Consistent temperature dependence of respiration across ecosystems contrasting in thermal history

Ecosystem respiration is a primary component of the carbon cycle and understanding the mechanisms that determine its temperature dependence will be important for predicting how rates of carbon efflux might respond to global warming. We used a rare model system, comprising a network of geothermally heated streams ranging in temperature from 5 °C to 25 °C, to explore the nature of the relationship between respiration and temperature. Using this ‘natural experiment’, we tested whether the natal thermal regime of stream communities influenced the temperature dependence of respiration in the absence of other potentially confounding variables. An empirical survey of 13 streams across the thermal gradient revealed that the temperature dependence of whole‐stream respiration was equivalent to the average activation energy of the respiratory complex (0.6–0.7 eV). This observation was also consistent for in‐situ benthic respiration. Laboratory experiments, incubating biofilms from four streams across the thermal gradient at a range of temperatures, revealed that the activation energy and Q₁₀ of respiration were remarkably consistent across streams, despite marked differences in their thermal history and significant turnover in species composition. Furthermore, absolute rates of respiration at standardised temperature were also unrelated to ambient stream temperature, but strongly reflected differences in biofilm biomass. Together, our results suggest that the core biochemistry, which drives the kinetics of oxidative respiratory metabolism, may be well conserved among diverse taxa and environments, and that the intrinsic sensitivity of respiration to temperature is not influenced by ambient environmental temperature.     

Redundant functions of Rac GTPases in inner ear morphogenesis

Development of the mammalian inner ear requires coordination of cell proliferation, cell fate determination and morphogenetic movements. While significant progress has been made in identifying developmental signals required for inner ear formation, less is known about how distinct signals are coordinated by their downstream mediators. Members of the Rac family of small GTPases are known regulators of cytoskeletal remodeling and numerous other cellular processes. However, the function of Rac GTPases in otic development is largely unexplored. Here, we show that Rac1 and Rac3 redundantly regulate many aspects of inner ear morphogenesis. While no morphological defects were observed in Rac3(-/-) mice, Rac1(CKO); Rac3(-/-) double mutants displayed enhanced vestibular and cochlear malformations compared to Rac1(CKO) single mutants. Moreover, in Rac1(CKO); Rac3(-/-) mutants, we observed compromised E-cadherin-mediated cell adhesion, reduced cell proliferation and increased cell death in the early developing otocyst, leading to a decreased size and malformation of the membranous labyrinth. Finally, cochlear extension was severely disrupted in Rac1(CKO); Rac3(-/-) mutants, accompanied by a loss of epithelial cohesion and formation of ectopic sensory patches underneath the cochlear duct. The compartmentalized expression of otic patterning genes within the Rac1(CKO); Rac3(-/-) mutant otocyst was largely normal, however, indicating that Rac proteins regulate inner ear morphogenesis without affecting cell fate specification. Taken together, our results reveal an essential role for Rac GTPases in coordinating cell adhesion, cell proliferation, cell death and cell movements during otic development.     

Force-Induced Changes in Subnuclear Movement and Rheology

Extracellular mechanical forces result in changes in gene expression, but it is unclear how cells are able to permanently adapt to new mechanical environments because chemical signaling pathways are short-lived. We visualize force-induced changes in nuclear rheology to examine short- and long-time genome organization and movements. Punctate labels in the nuclear interior of HeLa, human umbilical vein endothelial, and osteosarcoma (Saos-2) cells allow tracking of nuclear movements in cells under varying levels of shear and compressive force. Under adequate shear stress two distinct regimes develop in cells under mechanical stimulation: an initial event of increased intranuclear movement followed by a regime of intranuclear movements that reflect the dose of applied force. At early times there is a nondirectionally oriented response with a small increase in nuclear translocations. After 30 min, there is a significant increase in nuclear movements, which scales with the amount of shear or compressive stress. The similarities in the nuclear response to shear and compressive stress suggest that the nucleus is a mechanosensitive element within the cell. Thus, applied extracellular forces stimulate intranuclear movements, resulting in repositioning of nuclear bodies and the associated chromatin within the nucleus.     

