Mathematical model of fructan biosynthesis and polymer length distribution in plants

Background and Aims

There are many unresolved issues concerning the biochemistry of fructan biosynthesis. The aim of this paper is to address some of these by means of modelling mathematically the biochemical processes.

Methods

A model has been constructed for the step-by-step synthesis of fructan polymers. This is run until a steady state is achieved for which a polymer distribution is predicted. It is shown how qualitatively different distributions can be obtained.

Key Results

It is demonstrated how a set of experimental results on polymer distribution can by simulated by a simple parameter adjustments.

Conclusions

Mathematical modelling of fructan biosynthesis can provide a useful tool for helping elucidate the details of the biosynthetic processes.     

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.     

A Systematic Review of MicroRNA in Glioblastoma Multiforme: Micro-modulators in the Mesenchymal Mode of Migration and Invasion

Glioblastoma multiforme (GBM) is an incurable form of brain cancer with a very poor prognosis. Because of its highly invasive nature, it is impossible to remove all tumor cells during surgical resection, making relapse inevitable. Further research into the regulatory mechanism underpinning GBM pathogenesis is therefore warranted, and over the past decade, there has been an increased focus on the functional role of microRNA (miRNA). This systematic review aims to present a comprehensive overview of all the available literature on the expression profiles and function of miRNA in GBM. Here, we have reviewed 163 papers and identified 253 upregulated, 95 downregulated, and 17 disputed miRNAs with respect to expression levels; 85 % of these miRNAs have not yet been functionally characterized. A focus in this study has been 26 interesting miRNAs involved in the mesenchymal mode of migration and invasion, demonstrating the importance of miRNAs in the context of the cellular niche. Both oncogenic and tumor-suppressive miRNAs were found to affect target genes involved in cell migration, cytoskeletal rearrangement, invasiveness, and angiogenesis. Clearly, the distinct functional properties of these miRNAs need further investigation and might hold a great potential in future molecular therapies targeting GBM.     

Effect of four plant species on soil 15N-access and herbage yield in temporary agricultural grasslands

Background and aims

We carried out field experiments to investigate if an agricultural grassland mixture comprising shallow- (perennial ryegrass: Lolium perenne L.; white clover: Trifolium repens L.) and deep- (chicory: Cichorium intybus L.; Lucerne: Medicago sativa L.) rooting grassland species has greater herbage yields than a shallow-rooting two-species mixture and pure stands, if deep-rooting grassland species are superior in accessing soil ¹⁵N from 1.2 m soil depth compared with shallow-rooting plant species and vice versa, if a mixture of deep- and shallow-rooting plant species has access to greater amounts of soil ¹⁵N compared with a shallow-rooting binary mixture, and if leguminous plants affect herbage yield and soil ¹⁵N-access.

Methods

¹⁵N-enriched ammonium-sulphate was placed at three different soil depths (0.4, 0.8 and 1.2 m) to determine the depth dependent soil ¹⁵N-access of pure stands, two-species and four-species grassland communities.

Results

Herbage yield and soil ¹⁵N-access of the mixture including deep- and shallow-rooting grassland species were generally greater than the pure stands and the two-species mixture, except for herbage yield in pure stand lucerne. This positive plant diversity effect could not be explained by complementary soil ¹⁵N-access of the different plant species from 0.4, 0.8 and 1.2 m soil depths, even though deep-rooting chicory acquired relatively large amounts of deep soil ¹⁵N and shallow-rooting perennial ryegrass when grown in a mixture relatively large amounts of shallow soil ¹⁵N. Legumes fixed large amounts of N₂, added and spared N for non-leguminous plants, which especially stimulated the growth of perennial ryegrass.

Conclusions

Our study showed that increased plant diversity in agricultural grasslands can have positive effects on the environment (improved N use may lead to reduced N leaching) and agricultural production (increased herbage yield). A complementary effect between legumes and non-leguminous plants and increasing plant diversity had a greater positive impact on herbage yield compared with complementary vertical soil ¹⁵N-access.     

Bicarbonate as tracer for assimilated C and homogeneity of 14C and 15N distribution in plants by alternative labeling approaches

Aims

Application of carbon (C) and nitrogen (N) isotopes is an essential tool to study C and N flows in plant-soil-microorganisms systems. When targeting single plants in a community the tracers need to be added via e.g., leaf-labeling or stem-feeding approaches. In this study we: (i) investigated if bicarbonate can be used to introduce ¹⁴C (or ¹³C) into white clover and ryegrass, and (ii) compared the patterns of ¹⁴C and ¹⁵N allocation in white clover and ryegrass to evaluate the homogeneity of tracer distribution after two alternative labeling approaches.

Methods

Perennial ryegrass and white clover were pulse labeled with ¹⁵N urea via leaf-labeling and ¹⁴C either via a ¹⁴CO₂ atm or with ¹⁴C bicarbonate through leaf-labeling. Plants were sampled 4 days after labeling and prepared for bulk isotope analysis and for ¹⁴C imaging to identify plant parts with high and low ¹⁴C activity. Subsequently, plant parts with high and low ¹⁴C activity were separated and analyzed for ¹⁵N enrichment.

Results

Bicarbonate applied by leaf-labeling efficiently introduced ¹⁴C into both white clover and ryegrass, although the ¹⁴C activity in particular for white clover was found predominantly in the labeled leaf. Using ¹⁴C imaging for identification of areas with high (hotspots) and low ¹⁴C activity showed that ¹⁴C was incorporated very heterogeneously both when using bicarbonate and CO₂ as expected when using pulse labeling. Subsequent analysis of ¹⁵N enrichment in plant parts with high and low ¹⁴C activity showed that ¹⁵N also had a heterogeneous distribution (up to two orders of magnitude).

