thoughtful assessment of the disease is required. The resistance of brain tumors to most forms of conventional therapy has led researchers to explore the underlying biology in search of new vulnerabilities and biomarkers. The unique metabolism of brain tumors represents one potential vulnerability and the basis for a system of classification. Read More

View Article and Full-Text PDF
February 2021

The synergistic anti-depression effects of different efficacy groups of Xiaoyaosan as demonstrated by the integration of network pharmacology and serum metabolomics.

J Pharm Biomed Anal 2021 Apr 4;197:113949. Epub 2021 Feb 4.

Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China; Shanxi Key Laboratory of Active Constituents Research and Utilization of TCM, Taiyuan 030006, China.

Compatibility investigations are vital but also the most difficult aspect of traditional Chinese medicine (TCM) prescriptions. Previous researches have demonstrated that Xiaoyaosan (XYS) is an effective treatment for depression. However, the compatibility rules of XYS and the underlying mechanisms remain unclear. Read More

View Article and Full-Text PDF

Ecotoxicological effects of erythromycin on a multispecies biofilm model, revealed by metagenomic and metabolomic approaches.

Environ Pollut 2021 May 11;276:116737. Epub 2021 Feb 11.

School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China; The University of Hong Kong-Shenzhen Institute of Research and Innovation (HKU-SIRI), Shenzhen, Guangdong Province, China. Electronic address:

The presence of antibiotics such as erythromycin, even in trace amounts, has long been acknowledged for negatively impacting ecosystems in freshwater environments. Although many studies have focused on the impact of antibiotic pollution at a macroecological level, the impact of erythromycin on microecosystems, such as freshwater biofilms, is still not fully understood. This knowledge gap may be attributed to the lack of robust multispecies biofilm models for fundamental investigations. Read More

View Article and Full-Text PDF

Immune checkpoint inhibitors.

J Exp Med 2021 Mar;218(3)

Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China.

Three papers by James Allison and Tasuku Honjo published in JEM between 1995 and 2000 crystallized seminal insights into the role of CTLA-4 and PD-1 in immunosuppression (Krummel and Allison. 1995. J. Read More

View Article and Full-Text PDF

Comparison of lipidome profiles of Caenorhabditis elegans-results from an inter-laboratory ring trial.

Metabolomics 2021 02 17;17(3):25. Epub 2021 Feb 17.

Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany.

Introduction: Lipidomic profiling allows 100s if not 1000s of lipids in a sample to be detected and quantified. Modern lipidomics techniques are ultra-sensitive assays that enable the discovery of novel biomarkers in a variety of fields and provide new insight in mechanistic investigations. Despite much progress in lipidomics, there remains, as for all high throughput "omics" strategies, the need to develop strategies to standardize and integrate quality control into studies in order to enhance robustness, reproducibility, and usability of studies within specific fields and beyond. Read More

View Article and Full-Text PDF
February 2021

Comprehensive two-dimensional gas chromatography as a boosting technology in food-omic investigations.

J Sep Sci 2021 Feb 14. Epub 2021 Feb 14.

Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy.

This review focuses on the role that comprehensive two-dimensional gas chromatography can play within the investigation workflows of food-omics and related disciplines and subdisciplines, including food metabolomics, nutrimetabolomics, sensomics, and food safety. After a short introductory survey, discussing the intriguing context of system biology and integrationist approaches of investigation, the concepts of analytical dimensions and the key characteristics of comprehensive two-dimensional gas chromatography are introduced. Through a selection of relevant examples, the boosting role of comprehensive two-dimensional gas chromatography within food-omics is described, providing to the reader evidence of how comprehensive multidimensional separations based platforms have introduced new concepts and tools in the analytical measurement of complex biological samples. Read More

View Article and Full-Text PDF
February 2021

The genetics of mitochondrial disease: dissecting mitochondrial pathology using multi-omic pipelines.

J Pathol 2021 Feb 14. Epub 2021 Feb 14.

Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.

Mitochondria play essential roles in numerous metabolic pathways including the synthesis of adenosine triphosphate through oxidative phosphorylation. Clinically, mitochondrial diseases occur when there is mitochondrial dysfunction - manifesting at any age and affecting any organ system; tissues with high energy requirements, such as muscle and the brain, are often affected. The clinical heterogeneity is parallel to the degree of genetic heterogeneity associated with mitochondrial dysfunction. Read More

View Article and Full-Text PDF
February 2021

A metabolic investigation of arterialized venous flaps in rabbits using mass spectrometry-based metabolomics.

