Short Citation:
Alaska Fisheries Science Center, 2021: AFSC/RACE/SAP/Shavey: DNA extraction from archived Giemsa-stained blood smears using polymerase chain reaction to detect host and parasitic DNA, https://www.fisheries.noaa.gov/inport/item/35937.

Item Identification

Title: AFSC/RACE/SAP/Shavey: DNA extraction from archived Giemsa-stained blood smears using polymerase chain reaction to detect host and parasitic DNA
Short Name: AFSC/RACE/SAP/Shavey: DNA extraction from archived Giemsa-stained blood smears using polymerase chain reaction to detect host and parasitic DNA
Status: Completed
Abstract:

These are the data from a laboratory experiment in which DNA content was removed from blood smears and extracted. The blood smears were either stained with Giemsa-stain or remained un-stained. Some of the un-stained smears were coverslipped. Host and parasitic DNA was amplified using conventional PCR.

Purpose:

To identify a new technique of removing contents from blood smears and to evalutate the effects of Giemsa-staining and coverslipping for DNA amplication.

Notes:

Loaded by FGDC Metadata Uploader, batch 9574, 12-13-2016 12:44

The following FGDC sections are not currently supported in InPort, but were preserved and will be included in the FGDC export:

- Taxonomy (FGDC:taxonomy)

Keywords

Theme Keywords

Thesaurus Keyword
UNCONTROLLED
ISO19115 Biota
ISO19115 Oceans
None Blood Smear
None disease
None DNA Extraction

Spatial Keywords

Thesaurus Keyword
UNCONTROLLED
None Alaska
None Bering Sea
None Gulf of Alaska
None Newfoundland, Canada
None SE Alaska
None Washington State Coast

Physical Location

Organization: Alaska Fisheries Science Center
City: Seattle
State/Province: WA
Country: USA

Data Set Information

Data Set Scope Code: Data Set
Data Set Type: MS Excel
Maintenance Frequency: None Planned
Data Presentation Form: Table (digital)
Distribution Liability:

The user is responsible for the results of any application of this data for other than its intended purpose.

NOAA denies liability if the data are misused.

Support Roles

Data Steward

CC ID: 362711
Date Effective From: 2016-12-13
Date Effective To:
Contact (Person): Lang, Christie
Email Address: christie.lang@noaa.gov

Distributor

CC ID: 362778
Date Effective From: 2016-12-13
Date Effective To:
Contact (Person): Foy, Robert
Email Address: robert.foy@noaa.gov

Metadata Contact

CC ID: 362776
Date Effective From: 2016-12-13
Date Effective To:
Contact (Person): MC, Metadata Coordinators
Email Address: AFSC.metadata@noaa.gov

Originator

CC ID: 362779
Date Effective From: 2016-12-13
Date Effective To:
Contact (Organization): Alaska Fisheries Science Center (AFSC)
Address: 7600 Sand Point Way N.E., Building 4
Seattle, WA 98115
USA
URL: http://www.afsc.noaa.gov
Business Hours: 0700-1700 Pacific Time

Point of Contact

CC ID: 362777
Date Effective From: 2016-12-13
Date Effective To:
Contact (Person): Lang, Christie
Email Address: christie.lang@noaa.gov

Extents

Currentness Reference: Ground Condition

Extent Group 1

Extent Group 1 / Geographic Area 1

CC ID: 362775
W° Bound: -178.51
E° Bound: -53.11
N° Bound: 61.67
S° Bound: 49.63
Description

Eastern Bering Sea, Alaska; Gulf of Alaska; Southeast Alaska, Washington State Coast, North Atlantic Coast

Extent Group 1 / Time Frame 1

CC ID: 362774
Time Frame Type: Range
Start: 1988
End: 2004

Access Information

Security Class: Unclassified
Data Access Procedure:

unknown

Data Access Constraints:

There are no legal restrictions on access to the data. They reside in public domain and can be freely distributed.

Data Use Constraints:

User must read and fully comprehend the metadata prior to use. Applications or inferences derived from the data should be carefully considered for accuracy. Acknowledgementof NOAA/NMFS/AFSC, as the source from which these data were obtained in any publications and/or other representations of these, data is suggested.

Distribution Information

Technical Environment

Description:

Excel

Data Quality

Accuracy:

Data is submitted through a thorough QA/QC process.

Completeness Report:

Due to small sample size, only blood smears with high parasite ratings were used in statistical analysis. Crab morphometrics are not available for some samples. BCS smears were rated with trophont stage. Two samples used in analysis had a trophont and prespore stage (thought to be advanced stage) and those samples were grouped as highest trophont stage (T5).

Conceptual Consistency:

Data is checked for values outside range.

Quality Control Procedures Employed:

Data is checked for values outside range.

