Regenerating zebrafish scales express a subset of evolutionary conserved genes involved in human skeletal disease

BACKGROUND: Scales are mineralised exoskeletal structures that are part of the dermal skeleton. Scales have been mostly lost during evolution of terrestrial vertebrates whilst bony fish have retained a mineralised dermal skeleton in the form of fin rays and scales. Each scale is a mineralised collagen plate that is decorated with both matrix-building and resorbing cells. When removed, an ontogenetic scale is quickly replaced following differentiation of the scale pocket-lining cells that regenerate a scale. Processes promoting de novo matrix formation and mineralisation initiated during scale regeneration are poorly understood. Therefore, we performed transcriptomic analysis to determine gene networks and their pathways involved in dermal scale regeneration. RESULTS: We defined the transcriptomic profiles of ontogenetic and regenerating scales of zebrafish and identified 604 differentially expressed genes (DEGs). These were enriched for extracellular matrix, ossification, and cell adhesion pathways, but not in enamel or dentin formation processes indicating that scales are reminiscent to bone. Hypergeometric tests involving monogenetic skeletal disorders showed that DEGs were strongly enriched for human orthologues that are mutated in low bone mass and abnormal bone mineralisation diseases (P< 2× 10(−3)). The DEGs were also enriched for human orthologues associated with polygenetic skeletal traits, including height (P< 6× 10(−4)), and estimated bone mineral density (eBMD, P< 2× 10(−5)). Zebrafish mutants of two human orthologues that were robustly associated with height (COL11A2, P=6× 10(−24)) or eBMD (SPP1, P=6× 10(−20)) showed both exo- and endo- skeletal abnormalities as predicted by our genetic association analyses; col11a2(Y228X/Y228X) mutants showed exoskeletal and endoskeletal features consistent with abnormal growth, whereas spp1(P160X/P160X) mutants predominantly showed mineralisation defects. CONCLUSION: We show that scales have a strong osteogenic expression profile comparable to other elements of the dermal skeleton, enriched in genes that favour collagen matrix growth. Despite the many differences between scale and endoskeletal developmental processes, we also show that zebrafish scales express an evolutionarily conserved sub-population of genes that are relevant to human skeletal disease. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-021-01209-8

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The current assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n=14) containing 32,928 and 36,697 protein-coding genes, respectively. The Petunia lineage has experienced at least two rounds of paleohexaploidization, the older gamma hexaploidy event, which is shared with other Eudicots, and the more recent Solanaceae paleohexaploidy event that is shared with tomato and other Solanaceae species. Transcription factors that were targets of selection during the shift from bee- to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral color patterns and pollination systems. The high quality genome sequences will enhance the value of Petunia as a model system for basic and applied research on a variety of unique biological phenomena

Massive indexed parallel identification of transposon flanking sequences

International audienceThe large scale sequencing of insertion element flanking sequences has revolutionized reverse genetics in plant research: Insertion mutants can now simply be identified in silico by BLAST searching the resulting flanking sequence databases. The development of next-generation sequencing technologies has further facilitated the creation of flanking sequence collections derived from entire mutant populations. Here we describe a highly efficient and widely applicable method that we developed to amplify, sequence, and identify dTph1 transposon flanking sequences from a library of 1000 Petunia W138 individuals simultaneously

Differential Recruitment of WOX Transcription Factors for Lateral Development and Organ Fusion in Petunia and Arabidopsis[W]

Petal fusion in petunia (Petunia × hybrida) results from lateral expansion of the five initially separate petal primordia, forming a ring-like primordium that determines further development. Here, we show that MAEWEST (MAW) and CHORIPETALA SUZANNE (CHSU) are required for petal and carpel fusion, as well as for lateral outgrowth of the leaf blade. Morphological and molecular analysis of maw and maw chsu double mutants suggest that polarity defects along the adaxial/abaxial axis contribute to the observed reduced lateral outgrowth of organ primordia. We show that MAW encodes a member of the WOX (WUSCHEL-related homeobox) transcription factor family and that a partly similar function is redundantly encoded by WOX1 and PRESSED FLOWER (PRS) in Arabidopsis thaliana, indicating a conserved role for MAW/WOX1/PRS genes in regulating lateral organ development. Comparison of petunia maw and Arabidopsis wox1 prs phenotypes suggests differential recruitment of WOX gene function depending on organ type and species. Our comparative data together with previous reports on WOX gene function in different species identify the WOX gene family as highly dynamic and, therefore, an attractive subject for future evo-devo studies

