Biology Commons^™

Time Series Data For 3b Image Processing, George Mcnamara

George McNamara

Time series data for 3B image processing

Four time series data sets of Stellaris single molecules RNA FISH (fluorescence in situ hybridization). All four datasets are 301 imaqe planes. FISH probes are to TOP1 mRNA (Topoisomerase I)in Saos osterosarcoma cells.

One dataset is 10 millisecond exposures (very dim), acquired in Streaming acquisition mode (no hardware overhead).

The other three datasets are a three consecutive planes of the same XY field of view.

I have included image processing results for:

PiMP - a fast method developed by Sebastian Munck et al 2012, http://www.ncbi.nlm.nih.gov/pubmed/?term=22357945

and greatly improved performance by Glen Macdonald (Seattle). …

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

Video Codec Performance (Excel Spreadsheet), George Mcnamara

George McNamara

Video codec performance (Excel spreadsheet). Movie was made in 2005-2006 when I worked at City of Hope National Medical Center. VTLF refers to Video Timelapse Light Facility. Videos were outputted from MetaMorph as AVI files. Personally, I always recommend uncompressed video files fro scientific uses. I also encourage posting the original scientific data format (ex. .lsm, .zvi, .lif, .stk).

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 …

Characterization Of Genes Required For Preimplantation Embryo Development, Marc P. Maserati Jr

Marc P Maserati Jr

Preimplantation embryo development in the mouse is a time of rapid cellular morphological and molecular changes leading to embryo implantation for the generation of offspring. The Mager lab studies these events occuring between fertilization and implantation in order to better understand the initial events which set the stage for all future aspects of development. The result of this research impacts many scientific disciplines including in-vitro based means of embryo culture, establishment of epigenetic marks, differentiation and cellular reprogramming and can be used in translational research for the improvement of in-vitro culture techniques and develop novel therapies such as cell replacement …

Halloween 2012 Jack O'Lanterns Trick Or Treat, George Mcnamara

George McNamara

Halloween 2012 makes trick or treating more visual and interactive than in past years.

the download is a ZIP file containing three files.

Print out the (unnumbered) image on as large and nice printer paper as possible - I used glossy 44" wide here in Miami (University of Miami, MillerSchool of Medicine, Calder Library, Biomedical Communications dept - I also made another print on "fabric", also 44" wide to take with me to an HHMI Janelia Farm conference on 'turning images into knowledge' that ends on Oct 31 - might stay up for a second conference, "GFP..." that start Nov …

Mcnamara 20120831fri-20120904tue Cosmic Ray Particles By Ccd Imaging, George Mcnamara

George McNamara

McNamara 20120831Fri-20120904Tue Cosmic Ray Particles by CCD imaging.zip contains image files in support of a Microscopy Today article - please see

http://www.microscopy-today.com/

Cosmic Ray Particles Images With Orca-Ii Erg, George Mcnamara

George McNamara

Cosmic ray particles image series acquired using a Hamamatsu ORCA-II ERG scientific grade CCD camera, cooled to -60 C. Each image is a consecutive 600 second (10 minute) exposure time with no light to the camera.

While processing the data, I discoverd that the background changed around planes 25 and 227 (see Excel file and jpeg screenshots), so I also processed only planes 025-227 (203 planes total, 2030 minutes, 33.83 hours). the CCD industry "rule of thumb" for a "typical" CCD sensor (i.e. 1/3" CCD) is that one cosmic ray particle strikes a sensor approximately every 30 seconds (assuming not …

Flatbed Scanner Report - Optical Density Dynamic Range, George Mcnamara

George McNamara

George McNamara (now at University of Miami) report for Hua Yu and Richard Jove, City of Hope National Medical Center, on optical density dynamic range of several flatbed scanners.

Introduction To Nanoscopy Nano-Talk, George Mcnamara

George McNamara

T7-1 is the designation for the LMRG Nanoscopy session at ABRF in Orlando, FL, on March 20, 2012. The PDF file here is a draft of my presentation.

May not be very helpful since (1) would probably help to know what is in my head and each slide will [hopefully] prompt me to say, and (2) 10 minute talk so I am going to push the "next slide" button after saying very little.

__________________

Publisher statement:

The T7-1 Introduction to Nanoscopy Nano Talk is copyrighted (c) George McNamara, 2012. Except for (1) screenshots from research articles (which are copyrighted by …

Pubspectra - Open Data Access Fluorescence Spectra, George Mcnamara

George McNamara

The Internet is enabling greater access to spectral imaging publications, spectral graphs, and data than that was available a generation ago. The spectral imaging systems discussed in this issue of Cytometry work because reagent and hardware spectra are reproducible, reusable, and provide input to spectral unmixing and spectral components recognition algorithms. These spectra need to be readily available in order to determine what to purchase, how to use it, and what the output means. We refer to several commercially sponsored and academic spectral web sites and discuss our spectral graphing and data sites. Sites include fluorescent dye graph servers from …

Mcnamara 2011 Feature Extraction (Image Analysis), George Mcnamara

George McNamara

Feature Extraction presentation and movies in a ZIP file from a presentation I gave at ISAC 2011 in Baltomore, Md.

