1,720,966 research outputs found
Corrigendum to ”Calreticulin is crucial for calcium homeostasis mediated adaptation and survival of thick ascending limb of Henle’s loop cells under osmotic stress” [Int. J. Biochem. Cell Biol. 43 (2011) 1187– 1197]
No full textAdaption of the global test idea to proteomics data with missing values
No full textMotivation: Global test procedures are frequently used in gene expression analysis to study the relationship between a functional subset of RNA transcripts and an experimental group factor. However, these procedures have been rarely used for the analysis of high-throughput data from other sources, such as proteome expression data. The main difficulties in transferring global test procedures from genomics to proteomics data are the more complicated way of obtaining functional annotations and the handling of missing values in some types of proteomics data. Results: We propose a simple mixed linear model in combination with a permutation procedure and missing values imputation to conduct global tests in proteomics experiments. This new approach is motivated by protein expression data obtained by means of 2-D gel electrophoresis within a mouse experiment of our current research. A simulation study yielded that power and testing level of the mixed model alone can be affected by missing values in the dataset. Imputation of missing values was able to correct for a bias in some simulation settings. Our new approach provides the possibility to rank Gene Ontology (GO) terms associated with protein sets. It is also helpful in the case in which a specific protein is represented by multiple spots on a 2-D gel by considering these spots also as a protein set. Analysis of our data points at correlations between the deficiency of the protein 'calreticulin' and protein sets related to biological processes in the heart muscle
Impact of the antiproliferative agent ciclopirox olamine treatment on stem cell proteome
Full text linkAIM: To investigate the proteome changes of stem cells due to ciclopirox olamine (CPX) treatment compared to control and retinoic acid treated cells. METHODS: Stem cells (SCs) are cells, which have the ability to continuously divide and differentiate into various other kinds of cells. Murine embryonic stem cells (ESCs) and multipotent adult germline stem cells (maGSCs) were treated with CPX, which has been shown to have an antiproliferative effect on stem cells, and compared to stem cells treated with retinoic acid (RA), which is known to have a differentiating effect on stem cells. Classical proteomic techniques like 2-D gel electrophoresis and differential in-gel electrophoresis (DIGE) were used to generate 2D protein maps from stem cells treated with RA or CPX as well as from non-treated stem cells. The resulting 2D gels were scanned and the digitalized images were collated with the help of Delta 2D software. The differentially expressed proteins were analyzed by a MALDI-TOF-TOF mass spectrometer, and the identified proteins were investigated and categorized using bioinformatics. RESULTS: Treatment of stem cells with CPX, a synthetic antifungal clinically used to treat superficial mycoses, resulted in an antiproliferative effect in vitro, without impairment of pluripotency. To understand the mechanisms induced by CPX treatments which results in arrest of cell cycle without any marked effect on pluripotency, a comparative proteomics study was conducted. The obtained data revealed that the CPX impact on cell proliferation was accompanied with a significant alteration in stem cell proteome. By peptide mass fingerprinting and tandem mass spectrometry combined with searches of protein sequence databases, a set of 316 proteins was identified, corresponding to a library of 125 non-redundant proteins. With proteomic analysis of ESCs and maGSCs treated with CPX and RA, we could identify more than 90 single proteins, which were differently expressed in both cell lines. We could highlight, that CPX treatment of stem cells, with subsequent proliferation inhibition, resulted in an alteration of the expression of 56 proteins compared to non-treated cells, and 54 proteins compared to RA treated cells. Bioinformatics analysis of the regulated proteins demonstrated their involvement in various biological processes. To our interest, a number of proteins have potential roles in the regulation of cell proliferation either directly or