Automated system and process for heterotrophic growth of plant tissue

A micropropagation system and process for promoting the growth of plant tissue in a sterile environment is provided. The system includes a bioreactor in which the explant tissue is contained and grown. A plurality of fluid reservoirs are connected to the bioreactor for supplying sugar, nutrients, hormones, and water to the plant material. A controller and an analyzer are also included for automating the system by controlling flow rates and by monitoring media concentrations and levels within the bioreactor. Specifically, the controller is capable of monitoring system conditions and making the desired corrections by receiving data from the chemical analyzer. In particular, the controller is capable of calculating and maintaining volume levels of liquid growth media within the bioreactor chamber and maintaining the proper concentrations and proportions of components in the growth media

NOVEL MECHANISMS OF TRANSCRIPTIONAL AND TRANSLATIONAL CONTROL OF HUMAN CYTOMEGALOVIRUS GENE EXPRESSION

Herpesvirus gene expression is dynamic and complex, with distinct complements of viral genes expressed at specific times in different infection contexts. These patterns of viral gene expression arise in part from the integration of multiple cellular and viral signals that affect the transcription and translation of viral genes. The use of alternative promoters provides an increased level of control, allowing different promoters to direct the transcription of the same gene in response to distinct temporal and contextual cues. While once considered rare, herpesvirus alternative promoter usage was recently found to be far more pervasive and impactful than previously thought. Here I show how host transcription factors Foxo3a and C/EBPβ differentially regulate alternative promoters to drive viral gene expression during human cytomegalovirus (HCMV) reactivation. At the post-transcriptional level, HCMV protein pTRS1 further modulates viral gene expression by antagonizing antiviral kinase PKR at multiple junctures. I describe a novel interaction of pTRS1 with cellular phosphatase PP1 to further enhance the effect of pTRS1 on inhibiting host antiviral responses. My work indicates that these strategies for nuanced control of viral gene expression is a crucial component of herpesvirus transcriptional and post-transcriptional gene regulation.Doctor of Philosoph

The Focal plane Detector Package on the TUNL Split-pole Spectrograph

A focal plane detector for the Enge Split-pole Spectrograph at Triangle Universities Nuclear Laboratory has been designed. The detector package consists of two position sensitive gas avalanche counters, a gas proportionality energy loss section, and a residual energy scintillator. This setup allows both particle identification and focal plane reconstruction. In this paper we will detail the construction of each section along with their accompanying electronics and data acquisition. Effects of energy loss throughout the detector, ray tracing procedures, and resolution as a function of fill pressure and bias voltage are also investigated. A measurement of the $^{27}\!$Al$(d,p)$ reaction is used to demonstrate detector performance and to illustrate a Bayesian method of energy calibration

Genome-wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis

Ash (Fraxinus spp.) is one of the most widely distributed tree genera in North America. Populations of ash in the United States and Canada have been decimated by the introduced pest Agrilus planipennis (Coleoptera: Buprestidae; emerald ash borer), having negative impacts on both forest ecosystems and economic interests. The majority of trees succumb to attack by A. planipennis, but some trees have been found to be tolerant to infestation despite years of exposure. Restriction site-associated DNA (RAD) sequencing was used to sequence ash individuals, both tolerant and susceptible to A. planipennis attack, in order to identify single nucleotide polymorphism (SNP) patterns related to tolerance and health declines. de novo SNPs were called using SAMtools and, after filtering criteria were implemented, a set of 17,807 SNPs were generated. Principal component analysis (PCA) of SNPs aligned individual trees into clusters related to geography; however, five tolerant trees clustered together despite geographic location. A subset of 32 outlier SNPs identified within this group, as well as a subset of 17 SNPs identified based on vigor rating, are potential candidates for the selection of host tolerance. Understanding the mechanisms of host tolerance through genome-wide association has the potential to restore populations with cultivars that are able to withstand A. planipennis infestation. This study was successful in using RAD-sequencing in order to identify SNPs that could contribute to tolerance of A. planipennis. This was a first step toward uncovering the genetic basis for host tolerance to A. planipennis. Future studies are needed to identify the functionality of the loci where these SNPs occur and how they may be related to tolerance of A. planipennis attack

