235 research outputs found
Automated Quantitative Assessment of Proteins' Biological Function in Protein Knowledge Bases
Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings
How to track cellular aging of mesenchymal stromal cells?
Mesenchymal stromal cells (MSC) are currently tested in a large number of
clinical trials and raise high hope in regenerative medicine. These cells
have to be expanded in vitro before transplantation and several studies
demonstrated that long-term culture evokes continuous changes in MSC:
proliferation rate decays, the cell size increases, differentiation
potential is affected, chromosomal instabilities may arise and molecular
changes are acquired. Long-term culture of cell preparations might also
have therapeutic consequences, although this has hardly been addressed in
ongoing trials so far. Reliable therapeutic regimens necessitate quality
control of cellular products. This research perspective summarizes
available methods to track cellular aging of MSC. We have demonstrated that
gene expression changes and epigenetic modifications are
continuously acquired during replicative senescence. Molecular analysis of
a suitable panel of genes might provide a robust tool to assess efficiency
and safety of long-term expansion
Hematopoietic bone marrow cells participate in endothelial, but not epithelial or mesenchymal cell renewal in adult rats
The extent to which bone marrow (BM) contributes to physiological cell renewal is still controversial. Using the marker human placental alkaline phosphatase (ALPP) which can readily be detected in paraffin and plastic sections by histochemistry or immunohistochemistry, and in ultrathin sections by electron microscopy after pre-embedding staining, we examined the role of endogenous BM in physiological cell renewal by analysing tissues from lethally irradiated wild-type inbred Fischer 344 (F344) rats transplanted (BMT) with unfractionated BM from ALPP-transgenic F344 rats ubiquitously expressing the marker. Histochemical, immunohistochemical and immunoelectron microscopic analysis showed that the proportion of ALPP+ capillary endothelial cells (EC) profoundly increased from 1 until 6 months after BMT in all organs except brain and adrenal medulla. In contrast, pericytes and EC in large blood vessels were ALPP–. Epithelial cells in kidney, liver, pancreas, intestine and brain were recipient-derived at all time-points. Similarly, osteoblasts, chondrocytes, striated muscle and smooth muscle cells were exclusively of recipient origin. The lack of mesenchymal BM-derived cells in peripheral tissues prompted us to examine whether BMT resulted in engraftment of mesenchymal precursors. Four weeks after BMT, all haematopoietic BM cells were of donor origin by flow cytometric analysis, whereas isolation of BM mesenchymal stem cells (MSC) failed to show engraftment of donor MSC. In conclusion, our data show that BM is an important source of physiological renewal of EC in adult rats, but raise doubt whether reconstituted irradiated rats are an apt model for BM-derived regeneration of mesenchymal cells in peripheral tissues
Histochemical structure and immunolocalisation of the hyaluronan system in the dromedary oviduct
miR-17, miR-19b, miR-20a, and miR-106a are down-regulated in human aging
Aging is a multifactorial process where deterioration of body functions is driven by stochastic damage while counteracted by distinct genetically encoded repair systems. To better understand the genetic component of aging, many studies have addressed the gene and protein expression profiles of various aging model systems engaging different organisms from yeast to human. The recently identified small non-coding miRNAs are potent post-transcriptional regulators that can modify the expression of up to several hundred target genes per single miRNA, similar to transcription factors. Increasing evidence shows that miRNAs contribute to the regulation of most if not all important physiological processes, including aging. However, so far the contribution of miRNAs to age-related and senescence-related changes in gene expression remains elusive. To address this question, we have selected four replicative cell aging models including endothelial cells, replicated CD8+ T cells, renal proximal tubular epithelial cells, and skin fibroblasts. Further included were three organismal aging models including foreskin, mesenchymal stem cells, and CD8+ T cell populations from old and young donors. Using locked nucleic acid-based miRNA microarrays, we identified four commonly regulated miRNAs, miR-17 down-regulated in all seven; miR-19b and miR-20a, down-regulated in six models; and miR-106a down-regulated in five models. Decrease in these miRNAs correlated with increased transcript levels of some established target genes, especially the cdk inhibitor p21/CDKN1A. These results establish miRNAs as novel markers of cell aging in humans
GiSAO.db: a database for ageing research
<p>Abstract</p> <p>Background</p> <p>Age-related gene expression patterns of <it>Homo sapiens </it>as well as of model organisms such as <it>Mus musculus</it>, <it>Saccharomyces cerevisiae</it>, <it>Caenorhabditis elegans </it>and <it>Drosophila melanogaster </it>are a basis for understanding the genetic mechanisms of ageing. For an effective analysis and interpretation of expression profiles it is necessary to store and manage huge amounts of data in an organized way, so that these data can be accessed and processed easily.</p> <p>Description</p> <p>GiSAO.db (Genes involved in senescence, apoptosis and oxidative stress database) is a web-based database system for storing and retrieving ageing-related experimental data. Expression data of genes and miRNAs, annotation data like gene identifiers and GO terms, orthologs data and data of follow-up experiments are stored in the database. A user-friendly web application provides access to the stored data. KEGG pathways were incorporated and links to external databases augment the information in GiSAO.db. Search functions facilitate retrieval of data which can also be exported for further processing.</p> <p>Conclusions</p> <p>We have developed a centralized database that is very well suited for the management of data for ageing research. The database can be accessed at <url>https://gisao.genome.tugraz.at</url> and all the stored data can be viewed with a guest account.</p
