Physics Commons^™

Model For Coordination Of Microtubule And Actin Dynamics In Growth Cone Turning, Erin M. Craig

All Faculty Scholarship for the College of the Sciences

In the developing nervous system, axons are guided to their synaptic targets by motile structures at the axon tip called growth cones, which reorganize their cytoskeleton in order to steer in response to chemotactic cues. Growth cone motility is mediated by an actin-adhesion “clutch” mechanism, in which mechanical attachment to a substrate, coupled with polarized actin growth, produces leading-edge protrusion. Several studies suggest that dynamic microtubules (MTs) in the growth cone periphery play an essential role in growth cone steering. It is not yet well-understood how the MT cytoskeleton and the dynamic actin-adhesion clutch system are coordinated to promote growth …

Raman Spectroscopy Detects Biochemical Changes Due To Different Cell Culture Environments In Live Cells In Vitro, Mahmoud Gargotti, Esen Efeoglu, Hugh Byrne, Alan Casey

Articles

The in vitro cell culture environment can impact on cell biochemistry and cell cycle. The manifestation of such substrate-induced changes in cell cycle in the Raman microspectroscopic profiles of cell cultures is investigated at the level of nucleolus, nucleus and cytoplasm. HeLa immortalised human cervical cells and HaCaT dermal cells were cultured on three different substrates, conventional polystyrene cell culture dishes, CaF2 slides as a commonly used Raman substrate, and glass slides coated with Collagen Rat Tail, as a mimic of the extra cellular matrix (ECM) environment. A cell cycle study, based on percentage DNA content, as determined using Propidium …

Structural And Wetting Properties Of Nature's Finest Silks (Order Embioptera), Grace Y. Stokes, Evangelea N. Dicicco, Trevor J. Moore, Vivian C. Cheng, Kira Y. Wheeler, John Soghigian, Richard P. Barber Jr., Janice Edgerly-Rooks

Physics

Insects from the order Embioptera (webspinners) spin silk fibres which are less than 200 nm in diameter. In this work, we characterized and compared the diameters of single silk fibres from nine species—Antipaluria urichi, Pararhagadochir trinitatis, Saussurembia calypso, Diradius vandykei, Aposthonia ceylonica, Haploembia solieri, H. tarsalis, Oligotoma nigra and O. saundersii. Silk from seven of these species have not been previously quantified. Our studies cover five of the 10 named taxonomic families and represent about one third of the known taxonomic family-level diversity in the order Embioptera. Naturally spun silk varied …

Estimating And Correcting Interference Fringes In Infrared Spectra In Infrared Hyperspectral Imaging, Ghazal Azarfar, Ebrahim Aboualizadeh, Nicholas Walter,, Simona Ratti, Camilla Olivieri, Alessandra Alessandra, Michael Nasse, Achim Kohler, Mario Giordano, Carol Hirschmugl

Physics Faculty Articles

Short-term acclimation response of individual cells of Thalassiosira weissflogii was monitored by Synchrotron FTIR imaging over the span of 75 minutes. The cells, collected from batch cultures, were maintained in a constant flow of medium, at an irradiance of 120 μmol m−2 s−1 and at 20 °C. Multiple internal reflections due to the micro fluidic channel were modeled, and showed that fringes are additive sinusoids to the pure absorption of the other components of the system. Preprocessing of the hyperspectral cube (x, y, Abs(λ)) included removing spectral fringe using an EMSC approach. Principal component analysis of the time series of …

E. Coli Elongation Factor Tu Bound To A Gtp Analogue Displays An Open Conformation Equivalent To The Gdp-Bound Form, Jesper S. Johansen, Darius Kavaliauskas, Shawn H. Pfeil, Mickael Blaise, Barry C. Cooperman, Yale E. Goldman, Søren S. Thirup, Charlotte R. Knudsen

Physics & Engineering Faculty Publications

According to the traditional view, GTPases act as molecular switches, which cycle between distinct ‘on’ and ‘off’ conformations bound to GTP and GDP, respectively. Translation elongation factor EF-Tu is a GTPase essential for prokaryotic protein synthesis. In its GTP-bound form, EF-Tu delivers aminoacylated tRNAs to the ribosome as a ternary complex. GTP hydrolysis is thought to cause the release of EF-Tu from aminoacyl-tRNA and the ribosome due to a dramatic conformational change following Pi release. Here, the crystal structure of Escherichia coli EF-Tu in complex with a non-hydrolysable GTP analogue (GDPNP) has been determined. Remarkably, the overall conformation of EF-Tu·GDPNP …

