Advanced Research
Internship Program 2019
ARIP 2019 Syllabus
This syllabus reflects the activities that interns participated in during ARIP 2019. See below the syllabus for links to the reference data posted by all the intern participants.
| WORK DAY |
DATE | L = lecture ACTIVITY |
|---|---|---|
| On-Line July 8–13 | Research reading | |
| 0 | Su 14 July |
Arrivals in L.A. G: Welcome dinner and orientation |
| 1 | Mo 15 July |
[9:00am] L: Introduction to the program T: Behind-the-scenes tour at Natural History Museum of L.A. County L: Molecular techniques, DNA, and PCR |
| 2 | Tu 16 July |
F: [At marina at 10am] Collecting at King Harbor Marina floating dock T: Crustacea dissection and seafood lunch R: Sample sorting, identification, photography, and tissue sampling |
| 3 | We 17 July |
[8am] R: DNA extraction from specimens G: Begin Materials & Methods written activity T: California Science Center: IMAX movie (12:00pm), Space Shuttle, Ecosystems T: Visit USC campus and admissions (3:15pm – 4:45pm) |
| 4 | Th 18 July |
[8am] R: DNA amplification of specimen extracts G: Continue Materials & Methods written activity G: Research presentation topic selection R: PCR product gels (then PCR product sent out for sequencing) [7pm] L: Zócalo Public Square Event at Natural History Museum |
| 5 | Fr 19 July |
[5:30am] F: Intertidal collecting trip to San Pedro (sunrise 5:56am, low tide -0.23 ft at 6:31am) T: Visit Marine Mammal Care Center T: Visit and picnic lunch at Korean Friendship Bell T: Visit Cabrillo Marine Aquarium |
| 6 | Sa 20 July |
T: Visit Malibu, Pepperdine University T: Santa Monica Mountains Recreation Area |
| 7 | Su 21 July |
[9am] R: DNA sequence processing G: Continue Materials & Methods written activity G: Research presentation discussion G: Scientific communication G: Research presentation prep T: Visit Butterfly Pavilion and exhibits at NHMLA |
| 8 | Mo 22 July |
[9:45am] F: Collection tours in other NHM sections
G: Materials & Methods section writing R: Specimen data and specimen photo posting to Barcode of Life Database |
| 9 | Tu 23 July |
[9:30am] T: Visit La Brea Tar Pits, Farmers Market, and The Grove T: Visit UCLA campus |
| 10 | We 24 July |
[9am] R: Molecular sequence and tracefile posting to Barcode of Life Database G: Research presentation rehearsal and critique G: Lunch in the lab G: Writing good résumés, getting good letters of recommendation, U.S. colleges G: Materials and Methods section wrapup |
| 11 | Th 25 July | [7:30am] T: Day trip to Catalina Island — USC Wrigley Marine Science Center |
| 12 | Fr 26 July | [9am] Organize for Research Presentations 10:00am – 11:15am Research presentations 11:15am – 12:30pm Lunch 12:30am – 01:45pm Research presentations 04:00pm Closing ceremony 06:00pm Farewell dinner |
| 13 | Sa 27 July | Departures |
Reference Barcode Sequences
All interns this year succeeded in generating at least one reference barcode sequence, registered at the international genetic barcode reference library Barcode of Life Database (BOLD).
The links here lead to the full reference records, including specimen information, photographs, sequences, and sequencing tracefiles.
NOTE: because it takes BOLD a few weeks to make “public” records public, the links below may not work until sometime in August 2019.
