ARIP 2017

Page Contents

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 BOLDTaxonInterns responsible for data
BOLD ID ARIQ001-17GastropodaBryant Hwang, David Choi
BOLD ID ARIQ002-17IdoteidaeBryant Hwang, David Choi
BOLD ID ARIQ004-17Scalibregma californicumJasmine Noh, Grace Park
BOLD ID ARIQ005-17PolyplacophoraAudrey Yeh, Erica Kim
BOLD ID ARIQ006-17Platynereis bicanaliculataBryant Hwang, David Choi
BOLD ID ARIQ007-17Piromis harrisaeGrace Park
BOLD ID ARIQ008-17GastropodaSooyun Jang
BOLD ID ARIQ009-17Watersipora subtorquataBryant Hwang, David Choi
BOLD ID ARIQ010-17CaprellidaeJessica Yeh
BOLD ID ARIQ011-17Watersipora subtorquataAlyssa Yeh, Ho Jung Chung
BOLD ID ARIQ012-17GammaridaeBryant Hwang, David Choi
BOLD ID ARIQ013-17MysidaJasmine Noh, Grace Park
BOLD ID ARIQ015-17ParacerceisErica Kim, Audry Yeh
BOLD ID ARIQ016-17Crepipatella lingulataSooyun Jang
BOLD ID ARIQ017-17NereisAudrey Yeh, Erica Kim
BOLD ID ARIQ018-17CaprellidaeIn Su Park, Grace Na
BOLD ID ARIQ019-17PolyplacophoraAlyssa Yeh, Ho Jung Chung
BOLD ID ARIQ021-17Platynereis bicanaliculataJasmine Noh, Grace Park
BOLD ID ARIQ022-17MajidaeSooyun Jang
BOLD ID ARIQ023-17OphiuroideaIsaac Y Lee
BOLD ID ARIQ024-17NicoleaAudrey Yeh, Erica Kim
BOLD ID ARIQ025-17SphaeromatidaeAlyssa Yeh, Ho Jung Chung
BOLD ID ARIQ026-17CaprellidaeGrace Na, In Su Park
BOLD ID ARIQ027-17MysidaeJessica Yeh
BOLD ID ARIQ028-17NereisJessica Yeh
BOLD ID ARIQ029-17DecapodaHo Jung Chung
BOLD ID ARIQ030-17Watersipora subtorquataBlake 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.


L = lecture
G = group discussion/activity
F = field collecting
T = tour/trip
R = research lab 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

Trees and phylogeny lecture

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

DNA extraction protocol

Day 1 (Monday) Documents

Introduction to ARIP
The DISCO program
Finding the scientific literature (sample paper)
Animal diversity