The modelled growth of mycorrhizal and non-mycorrhizal plants under constant versus variable soil nutrient concentration

We studied the response of mycorrhizal and non-mycorrhizal plants to variation in soil nutrient concentration. A model for the relative growth rate (RGR) of plant biomass was constructed with soil nutrients as an explanatory variable. A literature survey was carried out to find the relative magnitudes of parameter values for mycorrhizal and non-mycorrhizal plants. Mycorrhizal plants had higher RGR at low nutrient concentrations and non-mycorrhizal plants at high nutrient concentrations. The RGR of mycorrhizal and non-mycorrhizal plants at constant versus log-normally distributed soil nutrient concentration were compared to see the effect of mycorrhizal status on responses to variation. Variation in nutrient concentration generally reduced RGR, especially in mycorrhizal plants. The RGR of a non-mycorrhizal plant may increase with variation where a growth function threshold exists, i.e. a soil nutrient concentration that must be exceeded to allow growth. Mycorrhizal plants appeared more sensitive to variation in nutrient concentration than non-mycorrhizal plants due to the higher affinity of mycorrhizal roots at low nutrient levels. However, this prediction may be reversed if mycorrhizal symbiosis considerably stabilises flow of nutrients to plant physiological processes, such that mycorrhizal plants experience less variation in soil nutrient concentration than non-mycorrhizal plants. Our results also attain broader significance by suggesting a general trade-off between competitive ability in a constant versus variable resource availability.     

AutoFACT: AnAutomaticFunctionalAnnotation andClassificationTool

Background  

Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets.     

A DNA vaccine prime followed by a liposome-encapsulated protein boost confers enhanced mucosal immune responses and protection

A variety of DNA vaccine prime and recombinant viral boost immunization strategies have been developed to enhance immune responses in humans, but inherent limitations to these strategies exist. There is still an overwhelming need to develop safe and effective approaches that raise broad humoral and T cell-mediated immune responses systemically and on mucosal surfaces. We have developed a novel mucosal immunization regimen that precludes the use of viral vectors yet induces potent T cell responses. Using hepatitis B surface Ag (HBsAg), we observed that vaccination of BALB/c mice with an i.m. HBsAg-DNA vaccine prime followed by an intranasal boost with HBsAg protein encapsulated in biologically inert liposomes enhanced humoral and T cell immune responses, particularly on mucosal surfaces. Intranasal live virus challenge with a recombinant vaccinia virus expressing HBsAg revealed a correlation between T cell immune responses and protection of immunized mice. A shortened immunization protocol was developed that was successful in both adult and neonatal mice. These results support the conclusion that this new approach is capable of generating a Th-type-1-biased, broad spectrum immune response, specifically at mucosal surfaces. The success of this design may provide a safe and effective vaccination alternative for human use.     

Selective MicroRNA-Offset RNA Expression in Human Embryonic Stem Cells

Small RNA molecules, including microRNAs (miRNAs), play critical roles in regulating pluripotency, proliferation and differentiation of embryonic stem cells. miRNA-offset RNAs (moRNAs) are similar in length to miRNAs, align to miRNA precursor (pre-miRNA) loci and are therefore believed to derive from processing of the pre-miRNA hairpin sequence. Recent next generation sequencing (NGS) studies have reported the presence of moRNAs in human neurons and cancer cells and in several tissues in mouse, including pluripotent stem cells. In order to gain additional knowledge about human moRNAs and their putative development-related expression, we applied NGS of small RNAs in human embryonic stem cells (hESCs) and fibroblasts. We found that certain moRNA isoforms are notably expressed in hESCs from loci coding for stem cell-selective or cancer-related miRNA clusters. In contrast, we observed only sparse moRNAs in fibroblasts. Consistent with earlier findings, most of the observed moRNAs derived from conserved loci and their expression did not appear to correlate with the expression of the adjacent miRNAs. We provide here the first report of moRNAs in hESCs, and their expression profile in comparison to fibroblasts. Moreover, we expand the repertoire of hESC miRNAs. These findings provide an expansion on the known repertoire of small non-coding RNA contents in hESCs.     

Diatom assemblages in sediments of Lake Juusa, Southern Estonia with an assessment of their habitat

Diatom analysis of surface sediments and two sediment cores from different sedimentation areas of a small closed lake was undertaken with the aim of acquiring knowledge on the dependence of the distribution of diatom assemblages on lake bathymetry. Lake Juusa was selected for the study because we have for this lake a large data set about the lithological composition of sediments and macrofossil and cladoceran records for the Holocene. A high carbonate content (20–60%) in the sediment sequence indicates high carbonacity and relatively stable pH values during the Holocene. On the basis of comprehensive analysis, abrupt water-level fluctuations and changes in the trophic status were established. Results of this study showed that the fluctuations of the water-level were the leading factor determining the habitats of diatom assemblages in the lake. In the surface sediment samples planktonic species such as Cyclotella spp., Stephanodiscus spp. and Aulacoseira spp. had a depth optimum at 3–4 m and the most abundant periphytic taxa were distributed mostly at depths shallower than 3.5 m. The same regularity was established in sediment cores where a good correlation between planktonic species and lake water depth was found in sediments accumulated at water depths >4 m. Lake Juusa appears to be a proper site for detailed environmental reconstructions over the Holocene, and the results will give us a good opportunity to analyse the history of water-level fluctuations in other small Estonian lakes. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: K. Martens     

