Tracing the evolution of bioluminescent light organs across the deep-sea shrimp family Sergestidae using a genomic skimming and phylogenetic approach

Deep-sea shrimp of the family Sergestidae Dana, 1852 provide a unique system for studying the evolution of bioluminescence. Most species within the family possess autogenic bioluminescent photophores in one of three distinct forms: lensed photophores; non-lensed photophores; or internal organs of Pesta. This morphological diversity across the Sergestidae has resulted in recent major taxonomic revisions, dividing the two major genera (Sergia Stimpson, 1860 and Sergestes Milne Edwards, 1830) into 15. The present study capitalises on molecular data to construct an updated genus-level phylogeny of sergestid shrimp. DNA was successfully extracted from ~87 individuals belonging to 13 of the 15 newly proposed genera. A ‘genome skimming’ approach was implemented, allowing the capture of mitochondrial genomic data across 19 sergestid species. Additional individuals have been incorporated into the phylogeny through Sanger sequencing of both nuclear (H3 and NAK) and mitochondrial (16S and COI) genes. The resulting molecular phylogeny is compared with previous morphological trees with specific attention to genus-level relationships. The -sergestes group was rendered non-monophyletic and the -sergia group was recovered as monophyletic. Ancestral state reconstructions of light organ type indicate that organs of Pesta is the ancestral state for the family. Non-lensed photophores evolved once across the -sergia group, but were later lost in the deepest living genus, Sergia. Lensed photophores also evolved once within the genera Prehensilosergia Vereshchaka, Olesen & Lunina, 2014, Lucensosergia Vereshchaka, Olesen & Lunina, 2014 and Challengerosergia Vereshchaka, Olesen & Lunina, 2014. These findings identify preliminary patterns across light organ type and species’ depth distributions; however, future research that incorporates finer-scale depth data and more species is needed to confirm our findings.

Organ accompaniment to silent films, part 3 – the activity of Robert Hope-Jones and its importance

The idea to write music for silent films, both in a form of written-down scores and composed live has experienced its renaissance for more than ten years. Thanks to a quite decent number of preserved theatre instruments and also due to the globalisation and wide data flow options connected with it, the knowledge and interest in Anglo-Saxon tradition of organ accompaniment in cinema were able to spread away from its place of origin. The article is the third part of four attempts to present the phenomenon of combination of the art of organ improvisation with cinematography and it was based on the fragments of the doctoral thesis entitled “Current methods of organ improvisation as performance means in the accompaniment for silent films based on the selected musical and visual work”. The dissertation was written under the supervision of prof. dr hab. Elżbieta Karolak and was defended at the Ignacy Jan Paderewski Academy of Music in Poznań in 2020. The article focuses on the profile of Robert Hope-Jones, an eccentric creator of cinema organ. It describes the period preceding the time when typical theatre instruments called “Mighty Wurlitzer” acquired their final shape, i.e., from the introduction of first electromagnetic tracture innovations in England, to the establishment of Hope Jones’s collaboration with the Wurlitzer company in the United States of America and the creation of instruments of the Unit Organ type.

Evolutionary dynamics of circular RNAs in primates

Many primate genes produce circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear. By comparing tissue-specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related to species identity than organ type. However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution. By comparing to species-specific circRNAs, we identified that the downstream intron of the conserved circRNAs display a dramatic lengthening during evolution due to the insertion of novel retrotransposons. Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.

Context-Dependent Roles of Claudins in Tumorigenesis

The barrier and fence functions of the claudin protein family are fundamental to tissue integrity and human health. Increasing evidence has linked claudins to signal transduction and tumorigenesis. The expression of claudins is frequently dysregulated in the context of neoplastic transformation. Studies have uncovered that claudins engage in nearly all aspects of tumor biology and steps of tumor development, suggesting their promise as targets for treatment or biomarkers for diagnosis and prognosis. However, claudins can be either tumor promoters or tumor suppressors depending on the context, which emphasizes the importance of taking various factors, including organ type, environmental context and genetic confounders, into account when studying the biological functions and targeting of claudins in cancer. This review discusses the complicated roles and intrinsic and extrinsic determinants of the context-specific effects of claudins in cancer.

