Biology subjects

Fox, S. E.

Publications and source records attributed to Fox, S. E..

5 recordsLinked to original sources

bioRxiv2023

Comparative Analysis of Salinity Response Transcriptomes in Salt-Tolerant Pokkali and Susceptible IR29 Rice

Rice is a major cereal crop responsible for feeding the worlds population. To improve grain yield and quality, meet growing demand, and face the challenges posed by abiotic and biotic stress, it is imperative to explore genetic diversity in rice for candidate genes and loci that may contribute to stress tolerance. High salinity abiotic stress in the rice growth environment affects growth, yield, and quality. Therefore, we conducted a salt stress-responsive RNA-Seq-based transcriptome study of two rice (Oryza sativa) varieties, the salt-tolerant Pokkali and the salt-sensitive breeding line IR29. To identify early and late salinity response genes, we collected samples from the treated and untreated plants in this study at 1, 2, 5, 10, and 24 hours after treatment with 300 mM NaCl solution. We identified 7,209 and 6,595 salt-induced differentially expressed transcripts from Pokkali and IR29, respectively, over all time points. We identified [~]190,000 single nucleotide polymorphism (SNP) sites and [~]40,000 simple sequence repeat (SSR) sites, allowing analysis of their consequences on genetic diversity, transcript structure, gene function, and differential expression. We identified and validated the polymorphic SSRs in the differentially expressed salt-responsive genes Respiratory Burst Oxidase Homolog B (RBOHB) and Rice Salt Sensitive 1 (RSS1) that underly nearby salt tolerance QTLs. This study provides insight into transcriptional programming during salt stress, evidence for improving Oryza genome annotations, and reveals SNP and SSR sites associated with differential gene expression and potential gene function.

plant biology↗

bioRxiv2022

A Camera-Assisted Pathology Microscope to Capture the Lost Data in Clinical Glass Slide Diagnosis

Digital pathology, or the practice of acquiring, managing, and interpreting high-resolution digital images from glass pathology slides, holds much promise in precision medicine, potentially transforming diagnosis and prognosis based on computational image biomarkers derived from digital tissue images. However, for all its promise, digital imaging in pathology has not yet become an integral part of the clinical workflow as it has in radiology due to high cost, workflow disruptions, burdensome data sizes and IT requirements, and additional dedicated personnel requirements. Consequently, pathology retains the 150-year-old analog workflow, and the vast majority of slides used in clinical diagnosis are never digitized. Furthermore, there is a missed opportunity to capture the image information and associated data on search processes that led to the clinical diagnosis, which could serve as the foundation for computational clinical decision support. This paper describes an approach for slide digitization during clinical review using a camera attached to a standard brightfield pathology microscope. While a pathologist reviews a glass slide using the eyepiece oculars, the continuously running camera digitizes a complete record of the slide review, resulting in multi-resolution slide images and spatiotemporal saliency maps of the slide review. Unlike other approaches, the pathologist does not stop to review the video stream or monitor the acquisition of video frames but performs the diagnostic review at the microscope using the standard clinical protocol. This hybrid analog-digital approach combines the benefits of digital slide analysis, including annotation, computation, and the ability to confirm the completeness and quality of the glass slide review with the ease of using the microscope for primary diagnosis. Furthermore, a record of the pathologists attention during the review, including their search path, magnification level, and dwell times at each location on the slide, is obtained. In the future, this approach could enable the development and application of new and emerging computational decision-support algorithms in real-time to provide feedback to the pathologist, reduce diagnostic errors, and improve disease diagnosis and prognosis.

bioengineering↗

bioRxiv2020

Multiscale three-dimensional pathology findings of COVID-19 diseased lung using high-resolution cleared tissue microscopy

The study of pulmonary samples from individuals who have died as a direct result of COVID-19 infection is vital to our understanding of the pathogenesis of this disease. Histopathologic studies of lung tissue from autopsy of patients with COVID-19 specific mortality are only just emerging. All existing reports have relied on traditional 2-dimensional slide-based histological methods for specimen preparation. However, emerging methods for high-resolution, massively multiscale imaging of tissue microstructure using fluorescence labeling and tissue clearing methods enable the acquisition of tissue histology in 3-dimensions, that could open new insights into the nature of SARS-Cov-2 infection and COVID-19 disease processes. In this article, we present the first 3-dimensional images of lung autopsy tissues taken from a COVID-19 patient, including 3D "virtual histology" of cubic-millimeter volumes of the diseased lung, providing unique insights into disease processes contributing to mortality that could inform frontline treatment decisions.

pathology↗

bioRxiv2018

Place cell firing cannot support navigation without intact septal circuits

Though it has been known for over half a century that interference with the normal activity of septohippocampal neurons can abolish hippocampal theta rhythmicity, a definitive answer to the question of its function has remained elusive. To clarify the role of septal circuits and theta in location specific activity of place cells and spatial behavior, three drugs were delivered to the medial septum of rats: tetracaine, a local anesthetic; muscimol, a GABA-A agonist; and gabazine, a GABA-A antagonist. All three drugs disrupted normal oscillatory activity in the hippocampus. However, tetracaine and muscimol both reduced spatial firing and interfered with the rats ability to navigate to a hidden goal. After gabazine, location specific firing was preserved in the absence of theta, but rats were unable to accurately locate the hidden goal. These results indicate that theta is unnecessary for location specific firing of hippocampal cells, and that place cell activity cannot support accurate navigation when septal circuits are disrupted.

neuroscience↗

bioRxiv2018

Measurement of the Topological Dimension of Hippocampal Place Cell Activity

The fundamental property of topological dimension of neural activity has never been measured before. We measured the topological dimension of the activity of 89 rat hippocampal place cells recorded during foraging using the neighborhood boundary countdown method. Points were rate vectors forming a manifold in an 89 dimensional rate space Since a boundary has one less dimension than the neighborhood it encloses, reducing the dimension in sequential radial cuts finally arrives at boundary that is two points. The number of cuts required is the topological dimension of the set. Due to sparsity, we used a shell-like boundary with thickness. As expected, we found the large inductive dimension of this set of points to be two. To examine the robustness of the method, we used both real and modeled place cells and varied the number of neurons, duration of the time step and smoothing, radius and thickness for the boundary, decrement of the radius with each cut, requirements for the center point, and number of points in the final cluster. With the exception of shell thickness, the result was insensitive to these variations. Knowing the topological dimension allows application of rigorous topological principles to the activity of neuron populations. The method potentially can be applied to other neural classes and other behaviors, to enumerate firing variables when they are unknown, even count the factors influencing neural activity in sleep.

neuroscience↗