Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype.

Cucumis melo displays a large diversity of horticultural groups with cantaloupe melon the most cultivated type. Using a combination of single-molecule sequencing, 10X Genomics link-reads, high-density optical and genetic maps, and chromosome conformation capture (Hi-C), we assembled a chromosome scale C. melo var. cantalupensis Charentais mono genome. Integration of RNA-seq, MeDip-seq, ChIP-seq, and Hi-C data revealed a widespread compartmentalization of the melon genome, segregating constitutive heterochromatin and euchromatin. Genome-wide comparative and evolutionary analysis between melon botanical groups identified Charentais mono genome increasingly more divergent from Harukei-3 (reticulatus), Payzawat (inodorus), and HS (ssp. agrestis) genomes. To assess the paleohistory of the Cucurbitaceae, we reconstructed the ancestral Cucurbitaceae karyotype and compared it to sequenced cucurbit genomes. In contrast to other species that experienced massive chromosome shuffling, melon has retained the ancestral genome structure. We provide comprehensive genomic resources and new insights in the diversity of melon horticultural groups and evolution of cucurbits.

Integrative genome-wide analysis reveals the role of WIP proteins in inhibition of growth and development.

In cucurbits, CmWIP1 is a master gene controlling sex determination. To bring new insight in the function of CmWIP1, we investigated two Arabidopsis WIP transcription factors, AtWIP1/TT1 and AtWIP2/NTT. Using an inducible system we showed that WIPs are powerful inhibitor of growth and inducer of cell death. Using ChIP-seq and RNA-seq we revealed that most of the up-regulated genes bound by WIPs display a W-box motif, associated with stress signaling. In contrast, the down-regulated genes contain a GAGA motif, a known target of polycomb repressive complex. To validate the role of WIP proteins in inhibition of growth, we expressed AtWIP1/TT1 in carpel primordia and obtained male flowers, mimicking CmWIP1 function in melon. Using other promoters, we further demonstrated that WIPs can trigger growth arrest of both vegetative and reproductive organs. Our data supports an evolutionary conserved role of WIPs in recruiting gene networks controlling growth and adaptation to stress.

New psychoactive substance use as a survival strategy in rural marginalised communities in Hungary.

BACKGROUND: New psychoactive substance (NPS) use has become a widespread phenomenon among marginalised communities in Hungary. Since 2010, a growing number of reports in grey literature and anecdotal information among professionals have become available on NPS use among previously unaffected groups, such as people living in rural, socioeconomically deprived communities. In our research, we aimed to explore NPS use among these communities. METHODS: We conducted a mixed method research with convergent parallel design. Data collection took place in 2017 in marginalised communities in villages in two regions in Hungary, where 150 questionnaires were recorded and 50 interviews were conducted with current NPS users. RESULTS: According to the survey results, NPS is very easy to access, synthetic cannabinoid receptor agonist (SCRA) are easily bought in marginalised rural communities (79% found SCRA easy to obtain). Both SCRA and synthetic cathinones are used regularly; 57% of SCRA users and 37% of synthetic cathinone users used the respective substance at least once a week in the past 30 days. Besides NPS, sedative use (without prescription) and alcohol consumption are common among the respondents. 17% of the sample has already injected NPS. The overwhelming majority of the respondents rated regular consumption of NPS as "very dangerous" (SCRA: 75%, synthetic cathinones 72%). NPS users have limited knowledge of consequences and the social and health treatment options available. Most themes in the interviews are associated with surviving stress, crisis and anxiety, as well as the wish to escape from insecurity and chaotic life. Positive effects of substance use (community, joy, energy) are rarely present. CONCLUSION: People who use drugs (PWUD) living in these rural communities face the consequences of the rural risk environment: easy access to NPS, inadequate access to services, poor labour market situation and attributions of marginalised groups, for example disaffiliation. NPS use is not a recreational activity in this population; individuals mainly use NPS to get away from reality, problems, pain, poverty and marginalisation. NPS use is a survival strategy. Effective responses have to address substance use and social integration; we need complex interventions addressing structural factors.

TCTP and CSN4 control cell cycle progression and development by regulating CULLIN1 neddylation in plants and animals.

