PRFS-Based MR Thermometry Versus an Alternative T1 Magnitude Method – Comparative Performance Predicting Thermally Induced Necrosis in Hepatic Tumor Ablation

Objective

To compare the accuracy of a semi-quantitative proton resonance frequency shift (PRFS) thermal mapping interface and an alternative qualitative T1 thermometry model in predicting tissue necrosis in an established routine setting of MRI-guided laser ablation in the human liver.

Materials and Methods

34 cases of PRFS-guided (GRE) laser ablation were retrospectively matched with 34 cases from an earlier patient population of 73 individuals being monitored through T1 magnitude image evaluation (FLASH 2D). The model-specific real-time estimation of necrotizing thermal impact (above 54 °C zone and T1 signal loss, respectively) was correlated in size with the resulting necrosis as shown by lack of enhancement on the first-day contrast exam (T1). Matched groups were compared using the Mann-Whitney test.

Results

Online PRFS guidance was available in 33 of 34 cases. Positive size correlation between calculated impact zone and contrast defect at first day was evident in both groups (p < 0.0004). The predictive error estimating necrosis was median 21 % (range 1 % - 52 %) in the PRFS group and 61 % (range 22 - 84 %) in the T1 magnitude group. Differences in estimating lethal impact were significant (p = 0.004), whereas the real extent of therapy-induced necrosis showed no significant difference (p > 0.28) between the two groups.

Conclusion

PRFS thermometry is feasible in a clinical setting of thermal hepatic tumor ablation. As an interference-free MR-tool for online therapy monitoring its accuracy to predict tissue necrosis is superior to a competing model of thermally induced alteration of the T1 magnitude signal.     

Climate change amplifies gross nitrogen turnover in montane grasslands of Central Europe in both summer and winter seasons

The carbon‐ and nitrogen‐rich soils of montane grasslands are exposed to above‐average warming and to altered precipitation patterns as a result of global change. To investigate the consequences of climatic change for soil nitrogen turnover, we translocated intact plant–soil mesocosms along an elevational gradient, resulting in an increase of the mean annual temperature by approx. 2 °C while decreasing precipitation from approx. 1500 to 1000 mm. Following three years of equilibration, we monitored the dynamics of gross nitrogen turnover and ammonia‐oxidizing bacteria (AOB) and archaea (AOA) in soils over an entire year. Gross nitrogen turnover and gene levels of AOB and AOA showed pronounced seasonal dynamics. Both summer and winter periods equally contributed to cumulative annual N turnover. However, highest gross N turnover and abundance of ammonia oxidizers were observed in frozen soil of the climate change site, likely due to physical liberation of organic substrates and their rapid turnover in the unfrozen soil water film. This effect was not observed at the control site, where soil freezing did not occur due to a significant insulating snowpack. Climate change conditions accelerated gross nitrogen mineralization by 250% on average. Increased N mineralization significantly stimulated gross nitrification by AOB rather than by AOA. However, climate change impacts were restricted to the 2–6 cm topsoil and rarely occurred at 12–16 cm depth, where generally much lower N turnover was observed. Our study shows that significant mineralization pulses occur under changing climate, which is likely to result in soil organic matter losses with their associated negative impacts on key soil functions. We also show that N cycling processes in frozen soil can be hot moments for N turnover and thus are of paramount importance for understanding seasonal patterns, annual sum of N turnover and possible climate change feedbacks.     

The glycoprotein cytoplasmic tail of Uukuniemi virus (Bunyaviridae) interacts with ribonucleoproteins and is critical for genome packaging

We have analyzed the importance of specific amino acids in the cytoplasmic tail of the glycoprotein G(N) for packaging of ribonucleoproteins (RNPs) into virus-like particles (VLPs) of Uukuniemi virus (UUK virus), a member of the Bunyaviridae family. In order to study packaging, we added the G(N)/G(C) glycoprotein precursor (p110) to a polymerase I-driven minigenome rescue system to generate VLPs that are released into the supernatant. These particles can infect new cells, and reporter gene expression can be detected. To determine the role of UUK virus glycoproteins in RNP packaging, we performed an alanine scan of the glycoprotein G(N) cytoplasmic tail (amino acids 1 to 81). First, we discovered three regions in the tail (amino acids 21 to 25, 46 to 50, and 71 to 81) which are important for minigenome transfer by VLPs. Further mutational analysis identified four amino acids that were important for RNP packaging. These amino acids are essential for the binding of nucleoproteins and RNPs to the glycoprotein without affecting the morphology of the particles. No segment-specific interactions between the RNA and the cytoplasmic tail could be observed. We propose that VLP systems are useful tools for analyzing protein-protein interactions important for packaging of viral genome segments, assembly, and budding of other members of the Bunyaviridae family.     

