Micropattern traction microscopy: a technique for the simplification of cellular traction force measurements

Thesis (Ph.D.)--Boston UniversityCells respond to a number of cues that affect how they interact with their surrounding environment, such as topology, the presentation of adhesive ligands, and stiffness. Recent advancements in the field ofmechanobiology have revealed that one of the main ways in which cells sense these cues is through contractile forces. Mechanobiology research seeks to understand how environmental cues affect the forces that cells exert on their surronnding environment and how these mechanical forces are communicated to the cell and transformed into biochemical signals. Therefore, quantitative methods have been developed to determine cell contractility on soft, optically transparent, deformable surfaces by quantifying substrate deformation in terms of cellular traction forces. However, the currently available tools that are used to study cell interactions are limited in their applicability due to the need for specialized technical expertise that is not amenable to the widespread adaptation of these techniques. Therefore, we have sought to develop a novel traction force microscopy technique known as micropattem traction microscopy. With this technique, we hope to greatly simplify the current traction force microscopy techniques and provide a method which will be able to be adopted by a wide range of laboratories. This dissertation describes the process ofthe development and application of this novel traction force technique to probe questions in mechanobiology that have not been previously broached due to the lack of appropriate tools. The technique itself uses indirect microcontact printing to create a regularized array of fluorescent protein onto a glass substrate, which is then transferred to an optically transparent, soft, elastic polyacrylamide hydrogel. Cells, limited by their ability to adhere only to patterned regions, will deform the pattern at these defined points. Thus, with knowledge of the bulk elastic properties ofthe substrate and a priori knowledge of the pattern, we are able to quantify the force a cell is exerting without its removal. We also developed and released a robust, automated MATLAB program that will aid users in the calculation of traction forces so that people with limited experience with programming can utilize the program without significant investments into training. This indirect approach allows for not only individual proteins, but also for multiple, spatially distinct, fluorescent proteins such as fibronectin and gelatin to be simultaneously patterned onto this surface as well. The ability to pattern multiple proteins in a spatially defmed region significantly aids in giving users control over as many parameters as possible. Finally, we will explore the current and future potential that this technique has to offer to researchers in the field of mechanobiology

Crops, Rumps and Woolly Jumpers: An Innovative Extension Approach Enabling the Complexities of Mixed Farming to Be Shared and Understood

The sheep-wheat belt of southern Australia accounts for about 19% and 57% of total Australian beef and sheep production, respectively. Most farm businesses in this zone are family owned and contain a mix of livestock and cropping enterprises. While the focus of most research, development and extension for mixed farming systems focuses on single components of the system (lamb, wool, beef, pastures, crops), the systems are complex and dynamic and cannot be understood by analysing the components in isolation. The enterprise synergies are dependent on economic, environmental and social factors. The farmers themselves are best equipped to explain the system function and the interplay between the components. The traditional conference format with technical experts presenting their findings was deemed to be inadequate to relay the complexity of mixed farming systems, stifling two-way information flow and the opportunity for experts to acquire tacit knowledge held by farmers. This paper out-lines an innovative extension approach based on story telling, video footage and discussion, providing technical experts with an opportunity to appreciate the complexity and farmer decision processes. This approach fostered audience participation and interaction, leading to a better understanding of the complexities of mixed farming and how conflicts between diversification and specialisation may be resolved by the management team. Facilitated discussion also highlighted potential areas of research, development and extension

The Zwicky Transient Facility: Surveys and Scheduler

We present a novel algorithm for scheduling the observations of time-domain imaging surveys. Our Integer Linear Programming approach optimizes an observing plan for an entire night by assigning targets to temporal blocks, enabling strict control of the number of exposures obtained per field and minimizing filter changes. A subsequent optimization step minimizes slew times between each observation. Our optimization metric self-consistently weights contributions from time-varying airmass, seeing, and sky brightness to maximize the transient discovery rate. We describe the implementation of this algorithm on the surveys of the Zwicky Transient Facility and present its on-sky performance.Comment: Published in PASP Focus Issue on the Zwicky Transient Facility (https://dx.doi.org/10.1088/1538-3873/ab0c2a). 13 Pages, 11 Figure

