Plant Metabolomics Reviews

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Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris.

August 11, 2017 - 10:29am
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Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris.

Microbiology. 2017 Aug 10;:

Authors: Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ

Abstract
Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features. Traditional analyses of Xanthomonas metabolism missed the Embden-Meyerhof-Parnas pathway (glycolysis) as being a route by which energy and molecular building blocks are derived from glucose. As a consequence of the emerging full picture of their metabolism process, xanthomonads were discovered to have three alternative catabolic pathways and they use an unusual and reversible phosphofructokinase as a key enzyme. In this review, we summarize the synthetic and systems biology methods and the bioinformatics tools applied to reconstruct their metabolic network and reveal the dynamic fluxes within their complex carbohydrate metabolism. This is based on insights from omics disciplines; in particular, genomics, transcriptomics, proteomics and metabolomics. Analysis of high-throughput omics data facilitates the reconstruction of organism-specific large- and genome-scale metabolic networks. Reconstructed metabolic networks are fundamental to the formulation of metabolic models that facilitate the simulation of actual metabolic activities under specific environmental conditions.

PMID: 28795660 [PubMed - as supplied by publisher]

Uptake and transformations of engineered nanomaterials: Critical responses observed in terrestrial plants and the model plant Arabidopsis thaliana.

August 11, 2017 - 10:29am
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Uptake and transformations of engineered nanomaterials: Critical responses observed in terrestrial plants and the model plant Arabidopsis thaliana.

Sci Total Environ. 2017 Aug 05;607-608:1497-1516

Authors: Montes A, Bisson MA, Gardella JA, Aga DS

Abstract
With the applications of engineered nanomaterials (ENMs) continually expanding and production quickly growing, residues of ENMs will end up in the environment at levels that may be harmful to non-target organisms. Many of the tunable properties that have made them desirable, such as type, size, charge, or coating, also contribute to the current difficulties in understanding the fate of ENMs in the environment. This review article focuses on studies that investigate plant-ENM interactions, including techniques used to study these interactions and documented plant responses due to the phytotoxic effects of ENMs. The many variables which can be altered for an experiment, such as type, size, and concentration of ENMs, make it difficult to formulate generalizations about the uptake mechanism involved, or to make an inference on the subcellular localization and distribution of the internalized ENMs in plant tissue. In order to avoid these challenges, studies can utilize a model organism such as Arabidopsis thaliana, and a combination of analytical techniques that can reveal complementary information in order to assess how the different experimental conditions influence the uptake and phytotoxicity of ENMs. This review presents recent studies regarding plant-ENM interactions employing Arabidopsis to demonstrate how the use of this model plant can advance our understanding of plant-ENM interactions and guide additional studies using other plant species. Overarching results suggest that more sensitive tests and consistency in experimental designs are needed to fully assess and understand the phytotoxic effects of ENMs in the environment.

PMID: 28793406 [PubMed - as supplied by publisher]

Hyphenated MS-based targeted approaches in metabolomics.

August 10, 2017 - 7:26am
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Hyphenated MS-based targeted approaches in metabolomics.

Analyst. 2017 Aug 09;:

Authors: Begou O, Gika HG, Wilson ID, Theodoridis G

Abstract
While global metabolic profiling (untargeted metabolomics) has been the center of much interest and research activity in the past few decades, more recently targeted metabolomics approaches have begun to gain ground. These analyses are, to an extent, more hypothesis-driven, as they focus on a set of pre-defined metabolites and aim towards their determination, often to the point of absolute quantification. The continuous development of the technological platforms used in these studies facilitates the analysis of large numbers of well-characterized metabolites present in complex matrices. The present review describes recent developments in the hyphenated chromatographic methods most often applied in targeted metabolomic/lipidomic studies (LC-MS/MS, CE-MS/MS, and GC-MS/MS), highlighting applications in the life and food/plant sciences. The review also underlines practical challenges-limitations that appear in such approaches.

PMID: 28792021 [PubMed - as supplied by publisher]

Arsenic Hyperaccumulation Strategies: An Overview.

August 5, 2017 - 10:27am
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Arsenic Hyperaccumulation Strategies: An Overview.

