Pathway Mapping Research Articles

Mapping of pathways of care, assessment of delays and gap analysis in provision of care following road traffic injury among patients in selected tertiary hospitals in urban Karnataka, South India

Background: Evidence-based public health advocates decision making based on best available scientific evidence, hence it is important to gather evidence of current scenario of trauma care. Aim & Objective: To determine pathways of care and delays among Road Traffic Injury patients and assess gaps in resources. Settings and Design: This cross-sectional study was conducted in selected tertiary care hospitals in Mangaluru taluk, Karnataka. Methods and Material: Participants were administered validated proformas on prehospital and hospital care. WHO trauma care checklist was used for capacity assessment and gap analysis. Statistical analysis used: Time intervals are expressed as measures of central tendency and dispersion. Descriptive analysis is given as percentages and proportions. Results: Median pre-hospital time was 30 minutes. Overall, 67.5% of the patients reached within golden hour. Majority (64.1%) were directly transported to current hospital. All patients received first aid, but only 0.8% received it at the RTI site. First aid was mostly administered by doctors (68.7%) or nursing staff (31.1%) and none by bystander. Insurance coverage was 32.8% and 87.9% incurred out of pocket expenditures. Scores were low in GP level hospital. Conclusions: Although transport was within the golden hour, pre-hospital care was poor. Out of pocket expenditures were high.

Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors.

Helicobacter pylori (H. pylori) is known to be a major pathogen causing gastric diseases through its direct localization in gastric epithelium cells. H. pylori releases outer membrane vesicles (OMVs) throughout the growth process. The content, function, and mechanism of H. pylori OMVs in gastric epithelial cells remain unclear. In this study, we extracted and characterized H. pylori OMVs of two strains (standard strain NCTC11637 and clinical strain Hp-400) and analyzed the specific content by proteomic technology. We identified more than 400 proteins in H. pylori OMVs. In addition, we investigated the impact of H. pylori OMVs on cellular functions by detecting proteomic changes in GES1 cells. GES1 cells cocultured with increasing concentrations of H. pylori OMVs were subjected to quantitative proteomic analyses using label-free methods for relative quantitation. The results showed that a total of 4261 proteins were verified, 153 of which were significantly altered in abundance when cocultured with NCTC11637 OMVs, and a total of 4234 proteins in Hp-400 OMVs, 390 of which were significantly altered. Gene ontology analysis and Kyoto encyclopedia of genes and genomes pathway mapping identified significantly altered inflammatory and cancer signaling pathways, including metabolic pathways and the PI3K-Akt signaling pathway. Furthermore, we explored the proteomic changes in GES1 cells induced by H. pylori. Bioinformatics analysis showed that changes in multiple pathways coincided with OMV-mediated proteomic changes. Based on these results, H. pylori induced pathogenicity in epithelial cells at least partially by secreting OMVs that mediated dramatic and specific proteomic changes in host cells. Data are available via ProteomeXchange with identifiers PXD025216, PXD025259, and PXD025281.

Groundwater Pathway Mapping Using Electrical Resistivity Tomography (ERT) Method

Geophysical electrical resistivity method has been one of the more popular non-destructive method to explore the subsurface. Geophysical electrical resistivity tomography (ERT) subsurface profiling was conducted to map the groundwater path along the embankment. The groundwater path able to decrease the slope stability, thus its need to locate the position for conduct the slope remediation via subsoil drainage. In this study, Terrameter LS2 model, electrodes, cables, battery, and cable connectors were the equipment used for measurement. This study uses cable spread line at 200m with 2.5m spacing between electrodes by using gradient protocol. The resistivity data was analyzed using RES2DINV software. The interpretation of groundwater path is based on the resistivity values less than 100 ohm.m, which is interpreted as saturated materials. This study demonstrates the efficiency of application of electrical resistivity tomography (ERT) in detecting the groundwater pathways. This investigation will help in sustaining the slope stability via indicating the position of groundwater pathways, and thus implementing the slope remediation work.

