Genome-Wide In Silico Analysis and Expression Profiling of Phosphoenolpyruvate Carboxylase Genes in Loquat, Apple, Peach, Strawberry and Pear

Phosphoenolpyruvate carboxylase (PEPC) genes have multiple potential roles in plant metabolism such as regulation and accumulation of organic acids in fruits, movement of guard cells and stress tolerance, etc. However, the systematic identification and characterization of PEPC genes in Rosaceae species i.e., loquat, apple, peach, strawberry, and pear are yet to be performed. In present study, 27 putative PEPC genes (loquat 4, apple 6, peach 3, strawberry 9, and pear 5) were identified. To further investigate the role of those PEPC genes, comprehensive bioinformatics and expression analysis were performed. In bioinformatic analysis, the physiochemical properties, conserved domains, gene structure, conserved motif, phylogenetic and syntenic analysis of PEPC genes were performed. The result revealed that the PEPcase superfamily domain was conserved in all examined PEPC proteins. Most of the PEPC proteins were predicted to be localized in cytonuclear. Genomic structural and motif analysis showed that the exon and motif number of each PEPC gene ranged dramatically, from 8 to 20, and 7 to 10, respectively. Syntenic analysis indicated that the segmental or whole-genome duplication played a vital role in extension of PEPC gene family in Rosacea species. The Ka and Ks values of duplicated genes depicted that PEPC genes have undergone a strong purifying selection. Furthermore, the expression analysis of PEPC genes in root, mature leaf, stem, full-bloom flower, and ripened fruit of loquat, apple, peach, strawberry, and pear was performed. Some genes were differentially expressed in aforementioned plant tissues, signifying their role in plant metabolism. This study provides the first genome-wide identification, characterization, and expression profiling of PEPC gene family in Rosaceae species, and provides the foundation for further functional analysis.

Molecular Characterization of Infectious Bronchitis Virus Strain HH06 Isolated in a Poultry Farm in Northeastern China

Spike (S) glycoprotein is an important virulent factor for coronaviruses (CoVs), and variants of CoVs have been characterized based on S gene analysis. We present phylogenetic relationship of an isolated infectious bronchitis virus (IBV) strain with reference to the available genome and protein sequences based on network, multiple sequence, selection pressure, and evolutionary fingerprinting analysis in People's Republic of China. One hundred and elven strains of CoVs i.e., Alphacoronaviruses (Alpha-CoVs; n = 12), Betacoronaviruses (Beta-CoVs; n = 37), Gammacoronaviruses (Gamma-CoVs; n = 46), and Deltacoronaviruses (Delta-CoVs; n = 16) were selected for this purpose. Phylogenetically, SARS-CoV-2 and SARS-CoVs clustered together with Bat-CoVs and MERS-CoV of Beta-CoVs (C). The IBV HH06 of Avian-CoVs was closely related to Duck-CoV and partridge S14, LDT3 (teal and chicken host). Beluga whale-CoV (SW1) and Bottlenose dolphin-CoVs of mammalian origin branched distantly from other animal origin viruses, however, making group with Avian-CoVs altogether into Gamma-CoVs. The motif analysis indicated well-conserved domains on S protein, which were similar within the same phylogenetic class and but variable at different domains of different origins. Recombination network tree indicated SARS-CoV-2, SARS-CoV, and Bat-CoVs, although branched differently, shared common clades. The MERS-CoVs of camel and human origin spread branched into a different clade, however, was closely associated closely with SARS-CoV-2, SARS-CoV, and Bat-CoVs. Whereas, HCoV-OC43 has human origin and branched together with bovine CoVs with but significant distant from other CoVs like SARS CoV-2 and SARS-CoV of human origin. These findings explain that CoVs' constant genetic recombination and evolutionary process that might maintain them as a potential veterinary and human epidemic threat.

Genome-wide Identification and Expression Analysis of the Cucumber PP2C Genes Family

Background: Type 2C protein phosphatase (PP2Cs) is a negative regulator of ABA signaling pathway, which play important roles in stress signal transduction in plants. However, cucumber (Cucumis sativus L.), as an important economic vegetable, has little research on its PP2C genes family. Results: This study conducted a genome-wide investigation of CsPP2C gene family. Through bioinformatics analysis, 56 CsPP2C genes were identified in cucumber. Based on phylogenetic analysis, the PP2C genes of cucumber and Arabidopsis were divided into 13 groups. Gene structure and conserved motif analysis showed that CsPP2C genes in the same group had similar gene structure and conserved domains. Collinearity analysis showed that segmental duplication events played a key role in the expansion of cucumber PP2C genes family. In addition, the expression of CsPP2Cs under different abiotic treatments was analyzed by qRT-PCR. The results showed that CsPP2C family genes showed different expression patterns under ABA, drought, salt and cold treatment, and a significantly responsive gene CsPP2Cs was obtained (CsPP2C3). By predicting the cis-elements in the promoter, we found that all CsPP2C members contained ABA response elements (ABRE) and drought response elements (MYC). Additionally, the expression patterns of CsPP2C genes were specific in different tissues. Conclusions: The results of this study provide a reference for the genome-wide identification of PP2C gene family in other species, and provide a basis for future studies on the function of PP2C gene in cucumber.

