Adv Phage Genetics/BioS 318

Primary Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 6

Juniors: 3

Seniors: 3

Meetings per week: 3

Hours per week: 10.0

Adv. Phage Genetics/BioS 396

Primary Instructor: Vassie Ware

Type: Other

Hosts used: Streptomyces griseus

Number of students: 11

Sophomores: 1

Juniors: 7

Seniors: 3

Meetings per week: 3

Hours per week: 10.0

Students (sophomores, juniors, and seniors) in this course continue phage research after completing the year-long phage courses (started in their freshman year and continued into the sophomore year). This advanced course includes both microbiology and bioinformatics, depending on the individual interests of the students. Phage hunting may also be included using different hosts other than Mycobacterium smegmatis (e.g., Gordonia, Microbacterium, and Streptomyces).

Advanced Phage genetic

Primary Instructor: Vassie Ware

Additional Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 8

Juniors: 2

Seniors: 6

independent research students register for 1-3 credits

BioS 043 Phage Hunting

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: In situ (phage discovery/microbiology)

Hosts used: Mycobacterium smegmatis

Number of students: 12

Freshmen: 11

Sophomores: 1

Meetings per week: 2

Hours per week: 6.0

Also hunting with Microbacterium natoriense.

BioS 043-010

Primary Instructor: Vassie Ware

Additional Instructor: Vassie Ware

Type: In situ (phage discovery/microbiology)

Hosts used: No host information yet.

Number of students: 12

Freshmen: 12

Meetings per week: 2

Hours per week: 6.0

BioS 118

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: In silico (phage genomics/bioinformatics)

Hosts used: Mycobacterium smegmatis

Number of students: 17

Sophomores: 17

Meetings per week: 2

Hours per week: 6.0

Section will focus on annotation and in situ work.

BioS 118

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 11

Sophomores: 11

Meetings per week: 2

Hours per week: 5.0

Both in silico and in situ work are in this course

BioS 118

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: In silico (phage genomics/bioinformatics)

Hosts used: Mycobacterium smegmatis

Number of students: 16

Sophomores: 15

Juniors: 1

Meetings per week: 2

Hours per week: 6.0

In addition to phage genomics and bioinformatics, there are additional microbiology experiments that will be pursued.

BioS 118

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 16

Sophomores: 16

Meetings per week: 2

Hours per week: 6.0

BioS 118 -060

Primary Instructor: Margaret Kenna

Additional Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 12

Sophomores: 12

Meetings per week: 2

Hours per week: 5.0

bioinformatics and situ work

Bios 118 -23, 60 and 61

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: In silico (phage genomics/bioinformatics)

Hosts used: Mycobacterium smegmatis

Number of students: 17

Sophomores: 17

Meetings per week: 2

2.5

BioS 118 Phage Genetics Lab

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: In silico (phage genomics/bioinformatics)

Hosts used: Mycobacterium smegmatis

Number of students: 10

Sophomores: 10

Meetings per week: 2

Hours per week: 5.5

Bioinformatics work: Annotation of two genomes from DOGEMS analyses Wet lab experiments also include: 1)PCR to determine which phages correspond to specific contigs in DOGEMS samples 2) preparation of lysogens using phages from in situ phage hunting course last semester 3) immunity testing of phages on newly made lysogens and other lysogens

BioS 118 Phage Genetics Lab

Primary Instructor: Vassie Ware

Additional Instructor: Vassie Ware

Type: Other

Hosts used: Streptomyces griseus

Number of students: 26

Sophomores: 26

Meetings per week: 2

Hours per week: 6.0

BioS 118-10

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: In silico (phage genomics/bioinformatics)

Hosts used: Mycobacterium smegmatis, Rhodococcus erythropolis, Arthrobacter sp.

