Courses

Courses kdorfman Thu, 01/11/2024 - 18:27

Courses taught in ISB

Bio 499CB (Loomis Cancer)

Bio 499CB (Loomis Cancer) kdorfman Thu, 09/08/2022 - 20:59

Kari Loomis honors thesis seminar

Librarian does workshop on library research.

We do Bradford assay lab:

Explain Bradford assay.

Add some Bradford reagent to some BSA - Ask how much protein?

Need standards to compare to!

  • Bradford concentrate from Bio-Rad 500-0006
  • dilute 1:4 with water
  • Make BSA solution 0.1 mg/mL (dilute from the test 2 m/mL test solution
  • Students share a plate:
    • one uses top row
    • one uses bottom row
  • write a program on PS2

Student protocol:

  • Make a 2-fold dilution series of the BSA
    • 0.5 mL water in each tube (except the first)
    • 1 mL BSA into first tube
    • .5 mL to next tube, mix, transfer to next, etc.
  • Put 160 uL BSA into each well
  • put 160 uL water in one well. (Why?)
  • Add 40 uL Bradford
  • Read plate

Data management

  • Stupid Excel Tricks
  • Art of the standard curve
  • Make your own std curve.
  • How would you estimate the concentration of protein in a solution that had an Abs of:
    • 0.5
    • 0.4
    • 3
Raw data
Bradford processed data
preya_tina_9-9_ps2.xls
Nabil Amira Bradford_ps2.xls
pipette good_ps2.xls
Pipette Champions_ps2.xls
abe_cal_BRADplate_ps2.xls

Marine Biology

Marine Biology kdorfman Mon, 01/15/2024 - 17:32

Bio 424 Spring 2024 (Akiko Okusu)

Materials Request

Prep Instructions

Growth chamber spawning program

Growth chamber spawning program kdorfman Fri, 05/17/2024 - 19:17

Basic Parameters:

Light from 9 pm Sunday to 1 pm Monday, otherwise dark

Warm from 9 pm Sunday til 9 am Monday, otherwise cool

Day time temp light level
M 13:00 18 0
Sun 21:00 25 3
M 9:00 18 3
M 13:00 18 0

Schedule 3 programs, like this:

Program 1, repeat 6 times:

Day time temp light level
M 00:00 18 0

Program 2 (spawning), do once, following 6x Program 1

Day time temp light level
Sun 00:00 18 0
21:00 251 3

Program 3, do once

Day time temp light level
M 00:00 25 3
9:00 18 3
13:00 18 0

Return to Program 1

  1. There is a temperature spike when the light comes on, so leave the temp setting at 18 for an hour (until 22:00), then raise it to 25. ↩︎

Sea Water for 424

Sea Water for 424 kdorfman Mon, 01/15/2024 - 18:14

2 carboys SeaWater (31-35ppt salinity):

  • 31-35g InstantOcean Reef Salt in 1 L
  • Submerge a bubbler or a pump so that it is constantly being mixed

Nematostella SW is 1/3 ASW

F/2 Medium for algae (424)

F/2 Medium for algae (424) kdorfman Mon, 01/15/2024 - 18:16

5 liters of f/2 medium for algae.

L1 Medium Kit from Bigelow NCMA contains the nitrate, phosphate, trace minerals, and vitamins. Add the antibiotics from prep room freezer stocks.

Re-inoculate once during week of 1/15

TA & Students will re-inoculate once monthly

50 mL/month x 4 months x 16 students = 3200 mL

Make 4 L for the semester.