Spatial mapping of subcellular disease pathways and cytoarchitecture to anatomical brain regions for multi‐scale brain simulation with The Virtual Brain

AbstractBackgroundComprehensive knowledge bases as NeuroMMSig, a knowledge base of multimodal mechanistic signatures, catalog knowledge about Alzheimer's Disease (AD) and its underlying candidate mechanisms. Besides, digital atlases provide information about cytoarchitectonics and receptor densities, e.g. JuBrain at the EBRAINS platform of the Human Brain Project. However, a gap exists presently with respect to the integration of the various knowledge sources. The Virtual Brain (TVB) is a full brain simulation platform that integrates multimodal imaging data with mathematical brain networks. We present a methodology to map semantic information about AD to 3D brain atlases and to use it for simulations with TVB – increasing the biological plausibility of whole‐brain simulations and disease specificity.MethodOur framework allows topological assignment of brain‐related data from different sources to the Multimodal surface‐based cortical parcellation (MMP) of the Human Connectome Project. Our tool allows mapping of stochastic information from the literature database SCAIView to brain regions. The relevance score for a specific query is calculated for anatomy‐related words from the anatomic ontology Uberon, which we transfer by a unique matrix to MMP parcels. Re‐sampling by the fsaverage brain space of freesurfer allows interoperability with other atlases. In addition, atlas‐annotated data from EBRAINS and neuroimaging data are co‐registered with MMP, enabling knowledge integration into a standardized 3D brain space.ResultOur methodologic pipeline can be used as a software to map semantic information to the brain, which we demonstrate with NeuroMMSig pathways. We further demonstrate how the resulting maps constrain TVB simulations. Face validity is provided through reproducing group‐level (AD versus controls) results of simulations integrating subject‐specific positron emission tomography when semantic information about AD stages is integrated into TVB. We elucidate how brain maps derived from different semantic queries can change simulated brain dynamics fundamentally. Literature‐derived NMDA receptor densities show significant differences between AD and healthy controls. When used to constrain TVB models, this leads to an in silico disruption of functional subnetworks in AD.ConclusionWe developed a tool for mapping semantic knowledge to anatomical brain regions. This enables multi‐scale brain simulations with increases biological plausibility and disease‐specificity for translational research.

Front Cover: A Systematic Review of Metabolic Alterations Underlying IgE‐Mediated Food Allergy in Children

Mol. Nutr. Food Res. 2021, 65, 202100536 DOI: 10.1002/mnfr.202100536 IgE-mediated food allergies (IgE-FA) are considered a growing epidemic. Its pathogenic mechanisms remain however largely unknown. The authors performed a literature search followed by in-depth pathway mapping of IgE-FA in children, and revealed a shift in energy metabolism, next to aberrant metabolization of bile acids, lipids, nucleotides, fecal SCFAs and amino acids. As such, this work confirmed the unprecedented opportunities of metabolomics while offering a solid basis for future FA research. This is reported by Lynn Vanhaecke and co-workers in article number 2100536.

Transcriptome Analysis of Host Inflammatory Responses to the Ectoparasitic Mite Sarcoptes scabiei var. hominis.

