General Safety - Southeast Missouri State University

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LABORATORY METHODS IN BIO
TECHNOLOGY

(BIOLOGY
2
45)

Spring 201
3


Instructor
s
:

Jim Champine



224A

Rhodes Hall of Science



651
-
2
171
,
jchampine@semo.edu




Office Hours:

WR
F
9
-
11

A
M

Schedule:

Tues
day,
1
2
:30


2
:30 PM
, 22
0
/223

Rhodes



Thurs
day,
1
2
:30


3
:30 PM, 220
/223

Rhodes


Prerequisites:


BI 200 General Microbiology

(pre
-

or co
-
requisite)

Textbook:

Basic Laboratory Methods for Biotech
n
ology
, 2
nd

Edition, Seidman and Moore


Additional Resource
s
:


A Photographic
Atlas for the Microbiology Laboratory
,
4th

Edition
, L
eboffe and Pierce

Brock Biology of Microorganisms
, 1
3
th Edition, Madigan
,

Martinko
, Stahl and Clark


Course Webpage:

http://cstl
-
csm.semo.edu/champine/
teaching/
BI245/index.html





Goals of the Course

The principal goal of this course is to teach students the skills and dispositions necessary
to pursue a career in microbial, cellular, and molecular biology. These
disciplines cannot be
pursued without practice and understanding of laboratory research techniques. After the course
the student should be significantly better equipped to:

a. Carry out undergraduate research

b. Read and interpret primary literature

c. Fu
nction as a research technician

d. Undertake a graduate program


Course Organization

Class will meet
Tues
day (
1
2
:30


2
:30

PM
) and
Thurs
day

(
1
2
:30


3
:30

PM
) in either
220 or 223 Rhodes Hall. On average, each week will consist of 4 hours lab and 1 hour
lecture,
although there will be no clear cut distinction between the two.



Course Grading

There will be
600

possible points.

Up to
30

points extra credit will be awarded for
participation
, asking questions, being on time and prepared, and attendance
.

Th
e grading will be, in part, competency based
.

This means you need

to show
proficiency in four areas



general, culturing,

analysis, and nucleic acids. In each area
proficiencies will be demonstrated through UTests, homework, in
-
class activities, manuscri
pts,
and practical and written exams.






Grades will be assigned according to the following table.


Grading Element

Points

Homework
, Assignments, Competencies
(Utests), Presentation, Practicals,
Unknowns

2
00

Notebook

2
0+
30
+
50
=
1
00

Manuscripts

2
0+
30
+
50
=
1
00

Exams

2
00


A straight scale (90%A, 80%B, 70%C, 60%D) will be employed.


Student Learning Outcomes

1.

The students will develop a plan for preparing a standard laboratory solution from various
starting materials.

2.
Students will be able to calculate growth rate parameters for microorganisms.

3.
Students will demonstrate the ability to manipulate DNA by measuring the size of DNA
pieces they generated and electrophoresed


Questions, comments or requests regarding th
is course should be taken to your instructor
-

usually me, but in some cases Dr. Bluma.


Unanswered questions or unresolved issues involving
this class may be taken to Dr. Chris McGowan, Dean of the College of Science, Technology, and
Agriculture (
cwmcgowan@semo.edu
, 102 Rhodes Hall, 651
-
2163).



From the Bulletin


Attendance

Students are expected to attend all classes and to complete all assignments for courses in
which they are enrolled. An absence does not relieve the student of the responsibility to complete
all assignments. If an absence is associated with a university
-
san
ctioned activity, the instructor
will provide an opportunity for assignment make
-
up. However, it is the instructor’s decision to
provide, or not to provide, make
-
up work related to absences for any other reason.

A student not present for class during the

entire initial week of a scheduled course may
be removed

from the course roster unless the student notifies the instructor by the end of the first
week of an intention to attend the class. Questions regarding the removal process should be
directed to the
Registrar.


