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  1. Abstract Background

    Response to oxidative stress is universal in almost all organisms and the mitochondrial membrane protein, BbOhmm, negatively affects oxidative stress responses and virulence in the insect fungal pathogen,Beauveria bassiana. Nothing further, however, is known concerning howBbOhmmand this phenomenon is regulated.

    Results

    Threeoxidativestressresponse regulating Zn2Cys6transcription factors (BbOsrR1, 2, and 3) were identified and verified via chromatin immunoprecipitation (ChIP)-qPCR analysis as binding to theBbOhmmpromoter region, with BbOsrR2 showing the strongest binding. Targeted gene knockout ofBbOsrR1orBbOsrR3led to decreasedBbOhmmexpression and consequently increased tolerances to free radical generating compounds (H2O2and menadione), whereas the ΔBbOsrR2strain showed increasedBbOhmmexpression with concomitant decreased tolerances to these compounds. RNA and ChIP sequencing analysis revealed that BbOsrR1 directly regulated a wide range of antioxidation and transcription-associated genes, negatively affecting the expression of theBbClp1cyclin andBbOsrR2. BbClp1 was shown to localize to the cell nucleus and negatively mediate oxidative stress responses. BbOsrR2 and BbOsrR3 were shown to feed into the Fus3-MAPK pathway in addition to regulating antioxidation and detoxification genes. Binding motifs for the three transcription factors were found to partially overlap in the promoter region ofBbOhmmand other target genes. Whereas BbOsrR1 appeared to function independently, co-immunoprecipitation revealed complex formation between BbClp1, BbOsrR2, and BbOsrR3, with BbClp1 partially regulating BbOsrR2 phosphorylation.

    Conclusions

    These findings reveal a regulatory network mediated by BbOsrR1 and the formation of a BbClp1-BbOsrR2-BbOsrR3 complex that orchestrates fungal oxidative stress responses.

     
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  2. Unexpected long query latency of a database system can cause domino effects on all the upstream services and se- verely degrade end users’ experience with unpredicted long waits, resulting in an increasing number of users disengaged with the services and thus leading to a high user disengage- ment ratio (UDR). A high UDR usually translates to reduced revenue for service providers. This paper proposes UTSLO, a UDR-oriented SLO guaranteed system, which enables a database system to support multi-tenant UDR targets in a cost-effective fashion through UDR-oriented capacity plan- ning and dynamic UDR target enforcement. The former aims to estimate the feasibility of UDR targets while the latter dynamically tracks and regulates per-connection query la- tency distribution needed for accurate UDR target guarantee. In UTSLO, the database service capacity can be fully ex- ploited to efficiently accommodate tenants while minimizing resources required for UDR target guarantee. 
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    Free, publicly-accessible full text available November 1, 2024
  3. Abstract Background

    Analysis of the relationship between chromosomal structural variation (synteny breaks) and 3D-chromatin architectural changes among closely related species has the potential to reveal causes and correlates between chromosomal change and chromatin remodeling. Of note, contrary to extensive studies in animal species, the pace and pattern of chromatin architectural changes following the speciation of plants remain unexplored; moreover, there is little exploration of the occurrence of synteny breaks in the context of multiple genome topological hierarchies within the same model species.

    Results

    Here we used Hi-C and epigenomic analyses to characterize and compare the profiles of hierarchical chromatin architectural features in representative species of the cotton tribe (Gossypieae), includingGossypium arboreum,Gossypium raimondii, andGossypioides kirkii, which differ with respect to chromosome rearrangements. We found that (i) overall chromatin architectural territories were preserved inGossypioidesandGossypium, which was reflected in their similar intra-chromosomal contact patterns and spatial chromosomal distributions; (ii) the non-random preferential occurrence of synteny breaks in A compartment significantly associate with the B-to-A compartment switch in syntenic blocks flanking synteny breaks; (iii) synteny changes co-localize with open-chromatin boundaries of topologically associating domains, while TAD stabilization has a greater influence on regulating orthologous expression divergence than do rearrangements; and (iv) rearranged chromosome segments largely maintain ancestralin-cisinteractions.

    Conclusions

    Our findings provide insights into the non-random occurrence of epigenomic remodeling relative to the genomic landscape and its evolutionary and functional connections to alterations of hierarchical chromatin architecture, on a known evolutionary timescale.

     
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    Free, publicly-accessible full text available December 1, 2024
  4. Cytonuclear disruption may accompany allopolyploid evolution as a consequence of the merger of different nuclear genomes in a cellular environment having only one set of progenitor organellar genomes. One path to reconcile potential cytonuclear mismatch is biased expression for maternal gene duplicates (homoeologs) encoding proteins that target to plastids and/or mitochondria. Assessment of this transcriptional form of cytonuclear coevolution at the level of individual cells or cell types remains unexplored. Using single-cell (sc-) and single-nucleus (sn-) RNAseq data from eight tissues in three allopolyploid species, we characterized cell type–specific variations of cytonuclear coevolutionary homoeologous expression and demonstrated the temporal dynamics of expression patterns across development stages during cotton fiber development. Our results provide unique insights into transcriptional cytonuclear coevolution in plant allopolyploids at the single-cell level.

     
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    Free, publicly-accessible full text available October 3, 2024
  5. Abstract

    This research examines how team members’ passion for innovation compiles to contribute to team innovation. We argue that team mean passion influences team innovation by affecting team reflexivity, which is a key team process for members to collectively reflect on and adjust their efforts toward achieving innovation goals. The indirect effect of mean passion on team innovation via team reflexivity depends on the nature of passion—harmonious passion (HP) versus obsessive passion (OP)—and the diversity of the corresponding type of passion. Results from a two‐wave field study of 131 teams and a three‐wave field study of 155 teams support the differential effects of compiled HP and OP. Moreover, the effect of mean HP on team reflexivity and its indirect effect on team innovation via reflexivity were less positive when HP diversity was higher rather than lower, while the effect of mean OP on team reflexivity and its indirect effect on team innovation via reflexivity were less negative when OP diversity was higher rather than lower. This research offers important theoretical and practical implications for literatures on passion, teams, and team innovation.

     
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  6. Abstract Effective utilization of wild relatives is key to overcoming challenges in genetic improvement of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher high-quality genomes for tomato wild species are insufficient. Here, we report chromosome-scale tomato genomes from nine wild species and two cultivated accessions, representative of Solanum section Lycopersicon , the tomato clade. Together with two previously released genomes, we elucidate the phylogeny of Lycopersicon and construct a section-wide gene repertoire. We reveal the landscape of structural variants and provide entry to the genomic diversity among tomato wild relatives, enabling the discovery of a wild tomato gene with the potential to increase yields of modern cultivated tomatoes. Construction of a graph-based genome enables structural-variant-based genome-wide association studies, identifying numerous signals associated with tomato flavor-related traits and fruit metabolites. The tomato super-pangenome resources will expedite biological studies and breeding of this globally important crop. 
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