Scabies, a human skin infestation caused by the ectoparasitic mite Sarcoptes scabiei var. hominis, affects more than 200 million people globally. The prevailing knowledge of the disease process and host immune response mechanisms is limited. A better understanding of the host-parasite relationship is essential for the identification of novel vaccine and drug targets. Here we aimed to interrogate the transcriptomic profiles of mite-infested human skin biopsies with clinical manifestations of ordinary scabies subjects (“OS”; n = 05) and subjects naive to scabies (“control”; n = 03) using RNASeq data analysis. A combined clustering, network, and pathway mapping approach enabled us to identify key signaling events in the host immune and pro-inflammatory responses to S. scabiei infestation. The clustering patterns showed various differentially expressed genes including inflammatory responses and innate immunity genes (DEFB4A, IL-19, CXCL8, CSF3, SERPINB4, S100A7A, HRNR) and notably upregulation of the JAK-STAT pathway in scabies-infested samples. Mite-infested human skin biopsies (GSE178563) were compared with an ex-vivo porcine infested model (E-MTAB-6433) and human skin equivalents (GSE48459). Marked enrichment of immune response pathways (JAK-STAT signaling, IL-4 and IL-13 pathway, and Toll receptor cascade), chemokine ligands and receptors (CCL17, CCL18, CCL3L1, CCL3L3, CCR7), and cytokines (IL-13 and IL-20) were observed. Additionally, genes known for their role in psoriasis and atopic dermatitis were upregulated, e.g., IL-19. The detailed transcriptomic profile has provided an insight into molecular functions, biological processes, and immunological responses and increased our understanding about transcriptomic regulation of scabies in human.

Genome wide identification and analysis of WD40 domain containing proteins in Danio rerio

The WD40 domain is one of the most occurring domains in the eukaryotic genome. Recently it is also reported in prokaryotes. The protein with WD40 domain acts as scaffold proteins and helps in the assembly of multiprotein complexes. Genome wide identification and analysis of WD40 domain-containing proteins in Zebrafish was performed in the present work. Total 251 redundant proteins with WD40 domain (at least six WD40 repeats) were identified from WDSP software and further confirmed using ZFIN and NCBI database. Their chromosomal localization and domain architecture was analyzed. The DrWD40 genes are distributed on all the chromosomes with the maximum number (18) on chromosome 5. Based on the presence of other domains, DrWD40 proteins were classified into 18 classes. The coiled-coil domain was the most occurring domain along with the WD40 domain. In the KEGG pathway mapping, they show involvement in different pathways viz., RNA transport, mRNA surveillance, ribosome biogenesis, etc. In gene ontology analysis using DAVID and PANTHER software, it was found that they are involved in diverse biological processes and perform different molecular functions. WD40 proteins in Danio rerio predominantly participate in a binding activity such as actin filament binding, microtubule-binding, dynein binding, etc. They are mainly localized to the cytoplasm and nucleus. Our analysis highlighted the participation of DrWD40 proteins in diverse cellular and biological processes. A cluster of proteins with similar molecular and biological functions can be further studied.

Benefit of Action Naming Over Object Naming for Visualization of Subcortical Language Pathways in Navigated Transcranial Magnetic Stimulation-Based Diffusion Tensor Imaging-Fiber Tracking.

Visualization of functionally significant subcortical white matter fibers is needed in neurosurgical procedures in order to avoid damage to the language network during resection. In an effort to achieve this, positive cortical points revealed during preoperative language mapping with navigated transcranial magnetic stimulation (nTMS) can be employed as regions of interest (ROIs) for diffusion tensor imaging (DTI) fiber tracking. However, the effect that the use of different language tasks has on nTMS mapping and subsequent DTI-fiber tracking remains unexplored. The visualization of ventral stream tracts with an assumed lexico-semantic role may especially benefit from ROIs delivered by the lexico-semantically demanding verb task, Action Naming. In a first step, bihemispheric nTMS language mapping was administered in 18 healthy participants using the standard task Object Naming and the novel task Action Naming to trigger verbs in a small sentence context. Cortical areas in which nTMS induced language errors were identified as language-positive cortical sites. In a second step, nTMS-based DTI-fiber tracking was conducted using solely these language-positive points as ROIs. The ability of the two tasks’ ROIs to visualize the dorsal tracts Arcuate Fascicle and Superior Longitudinal Fascicle, the ventral tracts Inferior Longitudinal Fascicle, Uncinate Fascicle, and Inferior Fronto-Occipital Fascicle, the speech-articulatory Cortico-Nuclear Tract, and interhemispheric commissural fibers was compared in both hemispheres. In the left hemisphere, ROIs of Action Naming led to a significantly higher fraction of overall visualized tracts, specifically in the ventral stream’s Inferior Fronto-Occipital and Inferior Longitudinal Fascicle. No difference was found between tracking with Action Naming vs. Object Naming seeds for dorsal stream tracts, neither for the speech-articulatory tract nor the inter-hemispheric connections. While the two tasks appeared equally demanding for phonological-articulatory processes, ROI seeding through the task Action Naming seemed to better visualize lexico-semantic tracts in the ventral stream. This distinction was not evident in the right hemisphere. However, the distribution of tracts exposed was, overall, mirrored relative to those in the left hemisphere network. In presurgical practice, mapping and tracking of language pathways may profit from these findings and should consider inclusion of the Action Naming task, particularly for lesions in ventral subcortical regions.

