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2013

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Full-Text Articles in Life Sciences

Stellaris Fish Workshop Gadph And Dapi Z-Series, George Mcnamara Dec 2013

Stellaris Fish Workshop Gadph And Dapi Z-Series, George Mcnamara

George McNamara

Stellaris FISH workshop GADPH and DAPI Z-series at MD Anderson Cancer Center, Houston, TX.

The zip file contains raw and GPU deconvolved image data from a workshop Biosearch Technologies conducted for MDACC researchers in December 2013. Image data was acquired on a Leica DMI6000 microscope with Lumencor SOLA light engine, DAPI and Cy5 filter cubes, Hamamatsu ORCA FLASH4.0 sCMOS camera (500 ms exposure time per plane for Quasar 670).

Pixel size 100 nm XY.

Z-step size 200 nm.

32 planes (power of 2 is optimal for GPU deconvolution). With 500 ms exposure time, the Quasar 670 GADPH FISH probes ...


Geoexes - My Dos Executables - Use At Your Own Risk, George Mcnamara Dec 2013

Geoexes - My Dos Executables - Use At Your Own Risk, George Mcnamara

George McNamara

The downloadable ZIP file contains old Turbo Pascal programs I wrote. These ran in Microscoft DOS and in early Windows (ex. Windows 3.1) DOS shells. They may or may not work in recent (Windows 2000, XP, Vista, 7) cmd or command "shells". No warranty. Use at your own risk. I do not expect to ever program in Turbo Pascal again so if anyone wants to "take over" my old code (and adjust copyirght notices, warnings, etc), please email me. In particular, MATH.exe had 10,000 lines of pascal code in it. Another program is LUTSconv.exe which converted ...


Stellaris Fishing 20131125mon Part 1 Of 2, George Mcnamara Nov 2013

Stellaris Fishing 20131125mon Part 1 Of 2, George Mcnamara

George McNamara

Stellaris FISH dataset using three FISH probe sets. Slides courtesy of Biosearch Technologies,

https://www.biosearchtech.com/store/product.aspx?catid=224,318,324

see http://stellarisfish.smugmug.com/ for online gallery by Biosearch.

This experiment was to evaluate the crosstalk between the Biosearch fluorophores:

Quasar 570

CAL Fluor Red 610 (CFR 610)

Quasar 670

DAPI (DNA counterstain)

Autofluorescence (green, but sometimes showing up in other channels).

and our lab's Leica DMI6000 fluorescence microscope with Leica filter sets:

DAPI

GFP (L5)

Cy3 (N3)

Texas Red (TxRed2)

Cy5 (Y5)

I also acquired green channel and red channel with exciter filters ...


Stellaris Fishing 20131125mon Part 2 Of 2, George Mcnamara Nov 2013

Stellaris Fishing 20131125mon Part 2 Of 2, George Mcnamara

George McNamara

Stellaris FISH dataset using three FISH probe sets.

Slides courtesy of Biosearch Technologies,

https://www.biosearchtech.com/store/product.aspx?catid=224,318,324

see http://stellarisfish.smugmug.com/ for online gallery by Biosearch.

This experiment was to evaluate the crosstalk between the Biosearch fluorophores:

Quasar 570

CAL Fluor Red 610 (CFR 610)

Quasar 670

DAPI (DNA counterstain)

Autofluorescence (green, but sometimes showing up in other channels).

and our lab's Leica DMI6000 fluorescence microscope with Leica filter sets:

DAPI

GFP (L5)

Cy3 (N3)

Texas Red (TxRed2)

Cy5 (Y5)

I also acquired green channel and red channel with exciter filters ...


Leica Microscope Gpu Deconvolution Stellaris Fish Dataset #1, George Mcnamara Nov 2013

Leica Microscope Gpu Deconvolution Stellaris Fish Dataset #1, George Mcnamara

George McNamara

McNamara 20131101Fri Leica widefield microscope CUDA Deconvolution Stellaris FISH probe cultured cells dataset #1.zip

A text file in the zip archive has experiment details. I am posting this online so that researchers - whether academic or commercial - can evaluate the acquired data, the Bruce and Butte 2013 Optics Express ( http://www.opticsinfobase.org/oe/fulltext.cfm?uri=oe-21-4-4766 ) deconvolution result (note: I may not have used optimal settings), and to compare these deconvolution results to other methods. If anyone generates alternative spatial deconvolution output, such as from: * SVI Huygens * Media Cy AutoQuant * Agard's ER-Decon (Arigovindan 2013 PNAS) * Vicidomini SGP ...


