The Alaska Frozen Tissue Collection:

A Resource for Marine Biotechnology, Phase II

Principal Investigators:

Joseph A. Cook, Idaho State University

Gordon H. Jarrell, University of Alaska Fairbanks

Final Report

November 2002

OCS Study MMS 2002-027
This study was funded in part by the U.S. Department of the Interior, Minerals Management Service

(MMS), through Cooperative Agreement No. 1435-01-98-CA-30909, Task Order No. 15164, between

the MMS, Alaska Outer Continental Shelf Region, and the University of Alaska Fairbanks.

The opinions, findings, conclusions, or recommendations expressed in this report or product are those

of the authors and do not necessarily reflect the views of the Minerals Management Service, nor does

mention of trade names of commercial products constitute endorsement or recommendation for use

by the Federal Government.
1Depament of Biological Sciences

Idaho State University

Pocatello, ID 83209-8007

2University of Alaska Museum

University of Alaska Fairbanks

Fairbanks, AK 99775-6960

E-mail: cookjose@isu.edu

fnghj©uaf.edu

November2002
Some relevant UIRLs 13

Objective 3 20

Conclusions 21

Study Products 22

Reference 23

H
Figure 9. Individual specimen record 19

Figure 10. Funding and the development of AFTC 20

111
for three years before that), CMI has sustained the development of a unique addition to

the scientific infrastructure in Alaska. The AFTC provides a mechanism with established

protocols for sharing and preserving data from faunal investigations of the marine

environment. Essentially, the AFTC serves as an archive, storing and providing access

to zoological samples that would otherwise be difficult, expensive, and often impossible

to reacquire. We hope to show here that CMII, in supporting the AFTC, has catalyzed an

exemplary development. We will explain what the Collection is and why we believe that it

is important. We will describe the objectives of CMII support, and how we have succeeded

in meeting those objectives. In &ldition, we will describe how these activities have catalyzed

the development of a new, encompassing entitythe Arctic Archival Observatory (AAO).

What is the AFTC?

The Alaska Frozen Tissue Collection is an archive for biological samples housed at the

University of Alaska Museum (hAM) in Fairbanks. Physically, the Collection is comprised

of three ultra-cold chest freezers operated at 70° C. Each freezer is equipped with racks and

slotted boxes to hold approximately 60,000 samples, most of which are in 2-mL cryo-tubes.

The freezers connect to an alarm system monitored by the University's Safety Services

Department at all times. They also connect to a compressed carbon dioxide back-up system

that vents into the freezers in case of a continuing temperature rise.

1
Samples archived now contain data about present conditions and these

data can be rendered in the future.

New tools for rendering ecological, genetic, and pathological data from

small amounts of biological material are developing rapidly. (Stable

isotope ecology and DNA sequencing are prominent examples.)

Freezing biological materials preserves the broadest possible suite of

biochemical characteristics and thereby gives the greatest flexibility to

future investigators.

Samples collected for short-term goals should be sub-sampled and

archived for the long-term goal of monitoring change, and many such

samples from recent projects are invaluable when retrievable now.

High trophic level organisms are particularly sensitive bio-indicators

and are worth sampling now for potential use later.

2
world class. The counts in Table 1 do not include several substantial accessions awaiting data

entry and several accessions intended for UAM that are still in the hands of management

agencies.

Formal agreements for specimen deposition were reached with two Alaska Native marine

mammal co-management commissions: the Alaska Native Harbor Seal Commission

(ANIISC), and the Alaska Sea Otter and Steller Sea Lion Commission. Both organizations

were established under the Native co-management mandate of the Marine Mammal

Protection Act (MMPA), and give Native subsistence hunters substantial control over

scientific sampling and the disposition of scientific samples. Both commissions have agreed

to deposit samples collected by their members in the AFTC. No formal agreement exists with

the Alaska Eskimo Whaling Commission, but the Department of Wildlife Management at the

North Slope Borough regularly contributes samples from harvested bowhead whales and

many other marine mammals. Such long-term arrangements will steadily build chronological

samples relevant to environmental change and to parameters that may vary naturally over

time. The AFTC is eager to accommodate samples from resource management agencies,

either on a case-by-case basis for individual projects, or in broader, more formal, cooperative

agreements.

3
Half of the species in Table 1 are clearly dependent on polar pack ice and are likely already

affected by climate change. Two other species, Steller sea lions and harbor seals, are thought

to have declined precipitously in recent decades.

4

Spotted seal 64 639

Ringed seal 160 2807

Ribbon seal 33 308

Bearded seal 20 1392

Walrus 611 1199

Northern fur seal 13 31

Stetler sea lion 79 142

Polar bear 178 481

Sea otter 503 1334

Total 2429 9761
signatures in Pacific coast pinnipeds over the past 3000 years. It has also

ascertained that a large proportion of the pinniped bones recovered from

Paleo-Indian middens have been misidentified by archeologists.

