Evolution of carbon fluxes during initial soil formation along the forefield of Damma glacier, Switzerland

Soil carbon (C) fluxes, soil respiration and dissolved organic carbon (DOC) leaching were explored along the young Damma glacier forefield chronosequence (7-128years) over a three-year period. To gain insight into the sources of soil CO2 effluxes, radiocarbon signatures of respired CO2 were measured and a vegetation-clipping experiment was performed. Our results showed a clear increase in soil CO2 effluxes with increasing site age from 9±1 to 160±67gCO2-Cm−2year−1, which was linked to soil C accumulation and development of vegetation cover. Seasonal variations of soil respiration were mainly driven by temperature; between 62 and 70% of annual CO2 effluxes were respired during the 4-month long summer season. Sources of soil CO2 effluxes changed along the glacier forefield. For most recently deglaciated sites, radiocarbon-based age estimates indicated ancient C to be the dominant source of soil-respired CO2. At intermediate site age (58-78years), the contribution of new plant-fixed C via rhizosphere respiration amounted up to 90%, while with further soil formation, heterotrophically respired C probably from accumulated ‘older' soil organic carbon (SOC) became increasingly important. In comparison with soil respiration, DOC leaching at 10cm depth was small, but increased similarly from 0.4±0.02 to 7.4±1.6gDOCm−2year−1 over the chronosequence. A strong rise of the ratio of SOC to secondary iron and aluminium oxides strongly suggests that increasing DOC leaching with site age results from a faster increase of the DOC source, SOC, than of the DOC sink, reactive mineral surfaces. Overall, C losses from soil by soil respiration and DOC leaching increased from 9±1 to 70±17 and further to 168±68gCm−2year−1 at the <10, 58-78, and 110-128year old sites. By comparison, total ecosystem C stocks increased from 0.2 to 1.1 and to 3.1kgCm−2 from the young to intermediate and old sites. Therefore, the ecosystem evolved from a dominance of C accumulation in the initial phase to a high throughput system. We suggest that the relatively strong increase in soil C stocks compared to C fluxes is a characteristic feature of initial soil formation on freshly exposed rock

Protective distal side-to-side neurorrhaphy in proximal nerve injury-an experimental study with rats

Background Side-to-side neurorrhaphy may protect the denervated end organ and preserve the initial connection with proximal stump. We examined the effect of protective side-to-side anastomosis on nerve and end organ regeneration in proximal nerve injury model.Methods The left common peroneal nerve of 24 Sprague Dawley rats was proximally transected. In groups B and C, side-to-side neurorrhaphy was performed distally between the peroneal and tibial nerves without (group B) and with (group C) partial donor nerve axotomy inside the epineural window. Group A served as an unprotected control. After 26 weeks, the proximal transection was repaired with end-to-end neurorrhaphy on all animals. Regeneration was followed during 12 weeks with the walk track analysis. Morphometric studies and wet muscle mass calculations were conducted at the end of the follow-up period.Results The results of the walk track analysis were significantly better in groups B and C compared to group A. Groups B and C showed significantly higher wet mass ratios of the tibialis anterior and extensor digitorum longus muscle compared to group A. Group C showed significantly higher morphometric values compared to group A. Group B reached higher values of the fibre count, fibre density, and percentage of the fibre area compared to group A.Conclusions Protective distal side-to-side neurorrhaphy reduced muscle atrophy and had an improving effect on the morphometric studies and walk track analysis. Distal side-to-side neurorrhaphy does not prevent the regenerating axons to grow from the proximal stump to achieve distal nerve stump

Natural products in modern life science

With a realistic threat against biodiversity in rain forests and in the sea, a sustainable use of natural products is becoming more and more important. Basic research directed against different organisms in Nature could reveal unexpected insights into fundamental biological mechanisms but also new pharmaceutical or biotechnological possibilities of more immediate use. Many different strategies have been used prospecting the biodiversity of Earth in the search for novel structure–activity relationships, which has resulted in important discoveries in drug development. However, we believe that the development of multidisciplinary incentives will be necessary for a future successful exploration of Nature. With this aim, one way would be a modernization and renewal of a venerable proven interdisciplinary science, Pharmacognosy, which represents an integrated way of studying biological systems. This has been demonstrated based on an explanatory model where the different parts of the model are explained by our ongoing research. Anti-inflammatory natural products have been discovered based on ethnopharmacological observations, marine sponges in cold water have resulted in substances with ecological impact, combinatory strategy of ecology and chemistry has revealed new insights into the biodiversity of fungi, in depth studies of cyclic peptides (cyclotides) has created new possibilities for engineering of bioactive peptides, development of new strategies using phylogeny and chemography has resulted in new possibilities for navigating chemical and biological space, and using bioinformatic tools for understanding of lateral gene transfer could provide potential drug targets. A multidisciplinary subject like Pharmacognosy, one of several scientific disciplines bridging biology and chemistry with medicine, has a strategic position for studies of complex scientific questions based on observations in Nature. Furthermore, natural product research based on intriguing scientific questions in Nature can be of value to increase the attraction for young students in modern life science