indirectly. Furthermore the classification of the altered polypeptides according to their main known/postulated functions revealed that the majority of these proteins are involved in molecular functions like nucleotide binding and metal ion binding, and biological processes like nucleotide biosynthetic processes, gene expression, embryonic development, regulation of transcription, cell cycle processes, RNA and mRNA processing. Proteins, which are involved in nucleotide biosynthetic process and proteolysis, were downregulated in CPX treated cells compared to control, as well as in RA treated cells, which may explain the cell cycle arrest. Moreover, proteins which were involved in cell death, positive regulation of biosynthetic process, response to organic substance, glycolysis, anti-apoptosis, and phosphorylation were downregulated in RA treated cells compared to control and CPX treated cells. CONCLUSION: The CPX treatment of SCs results in downregulation of nucleotide binding proteins and leads to cell cycle stop without impairment of pluripotency
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Bedeutung der Calreticulin in Nierenfunktion und -Erkrankung: chronisch niedrige Calreticulin-Konzentration beeinträchtigt die Ca2+-Homöostase und führt zu mitochondrialer Dysfunktion und chronischer Nierenschädigung
No full textChronische Nierenerkrankung (CKD, chronic
kidney disease) ist weltweit zu einem großen Gesundheitsproblem
geworden. Das kontinuierliche Fortschreiten der CKD scheint das
Ergebnis der Selbsterhaltung der Mechanismen zu sein, die einer
anfänglichen Schädigung zugrunde liegen. Die Niere, als das
Blutfiltrationsorgan, ist stets toxische Metabolismus-Abfälle,
Wasserüberschuss und Ionen ausgesetzt. Mit dem Ziel, die
molekularen Mechanismen zu verstehen, die eine normal
funktionierende Niere zu einer kranken Niere überführen, wurden
proteomische Analyse von Nierenzellen unter verschiedenen
physiologischen Bedingungen wie osmotischer Stress, oxidativer
Stress und Zytokinbehandlung durchgeführt. Interessanteweise haben
die Daten gezeigt, dass Calreticulin, eine Ca2+-bindendes
Endoplasmatische Reticulum (ER)-Protein, eine starke
Expressionsregulierung aufweist. Innerhalb des ERs, spielt die
Calreticulin eine wichtige Rolle als Chaperon, die zur richtigen
Proteinfaltung beiträgt. Des Weitern kommt der Calreticulin als
Ca2+-bindendes ER Protein, eine wesentliche Rolle bei der
Regulierung der cytososlischen Calciumkonzentration zu. Der Ziel
dieser Studie war es, die mögliche Rolle von Calreticulin in der
Nierenerkrankungen zu studieren wie auch die Mechanismen zu
untersuchen, die dieses Protein mit der Regulierung der Funktion
der Nierenzellen und das Fortschreiten der Nierenschädigung
verbinden. Zur Verwirklichung der Ziele wurden sowohl in-vitro als
auch in vivo Studien durchgeführt. Kapitel 2 der Dissertation
beschäftigt sich mit der in-vitro-Untersuchungen: Kombination der
zweidimensionalen Gelelektrophorese (mit Fluoreszenz gefärbten
Proteine) und Massenspektrometrie, zeigt eine starke
Runterregulierung der Calreticulin-Expression in Nierenzellen unter
osmotischen Stress. Die Expressionsänderung der Calreticulin
korrelierte mit einer kontinuierlichen Steigerung der Konzentration
des freien intrazellulären Ca2+. Andererseits, die Hemmung der
Ca2+-Freisetzung, durch IP3R Antagonisten, verhinderte die
Expressionsänderung der Calreticulin unter Stressbedingungen. Dies
resultierte in einer erheblichen Beeinträchtigung des
Zellüberlebens.Chronic kidney disease (CKD) is becoming a
major public health problem worldwide. The persistent progression
of CKD is postulated to result from a self-perpetuating vicious
cycle of events activated after initial injury. Being a major
excretory and homeostatic organ of the body, kidney is continuously
exposed to toxic wastes, excess of water and ions. In an attempt to
understand the molecular mechanisms, which lead a normal
functioning kidney towards disease state, proteomic screening of
renal cells under various physiological conditions such as osmotic
stress, oxidative stress and cytokines were performed. The data
highlighted the expression regulation of an endoplasmic reticulum
resident Ca2+ binding protein, calreticulin. Within endoplasmic
reticulum (ER), calreticulin plays important function as a chaperon
directing proper conformation of proteins, as well as a major ER
Ca2+ binding protein, which controls cytosolic and ER Ca2+ levels.
