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

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

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

Mesenchymal Stem Cells in a Transgenic Mouse Model of Multiple System Atrophy: Immunomodulation and Neuroprotection

Mesenchymal stem cells (MSC) are currently strong candidates for cell-based therapies. They are well known for their differentiation potential and immunoregulatory properties and have been proven to be potentially effective in the treatment of a large variety of diseases, including neurodegenerative disorders. Currently there is no treatment that provides consistent long-term benefits for patients with multiple system atrophy (MSA), a fatal late onset α-synucleinopathy. Principally neuroprotective or regenerative strategies, including cell-based therapies, represent a powerful approach for treating MSA. In this study we investigated the efficacy of intravenously applied MSCs in terms of behavioural improvement, neuroprotection and modulation of neuroinflammation in the (PLP)-αsynuclein (αSYN) MSA model.MSCs were intravenously applied in aged (PLP)-αSYN transgenic mice. Behavioural analyses, defining fine motor coordination and balance capabilities as well as stride length analysis, were performed to measure behavioural outcome. Neuroprotection was assessed by quantifying TH neurons in the substantia nigra pars compacta (SNc). MSC treatment on neuroinflammation was analysed by cytokine measurements (IL-1α, IL-2, IL-4, IL-5, IL-6, IL-10, IL-17, GM-CSF, INFγ, MCP-1, TGF-β1, TNF-α) in brain lysates together with immunohistochemistry for T-cells and microglia. Four weeks post MSC treatment we observed neuroprotection in the SNc, as well as downregulation of cytokines involved in neuroinflammation. However, there was no behavioural improvement after MSC application.To our knowledge this is the first experimental approach of MSC treatment in a transgenic MSA mouse model. Our data suggest that intravenously infused MSCs have a potent effect on immunomodulation and neuroprotection. Our data warrant further studies to elucidate the efficacy of systemically administered MSCs in transgenic MSA models

Aging Stem Cells and Regenerative Biomedicine: Concepts, Opportunities and Technological Advances

Special Issue: “Stem Cell Aging and Regenerative Medicine

Open-ended question: is immortality exclusively inherent to the germ line?

All somatic cells are subject to aging. Germ line links generations, and thus, pluripotent germ cells are considered potentially immortal. The current understanding how the germ line escapes this otherwise inevitable phenomenon is outlined in this article

Controversial Issue: Is it safe to employ mesenchymal stem cells in cell-based therapies?

The prospective clinical use of multipotent mesenchymal stromal stem cells (MSC) holds enormous promise for the treatment of a large number of degenerative and age-related diseases. However, the challenges and risks for cell-based therapies are multifaceted. The risks for patients receiving stem cells, which have been expanded in vitro in the presence of xenogenic compounds, can hardly be anticipated and methods for the culture and manipulation of “safe” MSC ex vivo are being investigated. During in vitro expansion, stem cells experience a long replicative history and are thus subject to damage from intracellular and extracellular influences. While murine MSC are prone to cellular transformation in culture, human MSC do not transform. One reason for this striking difference is that during long-term culture, human MSC finally become replicatively senescent. In consequence, this greatly restricts their proliferation and differentiation efficiency. It however also limits the yield of sufficient numbers of cells needed for therapy. Another issue is to eliminate contamination of expanding cells with serumbound pathogenic agents in order to reduce the risks for infection. A recent technical advancement, which applies human serum platelet lysates as an alternative source for growth factors and essential supplements, allows the unimpaired proliferation of MSC in the absence of animal sera. Here, we present an update regarding cellular senescence of MSC and recent insights concerning potential risks associated with their clinical use

A Poly-(ethylene glycol)-diacrylate 3D-Printed Micro-Bioreactor for Direct Cell Biological Implant-Testing on the Developing Chicken Chorioallantois Membrane

Advancements in biomaterial manufacturing technologies calls for improved standards of fabrication and testing. Currently 3D-printable resins are being formulated which exhibit the potential to rapidly prototype biocompatible devices. For validation purposes, 3D-printed materials were subjected to a hierarchical validation onto the chorioallantoic membrane of the developing chicken, better known as the HET CAM assay. Working along these lines, prints made from poly-(ethylene glycol)-diacrylate (PEGDA), which had undergone appropriate post-print processing, outperformed other commercial resins. This material passed all tests without displaying adverse effects, as experienced with other resin types. Based on this finding, the micro bioreactors (MBR) design, first made of PDMS and that also passed with cell tests on the HET-CAM, was finally printed in PEGDA, and applied in vivo. Following this workflow shows the applicability of 3D-printable resins for biomedical device manufacturing, consents to adherence to the present standards of the 3R criteria in material research and development, and provides flexibility and fast iteration of design and test cycles for MBR adaptation and optimization