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

Standke, Heidi G / Kraus, Allison

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
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Article ; Online: Proline and lysine residues provide modulatory switches in amyloid formation: Insights from prion protein.

Kraus, Allison

Prion

2016 Volume 10, Issue 1, Page(s) 57–62

Abstract: Amyloidogenic proteins have an increased propensity to reorganize into the highly structured, β sheet rich structures that characterize amyloid. The probability of attaining these highly structured assemblies is influenced by multiple factors, including ... ...

Abstract	Amyloidogenic proteins have an increased propensity to reorganize into the highly structured, β sheet rich structures that characterize amyloid. The probability of attaining these highly structured assemblies is influenced by multiple factors, including amino acid composition and environmental conditions. Evolutionary selection for amino acid sequences that prevent amyloid formation could further modulate amyloid-forming propensity. Indeed, we have recently identified specific proline and lysine residues, contained within a highly conserved central region of prion protein (PrP), that impede PrP amyloid formation in vitro. These prolines are mutated in certain forms of the human familial genetic disease, Gerstmann-Straüssler-Schneiker (GSS) syndrome. Here, I discuss the influence of these proline and lysine residues on PrP amyloid formation and how such anti-amyloidogenic primary amino acid sequences might be modulated to influence protein amyloidogenicity.
MeSH term(s)	Amino Acid Sequence ; Amyloid/chemistry ; Amyloid/genetics ; Amyloid/metabolism ; Humans ; Lysine/chemistry ; Lysine/genetics ; Lysine/metabolism ; Mutation ; Prion Proteins/chemistry ; Prion Proteins/genetics ; Prion Proteins/metabolism ; Proline/chemistry ; Proline/genetics ; Proline/metabolism
Chemical Substances	Amyloid ; Prion Proteins ; Proline (9DLQ4CIU6V) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ISSN	1933-690X
ISSN (online)	1933-690X
DOI	10.1080/19336896.2015.1132138
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Article ; Online: Adaptive body image can be contagious: An examination of college women facing situational body image threats.

Miller, Kathryn E / Kelly, Allison C / Kraus, Giselle E

Body image

2022 Volume 42, Page(s) 222–236

Abstract: The present research examined whether and which adaptive body image displays in peers can promote more adaptive body image in self. In two studies, female-identified undergraduates recalled a personally distressing body image event. In Study 1, ... ...

Abstract	The present research examined whether and which adaptive body image displays in peers can promote more adaptive body image in self. In two studies, female-identified undergraduates recalled a personally distressing body image event. In Study 1, participants (N = 158) then heard an alleged female-identified peer responding to her own distressing body image event with either self-compassion, self-esteem enhancement, or distraction. Participants across conditions reported increased body acceptance and body image-related self-compassion, and decreased body image distress, but changes did not vary by condition. Study 2 sought to determine which component(s) common to Study 1's conditions explained the benefits participants experienced. Participants (N = 207) listened to an alleged peer: describe body image distress with which she coped adaptively; express body image distress but no adaptive coping; or deny body image distress and relate positively to her body. Hearing a peer cope adaptively with body image distress yielded the greatest body image benefits, whereas hearing a peer deny body image distress was generally least helpful. Results suggest that learning how a peer copes adaptively with body image distress may be most helpful in the face of personal body image distress, and support the overarching theory that adaptive body image may be socially transmissible.
MeSH term(s)	Adaptation, Psychological ; Body Image/psychology ; Empathy ; Female ; Humans ; Self Concept ; Students ; Universities
Language	English
Publishing date	2022-07-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2211449-X
ISSN	1873-6807 ; 1740-1445
ISSN (online)	1873-6807
ISSN	1740-1445
DOI	10.1016/j.bodyim.2022.06.008
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Article ; Online: Structural biology of ex vivo mammalian prions.

