A young scientist observes Brook Trout housed in EESC's artificial stream lab.
Clayton Raines
Clay is a Fish Biologist at the USGS Eastern Ecological Science Center, National Fish Health Research Laboratory in Kearneysville, WV.
I am currently serving as Fish Biologist at the USGS National Fish Health Research Laboratory. I previously worked as a biologist with the WV DNR, as well as the Tennessee Aquarium Conservation Institute where I oversaw restoration and monitoring efforts for threatened and endangered freshwater species as well as conducted research on a variety of fisheries management topics. Additionally, I studied Southeast reservoir fish ecology and physiology as a graduate research assistant at Mississippi State University. I also completed a GIS internship with Jefferson County Planning and Zoning, as well as conducting research at The Conservation Fund’s Freshwater Institute and USDA Appalachian Fruit Research Station.
Science and Products
Osprey (Pandion haliaetus) Population and the Availability of Menhaden (Brevoortia tyrannus) as Their Food Source in Chesapeake Bay: Historical and Present-day Comparison
USGS is collaborating with many biologists in analysis of data on osprey ( Pandion haliaetus ) and their prey (menhaden, Brevoortia tyrannus , and other species of fish) in the middle and lower Chesapeake Bay and its tributaries. The data compiled and collected will help determine if a lack of menhaden or other environmental factors are affecting osprey reproductive success in portions of the...
Functional and Molecular Bioassay Core Technology Team
About the Research The Functional and Molecular Bioassay Core Technology Team (CTT) as part of the Environmental Health Program utilizes reporter assays, quantitative gene expression analyses, and high-throughput sequencing methods to produce functional endpoints across a broad scope of environmental topics and sample matrices.
AquaDePTH-Aquatic Disease and Pathogen Repository
The Aquatic Disease and Pathogen Repository (AquaDePTH) will be a public-facing national repository to support biosurveillance of aquatic animal diseases and pathogens. By collating historically published data, plus new aquatic pathogen and disease information, stakeholders will be able monitor fish kill and aquatic pathogen trends spatially and temporally in freshwater and marine environments...
Investigating blotchy bass syndrome in black basses
Black basses (Micropterus spp) are enigmatic North American sportfishes that support the most economically valuable freshwater sport fishery in the United States and serve as keystone predators within aquatic ecosystems. Hyperpigmented melanistic lesions on the surface of black basses have been observed in a number of waterbodies across the country in increasing frequency. We have recently...
Observing an Artificial Stream Lab
A young scientist observes Brook Trout housed in EESC's artificial stream lab.
EESC Earth Day Crayfish Outreach
Brenna Raines (near) and Taylor Woods (far) display crayfish and other macroinvertebrates during the EESC earth day open house event in 2024
Brenna Raines (near) and Taylor Woods (far) display crayfish and other macroinvertebrates during the EESC earth day open house event in 2024
Macroinvertebrate Outreach at EESC Earth Day 2024
Brenna Raines (right) educates earth day guest Bennett Butts about macroinvertebrates.
Brenna Raines (right) educates earth day guest Bennett Butts about macroinvertebrates.
EESC Earth Day Photo Frame
A photo of a young earth day attendee using one of the earth day photo frames at earth day 2024.
A photo of a young earth day attendee using one of the earth day photo frames at earth day 2024.
Interns at the Waterfall
AFS Hutton Scholars Brennan Landerkin (left) and Emily Hunt (right) observing a tank of Atlantic Salmon (Salmo salar) at the Conservation Fund’s Freshwater Institute.
AFS Hutton Scholars Brennan Landerkin (left) and Emily Hunt (right) observing a tank of Atlantic Salmon (Salmo salar) at the Conservation Fund’s Freshwater Institute.
Interns collect salmon blood
Brennan and Emily collect and transfer salmon plasma to assess for PFAS
Brennan and Emily collect and transfer salmon plasma to assess for PFAS
Interns observe a salmon necropsy
Dr. John Davidson (right) provides instruction on salmon internal anatomy.