| ARIP Intern | BOLD Reference Barcode Record | Illustrative Barcode | Preliminary Identification |
|---|---|---|---|
| Hyojin Lee | ARIS001-19 |  | Caprella |
| Hyojin Lee | ARIS004-19 |  | Platynereis bicanaliculata |
| Chang Jun Son | ARIS009-19 |  | Caprellidae |
| Joshua Suo | ARIS011-19 |  | Caprellidae |
| Seung Hyuk Kim | ARIS003-19 |  | Caprellidae |
| Paul Kim | ARIS010-19 |  | Halosydna brevisetosa |
| Esther Cho | ARIS007-19 |  | Pachygrapsus crassipes |
| Leah Vozzi | ARIS002-19 |  | Amphipoda |
| Jun-Sang Park | ARIS005-19 |  | Idoteidae |
| Harry Cha | ARIS008-19 |  | Nereis pelagica |
| Eun Sang Park | ARIS006-19 |  | Amphipoda |
Sequencing tracefiles
Here are all the sequencing tracefiles, listed by Molecular ID:
6326_16Sar.ab1
6326_16Sbr.ab1
6327_16Sar.ab1
6327_16Sbr.ab1
6335_16Sar.ab1
6335_16Sbr.ab1
6338_16Sar.ab1
6338_16Sbr.ab1
6340_16Sar.ab1
6340_16Sbr.ab1
6344_16Sar.ab1
6344_16Sbr.ab1
6347_16Sar.ab1
6347_16Sbr.ab1
6350_16Sar.ab1
6350_16Sbr.ab1
6353_16Sar.ab1
6353_16Sbr.ab1
6356_16Sar.ab1
6356_16Sbr.ab1
6357_16Sar.ab1
6357_16Sbr.ab1
8183_jgHCO.ab1
8183_jgLCO.ab1
8184_jgHCO.ab1
8184_jgLCO.ab1
8186_jgHCO.ab1
8186_jgLCO.ab1
8187_jgHCO.ab1
8187_jgLCO.ab1
8189_jgHCO.ab1
8189_jgLCO.ab1
8196_jgHCO.ab1
8196_jgLCO.ab1
8197_jgHCO.ab1
8197_jgLCO.ab1
8198_jgHCO.ab1
8198_jgLCO.ab1
8200_jgHCO.ab1
8200_jgLCO.ab1
8202_jgHCO.ab1
8202_jgLCO.ab1
8203_jgHCO.ab1
8203_jgLCO.ab1
8205_jgHCO.ab1
8205_jgLCO.ab1
8206_jgHCO.ab1
8206_jgLCO.ab1
8207_jgHCO.ab1
8207_jgLCO.ab1
8208_jgHCO.ab1
8208_jgLCO.ab1
8210_jgHCO.ab1
8210_jgLCO.ab1
8211_jgHCO.ab1
8211_jgLCO.ab1
8212_jgHCO.ab1
8212_jgLCO.ab1
8213_jgHCO.ab1
8213_jgLCO.ab1
8214_jgHCO.ab1
8214_jgLCO.ab1
8215_jgHCO.ab1
8215_jgLCO.ab1
8216_jgHCO.ab1
8216_jgLCO.ab1
8218_jgHCO.ab1
8218_jgLCO.ab1
8222_jgHCO.ab1
8222_jgLCO.ab1
8224_jgHCO.ab1
8224_jgLCO.ab1
8225_jgHCO.ab1
8225_jgLCO.ab1
8226_jgHCO.ab1
8226_jgLCO.ab1
8227_jgHCO.ab1
8227_jgLCO.ab1
8228_jgHCO.ab1
8228_jgLCO.ab1
Specimen and extract IDs
| Collection ID | Specimen ID | BOLD Museum ID | Molecular ID | Description |
|---|---|---|---|---|
| 20192 | 12905 | LACM:DISCO:12905 | 8175 | JC — Phillipines — gnathiid |
| 20192 | 12906 | LACM:DISCO:12906 | 8176 | JC — Phillipines — gnathiid |
| 20192 | 12907 | LACM:DISCO:12907 | 8177 | JC — Phillipines — gnathiid |
| 20192 | 12908 | LACM:DISCO:12908 | 8178 | JC — Phillipines — gnathiid |
| 20192 | 12909 | LACM:DISCO:12909 | 8179 | JC — Phillipines — gnathiid |
| 20192 | 12910 | LACM:DISCO:12910 | 8180 | JC — Phillipines — gnathiid |
| 12900 | LACM:DISCO:12900 | 8181 | Paul Kim — blue crab | |
| 12900 | LACM:DISCO:12900 | 8182 | Joshua Suo — blue crab | |
| 12902 | LACM:DISCO:12902 | 8183 | Hyojin Lee — greenlip mussel | |
| 12902 | LACM:DISCO:12902 | 8184 | Leah Vozzi — greenlip mussel | |
| 12902 | LACM:DISCO:12902 | 8185 | Patrick Park — greenlip mussel | |
| 12902 | LACM:DISCO:12902 | 8186 | William Park — greenlip mussel | |
| 12902 | LACM:DISCO:12902 | 8187 | Victoria Westover — greenlip mussel | |
| 12903 | LACM:DISCO:12903 | 8188 | Harry Cha — little neck clam | |
| 12903 | LACM:DISCO:12903 | 8189 | Charles Son — little neck clam | |
| 12903 | LACM:DISCO:12903 | 8190 | Ania Webb — little neck clam | |
| 12904 | LACM:DISCO:12904 | 8191 | John Kim — manila clam | |
| 12904 | LACM:DISCO:12904 | 8192 | Ester Cho — manila clam | |
| 21105 | ? | 8193 | Joshua — spirorbid | |
| 21105 | 12912 | LACM:DISCO:12912 | 8194 | Joshua — caprellid |
| 21105 | 12980 | LACM:DISCO:12980 | 8195 | Joshua — polychaete |
| 21105 | 12933 | LACM:DISCO:12933 | 8196 | Charles — spirorbid |
| 21105 | 12917 | LACM:DISCO:12917 | 8197 | Charles — caprellid |