Front Cell Dev Biol. 2017;5:67

Authors: Souri Z, Karimi N, Sandalio LM

Abstract
Arsenic (As) pollution, which is on the increase around the world, poses a growing threat to the environment. Phytoremediation, an important green technology, uses different strategies, including As uptake, transport, translocation, and detoxification, to remediate this metalloid. Arsenic hyperaccumulator plants have developed various strategies to accumulate and tolerate high concentrations of As. In these plants, the formation of AsIII complexes with GSH and phytochelatins and their transport into root and shoot vacuoles constitute important mechanisms for coping with As stress. The oxidative stress induced by reactive oxygen species (ROS) production is one of the principal toxic effects of As; moreover, the strong antioxidative defenses in hyperaccumulator plants could constitute an important As detoxification strategy. On the other hand, nitric oxide activates antioxidant enzyme and phytochelatins biosynthesis which enhances As stress tolerance in plants. Although several studies have focused on transcription, metabolomics, and proteomic changes in plants induced by As, the mechanisms involved in As transport, translocation, and detoxification in hyperaccumulator plants need to be studied in greater depth. This review updates recent progress made in the study of As uptake, translocation, chelation, and detoxification in As hyperaccumulator plants.

PMID: 28770198 [PubMed]

Evolutionary Ecology of Multitrophic Interactions between Plants, Insect Herbivores and Entomopathogens.

August 2, 2017 - 7:27am
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Evolutionary Ecology of Multitrophic Interactions between Plants, Insect Herbivores and Entomopathogens.

J Chem Ecol. 2017 Jun;43(6):586-598

Authors: Shikano I

Abstract
Plants play an important role in the interactions between insect herbivores and their pathogens. Since the seminal review by Cory and Hoover (2006) on plant-mediated effects on insect-pathogen interactions, considerable progress has been made in understanding the complexity of these tritrophic interactions. Increasing interest in the areas of nutritional and ecological immunology over the last decade have revealed that plant primary and secondary metabolites can influence the outcomes of insect-pathogen interactions by altering insect immune functioning and physical barriers to pathogen entry. Some insects use plant secondary chemicals and nutrients to prevent infections (prophylactic medication) and medicate to limit the severity of infections (therapeutic medication). Recent findings suggest that there may be selectable plant traits that enhance entomopathogen efficacy, suggesting that entomopathogens could potentially impose selection pressure on plant traits that improve both pathogen and plant fitness. Moreover, plants in nature are inhabited by diverse communities of microbes, in addition to entomopathogens, some of which can trigger immune responses in insect herbivores. Plants are also shared by numerous other herbivorous arthropods with different modes of feeding that can trigger different defensive responses in plants. Some insect symbionts and gut microbes can degrade ingested defensive phytochemicals and be orally secreted onto wounded plant tissue during herbivory to alter plant defenses. Since non-entomopathogenic microbes and other arthropods are likely to influence the outcomes of plant-insect-entomopathogen interactions, I discuss a need to consider these multitrophic interactions within the greater web of species interactions.

PMID: 28526946 [PubMed - indexed for MEDLINE]

Omics approaches to probe markers of disease resistance in animal sciences.

July 25, 2017 - 10:32am
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Omics approaches to probe markers of disease resistance in animal sciences.

Mol Biosyst. 2016 Jun 21;12(7):2036-46

Authors: Guillemin N, Horvatić A, Kuleš J, Galan A, Mrljak V, Bhide M

Abstract
Omics technologies have been developed in recent decades and used in different thematics. More advancements were done in human and plant thematics. Omics is the conjugation of different techniques, studying all biological molecules (DNA, RNA, proteins, metabolites, etc.). Omics is then able to study entire pathways, elucidating phenotypes and their control. Thus, thanks to Omics, it is possible to have a broad overview of the linkage between genotypes and phenotypes. Disease phenotypes (tolerance or resistance) are important to understand in both production and health. Nowadays a plethora of research articles are presenting results in the field of natural disease resistance of animals using Omics technologies. Moreover, thanks to advanced high throughput technologies novel modes of infections (infection pathways) are coming to the surface. Such pathways are complex (hundreds to thousands of molecules implied, with complicated control mechanisms), and Omics can generate useful knowledge to understand those pathways. Here we aim to review several angles of Omics used to probe markers of disease resistance with recent publications and data on the field, and present perspectives and its utilization for a better understanding of diseases.

PMID: 27197117 [PubMed - indexed for MEDLINE]

High-Spatial Resolution Mass Spectrometry Imaging: Toward Single Cell Metabolomics in Plant Tissues.