Simulated interventions to ameliorate age-related bone loss indicate the importance of timing
Bone remodeling is the continuous process of bone resorption by osteoclasts and bone formation by osteoblasts, in order to maintain homeostasis. The activity of osteoclasts and osteoblasts is regulated by a network of signaling pathways, including Wnt, parathyroid hormone (PTH), RANKL/OPG and TGF-β, in response to stimuli such as mechanical loading. During aging there is a gradual loss of bone mass due to dysregulation of signaling pathways. This may be due to a decline in physical activity with age and/or changes in hormones and other signaling molecules. In particular, hormones such as PTH have a circadian rhythm which may be disrupted in aging. Due to the complexity of the molecular and cellular networks involved in bone remodeling, several mathematical models have been proposed to aid understanding of the processes involved. However, to date there are no models which explicitly consider the effects of mechanical loading, the circadian rhythm of PTH and the dynamics of signaling molecules on bone remodeling. Therefore, we have constructed a network model of the system using a modular approach which will allow further modifications as required in future research. The model was used to simulate the effects of mechanical loading and also the effects of different interventions such as continuous or intermittent administration of PTH. Our model predicts that the absence of regular mechanical loading and/or an impaired PTH circadian rhythm leads to a gradual decrease in bone mass over time which can be restored by simulated interventions and that the effectiveness of some interventions may depend on their timing
Identification of evolutionarily conserved genetic regulators of cellular aging
To identify new genetic regulators of cellular aging and senescence, we performed genome-wide comparative RNA profiling with selected human cellular model systems, reflecting replicative senescence, stress-induced premature senescence, and distinct other forms of cellular aging. Gene expression profiles were measured, analyzed, and entered into a newly generated database referred to as the GiSAO database. Bioinformatic analysis revealed a set of new candidate genes, conserved across the majority of the cellular aging models, which were so far not associated with cellular aging, and highlighted several new pathways that potentially play a role in cellular aging. Several candidate genes obtained through this analysis have been confirmed by functional experiments, thereby validating the experimental approach. The effect of genetic deletion on chronological lifespan in yeast was assessed for 93 genes where (i) functional homologues were found in the yeast genome and (ii) the deletion strain was viable. We identified several genes whose deletion led to significant changes of chronological lifespan in yeast, featuring both lifespan shortening and lifespan extension. In conclusion, an unbiased screen across species uncovered several so far unrecognized molecular pathways for cellular aging that are conserved in evolution
Diversity of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in indigenous chickens
In vivo biofunctional evaluation of hydrogels for disc regeneration
Purpose Regenerative strategies aim to restore the original
biofunctionality of the intervertebral disc. Different
biomaterials are available, which might support disc
regeneration. In the present study, the prospects of success
of two hydrogels functionalized with anti-angiogenic peptides
and seeded with bone marrow derived mononuclear
cells (BMC), respectively, were investigated in an ovine
nucleotomy model.
Methods In a one-step procedure iliac crest aspirates
were harvested and, subsequently, separated BMC were
seeded on hydrogels and implanted into the ovine disc. For
the cell-seeded approach a hyaluronic acid-based hydrogel
was used. The anti-angiogenic potential of newly developed
VEGF-blockers was investigated on ionically crosslinked
metacrylated gellan gum hydrogels. Untreated discs
served as nucleotomy controls. 24 adult merino sheep were
used. After 6 weeks histological, after 12 weeks histological
and biomechanical analyses were conducted.
Results Biomechanical tests revealed no differences
between any of the implanted and nucleotomized discs. All
implanted discs significantly degenerated compared to
intact discs. In contrast, there was no marked difference
between implanted and nucleotomized discs. In tendency,
albeit not significant, degeneration score and disc height
index deteriorated for all but not for the cell-seeded
hydrogels from 6 to 12 weeks. Cell-seeded hydrogels
slightly decelerated degeneration.
Conclusions None of the hydrogel configurations was
able to regenerate biofunctionality of the intervertebral
disc. This might presumably be caused by hydrogel
extrusion. Great importance should be given to the development
of annulus sealants, which effectively exploit the
potential of (cell-seeded) hydrogels for biological disc
regeneration and restoration of intervertebral disc
functioningThis work was supported by the EU-project Disc Regeneration (NMP3-LA-2008-213904). Technical assistance of Iris Baum and the whole animal surgery team of the Institute of Orthopaedic Research and Biomechanics, Ulm, are gratefully acknowledged. DDAHA hydrogels were kindly provided by Cristina Longinotti (DDAHA, Anika Therapeutics, Abano Therme, Italy)
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