Dr. John Davidson (right) provides instruction on salmon internal anatomy.
Brennan and Emily assess habitat in a spillway plunge pool.
Brennan and Emily assess habitat in a spillway plunge pool
Brennan and Emily assess habitat in a spillway plunge pool
Interns Conducting Fish Habitat Research
Brennan and Emily conducting fish habitat surveys in Catoctin Mountain Park.
Brennan and Emily conducting fish habitat surveys in Catoctin Mountain Park.
2022 Blotchy Bass Syndrome Biosurveillance Project
Blotchy bass syndrome (BBS) is the presence of hyperpigmentation (melanosis) on the external surface of black basses. This condition has received increased attention from anglers and resource managers in recent years and is a popular topic of discussion and reporting on angling websites and blogging platforms.
Blotchy bass syndrome (BBS) is the presence of hyperpigmentation (melanosis) on the external surface of black basses. This condition has received increased attention from anglers and resource managers in recent years and is a popular topic of discussion and reporting on angling websites and blogging platforms.
2022 Blotchy Bass Syndrome Biosurveillance Project
Blotchy bass syndrome (BBS) is the presence of hyperpigmentation (melanosis) on the external surface of black basses. This condition has received increased attention from anglers and resource managers in recent years and is a popular topic of discussion and reporting on angling websites and blogging platforms.
Blotchy bass syndrome (BBS) is the presence of hyperpigmentation (melanosis) on the external surface of black basses. This condition has received increased attention from anglers and resource managers in recent years and is a popular topic of discussion and reporting on angling websites and blogging platforms.
nCounterMax Automated Prep Station
image of the automated prep station for the Nanostring nCounter Max. The device prepares cartridges for CodeSet Gene Expression Analysis
image of the automated prep station for the Nanostring nCounter Max. The device prepares cartridges for CodeSet Gene Expression Analysis
Blotchy Swab
A dermal swab being used on a Largemouth Bass at a Bass Pro Shops retail store with a presumptive case of blotchy bass syndrome. We can see the transfer of pigmented epidermal tissue to the swab changing its color. The collected swabs can be used to isolate DNA and RNA which can be used to identify pathogens including those associated with hyperpigmentation.
A dermal swab being used on a Largemouth Bass at a Bass Pro Shops retail store with a presumptive case of blotchy bass syndrome. We can see the transfer of pigmented epidermal tissue to the swab changing its color. The collected swabs can be used to isolate DNA and RNA which can be used to identify pathogens including those associated with hyperpigmentation.
C. Raines Blotchy Bass Swab
Clay Raines, a USGS scientist, performing a dermal swab on a Largemouth Bass at a Bass Pro Shops retail store with a presumptive case of blotchy bass syndrome. The collected swabs can be used to isolate DNA and RNA which can be used to identify pathogens including those associated with hyperpigmentation.
Clay Raines, a USGS scientist, performing a dermal swab on a Largemouth Bass at a Bass Pro Shops retail store with a presumptive case of blotchy bass syndrome. The collected swabs can be used to isolate DNA and RNA which can be used to identify pathogens including those associated with hyperpigmentation.
Spike of RHV virus
Spike of RHV virus as extraction control in the Biosafety Level-3 Lab. Photos take in the BSL-3 lab are often fuzzy due to phones being kept in sealed plastic for safety.
Spike of RHV virus as extraction control in the Biosafety Level-3 Lab. Photos take in the BSL-3 lab are often fuzzy due to phones being kept in sealed plastic for safety.
Transfer or RNA Spin Columns 2
Transfer of RNA spin columns into collection tubes (also pictured Chris Ottinger and Colleen Young)
Transfer of RNA spin columns into collection tubes (also pictured Chris Ottinger and Colleen Young)
Transfer or RNA Spin Columns 1
Transfer of RNA spin columns into collection tubes (with Chris Ottinger and Colleen Young)
Transfer of RNA spin columns into collection tubes (with Chris Ottinger and Colleen Young)
Processing Filtered Samples
1x filtered samples processed via vacuum manifold RNA column filtration. Photos take in the BSL-3 lab are often fuzzy due to phones being kept in sealed plastic for safety.
