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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

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 ...


A Tale Of Two Sirtuins: The Impact Of Sirt1 And Sirt3 On The Pathophysiology Of Shock, Carrie Adelia Sims Jan 2018

A Tale Of Two Sirtuins: The Impact Of Sirt1 And Sirt3 On The Pathophysiology Of Shock, Carrie Adelia Sims

Publicly Accessible Penn Dissertations

Both acute blood loss and severe infection activate common cellular pathways leading to shock – a pathologic condition characterized by systemic inflammation, oxidative stress, and mitochondrial dysfunction. Sirtuins, a highly conserved group of NAD-dependent enzymes, play a critical role in cellular survival and many of the benefits associated with sirtuin activation are thought to be secondary to decreased inflammation, reduced oxidative stress, and improved mitochondrial physiology. As such, we hypothesized that sirtuin pathways play a crucial role in shock and could be could be targeted to improve outcomes following acute blood loss and severe infection. In a series of in vivo ...


Histone Deacetylase 3 And The Epigenomic Regulation Of Brown Adipose Physiology, Matthew Joseph Emmett Jan 2017

Histone Deacetylase 3 And The Epigenomic Regulation Of Brown Adipose Physiology, Matthew Joseph Emmett

Publicly Accessible Penn Dissertations

Brown adipose tissue (BAT) is a thermogenic organ, which helps to protect body temperature against cold and can counteract metabolic disease. Numerous pathways modulate the activity of BAT in a highly regulated and coordinated manner to exert tight control over its immense calorie burning capacity. However, less is known regarding the transcriptional and epigenomic mechanisms controlling the thermogenic gene program of brown adipocytes. Here, we show that histone deacetylase 3 (HDAC3) is required for the activation of BAT enhancers to ensure thermogenic aptitude, thus enabling survival of dangerously cold environmental temperature. Loss of HDAC3 leads to deficient expression of uncoupling ...


Nampt-Mediated Nad+ Homeostasis In Skeletal Muscle: Implications For Healthy Aging, David Frederick Jan 2016

Nampt-Mediated Nad+ Homeostasis In Skeletal Muscle: Implications For Healthy Aging, David Frederick

Publicly Accessible Penn Dissertations

Mammalian skeletal muscle is a highly dynamic organ capable of structural and metabolic remodeling in response to exercise demands, nutrient supply, and environmental insults. Muscle also plays a central role in the maintenance of whole-body energy balance, capable of both storing and oxidizing carbohydrate and lipid fuels. The course of natural aging leads to a gradual decline in the mass, strength, and oxidative capacity of skeletal muscle, which increases the susceptibility of the elderly to frailty and metabolic diseases, such as Type II Diabetes. Ectopic muscle lipids can also exacerbate the metabolic complications of obesity, prompting interest in new means ...


Spontaneous Pancreatitis Caused By Tissue-Specific Gene Ablation Of Hhex In Mice, Mark Ferreira Jan 2015

Spontaneous Pancreatitis Caused By Tissue-Specific Gene Ablation Of Hhex In Mice, Mark Ferreira

Publicly Accessible Penn Dissertations

Background & Aims: Perturbations in pancreatic ductal bicarbonate secretion often result in chronic pancreatitis. Although the physiological mechanism of ductal secretion is known, its transcriptional control is not well characterized. Here, we investigate the role of the transcription factor Hematopoietically-expressed homeobox protein (Hhex) in pancreatic secretion and pancreatitis.

Methods: We derived mice with pancreas-specific, Cre-mediated Hhex gene ablation to determine the requirement of Hhex in the pancreatic duct in early life and in adult stages. Histological and immunostaining analyses were used to detect the presence of pathology. Pancreatic primary ductal cells (PDCs) were isolated to discover differentially expressed transcripts upon acute ...


A Microfluidic Approach For Investigating The Role Of Intrathrombus Transport In Thrombosis And Hemostasis, Ryan W. Muthard Jan 2014

A Microfluidic Approach For Investigating The Role Of Intrathrombus Transport In Thrombosis And Hemostasis, Ryan W. Muthard

Publicly Accessible Penn Dissertations

Biological and physical factors interact to modulate blood response in a wounded vessel, resulting in a hemostatic clot or an occlusive thrombus. Wall shear stress (τw) and pressure differential (ΔP) across the wound from the lumen to the extravascular compartment may impact hemostasis. This thesis describes the design of a microfluidic device capable of flowing human blood over a side channel plugged with collagen (± tissue factor) while independently controlling ΔP and τw. Using this device we were able to investigate the impact of physiologic hemodynamics on the growth and architecture of human blood clots. Our results revealed ...


Synergy Between Insulin-Like Growth Factor-I (Igf-I) E-Peptides And Igf-I Signaling Alters Growth In Skeletal Muscle, Becky Kathleen Brisson Jan 2012

Synergy Between Insulin-Like Growth Factor-I (Igf-I) E-Peptides And Igf-I Signaling Alters Growth In Skeletal Muscle, Becky Kathleen Brisson

Publicly Accessible Penn Dissertations

Insulin-like growth factor-I (IGF-I) is a potent growth factor that regulates and promotes growth in many types of cells and tissues, including skeletal muscle. The igf1 gene encodes mature IGF-I and a carboxy-terminal extension called the E-peptide. In rodents, alternative splicing and post-translational processing produce two E-peptides (EA and EB). The mature IGF-I produced by both isoforms is identical, while EA and EB share less than 50% homology. EB has been studied extensively and has been reported to promote cell proliferation and migration independently of IGF-I and its receptor (IGF-IR) in culture, but the mechanism by which EB causes these ...


The Evolution Of Platelet Responses To Collagen Under Conditions Of Hemodynamic Flow, Alec A. Schmaier Aug 2010

The Evolution Of Platelet Responses To Collagen Under Conditions Of Hemodynamic Flow, Alec A. Schmaier

Publicly Accessible Penn Dissertations

Collagen activates platelets through the immune-type GPVI receptor, but the mechanism by which this receptor has adapted to function in platelets under conditions of rapid blood flow is unclear. Additionally, it is unknown if responses to collagen are conserved in nucleated thrombocytes found in non-mammalian vertebrates, which do not express GPVI. Here we show that the GPVI proline-rich domain accelerates GPVI signaling kinetics and is required for maximal adhesion to collagen under flow. The proline-rich domain accelerates signaling through binding and directly activating the Src-family kinase Lyn. Chicken thrombocytes are potently activated by collagen but do not form 3-dimensional aggregates ...