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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 images …

Conservation In The Context Of Climate Change: Practical Guidelines For Land Protection At Local Scales, Kevin Ruddock, Peter August, Christopher Damon, Charles Labash, Pamela Rubinoff, Donald Robadue Jr.

Peter August

Climate change will affect the composition of plant and animal communities in many habitats and geographic settings. This presents a dilemma for conservation programs – will the portfolio of protected lands we now have achieve a goal of conserving biodiversity in the future when the ecological communities occurring within them change? Climate change will significantly alter many plant communities, but the geophysical underpinnings of these landscapes, such as landform, elevation, soil, and geological properties, will largely remain the same. Studies show that extant landscapes with a diversity of geophysical characteristics support diverse plant and animal communities. Therefore, geophysically diverse landscapes …

The Empire Of Cancer: Gene Patents And Cancer Voices, Matthew Rimmer

Matthew Rimmer

In his book, The Emperor of All Maladies, Siddhartha Mukherjee writes a history of cancer — ‘It is a chronicle of an ancient disease — once a clandestine, “whispered-about” illness — that has metamorphosed into a lethal shape-shifting entity imbued with such penetrating metaphorical, medical, scientific, and political potency that cancer is often described as the defining plague of our generation’.Increasingly, an important theme in the history of cancer is the role of law, particularly in the field of intellectual property law. It is striking that a number of contemporary policy debates over intellectual property and public health have concerned …

Definition Of An Hla-Dpw2-Restricted Epitope On Ns3, Recognized By A Dengue Virus Serotype-Cross-Reactive Human Cd4+ Cd8- Cytotoxic T-Cell Clone, Ichiro Kurane, Li Chen Dai, Peter G. Livingston, Elaine Reed, Francis A. Ennis

Li Dai

We previously reported that the clone JK34 was cross-reactive for dengue virus types 1, 2, 3, and 4 and recognized NS3 (I. Kurane, M. A. Brinton, A. L. Samson, and F. A. Ennis, J. Virol. 65:1823-1828, 1991). In the present experiments, we defined the epitope at the amino acid level, with 93 15-mer overlapping peptides which cover the entire NS3. A peptide 4 which contains amino acids 251 to 265 of NS3 sensitized the autologous B lymphoblastoid cell line (LCL) to the lysis by JK34. The smallest peptide recognized by JK34 was a 10-mer peptide which contains amino acids 255 …

Mutation Of Human Immunodeficiency Virus Type 1 At Amino Acid 585 On Gp41 Results In Loss Of Killing By Cd8+ A24-Restricted Cytotoxic T Lymphocytes, Li Chen Dai, Kim West, Rebecca A. Littaua, Kazuo Takahashi, Francis A. Ennis

Li Dai

A human leukocyte antigen A24-restricted CD8+ cytotoxic T-cell clone specific for gp41 of human immunodeficiency virus type 1 was isolated from an infected individual. The epitope was localized to amino acids 584 to 591 (YLKDQQLL, NL43 env sequence) of gp41 by using a panel of recombinant vaccinia viruses that contain truncated env genes and synthetic peptides. The clone killed autologous B-lymphoblastoid cell lines pulsed with a synthetic peptide reflecting the sequence of the IIIB and MN strains. This clone, however, failed to kill target cells pulsed with the peptides that have a mutation from Lys to Arg or Gln at …

A Prospective Study Of The Transient Decrease In Ovarian Cancer Risk Following Childbirth, Qin Liu, Mats Lambe, Inkyung Baik, Sven Cnattingius, Tomas Riman, Anders R. Ekbom, Hans-Olov Adami, Chung-Cheng Hsieh

Qin Liu

Epidemiologic evidence shows that the risk of ovarian cancer is decreased following childbirth. We examined the time points when the decreased risk of postpartum maternal ovarian cancer reaches the lowest point and whether the protective effect diminishes over time. A case-control study nested within the Swedish Fertility Register included 10,086 cases of epithelial ovarian cancer recorded in the Swedish Cancer Register from 1961 to 2001. From the Fertility Register, 49,249 eligible subjects matched to the cases by age were selected as controls. The analysis contrasted risk between adjacent parities through logistic regression models that included indicator variables representing each year …