New Frontiers in Food Production Beyond LEO

New technologies will be needed as mankind moves towards exploration of cislunar space, the Moon and Mars. Although many advances in our understanding of the effects of spaceflight on plant growth have been achieved in the last 40 years, spaceflight plant growth systems have been primarily designed to support space biology studies. Recently, the need for a sustainable and robust food system for future missions beyond Low Earth Orbit (LEO) has identified gaps in current technologies for food production. The goal is to develop safe and sustainable food production systems with reduced resupply mass and crew time compared to current systems

Panic at the ISCO: the visible accretion disks powering optical variability in ZTF AGN

About 3-10% of Type I active galactic nuclei (AGN) have double-peaked broad Balmer lines in their optical spectra originating from the motion of gas in their accretion disk. Double-peaked profiles arise not only in AGN, but occasionally appear during optical flares from tidal disruption events and changing-state AGN. In this paper we identify 250 double-peaked emitters (DPEs) amongst a parent sample of optically variable broad-line AGN in the Zwicky Transient Facility (ZTF) survey, corresponding to a DPE fraction of 19%. We model spectra of the broad H alpha emission line regions and provide a catalog of the fitted accretion disk properties for the 250 DPEs. Analysis of power spectra derived from the 5 year ZTF light curves finds that DPEs have similar amplitudes and power law indices to other broad-line AGN, but have lower turnover frequencies. Follow-up spectroscopy of 12 DPEs reveals that ~50% display significant changes in the relative strengths of their red and blue peaks over long 10-20 year timescales, indicating that broad-line profile changes arising from spiral arm or hotspot rotation are common amongst optically variable DPEs. Analysis of the accretion disk parameters derived from spectroscopic modeling provides evidence that DPEs are not in a special accretion state, but are simply normal broad-line AGN viewed under the right conditions for the accretion disk to be easily visible. We compare the radio variability properties of the two samples and present radio jet imaging of 3 DPEs with disks of inclination angle 14-35 degrees. We discuss some objects with notable light curves or unusual broad line profiles which are outliers amongst the variable DPE population. We include inspiraling SMBH binary candidate SDSSJ1430+2303 in our analysis, and discuss how its photometric and spectroscopic variability is consistent with the disk-emitting AGN population in ZTF.Comment: Submitted to ApJ. 30 pages, 10 figures, 4 tables. Comments welcome

SN 2020jgb: A Peculiar Type Ia Supernova Triggered by a Massive Helium-Shell Detonation in a Star-Forming Galaxy

The detonation of a thin ($\lesssim$$0.03\,\mathrm{M_\odot}$) helium shell (He-shell) atop a $\sim$$1\,\mathrm{M_\odot}$ white dwarf (WD) is a promising mechanism to explain normal Type Ia supernovae (SNe Ia), while thicker He-shells and less massive WDs may explain some recently observed peculiar SNe Ia. We present observations of SN 2020jgb, a peculiar SN Ia discovered by the Zwicky Transient Facility (ZTF). Near maximum light, SN 2020jgb is slightly subluminous (ZTF $g$-band absolute magnitude $M_g$ between $-18.2$ and $-18.7$ mag depending on the amount of host galaxy extinction) and shows an unusually red color ($g_\mathrm{ZTF}-r_\mathrm{ZTF}$ between 0.4 and 0.2 mag) due to strong line-blanketing blueward of $\sim$5000 $\r{A}$. These properties resemble those of SN 2018byg, a peculiar SN Ia consistent with a thick He-shell double detonation (DDet) SN. Using detailed radiative transfer models, we show that the optical spectroscopic and photometric evolution of SN 2020jgb are broadly consistent with a $\sim$$0.95\,\mathrm{M_\odot}$ (C/O core + He-shell; up to $\sim$$1.00\,\mathrm{M_\odot}$ depending on the total host extinction) progenitor ignited by a thick ($\sim$$0.13\,\mathrm{M_\odot}$) He-shell. We detect a prominent absorption feature at $\sim$1 $\mu\mathrm{m}$ in the near-infrared (NIR) spectrum of SN 2020jgb, which could originate from unburnt helium in the outermost ejecta. While the sample size is limited, similar 1 $\mu\mathrm{m}$ features have been detected in all the thick He-shell DDet candidates with NIR spectra obtained to date. SN 2020jgb is also the first subluminous, thick He-shell DDet SN discovered in a star-forming galaxy, indisputably showing that He-shell DDet objects occur in both star-forming and passive galaxies, consistent with the normal SN Ia population.Comment: 23 pages, 10 figures. Updated to accepted version (ApJ

