NanoJ: a high-performance open-source super-resolution microscopy toolbox

Super-resolution microscopy (SRM) has become essential for the study of nanoscale biological processes. This type of imaging often requires the use of specialised image analysis tools to process a large volume of recorded data and extract quantitative information. In recent years, our team has built an open-source image analysis framework for SRM designed to combine high performance and ease of use. We named it NanoJ—a reference to the popular ImageJ software it was developed for. In this paper, we highlight the current capabilities of NanoJ for several essential processing steps: spatio-temporal alignment of raw data (NanoJ-Core), super-resolution image reconstruction (NanoJ-SRRF), image quality assessment (NanoJ-SQUIRREL), structural modelling (NanoJ-VirusMapper) and control of the sample environment (NanoJ-Fluidics). We expect to expand NanoJ in the future through the development of new tools designed to improve quantitative data analysis and measure the reliability of fluorescent microscopy studies

Crenarchaeal CdvA Forms Double-Helical Filaments Containing DNA and Interacts with ESCRT-III-Like CdvB

International audienceBACKGROUND: The phylum Crenarchaeota lacks the FtsZ cell division hallmark of bacteria and employs instead Cdv proteins. While CdvB and CdvC are homologues of the eukaryotic ESCRT-III and Vps4 proteins, implicated in membrane fission processes during multivesicular body biogenesis, cytokinesis and budding of some enveloped viruses, little is known about the structure and function of CdvA. Here, we report the biochemical and biophysical characterization of the three Cdv proteins from the hyperthermophilic archaeon Metallospherae sedula. METHODOLOGY/PRINCIPAL FINDINGS: Using sucrose density gradient ultracentrifugation and negative staining electron microscopy, we evidenced for the first time that CdvA forms polymers in association with DNA, similar to known bacterial DNA partitioning proteins. We also observed that, in contrast to full-lengh CdvB that was purified as a monodisperse protein, the C-terminally deleted CdvB construct forms filamentous polymers, a phenomenon previously observed with eukaryotic ESCRT-III proteins. Based on size exclusion chromatography data combined with detection by multi-angle laser light scattering analysis, we demonstrated that CdvC assembles, in a nucleotide-independent way, as homopolymers resembling dodecamers and endowed with ATPase activity in vitro. The interactions between these putative cell division partners were further explored. Thus, besides confirming the previous observations that CdvB interacts with both CdvA and CdvC, our data demonstrate that CdvA/CdvB and CdvC/CdvB interactions are not mutually exclusive. CONCLUSIONS/SIGNIFICANCE: Our data reinforce the concept that Cdv proteins are closely related to the eukaryotic ESCRT-III counterparts and suggest that the organization of the ESCRT-III machinery at the Crenarchaeal cell division septum is organized by CdvA an ancient cytoskeleton protein that might help to coordinate genome segregation

A unique cell division machinery in the Archaea

In contrast to the cell division machineries of bacteria, euryarchaea, and eukaryotes, no division components have been identified in the second main archaeal phylum, Crenarchaeota. Here, we demonstrate that a three-gene operon, cdv, in the crenarchaeon Sulfolobus acidocaldarius, forms part of a unique cell division machinery. The operon is induced at the onset of genome segregation and division, and the Cdv proteins then polymerize between segregating nucleoids and persist throughout cell division, forming a successively smaller structure during constriction. The cdv operon is dramatically down-regulated after UV irradiation, indicating division inhibition in response to DNA damage, reminiscent of eukaryotic checkpoint systems. The cdv genes exhibit a complementary phylogenetic range relative to FtsZ-based archaeal division systems such that, in most archaeal lineages, either one or the other system is present. Two of the Cdv proteins, CdvB and CdvC, display homology to components of the eukaryotic ESCRT-III sorting complex involved in budding of luminal vesicles and HIV-1 virion release, suggesting mechanistic similarities and a common evolutionary origin

Tra risultati scientifici, radici ideologiche e orizzonti culturali condivisi. Un\u2019analisi culturale della ricerca scientifica in Media Education (versione italiana)

L'articolo riflette sulle iscrizioni \u201cideologiche\u201d della ricerca scientifica in Media Education. - Sulla scorta degli studi culturali anglosassoni , adotta l'approccio che l\u2019educazione ai media da sempre applica allo studio dei media e dei loro testi: l\u2019analisi critica e la decostruzione dei dispositivi retorici del testo. In questo caso i testi oggetto di analisi sono: alcuni classici dispositivi metodologici tipicamente usati nelle ricerche in Media education(i.e. le griglie utilizzate per l'analisi comparativa dei contenuti televisivi) e alcuni risultati ormai stabilizzati della ricerca in questo settore (i.e. la desensibilizzazione come effetto dell'esposizione protratta alla violenza rappresentata). La meta analisi di metodi e risultati della ricerca nel settore (intesi come dispositivi discorsivi) rivela la radice inevitabilmente ideologica di questa (come altre) impresa scientifica. Al di l\ue0 delle misure di controllo utilizzate (intercorder agreement, significativit\ue0 statistica, etc..), anche solo tratti considerati pertinenti e distintivi rispetto alla descrizione dei contenuti mediatici ma anche le parole utilizzate per descrivere i risultati delle ricerche rivelano quanto la ricerca stessa sia dipendente da assunti, idee, rappresentazioni del tutto culturali circa fenomeni quali "intelligenza", "identit\ue0", "genere" , ma anche da precise idee per nulla scientifiche circa ci\uf2 che \ue9 auspicabile e ci\uf2 che non lo \ue9 rispetto allo sviluppo dei bambini. Questa meta analisi consente di mostrare che la ricerca in questo ambito, persino quella a carattere "puramente" descrittivo o rigorosamente sperimentale, non \ue9 value & context-free. Essa si radica in un orizzonte morale e dipende dai punti di vista e valori inscrutti nei dispositivi discorsivi condivisi e legittimati dalla comunit\ue0 scientifica

Management of the neck in the setting of definitive chemoradiation: Is there a consensus? A GETTEC study

Background. The management of the neck remains controversial in the definitive chemoradiation setting of advanced N2-3 head and neck squamous cell carcinoma. Most published data favor omission of neck dissection (ND) after complete response for N2-3 or selective ND for residual disease Methods. We studied the patterns of care in the French-Belgian Groupe d'Etude des Tumeurs de la Tête Et du Cou (GETTEC) through a questionnaire-based survey. Results. Eighteen percent of institutions never performed up-front ND, 20% rarely, 40% sometimes, 14% often, and 8% systematically. Induction chemotherapy was indicated in 30% of the cases, and most ND were performed either between induction and radiation or after chemoradiation for residual disease. Response to chemoradiation was assessed by computed tomographic scan and positron emission tomography in 72% of cases. Selective ND was more common than radical ND. Conclusions. Omission of ND based on computed tomographic scan and positron emission tomography-based complete response to chemoradiation is the most common strategy for advanced nodal disease among centers. However, neck management strategies vary among institutions, and some institutions continue advocating systematic ND before irradiation. The new treatment options and the changing epidemiology, namely docetaxel-based induction chemotherapy and human papilloma virus-related head and neck squamous cell carcinoma having better response profiles and prognosis, are adding to the nonconsensual approach. The best therapeutic index in terms of neck management remains to be defined in this evolving context. © 2012 Society of Surgical Oncology