Analysis of the Petunia TM6 MADS Box Gene Reveals Functional Divergence within the DEF/AP3 Lineage

Antirrhinum majus DEFICIENS (DEF) and Arabidopsis thaliana APETALA3 (AP3) MADS box proteins are required to specify petal and stamen identity. Sampling of DEF/AP3 homologs revealed two types of DEF/AP3 proteins, euAP3 and TOMATO MADS BOX GENE6 (TM6), within core eudicots, and we show functional divergence in Petunia hybrida euAP3 and TM6 proteins. Petunia DEF (also known as GREEN PETALS [GP]) is expressed mainly in whorls 2 and 3, and its expression pattern remains unchanged in a blind (bl) mutant background, in which the cadastral C-repression function in the perianth is impaired. Petunia TM6 functions as a B-class organ identity protein only in the determination of stamen identity. Atypically, Petunia TM6 is regulated like a C-class rather than a B-class gene, is expressed mainly in whorls 3 and 4, and is repressed by BL in the perianth, thereby preventing involvement in petal development. A promoter comparison between DEF and TM6 indicates an important change in regulatory elements during or after the duplication that resulted in euAP3- and TM6-type genes. Surprisingly, although TM6 normally is not involved in petal development, 35S-driven TM6 expression can restore petal development in a def (gp) mutant background. Finally, we isolated both euAP3 and TM6 genes from seven solanaceous species, suggesting that a dual euAP3/TM6 B-function system might be the rule in the Solanaceae

Until the Last Fallen Soldieris Buried : The Second World War, Remembrance and Community in St Petersburg and Leningrad oblast

Avhandlingen undersöker minnespraktiker kring andra världskriget i S:t Petersburg med omnejd, en stad som under namnet Leningrad 1941–44 var belägrad av tyskarna i över två år. På fronterna runt den omringade staden rasade under drygt två år hårda strider. Skogarna och myrarna där är fortfarande fulla av spår av kriget och marken gömmer kvarlevor av de soldater som fick sätta livet till under striderna. Avhandlingens empiriska fokus är den rörelse som arbetar för att dessa soldater till slut ska få en begravning och kunna identifieras. I avhandlingen speglas olika aspekter av verksamheten: vikten av ett namn, begravningarna, gemensamhetsskapandet, platsen och krigets spår i landskapet. Sökandet sätts också in i en större samhällelig kontext. Minnet av kriget är en viktig källa till stolthet i Ryssland, och segerdagen 9 maj har hög officiell status och stor folklig uppslutning. Det stora lidandet och uppoffringen bidrar till att göra kriget heligt, både då och nu. Det finns en föreställning om att de nu levande har skyldigheter mot det förflutna – en plikt att minnas. Sökarbetet är en komplex kamp mellan identifikation med och kritik av bärande nationella myter. Avhandlingen utforskar spänningsfältet minne och glömska och undersöker hur minnet av andra världskriget får bestående och ritualiserad mening, samt hur meningsskapandet förändras över tid och i olika sammanhang.In this dissertation commemorative practices in St Petersburg and Leningrad oblast relating to the Second World War are investigated. The city of Leningrad was besieged by the Germans for more than two years 1941–44 and on the fronts around the city raged fierce battles. The woods and bogs here are still full of traces from the war, and the ground hides the remains of fallen soldiers. The empirical focus of the dissertation is the Russian voluntary movement working to find, bury, and if possible identify these soldiers. Different aspects of the activity are investigated: the importance of a name, the funerals, community building, the place, and the traces of war in the landscape. The search for fallen soldiers is related to a wider societal context. The war is an important source of national pride in Russia, and Victory Day May 9th is a holiday with high official status as well as popular enthusiasm. The suffering and sacrifice from the war contributes to making it sacred, both then and now. There is a widespread idea that the now living have obligations to the past – a duty to remember. The search activity is a complex struggle between identification with and critique of national myths. The dissertation explores the tension between memory and forgetting, and investigates how the memory of the Second World War is imbued with lasting and ritualised meaning, and how meaning is changed over time and in different contexts

"Defenders of their faith" : power and party in the Anglican Diocese of Sydney, 1909-1938

