Day 3 :
- Track 3: Next Genetaion Sequencing Track 4: Cancer Genomics Track 9: Bioinformatics in Genomics, Proteomics and Computational Biology Track 14: mRNA analysis
Chair
Gerald J Wyckoff
University of Missouri, USA
Session Introduction
Aditi Nadkarni
New York University, USA
Title: The relationship between NER and TCR in the repair of DNA adducts
Biography:
Aditi Nadkarni is an Associate Research Scientist at New York University’s Department of Biology where she conducts research in the fi elds of carcinogenesis, DNA repair and genomics using human cells. Her previous work includes preclinical analysis of DNA repair inhibitors in glioma cells during a Post-doctoral Fellowship at Mayo Clinic and characterization of a breast cancer genetic mutant during her PhD research at University of Toledo.
Abstract:
Exposure to Polycyclic Aromatic Hydrocarbons (PAHs) can give rise to DNA adducts that alter essential cellular functions such as replication and transcription and induce genome instability. DNA repair mitigates the deleterious eff ects of DNA damage. Nucleotide Excision Repair (NER) detects and removes bulky DNA adducts that disrupt base pairing and distort the DNA helix whereas Transcription-Coupled DNA Repair (TCR) removes DNA adducts that impede RNA polymerase elongation during gene expression. Site-specifi c DNA lesions were used to examine the relationship between NER and TCR in the repair of PAH-induced adducts. In addition, the consequences to gene expression and mRNA integrity of damage that escapes repair or is repaired slowly was also studied. Th e results indicate that TCR slowly repairs DNA adducts that block transcription but escape removal by NER. Furthermore, the absence of NER or TCR in cells defective in either or both pathways results in decreased gene expression and alterations to the sequence of the mRNA produced. Th ese fi ndings enhance our understanding of DNA repair and its role in processing DNA damage that impedes gene expression in human cells.
Gerald J Wyckoff
University of Missouri, USA
Title: Sparse-matrix analysis of small molecules and protein targets for drug discovery
Biography:
Gerald J Wyckoff is a Molecular Evolutionary Geneticist. He was trained in fi nding faint signatures of positive selection in a sea of genomic noise. This led him to become involved with large scale genomic, and later proteomic, projects and these are his areas of interest. This has allowed him to extend his knowledge in drug discovery towards chemical information signatures for high-throughput screening of compounds.
Abstract:
We have established a rapid and practical methodology for the clustering of small molecule similarity. Th is is a known technique for analysis of next-gen sequence, expression data and other types of “big data”. However, this technique has not been deployed for small molecules because there has not been a good methodology for representing chemical similarity that lends itself to clustering across broad ranges of molecule similarity. We have developed a chemical fi ngerprinting system from earlier work that gives a bitwise score or “signature” for any molecule that can be represented in three-dimensional space (normally in a PDB or PDBQT fi le). Because of this, the mathematical difference between two small molecules bitwise scores acts as a traditional ‘distance” measure would enabling clustering of small molecules. When matched with traditional protein phylogenetic clustering, we derive a “sparse matrix” graph. Th e X-axis is populated by clustered small molecules; the Y-axis is populated by phylogenetically clustered protein targets. In the center of the graph, we record if a small molecule is known to interact with a specifi c protein target. Th ese graphs enable drug discovery. Structure-based virtual screening is an important tool in the drug discovery process. Th e use of computational tools has allowed for the screening of large libraries of chemical compounds to identify putative ligand-receptor interactions. Th e identifi cation of valid targets and therapeutic compounds has long-term importance both to public health and the economic strength of the pharmaceutical industry. Extending this technology by enabling small molecule clustering and results visualization is the next logical evolution of the technology.
Gulnaz T Javan
Alabama State University, USA
Title: Using high-throughput sequencing of the thanatomicrobiome of criminal cases
Biography:
Gulnaz T Javan graduated with a PhD in Forensic Science from Istanbul University, Istanbul, Turkey in 2003. Her current projects employ next generation sequencing and fl ow cytometry, of cadaver tissues, microbial diversity in soil under decomposing cadavers, and entomology, to determine corpses’ PMIs. She received a $200,000 NSF grant for the project, "Life after Death - The Thanatomicrobiome.” She introduced a new term, Thanatomicrobiome, at the 66th Annual American Academy Forensic Science Meeting (AAFS) in 2014.
