Evolutionary Analyses Reveal Diverged Patterns of SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family in Oryza Genus

The SPL (SQUAMOSA promoter binding protein-like) gene family is one of the plant-specific transcription factor families and controls a considerable number of biological functions, including floral development, phytohormone signaling, and toxin resistance. However, the evolutionary patterns and driving forces of SPL genes in the Oryza genus are still not well-characterized. In this study, we investigated a total of 105 SPL genes from six AA genome Oryza representative species (O. barthii, O. glumipatula, O. nivara, O. rufipogon, O. glaberrima, and O. sativa). Phylogenetic and motif analyses indicated that SPL proteins could be divided into two distinct lineages (I and II), and further studies showed lineage II consisted of three clades (IIA, IIB, and IIC). We found that clade I had comparable structural features with clade IIA, whereas genes in clade IIC displayed intrinsic differences, such as lower exon numbers and the presence of miR156 regulation elements. Nineteen orthologous groups of OsSPLs in Oryza were also identified, and most exons within those genes maintained constant length, whereas length of intron changed relatively. All groups were constrained by stronger purifying selection and diversified continually including alterative gene number, intron length, and miR156 regulation. Subsequently, cis-acting element analyses revealed the potential role of SPLs in wild rice, which might participate in light-responsive, phytohormone response, and plant growth and development. Our results shed light on that different evolutionary rates and duplication events might result in divergent evolutionary patterns in each lineage of SPL genes, providing a guide in exploring diverse function in the rice gene family among six closely related Oryza species

A Method for Filtering Pages by Similarity Degree based on Dynamic Programming

To obtain the target webpages from many webpages, we proposed a Method for Filtering Pages by Similarity Degree based on Dynamic Programming (MFPSDDP). The method needs to use one of three same relationships proposed between two nodes, so we give the definition of the three same relationships. The biggest innovation of MFPSDDP is that it does not need to know the structures of webpages in advance. First, we address the design ideas with queue and double threads. Then, a dynamic programming algorithm for calculating the length of the longest common subsequence and a formula for calculating similarity are proposed. Further, for obtaining detailed information webpages from 200,000 webpages downloaded from the famous website “www.jd.com„, we choose the same relationship Completely Same Relationship (CSR) and set the similarity threshold to 0.2. The Recall Ratio (RR) of MFPSDDP is in the middle in the four filtering methods compared. When the number of webpages filtered is nearly 200,000, the PR of MFPSDDP is highest in the four filtering methods compared, which can reach 85.1%. The PR of MFPSDDP is 13.3 percentage points higher than the PR of a Method for Filtering Pages by Containing Strings (MFPCS)

FilteredWebHtmlDataBase

This dataset is used in my study about my manuscript "A Method for Filtering Pages by Similarity Degree based on Dynamic Programming". The data file is FilteredWebHtmlDataBase.mdf. The log file is FilteredWebHtmlDataBase_log.ldf. The database is SQL Server 2017. The downloaded url of the data file is https://pan.baidu.com/s/1N56EzVhW0M-qPWZQzORGtw. The downloaded url of the log file is https://pan.baidu.com/s/1qwqD7CNCqjwRs1tgvpuYUQ

A Reliability Calculation Method for Web Service Composition Using Fuzzy Reasoning Colored Petri Nets and Its Application on Supercomputing Cloud Platform

In order to develop a Supercomputing Cloud Platform (SCP) prototype system using Service-Oriented Architecture (SOA) and Petri nets, we researched some technologies for Web service composition. Specifically, in this paper, we propose a reliability calculation method for Web service compositions, which uses Fuzzy Reasoning Colored Petri Net (FRCPN) to verify the Web service compositions. We put forward a definition of semantic threshold similarity for Web services and a formal definition of FRCPN. We analyzed five kinds of production rules in FRCPN, and applied our method to the SCP prototype. We obtained the reliability value of the end Web service as an indicator of the overall reliability of the FRCPN. The method can test the activity of FRCPN. Experimental results show that the reliability of the Web service composition has a correlation with the number of Web services and the range of reliability transition values

The Precoder Design with Covariance Feedback for Simultaneous Information and Energy Transmission Systems

We consider the optimal precoder design with the assumption that the transmitter only has channel covariance information, for the multi-input multi-output (MIMO) information and energy transmission system. The objective of the system design is to maximize the average system information rate, meanwhile meeting the minimum energy requirement of the energy receiver. Following this objective, we formulate the problem as a semidefinite programming (SDP) and further transform it into a dual problem. Two methods are proposed to solve this problem: the first method decomposes the transmission covariance as a product of precoders so that the constrained optimization becomes an unconstrained one, whereas the second method derives the structure of the optimal transmission covariance analytically. Both methods are proved to be convergent and their overheads and complexity are also analyzed. The achievable rate-energy (R-E) regions for the proposed methods are presented in the simulation. Under various system settings, the superiority of the proposed methods is shown by comparing with a few existing transmission schemes

