Wortmannin Blocks Goldfish Retinal Phosphatidylinositol 3-Kinase and Neurite Outgrowth

The goldfish retina has been used extensively for the study of nerve regeneration. A role for phosphatidylinositol 3-kinase (PI3K) in neurite outgrowth from goldfish retinal explants has been examined by means of wortmannin (WT), a selective inhibitor of the enzyme. The presence of PI3K in retinal extracts was determined by means of immunoprecipitation as well as by an in vitro assay system for catalytic activity. The relative amount of the p85 subunit of PI3K detected by western blot in the retina following optic nerve crush was unchanged. WT inhibited goldfish brain PI3K activity at concentrations as low as 10 −9 M, approximating that reported for inhibition of mammalian PI3K's. Daily addition of 10 −8 M WT to retinal explants, activated by prior crush of the optic nerve, significantly inhibited neurite outgrowth during a 7 day in vitro culture period, while a single addition of WT to freshly explanted retina had no effect on neurite outgrowth. These results suggest that a PI3K-mediated process may be critical for nerve regrowth.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45415/1/11064_2004_Article_421925.pd

Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers

<p>Abstract</p> <p>Background</p> <p>Maturation inhibitors such as Bevirimat are a new class of antiretroviral drugs that hamper the cleavage of HIV-1 proteins into their functional active forms. They bind to these preproteins and inhibit their cleavage by the HIV-1 protease, resulting in non-functional virus particles. Nevertheless, there exist mutations in this region leading to resistance against Bevirimat. Highly specific and accurate tools to predict resistance to maturation inhibitors can help to identify patients, who might benefit from the usage of these new drugs.</p> <p>Results</p> <p>We tested several methods to improve Bevirimat resistance prediction in HIV-1. It turned out that combining structural and sequence-based information in classifier ensembles led to accurate and reliable predictions. Moreover, we were able to identify the most crucial regions for Bevirimat resistance computationally, which are in line with experimental results from other studies.</p> <p>Conclusions</p> <p>Our analysis demonstrated the use of machine learning techniques to predict HIV-1 resistance against maturation inhibitors such as Bevirimat. New maturation inhibitors are already under development and might enlarge the arsenal of antiretroviral drugs in the future. Thus, accurate prediction tools are very useful to enable a personalized therapy.</p

Prediction of Co-Receptor Usage of HIV-1 from Genotype

Human Immunodeficiency Virus 1 uses for entry into host cells a receptor (CD4) and one of two co-receptors (CCR5 or CXCR4). Recently, a new class of antiretroviral drugs has entered clinical practice that specifically bind to the co-receptor CCR5, and thus inhibit virus entry. Accurate prediction of the co-receptor used by the virus in the patient is important as it allows for personalized selection of effective drugs and prognosis of disease progression. We have investigated whether it is possible to predict co-receptor usage accurately by analyzing the amino acid sequence of the main determinant of co-receptor usage, i.e., the third variable loop V3 of the gp120 protein. We developed a two-level machine learning approach that in the first level considers two different properties important for protein-protein binding derived from structural models of V3 and V3 sequences. The second level combines the two predictions of the first level. The two-level method predicts usage of CXCR4 co-receptor for new V3 sequences within seconds, with an area under the ROC curve of 0.937±0.004. Moreover, it is relatively robust against insertions and deletions, which frequently occur in V3. The approach could help clinicians to find optimal personalized treatments, and it offers new insights into the molecular basis of co-receptor usage. For instance, it quantifies the importance for co-receptor usage of a pocket that probably is responsible for binding sulfated tyrosine

INTCare: a knowledge discovery based intelligent decision support system for intensive care medicine

This paper introduces the INTCare system, an intelligent information system based on a completely automated Knowledge Discovery process and on the Agents paradigm. The system was designed to work in Hospital Intensive Care Units, supporting the physicians’ decisions by means of prognostic Data Mining models. In particular, these techniques were used to predict organ failure and mortality assessment. The main intention is to change the current reactive behaviour to a pro-active one, enhancing the quality of service. Current applications and experimentations, the functional and structural aspects, and technological options are presented

Machine learning on normalized protein sequences

<p>Abstract</p> <p>Background</p> <p>Machine learning techniques have been widely applied to biological sequences, e.g. to predict drug resistance in HIV-1 from sequences of drug target proteins and protein functional classes. As deletions and insertions are frequent in biological sequences, a major limitation of current methods is the inability to handle varying sequence lengths.</p> <p>Findings</p> <p>We propose to normalize sequences to uniform length. To this end, we tested one linear and four different non-linear interpolation methods for the normalization of sequence lengths of 19 classification datasets. Classification tasks included prediction of HIV-1 drug resistance from drug target sequences and sequence-based prediction of protein function. We applied random forests to the classification of sequences into "positive" and "negative" samples. Statistical tests showed that the linear interpolation outperforms the non-linear interpolation methods in most of the analyzed datasets, while in a few cases non-linear methods had a small but significant advantage. Compared to other published methods, our prediction scheme leads to an improvement in prediction accuracy by up to 14%.</p> <p>Conclusions</p> <p>We found that machine learning on sequences normalized by simple linear interpolation gave better or at least competitive results compared to state-of-the-art procedures, and thus, is a promising alternative to existing methods, especially for protein sequences of variable length.</p