Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii.

BACKGROUND: Restorative regeneration, the capacity to reform a lost body part following amputation or injury, is an important and still poorly understood process in animals. Annelids, or segmented worms, show amazing regenerative capabilities, and as such are a crucial group to investigate. Elucidating the molecular mechanisms that underpin regeneration in this major group remains a key goal. Among annelids, the nereididae Platynereis dumerilii (re)emerged recently as a front-line regeneration model. Following amputation of its posterior part, Platynereis worms can regenerate both differentiated tissues of their terminal part as well as a growth zone that contains putative stem cells. While this regeneration process follows specific and reproducible stages that have been well characterized, the transcriptomic landscape of these stages remains to be uncovered. RESULTS: We generated a high-quality de novo Reference transcriptome for the annelid Platynereis dumerilii. We produced and analyzed three RNA-sequencing datasets, encompassing five stages of posterior regeneration, along with blastema stages and non-amputated tissues as controls. We included two of these regeneration RNA-seq datasets, as well as embryonic and tissue-specific datasets from the literature to produce a Reference transcriptome. We used this Reference transcriptome to perform in depth analyzes of RNA-seq data during the course of regeneration to reveal the important dynamics of the gene expression, process with thousands of genes differentially expressed between stages, as well as unique and specific gene expression at each regeneration stage. The study of these genes highlighted the importance of the nervous system at both early and late stages of regeneration, as well as the enrichment of RNA-binding proteins (RBPs) during almost the entire regeneration process. CONCLUSIONS: In this study, we provided a high-quality de novo Reference transcriptome for the annelid Platynereis that is useful for investigating various developmental processes, including regeneration. Our extensive stage-specific transcriptional analysis during the course of posterior regeneration sheds light upon major molecular mechanisms and pathways, and will foster many specific studies in the future.

The success of the bloom-forming cyanobacteria Planktothrix: Genotypes variability supports variable responses to light and temperature stress.

Cyanobacterial blooms can modify the dynamic of aquatic ecosystems and have harmful consequences for human activities. Moreover, cyanobacteria can produce a variety of cyanotoxins, including microcystins, but little is known about the role of environmental factors on the prevalence of microcystin producers in the cyanobacterial bloom dynamics. This study aimed to better understand the success of Planktothrix in various environments by unveiling the variety of strategies governing cell responses to sudden changes in light intensity and temperature. The cellular responses (photosynthesis, photoprotection, heat shock response and metabolites synthesis) of four Planktothrix strains to high-light or high-temperature were studied, focusing on how distinct ecotypes (red- or green-pigmented) and microcystin production capability affect cyanobacteria's ability to cope with such abiotic stimuli. Our results showed that high-light and high-temperature impact different cellular processes and that Planktothrix responses are heterogeneous, specific to each strain and thus, to genotype. The ability of cyanobacteria to cope with sudden increase in light intensity and temperature was not related to red- or green-pigmented ecotype or microcystin production capability. According to our results, microcystin producers do not cope better to high-light or high-temperature and microcystin content does not increase in response to such stresses.

Development of a new extraction method based on high-intensity ultra-sonication to study RNA regulation of the filamentous cyanobacteria Planktothrix.

Efficient RNA extraction methods are needed to study transcript regulation. Such methods must lyse the cell without degrading the genetic material. For cyanobacteria this can be particularly challenging because of the presence of the cyanobacteria cell envelope. The great breath of cyanobacterial shape and size (unicellular, colonial, or filamentous multicellular) created a variety of cell lysis methods. However, there is still a lack of reliable techniques for nucleic acid extraction for several types of cyanobacteria. Here we designed and tested 15 extraction methods using physical, thermic or chemical stress on the filamentous cyanobacteria Planktothrix agardhii. Techniques based on the use of beads, sonication, and heat shock appeared to be too soft to break the Planktothrix agardhii cell envelope, whereas techniques based on the use of detergents degraded the cell envelope but also the RNA. Two protocols allowed to successfully obtain good-quality RNA. The first protocol consisted to manually crush the frozen cell pellet with a pestle and the second was based on the use of high-intensity ultra-sonication. When comparing these two, the high-intensity ultra-sonication protocol was less laborious, faster and allowed to extract 3.5 times more RNA compared to the liquid nitrogen pestle protocol. The high-intensity ultra-sonication protocol was then tested on five Planktothrix strains, this protocol allowed to obtain >8.5 µg of RNA for approximatively 3.5 × 108 cells. The extracted RNA were characterized by 260/280 and 260/230 ratio > to 2, indicating that the samples were devoid of contaminant, and RNA Quality Number > to 7, meaning that the integrity of RNA was preserved with this extraction method. In conclusion, the method we developed based on high-intensity ultra-sonication proved its efficacy in the extraction of Planktothrix RNA and could be helpful for other types of samples.