Proteolytic cleavage and phosphorylation of a tumor-associated ErbB4 isoform promote ligand-independent survival and cancer cell growth

The ErbB1 and ErbB2 receptors are oncogenes with therapeutic significance in human cancer, whereas the transforming potential of the related ErbB4 receptor has remained controversial. Here, we have addressed whether four alternatively spliced ErbB4 isoforms differ in regulating cellular responses relevant for tumor growth. We show that the two tumor necrosis factor-α converting enzyme (TACE)-cleavable ErbB4 isoforms (the juxtamembrane [JM]-a isoforms) were overexpressed in a subset of primary human breast cancers together with TACE. The overexpression of the JM-a cytoplasmic (CYT)-2 ErbB4 isoform promoted ErbB4 phosphorylation, survival of interleukin-3-dependent cells, and proliferation of breast cancer cells even in the absence of ligand stimulation, whereas activation of the other three ErbB4 isoforms required ligand stimulation. Ligand-independent cellular responses to ErbB4 JM-a CYT-2 overexpression were regulated by both tyrosine kinase activity and a two-step proteolytic generation of an intracellular receptor fragment involving first a TACE-like proteinase, followed by γ-secretase activity. These data suggest a novel transforming mechanism for the ErbB4 receptor in human breast cancer that is 1) specific for a single receptor isoform and 2) depends on proteinase cleavage and kinase activity but not ligand activation of the receptor.     

Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation

We characterize allelic and gene expression variation between populations of the Glanville fritillary butterfly (Melitaea cinxia) from two fragmented and two continuous landscapes in northern Europe. The populations exhibit significant differences in their life history traits, e.g. butterflies from fragmented landscapes have higher flight metabolic rate and dispersal rate in the field, and higher larval growth rate, than butterflies from continuous landscapes. In fragmented landscapes, local populations are small and have a high risk of local extinction, and hence the long-term persistence at the landscape level is based on frequent re-colonization of vacant habitat patches, which is predicted to select for increased dispersal rate. Using RNA-seq data and a common garden experiment, we found that a large number of genes (1,841) were differentially expressed between the landscape types. Hexamerin genes, the expression of which has previously been shown to have high heritability and which correlate strongly with larval development time in the Glanville fritillary, had higher expression in fragmented than continuous landscapes. Genes that were more highly expressed in butterflies from newly-established than old local populations within a fragmented landscape were also more highly expressed, at the landscape level, in fragmented than continuous landscapes. This result suggests that recurrent extinctions and re-colonizations in fragmented landscapes select a for specific expression profile. Genes that were significantly up-regulated following an experimental flight treatment had higher basal expression in fragmented landscapes, indicating that these butterflies are genetically primed for frequent flight. Active flight causes oxidative stress, but butterflies from fragmented landscapes were more tolerant of hypoxia. We conclude that differences in gene expression between the landscape types reflect genomic adaptations to landscape fragmentation.     

Identification of novel virulence-associated loci in uropathogenic Escherichia coli by suppression subtractive hybridization

To identify novel virulence-associated genes in uropathogenic Escherichia coli (UPEC) strains, a suppression subtractive hybridization strategy was applied to genomic DNA of four clinical UPEC isolates from patients suffering from cystitis or pyelonephritis. The genomic DNA of four isolates (tester strains) was subtracted from the DNA of two different driver strains, the well characterized UPEC strain CFT073 and the non-pathogenic E. coli K-12 strain MG1655. We determined the sequence of 172 tester strain-specific DNA fragments, 86 of which revealed only low or no homology to nucleotide sequences of public databases. We further determined the virulence association of the 86 novel DNA fragments using each DNA fragment as a probe in Southern hybridizations of a reference strain collection consisting of 60 extraintestinal pathogenic E. coli isolates, and 40 non-virulent E. coli strains from stool samples. From this, 19 novel DNA fragments were demonstrated to be significantly associated with virulent strains and thus may represent new virulence traits. Our results support the idea of a considerable genetic variability among UPEC strains and suggest that novel genomic determinants might contribute to virulence of UPEC.     

Intra-lake heterogeneity of sedimentary cladoceran (Crustacea) assemblages forced by local hydrology

Intra-lake variation of fossil Cladocera (Crustacea) assemblages in 31 surface sediment samples in Lake Pieni-Kauro and River Saavanjoki, eastern Finland, was examined with an objective to identify habitat specificity of Cladocera in relation to local hydrology-related environmental factors. The surface sediment assemblages showed high levels of heterogeneity, mainly as to water depth and lentic–lotic gradients in the lake–river complex. This was evident from the principal component analysis which indicated a major trend from shallow to deep samples and a secondary trend from lentic to lotic samples, and from redundancy analysis (RDA), which recognized water depth and river flow as the most important environmental variables in explaining cladoceran variability within the dataset. According to the RDA and generalized linear models, Daphnia spp., Bosmina (Eubosmina), and Alona quadrangularis showed association with deep water localities, whereas Bosmina longirostris and Alona affinis preferred littoral habitats. Acroperus harpae and Chydorus sphaericus s.l. appeared to favor lotic habitats. The results propose that littoral taxa are primarily deposited postmortem or after molting close to their shallow water habitats, while planktonic cladocerans accumulate principally in deepwater locations. Accordingly, it appears that in heterogeneous basins intra-lake surface sediment samples integrate locally living fauna that is driven by local hydrology-related factors, such as water depth, sediment properties, macrophytes, and river flow and coupling biotic interactions.