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An investigation into the role of mitochondrial dysfunction in South African Parkinson’s disease patients
Get PDFThesis (MScMedSC)--Stellenbosch University, 2012.BibliographyENGLISH ABSTRACT: Parkinson’s disease (PD) is a neurodegenerative movement disorder characterized by the loss of dopaminergic neurons in the substantia nigra of the midbrain. Although the aetiology of PD is still not fully understood, it is thought to involve a combination of environmental (such as exposure to pesticides and neurotoxins) and genetic factors. A number of PD-causing genes have been found including SNCA, LRRK2, EIF4G1 and VPS35 (for autosomal dominant forms of PD) and parkin, PINK1, DJ-1 and ATP13A2 (for autosomal recessive forms of PD – arPD). Mutations in the parkin gene are the predominant cause of arPD. Parkin plays a role in the ubiquitin-proteasomal system which degrades damaged and unwanted proteins in the cell and it is also thought to be involved in maintaining healthy mitochondria. Numerous studies have implicated mitochondrial function in the pathogenesis of PD. Therefore the aim of the present study was to investigate the role of mitochondrial dysfunction in PD patients with parkin-null mutations.
Four South African PD patients, each harbouring two parkin-null mutations, were recruited for this study. A muscle biopsy was performed for analysis of mitochondrial morphology using histology and transmission electron microscopy (TEM). Skin biopsies were taken, from which fibroblasts were cultured. These fibroblasts were used in i) mitochondrial morphological assessments using TEM, ii) mitochondrial network analysis, iii) functional studies via ROS measurement and iv) analysis of the proteome using a LTQ Orbitrap Velos mass spectrometer. In addition, RNA was isolated from peripheral blood samples for gene expression studies using the RT² Profiler PCR Array (SABiosciences, USA) and the RT² PCR Primer Assay (SABiosciences, USA). Heterozygous family members (carriers) and wild-type controls were also recruited for this study. Results from the histological and TEM analysis from the muscle biopsy observed subtle mitochondrial changes including the presence of type II fibres, atrophic fibres, the presence of lipids, and wrinkling of the sarcolemmal membrane. Enlarged mitochondria were also observed in one patient. TEM analysis on the patient’s fibroblasts observed an increase in the number of electron dense vacuoles, speculated to be autolysosomes. The mitochondrial network in two of the patients’ fibroblasts showed fragmented and dot-like networks which are indicative of damaged mitochondria. An increase in mitochondrial ROS levels was observed in three of the four patients. Expression studies found down-regulation of 14 genes from four of the five mitochondrial complexes and a total of 688 proteins were found only in the control and not in the patient fibroblasts. Some of these proteins are known to be part of the ‘mitochondrial dysfunction’ pathway.
Taken together, these results indicate that the absence of parkin results in a number of mitochondrial alterations. Based on these findings, a model of PD was proposed: It is speculated that when parkin is absent, electron transport chain complex genes are down-regulated. This results in impaired oxidative phosphorylation, causing an increase in the production of mitochondrial ROS and subsequent oxidative stress. Mitochondria are then damaged; resulting in the fragmentation of the mitochondrial network. The impaired mitochondria are thus tagged for degradation, causing the recruitment of autolysosomes which engulf the mitochondria via mitophagy. Ultimately, as the compensatory mechanisms fail, this triggers the consequential cascade of cellular apoptotic events.
This study has elucidated the effect of parkin on the mitochondria, and can act as a ‘stepping stone’ towards future development of therapeutic strategies and/or biochemical markers that will benefit not only patients with PD but also other neurodegenerative disorders.AFRIKAANSE OPSOMMING: Parkinson se siekte (PS) is ‘n neurodegeneratiewe bewegings-afwyking gedefineer deur die verlies van dopaminergiese neurone in die substantia nigra van die midde brein. Alhoewel die spesifieke oorsprong van die afwyking nog nie ten volle begryp is nie, word bydraes van beide omgewings faktore (bv. blootstelling aan plaagdoders en neurotoksienes) asook genetiese faktore gespekuleer. Vanuit ‘n genetiese aspek is ‘n aantal gene al geassosieer met PS. Hierdie gene sluit in SNCA, LRRK2, EIF4G1 en VPS35 (vir outosomale dominante vorms van PS) en parkin, PINK1, DJ-1, en ATP13A2 (vir outosomale resessiewe vorms van PS - orPS). Mutasies in die parkin geen is aangedui as die hoof oorsaak van orPS. Parkin speel ‘n rol in die ubiquitine-proteasomale sisteem wat beskadige en ongewensde proteïne binne in die sel verwyder en is verdink om by te dra tot die instandhouding van gesonde mitokondria. Mitokondriese wanfunksionering is ook deur talle studies gewys as ‘n bydraende faktor in die patologie van PS. Die doel van die studie is om ondersoek in te stel tot die spesifieke rol wat mitokondriese wanfunsionering speel in PS pasiënte met parkin-nul mutasies.
