Tumor Necrosis Factor Alpha and Insulin-Like Growth Factor 1 Induced Modifications of the Gene Expression Kinetics of Differentiating Skeletal Muscle Cells

Introduction TNF-alpha levels are increased during muscle wasting and chronic muscle degeneration and regeneration processes, which are characteristic for primary muscle disorders. Pathologically increased TNF-alpha levels have a negative effect on muscle cell differentiation efficiency, while IGF1 can have a positive effect;therefore, we intended to elucidate the impact of TNF-alpha and IGF1 on gene expression during the early stages of skeletal muscle cell differentiation. Methodology/Principal Findings This study presents gene expression data of the murine skeletal muscle cells PMI28 during myogenic differentiation or differentiation with TNF-alpha or IGF1 exposure at 0 h, 4 h, 12 h, 24 h, and 72 h after induction. Our study detected significant coregulation of gene sets involved in myoblast differentiation or in the response to TNF-alpha. Gene expression data revealed a time-and treatment-dependent regulation of signaling pathways, which are prominent in myogenic differentiation. We identified enrichment of pathways, which have not been specifically linked to myoblast differentiation such as doublecortin-like kinase pathway associations as well as enrichment of specific semaphorin isoforms. Moreover to the best of our knowledge, this is the first description of a specific inverse regulation of the following genes in myoblast differentiation and response to TNF-alpha: Aknad1, Cmbl, Sepp1, Ndst4, Tecrl, Unc13c, Spats2l, Lix1, Csdc2, Cpa1, Parm1, Serpinb2, Aspn, Fibin, Slc40a1, Nrk, and Mybpc1. We identified a gene subset (Nfkbia, Nfkb2, Mmp9, Mef2c, Gpx, and Pgam2),which is robustly regulated by TNF-alpha across independent myogenic differentiation studies. Conclusions This is the largest dataset revealing the impact of TNF-alpha or IGF1 treatment on gene expression kinetics of early in vitro skeletal myoblast differentiation. We identified novel mRNAs, which have not yet been associated with skeletal muscle differentiation or response to TNF-alpha. Results of this study may facilitate the understanding of transcriptomic networks underlying inhibited muscle differentiation in inflammatory diseases

Efficiency and adaptability of the benthic methane filter at Quepos Slide cold seeps, offshore Costa Rica

Large amounts of methane are delivered by fluids through the erosive forearc of the convergent margin offshore Costa Rica and lead to the formation of cold seeps at the sediment surface. Besides mud extrusion, numerous cold seeps are created by landslides induced by seamount subduction or fluid migration along major faults. Most of the dissolved methane reaching the seafloor at cold seeps is oxidized within the benthic microbial methane filter by anaerobic oxidation of methane (AOM). Measurements of AOM and sulfate reduction as well as numerical modeling of porewater profiles revealed a highly active and efficient benthic methane filter at Quepos Slide site; a landslide on the continental slope between the Nicoya and Osa Peninsula. Integrated areal rates of AOM ranged from 12.9 ± 6.0 to 45.2 ± 11.5 mmol m-2 d-1, with only 1 to 2.5% of the upward methane flux being released into the water column. Additionally, two parallel sediment cores from Quepos Slide were used for in vitro experiments in a recently developed Sediment-F low-Through (SLOT) system to simulate an increased fluid and methane flux from the bottom of the sediment core. The benthic methane filter revealed a high adaptability whereby the methane oxidation efficiency responded to the increased fluid flow within 150–170 days. To our knowledge, this study provides the first estimation of the natural biogeochemical response of seep sediments to changes in fluid flow

Microbial activity and carbonate isotope signatures as a tool for identification of spatial differences in methane advection: a case study at the Pacific Costa Rican margin

Subduction of the oceanic Cocos plate offshore Costa Rica causes strong advection of methane-charged fluids. Presented here are the first direct measurements of microbial anaerobic oxidation of methane (AOM) and sulfate reduction (SR) rates in sediments from the two mounds, applying radiotracer techniques in combination with numerical modeling. In addition, analysis of carbonate δ18O, δ13C, and 87Sr / 86Sr signatures constrain the origin of the carbonate-precipitating fluid. Average rates of microbial activities showed differences with a factor of 4.8 to 6.3 between Mound 11 [AOM 140.71 (±40.84 SD); SR 117.25 (±82.06 SD) mmol m−2 d−1, respectively] and Mound 12 [AOM 22.37 (±0.85 SD); SR 23.99 (±5.79 SD) mmol m−2 d−1, respectively]. Modeling results yielded flow velocities of 50 cm a−1 at Mound 11 and 8–15 cm a−1 at Mound 12. Analysis of oxygen and carbon isotope variations of authigenic carbonates from the two locations revealed higher values for Mound 11 (δ18O: 4.7 to 5.9‰, δ13C: −21.0 to −29.6‰), compared to Mound 12 (δ18O: 4.1 to 4.5‰, δ13C: −45.7 to −48.9‰). Analysis of carbonates 87Sr / 86Sr indicated temporal changes of deep-source fluid admixture at Mound 12. The present study is in accordance with previous work supporting considerable differences of methane flux between the two Mounds. It also strengthens the hypothesis of a predominantly deep fluid source for Mound 11 versus a rather shallow source of biogenic methane for Mound 12. The results demonstrate that methane-driven microbial activity is a valid ground truthing tool for geophysical measurements of fluid advection and constraining of recent methane fluxes in the study area. The study further shows that the combination of microbial rate measurements, numerical modeling, and authigenic carbonate analysis provide a suitable approach to constrain temporal and spatial variations of methane charged fluid flow at the Pacific Costa Rican margin

