Capabilities and limitations of gel electrophoresis for elemental speciation : a laboratory's experience

Gel electrophoresis is a fractionation/separation technique that yields valuable information in the field of metalloproteomics, often referred to as metallomics. This paper is based on four years of practical experience of the authors' lab in this domain and highlights the capabilities and limitations of gel electrophoresis. Pitfalls of the technique were recognized by identifying the origin of artefacts in the separation, species degradation being the most important. Gel electrophoresis can be accomplished under either native or denaturing conditions. The speciation of vanadium and selenium among serum and yeast proteins, respectively, is sued to illustrate these two major modes. The most powerful approach is two-dimensional denaturing gel electrophoresis. This review of the methods used in our laboratory also descries the application of the two major detection techniques, autoradiography on the one hand and electrothermal vaporization - or laser ablation (LA)-inductively coupled plasma-mass spectrometry (ICP-MS) on the other

Problems and opportunities of applying data-& audio-mining techniques to ethnic music

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Using local texture maps of brain MR images to detect Mild Cognitive Impairment

Early detection of Alzheimer's disease is expected to aid in the development and monitoring of more effective treatments. Classification methods have been proposed to distinguish Alzheimer's patients from normal controls using Magnetic Resonance Images. However, their performance drops when classifying patients at a prodromal stage, such as in Mild Cognitive Impairment. Most often, the features used in these classification tasks are related to structural measures such as volume, shape and tissue density. However, microstructural changes have been shown to arise even earlier than these larger-scale alterations. Taking this into account, we propose the use of local statistical texture maps that make no assumptions regarding the location of the affected brain regions. Each voxel contains texture information from its local neighborhood and is used as a feature in the classification of normal controls and Mild Cognitive Impairment patients. The proposed approach obtained an accuracy of 87% (sensitivity 85%, specificity 95%) with Support Vector Machines, outperforming the 63% achieved by the local gray matter density feature

Golgi targeting of Drosophila melanogaster β4GalNAcTB requires a DHHC protein family–related protein as a pilot

Drosophila melanogaster β4GalNAcTB mutant flies revealed that this particular N-acetylgalactosaminyltransferase is predominant in the formation of lacdiNAc (GalNAcβ1,4GlcNAc)-modified glycolipids, but enzymatic activity could not be confirmed for the cloned enzyme. Using a heterologous expression cloning approach, we isolated β4GalNAcTB together with β4GalNAcTB pilot (GABPI), a multimembrane-spanning protein related to Asp-His-His-Cys (DHHC) proteins but lacking the DHHC consensus sequence. In the absence of GABPI, inactive β4GalNAcTB is trapped in the endoplasmic reticulum (ER). Coexpression of β4GalNAcTB and GABPI generates the active enzyme that is localized together with GABPI in the Golgi. GABPI associates with β4GalNAcTB and, when expressed with an ER retention signal, holds active β4GalNAcTB in the ER. Importantly, treatment of isolated membrane vesicles with Triton X-100 disturbs β4GalNAcTB activity. This phenomenon occurs with multimembrane-spanning glycosyltransferases but is normally not a property of glycosyltransferases with one membrane anchor. In summary, our data provide evidence that GABPI is required for ER export and activity of β4GalNAcTB

Metal transfer to sediments, invertebrates and fish following waterborne exposure to silver nitrate or silver sulfide nanoparticles in an indoor stream mesocosm

The fate of engineered nanomaterials in ecosystems is unclear. An aquatic stream mesocosm explored the fate and bioaccumulation of silver sulfide nanoparticles (AgS NPs) compared to silver nitrate (AgNO). The aims were to determine the total Ag in water, sediment and biota, and to evaluate the bioavailable fractions of silver in the sediment using a serial extraction method. The total Ag in the water column from a nominal daily dose of 10 μg L of Ag for the AgNO or AgS NP treatments reached a plateau of around 13 and 12 μg L, respectively, by the end of the study. Similarly, the sediment of both Ag-treatments reached ~380 μg Ag kg, and with most of it being acid-extractable/labile. The biota accumulated 4–59 μg Ag g dw, depending on the type of Ag-treatment and organism. The oligochaete worm, Lumbriculus variegatus, accumulated Ag from the AgS exposure over time, which was similar to the AgNO treatment by the end of the experiment. The planarian, Girardia tigrina, and the chironomid larva, Chironomus riparius, showed much higher Ag concentrations than the oligochaete worms; and with a clearer time-dependent statistically significant Ag accumulation relative to the untreated controls. For the pulmonate snail, Physa acuta, bioaccumulation of Ag from AgNO and AgS NP exposures was observed, but was lower from the nano treatment. The AgNO exposure caused appreciable Ag accumulation in the water flea, Daphnia magna, but accumulation was higher in the AgS NP treatment (reaching 59 μg g dw). In the rainbow trout, Oncorhynchus mykiss, AgNO, but not AgS NPs, caused total Ag concentrations to increase in the tissues. Overall, the study showed transfer of total Ag from the water column to the sediment, and Ag bioaccumulation in the biota, with Ag from AgS NP exposure generally being less bioavailable than that from AgNO.This work was supported by the project NanoFASE (Nanomaterial Fate and Speciation in the Environment), financed by the European Union's Horizon 2020 research and innovation programme under grant agreement no 646002. RDH was partly supported by NanoHarmony under grant agreement 885931 in Horizon 2020 while redrafting the main text. PVS was awarded with a PhD grant (SFRH/BD/51571/2014) by FCT – Fundação para a Ciência e a Tecnologia. SL and PVS received additional financial support from FCT/MCTES, through national funds, to CESAM (UIDP/50017/2020+UIDB/50017/2020+ LA/P/0094/2020)

Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information

Genome-wide association studies have generated an increasing number of common genetic variants associated with neurological and psychiatric disease risk. An improved understanding of the genetic control of gene expression in human brain is vital considering this is the likely modus operandum for many causal variants. However, human brain sampling complexities limit the explanatory power of brain-related expression quantitative trait loci (eQTL) and allele-specific expression (ASE) signals. We address this, using paired genomic and transcriptomic data from putamen and substantia nigra from 117 human brains, interrogating regulation at different RNA processing stages and uncovering novel transcripts. We identify disease-relevant regulatory loci, find that splicing eQTLs are enriched for regulatory information of neuron-specific genes, that ASEs provide cell-specific regulatory information with evidence for cellular specificity, and that incomplete annotation of the brain transcriptome limits interpretation of risk loci for neuropsychiatric disease. This resource of regulatory data is accessible through our web server, http://braineacv2.inf.um.es/

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

Background Genome-wide association studies (GWAS) in Parkinson's disease have increased the scope of biological knowledge about the disease over the past decade. We aimed to use the largest aggregate of GWAS data to identify novel risk loci and gain further insight into the causes of Parkinson's disease. Methods We did a meta-analysis of 17 datasets from Parkinson's disease GWAS available from European ancestry samples to nominate novel loci for disease risk. These datasets incorporated all available data. We then used these data to estimate heritable risk and develop predictive models of this heritability. We also used large gene expression and methylation resources to examine possible functional consequences as well as tissue, cell type, and biological pathway enrichments for the identified risk factors. Additionally, we examined shared genetic risk between Parkinson's disease and other phenotypes of interest via genetic correlations followed by Mendelian randomisation. Findings Between Oct 1, 2017, and Aug 9, 2018, we analysed 7·8 million single nucleotide polymorphisms in 37 688 cases, 18 618 UK Biobank proxy-cases (ie, individuals who do not have Parkinson's disease but have a first degree relative that does), and 1·4 million controls. We identified 90 independent genome-wide significant risk signals across 78 genomic regions, including 38 novel independent risk signals in 37 loci. These 90 variants explained 16–36% of the heritable risk of Parkinson's disease depending on prevalence. Integrating methylation and expression data within a Mendelian randomisation framework identified putatively associated genes at 70 risk signals underlying GWAS loci for follow-up functional studies. Tissue-specific expression enrichment analyses suggested Parkinson's disease loci were heavily brain-enriched, with specific neuronal cell types being implicated from single cell data. We found significant genetic correlations with brain volumes (false discovery rate-adjusted p=0·0035 for intracranial volume, p=0·024 for putamen volume), smoking status (p=0·024), and educational attainment (p=0·038). Mendelian randomisation between cognitive performance and Parkinson's disease risk showed a robust association (p=8·00 × 10−7). Interpretation These data provide the most comprehensive survey of genetic risk within Parkinson's disease to date, to the best of our knowledge, by revealing many additional Parkinson's disease risk loci, providing a biological context for these risk factors, and showing that a considerable genetic component of this disease remains unidentified. These associations derived from European ancestry datasets will need to be followed-up with more diverse data. Funding The National Institute on Aging at the National Institutes of Health (USA), The Michael J Fox Foundation, and The Parkinson's Foundation (see appendix for full list of funding sources)

Assessing associations between the AURKAHMMR-TPX2-TUBG1 functional module and breast cancer risk in BRCA1/2 mutation carriers

While interplay between BRCA1 and AURKA-RHAMM-TPX2-TUBG1 regulates mammary epithelial polarization, common genetic variation in HMMR (gene product RHAMM) may be associated with risk of breast cancer in BRCA1 mutation carriers. Following on these observations, we further assessed the link between the AURKA-HMMR-TPX2-TUBG1 functional module and risk of breast cancer in BRCA1 or BRCA2 mutation carriers. Forty-one single nucleotide polymorphisms (SNPs) were genotyped in 15,252 BRCA1 and 8,211 BRCA2 mutation carriers and subsequently analyzed using a retrospective likelihood appr