Western New York

Genetics in Research

PartnershipExpanding Exposure, Career Exploration and Interactive Projects in Basic Genome Analysis and Bioinformatics

Program Overview – National Science Foundation ITEST

Strategies Project• Recruitment of 30 high school science teachers and 150 students per year to be involved in the annotation process (3 years total funding).

• July 2015 : session to teach the fundamentals of genome annotation to the high school teachers and to discuss fall program involving high school student participants

• September - November 2015: 4 semester 1 activities to build student interest in the project

• January to May, 2016: Students work on gene annotations• May 2016: Capstone symposium to bring teachers and their

student participants to UB to present their data in poster format and network with other participants and representatives of bioinformatics related programs in the area.

Goals for Teacher / Student Involvement

• to allow high school students and teachers to be current participants in science

• to stimulate the interest of students in pursuing careers in science and technology through the use of a unique, interactive learning environment: GENI-ACT

• to encourage teachers to incorporate teaching of bioinformatics and genomics into their classrooms wherever possible.

How do we test if this program is effective?

We need 2 groups of student participants (randomly assigned by our assessment partners):

• Experimental group – taking part in annotations exercises

• Control group – not taking part in the annotation exercises

Both groups take pre and post surveys and perhaps are interviewed about topics related to project

GENI-ACT Annotation Workflow

GENI-ACT Workshop

Course Setup

Student Pre-survey

Gene/PathwayAssignments

Progress

Student Post-survey Capstone Symposium

Complete Annotation Modules

Online Lab Notebook

IMG/EDU and other online tools

5

Control Group Intervention Group

Why sequence and annotate the Kytococcus sedentarius genome? • Formally known

as Micrococcus sedentarius

• Summary of Biology

• Genome Information

Pathology Associated with Kytococcus sedentarius

• Pitted Keratolysis (images on next slide)• Associated with pits in skin on the plantar

surfaces of the feet and toes• Strong foot odor• Two extracellular proteases isolated that can

degrade human keratin and thus contribute to pitting of skin

• Generally not invasive beyond stratum corneum in immunocompetent patients.

Pitted Keratolysis

http://emedicine.medscape.com/article/1053078-overview

What does it mean to annotate a gene?

• Bioinformatics – can be thought of as in silico biology as opposed to in vivo or in vitro biology

Annotation

• Annotation is the process of assigning biological information to sequencing data. It consists of essentially 2 different processes:• Gene calling – identification of genes• Function prediction – determining the

biological function of the identified genes.

http://www.nature.com/nrg/journal/v2/n7/abs/nrg0701_493a.html

Kytococcus sedentarius Gene Annotation

• The genome of Kytococcus sedentarius has been sequenced and subjected to computer-based gene calling and annotation…..so why are we doing manual annotations?

• Up to 35% of computer gene calls and annotations are incorrect.

• Automated annotations miss things.• The logic of bioinformatic algorithms illustrates

principles of biology.

Dr. Cheryl Kerfeld, JGI, personal communication

Genomics Education National Initiative Annotation Collaboration

Toolkit• Web-based tools• Contains modular framework for

annotation• Stimulates collaboration within

and between institutions• Designed to suit basic and

advanced annotation

Modules Activites Questions Investigated

Module 1- Basic Information Module

DNA Coordinates and Sequence, Protein Sequence

What is the sequence of my gene and protein? Where is it located in the genome?

Module 2- Sequence-Based Similarity Data

Blast, CDD, T-Coffee, WebLogo

Is my sequence similar to other sequences in Genbank?

Module 3- Cellular Localization Data

Gram Stain, TMHMM, SignalP, PSORT, Phobius

Is my protein in the cytoplasm, secreted or embedded in the membrane?

Module 4- Alternative Open Reading Frame

IMG Sequence Viewer For Alternate ORF Search

Has the amino acid sequence of my protein been called correctly by the computer?

Modules Activites Questions Investigated

Module 5- Structure-Based Evidence

TIGRfam, Pfam, PDB Are there functional domains in my protein?

Module 6- Enzymatic Function

KEGG, MetaCyc, E.C. Number,

In what process does my protein take part?

Module 7- Gene Duplication/Gene Degradation

Paralog, Pseudogene Are there other forms of my gene in Kytococcus? Is my gene functional?

Module 8- Evidence for Horizontal Gene Transfer

Phylogenetic Tree, Has my gene co-evolved with Kytococcus?

Module 9- RNA RFAM Does my gene encode a functional RNA?

Capstone Symposium

Now lets take a closer look at GENI-ACT

http://geni-act.org

Contact Information:Stephen T. Koury, Ph.D.Department of Biotechnical and Clinical Laboratory SciencesUniversity at Buffalo, 26 Cary Hall3435 Main StreetBuffalo, NY 14214

Phone:  716-829-5188Fax:    716-829-3601Email: stvkoury@buffalo.eduhttp://buffalo.academia.edu/StephenKouryhttp://ubwp.buffalo.edu/wnygirp/