References of "Gu, Wei 50001901"
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See detailA rare loss-of function variant of ADAM17 is associated with late-onset familial Alzheimer disease
Hartl, Daniela; May, Patrick UL; Gu, Wei UL et al

in Molecular Psychiatry (2018)

Common variants of about 20 genes contributing to AD risk have so far been identified through genome-wide association studies (GWAS). However, there is still a large proportion of heritability that might ... [more ▼]

Common variants of about 20 genes contributing to AD risk have so far been identified through genome-wide association studies (GWAS). However, there is still a large proportion of heritability that might be explained by rare but functionally important variants. One of the so far identified genes with rare AD causing variants is ADAM10. Using whole-genome sequencing we now identified a single rare nonsynonymous variant (SNV) rs142946965 [p.R215I] in ADAM17 co-segregating with an autosomal-dominant pattern of late-onset AD in one family. Subsequent genotyping and analysis of available whole-exome sequencing data of additional case/control samples from Germany, the UK and the USA identified five variant carriers among AD patients only. The mutation inhibits pro-protein cleavage and the formation of the active enzyme, thus leading to loss-of-function of ADAM17 α-secretase. Further, we identified a strong negative correlation between ADAM17 and APP gene expression in human brain and present in vitro evidence that ADAM17 negatively controls the expression of APP. As a consequence, p.R215I mutation of ADAM17 leads to elevated Aß formation in vitro. Together our data supports a causative association of the identified ADAM17 variant in the pathogenesis of AD. [less ▲]

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See detailSmartR: An open-source platform for interactive visual analytics for translational research data.
Herzinger, Sascha UL; Gu, Wei UL; Satagopam, Venkata UL et al

in Bioinformatics (Oxford, England) (2017)

In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre ... [more ▼]

In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre-clinical, or OMICS data combined with strong visual analytical capabilities will significantly accelerate the scientific progress by making data more accessible and hypothesis generation easier. The open data warehouse tranSMART is capable of storing a variety of data types and has a growing user community including both academic institutions and pharmaceutical companies. tranSMART, however, currently lacks interactive and dynamic visual analytics and does not permit any post-processing interaction or exploration. For this reason, we developed SmartR , a plugin for tranSMART, that equips the platform not only with several dynamic visual analytical workflows, but also provides its own framework for the addition of new custom workflows. Modern web technologies such as D3.js or AngularJS were used to build a set of standard visualizations that were heavily improved with dynamic elements. Contact: reinhard.schneider@uni.lu. Supplementary information: Supplementary data are available at Bioinformatics online. Availability: : The source code is licensed under the Apache 2.0 License and is freely available on GitHub: https://github.com/transmart/SmartR. [less ▲]

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See detailIDENTIFICATION OF A RARE GENE VARIANT THAT IS ASSOCIATED WITH FAMILIAL ALZHEIMER DISEASE AND REGULATES APP EXPRESSION
Hartl, Daniela; May, Patrick UL; Gu, Wei UL et al

in Alzheimer's & Dementia : The Journal of the Alzheimer's Association (2017), 13(7, Supplement), 648

Background Genetic mutations leading to familial forms of Alzheimer disease (AD) have so far been reported for a few genes including APP, PSEN1 and PSEN2, UNC5C, PLD3, ABCA7, TTC3, and possibly ADAM10 ... [more ▼]

Background Genetic mutations leading to familial forms of Alzheimer disease (AD) have so far been reported for a few genes including APP, PSEN1 and PSEN2, UNC5C, PLD3, ABCA7, TTC3, and possibly ADAM10. With the advent of whole exome and whole genome sequencing approaches new genes and mutations are likely to be identified. Methods We analyzed the genetic cause of AD in a large multiplex family with an autosomal-dominant pattern of inheritance with LOAD. The family lacked pathogenic mutations of known AD genes. We performed whole-genome sequencing (WGS) in six family members (two affected and four unaffected) and prioritized rare, potential damaging, variants that segregated with disease. Variants were further characterized by subsequent molecular analyzes in human brain and cell culture models. Results We identified a single rare nonsynonymous variant co-segregating with AD. The mutation inhibits pro-protein cleavage and the formation of the active enzyme, thus leading to a loss-of-function of the gene. We further found a strong negative correlation between the identified gene and APP gene expression in human brain and in cells over-expressing the gene. The negative regulation of APP expression was only observed for the wt gene, but not for mutated forms, thus causing beside the loss of enzyme function a decoupling of both APPexpression and subsequent beta-amyloid formation. The identity of the gene will be presented on the conference. Conclusions This novel pathway strongly supports a causative association of the identified gene with the pathogenesis of AD. [less ▲]

