151 research outputs found
Determining the Location of the Alpha-Synuclein Dimer Interface using Native Top-Down Fragmentation and Isotope Depletion-Mass Spectrometry
No full textAlpha-synuclein (αSyn), a 140-residue intrinsically disordered protein, comprises the primary proteinaceous component of pathology-associated Lewy body inclusions in Parkinson’s disease (PD). Due to its association with PD αSyn is studied extensively; however the endogenous structure and physiological roles of this protein are yet to be fully understood. Here, ion mobility-mass spectrometry and native top-down electron capture dissociation fragmentation have been used to elucidate the structural properties associated with a stable, naturally-occurring dimeric species of αSyn. This stable dimer appears in both wild-type (WT) αSyn and the PD-associated variant A53E. Furthermore, we integrated a novel method for generating isotopically depleted protein into our native top-down workflow. Isotope depletion increases signal-to-noise ratio and reduces the spectral complexity of fragmentation data, enabling the monoisotopic peak of low abundant fragment ions to be observed. This enables the accurate and confident assignment of fragments unique to the αSyn dimer to be assigned, and structural information about this species to be inferred. Using this approach, we were able to identify fragments unique to the dimer, which demonstrates a C-terminal to C-terminal interaction between the monomer subunits. The approach in this study holds promise for further investigation into the structural properties of endogenous multimeric species of αSyn. The data relates to the following publication:
Kiani Jeacock, Alexandre Chappard, Kelly J. Gallagher, C. Logan Mackay, David P. A. Kilgour, Mathew H. Horrocks, Tilo Kunath and David J. Clarke. 'Determining the Location of the Alpha-Synuclein Dimer Interface using Native Top-Down Fragmentation and Isotope Depletion-Mass Spectrometry.' J. Am. Soc Mass Spec. (in submission)
Determining the Location of the Alpha-Synuclein Dimer Interface using Native Top-Down Fragmentation and Isotope Depletion-Mass Spectrometry
No full textAlpha-synuclein (αSyn), a 140-residue intrinsically disordered protein, comprises the primary proteinaceous component of pathology-associated Lewy body inclusions in Parkinson’s disease (PD). Due to its association with PD αSyn is studied extensively; however the endogenous structure and physiological roles of this protein are yet to be fully understood. Here, ion mobility-mass spectrometry and native top-down electron capture dissociation fragmentation have been used to elucidate the structural properties associated with a stable, naturally-occurring dimeric species of αSyn. This stable dimer appears in both wild-type (WT) αSyn and the PD-associated variant A53E. Furthermore, we integrated a novel method for generating isotopically depleted protein into our native top-down workflow. Isotope depletion increases signal-to-noise ratio and reduces the spectral complexity of fragmentation data, enabling the monoisotopic peak of low abundant fragment ions to be observed. This enables the accurate and confident assignment of fragments unique to the αSyn dimer to be assigned, and structural information about this species to be inferred. Using this approach, we were able to identify fragments unique to the dimer, which demonstrates a C-terminal to C-terminal interaction between the monomer subunits. The approach in this study holds promise for further investigation into the structural properties of endogenous multimeric species of αSyn. The data relates to the following publication: Kiani Jeacock, Alexandre Chappard, Kelly J. Gallagher, C. Logan Mackay, David P. A. Kilgour, Mathew H. Horrocks, Tilo Kunath and David J. Clarke. 'Determining the Location of the Alpha-Synuclein Dimer Interface using Native Top-Down Fragmentation and Isotope Depletion-Mass Spectrometry.' J. Am. Soc Mass Spec. (in submission)
Cognitive System Dynamics
No full textCognitive System Dynamics (CSD) is an original research framework developed by Aryo Kiani to explore how beliefs evolve, persist, and distort under recursive cognitive feedback. It integrates system-level modeling methods with a novel epistemological foundation to address longstanding challenges in the study of bias, misinformation, and rational failure.
This project space is a timestamped, author-verified archive for foundational materials supporting the development of the CSD research program. Select preprints, diagrams, and working papers are made publicly visible for scholarly dialogue and citation. All documents are shared with full attribution requirements under a CC BY-NC-ND 4.0 license.
Collaboration requests and formal inquiries are welcome via the contact information on ParadigmDynamics.or
Investigating the structure of alpha-synuclein using mass spectrometry
No full textThe pathological hallmark of Parkinson’s disease (PD) are Lewy bodies (LBs),
insoluble inclusions observed in dopaminergic neurons in the brains of PD patients.