Number of students: 11

Sophomores: 11

Meetings per week: 2

Hours per week: 6.0

Note that the first semester of Lehigh's SEA-PHAGES course (in situ: phage hunting) is offered in the spring semester to first year students. The second course (annotation and independent research projects) is offered to sophomores (and others) who continue from the previous spring semester. No sequencing is expected for this section. Instead sequencing will be performed during the summer 2015 after the spring in situ semester. Number of in situ sections for Spring 2015 will be determined by January 2015.

BioS 318

Primary Instructor: Vassie Ware

Additional Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 12

Sophomores: 3

Juniors: 2

Seniors: 7

Meetings per week: 2

Hours per week: 10.0

BioS 318

Primary Instructor: Vassie Ware

Additional Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 9

Juniors: 3

Seniors: 6

Meetings per week: 3

Hours per week: 10.0

Students follow up with experiments from SEA-GENES, new in situ work in microbiology and molecular biology, annotation work for new phage genomes

BioS 318

Primary Instructor: Vassie Ware

Additional Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 12

Sophomores: 5

Juniors: 5

Seniors: 2

Meetings per week: 3

Hours per week: 10.0

BioS 318

Primary Instructor: Vassie Ware

Additional Instructor: Michael Kuchka

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 13

Sophomores: 2

Juniors: 4

Seniors: 7

Meetings per week: 2

Hours per week: 10.0

Independent phage research includes in situ work from SEA-GENES, SEA-PHAGES, and in silico work

BioS 318

Primary Instructor: Vassie Ware

Type: Other

Hosts used: No host information yet.

Number of students: 10

Sophomores: 4

Juniors: 6

phage discovery for some students, bioinformatics for others

BioS 318

Primary Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 8

Juniors: 5

Seniors: 3

Meetings per week: 2

Hours per week: 6.0

In situ and in silico work is pursued by students in this course.

BioS 318 Adv. Phage Genetics

Primary Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 9

Juniors: 8

Seniors: 1

Meetings per week: 3

Hours per week: 10.0

students take this course for a variable number of credits (1-3) depending on the nature of the experiments undertaken. This is a hybrid course with wet lab experimentation and advanced bioinformatics analyses as well.

BioS 318 Adv. Phage Genetics

Primary Instructor: Vassie Ware

Additional Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 16

Sophomores: 6

Juniors: 3

Seniors: 7

Meetings per week: 2

Hours per week: 10.0

This sections includes both bioinformatics and wet bench work, where students study contributions of specific genes to the lysogenic cycle of temperate phages and to immunity relationships between phages.

BioS 318 Advance Phage Genetic

Primary Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 10

Sophomores: 1

Juniors: 8

Seniors: 1

Meetings per week: 3

Hours per week: 10.0

also using host, Streptomyces griseus. Students carry out independent research projects, including genome annotation, immunity studies, phage genome mutagenesis, RNAseq analysis, phage hunting in new hosts, etc.

BioS 318: Advanced Phage Lab

Primary Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 12

Juniors: 11

Seniors: 1

Meetings per week: 3

Hours per week: 10.0

bioinformatics and in situ research

BioS 391-25 Independent Phage

Primary Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 5

Juniors: 4

Seniors: 1

Meetings per week: 2

Hours per week: 10.0

Collaborative and independent research on phage Butters to uncover functions of novel phage genes. No sequencing is expected for this section.

Bios 391-25: Independent Phage

Primary Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 10

Sophomores: 6

Juniors: 3

Seniors: 1

Meetings per week: 2

Hours per week: 10.0

Collaborative and independent research on mycobacteriophages Butters, Sneeze, and K cluster phages. Phage hunting for Rhodococcus phages.

BioS 396 Adv Phage Res Lab

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 11

Sophomores: 7

Seniors: 4

Meetings per week: 3

Hours per week: 10.0

BioS 396 Advanced Phage Lab

Primary Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 6

Juniors: 6

Meetings per week: 3

Hours per week: 10.0

Students undertake independent phage research based on work uncovered in the yearlong phage courses.

