Maize Transposable Elements Ac/Ds as Insertion Mutagenesis Tools in Candidaalbicans

In non-model systems genetic research is often limited by the lack of techniques for the generation and identification of gene mutations. One approach to overcome this bottleneck is the application of transposons for gene tagging. We have established a two-element transposon tagging system, based on the transposable elements Activator (Ac)/Dissociation (Ds) from maize, for in vivo insertion mutagenesis in the fungal human pathogen Candida albicans. A non-autonomous Ds transposon carrying a selectable marker was constructed into the ADE2 promoter on chromosome 3 and a codon usage-adapted Ac transposase gene was inserted into the neutral NEUT5L locus on chromosome 5. In C. albicans cells expressing the transposase the Ds element efficiently excised and reintegrated elsewhere in the genome, which makes the Ac/Ds transposons promising tools for saturating insertion mutagenesis in clinical strains of C. albicans

New “haploid biofilm model” unravels IRA2 as a novel regulator of Candida albicans biofilm formation

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Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma

Diffuse intrinsic pontine glioma (DIPG) is an aggressive incurable brainstem tumor that targets young children. Complete resection is not possible, and chemotherapy and radiotherapy are currently only palliative. This study aimed to identify potential therapeutic agents using a computational pipeline to perform an in silico screen for novel drugs. We then tested the identified drugs against a panel of patient-derived DIPG cell lines. Using a systematic computational approach with publicly available databases of gene signature in DIPG patients and cancer cell lines treated with a library of clinically available drugs, we identified drug hits with the ability to reverse a DIPG gene signature to one that matches normal tissue background. The biological and molecular effects of drug treatment was analyzed by cell viability assay and RNA sequence. In vivo DIPG mouse model survival studies were also conducted. As a result, two of three identified drugs showed potency against the DIPG cell lines Triptolide and mycophenolate mofetil (MMF) demonstrated significant inhibition of cell viability in DIPG cell lines. Guanosine rescued reduced cell viability induced by MMF. In vivo, MMF treatment significantly inhibited tumor growth in subcutaneous xenograft mice models. In conclusion, we identified clinically available drugs with the ability to reverse DIPG gene signatures and anti-DIPG activity in vitro and in vivo. This novel approach can repurpose drugs and significantly decrease the cost and time normally required in drug discovery

Regulation of Yeast Actin Cytoskeleton-Regulatory Complex Pan1p/Sla1p/End3p by Serine/Threonine Kinase Prk1p

The serine/threonine kinase Prk1p is known to be involved in the regulation of the actin cytoskeleton organization in budding yeast. One possible function of Prk1p is the negative regulation of Pan1p, an actin patch regulatory protein that forms a complex in vivo with at least two other proteins, Sla1p and End3p. In this report, we identified Sla1p as another substrate for Prk1p. The phosphorylation of Sla1p by Prk1p was established in vitro with the use of immunoprecipitated Prk1p and in vivo with the use of PRK1 overexpression, and was further supported by the finding that immunoprecipitated Sla1p contained PRK1- and ARK1-dependent kinase activities. Stable complex formation between Prk1p and Sla1p/Pan1p in vivo could be observed once the phosphorylation reaction was blocked by mutation in the catalytic site of Prk1p. Elevation of Prk1p activities in wild-type cells resulted in a number of deficiencies, including those in colocalization of Pan1p and Sla1p, endocytosis, and cell wall morphogenesis, likely attributable to a disintegration of the Pan1p/Sla1p/End3p complex. These results lend a strong support to the model that the phosphorylation of the Pan1p/Sla1p/End3p complex by Prk1p is one of the important mechanisms by which the organization and functions of the actin cytoskeleton are regulated

Siam-Sort: Multi-Target Tracking in Video SAR Based on Tracking by Detection and Siamese Network

Shadows are widely used in the tracking of moving targets by video synthetic aperture radar (video SAR). However, they always appear in groups in video SAR images. In such cases, track effects produced by existing single-target tracking methods are no longer satisfactory. To this end, an effective way to obtain the capability of multiple target tracking (MTT) is in urgent demand. Note that tracking by detection (TBD) for MTT in optical images has achieved great success. However, TBD cannot be utilized in video SAR MTT directly. The reasons for this is that shadows of moving target are quite different from in video SAR image than optical images as they are time-varying and their pixel sizes are small. The aforementioned characteristics make shadows in video SAR images hard to detect in the process of TBD and lead to numerous matching errors in the data association process, which greatly affects the final tracking performance. Aiming at the above two problems, in this paper, we propose a multiple target tracking method based on TBD and the Siamese network. Specifically, to improve the detection accuracy, the multi-scale Faster-RCNN is first proposed to detect the shadows of moving targets. Meanwhile, dimension clusters are used to accelerate the convergence speed of the model in the training process as well as to obtain better network weights. Then, SiamNet is proposed for data association to reduce matching errors. Finally, we apply a Kalman filter to update the tracking results. The experimental results on two real video SAR datasets demonstrate that the proposed method outperforms other state-of-art methods, and the ablation experiment verifies the effectiveness of multi-scale Faster-RCNN and SimaNet

Off-Grid RFI Suppression Method in Synthetic Aperture Radar Based on Mismatch Reconstruction and Dictionary Rotation

