Bulletin of the American Physical Society
2014 Annual Meeting of the Mid-Atlantic Section of the APS
Volume 59, Number 9
Friday–Sunday, October 3–5, 2014; University Park, Pennsylvania
Session H7: Biological and Medical Physics |
Hide Abstracts |
Chair: Colin Campbell, Pennsylvania State University Room: Life Sciences Building 013 |
Sunday, October 5, 2014 9:00AM - 9:36AM |
H7.00001: Stochastic expression and epigenetic memory of the HO promoter Invited Speaker: Lucy Bai Eukaryotic gene regulation usually involves sequence-specific transcription factors and sequence-nonspecific cofactors. Large effort has been made to understand how these factors affect the average gene expression level among a population. However, little is known about how they regulate gene expression in individual cells. In this work, we address this question by mutating multiple factors in the regulation pathway of the yeast HO promoter and probing the corresponding promoter activity in single cells using time-lapse fluorescence microscopy. We show that the HO promoter fires in a stochastic, ``on or off'' fashion in wild type cells as well as in different genetic backgrounds. Many chromatin-related co-factors that affect the average level of HO expression do not actually affect the firing amplitude of the HO promoter; instead they affect the firing frequency among individual cell cycles. With certain mutations, the bimodal expression exhibits short-term epigenetic memory across the mitotic boundary. The memory is propagated in ``cis'' and caused by enhanced activator binding after a previous ``on'' cycle. Finally, we proposed a novel model that the short transcriptional memory is a result of slow turnover of the histone acetylation marks. [Preview Abstract] |
Sunday, October 5, 2014 9:36AM - 9:48AM |
H7.00002: Physics Has Often Been in the Forefront of Fundamental Advances in Biology and Medicine Ronald Aaron At a time when the physical structure of a living cell was essentially unknown, and the existence of an enveloping membrane was only a hypothesis, Julius Bernstein (between 1868 and 1912) developed the hypothesis that the cell is composed of an electrolytic interior surrounded by a thin membrane impermeable to ions. Furthermore he basically proposed the sodium-potassium pump! Max Delbruck in the early 1930's was inspired by new data concerning fruit flies; namely, that when exposed to X-rays and ultraviolet radiation, their mutation was proportional to the concentration of free radicals. Based on this information Delbruck proposed that the gene was a single long-chain molecule and shared a Nobel Prize with Salvador Lurie in 1969. In this presentation we discuss the above, and further such examples, and suggest what is special about the science of physics that produces such remarkable forefront discoveries. [Preview Abstract] |
Sunday, October 5, 2014 9:48AM - 10:00AM |
H7.00003: Heme electronic structure calculations with band parameters from optical absorption spectra Arthur Brill, Mark Carlson Central energies, bandwidths, peak absorptivities, oscillator strengths and transition dipole matrix elements are available from bandanalysis of optical absorption spectra for the visible and near UV regions of the aquo, fluoride, azide and cyanide complexes of horse metmyoglobin (M. L. Carlson and A. S. Brill, paper in preparation). The circular orbit model of porphin structure is applicable to related structures such as heme, and is useful for identifying $\pi-\pi$ transitions responsible for the B bands in the Soret and the Q bands in the visible. The other transitions from this bandanalysis are identified as visible n-$\pi$ (four for the aquo complex, five for both the F$^-$ and CN$^-$ complexes, six for the NH$_3^-$ complex) and near ultraviolet beyond the Soret (seven for the aquo, fluoride and cyanide complexes, six for the azide). With the circular orbit model, average inner and outer radii of the structure of the heme chromophore are calculable from the lower and higher pairs of band center energies of $\pi-\pi$ transitions. These radial distances are in approximate agreement with structural data from x-ray diffraction. [Preview Abstract] |
Sunday, October 5, 2014 10:00AM - 10:12AM |
H7.00004: Adaptation in variable action sequences Jason D. Wittenbach, Dezhe Z. Jin Sequential behavior is seen throughout the animal kingdom. Often times the actions that comprise a sequential behavior can be placed in different orders within the sequence, creating a variable action sequence. Examples of variable actions sequence range from the simple grooming patterns of mice to the complex patterns and rules of human speech. Understanding how neural circuits can encode and generate the patterns seen in such variable action sequences is an important step in unraveling how the brain generates complex behavior. One popular model system for studying variable action sequences is the Bengalese finch - a songbird with a complex and variable song. The Bengalese finch song exhibits repetition adaptation: a phenomenon where repeated elements become less likely to continue repeating the longer the repetition continues. We propose a model for the neural circuit that the Bengalese finch uses to produce the patterns of its song. This model reproduces the previously unexplained repetition adaptation. We also present a simplified dynamical system that shows how many systems with slowly changing parameters can exhibit a similar phenomenon. [Preview Abstract] |
Sunday, October 5, 2014 10:12AM - 10:24AM |
H7.00005: Phase Diagram for a Model of Truncated $\beta $B1-Crystallin Thienbao Nguyen, James Gunton $\beta $B1-Crystallin proteins, found in the eye lens, self assemble into various oligomer sizes that can affect transparency and refractive power of the lens. Knowing the phase diagrams is an important aspect of understanding this self-assembly. There exists an experimental measurement of the effect of truncation of the protein's N-terminus, which has been associated with aging, on the self-assembly and phase transition properties of the protein solution. By studying the behavior of a native state $\beta $B1 and a truncated version, it was found that the protein undergoes two interesting phase transitions. The first transition corresponds to the fluid-solid solubility line, below which is found rod like structures that crystallize over time. Further below the solubility line is the second transition, which is a liquid-liquid phase separation accompanied by by gelation of the protein rich phase. We propose a phenomenological coarse-grained model, and use a Monte Carlo method simulation to determine the phase transition with the goal of explaining the solubility line and found self-assembly structures in the experimental work. [Preview Abstract] |