Translationally Controlled Tumor Protein (TCTP) controls growth by regulating the G1/S transition during cell cycle progression. Our genetic interaction studies show that TCTP fulfills this role by interacting with CSN4, a subunit of the COP9 Signalosome complex, known to influence CULLIN-RING ubiquitin ligases activity by controlling CULLIN (CUL) neddylation status. In agreement with these data, downregulation of CSN4 in Arabidopsis and in tobacco cells leads to delayed G1/S transition comparable to that observed when TCTP is downregulated. Loss-of-function of AtTCTP leads to increased fraction of deneddylated CUL1, suggesting that AtTCTP interferes negatively with COP9 function. Similar defects in cell proliferation and CUL1 neddylation status were observed in Drosophila knockdown for dCSN4 or dTCTP, respectively, demonstrating a conserved mechanism between plants and animals. Together, our data show that CSN4 is the missing factor linking TCTP to the control of cell cycle progression and cell proliferation during organ development and open perspectives towards understanding TCTP's role in organ development and disorders associated with TCTP miss-expression.

Biosynthesis of 2-Phenylethanol in Rose Petals Is Linked to the Expression of One Allele of RhPAAS.

Floral scent is one of the most important characters in horticultural plants. Roses (Rosa spp.) have been cultivated for their scent since antiquity. However, probably by selecting for cultivars with long vase life, breeders have lost the fragrant character in many modern roses, especially the ones bred for the cut flower market. The genetic inheritance of scent characters has remained elusive so far. In-depth knowledge of this quantitative trait is thus very much needed to breed more fragrant commercial cultivars. Furthermore, rose hybrids harbor a composite genomic structure, which complexifies quantitative trait studies. To understand rose scent inheritance, we characterized a segregating population from two diploid cultivars, Rosa × hybrida cv H190 and Rosa wichurana, which have contrasting scent profiles. Several quantitative trait loci for the major volatile compounds in this progeny were identified. One among these loci contributing to the production of 2-phenylethanol, responsible for the characteristic odor of rose, was found to be colocalized with a candidate gene belonging to the 2-phenylethanol biosynthesis pathway: the PHENYLACETALDEHYDE SYNTHASE gene RhPAAS An in-depth allele-specific expression analysis in the progeny demonstrated that only one allele was highly expressed and was responsible for the production of 2-phenylethanol. Unexpectedly, its expression was found to start early during flower development, before the production of the volatile 2-phenylethanol, leading to the accumulation of glycosylated compounds in petals.

The Rosa genome provides new insights into the domestication of modern roses.

Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis 'Old Blush'. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of 'La France', one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals.

The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT is a new player in the microRNA pathway.

In Arabidopsis, the F-box HAWAIIAN SKIRT (HWS) protein is important for organ growth. Loss of function of HWS exhibits pleiotropic phenotypes including sepal fusion. To dissect the HWS role, we EMS-mutagenized hws-1 seeds and screened for mutations that suppress hws-1 associated phenotypes. We identified shs-2 and shs-3 (suppressor of hws-2 and 3) mutants in which the sepal fusion phenotype of hws-1 was suppressed. shs-2 and shs-3 (renamed hst-23/hws-1 and hst-24/hws-1) carry transition mutations that result in premature terminations in the plant homolog of Exportin-5 HASTY (HST), known to be important in miRNA biogenesis, function and transport. Genetic crosses between hws-1 and mutant lines for genes in the miRNA pathway also suppress the phenotypes associated with HWS loss of function, corroborating epistatic relations between the miRNA pathway genes and HWS. In agreement with these data, accumulation of miRNA is modified in HWS loss or gain of function mutants. Our data propose HWS as a new player in the miRNA pathway, important for plant growth.

Roles of the Translationally Controlled Tumor Protein (TCTP) in Plant Development.

The Translationally Controlled Tumor Protein (TCTP) is a conserved protein which expression was associated with several biochemical and cellular functions. Loss-of-function mutants are lethal both in animals and in plants, making the identification of its exact role difficult. Recent data using the model plant Arabidopsis thaliana provided the first viable adult knockout for TCTP and helped addressing the biological role of TCTP during organ development and the functional conservation between plants and animals. This chapter summarizes our up to date knowledge about the role of TCTP in plants and discuss about conserved functions and mechanisms between plants and animals.

HAWAIIAN SKIRT controls size and floral organ number by modulating CUC1 and CUC2 expression.

