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Timelapse Data - Gm Imaging Cytometer Needs Stitching Part 1 Of 2, George McNamara 2014 The University of Texas

Timelapse Data - Gm Imaging Cytometer Needs Stitching Part 1 Of 2, George Mcnamara

George McNamara

Timelapse data - GM imaging cytometer needs stitching part 1 of 2

Imaging challenge: align multiple time series over time to overcome "stage slop" in the imaging cytometer used in this experiment.

http://works.bepress.com/gmcnamara/53 (this)

and

http://works.bepress.com/gmcnamara/54 (next)

are zip files containing 8-bit stacks (MetaMorph multiplane TIFF files) acquired on an imaging cytometer.

"53" is the brightfield data, raw and automatic aligned stacks in MetaMorph (Apps menu, MM7.8.6).

"54" is GFP fluorescence, raw and automatic aligned stacks in MetaMorph (Apps menu, MM7.8.6). The GFP fluorescence decreases over time ...


Timelapse Data - Gm Imaging Cytometer Needs Stitching Part 2 Of 2, George McNamara 2014 The University of Texas

Timelapse Data - Gm Imaging Cytometer Needs Stitching Part 2 Of 2, George Mcnamara

George McNamara

Timelapse data - GM imaging cytometer needs stitching part 2 of 2

Imaging challenge: align multiple time series over time to overcome "stage slop" in the imaging cytometer used in this experiment.

http://works.bepress.com/gmcnamara/53 (previous) and http://works.bepress.com/gmcnamara/54 (this)

are zip files containing 8-bit stacks (MetaMorph multiplane TIFF files) acquired on an imaging cytometer.

"53" is the brightfield data, raw and automatic aligned stacks in MetaMorph (Apps menu, MM7.8.6). "54" is GFP fluorescence, raw and automatic aligned stacks in MetaMorph (Apps menu, MM7.8.6). The GFP fluorescence decreases over time ...


Rictor/Mtorc2 Loss In The Myf5 Lineage Reprograms Brown Fat Metabolism And Protects Mice Against Obesity And Metabolic Disease, Chien-Min Hung, Camila Martinez Calejman, Joan Sanchez-Gurmaches, Huawei Li, Clary B. Clish, Simone Hettmer, Amy J. Wagers, David A. Guertin 2014 University of Massachusetts Medical School

Rictor/Mtorc2 Loss In The Myf5 Lineage Reprograms Brown Fat Metabolism And Protects Mice Against Obesity And Metabolic Disease, Chien-Min Hung, Camila Martinez Calejman, Joan Sanchez-Gurmaches, Huawei Li, Clary B. Clish, Simone Hettmer, Amy J. Wagers, David A. Guertin

GSBS Student Publications

The in vivo functions of mechanistic target of rapamycin complex 2 (mTORC2) and the signaling mechanisms that control brown adipose tissue (BAT) fuel utilization and activity are not well understood. Here, by conditionally deleting Rictor in the Myf5 lineage, we provide in vivo evidence that mTORC2 is dispensable for skeletal muscle development and regeneration but essential for BAT growth. Furthermore, deleting Rictor in Myf5 precursors shifts BAT metabolism to a more oxidative and less lipogenic state and protects mice from obesity and metabolic disease at thermoneutrality. We additionally find that Rictor is required for brown adipocyte differentiation in vitro and ...


Fty720 (Fingolimod) Provides Insight Into The Molecular Mechanisms Of Multiple Sclerosis, Madelyn Elizabeth Crawford 2014 University of Tennessee, Knoxville

Fty720 (Fingolimod) Provides Insight Into The Molecular Mechanisms Of Multiple Sclerosis, Madelyn Elizabeth Crawford

Pursuit - The Journal of Undergraduate Research at the University of Tennessee

Multiple sclerosis (MS) is a neurodegenerative disorder caused by a prolonged immune- mediated inflammatory response that targets myelin. Nearly all of the drugs approved for the treatment of MS are general immunosuppressants or only function in symptom management. The oral medication fingolimod, however, is reported to have direct therapeutic effects on cells of the central nervous system in addition to immunomodulatory functions. Fingolimod is known to interact with sphingosine-1-phosphate (S1P) receptors, and the most widely- accepted theory for its mechanism of action is functional antagonism of the receptor. This review examines significant neuromodulatory effects achieved by functional antagonism of the ...