A transient homotypic interaction model for the influenza A virus NS1 protein effector domain

Influenza A virus NS1 protein is a multifunctional virulence factor consisting of an RNA binding domain (RBD), a short linker, an effector domain (ED), and a C-terminal 'tail'. Although poorly understood, NS1 multimerization may autoregulate its actions. While RBD dimerization seems functionally conserved, two possible apo ED dimers have been proposed (helix-helix and strand-strand). Here, we analyze all available RBD, ED, and full-length NS1 structures, including four novel crystal structures obtained using EDs from divergent human and avian viruses, as well as two forms of a monomeric ED mutant. The data reveal the helix-helix interface as the only strictly conserved ED homodimeric contact. Furthermore, a mutant NS1 unable to form the helix-helix dimer is compromised in its ability to bind dsRNA efficiently, implying that ED multimerization influences RBD activity. Our bioinformatical work also suggests that the helix-helix interface is variable and transient, thereby allowing two ED monomers to twist relative to one another and possibly separate. In this regard, we found a mAb that recognizes NS1 via a residue completely buried within the ED helix-helix interface, and which may help highlight potential different conformational populations of NS1 (putatively termed 'helix-closed' and 'helix-open') in virus-infected cells. 'Helix-closed' conformations appear to enhance dsRNA binding, and 'helix-open' conformations allow otherwise inaccessible interactions with host factors. Our data support a new model of NS1 regulation in which the RBD remains dimeric throughout infection, while the ED switches between several quaternary states in order to expand its functional space. Such a concept may be applicable to other small multifunctional proteins

On the alleged simplicity of impure proof

Roughly, a proof of a theorem, is “pure” if it draws only on what is “close” or “intrinsic” to that theorem. Mathematicians employ a variety of terms to identify pure proofs, saying that a pure proof is one that avoids what is “extrinsic,” “extraneous,” “distant,” “remote,” “alien,” or “foreign” to the problem or theorem under investigation. In the background of these attributions is the view that there is a distance measure (or a variety of such measures) between mathematical statements and proofs. Mathematicians have paid little attention to specifying such distance measures precisely because in practice certain methods of proof have seemed self- evidently impure by design: think for instance of analytic geometry and analytic number theory. By contrast, mathematicians have paid considerable attention to whether such impurities are a good thing or to be avoided, and some have claimed that they are valuable because generally impure proofs are simpler than pure proofs. This article is an investigation of this claim, formulated more precisely by proof- theoretic means. After assembling evidence from proof theory that may be thought to support this claim, we will argue that on the contrary this evidence does not support the claim

Qualitative Analysis of String Cosmologies

A qualitative analysis is presented for spatially flat, isotropic and homogeneous cosmologies derived from the string effective action when the combined effects of a dilaton, modulus, two-form potential and central charge deficit are included. The latter has significant effects on the qualitative dynamics. The analysis is also directly applicable to the anisotropic Bianchi type I cosmology.Comment: 13 pages, 4 postscript figures, accepted to Physical Review

Snowpack Relative Permittivity and Density Derived from Near-Coincident Lidar and Ground-Penetrating Radar

Depth-based and radar-based remote sensing methods (e.g., lidar, synthetic aperture radar) are promising approaches for remotely measuring snow water equivalent (SWE) at high spatial resolution. These approaches require snow density estimates, obtained from in-situ measurements or density models, to calculate SWE. However, in-situ measurements are operationally limited, and few density models have seen extensive evaluation. Here, we combine near-coincident, lidar-measured snow depths with ground-penetrating radar (GPR) two-way travel times (twt) of snowpack thickness to derive \u3e20 km of relative permittivity estimates from nine dry and two wet snow surveys at Grand Mesa, Cameron Pass, and Ranch Creek, Colorado. We tested three equations for converting dry snow relative permittivity to snow density and found the Kovacs et al. (1995) equation to yield the best comparison with in-situ measurements (RMSE = 54 kg m−3). Variogram analyses revealed a 19 m median correlation length for relative permittivity and snow density in dry snow, which increased to \u3e 30 m in wet conditions. We compared derived densities with estimated densities from several empirical models, the Snow Data Assimilation System (SNODAS), and the physically based iSnobal model. Estimated and derived densities were combined with snow depths and twt to evaluate density model performance within SWE remote sensing methods. The Jonas et al. (2009) empirical model yielded the most accurate SWE from lidar snow depths (RMSE = 51 mm), whereas SNODAS yielded the most accurate SWE from GPR twt (RMSE = 41 mm). Densities from both models generated SWE estimates within ±10% of derived SWE when SWE averaged \u3e 400 mm, however, model uncertainty increased to \u3e 20% when SWE averaged \u3c 300 mm. The development and refinement of density models, particularly in lower SWE conditions, is a high priority to fully realize the potential of SWE remote sensing methods

