Evaluation of peak-picking algorithms for protein mass spectrometry

Peak picking is an early key step in MS data analysis. We compare three commonly used approaches to peak picking and discuss their merits by means of statistical analysis. Methods investigated encompass signal-to-noise ratio, continuous wavelet transform, and a correlation-based approach using a Gaussian template. Functionality of the three methods is illustrated and discussed in a practical context using a mass spectral data set created with MALDI-TOF technology. Sensitivity and specificity are investigated using a manually defined reference set of peaks. As an additional criterion, the robustness of the three methods is assessed by a perturbation analysis and illustrated using ROC curves

The Functional Study of the N-Terminal Region of Influenza B Virus Nucleoprotein

Influenza nucleoprotein (NP) is a major component of the ribonucleoprotein (vRNP) in influenza virus, which functions for the transcription and replication of viral genome. Compared to the nucleoprotein of influenza A (ANP), the N-terminal region of influenza B nucleoprotein (BNP) is much extended. By virus reconstitution, we found that the first 38 residues are essential for viral growth. We further illustrated the function of BNP by mini-genome reconstitution, fluorescence microscopy, electron microscopy, light scattering and gel shift. Results show that the N terminus is involved in the formation of both higher homo-oligomers of BNP and BNP-RNA complex

Intermedin attenuates LPS-induced inflammation in the rat testis

First reported as a vasoactive peptide in the cardiovascular system, intermedin (IMD), also known as adrenomedullin 2 (ADM2), is a hormone with multiple potent roles, including its antioxidant action on the pulmonary, central nervous, cardiovascular and renal systems. Though IMD may play certain roles in trophoblast cell invasion, early embryonic development and cumulus cell-oocyte interaction, the role of IMD in the male reproductive system has yet to be investigated. This paper reports our findings on the gene expression of IMD, its receptor components and its protein localization in the testes. In a rat model, bacterial lippolysaccharide (LPS) induced atypical orchitis, and LPS treatment upregulated the expression of IMD and one of its receptor component proteins, i.e. receptor activity modifying protein 2 (RAMP2). IMD decreased both plasma and testicular levels of reactive oxygen species (ROS) production, attenuated the increase in the gene expression of the proinflammatory cytokines tumor necrosis factor alpha (TNFα), interleukin 6 (IL6) and interleukin 1 beta (IL1β), rescued spermatogenesis, and prevented the decrease in plasma testosterone levels caused by LPS. The restorative effect of IMD on steroidogenesis was also observed in hydrogen peroxide-treated rat primary Leydig cells culture. Our results indicate IMD plays an important protective role in spermatogenesis and steroidogenesis, suggesting therapeutic potential for IMD in pathological conditions such as orchitis.published_or_final_versio

Wandering behaviour prevents inter and intra oceanic speciation in a coastal pelagic fish

Small pelagic fishes have the ability to disperse over long distances and may present complex evolutionary histories. Here, Old World Anchovies (OWA) were used as a model system to understand genetic patterns and connectivity of fish between the Atlantic and Pacific basins. We surveyed 16 locations worldwide using mtDNA and 8 microsatellite loci for genetic parameters, and mtDNA (cyt b; 16S) and nuclear (RAG1; RAG2) regions for dating major lineage-splitting events within Engraulidae family. The OWA genetic divergences (0-0.4%) are compatible with intra-specific divergence, showing evidence of both ancient and contemporary admixture between the Pacific and Atlantic populations, enhanced by high asymmetrical migration from the Pacific to the Atlantic. The estimated divergence between Atlantic and Pacific anchovies (0.67 [0.53-0.80] Ma) matches a severe drop of sea temperature during the Gunz glacial stage of the Pleistocene. Our results support an alternative evolutionary scenario for the OWA, suggesting a coastal migration along south Asia, Middle East and eastern Africa continental platforms, followed by the colonization of the Atlantic via the Cape of the Good Hope.Portuguese Foundation for Science & Technology (FCT) [SFRH/BD/36600/2007]; FCT [UID/MAR/04292/2013, SFRH/BPD/65830/2009]; FCT strategic plan [UID/Multi/04326/2013]info:eu-repo/semantics/publishedVersio

Incremental prognostic value of global longitudinal strain in patients with type 2 diabetes mellitus

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Evaluation of moderate alcohol use and cognitive function among men using a mendelian randomization design in the guangzhou biobank cohort study