1x filtered samples processed via vacuum manifold RNA column filtration. Photos take in the BSL-3 lab are often fuzzy due to phones being kept in sealed plastic for safety.
Science and Products
Osprey (Pandion haliaetus) Population and the Availability of Menhaden (Brevoortia tyrannus) as Their Food Source in Chesapeake Bay: Historical and Present-day Comparison
USGS is collaborating with many biologists in analysis of data on osprey ( Pandion haliaetus ) and their prey (menhaden, Brevoortia tyrannus , and other species of fish) in the middle and lower Chesapeake Bay and its tributaries. The data compiled and collected will help determine if a lack of menhaden or other environmental factors are affecting osprey reproductive success in portions of the...
Functional and Molecular Bioassay Core Technology Team
About the Research The Functional and Molecular Bioassay Core Technology Team (CTT) as part of the Environmental Health Program utilizes reporter assays, quantitative gene expression analyses, and high-throughput sequencing methods to produce functional endpoints across a broad scope of environmental topics and sample matrices.
AquaDePTH-Aquatic Disease and Pathogen Repository
The Aquatic Disease and Pathogen Repository (AquaDePTH) will be a public-facing national repository to support biosurveillance of aquatic animal diseases and pathogens. By collating historically published data, plus new aquatic pathogen and disease information, stakeholders will be able monitor fish kill and aquatic pathogen trends spatially and temporally in freshwater and marine environments...
Investigating blotchy bass syndrome in black basses
Black basses (Micropterus spp) are enigmatic North American sportfishes that support the most economically valuable freshwater sport fishery in the United States and serve as keystone predators within aquatic ecosystems. Hyperpigmented melanistic lesions on the surface of black basses have been observed in a number of waterbodies across the country in increasing frequency. We have recently...
Observing an Artificial Stream Lab
A young scientist observes Brook Trout housed in EESC's artificial stream lab.
A young scientist observes Brook Trout housed in EESC's artificial stream lab.
EESC Earth Day Crayfish Outreach
Brenna Raines (near) and Taylor Woods (far) display crayfish and other macroinvertebrates during the EESC earth day open house event in 2024
Brenna Raines (near) and Taylor Woods (far) display crayfish and other macroinvertebrates during the EESC earth day open house event in 2024
Macroinvertebrate Outreach at EESC Earth Day 2024
Brenna Raines (right) educates earth day guest Bennett Butts about macroinvertebrates.
Brenna Raines (right) educates earth day guest Bennett Butts about macroinvertebrates.
EESC Earth Day Photo Frame
A photo of a young earth day attendee using one of the earth day photo frames at earth day 2024.
A photo of a young earth day attendee using one of the earth day photo frames at earth day 2024.
Interns at the Waterfall
AFS Hutton Scholars Brennan Landerkin (left) and Emily Hunt (right) observing a tank of Atlantic Salmon (Salmo salar) at the Conservation Fund’s Freshwater Institute.
AFS Hutton Scholars Brennan Landerkin (left) and Emily Hunt (right) observing a tank of Atlantic Salmon (Salmo salar) at the Conservation Fund’s Freshwater Institute.
Interns collect salmon blood
Brennan and Emily collect and transfer salmon plasma to assess for PFAS
Brennan and Emily collect and transfer salmon plasma to assess for PFAS
Interns observe a salmon necropsy
Dr. John Davidson (right) provides instruction on salmon internal anatomy.
Dr. John Davidson (right) provides instruction on salmon internal anatomy.
Brennan and Emily assess habitat in a spillway plunge pool.
Brennan and Emily assess habitat in a spillway plunge pool
Brennan and Emily assess habitat in a spillway plunge pool
Interns Conducting Fish Habitat Research
Brennan and Emily conducting fish habitat surveys in Catoctin Mountain Park.
Brennan and Emily conducting fish habitat surveys in Catoctin Mountain Park.