In the process of radio frequency interference (RFI) suppression for synthetic aperture radar (SAR), when frequencies of RFIs are not located on discrete grids of the frequency spectrum, i.e., RFIs are off-grid, energies of RFIs will spread out, degrading suppression performances of lots of existing methods. To this end, aiming at the off-grid RFI suppression problem, in this article, a mismatch reconstruction and dictionary rotation-based RFI suppression method is proposed. First, using the defined support set, an optimization model is constructed to reconstruct mismatches of off-grid RFIs. Then, these mismatch variables are utilized to rotate the original Fourier transform-based dictionary so that frequencies of RFIs can be well matched. The energies of RFIs can be refocused under the representation of rotated dictionaries. At this time, we construct and solve another optimization problem to subtract RFIs and obtain the cleaned SAR signals. The real-world SAR data and simulated RFI data-based experiments demonstrate the effectiveness of the proposed method

Identification of Novel Recognition Motifs and Regulatory Targets for the Yeast Actin-regulating Kinase Prk1p

Prk1p is a serine/threonine kinase involved in the regulation of the actin cytoskeleton organization in the yeast Saccharomyces cerevisiae. Previously, we have identified LxxQxTG as the phosphorylation site of Prk1p. In this report, the recognition sequence for Prk1p is investigated more thoroughly. It is found that the presence of a hydrophobic residue at the position of P-5 is necessary for Prk1p phosphorylation and L, I, V, and M are all able to confer the phosphorylation at various efficiencies. The residue flexibility at P-2 has also been identified to include Q, N, T, and S. A homology-based three-dimensional model of the kinase domain of Prk1p provided some structural interpretations for these substrate specificities. The characterization of the [L/I/V/M]xx[Q/N/T/S]xTG motif led to the identification of a spectrum of potential targets for Prk1p from yeast genome. One of them, Scd5p, which contains three LxxTxTG motifs and is previously known to be important for endocytosis and actin organization, has been chosen to demonstrate its relationship with Prk1p. Phosphorylation of Scd5p by Prk1p at the three LxxTxTG motifs could be detected in vitro and in vivo, and deletion of PRK1 suppressed the defects in actin cytoskeleton and endocytosis in one of the scd5 mutants. These results allowed us to conclude that Scd5p is likely another regulatory target of Prk1p

Direction-of-Arrival Estimation for Circulating Space-Time Coding Arrays: From Beamspace MUSIC to Spatial Smoothing in the Transform Domain

As a special type of coherent collocated Multiple-Input Multiple-Output (MIMO) radar, a circulating space-time coding array (CSTCA) transmits an identical waveform with a tiny time shift. It provides a simple way to achieve a full angular coverage with a stable gain and a low sidelobe level (SLL) in the range domain. In this paper, we address the problem of direction-of-arrival (DOA) estimation in CSTCA. Firstly, we design a novel two-dimensional space-time matched filter on receiver. It jointly performs equivalent transmit beamforming in the angle domain and waveform matching in the fast time domain. Multi-beams can be formed to acquire controllable transmit freedoms. Then, we propose a beamspace multiple signal classification (MUSIC) algorithm applicable in case of small training samples. Next, since targets at the same range cell show characteristics of coherence, we devise a transformation matrix to restore the rotational invariance property (RIP) of the receive array. Afterwards, we perform spatial smoothing in element domain based on the transformation. In addition, the closed-form expression of Cramer-Rao lower bound (CRLB) for angle estimation is derived. Theoretical performance analysis and numerical simulations are presented to demonstrate the effectiveness of proposed approaches

Multi-Resolution STAP for Enhanced Ultra-Low-Altitude Target Detection

In this paper, an ultra-low-altitude target (ULAT) detection approach, referred to as the multi-resolution space-time adaptive processing (STAP), is proposed to enhance the target detection performance in a missile-borne radar system. In this respect, the whole base band is divided into a series of equal-width and center-frequency-diverse sub-bands with the frequency diversity technique, which enhances the multipath-target coupled (MTC) effect with the decreased range resolution. Hence, it is feasible to exploit the multipath signal power to improve the output signal-to-clutter-plus-noise ratio (SCNR) performance of sub-band STAP. In this regard, the mechanism of the MTC effect is analyzed numerically for the efficient sub-band STAP. However, such SCNR improvement is achieved at the cost of target tracking performance loss. Hence, the full-band STAP is further applied for multipath-target separation based on the target range-Doppler locations detected by the joint multiple sub-bands ΣΔ-STAP, which also alleviates the dynamic target attenuation and the corresponding target Doppler history corruption within the long coherent processing interval (CPI). On this basis, the SCNR performance is further improved by applying coherent accumulation among sub-CPIs, in which the clutter suppression performance degradation and coherent accumulation loss of STAP are alleviated within the sub-CPIs. Numerical and measured results corroborate the effectiveness of ULAT detection with the considered multi-resolution STAP

Waveform Design and Signal Processing Method of a Multifunctional Integrated System Based on a Frequency Diverse Array

A Frequency Diverse Array (FDA), developed innovatively based on phased array radar, can obtain an angle-range-time-dependent multidimensional transmit beampattern by modulating frequencies across different transmit antenna elements, which considerably increases the beam control ability and signal processing dimension. After joint transmit-receive processing, an FDA can be applied to various areas, such as multidimensional parameter joint estimation, mainlobe deceptive jammer suppression, ambiguous clutter suppression, and high-resolution and wide-swath imaging. This study investigates the waveform design and signal processing method of a multifunctional integrated system based on an FDA from the system level, with emphasis on new signal processing methods for integrated detection and estimation, integrated ambiguity resolution and jammer suppression, as well as integrated Synthetic Aperture Radar (SAR) imaging and moving target detection. Moreover, the application prospects of FDA multifunctional integrated systems are provided