Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences

Minimotif Miner (MnM available at http://minimotifminer.org or http://mnm.engr.uconn.edu) is an online database for identifying new minimotifs in protein queries. Minimotifs are short contiguous peptide sequences that have a known function in at least one protein. Here we report the third release of the MnM database which has now grown 60-fold to approximately 300 000 minimotifs. Since short minimotifs are by their nature not very complex we also summarize a new set of false-positive filters and linear regression scoring that vastly enhance minimotif prediction accuracy on a test data set. This online database can be used to predict new functions in proteins and causes of disease

Reviews of

Antibiotic Switch therapy is defined by the switch of intravenous antibiotic therapy to oral form. This research aimed to learn about the relationship of switch therapy toward the value of wound healing, lenght of stay and the antibiotic expenditure. The data of this cross sectional study was collected from medical record and by direct investigation to patients for their macroscopis the wound healings value. T-test was used to compared the relationship of the patient wound healings value, lenght of stay and the antibiotic expenditure between the those with and accurate switch therapy and those without it. The result showed that there was no different of wound healing value between those groups of patients (P>0,1). On the other hand, lenght of stay and antibiotic expenditure of the patient with the accurate switch therapy was cuted on the patient with the accurate switch therapy. These indicated that accuracy of switch therapy will proceed a benefit outcome to the patient with appendicitis, especially to there lenght of stay and antibiotic expenditure as well

Evaluation of the New Architect Cytomegalovirus Immunoglobulin M (IgM), IgG, and IgG Avidity Assays▿

A panel of new cytomegalovirus (CMV) assays for use on the Architect instrument has been developed, including a CMV avidity assay based on a new technology. The purpose of this study was to compare the performance characteristics of the fully automated CMV immunoglobulin M (IgM), IgG, and IgG avidity tests on the Architect instrument with those of other available assays. A total of 503 consecutive fresh patient serum specimens (routine serum specimens) and 96 serum specimens from 33 pregnant women with a recent CMV primary infection (seroconversion serum specimens) were tested for CMV IgM and IgG by the Architect (Abbott), Vidas (BioMérieux), and Enzygnost (Siemens) assays. The seroconversion sera and 100 preselected serum specimens IgM negative and IgG positive by the AxSYM assay were also tested by the IgG avidity tests on the Architect and Vidas instruments. The relative agreements for CMV IgM determination with routine sera between the Architect assay and the Vidas, Enzygnost, and AxSYM assays were 97%, 94%, and 93%, respectively, for the CMV IgM tests and 99%, 98%, and 98%, respectively, for the CMV IgG tests. The specificities of the CMV IgG avidity test were 98% for the Architect assay and 76% for the Vidas assay. No high CMV IgG avidity test results were found within the first 3 months after seroconversion by either of those assays. The correlation between the results of the newly developed CMV IgM and IgG tests on the Architect instrument with the Vidas and Enzygnost assays was excellent (≥94%). The CMV IgG avidity test reliably excluded patients with recent infections and showed an excellent specificity (98%)

Hospital outbreak of gastroenteritis due to norovirus in Belgium

We report an outbreak of gastroenteritis due to Norovirus in a care unit in a Belgian hospital involving thirty-three people. The origin of the outbreak was traced to one nursing assistant. The virus strain identified by reverse transcription polymerase chain reaction and electron microscopy belonged to the genogroup II

HIV-1 Nef protein: purification, crystallizations, and preliminary X-ray diffraction studies.

Human immunodeficiency virus Nef protein accelerates virulent progression of AIDS by its interaction with specific cellular proteins involved in cellular activation and signal transduction. Here we report the purification and crystallization of the conserved core of HIV-1LAI Nef protein in the unliganded form and in complex with the wild-type SH3 domain of the P59fyn protein-tyrosine kinase. One-dimensional NMR experiments show that full-length protein and truncated fragment corresponding to the product of HIV-1 protease cleavage have a well-folded compact tertiary structure. The ligand-free HIV-1 Nefcore protein forms cubic crystals belonging to space group P23 with unit cell dimensions of a = b = c = 86.4 A. The Nef-Fyn SH3 cocrystals belong to the space group P6(1)22 or its enantiomorph, P6(5)22, with unit cell dimensions of a = b = 108.2 A and c = 223.7 A. Both crystal forms diffract to a resolution limit of 3.0 A resolution using synchrotron radiation, and are thus suitable for X-ray structure determination