Calcium in isolated mitochondria from the left ventricular wall

The content of calcium per mg mitochondrial protein has been measured by conventional biochemical methods in myocardial tissue of some mammalian species. In addition, a method is presented for (1) the analysis of mitochondrial volumes in the same tissues and (2) calculating the amount of calcium in units of 10(6) mitochondria. It appears that a highly significant correlation exists between the calcium content and the number of mitochondria, with a positive correlation coefficient of 0.92. The mean mitochondrial volume in fractions of the rabbit myocardium was found to be 1.3386 micron3. Electron microscopic studies demonstrate pure mitochondrial fractions and only moderate structural alterations. The method described may represent a useful supplement for the estimation of calcium fluxes in mitochondria and of alterations in their volume, number and structure under conditions of myocardial ischemia.     

Widespread seafloor anoxia during generation of the Ediacaran Shuram carbon isotope excursion

Reconstructing the oxygenation history of Earth's oceans during the Ediacaran period (635 to 539 million years ago) has been challenging, and this has led to a polarizing debate about the environmental conditions that played host to the rise of animals. One focal point of this debate is the largest negative inorganic C-isotope excursion recognized in the geologic record, the Shuram excursion, and whether this relic tracks the global-scale oxygenation of Earth's deep oceans. To help inform this debate, we conducted a detailed geochemical investigation of two siliciclastic-dominated successions from Oman deposited through the Shuram Formation. Iron speciation data from both successions indicate formation beneath an intermittently anoxic local water column. Authigenic thallium (Tl) isotopic compositions leached from both successions are indistinguishable from bulk upper continental crust (ε²⁰⁵Tl_A ≈ −2) and, by analogy with modern equivalents, likely representative of the ancient seawater ε²⁰⁵Tl value. A crustal seawater ε²⁰⁵Tl value requires limited manganese (Mn) oxide burial on the ancient seafloor, and by extension widely distributed anoxic sediment porewaters. This inference is supported by muted redox-sensitive element enrichments (V, Mo, and U) and consistent with some combination of widespread (a) bottom water anoxia and (b) high sedimentary organic matter loading. Contrary to a classical hypothesis, our interpretations place the Shuram excursion, and any coeval animal evolutionary events, in a predominantly anoxic global ocean.     

FGF10 maintains distal lung bud epithelium and excessive signaling leads to progenitor state arrest,distalization, and goblet cell metaplasia

Background  

Interaction with the surrounding mesenchyme is necessary for development of endodermal organs, and Fibroblast growth factors have recently emerged as mesenchymal-expressed morphogens that direct endodermal morphogenesis. The fibroblast growth factor 10 (Fgf10) null mouse is characterized by the absence of lung bud development. Previous studies have shown that this requirement for Fgf10 is due in part to its role as a chemotactic factor during branching morphogenesis. In other endodermal organs Fgf10 also plays a role in regulating differentiation.     

A community resource benchmarking predictions of peptide binding to MHC-I molecules

Recognition of peptides bound to major histocompatibility complex (MHC) class I molecules by T lymphocytes is an essential part of immune surveillance. Each MHC allele has a characteristic peptide binding preference, which can be captured in prediction algorithms, allowing for the rapid scan of entire pathogen proteomes for peptide likely to bind MHC. Here we make public a large set of 48,828 quantitative peptide-binding affinity measurements relating to 48 different mouse, human, macaque, and chimpanzee MHC class I alleles. We use this data to establish a set of benchmark predictions with one neural network method and two matrix-based prediction methods extensively utilized in our groups. In general, the neural network outperforms the matrix-based predictions mainly due to its ability to generalize even on a small amount of data. We also retrieved predictions from tools publicly available on the internet. While differences in the data used to generate these predictions hamper direct comparisons, we do conclude that tools based on combinatorial peptide libraries perform remarkably well. The transparent prediction evaluation on this dataset provides tool developers with a benchmark for comparison of newly developed prediction methods. In addition, to generate and evaluate our own prediction methods, we have established an easily extensible web-based prediction framework that allows automated side-by-side comparisons of prediction methods implemented by experts. This is an advance over the current practice of tool developers having to generate reference predictions themselves, which can lead to underestimating the performance of prediction methods they are not as familiar with as their own. The overall goal of this effort is to provide a transparent prediction evaluation allowing bioinformaticians to identify promising features of prediction methods and providing guidance to immunologists regarding the reliability of prediction tools.     

