Investigation on Geometry Computation of Spaceborne GNSS-R Altimetry over Topography: Modeling and Validation

The spaceborne Global Navigation Satellite Systems Reflectometry (GNSS-R) offers versatile Earth surface observation. While the accuracy of the computed geometry, required for the implementation of the technique, degrades when Earth’s surface topography is complicated, previous studies ignored the effects of the local terrain surrounding the ideal specular point at a suppositional Earth reference surface. The surface slope and its aspect have been confirmed that it can lead to geolocation-related errors in the traditional radar altimetry, which will be even more intensified in tilt observations. In this study, the effect of large-scale slope on the spaceborne GNSS-R technique is investigated. We propose a new geometry computation strategy based on the property of ellipsoid to carry out forward and inverse calculations of path geometries. Moreover, it can be extended to calculate unusual reflected paths over versatile Earth’s topography by taking the surface slope and aspects into account. A simulation considering the slope effects demonstrates potential errors as large as meters to tens kilometers in geolocation and height estimations in the grazing observation condition over slopes. For validation, a single track over the Greenland surface received by the TechDemoSat 1 (TDS-1) satellite with a slope range from 0% to 1% was processed and analyzed. The results show that using the TanDEM-X 90 m Digital Elevation Model (DEM) as a reference, a slope of 0.6% at an elevation angle of 54 degrees can result in a geolocation inaccuracy of 10 km and a height error of 50 m. The proposed method in this study greatly reduces the standard deviation of geolocations of specular points from 4758 m to 367 m, and height retrievals from 28 m to 5.8 m. Applications associated with topography slopes, e.g., cryosphere could benefit from this method

The regulatory mechanisms and physiological functions of an outer membrane protein opmpW during anaerobic adaptation in Escherichia coli

ompW encodes a widespread outer-membrane porin protein in Gram-negative bacteria. It has been implicated in bacterial responses to various antibiotics and environmental substances such as antibiotics, drugs and mouse mucus etc. Little is known, however, about its regulation and physiological roles during bacterial stress responses. Recently, comparative genomics studies revealed that the ompW gene is a core regulon of the global transcription factor FNR (Fumarate Nitrate Reduction) which mediates the transition from aerobic to anaerobic lifestyle of facultative bacteria. Anaerobiosis represents a predominant challenge encountered by many bacteria in their natural ecological niches and human hosts. This thesis thus aims to elucidate the molecular mechanism of FNR-dependent regulation of ompW expression and its relevance to the anaerobic adaption of the model facultative bacterium E. coli. Regulation of ompW expression by several other key physiological signals related to the anaerobiosis of E. coli, as well as the physiological significance, is also explored systematically. In the first half of the thesis, FNR-dependent regulation of ompW is confirmed by in vivo transcriptional activity assay, and then further confirmed at mRNA and protein level by RT-qPCR and western blotting. EMSA combined with transcriptional activity assay reveals that FNR directly binds with two sites centered at -81.5 and -126.5 bp respectively on ompW promoter (PompW). While binding to the -81.5 site by FNR activates the transcription of ompW, interaction with the -126.5 site represses it, and repression through the -126.5 site is dependent on primary occupancy of the -81.5 site by FNR. Based on these molecular mechanisms, a novel regulatory model of ompW expression during anaerobic adaptation of E. coli is proposed. Growth competition assay further confirmed the physiological significance of this fine-tuned regulation of ompW by FNR in facilitating the fitness and adaptation of E. coli during the transition from aerobic to micro-aerobic and anaerobic lifestyles. In the second half of the thesis, it is demonstrated that two other physiological signals related to the anaerobiosis of E. coli participate in the regulation of ompW, i.e. carbon and electron sources. The molecular mechanisms of how the relevant transcription factors, namely CRP and NarXL, mediate ompW transcription were elucidated: CRP activates the transcription of ompW by binding with the -42.5 site on PompW when glucose is absent; NarL represses the expression of ompW via its binding with the -18.5 site on PompW in the presence of nitrate (the most preferred electron source of E. coli during anaerobic growth). Fumarate is estimated to enter the central channel of OmpW and rescues OmpW-mediated colicin S4 killing of E. coli, suggesting OmpW is a receptor for fumarate and revealing its role in facilitating C4-dicarboxylates utilization. In summary, my study reveals a previously unrecognized, highly co-ordinated and dynamic regulation network for the expression of the widely distributed Gram-negative bacterial minor porin protein OmpW. Given the high conservancy of both the ompW gene and its promoter regions in several pathogenic bacterial species, my study contributes to the understanding of the pathogenicity of these species in the host relevant environment of anaerobiosis.published_or_final_versionBiological SciencesDoctoralDoctor of Philosoph

