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  • 1
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    Online Resource
    Toxicity of ZnO and TiO2 to Escherichia coli cells
    Springer Science and Business Media LLC ; 2016
    In:  Scientific Reports Vol. 6, No. 1 ( 2016-10-12)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2016-10-12)
    Abstract: We performed a comprehensive investigation of the toxicity of ZnO and TiO 2 nanoparticles using Escherichia coli as a model organism. Both materials are wide band gap n-type semiconductors and they can interact with lipopolysaccharide molecules present in the outer membrane of E. coli , as well as produce reactive oxygen species (ROS) under UV illumination. Despite the similarities in their properties, the response of the bacteria to the two nanomaterials was fundamentally different. When the ROS generation is observed, the toxicity of nanomaterial is commonly attributed to oxidative stress and cell membrane damage caused by lipid peroxidation. However, we found that significant toxicity does not necessarily correlate with up-regulation of ROS-related proteins. TiO 2 exhibited significant antibacterial activity, but the protein expression profile of bacteria exposed to TiO 2 was different compared to H 2 O 2 and the ROS-related proteins were not strongly expressed. On the other hand, ZnO exhibited lower antibacterial activity compared to TiO 2 , and the bacterial response involved up-regulating ROS-related proteins similar to the bacterial response to the exposure to H 2 O 2 . Reasons for the observed differences in toxicity and bacterial response to the two metal oxides are discussed.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/srep35243
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
    detail.hit.zdb_id: 2615211-3
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  • 2
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    Association between phospholipid metabolism in plasma and spontaneous preterm birth: a discovery lipidomic analysis in the cork pregnancy cohort
    Springer Science and Business Media LLC ; 2020
    In:  Metabolomics Vol. 16, No. 2 ( 2020-02)
    Details
    In: Metabolomics, Springer Science and Business Media LLC, Vol. 16, No. 2 ( 2020-02)
    Abstract: Preterm birth (PTB) is defined as birth occurring before 37 weeks’ gestation, affects 5–9% of all pregnancies in developed countries, and is the leading cause of perinatal mortality. Spontaneous preterm birth (sPTB) accounts for 31–50% of all PTB, but the underlying pathophysiology is poorly understood. Objective This study aimed to decipher the lipidomics pathways involved in pathophysiology of sPTB. Methods Blood samples were taken from SCreening fOr Pregnancy Endpoints (SCOPE), an international study that recruited 5628 nulliparous women, with a singleton low-risk pregnancy. Our analysis focused on plasma from SCOPE in Cork. Discovery profiling of the samples was undertaken using liquid chromatography-mass spectrometry Lipidomics, and features significantly altered between sPTB (n = 16) and Control (n = 32) groups were identified using empirical Bayes testing, adjusting for multiple comparisons. Results Twenty-six lipids showed lower levels in plasma of sPTB compared to controls (adjusted p  〈  0.05), including 20 glycerophospholipids (12 phosphatidylcholines, 7 phosphatidylethanolamines, 1 phosphatidylinositol) and 6 sphingolipids (2 ceramides and 4 sphingomyelines). In addition, a diaglyceride, DG (34:4), was detected in higher levels in sPTB compared to controls. Conclusions We report reduced levels of plasma phospholipids in sPTB. Phospholipid integrity is linked to biological membrane stability and inflammation, while storage and breakdown of lipids have previously been implicated in pregnancy complications. The contribution of phospholipids to sPTB as a cause or effect is still unclear; however, our results of differential plasma phospholipid expression represent another step in advancing our understanding of the aetiology of sPTB. Further work is needed to validate these findings in independent pregnancy cohorts.