Sylvia Brunner, working with Peter Shaughnessy and Michael Bryden

at the University of Sydney, spent one month in August and September

1998 measuring all otariid seal skulls in the collection for a taxonomic

revision of sea lions and fur seals. Dr. Brunner's project involved an

18-month tour to many of the world's major collections of marine

mammals.

Tyson Sacco, a doctoral student from UCLA, visited the collection for

two weeks to measure 303 bear skulls, including 73 polar bears, for his

dissertation project, "Ecomorphology and Evolutionaiy Biology of the

Ursidae".

Some of the earliest specimens to be catalogued into the AFTC are blood

samples from Antarctic Weddell seals collected in 1991. Donald Siniff

of the University of Minnesota requested four of these in May 1999 for

paternity analyses (at Curtis Strobeck's lab, University of Alberta) in

order to complete a pedigree of the White Island population and test

5
Tissue samples from a walius and a harbor porpoise were also sent to

Klaus Koepfli. The samples will be used to characterize the molecular

evolution of a gene in the pathway that synthesizes cellular cholesterol.

Educational donations of a belukha skull were made to Kate Wynne of

the UAF Marine Advisory Program at Kodiak and of a sea otter skull to

Kay Furman of the Staatliches Museum fir Naturkunde, Oldenburg,

Germany. A polar bear skull was loaned to Brendan Kelly (University

of Alaska Southeast) for a student project on bear craniology.

Samples of two abnormal harbor seals, submitted by subsistence hunters,

were sent to Kathy Burek, a veterinary pathologist in Eagle River, Alaska.

One was diagnosed as having complications resulting from lung worm

infestation. The other appeared to have a liver parasite, but the organism

could not be identified.

Edward Miller from the Memorial University of Newfoundland spent ten

days at the Museum working with bacula from sea otters and seals. He

took measurements of 287 specimens.

6
p. 291304. In A.E. Dizon, S.J. Chivers and W.F. Perrin [eds.], Molecular Genetics of

Marine Mamma!s. Special Publication 3 by the Society for Marine Mammalogy.

Sche!l, D.M. 2000. Declining carrying capacity in the Bering Sea: Isotopic evidence from

whale baleen. Limnol. Oceanogr. 45:459-462.

Sche!l, D.M. 2001. Carbon isotope ratio variations in Bering Sea biota: The ro!e of

anthropogenic carbon dioxide. Lmmol. Oceanogr. 46:999-1000.

Schell, D.M., V.J. Rowntree and C.J. Pfeiffer. 2000. Stable-isotope and electronmicroscopic evidence that cyamids (Crustacea: Amphipoda) feed on whale skin. Can. J.

Zoo!. 78:721-727.

Shields, G.F., D. Adams, G. Gamer, M. Lae!!e, J. Pietsch, M. Ramsay, C. Schwartz, K. Titus

and S. Wi!liamson. 2000. Phy!ogeography of mitochondria! DNA variation in brown

bears and po!ar bears. Mo!. Phy!ogenet. Evol. 15:319-326.

7
I 1991 1992 1993 1994 1995

Figure 1. Total number of mammal specimens loaned to researchers by UAM.

b.) Develop additional backup systems for the freezers and an automated object-tracking

system.

The AFTC freezers have alarms set to go off in the event of a 100 rise in cabinet temperature.

They are hooked into a common system that sounds locally and is also connected to the

University's Silent Night® remote system. Thus, alarms are monitored by the university

Safety Services Department dispatcher's desk at all times. In addition to the alarms, the

freezers are manifolded to three 50-pound tanks of compressed carbon dioxide. Regulators on

the freezer cabinets are set to vent the compressed gas in the event of a 150 temperature rise.

Object tracking, through a system of barcoded specimens and containers, has been

implemented in the data model, but only barcoding of containers is in full practice. There

8

1996 1997 1998 1999 2000 2001

AAO
Business Logic Server (BLS)

(Versata on Solaris and NT)

A

Figure 2. Three-tiered architecture.

The significance of the three-tiered system is its platform independence and modularity. For

example, although (for reasons of institutional licensing) Berkeley's MVZ is using Sybase,

9

(PERL scripts)

Tier 2

Tier 1

Versata Development Studio

& Development BLS (NT)

Relational (SQL) Data

(Oracle on Solans)
specimens. An environmental sample might be almost anything removed from the

environment and archived for further studyfor example, a frozen benthic core, the

preserved result of an oceanographic irawl, a sample of invertebrates sorted or identified

only as far a higher taxonomic category, etc. Like museum specimens, enviromnental

samples have the attributes of our data model such as a "Collecting event", involvement

in transactions, and physical storage locations. They differ from conventional museum

specimens in that they lack precise taxonomic attributes, or they lack all taxonomic attributes.

