The community of needle endophytes reflects the current physiological state of Norway spruce

This study investigated fungal endophytes in the needles of Norway spruce (Picea abies) cuttings in relation to host tree growth. We also determined the prevalence of endophytes in needles incubated for six months. The cuttings originated from clonal origins showing slow- and fast-growth in long-term field trials but the heritable differences in growth rate were not yet detected among the studied cutting. Endophytes were isolated from surface-sterilized needles with culture-free DNA techniques. No significant differences were observed between endophyte communities of slow- and fast-growing clonal origins. However, the endophyte community correlated with the current growth rate of cuttings suggesting that endophytes reflect short- rather than long-term performance of a host. The concentration of condensed tannins was similar in slow- and fast-growing clonal origins but it showed a negative relationship with endophyte species richness, implying that these secondary compounds may play an important role in spruce tolerance against fungal infections. More than a third of endophyte species were detected in both fresh and decomposing needles, indicating that many needle endophytes are facultative saprotrophs. Several potentially pathogenic fungal species were also found within the community of saprotrophic endophytes.     

Revealing secrets of the enigmatic omega subunit of bacterial RNA polymerase

The conserved omega (ω) subunit of RNA polymerase (RNAP) is the only nonessential subunit of bacterial RNAP core. The small ω subunit (7 kDa–11.5 kDa) contains three conserved α helices, and helices α2 and α3 contain five fully conserved amino acids of ω. Four conserved amino acids stabilize the correct folding of the ω subunit and one is located in the vicinity of the β′ subunit of RNAP. Otherwise ω shows high variation between bacterial taxa, and although the main interaction partner of ω is always β′, many interactions are taxon‐specific. ω‐less strains show pleiotropic phenotypes, and based on in vivo and in vitro results, a few roles for the ω subunits have been described. Interactions of the ω subunit with the β′ subunit are important for the RNAP core assembly and integrity. In addition, the ω subunit plays a role in promoter selection, as ω‐less RNAP cores recruit fewer primary σ factors and more alternative σ factors than intact RNAP cores in many species. Furthermore, the promoter selection of an ω‐less RNAP holoenzyme bearing the primary σ factor seems to differ from that of an intact RNAP holoenzyme.     

Modeling Signal Transduction Leading to Synaptic Plasticity: Evaluation and Comparison of Five Models

An essential phenomenon of the functional brain is synaptic plasticity which is associated with changes in the strength of synapses between neurons. These changes are affected by both extracellular and intracellular mechanisms. For example, intracellular phosphorylation-dephosphorylation cycles have been shown to possess a special role in synaptic plasticity. We, here, provide the first computational comparison of models for synaptic plasticity by evaluating five models describing postsynaptic signal transduction networks. Our simulation results show that some of the models change their behavior completely due to varying total concentrations of protein kinase and phosphatase. Furthermore, the responses of the models vary when models are compared to each other. Based on our study, we conclude that there is a need for a general setup to objectively compare the models and an urgent demand for the minimum criteria that a computational model for synaptic plasticity needs to meet.     

Decreased free water clearance is associated with worse respiratory outcomes in premature infants

Objective

The goal was to elucidate predictors of decreased free water clearance (DFWC) in very low birth weight (VLBW) infants. We hypothesized that DFWC and fluid retention are linked to the severity of pulmonary problems and prolonged respiratory support, especially to nCPAP treatment.

Methods

The investigation was carried out at Tampere University Hospital between 2001 and 2006. The study population comprised 74 VLBW infants born at 29.21 (24.57–34.14) weeks of gestation. Median birth weight was 1175 (575–1490) grams. We measured plasma and urine osmolality and 24-hour urine volume to calculate free water clearance (FWC) for each infant. If FWC was less than 30 ml/kg/day the infant was classified as having DFWC.

Results

There were 38 (51.4%) infants with DFWC in the study population. The median duration of the observed DFT period was 14 (4–44) days. The gestational age at birth was lower for DFWC infants compared to infants with normal FWC (NFWC), 28.29 (24.57–32.86) vs. 30.00 (25.57–34.14) weeks (p = 0.001). DFWC infants also needed longer ventilator treatment, 2 (0–23) vs. 0.50 (0–23) days (p = 0.046), nCPAP treatment 30 (0–100) vs. 3 (0–41) days (p<0.0001) and longer oxygen supplementation 47 (0–163) vs. 22 (0–74) days (p = 0.011) than NFWC infants. All values presented here are medians with ranges.

