Advanced Research
Internship Program 2017
Published Reference Sequences
We have completed the Advanced Research Internship Program (ARIP) for 2017, in collaboration with the AGM Institute.
A core component of the ARIP program is that students have the opportunity to make a genuine contribution to an ongoing research program. In this case, it is the DISCO (Diversity Initiative for the Southern California Ocean) project, which aims to develop genetic barcode identification tools for the marine invertebrates of Southern California.
We are pleased to announce that every single ARIP 2017 student succeeded in taking at least one specimen from field collection, through lab processing, photography, molecular sequencing, and posting to the BOLD database. This table gives links to their publicly accessible research data:
| Specimen/Sequence at BOLD | Taxon | Interns responsible for data |
|---|---|---|
| BOLD ID ARIQ001-17 | Gastropoda | Bryant Hwang, David Choi |
| BOLD ID ARIQ002-17 | Idoteidae | Bryant Hwang, David Choi |
| BOLD ID ARIQ004-17 | Scalibregma californicum | Jasmine Noh, Grace Park |
| BOLD ID ARIQ005-17 | Polyplacophora | Audrey Yeh, Erica Kim |
| BOLD ID ARIQ006-17 | Platynereis bicanaliculata | Bryant Hwang, David Choi |
| BOLD ID ARIQ007-17 | Piromis harrisae | Grace Park |
| BOLD ID ARIQ008-17 | Gastropoda | Sooyun Jang |
| BOLD ID ARIQ009-17 | Watersipora subtorquata | Bryant Hwang, David Choi |
| BOLD ID ARIQ010-17 | Caprellidae | Jessica Yeh |
| BOLD ID ARIQ011-17 | Watersipora subtorquata | Alyssa Yeh, Ho Jung Chung |
| BOLD ID ARIQ012-17 | Gammaridae | Bryant Hwang, David Choi |
| BOLD ID ARIQ013-17 | Mysida | Jasmine Noh, Grace Park |
| BOLD ID ARIQ015-17 | Paracerceis | Erica Kim, Audry Yeh |
| BOLD ID ARIQ016-17 | Crepipatella lingulata | Sooyun Jang |
| BOLD ID ARIQ017-17 | Nereis | Audrey Yeh, Erica Kim |
| BOLD ID ARIQ018-17 | Caprellidae | In Su Park, Grace Na |
| BOLD ID ARIQ019-17 | Polyplacophora | Alyssa Yeh, Ho Jung Chung |
| BOLD ID ARIQ021-17 | Platynereis bicanaliculata | Jasmine Noh, Grace Park |
| BOLD ID ARIQ022-17 | Majidae | Sooyun Jang |
| BOLD ID ARIQ023-17 | Ophiuroidea | Isaac Y Lee |
| BOLD ID ARIQ024-17 | Nicolea | Audrey Yeh, Erica Kim |
| BOLD ID ARIQ025-17 | Sphaeromatidae | Alyssa Yeh, Ho Jung Chung |
| BOLD ID ARIQ026-17 | Caprellidae | Grace Na, In Su Park |
| BOLD ID ARIQ027-17 | Mysidae | Jessica Yeh |
| BOLD ID ARIQ028-17 | Nereis | Jessica Yeh |
| BOLD ID ARIQ029-17 | Decapoda | Ho Jung Chung |
| BOLD ID ARIQ030-17 | Watersipora subtorquata | Blake Han, Isaac Lee |
ARIP 2017 Syllabus
Program participants should refer to this web page (see below the syllabus) for information and assignments for the online week, beginning July 10, 2017.
We followed this syllabus, with occasional adaptations for immediate events. Note that this outline is subject to change as we adapt to program needs.
| WORK DAY |
DATE | L = lecture ACTIVITY |
|---|---|---|
| On-Line July 10–15 | Research reading | |
| 0 | Su 16 July | Arrivals in L.A. G: Welcome dinner and orientation |
| 1 | Mo 17 July | L: Introduction to the program (in Mark Ridley Thomas Center) T: Behind-the-scenes tour at Natural History Museum of L.A. County G: Using the scientific literature L: Animal diversity R: Begin sorting samples from seafloor grab |
| 2 | Tu 18 July | F: Collecting at King Harbor marina floating dock T: Seafood lunch and crustacea dissection R: Sample sorting, identification, and processing |
| 3 | We 19 July | R: DNA extraction from specimens (8am) T: Visit USC campus and admissions (11:45am – 1:15pm) T: California Science Center: space shuttle (2pm), ecosystems, IMAX movie (4pm) R: PCR prep tutorial |
| 4 | Th 20 July | R: DNA amplification of specimen extracts (8am at USC lab) G: Scientific communication; research presentation workshop G: Begin Materials & Methods written activity R: Sequencing gels (then PCR product sent out for sequencing) |
| 5 | Fr 21 July | T: Visit Malibu, Pepperdine University T: Santa Monica Mountains Recreation Area |
| 6 | Sa 22 July | T: Day trip to Catalina Island — USC Wrigley Marine Science Center |
| 7 | Su 23 July | R: DNA sequence processing L: Channel Islands; Chaparral; E/V Nautilus G: Writing good résumés and getting good letters of recommendation G: Research presentation discussion |
| 8 | Mo 24 July | T: Visit La Brea Tar Pits Museum T: Visit Farmers Market and The Grove |
| 9 | Tu 25 July | F: Intertidal collecting trip to San Pedro (sunrise 6a, tide -1.0 ft at 5:34) T: Beach time at Cabrillo Beach T: Visit Cabrillo Marine Aquarium (noon) G: Research presentation prep L: Trees and phylogeny T: Visit Butterfly Pavilion and visiting exhibit (Extreme Mammals) at NHMLA |
| 10 | We 26 July | R: Specimen data and specimen photo posting to Barcode of Life Database G: Research presentation prep |
| 11 | Th 27 July | R: Molecular sequence and tracefile posting to Barcode of Life Database G: Getting into U.S. colleges and college life G: Lunch in the lab G: Materials & Methods revisions |
| 12 | Fr 28 July |
10:00a – 11:00a Research talks (5) 11:30a – 12:30p Lunch 12:30a – 01:30p Research talks (5) 01:30p – 02:30p Break 02:30p – 03:15p Research talks (4) 04:00p Closing ceremony (in NHMLA MBC lab) 06:00p Farewell dinner |
| 13 | Sa 29 July | Departures |
Day 11 (Thursday) Documents
Talking Science, Speaking Powerpoint
Reference formatting guidance
Tracefile and sequence uploading
Day 10 (Wednesday) Documents
Sample ImageData.xls spreadsheet contents
Guidance on entering BOLD specimen data
Day 9 (Tuesday) Documents
Day 3 (Wednesday) Documents
Molecular replication lecture
Polymerase chain reaction (PCR) video I
Polymerase chain reaction (PCR) video II
Here is the paper on the molecular primers (the “Geller primers”) that you will use:
Geller, J., C. Meyer, M. Parker, and H. Hawk. 2013.
Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates
and application in all-taxa biotic surveys. Molecular Ecology Resources 13:851–861.
Day 2 (Tuesday) Documents
Day 1 (Monday) Documents
Introduction to ARIP
The DISCO program
Finding the scientific literature
(sample paper)
Animal diversity