Therefore, ignoring taxonomy and increasing the allowable vocabulary in other descriptive

fields can allow their inclusion in a museum data model.

We believe that this will be a major extension of the system's utility for environmental

researchers. For example, a benthic ecologist looking for specimens or records of a particular

polychaete worm could first search the Museum's collection of marine invertebrates by

taxonomy and learn what is known based on the collection. Dissatisfied with this information

and believing the species may occur in, say, Shelikof Strait, he or she could then go to the

data interface for environmental samples and search for benthic-grab samples taken at

appropriate depths in Shelikof Strait. Having located appropriate samples, the ecologist

can request and analyze them, rather than chartering a ship or speculating vaguely in the

literature.

10
or data repositories, can be engaged by mechanisms similar to our

connection to GenBank when they put adequately standardized data

into online databases.

An important feature of the database structure is the incorporation of "PROJECTS" (Figure 3).

Projects that contribute specimens (such as the Alaska Native Harbor Seal Commission),

projects that use specimens, and projects that do both can be related to each other through

data on specimen sources ("ACCESSIONS") and specimen usage ("LOANS", which includes

subsampling for destructive analysis). We have now implemented most of this structure but

we have not yet incorporated data on loans, nor have we systematically associated accessions

with projects. This will be straightforward once we have developed our internal interface for

managing loans. Nevertheless, there is now a web interface that displays the available project

data, including the ANHSC.

11
ppyg g

Survey topographic maps for Alaska and aerial photographs, where these are available.

Given such high-resolution mapping capacity, the precision of geographic coordinates will

become an obvious issue. The Arctos database accommodates an estimate of maximum

error and multiple determinations of latitude and longitude for a single locality. We are

currently retroactively determining maximum error (precision), and providing additional

determinations where more precision or corrections are justified. NSF is funding our

geo-referencing effort under a grant through MVZ to 17 North American mammal

collections. All 17 collections will then share a common interface. Web clients will be

able to search the AFTC's holdings in conjunction with essentially all of the computerized

North American holdings of mammal tissues.

With the MVZ, we are attempting the most comprehensive, powerful system ever

implemented within the arena of scientific museum collections. The University of Alaska

Museum, in large part because of CMI support for the AFTC, has been able to demonstrate

the utility of such a system to the National Science Foundation. We have been fortunate: a

smaller museum could not attract the resources; the largest museums have too much inertia to

innovate. Also, we have attracted a committed group of students and information technology

(IT) professionals, happy to be developing global scientific infrastructure, not merely

expanding the Internet's role as worldwide Yellow Pages.

12
13
Figure 4. Initial project query screen. From here, web users can search on projects which

have used Museum specimens, including tissue samples.

14

AAO home I UAM home

The University of Aiaska Museum at the Uriiv&sity of Aska Fairbanks, Fairbanks, AK

1YOA 99775-6960

Syct DaJ& CP.1t.

r - -
Figure 5. Project list. A list of projects meeting the parameters specified in the project query

screen, in this case all projects containing the character string "pinniped" in the

title. Clicking on "View Project" takes the user to a description of the project.

15

- Nliew Project

Stable-isotope analysis of changing pinniped distributions in

California.

JRobertK.Burtan,PauIL.Koch Dates: 07-AUG-97 - 17-FEB-99

- Docer Lone
commonly represented in Coastanoan rniddens from 300

to 8000 years BP. It appears that the breeding behavior,

presence of breeding colonies, and competition between

similar pinniped species have all changed considerably

over the last several hundred to several thousand years.

We have sampled a number of specimens from

collections at the California Academy of Sciences, as

well as San Jose State University, the Moss Landing

MarineLabs. andthe University of California at Santa. - Done

Figure 6. Project description. Individual projects are described in an abstract and the user has

the option of viewing specimen lists related to the project, or of viewing projects

that contributed specimens, or used specimens contributed by the present project

(if any). This screen executes the circuit diagramed in Figure 2.

16
imier Done

Figure 7. Specimen query screen. From this screen, the user can generate a list of specimens

meeting a variety of taxonomic and geographic parameters.

17

C.ntixejit/Oceaii TEl

Island

Icland Group Iean Islands

garth 1 Near Form
ext 10

Benanewseerch I ProjectsSeerch I SpecinienSeerch Previous Page

orerl Done

Figure 8. Initial query result. The user sees a list of specimens retrieved by the specified

search parameters. From here the user can choose a) a more detailed specimen

matrix, b) to download the result as a text file to import into the user's system.,

c) to view the resulting localities on the Xerox Corporation's map server (if there

are fifty or less specimen records), d) to view the Museum's specimen usage

protocols, or e) to view an individual specimen record.

