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Full-Text Articles in Physics

9th Annual Postdoctoral Science Symposium, University Of Texas Md Anderson Cancer Center Postdoctoral Association Sep 2019

9th Annual Postdoctoral Science Symposium, University Of Texas Md Anderson Cancer Center Postdoctoral Association

MD Anderson Cancer Center Postdoctoral Association Annual Postdoctoral Science Symposium Abstracts

The mission of the Annual Postdoctoral Science Symposium (APSS) is to provide a platform for talented postdoctoral fellows throughout the Texas Medical Center to present their work to a wider audience. The MD Anderson Postdoctoral Association convened its inaugural Annual Postdoctoral Science Symposium (APSS) on August 4, 2011.

The APSS provides a professional venue for postdoctoral scientists to develop, clarify, and refine their research as a result of formal reviews and critiques of faculty and other postdoctoral scientists. Additionally, attendees discuss current research on a broad range of subjects while promoting academic interactions and enrichment and developing new collaborations.


Hcp: A Matlab Package To Create Beautiful Heatmaps With Richly Annotated Covariates, Manuela Salvucci, Jochen Hm Prehn Jun 2019

Hcp: A Matlab Package To Create Beautiful Heatmaps With Richly Annotated Covariates, Manuela Salvucci, Jochen Hm Prehn

Physiology and Medical Physics Articles

HCP (HeatmapCovariatePlot) provides a simple high level application programming interface (API) to design elaborated visualizations in a modular fashion. The user can select which elements to include, covariate row annotations and/or heatmaps, by invoking the AddCovariateRow or the AddHeatmap methods. Elements can be vertically stacked and also grouped in functionally related sub-blocks encapsulated by the AddSubBlock method to adjust the figure layout. The plotting options in HCP are chosen sensibly to create production-quality out-of-the-box visualizations in most use-case. HCP features several plotting options to adjust the plot aesthetics to cater for the user preferences in terms of colormaps, labelling ...


Systems Biology Identifies Preserved Integrity But Impaired Metabolism Of Mitochondria Due To A Glycolytic Defect In Alzheimer's Disease Neurons., Pierre Theurey, Niamh M. Connolly, Ilaria Fortunati, Emy Basso, Susette Lauwen, Camilla Ferrante, Catarina Moreira Pinho, Alvin Joselin, Anna Gioran, Daniele Bano, David S. Park, Maria Ankarcrona, Paola Pizzo, Jochen Hm Prehn Jun 2019

Systems Biology Identifies Preserved Integrity But Impaired Metabolism Of Mitochondria Due To A Glycolytic Defect In Alzheimer's Disease Neurons., Pierre Theurey, Niamh M. Connolly, Ilaria Fortunati, Emy Basso, Susette Lauwen, Camilla Ferrante, Catarina Moreira Pinho, Alvin Joselin, Anna Gioran, Daniele Bano, David S. Park, Maria Ankarcrona, Paola Pizzo, Jochen Hm Prehn

Physiology and Medical Physics Articles

Mitochondrial dysfunction is implicated in most neurodegenerative diseases, including Alzheimer's disease (AD). We here combined experimental and computational approaches to investigate mitochondrial health and bioenergetic function in neurons from a double transgenic animal model of AD (PS2APP/B6.152H). Experiments in primary cortical neurons demonstrated that AD neurons had reduced mitochondrial respiratory capacity. Interestingly, the computational model predicted that this mitochondrial bioenergetic phenotype could not be explained by any defect in the mitochondrial respiratory chain (RC), but could be closely resembled by a simulated impairment in the mitochondrial NADH flux. Further computational analysis predicted that such an impairment would ...


Experimental Evidence Supportive Of The Quantum Dna Model, F. Matthew Mihelic May 2019

Experimental Evidence Supportive Of The Quantum Dna Model, F. Matthew Mihelic

Faculty Publications

The DNA molecule can be modeled as a quantum logic processor in which electron spin qubits are held coherently in each nucleotide in a logically and thermodynamically reversible enantiomeric symmetry, and can be coherently conducted along the pi-stacking interactions of aromatic nucleotide bases, while simultaneously being spin-filtered via the helicity of the DNA molecule. Entangled electron pairs can be separated by that spin-filtering, held coherently at biological temperatures in the topologically insulated nucleotide quantum gates, and incorporated into separate DNA strands during DNA replication. Two separate DNA strands that share quantum entangled electrons can be mitotically divided into individual cells ...


Meta-Analysis Of The Molecular Associations Of Mucinous Colorectal Cancer., Ian S. Reynolds, S J Furney, Elaine W. Kay, Deborah A. Mcnamara, Jochen Hm Prehn, John P. Burke May 2019

Meta-Analysis Of The Molecular Associations Of Mucinous Colorectal Cancer., Ian S. Reynolds, S J Furney, Elaine W. Kay, Deborah A. Mcnamara, Jochen Hm Prehn, John P. Burke

Physiology and Medical Physics Articles

BACKGROUND: Mucinous differentiation occurs in 5-15 per cent of colorectal adenocarcinomas. This subtype of colorectal cancer responds poorly to chemoradiotherapy and has a worse prognosis. The genetic aetiology underpinning this cancer subtype lacks consensus. The aim of this study was to use meta-analytical techniques to clarify the molecular associations of mucinous colorectal cancer.

