More Fish (1 Of 4), 2014 M.D. Anderson Cancer Center
More Fish (1 Of 4), George Mcnamara
George McNamara
More Stellaris FRISH and GPU Deconvolution, 20140313Thur - part 1 of 4
Please see other content in the FISH Imaging section of
http://works.bepress.com/gmcnamara/subject_areas.html
for details on the microscope. Briefly: Leica DMI6000 inverted microscope, SOLA lamp, Hamamatsu FLASH4.0 sCMOS camera, 100 nm XY, 200 nm Z pixels, 32 planes (16 um Z), MetaMorph 7.8 acquisition software.
Four zip files:
http://works.bepress.com/gmcnamara/43
http://works.bepress.com/gmcnamara/44
http://works.bepress.com/gmcnamara/45
http://works.bepress.com/gmcnamara/46
with two dataset (001, 002), raw and deconvolved using Bruce & Butte GPU deconvolution in Fiji ImageJ,
http://www.ncbi.nlm.nih.gov/pubmed/23482010
http://www.opticsinfobase.org/vjbo/fulltext.cfm?uri=oe-21-4-4766&id=249375 (free download, as are all Optics Express papers).
http://tcell.stanford.edu/software.html
http://lists.umn.edu/cgi-bin/wa?A2=ind1312&L=confocalmicroscopy&P=5534
Note: "001 raw" (bepress 43) contains my "imaging SOP" …
More Fish (2 Of 4), 2014 M.D. Anderson Cancer Center
More Fish (2 Of 4), George Mcnamara
George McNamara
More Stellaris FISH and GPU Deconvolution, 20140313Thur - part 2 of 4
Please see other content in the FISH Imaging section of
http://works.bepress.com/gmcnamara/subject_areas.html
for details on the microscope. Briefly: Leica DMI6000 inverted microscope, SOLA lamp, Hamamatsu FLASH4.0 sCMOS camera, 100 nm XY, 200 nm Z pixels, 32 planes (16 um Z), MetaMorph 7.8 acquisition software.
Four zip files:
http://works.bepress.com/gmcnamara/43
http://works.bepress.com/gmcnamara/44
http://works.bepress.com/gmcnamara/45
http://works.bepress.com/gmcnamara/46
with two dataset (001, 002), raw and deconvolved using Bruce & Butte GPU deconvolution in Fiji ImageJ,
http://www.ncbi.nlm.nih.gov/pubmed/23482010
http://www.opticsinfobase.org/vjbo/fulltext.cfm?uri=oe-21-4-4766&id=249375 (free download, as are all Optics Express papers).
http://tcell.stanford.edu/software.html
http://lists.umn.edu/cgi-bin/wa?A2=ind1312&L=confocalmicroscopy&P=5534
Note: "001 raw" (bepress 43) contains my "imaging SOP" …
More Fish (3 Of 4), 2014 M.D. Anderson Cancer Center
More Fish (3 Of 4), George Mcnamara
George McNamara
More Stellaris FISH and GPU Deconvolution, 20140313Thur - part 3 of 4
Please see other content in the FISH Imaging section of
http://works.bepress.com/gmcnamara/subject_areas.html
for details on the microscope. Briefly: Leica DMI6000 inverted microscope, SOLA lamp, Hamamatsu FLASH4.0 sCMOS camera, 100 nm XY, 200 nm Z pixels, 32 planes (16 um Z), MetaMorph 7.8 acquisition software.
Four zip files:
http://works.bepress.com/gmcnamara/43
http://works.bepress.com/gmcnamara/44
http://works.bepress.com/gmcnamara/45
http://works.bepress.com/gmcnamara/46
with two dataset (001, 002), raw and deconvolved using Bruce & Butte GPU deconvolution in Fiji ImageJ,
http://www.ncbi.nlm.nih.gov/pubmed/23482010
http://www.opticsinfobase.org/vjbo/fulltext.cfm?uri=oe-21-4-4766&id=249375 (free download, as are all Optics Express papers).
http://tcell.stanford.edu/software.html
http://lists.umn.edu/cgi-bin/wa?A2=ind1312&L=confocalmicroscopy&P=5534
Note: "001 raw" (bepress 43) contains my "imaging SOP" …
More Fish (4 Of 4), 2014 M.D. Anderson Cancer Center
More Fish (4 Of 4), George Mcnamara
George McNamara
More Stellaris FISH and GPU Deconvolution, 20140313Thur - part 4 of 4
Please see other content in the FISH Imaging section of
http://works.bepress.com/gmcnamara/subject_areas.html
for details on the microscope. Briefly: Leica DMI6000 inverted microscope, SOLA lamp, Hamamatsu FLASH4.0 sCMOS camera, 100 nm XY, 200 nm Z pixels, 32 planes (16 um Z), MetaMorph 7.8 acquisition software.
