Sunnie Grace McCalla (Former Employee)
Science and Products
Flocks of a feather dock together: Using Docker and HTCondor to link high-throughput computing across the USGS
USGS scientists often face computationally intensive tasks that require high-throughput computing capabilities. Several USGS facilities use HTCondor to run their computational pools but are not necessarily connected to the larger USGS pool. This project demonstrated how to connect HTCondor pools by flocking, or coordinating, within the USGS. In addition to flocking the Upper Midwest Environmental
Hunting Invasive Species with HTCondor: High Throughput Computing for Big Data and Next Generation Sequencing
Large amounts of data are being generated that require hours, days, or even weeks to analyze using traditional computing resources. Innovative solutions must be implemented to analyze the data in a reasonable timeframe. The program HTCondor (https://research.cs.wisc.edu/htcondor/) takes advantage of the processing capacity of individual desktop computers and dedicated computing resources as a sing
Ethanol and sodium acetate as a preservation method to delay degradation of environmental DNA: Data
This data contains environmental DNA (eDNA) sample assay results that were collected from water samples taken from a tank housing Asian carp and placed either on ice or at room temperature. At both treatment temperatures, water samples were left untreated or were treated with an ethanol and sodium acetate solution (EtOH-NaAc). This was done to evaluate an ethanol and sodium acetate solution to mai
Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor
Biologists and environmental scientists now routinely solve computational problems that were unimaginable a generation ago. Examples include processing geospatial data, analyzing -omics data, and running large-scale simulations. Conventional desktop computing cannot handle these tasks when they are large, and high-performance computing is not always available nor the most appropriate solution for
Authors
Richard A. Erickson, Michael N. Fienen, S. Grace McCalla, Emily L. Weiser, Melvin L. Bower, Jonathan M. Knudson, Greg Thain
The complete mitochondrial genome of Hine’s emerald dragonfly (Somatochlora hineana Williamson) via NGS sequencing
Here, we report the complete mitochondrial genome of the endangered Hine’s emerald dragonfly (HED), Somatochlora hineana Williamson. Data were generated via next generation sequencing (NGS) and assembled using a mitochondrial baiting and iterative mapping approach. The full length circular genome is 15,705 bp with 26.6% GC content. It contains the typical metazoan set of 37 genes: 13 protein-codin
Authors
Craig Jackson, S. Grace McCalla, Jon Amberg, Daniel Soluk, Hugh Britten
Ethanol and sodium acetate as a preservation method to delay degradation of environmental DNA
Environmental DNA (eDNA) samples that are collected from remote locations depend on rapid stabilization of the DNA. The degradation of eDNA in water samples is minimized when samples are stored at ≤ 4 °C. Developing a preservation technique to maintain eDNA integrity at room temperature would allow a wider range of locations to be sampled. We evaluated an ethanol and sodium acetate solution to mai
Authors
Bridget A. Ladell, Liza R. Walleser, S. Grace McCalla, Richard A. Erickson, Jon Amberg
Evidence of Asian carp spawning upstream of a key choke point in the Mississippi River
Bighead Carp Hypophthalmichthys nobilis, Silver Carp H. molitrix, and Grass Carp Ctenopharyngodon idella(collectively termed “Asian carp”) were introduced into North America during the 1960s and 1970s and have become established in the lower Mississippi River basin. Previously published evidence for spawning of these species in the upper Mississippi River has been limited to an area just downstrea
Authors
James H. Larson, Brent C. Knights, S. Grace McCalla, Emy Monroe, Maren T. Tuttle-Lau, Duane Chapman, Amy E. George, Jonathan M. Vallazza, Jon Amberg
Detecting the movement and spawning activity of bigheaded carps with environmental DNA
Bigheaded carps are invasive fishes threatening to invade the Great Lakes basin and establish spawning populations, and have been monitored using environmental DNA (eDNA). Not only does eDNA hold potential for detecting the presence of species, but may also allow for quantitative comparisons like relative abundance of species across time or space. We examined the relationships among bigheaded carp
Authors
Richard A. Erickson, Christopher B. Rees, Alison A. Coulter, Christopher M. Merkes, S. Grace McCalla, Katherine F Touzinsky, Liza R. Walleser, Reuben R. Goforth, Jon Amberg
Genetic analysis shows that morphology alone cannot distinguish asian carp eggs from those of other cyprinid species