Vier Suid-Afrikaanse PS-pasiënte, elk met twee parkin-nul mutasies, is gebruik vir die studie. Deur middel van spierbiopsies is monsters verkry vir mitokondriese morfologiese analises met behulp van histologiese en elektron-oordrag mikroskopie tegnieke (TEM). Vel biopsies is ook geneem en fibroblaste is gekweek vir die gebruik in: i) mitokondriese morfologiese assesering; ii) mitokondriese netwerk analiese; iii) funksionele studies waar vlakke van reaktiewe suurstof spesies (ROS) gemeet is; iv) proteoom analiese met behup van ‘n LTQ Orbitrap Velos massa spektrometer. RNA is ook geisoleer vanaf perifere bloedmonsters vir die gebruik in geen-uitdrukkings studies met behulp van ‘n RT² Profiler PCR Array en ‘n RT² Primer Assay. Selle vanaf famielie lede wat heterosigotiese draers is van die mutasie, asook normale (geen parkin mutasie) selle is gebruik as kontroles in die studie. TEM resultate vanaf die spier monsters het subtiele mitokondriese veranderinge getoon. Hierdie sluit in die teenwoordigheid van tipe II vesels, atrofiese vesels, teenwoordigheid van lipiedes, assook waarnemings van rimpeling van die sarcolemmal membraan. Vergrote mitokondrias is ook in een van die pasiënte opgelet. TEM resultate vanaf die fibroblaste het toename in die aantal elektron-digte vakuole vertoon, moontlik geidentifiseer as autolisosome. Gefragmenteerde en onderbreekte mitokondria netwerke is gelet tydens netwerk analiese van die fibroblaste, ‘n indikasie van beskadigde mitokondria. ‘n Toename in mitokondriese ROS vlakke is gevind in drie van die vier pasiënte. Af-regulering van 14 gene, geassosieerd met vier uit die vyf mitokondria komplekse, is verneem tydens die geen-uitdrukkings studie. Saam met dit is ‘n totaal van 688 proteïene geidentifiseer wat slegs teenwoordig is in die kontrole monsters en nie in die pasiënt monsters nie. Hierdie proteïene is almal uitgedruk en betrokke in die mitokondriese wanfunsionerings-weë.
Hierdie resultate dui dat die afwesigheid van parkin mitokondriese afwykings tot gevolg het wat kan lei tot die afsterwing van selle. Dit dra ook by tot die vorming van ‘n beter-verstaande siekte-model vir PS: Mutasies in parkin (wat lei tot die afwesigheid van parkin) kan dus moontlik lei tot die af-regulasie van gene geassosieerd met die elektron-vervoer ketting komplekse in die mitokondria. Dit lei tot gebrekkige oksidatiewe fosforilering en veroorsaak ‘n toename in die vorming van ROS, wat dan ‘n toename in oksidatiewe stres binne in die sel tot gevolg het. Uiteindelik lei dit dus tot die beskadiging van die mitokondria wat gepaard gaan met fragmentering van die mitokondriese netwerk. Beskadigde mitokondrias word geetiketeer vir afbraking. Hierdie etiketering aktiveer omringende autophagosome wat die beskadigde mitokondrias dan verwyder deur middel van ‘n verswelgende proses genaamd mitophagy. Dit veroorsaak die aktivering van ‘n aantal gekorreleerde sellulêre prosesse wat lei tot apoptose (afsterwing van die sel).