The Role Of The N-Terminus On The Enzymatic Activity Of Dutpase From Dictyostelium Discoideum, Kyle C. Varon 2014 University of Nebraska - Lincoln

The Role Of The N-Terminus On The Enzymatic Activity Of Dutpase From Dictyostelium Discoideum, Kyle C. Varon

Dissertations and Theses in Biological Sciences

The enzyme deoxyuridine triphosphatase (dUTPase) (EC 3.6.1.23) converts dUTP to dUMP, thus shifting the dUTP to dUMP ratio in the cell. The molecule dUTP is subject to mis-incorporation into DNA due to lack of distinguishing by DNA polymerase. Uracil incorporation can be repaired with base excision repair mechanisms but may create overwhelming DNA strand breaks proving to be detrimental to the cell. Most dUTPases of eukaryotes are homotrimeric and contain five highly conserved motifs responsible for catalysis and substrate binding. Many dUTPases of eukaryotes possess a leading and core region in their sequence. The core region is ...


Vitamin A Deficiency Causes Ovulation Abnormalities In Mice, Rebecca Ursin 2014 DePaul University

Vitamin A Deficiency Causes Ovulation Abnormalities In Mice, Rebecca Ursin

DePaul Discoveries

Retinoic acid (RA) is an active metabolite of vitamin A (VA) and is involved in tissue organization, patterning, and growth. RA has been shown to regulate male reproduction, however information on its role in ovary development is limited. To investigate the functions of RA in the ovary, we examined its role in ovary development and ovulation using an in vivo dietary VA-deprivation animal model. Our preliminary results have shown that VA deficiency causes a variety of ovarian pathologies, including reduced numbers of total follicles and corpus lutea, formation of hemorrhagic and atretic follicles, and formation of bursa and follicular cysts ...


Determining The Potential Activity Of Wnt Signaling During Zebrafish Oocyte Maturation, Nathan Pincus 2014 University of Puget Sound

Determining The Potential Activity Of Wnt Signaling During Zebrafish Oocyte Maturation, Nathan Pincus

Honors Program Theses

During maturation, the oocyte (immature egg) progresses from prophase I to metaphase II of meiosis and a multitude of cellular changes occur. In zebrafish, oocyte maturation is triggered by 17α,20β-dihydroprogesterone (DHP), which binds to a membrane-bound receptor, however the extent of communication between the oocyte and its environment is not fully understood. Wnt signaling pathways are known to regulate gene expression, cell behavior, cell adhesion, and cell polarity, as well as play an essential role in embryonic development. In this study, I investigated the potential activity of Wnt signaling pathways during zebrafish oocyte maturation by examining the gene expression ...


Tattletales And T-Bow Update 20140602mon, George McNamara 2014 The University of Texas

Tattletales And T-Bow Update 20140602mon, George Mcnamara

George McNamara

Tattletales and T-Bow Update 20140602Mon

http://works.bepress.com/gmcnamara/42

Please see also http://works.bepress.com/gmcnamara/26

Tattletales: multiplex fluorescent protein biosensors by spatial localization with TALE-FPs, Cas9-FPs, ZF-FPs, LacI-FPs, TetR-FPs, etc.

T-Bow: Rainbow T-cells and Tumor cells (and ES cells, iPS cells, other cells and organisms). You can think of this as "Brainbow meets TALENs/Cas9/ZFNs/other DNA sequence specific binding proteins".

If not familiar with Brainbow, see

http://en.wikipedia.org/wiki/Brainbow

If not familiar with TALENs, Cas9, etc, see

http://www.addgene.org/genome_engineering/

Big idea: localizing fluorescent proteins - and/or Nano-Lanterns ...


Chlorovirus Skp1 And Core Ankyrin-Repeat Protein Interplay And Mimicry Of Cellular Ubiquitin Ligase Machinery, Eric Andrew Noel 2014 University of Nebraska - Lincoln

Chlorovirus Skp1 And Core Ankyrin-Repeat Protein Interplay And Mimicry Of Cellular Ubiquitin Ligase Machinery, Eric Andrew Noel

Dissertations and Theses in Biological Sciences

The ubiquitin-proteasome system is a common target of several unrelated viruses that have evolved convergent strategies to redirect host ubiquitin machinery to serve their own needs. Members of the genus Chlorovirus, a group of large dsDNA viruses that infect certain freshwater chlorella-like green algae, encode a conserved Skp1 homolog and ankyrin-repeat (ANK) proteins, some of which contain C-terminal domains characteristic of cellular F-boxes or related viral PRANC domains. These observations suggested that this unique combination of chlorovirus proteins either interact with or imitate the key components of the SCF (Skp1-Cul1-F-box) ubiquitin ligases. Using mass spectrometry, we identified two functional classes ...


