Recent Applications of RNA Sequencing in Food and Agriculture

RNA sequencing (RNA-Seq) is the leading, routine, high-throughput, and cost-effective next-generation sequencing (NGS) approach for mapping and quantifying transcriptomes, and determining the transcriptional structure. The transcriptome is a complete collection of transcripts found in a cell or tissue or organism at a given time point or specific developmental or environmental or physiological condition. The emergence and evolution of RNA-Seq chemistries have changed the landscape and the pace of transcriptome research in life sciences over a decade. This chapter introduces RNA-Seq and surveys its recent food and agriculture applications, ranging from differential gene expression, variants calling and detection, allele-specific expression, alternative splicing, alternative polyadenylation site usage, microRNA profiling, circular RNAs, single-cell RNA-Seq, metatranscriptomics, and systems biology. A few popular RNA-Seq databases and analysis tools are also presented for each application. We began to witness the broader impacts of RNA-Seq in addressing complex biological questions in food and agriculture

The space coronagraph optical bench (SCoOB): 2. wavefront sensing and control in a vacuum-compatible coronagraph testbed for spaceborne high-contrast imaging technology

The 2020 Decadal Survey on Astronomy and Astrophysics endorsed space-based high contrast imaging for the detection and characterization of habitable exoplanets as a key priority for the upcoming decade. To advance the maturity of starlight suppression techniques in a space-like environment, we are developing the Space Coronagraph Optical Bench (SCoOB) at the University of Arizona, a new thermal vacuum (TVAC) testbed based on the Coronagraphic Debris Exoplanet Exploring Payload (CDEEP), a SmallSat mission concept for high contrast imaging of circumstellar disks in scattered light. When completed, the testbed will combine a vector vortex coronagraph (VVC) with a Kilo-C microelectromechanical systems (MEMS) deformable mirror from Boston Micromachines Corp (BMC) and a self-coherent camera (SCC) with a goal of raw contrast surpassing $10^{-8}$ at visible wavelengths. In this proceedings, we report on our wavefront sensing and control efforts on this testbed in air, including the as-built performance of the optical system and the implementation of algorithms for focal-plane wavefront control and digging dark holes (regions of high contrast in the focal plane) using electric field conjugation (EFC) and related algorithms.Comment: 7 pages, 5 figures, SPIE Astronomical Telescopes and Instrumentation 202

The Space Coronagraph Optical Bench (SCoOB): 1. Design and Assembly of a Vacuum-compatible Coronagraph Testbed for Spaceborne High-Contrast Imaging Technology

The development of spaceborne coronagraphic technology is of paramount importance to the detection of habitable exoplanets in visible light. In space, coronagraphs are able to bypass the limitations imposed by the atmosphere to reach deeper contrasts and detect faint companions close to their host star. To effectively test this technology in a flight-like environment, a high-contrast imaging testbed must be designed for operation in a thermal vacuum (TVAC) chamber. A TVAC-compatible high-contrast imaging testbed is undergoing development at the University of Arizona inspired by a previous mission concept: The Coronagraphic Debris and Exoplanet Exploring Payload (CDEEP). The testbed currently operates at visible wavelengths and features a Boston Micromachines Kilo-C DM for wavefront control. Both a vector vortex coronagraph and a knife-edge Lyot coronagraph operating mode are under test. The optics will be mounted to a 1 x 2 meter pneumatically isolated optical bench designed to operate at 10^-8 torr and achieve raw contrasts of 10^-8 or better. The validation of our optical surface quality, alignment procedure, and first light results are presented. We also report on the status of the testbed's integration in the vaccum chamber.Comment: 14 pages, 9 figure