2022 Blotchy Bass Syndrome Biosurveillance Project
Blotchy bass syndrome (BBS) is the presence of hyperpigmentation (melanosis) on the external surface of black basses. This condition has received increased attention from anglers and resource managers in recent years and is a popular topic of discussion and reporting on angling websites and blogging platforms.
Blotchy bass syndrome (BBS) is the presence of hyperpigmentation (melanosis) on the external surface of black basses. This condition has received increased attention from anglers and resource managers in recent years and is a popular topic of discussion and reporting on angling websites and blogging platforms.
2022 Blotchy Bass Syndrome Biosurveillance Project
Blotchy bass syndrome (BBS) is the presence of hyperpigmentation (melanosis) on the external surface of black basses. This condition has received increased attention from anglers and resource managers in recent years and is a popular topic of discussion and reporting on angling websites and blogging platforms.
Blotchy bass syndrome (BBS) is the presence of hyperpigmentation (melanosis) on the external surface of black basses. This condition has received increased attention from anglers and resource managers in recent years and is a popular topic of discussion and reporting on angling websites and blogging platforms.
nCounterMax Automated Prep Station
image of the automated prep station for the Nanostring nCounter Max. The device prepares cartridges for CodeSet Gene Expression Analysis
image of the automated prep station for the Nanostring nCounter Max. The device prepares cartridges for CodeSet Gene Expression Analysis
Blotchy Swab
A dermal swab being used on a Largemouth Bass at a Bass Pro Shops retail store with a presumptive case of blotchy bass syndrome. We can see the transfer of pigmented epidermal tissue to the swab changing its color. The collected swabs can be used to isolate DNA and RNA which can be used to identify pathogens including those associated with hyperpigmentation.
A dermal swab being used on a Largemouth Bass at a Bass Pro Shops retail store with a presumptive case of blotchy bass syndrome. We can see the transfer of pigmented epidermal tissue to the swab changing its color. The collected swabs can be used to isolate DNA and RNA which can be used to identify pathogens including those associated with hyperpigmentation.
C. Raines Blotchy Bass Swab
Clay Raines, a USGS scientist, performing a dermal swab on a Largemouth Bass at a Bass Pro Shops retail store with a presumptive case of blotchy bass syndrome. The collected swabs can be used to isolate DNA and RNA which can be used to identify pathogens including those associated with hyperpigmentation.
Clay Raines, a USGS scientist, performing a dermal swab on a Largemouth Bass at a Bass Pro Shops retail store with a presumptive case of blotchy bass syndrome. The collected swabs can be used to isolate DNA and RNA which can be used to identify pathogens including those associated with hyperpigmentation.
Spike of RHV virus
Spike of RHV virus as extraction control in the Biosafety Level-3 Lab. Photos take in the BSL-3 lab are often fuzzy due to phones being kept in sealed plastic for safety.
Spike of RHV virus as extraction control in the Biosafety Level-3 Lab. Photos take in the BSL-3 lab are often fuzzy due to phones being kept in sealed plastic for safety.
Transfer or RNA Spin Columns 2
Transfer of RNA spin columns into collection tubes (also pictured Chris Ottinger and Colleen Young)
Transfer of RNA spin columns into collection tubes (also pictured Chris Ottinger and Colleen Young)
Transfer or RNA Spin Columns 1
Transfer of RNA spin columns into collection tubes (with Chris Ottinger and Colleen Young)
Transfer of RNA spin columns into collection tubes (with Chris Ottinger and Colleen Young)
Processing Filtered Samples
1x filtered samples processed via vacuum manifold RNA column filtration. Photos take in the BSL-3 lab are often fuzzy due to phones being kept in sealed plastic for safety.
1x filtered samples processed via vacuum manifold RNA column filtration. Photos take in the BSL-3 lab are often fuzzy due to phones being kept in sealed plastic for safety.
*Disclaimer: Listing outside positions with professional scientific organizations on this Staff Profile are for informational purposes only and do not constitute an endorsement of those professional scientific organizations or their activities by the USGS, Department of the Interior, or U.S. Government