Branching Into Rnai: Synthesis, Characterization And Biology Of Branch And Hyperbranch Sirnas, Anthony Muriithi Maina 2014 Seton Hall University

Branching Into Rnai: Synthesis, Characterization And Biology Of Branch And Hyperbranch Sirnas, Anthony Muriithi Maina

Seton Hall University Dissertations and Theses (ETDs)

The cancer epidemic continues to afflict millions of humans world-wide each year and despite a renewed hope with the development of new and improved forms of therapy, a cure for cancer remains an elusive goal. This is partly related to the rise of resilient forms of tumors that have evolved with resistance towards conventional chemotherapy and radiation treatments. Moreover, these non-specific therapeutic regimens are highly toxic, leading to severe immunosuppressive effects which poisons the body and compromises the road towards remission. In an effort to mitigate these limitations, cancer-targeting approaches are currently experiencing a renaissance in the translation of new ...


The Role Of Integrins In Support Of Pancreatic Function, Survival And Maturation, Matthew Riopel 2014 Western University

The Role Of Integrins In Support Of Pancreatic Function, Survival And Maturation, Matthew Riopel

University of Western Ontario - Electronic Thesis and Dissertation Repository

The pancreas is a glandular organ composed of endocrine and exocrine compartments. Integrins are cell adhesion molecules that connect cells to the extracellular matrix (ECM). Integrins modulate a variety of cellular effects, yet their mechanism of action in the developed pancreas is not well understood. Fibrin is a provisional ECM protein that contains ligands for integrin receptors. Fibrin is capable of supporting islet health, but it is unclear how fibrin exerts its effects. The objective of this thesis is to understand the role of integrin receptors on in vivo pancreatic cell function, survival, and proliferation. In addition, this thesis investigates ...


Multiple Transcription Factors Directly Regulate Hox Gene Lin-39 Expression In Ventral Hypodermal Cells Of The C. Elegans Embryo And Larva, Including The Hypodermal Fate Regulators Lin-26 And Elt-6, Wan-Ju Liu, John S. Reece-Hoyes, Albertha J. M. Walhout, David M. Eisenmann 2014 University of Massachusetts Medical School

Multiple Transcription Factors Directly Regulate Hox Gene Lin-39 Expression In Ventral Hypodermal Cells Of The C. Elegans Embryo And Larva, Including The Hypodermal Fate Regulators Lin-26 And Elt-6, Wan-Ju Liu, John S. Reece-Hoyes, Albertha J. M. Walhout, David M. Eisenmann

Program in Systems Biology Publications and Presentations

BACKGROUND: Hox genes encode master regulators of regional fate specification during early metazoan development. Much is known about the initiation and regulation of Hox gene expression in Drosophila and vertebrates, but less is known in the non-arthropod invertebrate model system, C. elegans. The C. elegans Hox gene lin-39 is required for correct fate specification in the midbody region, including the Vulval Precursor Cells (VPCs). To better understand lin-39 regulation and function, we aimed to identify transcription factors necessary for lin-39 expression in the VPCs, and in particular sought factors that initiate lin-39 expression in the embryo.

RESULTS: We used the ...


Phenotypic Variation In The Model Organism, Danio Rerio, Rachel D. Champaigne, Kim H. Brown 2014 Portland State University

Phenotypic Variation In The Model Organism, Danio Rerio, Rachel D. Champaigne, Kim H. Brown

Student Research Symposium

Model organisms are used to study evolutionary conserved traits. Zebrafish (Danio rerio) are used a model organism because of their highly fecundity, external fertilization, and robust nature, making them highly adaptable to environmental and genetic variation. In an effort to limit data variation that lies outside of topic interest, phenotypic measures of variation must be performed, understood, and taken into consideration for future studies. A common measurement of phenotypic variation in fish is in the maximum (Ucrit) swimming speeds. Inter and intra-strain variation in zebrafish Ucrit swimming speeds will be observed in a swim tunnel. Baseline values will be recorded ...


Transcriptome Analysis Of Sea Lamprey Embryogenesis, Zakary Ilya Yermolenko 2014 Seton Hall University

Transcriptome Analysis Of Sea Lamprey Embryogenesis, Zakary Ilya Yermolenko

Seton Hall University Dissertations and Theses (ETDs)

The sea lamprey (Petromyzon marinus) has survived throughout evolution for hundreds of millions of years. It is considered an invasive species to the Great Lakes that has caused dramatic changes in the ecosystem for fish communities resulting in the collapse of a fishing industry that was previously valued at billions of dollars. Successful management of the sea lamprey is essential to a sustainable fishing industry and biodiversity. Therefore sea lamprey embryos were studied at various stages of development by growing them in a simulated habitat. RNAs from adult female ovaries and embryos at different time points during embryogenesis were extracted ...


Timelapse Data - Gm Vandana 20140502fri Part 1 Of 2, George McNamara 2014 The University of Texas

Timelapse Data - Gm Vandana 20140502fri Part 1 Of 2, George Mcnamara

George McNamara

Timelapse data - GM Vandana 20140502Fri part 1 of 2

(positions 1, 2 and 3).