Artikis, Efrosini / Kraus, Allison / Caughey, Byron

The Journal of biological chemistry

2022 Volume 298, Issue 8, Page(s) 102181

Abstract: The structures of prion protein (PrP)-based mammalian prions have long been elusive. However, cryo-EM has begun to reveal the near-atomic resolution structures of fully infectious ex vivo mammalian prion fibrils as well as relatively innocuous synthetic ... ...

Abstract	The structures of prion protein (PrP)-based mammalian prions have long been elusive. However, cryo-EM has begun to reveal the near-atomic resolution structures of fully infectious ex vivo mammalian prion fibrils as well as relatively innocuous synthetic PrP amyloids. Comparisons of these various types of PrP fibrils are now providing initial clues to structural features that correlate with pathogenicity. As first indicated by electron paramagnetic resonance and solid-state NMR studies of synthetic amyloids, all sufficiently resolved PrP fibrils of any sort (n > 10) have parallel in-register intermolecular β-stack architectures. Cryo-EM has shown that infectious brain-derived prion fibrils of the rodent-adapted 263K and RML scrapie strains have much larger ordered cores than the synthetic fibrils. These bona fide prion strains share major structural motifs, but the conformational details and the overall shape of the fibril cross sections differ markedly. Such motif variations, as well as differences in sequence within the ordered polypeptide cores, likely contribute to strain-dependent templating. When present, N-linked glycans and glycophosphatidylinositol (GPI) anchors project outward from the fibril surface. For the mouse RML strain, these posttranslational modifications have little effect on the core structure. In the GPI-anchored prion structures, a linear array of GPI anchors along the twisting fibril axis appears likely to bind membranes in vivo, and as such, may account for pathognomonic membrane distortions seen in prion diseases. In this review, we focus on these infectious prion structures and their implications regarding prion replication mechanisms, strains, transmission barriers, and molecular pathogenesis.
MeSH term(s)	Amyloid/chemistry ; Animals ; Biology ; Mammals/metabolism ; Mice ; Prion Diseases/metabolism ; Prion Proteins ; Prions/metabolism ; Scrapie/metabolism ; Sheep
Chemical Substances	Amyloid ; Prion Proteins ; Prions
Language	English
Publishing date	2022-06-23
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.102181
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Article ; Online: Defining the Protein Seeds of Neurodegeneration using Real-Time Quaking-Induced Conversion Assays.

Manca, Matteo / Kraus, Allison

Biomolecules

2020 Volume 10, Issue 9

Abstract: Neurodegenerative diseases are characterized by the accumulation of disease-related misfolded proteins. It is now widely understood that the characteristic self-amplifying (i.e., seeding) capacity once only attributed to the prions of transmissible ... ...

Abstract	Neurodegenerative diseases are characterized by the accumulation of disease-related misfolded proteins. It is now widely understood that the characteristic self-amplifying (i.e., seeding) capacity once only attributed to the prions of transmissible spongiform encephalopathy diseases is a feature of other misfolded proteins of neurodegenerative diseases, including tau, Aβ, and αSynuclein (αSyn). Ultrasensitive diagnostic assays, known as real-time quaking-induced conversion (RT-QuIC) assays, exploit these seeding capabilities in order to exponentially amplify protein seeds from various biospecimens. To date, RT-QuIC assays have been developed for the detection of protein seeds related to known prion diseases of mammals, the αSyn aggregates of Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy, and the tau aggregates of Alzheimer's disease, chronic traumatic encephalopathy, and other tauopathies including progressive supranuclear palsy. Application of these assays to premortem human biospecimens shows promise for diagnosis of neurodegenerative disease and is an area of active investigation. RT-QuIC assays are also powerful experimental tools that can be used to dissect seeding networks within and between tissues and to evaluate how protein seed distribution and quantity correlate to disease-related outcomes in a host. As well, RT-QuIC application may help characterize molecular pathways influencing protein seed accumulation, transmission, and clearance. In this review we discuss the application of RT-QuIC assays as diagnostic, experimental, and structural tools for detection and discrimination of PrP prions, tau, and αSyn protein seeds.
MeSH term(s)	Animals ; Biomarkers/chemistry ; Biomarkers/metabolism ; Brain/metabolism ; Computer Systems ; High-Throughput Screening Assays/methods ; Humans ; Models, Neurological ; Nerve Tissue Proteins/chemistry ; Nerve Tissue Proteins/metabolism ; Neurodegenerative Diseases/diagnosis ; Neurodegenerative Diseases/etiology ; Neurodegenerative Diseases/metabolism ; Prions/chemistry ; Prions/metabolism ; Protein Aggregates ; Protein Folding ; Proteostasis Deficiencies/etiology ; Proteostasis Deficiencies/metabolism ; alpha-Synuclein/chemistry ; alpha-Synuclein/metabolism ; tau Proteins/chemistry ; tau Proteins/metabolism
Chemical Substances	Biomarkers ; Nerve Tissue Proteins ; Prions ; Protein Aggregates ; alpha-Synuclein ; tau Proteins
Language	English
Publishing date	2020-08-25
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom10091233
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Article: A survey of practices and perceptions of vulvar biopsies in academic dermatology.