Feature extraction is one phrase for image analysis.

Rogers Pmn Movie - Background Information, George Mcnamara

George McNamara

Please see

http://mdc.custhelp.com/app/answers/detail/a_id/18689/~/metamatters-newsletters

for my series of MetaMorph MetaMatters articles in volume 2, numbers 3 through 6, on the Rogers PMN Panorama data set.

http://mdc.custhelp.com/app/answers/detail/a_id/18689/~/metamatters-newsletters

Brief summary (for more, see the Word doc)

Determining The Optimal Concentration Of Mannose As An Effective Selection Agent For Transformed Oil Palm Cells Using The Phosphomannose Isomerase (Pmi) Gene As A Positive Selectable Marker, Norzulaani Khalid

Norzulaani Khalid

The elimination of antibiotic or herbicide resistance gene usage in genetically modified plants is being encouraged due to public concern. In response to this, alternative selection systems for the recovery of transgenic oil palm were developed using positive selectable markers. To establish a selection system that utilises the phosphomannose isomerase (pmi) gene for oil palm transformation, we first determined the optimal mannose concentration for selecting the transformed cells. Non-transformed embryogenic calli were cultured on media containing various combinations and concentrations of mannose and a usable source of carbon, i.e. sucrose, ranging in content from 0 to 30 g litre . …

Boesenbergia Rotunda: From Ethnomedicine To Drug Discovery, Norzulaani Khalid

Norzulaani Khalid

Boesenbergia rotunda is a herb from the Boesenbergia genera under the Zingiberaceae family. B. rotunda is widely found in Asian countries where it is commonly used as a food ingredient and in ethnomedicinal preparations. The popularity of its ethnomedicinal usage has drawn the attention of scientists worldwide to further investigate its medicinal properties. Advancement in drug design and discovery research has led to the development of synthetic drugs from B. rotunda metabolites via bioinformatics and medicinal chemistry studies. Furthermore, with the advent of genomics, transcriptomics, proteomics, and metabolomics, new insights on the biosynthetic pathways of B. rotunda metabolites can be …

In Vitro Plant Regeneration, Antioxidant And Antibacterial Studies On Broccoli, Brassica Oleracea Var. Italica, Rosna Binti Mat Taha

Rosna Binti Mat Taha

Leaf and shoot tip explant of Brassica oleracea var. italica were inoculated on Murashige and Skoog (MS) basal medium supplemented with various concentrations of (BAP) and (IBA), alone and in combinations to achieve plant regeneration. Subsequently, antioxidant and antibacterial activities were determined from In vitro and In vivo plant parts. The highest mean numbers of shoot was observed on combinations of 1 mg l(-1) and 1.5 mg l(-1) of BAP and IBA, 9.49 and 8.69, respectively. The highest number of shoot produced (11.55) per shoot tip explant was recorded on 2.5 mg l(-1) BAP. In addition, highest percentage of roots …

Mcnamara 2011 Mpmicro - Multi-Probe Microscopy (10/31/2011), George Mcnamara

George McNamara

Multi-Probe Microscopy is an ~1500 page Word document summarizing what I know and/or found interesting in light microscopy, fluorescence microscopy and digital image analysis, from 1995-2005. Very little has been updated since 2005.

Optimization Of Two-Dimensional Gel Electrophoresis Protocols For Boesenbergia Rotunda In Vitro Suspension Culture, Norzulaani Khalid

Norzulaani Khalid

Boesenbergia rotunda belongs to the Zingiberaceae family and is abundant in the Southeast Asia. It is widely used as food ingredient and traditional medicine. Biologically, the plant extract contains pharmaceutically important bioactive compounds that exhibit anti-HIV protease, antibacterial, antifungal, anti-inflammatory, anti-tumor and antioxidant activities. Proteomics approaches to study the proteins and/or enzymes involved in the biosynthesis of these compounds are challenging due to the complexity of plant samples and the presence of interfering substances. Here, we describe the development a highly robust and reproducible two-dimensional gel electrophoresis (2DE) protocols for resolving the proteome of B. rotunda suspension cultures.

Effect Of Benzylaminopurine (Bap) Pulsing On In Vitro Shoot Multiplication Of Musa Acuminata (Banana) Cv. Berangan, Norzulaani Khalid

Norzulaani Khalid

MS (Murashige and Skoog) media supplemented with benzylaminopurine (BAP) showed that the number of bud formation in shoot cultures of Musa acuminata cv.Berangan during the initiation stage increased proportionately with the concentrations used (11, 22 and 33 μM). However, the highest concentration of BAP (33 μM) simultaneously increased the formation of abnormal shoots. After the first apical bud appeared, explants were transferred to MS medium with lower concentrations of BAP either with or without indole acetic acid (IAA). Proliferation media supplemented with IAA showed enhanced shoot multiplication and elongation but did not help to reduce the abnormality index that occurred

Rapid Micropropagation Of Boesenbergia Rotunda (L.) Mansf. Kulturpfl. (A Valuable Medicinal Plant) From Shoot Bud Explants, Norzulaani Khalid