Zebrafish (Danio rerio Hamilton) are increasingly used as a model to study the effects of chronic stress on brain and behaviour. In rodents, unpredictable chronic stress (UCS) has a stronger effect on physiology and behaviour during the active phase than during the resting phase. Here, we applied UCS during the daytime (active phase) for 7 and 14 days or during the night-time (resting phase) for 7 nights in an in-house-reared Tuebingen long-fin (TLF) zebrafish strain. Following UCS, inhibitory avoidance learning was assessed using a 3 day protocol where fish learn to avoid swimming from a white to a black compartment where they will receive a 3 V shock. Latencies of entering the black compartment were recorded before training (day 1; first shock) and after training on day 2 (second shock) and day 3 (no shock, tissue sampling). Fish whole-body cortisol content and expression levels of genes related to stress, fear and anxiety in the telencephalon were quantified. Following 14 days of UCS during the day, inhibitory avoidance learning decreased (lower latencies on days 2 and 3); minor effects were found following 7 days of UCS. Following 7 nights of UCS, inhibitory avoidance learning decreased (lower latency on day 3). Whole-body cortisol levels showed a steady increase compared with controls (100%) from 7 days of UCS (139%), to 14 days of UCS (174%) to 7 nights of UCS (231%), suggestive of an increasing stress load. Only in the 7 nights of UCS group did expression levels of corticoid receptor genes (mr, grα, grβ) and of bdnf increase. These changes are discussed as adaptive mechanisms to maintain neuronal integrity and prevent overload, and as being indicative of a state of high stress load. Overall, our data suggest that stressors during the resting phase have a stronger impact than during the active phase. Our data warrant further studies on the effect of UCS on stress axis-related genes, especially grβ; in mammals this receptor has been implicated in glucocorticoid resistance and depression

Toward the Analysis of the Petunia MADS Box Gene Family by Reverse and Forward Transposon Insertion Mutagenesis Approaches: B, C, and D Floral Organ Identity Functions Require SEPALLATA-Like MADS Box Genes in Petunia

We have initiated a systematic functional analysis of the MADS box, intervening region, K domain, C domain-type MADS box gene family in petunia. The starting point for this has been a reverse-genetics approach, aiming to select for transposon insertions into any MADS box gene. We have developed and applied a family signature insertion screening protocol that is highly suited for this purpose, resulting in the isolation of 32 insertion mutants in 20 different MADS box genes. In addition, we identified three more MADS box gene insertion mutants using a candidate-gene approach. The defined insertion lines provide a sound foundation for a systematic functional analysis of the MADS box gene family in petunia. Here, we focus on the analysis of Floral Binding Protein2 (FBP2) and FBP5 genes that encode the E-function, which in Arabidopsis has been shown to be required for B and C floral organ identity functions. fbp2 mutants display sepaloid petals and ectopic inflorescences originating from the third floral whorl, whereas fbp5 mutants appear as wild type. In fbp2 fbp5 double mutants, reversion of floral organs to leaf-like organs is increased further. Strikingly, ovules are replaced by leaf-like structures in the carpel, indicating that in addition to the B- and C-functions, the D-function, which specifies ovule development, requires E-function activity. Finally, we compare our data with results obtained using cosuppression approaches and conclude that the latter might be less suited for assigning functions to individual members of the MADS box gene family

Divergent Functional Diversification Patterns in the SEP/AGL6/AP1 MADS-box Transcription Factor Superclade

International audienceMembers of SEPALLATA (SEP) and APETALA1 (AP1)/SQUAMOSA (SQUA) MADS-box transcriptionfactor subfamilies play key roles in floral organ identity determination and floral meristem determinacyin the Rosid species Arabidopsis. Here, we present a functional characterization of the seven SEP/AGL6and four AP1/SQUA genes in the distant Asterid species Petunia x hybrida petunia. Based on the analysisof single and higher order mutants, we report that the petunia SEP1/SEP2/SEP3 orthologs together withAGL6 encode classical SEP floral organ identity and floral termination functions, with a master role forthe petunia SEP3 ortholog FLORAL BINDING PROTEIN 2 (FBP2). By contrast, the FBP9 subclademembers FBP9 and FBP23, for which no clear ortholog is present in Arabidopsis, play a major role indetermining floral meristem identity together with FBP4, while contributing only moderately to floralorgan identity. In turn, the four members of the petunia AP1/SQUA subfamily redundantly are requiredfor inflorescence meristem identity, and act as B-function repressors in the first floral whorl, togetherwith BEN/ROB genes. Overall, these data together with studies in other species suggest majordifferences in the functional diversification of the SEP/AGL6 and AP1/SQUA MADS-box subfamiliesduring angiosperm evolution