Four zip files:
http://works.bepress.com/gmcnamara/43
http://works.bepress.com/gmcnamara/44
http://works.bepress.com/gmcnamara/45
http://works.bepress.com/gmcnamara/46
with two dataset (001, 002), raw and deconvolved using Bruce & Butte GPU deconvolution in Fiji ImageJ,
http://www.ncbi.nlm.nih.gov/pubmed/23482010
http://www.opticsinfobase.org/vjbo/fulltext.cfm?uri=oe-21-4-4766&id=249375 (free download, as are all Optics Express papers).
http://tcell.stanford.edu/software.html
http://lists.umn.edu/cgi-bin/wa?A2=ind1312&L=confocalmicroscopy&P=5534
Note: "001 raw" (bepress 43) contains my "imaging SOP" …
Different Expression Of Placental Pyruvate Kinase M2 In Normal, Preeclamptic, And Intrauterine Growth Restriction Pregnancies, 2014 Brigham Young University - Provo
Different Expression Of Placental Pyruvate Kinase M2 In Normal, Preeclamptic, And Intrauterine Growth Restriction Pregnancies, Brigham L. Bahr
Theses and Dissertations
This thesis will be organized into two chapters discussing the placental expression of two proteins, pyruvate kinase M2 (PKM2) and heat shock protein 27 (HSP 27), in human placentas. Understanding the mechanisms of placental metabolism in healthy and diseased placentas helps us understand how placenta disorders occur and how we can treat these disorders. The goal is to investigate these proteins to gain an understanding of their roles in placental disorders and help decrease maternal and fetal mortality rates. Chapter one covers the background of pyruvate kinase M2 (PKM2) in cancer and embryonic tissues, and the expression of PKM2 in …
Design And Synthesis Of 4-N-Alkanoyl And 4-N-Alkyl Gemcitabine Analogues Suitable For Positron Emission Tomography, 2014 Florida International University
Design And Synthesis Of 4-N-Alkanoyl And 4-N-Alkyl Gemcitabine Analogues Suitable For Positron Emission Tomography, Jesse E. Pulido
FIU Electronic Theses and Dissertations
Gemcitabine is a highly potent chemotherapeutic nucleoside agent used in the treatment of several cancers and solid tumors. However, it is therapeutically limitated because of toxicity to normal cells and its rapid intracellular deamination by cytidine deaminase into the inactive uracil derivative. Modification at the 4-(N) position of gemcitabine's exocyclic amine to an -amide functionality is a well reported prodrug strategy which has been that confers a resistance to intracellular deamination while also altering pharmacokinetics of the parent drug. Coupling of gemcitabine to carboxylic acids with varying terminal moieties afforded the 4-N-alkanoylgemcitabines whereas reaction of 4-N …
Evaluation Of Novel Oral Vaccine Candidates And Validation Of A Caprine Model Of Johne’S Disease, 2014 University of Georgia
Evaluation Of Novel Oral Vaccine Candidates And Validation Of A Caprine Model Of Johne’S Disease, Murray E. Hines Ii, Sue E. Turnquist, Marcia R.S. Ilha, Sreekumari Rajeev, Arthur L. Jones, Lisa Whittington, John P. Bannantine, Raul G. Barletta, Yrjö T. Gröhn, Robab Katani, Adel M. Talaat, Lingling Li, Vivek Kapur
School of Veterinary and Biomedical Sciences: Faculty Publications
Johne’s disease (JD) caused by Mycobacterium avium subspecies paratuberculosis (MAP) is a major threat to the dairy industry and possibly some cases of Crohn’s disease in humans. A MAP vaccine that reduced of clinical disease and/or reduced fecal shedding would aid in the control of JD. The objectives of this study were (1) to evaluate the efficacy of 5 attenuated strains of MAP as vaccine candidates compared to a commercial control vaccine using the protocol proposed by the Johne’s Disease Integrated Program (JDIP) Animal Model Standardization Committee (AMSC), and (2) to validate the AMSC Johne’s disease go at challenge model. …
Seorious Business: Structural Proteins In Sieve Tubes And Their Involvement In Sieve Element Occlusion [Review Article], 2014 Selected Works
Seorious Business: Structural Proteins In Sieve Tubes And Their Involvement In Sieve Element Occlusion [Review Article], Michael Knoblauch, Daniel R. Froelich, William F. Pickard, Winfried S. Peters
Winfried S. Peters
