1,721,054 research outputs found
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
Investigating the role of orphan GPR50 in normal brain function and mental illness
Get PDFG protein-coupled receptors (GPCRs) form a link between the cell and their
environment when signaling pathways are activated upon ligand binding. However,
the ligands and functions for many GPCRs remain to be determined. G protein-coupled
receptor 50 (GPR50) is one such orphan, and its exact role is yet unknown.
There is however emerging functional and genetic evidence suggesting a function for
GPR50 in psychiatric illness and lipid metabolism. It was hypothesised that
investigating GPR50’s protein-protein interactions would lead to a greater
understanding of the role of GPR50 in normal brain functioning and in mental
illness. Putative protein interactors were initially isolated by a yeast two-hybid study
and were further tested here. To address GPR50’s links to mental illness, the
GPR50∆502-505 deletion variant associated with mood disorders was also investigated.
To test this hypothesis I sought to confirm some of the key yeast two-hybrid
interactions. Using co-immunoprecipitation and immunocytochemistry the
interaction of GPR50 with reticulon family members Nogo-A, Nogo-C and RTN3,
and with cell-cell adhesion molecule CDH8 and lipid-associated protein ABCA2
were validated.
In order to identify the location of interactions, subcellular fractionation of mouse
brain and rt-PCR and immunohistochemistry in developing and adult mouse brain
were performed. GPR50 and several interactors were found to be enriched at the
synapse by subcellular fractionation of whole adult brain, and at embryonic day 18
(E18) and 5 weeks by rt-PCR. Colocalisation of GPR50 and interactors was found in
the amygdala, hypothalamus, cortex and specific brain stem nuclei by
immunohistochemistry. The discovery of GPR50 expression in noradrenergic,
serotonergic and dopaminergic nuclei in the adult brain stem suggests a further role
for GPR50 in neurotransmitter signaling and stress.
To investigate the function of GPR50 two assays were performed that measure
processes which are known to be affected by Nogo and RTN3: The first assay was a
neurite outgrowth assay in Neuroscreen-1 cells, a PC12 cell clone. A significant
increase in neurite length was detected after transient overexpression of GPR50 and
this effect was increased in the GPR50∆502-505/T532A variant. Additionally GPR50-overexpression resulted in an increase in filopodia formation suggesting a role in
actin dynamics. As a second functional assay in vitro BACE1 activity assays were
performed in HEK293 cells. GPR50 but not GPR50∆502-505/T532A overexpression
resulted in a significant increase in BACE1 activity.
Lastly a final series of pilot experiments were performed to gain insight into the
secondary structure of the C-terminal domain and the effects of the polymorphisms
on structure. The 35kDa GPR50 C-terminal domain was purified and Circular
Dichroism studies indicated a predominantly unstructured protein with increased a-
helical content in the GPR50∆502-505 variant.
The results in this thesis indicate a role for GPR50 in neuronal development and
synaptic functioning. The results also strengthen an association with major mental
illness, with links to several disease mechanisms
Genome wide gene expression analysis of two ENU mouse models of major mental illness
Get PDFMajor mental illness is now recognised as one of the leading causes of adult
morbidity. Of the adult onset psychiatric disorders, the functional psychoses
(schizophrenia, bipolar disorder and recurrent major depression) are the most severe
and most common in the general population. Evidence suggests that certain genetic
factors influence an individual’s susceptibility to developing these disorders when
combined with appropriate social and environmental conditions. Several good
candidate genes have been identified. Of relevance to this study is Disrupted in
Schizophrenia 1 (DISC1) which was identified in a large Scottish family that carried a
balanced translocation (t1:11) and had a history of major mental illness. In 2008, two
ENU mutant mouse models with missense mutations in exon 2 of Disc1 were
characterised and found to have behavioural and neuroanatomical phenotypes
consistent with schizophrenia and major depression. The primary aim of this thesis is
to further analyse these mouse models by performing whole genome gene expression
studies and secondary protein analysis to identify genes involved in the aetiology of
schizophrenia and major depression.