July 8, 2017 - 7:34am
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High-Spatial Resolution Mass Spectrometry Imaging: Toward Single Cell Metabolomics in Plant Tissues.

Chem Rec. 2017 Jul 07;:

Authors: Hansen RL, Lee YJ

Abstract
Mass spectrometry imaging (MSI) is a powerful tool that has advanced our understanding of complex biological processes by enabling unprecedented details of metabolic biology to be uncovered. Through the use of high-spatial resolution MSI, metabolite localizations can be obtained with high precision. Here we describe our recent progress to enhance the spatial resolution of matrix-assisted laser desorption/ionization (MALDI) MSI from ∼50 μm with the commercial configuration to ∼5 μm. Additionally, we describe our efforts to develop a 'multiplex MSI' data acquisition method to allow more chemical information to be obtained on a single tissue in a single instrument run, and the development of new matrices to improve the ionization efficiency for a variety of small molecule metabolites. In combination, these contributions, along with the efforts of others, will bring MSI experiments closer to achieving metabolomic scale.

PMID: 28685965 [PubMed - as supplied by publisher]

A Concise Review on Multi-Omics Data Integration for Terroir Analysis in Vitis vinifera.

July 6, 2017 - 10:25am

A Concise Review on Multi-Omics Data Integration for Terroir Analysis in Vitis vinifera.

Front Plant Sci. 2017;8:1065

Authors: Fabres PJ, Collins C, Cavagnaro TR, Rodríguez López CM

Abstract
Vitis vinifera (grapevine) is one of the most important fruit crops, both for fresh consumption and wine and spirit production. The term terroir is frequently used in viticulture and the wine industry to relate wine sensory attributes to its geographic origin. Although, it can be cultivated in a wide range of environments, differences in growing conditions have a significant impact on fruit traits that ultimately affect wine quality. Understanding how fruit quality and yield are controlled at a molecular level in grapevine in response to environmental cues has been a major driver of research. Advances in the area of genomics, epigenomics, transcriptomics, proteomics and metabolomics, have significantly increased our knowledge on the abiotic regulation of yield and quality in many crop species, including V. vinifera. The integrated analysis of multiple 'omics' can give us the opportunity to better understand how plants modulate their response to different environments. However, 'omics' technologies provide a large amount of biological data and its interpretation is not always straightforward, especially when different 'omic' results are combined. Here we examine the current strategies used to integrate multi-omics, and how these have been used in V. vinifera. In addition, we also discuss the importance of including epigenomics data when integrating omics data as epigenetic mechanisms could play a major role as an intermediary between the environment and the genome.

PMID: 28676813 [PubMed - in process]

Metabolomic Tools to Assess the Chemistry and Bioactivity of Endophytic Aspergillus Strain.

July 4, 2017 - 7:25am

Metabolomic Tools to Assess the Chemistry and Bioactivity of Endophytic Aspergillus Strain.

Chem Biodivers. 2017 Jul 03;:

Authors: Tawfike AF, Tate R, Abbott G, Young L, Viegelmann C, Schumacher M, Diederich M, Edrada-Ebel RA

Abstract
Endophytic fungi associated with medicinal plants are a potential source of novel chemistry and biology that may find applications as pharmaceutical and agrochemical drugs. In this study, a combination of metabolomics and bioactivity-guided approaches were employed to isolate anticancer secondary metabolites from an endophytic Aspergillus aculeatus. The endophyte was isolated from the Egyptian medicinal plant Terminalia laxiflora and identified using molecular biological methods. Metabolomics and dereplication studies were accomplished by utilizing the MZmine software coupled with the universal Dictionary of Natural Products database. Metabolic profiling, with aid of multivariate data analysis, was performed at different stages of the growth curve to choose the optimised method suitable for up-scaling. The optimised culture method yielded a crude extract abundant with biologically-active secondary metabolites. Crude extracts were fractionated using different high-throughput chromatographic techniques. Purified compounds were identified by HRESI-MS, 1D and 2D-NMR. This study introduced a new method of dereplication utilising both high-resolution mass spectrometry and NMR spectroscopy. The metabolites were putatively identified by applying a chemotaxonomic filter. We also present a short review on the diverse chemistry of terrestrial endophytic strains of Aspergillus, which has become a part of our dereplication work and this will be of wide interest to those working in this field. This article is protected by copyright. All rights reserved.