Opti-Owecs: Final Report Vol. 0: Executive Summary

It was the particular mission of the project 'Structural and Economic Optimisation of Bottom-Mounted Offshore Wind Energy Converters' (Opti-OWECS) to extend the state-of-the-art, to determine required methods and to demonstrate practical solutions which will significantly reduce the electricity cost. This will facilitate the exploitation of true offshore sites on a commercial base in a medium time scale of 5 to 10 years from now. In several fields, e.g. support structure design, installation of the offshore wind energy converters, operation and maintenance, dynamics of the entire offshore wind energy converter, structural reliability considerations, etc., the study demonstrated new propositions which will contribute significantly to a mature offshore wind energy technology. This was achieved due to a smooth cooperation of leading industrial engineers and researchers from the wind energy field, offshore technology and power management. Moreover, an innovative design methodology devoted particularly to offshore wind energy conversion systems (OWECS) was developed and successfully demonstrated. The so-called 'integrated OWECS design approach' considers the components of an offshore wind farm as parts of an entire system. Therefore interactions between sub-systems are considered in a complete and practical form as possible so that the design solution is governed by overall criteria such as: levelised production costs, adaptation to the actual site conditions, dynamics of the entire system, installation effort as well as OWECS availability. Furthermore, a novel OWECS cost model was developed which led among other work of the project to the identification of the main cost drivers, i.e. annual mean wind speed, distance from shore, operation and maintenance aspects including wind turbine reliability and availability. A link between these results and a database of the offshore wind energy potential in Europe, developed by the previous Joule project JOUR 0072, facilitated the first estimate of energy cost consistent over entire regions of Northern Europe. The European Commission has supported the project in the scope of the framework of the Non Nuclear Energy Programme JOULE Ill (Research and Technical Development) under grant JOR3-CT95-0087

TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays

<p>Abstract</p> <p>Background</p> <p>High-throughput genotyping microarrays assess both total DNA copy number and allelic composition, which makes them a tool of choice for copy number studies in cancer, including total copy number and loss of heterozygosity (LOH) analyses. Even after state of the art preprocessing methods, allelic signal estimates from genotyping arrays still suffer from systematic effects that make them difficult to use effectively for such downstream analyses.</p> <p>Results</p> <p>We propose a method, TumorBoost, for normalizing allelic estimates of one tumor sample based on estimates from a single matched normal. The method applies to any paired tumor-normal estimates from any microarray-based technology, combined with any preprocessing method. We demonstrate that it increases the signal-to-noise ratio of allelic signals, making it significantly easier to detect allelic imbalances.</p> <p>Conclusions</p> <p>TumorBoost increases the power to detect somatic copy-number events (including copy-neutral LOH) in the tumor from allelic signals of Affymetrix or Illumina origin. We also conclude that high-precision allelic estimates can be obtained from a single pair of tumor-normal hybridizations, if TumorBoost is combined with single-array preprocessing methods such as (allele-specific) CRMA v2 for Affymetrix or BeadStudio's (proprietary) XY-normalization method for Illumina. A bounded-memory implementation is available in the open-source and cross-platform R package <it>aroma.cn</it>, which is part of the Aroma Project (<url>http://www.aroma-project.org/</url>).</p

Targeted resequencing of candidate genes using selector probes

Targeted genome enrichment is a powerful tool for making use of the massive throughput of novel DNA-sequencing instruments. We herein present a simple and scalable protocol for multiplex amplification of target regions based on the Selector technique. The updated version exhibits improved coverage and compatibility with next-generation-sequencing (NGS) library-construction procedures for shotgun sequencing with NGS platforms. To demonstrate the performance of the technique, all 501 exons from 28 genes frequently involved in cancer were enriched for and sequenced in specimens derived from cell lines and tumor biopsies. DNA from both fresh frozen and formalin-fixed paraffin-embedded biopsies were analyzed and 94% specificity and 98% coverage of the targeted region was achieved. Reproducibility between replicates was high (R2 = 0, 98) and readily enabled detection of copy-number variations. The procedure can be carried out in <24 h and does not require any dedicated instrumentation

Immunohistochemical expression of promyelocytic leukemia body in soft tissue sarcomas