    Type of Medium: Online Resource
    ISSN: 1573-3882 , 1573-3890
    URL: Article
    DOI: 10.1007/s11306-020-1639-6
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2182289-X
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  • 3
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    Dynamic changes in the brain protein interaction network correlates with progression of Aβ42 pathology in Drosophila
    Springer Science and Business Media LLC ; 2020
    In:  Scientific Reports Vol. 10, No. 1 ( 2020-10-28)
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    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2020-10-28)
    Abstract: Alzheimer’s disease (AD), the most prevalent form of dementia, is a progressive and devastating neurodegenerative condition for which there are no effective treatments. Understanding the molecular pathology of AD during disease progression may identify new ways to reduce neuronal damage. Here, we present a longitudinal study tracking dynamic proteomic alterations in the brains of an inducible Drosophila melanogaster model of AD expressing the Arctic mutant Aβ42 gene. We identified 3093 proteins from flies that were induced to express Aβ42 and age-matched healthy controls using label-free quantitative ion-mobility data independent analysis mass spectrometry. Of these, 228 proteins were significantly altered by Aβ42 accumulation and were enriched for AD-associated processes. Network analyses further revealed that these proteins have distinct hub and bottleneck properties in the brain protein interaction network, suggesting that several may have significant effects on brain function. Our unbiased analysis provides useful insights into the key processes governing the progression of amyloid toxicity and forms a basis for further functional analyses in model organisms and translation to mammalian systems.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-020-74748-9
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2615211-3
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  • 4
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    Glycerophospholipid and detoxification pathways associated with small for gestation age pathophysiology: discovery metabolomics analysis in the SCOPE cohort
    Springer Science and Business Media LLC ; 2021
    In:  Metabolomics Vol. 17, No. 1 ( 2021-01)
    Details
    In: Metabolomics, Springer Science and Business Media LLC, Vol. 17, No. 1 ( 2021-01)
    Abstract: Small for gestational age (SGA) may be associated with neonatal morbidity and mortality. Our understanding of the molecular pathways implicated is poor. Objectives Our aim was to determine the metabolic pathways involved in the pathophysiology of SGA and examine their variation between maternal biofluid samples. Methods Plasma (Cork) and urine (Cork, Auckland) samples were collected at 20 weeks’ gestation from nulliparous low-risk pregnant women participating in the SCOPE study. Women who delivered an SGA infant (birthweight  〈  10th percentile) were matched to controls (uncomplicated pregnancies). Metabolomics (urine) and lipidomics (plasma) analyses were performed using ultra performance liquid chromatography-mass spectrometry. Features were ranked based on FDR adjusted p-values from empirical Bayes analysis, and significant features putatively identified. Results Lipidomics plasma analysis revealed that 22 out of the 33 significantly altered lipids annotated were glycerophospholipids; all were detected in higher levels in SGA. Metabolomic analysis identified reduced expression of metabolites associated with detoxification (D-Glucuronic acid, Estriol-16-glucuronide), nutrient absorption and transport (Sulfolithocholic acid) pathways. Conclusions This study suggests higher levels of glycerophospholipids, and lower levels of specific urine metabolites are implicated in the pathophysiology of SGA. Further research is needed to confirm these findings in independent samples.
    Type of Medium: Online Resource
    ISSN: 1573-3882 , 1573-3890
    URL: Article
    DOI: 10.1007/s11306-020-01740-9
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
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  • 5
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    A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
    Springer Science and Business Media LLC ; 2022
    In:  Scientific Data Vol. 9, No. 1 ( 2022-03-30)
    Details
    In: Scientific Data, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2022-03-30)
    Abstract: In the last decade, a revolution in liquid chromatography-mass spectrometry (LC-MS) based proteomics was unfolded with the introduction of dozens of novel instruments that incorporate additional data dimensions through innovative acquisition methodologies, in turn inspiring specialized data analysis pipelines. Simultaneously, a growing number of proteomics datasets have been made publicly available through data repositories such as ProteomeXchange, Zenodo and Skyline Panorama. However, developing algorithms to mine this data and assessing the performance on different platforms is currently hampered by the lack of a single benchmark experimental design. Therefore, we acquired a hybrid proteome mixture on different instrument platforms and in all currently available families of data acquisition. Here, we present a comprehensive Data-Dependent and Data-Independent Acquisition (DDA/DIA) dataset acquired using several of the most commonly used current day instrumental platforms. The dataset consists of over 700 LC-MS runs, including adequate replicates allowing robust statistics and covering over nearly 10 different data formats, including scanning quadrupole and ion mobility enabled acquisitions. Datasets are available via ProteomeXchange (PXD028735).