PMID: 28672096 [PubMed - as supplied by publisher]

Experimental design and reporting standards for metabolomics studies of mammalian cell lines.

July 3, 2017 - 10:30am

Experimental design and reporting standards for metabolomics studies of mammalian cell lines.

Cell Mol Life Sci. 2017 Jul 01;:

Authors: Hayton S, Maker GL, Mullaney I, Trengove RD

Abstract
Metabolomics is an analytical technique that investigates the small biochemical molecules present within a biological sample isolated from a plant, animal, or cultured cells. It can be an extremely powerful tool in elucidating the specific metabolic changes within a biological system in response to an environmental challenge such as disease, infection, drugs, or toxins. A historically difficult step in the metabolomics pipeline is in data interpretation to a meaningful biological context, for such high-variability biological samples and in untargeted metabolomics studies that are hypothesis-generating by design. One way to achieve stronger biological context of metabolomic data is via the use of cultured cell models, particularly for mammalian biological systems. The benefits of in vitro metabolomics include a much greater control of external variables and no ethical concerns. The current concerns are with inconsistencies in experimental procedures and level of reporting standards between different studies. This review discusses some of these discrepancies between recent studies, such as metabolite extraction and data normalisation. The aim of this review is to highlight the importance of a standardised experimental approach to any cultured cell metabolomics study and suggests an example procedure fully inclusive of information that should be disclosed in regard to the cell type/s used and their culture conditions. Metabolomics of cultured cells has the potential to uncover previously unknown information about cell biology, functions and response mechanisms, and so the accurate biological interpretation of the data produced and its ability to be compared to other studies should be considered vitally important.

PMID: 28669031 [PubMed - as supplied by publisher]

The use of metabolomic quantitative trait locus mapping and osmotic adjustment traits for the improvement of crop yields under environmental stresses.

July 3, 2017 - 10:30am

The use of metabolomic quantitative trait locus mapping and osmotic adjustment traits for the improvement of crop yields under environmental stresses.

Semin Cell Dev Biol. 2017 Jun 28;:

Authors: Adbelrahman M, Burritt DJ, Tran LP

Abstract
The sustainable production of food to feed an increasing world population is a major challenge for plant scientists, especially due to the unpredictable and dynamic nature of global climatic conditions. Heat waves, drought, increased soil salinity, unseasonal cold and flooding are all becoming more common climate-related causes of stress for crop plants, and are already affecting yields and the geographical distributions of optimal growing regions for many crops. Therefore, the development and application of multi-faceted strategies, including sustainable agricultural practices and the development and cultivation of intraspecific hybrids containing genetic traits associated with abiotic stress tolerance from wild relatives, will either alone or together be essential to sustainably grow high-yielding crops under increasingly stressful environmental conditions. The development of abiotic stress-resilient crops requires an in-depth knowledge of plant development and of the biological processes that enable plants to survive in stressful environments, and this knowledge can be obtained from "omic" studies, such as bioinformatics, genomics, transcriptomics, proteomics and metabolomics. The plant metabolome can provide a snapshot of the physiological and biochemical status of a plant cell under normal or stressful conditions, and thus it is closely related to the plant phenotypes. Analysis of the metabolomes of plants growing under stressful conditions can be used to identify stress resistance-associated metabolites, or biomarkers, which can then be used by plant breeders as selective markers to help identify the phenotypes, resulted from the complex interactions between genotype and environment, associated with stress-tolerant crop plants. Osmotic adjustment is an important metabolic adaptation mechanism which helps plants survive abiotic stress and can support higher crop yield under stressful environmental conditions. This review highlights the recent advances in our understanding of the functions of abiotic stress-responsive metabolites, with an emphasis on the use of metabolomic quantitative trait locus mapping and osmotic adjustment agronomic traits, for the improvement of crop yields under environmental stresses.

PMID: 28668354 [PubMed - as supplied by publisher]

Proteomes and phosphoproteomes of anther and pollen: Availability and progress.

July 1, 2017 - 7:27am

Proteomes and phosphoproteomes of anther and pollen: Availability and progress.