Biosimulation Using the Cellworks Computational Omics Biology Model (CBM)-Based Assessment of Cytarabine (ARA-C) and Anthracycline Response and Novel Biomarker Response Criteria for the Addition of Etoposide (VP16) in Acute Myeloid Leukemia (AML)

Biosimulation Using the Cellworks Computational Omics Biology Model (CBM)-Based Assessment of Cytarabine (ARA-C) and Anthracycline Response and Novel Biomarker Response Criteria for the Addition of Etoposide (VP16) in Acute Myeloid Leukemia (AML)

A modular map of Bradykinin-mediated inflammatory signaling network.

Bradykinin, a member of the kallikrein-kinin system (KKS), is associated with an inflammatory response pathway with diverse vascular permeability functions, including thrombosis and blood coagulation. In majority, bradykinin signals through Bradykinin Receptor B2 (B2R). B2R is a G protein-coupled receptor (GPCR) coupled to G protein family such as Gαqs, Gαq/Gα11, Gαi1, and Gβ1γ2. B2R stimulation leads to the activation of a signaling cascade of downstream molecules such as phospholipases, protein kinase C, Ras/Raf-1/MAPK, and PI3K/AKT and secondary messengers such as inositol-1,4,5-trisphosphate, diacylglycerol and Ca2+ ions. These secondary messengers modulate the production of nitric oxide or prostaglandins. Bradykinin-mediated signaling is implicated in inflammation, chronic pain, vasculopathy, neuropathy, obesity, diabetes, and cancer. Despite the biomedical importance of bradykinin, a resource of bradykinin-mediated signaling pathway is currently not available. Here, we developed a pathway resource of signaling events mediated by bradykinin. By employing data mining strategies in the published literature, we describe an integrated pathway reaction map of bradykinin consisting of 233 reactions. Bradykinin signaling pathway events included 25 enzyme catalysis reactions, 12 translocations, 83 activation/inhibition reactions, 11 molecular associations, 45 protein expression and 57 gene regulation events. The pathway map is made publicly available on the WikiPathways Database with the ID URL: https://www.wikipathways.org/index.php/Pathway:WP5132. The bradykinin-mediated signaling pathway map will facilitate the identification of novel candidates as therapeutic targets for diseases associated with dysregulated bradykinin signaling.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12079-021-00652-0.

Pongol Methyl Ether Inhibits Akt and Suppresses Cancer Stem Cell Phenotypes in Lung Cancer Cells