Profiles Of Human Serum Antibody Responses Elicited By Three Leading Hiv Vaccines Focusing On The Induction Of Env-Specific Antibodies, Michael Vaine, Shixia Wang, Qin Liu, James Arthos, David C. Montefiori, Paul Goepfert, M. Juliana Mcelrath, Shan Lu

Qin Liu

In the current report, we compared the specificities of antibody responses in sera from volunteers enrolled in three US NIH-supported HIV vaccine trials using different immunization regimens. HIV-1 Env-specific binding antibody, neutralizing antibody, antibody-dependent cell-mediated cytotoxicity (ADCC), and profiles of antibody specificity were analyzed for human immune sera collected from vaccinees enrolled in the NIH HIV Vaccine Trial Network (HVTN) Study #041 (recombinant protein alone), HVTN Study #203 (poxviral vector prime-protein boost), and the DP6-001 study (DNA prime-protein boost). Vaccinees from HVTN Study #041 had the highest neutralizing antibody activities against the sensitive virus along with the highest binding antibody …

Correlation Of Umbilical Cord Blood Hormones And Growth Factors With Stem Cell Potential: Implications For The Prenatal Origin Of Breast Cancer Hypothesis, Todd M. Savarese, William C. Strohsnitter, Hoi Pang Low, Qin Liu, Inkyung Baik, William C. Okulicz, David P. Chelmow, Pagona Lagiou, Peter J. Quesenberry, Kenneth L. Noller, Chung-Cheng Hsieh

Qin Liu

INTRODUCTION: Prenatal levels of mitogens may influence the lifetime breast cancer risk by driving stem cell proliferation and increasing the number of target cells, and thereby increasing the chance of mutation events that initiate oncogenesis. We examined in umbilical cord blood the correlation of potential breast epithelial mitogens, including hormones and growth factors, with hematopoietic stem cell concentrations serving as surrogates of overall stem cell potential. METHODS: We analyzed cord blood samples from 289 deliveries. Levels of hormones and growth factors were correlated with concentrations of stem cell and progenitor populations (CD34+ cells, CD34+CD38- cells, CD34+c-kit+ cells, and granulocyte-macrophage colony-forming …

A Functional Notch-Survivin Gene Signature In Basal Breast Cancer, Connie Wing-Ching Lee, Karl Simin, Qin Liu, Janet Plescia, Minakshi Guha, Ashraf Khan, Chung-Cheng Hsieh, Dario C. Altieri

Qin Liu

INTRODUCTION: Basal-type, or triple-negative, breast cancer (lacking estrogen receptor, progesterone receptor, and human epidermal growth factor receptor-2 expression) is a high-risk disease for which no molecular therapies are currently available. We studied genetic signatures of basal breast cancer potentially suitable for therapeutic intervention. METHODS: We analyzed protein expression of the Notch-1 intracellular domain and survivin by immunohistochemistry in a series of basal breast cancer patients. A hierarchical clustering and overall survival analysis was carried out on a microarray mRNA database of 232 breast cancer patients. Fifteen published mRNA datasets containing estrogen receptor-negative or estrogen receptor-positive samples were subjected to meta-analysis …

Environmental And Socio-Economic Considerations For Aquaculture In Jervis Bay, Nsw, Alyssa Joyce, Ana M. Rubio, Pia C. Winberg

Dr Pia C Winberg

No abstract provided.

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 Fractint MAP lookup tables …

Impact Of Vehicular Traffic On Herpetofaunal Mortality In A Savannah Forest, Eastern Sri Lanka, Sujan Henkanaththegedara, Suranjan Karunarathna, A. A. Thasun Amarasinghe

Sujan Henkanaththegedara

Biology Department Receives Grant To Assess Juvenile Horseshoe Crab Populations In Long Island Sound, Jennifer Mattei

Jennifer Mattei

No abstract provided.

Biology Department Receives Grant To Assess Juvenile Horseshoe Crab Populations In Long Island Sound, Mark Beekey

Mark Beekey

No abstract provided.