The main protein component of LBs is alpha-synuclein (αSyn), a 140-residue
intrinsically disordered protein. Around 10% of PD cases are associated with genetic
mutations, including single-point variants of αSyn; and under physiological
conditions, the protein carries a constitutive N-terminal acetylation modification.
Thus, the structural and functional properties associated with αSyn are vitally
important to investigate in order to further understanding of how this protein
contributes to disease.
Here, we report the first full biophysical characterisation and cross-comparison
of wild-type (WT) αSyn and a panel of PD-associated variants, using circular dichroism
spectroscopy, fluorescence aggregation assays, native mass spectrometry, and ion
mobility-mass spectrometry (IM-MS). We uncover that the different variants occupy
different conformational spaces in the gas phase, and that the monomeric proteins
do not exhibit a completely unfolded structure, as expected for a disordered protein.
The N-terminal acetylated variants of αSyn are a more physiologically relevant
model, with the constitutive modification being important for the formation of a
transient N-terminal α-helix which mediates the binding of αSyn to various cellular
lipid membranes. Here, we studied the effect of this modification on the structure
and function of the panel of αSyn variants.
The native state of αSyn is highly disputed, with several reports proposing the
existence of naturally occurring multimers of the protein that may be involved in the
physiological role of αSyn. However, these species have not been studied extensively
and their role is not fully understood. Here, IM-MS and native top-down
fragmentation using electron capture dissociation were used to elucidate the
structural properties associated with a stable dimeric species of αSyn. In addition, we
integrated a novel method for generating isotopically depleted protein into our
native top-down workflow. Isotope depletion increases signal to noise ratio and/or
reduces the spectral complexity of fragmentation data, enabling the monoisotopic
peak of low abundant fragment ions to be observed. Using this new workflow, we
were able to infer structural information about this previously unreported αSyn
dimer interface.
Overall, this body of work aims to highlight native mass spectrometry as an
important tool for investigating challenging structural biology problems, such as
intrinsically disordered and aggregating proteins. This work also represents a
comprehensive structural study of physiologically relevant WT αSyn and PDassociated
variants in the gas phase. We showed that the N-terminal acetylation of
αSyn and various PD-associated variants alters all aspects of structure and function
of the protein, highlighting the need for physiologically relevant modifications to be
used in in vitro studies. We also provide conclusive evidence for a C-C terminal
interaction between the monomer units forming the stable dimeric species of αSyn,
presenting important structural data on endogenous αSyn multimers
Probing TDP-43 condensation using an in silico designed aptamer
No full textAptamers are artificial oligonucleotides binding to specific molecular targets. They have a promising role in therapeutics and diagnostics but are often difficult to design. Here, we exploited the catRAPID algorithm to generate aptamers targeting TAR DNA-binding protein 43 (TDP-43), whose aggregation is associated with Amyotrophic Lateral Sclerosis. On the pathway to forming insoluble inclusions, TDP-43 adopts a heterogeneous population of assemblies, many smaller than the diffraction-limit of light. We demonstrated that our aptamers bind TDP-43 and used the tightest interactor, Apt-1, as a probe to visualize TDP-43 condensates with super-resolution microscopy. At a resolution of 10 nanometers, we tracked TDP-43 oligomers undetectable by standard approaches. In cells, Apt-1 interacts with both diffuse and condensed forms of TDP-43, indicating that Apt-1 can be exploited to follow TDP-43 phase transition. The de novo generation of aptamers and their use for microscopy opens a new page to study protein condensation.</p
Spark plasma sintering of Stellite®-6 superalloy
No full textThis paper aims at studying microstructure and mechanical properties of spark plasma sintered (SPSed) Stellite®-6 cobalt-based superalloy. SPS is a sintering technique, based on a relatively fast resistance heating using a pulsed current. Fast sintering process, associated with minimum grain growth, results in excellent mechanical properties. Samples were sintered at temperatures ranging from 950 to 1100 °C. Microstructure of samples were studied using scanning electron microscope (SEM), energy-dispersive X-ray spectroscope (EDS), X-Ray diffraction (XRD), and optical microscope. Hardness, impact test, as well as room and high temperature compression tests were used to evaluate the effects of sintering temperature and duration on the mechanical properties of SPSed samples. Results show that optimum mechanical properties can be obtained after sintering at 1050 °C for 10 min. The correlation between sintering parameters, microstructure, and mechanical properties are discussed.Accepted Author ManuscriptElectronic Components, Technology and Material
Author response
No full textDecision making often involves a tradeoff between speed and accuracy. Previous studies indicate that neural activity in the lateral intraparietal area (LIP) represents the gradual accumulation of evidence toward a threshold level, or evidence bound, which terminates the decision process. The level of this bound is hypothesized to mediate the speed-accuracy tradeoff. To test this, we recorded from LIP while monkeys performed a motion discrimination task in two speed-accuracy regimes. Surprisingly, the terminating threshold levels of neural activity were similar in both regimes. However, neurons recorded in the faster regime exhibited stronger evidence-independent activation from the beginning of decision formation, effectively reducing the evidence-dependent neural modulation needed for choice commitment. Our results suggest that control of speed vs accuracy may be exerted through changes in decision-related neural activity itself rather than through changes in the threshold applied to such neural activity to terminate a decision
Synthesis and characterization of black amorphous titanium oxide nanoparticles by spark discharge method
No full textChantal Akerman, entre autoethnographie et banal : un féminisme des interstices.