METHODS: This study adhered to MOOSE guidelines. Databases were searched for studies comparing KRAS, BRAF, microsatellite instability (MSI), CpG island methylator phenotype (CIMP), p53 and p27 status between patients with mucinous and non-mucinous colorectal adenocarcinoma. A random-effects model was used for analysis.

RESULTS: Data from 46 studies ...


A Machine Learning Platform To Optimize The Translation Of Personalized Network Models To The Clinic., Manuela Salvucci, Arman Rahman, Alexa J. Resler, Girish M. Udupi, Deborah A. Mcnamara, Elaine W. Kay, Pierre Laurent-Puig, Daniel B. Longley, Patrick G. Johnston, Mark Lawler, Richard Wilson, Manuel Salto-Tellez, Sandra Van Schaeybroeck, Mairin Rafferty, William M. Gallagher, Markus Rehm, Jochen Hm Prehn Apr 2019

A Machine Learning Platform To Optimize The Translation Of Personalized Network Models To The Clinic., Manuela Salvucci, Arman Rahman, Alexa J. Resler, Girish M. Udupi, Deborah A. Mcnamara, Elaine W. Kay, Pierre Laurent-Puig, Daniel B. Longley, Patrick G. Johnston, Mark Lawler, Richard Wilson, Manuel Salto-Tellez, Sandra Van Schaeybroeck, Mairin Rafferty, William M. Gallagher, Markus Rehm, Jochen Hm Prehn

Physiology and Medical Physics Articles

PURPOSE: Dynamic network models predict clinical prognosis and inform therapeutic intervention by elucidating disease-driven aberrations at the systems level. However, the personalization of model predictions requires the profiling of multiple model inputs, which hampers clinical translation.

PATIENTS AND METHODS: We applied APOPTO-CELL, a prognostic model of apoptosis signaling, to showcase the establishment of computational platforms that require a reduced set of inputs. We designed two distinct and complementary pipelines: a probabilistic approach to exploit a consistent subpanel of inputs across the whole cohort (Ensemble) and a machine learning approach to identify a reduced protein set tailored for individual patients (Tree ...


The Effects Of Organic And Inorganic Nanoparticles On Bacterial Deactivation, Lauren Cooper Apr 2019

The Effects Of Organic And Inorganic Nanoparticles On Bacterial Deactivation, Lauren Cooper

Honors College Capstone Experience/Thesis Projects

Antibacterial resistance is one of the greatest problems in modern medicine, as healthcare professionals are experiencing more and more difficulty in providing effective care. As such, alternative methods of treatment are needed in order to overcome this issue. One recently proposed method of alternative treatment is photodynamic therapy. Photodynamic therapy is a light-based method of treatment that utilizes (1) a photosensitizing agent, (2) light, (3) produced oxygen species. When the photosensitizing agent is injected into an infected region of interest and then irradiated with a certain wavelength of light, the agent is photoactivated and begins to produce harmful forms of ...


A Theoretical Model Of Underground Dipole Antennas For Communications In Internet Of Underground Things, Abdul Salam, Mehmet C. Vuran, Xin Dong, Christos Argyropoulos, Suat Irmak Feb 2019

A Theoretical Model Of Underground Dipole Antennas For Communications In Internet Of Underground Things, Abdul Salam, Mehmet C. Vuran, Xin Dong, Christos Argyropoulos, Suat Irmak

Faculty Publications

The realization of Internet of Underground Things (IOUT) relies on the establishment of reliable communication links, where the antenna becomes a major design component due to the significant impacts of soil. In this paper, a theoretical model is developed to capture the impacts of change of soil moisture on the return loss, resonant frequency, and bandwidth of a buried dipole antenna. Experiments are conducted in silty clay loam, sandy, and silt loam soil, to characterize the effects of soil, in an indoor testbed and field testbeds. It is shown that at subsurface burial depths (0.1-0.4m), change in soil ...