To make (in a sterile hood)L F/2 medium for algae
add: mL NaNO3 (75g/L)
add: mL NaHPO4 (5 g/L)
add: mL trace minerals
add: mL vitamins
add: mL kanamycin
add: mL ampicillin
add: mL streptomycin

Plus ASW to final volume

Filter sterilize

F/2 medium for algae

Trace minerals for F/2

Trace minerals for F/2 kdorfman Mon, 06/24/2024 - 15:46

Buy L1 Medium Kit from Bigelow NCMA

Replacement trace minerals solution

Component Concentration in final medium
Na2EDTA · 2H2O 1.17 x 10-5 M
FeCl3 · 6H2O 1.17 x 10-5 M
MnCl2·4 H2O 9.00 x 10-7 M
ZnSO4 · 7H2O 8.00 x 10-8 M
CoCl2 · 6H2O 5.00 x 10-8 M
CuSO4 · 5H2O 1.00 x 10-8 M
Na2MoO4 · 2H2O 8.22 x 10-8 M
H2SeO3 1.00 x 10-8 M
NiSO4 1.00 x 10-8 M
Na3VO4 1.00 x 10-8 M
K2CrO4 1.00 x 10-8 M

Vitamins for F/2

Vitamins for F/2 kdorfman Mon, 06/24/2024 - 15:51

Buy L1 Medium Kit from Bigelow NCMA

Replacement Vitamin Stock Solution

Component Concentration in Final Medium
thiamine · HCl (vit. B1) 2.96 x 10-7 M
biotin (vit. H) 2.05 x 10-9 M
cyanocobalamin (vit. B12) 3.69 x 10-10 M

Perfect Plant 2024

Perfect Plant 2024 kdorfman Wed, 01/10/2024 - 21:51

Bio 427 - Madelaine Bartlett

Wednesdays

Date subject prep
2/7 plant architecture Find the leaf. lycophytes, bryophytes, diversity, alstoemeria, Ruscus
2/14 ferns and lycophytes ???? clv1 and wus mutants? from maize, tomato, arabidopsis; moss phyllotaxy
2/21 seed plants life cycles - moss gametophytes, sporophytes; tree thinking/traits on a tree. moss gametophytes, fern gametophytes, prepared slides
2/28 individual plant 1
3/6 fruit diversity fruit diversity (grocery store) including Citrus diversity; fas PCR, fruit description
3/13 exam 1
3/20 spring break
3/27 ABC model arabidopsis and maize ABC(E) mutants
4/3 individual plant 2
4/10 floral diversity grocery store floral diversity
4/17 exam 2
4/24 leaf development patterning mutants - ask Aman, Annis
5/1 leaf diversity Leaf morphological and anatomical diversity (C3 and C4), practice making hand sections
5/8 presentations

Prep pages

2024/02/07

2024/02/07 kdorfman Thu, 01/11/2024 - 18:47

Perfect Plant Lab 1

Topic: Major lineages of land plants, basics of plant architecture

Plants needed: NHC diversity; maize, arabidopsis, tomato

Prepared slides: Meristems

Materials:

  • dissection tools
  • hand section materials
  • microscopes

2024/02/14

2024/02/14 kdorfman Thu, 01/11/2024 - 19:01

Perfect Plant Lab 2

Topic: Fern lifecycle

Resources: C-fern Manual

Materials: dissection and hand section materials, microscopes

Plants: C-fern gametophytes; NHC diversity

Prep: Sow Arabidopsis ABC mutants

2024/02/21

2024/02/21 kdorfman Thu, 01/11/2024 - 19:06

Perfect Plant Lab 3

Topic: Seed plants

Plants needed: meristem mutants; NHC diversity

Prepared Slides: gametophytes; embryos

Materials: dissection and hand section materials, microscopes; maybe stuff for pollen tube growth

2024/02/28

2024/02/28 kdorfman Tue, 01/16/2024 - 21:37

Individual Plant Day 1

2024/03/27

2024/03/27 kdorfman Sun, 01/28/2024 - 15:54

Arabidopsis mutants:

Stock # tape color allele gene
CS3085 teal ap3-1 AT3G54340
CS3082 green ap2-1;ap2-2 AT4G36920
CS8066 red (clv3-2) AT2G27250
CS45 blue clv1-1 AT1G75820
CS77 lavender pi-1 AT5G20240
CS25 pink ag-1 AT4G18960
CS6291 orange ap1-7 AT1G69120
CS15 yellow wus-1 AT2G17950