Methane-producing microbial community in a coal bed of the Illinois basin

A series of molecular and geochemical studies were performed to study microbial, coal bed methane formation in the eastern Illinois Basin. Results suggest that organic matter is biodegraded to simple molecules, such as H(2) and CO(2), which fuel methanogenesis and the generation of large coal bed methane reserves. Small-subunit rRNA analysis of both the in situ microbial community and highly purified, methanogenic enrichments indicated that Methanocorpusculum is the dominant genus. Additionally, we characterized this methanogenic microorganism using scanning electron microscopy and distribution of intact polar cell membrane lipids. Phylogenetic studies of coal water samples helped us develop a model of methanogenic biodegradation of macromolecular coal and coal-derived oil by a complex microbial community. Based on enrichments, phylogenetic analyses, and calculated free energies at in situ subsurface conditions for relevant metabolisms (H(2)-utilizing methanogenesis, acetoclastic methanogenesis, and homoacetogenesis), H(2)-utilizing methanogenesis appears to be the dominant terminal process of biodegradation of coal organic matter at this location.     

Quercitol and osmotic adaptation of field-grown Eucalyptus under seasonal drought stress

This study investigated the role of quercitol in osmotic adjustment in field-grown Eucalyptus astringens Maiden subject to seasonal drought stress over the course of 1 year. The trees grew in a native woodland and a farm plantation in the semi-arid wheatbelt region of south Western Australia. Plantation trees allocated relatively more biomass to leaves than woodland trees, but they suffered greater drought stress over summer, as indicated by lower water potentials, CO₂ assimilation rates and stomatal conductances. In contrast, woodland trees had relatively fewer leaves and suffered less drought stress. Plantation trees under drought stress engaged in osmotic adjustment, but woodland trees did not. Quercitol made a significant contribution to osmotic adjustment in drought-stressed trees (25% of total solutes), and substantially more quercitol was measured in the leaves of plantation trees (5% dry matter) than in the leaves of woodland trees (2% dry matter). We found no evidence that quercitol was used as a carbon storage compound while starch reserves were depleted under drought stress. Differences in stomatal conductance, biomass allocation and quercitol production clearly indicate that E. astringens is both morphologically and physiologically 'plastic' in response to growth environment, and that osmotic adjustment is only one part of a complex strategy employed by this species to tolerate drought.     

Brief communication: Two and three-dimensional analysis of bone mass and microstructure in a bog body from the Iron Age

Human remains from peat bogs, called "bog bodies," have yielded valuable insights into human history because of their excellent preservation of soft tissue. On the other hand, the acidic environment of the peat leads to an extensive demineralization of skeletal elements, complicating their analysis. We studied the skeleton of the bog body "Moora" dated to approximately 650 B.C. Nondestructive evaluation of the bone was made using contact X-rays, peripheral quantitative computed tomography (pQCT) analysis, multislice computed tomography (CT) and high resolution micro computed tomography (microCT) imaging. Two thousand seven hundred years in the acidic environment of the bog led to a loss of 92.7% of bone mineral density. Despite this demineralization and in contrast to other bog bodies, the spatial structure of the bones of "Moora" is exceptionally well preserved. We found Harris lines and were able to obtain the first three-dimensional data on the trabecular microstructure of the bone of a young woman from the early Iron Age.     

A miniaturized high-throughput screening assay for fucosyltransferase VII

Fucosyltransferase VII (FucTVII) is a very promising drug target for treatment of inflammatory skin diseases. Its activity is required for synthesis of the sialyl-Lewis X glycoepitopes on the E- and P-selectin ligands, necessary for lymphocyte migration into the skin. High-throughput screening (HTS) of large chemical libraries has become the main source of novel chemical entities for the pharmaceutical industry. The screening of very large compound collections requires the use of specialized assay techniques that minimize time and costs. We describe the development of a miniaturized scintillation proximity assay for human FucTVII based on a oligosaccharide acceptor substrate that is identical to the glycosylation of the physiological substrate. In addition to assay development, the assay performance in a HTS campaign is shown. We screened 798,131 compounds from the Schering AG HTS library and identified 233 IC50 hits; 229 hits were FucTVII specific in so far as they did not inhibit either alpha-fucosidase or galactosyltransferase. In addition to screening a drug-like small-molecule collection, we worked on rational approaches to develop inhibitors or glycosidic decoys based on oligosaccharide-substrate analogues. The structure-activity relationship observed thereby is very narrow and shows strict requirements that are consistent with the described substrate specificity of FucTVII.     

DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA

We show that DNA molecules amplified by PCR from DNA extracted from animal bones and teeth that vary in age between 25 000 and over 50 000 years carry C→T and G→A substitutions. These substitutions can reach high proportions among the molecules amplified and are due to the occurrence of modified deoxycytidine residues in the template DNA. If the template DNA is treated with uracil N-glycosylase, these substitutions are dramatically reduced. They are thus likely to result from deamination of deoxycytidine residues. In addition, ‘jumping PCR’, i.e. the occurrence of template switching during PCR, may contribute to these substitutions. When DNA sequences are amplified from ancient DNA extracts where few template molecules initiate the PCR, precautions such as DNA sequence determination of multiple clones derived from more than one independent amplification are necessary in order to reduce the risk of determination of incorrect DNA sequences. When such precautionary measures are taken, errors induced by damage to the DNA template are unlikely to be more frequent than ~0.1% even under the unlikely scenario where each amplification starts from a single template molecule.     