When Ron Met Tam In Mesothelioma: All Druggable For One, And One Drug For All?, Anne-Marie Baird, David Easty, Monika A. Jarzabek, Liam Shiels, Alex Soltermann, Sonja Klebe, Stéphane Raeppel, Lauren Macdonagh, Chengguang Wu, Kim Griggs, Michaela B. Kirschner, Bryan Stanfill, Daisuke Nonaka, Chandra M. Goparaju, Bruno Murer, Dean A. Fennell, Dearbhaile M. O'Donnell, Martin P. Barr, Luciano Mutti, Glen Reid, Stephen Finn, Sinead Cuffe, Harvey I. Pass, Isabelle Opitz, Annette Byrne, Kenneth J. O'Byrne, Steven G. Gray Feb 2019

When Ron Met Tam In Mesothelioma: All Druggable For One, And One Drug For All?, Anne-Marie Baird, David Easty, Monika A. Jarzabek, Liam Shiels, Alex Soltermann, Sonja Klebe, Stéphane Raeppel, Lauren Macdonagh, Chengguang Wu, Kim Griggs, Michaela B. Kirschner, Bryan Stanfill, Daisuke Nonaka, Chandra M. Goparaju, Bruno Murer, Dean A. Fennell, Dearbhaile M. O'Donnell, Martin P. Barr, Luciano Mutti, Glen Reid, Stephen Finn, Sinead Cuffe, Harvey I. Pass, Isabelle Opitz, Annette Byrne, Kenneth J. O'Byrne, Steven G. Gray

Physiology and Medical Physics Articles

Malignant pleural mesothelioma (MPM) is an aggressive inflammatory cancer with a poor survival rate. Treatment options are limited at best and drug resistance is common. Thus, there is an urgent need to identify novel therapeutic targets in this disease in order to improve patient outcomes and survival times. MST1R (RON) is a trans-membrane receptor tyrosine kinase (RTK), which is part of the c-MET proto-oncogene family. The only ligand recognized to bind MST1R (RON) is Macrophage Stimulating 1 (MST1), also known as Macrophage Stimulating Protein (MSP) or Hepatocyte Growth Factor-Like Protein (HGFL). In this study, we demonstrate that the MST1-MST1R (RON ...


Volume 11, Jacob Carney, Ryan White, Joseph Hyman, Jenny Raven, Megan Garrett, Ibrahim Kante, Summer Meinhard, Lauren Johnson, William "Editha" Dean Howells, Laura Gottschalk, Christopher Siefke, Pink Powell, Natasha Woodmancy, Katharine Colley, Abbey Mays, Charlotte Potts Jan 2019

Volume 11, Jacob Carney, Ryan White, Joseph Hyman, Jenny Raven, Megan Garrett, Ibrahim Kante, Summer Meinhard, Lauren Johnson, William "Editha" Dean Howells, Laura Gottschalk, Christopher Siefke, Pink Powell, Natasha Woodmancy, Katharine Colley, Abbey Mays, Charlotte Potts

Incite: The Journal of Undergraduate Scholarship

Table of Contents:

Introduction, Dr. Roger A. Byrne, Dean

From the Editor, Dr. Larissa "Kat" Tracy

From the Designers, Rachel English, Rachel Hanson

Synthesis of 3,5-substituted Parabens and their Antimicrobial Properties, Jacob Coarney, Ryan White

Chernobyl: Putting "Perestroika" and "Glasnot" to the Test, Joseph Hyman

Art by Jenny Raven

Watering Down Accessibility: The Issue with Public Access to Alaska's Federal Waterways, Meagan Garrett

Why Has the Democratic Republic of the Congo outsourced its Responsibility to Educate its Citizens? Ibrahim Kante

Art by Summer Meinhard

A Computational Study of Single Molecule Diodes, Lauren Johnson

Satire of the State through ...


Post-Treatment De-Phosphorylation Of P53 Correlates With Dasatinib Responsiveness In Malignant Melanoma., Josip Skoko, Jan Rožanc, Emilie M. Charles, Leonidas G. Alexopoulos, Markus Rehm Dec 2018

Post-Treatment De-Phosphorylation Of P53 Correlates With Dasatinib Responsiveness In Malignant Melanoma., Josip Skoko, Jan Rožanc, Emilie M. Charles, Leonidas G. Alexopoulos, Markus Rehm

Physiology and Medical Physics Articles

BACKGROUND: Dasatinib (Sprycel) was developed as a tyrosine kinase inhibitor targeting Bcr-Abl and the family of Src kinases. Dasatinib is commonly used for the treatment of acute lymphoblastic and chronic myelogenous leukemia. Previous clinical studies in melanoma returned inconclusive results and suggested that patients respond highly heterogeneously to dasatinib as single agent or in combination with standard-of-care chemotherapeutic dacarbazine. Reliable biomarkers to predict dasatinib responsiveness in melanoma have not yet been developed.

RESULTS: Here, we collected comprehensive in vitro data from experimentally well-controlled conditions to study the effect of dasatinib, alone and in combination with dacarbazine, on cell proliferation and ...