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See detailRare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease
Sims, Rebecca; van der Lee, Sven J.; Naj, Adam C. et al

in Nature Genetics (2017), 49

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See detailIntegration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases.
Satagopam, Venkata UL; Gu, Wei UL; Eifes, Serge et al

in Big data (2016), 4(2), 97-108

Translational medicine is a domain turning results of basic life science research into new tools and methods in a clinical environment, for example, as new diagnostics or therapies. Nowadays, the process ... [more ▼]

Translational medicine is a domain turning results of basic life science research into new tools and methods in a clinical environment, for example, as new diagnostics or therapies. Nowadays, the process of translation is supported by large amounts of heterogeneous data ranging from medical data to a whole range of -omics data. It is not only a great opportunity but also a great challenge, as translational medicine big data is difficult to integrate and analyze, and requires the involvement of biomedical experts for the data processing. We show here that visualization and interoperable workflows, combining multiple complex steps, can address at least parts of the challenge. In this article, we present an integrated workflow for exploring, analysis, and interpretation of translational medicine data in the context of human health. Three Web services-tranSMART, a Galaxy Server, and a MINERVA platform-are combined into one big data pipeline. Native visualization capabilities enable the biomedical experts to get a comprehensive overview and control over separate steps of the workflow. The capabilities of tranSMART enable a flexible filtering of multidimensional integrated data sets to create subsets suitable for downstream processing. A Galaxy Server offers visually aided construction of analytical pipelines, with the use of existing or custom components. A MINERVA platform supports the exploration of health and disease-related mechanisms in a contextualized analytical visualization system. We demonstrate the utility of our workflow by illustrating its subsequent steps using an existing data set, for which we propose a filtering scheme, an analytical pipeline, and a corresponding visualization of analytical results. The workflow is available as a sandbox environment, where readers can work with the described setup themselves. Overall, our work shows how visualization and interfacing of big data processing services facilitate exploration, analysis, and interpretation of translational medicine data. [less ▲]

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See detailThe miRNome of Alzheimer's disease: consistent downregulation of the miR-132/212 cluster
Pichler, Sabrina; Gu, Wei UL; Hartl, Daniela et al

in Neurobiology of Aging (2016), 50

MicroRNAs (miRNAs) are small noncoding RNA molecules, with essential functions in RNA silencing and post-transcriptional regulation of gene expression. miRNAs appear to regulate the development and ... [more ▼]

MicroRNAs (miRNAs) are small noncoding RNA molecules, with essential functions in RNA silencing and post-transcriptional regulation of gene expression. miRNAs appear to regulate the development and function of the nervous system. Alterations of miRNA expression have been associated with Alzheimer's disease (AD). To characterize the AD miRNA signature, we examined genome-wide miRNA and mRNA expression patterns in the temporal cortex of AD and control samples. We validated our miRNA results by semiquantitative real-time polymerase chain reaction (PCR) in independent prefrontal cortex. Furthermore, we separated gray and white matter brain sections to identify the cellular origin of the altered miRNA expression. We observed genome-wide downregulation of hsa-miR-132-3p and hsa-miR-212-3p in AD with a stronger decrease in gray matter AD samples. We further identified 10 differently expressed transcripts achieving genome-wide levels of significance. Significantly deregulated miRNAs and mRNAs were correlated and examined for potential binding sites (in silico). This miRNome-wide study in AD provides supportive evidence and corroborates an important contribution of miR-132/212 and corresponding target mRNAs to the pathogenesis of AD. [less ▲]

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See detailAmyloid-β Protein Precursor Cleavage Products in Postmortem Ventricular Cerebrospinal Fluid of Alzheimer’s Disease Patients
Hartl, Daniela; Gu, Wei UL; Mayhaus, Manuel et al

in Journal of Alzheimer's Disease [=JAD] (2015), 47(2), 365-372

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See detailReproducible Research Results R3
Trefois, Christophe UL; Jarosz, Yohan UL; Gu, Wei UL et al

Poster (2014, December)

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See detailFrontotemporal dementia and its subtypes: a genome-wide association study.
Ferrari, Raffaele; Hernandez, Dena G.; Nalls, Michael A. et al

in Lancet neurology (2014), 13(7), 686-99

BACKGROUND: Frontotemporal dementia (FTD) is a complex disorder characterised by a broad range of clinical manifestations, differential pathological signatures, and genetic variability. Mutations in three ... [more ▼]

