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  1. Article ; Online: Seed amplification and RT-QuIC assays to investigate protein seed structures and strains.

    Standke, Heidi G / Kraus, Allison

    Cell and tissue research

    2022  Volume 392, Issue 1, Page(s) 323–335

    Abstract: The accumulation of misfolded proteins as amyloid fibrils in the brain is characteristic of most neurodegenerative disorders. These misfolded proteins are capable of self-amplifying through protein seeding mechanisms, leading to accumulation in the host. ...

    Abstract The accumulation of misfolded proteins as amyloid fibrils in the brain is characteristic of most neurodegenerative disorders. These misfolded proteins are capable of self-amplifying through protein seeding mechanisms, leading to accumulation in the host. First shown for PrP prions and prion diseases, it is now recognized that self-propagating misfolded proteins occur broadly in neurodegenerative diseases and include amyloid-β (Aβ) and tau in Alzheimer's disease (AD), tau in chronic traumatic encephalopathy (CTE), Pick's disease (PiD), corticobasal degeneration (CBD), and progressive supranuclear palsy (PSP), and α-synuclein (α-syn) in Parkinson's disease (PD) and Lewy body dementias (LBD). Techniques able to directly measure these bioactive protein seeds include the real-time quaking-induced conversion (RT-QuIC) assays. Initially developed for the detection of PrP prions and subsequently for the detection of other misfolded protein seeds, these assays take advantage of the mechanism of protein-based self-propagation to result in exponential amplification of the initial protein seeds from biospecimens. Disease-specific "protein seeds" recruit and template the misfolding of native recombinant protein substrates to elongate amyloid fibrils. The amplification power of these assays allows for detection of minute amounts of disease-specific protein seeds to better support early and accurate diagnosis. In addition to the diagnostic capabilities, assay readouts have been shown to reveal biochemical, structural, and kinetic information of protein seed self-propagation. This review examines the various protein seed amplification assays currently available for distinct neurodegenerative diseases, with a focus on RT-QuIC assays, along with the insights their readouts provide into protein seed structures and strain differences.
    MeSH term(s) Humans ; Amyloid/metabolism ; Alzheimer Disease/diagnosis ; Prions/metabolism ; alpha-Synuclein/metabolism ; Lewy Body Disease/metabolism ; Brain/metabolism
    Chemical Substances Amyloid ; Prions ; alpha-Synuclein
    Language English
    Publishing date 2022-03-08
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 125067-x
    ISSN 1432-0878 ; 0302-766X
    ISSN (online) 1432-0878
    ISSN 0302-766X
    DOI 10.1007/s00441-022-03595-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Purification and Biochemical Characterization of the DNA Binding Domain of the Nitrogenase Transcriptional Activator NifA from Gluconacetobacter diazotrophicus.

    Standke, Heidi G / Kim, Lois / Owens, Cedric P

    The protein journal

    2023  Volume 42, Issue 6, Page(s) 802–810

    Abstract: NifA is a ... ...

    Abstract NifA is a σ
    MeSH term(s) Nitrogenase/genetics ; Nitrogenase/metabolism ; Bacterial Proteins/chemistry ; Transcription Factors/genetics ; Nitrogen Fixation/genetics ; DNA/metabolism ; Genes, Bacterial
    Chemical Substances Nitrogenase (EC 1.18.6.1) ; Bacterial Proteins ; Transcription Factors ; DNA (9007-49-2)
    Language English
    Publishing date 2023-10-03
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2143071-8
    ISSN 1875-8355 ; 1572-3887
    ISSN (online) 1875-8355
    ISSN 1572-3887
    DOI 10.1007/s10930-023-10158-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Pathogenic prion structures at high resolution.

    Caughey, Byron / Standke, Heidi G / Artikis, Efrosini / Hoyt, Forrest / Kraus, Allison

    PLoS pathogens

    2022  Volume 18, Issue 6, Page(s) e1010594

    MeSH term(s) Humans ; PrPSc Proteins/chemistry ; Prion Diseases ; Prions/chemistry
    Chemical Substances PrPSc Proteins ; Prions
    Language English
    Publishing date 2022-06-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural
    ZDB-ID 2205412-1
    ISSN 1553-7374 ; 1553-7374
    ISSN (online) 1553-7374
    ISSN 1553-7374
    DOI 10.1371/journal.ppat.1010594
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Selective tau seeding assays and isoform-specific antibodies define neuroanatomic distribution of progressive supranuclear palsy pathology arising in Alzheimer's disease.