BioS 43

Primary Instructor: Margaret Kenna

Additional Instructor: Vassie Ware

Type: In situ (phage discovery/microbiology)

Hosts used: Mycobacterium smegmatis

Number of students: 18

Freshmen: 18

Meetings per week: 2

Hours per week: 3.0

BioS 43 Phage Hunting Lab

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: In situ (phage discovery/microbiology)

Hosts used: Mycobacterium smegmatis

Number of students: 16

Freshmen: 16

Meetings per week: 2

Hours per week: 6.0

BioS 43-010

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: In situ (phage discovery/microbiology)

Hosts used: Mycobacterium smegmatis

Number of students: 10

Freshmen: 10

Meetings per week: 2

Hours per week: 5.5

BioS 43-011

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: In situ (phage discovery/microbiology)

Hosts used: Mycobacterium smegmatis

Number of students: 9

Freshmen: 9

Meetings per week: 2

Hours per week: 5.5

BioS 43: Phage Hunting

Primary Instructor: Vassie Ware

Type: In situ (phage discovery/microbiology)

Hosts used: Mycobacterium smegmatis

Number of students: 11

Freshmen: 10

Sophomores: 1

Meetings per week: 2

Hours per week: 5.5

BIOS-043-060, 061-SP16-Phage H

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: In situ (phage discovery/microbiology)

Hosts used: Mycobacterium smegmatis

Number of students: 24

Freshmen: 23

Sophomores: 1

Meetings per week: 2

Hours per week: 6.0

BioS043

Primary Instructor: Vassie Ware

Type: In situ (phage discovery/microbiology)

Hosts used: Mycobacterium smegmatis

Number of students: 18

Freshmen: 18

Meetings per week: 2

Hours per week: 2.6

Bios043-61

Primary Instructor: Vassie Ware

Additional Instructor: Vassie Ware

Type: In situ (phage discovery/microbiology)

Hosts used: No host information yet.

Number of students: 11

Freshmen: 10

Seniors: 1

Meetings per week: 2

Hours per week: 6.0

BioS095

Primary Instructor: Vassie Ware

Type: In situ (phage discovery/microbiology)

Hosts used: Mycobacterium smegmatis

Number of students: 17

Freshmen: 17

Meetings per week: 2

Hours per week: 6.0

BioS118 Phage Genetics

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: In silico (phage genomics/bioinformatics)

Hosts used: Mycobacterium smegmatis

Number of students: 16

Sophomores: 16

Meetings per week: 2

Hours per week: 6.0

bios396Advanced phage research

Primary Instructor: Vassie Ware

Additional Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 7

Sophomores: 1

Juniors: 3

Seniors: 3

bios396Advanced phage research

Primary Instructor: Vassie Ware

Additional Instructor: Vassie Ware

Type: Other

Hosts used: Mycobacterium smegmatis

Number of students: 6

Juniors: 3

Seniors: 3

Phage Genetics BioS 118

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: In silico (phage genomics/bioinformatics)

Hosts used: Mycobacterium smegmatis

Number of students: 6

Sophomores: 6

Meetings per week: 2

Hours per week: 6.0

Two students in this section did not take the hunting portion so they will hunt in natoriense.

Phage Genetics Bios118

Primary Instructor: Vassie Ware

Type: In silico (phage genomics/bioinformatics)

Hosts used: Mycobacterium smegmatis

Number of students: 15

Sophomores: 15

Meetings per week: 2

Hours per week: 5.0

Phage Genetics Lab/BioS 118

Primary Instructor: Vassie Ware

Additional Instructor: Margaret Kenna

Type: In silico (phage genomics/bioinformatics)

Hosts used: Mycobacterium smegmatis

Number of students: 10

Sophomores: 10

Meetings per week: 2

Hours per week: 6.0

Lehigh does phage hunting in the spring semester. The spring phage hunting course substitutes for the first core laboratory course required in the biology curriculum, taken by freshmen. The fall semester course is dedicated to phage genomics and additional microbiology laboratory experiments. This course substitutes for the second required core lab course in the biology curriculum. Sophomores are typically enrolled in this course.