PlanMine 3.0-improvements to a mineable resource of flatworm biology and biodiversity

Flatworms (Platyhelminthes) are a basally branching phylum that harbours a wealth of fascinating biology, including planarians with their astonishing regenerative abilities and the parasitic tape worms and blood flukes that exert a massive impact on human health. PlanMine (http://planmine.mpi-cbg.de/) has the mission objective of providing both a mineable sequence repository for planarians and also a resource for the comparative analysis of flatworm biology. While the original PlanMine release was entirely based on transcriptomes, the current release transitions to a more genomic perspective. Building on the recent availability of a high quality genome assembly of the planarian model species Schmidtea mediterranea, we provide a gene prediction set that now assign existing transcripts to defined genomic coordinates. The addition of recent single cell and bulk RNA-seq datasets greatly expands the available gene expression information. Further, we add transcriptomes from a broad range of other flatworms and provide a phylogeny-aware interface that makes evolutionary species comparisons accessible to non-experts. At its core, PlanMine continues to utilize the powerful InterMine framework and consistent data annotations to enable meaningful inter-species comparisons. Overall, PlanMine 3.0 thus provides a host of new features that makes the fascinating biology of flatworms accessible to the wider research community.

The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea

In multicellular organisms, cell type diversity and fate depend on specific sets of transcript isoforms generated by post-transcriptional RNA processing. Here, we used Schmidtea mediterranea, a flatworm with extraordinary regenerative abilities and a large pool of adult stem cells, as an in vivo model to study the role of Uridyl-rich small nuclear RNAs (UsnRNAs), which participate in multiple RNA processing reactions including splicing, in stem cell regulation. We characterized the planarian UsnRNA repertoire, identified stem cell-enriched variants and obtained strong evidence for an increased rate of UsnRNA 3'-processing in stem cells compared to their differentiated counterparts. Consistently, components of the Integrator complex showed stem cell-enriched expression and their depletion by RNAi disrupted UsnRNA processing resulting in global changes of splicing patterns and reduced processing of histone mRNAs. Interestingly, loss of Integrator complex function disrupted both stem cell maintenance and regeneration of tissues. Our data show that the function of the Integrator complex in UsnRNA 3'-processing is conserved in planarians and essential for maintaining their stem cell pool. We propose that cell type-specific modulation of UsnRNA composition and maturation contributes to in vivo cell fate choices, such as stem cell self-renewal in planarians.

Monocyte enrichment from leukapharesis products for the generation of DCs by plastic adherence, or by positive or negative selection

BACKGROUND

DCs for use in immunotherapy are frequently generated from peripheral blood monocytes. However, there are different approaches to monocyte enrichment.

METHOD

Plastic adherence is a widely used method for the enrichment of monocytes collected in a leukapheresis procedure. Alternatively,monocytes may be enriched by positive selection using magnetic beads coupled to CD14 Abs, or by cell depletion using beads coupled to Abs against CD2 and CD19 to remove non-monocytes.

RESULTS

Positive selection resulted in the highest purity of immature DCs (97 +/- 1%), but in a low yield (8 +/- 3%). In contrast, depletion of non-monocytes gave a good yield (21 +/- 6%), but insufficient purity (42 +/- 10%). Conventional adherence procedures resulted in a good yield (25 +/- 5%) and reasonable purity (72 +/- 4%). All three monocyte enrichment procedures resulted in DCs that underwent maturation upon exposure to a combination of lipopolysaccharide and IFN-gamma. These DCs had a typical immune phenotype, they released similar amounts of IL-12, and had the capacity to support MLR.

CONCLUSION

Our data provide a basis to choose a monocyte enrichment procedure that favors high purity or a high yield. However, if a manual open system suffices, plastic adherence is a reasonable alternative.

Farm and personal characteristics of the clientele of a community-based animal-health service programme in northern Malawi

The social background, farm characteristics, indicators of income and self-evaluation returns of 96 randomly selected users of a Basic Animal Health Service (BAHS) programme in northern Malawi were compared with those of 96 matched past-users and 96 non-users, respectively. All 288 farms were visited between July and October 1997. Data analysis was performed using univariate and multivariate techniques. The results showed that, on average, BAHS users had larger cattle herds (16.3) than part-users (14.7) or non-users (12.4). Similarly, the annual yields of crops were higher for users compared to either of the other groups. Users occupied better houses and owned a larger number of farm and household items than did part-users or non-users. A third of all farmers were engaged in additional income generation to lessen the risk of poverty. However, analysis of the livestock management and the educational background of the farmers suggested that usage of the BAHS programme was not only determined by already existing 'wealth'. Improved livestock husbandry and management measures, which do not require capital investment, were more frequently applied by users compared to either of the other groups. Non-users and part-users had attained a lower level of education, were less open towards improved farming methods and felt less knowledgeable than BAHS users. The average straight-line distances from farms using BAHS to their respective village animal health worker (2.2 km) or veterinary assistant (2.9 km) were similar but varied according to ecological zone. Intensified extension and awareness meetings in villages will be required to get more non-users involved in BAHS.

Characteristics and performance of village animal health workers and veterinary assistants in northern Malawi

Fourty-two village animal health workers called keymen (KM) and 84 veterinary assistants (VA) involved in a Basic Animal Health Service (BAHS) Programme in northern Malawi were interviewed during 1998. The general characteristics and perceptions of both groups were analysed using uni- and multivariate techniques. Detailed sales and treatment patterns of six KM and 12 VA were evaluated for the period September 1996 to August 1997. Results indicated an overall job-satisfaction for 82% of KM and 83 % of VA. Estimated weekly involvement in livestock service delivery, particularly of KM, was 3.7 days on average. Total annual drug sales of KM and VA between 1996 and 1997 on average were equivalent to US$ 124 and US$ 218 respectively. Most livestock remedies were issued for treatment of calves, followed by adult cattle, chickens and small ruminants. The changes suggested by VA and KM in order to improve field performance focused on regular refresher training by the BAHS programme.

Comparison between a live and an inactivated vaccine against Newcastle disease in village chickens. A field study in northern Malawi

A total of 156 chickens in two villages in Malawi were marked and sampled. One hundred and fifteen of these were vaccinated against Newcastle disease immediately after blood sampling, using the V4 heat-resistant strain applied by eye-drop in one village and the inactivated Newcavac vaccine in the other village. A second blood sample was collected 4 weeks after vaccination. The samples were examined using an indirect ELISA test kit. The titre group median ranged from 2 to 3 before vaccination. Both vaccines led to a positive immune response. Newcavac induced higher and more homogeneous titres compared with the V4 vaccine. There was also an increase in the median of the control group where V4 live vaccine had been applied. The differences between the median titres induced by V4, Newcavac and controls were statistically significant.