Advancing Raman Microspectroscopy For Cellular And Subcellular Analysis: Towards In Vitro High Content Spectralomic Analysis, Hugh Byrne, Franck Bonnier, Alan Casey, Marcus Maher, Jennifer Mcintyre, Esen Efeoglu, Zeineb Farhane

Articles

In the confocal mode, Raman microspectroscopy can profile the biochemical content of biological cells at a subcellular level, and any changes to it by exogenous agents, such as therapeutic drugs or toxicants. As an exploration of the potential of the technique as a high content, label free analysis technique, this report reviews work to monitor the spectroscopic signatures associated with the uptake and response pathways of commercial chemotherapeutic agents and polymeric nanoparticles by human lung cells. It is demonstrated that the signatures are reproducible and characteristic of the cellular event, and can be used, for example, to identify the mode …

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 for lactic acid and …

Spectroscopy And Formation Of Lanthanum-Hydrocarbon Radicals Formed By Association And Carbon-Carbon Bond Cleavage Of Isoprene, Wenjin Cao, Dilkrushi Hewage, Dong-Sheng Yang

Chemistry Faculty Publications

La atom reaction with isoprene is carried out in a laser-vaporization molecular beam source. The reaction yields an adduct as the major product and C—C cleaved and dehydrogenated species as the minor ones. La(C₅H₈), La(C₂H₂), and La(C₃H₄) are characterized with mass-analyzed threshold ionization (MATI) spectroscopy and quantum chemical computations. The MATI spectra of all three species exhibit a strong origin band and several weak vibronic bands corresponding to La-ligand stretch and ligand-based bend excitations. La(C₅H₈) is a five-membered metallacycle, whereas La(C₂H_{2 …}

Collective Gradient Sensing In Fish Schools, James G. Puckett, Aawaz R. Pokhrel, Julia A. Giannini

Physics and Astronomy Faculty Publications

Throughout the animal kingdom, animals frequently benefit from living in groups. Models of collective behaviour show that simple local interactions are sufficient to generate group morphologies found in nature (swarms, flocks and mills). However, individuals also interact with the complex noisy environment in which they live. In this work, we experimentally investigate the group performance in navigating a noisy light gradient of two unrelated freshwater species: golden shiners (Notemigonuscrysoleucas) and rummy nose tetra (Hemigrammus bleheri). We find that tetras outperform shiners due to their innate individual ability to sense the environmental gradient. Using numerical simulations, we examine how group performance …

Computational Analysis Of Poliovirus Structural Dynamics Using A Coarse-Grained Model, Maneesh Koneru

University Scholar Projects

Though eradicated in most of the world, poliovirus remains a common model virus for a family of mammalian viruses known as Picornaviruses. Despite the development of a vaccination, little is understood about the infection process, particularly the mechanism of cell entry. Experimental studies have attempted to elucidate the dynamics of this process and have proposed pathways focused on VP4, the smallest of the four peptides which makes up the viral capsid, and its interaction with the pentameric interfaces of the five fold axes. This study utilizes coarse-grained molecular dynamics to supplement these proposed mechanisms with simplified simulations which reduce the …

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 with …

Vibration Response: Mapping The Behavioral Response Of Fruit Fly Larvae To Mechanical Stimuli, Alexander Berne

2018 Entries

Drosophila larvae are capable of a wide array of simple, quantifiable behavioral responses to stimuli, which makes the organism a useful tool for deconstructing biotic behavior for wider application. To this end, an understanding of the response to mechanical stimulation remains relatively unexplored in this organism, and warrants investigation. This research aims to map the fruit fly’s behavior as a function of a generalized mechanical stimulus, namely, vibration.