The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT (HWS) affects organ growth and the timing of floral organ abscission. The loss-of-function hws-1 mutant exhibits fused sepals and increased organ size. To understand the molecular mechanisms of HWS during plant development, we mutagenized hws-1 seeds with ethylmethylsulphonate (EMS) and screened for mutations suppressing hws-1 associated phenotypes. We isolated the shs1/hws-1 (suppressor of hws-1) mutant in which hws-1 sepal fusion phenotype was suppressed. The shs1/hws-1 mutant carries a G→A nucleotide substitution in the MIR164 binding site of CUP-SHAPED COTYLEDON 1 (CUC1) mRNA. CUC1 and CUP-SHAPED COTYLEDON 2 (CUC2) transcript levels were altered in shs1, renamed cuc1-1D, and in hws-1 mutant. Genetic interaction analyses using single, double and triple mutants of cuc1-1D, cuc2-1D (a CUC2 mutant similar to cuc1-1D), and hws-1, demonstrate that HWS, CUC1 and CUC2 act together to control floral organ number. Loss of function of HWS is associated with larger petal size due to alterations in cell proliferation and mitotic growth, a role shared with the CUC1 gene.

Somatosensory Amplification Is a Predictor of Self-Reported Side Effects in the Treatment of Primary Hypertension: a Pilot Study.

PURPOSE: Side effects consist of drug-specific and non-specific symptoms. Both components are based on bodily sensations that a person perceives after taking a drug and subsequently attributes to the drug. We suggest that somatosensory amplification (SSA) may explain a proportion of inter-individual differences in reports of side effects that cannot be accounted for by drug-specific safety profiles. This hypothesis was investigated in hypertensive patients starting a new pharmacotherapy. METHOD: This longitudinal study included 50 patients (66 % women, aged 55 ± 14 years) with a diagnosis of primary hypertension. Patients completed the Somatosensory Amplification Scale (SSAS), started to take their new medication, and recorded side effects on a daily basis for 4 weeks. RESULTS: After controlling for age, gender, number of pills taken, and previous personal and family experiences with medication side effects in the regression analyses, SSAS scores remained a significant predictor of reported side effects over the entire study period (weeks 1 and 2: ß = .621, p < .001; weeks 3 and 4: ß = .493, p = .003). In a subsample comprising patients taking the four most commonly used drug regimes, SSAS was a significant predictor of side effects, even when controlling for type of medication. CONCLUSION: In this sample of patients undergoing anti-hypertensive pharmacotherapy, higher SSA scores predicted increased reports of medication side effects. To account for this tendency and to improve compliance with medication regimes, this group may require special education about the nocebo phenomenon.

Single Cell Wall Nonlinear Mechanics Revealed by a Multiscale Analysis of AFM Force-Indentation Curves.

Individual plant cells are rather complex mechanical objects. Despite the fact that their wall mechanical strength may be weakened by comparison with their original tissue template, they nevertheless retain some generic properties of the mother tissue, namely the viscoelasticity and the shape of their walls, which are driven by their internal hydrostatic turgor pressure. This viscoelastic behavior, which affects the power-law response of these cells when indented by an atomic force cantilever with a pyramidal tip, is also very sensitive to the culture media. To our knowledge, we develop here an original analyzing method, based on a multiscale decomposition of force-indentation curves, that reveals and quantifies for the first time the nonlinearity of the mechanical response of living single plant cells upon mechanical deformation. Further comparing the nonlinear strain responses of these isolated cells in three different media, we reveal an alteration of their linear bending elastic regime in both hyper- and hypotonic conditions.

A comparative mechanical analysis of plant and animal cells reveals convergence across kingdoms.

Plant and animals have evolved different strategies for their development. Whether this is linked to major differences in their cell mechanics remains unclear, mainly because measurements on plant and animal cells relied on independent experiments and setups, thus hindering any direct comparison. In this study we used the same micro-rheometer to compare animal and plant single cell rheology. We found that wall-less plant cells exhibit the same weak power law rheology as animal cells, with comparable values of elastic and loss moduli. Remarkably, microtubules primarily contributed to the rheological behavior of wall-less plant cells whereas rheology of animal cells was mainly dependent on the actin network. Thus, plant and animal cells evolved different molecular strategies to reach a comparable cytoplasmic mechanical core, suggesting that evolutionary convergence could include the internal biophysical properties of cells.

Genetic and phenotypic analyses of petal development in Arabidopsis.

The link between gene regulation/function and organ shape (morphogenesis) is poorly understood and remains one of the major issues in developmental biology. Petals are attractive model organs for studying organogenesis mainly because they have a simple laminar structure with a small number of cell types. Moreover, because petals are dispensable for plant growth and reproduction, one can experimentally manipulate petal development and dissect the genetic mechanisms behind the changes without serious effects on plant viability. Here, we describe the methods used to study petal development at the molecular, cytological, and genetic level, and more specifically mitotic and post-mitotic growth control during petal morphogenesis.

Virus-like particle vaccine induces cross-protection against human metapneumovirus infections in mice.