Bright-Moon Sky as a Wide-Field Linear Polarimetric Flat Source for Calibration

Next-generation wide-field optical polarimeters like the Wide-Area Linear Optical Polarimeters (WALOPs) have a field of view (FoV) of tens of arcminutes. For efficient and accurate calibration of these instruments, wide-field polarimetric flat sources will be essential. Currently, no established wide-field polarimetric standard or flat sources exist. This paper tests the feasibility of using the polarized sky patches of the size of around ten-by-ten arcminutes, at a distance of up to 20 degrees from the Moon, on bright-Moon nights as a wide-field linear polarimetric flat source. We observed 19 patches of the sky adjacent to the bright-Moon with the RoboPol instrument in the SDSS-r broadband filter. These were observed on five nights within two days of the full-Moon across two RoboPol observing seasons. We find that for 18 of the 19 patches, the uniformity in the measured normalized Stokes parameters $q$ and $u$ is within 0.2 %, with 12 patches exhibiting uniformity within 0.07 % or better for both $q$ and $u$ simultaneously, making them reliable and stable wide-field linear polarization flats. We demonstrate that the sky on bright-Moon nights is an excellent wide-field linear polarization flat source. Various combinations of the normalized Stokes parameters $q$ and $u$ can be obtained by choosing suitable locations of the sky patch with respect to the MoonComment: 8 pages including appendix, 6 figures and 3 tables. Submitted to Astronomy and Astrophysics for review. Comments are welcom

Starlight-polarization-based tomography of the magnetized ISM: Pasiphae's line-of-sight inversion method

We present the first Bayesian method for tomographic decomposition of the plane-of-sky orientation of the magnetic field with the use of stellar polarimetry and distance. This standalone tomographic inversion method presents an important step forward in reconstructing the magnetized interstellar medium (ISM) in 3D within dusty regions. We develop a model in which the polarization signal from the magnetized and dusty ISM is described by thin layers at various distances. Our modeling makes it possible to infer the mean polarization (amplitude and orientation) induced by individual dusty clouds and to account for the turbulence-induced scatter in a generic way. We present a likelihood function that explicitly accounts for uncertainties in polarization and parallax. We develop a framework for reconstructing the magnetized ISM through the maximization of the log-likelihood using a nested sampling method. We test our Bayesian inversion method on mock data taking into account realistic uncertainties from $Gaia$ and as expected for the optical polarization survey PASIPHAE according to the currently planned observing strategy. We demonstrate that our method is effective in recovering the cloud properties as soon as the polarization induced by a cloud to its background stars is higher than $\sim 0.1\%$, for the adopted survey exposure time and level of systematic uncertainty. Our method makes it possible to recover not only the mean polarization properties but also to characterize the intrinsic scatter, thus opening ways to characterize ISM turbulence and the magnetic field strength. Finally, we apply our method to an existing dataset of starlight polarization with known line-of-sight decomposition, demonstrating agreement with previous results and an improved quantification of uncertainties in cloud properties.Comment: 28 pages, including 2 appendices, submitted to A&

Approaches to lowering the cost of large space telescopes

New development approaches, including launch vehicles and advances in sensors, computing, and software, have lowered the cost of entry into space, and have enabled a revolution in low-cost, high-risk Small Satellite (SmallSat) missions. To bring about a similar transformation in larger space telescopes, it is necessary to reconsider the full paradigm of space observatories. Here we will review the history of space telescope development and cost drivers, and describe an example conceptual design for a low cost 6.5 m optical telescope to enable new science when operated in space at room temperature. It uses a monolithic primary mirror of borosilicate glass, drawing on lessons and tools from decades of experience with ground-based observatories and instruments, as well as flagship space missions. It takes advantage, as do large launch vehicles, of increased computing power and space-worthy commercial electronics in low-cost active predictive control systems to maintain stability. We will describe an approach that incorporates science and trade study results that address driving requirements such as integration and testing costs, reliability, spacecraft jitter, and wavefront stability in this new risk-tolerant "LargeSat" context.Comment: Presented at SPIE, Optics+Photonics 2023, Astronomical Optics: Design, Manufacture, and Test of Space and Ground Systems IV in San Diego, CA, US

Transcriptome Analysis Using RNA Sequencing for Finding Genes Related to Fiber in Cotton: A Review