Academic Honesty

Academic honesty is one of the most important qualities influencing the character and
vitality of an

educational institution. Academic misconduct or dishonesty is inconsistent with
membership in an academic community and canno
t be accepted. Violations of academic honesty
represent a serious breach of discipline and may be considered grounds for disciplinary action,
including dismissal from the University. Academic dishonesty is defined to include those acts
which would deceive,

cheat, or defraud so as to promote or enhance one’s scholastic record.
Knowingly or actively assisting any person in the commission of an above
-
mentioned act is also
academic dishonesty. Students are responsible for upholding the principles of academic ho
nesty
in accordance with the “University Statement of Student Rights” found in the STUDENT
HANDBOOK. The University requires that all assignments submitted to faculty members by
students be the work of the individual student submitting the work. An excepti
on would be group
projects assigned by the instructor. In this situation, the work must be that of the group.
Academic dishonesty includes:


Plagiarism.
In speaking or writing, plagiarism is the act of passing someone else’s work off as
one’s own. In addit
ion, plagiarism is defined as using the essential style and manner of
expression of a source as if it were one’s own. If there is any doubt, the student should consult
his/her instructor or any manual of term paper or report writing. Violations of academic

honesty
include:

1. Presenting the exact words of a source without quotation marks;

2. Using another student’s computer source code or algorithm or copying a laboratory report;
or

3. Presenting information, judgments, ideas, or facts summarized from a sou
rce without giving
credit.


Cheating.
Cheating includes using or relying on the work of someone else in an inappropriate
manner.

It includes, but is not limited to, those activities where a student:

1. Obtains or attempts to obtain unauthorized knowledge
of an examination’s contents prior to
the time of that examination.

2. Copies another student’s work or intentionally allows others to copy assignments,
examinations,

source codes or designs;

3. Works in a group when she/he has been told to work individual
ly;

4. Uses unauthorized reference material during an examination; or

5. Have someone else take an examination or takes the examination for another


Civility

Every student at Southeast is obligated at all times to assume responsibility for his/her actions,

to
respect constituted authority, to be truthful, and to respect the rights of others, as to respect private and
public property. In their academic activities, students are expected to maintain high standards of
honesty and integrity and abide by the Uni
versity’s Policy on Academic Honesty. Alleged violations of
the Code of Student Conduct are adjudicated in accordance with the established procedures of the
judicial system.


Disabilities

Southeast Missouri State University and Disability Support Serv
ices remain committed to making every
reasonable educational accommodation for students with disabilities. Many services and
accommodations which aid a student’s educational experience are available for students with various
types of disabilities. It is th
e student’s responsibility to contact Disability Support Services to become
registered as a student with a disability in order to have accommodations implemented.
Accommodations are implemented on a case by case basis. For more information visit the follow
ing
site:
www.semo.edu/lapdss

or contact Disability Support Services at 573
-
651
-
2273




LABORATORY METHODS IN

BIOTECHNOLOGY

(BIOLOGY 2
45)

TENTATIVE ACTIVITY

SCHEDULE

and TOPIC OUTLINE

Date

#

Activity or
Topic


Chapter; Pages from Seidman and Moore

Brock, (Leboffe & Pierce),
Assignments, and Resources

1/1
5

T

1

Practical Exam I



1/
17

R

2

Course orientation


Notebooks

Manuscripts

Handling Liquids

Calibrating Pipettors

1.I.A
-
C; pp. 3
-
8

13; pp. 214
-
229

17.III.A
-
C; pp. 307
-
314

17.I
-
II.E; pp.296
-
307

20; pp.348
-
368

(1
-
6, 31
-
37)


1/19 F


Microscopy make up
(
2
:30
-
3
:30, 315 RH)



