Rashid Kaveh*, Benoit Van Aken Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA Objectives Conclusion.

Slides:



Advertisements
Similar presentations
Analysis of Microarray Genomic Data of Breast Cancer Patients Hui Liu, MS candidate Department of statistics Prof. Eric Suess, faculty mentor Department.
Advertisements

BiGCaT Bioinformatics Hunting strategy of the bigcat.
Effects of Caffeine and Ibuprofen on the Growth of Arab Kyle Butzine, Jasmine Crafton, and Dr. Catherine Chan University of Wisconsin – Whitewater, Department.
The Effects of Caffeine and Triclocarban on Gammarus pseudolimnaeus Jim Fietzer Department of Biological Sciences, University of Wisconsin – Whitewater.
Microarray technology and analysis of gene expression data Hillevi Lindroos.
Getting the numbers comparable
Microarrays Dr Peter Smooker,
DNA Microarray Bioinformatics - #27612 Normalization and Statistical Analysis.
27803::Systems Biology1CBS, Department of Systems Biology Schedule for the Afternoon 13:00 – 13:30ChIP-chip lecture 13:30 – 14:30Exercise 14:30 – 14:45Break.
ONCOMINE: A Bioinformatics Infrastructure for Cancer Genomics
Scientific Data Mining: Emerging Developments and Challenges F. Seillier-Moiseiwitsch Bioinformatics Research Center Department of Mathematics and Statistics.
DNA Arrays …DNA systematically arrayed at high density, –virtual genomes for expression studies, RNA hybridization to DNA for expression studies, –comparative.
Comparative Genomic Hybridization (CGH). Outline Introduction to gene copy numbers and CGH technology DNA copy number alterations in breast cancer (Pollack.
27803::Systems Biology1CBS, Department of Systems Biology Schedule for the Afternoon 13:00 – 13:30ChIP-chip lecture 13:30 – 14:30Exercise 14:30 – 14:45Break.
CISC667, F05, Lec24, Liao1 CISC 667 Intro to Bioinformatics (Fall 2005) DNA Microarray, 2d gel, MSMS, yeast 2-hybrid.
Microarrays: Theory and Application By Rich Jenkins MS Student of Zoo4670/5670 Year 2004.
ICA-based Clustering of Genes from Microarray Expression Data Su-In Lee 1, Serafim Batzoglou 2 1 Department.
STAT115 STAT215 BIO512 BIST298 Introduction to Computational Biology and Bioinformatics Spring 2015 Xiaole Shirley Liu Please Fill Out Student Sign In.
Why microarrays in a bioinformatics class? Design of chips Quantitation of signals Integration of the data Extraction of groups of genes with linked expression.
Genomics I: The Transcriptome RNA Expression Analysis Determining genomewide RNA expression levels.
and analysis of gene transcription
Paola CASTAGNOLI Maria FOTI Microarrays. Applicazioni nella genomica funzionale e nel genotyping DIPARTIMENTO DI BIOTECNOLOGIE E BIOSCIENZE.
This Week: Mon—Omics Wed—Alternate sequencing Technologies and Viromics paper Next Week No class Mon or Wed Fri– Presentations by Colleen D and Vaughn.
A Bioinformatics Meta-analysis of Differentially Expressed Genes in Colorectal Cancer Simon Chan, Thursday Trainee Seminar – October 11.
Amandine Bemmo 1,2, David Benovoy 2, Jacek Majewski 2 1 Universite de Montreal, 2 McGill university and Genome Quebec innovation centre Analyses of Affymetrix.
A New Oklahoma Bioinformatics Company. Microarray and Bioinformatics.
Significance Caffeine and ibuprofen may negatively affect plant growth.  Caffeine and ibuprofen generally exist at concentrations below 1 ppm in surface.
©Edited by Mingrui Zhang, CS Department, Winona State University, 2008 Identifying Lung Cancer Risks.
Development of Western Blots for Actin without the use of radioactivity Geoff Theobald STEP Summer Internship Program June 2003.
Scenario 6 Distinguishing different types of leukemia to target treatment.
Griffiths, M., Marks, H. P., & Young, F. G. (1941). Influence of (Œstrogens and Androgens on Glycogen Storage in the Fasting Rat. Nature, 147 (3725), 359–359.
Ranjit Ganta, Raj Acharya, Shruthi Prabhakara Department of Computer Science and Engineering, Penn State University DATA WAREHOUSE FOR BIO-GEO HEALTH CARE.
Ritesh Krishna Department Of Computer Science WPCCS July 1, 2008.
Data Mining the Yeast Genome Expression and Sequence Data Alvis Brazma European Bioinformatics Institute.
Phytoremediation and Phytosensing of Explosives: The Target genes By: Ariel Moore.
Abstract: The development of wheat and barley microarrays for gene expression analyses have opened the ability to identify genes whose expression patterns.
Overview of Microarray. 2/71 Gene Expression Gene expression Production of mRNA is very much a reflection of the activity level of gene In the past, looking.
ANALYSIS OF GENE EXPRESSION DATA. Gene expression data is a high-throughput data type (like DNA and protein sequences) that requires bioinformatic pattern.
Gene Expression Analysis Gabor T. Marth Department of Biology, Boston College BI420 – Introduction to Bioinformatics.
Genomics A Systematic Study of the Locations, Functions and Interactions of Many Genes at Once.
Genomics A Systematic Study of the Locations, Functions and Interactions of Many Genes at Once.
Statistical Analysis for Expression Experiments Heather Adams BeeSpace Doctoral Forum Thursday May 21, 2009.
Sequencing of the 1 st Intron: 30 DNA samples: (15 from 1997 & 15 from 2004) Amplified 3 B. rapa FLC genes of the 1 st intron using PCR Visualized DNA.
Graduate Research with Bioinformatics Research Mentors Nancy Warter-Perez, ECE Robert Vellanoweth Chem and Biochem Fellow Sean Caonguyen 8/20/08.
Date of download: 6/3/2016 Copyright © 2016 American Medical Association. All rights reserved. From: Novel Integrative Methods for Gene Discovery Associated.
Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation Rendong Yang and Zhen Su Division of Bioinformatics,
We thank the Office of Research and Sponsored Programs for supporting this research, and Learning & Technology Services for printing this poster. An Approach.
Figure S1 (a) (b) Fig. S1. Hydroponics culture of Arabidopsis thaliana. (a) Illustration of the hydroponics system in the growth chamber. (b) close-up.
STAT115 STAT215 BIO512 BIST298 Introduction to Computational Biology and Bioinformatics Spring 2016 Xiaole Shirley Liu.
Risheng Chen et al BMC Genomics
KEY CONCEPT Entire genomes are sequenced, studied, and compared.
The Basis of ABA phenotypes in Arabidopsis det1 mutants
Genomics A Systematic Study of the Locations, Functions and Interactions of Many Genes at Once.
Xiaopeng Min, Li Wang, Yin Wang (Advisor)
Conclusions and future work
Molecular analyses of the interaction of microbes and marsh grasses  Spartina alterniflora and Phragmites australis Lathadevi K. Chintapenta1; Venkateswara.
The impacts of antihistamines drugs in the mussel species Mytillus edulis: biochemical alterations induced after chronic exposure to cetirizine Miguel.
Ganesan Raja, Siwon Kim, Dahye Yoon, Heonho Lee and Suhkmann Kim*
Global Transcriptional Dysregulation in Breast Cancer
Proteomic and Morphological Analyses of Post-Flooding Recovery in Soybean Root Exposed to Aluminum Oxide Nanoparticles ○Farhat YASMEEN 1, 2, Naveed Iqbal.
Microarray Technology and Applications
Characterization of microRNA transcriptome in tumor, adjacent, and normal tissues of lung squamous cell carcinoma  Jun Wang, MD, PhD, Zhi Li, MD, PhD,
Volume 7, Issue 6, Pages (June 2014)
Volume 7, Issue 2, Pages (February 2014)
Volume 8, Issue 5, Pages (May 2015)
KEY CONCEPT Entire genomes are sequenced, studied, and compared.
Schematic representation of a transcriptomic evaluation approach.
Volume 2, Issue 2, Pages (March 2009)
OSPW After Ozonation with 80 mg O3/L
Transcriptome profiling of PD-L1 antibody–treated macrophages showed inflammatory phenotype, increased survival and proliferation, and decreased apoptosis.
Presentation transcript:

