Dual RNA-Seq of Trunk Kidneys Extracted From Channel Catfish Infected With Yersinia ruckeri Reveals Novel Insights Into Host-Pathogen Interactions

Host-pathogen intectarions are complex, involving large dynamic changes in gene expression through the process of infection. These interactions are essential for understanding anti-infective immunity as well as pathogenesis. In this study, the host-pathogen interaction was analyzed using a model of acute infection where channel catfish were infected with Yersinia ruckeri. The infected fish showed signs of body surface hyperemia as well as hyperemia and swelling in the trunk kidney. Double RNA sequencing was performed on trunk kidneys extracted from infected channel catfish and transcriptome data was compared with data from uninfected trunk kidneys. Results revealed that the host-pathogen interaction was dynamically regulated and that the host-pathogen transcriptome fluctuated during infection. More specifically, these data revealed that the expression levels of immune genes involved in Cytokine-cytokine receptor interactions, the NF-kappa B signaling pathway, the JAK-STAT signaling pathway, Toll-like receptor signaling and other immune-related pathways were significantly upregulated. Y. ruckeri mainly promote pathogenesis through the flagellum gene fliC in channel catfish. The weighted gene co-expression network analysis (WGCNA) R package was used to reveal that the infection of catfish is closely related to metabolic pathways. This study contributes to the understanding of the host-pathogen interaction between channel catfish and Y. ruckeri, more specifically how catfish respond to infection through a transcriptional perspective and how this infection leads to enteric red mouth disease (ERM) in these fish

Insect-Microorganism Interaction Has Implicates on Insect Olfactory Systems

Olfaction plays an essential role in various insect behaviors, including habitat selection, access to food, avoidance of predators, inter-species communication, aggregation, and reproduction. The olfactory process involves integrating multiple signals from external conditions and internal physiological states, including living environments, age, physiological conditions, and circadian rhythms. As microorganisms and insects form tight interactions, the behaviors of insects are constantly challenged by versatile microorganisms via olfactory cues. To better understand the microbial influences on insect behaviors via olfactory cues, this paper summarizes three different ways in which microorganisms modulate insect behaviors. Here, we deciphered three interesting aspects of microorganisms-contributed olfaction: (1) How do volatiles emitted by microorganisms affect the behaviors of insects? (2) How do microorganisms reshape the behaviors of insects by inducing changes in the synthesis of host volatiles? (3) How do symbiotic microorganisms act on insects by modulating behaviors

Partial Least Squares-Discriminant Analysis of the Major and Trace Elements and their Evolutionary Characteristics from the Jinchuan Ni-Cu-(PGE) Sulfide Deposit, NW China

The world-renowned Jinchuan Cu-Ni-(PGE) sulfide deposit consists of four mainly independent intrusive units from west to east, namely Segments III, I, II-W, and II-E, and the main sulfide types are the disseminated, net-textured, massive, and Cu-rich ores. Due to the similar geochemical characteristics of each segment, there is no convenient method to distinguish them and explain their respective variations. Meanwhile, considering that the division of different types of ores is confusing and their formation is still controversial, direct classification using elemental discrimination maps can facilitate subsequent mining and research. In this paper, we report the new major and trace elements data from the Jinchuan deposit and collect the published data to construct a database of 10 major elements for 434 samples and 33 trace elements for 370 samples, respectively, and analyze the data based on multivariate statistical analysis for the first time. Robust estimation of compositional data (robCompositions) was applied to investigate censored geochemical data, and the input censored data were transformed using the centered log-ratios (clr) to overcome the closure effect on compositional data. Exploratory data analysis (EDA) was used to characterize the spatial distribution and internal structural features of the data. The transformed data were classified by partial least squares-discriminant analysis (PLS-DA) to identify different compositional features for each segment and ore type. The receiver operator characteristic (ROC) curve was used to verify the model results, which showed that the PLS-DA model we constructed was reliable. The main discriminant elements were obtained by PLS-DA of the major and trace elements, and based on these elements, we propose the plot of SiO2 + Al2O3 vs. CaO + Na2O + K2O and Cs + Ce vs. Th + U to discriminate the different segments of the Jinchuan deposit, and the Al2O3 + CaO vs. Fe2O3T + Na2O and Co + Cu vs. Rb + Th + U to discriminate the different ore types. In addition, we predict that there are still considerable metal reserves at the bottom of Segment I