Cancer stem cells (CSCs) are an important therapeutic target. The therapeutic agents targeting CSCs should lead to improved clinical outcomes. Here we have demonstrated the CSC-suppressing activity of pongol methyl ether (PME), a pure compound from Millettia erythrocalyx. Methods: CSC-suppressing effects were evaluated by spheroid formation assay and detection of CSC markers. The related CSC cell signals were evaluated by Western blot, immunofluorescence and molecular docking analysis. Proteins affected by PME treatment were subjected to bioinformatic analysis. Protein–protein interaction (PPI) networks were constructed by the Search Tool for Interactions of Chemicals (STITCH). The Kyoto Encyclopedia of Genes and Genomes (KEGG) mapper were used to confirm the underlying pathways. Results: PME (5–25 µM) significantly suppressed the ability of lung cancer cells to form colonies, grow in an anchorage-independent manner and generate tumour spheroids. PME at 25 µM significantly decreased the CSC markers (CD133 and ALDH1A1) and pluripotent transcription factors (Oct4 and Nanog). Akt, the key upstream signal of CSC control, was significantly decreased by the PME treatment. The molecular docking indicated that PME was bound to Akt-1 with a binding affinity of −9.2 kcal/mol greater than the Akt-1 inhibitor (reference compound; CQW). The STITCH network identified a total of 15 proteins interacted in PPI networks, and Akt-1 was identified as a central protein. The KEGG mapper indicated that the selected CSC markers were mostly involved in the ‘signalling pathways regulating pluripotency of stem cells’ pathway map and Akt, Oct4 and Nanog were the regulatory proteins in the dominant pathway. In addition, PME (10–25 µM) can suppress spheroid formation and reduce CSC-specific marker expression in patient-derived primary lung cancer cells. Conclusions: Our study revealed a novel pharmacological effect and the underlying mechanism of PME that can attenuate CSC phenotypes in lung cancer cells and may be developed for lung cancer therapy.

A Systematic Review of Metabolic Alterations Underlying IgE-Mediated Food Allergy in Children.

Immunoglobulin E-mediated food allergies (IgE-FA) are characterized by an ever-increasing prevalence, currently reaching up to 10.4% of children in the European Union. Metabolomics has the potential to provide a deeper understanding of the pathogenic mechanisms behind IgE-FA. In this work, literature is systematically searched using Web of Science, PubMed, Scopus, and Embase, from January 2010 until May 2021, including human and animal metabolomic studies on multiple biofluids (urine, blood, feces). In total, 15 studies on IgE-FA are retained and a dataset of 277 potential biomarkers is compiled for in-depth pathway mapping. Decreased indoleamine 2,3-dioxygenase-1 (IDO- 1) activity is hypothesized due to altered plasma levels of tryptophan and its metabolites in IgE-FA children. In feces of children prior to IgE-FA, aberrant metabolization of sphingolipids and histidine is noted. Decreased fecal levels of (branched) short chain fatty acids ((B)SCFAs) compel a shift towards aerobic glycolysis and suggest dysbiosis, associated with an immune system shift towards T-helper 2 (Th2) responses. During animal anaphylaxis, a similar switch towards glycolysis is observed, combined with increased ketogenic pathways. Additionally, altered histidine, purine, pyrimidine, and lipid pathways are observed. To conclude, this work confirms the unprecedented opportunities of metabolomics and supports the in-depth pathophysiological qualification in the quest towards improved diagnostic and prognostic biomarkers for IgE-FA.

Hedera rhombea inhibits the biofilm formation of Candida, thereby increases the susceptibility to antifungal agent, and reduces infection

Candida is an opportunistic pathogen and a common cause of fungal infections worldwide. Anti-fungal use against Candida infections has resulted in the appearance of resistant strains. The limited choice of anti-fungal therapy means alternative strategies are needed to control fungal infectious diseases. The aim of this study was to evaluate the inhibition of Candida biofilm formation by Hedera rhombea (Korean name: songak) extract. Biofilm formation was assessed using the crystal violet assay which showed a dose dependent reduction in the presence of extract with the biofilm formation inhibitory concentration of C. albicans (IC50 = 12.5μg/ml), C. tropicalis var. tropicalis (IC50 = 25μg/ml), C. parapsilosis var. parapsilosis (IC50 = 6.25μg/ml), C. glabrata (IC50 = 6.25μg/ml), C. tropicalis (IC50 = 12.5μg/ml), and C. parapsilosis (IC50 = 12.5μg/ml) without directly reducing Candida growth. Treatment with 6.25μg/mL of extract increased the antifungal susceptibility to miconazole from 32% decreasing of fungal growth to 98.8% of that based on the fungal growth assay. Treatment of extract dose-dependently reduced the dimorphic transition of Candida based on the dimorphic transition assay and treatment of 3.125μg/mL of extract completely blocked the adherence of Candida to the HaCaT cells. To know the molecular mechanisms of biofilm formation inhibition by extract, qRT-PCR analysis was done, and the extract was found to dose dependently reduce the expression of hyphal-associated genes (ALS3, ECE1, HWP1, PGA50, and PBR1), extracellular matrix genes (GSC1, ZAP1, ADH5, and CSH1), Ras1-cAMP-PKA pathway genes (CYR1, EFG1, and RAS1), Cph2-Tec1 pathway gene (TEC1) and MAP kinases pathway gene (HST7). In this study, Hedera rhombea extract showed inhibition of fungal biofilm formation, activation of antifungal susceptibility, and reduction of infection. These results suggest that fungal biofilm formation is good screen for developing the antifungal adjuvant and Hedera rhombea extract should be a good candidate against biofilm-related fungal infection.