Dual-Center, Dual-Platform Microrna Profiling Identifies Potential Plasma Biomarkers Of Adult Temporal Lobe Epilepsy., Rana Raoof, Sebastian Bauer, Hany El Naggar, Gary P Brennan, Elizabeth Brindley, Thomas Hill, Hazel Mcardle, Elaine Spain, Robert J Forster, Jochen Hm Prehn, Hajo Hamer, Norman Delanty, Felix Rosenow, Catherine Mooney, David C. Henshall Dec 2018

Dual-Center, Dual-Platform Microrna Profiling Identifies Potential Plasma Biomarkers Of Adult Temporal Lobe Epilepsy., Rana Raoof, Sebastian Bauer, Hany El Naggar, Gary P Brennan, Elizabeth Brindley, Thomas Hill, Hazel Mcardle, Elaine Spain, Robert J Forster, Jochen Hm Prehn, Hajo Hamer, Norman Delanty, Felix Rosenow, Catherine Mooney, David C. Henshall

Physiology and Medical Physics Articles

BACKGROUND: There are no blood-based molecular biomarkers of temporal lobe epilepsy (TLE) to support clinical diagnosis. MicroRNAs are short noncoding RNAs with strong biomarker potential due to their cell-specific expression, mechanistic links to brain excitability, and stable detection in biofluids. Altered levels of circulating microRNAs have been reported in human epilepsy, but most studies collected samples from one clinical site, used a single profiling platform or conducted minimal validation.

METHOD: Using a case-control design, we collected plasma samples from video-electroencephalogram-monitored adult TLE patients at epilepsy specialist centers in two countries, performed genome-wide PCR-based and RNA sequencing during the discovery phase ...


The Significance Of Mucin Pools Following Neoadjuvant Chemoradiotherapy For Locally Advanced Rectal Cancer., Ian S. Reynolds, Deborah A. Mcnamara, Elaine W. Kay, Brian O'Neill, Joseph Deasy, John P. Burke Dec 2018

The Significance Of Mucin Pools Following Neoadjuvant Chemoradiotherapy For Locally Advanced Rectal Cancer., Ian S. Reynolds, Deborah A. Mcnamara, Elaine W. Kay, Brian O'Neill, Joseph Deasy, John P. Burke

Physiology and Medical Physics Articles

BACKGROUND: Neoadjuvant chemo-radiotherapy is utilized for locally advanced rectal cancer to optimize local control. A subset of patients form mucin pools following radiotherapy but the association between mucin pools and pathological and oncological outcomes following curative proctectomy for rectal cancer remains unknown.

OBJECTIVE: The aim of this study was to determine the significance of mucin pool formation after neoadjuvant chemoradiotherapy for rectal cancer.

METHODS: This is a retrospective analysis of a prospectively maintained rectal cancer database. Patients who underwent curative proctectomy for rectal cancer following long course chemoradiotherapy between January 2007 and December 2016 were eligible for inclusion.

RESULTS: A ...


Optimization Of Detergent-Mediated Reconstitution Of Influenza A M2 Protein Into Proteoliposomes, Catherine Hirshfeld Crouch, Margaret H. Bost , '17, Tae H. Kim , '14, Bryan M. Green , '16, Douglas Stuart Arbuckle , '17, Carl H. Grossman, Kathleen P. Howard Dec 2018

Optimization Of Detergent-Mediated Reconstitution Of Influenza A M2 Protein Into Proteoliposomes, Catherine Hirshfeld Crouch, Margaret H. Bost , '17, Tae H. Kim , '14, Bryan M. Green , '16, Douglas Stuart Arbuckle , '17, Carl H. Grossman, Kathleen P. Howard

Physics & Astronomy Faculty Works

We report the optimization of detergent-mediated reconstitution of an integral membrane-bound protein, full-length influenza M2 protein, by direct insertion into detergent-saturated liposomes. Detergent-mediated reconstitution is an important method for preparing proteoliposomes for studying membrane proteins, and must be optimized for each combination of protein and membrane constituents used. The purpose of the reconstitution was to prepare samples for site-directed spin-labeling electron paramagnetic resonance (SDSL-EPR) studies. Our goals in optimizing the protocol were to minimize the amount of detergent used, reduce overall proteoliposome preparation time, and confirm the removal of all detergent. The liposomes were comprised of (1-palmitoyl-2-oleyl-sn-glycero-phosphocholine (POPC) and 1-palmitoyl-2-oleyl-sn-glycero-3- ...


Exploring The Neural Mechanisms Of Physics Learning, Jessica E. Bartley Nov 2018

Exploring The Neural Mechanisms Of Physics Learning, Jessica E. Bartley

FIU Electronic Theses and Dissertations

This dissertation presents a series of neuroimaging investigations and achievements that strive to deepen and broaden our understanding of human problem solving and physics learning. Neuroscience conceives of dynamic relationships between behavior, experience, and brain structure and function, but how neural changes enable human learning across classroom instruction remains an open question. At the same time, physics is a challenging area of study in which introductory students regularly struggle to achieve success across university instruction. Research and initiatives in neuroeducation promise a new understanding into the interactions between biology and education, including the neural mechanisms of learning and development. These ...


