BacStalk: A comprehensive and interactive image analysis software tool for bacterial cell biology

Prokaryotic cells display a striking subcellular organization. Studies of the underlying mechanisms in different species have greatly enhanced our understanding of the morphological and physiological adaptation of bacteria to different environmental niches. The image analysis software tool BacStalk is designed to extract comprehensive quantitative information from the images of morphologically complex bacteria with stalks, flagella, or other appendages. The resulting data can be visualized in interactive demographs, kymographs, cell lineage plots, and scatter plots to enable fast and thorough data analysis and representation. Notably, BacStalk can generate demographs and kymographs that display fluorescence signals within the two-dimensional cellular outlines, to accurately represent their subcellular location. Beyond organisms with visible appendages, BacStalk is also suitable for established, non-stalked model organisms with common or uncommon cell shapes. BacStalk, therefore, contributes to the advancement of prokaryotic cell biology and physiology, as it widens the spectrum of easily accessible model organisms and enables highly intuitive and interactive data analysis and visualization.     

Systematic review and meta-analysis of PIT tagging effects on mortality and growth of juvenile salmonids

Reviews in Fish Biology and Fisheries - A systematic review and meta-analysis was conducted to evaluate the appropriate tag:fish size ratio when tagging juvenile salmonids (genera Oncorhynchus,...     

Growth-enhanced salmon modify stream ecosystem functioning

Use of fast-growing domesticated and/or genetically modified strains of fish is becoming increasingly common in aquaculture, increasing the likelihood of deliberate or accidental introductions into the wild. To date, their ecological impacts on ecosystems remain to be quantified. Here, using a controlled phenotype manipulation by implanting growth hormone in juvenile Atlantic salmon (Salmo salar), we found that growth-enhanced fish display changes in several phenotypic traits known to be important for ecosystem functioning, such as habitat use, morphology and excretion rate. Furthermore, these phenotypic changes were associated with significant impacts on the invertebrate community and key stream ecosystem functions such as primary production and leaf-litter decomposition. These findings provide novel evidence that introductions of growth-enhanced fish into the wild can affect the functioning of natural ecosystems and represent a form of intraspecific invasion. Consequently, environmental impact assessments of growth-enhanced organisms need to explicitly consider ecosystem-level effects.     

Lake morphometry determines Dreissena invasion dynamics

Predicting the ecosystem effects of invasive species and the best control strategies requires understanding population dynamics and population regulation. Invasive bivalves zebra and quagga mussels (Dreissena spp.) are considered the most aggressive invaders in freshwaters and have become major drivers of ecosystem processes in the Laurentian Great Lakes. Combining all lake-wide studies of Dreissena spp. conducted in the Great Lakes, we found that invasion dynamics are largely governed by lake morphometry. Where both species are present, quagga mussels generally become dominant in 8–13 years. Thereafter, zebra mussels remain common in shallow lakes and embayments and lake-wide Dreissena density may remain similar, while in deep lakes quagga led to a near-complete displacement of zebra mussels and an ensuing dramatic increase in overall dreissenid density. In deep lakes, overall Dreissena biomass peaked later and achieved?~?threefold higher levels than in shallow lakes. Comparison with 21 waterbodies in North America and Europe colonized by both dreissenids confirmed that patterns of invasion dynamics found in the Great Lakes are very consistent with other waterbodies, and thus can be generalized to other lakes. Our biophysical model predicted that the long-term reduction in primary producers by mussel grazing may be fourfold less in deep compared to shallow lakes due to thermal stratification and a smaller proportion of the epilimnion in contact with the bottom. While this impact remains greatest in shallow areas, we show that when lakes are vertically well-mixed, dreissenid grazing impact may be greatest offshore, revealing a potentially strong offshore carbon and phosphorus sink.

     

Production of phosphatidylinositol 5‐phosphate via PIKfyve and MTMR3 regulates cell migration

Although phosphatidylinositol 5‐phosphate (PtdIns5P) is present in many cell types and its biogenesis is increased by diverse stimuli, its precise cellular function remains elusive. Here we show that PtdIns5P levels increase when cells are stimulated to move and we find PtdIns5P to promote cell migration in tissue culture and in a Drosophila in vivo model. First, class III phosphatidylinositol 3‐kinase, which produces PtdIns3P, was shown to be involved in migration of fibroblasts. In a cell migration screen for proteins containing PtdIns3P‐binding motifs, we identified the phosphoinositide 5‐kinase PIKfyve and the phosphoinositide 3‐phosphatase MTMR3, which together constitute a phosphoinositide loop that produces PtdIns5P via PtdIns(3,5)P₂. The ability of PtdIns5P to stimulate cell migration was demonstrated directly with exogenous PtdIns5P and a PtdIns5P‐producing bacterial enzyme. Thus, the identified phosphoinositide loop defines a new role for PtdIns5P in cell migration.     