Kras activation in endometrial organoids drives cellular transformation and epithelial-mesenchymal transition

KRAS, an oncogene, is frequently activated by mutations in many cancers. Kras-driven adenocarcinoma development in the lung, pancreas, and biliary tract has been extensively studied using gene targeting in mice. By taking the organoid- and allograft-based genetic approach to these organs, essentially the same results as in vivo models were obtained in terms of tumor development. To verify the applicability of this approach to other organs, we investigated whether the combination of Kras activation and Pten inactivation, which gives rise to endometrial tumors in mice, could transform murine endometrial organoids in the subcutis of immunodeficient mice. We found that in KrasG12D-expressing endometrial organoids, Pten knockdown did not confer tumorigenicity, but Cdkn2a knockdown or Trp53 deletion led to the development of carcinosarcoma (CS), a rare, aggressive tumor comprising both carcinoma and sarcoma. Although they originated from epithelial cells, some CS cells expressed both epithelial and mesenchymal markers. Upon inoculation in immunodeficient mice, tumor-derived round organoids developed carcinoma or CS, whereas spindle-shaped organoids formed monophasic sarcoma only, suggesting an irreversible epithelial-mesenchymal transition during the transformation of endometrial cells and progression. As commonly observed in mutant Kras-driven tumors, the deletion of the wild-type Kras allele was identified in most induced tumors, whereas some epithelial cells in CS-derived organoids were unexpectedly negative for KrasG12D. Collectively, we showed that the oncogenic potential of KrasG12D and the histological features of derived tumors are context-dependent and varies according to the organ type and experimental settings. Our findings provide novel insights into the mechanisms underlying tissue-specific Kras-driven tumorigenesis.

Evolutionary dynamics of circular RNAs in primates

Many primate genes produce noncoding circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear. By comparing tissue specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related to species identity than organ type. However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution. These circRNAs are defined by an extended downstream intron that has shown dramatic lengthening during evolution due to the insertion of novel retrotransposons. Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.

Revealing the Tomato Endophyte Bacteria Communities Under Long-term Organic and Conventional Agricultural Practice System

Purpose: Microorganisms associated with the plant can contribute to plant health. Discrepancy both soil microbial structure and physicochemical properties observed in the organic and conventional agricultural systems. However, very little is known about the diversity of endophytic bacterial communities in plants grown in separate manipulation systems. The goal of this work was to get a broader overview of the diversity and dynamics of the tomato endophytic bacteria in the different agricultural practice systems.Methods: The structure of tomato endophyte bacterial communities under different growing stage (seeding stage, flowering stage, fruiting stage and harvesting stage), agricultural manipulation practices (organic and conventional systems) and organ-type (root or stem) were explored by using 16S rRNA gene profiling in this study.Results: A total of 2,014,992 16S rRNA gene sequences were obtained. These sequences revealed large-scale functional taxonomy units (OTUs). That is, there are 648 different OTUs in libraries, and 96 OTUs are common. Tomato endophyte bacteria consisted mainly of four phyllum, of which Proteobacteria was the most represented, followed by Firmcutes, Bacteroides, Actinobacteria, Gamma proteobacteria, the most abundant class are proteobacteria, bacteriobacteria, and so on. Proteobacteria are low. Enterobacteriaceae, Vecella, Bacillus, Mesorizobium and Chrysobacterium were shared by all plant development stage. Rich endophytic bacterial diversity was observed at the seedling stage（TI）, and endophytic bacterial diversity at the flowering stage （T2）and fruiting stage （T4）was low. Significant difference in endophytic bacterial communities emerged from roots and different host biographical stages, and tomato exerts greater influence on endophyte bacteria compared to organ type (main) agricultural manipulation methods.Conclusions: Tomato endophyte microbiota have a distinct structure in different plant development stage. Bacillus.spp were enriched seeding stage (TI) and decreased in the fruiting stage while Mesorhizobium.spp increased during in the fruiting stage(T4). Tomato have distinct endosphere microbiota by comparing beta diversity of microbiota in all crop season, compared with the manipulation resume and organ niche. And a strong correlation was observed between the structure of the microbiota in the whole dataset and soil chemistry which indicated that the soil type and treatment affected the endosphere microbiota of tomato. Organ niche exert more influence on the tomato microbiota compared with agricultural treatments between organic-farming and conventional farming.