Phosphoprotein Patterns Predict Trametinib Responsiveness And Optimal Trametinib Sensitisation Strategies In Melanoma., Jan Rožanc, Theodore Sakellaropoulos, Asier Antoranz, Cristiano Guttà, Biswajit Podder, Vesna Vetma, Nicole Rufo, Patrizia Agostinis, Vaia Pliaka, Thomas Sauter, Dagmar Kulms, Markus Rehm, Leonidas G. Alexopoulos Oct 2018

Phosphoprotein Patterns Predict Trametinib Responsiveness And Optimal Trametinib Sensitisation Strategies In Melanoma., Jan Rožanc, Theodore Sakellaropoulos, Asier Antoranz, Cristiano Guttà, Biswajit Podder, Vesna Vetma, Nicole Rufo, Patrizia Agostinis, Vaia Pliaka, Thomas Sauter, Dagmar Kulms, Markus Rehm, Leonidas G. Alexopoulos

Physiology and Medical Physics Articles

Malignant melanoma is a highly aggressive form of skin cancer responsible for the majority of skin cancer-related deaths. Recent insight into the heterogeneous nature of melanoma suggests more personalised treatments may be necessary to overcome drug resistance and improve patient care. To this end, reliable molecular signatures that can accurately predict treatment responsiveness need to be identified. In this study, we applied multiplex phosphoproteomic profiling across a panel of 24 melanoma cell lines with different disease-relevant mutations, to predict responsiveness to MEK inhibitor trametinib. Supported by multivariate statistical analysis and multidimensional pattern recognition algorithms, the responsiveness of individual cell lines ...


Copy Number Load Predicts Outcome Of Metastatic Colorectal Cancer Patients Receiving Bevacizumab Combination Therapy., Dominiek Smeets, Ian S. Miller, Darran P. O'Connor, Sudipto Das, Bruce Moran, Bram Boeckx, Timo Gaiser, Johannes Betge, Ana Barat, Rut Klinger, Nicole Ct Van Grieken, Chiara Cremolini, Hans Prenen, Massimiliano Mazzone, Jeroen Depreeuw, Orna Bacon, Bozena Fender, Joseph Brady, Bryan T. Hennessy, Deborah A. Mcnamara, Elaine W. Kay, Henk M. Verheul, Neerincx Maarten, William M. Gallagher, Verena Murphy, Jochen Hm Prehn, Miriam Koopman, Cornelis Ja Punt, Fotios Loupakis, Matthias Pa Ebert, Bauke Ylstra, Diether Lambrechts, Annette Byrne Oct 2018

Copy Number Load Predicts Outcome Of Metastatic Colorectal Cancer Patients Receiving Bevacizumab Combination Therapy., Dominiek Smeets, Ian S. Miller, Darran P. O'Connor, Sudipto Das, Bruce Moran, Bram Boeckx, Timo Gaiser, Johannes Betge, Ana Barat, Rut Klinger, Nicole Ct Van Grieken, Chiara Cremolini, Hans Prenen, Massimiliano Mazzone, Jeroen Depreeuw, Orna Bacon, Bozena Fender, Joseph Brady, Bryan T. Hennessy, Deborah A. Mcnamara, Elaine W. Kay, Henk M. Verheul, Neerincx Maarten, William M. Gallagher, Verena Murphy, Jochen Hm Prehn, Miriam Koopman, Cornelis Ja Punt, Fotios Loupakis, Matthias Pa Ebert, Bauke Ylstra, Diether Lambrechts, Annette Byrne

Physiology and Medical Physics Articles

Increased copy number alterations (CNAs) indicative of chromosomal instability (CIN) have been associated with poor cancer outcome. Here, we study CNAs as potential biomarkers of bevacizumab (BVZ) response in metastatic colorectal cancer (mCRC). We cluster 409 mCRCs in three subclusters characterized by different degrees of CIN. Tumors belonging to intermediate-to-high instability clusters have improved outcome following chemotherapy plus BVZ versus chemotherapy alone. In contrast, low instability tumors, which amongst others consist of POLE-mutated and microsatellite-instable tumors, derive no further benefit from BVZ. This is confirmed in 81 mCRC tumors from the phase 2 MoMa study involving BVZ. CNA clusters overlap ...


Low Cleaved Caspase-7 Levels Indicate Unfavourable Outcome Across All Breast Cancers., Andreas U Lindner, Federico Lucantoni, Damir Varešlija, Alexa Resler, Brona M Murphy, William M Gallagher, Arnold D K Hill, Leonie S. Young, Jochen H.M. Prehn Oct 2018

Low Cleaved Caspase-7 Levels Indicate Unfavourable Outcome Across All Breast Cancers., Andreas U Lindner, Federico Lucantoni, Damir Varešlija, Alexa Resler, Brona M Murphy, William M Gallagher, Arnold D K Hill, Leonie S. Young, Jochen H.M. Prehn

Physiology and Medical Physics Articles

Elevated levels of the anti-apoptotic BCL2 protein associate with favourable outcome in breast cancer. We investigated whether executioner caspase activation downstream of mitochondrial apoptosis was associated with, or independent, of BCL2's prognostic signature in breast cancer. Levels of pro- and anti-apoptotic BCL2 family proteins were quantified in triple negative breast cancer (TNBC) samples and utilised to calculate BCL2 profiles of 845 breast cancer patients. Biomarkers including single apoptosis proteins and network-enriched apoptosis system signatures were evaluated using uni- and multi-variate Cox-models. In both TNBC and non-TNBC breast cancer, the anti-apoptotic BCL2 protein was particularly abundant when compared to other ...