Identification Of Disufide Bond Formation Between Mitoneet And Glutamate Dehydrogenase 1, Morgan E. Roberts, Jacquelyn P. Crail, Megan M. Laffoon, William G. Fernandez, Michael A. Menze, Mary E. Konkle

Michael Menze

MitoNEET is a protein that was identified as a drug target for diabetes, but its cellular function as well as its role in diabetes remains elusive. Protein pull-down experiments identified glutamate dehydrogenase 1 (GDH1) as a potential binding partner. GDH1 is a key metabolic enzyme with emerging roles in insulin regulation. MitoNEET forms a covalent complex with GDH1 through disulfide bond formation and acts as an activator. Proteomic analysis identified the specific cysteine residues that participate in the disulfide bond. This is the first report that effectively links mitoNEET to activation of the insulin regulator GDH1.

Differential Habitat Use By Common Watersnakes (Nerodia Sipedon), Lorin A. Neuman-Lee, Andrew M. Durso, Nicholas M. Kiriazis, Melanie J. Olds, Stephen J. Mullin

Stephen J. Mullin

Understanding intraspecific variation in habitat use is important for the management of any species. In many studies of reptiles, habitat use by juveniles is poorly understood when compared to their adult conspecifics because of capture biases and logistical constraints. We compared habitat use between sexes and age classes of Common Watersnakes (Nerodia sipedon) at a reservoir in central Illinois. Juvenile N. sipedon occurred more frequently in habitat with high canopy cover, whereas adult N. sipedon, especially reproductive females, were found exclusively in habitat with no canopy cover. Adult males used both locations equally. We emphasize the need to investigate ontogenetic …

The North American Carbon Program Multi-Scale Synthesis And Terrestrial Model Intercomparison Project – Part 1: Overview And Experimental Design, D. N. Huntzinger, C. Schwalm, A, M, Michalak, K. Schaefer, A. W. King, Y. Wei, A. Jacobson, S. Liu, R. B. Cook, W. M. Post, G. Berthier, D Hayes, M. Huang, A. Ito, H. Lei, Chaoqun (Crystal) Lu, J. Mao, C. H. Peng, S. Peng, B. Poulter, D. Ricciuto, X. Shi, Hanqin Tian, W. Wang, N. Zeng, F. Zhao, Q. Zhu

Chaoqun (Crystal) Lu

Terrestrial biosphere models (TBMs) have become an integral tool for extrapolating local observations and understanding of land–atmosphere carbon exchange to larger regions. The North American Carbon Program (NACP) Multi-scale synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal model intercomparison and evaluation effort focused on improving the diagnosis and attribution of carbon exchange at regional and global scales. MsTMIP builds upon current and past synthesis activities, and has a unique framework designed to isolate, interpret, and inform understanding of how model structural differences impact estimates of carbon uptake and release. Here we provide an overview of the MsTMIP effort …

Effects Of Rest Interval Length On Smith Machine Bench Press Performance And Perceived Exertion In Trained Men, Ramires A. Tibana, Denis C. Vieira, Vitor Tajra, Martim Bottaro, Belmiro F. De Salles, Jeffrey Willardson, Jonato Prestes

Jeffrey Willardson

This study compared two different rest intervals (RI) between sets of resistance exercise. Ten resistance-trained men (M age = 24.3, SD = 3.5 yr.; M weigh t= 80.0 kg, SD = 15.3; M height = 1.75 m, SD = 0.04) performed five sets of Smith machine bench presses at 60% of one repetition maximum, either with 1.5 min. or 3 min. RI between sets. Their repetition performance, total training volume, velocity, fatigue, rating of perceived exertion, and muscular power were measured. All of these measures indicated that performance was significantly better and fatigue was significantly lower in the 3 min. …

Adult Mortality And Progeny Production Assessment Of Callosobruchus Maculatus (Coleoptera: Bruchidae) Exposed To Sayan®, Adel Khashaveh

Adel Khashaveh

The insecticidal efficacy of Sayan®, an Iranian formulation of diatomaceous earth, was evaluated against adults of Cowpea weevil, Callosobruchus maculatus (Coleoptera: Bruchidae) on cowpea. Sayan® was applied at the dose rates of 0.0, 0.1, 0.2, 0.5, 1.0 g/kg. One kg of cowpea was treated with appropriate dose rate and after one day, four samples of 50 g of each were taken as replication. Twenty five adults were introduced into each replication. The number of dead adults was counted after 24 and 72 h exposure. After mortality count, all surviving insects were removed and the samples retained under the same conditions …

La Diversidad De Los Analisis De Diversidad [The Diversity Of Diversity Analyses], Victor D. Carmona