Data-driven quantitative modeling of bacterial active nematics

International audienceSignificance Active nematics are nonequilibrium fluids consisting of elongated units driven at the individual scale. They spontaneously exhibit complex spatiotemporal dynamics and have attracted the attention of scientists from many disciplines. Here, we introduce an experimental system (made of filamentous bacteria) and a type of microscopic model for active nematics. Simultaneous measurements of orientation and velocity fields yield comprehensive experimental data that can be used to identify optimal values for all important parameters in the model. At these optimal parameters, the model quantitatively reproduces all experimentally measured features. This, in turn, reveals key processes governing active nematics. Our versatile approach successfully combines quantitative experiments and data-driven modeling; it can be used to study other dense active systems

Vertical and horizontal gene transfer tradeoffs direct plasmid fitness

Abstract Plasmid fitness is directed by two orthogonal processes—vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here, we present evidence for the presence, consequences, and molecular basis of a conjugation‐growth tradeoff across 40 plasmids derived from clinical Escherichia coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance

Evaluation of young consumer preference in three commercial Japonica rice varieties via hedonic and Just-About-Right tests

This research investigated the consumer preferences in three Japonica rice varieties with rounded,oval,and long shapes via hedonic and Just-About-Right tests.The results showed that young consumers preferred the raw rice variety with oval shape,full,translucent,shiny,and in moderate size,and cooked rice with characteristics in white color,glossy,slightly sticky,soft,slightly chewy,rich aroma,sweet and aftertaste in sweetness.The penalty analysis indicated the potential improving tendency in future breeding based on sensory attributes for each variety.The result might offer some information and directions on rice breeding and quality evaluation to meet consumers' expectations in the future

Investigation on Geometry Computation of Spaceborne GNSS-R Altimetry over Topography: Modeling and Validation

The space borne Global Navigation Satellite Systems Reflectometry (GNSS-R) offers versatile Earth surface observation. While the accuracy of the computed geometry, required for the implementation of the technique, degrades when Earth’s surface topography is complicated, previous studies ignored the effects of the local terrain surrounding the ideal specular point at a suppositional Earth reference surface. The surface slope and its aspect have been confirmed that it can lead to geolocation-related errors in the traditional radar altimetry, which will be even more intensified in tilt observations. In this study, the effect of large-scale slope on the spaceborne GNSS-R technique is investigated. We propose a new geometry computation strategy based on the property of ellipsoid to carry out forward and inverse calculations of path geometries. Moreover, it can be extended to calculate unusual reflected paths over versatile Earth’s topography by taking the surface slope and aspects into account. A simulation considering the slope effects demonstrates potential errors as large as meters to tens kilometers in geolocation and height estimations in the grazing observation condition over slopes. For validation, a single track over the Greenland surface received by the TechDemoSat 1 (TDS-1) satellite with a slope range from 0% to 1% was processed and analyzed. The results show that using the TanDEM-X 90 m Digital Elevation Model (DEM) as a reference, a slope of 0.6% at an elevation angle of 54 degrees can result in a geolocation inaccuracy of 10 km and a height error of 50 m. The proposed method in this study greatly reduces the standard deviation of geolocations of specular points from 4758 m to 367 m, and height retrievals from 28 m to 5.8 m. Applications associated with topography slopes, e.g., cryosphere could benefit from this method.This research was funded by the Natural Science Foundation of China (Grant No. 41830110 and No. 42174018), the Fundamental Research Funds for the Central Universities (Grant No. B200203110), Postgraduate Research & Practice Innovation Program of Jiangsu Province (KYCX20_0489), and the State Scholarship Fund from Chinese Scholarship Council (No. 202006710115)