Conclusions

DFWC appears to be frequently connected with exacerbation and prolongation of pulmonary problems in VLBW infants. Cautious fluid administration seems to be indicated in VLBW infants with prolonged respiratory problems and DFWC.     

Water colour, phosphorus and alkalinity are the major determinants of the dominant phytoplankton species in European lakes

Analysis of phytoplankton data from about 1,500 lakes in 20 European countries has revealed that two-thirds of the species that dominate lakes during the summer are dominant right across Europe. Using Canonical Correspondence Analyses, we have examined how both habitat conditions within lakes and environmental factors over broad geographical scales explained the distribution of the 151 most common summer dominant species. The distributions of these species were best explained by water colour and latitude, although alkalinity and total phosphorus also appeared to be important explanatory factors. Contrary to our original hypothesis, summer water temperatures had a negligible impact on the distribution of dominants, although, due to the restricted summer season we examined, only a limited temperature gradient was present in the dataset. Cryptophytes occurred more frequently among dominants in Northern Europe whereas cyanobacteria and dinophytes dominated more in Central and Southern Europe. Our analyses suggest that besides nutrient concentrations, other water chemistry variables, such as alkalinity and the content of humic substances, have at least as important a role in determining the distribution of the dominant phytoplankton species in European lakes.     

Interactions between invading benthivorous fish and native whitefish in subarctic lakes

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Comparison of the transmembrane helices of bovine rhodopsin in the crystal structure and the C α template based on cryo-electron microscopy maps and sequence analysis of the G protein-coupled receptors

G protein-coupled receptors (GPCR) are activated by a diverse array of extracellular signals, ranging from light to polypeptide molecules. The receptors propagate these signals intracellularly using G protein secondary messenger pathways. A common feature in the architecture of these receptors is their seven transmembrane domains. The first crystal structure of a GPCR, bovine rhodopsin, has recently been solved at 2.8 Å. We compared the seven membrane-spanning helices (TMH) from the crystal structure of bovine rhodopsin with those from the low-resolution model of bovine rhodopsin based on the cryo-electron microscopy structure of frog rhodopsin developed by Dr Joyce Baldwin. The model developed by Baldwin used a consensus sequence approach to predict the rotational position of each helix with respect to the other six helices. Superposition of the entire helix bundle of the Baldwin model with the crystal structure gave a RMS difference (RMSD) of 3.2 Å for the 198 C f atoms which suggests a high level of similarity in the arrangement of the helices. Except for TMH IV (RMSD of 4.0 Å), the position of corresponding helices within the helix bundle overlapped well. The superposition of individual helices showed that the RMSD values over 3 Å in the global superposition were largely due to one or more of the following: (i) differences in the unraveling and kinks for these helices, (ii) translation of TMH perpendicular to the membrane and (iii) rotation of helices up to 31°, except for TMH IV in which an additional contribution to the RMSD came from the aforementioned observation. As other crystal structures of GPCRs become available, a comparison with the Baldwin consensus model may reveal larger differences than those observed here.     

Antagonistic crosstalk between NF-κB and SIRT1 in the regulation of inflammation and metabolic disorders

Recent studies have indicated that the regulation of innate immunity and energy metabolism are connected together through an antagonistic crosstalk between NF-κB and SIRT1 signaling pathways. NF-κB signaling has a major role in innate immunity defense while SIRT1 regulates the oxidative respiration and cellular survival. However, NF-κB signaling can stimulate glycolytic energy flux during acute inflammation, whereas SIRT1 activation inhibits NF-κB signaling and enhances oxidative metabolism and the resolution of inflammation. SIRT1 inhibits NF-κB signaling directly by deacetylating the p65 subunit of NF-κB complex. SIRT1 stimulates oxidative energy production via the activation of AMPK, PPARα and PGC-1α and simultaneously, these factors inhibit NF-κB signaling and suppress inflammation. On the other hand, NF-κB signaling down-regulates SIRT1 activity through the expression of miR-34a, IFNγ, and reactive oxygen species. The inhibition of SIRT1 disrupts oxidative energy metabolism and stimulates the NF-κB-induced inflammatory responses present in many chronic metabolic and age-related diseases. We will examine the molecular mechanisms of the antagonistic signaling between NF-κB and SIRT1 and describe how this crosstalk controls inflammatory process and energy metabolism. In addition, we will discuss how disturbances in this signaling crosstalk induce the appearance of chronic inflammation in metabolic diseases.