Fruit fly larvae are placed in a light and temperature controlled environment, and observed crawling on vibrating agar plates with CCD cameras controlled through LabVIEW. Larvae are monitored for their instantaneous speed, …

Reference Dependence Of The Two-Determinant Coupled-Cluster Method For Triplet And Open-Shell Singlet States Of Biradical Molecules, Jesse J. Lutz, Marcel Nooijen, Ajith Perera, Rodney J. Bartlett

Faculty Publications

We study the performance of the two-determinant (TD) coupled-cluster (CC) method which, unlike conventional ground-state single-reference (SR) CC methods, can, in principle, provide a naturally spin-adapted treatment of the lowest-lying open-shell singlet (OSS) and triplet electronic states. Various choices for the TD-CC reference orbitals are considered, including those generated by the multi-configurational self-consistent field method. Comparisons are made with the results of high-level SR-CC, equation-of-motion (EOM) CC, and multi-reference EOM calculations performed on a large test set of over 100 molecules with low-lying OSS states. It is shown that in cases where the EOMCC reference function is poorly described, TD-CC …

Universality Of Quantum Information In Chaotic Cfts, Nima Lashkari, Anatoly Dymarsky, Hong Liu

Physics and Astronomy Faculty Publications

We study the Eigenstate Thermalization Hypothesis (ETH) in chaotic conformal field theories (CFTs) of arbitrary dimensions. Assuming local ETH, we compute the reduced density matrix of a ball-shaped subsystem of finite size in the infinite volume limit when the full system is an energy eigenstate. This reduced density matrix is close in trace distance to a density matrix, to which we refer as the ETH density matrix, that is independent of all the details of an eigenstate except its energy and charges under global symmetries. In two dimensions, the ETH density matrix is universal for all theories with the …

Hard-Sphere-Like Dynamics In Highly Concentrated Alpha-Crystallin Suspensions, Preeti Vodnala, Laurence Lurio, Michael C. Vega, Elizabeth Gaillard

Faculty Peer-Reviewed Publications

The dynamics of concentrated suspensions of the eye-lens protein alpha crystallin have been measured using x-ray photon correlation spectroscopy. Measurements were made at wave vectors corresponding to the first peak in the hard-sphere structure factor and volume fractions close to the critical volume fraction for the glass transition. Langevin dynamics simulations were also performed in parallel to the experiments. The intermediate scattering function f(q,τ) could be fit using a stretched exponential decay for both experiments and numerical simulations. The measured relaxation times show good agreement with simulations for polydisperse hard-sphere colloids.

A Machine Learning Algorithm For Identifying And Tracking Bacteria In Three Dimensions Using Digital Holographic Microscopy, Manuel Bedrossian, Marwan El-Kholy, Daniel Neamati, Jay Nadeau

Physics Faculty Publications and Presentations

Digital Holographic Microscopy (DHM) is an emerging technique for three-dimensional imaging of microorganisms due to its high throughput and large depth of field relative to traditional microscopy techniques. While it has shown substantial success for use with eukaryotes, it has proven challenging for bacterial imaging because of low contrast and sources of noise intrinsic to the method (e.g. laser speckle). This paper describes a custom written MATLAB routine using machine-learning algorithms to obtain three-dimensional trajectories of live, lab-grown bacteria as they move within an essentially unrestrained environment with more than 90% precision. A fully annotated version of the software used …

Lanthanum-Mediated Dehydrogenation Of Butenes: Spectroscopy And Formation Of La(C4H6) Isomers, Wenjin Cao, Dilkrushi Hewage, Dong-Sheng Yang

Chemistry Faculty Publications

La atom reactions with 1-butene, 2-butene, and isobutene are carried out in a laser-vaporization molecular beam source. The three reactions yield the same La-hydrocarbon products from the dehydrogenation and carbon-carbon bond cleavage and coupling of the butenes. The dehydrogenated species La(C₄H₆) is the major product, which is characterized with mass-analyzed threshold ionization (MATI) spectroscopy and quantum chemical computations. The MATI spectrum of La(C₄H₆) produced from the La+1-butene reaction exhibits two band systems, whereas the MATI spectra produced from the La+2-butene and isobutene reactions display only a single band system. Each of these …

Detection And Characterization Of The Tin Dihydride (Snh2 And Snd2) Molecule In The Gas Phase, Tony C. Smith, Dennis J. Clouthier