AtPTR4 and AtPTR6 are differentially expressed,tonoplast-localized members of the peptide transporter/nitrate transporter 1 (PTR/NRT1) family

Members of the peptide transporter/nitrate transporter 1 (PTR/NRT1) family in plants transport a variety of substrates like nitrate, di- and tripepetides, auxin and carboxylates. We isolated two members of this family from Arabidopsis, AtPTR4 and AtPTR6, which are highly homologous to the characterized di- and tripeptide transporters AtPTR1, AtPTR2 and AtPTR5. All known substrates of members of the PTR/NRT1 family were tested using heterologous expression in Saccharomyces cerevisiae mutants and oocytes of Xenopus laevis, but none could be identified as substrate of AtPTR4 or AtPTR6. AtPTR4 and AtPTR6 show distinct expression patterns, while AtPTR4 is expressed in the vasculature of the plants, AtPTR6 is highly expressed in pollen and during senescence. Phylogenetic analyses revealed that AtPTR2, 4 and 6 belong to one clade of subgoup II, whereas AtPTR1 and 5 are found in a second clade. Like AtPTR2, AtPTR4-GFP and AtPTR6-GFP fusion proteins are localized at the tonoplast. Vacuolar localization was corroborated by co-localization of AtPTR2-YFP with the tonoplast marker protein GFP-AtTIP2;1 and AtTIP1;1-GFP. This indicates that the two clades reflect different intracellular localization at the tonoplast (AtPTR2, 4, 6) and plasma membrane (AtPTR1, 5), respectively.     

Chemokine release by neutrophils in chronic obstructive pulmonary disease

Neutrophils are among the first cells to arrive at the site of injury. Chemokines secreted by neutrophils affect the migration of both neutrophils and other inflammatory cells, such as monocytes. It has been reported that LPS-induced release of IL-8 (CXCL-8) by neutrophils is amplified by neutrophil-derived TNF-α. We hypothesize that chemokine release by neutrophils is altered in chronic obstructive pulmonary disease (COPD) compared with healthy controls and that TNF-α may be involved in this alteration. Peripheral blood neutrophils isolated from smokers with COPD (n?=?12), smokers without COPD (n?=?12) and healthy, non-smokers (n?=?12) were stimulated with LPS, TNF-α or organic dust. Anti-TNF-α Ab (infliximab) was used to study the effect of neutrophil-derived TNF-α. Release of CXCL-8, macrophage inflammatory protein-1 α (MIP-1α, CCL-3), monocyte chemotactic protein-1 (MCP-1, CCL-2) and TNF-α was measured. Neutrophils spontaneously released CXCL-8, CCL-2 and CCL-3. Inhibition of TNF-α reduced the spontaneous release of CXCL-8 and CCL-3. Stimulation with LPS and organic dust increased the release of CXCL-8 and CCL-3 (but not CCL-2) which was reduced by inhibition of TNF-α. In the COPD group, inhibition of TNF-α failed to inhibit the release of LPS-induced CXCL-8. The role of neutrophils as cytokine and chemokine producers was confirmed. Neutrophil-derived TNF-α contributed to the release of chemokines after stimulation with LPS and organic dust, as the response was inhibited by infliximab. In the COPD group, infliximab did not significantly inhibit the release of CXCL-8, suggesting that the role of TNF-α is altered in COPD.     

Between Metabolite Relationships: an essential aspect of metabolic change

Not only the levels of individual metabolites, but also the relations between the levels of different metabolites may indicate (experimentally induced) changes in a biological system. Component analysis methods in current 'standard' use for metabolomics, such as Principal Component Analysis (PCA), do not focus on changes in these relations. We therefore propose the concept of 'Between Metabolite Relationships' (BMRs): common changes in the covariance (or correlation) between all metabolites in an organism. Such structural changes may indicate metabolic change brought about by experimental manipulation but which are lost with standard data analysis methods. These BMRs can be analysed by the INdividual Differences SCALing (INDSCAL) method. First the BMR quantification is described and subsequently the INDSCAL method. Finally, two studies illustrate the power and the applicability of BMRs in metabolomics. The first study is about the induced plant response of cabbage to herbivory, of which BMRs are a considerable part. In the second study-a human nutritional intervention study of green tea extract-standard data analysis tools did not reveal any metabolic change, although the BMRs were considerably affected. The presented results show that BMRs can be easily implemented in a wide variety of metabolomic studies. They provide a new source of information to describe biological systems in a way that fits flawlessly into the next generation of systems biology questions, dealing with personalized responses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-011-0316-1) contains supplementary material, which is available to authorized users.