BACKGROUND: Frontotemporal dementia (FTD) is a complex disorder characterised by a broad range of clinical manifestations, differential pathological signatures, and genetic variability. Mutations in three genes-MAPT, GRN, and C9orf72-have been associated with FTD. We sought to identify novel genetic risk loci associated with the disorder. METHODS: We did a two-stage genome-wide association study on clinical FTD, analysing samples from 3526 patients with FTD and 9402 healthy controls. To reduce genetic heterogeneity, all participants were of European ancestry. In the discovery phase (samples from 2154 patients with FTD and 4308 controls), we did separate association analyses for each FTD subtype (behavioural variant FTD, semantic dementia, progressive non-fluent aphasia, and FTD overlapping with motor neuron disease [FTD-MND]), followed by a meta-analysis of the entire dataset. We carried forward replication of the novel suggestive loci in an independent sample series (samples from 1372 patients and 5094 controls) and then did joint phase and brain expression and methylation quantitative trait loci analyses for the associated (p<5 x 10(-8)) single-nucleotide polymorphisms. FINDINGS: We identified novel associations exceeding the genome-wide significance threshold (p<5 x 10(-8)). Combined (joint) analyses of discovery and replication phases showed genome-wide significant association at 6p21.3, HLA locus (immune system), for rs9268877 (p=1.05 x 10(-8); odds ratio=1.204 [95% CI 1.11-1.30]), rs9268856 (p=5.51 x 10(-9); 0.809 [0.76-0.86]) and rs1980493 (p value=1.57 x 10(-8), 0.775 [0.69-0.86]) in the entire cohort. We also identified a potential novel locus at 11q14, encompassing RAB38/CTSC (the transcripts of which are related to lysosomal biology), for the behavioural FTD subtype for which joint analyses showed suggestive association for rs302668 (p=2.44 x 10(-7); 0.814 [0.71-0.92]). Analysis of expression and methylation quantitative trait loci data suggested that these loci might affect expression and methylation in cis. INTERPRETATION: Our findings suggest that immune system processes (link to 6p21.3) and possibly lysosomal and autophagy pathways (link to 11q14) are potentially involved in FTD. Our findings need to be replicated to better define the association of the newly identified loci with disease and to shed light on the pathomechanisms contributing to FTD. FUNDING: The National Institute of Neurological Disorders and Stroke and National Institute on Aging, the Wellcome/MRC Centre on Parkinson's disease, Alzheimer's Research UK, and Texas Tech University Health Sciences Center. [less ▲]

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See detailGene-wide analysis detects two new susceptibility genes for Alzheimer's disease.
Escott-Price, Valentina; Bellenguez, Celine; Wang, Li-San et al

in PloS one (2014), 9(6), 94661

BACKGROUND: Alzheimer's disease is a common debilitating dementia with known heritability, for which 20 late onset susceptibility loci have been identified, but more remain to be discovered. This study ... [more ▼]

BACKGROUND: Alzheimer's disease is a common debilitating dementia with known heritability, for which 20 late onset susceptibility loci have been identified, but more remain to be discovered. This study sought to identify new susceptibility genes, using an alternative gene-wide analytical approach which tests for patterns of association within genes, in the powerful genome-wide association dataset of the International Genomics of Alzheimer's Project Consortium, comprising over 7 m genotypes from 25,580 Alzheimer's cases and 48,466 controls. PRINCIPAL FINDINGS: In addition to earlier reported genes, we detected genome-wide significant loci on chromosomes 8 (TP53INP1, p = 1.4x10-6) and 14 (IGHV1-67 p = 7.9x10-8) which indexed novel susceptibility loci. SIGNIFICANCE: The additional genes identified in this study, have an array of functions previously implicated in Alzheimer's disease, including aspects of energy metabolism, protein degradation and the immune system and add further weight to these pathways as potential therapeutic targets in Alzheimer's disease. [less ▲]

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See detailMeta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease
Lambert, Jean-Charles; Ibrahim-Verbaas, Carla A.; Harold, Denise et al

in Nature Genetics (2013), 45

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See detailHydrogen-Bonded Networks Along and Bifurcation of the E-Pathway in Quinol:Fumarate Reductase
Herzog, Elena; Gu, Wei UL; Juhnke, Hanno D. et al

in Biophysical Journal (2012), 103(6), 1305-1314

The E-pathway of transmembrane proton transfer has been demonstrated previously to be essential for catalysis by the diheme-containing quinol:fumarate reductase (QFR) of Wolinella succinogenes. Two ... [more ▼]

