Cyclops response elements in the evolution and function of root endosymbioses in Lotus japonicus

Plant growth is dependent on sufficient supply of nitrogen, an essential component for important macromolecules such as proteins and nucleic acids. A small group of plants belonging to four orders - Fabales, Fagales, Cucurbitales and Rosales (the FaFaCuRo clade) - have evolved the ability to engage in a mutually beneficial interaction, namely the nitrogen-fixing root nodule symbiosis (RNS). Fixed nitrogen is supplied by the bacterial symbiont to the plant host, hence helping the host to overcome nitrogen limitation. RNS development is a complex procedure that involves massive transcriptional reprogramming carried out by a cohort of cis- and trans-acting regulators. The evolutionary steps leading to the emergence of RNS have been at the center of interest for decades. Understanding the main genetic differences between plants that can form RNS and those that cannot is assumed to provide the key for installing RNS in important crop plants that are currently unable to engage in RNS. Evolution of cis- and trans-acting elements has played key roles in the evolution of novel biological traits. This work focussed on two cis-regulatory elements that have played distinct roles in the evolution and maintenance of RNS. One cis-element, PACE (Predisposition Associated Cis- regulatory Element) was identified via a phylogenomic approach. PACE was discovered to be exclusively present in species within the FaFaCuRo clade in the promoter of the Nodule Inception (NIN) gene that encodes a master transcription factor (TF) positioned at the top of the transcriptional regulatory hierarchy specific for RNS. PACE confers responsiveness to bacterial signals and dictates gene expression in cortical cells forming infection threads (ITs), a tube-like plant-derived structure through which bacteria enter the root. PACE is essential for restoring IT formation in the Lotus japonicus nin-15 mutant even when engineered into the NIN promoter of tomato, a species outside of the FaFaCuRo clade. PACE contains the binding site of a TF Cyclops that is indispensable for transcriptional rewiring during RNS as well as for the evolutionarily older arbuscular mycorrhizal symbiosis. P ACE confers transactivation mediated by Cyclops in combination with the Calcium and Calmodulin-dependent protein kinase (CCaMK). These results suggested that PACE allows the induction of NIN via the symbiosis-induced signalling cascade common for RNS and AM. The phylogenetic restriction of PACE is congruent with that of RNS and consistent with an emergence in the last common ancestor of the FaFaCuRo clade. A related, yet functionally distinct cis-element was identified in the promoter of the Calcium Binding Protein 1 (CBP1) gene utilising the transgenic line T90 that originated from a promoter tagging program of L. japonicus. T90 carries a promoterless GUS gene that is specifically induced during RNS and AM. Dissection of the regulatory region of the T90 GUS gene led to the identification of one cis-regulatory element required for reporter expression in the epidermis and a second element, CYC-RECBP1 (Cyclops response element in the CBP1 promoter), necessary and sufficient for transactivation mediated by CCaMK/Cyclops and driving gene expression during both AM and RNS. The lack of GUS expression in three T90 white mutants that were identified from an ethyl methanesulfonate-mutagenised T90 population could be traced to DNA hypermethylation detected in and around CYC-RECBP1. Two additional regulatory regions also impact CBP1 expression. This work showcases Cyclops response elements as an essential building block for engineering RNS in crops, with a long-term goal of reducing agricultural fertiliser application

Collaborative Game Mosaics

Imagine two players are playing a strategy board game. With one player holding black stones and the other player holding white stones, they take turns to place their pieces. After a while, they start to recognize some patterns. With three colors in front of them, black, white, and the color of the game board, they are curious about if they can form a recognizable image. Instead of playing the game to win, they start to collaborate with each other to form a mosaic. Later, they invite more players and provide them their own stones in different shades of gray. The goal of this project is to use mathematical optimization techniques to design mosaics that simultaneously resemble well-known images and look like the current state of a board game like Gomoku or something that could be played on a Go board or chessboard. The work described here builds upon techniques devised by Professor Robert Bosch and some of his students. The paper will be structured as follows: First, we will discuss the data, variables, objective function, and universal constraints. Then we will explore constraints for two specific games, Gomoku and chess. Next, we will present several examples, sharing both images and statistics, and we will talk about methods we have devised for improving the results. We will conclude with a discussion of future directions for our research