Abstract:
The study of the postmortem microbial transformations aft er human death has yet to be fully investigated. In the present study, a new term, ‘thanatomicrobiome’, which refers to the microbiome existing in the internal organs and blood of a human host aft er death, is introduced. The objectives of this study were to (i) establish the best method for extracting and sampling DNA from four internal organs (liver, spleen, heart, and brain) and blood of cadavers with PMIs 20-240 hours using the Roche 454 platform; (ii) demonstrate that the method is feasible to survey the 16S rRNA genes of the microbiome using the IlluminaMiSeq platform; and (iii) compare the beta diversity of the microbiomes by cause of death and gender. Th e results of the fi rst objective demonstrated that the conventional phenol/chloroform method, followed by bead-beating and ethanol precipitation, was superior for extracting thanatomicrobiome DNA from the four organ tissues and blood of cadavers. Th e results of the second objective showed that the thanatomicrobiome is similar among the organ tissues and blood sample of the same cadaver. Additionally, facultative anaerobic bacteria, such as Lactobacillus, predominate in organ tissues and blood samples of cadavers with short PMIs and obligate anaerobic bacteria such as Clostridium, predominate in cadavers with longer PMIs. Th e third objective demonstrated that there are observable trends among taxa of same gender and cause of death. To date, this is the fi rst study of its kind to examine the microorganisms associated with internal organ tissues of cadavers using culture-independent methods.
Heba Bassiony
Cairo University, Egypt
Title: Evaluation of antitumor potential of magnetite nanoparticles on Ehrlich solid carcinoma bearing mice
Biography:
Heba Bassiony is an Assistant Lecturer at Zoology department, Faculty of Science; Cairo University. She has completed her PhD recently in 2015 from Faculty of Science, Cairo University in the fi eld of cytology and molecular biology. She has published two papers in reputed journals and third paper is in submission. She is interested in cancer research and molecular biology.
Abstract:
Magnetite Nanoparticles (MNPs) have been widely used as contrast agents and have promising approaches in cancer treatment. In the present study, we used Ehrlich Solid Carcinoma (ESC) bearing mice as a model to investigate MNPs antitumor activity, their effect on expression of p53 and p16 genes as an indicator for apoptotic induction in tumor tissues. MNPs coated with ascorbic acid (size: 25.0±5.0 nm) were synthesized by co-precipitation method and characterized. Ehrlich mice model were treated with MNPs using 60 mg/Kg day by day for 14 injections; intratumorally (IT) or intraperitoneally (IP). Tumor size, pathological changes and iron content in tumor and normal muscle tissues were assessed. We also assessed changes in expression levels of p53 and p16 genes in addition to p53 protein level by immunohistochemistry. Our results revealed that tumor growth was signifi cantly reduced by IT and IP MNPs injection compared to untreated tumor. A signifi cant increase in p53 and p16 mRNA expression was detected in Ehrlich solid tumors of IT and IP treated groups compared to untreated Ehrlich solid tumor. Th is increase was accompanied with increase in p53 protein expression. It is worth mentioning that no signifi cant diff erence in expression of p53 and p16 could be detected between IT ESC and control group. MNPs might be more eff ective in breast cancer treatment if injected intratumorally to be directed to the tumor tissues.
Daniel J Cooper
University of Texas at San Antonio, USA
Title: Co-regulation of pluripotency and enhanced genetic integrity at the genomic level
Biography:
Daniel J Cooper has completed his PhD in Cell and Molecular Biology at the University of Texas at San Antonio in May of 2015, focusing on mechanisms maintaining genetic integrity in pluripotent stem cells. He is currently a Postdoctoral Associate at the University of Miami Miller School of Medicine’s Project to Cure Paralysis.