18

UAM 507740 (Eumetopiasjubatus (United States (Alaska (Pribilof Islands

AM 507741 Eumetopiasjubatus lUthtedStates (Alaska (Peibiof Islands
AAO home I UAM home

The University of Alaska Museum at the University of Alaska Fairbanks. Fairbanks, AK

*M1rI AA& 99775-6960.

FAIRBANKS ca'&ea

.siiert Done

Figure 9. Individual specimen record. At this level, virtually all of the Museum's information

about a specimen is displayed. This belukha whale from Cook Inlet has an

identifying number with the Alaska Marine Mammal Tissue Archival Project.

19
95 96 97 98 99 00 01 02 03 04 05

CMI-funded

AFTC coordinator

(half-time grad assistant)

CMI-funded

AFTC subsistence

coordinator

(half-time grad assistant)

Figure 10. Funding and the development of AFTC.

20

State1unded

coordinator of AFTC

(full-time staff)

State-funding
more comprehensive, general resource.

The product of this project is thus a firmly institutionalized resource for the preservation and

distribution of environmental samples. The AFTC has grown from a single freezer in the

Museum's Mammal Collection, into a separate Museum department with its own full-time,

state-funded coordinator. It is now one of the largest collections of its type in the world. The

supporting information technology has evolved from a few data tables operated on locally

networked personal computers into a state-of-the-art, enterprise system operated on the world

wide web. The AFTC has become the primary regional archive for frozen biological samples

as a direct result of CMI's interest in promoting "projects which design or establish

mechanisms or protocols for the sharing of data..." (Technical Framework Issue 4).

21
Proceedings Seventh MMS Information Transfer Meeting. Alaska OCS Region, Minerals

Management Service, January 1999, Anchorage.

(The 5 April 1999 edition of the Fairbanks News-Miner featured Gordon Jarrell on the front

page with an extensive description of management and use of scientific collections

including the AFTC. The article was subsequently carried in the Ketchikan Daily News.)

Jarrell, G.H. 1999. Contributing to the Alaska Frozen Tissue Collection. Alaska Sea Otter

and Steller Sea Lion Commission, November 1999, Anchorage.

Jarrell, G.H. 1999. The Alaska Frozen Tissue Collection: A resource for biotechnology.

MMS Beaufort Information Update, Barrow.

Jarrell, G.H. 2000. The Alaska Frozen Tissue Collection: A resource for biotechnology.

Alaska Native Harbor Seal Commission, Annual Meeting, April, Angoon.

Jarrell, (3.H. 2000. The Alaska Department of Fish and Game's contributions to the Alaska

Frozen Tissue Collection. ADF&G Seminar, April, Juneau.

Jarrell, G.H. 2000. The Arctic Archival Observatory and its relationship to the Alaska

Frozen Tissue Collection. Minerals Management Service Seminar, May, Anchorage.

22
23
for most of our nationally owned public lands and natural resources. This includes fostering

sound use of our land and water resources; protecting our fish, wildlife, and biological diversity;

preserving the environmental and cultural values of our national parks and historical places;

and providing for the enjoyment of life through outdoor recreation. The Department assesses

our energy and mineral resources and works to ensure that their development is in the best

interests of all our people by encouraging stewardship and citizen participation in their care.

The Department also has a major responsibility for American Indian reservation communities

and for people who live in island territories under U.S. administration.

The Minerals Management Service Mission

As a bureau of the Department of the Interior, the Minerals Management Service s (MMS)

primary responsibilities are to manage the mineral resources located on the Nation s Outer

Continental Shelf (OCS), collect revenue from the Federal OCS and onshore Federal and

Indian lands, and distribute those revenues.

Moreover, in working to meet its responsibilities, the Offshore Minerals Management

Program administers the OCS competitive leasing program and oversees the safe and

environmentally sound exploration and production of our Nation s offshore natural gas, oil and

other mineral resources. The MMS Royalty Management Program meets its responsibilities

by ensuring the efficient, timely and accurate collection and disbursement of revenue from

mineral leasing and production due to Indian tribes and allottees, States and the U.S. Treasury.

The MMS strives to fulfill its responsibilities through the general guiding principals of: (1) being

responsive to the publics concerns and interests by maintaining a dialogue with al! potentially

affected parties and (2) carrying out its programs with an emphasis on working to enhance the

quatity of life for all Americans by lending MMS assistance and expertise to economic

development and environmental protection.