Metabolic Targeting Of Breast Cancer Cells With The 2-Deoxy-D-Glucose And The Mitochondrial Bioenergetics Inhibitor Mdivi-1., Federico Lucantoni, Heiko Düssmann, Jochen Hm Prehn Sep 2018

Metabolic Targeting Of Breast Cancer Cells With The 2-Deoxy-D-Glucose And The Mitochondrial Bioenergetics Inhibitor Mdivi-1., Federico Lucantoni, Heiko Düssmann, Jochen Hm Prehn

Physiology and Medical Physics Articles

Breast cancer cells have different requirements on metabolic pathways in order to sustain their growth. Triple negative breast cancer (TNBC), an aggressive breast cancer subtype relies mainly on glycolysis, while estrogen receptor positive (ER+) breast cancer cells possess higher mitochondrial oxidative phosphorylation (OXPHOS) levels. However, breast cancer cells generally employ both pathways to sustain their metabolic needs and to compete with the surrounding environment. In this study, we demonstrate that the mitochondrial fission inhibitor MDIVI-1 alters mitochondrial bioenergetics, at concentrations that do not affect mitochondrial morphology. We show that this effect is accompanied by an increase in glycolysis consumption. Dual ...


Riluzole Does Not Improve Lifespan Or Motor Function In Three Als Mouse Models., Marion C. Hogg, Luise Halang, Ina Woods, Karen S. Coughlan, Jochen Hm Prehn Aug 2018

Riluzole Does Not Improve Lifespan Or Motor Function In Three Als Mouse Models., Marion C. Hogg, Luise Halang, Ina Woods, Karen S. Coughlan, Jochen Hm Prehn

Physiology and Medical Physics Articles

BACKGROUND: Riluzole is the most widespread therapeutic for treatment of the progressive degenerative disease amyotrophic lateral sclerosis (ALS). Riluzole gained FDA approval in 1995 before the development of ALS mouse models. We assessed riluzole in three transgenic ALS mouse models: the SOD1

METHODS: Age, sex and litter-matched mice were treated with riluzole (22 mg/kg) in drinking water or vehicle (DMSO) from symptom onset. Lifespan was assessed and motor function tests were carried out twice weekly to determine whether riluzole slowed disease progression.

RESULTS: Riluzole treatment had no significant benefit on lifespan in any of the ALS mouse models tested ...


Activities And Classroom Demonstrations In Biological Physics: A Resource Document, Philip C. Nelson, William Berner Jul 2018

Activities And Classroom Demonstrations In Biological Physics: A Resource Document, Philip C. Nelson, William Berner

Department of Physics Papers

We give detailed recipes for a number of classroom demonstrations relevant to biological physics instruction. We developed them mainly for use in 2nd-3rd year undergraduate Physics courses. But you can (and we do) use them for primary school, through high school, up to PhD candidates. You adapt the words for each audience, but a phenomenon is a phenomenon.

We also outline a 1-hour introduction to Python for undergraduate scientific computing.

Finally we document some outcomes from courses taught at U Pennsylvania using these resources and others cited here. This material was presented at a workshop at the AAPT meeting in ...


Anti-Angiogenic Drug Scheduling Optimisation With Application To Colorectal Cancer., Marc Sturrock, Ian S. Miller, Guiyeom Kang, N Hannis Arba'ie, Alice C. O'Farrell, Ana Barat, Gemma Marston, Patricia L. Coletta, Annette Byrne, Jochen Hm Prehn Jul 2018

Anti-Angiogenic Drug Scheduling Optimisation With Application To Colorectal Cancer., Marc Sturrock, Ian S. Miller, Guiyeom Kang, N Hannis Arba'ie, Alice C. O'Farrell, Ana Barat, Gemma Marston, Patricia L. Coletta, Annette Byrne, Jochen Hm Prehn

Physiology and Medical Physics Articles

Bevacizumab (bvz) is a first choice anti-angiogenic drug in oncology and is primarily administered in combination with chemotherapy. It has been hypothesized that anti-angiogenic drugs enhance efficacy of cytotoxic drugs by "normalizing" abnormal tumor vessels and improving drug penetration. Nevertheless, the clinical relevance of this phenomenon is still unclear with several studies over recent years suggesting an opposing relationship. Herein, we sought to develop a new computational tool to interrogate anti-angiogenic drug scheduling with particular application in the setting of colorectal cancer (CRC). Specifically, we have employed a mathematical model of vascular tumour growth which interrogates the impact of anti-angiogenic ...