Genome-wide in silico analysis of long intergenic non-coding RNAs from rice peduncles at the heading stage.

The online version contains supplementary material available at 10.1007/s12298-021-01059-2.

IMFLer: A Web Application for Interactive Metabolic Flux Analysis and Visualization.

Increasing genome-wide data in biological sciences and medicine has contributed to the development of a variety of visualization tools. Several automatic, semiautomatic, and manual visualization tools have already been developed. Some even have integrated flux balance analysis (FBA), but in most cases, it depends on separately installed third party software that is proprietary and does not allow customization of its functionality and has many restrictions for easy data distribution and analysis. In this study, we present an interactive metabolic flux analyzer and visualizer (IMFLer)-a static single-page web application that enables the reading and management of metabolic model layout maps, as well as immediate visualization of results from both FBA and flux variability analysis (FVA). IMFLer uses the Escher Builder tool to load, show, edit, and save metabolic pathway maps. This makes IMFLer an attractive and easily applicable tool with a user-friendly interface. Moreover, it allows to faster interpret results from FBA and FVA and improves data interoperability by using a standardized file format for the genome-scale metabolic model. IMFLer is a fully open-source tool that enables the rapid visualization and interpretation of the results of FBA and FVA with no time setup and no programming skills required, available at https://lv-csbg.github.io/IMFLer/.

Intraoperative mapping and monitoring of the optic pathway

The identification of the visual pathway during surgery for tumors in visual areas is challenging. We present our experience in visual pathway mapping and monitoring, describing the role of direct mapping of the optic radiations and different techniques of VEPs monitoring, employing both Scalp Recording (SR) and the use of strip electrode positioned over the primary visual cortex for Direct Cortical Recording (DCR).

"The full mapping of low-lying excited state relaxation dynamic pathways for acetophenone "

"The full mapping of low-lying excited state relaxation dynamic pathways for acetophenone "

Intravenous administration of three multiwalled carbon nanotubes to female rats and their effect on urinary biochemical profile.

This study was conducted to investigate the influence of outer diameter (OD) and length (L) of multiwalled carbon nanotubes (MWCNTs) on biodistribution and the perturbation of endogenous metabolite profiles. Three different-sized carboxylated MWCNTs (NIEHS-12-2: L 0.5-2μm, OD 10-20 nm, NIEHS-13-2: L 0.5-2μm, OD 30-50 nm, and NIEHS-14-2: L 10-30 μm, OD 10-20 nm) in water were administered to female Sprague-Dawley rats as a single intravenous dose of 1mg/kg MWCNTs. Biodistribution in liver, lung, spleen, and lymph nodes was evaluated in tissue sections at 1 and 7days' post-dosing using enhanced darkfield microscopy and hyperspectral imaging. Nuclear magnetic resonance (NMR) analysis was used for biochemical profiling and pathway mapping of endogenous metabolites in urine collected at 24-h intervals prior to dosing, at Day 1 and Day 7. At Day 1 and Day 7, all three MWCNTs were observed in liver. NIEHS-12-2 was observed in spleen, whereas NIEHS-13-2 and NIEHS-14-2 were not. All three MWCNTs were observed in lymph nodes and lung at Day 7. The urinary biochemical profile showed the highest positive fold change (FC) at Day 7 for the metabolites acetate, alanine, and lactate, whereas 1-methylnicotinamide, 2-oxoglutarate, and hippurate had some of the lowest FCs for all three MWCNTs. This study demonstrates that the observed tissue location of MWCNTs is size dependent. Overlaps in the perturbation of endogenous metabolite profiles were found regardless of their size, and the biochemical responses were more profound at Day 7 compared with Day 1, indicating a delayed biological response to MWCNTs.