Human metapneumovirus (HMPV) is a paramyxovirus that causes acute respiratory-tract infections in children and adults worldwide. A safe and effective vaccine could decrease the burden of disease associated with this novel pathogen. We engineered HMPV viral-like particles (HMPV-VLPs) derived from retroviral core particles that mimic the properties of the viral surface of two HMPV viruses of either lineage A or B. These VLPs functionally display F and G HMPV surface glycoproteins. When injected in mice, HMPV-VLPs induce strong humoral immune response against both homologous and heterologous strains. Moreover, the induced neutralizing antibodies prevented mortality upon subsequent infection of the lungs with both homologous and heterologous viruses. Upon challenge, viral titers in the lungs of immunized animals were significantly reduced as compared to those of control animals. In conclusion, a HMPV-VLP vaccine that induces cross-protective immunity in mice is a promising approach to prevent HMPV infections.

Generation of transgenic mice expressing EGFP protein fused to NP68 MHC class I epitope using lentivirus vectors.

Immune tolerance to self-antigens is a complex process that utilizes multiple mechanisms working in concert to maintain homeostasis and prevent autoimmunity. Considerable progress in deciphering the mechanisms controlling the activation or deletion of T cells has been made by using T cell receptor (TCR) transgenic mice. One such model is the F5 model in which CD8 T cells express a TCR specific for an epitope derived from the influenza NP68 protein. Our aim was to create transgenic mouse models expressing constitutively the NP68 epitope fused to enhanced green fluorescent protein (EGFP) in order to assess unambiguously the relative levels of NP68 epitope expressed by single cells. We used a lentiviral-based approach to generate two independent transgenic mouse strains expressing the fusion protein EGFP-NP68 under the control of CAG (CMV immediate early enhancer and the chicken ß-actin promoter) or spleen focus-forming virus (SFFV) promoters. Analysis of the pattern of EGFP expression in the hematopoietic compartment showed that CAG and SFFV promoters are differentially regulated during T cell development. However, both promoters drove high EGFP-NP68 expression in dendritic cells (pDCs, CD8α(+) cDCs, and CD8α(-) cDCs) from spleen or generated in vitro following differentiation from bone-marrow progenitors. NP68 epitope was properly processed and successfully presented by dendritic cells (DCs) by direct presentation and cross-presentation to F5 CD8 T cells. The models presented here are valuable tools to investigate the priming of F5 CD8 T cells by different subsets of DCs.

Protection against henipavirus infection by use of recombinant adeno-associated virus-vector vaccines.

Nipah virus (NiV) and Hendra virus (HeV) are closely related, recently emerged paramyxoviruses that are capable of causing considerable morbidity and mortality in several mammalian species, including humans. Henipavirus-specific vaccines are still commercially unavailable, and development of novel antiviral strategies to prevent lethal infections due to henipaviruses is highly desirable. Here we describe the development of adeno-associated virus (AAV) vaccines expressing the NiV G protein. Characterization of these vaccines in mice demonstrated that a single intramuscular AAV injection was sufficient to induce a potent and long-lasting antibody response. Translational studies in hamsters further demonstrated that all vaccinated animals were protected against lethal challenge with NiV. In addition, this vaccine induced a cross-protective immune response that was able to protect 50% of the animals against a challenge by HeV. This study presents a new efficient vaccination strategy against henipaviruses and opens novel perspectives on the use of AAV vectors as vaccines against emergent diseases.

Nipah virus uses leukocytes for efficient dissemination within a host.

Nipah virus (NiV) is a recently emerged zoonotic paramyxovirus whose natural reservoirs are several species of Pteropus fruit bats. NiV provokes a widespread vasculitis often associated with severe encephalitis, with up to 75% mortality in humans. We have analyzed the pathogenesis of NiV infection, using human leukocyte cultures and the hamster animal model, which closely reproduces human NiV infection. We report that human lymphocytes and monocytes are not permissive for NiV and a low level of virus replication is detected only in dendritic cells. Interestingly, despite the absence of infection, lymphocytes could efficiently bind NiV and transfer infection to endothelial and Vero cells. This lymphocyte-mediated transinfection was inhibited after proteolytic digestion and neutralization by NiV-specific antibodies, suggesting that cells could transfer infectious virus to other permissive cells without the requirement for NiV internalization. In NiV-infected hamsters, leukocytes captured and carried NiV after intraperitoneal infection without themselves being productively infected. Such NiV-loaded mononuclear leukocytes transfer lethal NiV infection into naïve animals, demonstrating efficient virus transinfection in vivo. Altogether, these results reveal a remarkable capacity of NiV to hijack leukocytes as vehicles to transinfect host cells and spread the virus throughout the organism. This mode of virus transmission represents a rapid and potent method of NiV dissemination, which may contribute to its high pathogenicity.