Application of a spectrofluorimetric tool (bbe BenthoTorch) for monitoring potentially toxic benthic cyanobacteria in rivers.

Over the last decade reports of animal poisoning following accidental consumption of neurotoxin-producing benthic cyanobacteria (mainly Phormidium spp.) have increased. There is a need for rapid and cost-effective tools to survey benthic cyanobacteria. In this study we assessed the performance of the BenthoTorch, a fluorometric probe that provides in situ estimations of cyanobacteria, diatoms and green algae biomass in biofilms. Biofilms (n = 288) were analysed from two rivers in France and eight in New Zealand. Correlations between chlorophyll-a measured using the BenthoTorch and spectrophotometry were higher for thin (<2 mm) compared to thick (>2 mm) biofilms (r(2) = 0.58 and 0.27 respectively; p < 0.001). When cyanobacteria represented less than 50% of the total biomass (based on biovolumes), microscopic and BenthoTorch compositional estimations were significantly correlated (r(2) = 0.53, p < 0.001). Conversely, there was no correlation when cyanobacteria exceeded 50% of the total biomass. Under this scenario diatoms were overestimated. Our results suggest that the observed biases occur because the BenthoTorch only measures the upper biofilm layer and it underestimates the biomass of phycoerythrin-containing cyanobacteria. To improve the performance of this sensor and render it a useful tool for a rapid evaluation of benthic cyanobacterial biomass in rivers, we propose that: (i) the algorithms based on the LEDs responses currently available on this tool need revision, (ii) new excitation wavelengths should be included that allow the fingerprints of phycoerythrin-containing cyanobacteria to be discriminated, and (iii) a sensor that penetrates the biofilms is needed to obtain more accurate estimates of cyanobacterial biomass.

Observational case series on adalimumab-induced paradoxical hidradenitis suppurativa.

INTRODUCTION: Although the efficacy of TNF blockers has been demonstrated in hidradenitis suppurativa (HS), many paradoxical effects have also been described with TNF antagonists. We wished to describe patients with adalimumab (ADA)-induced paradoxical HS. METHODS: This is a retrospective descriptive case series of four patients with ADA-induced paradoxical HS. RESULTS: All the patients had a good response to TNFa antagonist therapy at the time of HS occurrence. The time from TNFa antagonist initiation to HS onset or exacerbation ranged from a few weeks to 24 months. The outcome of HS was variable. Systemic antibiotics were required in all the cases to control HS. TNF blockers were continued in three cases with a switch to another anti-TNF class in one case. Switch to ustekinumab was prescribed in one patient with SA and Crohn's disease. CONCLUSION: Although the imputability of TNF blockers in paradoxical HS is still debatable, further research and observation are needed to confirm and distinguish patients with genetic and clinical predisposition in the onset or exacerbation of HS during anti-TNF treatment.

Sentinel lymph node biopsy in melanoma: our 8-year clinical experience in a single French institute (2002-2009).

BACKGROUND: Since the introduction of sentinel lymph node biopsy (SLNB), its use as a standard of care for patients with clinically node-negative cutaneous melanoma remains controversial. We wished to evaluate our experience of SLNB for melanoma. METHODS: A single center observational cohort of 203 melanoma patients with a primary cutaneous melanoma (tumour thickness > 1 mm) and without clinical evidence of metastasis was investigated from 2002 to 2009. Head and neck melanoma were excluded. SLN was identified following preoperative lymphoscintigraphy and intraoperative gamma probe interrogation. RESULTS: The SLN identification rate was 97%. The SLN was tumor positive in 44 patients (22%). Positive SLN was significantly associated with primary tumor thickness and microscopic ulceration. The median follow-up was 39.5 (5-97) months. Disease progression was significantly more frequent in SLN positive patients (32% vs 13%, p = 0.002). Five-year DFS and OS of the entire cohort were 79.6% and 84.6%, respectively, with a statistical significant difference between SLN positive (58.7% and 69.7%) and SLN negative (85% and 90.3%) patients (p = 0.0006 and p = 0.0096 respectively). Postoperative complications after SLNB were observed in 12% of patients. CONCLUSION: Our data confirm previous studies and support the clinical usefulness of SLNB as a reliable and accurate staging method in patients with cutaneous melanoma. However, the benefit of additional CLND in patients with positive SLN remains to be demonstrated.