Rashid Kaveh*, Benoit Van Aken Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA Objectives Conclusion Background Results Temple University College of Engineering The anti-influenza drugs, oseltamivir phosphate (OSP) and zanamivir (ZAN), are major medications currently used for the treatment of influenza. These drugs have been detected in municipal wastewater and water catchments. They are likely to contaminate agricultural plants through irrigation with reclamation water and/or land application of biosolids. However, little is known about the effects of antiviral drugs on plants at the molecular level. Methods Transcriptional analysis showed changes in genes expression that may reflect oxidative stress in exposed plants. The enzymatic functions and processes may lead to the drugs detoxification in the plant tissue this may help phytoremediation technologies to decrease the concentration of the drugs in the environment. Whole genome expression analysis may be useful for the detection of chronic toxicity of emerging contaminants on plants, even when short-term exposure does not result in observable physiological effects. To understand the potential physiological and transcriptional responses of the model plant Arabidopsis thaliana (A. thaliana) to different contamination levels of the antiviral drugs, OSP and ZAN using whole genome expression microarray. Toxicity testing: A. thaliana was planted on gel medium in vented Magenta boxes under sterile conditions. The gel contained 0, 5, 20, and 100 mg/L on OSP and ZAN, separately. Exposure length was three weeks with incubation under 16 h/day fluorescent light. Molecular techniques: A. thaliana plants exposed to 20 mg/L OSP and ZAN were chosen for transcriptional analysis. Plants were kept is RNAlater storage solution. RNA was extracted using TRIzol ® Plus RNA Purification kit. RNA transcription to cDNA. RNA validity testing by RT-qPCR. Microarray analysis performed using Affimetrix Arabidopsis Gene 1.0 ST Array. Genomic data analysis: Data normalization by Affymetrix Gene Expression Console with Robust Multi-Array Average normalization algorithm BRB-ArrayTools package for statistical analysis and gene ontology analysis, BLAST2GO ® online data bases were used. Fig. 4. Major gene ontology (GO) process categories Acknowledgement: Dr. Yuesheng Li, Genomic facility, Fox Chase Cancer Center, Philadelphia. References Hruz, T. et al. (2008). Genevestigator V3: a reference expression database for the meta-analysis of transcriptomes. Advances in Bioinformatics, 5 pages. Kaveh, R. et al. (2013). Changes in Arabidopsis thaliana Gene Expression in Response to Silver Nanoparticles and Silver Ions. Environmental Science and Technology, Genetic Response of Plants Exposed to Anti-Influenza Drugs Fig.‎ 1. Exposure to a) No drugs, b) OSP 20 mg/L, c) ZAN 20 mg/L. Fig. 2. A. thaliana fresh weight after exposure to OSP and ZAN for three weeks. OSP samples are correlated with the applied concentrations. Biomass and physiological effect: Genetic response: Fig. 3. Number of genes significantly up-and down-regulated by exposure to the antiviral drugs Genes up-regulated (>2) Genes down-regulated (<0.5) OSP ZAN Fig. 5. Major gene ontology (GO) function categories a) b)c)