Fish eggs and embryos (hereafter collectively referred to as “eggs”) were collected in the upper Mississippi River main stem (~300 km upstream of previously reported spawning by invasive Asian carp) during summer 2013. Based on previously published morphological characteristics, the eggs were identified as belonging to Asian carp. A subsample of the eggs was subsequently analyzed by using molecular
Authors
James H. Larson, S. Grace McCalla, Duane Chapman, Christopher B. Rees, Brent C. Knights, Jonathan M. Vallazza, Amy E. George, William B. Richardson, Jon Amberg
Improving efficiency and reliability of environmental DNA analysis for silver carp
Natural resource agencies have established surveillance programs which use environmental DNA (eDNA) for the early detection of bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix before they establish populations within the Great Lakes. This molecular monitoring technique must be highly accurate and precise for confident interpretation and also efficient, both in de
Authors
Jon J. Amberg, S. Grace McCalla, Emy Monroe, Richard Lance, Kelly Baerwaldt, Mark P. Gaikowski
Persistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data
The prevention of non-indigenous aquatic invasive species spreading into new areas is a goal of many resource managers. New techniques have been developed to survey for species that are difficult to capture with conventional gears that involve the detection of their DNA in water samples (eDNA). This technique is currently used to track the invasion of bigheaded carps (silver carp and bighead carp;
Authors
Christopher M. Merkes, S. Grace McCalla, Nathan R. Jensen, Mark P. Gaikowski, Jon J. Amberg
Detection of environmental DNA of Bigheaded Carps in samples collected from selected locations in the St. Croix River and in the Mississippi River
The use of molecular methods, such as the detection of environmental deoxyribonucleic acid (eDNA), have become an increasingly popular tool in surveillance programs that monitor for the presence of invasive species in aquatic systems. One early application of these methods in aquatic systems was surveillance for DNA of Asian carps (specifically bighead carp Hypophthalmichthys nobilis and silver ca
Authors
Jon J. Amberg, S. Grace McCalla, Loren Miller, Peter Sorensen, Mark P. Gaikowski
Science and Products
Flocks of a feather dock together: Using Docker and HTCondor to link high-throughput computing across the USGS
USGS scientists often face computationally intensive tasks that require high-throughput computing capabilities. Several USGS facilities use HTCondor to run their computational pools but are not necessarily connected to the larger USGS pool. This project demonstrated how to connect HTCondor pools by flocking, or coordinating, within the USGS. In addition to flocking the Upper Midwest Environmental
Hunting Invasive Species with HTCondor: High Throughput Computing for Big Data and Next Generation Sequencing
Large amounts of data are being generated that require hours, days, or even weeks to analyze using traditional computing resources. Innovative solutions must be implemented to analyze the data in a reasonable timeframe. The program HTCondor (https://research.cs.wisc.edu/htcondor/) takes advantage of the processing capacity of individual desktop computers and dedicated computing resources as a sing
Ethanol and sodium acetate as a preservation method to delay degradation of environmental DNA: Data
This data contains environmental DNA (eDNA) sample assay results that were collected from water samples taken from a tank housing Asian carp and placed either on ice or at room temperature. At both treatment temperatures, water samples were left untreated or were treated with an ethanol and sodium acetate solution (EtOH-NaAc). This was done to evaluate an ethanol and sodium acetate solution to mai
Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor
Biologists and environmental scientists now routinely solve computational problems that were unimaginable a generation ago. Examples include processing geospatial data, analyzing -omics data, and running large-scale simulations. Conventional desktop computing cannot handle these tasks when they are large, and high-performance computing is not always available nor the most appropriate solution for
Authors
Richard A. Erickson, Michael N. Fienen, S. Grace McCalla, Emily L. Weiser, Melvin L. Bower, Jonathan M. Knudson, Greg Thain
The complete mitochondrial genome of Hine’s emerald dragonfly (Somatochlora hineana Williamson) via NGS sequencing