Victor D. Carmona-Galindo

There is a lack of consistency with respect to the use of the terms like species richness, diversity and biodiversity, which extends to the analysis of diversity indices and the merit of using diversity indices in the evaluation (comparison and contrast) of biological communities. The purpose of this article is to provide working definitions for these terms and cite examples from the primary literature that demonstrate the utility of estimating richness, evaluating proportional abundance patterns, as well as comparing indices of diversity and similarity to study patterns of biological organization at different ecological scales. Additionally, we provide a manual in …

Phosphatidic Acid Interacts With A Myb Transcription Factor And Regulates Its Nuclear Localization And Function In Arabidopsis, Xuemin Wang, Hongyan Yao, Geliang Wang, Liang Guo

Xuemin (Sam) Wang

Ultra-Deep Pyrosequencing Of Partial Surface Protein Genes From Infectious Salmon Anaemia Virus (Isav) Suggest Novel Mechanisms Involved In Transition To Virulence, Torstein Tengs Dr.

Dr. Torstein Tengs

Uncultivable HPR0 strains of infectious salmon anaemia viruses (ISAVs) infecting gills are non-virulent putative precursors of virulent ISAVs (vISAVs) causing systemic disease in farmed Atlantic salmon (Salmo salar). The transition to virulence involves two molecular events, a deletion in the highly polymorphic region (HPR) of the hemagglutinin-esterase (HE) gene and a Q266→L266 substitution or insertion next to the putative cleavage site (R267) in the fusion protein (F). We have performed ultra-deep pyrosequencing (UDPS) of these gene regions from healthy fish positive for HPR0 virus carrying full-length HPR sampled in a screening program, and a vISAV strain from an ISA outbreak …

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 in our ASI excitation wheel:

GFP + 492 exciter

Texas Red (TxRed2) + 572 …

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 in our ASI excitation wheel:

GFP + 492 exciter

Texas Red (TxRed2) + 572 …

Applying Life Cycle Assessment (Lca) To Aquaculture: A Case Study Of The Tasmanian Salmon Industry, A White, Daryl Mcphee, Tor Hundloe

Daryl McPhee

No abstract provided.

Future Management And Governance Of The Queensland East Coast Inshore Finfish Fishery, Daryl Mcphee

Daryl McPhee

No abstract provided.

Marine Park Planning And Fisheries Management In Australia: Understanding The Conflict And Designing A Better Future, Daryl Mcphee

Daryl McPhee

No abstract provided.

Likely Effectiveness Of Netting Or Other Capture Programs As A Shark Hazard Mitigation Strategy Under Western Australian Conditions, Daryl Mcphee

Daryl McPhee

No abstract provided.

Impacts Of The Moreton Bay Marine Park Rezoning On Commercial Fishermen, Casper Van De Greer, Morena Mills, Vanessa Adams, Robert Pressey, Daryl Mcphee

Daryl McPhee

The design of marine protected areas now typically incorporates socioeconomic data to minimize potential negative impacts on stakeholders. However, these data have limitations that are not well understood. Furthermore, whether the application of socioeconomic data in planning actually reduces avoidable negative impacts on stakeholders is rarely evaluated.

This study assessed impacts on commercial fishermen of the rezoning of the Moreton Bay Marine Park, in south eastern Queensland. Specifically, this study (1) compared estimates of opportunity costs of new no-take zones from before and after the rezoning was implemented, and (2) identified impacts of the new zoning scheme on fishing businesses …

Homeotic Gene Teashirt (Tsh) Has A Neuroprotective Function In Amyloid-Beta 42 Mediated Neurodegeneration., Michael M. Moran, Madhuri Kango-Singh, Amit Singh

Amit Singh

Background: Alzheimer's disease (AD) is a debilitating age related progressive neurodegenerative disorder characterized by the loss of cognition, and eventual death of the affected individual. One of the major causes of AD is the accumulation of Amyloid-beta 42 (Aβ42) polypeptides formed by the improper cleavage of amyloid precursor protein (APP) in the brain. These plaques disrupt normal cellular processes through oxidative stress and aberrant signaling resulting in the loss of synaptic activity and death of the neurons. However, the detailed genetic mechanism(s) responsible for this neurodegeneration still remain elusive. Methodology/ Principle Findings: We have generated a transgenic Drosophila eye model …