Skin Disease And Non-Syndromic Hearing Loss-Linked Cx30 Mutations Exhibit Several Distinct Cellular Pathologies, 2014 Western University
Skin Disease And Non-Syndromic Hearing Loss-Linked Cx30 Mutations Exhibit Several Distinct Cellular Pathologies, Amy Berger, John Kelly, Patrick Lajoie, Qing Shao, Dale Laird
Anatomy and Cell Biology Publications
Connexin 30 (Cx30), a member of the large gap junction protein family, plays a role in the homeostasis of the epidermis and inner ear through gap junctional intercellular communication (GJIC). Here, we investigated the underlying mechanisms of four autosomal dominant Cx30 gene mutations linked to hearing loss and/or various skin diseases. First, the T5M mutant linked to non-syndromic hearing loss formed functional gap junction channels and hemichannels, similar to wild type Cx30. The loss-of-function V37E mutant associated with Clouston syndrome or keratitis-ichthyosis-deafness syndrome was retained in the endoplasmic reticulum and significantly induced apoptosis. The G59R mutant linked to Vohwinkel and …
Recent Advances In The Molecular Characterization Of Circulating Tumor Cells, 2014 Western University
Recent Advances In The Molecular Characterization Of Circulating Tumor Cells, Lori E. Lowes, Alison L. Allan
Anatomy and Cell Biology Publications
Although circulating tumor cells (CTCs) were first observed over a century ago, lack of sensitive methodology precluded detailed study of these cells until recently. However, technological advances have now facilitated the identification, enumeration, and characterization of CTCs using a variety of methods. The majority of evidence supporting the use of CTCs in clinical decision-making has been related to enumeration using the CellSearch((R)) system and correlation with prognosis. Growing evidence also suggests that CTC monitoring can provide an early indication of patient treatment response based on comparison of CTC levels before and after therapy. However, perhaps the greatest potential that CTCs …
Cluster M Mycobacteriophages Bongo, Pegleg, And Rey With Unusually Large Repertoires Of Trna Isotopes, 2014 University of Pittsburgh - Main Campus
Cluster M Mycobacteriophages Bongo, Pegleg, And Rey With Unusually Large Repertoires Of Trna Isotopes, Welkin H. Pope, Kirk R. Anders, Madison Baird, Charles A. Bowman, Michelle M. Boyle, Gregory W. Broussard, Tiffany Chow, Kari L. Clase, Shannon Cooper, Kathleen A. Cornely, Randall J. Dejong, Veronique A. Delesalle, Lisa Deng, David Dunbar, Nicholas P. Edgington, Christina M. Ferreira, Kathleen Weston Hafer, Grant A. Hartzog, J. Robert Hatherill, Lee E. Hughes, Khristina Ipapo, Gregory P. Krukonis, Christopher G. Meier, Denise L. Monti, Matthew R. Olm, Shallee T. Page, Craig L. Peebles, Claire A. Rinehart, Michael R. Rubin, Daniel A. Russell, Erin R. Sanders, Morgan Schoer, Christopher D. Shaffer, James Wherley, Edwin Vazquez, Han Yuan, Daiyuan Zhang, Steven G. Cresawn, Deborah Jacobs-Sera, Roger W. Hendrix, Graham F. Hatfull
Biology Faculty Publications
Genomic analysis of a large set of phages infecting the common hostMycobacterium smegmatis mc2155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average …
Chip-Seq And Rna-Seq Reveal An Amrz-Mediated Mechanism For Cyclic Di-Gmp Synthesis And Biofilm Development By Pseudomonas Aeruginosa, 2014 The Ohio State University
Chip-Seq And Rna-Seq Reveal An Amrz-Mediated Mechanism For Cyclic Di-Gmp Synthesis And Biofilm Development By Pseudomonas Aeruginosa, Christopher J. Jones, David Newsom, Benjamin Kelly, Yasuhiko Irie, Laura K. Jennings, Binjie Xu, Dominique H. Limoli, Joe J. Harrison, Matthew R. Parsek, Peter White, Daniel J. Wozniak
Biology Faculty Publications
The transcription factor AmrZ regulates genes important for P. aeruginosa virulence, including type IV pili, extracellular polysaccharides, and the flagellum; however, the global effect of AmrZ on gene expression remains unknown, and therefore, AmrZ may directly regulate many additional genes that are crucial for infection. Compared to the wild type strain, a ΔamrZ mutant exhibits a rugose colony phenotype, which is commonly observed in variants that accumulate the intracellular second messenger cyclic diguanylate (c-di-GMP). Cyclic di-GMP is produced by diguanylate cyclases (DGC) and degraded by phosphodiesterases (PDE). We hypothesized that AmrZ limits the intracellular accumulation of c-di-GMP through transcriptional repression …