Chemistry Faculty Publications

The SnH₂ and SnD₂ molecules have been detected for the first time in the gas phase by laser-induced fluorescence (LIF) and emission spectroscopic techniques through the ùB₁–X̃¹A₁ electronic transition. These reactive species were prepared in a pulsed electric discharge jet using (CH₃)₄Sn or SnH₄/SnD₄ precursors diluted in high pressure argon. Transitions to the electronic excited state of the jet-cooled molecules were probed with LIF, and the ground state energy levels were measured from single rovibronic level emission spectra. The LIF spectrum of SnD_{2 …}

Modulation Of The Navigational Strategy Of Insects In Controlled Temperature Environments, Joseph Shomar, Anggie Ferrer, Josh Forer, Tom Zhang, Mason Klein

2018 Entries

With its small size and limited motor tool set, the Drosophila larva is a good system to study how animals alter specific elements of their behavior to search and reach optimal environmental conditions. We aim to understand the larva’s response to temperature across development, in sensory gradients, and to distinguish behavioral modulations based on physical changes from those due to sensory input. PID-controlled instruments drive temporal or spatial temperature gradients; combined with a moat system to replenish gels at high temperature, we can explore the larva’s full behavioral profile. Many larvae are simultaneously observed during free navigation in three different …

Three-Dimensional Imaging Of Kndy Neurons In The Mammalian Brain Using Optical Tissue Clearing And Multiple-Label Immunocytochemistry, Aleisha M. Moore, Kathryn A. Lucas, Robert L. Goodman, Lique M. Coolen, Michael N. Lehman

Faculty & Staff Scholarship

Kisspeptin/Neurokinin B/Dynorphin (KNDy) neurons of the arcuate nucleus (ARC) play a key role in the regulation of fertility. The ability to detect features of KNDy neurons that are essential for fertility may require three-dimensional (3D) imaging of the complete population. Recently developed protocols for optical tissue clearing permits 3D imaging of neuronal populations in un-sectioned brains. However, these techniques have largely been described in the mouse brain. We report 3D imaging of the KNDy cell population in the whole rat brain and sheep hypothalamus using immunolabelling and modification of a solvent-based clearing protocol, iDISCO. This study expands the use of …

Macrophage Sensing Of Single- Walled Carbon Nanotubes Via Toll- Like Receptors, Sourav P. Mukherjee, Olesja Bondarenko, Pekka Kohonen, Fernando T. Andon, Tana Brzicova, Isabel Gessner, Sanjay Mathur, Massimo Bottini, Paolo Calligari, Lorenzo Stella, Elena Kisin, Anna Shvedova, Reija Autio, Heli Salminen-Mankonen, Ritta Lahesmaa, Bengt Fadeel

Faculty & Staff Scholarship

Carbon-based nanomaterials including carbon nanotubes (CNTs) have been shown to trigger

inflammation. However, how these materials are ‘sensed’ by immune cells is not known. Here we compared the effects of two carbon-based nanomaterials, single-walled CNTs (SWCNTs) and graphene oxide (GO), on primary human monocyte-derived macrophages. Genome-wide transcriptomics assessment was performed at sub-cytotoxic doses. Pathway analysis of the microarray data revealed pronounced effects on chemokine-encoding genes in macrophages exposed to SWCNTs, but not in response to GO, and these results were validated by multiplex array-based cytokine and chemokine profiling. Conditioned medium from SWCNT-exposed cells acted as a chemoattractant for dendritic cells. …

Comparison Between The Water Activation Effects By Pulsed And Sinusoidal Helium Plasma Jets, Han Xu, Dingxin Liu, Wenjie Xia, Chen Chen, Weitao Wang, Zhijie Liu, Xiaohua Wang, Michael G. Kong

Bioelectrics Publications

Comparisons between pulsed and sinusoidal plasma jets have been extensively reported for the discharge characteristics and gaseous reactive species, but rarely for the aqueous reactive species in water solutions treated by the two types of plasma jets. This motivates us to compare the concentrations of aqueous reactive species induced by a pulsed and a sinusoidal plasma jet, since it is widely reported that these aqueous reactive species play a crucial role in various plasma biomedical applications. Experimental results show that the aqueous H₂O₂, OH/O₂⁻, and O₂⁻/ONOO⁻ induced by the …