Biomed Chromatogr 2021 Feb 10:e5089. Epub 2021 Feb 10.

Department of Orthopaedics (Division of Hand Surgery), The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.

An arterialized venous flap (AVF) is an ideal choice of flap to repair wounds. However, the survival of these flaps remains the source of some concern. This study used metabolomic analysis to investigate the mechanisms underlying survival in AVF flaps in order to guide the clinical application of these flaps. Read More

View Article and Full-Text PDF
February 2021

The Metabolomic Analysis of Human Milk Offers Unique Insights into Potential Child Health Benefits.

Curr Nutr Rep 2021 Mar 8;10(1):12-29. Epub 2021 Feb 8.

Department of Food Science, Aarhus University, Agro Food Park 48, DK-8200, Aarhus N, Denmark.

Purpose Of Review: Human milk is the gold standard of infant nutrition. The milk changes throughout lactation and is tailored for the infant providing the nutrients, minerals and vitamins necessary for supporting healthy infant growth. Human milk also contains low molecular weight compounds (metabolites) possibly eliciting important bioactivity. Read More

View Article and Full-Text PDF

Identification of novel 1,4-dioxane degraders and related genes from activated sludge by taxonomic and functional gene sequence analysis.

J Hazard Mater 2021 Jan 23;412:125157. Epub 2021 Jan 23.

Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, USA.

This study used integrated omics technologies to investigate the potential novel pathways and enzymes for 1,4-dioxane degradation by a consortium enriched from activated sludge of a domestic wastewater treatment plant. An unclassified genus belonging to Xanthobacteraceae increased significantly after magnetic nanoparticle-mediated isolation for 1,4-dioxane degraders. Species with relatively higher abundance (> 0. Read More

View Article and Full-Text PDF
January 2021

Cross-reactivity between cancer and microbial antigens.

Oncoimmunology 2021 Jan 20;10(1):1877416. Epub 2021 Jan 20.

Gustave Roussy Comprehensive Cancer Institute, Villejuif, France.

View Article and Full-Text PDF
January 2021

Lower Airway Dysbiosis Exacerbates Lung Cancer.

Cancer Discov 2021 Feb;11(2):224-226

Gustave Roussy Comprehensive Cancer Institute, Villejuif, France.

Accumulating evidence supports the impact of the gut microbiota on the clinical efficacy of cancer immunotherapies against extraintestinal tumors, but it has not yet been addressed whether local commensals could also dictate the prognosis of patients with cancer. In this issue of , Tsay and colleagues demonstrate that the lower airway microbiota may harbor oral commensals that turn on IL17-mediated inflammatory pathways and reprogram host transcription to exacerbate lung cancer progression.. Read More

View Article and Full-Text PDF
February 2021

Characterization of human bone marrow niches with metabolome and transcriptome profiling.

J Cell Sci 2021 Mar 11;134(6). Epub 2021 Mar 11.

Department of Pediatric Metabolism, Institute of Child Health, Hacettepe University, Sıhhıye, Ankara 06100, Turkey

Bone marrow (BM) niches are special microenvironments that work in harmony with each other for the regulation and maintenance of hematopoiesis. Niche investigations have thus far been limited to various model organisms and animal studies; therefore, little is known about different niches in healthy humans. In this study, a special harvesting method for the collection of BM from two different anatomical regions in the iliac crest of humans was used to investigate the presence of different niches in BM. Read More

View Article and Full-Text PDF

Different Blood Metabolomics Profiles in Infants Consuming a Meat- or Dairy-Based Complementary Diet.

Nutrients 2021 Jan 27;13(2). Epub 2021 Jan 27.

Section of Nutrition, Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.

Background: Research is limited in evaluating the mechanisms responsible for infant growth in response to different protein-rich foods; Methods: Targeted and untargeted metabolomics analysis were conducted on serum samples collected from an infant controlled-feeding trial that participants consumed a meat- vs. dairy-based complementary diet from 5 to 12 months of age, and followed up at 24 months.

Results: Isoleucine, valine, phenylalanine increased and threonine decreased over time among all participants; Although none of the individual essential amino acids had a significant impact on changes in growth Z scores from 5 to 12 months, principal component heavily weighted by BCAAs (leucine, isoleucine, valine) and phenylalanine had a positive association with changes in length-for-age Z score from 5 to 12 months. Read More

View Article and Full-Text PDF
January 2021

Subversion of calreticulin exposure as a strategy of immune escape.

Cancer Cell 2021 Jan 22. Epub 2021 Jan 22.

Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China; Faculty of Medicine, Université Paris Saclay, Le Kremlin-Bicêtre, France; Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; INSERM U1015, Villejuif, France; Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428 BIOTHERIS, Villejuif, France.

In this issue, Lin et al. report that, in malignant cells, stanniocalcin-1 (STC1) prevents the cell surface exposure of the "eat me" signal calreticulin, thereby avoiding phagocytosis by antigen-presenting cells. STC1 overexpression joins an arsenal of mechanisms through which tumor cells suppress calreticulin exposure and escape from immunosurveillance. Read More

View Article and Full-Text PDF
January 2021

Mycotoxins, Pesticide Residues, and Heavy Metals Analysis of Croatian Cereals.

Microorganisms 2021 Jan 21;9(2). Epub 2021 Jan 21.

Department of Food Technology, University North, Trg dr. Žarka Dolinara 1, 48000 Koprivnica, Croatia.

Cereals are still one of the most important food and feed sources, thus determining cereal's safety, i.e., compliance with legislation, is extremely important. Read More

View Article and Full-Text PDF
January 2021

Comprehensive identification of non-volatile bitter-tasting compounds in Zanthoxylum bungeanum Maxim. by untargeted metabolomics combined with sensory-guided fractionation technique.

Food Chem 2021 Jun 14;347:129085. Epub 2021 Jan 14.

College of Food Science, Southwest University, 2 Tiansheng Road, Beibei, Chongqing, 400715, PR China; Laboratory of Quality & Safety Risk Assessment for Agro-products on Storage and Preservation (Chongqing), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Chongqing, 400715, PR China; Chinese-Hungarian Cooperative Research Centre for Food Science, Chongqing, 400715, PR China. Electronic address:

Zanthoxylum Bungeanum Maxim. is an important seasoning in Chinese cooking, but its bitter taste limits its use by some consumers. In this study, metabolomic analysis based on ultra-high-performance liquid chromatograph-tandem mass spectrometry (UPLC-MS) was used to screen out a vast number of potential non-volatile bitter compounds in Z. Read More

View Article and Full-Text PDF

Bioelectrochemically enhanced degradation of bisphenol S: mechanistic insights from stable isotope-assisted investigations.

iScience 2021 Jan 30;24(1):102014. Epub 2020 Dec 30.

Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.

Electroactive microbes is the driving force for the bioelectrochemical degradation of organic pollutants, but the underlying microbial interactions between electrogenesis and pollutant degradation have not been clearly identified. Here, we combined stable isotope-assisted metabolomics (SIAM) and C-DNA stable isotope probing (DNA-SIP) to investigate bisphenol S (BPS) enhanced degradation by electroactive mixed-culture biofilms (EABs). Using SIAM, six C fully labeled transformation products were detected originating via hydrolysis, oxidation, alkylation, or aromatic ring-cleavage reactions from C-BPS, suggesting hydrolysis and oxidation as the initial and key degradation pathways for the electrochemical degradation process. Read More

View Article and Full-Text PDF
January 2021

Degradation of the polar lipid and fatty acid molecular species in extra virgin olive oil during storage based on shotgun lipidomics.

J Chromatogr A 2021 Feb 14;1639:461881. Epub 2021 Jan 14.

Department of Chemistry, Università di Roma "La Sapienza", Piazzale Aldo Moro 5, Rome 00185, Italy.

Among the bioactive compounds present in extra-virgin olive oil, polar lipids and free fatty acids are minor compounds with well-known nutritional values and have been studied for traceability and adulteration investigations as well. In the present paper, the simultaneous characterization of polar lipids and free fatty acids in a pool of fifteen EVOO samples was achieved by means of reversed phase C18 analysis coupled to negative polarity high-resolution mass spectrometry. A total of 24 polar lipids, comprising 19 phospholipids and 5 sulfolipids, and 27 free fatty acids were tentatively identified, including several odd-chain and very long-chain fatty acids at trace levels. Read More

View Article and Full-Text PDF
February 2021

The complexities of the diet-microbiome relationship: advances and perspectives.

Genome Med 2021 Jan 20;13(1):10. Epub 2021 Jan 20.

The Department of Twin Research, St Thomas' Hospital, King's College London, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK.

Personalised dietary modulation of the gut microbiota may be key to disease management. Current investigations provide a broad understanding of the impact of diet on the composition and activity of the gut microbiota, yet detailed knowledge in applying diet as an actionable tool remains limited. Further to the relative novelty of the field, approaches are yet to be standardised and extremely heterogeneous research outcomes have ensued. Read More

View Article and Full-Text PDF
January 2021