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Articles 1 - 21 of 21

Full-Text Articles in Life Sciences

Micrornas Are Necessary For Bmp-7-Induced Dendritic Growth In Cultured Rat Sympathetic Neurons, Vidya Chandrasekaran Sep 2019

Micrornas Are Necessary For Bmp-7-Induced Dendritic Growth In Cultured Rat Sympathetic Neurons, Vidya Chandrasekaran

Vidya Chandrasekaran

Neuronal connectivity is dependent on size and shape of the dendritic arbor. However, mechanisms controlling dendritic arborization, especially in the peripheral nervous system, are not completely understood. Previous studies have shown that bone morphogenetic proteins (BMPs) are important initiators of dendritic growth in peripheral neurons. In this study, we examined the hypothesis that post-transcriptional regulation mediated by microRNAs (miRNAs) is necessary for BMP-7-induced dendritic growth in these neurons. To examine the role of miRNAs in BMP-7-induced dendritic growth, microarray analyses was used to profile miRNA expression in cultured sympathetic neurons from the superior cervical ganglia of embryonic day 21 rat ...


Outward Currents Contributing To Inspiratory Burst Termination In Prebotzinger Complex Neurons Of Neonatal Mice Studied In Vitro, Rebecca Kray, Adam M. Goodreau, Thomas B. Arnold, Christopher A. Del Negro Jul 2019

Outward Currents Contributing To Inspiratory Burst Termination In Prebotzinger Complex Neurons Of Neonatal Mice Studied In Vitro, Rebecca Kray, Adam M. Goodreau, Thomas B. Arnold, Christopher A. Del Negro

Christopher Del Negro

We studied pre-Botzinger(preBotC) inspiratory interneurons to determine the cellular mechanisms that influence burst termination in a mammalian central pattern generator. Neonatal mouse slice preparations that retain pre-BoTC neurons generate respiratory motor rhythms in vitro. Inspiratory-related bursts rely on inward currents that flux Na+, thus outward currents coupled to Na+ accumulation are logical candidates for assisting in, or causing, burst termination. We examined Na+/K+/ATPase electrogenic pump current (Ipump), Na+-dependent K+ current, and ATP-dependent K+ current (IK-ATP). The pharmacological blockade of IPUMP, IK-Na, or IK-ATP caused pathological depolarization akin to a burst that ...


Data Collection Curated With An Application Ontology Describes The Methods And Results Upon Performing An Ex-Vivo Voltage-Clamp Assay On Outer Hair Cells Of The Mammalian Cochlea, Brenda Farrell, Jason Bengtson Jan 2019

Data Collection Curated With An Application Ontology Describes The Methods And Results Upon Performing An Ex-Vivo Voltage-Clamp Assay On Outer Hair Cells Of The Mammalian Cochlea, Brenda Farrell, Jason Bengtson

BCM Research Data

This data collection describes the electrical properties of outer hair cells isolated from the mammalian cochlea of the domestic guinea pig. This data was obtained by performing whole-cell patch clamp voltage clamp assay on cells and monitoring the electrical admittance during a DC voltage ramp. The membrane capacitance was then calculated at each membrane potential from this admittance, and the voltage-independent and voltage-dependent membrane capacitance was determined upon further analysis. In some case the DC conductance was also measured by interrogation of the cell with voltage-step function which was calculated from the change in the mean steady-state current with respect ...


The Effects Of Ethanol On Diverse Components Of Choice In The Rat: Reward Discrimination, Preference And Relative Valuation, Howard C. Cromwell, Justin J. Mcgraw, Luke Zona Jun 2017

The Effects Of Ethanol On Diverse Components Of Choice In The Rat: Reward Discrimination, Preference And Relative Valuation, Howard C. Cromwell, Justin J. Mcgraw, Luke Zona

Howard Casey Cromwell

Alcohol consumption impairs judgment and choice. How alcohol alters these crucial processes is primarily unknown. Choice can be fractionated into different components including reward discrimination, preference and relative valuation that can function together or in isolation depending upon diverse factors including choice context. We examined the diverse components and contextual effects by analyzing the effects of alcohol drinking on choice behavior in a task with a reduced level of temporal and spatial constraints. Rats were trained to drink 10% ethanol during 6 weeks of behavior testing using a combined sucrose-fade and two-bottle free-choice procedure. Two different sucrose pellet outcomes (e ...


Diabetic Peripheral Neuropathy, Michael Bradshaw, Jeffrey Brown, Kyril Cole, Whitney Harris, Kody Hasebi, Ysabella Del Rosario, Sara Werner, Bryan Witt, Alonzo Cook Feb 2017

Diabetic Peripheral Neuropathy, Michael Bradshaw, Jeffrey Brown, Kyril Cole, Whitney Harris, Kody Hasebi, Ysabella Del Rosario, Sara Werner, Bryan Witt, Alonzo Cook

Biomedical Engineering Western Regional Conference

No abstract provided.


Code For "Noise-Enhanced Coding In Phasic Neuron Spike Trains", Cheng Ly, Brent D. Doiron Jan 2017

Code For "Noise-Enhanced Coding In Phasic Neuron Spike Trains", Cheng Ly, Brent D. Doiron

Statistical Sciences and Operations Research Data

This zip file contains Matlab scripts and ode (XPP) files to calculate the statistics of the models in "Noise-Enhanced Coding in Phasic Neuron Spike Trains". This article is published in PLoS ONE.