    Coughlin, David G / Goodwill, Vanessa S / Standke, Heidi G / Kim, Yongya / Coley, Nicolas / Pizzo, Donald P / Galasko, Douglas / Kraus, Allison / Hiniker, Annie

    Acta neuropathologica

    2022  Volume 144, Issue 4, Page(s) 789–792

    MeSH term(s) Alzheimer Disease/pathology ; Carbolines ; Humans ; Protein Isoforms ; Supranuclear Palsy, Progressive/pathology ; tau Proteins
    Chemical Substances Carbolines ; Protein Isoforms ; tau Proteins
    Language English
    Publishing date 2022-08-18
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1079-0
    ISSN 1432-0533 ; 0001-6322
    ISSN (online) 1432-0533
    ISSN 0001-6322
    DOI 10.1007/s00401-022-02480-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Tau seeds occur before earliest Alzheimer's changes and are prevalent across neurodegenerative diseases.

    Manca, Matteo / Standke, Heidi G / Browne, Danielle F / Huntley, Mikayla L / Thomas, Olivia R / Orrú, Christina D / Hughson, Andrew G / Kim, Yongya / Zhang, Jing / Tatsuoka, Curtis / Zhu, Xiongwei / Hiniker, Annie / Coughlin, David G / Galasko, Douglas / Kraus, Allison

    Acta neuropathologica

    2023  Volume 146, Issue 1, Page(s) 31–50

    Abstract: Tau neurofibrillary tangles are a hallmark of Alzheimer's disease neuropathological change. However, it remains largely unclear how distinctive Alzheimer's disease tau seeds (i.e. 3R/4R) correlate with histological indicators of tau accumulation. ... ...

    Abstract Tau neurofibrillary tangles are a hallmark of Alzheimer's disease neuropathological change. However, it remains largely unclear how distinctive Alzheimer's disease tau seeds (i.e. 3R/4R) correlate with histological indicators of tau accumulation. Furthermore, AD tau co-pathology is thought to influence features and progression of other neurodegenerative diseases including Lewy body disease; yet measurements of different types of tau seeds in the setting of such diseases is an unmet need. Here, we use tau real-time quaking-induced conversion (RT-QuIC) assays to selectively quantitate 3R/4R tau seeds in the frontal lobe which accumulates histologically identifiable tau pathology at late disease stages of AD neuropathologic change. Seed quantitation across a spectrum of neurodegenerative disease cases and controls indicated tau seeding activity can be detected well before accompanying histopathological indication of tau deposits, and even prior to the earliest evidence of Alzheimer's-related tau accumulation anywhere in the brain. In later stages of AD, 3R/4R tau RT-QuIC measures correlated with immunohistochemical tau burden. In addition, Alzheimer's tau seeds occur in the vast majority of cases evaluated here inclusive of primary synucleinopathies, frontotemporal lobar degeneration and even controls albeit at multi-log lower levels than Alzheimer's cases. α-synuclein seeding activity confirmed synucleinopathy cases and further indicated the co-occurrence of α-synuclein seeds in some Alzheimer's disease and primary tauopathy cases. Our analysis indicates that 3R/4R tau seeds in the mid-frontal lobe correlate with the overall Braak stage and Alzheimer's disease neuropathologic change, supporting the quantitative predictive value of tau RT-QuIC assays. Our data also indicate 3R/4R tau seeds are elevated in females compared to males at high (≥ IV) Braak stages. This study suggests 3R/4R tau seeds are widespread even prior to the earliest stages of Alzheimer's disease changes, including in normal, and even young individuals, with prevalence across multiple neurodegenerative diseases to further define disease subtypes.
    MeSH term(s) Female ; Humans ; Male ; alpha-Synuclein ; Alzheimer Disease/pathology ; Neurodegenerative Diseases ; Synucleinopathies ; tau Proteins ; Tauopathies/pathology
    Chemical Substances alpha-Synuclein ; tau Proteins ; MAPT protein, human
    Language English
    Publishing date 2023-05-08
    Publishing country Germany
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1079-0
    ISSN 1432-0533 ; 0001-6322
    ISSN (online) 1432-0533
    ISSN 0001-6322
    DOI 10.1007/s00401-023-02574-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Cryo-EM structure of anchorless RML prion reveals variations in shared motifs between distinct strains.

    Hoyt, Forrest / Standke, Heidi G / Artikis, Efrosini / Schwartz, Cindi L / Hansen, Bryan / Li, Kunpeng / Hughson, Andrew G / Manca, Matteo / Thomas, Olivia R / Raymond, Gregory J / Race, Brent / Baron, Gerald S / Caughey, Byron / Kraus, Allison

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 4005

    Abstract: Little is known about the structural basis of prion strains. Here we provide a high (3.0 Å) resolution cryo-electron microscopy-based structure of infectious brain-derived fibrils of the mouse anchorless RML scrapie strain which, like the recently ... ...