| 21105 | 12984 | LACM:DISCO:12984 | 8198 | Charles — nereid |
| 21105 | 12918 | LACM:DISCO:12918 | 8199 | Harry — caprellid |
| 21105 | 12934 | LACM:DISCO:12934 | 8200 | Harry — spirorbid |
| 21105 | 12986 | LACM:DISCO:12986 | 8201 | Harry — polychaete |
| 21105 | 12932 | LACM:DISCO:12932 | 8202 | John — spirorbid |
| 21105 | 12913 | LACM:DISCO:12913 | 8203 | John — caprellid |
| 21105 | 12982 | LACM:DISCO:12982 | 8204 | John — amphipod |
| 21105 | 12914 | LACM:DISCO:12914 | 8205 | Paul — caprellid |
| 21105 | 12926 | LACM:DISCO:12926 | 8206 | Paul — scale worm |
| 21105 | 12937 | LACM:DISCO:12937 | 8207 | Paul — spirorbid |
| 21105 | 12974 | LACM:DISCO:12974 | 8208 | Esther — spirorbid |
| 21105 | 12920 | LACM:DISCO:12920 | 8209 | Esther — caprellid |
| 21105 | 12927 | LACM:DISCO:12927 | 8210 | Esther — crab |
| 21105 | 12911 | LACM:DISCO:12911 | 8211 | Hyojin — caprellid |
| 21105 | 12930 | LACM:DISCO:12930 | 8212 | Hyojin — spirorbid |
| 21105 | 12976 | LACM:DISCO:12976 | 8213 | Hyojin — polychaete |
| 21105 | 12919 | LACM:DISCO:12919 | 8214 | Leah — caprellid |
| 21105 | 12925 | LACM:DISCO:12925 | 8215 | Leah — spirorbid |
| 21105 | 12935 | LACM:DISCO:12935 | 8216 | Leah — amphipod |
| 21105 | 12915 | LACM:DISCO:12915 | 8217 | Patrick — caprellid |
| 21105 | 12931 | LACM:DISCO:12931 | 8218 | Patrick — spirorbid |
| 21105 | 12938 | LACM:DISCO:12938 | 8219 | Patrick — nemertean |
| 21105 | 12916 | LACM:DISCO:12916 | 8220 | William — caprellid |
| 21105 | 12929 | LACM:DISCO:12929 | 8221 | William — spirorbid |
| 21105 | 12978 | LACM:DISCO:12978 | 8222 | William — idoteid |
| 21105 | 12922 | LACM:DISCO:12922 | 8223 | Victoria — caprellid |
| 21105 | 12923 | LACM:DISCO:12923 | 8224 | Victoria — spirorbid |
| 21105 | 12988 | LACM:DISCO:12988 | 8225 | Victoria — brittle star |
| 21105 | 12921 | LACM:DISCO:12921 | 8226 | Ania — caprellid |
| 21105 | 12924 | LACM:DISCO:12924 | 8227 | Ania — spirorbid |
| 21105 | 12990 | LACM:DISCO:12990 | 8228 | Ania — amphipod |
Specimen images
Here are the images we took of each specimen, listed by Specimen ID number. There may be one or more images for each specimen. If there is a missing Specimen ID number, it means that we missed taking any images of that specimen (which is not a problem). Click on the Specimen ID to get a listing of the images for that specimen, and download them directly from your browser.
12911 12912 12913 12914 12915 12916 12917 12918 12919 12920 12921 12922 12923 12924 12925 12926 12927 12928 12929 12930 12931 12932 12933 12934 12935 12937 12974 12976 12978 12980 12982 12984 12986 12988 12990
Download this spreadsheet and enter your image data into it to accompany your images as you upload them to BOLD: ImageData.xls
Collection information
| Collection ID | BOLD Collection Event ID | Collection information |
|---|---|---|
| 21105 | DISCO-CollectionID:21105 | Eastern Pacific, USA, California, Los Angeles County, Redondo Beach, King Harbor, in front of Quality Seafood, 33.842°N 118.391°W, dock fouling, hand, paint scraper, fixed and preserved in 95% ethanol, 16 Jul 2019, Coll. R. Wetzer, N.D. Pentcheff, A. Wall, J. Carrillo, A. Webb, V. Westover, ARIP 2019, Collection ID: 21105 |
Mon 15 July lectures
PDF versions of the two talks on Monday:
Food Security & DNA
Trees & Animal Diversity
First Week Online Activities
During this first, online week of the ARIP program, we have two goals. One is to familiarize you with reading real research papers: the scientific literature. The other goal is to familiarize you with some of the genetic biodiversity concepts you’ll be working with during the on-site two weeks of the internship.