Panez, Sheila / Sattler, Samantha / Dobry, Allison S / Kraus, Christina N

International journal of women's dermatology

2021 Volume 7, Issue 5Part B, Page(s) 763–765

Language	English
Publishing date	2021-10-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2832233-2
ISSN	2352-6475
ISSN	2352-6475
DOI	10.1016/j.ijwd.2021.10.011
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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
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Article ; Online: Impact of text-to-speech features on the reading comprehension of children with reading and language difficulties.

Keelor, Jennifer L / Creaghead, Nancy A / Silbert, Noah H / Breit, Allison D / Horowitz-Kraus, Tzipi

Annals of dyslexia

2023 Volume 73, Issue 3, Page(s) 469–486

Abstract: This study investigated the reading comprehension scores of students with reading and language difficulties after reading a passage with and without text-to-speech (TTS). Students, ages 8 to 12 years, read five passages under the following conditions: (a) ...

Abstract	This study investigated the reading comprehension scores of students with reading and language difficulties after reading a passage with and without text-to-speech (TTS). Students, ages 8 to 12 years, read five passages under the following conditions: (a) silent read, (b) read aloud, (c) listen only, (d) TTS with no highlighting, and (e) TTS with highlighting. Students answered multiple-choice comprehension questions following each condition. Mixed ANOVAs were performed to determine whether TTS improved reading comprehension. TTS significantly improved comprehension in comparison to no TTS, and specifically, TTS with no highlighting and TTS with highlighting resulted in significantly higher comprehension scores compared to silent read. No other significant differences were found across conditions including between the presentational features of TTS, specifically TTS with no highlighting and TTS with highlighting conditions. Students were grouped as dyslexia only or reading and language impairment based on their test results. Findings suggested that students with dyslexia only scored significantly higher on reading comprehension questions in all reading conditions and derived significantly more benefit in reading comprehension from TTS and the listen only condition compared to students with Reading and Language Impairment. Overall, TTS may be a helpful tool for supporting the reading comprehension of students with reading and language difficulties, particularly for students with dyslexia only; however, further studies are needed to explore the benefits of TTS' presentational features such as highlighting with students with reading and language difficulties.
MeSH term(s)	Humans ; Child ; Comprehension ; Dyslexia ; Speech ; Reading ; Language Development Disorders
Language	English
Publishing date	2023-04-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	11939-8
ISSN	1934-7243 ; 0736-9387
ISSN (online)	1934-7243
ISSN	0736-9387
DOI	10.1007/s11881-023-00281-9
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Article ; Online: ReaLigands: A Ligand Library Cultivated from Experiment and Intended for Molecular Computational Catalyst Design.