Population Fluctuations And Distribution Of Staging Eared Grebes (Podiceps Nigricollis) In North America, Anthony J. Roberts, Michael R. Conover, John Luft, John Neil Oct 2013

Population Fluctuations And Distribution Of Staging Eared Grebes (Podiceps Nigricollis) In North America, Anthony J. Roberts, Michael R. Conover, John Luft, John Neil

Wildland Resources Faculty Publications

Eared Grebes (Podiceps nigricollis Brehm, 1831) use saline ecosystems throughout much of their life cycle, and greater than 90% of the North American population stage during fall at two hypersaline lakes. At one of these lakes, Great Salt Lake (GSL), Utah, a commercial harvest of brine shrimp (Artemia franciscana Kellogg, 1906) cysts occurs during fall and may impact Eared Grebe populations. We used photo surveys on the other hypersaline lake, Mono Lake, California, and on the GSL, as well as aerial counts on the GSL, to describe population fluctuations of Eared Grebes staging on these lakes. The long-term (1997–2012 ...


Goby Climbing Selection, Dominica Versus Hawaii, Sandy M. Kawano, William C. Bridges, Heiko L. Schoenfuss, Takashi Maie, Richard W. Blob Sep 2013

Goby Climbing Selection, Dominica Versus Hawaii, Sandy M. Kawano, William C. Bridges, Heiko L. Schoenfuss, Takashi Maie, Richard W. Blob

All Data Sets

Data set containing morphology data that was used for the selection analyses in the article "Differences in locomotor behavior correspond to different patterns of morphological selection in two species of waterfall-climbing gobiid fishes" Evolutionary Ecology, September 2013, Volume 27, Issue 5, pp 949-969.


Hamamatsu Flash4.0 Scmos Exposure Time Series, George Mcnamara Aug 2013

Hamamatsu Flash4.0 Scmos Exposure Time Series, George Mcnamara

George McNamara

Hamamatsu FLASH4.0 scientific cMOS camera exposure time series are pairs of images of:

1 millisecond (00,001ms series)

10 millisecond (00,010ms series)

100 millisecond (00,100ms series)

1,000 millisecond (01,000ms series)

4,000 millisecond (04,000ms series)

10,000 millisecond (10,000ms series)

I also included:

* difference images (exposure 2 minus exposure 1 plus 100 intensity values).

* a series of eleven 1 second (1,000 ms) exposure time images in a multi-plane TIFF file (different images than the pair of 1,000ms images above).

* Stack Arithmetic: Median, Average, Minimum, Maximum, of the eleven plane series (Stack ...


A Discussion With Mary Gardiner About Lady Beetles, Matthew E. O'Neal, Erin W. Hodgson, Mary Gardiner Aug 2013

A Discussion With Mary Gardiner About Lady Beetles, Matthew E. O'Neal, Erin W. Hodgson, Mary Gardiner

Matthew E. O'Neal

Dr. Mary Gardiner, assistant professor at the Ohio State University, visited ISU and gave a seminar about her research on the ladybeetles. Ladybeetles can play a positive role by feeding on pest like the soybean aphid. Mary's research is focused on the exotic multi-colored asian ladybeetle. This species is a voracious predator of soybean aphids, but is also a pest in our homes and to grape growers. Mary is documenting the role landscape plays in the establishment of this species as part of her Buckeye Lady Beetle Blitz.