Conclusion

Bicarbonate can efficiently be used to introduce ¹⁴C or ¹³C into plant via the leaf-labeling method. Both ¹⁴C and ¹⁵N showed heterogeneous distribution in the plant, although the distribution of ¹⁵N was more even than that of ¹⁴C.     

Strigolactones fine-tune the root system

Strigolactones were originally discovered to be involved in parasitic weed germination, in mycorrhizal association and in the control of shoot architecture. Despite their clear role in rhizosphere signaling, comparatively less attention has been given to the belowground function of strigolactones on plant development. However, research has revealed that strigolactones play a key role in the regulation of the root system including adventitious roots, primary root length, lateral roots, root hairs and nodulation. Here, we review the recent progress regarding strigolactone regulation of the root system and the antagonism and interplay with other hormones.     

Receptor Tyrosine Kinase-like Orphan Receptor 2 (Ror2) Expression Creates a Poised State of Wnt Signaling in Renal Cancer

Expression of the receptor tyrosine kinase-like orphan receptor 2 (Ror2) has been identified in an increasing array of tumor types and is known to play a role as an important mediator of Wnt signaling cascades. In this study, we aimed to clarify Ror2 interactions with the Wnt pathways within the context of renal cell carcinoma (RCC). An examination of Ror2 expression in primary human RCC tumors showed a significant correlation with several Wnt signaling genes, including the classical feedback target gene Axin2. We provide evidence that Ror2 expression results in a partially activated state for canonical Wnt signaling through an increased signaling pool of β-catenin, leading to an enhancement of downstream target genes following Wnt3a stimulation in both renal and renal carcinoma-derived cells. Additionally, inhibition of low-density lipoprotein receptor-related protein 6 (LRP6) with either siRNA or dickkopf decreased the response to Wnt3a stimulation, but no change was seen in the increased β-catenin pool associated with Ror2 expression, suggesting that LRP6 cofactor recruitment is necessary for a Wnt3a-induced signal but that it does not participate in the Ror2 effect on β-catenin signaling. These results highlight a new role for Ror2 in conveying a tonic signal to stabilize soluble β-catenin and create a poised state of enhanced responsiveness to Wnt3a exogenous signals in RCC.     

NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ

Major histocompatibility complex class II (MHCII) molecules play an important role in cell-mediated immunity. They present specific peptides derived from endosomal proteins for recognition by T helper cells. The identification of peptides that bind to MHCII molecules is therefore of great importance for understanding the nature of immune responses and identifying T cell epitopes for the design of new vaccines and immunotherapies. Given the large number of MHC variants, and the costly experimental procedures needed to evaluate individual peptide–MHC interactions, computational predictions have become particularly attractive as first-line methods in epitope discovery. However, only a few so-called pan-specific prediction methods capable of predicting binding to any MHC molecule with known protein sequence are currently available, and all of them are limited to HLA-DR. Here, we present the first pan-specific method capable of predicting peptide binding to any HLA class II molecule with a defined protein sequence. The method employs a strategy common for HLA-DR, HLA-DP and HLA-DQ molecules to define the peptide-binding MHC environment in terms of a pseudo sequence. This strategy allows the inclusion of new molecules even from other species. The method was evaluated in several benchmarks and demonstrates a significant improvement over molecule-specific methods as well as the ability to predict peptide binding of previously uncharacterised MHCII molecules. To the best of our knowledge, the NetMHCIIpan-3.0 method is the first pan-specific predictor covering all HLA class II molecules with known sequences including HLA-DR, HLA-DP, and HLA-DQ. The NetMHCpan-3.0 method is available at http://www.cbs.dtu.dk/services/NetMHCIIpan-3.0.     

The influence of goethite and gibbsite on soluble nutrient dynamics and microbial community composition

Iron and aluminum (oxyhydr)oxides are ubiquitous in the soil environment and have the potential to strongly affect the properties of dissolved organic matter. We examined the effect of oxide surfaces on soluble nutrient dynamics and microbial community composition using an incubation of forest floor material in the presence of (1) goethite and quartz, (2) gibbsite and quartz, and (3) quartz surfaces. Forest floor material was incubated over a period of 154 days. Aqueous extracts of the incubations were harvested on days 5, 10, 20, 30, 60, 90, and 154, and concentrations of P, N, PO₄ ^3?, NO₂ ^?, NO₃ ^?, and organic C were measured in the solutions. Microbial community composition was examined through pyrosequencing of bacterial and fungal small subunit ribosomal RNA genes on selected dates throughout the incubation. Results indicated that oxide surfaces exerted strong control on soluble nutrient dynamics and on the composition of the decomposer microbial community, while possibly having a small impact on system-level respiration. Goethite and gibbsite surfaces showed preferential adsorption of P-containing and high molar mass organic solutes, but not of N-containing compounds. On average, organic C concentrations were significantly lower in water extractable organic matter (WEOM) solutions from oxide treatments than from the control treatment (P = 0.0037). Microbial community composition varied both among treatments and with increasing time of incubation. Variation in bacterial and fungal community composition exhibited strong-to-moderate correlation with length of incubation, and several WEOM physiochemical characteristics including apparent (weight averaged) molar mass, pH and electrical conductivity. Additionally, variation in bacterial community composition among treatments was correlated with total P (r = 0.60, P < 0.0001), PO₄ ^3? (r = 0.79, P < 0.0001), and organic C (r = 0.36, P = 0.015) concentrations; while variation in fungal communities was correlated with organic C concentrations (r = ?0.48, P = 0.0008) but not with phosphorus concentrations. The relatively small impact of oxide surfaces on system-level microbial respiration of organic matter despite their significant effects on microbial community composition and WEOM dynamics lends additional support to the theory of microbial functional redundancy.