Contrived Materials and a Data Set for the Evaluation of Liquid Biopsy Tests: A Blood Profiling Atlas in Cancer (BLOODPAC) Community Study.

The Blood Profiling Atlas in Cancer (BLOODPAC) Consortium is a collaborative effort involving stakeholders from the public, industry, academia, and regulatory agencies focused on developing shared best practices on liquid biopsy. This report describes the results from the JFDI (Just Freaking Do It) study, a BLOODPAC initiative to develop standards on the use of contrived materials mimicking cell-free circulating tumor DNA, to comparatively evaluate clinical laboratory testing procedures. Nine independent laboratories tested the concordance, sensitivity, and specificity of commercially available contrived materials with known variant-allele frequencies (VAFs) ranging from 0.1% to 5.0%. Each participating laboratory utilized its own proprietary evaluation procedures. The results demonstrated high levels of concordance and sensitivity at VAFs of >0.1%, but reduced concordance and sensitivity at a VAF of 0.1%; these findings were similar to those from previous studies, suggesting that commercially available contrived materials can support the evaluation of testing procedures across multiple technologies. Such materials may enable more objective comparisons of results on materials formulated in-house at each center in multicenter trials. A unique goal of the collaborative effort was to develop a data resource, the BLOODPAC Data Commons, now available to the liquid-biopsy community for further study. This resource can be used to support independent evaluations of results, data extension through data integration and new studies, and retrospective evaluation of data collection.

RUNX1 deficiency cooperates with SRSF2 mutation to induce multilineage hematopoietic defects characteristic of MDS.

Myelodysplastic syndromes (MDSs) are a heterogeneous group of hematologic malignancies with a propensity to progress to acute myeloid leukemia. Causal mutations in multiple classes of genes have been identified in patients with MDS with some patients harboring more than 1 mutation. Interestingly, double mutations tend to occur in different classes rather than the same class of genes, as exemplified by frequent cooccurring mutations in the transcription factor RUNX1 and the splicing factor SRSF2. This prototypic double mutant provides an opportunity to understand how their divergent functions in transcription and posttranscriptional regulation may be altered to jointly promote MDS. Here, we report a mouse model in which Runx1 knockout was combined with the Srsf2 P95H mutation to cause multilineage hematopoietic defects. Besides their additive and synergistic effects, we also unexpectedly noted a degree of antagonizing activity of single mutations in specific hematopoietic progenitors. To uncover the mechanism, we further developed a cellular model using human K562 cells and performed parallel gene expression and splicing analyses in both human and murine contexts. Strikingly, although RUNX1 deficiency was responsible for altered transcription in both single and double mutants, it also induced dramatic changes in global splicing, as seen with mutant SRSF2, and only their combination induced missplicing of genes selectively enriched in the DNA damage response and cell cycle checkpoint pathways. Collectively, these data reveal the convergent impact of a prototypic MDS-associated double mutant on RNA processing and suggest that aberrant DNA damage repair and cell cycle regulation critically contribute to MDS development.

Association of rhizobia with a marine polychaete.

We report the presence of Mesorhizobium, a genus best known for its nitrogen-fixing symbiosis with terrestrial legumes, associated with the marine polychaete Meganerilla bactericola (Annelida: Nerillidae). Abundant epibionts were previously described as coating the exterior of M. bactericola, which is found within the anoxic sulfide-oxidizing microbial mats of the Santa Barbara Basin, California, USA. 16S rRNA investigation of the bacterial community associated with this polychaete discovered the presence of bacteria belonging to Mesorhizobium. We identified these bacteria using phylogenetic analyses of 16S rRNA and three additional functional genes, nifH, atpD and recA, and group-specific fluorescence in situ hybridization (FISH).

How to get into bones: proton pump and carbonic anhydrase in Osedax boneworms.

Osedax are gutless siboglinid worms that thrive on vertebrate bones lying on the ocean floor, mainly those of whales. The posterior body of female Osedax penetrates into the bone forming extensions known as 'roots', which host heterotrophic symbiotic bacteria in bacteriocytes beneath the epidermis. The Osedax root epithelium presumably absorbs bone collagen and/or lipids, which are metabolized by the symbiotic bacteria that in turn serve for Osedax's nutrition. Here, we show that Osedax roots express extremely high amounts of vacuolar-H(+)-ATPase (VHA), which is located in the apical membrane and in cytoplasmic vesicles of root and ovisac epithelial cells. The enzyme carbonic anhydrase (CA), which catalyses the hydration of CO2 into H(+) and HCO3(-), is also expressed in roots and throughout Osedax body. These results suggest Osedax roots have massive acid-secreting capacity via VHA, fuelled by H(+) derived from the CA-catalysed hydration of CO2 produced by aerobic metabolism. We propose the secreted acid dissolves the bone carbonate matrix to then allow the absorption of bone-derived nutrients across the skin. In an exciting example of convergent evolution, this model for acid secretion is remarkably similar to mammalian osteoclast cells. However, while osteoclasts dissolve bone for repairing and remodelling, the Osedax root epithelium secretes acid to dissolve foreign bone to access nutrients.

The reproductive system of Osedax (Annelida, Siboglinidae): ovary structure, sperm ultrastructure, and fertilization mode.

