High Performance Computing Based Smart Scan for the Identification of Species Based Unique DNA...
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STEM CELLS, GENE THERAPY, BIOMARKERS AND DIAGNOSTIC TOOLS New Biotechnology · Volume 31S · July 2014 PC-06 High Performance Computing Based Smart Scan for the Identification of Species Based Unique DNA Sequences Kivanc Bilecen 1,∗ , Behnam Rahnama 2 , Ender Altiok 2 1 (1) Okan University, (2) Duzen Laboratories Group 2 Okan University Nucleic acid based tools and techniques such as PCR, RT- PCR, DNA microarrays and lately DNA-hybridization-on-a-chip devices provide reliable detection and identification of microor- ganisms. These platforms rely on the presence of target specific DNA sequences to be known in advance. These sequences, how- ever, can be hard to identify in close species or on the strain level. In this work we have developed a parallel algorithm to accurately specify and classify species and strain specific DNA sequences. The parallel implementation of the intelligent search algo- rithm runs on the parallel GPGPU cores on an HPC server. Each Kepler K20X computational card provides 2688 fine cores acces- sing to 6 GB of DDR5 shared memory. Such massive parallelization allows us to compare variable window size of base pairs in an unmatched performance in comparison with conventional meth- ods. The intelligent scan results bidirectional and circular stream search as well as comparing not only the same instance but also similarity scan up to a defined threshold. Well-established CUBLAS library allows comparison of the determinant of sample matrices in portion of microseconds rather than sequential scanning of each base pare. Our algorithm successfully identified unique markers (70 to 120 bp) to differentiate Bacillus cereus and B. subtilis. Locations of these markers on the chromosome have also been taken into account. Our second set will include Salmonella group as this group is highly important for the food industry. Our results will compare marker selection and validation studies, and also their identification power in PCR and RT-PCR. http://dx.doi.org/10.1016/j.nbt.2014.05.1866 PC-07 Influence of analgesia on circulating tumor cells in patients with colorectal carcinoma Hanuˇ s Slavík 1,∗ , Emil Berta 2 , Josef Srovnal 2 , Andrea Prokopova 2 , Lenka Radova 2 , David Vrana 3 , Marian Hajduch 2 1 Palack´ y University Olomouc 2 Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Czech Republic 3 Department of Oncology, Faculty of Medicine and Dentistry, Palacky Univer- sity, Czech Republic Introduction: Circulating tumor cells (CTC) can create metas- tases, which are responsible for 90% causes of deaths at patients with a cancer. CTC are located in a blood stream or bone marrow and they are most common cause of cancer recurrence after surgi- cal resection of the primary tumor. Presence of CTC has become an important prognostic and predictive factor, which is possible to study by molecular methods such as polymerase chain reaction (PCR). A correlation between recurrence of disease after surgery and analgesics or anesthetics used during or after surgery was also found. Analgesia and anesthesia can affect amount of CTC because of their immunomodulatory effects. Methods and patients: Influence of morphine and pir- itramide was studied in 121 patients with colorectal carcinoma in our research. Detection of CTC was based on real-time PCR in sam- ples from peripheral blood and bone marrow with using epithelial genes as markers (carcinoembryonic antigen - CEA and cytokeratin 20 - CK20). Afterward, the presence of CTC was evaluated depend- ing on the type of analgesia and disease-free and overall survival of patients. The main objective was to optimize analgesic techniques after surgery to decrease risk of cancer recurrence. Results: One month after surgery, morphine-based analge- sia usually induced higher level of CTC. Disease-free survival of patients was also shorter in case of morphine. Conclusion: Piritramide seems to be better analgesic tech- nique than morphine, which negatively influences prognosis of patients with colorectal carcinoma after surgery. Acknowledgement: This study was supported by grants IGA UP LF 2014 019, CZ.1.05/2.1.00/01.0030 and CZ.1.07/2.3.00/30.0004. http://dx.doi.org/10.1016/j.nbt.2014.05.1867 PC-08 Differential Expression of Circulating miRNAs Fol- lowing Resistance Exercise and Carbohydrate/Protein Supplementation Foued S. Espindola 1,∗ , Olga Bocanegra 2 , Renata Teixeira 2 , Maria Siqueira 2 , Matheus Gomes 2 , Miguel Diaz 2 1 Universidade Federal de Uberlândia 2 Institute of Genetics and Biochemistry - Universidade Federal de Uberlândia We investigated the levels of expression of 12 circulating miR- NAs (c-miRNAs) involved in cell proliferation, differentiation, angiogenesis, inflammation and glycemic control in response to resistance exercise (RE) and dietary supplementation. Twelve subjects performed 10 sets of 10 repetitions with 80% of their respective 1RM followed by either carbohydrate or carbo- hydrate/protein supplementation in a randomized single-blind counter-balanced design. Samples of blood were collected before RE, 03 and 24 hours afterwards. The relative expression data of all of the genes were analyzed using a two-way analysis of variance with repeated measures. The molecular response in the group that supplemented with protein was more pronounced for c-miRNAs involved in the regulation of myogenesis, particularly hsa-miR- 133a and 503. Both treatments revealed a differential expression of the c-miRNAs hsa-miR-126 and 16, which are associated with angiogenesis. We argue that hsa-miR-133a might be associated with satellite cell proliferation, and possibly partially responsible for muscle hypertrophy following RE. Further, both the up- and down-regulation of hsa-miR-126 and 16, respectively, are likely to reflect neovascularization. These findings support the hypothesis that circulating miRNAs bear paracrine-like functions and thus, are involved in cell-to-cell crosstalk. S106 www.elsevier.com/locate/nbt
Transcript of High Performance Computing Based Smart Scan for the Identification of Species Based Unique DNA...