Special Topic 1b (2): Stereochemistry And Optical Activity, Mike A. Christiansen Jul 2013

Special Topic 1b (2): Stereochemistry And Optical Activity, Mike A. Christiansen

Mike Christiansen

The purpose of this video is to help second-year organic chemistry students review the concepts and questions that most frequently appear on standardized entrance exams, like the MCAT, DAT, PCAT, and GRE. In this video I'll share a personal anecdote about sign language the International House of Pancakes (IHOP). Then I'll continue by explaining chirality and teaching you how to assign R and S configurations to molecules that have stereocenters (also called chiral centers). I'll teach you how to assign molecules as being enantiomers or diastereomers, how to assign alkenes as being E or Z, and how ...


Effects Of Increasing Age On Fecundity Of Old-Aged Canada Geese (Branta Canadensis), Michael R. Conover May 2013

Effects Of Increasing Age On Fecundity Of Old-Aged Canada Geese (Branta Canadensis), Michael R. Conover

Wildland Resources Faculty Publications

Conover, M. R. 2013. Effects of increasing age on fecundity of old-aged Canada geese (Branta canadensis). Waterbirds 36: 378-384.


Shape Changes In Hyoid Arch Elements In Four Shark Species, Isabel S. Nowinowski May 2013

Shape Changes In Hyoid Arch Elements In Four Shark Species, Isabel S. Nowinowski

Senior Honors Projects

The hyoid arch is critical in expanding the oral cavity during feeding and ventilation in fishes. The elements of the hyoid arch vary widely in morphology among fish taxa. The hyoid arch is medial to the jaws and is made up of paired hyomandibular cartilages (HY) dorsally, paired ceratohyal cartilages (CH) ventral to the HY, and a single, medial basihyal cartilage (BH) that interconnects the two sides. As the jaws open, the CH-BH complex is depressed expanding the floor of the oral cavity. The coracohyoideus muscle pulls the BH ventroposteriorly, which in turn swings the CH ventroposteriorly. As the coracohyoideus ...


A Need For Green: An Approach For Motivating Environmentally Sustainable Practices At The University Of Rhode Island, Alyssa Mason, Mary Vidal May 2013

A Need For Green: An Approach For Motivating Environmentally Sustainable Practices At The University Of Rhode Island, Alyssa Mason, Mary Vidal

Senior Honors Projects

“Never underestimate the power of a few committed people to change the world. Indeed, it is the only thing that ever has." -Margaret Meade

Colin Beavan’s No Impact Man details his yearlong experiment to live without creating any environmental impact. As sophomores we were inspired by Beavan’s journey but also skeptical of living a completely no-impact lifestyle as college-students. Although we were motivated to try to live sustainably, our efforts were dormant until our junior year. That year we decided that we would attempt to live up to the standards set forth by Beavan--understanding that some practices would ...


A Literature Review Of Risk Factors For The Development Of Breast Cancer: Risks And Prevention Methods, Anna K. Manneschmidt May 2013

A Literature Review Of Risk Factors For The Development Of Breast Cancer: Risks And Prevention Methods, Anna K. Manneschmidt

Chancellor’s Honors Program Projects

No abstract provided.


Responding To Farm-Related Injuries, Charles V. Schwab Apr 2013

Responding To Farm-Related Injuries, Charles V. Schwab

Charles V. Schwab

No abstract provided.


Flash4 Dark Reference Images, George Mcnamara Apr 2013

Flash4 Dark Reference Images, George Mcnamara

George McNamara

Hamamatsu FLASH4.0 dark reference images, acquired with 10 second exposure times, no light to camera. Camera offset (set by Hamamatsu( is ~100 (the average intensity of the first image is always ~1 intensity level higher - an odd feature, but trivial in practice for a 16-bit camera).

George McNamara, Ph.D.

Single Cells Analyst at L.J.N. Cooper Lab

University of Texas M.D. Anderson Cancer Center


Pubspectra Tattletales, George Mcnamara Feb 2013

Pubspectra Tattletales, George Mcnamara

George McNamara

Tattletales for Multiplex Fluorescent Reporters in Single Cells for Metabolomics

George McNamara

As of April 2013: L.J.N. Cooper & D.A. Lee Cellular Immunotherapy Lab, University of Texas M.D. Anderson Cancer Center, Houston, TX

