MicroRNA transcriptome profiles during swine skeletal muscle development

Background

Dietary polyunsaturated fatty acids (PUFA), in particular the long chain marine fatty acids docosahexaenoic (DHA) and eicosapentaenoic (EPA), are linked to many health benefits in humans and in animal models. Little is known of the molecular response to DHA and EPA of the small intestine, and the potential contribution of this organ to the beneficial effects of these fatty acids. Here, we assessed gene expression changes induced by DHA and EPA in the wildtype C57BL/6J murine small intestine using whole genome microarrays and functionally characterized the most prominent biological process.

Results

The main biological process affected based on gene expression analysis was lipid metabolism. Fatty acid uptake, peroxisomal and mitochondrial beta-oxidation, and omega-oxidation of fatty acids were all increased. Quantitative real time PCR, and -in a second animal experiment- intestinal fatty acid oxidation measurements confirmed significant gene expression differences and showed in a dose-dependent manner significant changes at biological functional level. Furthermore, no major changes in the expression of lipid metabolism genes were observed in the colon.

Conclusion

We show that marine n-3 fatty acids regulate small intestinal gene expression and increase fatty acid oxidation. Since this organ contributes significantly to whole organism energy use, this effect on the small intestine may well contribute to the beneficial physiological effects of marine PUFAs under conditions that will normally lead to development of obesity, insulin resistance and diabetes.     

Recolonization by benthic invertebrates after experimental disturbance in a Swiss prealpine river

1. Although the crucial point of disturbance experiments in streams is the extent to which they can simulate an actual spate, this aspect has been widely neglected in the design of such studies. Similarly, the influence of the specific hydrological disturbance regime of a stream on its benthic community has received much theoretical attention in recent years, but hypotheses have rarely been tested in the field. 2. Our field experiment compared the structure of the benthic invertebrate community in the prealpine River Necker in north-eastern Switzerland with predictions of the patch dynamics concept about the faunal composition of frequently disturbed streams. We also compared the resistance and resilience of the invertebrates between two sites in the River Necker. A similar substratum composition at both sites, but higher shear stress values both at baseflow and bankfull discharge at site 2, implied a higher disturbance frequency at the latter site. Five patches of stream bed of ≈ 9 m² were disturbed by kicking and raking at each site, while five similar areas served as controls. From each plot, six Surber samples were taken: the first immediately after the disturbance, and the following five 1, 3, 6, 10 and 30 days later. 3. Resilience of the total benthic invertebrate fauna was high. The total number of individuals recovered to undisturbed densities within 30 days at site 1 and 6 days at site 2. Taxon richness recovered within 3 days. In accordance with theory, taxa with high recolonization rates made up a major percentage of the total number of individuals, especially in disturbed plots. However, this percentage was lower at site 2 in spite of the higher disturbance frequency at this site. Rhithrogena spp., Leuctra spp. and the Simuliidae recovered faster to undisturbed densities at site 2. In contrast, absolute recolonization rates of these taxa were higher at site 1, where total invertebrate densities were more than twice as high as at site 2. 4. Our results suggest that the time since the last disturbance should be considered as an important factor in studies of benthic invertebrate communities in prealpine rivers, because disturbances can alter the community structure. In frequently disturbed streams, very short sampling intervals may be needed to detect differences in taxon-specific colonization rates. The specific hydrological disturbance regime of such streams is also important, because even within-stream differences in the resilience of the benthic invertebrate community are possible.     

Ultrastructure of the sodium pump: Comparison of thin sectioning, negative staining, and freeze-fracture of purified, membrane-bound (Na+, K+)-ATPase

Purified (Na+, K+)-ATPase was studied by electron microscopy after thin sectioning, negative staining, and freeze-fracturing, particular emphasis being paid to the dimensions and frequencies of substructures in the membranes. Ultrathin sections show exclusively flat or cup-shaped membrane fragments which are triple-layered along much of their length and have diameters of 0.1-0.6 μm. Negative staining revealed a distinct substructure of particles with diameters between 30 and 50 A and with a frequency of 12,500 +/- 2,400 (SD) per μm(2). Comparisons with sizes of the protein components suggest that each surface particle contains as its major component one large catalytic chain with mol wt close to 100,000 and that two surface particles unite to form the unit of (Na+,K+)-ATPase which binds one molecule of ATP or ouabain. The further observations that the surface particles protrude from the membrane surface and are observed on both membrane surfaces in different patterns and degrees of clustering suggest that protein units span the membrane and are capable of lateral mobility. Freeze-fracturing shows intramembranous particles with diameters of 90-110 A and distributed on both concave and convex fracture faces with a frequency of 3,410 +/- 370 per μm(2) and 390 +/- 170 per μm(2), respectively. The larger diameters and three to fourfold smaller frequency of the intramembranous particles as compared to the surface particles seen after negative staining may reflect technical differences between methods, but it is more likely that the intramembranous particle is an oliogomer composed of two or even more of the protein units which form the surface particles.     