My initial analysis used Illumina BeadChip microarray technology to identify 368
genes that were differentially expressed in ENU mutant animals under different
biological conditions, compared to appropriate control animals. Nine biological
groups were compared including one embryonic group at E13, and three groups
treated with appropriate anti-psychotic or anti-depressant drugs. Of the 368 genes
identified as differentially expressed, 46 were chosen for validation by qRT-PCR
based on fold-change, p-value, functional significance, overenrichment of GO terms,
pathway analysis and previous implications in major mental illness. NRXN1, NRXN3
and CDH11 were found to be significantly up-regulated in the schizophrenia mouse
model with EGR4 significantly down-regulated compared to C57BL/6J wild-type
controls. These findings were also replicated in an independent sample using wildtype
littermates. The mental retardation gene PAK3 was up-regulated in the
schizophrenia mouse model and expression levels were corrected to a level not
significantly different to wild-type, when treated with the PDE4 inhibitor Rolipram.
Semi-quantitative western blotting also confirmed the disregulation of EGR4 and
PAK3 at the protein level in these animals. RNA expression profiles were also
characterised for each of the genes above, and DISC1, through development. In summary this thesis describes the striking disregulation of four prominent genetic
candidates of major mental illness in an independent animal model. A first functional
link between DISC1 and NRXN1 is described suggesting, for the first time, a DISC1-
dependant mechanism for regulating neurexin gene expression
Characterising the role of GPR50 in neurodevelopment and lipid metabolism
Get PDFG-protein coupled receptor 50 (GPR50) is a genetic risk factor for psychiatric illness.
It is a member of the melatonin receptor family, which includes the well
characterised melatonin receptors 1 and 2 (MT1 and MT2). However, the ligand for
GPR50 remains elusive and little is known about GPR50 signalling pathways.
Despite this, GPR50 is known to enhance neurite outgrowth and inhibit the actions of
the neurite outgrowth inhibitor NOGO-A. Existing evidence also indicates a role in
lipid metabolism; GPR50 knockout mice displayed abnormalities in energy
homeostasis and weight control, whilst sequence variants are associated with altered
lipid levels in humans. Further, a yeast-2-hybrid screen identified SREBF2 and
ABCA2, regulators of lipid homeostasis, as GPR50 interactors. This thesis explores
the role of GPR50 in neuronal development and lipid metabolism.
The work presented in this thesis shows that GPR50 promotes neuronal
differentiation. Overexpression significantly increased the number of neurites per
cell in SH-SY5Y cells. Further, dendritic branching was enhanced by GPR50
transfection in hippocampal and cortical neurons (DIV 14). In hippocampal neurons,
GPR50 transfection also lead to a shift towards spine maturity although it had no
effect on spine morphology, suggesting GPR50 enhances spine development but may
not alter synaptic strength. The effect of GPR50 on neuronal morphology may be
driven by actin remodelling. Immunocytochemistry showed an enrichment of
GPR50 in highly dynamic regions of the membrane, i.e. the lamellipodia and
dendritic spines. Overexpression in SH-SY5Y cells also resulted in an increase in
WAVE-2 and phosphorylated RAC1/CDC42, key modulators of actin dynamics.
Additionally, GPR50 transfection altered the protein level and localisation of α-
catenin, another regulator of actin organisation, in HEK293 and SH-SY5Y cells
respectively. An involvement of GPR50 in lipid metabolism has also been demonstrated in this thesis. Verification of the Y2H study suggested GPR50 does not physically interact
with SREBF2 or ABCA2. However, ABCA2 appears to induce the intracellular
localisation of GPR50 in several cell lines. In SH-SY5Y cells, this was mimicked by
the inhibition of cholesterol trafficking, suggesting the translocation of GPR50 to the
plasma membrane is dependent on cholesterol transport. Further, the depletion of
lipoproteins resulted in the downregulation of GPR50, indicating a responsiveness to
lipid levels. Finally, GPR50 increased lipid metabolism, as seen by a decrease in
intracellular lipid droplets upon GPR50 overexpression.