The Effects Of Aging On Skeletal Muscle Ampk Activation And An Analysis Of Chronic Aicar Treatment On The Aging Phenotype, 2014 Brigham Young University - Provo
The Effects Of Aging On Skeletal Muscle Ampk Activation And An Analysis Of Chronic Aicar Treatment On The Aging Phenotype, Shalene E. Hardman
Theses and Dissertations
AMP-activated protein kinase (AMPK), a metabolic regulator, acts in opposition to many of the effects of aging and may provide insights into the development of sarcopenia. However, the effect of aging on AMPK activation is unclear. The purpose of this dissertation was to: 1) clarify the controversy concerning the activation of AMPK in response to endurance-like exercise in aged skeletal muscle; 2) address mechanisms for the age-associated alterations in AMPK activation; and 3) address the known benefits of chronic AICAR treatment in aged skeletal muscle. First, to clarify the effect of age on AMPK activation, young adult (YA) (8 mo.) …
Endocannabinoid Biosynthetic Enzyme Mrna: Patterns Of Expression In Hippocampus And Ventral Tegmental Area And Effects On Synaptic Plasticity, 2014 Brigham Young University - Provo
Endocannabinoid Biosynthetic Enzyme Mrna: Patterns Of Expression In Hippocampus And Ventral Tegmental Area And Effects On Synaptic Plasticity, Collin Brutch Merrill
Theses and Dissertations
Endocannabinoids (eCBs) are lipophilic signals that are produced by postsynaptic neurons in an activity-dependent manner, and signal in a retrograde fashion to modulate neurotransmitter release. As such, eCBs are highly involved in synaptic plasticity, a process that strengthens or weakens synapses. eCB-mediated synaptic plasticity is involved in many brain processes including learning, short-term memory, and adaptive reward, which are processed in the hippocampus and ventral tegmental area (VTA), respectively. However, the expression of eCB biosynthetic enzyme mRNA within hippocampal and VTA neurons, as well as the relationship between these mRNA species and the occurrence of synaptic plasticity, remains unclear. The …
Vaccines Within Vaccines: The Use Of Adenovirus Types 4 And 7 As Influenza Vaccine Vectors, 2014 University of Nebraska-Lincoln
Vaccines Within Vaccines: The Use Of Adenovirus Types 4 And 7 As Influenza Vaccine Vectors, Eric A. Weaver
Nebraska Center for Virology: Faculty Publications
Adenovirus Types 4 and 7 (Ad4 and Ad7) are associated with acute respiratory distress (ARD). In order to prevent widespread Ad-associated ARD (Ad-ARD) the United States military immunizes new recruits using a safe and effective lyophilized wildtype Ad4 and Ad7 delivered orally in an enteric-coated capsule. We cloned Ad4 and Ad7 and modified them to express either a GFP-Luciferase (GFPLuc) fusion gene or a centralized influenza H1 hemagglutinin (HA1-con). BALB/c mice were injected with GFPLuc expressing viruses intramuscularly (i.m.) and intranasally (i.n.). Ad4 induced significantly higher luciferase expression levels as compared with Ad7 by both routes. Ad7 transduction was restored …
Deep Rna Sequencing Reveals Hidden Features And Dynamics Of Early Gene Transcription In Paramecium Bursaria Chlorella Virus 1, 2014 Aix-Marseille Universite
Deep Rna Sequencing Reveals Hidden Features And Dynamics Of Early Gene Transcription In Paramecium Bursaria Chlorella Virus 1, Guillaume Blanc, Michael Mozar, Irina V. Agarkova, James R. Gurnon, Giane Yanai-Balser, Janet M. Rowe, Yuannan Xia, Jean-Jack Riethoven, David D. Dunigan, James L. Van Etten
Nebraska Center for Virology: Faculty Publications