18F-FDG PET Imaging of Murine Atherosclerosis: Association with Gene Expression of Key Molecular Markers

Aim

To study whether ¹⁸F-FDG can be used for in vivo imaging of atherogenesis by examining the correlation between ¹⁸F-FDG uptake and gene expression of key molecular markers of atherosclerosis in apoE^−/− mice.

Methods

Nine groups of apoE^−/− mice were given normal chow or high-fat diet. At different time-points, ¹⁸F-FDG PET/contrast-enhanced CT scans were performed on dedicated animal scanners. After scans, animals were euthanized, aortas removed, gamma counted, RNA extracted from the tissue, and gene expression of chemo (C-X-C motif) ligand 1 (CXCL-1), monocyte chemoattractant protein (MCP)-1, vascular cell adhesion molecule (VCAM)-1, cluster of differentiation molecule (CD)-68, osteopontin (OPN), lectin-like oxidized LDL-receptor (LOX)-1, hypoxia-inducible factor (HIF)-1α, HIF-2α, vascular endothelial growth factor A (VEGF), and tissue factor (TF) was measured by means of qPCR.

Results

The uptake of ¹⁸F-FDG increased over time in the groups of mice receiving high-fat diet measured by PET and ex vivo gamma counting. The gene expression of all examined markers of atherosclerosis correlated significantly with ¹⁸F-FDG uptake. The strongest correlation was seen with TF and CD68 (p<0.001). A multivariate analysis showed CD68, OPN, TF, and VCAM-1 to be the most important contributors to the uptake of ¹⁸F-FDG. Together they could explain 60% of the ¹⁸F-FDG uptake.

Conclusion

We have demonstrated that ¹⁸F-FDG can be used to follow the progression of atherosclerosis in apoE^−/− mice. The gene expression of ten molecular markers representing different molecular processes important for atherosclerosis was shown to correlate with the uptake of ¹⁸F-FDG. Especially, the gene expressions of CD68, OPN, TF, and VCAM-1 were strong predictors for the uptake.     

Combined ensiling and hydrothermal processing as efficient pretreatment of sugarcane bagasse for 2G bioethanol production

Background

Ensiling cannot be utilized as a stand-alone pretreatment for sugar-based biorefinery processes but, in combination with hydrothermal processing, it can enhance pretreatment while ensuring a stable long-term storage option for abundant but moist biomass. The effectiveness of combining ensiling with hydrothermal pretreatment depends on biomass nature, pretreatment, and silage conditions.

Results

In the present study, the efficiency of the combined pretreatment was assessed by enzymatic hydrolysis and ethanol fermentation, and it was demonstrated that ensiling of sugarcane bagasse produces organic acids that can partly degrade biomass structure when in combination with hydrothermal treatment, with the consequent improvement of the enzymatic hydrolysis of cellulose and of the overall 2G bioethanol process efficiency. The optimal pretreatment conditions found in this study were those using ensiling and/or hydrothermal pretreatment at 190 °C for 10 min as this yielded the highest overall glucose recovery yield and ethanol yield from the raw material (0.28–0.30 g/g and 0.14 g/g, respectively).

Conclusion

Ensiling prior to hydrothermal pretreatment offers a controlled solution for wet storage and long-term preservation for sugarcane bagasse, thus avoiding the need for drying. This preservation method combined with long-term storage practice can be an attractive option for integrated 1G/2G bioethanol plants, as it does not require large capital investments or energy inputs and leads to comparable or higher overall sugar recovery and ethanol yields.

     

Effects of Elevated Atmospheric Carbon Dioxide and Temperature on Soil Respiration in a Boreal Forest Using δ13C as a Labeling Tool

This study examines the effect of elevated atmospheric carbon dioxide [CO₂] (+340 ppm, ¹³C-depleted) and/or elevated air temperature (2.8–3.5°C) on the rate and δ¹³C of soil respiration. The study was conducted in a boreal Norway spruce forest using temperature-controlled whole-tree chambers and ¹³C as a marker for root respiration. The δ¹³C of needle carbohydrates was followed after the onset of the CO₂ treatment in August 2001 and during a 2.5-week period in the summer of 2002. Averaged over the growing seasons of 2002 and 2003, we observed a 48% and 62% increase, respectively, in soil respiration in response to elevated [CO₂], but no response to elevated air temperature. The percentage increase in response to elevated [CO₂] varied seasonally (between 10% and 190% relative to the control), but the absolute increase varied less (39 ± 11 mg C m⁻² h⁻¹; mean ± SD). Data on δ¹³C of soil respiration indicate that this increase in soil respiration rate resulted from increased root/rhizosphere respiration of recently fixed carbon. Our results support the hypothesis that root/rhizosphere respiration is sensitive to variation in substrate availability.