The data presented here extends previous work indicating a role of GPR50 in
neurodevelopment. It also highlights a potential mechanism by which GPR50
regulates neuronal morphology, i.e. via actin remodelling. Reports that GPR50 is
involved in energy homeostasis is also supported in this thesis, further, results
presented here suggest GPR50 is specifically involved in lipid metabolism. These
processes are often disrupted in mental illness, thus this work may provide a
functional link between GPR50 and psychiatric disorders
Genetic responses to environmental stress underlying major depressive disorder
Get PDFMajor depressive disorder (MDD) is a common psychiatric disorder and a
leading cause of disability worldwide. Such illness is the result of a complex
interplay between genetic susceptibility and environmental risk factors.
Adverse life events are experienced before the onset of depressive episodes
in most patients, with robust evidence for the role of stressful life events
(SLE) as a main trigger of depressive symptoms. However, not all individuals
develop depression after episodes of stress. Thus, an individual’s sensitivity
to stress is an important predictor of stress response that may mediate the
association between stress and depression. A deeper understanding of the
genetic mechanisms underlying stress-sensitivity and stress response is,
therefore, crucial to a better understanding of MDD and thus to improve
treatments for both depressive symptoms and other stress-related conditions.
This PhD thesis uses empirical data from white Caucasian population-based
samples. By incorporating in new hypothesis-free genome-wide association
studies and polygenic approaches quantitative measures of recent SLE and
neuroticism---a personality trait though to mediate or moderate the effects of
adversity on depression risk---, this PhD thesis identifies the genetic
influences to a proxy for sensitivity to environmental stress and genotype-byenvironment
interaction (GxE) effects underlying depressive symptoms.
Following an introductory chapter, chapter 2 conceptualizes a proxy for our
sensitivity to negative outcomes by modelling the interaction between genetic
variants and MDD status on neuroticism score through a genome-wide
interaction study. This chapter seeks to identify genetic variants contributing
to a potential endophenotype mediating the associations between stress and
depression, and examines whether genetic effects on such proxy for stress
sensitivity partially explains the genetic contributions to liability not
attributable to additive main effects. The strongest signals came from genetic
variants associated with the glucocorticoid receptor function. Therefore,
Chapter 3 assesses the enrichment of the genetic contributions to liability of
MDD within three glucocorticoid-related gene sets: one gene set reflecting
“up-stream” cortisol signalling genes and two gene sets reflecting “downstream”
cortisol response genes. Chapter 4 empirically tests and assesses
the diathesis-stress theory for depression; using polygenic risk scores
weighted by the additive effects of MDD derived from the Psychiatric Genetic
Consortium MDD genome-wide association study and self-reported
measures on recent SLE. This chapter provides evidence for the presence of
GxE effects between stress and common genetic variants on risk of
depressive symptoms. The empirical support for this theory validates other
GxE approaches applying a genome-wide approach to investigate the
causative effect of stress in the development of depressive symptoms. Thus,
chapter 5 presents findings from genome-wide by environment interaction
studies in two cohorts that seek to identify common variants displaying an
increased risk of liability to depressive symptoms in response to SLE.
Whether inclusion of GxE effects improves the prediction of liability to MDD
over that explained by genetic additive main effects alone is also tested.
Furthermore, two potential forms of gene-environment interplay (i.e. GxE and
gene-environment correlation) and their biological interpretation are
extensively discussed. Stress contributes to many human conditions.
Therefore, the GxE effects are also used to predict other stress-related
physical and mental conditions. This chapter reports evidence of a potential
shared aetiology between depression and other traits, such as schizotypal
personality or heart disease, due to genetic mechanism underlying the
effects of SLE. Finally, chapter 6 brings back the diathesis-stress model
investigated in chapter 4. This chapter incorporates into the diathesis
framework the genetics effects for stress sensitivity and stress response
estimated in chapters 2 and chapter 5, respectively, and assess their
relevance to the diathesis-stress theory. Genetic differences between women
and men in stress response underlying the aetiology of depression are also
discussed.