Data Management

Have Resources for Management of these Data Been Identified?: No
Approximate Percentage of Budget for these Data Devoted to Data Management: Unknown
Do these Data Comply with the Data Access Directive?: No
Is Access to the Data Limited Based on an Approved Waiver?: No
If Distributor (Data Hosting Service) is Needed, Please Indicate: Yes
Approximate Delay Between Data Collection and Dissemination: no delay
Actual or Planned Long-Term Data Archive Location: NCEI-MD
Approximate Delay Between Data Collection and Archiving: unknown
How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive?:

IT Security and Contingency Plan for the system establishes procedures and applies to the functions, operations, and resources necessary to recover and restore data as hosted in the Western Regional Support Center in Seattle, Washington, following a disruption.

Lineage

Process Steps

Process Step 1

CC ID: 362805
Description:

A subset of 76 blood smears that were prepared in the field from 1988 to 2004 were chosen based on smear preparation (Giemsa-stained vs. no stain and coverslipped vs no coverslip) and parasite status (parasite presence vs. no parasite). All content was removed from each smear using a pipette tip and sterile blade. DNA was extracted and amplified using crab host and parasite PCR primer sets.

Process Step 2

CC ID: 362955
Description:

SPNO is a number assigned to each collected crab. Duplicate numbers represent replicate smears taken from sample.

The sex of the crab is identified as: 1) Male, 2) Female, 3) Unknown. Individual crab carapaces were measured (1 mm), excluding spines, and are reported as size. Null or blank fields in data represent no size information reported for crab specimen.

Shell condition class serves as a semi-quantitative index of molt status and time in shell post-molt. Carapace shell condition was assessed for each Chionoecetes crab sampled and assigned to one of six classes according to specific criteria (0 = premolt or molting, 1 = soft and pliable, 2 = new hardshell both firm and clean, 3 = oldshell slightly worn, 4 = oldshell worn, 9 = no shell condition information reported for crab specimen). Collection location was not a factor, so only general location is listed.

Process Step 3

CC ID: 362956
Description:

Blood smears analyzed were either unstained (none), or fixed with methanol and Giemsa-stained for 30 minutes (Giemsa). Treatment of blood smears are identified as (0 = no cover slip, 1 = cover slip attached using mounting media).

30 fields at 250X were read to determine presence or absence of Hematodinium spp. parasite on blood smear. Results were documented as: (0 = Hematodinium parasite absent on smear, 1 = Hematodinium parasite present on smear). Hematodinium parasite presence on smear was identified as T-rating (0 = No rating due to parasite absence, T1 = Up to 10% Hematodinium parasite present on smear (trophont stage), T2 = 10 - 40% Hematodinium parasite present on smear (trophont stage), T3 = 40 - 60% Hematodinium parasite present on smear (trophont stage), T4 = 60 - 90% Hematodinium parasite present on smear (trophont stage), T4P1 = 60 - 90% Hematodinium parasite present on smear (trophont stage) and up to 10% Hematodium prespore stage, T5 = Above 90% Hematodinium parasite present on smear (trophont stage), T5P1 = Above 90% Hematodinium parasite present on smear (trophont stage) and up to 10% Hematodium prespore stage).

Process Step 4

CC ID: 362957
Description:

PCR assays: for 16S, COI, 18S and ITS Primer (0 = Did not use primer set on this sample, 1 = Used primer set on this sample). For 16S, COI, 18S and ITS Amplification (0 = No DNA amplification using this primer set, 1 = DNA was amplified using primer set, 9 = no amplification to report due to primer set not used in sample). Primer set descriptions: 16S = 16Sar-L (CgC CTg TTT ATC AAA AAC AT) & 16Sbr-H (CCg gTC TgA ACT CAg ATC ACg T) primer set used in PCR assay, targeting mitochondrial DNA 16S ribosomal RNA gene. COI = LCO1490 (ggT CAA CAA ATC ATA AAg ATA TTg g) & HCO2198 (TAA ACT TCA ggg TgA CCA AAA AAT CA) primer set used in PCR assay, targeting the mitochondrial cytochrome c oxidase subunit I gene. 18S = HF1487 (CCT ggC TCg ATA gAg TTg) & HR1654 (ggC TgC CgT CCg AAT TAT TCA C) primer set used in PCR assay, targeting the 18S ribosomal gene located at the small subunit 3'-end of the ribosomal RNA unit. ITS = HSP7f (AGT CAT CAG CTC GTG CTG A) & HSP9r (TTC ACG GAA TTC TGC AAT TCG) primer set used in PCR assay, targeting the first internal transcribed spacer of the ribosomal RNA unit. Statistical analysis: Blood smears were analyzed using two-sample t-test (0 = smear was not used in statistical analysis, 1 = smear was used in statistical analysis).

Child Items

Rubric scores updated every 15m

Rubric Score Type Title
Entity (ENT) Blood smear data

Catalog Details

Catalog Item ID: 35937
Metadata Record Created By: Christie Lang
Metadata Record Created: 2016-12-13 11:56+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2019-06-04 13:14+0000
Metadata Record Published: 2016-12-16
Owner Org: AFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Next Review Date: 2017-12-17