Hierdie studie dra by tot die verklaring van die spesifieke effek wat parkin mutasies het op die funksionering van die mitokondria. Resultate hier lê ook die grondslag vir toekomstige studies met die doel tot die ontwikkeling van terapeutiese strategeë en biochemiese merkers wat kan bydrae tot die genesing van beide pasiënte met PS, asook pasiënte met ander neurodegeneratiewe afwykings
Analysis of copy number variation and disease mechanisms underlying Parkinson’s disease
Get PDFThesis (PhD)--Stellenbosch University, 2016ENGLISH ABSTRACT : Parkinson’s disease (PD) is a neurodegenerative movement disorder characterized by the loss of
dopaminergic neurons in the substantia nigra of the midbrain. Although the aetiology of PD is still not
fully understood, it is thought to involve a combination of environmental and genetic factors. To date,
a number of PD-causing genes have been found. The PINK1 gene is of particular interest for this study,
and mutations in this gene result in autosomal recessive inheritance of early onset PD. PINK1 plays a
vital role in mitochondrial quality control and homeostasis, and in its absence it is thought to result in
an accumulation of dysfunctional mitochondria in neurons, culminating in neuronal cell death. Whilst
pharmacological and surgical interventions are available for PD, the current options exhibit adverse
side effects with long term treatment. There is a great need to develop new treatments with i. less side
effects and ii. that can simultaneously target the multiple pathways associated with this disorder. One
molecule is curcumin, the core component of the curry spice turmeric, which is well known for its
antioxidant and anti-inflammatory properties and has already been studied for its possible
neuroprotective role in Alzheimer’s disease.
The aim of the present study was to create a cellular model of PD by decreasing the expression of
PINK1 in SH-SY5Y neuroblastoma cells. Thereafter, we aimed to test the protective effects of curcumin
on this model in the presence and absence of a known stressor, paraquat. This study also aimed to detect
possible copy number variation (CNV) in PINK1 (and other PD-causing genes) in a cohort of South
African patients with PD, in order to obtain patient-derived fibroblasts to verify the results obtained
from the original cellular model.
PINK1 was knocked down using siRNA (Qiagen, USA) in SH-SY5Y neuroblastoma cells, and the
knock down was verified by quantitative real time PCR (qRTPCR) and western blotting. Thereafter,
PINK1 siRNA cells and control cells were separated into four treatment groups: i. untreated, ii. treated
with 25μM paraquat for 24hours, iii. pre-treated with 2μM curcumin for 1hour then treated with 25μM
paraquat for 24hours, or iv. treated with 2μM curcumin for 1hour, and various parameters of cellular
and mitochondrial function were measured. Cell viability was measured by an MTT assay. Western blot
analysis was performed using cleaved PARP and full-length caspase 3 markers to detect levels of
apoptosis, and LC3-II and p62 markers to detect autophagic flux. Mitochondrial respiration experiments
were completed on the Seahorse XF Analyser using the Mito Stress Test Kit and the Glycolysis Stress
Test. Flow cytometry was utilised to measure mitochondrial membrane potential (MMP) using the JC-
1 fluorochrome, and mitochondrial network was analysed by fluorescent microscopy. For CNV
detection, MLPA was performed on 210 South African PD patients and putative mutations were verified
by qRTPCR on the Lightcycler 96.
PINK1 was successfully knocked down at a gene and protein expression level. The PINK1 siRNA cells
exhibited a significant decrease in cell viability (p=0.0036), and an increase in apoptosis (p=0.0144). A
decrease in PINK1 expression also resulted in significantly decreased MMP (p=0.0008), mitochondrial
respiration (p=0.0015), ATP production (p=0.002) and glycolytic capacity (p=0.0445). No significant
changes were observed in the connectivity of the mitochondrial network, but autophagic flux was
significantly increased in the PINK1 siRNA cells, as detected by increased LC3-II levels (p=0.0152). As expected, paraquat-treated cells exhibited decreased cell viability, increased apoptosis, decreased
MMP, autophagic flux, and a more fragmented mitochondrial network. Paraquat treatment therefore
successfully acted as a stressor on the cells. Curcumin pre-treatment followed by paraquat treatment
rescued cell viability in control cells (p=0.003), and significantly decreased apoptosis in PINK1 siRNA
cells (p=0.0018). Curcumin protected mitochondrial dysfunction in PINK1 siRNA cells by increasing
MMP (p=0.0472) and maximal respiration (p=0.0014), as well as significantly increasing MMP
(p=0.0307) and maximal respiration (p=0.032) in control cells. Additionally, curcumin treatment
resulted in increased autophagic flux (p=0.0017) in stressed control cells. These results highlight a
protective effect of curcumin against paraquat and against the damaging effects on the mitochondria in
cells with decreased PINK1 expression.