Does functionalisation enhance CO2 uptake in interpenetrated MOFs? An examination of the IRMOF-9 series

The effect of pore functionalisation (-I, -OH, -OCH3) on a series of topologically equivalent, interpenetrated metal-organic frameworks (MOFs) was assessed by both simulation and experiment. Counter-intuitively, a decreased affinity for CO2 was observed in the functionalised materials, compared to the non-functionalised material. This result highlights the importance of considering the combined effects of network topology and chemical functionality in the design of MOFs for enhanced CO2 adsorptionRavichandar Babarao, Campbell J. Coghlan, Damien Rankine, Witold M. Bloch, Gemma K. Gransbury, Hiroshi Sato, Susumu Kitagawa, Christopher J. Sumby, Matthew R. Hill and Christian J. Doona

ZTF Early Observations of Type Ia Supernovae. III. Early-time Colors As a Test for Explosion Models and Multiple Populations

Colors of Type Ia supernovae (SNe Ia) in the first few days after explosion provide a potential discriminant between different models. In this paper, we present g-r colors of 65 SNe Ia discovered within 5 days from first light by the Zwicky Transient Facility in 2018, a sample that is about three times larger than that in the literature. We find that g-r colors are intrinsically rather homogeneous at early phases, with about half of the dispersion attributable to photometric uncertainties (σnoise ∼ σ int ∼ 0.18 mag). Colors are nearly constant starting from 6 days after first light (g-r ∼-0.15 mag), while the time evolution at earlier epochs is characterized by a continuous range of slopes, from events rapidly transitioning from redder to bluer colors (slope of ∼-0.25 mag day-1) to events with a flatter evolution. The continuum in the slope distribution is in good agreement both with models requiring some amount of 56Ni mixed in the outermost regions of the ejecta and with "double-detonation"models having thin helium layers MHe=0.01 M⊙) and varying carbon-oxygen core masses. At the same time, six events show evidence for a distinctive "red bump"signature predicted by double-detonation models with larger helium masses. We finally identify a significant correlation between the early-time g-r slopes and supernova brightness, with brighter events associated to flatter color evolution (p-value = 0.006). The distribution of slopes, however, is consistent with being drawn from a single population, with no evidence for two components as claimed in the literature based on B-V colors

ZTF Early Observations of Type Ia Supernovae. III. Early-time Colors As a Test for Explosion Models and Multiple Populations

Colors of Type Ia supernovae (SNe Ia) in the first few days after explosion provide a potential discriminant between different models. In this paper, we present g − r colors of 65 SNe Ia discovered within 5 days from first light by the Zwicky Transient Facility in 2018, a sample that is about three times larger than that in the literature. We find that g − r colors are intrinsically rather homogeneous at early phases, with about half of the dispersion attributable to photometric uncertainties (σ_(noise)∼σ_(int) ~ 0.18 mag). Colors are nearly constant starting from 6 days after first light (g − r ~ −0.15 mag), while the time evolution at earlier epochs is characterized by a continuous range of slopes, from events rapidly transitioning from redder to bluer colors (slope of ~−0.25 mag day⁻¹) to events with a flatter evolution. The continuum in the slope distribution is in good agreement both with models requiring some amount of ⁵⁶Ni mixed in the outermost regions of the ejecta and with "double-detonation" models having thin helium layers (M_(He) = 0.01 M_⊙) and varying carbon–oxygen core masses. At the same time, six events show evidence for a distinctive "red bump" signature predicted by double-detonation models with larger helium masses. We finally identify a significant correlation between the early-time g − r slopes and supernova brightness, with brighter events associated to flatter color evolution (p-value = 0.006). The distribution of slopes, however, is consistent with being drawn from a single population, with no evidence for two components as claimed in the literature based on B − V colors