Meta-Analysis of Salt Stress Transcriptome Responses in Different Rice Genotypes at the Seedling Stage

Rice (Oryza sativa L.) is one of the most important staple food crops worldwide, while its growth and productivity are threatened by various abiotic stresses, especially salt stress. Unraveling how rice adapts to salt stress at the transcription level is vital. It can provide valuable information on enhancing the salt stress tolerance performance of rice via genetic engineering technologies. Here, we conducted a meta-analysis of different rice genotypes at the seedling stage based on 96 public microarray datasets, aiming to identify the key salt-responsive genes and understand the molecular response mechanism of rice under salt stress. In total, 5559 genes were identified to be differentially expressed genes (DEGs) under salt stress, and 3210 DEGs were identified during the recovery process. The Gene Ontology (GO) enrichment results revealed that the salt-response mechanisms of shoots and roots were different. A close-knit signaling network, consisting of the Ca2+ signal transduction pathway, the mitogen-activated protein kinase (MAPK) cascade, multiple hormone signals, transcription factors (TFs), transcriptional regulators (TRs), protein kinases (PKs), and other crucial functional proteins, plays an essential role in rice salt stress response. In this study, many unreported salt-responsive genes were found. Besides this, MapMan results suggested that TNG67 can shift to the fermentation pathway to produce energy under salt stress and may enhance the Calvin cycle to repair a damaged photosystem during the recovery stage. Taken together, these findings provide novel insights into the salt stress molecular response and introduce numerous candidate genes for rice salt stress tolerance breeding

Engineering an AI-based forward-reverse platform for the design of cross-ribosome binding sites of a transcription factor biosensor

A cross-ribosome binding site (cRBS) adjusts the dynamic range of transcription factor-based biosensors (TFBs) by controlling protein expression and folding. The rational design of a cRBS with desired TFB dynamic range remains an important issue in TFB forward and reverse engineering. Here, we report a novel artificial intelligence (AI)-based forward-reverse engineering platform for TFB dynamic range prediction and de novo cRBS design with selected TFB dynamic ranges. The platform demonstrated superior in processing unbalanced minority-class datasets and was guided by sequence characteristics from trained cRBSs. The platform identified correlations between cRBSs and dynamic ranges to mimic bidirectional design between these factors based on Wasserstein generative adversarial network (GAN) with a gradient penalty (GP) (WGAN-GP) and balancing GAN with GP (BAGAN-GP). For forward and reverse engineering, the predictive accuracy was up to 98% and 82%, respectively. Collectively, we generated an AI-based method for the rational design of TFBs with desired dynamic ranges

Evolutionary Analysis of <i>GH3</i> Genes in Six <i>Oryza</i> Species/Subspecies and Their Expression under Salinity Stress in <i>Oryza sativa</i> ssp. <i>japonica</i>

Glycoside Hydrolase 3 (GH3), a member of the Auxin-responsive gene family, is involved in plant growth, the plant developmental process, and various stress responses. The GH3 gene family has been well-studied in Arabidopsis thaliana and Zea mays. However, the evolution of the GH3 gene family in Oryza species remains unknown and the function of the GH3 gene family in Oryza sativa is not well-documented. Here, a systematic analysis was performed in six Oryza species/subspecies, including four wild rice species and two cultivated rice subspecies. A total of 13, 13, 13, 13, 12, and 12 members were identified in O. sativa ssp. japonica, O. sativa ssp. indica, Oryza rufipogon, Oryza nivara, Oryza punctata, and Oryza glumaepatula, respectively. Gene duplication events, structural features, conserved motifs, a phylogenetic analysis, chromosome locations, and Ka/Ks ratios of this important family were found to be strictly conservative across these six Oryza species/subspecies, suggesting that the expansion of the GH3 gene family in Oryza species might be attributed to duplication events, and this expansion could occur in the common ancestor of Oryza species, even in common ancestor of rice tribe (Oryzeae) (23.07~31.01 Mya). The RNA-seq results of different tissues displayed that OsGH3 genes had significantly different expression profiles. Remarkably, the qRT-PCR result after NaCl treatment indicated that the majority of OsGH3 genes play important roles in salinity stress, especially OsGH3-2 and OsGH3-8. This study provides important insights into the evolution of the GH3 gene family in Oryza species and will assist with further investigation of OsGH3 genes&#8217; functions under salinity stress