The E-pathway of transmembrane proton transfer has been demonstrated previously to be essential for catalysis by the diheme-containing quinol:fumarate reductase (QFR) of Wolinella succinogenes. Two constituents of this pathway, Glu-C180 and heme bp ring C (b(D)-C-) propionate, have been validated experimentally. Here, we identify further constituents of the E-pathway by analysis of molecular dynamics simulations. The redox state of heme groups has a crucial effect on the connectivity patterns of mobile internal water molecules that can transiently support proton transfer from the b(D)-C-propionate to Glu-C180. The short H-bonding paths formed in the reduced states can lead to high proton conduction rates and thus provide a plausible explanation for the required opening of the E-pathway in reduced QFR. We found evidence that the b(D)-C-propionate group is the previously postulated branching point connecting proton transfer to the E-pathway from the quinol-oxidation site via interactions with the heme bp ligand His-C44. An essential functional role of His-C44 is supported experimentally by site-directed mutagenesis resulting in its replacement with Glu. Although the H44E variant enzyme retains both heme groups, it is unable to catalyze quinol oxidation. All results obtained are relevant to the QFR enzymes from the human pathogens Campylobacter jejuni and Helicobacter pylori. [less ▲]

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See detailCarbon Nanotube Wins the Competitive Binding over Proline-Rich Motif Ligand on SH3 Domain
Zuo, Guanghong; Gu, Wei UL; Fang, Haiping et al

in JOURNAL OF PHYSICAL CHEMISTRY C (2011), 115(25), 12322-12328

The binding competition between a proline-rich motif (PRM) ligand and a hydrophobic nanoparticle, the single-wall carbon nanotube (SWCNT), at the binding pocket of SH3 domain, has been investigated by ... [more ▼]

The binding competition between a proline-rich motif (PRM) ligand and a hydrophobic nanoparticle, the single-wall carbon nanotube (SWCNT), at the binding pocket of SH3 domain, has been investigated by molecular dynamics simulations. It is found that the SWCNT has a very high probability of occupying the binding pocket of the SH3 domain, which prevents the PRM ligand from binding to the pocket. The binding free energy landscapes show that the SWCNT has similar to 0.6 kcal/mol stronger binding affinity than the ligand in the three-way binding competition (SWCNT + ligand + protein). The potent binding affinity between the SWCNT and the SH3 domain is shown to be mainly from the pi-pi stacking interactions between the CNT and aromatic residues in the binding pocket. Our findings show that the existence of hydrophobic particles can greatly reduce the possibility of the regular binding of the ligand with the target protein, suggesting potential toxicity to proteins by hydrophobic nanoscale particles. [less ▲]

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See detailAdhesive water networks facilitate binding of protein interfaces
Ahmad, Mazen; Gu, Wei UL; Geyer, Tihamer et al

in Nature Communications (2011), 2

Water structure has an essential role in biological assembly. Hydrophobic dewetting has been documented as a general mechanism for the assembly of hydrophobic surfaces; however, the association mechanism ... [more ▼]

Water structure has an essential role in biological assembly. Hydrophobic dewetting has been documented as a general mechanism for the assembly of hydrophobic surfaces; however, the association mechanism of hydrophilic interfaces remains mysterious and cannot be explained by simple continuum water models that ignore the solvent structure. Here we study the association of two hydrophilic proteins using unbiased extensive molecular dynamics simulations that reproducibly recovered the native bound complex. The water in the interfacial gap forms an adhesive hydrogen-bond network between the interfaces stabilizing early intermediates before native contacts are formed. Furthermore, the interfacial gap solvent showed a reduced dielectric shielding up to distances of few nanometres during the diffusive phase. The interfacial gap solvent generates an anisotropic dielectric shielding with a strongly preferred directionality for the electrostatic interactions along the association direction. [less ▲]

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See detailDesign of a Gated Molecular Proton Channel
Gu, Wei UL; Zhou, Bo; Geyer, Tihamer et al

in Angewandte Chemie International Edition (2011), 50(3), 768-771

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See detailDownhill Binding Energy Surface of the Barnase-Barstar Complex
Wang, Ling; Siu, Shirley W. I.; Gu, Wei UL et al

in Biopolymers (2010), 93(11), 977-985

We have employed biased molecular dynamics simulations in explicit solvent to characterize the one-dimensional potential of mean force for the dissociation process of the barnase-barstar protein-protein ... [more ▼]