Vertical profiles of CH4 concentrations,dissolved substrates and processes involved in CH4 production in a flooded Italian rice field

Vertical profiles were measured in soil cores taken from flooded rice fields in the Po valley during July and August 1990. Methane concentrations generally increased with depth and reached maximum values of 150–500 μM in 5–13 cm depth. However, the shape of the profiles was very different when studying different soil cores. The CH₄ content of gas bubbles showed a similar variability which apparently was due to spatial rather than temporal inhomogeneities. Similar inhomogeneities were observed in the vertical profiles of acetate, propionate, lactate, and formate which showed maximum values of 1500, 66, 135, and 153, μM, respectively. However, maxima and minima of the vertical profiles of the different substates usually coincided in one particular soil core. Large inhomogeneities in the vertical profiles were also observed for the rates of total CH₄ production, however, the percentage contribution of H₂/CO₂ to CH₄ production was relatively homogeneous at 24 ± 7% (SD). Similarly, the H₂ content of gas bubbles was relatively constant at 93.3 ± 9.6 ppmv when randomly sampled in the rice field at different times of the day. A small contribution (6%) of H₂/CO₂ to acetate production was also observed. Vertical profiles of the respiratory index (RI) for [2-¹⁴C] acetate showed that acetate was predominantly degraded by methanogenesis in 5–11 cm depth, but by respiration in the surface soil (3 cm depth) and in soil layers below 13–16 cm depth which coincided with a transition of the colour (grey to reddish) and the physical characteristics (porosity, density) of the soil. The observations indicate that the microbial community which degrades organic matter to CH₄ is in itself relatively homogenous, but operates at highly variable rates within the soil structure. Author for correspondence     

T cell epitope definition by differential mass spectrometry: identification of a novel, immunogenic HLA-B8 ligand directly from renal cancer tissue

In this study, we describe a differential mass spectrometric technique for the immuno-proteomic analysis of the major histocompatibility complex (MHC) peptides of a renal cell carcinoma (RCC) biopsy compared with the healthy kidney tissue of the same patient after nephrectomy. Using a stable isotope labeling approach, we could directly compare and relatively quantify 43 MHC-peptide pairs, most of which were present in similar proportions on both normal kidney and tumor. Significantly, two dominant peptides of monoisotopic masses ([M+H](+)) 973.43 u and 967.59 u, respectively, were found exclusively in the tumor sample. One of these was identified as originating from heme oxygenase-1 (HO-1), a protein involved in induction of apoptosis resistance, immuno-suppression and neoangiogenesis and reported to be up-regulated in various cancer types. Moreover, the corresponding synthetic HO-1-derived peptide was shown to be immunogenic in vitro by generation of CD8+ T cell lines with peptide-specific cytolytic activity. Thus, this peptide is an example of a differentially identified T cell epitope that could be considered as a target for immunotherapy.     

Stress sensor triggers conformational response of the integral membrane protein microsomal glutathione transferase 1

Microsomal glutathione (GSH) transferase 1 (MGST1) is a trimeric, integral membrane protein involved in cellular response to chemical or oxidative stress. The cytosolic domain of MGST1 harbors the GSH binding site and a cysteine residue (C49) that acts as a sensor of oxidative and chemical stress. Spatially resolved changes in the kinetics of backbone amide H/D exchange reveal that the binding of a single molecule of GSH/trimer induces a cooperative conformational transition involving movements of the transmembrane helices and a reordering of the cytosolic domain. Alkylation of the stress sensor preorganizes the helices and facilitates the cooperative transition resulting in catalytic activation.     

PARma: identification of microRNA target sites in AGO-PAR-CLIP data

PARma is a complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites. It integrates specific characteristics of the experiments into a generative model. The model and a novel pattern discovery tool are iteratively applied to data to estimate seed activity probabilities, cluster confidence scores and to assign the most probable microRNA. Based on differential PAR-CLIP analysis and comparison to RIP-Chip data, we show that PARma is more accurate than existing approaches. PARma is available from http://www.bio.ifi.lmu.de/PARma