Drug and Alcohol Rehabilitation: SIGLOCPRED: An Algorithm to Predict Bacterial Signal Peptides and OMPS.

SIGLOCPRED: an algorithm to predict bacterial signal peptides and OMPS.

Filed under: Drug and Alcohol Rehabilitation

Bioinformation. 2012; 8(20): 970-3
Dhanaraj P, James JV, Michael PG, Muthiah I

There is a growing interest in Biological investigation to determine the location of proteins, to identify new potentially accessible drug targets. Signal peptide directs the transport of the protein to its location. Bacterial OMPs are essential for their survival in the host organism. SIGLOCPRED a signal peptide predictor for the bacterial proteins as well as OMP prediction has been developed. The signal peptide prediction is done based on the influence of the flanking residues on the signal peptide cleavage. A dataset of proteins with confirmed outer membrane location has being created, and the probable OMP polypeptide sequence is predicted. Since the algorithm uses confirmed datasets the prediction is more reliable and efficient. SIGLOCPRED is as efficient as many of the existing signal peptide predictors and can also predict OMPs in addition.
HubMed – drug

Pharmacy students’ attitudes toward reporting serious adverse drug events.

Filed under: Drug and Alcohol Rehabilitation

Am J Pharm Educ. 2012 Dec 12; 76(10): 194
Gavaza P, Bui B

Objectives. To determine pharmacy students’ attitude toward and knowledge of reporting serious adverse drug events (ADEs) to the Food and Drug Administration (FDA).Method. A 58-item survey questionnaire constructed to measure respondents’ intention to report ADEs (3 items), attitude toward reporting ADEs (20 items), knowledge of ADE reporting (9 items), and demographic data was administered to all third-year (final-year) pharmacy students at the Appalachian College of Pharmacy.Results. The majority of the 58 students who responded (91% response rate) intended (84%) and planned (85.3%) to report serious ADEs when they encounter them. Most respondents had favorable attitudes toward reporting serious ADEs to the FDA; respondents believed that reporting serious ADEs was valuable (5.6 ± 1.5, mean ± SD), good (3.0 ± 1.7), and beneficial (5.7 ± 1.5). Many students also believed that ADE reporting resulted in increased risk of malpractice, compromised relationships with physicians, broken trust with patients, disruption of the normal workflow, and was time consuming. Many students had inadequate knowledge on reporting ADEs.Conclusion. Although pharmacy students had strong intentions and favorable attitudes toward ADE reporting, they had inadequate knowledge of how to report serious ADEs.
HubMed – drug

Safety and Effectiveness of Gemcitabine in 855 Patients with Pancreatic Cancer under Japanese Clinical Practice Based on Post-marketing Surveillance in Japan.

Filed under: Drug and Alcohol Rehabilitation

Jpn J Clin Oncol. 2012 Dec 28;
Ioka T, Katayama K, Tanaka S, Takakura R, Ashida R, Kobayashi N, Taniai H

OBJECTIVE: When gemcitabine was approved as an anti-cancer drug, there were limited data for Japanese patients treated with gemcitabine. Generally, advanced or metastatic pancreatic cancer patients experience poor prognosis and suffer from debilitating disease-related symptoms. Reports and information on gemcitabine use within a large patient pool will be beneficial to aid physicians. Therefore, this post-marketing surveillance was conducted as a non-interventional, observational study on the use of gemcitabine in a clinical practice setting in Japan. METHODS: Patients had no previous treatment with gemcitabine and were diagnosed with pancreatic cancer by an attending physician. Patients were registered between May 2001 and December 2003 in Japan. The patients were treated with gemcitabine. Data such as patient background, treatment details, adverse events, tumor response, serum CA19-9 levels and drug-related symptom improvement were assessed. RESULTS: Of the 890 patients registered for the study, 855 were included in the analysis of gemcitabine for safety. Four hundred and forty-three (51.9%) patients reported drug-related adverse events, with 97 patients (11.4%) experiencing serious adverse events. The incidence of interstitial lung disease was 0.7% (six patients). Six hundred patients were evaluated for tumor response. The overall response rate was 6.0% and the disease control rate was 54.0%. CA19-9 decreased in 63.6% of the 335 evaluable patients, with a ?75% decrease seen in 19.4% of the total group. Drug-related symptom improvement was observed in 27.0% of the 686 evaluable patients. CONCLUSIONS: This large-scale surveillance could confirm the safety of gemcitabine for Japanese pancreatic cancer patients as well as elucidate the efficacy profile, measured by drug-related symptom improvement, for Japanese pancreatic cancer patients.
HubMed – drug

RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus.

Filed under: Drug and Alcohol Rehabilitation

Nucleic Acids Res. 2012 Dec 28;
Ishimaru D, Plant EP, Sims AC, Yount BL, Roth BM, Eldho NV, Pérez-Alvarado GC, Armbruster DW, Baric RS, Dinman JD, Taylor DR, Hennig M

Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem-loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop-loop interactions. We also show that loop-loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop-loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis.
HubMed – drug

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