Iterative Methods at Lower Precision

Since numbers in the computer are represented with a fixed number of bits, loss of accuracy during calculation is unavoidable. At high precision where more bits (e.g. 64) are allocated to each number, round-off errors are typically small. On the other hand, calculating at lower precision, such as half (16 bits), has the advantage of being much faster. This research focuses on experimenting with arithmetic at different precision levels for large-scale inverse problems, which are represented by linear systems with ill-conditioned matrices. We modified the Conjugate Gradient Method for Least Squares (CGLS) and the Chebyshev Semi-Iterative Method (CS) with Tikhonov regularization to do arithmetic at lower precision using the MATLAB chop function, and we ran experiments on applications from image processing and compared their performance at different precision levels. We concluded that CGLS is a more stable algorithm, but overflows easily due to the computation of inner products, while CS is less likely to overflow but it has more erratic convergence behavior. When the noise level is high, CS outperforms CGLS by being able to run more iterations before overflow occurs; when the noise level is close to zero, CS appears to be more susceptible to accumulation of round-off errors

Identification of multi-fault in rotor-bearing system using spectral kurtosis and EEMD

Condition monitoring and fault diagnosis via vibration signal processing play an important role to avoid serious accidents. Aiming at the complexity of multiple faults in a rotor-bearing system and drawback, the characteristic frequency of relevant fault could not be determined effectively with traditional method. The Spectral Kurtosis (SK) is useful for the bearing fault detection. Nevertheless, the simulation of experiment in this paper shows that the SK is unable to identify multi-fault of rotor-bearing system fully when different faults excite different resonance frequencies. A new multi-fault detection method based on EEMD and spectral kurtosis (SK) is proposed in order to overcoming the shortcoming. The proposed method is applied to multi-faults of rotor imbalance and faulty bearings. The superiority of the proposed method based on spectral kurtosis (SK) and EEMD is demonstrated in extracting fault characteristic information of rotating machinery

Blind source separation of rolling element bearing’ single channel compound fault based on Shift Invariant Sparse Coding

The mechanical vibration source signal collected by sensor often includes a variety of internal vibration source of contributions such as gears, bearings, shaft and so on. It is often hoped to achieve effective separation of the source signal in order to obtain better fault diagnosis result. Blind source separation of the failure signal of rolling element bearing is a challenging task due to the above reasons, especially in the case of single channel compound fault. A method of blind source separation of rolling element bearing’s single channel compound fault based on Shift-Invariant Sparse Coding (SISC) is proposed in the paper. The waveform characteristic of different fault signal has some difference in the structure even that the same impulse characteristics of signals are produced by different parts, and the difference can be captured by the SISC method with the following reasons: Firstly, a set of basis functions is trained and obtained by SISC feature self-study method (The number of the basis functions is big necessarily). Then the potential components are constructed using the corresponding obtained basis functions. At last, the clustering operation is carried out using the structural similarity of the potential components, and the clustering signals represent the different vibration source signals. Apply the traditional vibration signal handling method such as envelope demodulation to the obtained clustering signals respectively and better fault diagnosis results are obtained at last

A CCaMK/Cyclops response element in the promoter of Lotus japonicus calcium-binding protein 1 (CBP1) mediates transcriptional activation in root symbioses

Early gene expression in arbuscular mycorrhiza (AM) and the nitrogen-fixing root nodule symbiosis (RNS) is governed by a shared regulatory complex. Yet many symbiosis-induced genes are specifically activated in only one of the two symbioses. The Lotus japonicus T-DNA insertion line T90, carrying a promoterless uidA (GUS) gene in the promoter of Calcium Binding Protein 1 (CBP1) is exceptional as it exhibits GUS activity in both root endosymbioses. To identify the responsible cis- and trans-acting factors, we subjected deletion/modification series of CBP1 promoter : reporter fusions to transactivation and spatio-temporal expression analysis and screened ethyl methanesulphonate (EMS)-mutagenized T90 populations for aberrant GUS expression. We identified one cis-regulatory element required for GUS expression in the epidermis and a second element, necessary and sufficient for transactivation by the calcium and calmodulin-dependent protein kinase (CCaMK) in combination with the transcription factor Cyclops and conferring gene expression during both AM and RNS. Lack of GUS expression in T90 white mutants could be traced to DNA hypermethylation detected in and around this element. We concluded that the CCaMK/Cyclops complex can contribute to at least three distinct gene expression patterns on its direct target promoters NIN (RNS), RAM1 (AM), and CBP1 (AM and RNS), calling for yet-to-be identified specificity-conferring factors