The cotton crop is economically important and primarily grown for its fiber. Although the genus Gossypium consists of over 50 species, only four domesticated species produce spinnable fiber. However, the genes determine the molecular phenotype of fiber, and variation in their expression primarily contributes to associated phenotypic changes. Transcriptome analyses can elucidate the similarity or variation in gene expression (GE) among organisms at a given time or a circumstance. Even though several algorithms are available for analyzing such high-throughput data generated from RNA Sequencing (RNA-Seq), a reliable pipeline that includes a combination of tools such as an aligner for read mapping, an assembler for quantitating full-length transcripts, a differential gene expression (DGE) package for identifying differences in the transcripts across the samples, a gene ontology tool for assigning function, and enrichment and pathway mapping tools for finding interrelationships between genes based on their associated functions are needed. Therefore, this chapter first introduces the cotton crop, fiber phenotype, transcriptome, then discusses the basic RNA-Seq pipeline and later emphasizes various transcriptome analyses studies focused on genes associated with fiber quality and its attributes

Scalable growth models for time‐series multispectral images

Abstract Vegetation indices (VIs) are produced as a combination of different reflectance bands that are captured by multispectral images (MSIs). These indices, such as normalized difference vegetation index (NDVI), are reported to be proxy indicators of photosynthetic activity, plant canopy biomass, and leaf area index. To determine the utility of using VI derived from MSI to model plant growth, random regression (RR) models with linear splines and different orders of Legendre polynomials were applied to data collected (years 2019 and 2020) as part of the Genome‐to‐Fields initiative. Growth curves of maize (Zea mays L.) hybrids were modeled using both NDVI and cumulative NDVI (cNDVI) phenotypes. Due to the difference in MSI recording dates, and sparse overlap in hybrids between years, all the analyses were nested within a year. Results indicate that RR models using Legendre polynomials provide a robust and scalable method for modeling growth curves using phenotypes extracted from MSI; however, RR models using linear splines showed inconsistent convergence. Growth curves estimated using NDVI and cNDVI showed low‐to‐moderate heritability (0.11–0.44) and a range of genetic correlations (−0.15 to 0.97) with grain yield. This study demonstrates the utility of MSI for modeling genetic growth trends, with the best modeling results obtained when using Legendre polynomials and cNDVI

Stress-induced birefringence in the lenses of Wide-Area Linear Optical Polarimeter-South

Two unique wide-field and high-accuracy polarimeters named WALOP (Wide-Area Linear Optical Polarimeter)- North and WALOP-South are currently under development at the Inter-University Center for Astronomy and Astrophysics (IUCAA), India, to create a large area optical polarization map of the sky for the upcoming PASIPHAE sky survey. These instruments are designed to achieve a linear polarimetric measurement accuracy of 0.1% across a field of view (FoV) of 30×30 arcminutes. The WALOP-South instrument will be installed first on a 1 m telescope at the Sutherland Observatory, where the temperatures during the night can vary between 10 to -5°C. These temperature variations and the instrument's pointing to various non-zenithal positions in the sky can introduce stress birefringence in the lenses, leading to time-varying instrumental polarization. This work estimates stress-induced birefringence due to thermal, and gravity stresses on WALOP-South lenses. Using the optomechanical model of the WALOP-South, we carried out Finite Element Analysis (FEA) simulations in SolidWorks software to estimate the stresses for various scenarios of temperature, telescope pointing airmass, and lens mount material (aluminum and titanium). Further, we use the stress tensor analysis to estimate the principal stresses and their directions and consequent birefringence and retardance introduced in the lenses. The stressinduced birefringence will change the optical path length for orthogonal polarization states of the beam passing through the lenses and introduce phase retardation. Overall, with the lens mount design of the instrument, we find that the retardation and consequent instrumental polarization will be within the instrumental accuracy requirements. Additionally, the stress birefringence is found to be higher for aluminum compared to titanium mounts. We further incorporated this retardance in the instrument Mueller matrix estimation to understand its effects on the polarization measurements. © COPYRIGHT SPIE. Downloading of the abstract is permitted for personal use only.Immediate accessThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]