1/22
T

3

Cleaning Pipettors

Dimensional Analysis

14; pp. 230
-
236



1/2
4

R

4

Descriptive Statistics

Measurements

Weights

16.I.A
-
D; pp. 271
-
279

Unit V; pp. 293
-
295

19; pp. 333
-
347


1/
29

T

5

Water

Preparing Solutions

Concentration and Dilution

28
-
II.C; pp.524
-
537

14.V.A
-
D; pp. 241
-
245

26; pp.492
-
504. 27.I; pp.508
-
510.
27.III.A
-
IV.A; pp.514
-
518


1/31

R

6

pH
,
Weak Acids
,
CO
2
, and
Buffers

Solution Projects

22; pp.380
-
401

27.II; 510
-
514


2/2 S


University Lab Safety
Training



2/
5

T

7

Lab

Safety
Training
Make
-
up
day



2/
7

R

8

General

Safety

Chemical Safety

Reagents

Guest Speaker

Unit III
-
9; pp.133
-
145

11; pp.161
-
183




Date

#

Activity or Topic

Chapter; Pages from Seidman

and Moore

Brock, (Leboffe & Pierce),
Assignments, and Resources

2/1
2

T

9

Filtration and
Centrifugation


Media

28.II.C.v; pp.526

Unit VIII 31
-
32; pp.588
-
620

Brock 26.3, p. 760
-
762

(228)

Brock 4.1
-
4.4, p. 85
-
91

2/1
4

R

10

Preparing Agar Plates

Media Projects

30
-
IV.D; pp.563
-
587

Brock 26.1, p. 756
-
759

2/19

T

11

Agar Day

Measures of Microbial
Growth



Brock 5.9
-
5.11, 128
-
132

2/
21

R

12

VCC


and OD



12; pp. 184
-
213

(217
-
220)

Brock 31.4, p. 888
-
892

2/2
6

T

13

Bacterial Growth Curves


Growth Rate Kinetics
Batch Culture Growth
Cycle

14.V.F; pp.
246
-
250

23.I.
-
III.C; pp.403
-
415

15.II.A; pp. 263
-
267

Brock 5.5
-
5.6, p.123
-
126

Brock 6.7, p.125
-
126

2/28

R

14

Viral Growth Curves

Guest speaker


Brock 9.1
-
9.5, p. 237
-
242
(117
-
119)

3/
5

T

15

Exam I


through Batch
culture growth cycle




3/
7

R

16

Plaque
Assay


(220
-
221)



Date

#

Activity or Topic

Chapter; Pages from Seidman and Moore

Brock, (Leboffe & Pierce),
Assignments, and Resources

3/12

T

17

Using the Avanti

Spectrophotometry

Pigment Spectra

23.IV; pp.415
-
425

25.I
-
II.; pp.463
-
464

Brock 13.1
-
13.5, p. 346
-
352

3/14
R

18

End Point
Determination

Glucose Measurement

25.III.A
-
B ; pp.464
-
467




3/18
-
3/22

Spring

break, no classes


3/
26

T

19

Protein Determination

Bradford Assay

15.I.C; pp.257
-
260

25.IV.A; p.472

25.V.C; pp.477
-
478


3/
28

R

20

SDS Page

29
-
II.F; pp.542
-
550

33;
pp.621
-
638

(106
-
107)

4/2

T

21

Chromosomal DNA
Extraction

29.III
-
App.; pp.550
-
562

(109)

4/4

R

22

Agarose Gel
Electrophoresis





(110)

4/
9

T

23

DNA Concentration

25.V.D; pp.478
-
482


4/
11

R

24

Guest speaker





Date

#

Activity or Topic

Chapter; Pages from Seidman and Moore

Brock, (Leboffe & Pierce),
Assignments, and Resources

4/16

T

25

Plasmid Extraction

26.App.; pp.505
-
507


4/1
8

R

26

Lambda Restriction
Enzyme Analysis


Brock 11.1, 292
-
293

4/
23

T

27

Polymerase Chain
Reaction


Brock
6.11, 169

(111
-
112)

4/
25
R

28

Plasmid Unknown

Guest speaker



4/30

T

29

Use
s

of Radiation

in
Research

Irradiation of Food



5/
2

R

30

Radiation Safety

15; pp. 267
-
270

Brock 20.2, p. 673
-
675

5/8 T


Exam I
I



Virus through
Radiation



items

in italics are lab activities and require a notebook entry