Email: gtmcnamara@mdanderson.org, geomcnamara@earthlink.net

Tattletales is my concept for spatial multiplexing many fluorescent protein (FP) biosensors in the same live cell. For example, there are excellent FP biosensors to Ca++ ions, pH, glucose, ribose, glutamine, glutamate, ATP, redox, ROS, pyruvate, cAMP, cGMP, IP3, PI(3,4,5)P3, cell cycle indicators (Fucci2), PKA, PKC, photsphatases, caspase(s) [1, 2]. However, these are typically used one biosensor per experiment, due in part to flooding the cell with soluble biosensor. That is, conventionally, either a metabolite (glucose) reporter or a signal transduction (Ca++) reporter can be imaged. By flooding the cell with the reporter, signal to noise ratio is compromized by autofluorescence.

Tattletales takes advantage of spatial multiplexing to both increase the number of different reporters, and improve signal to noise ratio by localizing each biosensor to a small volume. I started with the observation by Robinett et al [3] who localized 512 GFP-nls-LacI to a 256 LacO array as a 200 nm diameter diffraction limited spot (nuclear background due to overexpression). Many thousands of DNA binding proteins, of known sequence specifities, exist (LacI, TetR, GalR, etc for cell line studies; ZF-FPs, TALE-FPs to STRs, telomere repeat binding factors-FPs, etc for primary cells) and can be fused (as cDNAs) to different fluorescent proteins and FP biosensors.

Many biosensors are available as affinity series [1, 4], now enabling extended dynamic range. I realized that spatial multiplexing of many DNA binding protein-reporters by localizing to different spots in the cell nucleus and distinguished by combinatorial addressing, where N address colors provide 2^N addresses (example, 3 colors is 2^3 = 8 combinations). Multiplexing ...


Ungulate Damage To Safflower In Utah, Michael J. Haney, Michael R. Conover Feb 2013

Ungulate Damage To Safflower In Utah, Michael J. Haney, Michael R. Conover

Wildland Resources Faculty Publications

In Utah, farmers are concerned that ungulates are damaging safflower (Carthamus tinctorius) fields. We examined elk (Cervus elaphus) and mule deer (Odocoileus hemionus) damage to safflower production in San Juan County, Utah during 2009 and 2010. We collected data on damaged safflower plants within 28 fields, totaling 1,581 ha (13 fields totaling 963 ha during 2009; 15 fields totaling 618 ha during 2010). We compared 3 methods to assess yield losses: ungulate-proof exclosures, adjacent plant compensation method, and counting the number of damaged plants in 50-m transects (safflower count method). Exclosures were of limited use because they could not ...


Helix Turn Helix Domain, David J. Hall Jan 2013

Helix Turn Helix Domain, David J. Hall

Protein Domains

Helix turn helix domain #3V1A. The helix-turn helix is a DNA-binding domain. The two alpha helices are the reading or recognition helices, which bind in a groove in the DNA and recognize specific gene regulatory sequences in the DNA.


Ig Domain, David J. Hall Jan 2013

Ig Domain, David J. Hall

Protein Domains

Ig domain #2CKN. This particular domain is named for the first protein in which it was found, the immunoglobulin. An immunoglobulin is a antibody. Antibodies are generated by our immune system to recognize the specific size, shape and charge of pathogens. This domain is also found on the extracellular portion of many receptors including the interleukin-1 family of receptors.


Sh3 Domain, David J. Hall Jan 2013

Sh3 Domain, David J. Hall

Protein Domains

SH3 domain #1NEB. Src-homology 3 (SH3) domains bind to Pro-rich peptides that form a left-handed poly-Pro type II helix, with the minimal consensus Pro-X-X-Pro. Each Pro is usually preceeded by an aliphatic residue. Each in the aliphatic-Pro pair binds to a hydrophobic pocket on the SH3 domain.


Sh2 Domain, David J. Hall Jan 2013

Sh2 Domain, David J. Hall

Protein Domains

SH2 domain #1BFJ. Src-homology 2 (SH2) domains are modules of ~100 amino acids that bind to specific phospho tyrosine (pY) containing peptide motifs. Conventional SH2 domains have a conserved pocket that recognizes pY, and a more variable pocket that binds 3-6 residues C-terminal to the pY and confers specificity.