    Type of Medium: Online Resource
    ISSN: 2052-4463
    URL: Article
    DOI: 10.1038/s41597-022-01216-6
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2775191-0
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  • 6
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    Mass spectrometry-based metabolomics for the discovery of candidate markers of flavonoid and polyphenolic intake in adults
    Springer Science and Business Media LLC ; 2021
    In:  Scientific Reports Vol. 11, No. 1 ( 2021-03-11)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2021-03-11)
    Abstract: Robust biological markers of dietary exposure are essential in improving the understanding of the link between diet and health outcomes. Polyphenolic compounds, including flavonoids, have been proposed to mitigate the risk of chronic diseases where oxidative stress and inflammation play a central role. Biomarkers can provide objective measurement of the levels of polyphenolic compounds. In this study, we provide methodology to identify potential candidate markers of polyphenol intake in human serum. Seventeen participants from the UK arm of the Global Allergy and Asthma Network of Excellence (GA 2 LEN) had their dietary intake estimated using a validated food frequency questionnaire, and serum samples were assessed using mass spectrometry to identify potential candidate markers. 144 features were assigned identities, of these we identified four biologically relevant compounds (rhamnazin 3-rutinoside, 2-galloyl-1,4-galactarolactone methyl ester, 2″,32″-di-O-p-coumaroylafzelin and cyclocommunin), which were significantly increased in the serum of participants with high predicted level of fruit and vegetable intake. 2-galloyl-1,4-galactarolactone methyl ester was strongly correlated with total flavonoids (r = 0.62; P  = 0.005), flavan-3-ols (r = 0.67; P  = 0.002) as well as with other four subclasses. Rhamnazin 3-rutinoside showed strong correlation with pro-anthocyanidins (r = 0.68; P  = 0.001), flavones (r = 0.62; P  = 0.005). Our results suggest that serum profiling for these compounds might be an effective way of establishing the relative intake of flavonoids and could contribute to improve the accuracy of epidemiological methods to ascertain flavonoid intake.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-021-85190-w
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2615211-3
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  • 7
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    Specificity of the osmotic stress response in Candida albicans highlighted by quantitative proteomics
    Springer Science and Business Media LLC ; 2018
    In:  Scientific Reports Vol. 8, No. 1 ( 2018-09-27)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2018-09-27)
    Abstract: Stress adaptation is critical for the survival of microbes in dynamic environments, and in particular, for fungal pathogens to survive in and colonise host niches. Proteomic analyses have the potential to significantly enhance our understanding of these adaptive responses by providing insight into post-transcriptional regulatory mechanisms that contribute to the outputs, as well as testing presumptions about the regulation of protein levels based on transcript profiling. Here, we used label-free, quantitative mass spectrometry to re-examine the response of the major fungal pathogen of humans, Candida albicans , to osmotic stress. Of the 1,262 proteins that were identified, 84 were down-regulated in response to 1M NaCl, reflecting the decrease in ribosome biogenesis and translation that often accompanies stress. The 64 up-regulated proteins included central metabolic enzymes required for glycerol synthesis, a key osmolyte for this yeast, as well as proteins with functions during stress. These data reinforce the view that adaptation to salt stress involves a transient reduction in ribosome biogenesis and translation together with the accumulation of the osmolyte, glycerol. The specificity of the response to salt stress is highlighted by the small proportion of quantified C. albicans proteins (5%) whose relative elevated abundances were statistically significant.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-018-32792-6
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
    detail.hit.zdb_id: 2615211-3
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  • 8
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    Development of a rapid profiling method for the analysis of polar analytes in urine using HILIC–MS and ion mobility enabled HILIC–MS
    Springer Science and Business Media LLC ; 2019
    In:  Metabolomics Vol. 15, No. 2 ( 2019-2)
    Details
    In: Metabolomics, Springer Science and Business Media LLC, Vol. 15, No. 2 ( 2019-2)
    Type of Medium: Online Resource
    ISSN: 1573-3882 , 1573-3890
    URL: Article
    DOI: 10.1007/s11306-019-1474-9
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
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  • 9
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    A multiple reaction monitoring method for determining peanut (Arachis hypogea) allergens in serum using quadrupole and time-of-flight mass spectrometry
    Springer Science and Business Media LLC ; 2020
    In:  Analytical and Bioanalytical Chemistry Vol. 412, No. 12 ( 2020-05), p. 2815-2827
    Details
    In: Analytical and Bioanalytical Chemistry, Springer Science and Business Media LLC, Vol. 412, No. 12 ( 2020-05), p. 2815-2827
    Abstract: Peanut is a major cause of severe IgE-mediated food allergic reactions, which can be exacerbated by factors, such as exercise, that may increase allergen uptake into the circulation. Enzyme-linked immunosorbent assays (ELISAs) have been used to determine allergen uptake into serum, but there are concerns over their specificity and a confirmatory method is required. Mass spectrometry (MS) methods have the potential to provide rigorous alternatives for allergen determination. A suite of peptide targets representing the major clinically relevant peanut allergens previously applied in food analysis were used to develop a targeted multiple reaction monitoring (MRM) method for determination of peanut in serum. Depletion of serum using affinity chromatography was found to be essential to allow detection of the peptide targets. A comparison of triple quadrupole and Q-TOF methods showed that one Ara h 2 peptide was only detected by the Q-TOF, the other peptide targets giving similar assay sensitivities with both MS platforms, although transitions for all the peptides were detected more consistently with the Q-TOF. The Q-TOF MRM assay detected peanut from spiked serum more effectively than the triple quadrupole assay, with Ara h 3 being detected down to 3 mg total peanut protein/L of serum, comparable with an Ara h 3–specific ELISA. The poor recoveries observed for both methods are likely due to loss of peanut immune complexes during the serum depletion process. Nevertheless, the Q-TOF MRM method has much promise to confirm the uptake of peanut proteins in serum samples providing immune complexes can be disrupted effectively prior to depletion.
    Type of Medium: Online Resource
    ISSN: 1618-2642 , 1618-2650
    URL: Article
    DOI: 10.1007/s00216-020-02508-9
    RVK:
    VA 4300
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 1459122-4
    detail.hit.zdb_id: 2071767-2
    SSG: 12
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