Characterization of SPX exclusive family members in plant Pi sensing and regulation

The macronutrient phosphorus is vital to plant growth but the readily absorbed form of inorganic phosphate (Pi) is often environmentally limited. To increase Pi acquisition and use efficiency, plants have developed strategies involving a group of proteins, characterized by a highly conserved N-terminal SPX domain, which play critical roles. In this project, 14 SPX domain-containing proteins were identified in potato (Solanum tuberosum) and classified into four plant SPX domain-containing protein families. Gene expression analysis of SPX-exclusive family members using quantitative real-time PCR showed StSPX2, StSPX3 and StSPX5 are transcriptionally up-regulated during Pi starvation responses, suggesting the pervasive involvement of SPX proteins in Pi regulation among different plant species. The P1BS cis-element was also found in the promoter region of potato SPX genes, suggesting these genes are likely to be regulated by a potato homologue of AtPHR1, a Myb-CC family transcription factor which binds this sequence in other plant species. Recent studies in Arabidopsis demonstrated the SPX exclusive family protein AtSPX1 can compete with DNA to physically interact with the transcription factor AtPHR1 in a Pi-dependent way. However, the interaction mechanism is poorly understood. To investigate this, Glutathione-S-transferase-SPX1 and Maltose-binding-protein-PHR1 fusion proteins were expressed and purified from E. coli. AtPHR1 was shown to be a monomeric protein in solution that dimerizes upon associating with P1BS. SPR data also showed that AtSPX1 cannot displace AtPHR1 associated with DNA, but only interact with monomeric AtPHR1 in the presence of either 5 mM Pi or 500 µM InsP6. Therefore I propose a new model that in the Pi restored condition, AtSPX1 can bind to monomeric AtPHR1 and therefore regulate PSI gene expression by tuning the AtPHR1-DNA binding equilibrium. This regulation also generates a negative feedback loop on the expression of AtSPX1 itself, providing a tight control of PSI gene expression under Pi sufficient conditions

Experimental Study on Seismic Performance of Prefabricated Utility Tunnel

Utility tunnel is a kind of underground tunnel structure that carries more than two types of public utility lines, and the utility tunnels built by the prefabricated method have been adopted in many modern cities due to their easy maintenance and environmental protection capabilities. However, knowledge about the seismic performance of the prefabricated utility tunnel and pipelines inside is quite limited. In this paper, a prefabricated utility tunnel newly built in Xi’an, China, is taken as the prototype; a series of shaking table tests are conducted to investigate the seismic performance of the prefabricated utility tunnel in loess foundation, using El Centro earthquake wave as the input loading. Details of the experimental setup focus on the design of the soil container, scaled model (1 : 10), sensor arrangement, and test cases. Dynamic responses including evaluation of boundary effect, the amplification factor of the ground and structure, distribution of soil pressure, characteristics of predominant frequencies, and the damage phenomena are analyzed. Dynamic strain obtained by Fiber Bragg Grating sensors releases the critical positions of the prefabricated utility tunnel during the earthquake. Moreover, the dynamic responses of the pipelines contained in the utility tunnel are also analyzed. From aforementioned results, the seismic performance of the prefabricated utility tunnel has been revealed. The results will provide a reference for the seismic design of prefabricated utility tunnels. Document type: Articl

Bubble-Wall Plot: A New Tool for Data Visualization

This research aimed to design a new tool for data visualization with performed features - named Bubble-Wall Plot and assumed that it could be an effective tool for developing data visualization systems. This research reviewed seven data visualization approaches for identifying the outliers, including Line Charts, Parallel Coordinates Plot, Scatter Plots, TreeMap, Glyphs, Pixel-based techniques, and Redial visualizations. The challenges for current data visualization approaches were also summarized. Two principles were addressed to design the new tool- keep it simple strategy with the smallest strategy. As a result, the newly designed Bubble-Wall Plot has successfully been adopted to develop a warning system for identifying the outliers in a Case Study company, which was deployed for user acceptance testing in May 2021. The main contribution is that this newly designed tool with the simplest style was well-designed and proven to effectively develop a warning visualization system

Phosphoric Metabolites Link Phosphate Import and Polysaccharide Biosynthesis for Candida albicans Cell Wall Maintenance

ACKNOWLEDGMENTS We declare no conflicts of interest. We thank Jesús Pla for his kind gift of the anti-Mkc1 antibody and Kristin Moffitt and Richard Malley for generous advice in ELISA technology and use of the ELISA reader. We thank Tahmeena Chowdhury for scientific discussions leading up to this work. We thank the Candida Genome Database. N.-N.L., M.A.-Z., W.Q., and J.R.K. were supported by R21 AI137716 and by Boston Children’s Hospital Department of Pediatrics. M.A.-Z. was partially funded by the Alfonso Martin Escudero Foundation. J.D.-A. and O.L. were funded by the Boston Children’s Hospital Department of Pediatrics and U19 AI118608-01A1. N.A.R.G. was supported by the Wellcome Trust and the Medical Research Council Centre for Medical Mycology (MR/N006364/1).Peer reviewedPublisher PD

Dense sampling of bird diversity increases power of comparative genomics

© 2020, The Author(s). Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species

Intersection of phosphate transport, oxidative stress and TOR signalling in Candida albicans virulence