STEM CELLS, GENE THERAPY, BIOMARKERS ANDDIAGNOSTIC TOOLS New Biotechnology · Volume 31S · July 2014
PC-06
High Performance Computing Based Smart Scan for theIdentification of Species Based Unique DNA Sequences
Kivanc Bilecen1,∗ , Behnam Rahnama2, Ender Altiok2
1 (1) Okan University, (2) Duzen Laboratories Group2 Okan University
Nucleic acid based tools and techniques such as PCR, RT-PCR, DNA microarrays and lately DNA-hybridization-on-a-chipdevices provide reliable detection and identification of microor-ganisms. These platforms rely on the presence of target specificDNA sequences to be known in advance. These sequences, how-ever, can be hard to identify in close species or on the strain level.In this work we have developed a parallel algorithm to accuratelyspecify and classify species and strain specific DNA sequences.
The parallel implementation of the intelligent search algo-rithm runs on the parallel GPGPU cores on an HPC server. EachKepler K20X computational card provides 2688 fine cores acces-sing to 6 GB of DDR5 shared memory. Such massive parallelizationallows us to compare variable window size of base pairs in anunmatched performance in comparison with conventional meth-ods. The intelligent scan results bidirectional and circular streamsearch as well as comparing not only the same instance but alsosimilarity scan up to a defined threshold. Well-established CUBLASlibrary allows comparison of the determinant of sample matrices inportion of microseconds rather than sequential scanning of eachbase pare.
Our algorithm successfully identified unique markers (70 to120 bp) to differentiate Bacillus cereus and B. subtilis. Locationsof these markers on the chromosome have also been taken intoaccount. Our second set will include Salmonella group as thisgroup is highly important for the food industry. Our results willcompare marker selection and validation studies, and also theiridentification power in PCR and RT-PCR.
http://dx.doi.org/10.1016/j.nbt.2014.05.1866
PC-07
Influence of analgesia on circulating tumor cells inpatients with colorectal carcinoma
Hanus Slavík1,∗ , Emil Berta2, Josef Srovnal2, Andrea Prokopova2,Lenka Radova2, David Vrana3, Marian Hajduch2
1 Palacky University Olomouc2 Institute of Molecular and Translational Medicine, Faculty of Medicine andDentistry, Palacky University, Czech Republic3 Department of Oncology, Faculty of Medicine and Dentistry, Palacky Univer-sity, Czech Republic
Introduction: Circulating tumor cells (CTC) can create metas-tases, which are responsible for 90% causes of deaths at patientswith a cancer. CTC are located in a blood stream or bone marrowand they are most common cause of cancer recurrence after surgi-cal resection of the primary tumor. Presence of CTC has becomean important prognostic and predictive factor, which is possibleto study by molecular methods such as polymerase chain reaction
(PCR). A correlation between recurrence of disease after surgeryand analgesics or anesthetics used during or after surgery was alsofound. Analgesia and anesthesia can affect amount of CTC becauseof their immunomodulatory effects.
Methods and patients: Influence of morphine and pir-itramide was studied in 121 patients with colorectal carcinoma inour research. Detection of CTC was based on real-time PCR in sam-ples from peripheral blood and bone marrow with using epithelialgenes as markers (carcinoembryonic antigen - CEA and cytokeratin20 - CK20). Afterward, the presence of CTC was evaluated depend-ing on the type of analgesia and disease-free and overall survival ofpatients. The main objective was to optimize analgesic techniquesafter surgery to decrease risk of cancer recurrence.
Results: One month after surgery, morphine-based analge-sia usually induced higher level of CTC. Disease-free survival ofpatients was also shorter in case of morphine.
Conclusion: Piritramide seems to be better analgesic tech-nique than morphine, which negatively influences prognosis ofpatients with colorectal carcinoma after surgery.
Acknowledgement: This study was supported bygrants IGA UP LF 2014 019, CZ.1.05/2.1.00/01.0030 andCZ.1.07/2.3.00/30.0004.
http://dx.doi.org/10.1016/j.nbt.2014.05.1867
PC-08
Differential Expression of Circulating miRNAs Fol-lowing Resistance Exercise and Carbohydrate/ProteinSupplementation
Foued S. Espindola1,∗ , Olga Bocanegra2, Renata Teixeira2, MariaSiqueira2, Matheus Gomes2, Miguel Diaz2
1 Universidade Federal de Uberlândia2 Institute of Genetics and Biochemistry - Universidade Federal de Uberlândia
We investigated the levels of expression of 12 circulating miR-NAs (c-miRNAs) involved in cell proliferation, differentiation,angiogenesis, inflammation and glycemic control in responseto resistance exercise (RE) and dietary supplementation. Twelvesubjects performed 10 sets of 10 repetitions with 80% oftheir respective 1RM followed by either carbohydrate or carbo-hydrate/protein supplementation in a randomized single-blindcounter-balanced design. Samples of blood were collected beforeRE, 03 and 24 hours afterwards. The relative expression data of allof the genes were analyzed using a two-way analysis of variancewith repeated measures. The molecular response in the group thatsupplemented with protein was more pronounced for c-miRNAsinvolved in the regulation of myogenesis, particularly hsa-miR-133a and 503. Both treatments revealed a differential expressionof the c-miRNAs hsa-miR-126 and 16, which are associated withangiogenesis. We argue that hsa-miR-133a might be associatedwith satellite cell proliferation, and possibly partially responsiblefor muscle hypertrophy following RE. Further, both the up- anddown-regulation of hsa-miR-126 and 16, respectively, are likely toreflect neovascularization. These findings support the hypothesisthat circulating miRNAs bear paracrine-like functions and thus, areinvolved in cell-to-cell crosstalk.
S106 www.elsevier.com/locate/nbt
