Exploiting performance characterization of BLAST in the grid

Sequence analysis has become essential to the study of genomes and biological research in general. Basic Local Alignment Search Tool (BLAST) leads the way as the most accepted method for performing necessary query searches and analysis of discovered genes. Combating growing data sizes, with the goal of speeding up job runtimes, scientist are resorting to grid computing technologies. However, grid environments are characterized by dynamic, heterogeneous, and transient state of available resources causing major hindrance to users when trying to realize user-desired levels of service. This paper analyzes performance characteristics of NCBI BLAST on several resources and captures influence of resource characteristics and job parameters on BLAST job runtime across those resources. Obtained results are summarized as a set of principles characterizing performance of NCBI BLAST across homogeneous and heterogeneous environments. These principles are then applied and verified through creation of a grid-enabled BLAST wrapper application called Dynamic BLAST. Results show runtime savings up to 50% and resource utilization improvement of approximately 40%.     

Rapid Identification of the Foodborne Pathogen Trichinella spp. by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Human trichinellosis occurs through consumption of raw or inadequately processed meat or meat products containing larvae of the parasitic nematodes of the genus Trichinella. Currently, nine species and three genotypes are recognized, of which T. spiralis, T. britovi and T. pseudospiralis have the highest public health relevance. To date, the differentiation of the larvae to the species and genotype level is based primarily on molecular methods, which can be relatively time consuming and labor intensive. Due to its rapidness and ease of use a matrix assisted laser desorption / ionization time of flight mass spectrometry (MALDI-TOF MS) reference spectra database using Trichinella strains of all known species and genotypes was created. A formicacid/acetonitrile protein extraction was carried out after pooling 10 larvae of each Trichinella species and genotype. Each sample was spotted 9 times using α-cyano 4-hydoxy cinnamic acid matrix and a MicroFlex LT mass spectrometer was used to acquire 3 spectra (m/z 2000 to 20000 Da) from each spot resulting in 27 spectra/species or genotype. Following the spectra quality assessment, Biotyper software was used to create a main spectra library (MSP) representing nine species and three genotypes of Trichinella. The evaluation of the spectra generated by MALDI-TOF MS revealed a classification which was comparable to the results obtained by molecular methods. Also, each Trichinella species utilized in this study was distinct and distinguishable with a high confidence level. Further, different conservation methods such as freezing and conservation in alcohol and the host species origin of the isolated larvae did not have a significant influence on the generated spectra. Therefore, the described MALDI-TOF MS can successfully be implemented for both genus and species level identification and represents a major step forward in the use of this technique in foodborne parasitology.     

A 16-Gene Signature Distinguishes Anaplastic Astrocytoma from Glioblastoma

Anaplastic astrocytoma (AA; Grade III) and glioblastoma (GBM; Grade IV) are diffusely infiltrating tumors and are called malignant astrocytomas. The treatment regimen and prognosis are distinctly different between anaplastic astrocytoma and glioblastoma patients. Although histopathology based current grading system is well accepted and largely reproducible, intratumoral histologic variations often lead to difficulties in classification of malignant astrocytoma samples. In order to obtain a more robust molecular classifier, we analysed RT-qPCR expression data of 175 differentially regulated genes across astrocytoma using Prediction Analysis of Microarrays (PAM) and found the most discriminatory 16-gene expression signature for the classification of anaplastic astrocytoma and glioblastoma. The 16-gene signature obtained in the training set was validated in the test set with diagnostic accuracy of 89%. Additionally, validation of the 16-gene signature in multiple independent cohorts revealed that the signature predicted anaplastic astrocytoma and glioblastoma samples with accuracy rates of 99%, 88%, and 92% in TCGA, {"type":"entrez-geo","attrs":{"text":"GSE1993","term_id":"1993"}}GSE1993 and {"type":"entrez-geo","attrs":{"text":"GSE4422","term_id":"4422"}}GSE4422 datasets, respectively. The protein-protein interaction network and pathway analysis suggested that the 16-genes of the signature identified epithelial-mesenchymal transition (EMT) pathway as the most differentially regulated pathway in glioblastoma compared to anaplastic astrocytoma. In addition to identifying 16 gene classification signature, we also demonstrated that genes involved in epithelial-mesenchymal transition may play an important role in distinguishing glioblastoma from anaplastic astrocytoma.     

Adrenergic stimulation of inositol-phosphate production in a genital tract smooth muscle cell line

Catecholamines are important in the modulation of smooth muscle contractile activity; this study was undertaken to evaluate adrenoceptor stimulation of intracellular inositol-phosphate production in a genital tract smooth muscle myocyte. DDT1 MF-2 smooth muscle myocytes, derived from a hamster ductus deferens leiomyosarcoma, were loaded with 3H-inositol, incubated in 10 mM LiCl, then stimulated with adrenergic agonists with and without antagonists. Subsequently, the inositol phosphates were isolated by anion-exchange chromatography. In the presence of norepinephrine (NE), inositol trisphosphate (IP3) was produced by 30 s and peaked at 2 min; inositol 1-phosphate was also apparent by 30 s, and continued to increase over 15 min. Clonidine (an alpha-2 agonist), isoproterenol, and NE in the presence of phentolamine or prazosin (an alpha-1 antagonist) failed to increase IP3. In contrast, NE in the presence of yohimbine (an alpha-2 antagonist) or propranolol stimulated IP3 production to levels comparable to that stimulated by NE alone. These studies provide evidence that inositol phosphate production is involved in alpha-1 adrenergic signal transduction in DDT1 MF-2 myocyte.     

Response of the seminal vesicles of the hypophysectomized catfish Heteropneustes fossilis (Bloch) to exogenous androgens,estrogen and corticosteroid†

The response of the regressed seminal vesicles of 136- and 102-day hypophysectomized catfish to 30-day treatment with various steroids has been studied. Hypophysectomy results in complete regression of the seminal vesicles within 40 days. Of the various andro gens tested, ethynyltestosterone and 17 α-methyltestosterone are equipotent in producing weight increment and initiation of secretory activity in the regressed seminal vesicles but are 2.5 times more potent than testosterone propionate. Olive oil, eslradiol benzoate and desoxycorticosterone acetate treatment induce neither secretory activity nor weight increments in the regressed seminal vesicles. The adrenal androgens, 4-androstenedione and dehydroepiandrosterone proved to be weak androgens. The data indicate that only androgens can restore secretory activity in the regressed seminal vesicles of the hypophy sectomized catfish.