Computer Design Of Microfluidic Mixers For Protein/Rna Folding Studies, Venkatesh Inguva, Sagar V. Kathuria, Osman Bilsel, Blair James Perot Jun 2018

Computer Design Of Microfluidic Mixers For Protein/Rna Folding Studies, Venkatesh Inguva, Sagar V. Kathuria, Osman Bilsel, Blair James Perot

Open Access Articles

Kinetic studies of biological macromolecules increasingly use microfluidic mixers to initiate and monitor reaction progress. A motivation for using microfluidic mixers is to reduce sample consumption and decrease mixing time to microseconds. Some applications, such as small-angle x-ray scattering, also require large ( > 10 micron) sampling areas to ensure high signal-to-noise ratios and to minimize parasitic scattering. Chaotic to marginally turbulent mixers are well suited for these applications because this class of mixers provides a good middle ground between existing laminar and turbulent mixers. In this study, we model various chaotic to marginally turbulent mixing concepts such as flow turning, flow ...


Multicomponent Analysis Using A Confocal Raman Microscope, Zhengyuan Tang, Sinead J. Barton, Thomas E. Ward, John P. Lowry, Michelle M. Doran, Hugh Byrne, Bryan M. Hennelly Jun 2018

Multicomponent Analysis Using A Confocal Raman Microscope, Zhengyuan Tang, Sinead J. Barton, Thomas E. Ward, John P. Lowry, Michelle M. Doran, Hugh Byrne, Bryan M. Hennelly

Articles

Measuring the concentration of multiple chemical components in a low volume aqueous mixture by Raman spectroscopy has received significant interest in the literature. All of the contributions to date focus on the design of optical systems that facilitate the recording of spectra with high signal-to-noise ratio, by collecting as many Raman scattered photons as possible. In this study, the confocal Raman microscope set-up is investigated for multicomponent analysis. Partial Least Squares Regression is used to quantify physiologically relevant aqueous mixtures of glucose, lactic acid, and urea. The predicted error is 17.81 mg/dL for glucose, 10.6 mg/dL ...


Bcl2 And Bcl(X)L Selective Inhibitors Decrease Mitochondrial Atp Production In Breast Cancer Cells And Are Synthetically Lethal When Combined With 2-Deoxy-D-Glucose., Federico Lucantoni, Heiko Düssmann, Irene Llorente-Folch, Jochen Hm Prehn May 2018

Bcl2 And Bcl(X)L Selective Inhibitors Decrease Mitochondrial Atp Production In Breast Cancer Cells And Are Synthetically Lethal When Combined With 2-Deoxy-D-Glucose., Federico Lucantoni, Heiko Düssmann, Irene Llorente-Folch, Jochen Hm Prehn

Physiology and Medical Physics Articles

Cancer cells display differences regarding their engagement of glycolytic vs. mitochondrial oxidative phosphorylation (OXPHOS) pathway. Triple negative breast cancer, an aggressive form of breast cancer, is characterized by elevated glycolysis, while estrogen receptor positive breast cancer cells rely predominantly on OXPHOS. BCL2 proteins control the process of mitochondrial outer membrane permeabilization during apoptosis, but also regulate cellular bioenergetics. Because BCL2 proteins are overexpressed in breast cancer and targetable by selective antagonists, we here analysed the effect of BCL2 and BCL(X)L selective inhibitors, Venetoclax and WEHI-539, on mitochondrial bioenergetics and cell death. Employing single cell imaging using a FRET-based ...


Increased A20-E3 Ubiquitin Ligase Interactions In Bid-Deficient Glia Attenuate Tlr3- And Tlr4-Induced Inflammation., Sinéad Kinsella, Michael Fichtner, Orla Watters, Hans-Georg König, Jochen Hm Prehn May 2018

Increased A20-E3 Ubiquitin Ligase Interactions In Bid-Deficient Glia Attenuate Tlr3- And Tlr4-Induced Inflammation., Sinéad Kinsella, Michael Fichtner, Orla Watters, Hans-Georg König, Jochen Hm Prehn

Physiology and Medical Physics Articles

Background: Chronic pro-inflammatory signaling propagates damage to neural tissue and affects the rate of disease progression. Increased activation of Toll-like receptors (TLRs), master regulators of the innate immune response, is implicated in the etiology of several neuropathologies including amyotrophic lateral sclerosis, Alzheimer’s disease, and Parkinson’s disease. Previously, we identified that the Bcl-2 family protein BH3-interacting domain death agonist (Bid) potentiates the TLR4-NF-κB pro-inflammatory response in glia, and specifically characterized an interaction between Bid and TNF receptor associated factor 6 (TRAF6) in microglia in response to TLR4 activation.