Paramecium bursaria chlorella virus 1 (PBCV-1) is the prototype of the genus Chlorovirus (family Phycodnaviridae) that infects the unicellular, eukaryotic green alga Chlorella variabilis NC64A. The 331-kb PBCV-1 genome contains 416 major open reading frames. A mRNA-seq approach was used to analyze PBCV-1 transcriptomes at 6 progressive times during the first hour of infection. The alignment of 17 million reads to the PBCV-1 genome allowed the construction of single-base transcriptome maps. Significant transcription was detected for a subset of 50 viral genes as soon as 7 min after infection. By 20 min post infection (p.i.), transcripts were detected for …
Inhibition Of Pim And Axl Kinases As Potential Treatments For A Variety Of Hematological Malignancies And Solid Tumors, 2014 Brigham Young University - Provo
Inhibition Of Pim And Axl Kinases As Potential Treatments For A Variety Of Hematological Malignancies And Solid Tumors, Kent James Carpenter
Theses and Dissertations
This thesis is divided into three chapters. In each case, the goal is to achieve inhibition of a growth kinase (PIM or AXL) and subsequent arrest of cell growth and induction of apoptosis (in vitro cell culture models) or decrease in tumor volume (in vivo xenograft studies). Chapter one and chapter two discuss inhibition of proviral integration site for Moloneymurine leukemia virus (PIM) kinases. The three PIM kinases, PIM-1, PIM-2, and PIM-3, are a subfamily of serine/threonine kinases that are known to be involved in signaling pathways as downstream effectors of signal transducer and activator of transcription-5 (STAT5) signaling and …
Immature Myeloid Cells Promote Tumor Formation Via Non-Suppressive Mechanism, 2014 University of South Florida
Immature Myeloid Cells Promote Tumor Formation Via Non-Suppressive Mechanism, Myrna Lillian Ortiz
USF Tampa Graduate Theses and Dissertations
ABSTRACT
Although there is ample evidence linking chronic inflammation with cancer, the cellular mechanisms involved in early events leading to tumor development remain unclear. Myeloid cells are an intricate part of inflammation. They consist of mature cells represented by macrophages, dendritic cells and granulocytes and a population of Immature Myeloid Cells (IMC), which in healthy individuals are cells in transition to mature cells. There is a substantial expansion of IMC in cancer and many other pathological conditions which is associated with pathologic activation of these cells. As a result, these cells acquire the ability to suppress immune responses and are …
Direct-To-Consumer Genetic Testing In The College Classroom: Knowledge, Attitudes, And Concerns Of Introductory Biology Students, 2014 Providence College
Direct-To-Consumer Genetic Testing In The College Classroom: Knowledge, Attitudes, And Concerns Of Introductory Biology Students, Nicanor Austriaco
Biology Faculty Publications
Pioneered by companies like 23andMe.com, deCODEme.com, and Navigenics.com, direct-to-consumer genetic testing refers to genetic tests that are marketed directly to consumers via television, print media, or the Internet. This kind of testing provides access to a customer’s genetic information without necessarily involving either a medical health care professional or a genetic counselor in the process. In recent years, a course offered to medical and graduate students at Stanford University has included an option for students to undergo personal genotyping, raising the possibility that direct-to-consumer genetic testing could also be incorporated into undergraduate biology courses to enhance student learning. In this …
3b Project Data - Raw Tiff Series And Cropped Series, 2014 M.D. Anderson Cancer Center
3b Project Data - Raw Tiff Series And Cropped Series, George Mcnamara
George McNamara
Fluorescence microscopy data acquired for 3B Bayesian localization microscopy.
Settings: 100 nm XY pixel size. 50 millisecond exposures, MetaMorph stream acquisition mode (as fast as possible). Stellaris FISH mammalian cells labeled with Quasar 670 fluorophores, one molecule per 20mer FISH probe, ~48 probes to TOP1 mRNA (Topoisomerase 1).
More on the 3B project and Stellaris FISH data at http://works.bepress.com/gmcnamara/38/
and at Susan Cox's web sites http://www.coxphysics.com/3b/ http://superresolved.com/