Norzulaani Khalid

A successful protocol was developed for mass propagation of Boesenbergia rotunda (L.) Mansf. Kulturpfl., an important medicinal plant. Numerous shoots were induced from young shoot bud of B. rotunda mature rhizome on Murashige and Skoog (1962) medium supplemented with 30.0 g/l sucrose, 2.0 g/l gelrite, different concentrations of 6-benzylaminopurine (BAP) and α-naphtaleneacetic acid (NAA). Plant medium supplemented with different concentrations of BAP alone or with NAA produced varying degree of multiple shoots. A supplementation of 2.0 mg/l BAP and 0.5 mg/l NAA gave the best result. Ninety percent of the explants induced multiple shoots within 10 to 14 days of …

Determining The Optimal Concentration Of Mannose As An Effective Selection Agent For Transformed Oil Palm Cells Using The Phosphomannose Isomerase (Pmi) Gene As A Positive Selectable Marker, Norzulaani Khalid

Norzulaani Khalid

The elimination of antibiotic or herbicide resistance gene usage in genetically modified plants is being encouraged due to public concern. In response to this, alternative selection systems for the recovery of transgenic oil palm were developed using positive selectable markers. To establish a selection system that utilises the phosphomannose isomerase (pmi) gene for oil palm transformation, we first determined the optimal mannose concentration for selecting the transformed cells. Non-transformed embryogenic calli were cultured on media containing various combinations and concentrations of mannose and a usable source of carbon, i.e. sucrose, ranging in content from 0 to 30 g litre . …

Total Phenolic Contents, Antioxidant And Antimicrobial Activities Of Bruguiera Gymnorrhiza, Rosna Binti Mat Taha

Rosna Binti Mat Taha

In the present work, the antioxidant and antibacterial activities of methanolic, ethanolic and chloroform crude extract of leaves and barks of Bruguiera gymnorrhiza were investigated. The antioxidant activity of the crude extracts were evaluated using the enzymatic and non enzymatic methods namely superoxide dismutase determination, reducing power assay and 2, 2-diphenyl-1-picrylhydrazil free radical scavenging assays. Folin-ciocalteu reagent method was used to estimate the amount of total phenolic compounds of the extracts. Ethanol extract of barks showed the best result in all antioxidant assays which was positively co-related with the total phenolic contents. There was no significant difference between the IC(50) …

Effect Of Picloram, Additives And Plant Growth Regulators On Somatic Embryogenesis Of Phyla Nodiflora (L.) Greene, Rosna Binti Mat Taha

Rosna Binti Mat Taha

The present study describes the plant regeneration via somatic embryogenesis in suspension culture derived from the leaf and stem explants of Phyla nodiflora. The medium type, plant growth regulators, complex extract (coconut milk and malt extract) and anti-oxidant (activated charcoal, ascorbic acid, Polyvinylpyrrolidone and citric acid) markedly influenced the embryo regeneration of P. nodiflora. MS with 2,4-D and activated charcoal (10 mg/L) gave the highest stimulation of embryogenic callus growth. Optimized callus was transfered into suspension culture, which showed the globular, heart shaped embryos in MS with 2,4-D + BA + picloram (0.1 mg/L), coconut milk (10 ml/L), citric acid …

Species Boundaries And Evolutionary Lineages In The Blue Green Damselfishes Chromis Viridis And Chromis Atripectoralis (Pomacentridae), Philadelphia University

Philadelphia University, Jordan

No abstract provided.

A Quantitative Taqman Mgb Real-Time Polymerase Chain Reaction Based Assay For Detection Of The Causative Agent Of Crayfish Plague Aphanomyces Astaci, Torstein Tengs

Dr. Torstein Tengs

Here we present the development and first validation of a TaqMan minor groove binder (MGB) real-time polymerase chain reaction (RT-PCR) method for quantitative and highly specific detection of Aphanomyces astaci, the causative agent of crayfish plague. The assay specificity was experimentally assessed by testing against DNA representative of closely related oomycetes, and theoretically assessed by additional sequence similarity analyses comparing the primers and probe sequences to available sequences in EMBL/GenBank. The target of the assay is a 59 bp unique sequence motif of A. astaci found in the internal transcribed spacer 1 of the nuclear ribosomal gene cluster. A standard …

A Kinetic Model For Growth And Biosynthesis Of Medium-Chain-Length Poly-(3-Hydroxyalkanoates) In Pseudomonas Putida, Irene Tan Kit Ping

Irene Tan Kit Ping

A kinetic model is presented giving a mathematical description of batch culture of Pseudomonas putida PGA1 grown using saponified palm kernel oil as carbon source and ammonium as the limiting nutrient. The growth of the micro-organism is well-described using. Tessier-type model which takes into account the inhibitory effect of ammonium at high concentrations. The ammonium consumption rate by the cells is related ill proportion to the rate of growth. The intracellular production of medium-chain-length poly(3-hydroxyalkanoates) (PHA(MCL)) by P. putida PGA1 cells is reasonably modeled by the modified Luedeking-Piret kinetics, which incorporate a function of product Synthesis inhibition (or reduction) by …