Understanding the content of these papers is very important for doing well in the internship. You will be expected to know these concepts and be able to work with them once you are here. We know they are complex ideas, and we know that learning them directly from the actual research literature (not popular articles) is difficult. But that’s why you are participating in this internship. You will work hard. In return, we will work hard to give you all the help and information you need to do well — that is why we are participating.
The way this will work is that there will be a series of daily reading assignments. Each day you will be required to complete a brief quiz about the reading for that day. That quiz will be available for only 24 hours — you must check in here and complete the quiz sometime during the 24 hour window for that day’s reading.
To be completely open with you: the purpose of those quizzes is not to grade or rank your performance, but to ensure that you do some of the reading each day. If you could leave it all to one session at the end, there is no way you could get good comprehension!
The materials are available to you now (see links lower on this page), so feel free to read ahead! But, again, you will have to return to this web page each day to complete each day’s questions on the assigned day.
What if I have questions about the material or the assignment?
Feel free to send email with questions to me (Dean Pentcheff). I’m managing the online
portion of the course (I’ll also be participating in leading the on-site part). You
can reach me at: pentcheff@nhm.org .
What if I will be unavailable or travelling on one or more of the assignment days?
Send me an email (to pentcheff@nhm.org)
and I’ll get the day’s questions to you by email so that you can
complete them on a different day.
What time of day will the day’s questions become available (and when will they disappear)?
Each day’s questions will become available at 00:01 (one minute into the day) on the
day of the assignment, and will close at 23:59 (one minute before midnight) on the
day of the assignment. All dates and times will be in Pacific Daylight Time (PDT UTC-7).
Online Day 1 (Monday) July 8 — Reading a scientific paper
We‘re starting easily. Today there are two online articles we‘d like you to read that will help you learn how to (constructively) read a scientific paper.
Reading 1: How to read a scientific paper
Reading 2: How to read and understand a scientific paper: a guide for non-scientists
Read both of these to prepare yourself for reading the scientific papers over the next few days. These guides refer to two kinds of scientific papers: primary research papers and review papers. Most of the papers we‘ll have you read are review papers — they summarize the work reported in many other papers. Because of that, they will not be broken into the structure of a typical primary research paper (Introduction, Materials and Methods, Results, and Discussion). However, the analysis you will need to do as you read (for example, looking up every single word you don‘t understand as you read) is the same for primary and review papers.
This quiz is now closed.
So that everyone can catch up, we will leave this first day’s quiz open for two days.
Online Day 2 (Tuesday) July 9 — Genetic barcoding
“Genetic barcoding” is a technique being applied to biodiversity research, and is a core technology you will use and learn in this internship. These two papers give a bit of perspective on the technique. The first was written over a decade ago as barcoding was just being developed. The second looks back over the decade of development and summarizes how the field has grown.
This quiz is now closed.
Online Day 3 (Wednesday) July 10 — Metabarcoding entire communities
One of the really exiting ways we can use genetic barcodes is to describe entire marine communities based just on seawater samples (by sequencing and identifying the DNA that organisms shed into the seawater). This paper is a recent example of that kind of work. (Note that this is a primary research paper, a report of novel work, unlike the rest of the papers we are having you read, which are review papers.)
This quiz is now closed.
I apologize for messing up the availability of the Day 3 quiz! That was entirely a technical error on my part, and was not your fault at all. To make sure you get a chance to answer the questions, I will leave this quiz open all day on Thursday (as well as Thursday’s quiz). Again — I apologize for the mistake! [Dean Pentcheff]
Online Day 4 (Thursday) July 11 — Barcoding and biomonitoring
A key application of barcoding, particularly of entire communities, is the potential it has for letting us monitor biological changes more frequently, more cheaply, and in more detail than traditional techniques.
This quiz is now closed.
Online Day 5 (Friday) July 12 — DNA extraction and taxonomy
For the first reading, we are jumping directly into some of the work you will do in the internship. In a theoretical way, you have read about DNA extractions for making genetic reference barcode sequences. A key step along the way is extraction and purification of DNA from your organism of choice. This first paper is the extraction protocol that you will be following in the lab. It is the protocol for using the popular “DNeasy Blood & Tissue” extraction kit. You will actually be carrying out this procedure, so read this carefully. You remember the Day 1 readings on how to read a scientific paper? Treat this like the Materials & Methods section of a research paper: look up the meaning of words you don’t understand; draw yourself diagrams of what actions are being described.
The science of taxonomy is the discipline of classifying organisms into some sort of understandable system. It has taken us a couple of centuries to name and describe about one million species. We think there are something like 10–100 million species on earth. Clearly, we have a lot of work to do. The second of these papers gives a little perspective on how genetic barcoding may help us — part of the reason we have initiated our whole research program here at the Natural History Museum.
Reading 1: Qiagen Corporation. 2006. DNeasy Blood and Tissue Handbook. Pp 28–30.
This quiz is now closed.
Thanks for participating in the online week! We will see you soon in Los Angeles.