Circadian Effects Of The Conditional Knockdown Of Serotonin In The Midbrain Raphe Nuclear Complex Of Adult Mice, Robert W. Woodruff Iii, Ashley Shemery, Alex Yaw, J. David Glass Mar 2016

Circadian Effects Of The Conditional Knockdown Of Serotonin In The Midbrain Raphe Nuclear Complex Of Adult Mice, Robert W. Woodruff Iii, Ashley Shemery, Alex Yaw, J. David Glass

Undergraduate Research Symposium

Hypothesis: The brain serotonin (5-HT) system is known to play a key role in regulating critical processes such as circadian clock timing, motivation, reward response and sleep. 5-HT knockout (SKO) mouse models have previously been used to understand 5-HT actions, but such global 5-HT depletion has profound non-targeted neurophysiological and developmental consequences. Therefore, conditional SKOs are needed. Here, we performed preliminary behavioral phenotyping in a conditional 5-HT knock down model where 5-HT synthesis blockade was targeted specifically to the midbrain raphe nuclear complex (site of hypothalamic serotonergic innervation) in adult mice.

Methods: Male Tph2-floxed mice were injected with AAV-Cre (experimental ...


Movement Path Tortuosity In Free Ambulation: Relationships To Age And Brain Disease, William Kearns, James Fozard, Vilis Nams Jan 2016

Movement Path Tortuosity In Free Ambulation: Relationships To Age And Brain Disease, William Kearns, James Fozard, Vilis Nams

William D. Kearns, PhD

Ambulation is defined by duration, distance traversed, number and size of directional changes and the interval separating successive movement episodes; more complex measures of ambulation can be created by aggregating these features. This review article of published findings defines random changes in direction during movement as “movement path tortuosity”, and relates tortuosity to the understanding of cognitive impairments of persons of all ages. Path tortuosity is quantified by subjecting tracking data to fractal analysis, specifically Fractal Dimension (Fractal D), which ranges from a value of 1 when the movement path is perfectly straight to a value of 2 when the ...


Synaptogyrin 3 Binds Amyloid Beta And May Alter Dopamine Transport In Alzheimer’S Disease, William Gierach Jan 2016

Synaptogyrin 3 Binds Amyloid Beta And May Alter Dopamine Transport In Alzheimer’S Disease, William Gierach

Undergraduate Honors Theses

Alzheimer’s Disease effects 35 million elderly individuals globally by causing dementia, memory loss and eventually death. Amyloid Beta (Aß), a neurotropic peptide and a hallmark of AD pathogenesis, disrupts cellular organization and impairs neuronal systems. The dopaminergic system regulates learning, motor function and behavior and malfunctions in early AD. Aß causes dopaminergic transmission to dysfunction by unknown mechanisms. To elucidate these mechanisms, we screened solubilized mouse synaptosomes for proteins that specifically bind Aß 1-42. 107 proteins that bound Aß were identified by mass spectrometry. Human orthologs were further screened in HEK293 cells for Aß binding. Of the thirteen proteins ...


Data From: A Stochastic Burst Follows The Periodic Morning Peak In Individual Drosophila Locomotion, Stanislav Lazopulo, Juan A. Lopez, Paul Levy, Sheyum Syed Jan 2015

Data From: A Stochastic Burst Follows The Periodic Morning Peak In Individual Drosophila Locomotion, Stanislav Lazopulo, Juan A. Lopez, Paul Levy, Sheyum Syed

Physics Data Sets

The data is associated to the article A Stochastic Burst Follows the Periodic Morning Peak in Individual Drosophila Locomotion published in PLoS ONE. The full text article can be found at https://doi.org/10.1371/journal.pone.0140481


Calciumsignalextract: A Matlab Gui To Automatically Extract The Activity Of Multiple Cells From Calcium Imaging Data, Stephan Meyer Zum Alten Borgloh Jan 2015

Calciumsignalextract: A Matlab Gui To Automatically Extract The Activity Of Multiple Cells From Calcium Imaging Data, Stephan Meyer Zum Alten Borgloh

Gilbert Laboratory

A Matlab GUI that automatically segments fluorescence image stacks into ROIs based on differential morphology and fluorescence activity of the individual cells. The time course data of each ROI gets extracted and plotted. External data from behavioral experiments and sensory stimuli can be integrated to compare for task and stimulus dependent neuronal events


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 ...


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.


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

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 4).

The other ...


Mcnamara 20120831fri-20120904tue Cosmic Ray Particles By Ccd Imaging, George Mcnamara Sep 2012

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 Aug 2012

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 ...


Pubspectra - Open Data Access Fluorescence Spectra, George Mcnamara Feb 2012

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 Feb 2012

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.


"The Natural History Of Truth: The Neurobiology Of Belief", Neil Greenberg Jan 2009

"The Natural History Of Truth: The Neurobiology Of Belief", Neil Greenberg

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

The pursuit of truth is woven into the fabric of every organism*. Any estimate of how best to survive and thrive in the reality in which we are immersed requires a sense of self, of the world, and of their relationship to each other. I wish to explore the idea that this pursuit has at its heart two complementary modes of reality testing utilizing separate cerebral systems which deal, respectively with the correspondence of experience with the world and the coherence of the experience with previous experiences: “is it real” and “does it fit?” At multiple levels of the nervous ...


"The Natural History Of Truth: The Neurobiology Of Belief", Neil Greenberg Dec 2008

"The Natural History Of Truth: The Neurobiology Of Belief", Neil Greenberg

Neil Greenberg

The pursuit of truth is woven into the fabric of every organism*. Any estimate of how best to survive and thrive in the reality in which we are immersed requires a sense of self, of the world, and of their relationship to each other. I wish to explore the idea that this pursuit has at its heart two complementary modes of reality testing utilizing separate cerebral systems which deal, respectively with the correspondence of experience with the world and the coherence of the experience with previous experiences: “is it real” and “does it fit?” At multiple levels of the nervous ...