Data from a project with Vandana Kaul, Univ Houston. Vandana and GM know the details of this experiment. Nikon BioStation IM, 20x effective magnification (Nikon 40x lens with de-zoom), 800x600 pixels (by 2x2 binning). Five positions (P1 ... P5), acquired at 1 frame per minute, playback 30 fps.


Timelapse Data - Gm Vandana 20140502fri Part 2 Of 2, George McNamara 2014 The University of Texas

Timelapse Data - Gm Vandana 20140502fri Part 2 Of 2, George Mcnamara

George McNamara

Timelapse data - GM Vandana 20140502Fri part 2 of 2

(positions 4 and 5 of 5).

Data from a project with Vandana Kaul, Univ Houston. Vandana and GM know the details of this experiment. Nikon BioStation IM, 20x effective magnification (Nikon 40x lens with de-zoom), 800x600 pixels (by 2x2 binning). Five positions (P1 ... P5), acquired at 1 frame per minute, playback 30 fps.

Videos 1, 2 and 3 are in "part 1" at

http://works.bepress.com/gmcnamara/48/


The Association Between The Il-1 Pathway, Isaac C. Wun 2014 Texas Medical Center Library

The Association Between The Il-1 Pathway, Isaac C. Wun

UT GSBS Dissertations and Theses (Open Access)

Cutaneous malignant melanoma (CMM) is a potentially lethal malignancy that warrants attention and further research, as it is known to that there is an increasing rate of incidence in theUnited States, and it is also known that exposure to UV light is its most crucial risk factor, and family history of melanoma is also an important risk factor. Melanoma is an aggressive and lethal cancer in humans. There are an estimated new 132,000 melanoma cases annually worldwide, and the trend has doubled in the past 20 years. However, attempts to treat melanoma have encountered considerable resistance and remained ineffective ...


Molecular Chaperone Tools For Use Against Neurodegenerative Diseases, Matthew Tinkham 2014 University of Rhode Island

Molecular Chaperone Tools For Use Against Neurodegenerative Diseases, Matthew Tinkham

Senior Honors Projects

A noted characteristic found in several neurodegenerative disorders, including Alzheimer’s Disease, Parkinson’s Disease, Huntington’s Disease and bovine spongiform encephalopathy, is the accumulation of amyloid plaques in the brain. Amyloid plaques contain deposits of fibrillar aggregates of misfolded proteins that disrupt normal functionality in neurons. Certain variants of these misfolded proteins are self-replicating; these self-replicating amyloids are termed prions (for infectious protein). We are interested in how protein misfolding contributes to amyloid formation and how molecular chaperone proteins can change the formation of amyloid deposits. Chaperone proteins function by catalyzing the proper folding of other proteins, the refolding ...


Defining The Sites Of Interaction Of The Fancd2, Fance, And Fancl Proteins, Joseph McClanaghan 2014 University of Rhode Island

Defining The Sites Of Interaction Of The Fancd2, Fance, And Fancl Proteins, Joseph Mcclanaghan

Senior Honors Projects

Fanconi anemia (FA) is a rare genetic disease characterized by congenital defects, bone marrow failure and increased cancer susceptibility. FA is caused by mutations in any one of 16 genes. These genes encode for proteins that function in the FA-BRCA pathway to repair damaged DNA. Because of its important r­­­ole in DNA repair, this pathway is considered a major cellular tumor suppressor pathway, i.e. is critical for the prevention of cancer. Underscoring this fact, several of the FA genes - including BRCA2, BRIP1, PALB2, and RAD51C - are bona fide breast and ovarian cancer susceptibility genes.

My project involves studying ...


Exploration Of Mutations In Erythroid 5-Aminolevulinate Synthase That Lead To Increased Porphyrin Synthesis, Erica Jean Fratz 2014 University of South Florida

Exploration Of Mutations In Erythroid 5-Aminolevulinate Synthase That Lead To Increased Porphyrin Synthesis, Erica Jean Fratz

Graduate School Theses and Dissertations

5-Aminolevulinate synthase (ALAS; EC 2.3.1.37) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the first committed step of heme biosynthesis in animals, the condensation of glycine and succinyl-CoA yielding 5-aminolevuliante (ALA), CoA, and CO2. Murine erythroid-specific ALAS (mALAS2) variants that cause high levels of PPIX accumulation provide a new means of targeted, and potentially enhanced, photosensitization. Transfection of HeLa cells with expression plasmids for mALAS2 variants, specifically for those with mutated mitochondrial presequences and a mutation in the active site loop, caused significant cellular accumulation of PPIX, particularly in the membrane. Light treatment of HeLa ...


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