Methods: We assessed the activation of mitogen-activated protein kinase (MAPK) and ...


Pleiotropic Activity Of Systemically Delivered Angiogenin In The Sod1, Martin Crivello, Saidhbhe L. O'Riordan, Ina Woods, Sarah Cannon, Luise Halang, Karen S. Coughlan, Marion C. Hogg, Sebastian A. Lewandowski, Jochen Hm Prehn May 2018

Pleiotropic Activity Of Systemically Delivered Angiogenin In The Sod1, Martin Crivello, Saidhbhe L. O'Riordan, Ina Woods, Sarah Cannon, Luise Halang, Karen S. Coughlan, Marion C. Hogg, Sebastian A. Lewandowski, Jochen Hm Prehn

Physiology and Medical Physics Articles

Loss-of-function mutations in the angiogenin (ANG) gene have been identified in familial and sporadic ALS patients. Previous work from our group identified human ANG (huANG) to protect motoneuronsin vitro, and provided proof-of-concept that daily intraperitoneal (i.p.) huANG injections post-symptom onset increased lifespan and delayed disease progression in SOD1G93A mice. huANG's mechanism of action remains less well understood. Here, we implemented a preclinical in vivo design to validate our previous results, provide pharmacokinetic and protein distribution data after systemic administration, and explore potential pleiotropic activities of huANG in vivo. SOD1G93A mice (n = 45) and non-transgenic controls (n = 31 ...


Characterization And Analysis Of Ultrathin Cigs Films And Solar Cells Deposited By 3-Stage Process, Grace Rajan, Krishna Aryal, Shankar Karki, Puruswottam Aryal, Robert W. Collins, Sylvain Marsillac May 2018

Characterization And Analysis Of Ultrathin Cigs Films And Solar Cells Deposited By 3-Stage Process, Grace Rajan, Krishna Aryal, Shankar Karki, Puruswottam Aryal, Robert W. Collins, Sylvain Marsillac

Electrical & Computer Engineering Faculty Publications

In view of the large-scale utilization of Cu(In,Ga)Se2 (CIGS) solar cells for photovoltaic application, it is of interest not only to enhance the conversion efficiency but also to reduce the thickness of the CIGS absorber layer in order to reduce the cost and improve the solar cell manufacturing throughput. In situ and real-time spectroscopic ellipsometry (RTSE) has been used conjointly with ex situ characterizations to understand the properties of ultrathin CIGS films. This enables monitoring the growth process, analyzing the optical properties of the CIGS films during deposition, and extracting composition, film thickness, grain size, and ...


Raman Spectral Analysis For Rapid Screening Of Dengue Infection, Tahir Mahmood, Haq Nawaz, A. Ditta, M.I. Majeed, M.A. Hanif, N. Rashid, H.N. Bhatti, H.F. Nargis, M. Saleem, Franck Bonnier, Hugh Byrne May 2018

Raman Spectral Analysis For Rapid Screening Of Dengue Infection, Tahir Mahmood, Haq Nawaz, A. Ditta, M.I. Majeed, M.A. Hanif, N. Rashid, H.N. Bhatti, H.F. Nargis, M. Saleem, Franck Bonnier, Hugh Byrne

Articles

Infection with the dengue virus is currently clinically detected according to different biomarkers in human blood plasma, commonly measured by enzyme linked immunosorbent assays, including non-structural proteins (Ns1), immunoglobulin M (IgM) and immunoglobulin G (IgG). However, there is little or no mutual correlation between the biomarkers, as demonstrated in this study by a comparison of their levels in samples from 17 patients. As an alternative, the label free, rapid screening technique, Raman spectroscopy has been used for the characterisation/diagnosis of healthy and dengue infected human blood plasma samples. In dengue positive samples, changes in specific Raman spectral bands associated ...


Apoptosis-Inducing Factor (Aif) In Physiology And Disease: The Tale Of A Repented Natural Born Killer., Daniele Bano, Jochen Hm Prehn Apr 2018

Apoptosis-Inducing Factor (Aif) In Physiology And Disease: The Tale Of A Repented Natural Born Killer., Daniele Bano, Jochen Hm Prehn

Physiology and Medical Physics Articles

Apoptosis-inducing factor (AIF) is a mitochondrial oxidoreductase that contributes to cell death programmes and participates in the assembly of the respiratory chain. Importantly, AIF deficiency leads to severe mitochondrial dysfunction, causing muscle atrophy and neurodegeneration in model organisms as well as in humans. The purpose of this review is to describe functions of AIF and AIF-interacting proteins as regulators of cell death and mitochondrial bioenergetics. We describe how AIF deficiency induces pathogenic processes that alter metabolism and ultimately compromise cellular homeostasis. We report the currently known AIFM1 mutations identified in humans and discuss the variability of AIFM1-related disorders in terms ...