Comprehensive LC-HRMS metabolomics analyses for the estimation of environmental inputs of altrenogest in pig breeding

Altrenogest (ALT), a synthetic progestogen, is used in pig farming for estrus synchronization in gilts. Residues of ALT and its metabolites may reach the aquatic environment via the spread of liquid manure and may present a risk for fish and other higher aquatic organisms due to its endocrine disrupting potential. A pilot study was conducted in which spot urine samples from ALT-treated and non-medicated gilts were collected. We applied LC-HRMS analysis to perform targeted analysis of ALT and known metabolites as well as non-targeted metabolomics analyses to find previously unknown metabolites. The targeted investigation showed that glucuronide conjugates of ALT and its photo-isomerization product are main urinary metabolites of ALT in gilts. Furthermore, an unknown isomerization product of ALT was observed at trace level, whereas ALT and ALT sulfate were not found. The chemometric analysis of non-targeted data revealed a clear difference between ALT-treated gilts and control animals. Furthermore, a hydroxylated ALT glucuronide was identified as highly significant in the ALT-treated group. Additional biomarker annotation and pathway mapping revealed changes in the metabolism of ALT-treated animals which can be explained by ALT's hormonal action. This study illustrates the exceptional potential of LC-HRMS and metabolomics for the detection of potentially new environmental contaminants with high biological activity. Further advantages of the method described are the sampling during routine breeding conditions, a relatively small number of animals required and no particular stress for the animals.

Transcriptomics analysis of genes induced by melatonin related to glucosinolates synthesis in broccoli hairy roots

ABSTRACT Glucoraphanin (GRA) is found in the seeds and vegetative organs of broccoli (Brassica oleracea L. var. italica Planch) as the precursor of anti-carcinogen sulforaphane (SF). The yield of GRA obtained from these materials is weak and the cost is high. In recent years, the production of plant secondary metabolites by large-scale hairy roots culture in vitro has succeeded in some species. Melatonin (MT) is a natural hormone which existed in numerous organisms. Studies have demonstrated that MT can improve the synthesis of secondary metabolites in plants. At present, it has not been reported that MT regulates the biosynthesis of glucoraphanin in broccoli hairy roots. In this study, the broccoli hairy roots that grew for 20 d were respectively treated by 500 µM MT for 0, 6, 12, 20 and 32. To explore the reason of changes in secondary metabolites and reveal the biosynthetic pathway of glucoraphanin at transcriptional level. Compared with 0 h, the yield of GRA under other treatments was increased, and the overall trend was firstly increased and then decreased. The total yield of GRA reached the highest at 12 h, which was 1.22-fold of 0 h. Then, the genome of broccoli as the reference, a total of 13234 differentially expressed genes (DEGs) were identified in broccoli hairy roots under treatment with 500 µM MT for 0, 6, 12, 20 and 32 h, respectively. Among these DEGs, 6266 (47.35%) were upregulated and 6968 (52.65%) were downregulated. It was found that the pathway of ‘Glucosinolates biosynthesis (ko00966)’ was enriched in the 16th place by Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of the upregulated DEGs. The expression of key genes in the GRA biosynthesis pathway was upregulated at all time points, and a deduced GRA biosynthesis pathway map was constructed for reference.