Genetics plays a significant role in the effects of stress. The findings
presented in this thesis emphasize the relevance of genetic effects for stress
sensitivity and stress response in depression and health in general. Overall,
this thesis presents a range of original studies in order to advance our
understanding of the genetic response to stress, comprehensively discussing
the limitations and pitfalls of this research area, and provides a basis for
future lines of research on gene-environment interplay in psychiatry
Using DNA methylation data and haplotypes to investigate predisposition to Alzheimer’s disease
Get PDFAlzheimer’s disease (AD) is a complex neurodegenerative disease resulting in cognitive decline, memory issues and alterations in mood, behaviour, and personality. AD is the most common form of dementia, which accounts for 50-75% of cases globally. Individuals with AD may become impulsive and disorientated in the early stages but as the disease progresses many require full time care support and die prematurely. AD pathophysiology is characterised by amyloid-beta plaques and tau neurofibrillary tangles within the brain. AD has a high heritability (60-80%) yet much of this remains largely unexplained. There are predicted to be between 100-10,000 causal variants; exemplifying the necessity to identify and characterise new genetic risk factors. In some cases, epigenetic changes in the genome may be studied to provide additional understanding into the effect the heritable risk of AD has on gene expression. Epigenetic changes may be investigated using polygenic risk scores (PRS) and epigenome wide association studies (EWAS), which may provide insight into an individual’s genetic susceptibility to AD and the association between AD and DNA methylation. Previously, Walker et al used 26 lead loci to identify 68 significant differentially methylated (DM) CpGs. Walker et al carried out meQTL analyses using the DM CpGs identified, finding 48 CpGs were associated in cis with genetic variants in the genome wide association study (GWAS) loci. The aim of the study was to use additional AD associated loci to identify and characterise further genome wide significant (GWS) DM loci, using individual SNPs and haplotypes. Additionally, the individual effects of functional haplotypes on epigenetic variation were investigated. The most recent and relevant AD-GWAS results were used in this study, with up to 75 AD risk loci identified, to generate an AD PRS. The AD PRS were used to identify significant AD associated, DM CpGs. meQTL analysis was carried out to investigate the association of the significant CpGs with the SNPs in the PRS. SORL1 and APOE have previously been identified as AD susceptibly genes, and functional studies have been carried out. The functional studies have identified SNPs within APOE and SORL1 which directly influence the function of the genes and protein production, altering an individual’s risk to AD. Therefore, haplotypes spanning these gene regions were used in meQTL analyses to consider whether the individual SNPs or haplotypes have a different association with DM at the significant CpGs. Further EWAS were carried out using only haplotypes which contain the AD-risk allele at the SNPs comprising the functional haplotype in SORL1 and APOE. Schwartzentruber et al and Bellenguez et al AD GWAS were identified as the most suitable for the PRS generation. EWAS meta-analyses using the Bellenguez et al and Schwartzentruber et al derived PRS identified 116 and 203 GWS DM CpGs, respectively. meQTL analyses identified 45/116 and 109/203 of these GWS CpGs were significantly associated with SNPs in the PRS.
With 31 and 21independant GWS lead CpGs identified using the Bellenguez et al and Schwartzentruber et al PRS in the EWAS, respectively. meQTL analysis found SNPs in the SORL1 region had the strongest association with DM at CpG sites, as opposed to haplotypes and/or when the APOE region were investigated.
Functional haplotypes dependent upon carrier status identified additional GWS DM CpGs and associated genes, of particular interest was FEM1C. Ultimately this study may allow further investigation into the importance and relevance of the GWS DM loci in AD progression, disease pathogenesis and aetiology
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
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