6 Works

Supplementary material from \"Impact of phylogeny on structural contact inference from protein sequence data\"

Nicola Dietler, Umberto Lupo & Anne-Florence Bitbol
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ancestry, their sequences also feature phylogenetic correlations, which can impair contact inference. We investigate this effect by generating controlled synthetic data from a minimal model where the importance of contacts and of phylogeny can be tuned. We demonstrate that...

The combined impact of persistent infections and human genetic variation on C-reactive protein levels

Flavia Hodel, Olivier Naret, Clara Bonnet, Nicole Brenner, Noemi Bender, Tim Waterboer, Pedro Marques-Vidal, Peter Vollenweider & Jacques Fellay
Abstract Multiple human pathogens establish chronic, sometimes life-long infections. Even if they are often latent, these infections can trigger some degree of local or systemic immune response, resulting in chronic low-grade inflammation. There remains an incomplete understanding of the potential contribution of both persistent infections and human genetic variation on chronic low-grade inflammation. We searched for potential associations between seropositivity for 13 persistent pathogens and the plasma levels of the inflammatory biomarker C-reactive protein (CRP),...

The combined impact of persistent infections and human genetic variation on C-reactive protein levels

Flavia Hodel, Olivier Naret, Clara Bonnet, Nicole Brenner, Noemi Bender, Tim Waterboer, Pedro Marques-Vidal, Peter Vollenweider & Jacques Fellay
Abstract Multiple human pathogens establish chronic, sometimes life-long infections. Even if they are often latent, these infections can trigger some degree of local or systemic immune response, resulting in chronic low-grade inflammation. There remains an incomplete understanding of the potential contribution of both persistent infections and human genetic variation on chronic low-grade inflammation. We searched for potential associations between seropositivity for 13 persistent pathogens and the plasma levels of the inflammatory biomarker C-reactive protein (CRP),...

Prominent astrocytic alpha-synuclein pathology with unique post-translational modification signatures unveiled across Lewy body disorders

Melek Firat Altay, Alan King Lun Liu, Janice L. Holton, Laura Parkkinen & Hilal A. Lashuel
Abstract Alpha-synuclein (aSyn) is a pre-synaptic monomeric protein that can form aggregates in neurons in Parkinson’s disease (PD), Parkinson’s disease with dementia (PDD) and dementia with Lewy bodies (DLB), and in oligodendrocytes in multiple system atrophy (MSA). Although aSyn in astrocytes has previously been described in PD, PDD and DLB, the biochemical properties and topographical distribution of astrocytic aSyn have not been studied in detail. Here, we present a systematic investigation of aSyn astrocytic pathology...

Prominent astrocytic alpha-synuclein pathology with unique post-translational modification signatures unveiled across Lewy body disorders

Melek Firat Altay, Alan King Lun Liu, Janice L. Holton, Laura Parkkinen & Hilal A. Lashuel
Abstract Alpha-synuclein (aSyn) is a pre-synaptic monomeric protein that can form aggregates in neurons in Parkinson’s disease (PD), Parkinson’s disease with dementia (PDD) and dementia with Lewy bodies (DLB), and in oligodendrocytes in multiple system atrophy (MSA). Although aSyn in astrocytes has previously been described in PD, PDD and DLB, the biochemical properties and topographical distribution of astrocytic aSyn have not been studied in detail. Here, we present a systematic investigation of aSyn astrocytic pathology...

Supplementary material from \"Impact of phylogeny on structural contact inference from protein sequence data\"

Nicola Dietler, Umberto Lupo & Anne-Florence Bitbol
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ancestry, their sequences also feature phylogenetic correlations, which can impair contact inference. We investigate this effect by generating controlled synthetic data from a minimal model where the importance of contacts and of phylogeny can be tuned. We demonstrate that...

Registration Year

  • 2023
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Affiliations

  • École Polytechnique Fédérale de Lausanne
    6
  • Swiss Institute of Bioinformatics
    4
  • University of Lausanne
    2
  • University College London
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  • German Cancer Research Center
    2
  • University of Oxford
    2
  • University Hospital of Lausanne
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