The Fibrin Matrix Regulates Angiogenic Responses within the Hemostatic Microenvironment through Biochemical Control

Conceptually, premature initiation of post-wound angiogenesis could interfere with hemostasis, as it relies on fibrinolysis. The mechanisms facilitating orchestration of these events remain poorly understood, however, likely due to limitations in discerning the individual contribution of cells and extracellular matrix. Here, we designed an in vitro Hemostatic-Components-Model (HCM) to investigate the role of the fibrin matrix as protein factor-carrier, independent of its cell-scaffold function. After characterizing the proteomic profile of HCM-harvested matrix releasates, we demonstrate that the key pro-/anti-angiogenic factors, VEGF and PF4, are differentially bound by the matrix. Changing matrix fibrin mass consequently alters the balance of releasate factor concentrations, with differential effects on basic endothelial cell (EC) behaviors. While increasing mass, and releasate VEGF levels, promoted EC chemotactic migration, it progressively inhibited tube formation, a response that was dependent on PF4. These results indicate that the clot’s matrix component initially serves as biochemical anti-angiogenic barrier, suggesting that post-hemostatic angiogenesis follows fibrinolysis-mediated angiogenic disinhibition. Beyond their significance towards understanding the spatiotemporal regulation of wound healing, our findings could inform the study of other pathophysiological processes in which coagulation and angiogenesis are prominent features, such as cardiovascular and malignant disease.     

Examination of brown adipose tissue thermogenesis of glutamate-induced obese rats by differential temperature measurements.

Differential temperature measurement between interscapular brown adipose tissue (BAT, Tbat), rectum (Trect) and a subcutaneous point in the back left of the vertebral column (Tsc) was useful for examination of BAT-thermogenesis in glutamate-induced obese Wistar-rats. Positive temperature gradients Tbat-Tsc pointed to a basal BAT-thermogenesis, whereas negative temperature gradients Tbat-Trect did not indicate that heat production in lean and obese rats. One may conclude from this, that inclusion of subcutaneous points outside the BAT improves sensitivity of differential temperature measurements for BAT-thermogenesis. Basal temperatures Tbat, Trect and Tsc were reduced in obese rats compared to lean rats, although thermoinsulation of obese rats is improved on account of their high fat content. This points to a diminished heat production in obese rats. Cold exposure at 4 degrees C elicited an increase of temperature gradients Tbat-Trect in lean as well as in obese rats, with positive values found only in lean rats. However, positive values Tbat-Tsc were calculated for both groups. Increases were noted only in lean rats. Injection of noradrenaline (0.5 mg/kg i.m.) was followed by positive temperature gradients Tbat-Trect and increased positive values for Tbat-Tsc, pointing to a remarkable activation of BAT-thermogenesis in lean and obese rats. These findings confirm, that glutamate-induced obese rats preserved the ability to activate BAT-thermogenesis. There were, however, hints of reduced heat production in BAT of obese rats, thus contributing to obesity despite normophagia.     

Assessment of Data Quality: Errors of Measurement and Errors of Process

As projects progress from pilot studies with few simple variables and small samples, the research process as a whole becomes qualitatively more complex and subject to an array of contamination by errors and mistakes. Data usually undergo a series of manipulations (e.g., recording, computer entry, transmission) prior to final statistical analysis. The process, then, consists of numerous operations only ending with eventual statistical analysis and write-up. We present a means of estimating the impact of process error in the same terms as psychometric reliability and discuss the implications for reducing the impact of errors on overall data quality.     

Hypoxia-based strategies for angiogenic induction

Therapeutic angiogenesis promises to aid the healing and regeneration of tissues suffering from a compromised vascular supply. Ischaemia therapy has so far primarily focused on delivering isolated angiogenic growth factors. The limited success of these strategies in clinical trials, however, is increasingly forcing researchers to recognize the difficulties associated with trying to mimic the angiogenic process, due to its natural complexity. Instead, a new school of thought is gradually emerging, focusing on how to induce angiogenesis at its onset, by utilizing hypoxia, the primary angiogenic stimulus in physiological, as well pathological states. This shift in therapeutic approach is underlined by the realization of the importance of depressed HIF-1 α-mediated gene programming in non-healing ischemic tissues, which could explain their apparent habituation to chronic hypoxic stress and the limited capacity to generate adaptive angiogenesis. Hypoxia-based strategies, then effectively aim to override the habituated angiogenic cellular response, re-start the regenerative process and drive it to completion. Here we make a distinction between those strategies that utilize hypoxia in vitro as a preconditioning tool to optimize the angiogenic potential of tissue/cells before transplantation, vs. strategies that aim to induce hypoxia-induced signaling in vivo, directly, through pharmacological means or gene transfer. We then discuss possible future directions for the field, as it moves into the phase of clinical trials.