COMMACK HIGH SCHOOL

Mission Statement

Students in this course will be exposed to the process of scientific investigation through collaboration with researchers at Stanford University. The overarching goal of Dr. Kim's lab at Stanford is to explore the function and development of insulin-producing cells in humans with the ultimate goal of curing type I and type II diabetes. The fruit fly is used as a model system because it has insulin-producing cells and many of the regulatory pathways are the same as in humans. A critical part of this work, as in all experiments involving fruit flies, is to be able to control gene expression as specifically as possible. Students will be involved in finding regions of DNA that control gene expression in fruit flies. To do this they will learn current techniques in fly biology, fluorescence microscopy, molecular biology and bioinformatics. Useful strains of flies made and characterized by students will be used by researchers in Dr. Kim's lab and made available to all scientists working on fruit flies (Info provided by Phillips Exeter Academy)

Stanford University & Commack High School Collaboration Publication

2023 Generation of LexA enhancer-trap lines in Drosophila by an international scholastic network

2019 An Interscholastic Network to Generate LexA Enhancer Trap Lines in Drosophila

Stan-X Website (Stanford University)

StanMack Info

StanMack Course Intro

Basics of Drosophilia Genetics

Genetic Terminology, Genetic Naming, and Writing Conventions

Sex Determination

Identifying Virginal Flies

Identifying Flies

Bio670 Manual

Card Sort: Female Vs Male Flies

Card Sort: Genotype to Phenotype

In-Class Crosses

Hand-outs

Nomenclature Rules Cheat Sheet

Nomenclature Student Assignment (Groo)

StanEx Fly Nomenclature Description Sheet

F0 Crossing Scheme Assignment

F0 (Reverse Cross) Crossing Scheme assignment

F1Crossing Scheme Assignment

Primer Sequences Kurt/Ulf and Plac1/Plac4 and SP1

Lutz Document on Analysis of Sequencing from Insertion Site Cloning

Sequence Data Assignment for Inverse PCR

NCBI- Blast Sequence Alignment

FlyBase Blast

Inverse PCR

P-element 5' --> 3': TTTCATCATG motif (at begining and end of p-elemnt)

Sau3AI Restriction Site: GATC (Replaced BfuCI Restriction Site: GATC)

HpaII Restriction Site: CCGG

+/+: Return sequence in database

+/- : Return reverse complement of what is in the database

5' --> 3' sequenced with Sp1 (5' end of p-element)

+/-: Coordinates decreasing, 5' --> 3' p-element orientation (add +1 to first nt match/duplicated nt: Reverse Complement)

+/+: Coordinates increasing, 3' -->5' p-element orientation (add +8 to first nt match/duplicated nt: 1st 8nt)

3' -->5' sequenced with Berta/Ulf (3' end of p-element)

+/+: Coordinates increasing, 5' --> 3' p-element orientation (add +8 to first nt match/duplicated nt: 1st 8nt)

+/-: Coordinates decreasing, 3' -->5' p-element orientation (add +1 to first nt match/duplicated nt: Reverse Complement)

Primer Design

The are different orientations but both are Dove primers so the Primer3 settings are:
Change NONE to Drosophila
Product size range: 601-700 701-850
Primer size: Min 18, Opt 23, Max 25
Tm Dove: Min 51, Opt 53, Max 55

If you needed a Chris Primer the Primer3 settings are:
Change NONE to Drosophila
Product size range: 601-700 701-850
Primer size: Min 18, Opt 23, Max 25
Tm Chris: Min 61, Opt 63, Max 65

Practice Sequence Data from Exeter Manual

StanEx Sequence Analysis