Riparian Corridors: A New Conceptual Framework for Assessing Nitrogen Buffering Across Biomes

Anthropogenic activities have more than doubled the amount of reactive nitrogen circulating on Earth, creating excess nutrients across the terrestrial-aquatic gradient. These excess nutrients have caused worldwide eutrophication, fundamentally altering the functioning of freshwater and marine ecosystems. Riparian zones have been recognized to buffer diffuse nitrate pollution, reducing delivery to aquatic ecosystems, but nutrient removal is not their only function in river systems. In this paper, we propose a new conceptual framework to test the capacity of riparian corridors to retain, remove, and transfer nitrogen along the continuum from land to sea under different climatic conditions. Because longitudinal, lateral, and vertical connectivity in riparian corridors influences their functional role in landscapes, we highlight differences in these parameters across biomes. More specifically, we explore how the structure of riparian corridors shapes stream morphology (the river's spine), their multiple functions at the interface between the stream and its catchment (the skin), and their biogeochemical capacity to retain and remove nitrogen (the kidneys). We use the nitrogen cycle as an example because nitrogen pollution is one of the most pressing global environmental issues, influencing directly and indirectly virtually all ecosystems on Earth. As an initial test of the applicability of our interbiome approach, we present synthesis results of gross ammonification and net nitrification from diverse ecosystems

Riparian corridors: A new conceptual framework for assessingt nitrogen buffering across biomes

Anthropogenic activities have more than doubled the amount of reactive nitrogen circulating on Earth, creating excess nutrients across the terrestrial-aquatic gradient. These excess nutrients have caused worldwide eutrophication, fundamentally altering the functioning of freshwater and marine ecosystems. Riparian zones have been recognized to buffer diffuse nitrate pollution, reducing delivery to aquatic ecosystems, but nutrient removal is not their only function in river systems. In this paper, we propose a new conceptual framework to test the capacity of riparian corridors to retain, remove, and transfer nitrogen along the continuum from land to sea under different climatic conditions. Because longitudinal, lateral, and vertical connectivity in riparian corridors influences their functional role in landscapes, we highlight differences in these parameters across biomes. More specifically, we explore how the structure of riparian corridors shapes stream morphology (the river's spine), their multiple functions at the interface between the stream and its catchment (the skin), and their biogeochemical capacity to retain and remove nitrogen (the kidneys). We use the nitrogen cycle as an example because nitrogen pollution is one of the most pressing global environmental issues, influencing directly and indirectly virtually all ecosystems on Earth. As an initial test of the applicability of our interbiome approach, we present synthesis results of gross ammonification and net nitrification from diverse ecosystems

Prophylactic Application of Nebulized Liposomal Amphotericin B in Hematologic Patients with Neutropenia

Background: Pulmonary invasive fungal infections (IFI) are well-recognized complications with high morbiditiy and mortality in patients with hematologic malignancies. Patients and Methods: Aerosolized liposomal amphotericin B (lipAmB) was evaluated as an antifungal prophylaxis in patients with an expected neutropenia of more than 10 days due to intensive chemotherapy or stem cell transplantation, in a prospective phase II trial. Results: 98 treatment episodes were included in the study and compared to 105 historical control patients. Inhalation was performed between 0 and 103 days. No severe side effects of therapy occurred. 40 patients considered inhalations as unpleasant, 2 as very unpleasant, mostly due to bad taste or cough. Few cases of definite or probable IFI were recorded, whereas a large number of patients were treated with systemic antifungal therapy for pneumonia or fever of unknown origin without a significant difference between study patients and controls. In a predefined subgroup analysis of 48 patients with newly diagnosed acute myeloid leukemia (AML), significantly more patients survived for 1 year in the AmB prophylaxis than in the control group (80% vs. 54%, p < 0.01). Conclusions: Inhalations of lipAmB are feasible and safe. Results in the subgroup of patients with AML together with data from other trials suggest further evaluation of effectiveness