<p>Abstract</p> <p>Background</p> <p>The function of promyelocytic leukemia (PML) bodies is not well known but plays an important role in controlling cell proliferation, apoptosis and senescence. This study was undertaken to analyze the clinical significance of PML body expression in primary tumor samples from malignant fibrous histiocytoma (MFH) and liposarcoma patients.</p> <p>Methods</p> <p>We studied MFH and liposarcoma samples from 55 patients for PML bodies. Fluorescent immunostaining of PML bodies was performed in the paraffin-embedded tumor sections.</p> <p>Results</p> <p>PML body immunostaining was identified in 63.9% of MFH and 63.2% of liposarcoma samples. PML body expression rates of all sarcoma cells were 1.5 ± 1.8% (range: 0–7.0) in MFH and 1.3 ± 1.4% (0–5.2) in liposarcoma samples. PML body expression (p = 0.0053) and a high rate of PML body expression (p = 0.0012) were significantly greater prognostic risk factors for death than the other clinical factors in MFH patients. All liposarcoma patients without expression of PML were disease free at the end of the study.</p> <p>Conclusion</p> <p>Our study suggests that the presence of PML bodies may indicate a poor prognosis for MFH and liposarcoma patients.</p

Inactivation of promoter 1B of APC causes partial gene silencing: evidence for a significant role of the promoter in regulation and causative of familial adenomatous polyposis

Familial adenomatous polyposis (FAP) is caused by germline mutations in the adenomatous polyposis coli (APC) gene. Two promoters, 1A and 1B, have been recognized in APC, and 1B is thought to have a minor role in the regulation of the gene. We have identified a novel deletion encompassing half of this promoter in the largest family (Family 1) of the Swedish Polyposis Registry. The mutation leads to an imbalance in allele-specific expression of APC, and transcription from promoter 1B was highly impaired in both normal colorectal mucosa and blood from mutation carriers. To establish the significance of promoter 1B in normal colorectal mucosa (from controls), expression levels of specific transcripts from each of the promoters, 1A and 1B, were examined, and the expression from 1B was significantly higher compared with 1A. Significant amounts of transcripts generated from promoter 1B were also determined in a panel of 20 various normal tissues examined. In FAP-related tumors, the APC germline mutation is proposed to dictate the second hit. Mutations leaving two or three out of seven 20-amino-acid repeats in the central domain of APC intact seem to be required for tumorigenesis. We examined adenomas from mutation carriers in Family 1 for second hits in the entire gene without any findings, however, loss of the residual expression of the deleterious allele was observed. Three major conclusions of significant importance in relation to the function of APC can be drawn from this study; (i) germline inactivation of promoter 1B is disease causing in FAP; (ii) expression of transcripts from promoter 1B is generated at considerable higher levels compared with 1A, demonstrating a hitherto unknown importance of 1B; (iii) adenoma formation in FAP, caused by impaired function of promoter 1B, does not require homozygous inactivation of APC allowing for alternative genetic models as basis for adenoma formation

Distinct Cytoplasmic and Nuclear Functions of the Stress Induced Protein DDIT3/CHOP/GADD153

DDIT3, also known as GADD153 or CHOP, encodes a basic leucine zipper transcription factor of the dimer forming C/EBP family. DDIT3 is known as a key regulator of cellular stress response, but its target genes and functions are not well characterized. Here, we applied a genome wide microarray based expression analysis to identify DDIT3 target genes and functions. By analyzing cells carrying tamoxifen inducible DDIT3 expression constructs we show distinct gene expression profiles for cells with cytoplasmic and nuclear localized DDIT3. Of 175 target genes identified only 3 were regulated by DDIT3 in both cellular localizations. More than two thirds of the genes were downregulated, supporting a role for DDIT3 as a dominant negative factor that could act by either cytoplasmic or nuclear sequestration of dimer forming transcription factor partners. Functional annotation of target genes showed cell migration, proliferation and apoptosis/survival as the most affected categories. Cytoplasmic DDIT3 affected more migration associated genes, while nuclear DDIT3 regulated more cell cycle controlling genes. Cell culture experiments confirmed that cytoplasmic DDIT3 inhibited migration, while nuclear DDIT3 caused a G1 cell cycle arrest. Promoters of target genes showed no common sequence motifs, reflecting that DDIT3 forms heterodimers with several alternative transcription factors that bind to different motifs. We conclude that expression of cytoplasmic DDIT3 regulated 94 genes. Nuclear translocation of DDIT3 regulated 81 additional genes linked to functions already affected by cytoplasmic DDIT3. Characterization of DDIT3 regulated functions helps understanding its role in stress response and involvement in cancer and degenerative disorders