Abstract:
One important but poorly characterized aspect of stem cells is their ability to maintain genetic integrity while pluripotent, when induced to diff erentiate and or when derived from diff erentiated cells by reprogramming. We tested the hypothesis that pluripotency and enhanced genetic integrity are mechanistically linked at the genomic level. We used computational methods to mine previously published databases describing gene expression in human and mouse ES, iPS and diff erentiated cells and found that 40-44% of DNA repair genes are up-regulated in ES and iPS cells while only 1-13% are down-regulated. Cell death genes showed overall diff erential expression between pluripotent and diff erentiated cells with 14-24% of genes downregulated and 12- 23% up-regulated in pluripotent cells. We then used Ingenuity Pathway Analysis (IPA) to examine direct interactions between three pluripotency factors, SOX2, OCT4 and NANOG and these diff erentially expressed genes. In addition, we examined interactions between pluripotency factors and intermediary transcription factors that are themselves, regulated by pluripotency factors and which in turn regulate downstream genetic integrity genes. Th e combination of direct and indirect interactions we detected accounted for regulation of 22-50% of diff erentially expressed genetic integrity genes by the three pluripotency factors investigated. Several of the pluripotency-genetic integrity network interactions predicted by computational methods were subsequently validated by ChIP-qPCR. Taken together, our data support our hypothesis that enhanced maintenance of genetic integrity is mechanistically linked to the epigenetic state of pluripotency at the genomic level. In addition, these fi ndings demonstrate how a small number of key factors can regulate large numbers of downstream genes.
Jumoke Soyemi
The Federal Polytechnic, Nigeria
Title: Comparison of computational models in prediction of adverse drug reactions
Biography:
Jumoke Soyemi completed her BSc (Computer Science) at Obafemi Awolowo University, Ile-Ife in 1999, MSc (Computer Science) at University of Ibadan in 2004 and is presently pursuing her PhD (Bioinformatics) at Covenant University, Ota under the Covenant University Bioinformatics Research cluster (CUBRe). Her PhD is supported by h3abionet grant.
Abstract:
Computational pharmacology is the application of bioinformatics and computational biology with relevance to pharmacology including understanding of drug action, adverse drug reaction, identification of drug targets and drug design. Early and accurate identifi cation of Adverse Drug Reactions (ADR) is critically important for drug development and clinical safety. Oft en times the adverse eff ect of drugs are not discovered until years later aft er the drugs’ release to the market. Th e post hoc analysis is usually unable to detect rare or delayed on-set ADR until clinical evidence accumulates. Th e process of drug development and ADRs discovery takes years, meaning that a lot of harm would have been caused to lives before evidences are accumulated, therefore developing a computational pharmacology model that can be used to make informed decisions to decrease attrition rate in the process of drug development with improve number of drugs having an acceptable benefi t and risk ratio is paramount. Th is paper reviews and compares computational methods of the few works that has been done so far to address this issue and hence looks at the applicable methods that can be used in drug to ADR prediction.
Binay Kumar Raut
Kathmandu University of Medical Sciences, Nepal
Title: Cytogenetic investigations in bone marrow cancers and cancer predisposing chromosomal instability syndromes
Biography:
Binay Kumar Raut is working as a Lecturer in Biochemistry at Kathmandu University School of Medical Sciences, Nepal. He is interested to conduct research in Biochemistry. He authored many publications which mainly concentrates prevalence of iron deficiency in Pregnant women and Oncogenes responsible for Bone Marrow Cancer.
Abstract:
Background: Leukemia is a neoplastic proliferation of hematopoietic cells. Leukemia can be classifi ed as either myelocytic (myeloid) or lymphocytic (lymphoid) depending on the lineage of the leukemic cells and chronic and acute depending on the clinical course. Aim: Th e aim of the present study was to detect structural abnormalities by using automated karyotyping (IKAROS) soft ware in Leukemia cancer (CML, AML, ALL and CLL) samples. Methods: Conventional cytogenetics: Peripheral Blood Culture (PBC) and bone marrow aspirate supplemented with mitogen Phytohemagglutinin (PHA) metaphase chromosomes were harvested aft er 72 hours for chromosome analysis. Image acquisition and analysis was performed by using automated karyotyping (IKAROS) soft ware based on GTG banding. Results: Philadelphia chromosome involving the reciprocal translocation between the long arms of chromosomes 9 and 22 (46, XY, t (9; 22)) was observed in majority of Chronic Myeloid Leukemia (CML) patients of the present study. Also a high number of chromosomal structural aberrations were observed in Fanconi Anemia (FA) patient, a chromosomal instability syndrome predisposing to cancer. Conclusion: Conventional cytogenetics can be the method of choice in diagnosis of genetic conditions like CML but for other bone marrow cancers more studies with high sample numbers need to be carried out for determination of clear cut markers.