Chen, Shu-Sen / Meyer, Zack / Jensen, Brendan / Kraus, Alex / Lambert, Allison / Ess, Daniel H

Journal of chemical information and modeling

2023 Volume 63, Issue 23, Page(s) 7412–7422

Abstract: Computational catalyst design requires identification of a metal and ligand that together result in the desired reaction reactivity and/or selectivity. A major impediment to translating computational designs to experiments is evaluating ligands that are ... ...

Abstract	Computational catalyst design requires identification of a metal and ligand that together result in the desired reaction reactivity and/or selectivity. A major impediment to translating computational designs to experiments is evaluating ligands that are likely to be synthesized. Here, we provide a solution to this impediment with our ReaLigands library that contains >30,000 monodentate, bidentate (didentate), tridentate, and larger ligands cultivated by dismantling experimentally reported crystal structures. Individual ligands from mononuclear crystal structures were identified using a modified depth-first search algorithm and charge was assigned using a machine learning model based on quantum-chemical calculated features. In the library, ligands are sorted based on direct ligand-to-metal atomic connections and on denticity. Representative principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) analyses were used to analyze several tridentate ligand categories, which revealed both the diversity of ligands and connections between ligand categories. We also demonstrated the utility of this library by implementing it with our building and optimization tools, which resulted in the very rapid generation of barriers for 750 bidentate ligands for Rh-hydride ethylene migratory insertion.
MeSH term(s)	Ligands ; Small Molecule Libraries
Chemical Substances	Ligands ; Small Molecule Libraries
Language	English
Publishing date	2023-11-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c01310
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Article ; Online: Transmissibility versus Pathogenicity of Self-Propagating Protein Aggregates.

Caughey, Byron / Kraus, Allison

Viruses

2019 Volume 11, Issue 11

Abstract: The prion-like spreading and accumulation of specific protein aggregates appear to be central to the pathogenesis of many human diseases, including Alzheimer's and Parkinson's. Accumulating evidence indicates that inoculation of tissue extracts from ... ...

Abstract	The prion-like spreading and accumulation of specific protein aggregates appear to be central to the pathogenesis of many human diseases, including Alzheimer's and Parkinson's. Accumulating evidence indicates that inoculation of tissue extracts from diseased individuals into suitable experimental animals can in many cases induce the aggregation of the disease-associated protein, as well as related pathological lesions. These findings, together with the history of the prion field, have raised the questions about whether such disease-associated protein aggregates are transmissible between humans by casual or iatrogenic routes, and, if so, do they propagate enough in the new host to cause disease? These practical considerations are important because real, and perhaps even only imagined, risks of human-to-human transmission of diseases such as Alzheimer's and Parkinson's may force costly changes in clinical practice that, in turn, are likely to have unintended consequences. The prion field has taught us that a single protein, PrP, can aggregate into forms that can propagate exponentially in vitro, but range from being innocuous to deadly when injected into experimental animals in ways that depend strongly on factors such as conformational subtleties, routes of inoculation, and host responses. In assessing the hazards posed by various disease-associated, self-propagating protein aggregates, it is imperative to consider both their actual transmissibilities and the pathological consequences of their propagation, if any, in recipient hosts.
MeSH term(s)	Alzheimer Disease/etiology ; Alzheimer Disease/metabolism ; Alzheimer Disease/pathology ; Amyloid/chemistry ; Amyloid/metabolism ; Animals ; Humans ; Membrane Proteins/metabolism ; Parkinson Disease/etiology ; Parkinson Disease/metabolism ; Parkinson Disease/pathology ; Prion Diseases/metabolism ; Prion Diseases/pathology ; Prion Diseases/transmission ; Prions/metabolism ; Prions/pathogenicity ; Protein Aggregates ; Protein Folding ; Scrapie/etiology ; Scrapie/metabolism ; Synucleins/metabolism ; Virulence
Chemical Substances	Amyloid ; Membrane Proteins ; Prions ; Protein Aggregates ; Synucleins ; tau 40 protein, human
Language	English
Publishing date	2019-11-09
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v11111044
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