Proteomics. 2017 Jun 30;:

Authors: Zhang Z, Hu M, Feng X, Gong A, Cheng L, Yuan H

Abstract
In flowering plants, anther development plays crucial role in sexual reproduction. Within the anther, microspore mother cells meiosis produces microspores, which further develop into pollen grains that play decisive role in plant reproduction. Previous studies on anther biology mainly focused on single gene functions relying on genetic and molecular methods. Recently, anther development has been expanded from multiple OMICS approaches like transcriptomics, proteomics/phosphoproteomics, and metabolomics. The development of proteomics techniques allowing increased proteome coverage and quantitative measurements of proteins which can characterize proteomes and their modulation during normal development, biotic and abiotic stresses in anther development. In this review, we summarize the achievements of proteomics and phosphoproteomics with anther and pollen organs from model plant and crop species (i.e. Arabidopsis, rice, tobacco). The increased proteomic information facilitated translation of information from the models to crops and thus aid in agricultural improvement. This article is protected by copyright. All rights reserved.

PMID: 28665021 [PubMed - as supplied by publisher]

Oxidative stress and chronic inflammation in osteoarthritis: can NRF2 counteract these partners in crime?

June 30, 2017 - 1:24pm

Oxidative stress and chronic inflammation in osteoarthritis: can NRF2 counteract these partners in crime?

Ann N Y Acad Sci. 2017 Jun 29;:

Authors: Marchev AS, Dimitrova PA, Burns AJ, Kostov RV, Dinkova-Kostova AT, Georgiev MI

Abstract
Osteoarthritis (OA) is an age-related joint degenerative disease associated with pain, joint deformity, and disability. The disease starts with cartilage damage but then progressively involves subchondral bone, causing an imbalance between osteoclast-driven bone resorption and osteoblast-driven remodeling. Here, we summarize the data for the role of oxidative stress and inflammation in OA pathology and discuss how these two processes are integrated during OA progression, as well as their contribution to abnormalities in cartilage/bone metabolism and integrity. At the cellular level, oxidative stress and inflammation are counteracted by transcription factor nuclear factor erythroid p45-related factor 2 (NRF2), and we describe the regulation of NRF2, highlighting its role in OA pathology. We also discuss the beneficial effect of some phytonutrients, including the therapeutic potential of NRF2 activation, in OA.

PMID: 28662306 [PubMed - as supplied by publisher]

Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding.

June 20, 2017 - 10:41am
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Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding.

Front Plant Sci. 2017;8:757

Authors: Ghatak A, Chaturvedi P, Weckwerth W

Abstract
Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.

PMID: 28626463 [PubMed - in process]

Frontiers of high-throughput metabolomics.

June 20, 2017 - 10:41am
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Frontiers of high-throughput metabolomics.

Curr Opin Chem Biol. 2017 Feb;36:15-23

Authors: Zampieri M, Sekar K, Zamboni N, Sauer U

Abstract
Large scale metabolomics studies are increasingly used to investigate genetically different individuals and time-dependent responses to environmental stimuli. New mass spectrometric approaches with at least an order of magnitude more rapid analysis of small molecules within the cell's metabolome are now paving the way towards true high-throughput metabolomics, opening new opportunities in systems biology, functional genomics, drug discovery, and personalized medicine. Here we discuss the impact and advantages of the progress made in profiling large cohorts and dynamic systems with high temporal resolution and automated sampling. In both areas, high-throughput metabolomics is gaining traction because it can generate hypotheses on molecular mechanisms and metabolic regulation. We conclude with the current status of the less mature single cell analyses where high-throughput analytics will be indispensable to resolve metabolic heterogeneity in populations and compartmentalization of metabolites.

PMID: 28064089 [PubMed - indexed for MEDLINE]

The application of metabolomics for herbal medicine pharmacovigilance: a case study on ginseng.

June 20, 2017 - 10:41am
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The application of metabolomics for herbal medicine pharmacovigilance: a case study on ginseng.

Essays Biochem. 2016 Dec 15;60(5):429-435

Authors: Crighton E, Mullaney I, Trengove R, Bunce M, Maker G

Abstract
Herbal medicines are growing in popularity, use and commercial value; however, there remain problems with the quality and consequently safety of these products. Adulterated, contaminated and fraudulent products are often found on the market, a risk compounded by the fact that these products are available to consumers with little or no medical advice. Current regulations and quality control methods are lacking in their ability to combat these serious problems. Metabolomics is a biochemical profiling tool that may help address these issues if applied to quality control of both raw ingredients and final products. Using the example of the popular herbal medicine, ginseng, this essay offers an overview of the potential use of metabolomics for quality control in herbal medicines and also highlights where more research is needed.