    Abstract Little is known about the structural basis of prion strains. Here we provide a high (3.0 Å) resolution cryo-electron microscopy-based structure of infectious brain-derived fibrils of the mouse anchorless RML scrapie strain which, like the recently determined hamster 263K strain, has a parallel in-register β-sheet-based core. Several structural motifs are shared between these ex vivo prion strains, including an amino-proximal steric zipper and three β-arches. However, detailed comparisons reveal variations in these shared structural topologies and other features. Unlike 263K and wildtype RML prions, the anchorless RML prions lack glycophosphatidylinositol anchors and are severely deficient in N-linked glycans. Nonetheless, the similarity of our anchorless RML structure to one reported for wildtype RML prion fibrils in an accompanying paper indicates that these post-translational modifications do not substantially alter the amyloid core conformation. This work demonstrates both common and divergent structural features of prion strains at the near-atomic level.
    MeSH term(s) Amyloid ; Animals ; Brain/metabolism ; Cryoelectron Microscopy ; Mice ; Prions/metabolism ; Scrapie ; Sheep
    Chemical Substances Amyloid ; Prions
    Language English
    Publishing date 2022-07-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-30458-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Neuronal Ndst1 depletion accelerates prion protein clearance and slows neurodegeneration in prion infection.

    Aguilar-Calvo, Patricia / Malik, Adela / Sandoval, Daniel R / Barback, Christopher / Orrù, Christina D / Standke, Heidi G / Thomas, Olivia R / Dwyer, Chrissa A / Pizzo, Donald P / Bapat, Jaidev / Soldau, Katrin / Ogawa, Ryotaro / Riley, Mckenzie B / Nilsson, K Peter R / Kraus, Allison / Caughey, Byron / Iliff, Jeffrey J / Vera, David R / Esko, Jeffrey D /
    Sigurdson, Christina J

    PLoS pathogens

    2023  Volume 19, Issue 9, Page(s) e1011487

    Abstract: Select prion diseases are characterized by widespread cerebral plaque-like deposits of amyloid fibrils enriched in heparan sulfate (HS), a abundant extracellular matrix component. HS facilitates fibril formation in vitro, yet how HS impacts fibrillar ... ...

    Abstract Select prion diseases are characterized by widespread cerebral plaque-like deposits of amyloid fibrils enriched in heparan sulfate (HS), a abundant extracellular matrix component. HS facilitates fibril formation in vitro, yet how HS impacts fibrillar plaque growth within the brain is unclear. Here we found that prion-bound HS chains are highly sulfated, and that the sulfation is essential for accelerating prion conversion in vitro. Using conditional knockout mice to deplete the HS sulfation enzyme, Ndst1 (N-deacetylase / N-sulfotransferase) from neurons or astrocytes, we investigated how reducing HS sulfation impacts survival and prion aggregate distribution during a prion infection. Neuronal Ndst1-depleted mice survived longer and showed fewer and smaller parenchymal plaques, shorter fibrils, and increased vascular amyloid, consistent with enhanced aggregate transit toward perivascular drainage channels. The prolonged survival was strain-dependent, affecting mice infected with extracellular, plaque-forming, but not membrane bound, prions. Live PET imaging revealed rapid clearance of recombinant prion protein monomers into the CSF of neuronal Ndst1- deficient mice, neuronal, further suggesting that HS sulfate groups hinder transit of extracellular prion protein monomers. Our results directly show how a host cofactor slows the spread of prion protein through the extracellular space and identify an enzyme to target to facilitate aggregate clearance.
    MeSH term(s) Animals ; Mice ; Heparitin Sulfate/metabolism ; Mice, Knockout ; Neurons/enzymology ; Prion Diseases/metabolism ; Prion Proteins/genetics ; Prions/metabolism ; Sulfotransferases/genetics ; Sulfotransferases/metabolism
    Chemical Substances Heparitin Sulfate (9050-30-0) ; Prion Proteins ; Prions ; heparitin sulfotransferase (EC 2.8.2.8) ; Sulfotransferases (EC 2.8.2.-)
    Language English
    Publishing date 2023-09-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2205412-1
    ISSN 1553-7374 ; 1553-7374
    ISSN (online) 1553-7374
    ISSN 1553-7374
    DOI 10.1371/journal.ppat.1011487
    Database MEDical Literature Analysis and Retrieval System OnLINE

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