Therapeutic vaccination against autologous cancer stem cells with mRNA-transfected dendritic cells in patients with glioblastoma

Background

The growth and recurrence of several cancers appear to be driven by a population of cancer stem cells (CSCs). Glioblastoma, the most common primary brain tumor, is invariably fatal, with a median survival of approximately 1 year. Although experimental data have suggested the importance of CSCs, few data exist regarding the potential relevance and importance of these cells in a clinical setting.

Methods

We here present the first seven patients treated with a dendritic cell (DC)-based vaccine targeting CSCs in a solid tumor. Brain tumor biopsies were dissociated into single-cell suspensions, and autologous CSCs were expanded in vitro as tumorspheres. From these, CSC-mRNA was amplified and transfected into monocyte-derived autologous DCs. The DCs were aliquoted to 9–18 vaccines containing 10⁷ cells each. These vaccines were injected intradermally at specified intervals after the patients had received a standard 6-week course of post-operative radio-chemotherapy. The study was registered with the ClinicalTrials.gov identifier NCT00846456.

Results

Autologous CSC cultures were established from ten out of eleven tumors. High-quality RNA was isolated, and mRNA was amplified in all cases. Seven patients were able to be weaned from corticosteroids to receive DC immunotherapy. An immune response induced by vaccination was identified in all seven patients. No patients developed adverse autoimmune events or other side effects. Compared to matched controls, progression-free survival was 2.9 times longer in vaccinated patients (median 694 vs. 236 days, p = 0.0018, log-rank test).

Conclusion

These findings suggest that vaccination against glioblastoma stem cells is safe, well-tolerated, and may prolong progression-free survival.     

Prolonging the hydration and active metabolism from light periods into nights substantially enhances lichen growth

This study investigates how hydration during light and dark periods influences growth in two epiphytic old forest lichens, the green algal Lobaria pulmonaria and the cyanobacterial L. scrobiculata. The lichens were cultivated in growth chambers for 14 days (200 μmol m^?1 s^?2; 12 h photoperiod) at four temperature regimes (25/20 °C, 21/16 °C, 13/8 °C, and 6/1 °C; day/night temperatures) and two hydration regimes (12 h day-time hydration; 12 h day-time + 12 h night-time hydration). Growth was highly dynamic, showing that short-term growth experiments in growth cabinets have a high, but largely unexplored potential in functional lichen studies. The highest measured growth rates were not far from the maximal dry matter gain estimated from published net photosynthetic CO₂ uptake data. For the entire data set, photobiont type, temperature, hydration regime and specific thallus mass accounted for 46.6 % of the variation in relative growth rate (RGR). Both species showed substantially higher relative growth rates based on both biomass (RGR) and thallus area (RT_AGR) when they were hydrated day and night compared to hydration in light only. Chronic photoinhibition was substantial in thalli hydrated only during the day time and kept at the highest and lowest temperature regimes, resulting in exponential increases in RGR with increasing maximal PSII efficiency (F _v/F _m) in both species. However, the depression in F _v/F _m was stronger for the cyanolichen than for the cephalolichen at extreme temperatures. The growth-stimulating effect of night-time hydration suggests that nocturnal metabolic activity improves recovery of photoinhibition and/or enhances the conversion rate of photosynthates into thallus extension.     

Elemental stoichiometry of basal resources and benthic macroinvertebrates along a land use gradient in a Great Basin watershed

The effects of land use on the elemental stoichiometry of aquatic organisms have rarely been studied in semi-arid watersheds. In eight semi-arid sub-watersheds differing in land use, we determined which predictor variable(s) best explains the elemental variability in two basal food resources and benthic macroinvertebrates (BMI). The elemental composition of periphyton and seston was best explained by percentage of urban and agricultural areas, forested land and associated differences in SRP, DOC, and stream water N:P ratios. In contrast, consumer elemental stoichiometry was related to taxonomic identity and feeding mode. Elemental imbalances were higher for collector-gatherer than for scraper and collector-filterer. However, high spatial and temporal variability in the elemental composition of basal food resources obscured clear spatial patterns of imbalances between nutrient-poor upstream and nutrient-rich downstream sites. Results from this study suggest that land use can affect BMI due to alteration in stoichiometry of their food resources. However, taxonomy and allometry must be taken into account to better understand spatial and temporal changes in the elemental composition of BMI. Our results indicate the importance of considering multiple effects to accurately assess land use effects on producer and consumer stoichiometry, particularly the in highly variable Great Basin watersheds.