PMID: 27980093 [PubMed - indexed for MEDLINE]

Livestock metabolomics and the livestock metabolome: A systematic review.

May 23, 2017 - 10:19am
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Livestock metabolomics and the livestock metabolome: A systematic review.

PLoS One. 2017;12(5):e0177675

Authors: Goldansaz SA, Guo AC, Sajed T, Steele MA, Plastow GS, Wishart DS

Abstract
Metabolomics uses advanced analytical chemistry techniques to comprehensively measure large numbers of small molecule metabolites in cells, tissues and biofluids. The ability to rapidly detect and quantify hundreds or even thousands of metabolites within a single sample is helping scientists paint a far more complete picture of system-wide metabolism and biology. Metabolomics is also allowing researchers to focus on measuring the end-products of complex, hard-to-decipher genetic, epigenetic and environmental interactions. As a result, metabolomics has become an increasingly popular "omics" approach to assist with the robust phenotypic characterization of humans, crop plants and model organisms. Indeed, metabolomics is now routinely used in biomedical, nutritional and crop research. It is also being increasingly used in livestock research and livestock monitoring. The purpose of this systematic review is to quantitatively and objectively summarize the current status of livestock metabolomics and to identify emerging trends, preferred technologies and important gaps in the field. In conducting this review we also critically assessed the applications of livestock metabolomics in key areas such as animal health assessment, disease diagnosis, bioproduct characterization and biomarker discovery for highly desirable economic traits (i.e., feed efficiency, growth potential and milk production). A secondary goal of this critical review was to compile data on the known composition of the livestock metabolome (for 5 of the most common livestock species namely cattle, sheep, goats, horses and pigs). These data have been made available through an open access, comprehensive livestock metabolome database (LMDB, available at http://www.lmdb.ca). The LMDB should enable livestock researchers and producers to conduct more targeted metabolomic studies and to identify where further metabolome coverage is needed.

PMID: 28531195 [PubMed - in process]

Proteomics survey of Solanaceae family: Current status and challenges ahead.

May 23, 2017 - 10:19am
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Proteomics survey of Solanaceae family: Current status and challenges ahead.

J Proteomics. 2017 May 18;:

Authors: Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, Gupta R

Abstract
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions. Among the Solanaceae members, most of the research has been focused on tomato (42%) followed by potato (28%) and tobacco (20%), owing to their economic importance. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.
BIOLOGICAL SIGNIFICANCE: Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key players associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.

PMID: 28528990 [PubMed - as supplied by publisher]

Genomics of the Asian rice gall midge and its interactions with rice.

May 20, 2017 - 7:25am
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Genomics of the Asian rice gall midge and its interactions with rice.

Curr Opin Insect Sci. 2017 Feb;19:76-81

Authors: Sinha DK, Atray I, Agarrwal R, Bentur JS, Nair S

Abstract
Understanding virulence and manipulative strategies of gall formers will reveal new facets of plant defense and insect counter defense. Among the gall midges, the Asian rice gall midge (AGM) has emerged as a model for studies on plant-insect interactions. Data from several genomics, transcriptomics and metabolomics studies have revealed diverse strategies adopted by AGM to successfully invade the host while overcoming its defense. Adaptive skills of AGM transcend from its genomic and transcriptomic make-up. Information arising from studies on genetics, mitochondrial genome and miRNAs, amongst other parameters, highlights AGM's capacity to maneuver the host defense, reorient host metabolome and redirect its morphogenesis.

PMID: 28521946 [PubMed - in process]

More effort - more results: recent advances in integrative 'omics' data analysis.

May 20, 2017 - 7:25am
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More effort - more results: recent advances in integrative 'omics' data analysis.

Curr Opin Plant Biol. 2016 Apr;30:57-61

Authors: Rajasundaram D, Selbig J

Abstract
The development of 'omics' technologies has progressed to address complex biological questions that underlie various plant functions thereby producing copious amounts of data. The need to assimilate large amounts of data into biologically meaningful interpretations has necessitated the development of statistical methods to integrate multidimensional information. Throughout this review, we provide examples of recent outcomes of 'omics' data integration together with an overview of available statistical methods and tools.

PMID: 26890084 [PubMed - indexed for MEDLINE]

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