Benzyl 3-dehydr­oxy-1,2,5-oxadiazolo[3′,4′:2,3]oleanolate

The title compound, C37H50N2O3, is a benzyl ester derivative of oleanolic acid, a penta­cyclic triterpene, with a five-membered oxadiazole ring fused to the ring A. The triterpene A and C rings adopt slightly distorted half-chair conformations, whereas the remaining three six-membered rings are in chair forms

Graph Neural Network for spatiotemporal data: methods and applications

In the era of big data, there has been a surge in the availability of data containing rich spatial and temporal information, offering valuable insights into dynamic systems and processes for applications such as weather forecasting, natural disaster management, intelligent transport systems, and precision agriculture. Graph neural networks (GNNs) have emerged as a powerful tool for modeling and understanding data with dependencies to each other such as spatial and temporal dependencies. There is a large amount of existing work that focuses on addressing the complex spatial and temporal dependencies in spatiotemporal data using GNNs. However, the strong interdisciplinary nature of spatiotemporal data has created numerous GNNs variants specifically designed for distinct application domains. Although the techniques are generally applicable across various domains, cross-referencing these methods remains essential yet challenging due to the absence of a comprehensive literature review on GNNs for spatiotemporal data. This article aims to provide a systematic and comprehensive overview of the technologies and applications of GNNs in the spatiotemporal domain. First, the ways of constructing graphs from spatiotemporal data are summarized to help domain experts understand how to generate graphs from various types of spatiotemporal data. Then, a systematic categorization and summary of existing spatiotemporal GNNs are presented to enable domain experts to identify suitable techniques and to support model developers in advancing their research. Moreover, a comprehensive overview of significant applications in the spatiotemporal domain is offered to introduce a broader range of applications to model developers and domain experts, assisting them in exploring potential research topics and enhancing the impact of their work. Finally, open challenges and future directions are discussed

Diagnosis of rolling element bearing fault arising in gearbox based on sparse morphological component analysis

It is hard to diagnose the rolling element bearing fault occurring in gearbox due to the complexity and the probable mutual coupling among the kinds of signals. A novel diagnosis method of rolling element bearing fault arising in gearbox based on morphological component analysis (MCA) originating from sparse representation theory is proposed in the paper. By selecting proper dictionaries, different morphological components can be separated successfully from the complex rolling fault signal arising in gearbox, which helps to improve the efficiency and accuracy of diagnosis result. The effectiveness of the proposed method is verified through simulations firstly. Then the proposed method is used in fault feature extracting of complex vibration signals collected from rotating machinery, and the effectiveness of the proposed method is further verified. Besides, the advantage of the proposed method over other relative method is presented

Structural reconstruction of the catalytic center of LiPDF through multiple scattering calculation with MXAN

Abstract Peptide deformylase (PDF, EC 3.5.1.27) is essential for the normal growth of eubacterium but not for mammalians. Recently, PDF has been studied as a target for new antibiotics. In this paper, X-ray absorption spectroscopy was employed to determine the local structure around the zinc ion of PDF from Leptospira Interrogans in dry powder, because it is very difficult to obtain the crystallized sample of Li PDF. We performed X-ray absorption near edge structure (XANES) calculation and reconstructed successfully the local geometry of the active center, and the results from calculations show that a water molecule (Wat1) has moved towards the zinc ion and lies in the distance range to coordinate with the zinc ion weakly. In addition, the sensitivity of theoretical spectra to the different ligand bodies was evaluated in terms of goodness-of-fit