AUXIN RESPONSE FACTOR8 regulates Arabidopsis petal growth by interacting with the bHLH transcription factor BIGPETALp.

Plant organ growth and final size are determined by coordinated cell proliferation and expansion. The BIGPETALp (BPEp) basic helix-loop-helix (bHLH) transcription factor was shown to limit Arabidopsis thaliana petal growth by influencing cell expansion. We demonstrate here that BPEp interacts with AUXIN RESPONSE FACTOR8 (ARF8) to affect petal growth. This interaction is mediated through the BPEp C-terminal domain (SD(BPEp)) and the C-terminal domain of ARF8. Site-directed mutagenesis identified an amino acid consensus motif in SD(BPEp) that is critical for mediating BPEp-ARF8 interaction. This motif shares sequence similarity with motif III of ARF and AUXIN/INDOLE-3-ACETIC ACID proteins. Petals of arf8 mutants are significantly larger than those of the wild type due to increased cell number and increased cell expansion. bpe arf8 double mutant analyses show that during early petal development stages, ARF8 and BPEp work synergistically to limit mitotic growth. During late stages, ARF8 and BPEp interact to limit cell expansion. The alterations in cell division and cell expansion observed in arf8 and/or bpe mutants are associated with a change in expression of early auxin-responsive genes. The data provide evidence of an interaction between an ARF and a bHLH transcription factor and of its biological significance in regulating petal growth, with local auxin levels likely influencing such a biological function.

Jasmonate controls late development stages of petal growth in Arabidopsis thaliana.

In Arabidopsis, four homeotic gene classes, A, B, C and E, are required for the patterning of floral organs. However, very little is known about how the activity of these master genes is translated into regulatory processes leading to specific growth patterns and the formation of organs with specific shapes and sizes. Previously we showed that the transcript variant BPEp encodes a bHLH transcription factor that is involved in limiting petal size by controlling post-mitotic cell expansion. Here we show that the phytohormone jasmonate is required for control of BPEp expression. Expression of BPEp was negatively regulated in opr3 mutant flowers that are deficient in jasmonate synthesis. Moreover, the expression of BPEp was restored in opr3 flowers following exogenous jasmonate treatments. Expression of the second transcript variant BPEub, which originates from the same gene as BPEp via an alternative splicing event, was not affected, indicating that BPEp accumulation triggered by jasmonate occurs at the post-transcriptional level. Consistent with these data, opr3 exhibited an increase in petal size as a result of increased cell size, as well as a modified vein pattern, phenotypes that are similar to those of the bpe-1 mutant. Furthermore, exogenous treatments with jasmonate rescued petal phenotypes associated with loss of function of OPR3. Our data demonstrate that jasmonate signaling downstream of OPR3 is involved in the control of cell expansion and in limiting petal size, and that BPEp is a downstream target that functions as a component mediating jasmonate signaling during petal growth.

DNA vaccination with a single-plasmid construct coding for viruslike particles protects mice against infection with a highly pathogenic avian influenza A virus.

BACKGROUND: With seasonal outbreaks affecting millions of people each year and devastating pandemics, human influenza is a major health concern. The pandemic threat includes highly pathogenic avian influenza viruses (HPAIVs) that gained the ability to infect humans in Asia and quickly spread throughout the world. Major concerns have been raised regarding today's vaccine production systems against influenza viruses, and new strategies to design efficient vaccines are under intensive investigation. METHODS: We demonstrated elsewhere that viruslike particles (VLPs) incorporating HPAIV hemagglutinin induce strong humoral immune response when injected in mice. In the current study, we evaluated a novel strategy that combines the immunogenicity of influenza VLPs and the advantages of DNA vaccines. RESULTS: We developed minimal expression vectors encoding all genetic information necessary to produce H7N1 influenza VLPs. We showed that mice vaccinated with small DNA amounts developed specific, high-titer neutralizing antibodies against homologous H7N1 strain and were protected against lethal doses of an antigenically distinct H7N7 HPAIV. Moreover, using some of these constructs, we were able to raise cross-neutralizing antibodies against an unrelated H5N1 HPAIV. CONCLUSIONS: DNA vaccination with constructs coding for influenza VLP production is a promising strategy to induce protection against different influenza viruses.