Leaf gas exchange and nitrogen dynamics of N2-fixing, field-grown Alnus glutinosa under elevated atmospheric CO2

Few studies have investigated the effects of elevated CO₂ on the physiology of symbiotic N₂-fixing trees. Tree species grown in low N soils at elevated CO₂ generally show a decline in photosynthetic capacity over time relative to ambient CO₂ controls. This negative adjustment may be due to a reallocation of leaf N away from the photosynthetic apparatus, allowing for more efficient use of limiting N. We investigated the effect of twice ambient CO₂ on net CO₂ assimilation (A), photosynthetic capacity, leaf dark respiration, and leaf N content of N2-fixing Alnus glutinosa (black alder) grown in field open top chambers in a low N soil for 160 d. At growth CO₂, A was always greater in elevated compared to ambient CO₂ plants. Late season A vs. internal leaf p(CO₂) response curves indicated no negative adjustment of photosynthesis in elevated CO₂ plants. Rather, elevated CO₂ plants had 16% greater maximum rate of CO₂ fixation by Rubisco. Leaf dark respiration was greater at elevated CO₂ on an area basis, but unaffected by CO₂ on a mass or N basis. In elevated CO₂ plants, leaf N content (μg N cm^?2) increased 50% between Julian Date 208 and 264. Leaf N content showed little seasonal change in ambient CO₂ plants. A single point acetylene reduction assay of detached, nodulated root segments indicated a 46% increase in specific nitrogenase activity in elevated compared to ambient CO₂ plants. Our results suggest that N₂-fixing trees will be able to maintain high A with minimal negative adjustment of photosynthetic capacity following prolonged exposure to elevated CO₂ on N-poor soils.     

Modelling the role of agriculture for the 20th century global terrestrial carbon balance

In order to better assess the role of agriculture within the global climate‐vegetation system, we present a model of the managed planetary land surface, Lund–Potsdam–Jena managed Land (LPJmL), which simulates biophysical and biogeochemical processes as well as productivity and yield of the most important crops worldwide, using a concept of crop functional types (CFTs). Based on the LPJ‐Dynamic Global Vegetation Model, LPJmL simulates the transient changes in carbon and water cycles due to land use, the specific phenology and seasonal CO₂ fluxes of agricultural‐dominated areas, and the production of crops and grazing land. It uses 13 CFTs (11 arable crops and two managed grass types), with specific parameterizations of phenology connected to leaf area development. Carbon is allocated daily towards four carbon pools, one being the yield‐bearing storage organs. Management (irrigation, treatment of residues, intercropping) can be considered in order to capture their effect on productivity, on soil organic carbon and on carbon extracted from the ecosystem. For transient simulations for the 20th century, a global historical land use data set was developed, providing the annual cover fraction of the 13 CFTs, rain‐fed and/or irrigated, within 0.5° grid cells for the period 1901–2000, using published data on land use, crop distributions and irrigated areas. Several key results are compared with observations. The simulated spatial distribution of sowing dates for temperate cereals is comparable with the reported crop calendars. The simulated seasonal canopy development agrees better with satellite observations when actual cropland distribution is taken into account. Simulated yields for temperate cereals and maize compare well with FAO statistics. Monthly carbon fluxes measured at three agricultural sites also compare well with simulations. Global simulations indicate a ∼24% (respectively ∼10%) reduction in global vegetation (respectively soil) carbon due to agriculture, and 6–9 Pg C of yearly harvested biomass in the 1990s. In contrast to simulations of the potential natural vegetation showing the land biosphere to be an increasing carbon sink during the 20th century, LPJmL simulates a net carbon source until the 1970s (due to land use), and a small sink (mostly due to changing climate and CO₂) after 1970. This is comparable with earlier LPJ simulations using a more simple land use scheme, and within the uncertainty range of estimates in the 1980s and 1990s. The fluxes attributed to land use change compare well with Houghton's estimates on the land use related fluxes until the 1970s, but then they begin to diverge, probably due to the different rates of deforestation considered. The simulated impacts of agriculture on the global water cycle for the 1990s are∼5% (respectively∼20%) reduction in transpiration (respectively interception), and∼44% increase in evaporation. Global runoff, which includes a simple irrigation scheme, is practically not affected.     

中国横断山地区蓝藻型肺衣属地衣的三个新种

在形态和化学研究的基础上,结合分子生物学研究方法（ITS片段）,对中国横断山地区的830号与蓝细菌共生的肺衣属标本进行了分类学研究,共发现3个新种;其中,横断山肺衣L. hengduanensis的主要特征是具粉芽化裂芽,无脊肺衣L. irrugulosa的网脊不明显,以及宽叶肺衣L. latilobulata的裂片顶端宽且钝圆;3个种在ITS系统发育树上分别形成独立小枝。文中提供了中国肺衣属中与蓝细菌共生的物种检索表。     

Solvent-induced free energy landscape and solute-solvent dynamic coupling in a multielement solute

Molecular dynamics simulations using a simple multielement model solute with internal degrees of freedom and accounting for solvent-induced interactions to all orders in explicit water are reported. The potential energy landscape of the solute is flat in vacuo. However, the sole untruncated solvent-induced interactions between apolar (hydrophobic) and charged elements generate a rich landscape of potential of mean force exhibiting typical features of protein landscapes. Despite the simplicity of our solute, the depth of minima in this landscape is not far in size from free energies that stabilize protein conformations. Dynamical coupling between configurational switching of the system and hydration reconfiguration is also elicited. Switching is seen to occur on a time scale two orders of magnitude longer than that of the reconfiguration time of the solute taken alone, or that of the unperturbed solvent. Qualitatively, these results are unaffected by a different choice of the water-water interaction potential. They show that already at an elementary level, solvent-induced interactions alone, when fully accounted for, can be responsible for configurational and dynamical features essential to protein folding and function.