Here, we report the complete mitochondrial genome of the endangered Hine’s emerald dragonfly (HED), Somatochlora hineana Williamson. Data were generated via next generation sequencing (NGS) and assembled using a mitochondrial baiting and iterative mapping approach. The full length circular genome is 15,705 bp with 26.6% GC content. It contains the typical metazoan set of 37 genes: 13 protein-codin
Authors
Craig Jackson, S. Grace McCalla, Jon Amberg, Daniel Soluk, Hugh Britten
Ethanol and sodium acetate as a preservation method to delay degradation of environmental DNA
Environmental DNA (eDNA) samples that are collected from remote locations depend on rapid stabilization of the DNA. The degradation of eDNA in water samples is minimized when samples are stored at ≤ 4 °C. Developing a preservation technique to maintain eDNA integrity at room temperature would allow a wider range of locations to be sampled. We evaluated an ethanol and sodium acetate solution to mai
Authors
Bridget A. Ladell, Liza R. Walleser, S. Grace McCalla, Richard A. Erickson, Jon Amberg
Evidence of Asian carp spawning upstream of a key choke point in the Mississippi River
Bighead Carp Hypophthalmichthys nobilis, Silver Carp H. molitrix, and Grass Carp Ctenopharyngodon idella(collectively termed “Asian carp”) were introduced into North America during the 1960s and 1970s and have become established in the lower Mississippi River basin. Previously published evidence for spawning of these species in the upper Mississippi River has been limited to an area just downstrea
Authors
James H. Larson, Brent C. Knights, S. Grace McCalla, Emy Monroe, Maren T. Tuttle-Lau, Duane Chapman, Amy E. George, Jonathan M. Vallazza, Jon Amberg
Detecting the movement and spawning activity of bigheaded carps with environmental DNA
Bigheaded carps are invasive fishes threatening to invade the Great Lakes basin and establish spawning populations, and have been monitored using environmental DNA (eDNA). Not only does eDNA hold potential for detecting the presence of species, but may also allow for quantitative comparisons like relative abundance of species across time or space. We examined the relationships among bigheaded carp
Authors
Richard A. Erickson, Christopher B. Rees, Alison A. Coulter, Christopher M. Merkes, S. Grace McCalla, Katherine F Touzinsky, Liza R. Walleser, Reuben R. Goforth, Jon Amberg
Genetic analysis shows that morphology alone cannot distinguish asian carp eggs from those of other cyprinid species
Fish eggs and embryos (hereafter collectively referred to as “eggs”) were collected in the upper Mississippi River main stem (~300 km upstream of previously reported spawning by invasive Asian carp) during summer 2013. Based on previously published morphological characteristics, the eggs were identified as belonging to Asian carp. A subsample of the eggs was subsequently analyzed by using molecular
Authors
James H. Larson, S. Grace McCalla, Duane Chapman, Christopher B. Rees, Brent C. Knights, Jonathan M. Vallazza, Amy E. George, William B. Richardson, Jon Amberg
Improving efficiency and reliability of environmental DNA analysis for silver carp
Natural resource agencies have established surveillance programs which use environmental DNA (eDNA) for the early detection of bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix before they establish populations within the Great Lakes. This molecular monitoring technique must be highly accurate and precise for confident interpretation and also efficient, both in de
Authors
Jon J. Amberg, S. Grace McCalla, Emy Monroe, Richard Lance, Kelly Baerwaldt, Mark P. Gaikowski
Persistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data
The prevention of non-indigenous aquatic invasive species spreading into new areas is a goal of many resource managers. New techniques have been developed to survey for species that are difficult to capture with conventional gears that involve the detection of their DNA in water samples (eDNA). This technique is currently used to track the invasion of bigheaded carps (silver carp and bighead carp;
Authors
Christopher M. Merkes, S. Grace McCalla, Nathan R. Jensen, Mark P. Gaikowski, Jon J. Amberg
Detection of environmental DNA of Bigheaded Carps in samples collected from selected locations in the St. Croix River and in the Mississippi River
The use of molecular methods, such as the detection of environmental deoxyribonucleic acid (eDNA), have become an increasingly popular tool in surveillance programs that monitor for the presence of invasive species in aquatic systems. One early application of these methods in aquatic systems was surveillance for DNA of Asian carps (specifically bighead carp Hypophthalmichthys nobilis and silver ca
Authors
Jon J. Amberg, S. Grace McCalla, Loren Miller, Peter Sorensen, Mark P. Gaikowski