Sunday, October 5, 2014 10:24AM - 10:36AM |
H7.00006: A Model of Songbird Song Syntax using Bayesian Nonparametrics Sumithra Surendralal, Dezhe Z. Jin Bird songs are learned sequences of syllables governed by specific rules of arrangement, or syntax. How is syntax encoded in the bird's brain? How is it accessed to produce variability in the vocalizations? These questions are pertinent not only to birdsong, but also to other kinds of learned sequence generation in animals - motor movements, for example. As a first step in addressing these questions, we can construct a probabilistic model of the song syntax. An earlier study has shown that the song syntax of a Bengalese Finch can be described by a Partially Observable Markov Model (POMM), in which a many-to-one mapping scheme between the syllables and associated hidden states was invoked. However, the construction of this model was largely heuristic. We use a nonparametric Bayesian formulation, the Hierarchical Dirichlet Process - Hidden Markov Model, to develop a more principled method of constructing the POMM for birdsong. Importantly, the use of a nonparametric Bayesian inference technique allows us to automatically estimate the optimal number of hidden states in the model. We also make a case for a correspondence between the abstract states in our model and chain networks of neurons in the avian brain region called the HVC. [Preview Abstract] |
Sunday, October 5, 2014 10:36AM - 10:48AM |
H7.00007: Physics-based approaches for protein identification Oleg Obolensky, Yi-Kuo Yu In biomedical research it is often necessary to identify proteins present in a sample. Tandem mass spectrometry (MS/MS) techniques are routinely used for this purpose. The protein in question is digested into smaller pieces (peptides) and then these pieces are protonated and further fragmented in mass spectrometers. The obtained mass spectra are analyzed and the peptides (and eventually the original protein) are identified. Currently, mass spectrometry-based peptide identification methods rely solely on statistical analysis of the mass spectra, while information about physics of the peptide fragmentation processes is vastly underutilized. We demonstrate how the physical approaches can be applied to the problem of peptide identification and how they can complement the statistical analysis. In particular, we show that observability of more than 90 per cent of signal peaks in mass spectra of short singly charged peptides can be easily predicted by knowing the dissociation energies in the corresponding fragmentation channels. [Preview Abstract] |
Sunday, October 5, 2014 10:48AM - 11:00AM |
H7.00008: Modeling Bengalese finch syllable sequence generation with auditory feedback Seth Hulsey, Dezhe Jin The song of the Bengalese finch consists of variable sequences of discrete syllables. Auditory feedback is required for normal singing behavior. Disruption of auditory feedback significantly altered syllable sequencing and timing. Deafening led to the emergence of novel transitions and more complex syllable sequences. Here we construct a computational model of variable sequence generation in Bengalese finch that can explain these results. The model is based on the branched chain network of projection neurons in the premotor song nucleus HVC (proper name). Chains of HVC projection neurons are associated with song syllables. Feedback inhibition from inhibitory interneurons ensures that spiking activity propagates along a single chain at a time. Auditory feedback is provided by projections from NIf neurons to HVC neurons. Different sets of NIf neurons respond to different syllables and have distinctive connection patterns to the HVC chains. Auditory feedback in our model provides sequence-dependent feedback inputs to the HVC network that can control syllable transitions. Alteration of auditory feedback temporarily suppresses NIf input, altering syllable sequencing. Deafening leads to random activations of NIf neurons, encouragingnovel syllable transitions and randomizingsyllable sequences. Our model explains the neural mechanism underlying the effects of altered auditory feedback and deafening on Bengalese finch song sequencing. [Preview Abstract] |
Sunday, October 5, 2014 11:00AM - 11:12AM |
H7.00009: Identifying and controlling the dynamical repertoire of intracellular networks Jorge G.T. Za\~nudo, R\'eka Albert An important challenge when modeling large intracellular networks is to relate the network structure and function to its stable patterns of activity (attractors). Here we present an approach that can be efficiently applied to large network sizes (up to size 1000 and possibly beyond). Formulated in a discrete dynamic framework, this method is based on a topological criterion to find network motifs that stabilize in a fixed state. Combining these network motifs with network reduction techniques, our method predicts the dynamical repertoire of the network elements (fixed states or oscillations) in the model's attractors, and has also been shown to find all of the model's attractors. To illustrate the applicability of our method, we apply it to two different intracellular network models: the network involved in a type of T cell cancer (T cell large granular lymphocytic leukemia), and the network involved in the metastasis of a type of liver cancer (hepatocellular carcinoma). Interestingly, we find that the network motifs identified during our reduction method play a significant role in the cell fate decision mechanisms in both systems, and also provide insights into how to control the dynamics of the system. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700