Observational studies usually show that moderate alcohol use is associated with better cognitive function. Such studies are vulnerable to residual confounding arising from systematic differences between moderate alcohol users and others. A Mendelian randomization study carried out in a suitable population, such as southern Chinese men, in which alcohol use is low to moderate and is influenced by genotype, offers an alternative and superior approach for clarifying the causal effect of moderate alcohol use on cognitive function. The authors used aldehyde dehydrogenase 2 (ALDH2) genotype (AA, GA, or GG) as an instrumental variable in 2-stage least squares analysis to obtain unbiased estimates of the relation of alcohol consumption (measured in alcohol units (10 g ethanol) per day) with cognitive function, assessed from delayed 10-word recall score (n = 4,707) and Mini-Mental State Examination (MMSE) score (n = 2,284), among men from the Guangzhou Biobank Cohort Study (2003-2008). ALHD2 genotype was strongly associated with alcohol consumption, with an F statistic of 71.0 in 2-stage least squares analysis. Alcohol consumption was not associated with delayed 10-word recall score (-0.03 words per alcohol unit, 95% confidence interval:-0.18, 0.13) or MMSE score (0.06 points per alcohol unit, 95% confidence interval:-0.22, 0.34). Moderate alcohol use is unlikely to be cognitively protective. © The Author 2012. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved.postprin

Evaluation of a sponge assisted-granular anaerobic membrane bioreactor (SG-AnMBR) for municipal wastewater treatment

© 2017 Elsevier Ltd This study compared a conventional granular anaerobic membrane bioreactor (CG-AnMBR) with a sponge assisted-granular anaerobic membrane bioreactor (SG-AnMBR) in terms of treatment performance, granular sludge properties, membrane fouling behaviour and biogas production. The SG-AnMBR showed better organics and nutrient removal, and enhanced methane yield at 156.3 ± 5.8 mL CH4(STP)/g CODremoved. Granular sludge from the SG-AnMBR had superior quality with better settleability, larger particle size, higher EPS content and more granule abundance. The SG-AnMBR also exhibited slower fouling development with 50.7% lower total filtration resistance than those of the CG-AnMBR. Sponge addition effectively affected the concentration and properties of microbial products (e.g. soluble microbial products (SMP) and extracellular polymeric substances (EPS)) in granular sludge, cake layer as well as settling zone mixed liquor, thus alleviating the fouling propensity. The liquid chromatography-organic carbon detection (LC-OCD) analysis suggested that sponge addition reduced the concentrations of biopolymers, low molecular weight neutrals and acids, and building blocks of the foulants. Compared with the SG-AnMBR, GC-MS analysis confirmed the accumulation of volatile fatty acids, particularly acetic acid in the CG-AnMBR. It is evident that the SG-AnMBR could be a promising solution for improving overall G-AnMBR performance and substantially mitigating membrane fouling

Bioprocessing for elimination antibiotics and hormones from swine wastewater

© 2017 Elsevier B.V. Antibiotics and hormones in swine wastewater have become a critical concern worldwide due to the severe threats to human health and the eco-environment. Removal of most detectable antibiotics and hormones, such as sulfonamides (SAs), SMs, tetracyclines (TCs), macrolides, and estrogenic hormones from swine wastewater utilizing various biological processes were summarized and compared. In biological processes, biosorption and biodegradation are the two major removal mechanisms for antibiotics and hormones. The residuals in treated effluents and sludge of conventional activated sludge and anaerobic digestion processes can still pose risks to the surrounding environment, and the anaerobic processes’ removal efficiencies were inferior to those of aerobic processes. In contrast, membrane bioreactors (MBRs), constructed wetlands (CWs) and modified processes performed better because of their higher biodegradation of toxicants. Process modification on activated sludge, anaerobic digestion and conventional MBRs could also enhance the performance (e.g. removing up to 98% SMs, 88.9% TCs, and 99.6% hormones from wastewater). The hybrid process combining MBRs with biological or physical technology also led to better removal efficiency. As such, modified conventional biological processes, advanced biological technologies and MBR hybrid systems are considered as a promising technology for removing toxicants from swine wastewater

A novel mechanistic model for nitrogen removal in algal-bacterial photo sequencing batch reactors

© 2018 Elsevier Ltd A comprehensive mathematical model was constructed to evaluate the complex substrate and microbial interaction in algal-bacterial photo sequencing batch reactors (PSBR). The kinetics of metabolite, growth and endogenous respiration of ammonia oxidizing bacteria, nitrite oxidizing bacteria and heterotrophic bacteria were coupled to those of microalgae and then embedded into widely-used activated sludge model series. The impact of light intensity was considered for microalgae growth, while the effect of inorganic carbon was considered for each microorganism. The integrated model framework was assessed using experimental data from algal-bacterial consortia performing sidestream nitritation/denitritation. The validity of the model was further evaluated based on dataset from PSBR performing mainstream nitrification. The developed model could satisfactorily capture the dynamics of microbial populations and substrates under different operational conditions (i.e. feeding, carbon dosing and illuminating mode, light intensity, influent ammonium concentration), which might serve as a powerful tool for optimizing the novel algal-bacterial nitrogen removal processes