Phosphate is an essential macronutrient required for cell growth and division. Pho84 is the major high-affinity cell-surface phosphate importer of Saccharomyces cerevisiae and a crucial element in the phosphate homeostatic system of this model yeast. We found that loss of Candida albicans Pho84 attenuated virulence in Drosophila and murine oropharyngeal and disseminated models of invasive infection, and conferred hypersensitivity to neutrophil killing. Susceptibility of cells lacking Pho84 to neutrophil attack depended on reactive oxygen species (ROS): pho84-/- cells were no more susceptible than wild type C. albicans to neutrophils from a patient with chronic granulomatous disease, or to those whose oxidative burst was pharmacologically inhibited or neutralized. pho84-/- mutants hyperactivated oxidative stress signalling. They accumulated intracellular ROS in the absence of extrinsic oxidative stress, in high as well as low ambient phosphate conditions. ROS accumulation correlated with diminished levels of the unique superoxide dismutase Sod3 in pho84-/- cells, while SOD3 overexpression from a conditional promoter substantially restored these cells’ oxidative stress resistance in vitro. Repression of SOD3 expression sharply increased their oxidative stress hypersensitivity. Neither of these oxidative stress management effects of manipulating SOD3 transcription was observed in PHO84 wild type cells. Sod3 levels were not the only factor driving oxidative stress effects on pho84-/- cells, though, because overexpressing SOD3 did not ameliorate these cells’ hypersensitivity to neutrophil killing ex vivo, indicating Pho84 has further roles in oxidative stress resistance and virulence. Measurement of cellular metal concentrations demonstrated that diminished Sod3 expression was not due to decreased import of its metal cofactor manganese, as predicted from the function of S. cerevisiae Pho84 as a low-affinity manganese transporter. Instead of a role of Pho84 in metal transport, we found its role in TORC1 activation to impact oxidative stress management: overexpression of the TORC1-activating GTPase Gtr1 relieved the Sod3 deficit and ROS excess in pho84-/- null mutant cells, though it did not suppress their hypersensitivity to neutrophil killing or hyphal growth defect. Pharmacologic inhibition of Pho84 by small molecules including the FDA-approved drug foscarnet also induced ROS accumulation. Inhibiting Pho84 could hence support host defenses by sensitizing C. albicans to oxidative stress

A Bus Passenger Flow Prediction Model Fused with Point-of-Interest Data Based on Extreme Gradient Boosting

Bus operation scheduling is closely related to passenger flow. Accurate bus passenger flow prediction can help improve urban bus planning and service quality and reduce the cost of bus operation. Using machine learning algorithms to find the rules of urban bus passenger flow has become one of the research hotspots in the field of public transportation, especially with the rise of big data technology. Bus IC card data are an important data resource and are more valuable to passenger flow prediction in comparison with manual survey data. Aiming at the balance between efficiency and accuracy of passenger flow prediction for multiple lines, we propose a novel passenger flow prediction model based on the point-of-interest (POI) data and extreme gradient boosting (XGBoost), called PFP-XPOI. Firstly, we collected POI data around bus stops based on the Amap Web service application interface. Secondly, three dimensions were considered for building the model. Finally, the XGBoost algorithm was chosen to train the model for each bus line. Results show that the model has higher prediction accuracy through comparison with other models, and thus this method can be used for short-term passenger flow forecasting using bus IC cards. It plays a very important role in providing decision basis for more refined bus operation management

Pi sensing and signaling: from prokaryotic to eukaryotic cells

Phosphorus is one of the most important macronutrients and is indispensable for all organisms as a critical structural component as well as participating in intracellular signalling and energy metabolism. Sensing and signalling of phosphate (Pi) has been extensively studied and is well understood in single-cellular organisms like bacteria (Escherichia coli) and Saccharomyces cerevisiae. In comparison, the mechanism of Pi regulation in plants is less well understood despite recent advances in this area. In most soils the available Pi limits crop yield, therefore a clearer understanding of the molecular basis underlying Pi sensing and signalling is of great importance for the development of plants with improved Pi use efficiency. This mini-review compares some of the main Pi regulation pathways in prokaryotic and eukaryotic cells and identifies similarities and differences among different organisms, as well as providing some insight into future research

Wide-Dynamic-Range Zero-Bias Microwave Detector Using AlGaN/GaN Heterojunction Field-Effect Diode

An AlGaN/GaN HEMT-compatible lateral field-effect diode has been used for zero-bias microwave detector application. Using the versatile fluorine plasma ion treatment technique, we have been able to realize a diode that exhibits strong nonlinearity near zero bias, thus, eliminating DC supplies in microwave detector circuits. The AlGaN/GaN microwave detectors deliver high sensitivity, wide dynamic range and high temperature operating capability. The maximum zero-bias curvature coefficient (gamma) measured are 11.6 V-1 and 3.2 V-1 at 50 degrees C and 250 degrees C, respectively, yielding a directly-measured sensitivity (beta(v)) of 1027 mV/mW at 50 degrees C and 466 mV/mW at 250 degrees C. The peak conjugately-matched sensitivity (beta(v,opt)) is projected to be 9030 mV/mW at 2 GHz at 50 degrees C. At room temperature, the wide dynamic range of 53 and 54 dB at 2 and 5 GHz are observed, respectively, both of which are the highest values reported so far