2,146 research outputs found

    RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics

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    Statistically meaningful comparison/combination of peptide identification results from various search methods is impeded by the lack of a universal statistical standard. Providing an E-value calibration protocol, we demonstrated earlier the feasibility of translating either the score or heuristic E-value reported by any method into the textbook-defined E-value, which may serve as the universal statistical standard. This protocol, although robust, may lose spectrum-specific statistics and might require a new calibration when changes in experimental setup occur. To mitigate these issues, we developed a new MS/MS search tool, RAId_aPS, that is able to provide spectrum-specific E-values for additive scoring functions. Given a selection of scoring functions out of RAId score, K-score, Hyperscore and XCorr, RAId_aPS generates the corresponding score histograms of all possible peptides using dynamic programming. Using these score histograms to assign E-values enables a calibration-free protocol for accurate significance assignment for each scoring function. RAId_aPS features four different modes: (i) compute the total number of possible peptides for a given molecular mass range, (ii) generate the score histogram given a MS/MS spectrum and a scoring function, (iii) reassign E-values for a list of candidate peptides given a MS/MS spectrum and the scoring functions chosen, and (iv) perform database searches using selected scoring functions. In modes (iii) and (iv), RAId_aPS is also capable of combining results from different scoring functions using spectrum-specific statistics. The web link is http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/raid_aps/index.html. Relevant binaries for Linux, Windows, and Mac OS X are available from the same page.Comment: 34 pages, 10 figures, 1 supplementary information file (RAId_aPS_support.pdf). To view the supplementary file, please download and extract the gzipped tar source file listed under "Other formats

    Neurofilament light in plasma is a potential biomarker of central nervous system involvement in systemic lupus erythematosus

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    BACKGROUND: Neuropsychiatric manifestations (NP) are common in systemic lupus erythematosus (SLE). However, the pathophysiological mechanisms are not completely understood. Neurofilament light protein (NfL) is part of the neuronal cytoskeleton. Increased NfL concentrations, reflecting neurodegeneration, is observed in cerebrospinal fluid (CSF) in several neurodegenerative and neuroinflammatory conditions. We aimed to explore if plasma NfL could serve as a biomarker for central nervous system (CNS) involvement in SLE. METHODS: Sixty-seven patients with SLE underwent neurological examination; 52 underwent lumbar puncture, while 62 underwent cerebral magnetic resonance imaging (MRI). We measured selected auto-antibodies and other laboratory variables postulated to have roles in NP pathophysiology in the blood and/or CSF. We used SPM12 software for MRI voxel-based morphometry. RESULTS: Age-adjusted linear regression analyses revealed increased plasma NfL concentrations with increasing creatinine (β = 0.01, p < 0.001) and Q-albumin (β = 0.07, p = 0.008). We observed higher plasma NfL concentrations in patients with a history of seizures (β = 0.57, p = 0.014), impaired motor function (β = 0.36, p = 0.008), increasing disease activity (β = 0.04, p = 0.008), and organ damage (β = 0.10, p = 0.002). Voxel-based morphometry suggested an association between increasing plasma NfL concentrations and the loss of cerebral white matter in the corpus callosum and hippocampal gray matter. CONCLUSION: Increased plasma NfL concentrations were associated with some abnormal neurological, cognitive, and neuroimaging findings. However, plasma NfL was also influenced by other factors, such as damage accrual, creatinine, and Q-albumin, thereby obscuring the interpretation of how plasma NfL reflects CNS involvement. Taken together, NfL in CSF seems a better marker of neuronal injury than plasma NfL in patients with SLE

    Microfluidic systems for the analysis of the viscoelastic fluid flow phenomena in porous media

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    In this study, two microfluidic devices are proposed as simplified 1-D microfluidic analogues of a porous medium. The objectives are twofold: firstly to assess the usefulness of the microchannels to mimic the porous medium in a controlled and simplified manner, and secondly to obtain a better insight about the flow characteristics of viscoelastic fluids flowing through a packed bed. For these purposes, flow visualizations and pressure drop measurements are conducted with Newtonian and viscoelastic fluids. The 1-D microfluidic analogues of porous medium consisted of microchannels with a sequence of contractions/ expansions disposed in symmetric and asymmetric arrangements. The real porous medium is in reality, a complex combination of the two arrangements of particles simulated with the microchannels, which can be considered as limiting ideal configurations. The results show that both configurations are able to mimic well the pressure drop variation with flow rate for Newtonian fluids. However, due to the intrinsic differences in the deformation rate profiles associated with each microgeometry, the symmetric configuration is more suitable for studying the flow of viscoelastic fluids at low De values, while the asymmetric configuration provides better results at high De values. In this way, both microgeometries seem to be complementary and could be interesting tools to obtain a better insight about the flow of viscoelastic fluids through a porous medium. Such model systems could be very interesting to use in polymer-flood processes for enhanced oil recovery, for instance, as a tool for selecting the most suitable viscoelastic fluid to be used in a specific formation. The selection of the fluid properties of a detergent for cleaning oil contaminated soil, sand, and in general, any porous material, is another possible application

    Neurofilament light is a biomarker of brain involvement in lupus and primary Sjögren's syndrome