Ring Domain, David J. Hall Jan 2013

Ring Domain, David J. Hall

Protein Domains

Ring domain #1CHC. The RING finger is a specialized type of Zn finger consisting of 40–60 residues that binds two atoms of zinc, and is involved in mediating protein—protein interactions. Many zinc fingers bind nucleic acids. The presence of a RING finger domain is a characteristic of RING-class E3 ubiquitin protein ligases capable of transferring ubiquitin from an E2 enzyme to a substrate protein.


Beta Barrel, David J. Hall Jan 2013

Beta Barrel, David J. Hall

Protein Domains

Beta barrel (cyan fluorescent protein) #4AR7. This fluorescent protein is a variation of green fluorescent protein from a jellyfish and is the only domain that is a complete protein. The protein is routinely used to visualize a variety of biological processes. The beta barrel domain is a beta sheet wrapped around the fluorescent active site to provide structure.


Phi X 174, David J. Hall Jan 2013

Phi X 174, David J. Hall

Infectious Pathogens

Phi X 174 database number # 1CD3. Phi X 174 is a virus that infects bacteria and was the first DNA-based genome to be sequenced in 1977. This bacteriophage has a [+] circular single-stranded DNA genome. The assembly of the capsid has been successfully done in vitro and is the focus of many studies on self-assembly, drug delivery and nanotechnology.


Human Papilloma Virus 16, David J. Hall Jan 2013

Human Papilloma Virus 16, David J. Hall

Infectious Pathogens

Human Papilloma virus 16, database# 1DZL Infection by most papillomaviruses is either asymptomatic or causes small benign tumors, known as papillomas or warts (e.g. human papillomavirus HPV6 or HPV11). Papillomas caused by some types, however, such as human papillomaviruses 16 and 18, carry a risk of becoming cancerous. Human papilloma virus is a non-enveloped, double stranded, circular DNA virus.


Dengue Virus, David J. Hall Jan 2013

Dengue Virus, David J. Hall

Infectious Pathogens

Dengue virus, database # 1THD Dengue fever, is an infectious tropical disease caused by the dengue virus and transmitted by mosquito. Symptoms include fever, headache, muscle and joint pains, and a characteristic skin rash that is similar to measles. In a small proportion of cases the disease develops into the life-threatening dengue hemorrhagic fever. Dengue is a positive strand RNA virus that is part of the flavivirus family. Dengue is an enveloped virus meaning it has a nucleocapsid protecting the RNA and the nucleocapsid is surrounded by lipids (hence the name enveloped).


Hepatitis B, David J. Hall Jan 2013

Hepatitis B, David J. Hall

Infectious Pathogens

Hepatitis B, database # 2g33. Hepatitis B is an infectious inflammatory illness of the liver caused by the hepatitis B virus (HBV). Hepatitis B virus (HBV) is a member of the Hepadnavirus family.The virus particle, (virion) consists of an outer lipid envelope and an icosahedral nucleocapsid core composed of protein. These virions are 42 nM in diameter. The nucleocapsid encloses the viral DNA and a DNA polymerase that has reverse transcriptase activity.


Meyer Navigator: User Scanimage Functions To Show X/Y Positions Of The Stage/Objective In A Coordinate System, Stephan Meyer Zum Alten Borgloh Jan 2013

Meyer Navigator: User Scanimage Functions To Show X/Y Positions Of The Stage/Objective In A Coordinate System, Stephan Meyer Zum Alten Borgloh

Gilbert Laboratory

These Matlab functions extend Janelia Farms' ScanImage microscope control software. The functions allow the user to view, mark and track positions of the motor stage/objective in x, y, and z, which get displayed in a separate window. This helps to keep track of the stage movements, regions of interest and makes it easy to document areas imaged and map out the specimen being investigated. For detailed information about the functionality as well as installation, view the included manual file.


Holyoke Dam, Connecticut River, 2013, Brett Towler Jan 2013

Holyoke Dam, Connecticut River, 2013, Brett Towler

Fish Passage Data Archive

Holyoke River

Connecticut Dam

Massachusetts

Year data collected: 2013