Manipulation of the unfolded protein response: A pharmacological strategy against coronavirus infection.

Coronavirus infection induces the unfolded protein response (UPR), a cellular signalling pathway composed of three branches, triggered by unfolded proteins in the endoplasmic reticulum (ER) due to high ER load. We have used RNA sequencing and ribosome profiling to investigate holistically the transcriptional and translational response to cellular infection by murine hepatitis virus (MHV), often used as a model for the Betacoronavirus genus to which the recently emerged SARS-CoV-2 also belongs. We found the UPR to be amongst the most significantly up-regulated pathways in response to MHV infection. To confirm and extend these observations, we show experimentally the induction of all three branches of the UPR in both MHV- and SARS-CoV-2-infected cells. Over-expression of the SARS-CoV-2 ORF8 or S proteins alone is itself sufficient to induce the UPR. Remarkably, pharmacological inhibition of the UPR greatly reduced the replication of both MHV and SARS-CoV-2, revealing the importance of this pathway for successful coronavirus replication. This was particularly striking when both IRE1α and ATF6 branches of the UPR were inhibited, reducing SARS-CoV-2 virion release (~1,000-fold). Together, these data highlight the UPR as a promising antiviral target to combat coronavirus infection

Discovery of an intermediate-luminosity red transient in M51 and its likely dust-obscured, infrared-variable progenitor

We present the discovery of an optical transient (OT) in Messier 51, designated M51 OT2019-1 (also ZTF19aadyppr, AT 2019abn, ATLAS19bzl), by the Zwicky Transient Facility (ZTF). The OT rose over 15 days to an observed luminosity of $M_r=-13$ (${\nu}L_{\nu}=9\times10^6~L_{\odot}$), in the luminosity gap between novae and typical supernovae (SNe). Spectra during the outburst show a red continuum, Balmer emission with a velocity width of $\approx400$ km s$^{-1}$, Ca II and [Ca II] emission, and absorption features characteristic of an F-type supergiant. The spectra and multiband light curves are similar to the so-called "SN impostors" and intermediate-luminosity red transients (ILRTs). We directly identify the likely progenitor in archival Spitzer Space Telescope imaging with a $4.5~\mu$m luminosity of $M_{[4.5]}\approx-12.2$ and a $[3.6]-[4.5]$ color redder than 0.74 mag, similar to those of the prototype ILRTs SN 2008S and NGC 300 OT2008-1. Intensive monitoring of M51 with Spitzer further reveals evidence for variability of the progenitor candidate at [4.5] in the years before the OT. The progenitor is not detected in pre-outburst Hubble Space Telescope optical and near-IR images. The optical colors during outburst combined with spectroscopic temperature constraints imply a higher reddening of $E(B-V)\approx0.7$ mag and higher intrinsic luminosity of $M_r\approx-14.9$ (${\nu}L_{\nu}=5.3\times10^7~L_{\odot}$) near peak than seen in previous ILRT candidates. Moreover, the extinction estimate is higher on the rise than on the plateau, suggestive of an extended phase of circumstellar dust destruction. These results, enabled by the early discovery of M51 OT2019-1 and extensive pre-outburst archival coverage, offer new clues about the debated origins of ILRTs and may challenge the hypothesis that they arise from the electron-capture induced collapse of extreme asymptotic giant branch stars.Comment: 21 pages, 5 figures, published in ApJ