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    Background: To test the hypothesis that neuroflament light (NfL) in CSF is a biomarker of CNS involvement in patients with systemic lupus erythematosus (SLE) and primary Sjögren’s syndrome (pSS), we measured NfL in CSF from 52 patients with lupus and 54 with pSS and explored associations with clinical, structural, immunological and biochemical abnormalities. Methods: In CSF, we measured NfL, anti-P antibodies, protein S100B and TWEAK by ELISA and anti-NR2 antibodies by electrochemiluminescence. Anti-phospholipid antibodies and routine immunological tests were performed in blood. IgG and albumin were measured in CSF and serum for assessment of the blood–brain barrier function (Q-albumin) and intrathecal IgG production (IgG index). Cerebral MRI and neuropsychological testing were performed. Results: A multivariable regression model showed that increasing CSF anti-NR2 antibody levels were associated with increasing NfL levels in patients with SLE (B 1.27, 95% CI 0.88–1.65, p<0.001). Age contributed signifcantly in the model (B 0.04, 95% CI 0.03–0.05, p<0.001). Similar fndings were observed in the pSS group. Adjusted for age and sex, no associations were found between NfL levels and any MRI data. In SLE patients, higher NfL concentrations were associated with impairments in psychomotor speed and motor function, and in pSS with motor dysfunction. These associations remained in multivariable regression models. Conclusions: Increased concentration of NfL in CSF is a marker of cerebral involvement in patients with SLE and pSS, is strongly associated with the presence of anti-NR2 antibodies, and correlates with cognitive impairment in several domain

    Isolation and functional characterization of a cotton ubiquitination-related promoter and 5'UTR that drives high levels of expression in root and flower tissues

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    <p>Abstract</p> <p>Background</p> <p>Cotton (<it>Gossypium </it>spp.) is an important crop worldwide that provides raw material to 40% of the textile fiber industry. Important traits have been studied aiming the development of genetically modified crops including resistance to insect and diseases, and tolerance to drought, cold and herbicide. Therefore, the characterization of promoters and regulatory regions is also important to achieve high gene expression and/or a specific expression pattern. Commonly, genes involved in ubiquitination pathways are highly and differentially expressed. In this study, we analyzed the expression of a cotton ubiquitin-conjugating enzyme (E2) family member with no previous characterization.</p> <p>Results</p> <p>Nucleotide analysis revealed high identity with cotton <it>E2 </it>homologues. Multiple alignment showed a premature stop codon, which prevents the encoding of the conserved cysteine residue at the <it>E2 </it>active site, and an intron that is spliced in <it>E2 </it>homologues, but not in <it>GhGDRP85</it>. The <it>GhGDRP85 </it>gene is highly expressed in different organs of cotton plants, and has high transcript levels in roots. Its promoter (uceApro2) and the 5'UTR compose a regulatory region named uceA1.7, and were isolated from cotton and studied in <it>Arabidopsis thaliana</it>. uceA1.7 shows strong expression levels, equaling or surpassing the expression levels of CaMV35S. The uceA1.7 regulatory sequence drives GUS expression 7-fold higher in flowers, 2-fold in roots and at similar levels in leaves and stems. GUS expression levels are decreased 7- to 15-fold when its 5'UTR is absent in uceApro2.</p> <p>Conclusions</p> <p>uceA1.7 is a strong constitutive regulatory sequence composed of a promoter (uceApro2) and its 5'UTR that will be useful in genetic transformation of dicots, having high potential to drive high levels of transgene expression in crops, particularly for traits desirable in flower and root tissues.</p

    A new thiocyanoacetamide (2-cyano-2-p-nitrophenyl-N-benzylthioamide) reduces doxorubicin-induced in vitro toxicity in Sertoli cells by decreasing apoptosis and autophagy

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    Despite conflicting data on doxorubicin (DOX) reproductive toxicity, its chemotherapeutic potential sustains its use to treat different types of cancer. This work was designed to study the protective effect of a newly synthesized thiocyanoacetamide (TA), in comparison with selenium (Se), against doxorubicin-induced in vitro toxicity in rat Sertoli cells (SCs). DOX was administered alone or in combination with Se or TA. The possible protective role of increased concentrations of TA (0.25, 0.5 and 1 mM) or Se (12, 25 and 50 mu M) on SCs was tested against 1 mu M of DOX. From this screening, only the least toxic doses of TA and Se were used for further analysis. DOX cytotoxicity, as well as its impact on SCs viability, mitochondria) membrane potential (Delta Psi(m)), oxidative stress biomarkers, apoptosis and autophagy were assessed. Our results showed that DOX exerted its cytotoxic effect through a significant increase in cell death. DOX-mediated cell death was not related to autophagy nor to an overproduction of reactive oxygen species. It was rather due to apoptosis, as shown by the increased number of apoptotic cells and increased activity of caspase-3, or due to necrosis, as shown by the increase in lactate dehydrogenase (LDH) extracellular activity. Still, Bax and Bcl-2 protein expression levels, as well as Delta Psi(m) were not altered by the different treatments. Some individual doses of Se or TA induced a significant toxicity in SCs, however, when combined with DOX, there was a decrease in cell death, LDH extracellular activity, number of apoptotic cells and caspase-3 activity. Overall, our results indicate that DOX-mediated apoptosis in cultured SCs can possibly be averted through its association with specific doses of Se or TA. Nevertheless, TA showed a higher efficiency than Se in reducing DOX-induced toxicity in SCs by decreasing not only apoptosis, but also necrosis and autophagy. (C) 2019 Elsevier Inc. All rights reserved
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