Analysis of the Spatio-Temporal Evolution and Factors Influencing the Freight Network in the Middle Reaches of the Yangtze River

The study uses python software to crawl O-D big data on the freight information platform and construct a frequency matrix based on freight connections between cities, then forming a freight network. There are 31 cities in the middle reaches of the Yangtze river that form the subject of the research. The study adopts the methods of the node degree, community analysis, network motif analysis, and multielement regression analysis to assess the differences of the spatio-temporal evolution and factors influencing the freight network in 2014 and 2018. The following conclusions can be drawn: (1) the freight network has experienced a change in pattern from “island” to “radial,” and the tightness of the freight network is strengthened. (2) The circulation accumulation of elements causes the change of node degree to have a high tendency of agglomeration of capital and central cities. (3) The phenomenon of “enclave freight” and “freight union” exists in the inner-city group, but the “freight alliance” formed by the “enclave” is relatively loose. (4) With the increase in the scale of the freight network, the module characteristics are gradually simplified. (5) Science and technology run through the entire process of the formation and development of the urban freight network.

Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP

BackgroundCrosslinking and immunoprecipitation (CLIP) is a method used to identify in vivo RNA– protein binding sites on a transcriptome-wide scale. With the increasing amounts of available data for RNA-binding proteins (RBPs), it is important to understand to what degree the enriched motifs specify the RNA binding profiles of RBPs in cells.ResultsWe develop positionally-enriched k-mer analysis (PEKA), a computational tool for efficient analysis of enriched motifs from individual CLIP datasets, which minimises the impact of technical and regional genomic biases by internal data normalisation. We cross-validate PEKA with mCross, and show that background correction by size-matched input doesn’t generally improve the specificity of detected motifs. We identify motif classes with common enrichment patterns across eCLIP datasets and across RNA regions, while also observing variations in the specificity and the extent of motif enrichment across eCLIP datasets, between variant CLIP protocols, and between CLIP and in vitro binding data. Thereby we gain insights into the contributions of technical and regional genomic biases to the enriched motifs, and find how motif enrichment features relate to the domain composition and low-complexity regions (LCRs) of the studied proteins.ConclusionsOur study provides insights into the overall contributions of regional binding preferences, protein domains and LCRs to the specificity of protein-RNA interactions, and shows the value of cross-motif and cross-RBP comparison for data interpretation. Our results are presented for exploratory analysis via an online platform in an RBP-centric and motif-centric manner (https://imaps.goodwright.com/apps/peka/). PEKA is available from https://github.com/ulelab/peka.

CCCH Zinc Finger Genes in Barley: Genome-Wide Identification, Evolution, Expression and Haplotype Analysis

Background: CCCH transcription factors are important zinc finger transcription factors involved in the response to biotic and abiotic stress and physiological and developmental processes. Barley (Hordeum vulgare) is an agriculturally important cereal crop with multiple uses, such as brewing production, animal feed, and human food. The identification and assessment of new functional genes are important for the molecular breeding of barley. Results: In this study, a total of 35 protein-encoding CCCH genes unevenly dispersed on seven different chromosomes were identified in barley. Phylogenetic analysis categorized the barley CCCH genes (HvC3Hs) into seven subfamilies according to their distinct features, and this classification was supported by intron–exon structure and conserved motif analysis. Despite the large genome size of barley, the lower number of CCCH genes in barley might be attributed to the low frequency of segmental and tandem duplication events. Furthermore, the HvC3H genes displayed distinct expression profiles for different developmental processes and in response to various types of stresses. The expression of HvC3H9 was significantly induced by multiple types of abiotic stress and/or phytohormone treatment, which might make it an excellent target for the molecular breeding of barley. Genetic variation of HvC3Hs was characterized using publicly available exome-capture sequencing datasets. Clear genetic divergence was observed between wild and landrace barley populations in HvC3H genes. For most HvC3Hs, nucleotide diversity and the number of haplotype polymorphisms decreased during barley domestication. Conclusion: Overall, our study provides a comprehensive characterization of barley CCCH transcription factors, their diversity, and their biological functions.

Genome-wide analysis of the CalS gene family in cotton reveals their potential roles in fiber development and responses to stress

Callose deposition occurs during plant growth and development, as well as when plants are under biotic and abiotic stress. Callose synthase is a key enzyme for the synthesis of callose. In this study, 27, 28, 16, and 15 callose synthase family members were identified in Gossypium hirsutum, Gossypium barbadense, Gossypium raimondii, and Gossypium arboreum using the sequence of Arabidopsis callose synthase. The CalSs were divided into five groups by phylogenetic, gene structure, and conservative motif analysis. The conserved motifs and gene structures of CalSs in each group were highly similar. Based on the analysis of cis-acting elements, it is inferred that GhCalSs were regulated by abiotic stress. WGD/Segmental duplication promoted the amplification of the CalS gene in cotton, and purification selection had an important function in the CalS family. The transcriptome data and qRT-PCR under cold, heat, salt, and PEG treatments showed that GhCalSs were involved in abiotic stress. The expression patterns of GhCalSs were different in various tissues. We predicted that GhCalS4, which was highly expressed in fibers, had an important effect on fiber elongation. Hence, these results help us understand the role of GhCalSs in fiber development and stress response.