Lastly, MLPA analysis did not reveal any PINK1 CNV mutations in a total of 210 South African PD
patients, and fibroblasts were therefore not obtained. A number of false positive mutations were
identified that were not verified by qRTPCR. A common polymorphism M192L resulting in a false
positive PARK2 exon 5 deletion was found in a number of patients, all of whom were of Black or Mixed
Ancestry ethnic groups. One patient was shown to harbour a heterozygous deletion in PARK2 exon 4.
In conclusion, PINK1 siRNA-mediated knock down in SH-SY5Y neuroblastoma cells can be used as
a model of PD to study aspects of mitochondrial dysfunction. Furthermore, curcumin should be
considered as a possible therapeutic target for PD, as it exhibits protective effects against paraquat at a
mitochondrial level. Given the low toxicity of curcumin, and the fact that it is already part of a dietary
regimen in most populations worldwide, further studies on elucidating its biochemical and cellular
properties are therefore warranted. The use of natural compounds such as curcumin as therapeutic
agents is currently a topical and fast-growing area of research, and holds much promise for clinical
application in various diseases including neurodegenerative disorders such as Alzheimer’s disease and
PD.AFRIKAANSE OPSOMMING : Parkinson se siekte (PD) is 'n neurodegeneratiewe beweging versteuring wat gekenmerk word deur die
verlies van dopaminergiese neurone in die brein. Hoewel die etiologie van PD nog nie ten volle verstaan
is nie, is daar denke dat dit 'n kombinasie van die omgewing en genetiese faktore behels. Tot dus ver is
daar nog net ‘n aantal gene wat PD-veroorsaak gevind. Die PINK1 geen is van besondere belang vir
hierdie studie, en mutasies in dié geen veroorsaak outosomale resessiewe oorerwing van vroeë aanvang
PD. PINK1 speel 'n belangrike rol in die mitochondriale gehaltebeheer en homeostase, en in sy
afwesigheid is dit gedink om te lei tot 'n opeenhoping van disfunksionele mitochondria in die neurone,
wat kulmineer in neuronale sel dood. Terwyl farmakologiese en chirurgiese ingrepe beskikbaar is vir
PD, die huidige opsies wys duidelike newe-effekte met lang termyn behandeling. Daar is 'n groot
behoefte om nuwe behandelings te ontwikkel met i. minder newe-effekte en ii. wat gelyktydig die
verskeie paaie wat verband hou met hierdie versteuring kan teiken. Een molekule is curcumin, die hoof
komponent van die kerrie spesery borrie, wat wel bekend is vir, sy anti-oksidant en anti-inflammatoriese
eienskappe, en is reeds bestudeer vir sy moontlike beskermende rol in Alzheimer’s se siekte.
Die doel van hierdie projek is om 'n sellulêre model van PD te skep deur die vermindering van die
uitdrukking van PINK1 in SH-SY5Y neuroblastoom selle. Ons daarop gemik om die beskermende effek
van curcumin te toets in die teenwoordigheid en afwesigheid van 'n bekende stressor, parakwat in ons
model. ‘n Additionele doelwit is om moontlike kopiegetal variasie (CNV) in die PINK1 gene (en ander
PD veroorsaakende gene) op te tel in 'n groep van die Suid-Afrikaanse pasiënte met PD. Die doel van
hierdie was om pasiënt-afgeleibare fibroblaste te kry om die resultate te verifieer vanuit die
oorspronklike model.
SH-SY5Y neuroblastoom selle was gekweek, en PINK1 is platgeslaan deur gebruik te maak van siRNA
en HiPerfect Transfectie Reagens (Qiagen, VSA). Klop van PINK1 is bevestig deur kwantitatiewe real
time PCR (qRTPCR) en westelike klad. Daarna, PINK1 siRNA selle en beheer selle was óf i. nie
behandel nie, ii. behandel met 25 um paraquat vir 24 uur per dag, iii. vooraf behandel met 2μM curcumin
vir 1 uur dan behandel met 25 um paraquat vir 24 uur per dag, of iv. behandel met 2μM curcumin vir 1
uur, en verskeie parameters van sellulêre en mitochondriale funksie is gemeet. Lewensvatbaarheid van
die selle is gemeet deur 'n MTT toets. Westerne klad analise is uitgevoer met behulp van gekleefde
PARP en vollengte caspase 3 merkers om die vlakke van apoptose te meet, en LC3-II en p62 merkers
was gebruik om autophagic vloed op te spoor. Mitochondriale respirasie eksperimente is voltooi op die
Seahorse XF Analyser met behulp van die Mito Stres Test Kit en die Glikolise Stres Toets.