The purpose of this study was to investigate the potential role of
calreticulin and mechanisms connecting this protein in regulating
the renal cells function and progression of renal injury. In vitro
investigations described in Chapter 2 using two-dimensional
fluorescence difference gel electrophoresis combined with mass
spectrometry analysis revealed an expression alteration of
calreticulin in renal cells under osmotic stress conditions. It was
also found that downregulation of calreticulin is combined with
continuous change in the level of free intracellular Ca2+. On the
other hand, inhibition of the Ca2+ release, through IP3R
antagonist, prevented calreticulin expression alteration under
hyperosmotic stress, whereas the cell viability was significantly
impaired. An increase in ER Ca2+ storage with decreased cell
viability was observed in cells overexpressing wild type
calreticulin compared to no significant change in Ca2+ level and
viability in cells overexpressing mutant calreticulin, lacking the
Ca2+ binding domain. Furthermore, free Ca2+ level and cell survival
were significantly improved under osmotic stress conditions by
silencing calreticulin with siRNA. Taken together, our data clearly
highlight the crucial role of calreticulin in renal cells
functioning and survival through modulating Ca2+ homeostasis under
osmotic stress conditions. The work presented in Chapter 3 was
performed with adult heterozygote Calr+/- mice having chronic low
level of calreticulin to further investigate the in vivo impact of
downregulation of calreticulin on kidney structure and function. A
progression of renal injury evidenced by development of
glomerulosclerosis and tubulointerstitial damage was observed in
histological analysis of Calr+/- mice kidneys from different age
groups. The significant overexpression of cytosolic Ca2+ binding
proteins with an insignificant alteration of ER stress proteins,
suggested the role of intracellular Ca2+ homeostasis disturbance in
renal impairments in Calr+/- mice. It was also found that
endoplasmic reticulum stress protein markers are not significantly
induced. Proteomic analysis further highlighted the role of
oxidative stress and mitochondrial dysfunction in renal injury in
Calr+/- mice kidneys. Especially, the reactive oxidative species
scavenging enzyme, Sod1 expression was not only significantly
downregulated but also showed irregular aggregates with
immunohistochemical staining. Ultrastructural analysis further
indicated significantly impaired mitochondrial morphology
characterized by enlarged, swollen mitochondria with disturbed
membranous structures in Calr+/- mice. These morphological changes
were accompanied by biochemical abnormalities with specific
decreases in the activity of cytochrome c oxidase of the
mitochondrial electron transfer chain. Consequently, the oxidative
stress together with mitochondrial damage and energy imbalance
resulted in kidney injury in Calr+/- mice. In conclusion, the work
presented in this thesis, revealed for the first time, the role of
calreticulin in renal cells function and in the progression of
chronic kidney injury. The study also points out that low level of
calreticulin mediated Ca2+ homeostasis disturbances impacts the
mitochondrial morphology, function and expression of Sod1. It will
be interesting to investigate the exact mechanism by which
calreticulin modulates Sod1 downregulation, at the molecular level.
This should provide more concentrated foci for future
experimentation. However, our findings highlighted a new potential
mechanism of the progression of CKD and encourage new directions in
CKD research, which in turn should have impact on treatment
approach, diagnosis and prevention of CKD
Secretion of ERP57 is important for extracellular matrix accumulation and progression of renal fibrosis, and is an early sign of disease onset
Full text linkRenal fibrosis is characterized by excessive accumulation of extracellular matrix (ECM), which compromises organ function by replacing normal organ tissue. The molecular mechanisms leading to renal fibrosis are not fully understood. Here we demonstrated that TGF beta 1, AGT or PDGF stimulation of renal cells resulted in endoplasmic reticulum (ER) stress followed by activation of the protective unfolded protein response pathway and a high secretory level of protein disulfide isomerase ERP57 (also known as PDIA3). The TGF beta 1-induced impairment of ER function could be reversed by treatment with BMP7, suggesting a specific involvement in renal fibrosis. A clear correlation between the degree of fibrosis, ER stress and the level of ERP57 could be seen in fibrosis animal models and in biopsies of renal fibrosis patients. Protein interaction studies revealed that secreted ERP57 exhibits a strong interaction with ECM proteins. Knockdown of ERP57 or antibody-targeted inhibition of the secreted form significantly impaired the secretion and accumulation of ECM. Moreover, ERP57 was excreted in the early stages of chronic kidney disease, and its level in urine correlated with the degree of renal fibrosis, suggesting that the secretion of ERP57 represents one of the first signs of renal fibrosis onset and progression
Correction: Secretion of ERP57 is important for extracellular matrix accumulation and progression of renal fibrosis, and is an early sign of disease onset (doi:10.1242/jcs.125088)
No full textVariations on the Author
Full text link“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
Full text linkWe 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
- …
