Biomedical subjects

Reinhard Schneider

Publications and source records attributed to Reinhard Schneider.

5 recordsLinked to original sources

PubMed2006

Status of text-mining techniques applied to biomedical text.

Scientific progress is increasingly based on knowledge and information. Knowledge is now recognized as the driver of productivity and economic growth, leading to a new focus on the role of information in the decision-making process. Most scientific knowledge is registered in publications and other unstructured representations that make it difficult to use and to integrate the information with other sources (e.g. biological databases). Making a computer understand human language has proven to be a complex achievement, but there are techniques capable of detecting, distinguishing and extracting a limited number of different classes of facts. In the biomedical field, extracting information has specific problems: complex and ever-changing nomenclature (especially genes and proteins) and the limited representation of domain knowledge.

Abstracting and Indexing↗

PubMed2005

Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery.

Every entirely sequenced genome reveals 100 s to 1000 s of protein sequences for which the only annotation available is 'hypothetical protein'. Thus, in the human genome and in the genomes of pathogenic agents there could be 1000 s of potential, unexplored drug targets. Computational prediction of protein function can play a role in studying these targets. We shall review the challenges, research approaches and recently developed tools in the field of computational function-prediction and we will discuss the ways these issues can change the process of drug discovery.

Computational Biology↗

PubMed2005

L-Arginine does not affect renal morphology and cell survival in ischemic acute renal failure in rats.

BACKGROUND: L-Arginine (L-Arg), a substrate of nitric oxide synthases, improves renal function in ischemic acute renal failure (iARF). We evaluated whether L-Arg improves renal morphology and cell survival in the course of iARF. METHODS AND RESULTS: iARF was induced in rats by bilateral clamping of renal arteries for 45 min. L-Arg was applied intraperitoneally during clamping, and orally during 14 days of follow-up. Morphology and cell survival of renal cortical and medullar tissue was analyzed on days 1, 3, 7, and 14 of follow-up, using toluidine blue staining and immunohistochemistry of perfusion-fixated tissue, and Western blot analysis of tissue homogenate. Renal tubular injury showed typical features of necrosis and was most severe on days 1 and 3 after clamping, predominantly in S3 segments, with almost complete recovery by day 14. Enhanced medullar monocyte infiltration, determined by ED-1 expression as well as by immunohistochemistry, and enhanced expression of proliferating cell nuclear antigen (PCNA), indicative of proliferation and regeneration, accompanied these morphological changes. Compared to controls, L-Arg had no impact on renal morphology, ED-1, and PCNA expression. Furthermore, expression of markers of apoptosis Bcl-2, Bax, and cleaved caspase-3 was only slightly increased in iARF rats, compared to sham-operated animals, and was also not influenced by L-Arg. CONCLUSION: Despite its repeatedly reported positive impact on renal function as also shown in our model, L-Arg does not alter cell death and proliferation in the course of iARF in our model. Thus, different mechanisms have to be considered, in particular improved intrarenal hemodynamics.

Acute Kidney Injury↗

PubMed2003

L-Arginine counteracts nitric oxide deficiency and improves the recovery phase of ischemic acute renal failure in rats.

BACKGROUND: In ischemic acute renal failure (ARF), nitric oxide-dependent regulation of renal hemodynamics and glomerular function is disturbed. Previous studies indicate that the nitric oxide precursor l-arginine (l-Arg) has beneficial effects on renal function. Here we further analyzed the impact of l-Arg on functional and biochemical parameters of nitric oxide signaling during the course of ischemic ARF. METHODS: Ischemic ARF was induced in rats by bilateral clamping of renal arteries for 45 minutes. l-Arg was applied intraperitoneally during clamping, and orally during 14 days of follow-up. Glomerular filtration rate (GFR) and renal plasma flow (RPF) were measured, and biochemical parameters analyzed by protein immunoblots. RESULTS: Clamping resulted in 70% to 90% reduction of GFR and RPF, with a gradual recovery by day 14. Using an in situ assay with the oxidative fluorescent dye hydroethidine, increased tubular generation of O2- was detected in the early course of ischemic ARF, indicating enhanced oxidative stress. These findings were accompanied by up-regulation of the nitric oxide receptor, soluble guanylate cyclase, and by significant regulatory changes of inducible nitric oxide synthase (iNOS) and endothelial NOS expression. l-Arg had a beneficial effect on GFR and RPF, decreased O2- production, diminished up-regulation of soluble guanylate cyclase, and prevented up-regulation of iNOS. CONCLUSION: Ischemic ARF is accompanied by marked alterations in the expression of key enzymes of the nitric oxide pathway, indicative for deficiency of constitutive NOS activity. l-Arg supplementation reduces O2- generation and significantly improves the expression of nitric oxide signaling proteins as well as the recovery phase of ischemic ARF.

Acute Kidney Injury↗

PubMedDate not supplied

A bioinformatics perspective on proteomics: data storage, analysis, and integration.

The field of proteomics is advancing rapidly as a result of powerful new technologies and proteomics experiments yield a vast and increasing amount of information. Data regarding protein occurrence, abundance, identity, sequence, structure, properties, and interactions need to be stored. Currently, a common standard has not yet been established and open access to results is needed for further development of robust analysis algorithms. Databases for proteomics will evolve from pure storage into knowledge resources, providing a repository for information (meta-data) which is mainly not stored in simple flat files. This review will shed light on recent steps towards the generation of a common standard in proteomics data storage and integration, but is not meant to be a comprehensive overview of all available databases and tools in the proteomics community.

Computational Biology↗