Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics

This review explores the latest developments in Fourier transform mass spectrometry and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing high resolution mass spectrometry data

The Genome-Wide Early Temporal Response of Saccharomyces cerevisiae to Oxidative Stress Induced by Cumene Hydroperoxide

Oxidative stress is a well-known biological process that occurs in all respiring cells and is involved in pathophysiological processes such as aging and apoptosis. Oxidative stress agents include peroxides such as hydrogen peroxide, cumene hydroperoxide, and linoleic acid hydroperoxide, the thiol oxidant diamide, and menadione, a generator of superoxide, amongst others. The present study analyzed the early temporal genome-wide transcriptional response of Saccharomyces cerevisiae to oxidative stress induced by the aromatic peroxide cumene hydroperoxide. The accurate dataset obtained, supported by the use of temporal controls, biological replicates and well controlled growth conditions, provided a detailed picture of the early dynamics of the process. We identified a set of genes previously not implicated in the oxidative stress response, including several transcriptional regulators showing a fast transient response, suggesting a coordinated process in the transcriptional reprogramming. We discuss the role of the glutathione, thioredoxin and reactive oxygen species-removing systems, the proteasome and the pentose phosphate pathway. A data-driven clustering of the expression patterns identified one specific cluster that mostly consisted of genes known to be regulated by the Yap1p and Skn7p transcription factors, emphasizing their mediator role in the transcriptional response to oxidants. Comparison of our results with data reported for hydrogen peroxide identified 664 genes that specifically respond to cumene hydroperoxide, suggesting distinct transcriptional responses to these two peroxides. Genes up-regulated only by cumene hydroperoxide are mainly related to the cell membrane and cell wall, and proteolysis process, while those down-regulated only by this aromatic peroxide are involved in mitochondrial function

Label-free shotgun proteomics and metabolite analysis reveal a significant metabolic shift during citrus fruit development.

Label-free LC-MS/MS-based shot-gun proteomics was used to quantify the differential protein synthesis and metabolite profiling in order to assess metabolic changes during the development of citrus fruits. Our results suggested the occurrence of a metabolic change during citrus fruit maturation, where the organic acid and amino acid accumulation seen during the early stages of development shifted into sugar synthesis during the later stage of citrus fruit development. The expression of invertases remained unchanged, while an invertase inhibitor was up-regulated towards maturation. The increased expression of sucrose-phosphate synthase and sucrose-6-phosphate phosphatase and the rapid sugar accumulation suggest that sucrose is also being synthesized in citrus juice sac cells during the later stage of fruit development

Transcriptomic footprints disclose specificity of reactive oxygen species signaling in Arabidopsis

Reactive oxygen species ( ROS) are key players in the regulation of plant development, stress responses, and programmed cell death. Previous studies indicated that depending on the type of ROS ( hydrogen peroxide, superoxide, or singlet oxygen) or its subcellular production site ( plastidic, cytosolic, peroxisomal, or apoplastic), a different physiological, biochemical, and molecular response is provoked. We used transcriptome data generated from ROS-related microarray experiments to assess the specificity of ROS-driven transcript expression. Data sets obtained by exogenous application of oxidative stress-causing agents ( methyl viologen, Alternaria alternata toxin, 3-aminotriazole, and ozone) and from a mutant ( fluorescent) and transgenic plants, in which the activity of an individual antioxidant enzyme was perturbed ( catalase, cytosolic ascorbate peroxidase, and copper/zinc superoxide dismutase), were compared. In total, the abundance of nearly 26,000 transcripts of Arabidopsis ( Arabidopsis thaliana) was monitored in response to different ROS. Overall, 8,056, 5,312, and 3,925 transcripts showed at least a 3-, 4-, or 5- fold change in expression, respectively. In addition to marker transcripts that were specifically regulated by hydrogen peroxide, superoxide, or singlet oxygen, several transcripts were identified as general oxidative stress response markers because their steady-state levels were at least 5- fold elevated in most experiments. We also assessed the expression characteristics of all annotated transcription factors and inferred new candidate regulatory transcripts that could be responsible for orchestrating the specific transcriptomic signatures triggered by different ROS. Our analysis provides a framework that will assist future efforts to address the impact of ROS signals within environmental stress conditions and elucidate the molecular mechanisms of the oxidative stress response in plants