We have employed biased molecular dynamics simulations in explicit solvent to characterize the one-dimensional potential of mean force for the dissociation process of the barnase-barstar protein-protein complex. Unbinding of barstar from wild-type barnase was compared with dissociation from four charge-deletion mutants of barnase. Interestingly, we find in all cases that unbinding of barnase and barstar is an uphill process on a smooth, tilted energy landscape. The total free energy difference between the dissociated and bound state was similar for wild-type barnase-barstar and for the R87A mutant of barnase. The values for the three other mutant barnase mutants K27A, R59A, and R83Q were only about half as much. Besides, we have analyzed the conformational dynamics of important residues at the barnase-barstar interface. In the bound state, their conformational fluctuations are reduced relatively to the free state because of the formation of intermolecular contacts. Interestingly, we find that some residues also show decreased mobility at intermediate stages of the unbinding process suggesting that these residues may be involved in the first contacts being formed on binding. (C) 2010 Wiley Periodicals, Inc. Biopolymers 93: 977-985, 2010. [less ▲]

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See detailAtomistic Simulation of Water Percolation and Proton Hopping in Nation Fuel Cell Membrane
Devanathan, Ram; Venkatnathan, Arun; Rousseau, Roger et al

in Journal of Physical Chemistry B (2010), 114(43), 13681-13690

We have performed a detailed analysis of water clustering and percolation in hydrated Nafion configurations generated by classical molecular dynamics simulations. Our results show that at low hydration ... [more ▼]

We have performed a detailed analysis of water clustering and percolation in hydrated Nafion configurations generated by classical molecular dynamics simulations. Our results show that at low hydration levels H(2)O molecules are isolated and a continuous hydrogen-bonded network forms as the hydration level is increased. Our quantitative analysis has established a hydration level (lambda) between 5 and 6 H(2)O/SO(3)(-) as the percolation threshold of Nation. We have also examined the effect of such a network on proton transport by studying the structural diffusion of protons using the quantum hopping molecular dynamics method. The mean residence time of the proton on a water molecule decreases by 2 orders of magnitude when the lambda value is increased from 5 to 15. The proton diffusion coefficient in Nation at a lambda value of 15 is about 1.1 x 10(-5) cm(2)/s in agreement with experiment. The results provide quantitative atomic-level evidence of water network percolation in Nafion and its effect on proton conductivity. [less ▲]

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See detailTightly Connected Water Wires Facilitate Fast Proton Uptake at The Proton Entrance of Proton Pumping Proteins
Gu, Wei UL; Helms, Volkhard

in Journal of the American Chemical Society (2009), 131(6), 2080-

Tightly connected water wires (TCW) exist in systems with nonconfined water like the solvated membrane proton pump system. The TCWs that connect to the negatively charged proton entrance facilitate the ... [more ▼]

Tightly connected water wires (TCW) exist in systems with nonconfined water like the solvated membrane proton pump system. The TCWs that connect to the negatively charged proton entrance facilitate the fast proton uptake of the proton pump. They function as a direct proton bridge or/and stabilizer of protons within the Coulomb cage of the proton entrance. Negatively charged residue(s) at the proton entrance induce a large population of long TCWs. Additional negatively charged residues increase the population of such long TCWs and, thus, raise the possibility to capture proton from the solution. [less ▲]

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See detailMechanism of fast peptide recognition by SH3 domains
Ahmad, Mazen; Gu, Wei UL; Helms, Volkhard

in Angewandte Chemie International Edition (2008), 47(40), 7626-7630

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See detailDifferent protonation equilibria of 4-methylimidazole and acetic acid
Gu, Wei UL; Helms, Volkhard

in Chemphyschem : A European Journal of Chemical Physics and Physical Chemistry (2007), 8(17), 2445-2451

Dynamic protonation equilibria in water of one 4-methylimidazole molecule as well as for pairs and groups consisting of 4-methylimidazole, acetic acid and bridging water molecules are studied using Q-HOP ... [more ▼]

Dynamic protonation equilibria in water of one 4-methylimidazole molecule as well as for pairs and groups consisting of 4-methylimidazole, acetic acid and bridging water molecules are studied using Q-HOP molecular dynamics simulation. We find a qualitatively different protonation behavior of 4-methylimidazole compared to that of acetic acid. On one hand, deprotonoted, neutral 4-methylimidazole cannot as easily attract a freely diffusing extra proton from solution. Once the proton is bound however, it remains tightly bound on a time scale of tens of nanoseconds. In a linear chain composed of acetic acid, a separating water molecule and 4-methylimidazole, an excess proton is equally shared between 4-methylimidozole and water. When a water molecule is linearly placed between two acetic acid molecules, the excess proton is always found on the central water. On the other hand, an excess proton in a 4-methylimidazole-water-4-methylimidozole chain is always localized on one of the two 4-methylimidozoles. These findings are of interest to the discussion of proton transfer along chains of amino acids and water molecules in biomolecules. [less ▲]

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