Proteomic analysis of early phosphorylated proteins in acute pancreatitis model

Background and Objective: The exact mechanism of acute pancreatitis (AP), which is an inflammation of the pancreas, still remains unclear. In this study, we examined the protein phosphorylation changes during the early stage of AP in mice using proteomic analysis. Methods: AP model in mice was constructed using an intraperitoneal injection of cerulein. Blood samples and pancreas were collected at 1, 3, 6, 9h after the final injection (n=3 at each time point). Samples collected 3h after the final injection were separately mixed and named S (saline group) and C1 (cerulein group); samples collected 6h after the final injection from the cerulein group were mixed and named C2. Proteins from S, C1, and C2 were extracted, digested by trypsin, and subjected to LC-MS/MS analysis, bioinformatics analysis, and Western blotting. Results: A total of 549 sites (426 proteins) were upregulated, and 501 sites (367 proteins) were downregulated in C1 compared to S; while 491 phosphorylation sites (377 proteins) were upregulated and 367 sites (274 proteins) were downregulated in C2 compared to S. Motif analysis showed that proline-directed kinase and basophilic kinase had a key role during early AP. During an early AP stage, the cellular distributions of proteins slightly changed. The types of domains changed with the development of AP. Phosphorylation proteins associated with calcium signaling, especially IP3R mediated calcium release, lysosome and autophagosome pathway, pancreatic digestive activation, and secretion, were found to be involved in the development of early AP independent of NF-kB activation. Moreover, the MAPK family was found to have a greater impact at the early stage of AP. We also found differentially expressed phosphorylations of amylase and trypsinogen and increased phosphorylation of MAPK6 S189 in early AP. Conclusion: IP3R mediated calcium release and activation of MAPK family are key events promoting the development of early AP.

Eve, Magdalina, Samaritian... (To the Typology of Female Images in the Novel of L. M. Leonov “Thief”)

Purpose. The article presents the results of the analysis of key female images in the novel by L. M. Leonov “Thief”: Masha Dolomanova, Tatiana Vekshina, Zinaida Balueva, Ksenia Babkina – whose fates are united by a typological commonality. The relevance of the study is due to the rethinking of the role of women in the modern world and art, and the formation of heroines, unhappy men in the world of men, in the literature of the 20th century developed, including under the influence of post-revolutionary, post-war reality, under the influence of urbanization. Methodology. The study based on the works devoted to the poetics of motif, image. To achieve the goal, the following tasks were set: determination of artistically significant motives; comparison of plot lines with precedent texts (mostly biblical); explanation of details that clarify the essence of female images. Using the method of motif analysis, identified the main motives involved in creating the storylines of each heroine, and their variants. Results. The motif of violence is highlighted, which is presented in the following allomotives: sexual violence (including deprivation of innocence) – for all heroines, except for Zinaida Balueva; physical violence (beating) – images of Masha Dolomanova, Zinaida Balueva – and suicide (Ksenia Babkina); psychological abuse (like suppression of will, lack of care) – all heroines. Within the framework of the method of structural-typological analysis, female characters were correlated with the poles of the binary opposition between the evil wife and the good wife, ascending to the Holy Scriptures. It was found that, in addition to the motive of violence, which is present in the storyline of each heroine, but conditioned not by the will of the person, but by chance, Leonov’s female characters are united by the motive of temptation, temptation, which allows one to assess their individual position and explain the tragic outcome of life. Conclusion. The female images in the novel “Thief” are comparable with such biblical personalities as Eve, Mary Magdalene, an unnamed Samaritan woman, Tatiana the Martyr. Their fates are determined by the actions or desires of other heroes, which, given the fact that they have not found their own God, ultimately leads to despair and irrevocable death.

Mapping cis-regulatory elements in the midgestation mouse placenta

The placenta is a temporary organ that provides the developing fetus with nutrients, oxygen, and protection in utero. Defects in its development, which may be caused by misregulated gene expression, can lead to devastating outcomes for the mother and fetus. In mouse, placental defects during midgestation commonly lead to embryonic lethality. However, the regulatory mechanisms controlling expression of genes during this period have not been thoroughly investigated. Therefore, we generated and analyzed ChIP-seq data for multiple histone modifications known to mark cis-regulatory regions. We annotated active and poised promoters and enhancers, as well as regions generally associated with repressed gene expression. We found that poised promoters were associated with neuronal development genes, while active promoters were largely associated with housekeeping genes. Active and poised enhancers were associated with placental development genes, though only active enhancers were associated with genes that have placenta-specific expression. Motif analysis within active enhancers identified a large network of transcription factors, including those that have not been previously studied in the placenta and are candidates for future studies. The data generated and genomic regions annotated provide researchers with a foundation for future studies, aimed at understanding how specific genes in the midgestation mouse placenta are regulated.