1-Benzyl-3,5-bis­(4-chloro­benzyl­idene)piperidin-4-one

The title compound, C26H21Cl2NO, crystallizes with two symmetry-independent mol­ecules (A and B) in the asymmetric unit. In both mol­ecules, the central heterocyclic ring adopts a sofa conformation. The dihedral angles between the planar part of this central heterocyclic ring [maximum deviations of 0.011 (1) and 0.036 (1) Å in mol­ecules A and B, respectively] and the two almost planar [maximum deviations of 0.020 (1) and 0.008 (1) Å in A and 0.007 (1) and 0.011 (1) in B] side-chain fragments that include the aromatic ring and bridging atoms are 20.1 (1) and 31.2 (1)° in mol­ecule A, and 26.4 (1) and 19.6 (1)° in mol­ecule B. The dihedral angles between the planar part of the heterocyclic ring and the benzyl substituent are 79.7 (1) and 53.2 (1)° in mol­ecules A and B, respectively. In the crystal, weak inter­molecular C—H⋯O hydrogen bonds link the two independent mol­ecules into dimers

3,5-Bis(4-chloro­benzyl­idene)-1-methyl­piperidin-4-one

In the title mol­ecule, C20H17Cl2NO, the central heterocyclic ring adopts a flattened boat conformation. The dihedral angles between the planar part of this central heterocyclic ring [maximum deviation = 0.004 (1) Å] and the two almost planar side-chain fragments [maximum deviations = 0.015 (1) and 0.019 (1) Å], that include the aromatic ring and bridging atoms, are 18.1 (1) and 18.0 (1)°. In the crystal, pairs of weak inter­molecular C—H⋯O hydrogen bonds link mol­ecules into inversion dimers that form stacks along the a axis. The structure is further stabilized by weak inter­molecular C—H⋯π inter­actions involving the benzene rings

Functional Assessment of the Medicago truncatula

The Medicago truncatula NIP/LATD (for Numerous Infections and Polyphenolics/Lateral root-organ Defective) gene encodes a protein found in a clade of nitrate transporters within the large NRT1(PTR) family that also encodes transporters of dipeptides and tripeptides, dicarboxylates, auxin, and abscisic acid. Of the NRT1(PTR) members known to transport nitrate, most are low-affinity transporters. Here, we show that M. truncatula nip/latd mutants are more defective in their lateral root responses to nitrate provided at low (250 μm) concentrations than at higher (5 mm) concentrations; however, nitrate uptake experiments showed no discernible differences in uptake in the mutants. Heterologous expression experiments showed that MtNIP/LATD encodes a nitrate transporter: expression in Xenopus laevis oocytes conferred upon the oocytes the ability to take up nitrate from the medium with high affinity, and expression of MtNIP/LATD in an Arabidopsis chl1(nrt1.1) mutant rescued the chlorate susceptibility phenotype. X. laevis oocytes expressing mutant Mtnip-1 and Mtlatd were unable to take up nitrate from the medium, but oocytes expressing the less severe Mtnip-3 allele were proficient in nitrate transport. M. truncatula nip/latd mutants have pleiotropic defects in nodulation and root architecture. Expression of the Arabidopsis NRT1.1 gene in mutant Mtnip-1 roots partially rescued Mtnip-1 for root architecture defects but not for nodulation defects. This suggests that the spectrum of activities inherent in AtNRT1.1 is different from that possessed by MtNIP/LATD, but it could also reflect stability differences of each protein in M. truncatula. Collectively, the data show that MtNIP/LATD is a high-affinity nitrate transporter and suggest that it could have another function

Understanding Water-Stress Responses in Soybean Using Hydroponics System—A Systems Biology Perspective

This article discusses using a system of reduced complexity like hydroponics to identify the potential candidates for water-stress tolerance by plants

Local and Systemic Metabolic Responses during Light-Induced Rapid Systemic Signaling

This article reports that local application of light stress to one rosette leaf of bolting Arabidopsis (Arabidopsis thaliana) plants resulted in a metabolic response that encompassed local, systemic and transport tissues, demonstrating a high degree of physical and metabolic continuity between different tissues throughout the plant

Functional Assessment of the Medicago truncatula NIP/LATD Protein Demonstrates That It Is a High-Affinity Nitrate Transporter

Article on the functional assessment of the Medicago truncatula NIP/LATD protein demonstrating that it is a high-affinity nitrate transporter