Osedax is a genus of siboglinid annelids in which the females live on dead vertebrate bones on the seafloor. These females have a posterior end that lies within the bone and contains the ovarian tissue, as well as the "roots" involved with bone degradation and nutrition. The males are microscopic and live as "harems" in the lumen of the gelatinous tube that surrounds the female trunk, well away from the ovary. Females are known to spawn fertilized primary oocytes, suggesting internal fertilization. However, little is known about sperm transfer, sperm storage, or the location of fertilization, and the morphology of the female reproductive system has not been described and compared with the reproductive systems of other siboglinids. A 3D-reconstruction of the ovisac of Osedax showed ovarian tissue with multiple lobes and mature oocytes stored in a "uterus" before being released through the single oviduct. The oviduct emerges as a gonopore on the trunk and travels along the trunk to finally open to the seawater as a thin cylindrical tube among the crown of palps. Light and transmission electron microscopy of mature Osedax sperm revealed elongate heads consisting of a nucleus with helical grooves occupied by mitochondria. In contrast to other Siboglinidae, Osedax sperm are not packaged into spermatophores or spermatozeugmata, and Osedax females lack a discrete region for sperm storage. Transmission electron microscopy and fluorescence microscopy allowed detection of sperm associated with ovarian tissue of the female ovisac of four different Osedax species. This provides the first evidence for the site of internal fertilization in Osedax. A heart body was found in the circulatory system, as seen in other siboglinids and some other annelids. The possible presence of nephridia in the anterior ovisac region was also documented. These morphological features provide new insights for comparing the regionalization of Osedax females in relation to other siboglinids.

The Osedax trophosome: organization and ultrastructure.

The polychaete family Siboglinidae, which is currently construed as comprising the Frenulata, Monilifera (composed of Sclerolinum), Vestimentifera, and Osedax, has become known for its specialized symbiont-housing organ called the trophosome. This organ replaced the digestive system of the worms and is located in the elongated trunk region in Frenulata, Sclerolinum, and Vestimentifera. Currently two types of trophosomes have been described: in the taxa Frenulata and Sclerolinum the bacteriocytes originate from endoderm, and in Vestimentifera they originate from mesoderm. In Osedax, a trophosome was described as lacking (Rouse et al., 2004), but bacteriocytes are located in Osedax's characteristic root tissue. Here, we argue for a consistent name for the symbiont-housing tissue, namely trophosome, as in other siboglinids. In this study we provide morphological evidence that in Osedax the bacteriocytes are derived from somatic mesoderm. We show that the trophosome in Osedax is an apolar tissue composed of bacteriocytes and nonsymbiotic cells. As in vestimentiferans, a specific cell cycle was identified; however, in this case it is directed from the posterior to the anterior end of the worms instead of from the center toward the periphery. Comparison of all siboglinid trophosomes and re-evaluation of their body regions allows us to discuss whether the trophosomes are homologous and to hypothesize about the organization of the last common ancestor of Siboglinidae.

The skin of Osedax (Siboglinidae, Annelida): an ultrastructural investigation of its epidermis.

The symbiotic polychaetes of the genus Osedax living on the bones of whale carcasses have become known as bone-eating worms. It is believed that whale bones are the source of nutrition for those gutless worms and that fatty acids are produced by their symbionts and transferred to the host. However, the symbionts are of the heterotrophic group Oceanospirillales and as such are not able to synthesize organic carbon de novo. Also, they are not housed in close contact to the bone material. We studied the ultrastructure of the integument overlying the symbiont housing trophosome in the ovisac region and the roots region and of the symbiont-free trunk region of Osedax to investigate the host's possible contribution in feeding for the whole symbiosis. The epidermis differs conspicuously between the three regions investigated and clearly points to being correlated with different functions carried out by those regions. The ultrastructure of the integument of the root region changed towards the ovisac region and corresponds with the change of the ultrastructure observed in the Osedax trophosome. We suggest that the epidermis in the root region is tightly linked to bone degradation and nutrient uptake. The trunk region possess two types of unicellular gland cells, at least one of which seems to be involved in secretion of the gelatinous tube of adult Osedax females.

The effects of sulphide on growth and behaviour of the thiotrophic Zoothamnium niveum symbiosis.

Zoothamnium niveum (Ciliophora, Oligohymenophora) is a giant, colonial marine ciliate from sulphide-rich, shallow-water habitats, obligatorily associated with the ectosymbiotic, chemoautotrophic, sulphide-oxidizing bacterium 'Candidatus Thiobios zoothamnicoli'. The aims of this study were to characterize the natural habitat and investigate growth, reproduction, survival and maintenance of the symbiosis from Corsica, France (Mediterranean Sea) using a flow-through respirometer providing stable chemical conditions. We were able to successfully cultivate the Z. niveum symbiosis during its entire lifespan and document reproduction, whereby the optimum conditions were found to range from 3 to 33 micromol l(-1) sigmaH2S in normoxic seawater. Starting with an inoculum of 13 specimens, we found up to 173 new specimens that were asexually produced after only 11 days. Observed mean lifespan of the Z. niveum colonies was approximately 11 days and mean colony size reached 51 branches, from which rapid host division rates of up to every 4.1 hours were calculated. Comparing the ectosymbiotic population from Z. niveum colonies collected from their natural habitat with those cultivated under optimal conditions, we found significant differences in the bacterial morphology and the frequency of dividing cells on distinct host parts, which is most likely caused by behaviour of the host ciliate. Applying different sulphide concentrations we revealed that the symbiosis was not able to survive without sulphide and was harmed by high sulphide conditions. To our knowledge, this study reports the first successful cultivation of a thiotrophic ectosymbiosis.