No full textChantal Akerman is generally considered a feminist cineast by the commentators of her work, especially regarding her 1976 film Jeanne Dielman, 23 Quai du Commerce, 1080 Bruxelles. This film perfectly fits into the cognitive orientation of the women’s movement of the second wave in politicizing domestic work. I argue in this article that the feminist point of view of the author is graspable in two cinematic dispositives used throughout her work: firstly, the way she forces us to look at the banal generally devalued, and secondly, the autoethnographic component of her cinema affirming the fluidity of the subject and a situated point of view. Chantal Akerman is precursor of a practice theorized since the 1980s as a consequence of the « Crisis of representation », consisting in shifting the focus from to Other to the self
Investigating Leisure-Time Patterns of Individuals with Physical Disabilities: A Case Study of Individuals with Physical Disabilities in the City of Kashan
No full textInvestigating Leisure-Time Patterns of Individuals with Physical Disabilities: A Case Study of Individuals with Physical Disabilities in the City of Kashan
Mohsen Shaterian[1] , Sedighe Kiani Salmi[2] , Maryam Kamari[3]
Received: 13/05/2018 Accepted: 19/01/2019
Abstract
The study of how individuals with disabilities spend their leisure time in order to identify their limitations and weaknesses based on their viewpoints is an essential element in planning. The results will be effective in improving the services and investment with the goal of improving, at least, part of their leisure time quality. The purpose of this study is to identify how individuals with physical disabilities in Kashan spend their leisure time. The research tool for this applied study is a questionnaire with 66 items which was developed after the study of the background and theoretical foundations of the research with an approach to empowering individuals with physical disabilities in managing their leisure time. The tool was validated with the help of experts in the field and its reliability was caluculated using the Cronbach's alpha coefficient to be 0.776. The results of the questionnaire were analyzed using AMOS and SPSS softwares. Findings indicate that home-activities with a factor load of 0.93 had a greater role in the leisure time of individuals with physical disabilities. Socializing with friends with a factor load of 0.77 ranked in second followed by computer activities, mass media, and the family. The results of the study on the problems of individuals with physical disabilities in spending their
leisure time indicate that low safety of sports equipment and lack of proper equipment for exercise with a factor load of 0.90 are the main barriers to performing leisure time activities. Other important obstacles are a lack of leisure facilities such as benches and sports facilities, lack of standard footpaths, adequate floor coverings and parking spaces with regression weights of 0.88, 0.82, 0.81, 0.77 and 0.57, respectively. In order to improve the leisure-time patterns of individuals with physical disabilities community-based rehabilitation programs are required. In this regard, planning for and empowerment of individuals with physical disabilities can be more effective with six rehabilitational activities including family education, community education, individuals with physical disabilities referring to higher levels of support and guidance, providing rehabilitation aids, employment, and social support for individuals with physical disabilities.
Keywords: City of Kashan, Individuals with Physical Disabilities, Leisure-Time, Structural Equation Modeling
[1]. Associate Professor, Department of Geography and Ecotourism, Faculty of Natural
Resource and Earth Scince, University of Kashan. (Corresponding Author).
[email protected]
[2]. Assistant Professor, Department of Geography and ecotourism, faculty of natural resource
and EarthScinceUniversity of Kashan. [email protected]
[3]. MA Student of Cultural Studies, Faculty of Natural Resource and EarthScinceUniversity
of Kashan
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