Partial Least Squares-Discriminant Analysis of the Major and Trace Elements and their Evolutionary Characteristics from the Jinchuan Ni-Cu-(PGE) Sulfide Deposit, NW China

The world-renowned Jinchuan Cu-Ni-(PGE) sulfide deposit consists of four mainly independent intrusive units from west to east, namely Segments III, I, II-W, and II-E, and the main sulfide types are the disseminated, net-textured, massive, and Cu-rich ores. Due to the similar geochemical characteristics of each segment, there is no convenient method to distinguish them and explain their respective variations. Meanwhile, considering that the division of different types of ores is confusing and their formation is still controversial, direct classification using elemental discrimination maps can facilitate subsequent mining and research. In this paper, we report the new major and trace elements data from the Jinchuan deposit and collect the published data to construct a database of 10 major elements for 434 samples and 33 trace elements for 370 samples, respectively, and analyze the data based on multivariate statistical analysis for the first time. Robust estimation of compositional data (robCompositions) was applied to investigate censored geochemical data, and the input censored data were transformed using the centered log-ratios (clr) to overcome the closure effect on compositional data. Exploratory data analysis (EDA) was used to characterize the spatial distribution and internal structural features of the data. The transformed data were classified by partial least squares-discriminant analysis (PLS-DA) to identify different compositional features for each segment and ore type. The receiver operator characteristic (ROC) curve was used to verify the model results, which showed that the PLS-DA model we constructed was reliable. The main discriminant elements were obtained by PLS-DA of the major and trace elements, and based on these elements, we propose the plot of SiO2 + Al2O3 vs. CaO + Na2O + K2O and Cs + Ce vs. Th + U to discriminate the different segments of the Jinchuan deposit, and the Al2O3 + CaO vs. Fe2O3T + Na2O and Co + Cu vs. Rb + Th + U to discriminate the different ore types. In addition, we predict that there are still considerable metal reserves at the bottom of Segment I

PP2B and PP1 alpha cooperatively disrupt 7SK snRNP to release P-TEFb for transcription in response to Ca2+ signaling

The positive transcription elongation factor b (P-TEFb), consisting of Cdk9 and cyclin T, stimulates RNA polymerase II elongation and cotranscriptional pre-mRNA processing. To accommodate different growth conditions and transcriptional demands, a reservoir of P-TEFb is kept in an inactive state in the multisubunit 7SK snRNP. Under certain stress or disease conditions, P-TEFb is released to activate transcription, although the signaling pathway(s) that controls this is largely unknown. Here, through analyzing the UV- or hexamethylene bisacetamide (HMBA)-induced release of P-TEFb from 7SK snRNP, an essential role for the calcium ion (Ca2+)-calmodulin-protein phosphatase 2B (PP2B) signaling pathway is revealed. However, Ca2+ signaling alone is insufficient, and PP2B must act sequentially and cooperatively with protein phosphatase 1 alpha (PP1 alpha) to disrupt 7SK snRNP. Activated by UV/HMBA and facilitated by a PP2B-induced conformational change in 7SK snRNP, PP1 alpha releases P-TEFb through dephosphorylating phospho-Thr186 in the Cdk9 T-loop. This event is also necessary for the subsequent recruitment of P-TEFb by the bromodomain protein Brd4 to the preinitiation complex, where Cdk9 remains unphosphorylated and inactive until after the synthesis of a short RNA. Thus, through cooperatively dephosphorylating Cdk9 in response to Ca2+ signaling, PP2B and PP1 alpha alter the P-TEFb functional equilibrium through releasing P-TEFb from 7SK snRNP for transcription