Vloeisitometrie is gebruik om mitochondriale membraan potensiaal (MMP) te meet met behulp van die
JC-1 fluorochrome en die mitochondriale netwerk is geanaliseer deur fluorescent mikroskopie. Vir
CNV opsporing, was MLPA uitgevoer op 210 Suid-Afrikaanse PD pasiënte en vermeende mutasies is
bevestig deur qRTPCR op die Lightcycler 96.
PINK1 is suksesvol platgeslaan op 'n geen en proteïen uitdrukking vlak. Die PINK1 siRNA selle betoon
'n beduidende afname in lewensvatbaarheid sel (p = 0.0036), en 'n toename in apoptose (p=0.0144). 'n Afname in PINK1 uitdrukking het ook daartoe gelei na ‘n beduidende vermindering in MMP
(p=0.0008), mitochondriale respirasie (p=0.0015), ATP produksie (p=0.002) en glikolitiese kapasiteit
(p=0.0445). Geen beduidende veranderinge is waargeneem in die verbinding van die mitochondriale
netwerk nie, maar autophagic vloed het aansienlik toegeneem in die PINK1 siRNA selle, soos
waargeneem deur verhoogde vlakke in LC3-II (p=0.0152).
Soos verwag betoon, paraquat behandelde selle ‘n afname in sel lewensvatbaarheid, verhoogde
apoptose, afname in MMP, autophagic vloed, en 'n meer gefragmenteerde mitochondriale netwerk.
Parakwat behandeling het dus suksesvol opgetree as 'n stressor op die selle. Curcumin voorafbehandeling
gevolg deur paraquat behandeling het sel lewensvatbaarheid gered in beheer selle
(p=0.003), en aansienlik verminderde apoptose in PINK1 siRNA selle (p=0.0018) betoon. Curcumin
beskerm mitochondriale disfunksie deur die verhoging van MMP (p=0.0472, p=0.0307) en maksimale
respirasie (p=0.0014, p=0.032) in beide PINK1 siRNA en beheer selle. Additioneel, het curcumin
behandeling gelei tot ‘n verhoogde autophagic vloed (p=0.0017) in onderdrukte beheer selle. Hierdie
resultate beklemtoon die beskermende effek van curcumin teen parakwat en teen die skadelike resultaat
op die mitochondria in die selle met verlaagde PINK1 uitdrukking.
Laastens, MLPA ontleding het nie PINK1 CNV mutasies openbaar in 'n totaal van 210 Suid-Afrikaanse
PD pasiënte, en fibroblaste is dus nie verkry nie. 'n Aantal vals positiewe mutasies is geïdentifiseer wat
nie geverifieer is deur qRTPCR. 'n Algemene polimorfisme M192L is in 'n aantal pasiënte gevind wat
in 'n vals positiewe PARK2 ekson 5 eliminasie ontaard, waarvan almal swart of gemengde afkoms etiese
groepe is. Een pasiënt het getoon dat 'n heterosigotiese eliminasie in PARK2 ekson 4 bevind is.
Ten slotte, PINK1 siRNA-gemedieerde wat platgeslaan is in SH-SY5Y neuroblastoom selle kan gebruik
word as 'n model van PD om aspekte van mitochondriale disfunksie te bestudeer. Verder moet curcumin
beskou word as 'n moontlike terapeutiese teiken vir PD, omdat dit beskermende effekte teen parakwat
op 'n mitochondriale vlak vertoon. Gegewe die lae toksisiteit van curcumin en die feit dat dit reeds ‘n
deel vorm van die dieët in meeste populasie groepe wêreldwyd, is verdere studies op die biochemiese
en sellulêre eienskappe daarvan benodig. Die gebruik van natuurlike komposisies, soos curcumin as ‘n
terapeutiese middel is tans ‘n relevante en vinnig groeiende area van navorsing en toon baie belofte vir
kliniese toepassing in verskeie siektes soos Alzheimer’s siekte en PD.Doctora
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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