683 research outputs found

    History-Adjusted Marginal Structural Models to Estimate Time-Varying Effect Modification

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    Much of epidemiology and clinical medicine is focused on the estimation of treatments or interventions administered over time. In such settings of longitudinal treatment, time-dependent confounding is often an important source of bias. Marginal structural models are a powerful tool for estimating the causal effect of a treatment using observational data, particularly when time-dependent confounding is present. Recent statistical work presented a generalization of marginal structural models, called history-adjusted marginal structural models. Unlike standard marginal structural models, history-adjusted marginal structural models can be used to estimate modification of treatment effects by time-varying covariates. Estimation of time-dependent causal effect modification is frequently of great practical relevance. For example, clinical researchers are often interested in how the prognostic significance of a biomarker for treatment response can change over time. This article provides a practical introduction to the implementation and interpretation of history-adjusted marginal structural models. The method is illustrated using a clinical question drawn from the treatment of HIV infection. Observational cohort data from San Francisco, California, collected between 2000 and 2004, are used to estimate the effect of time until switching antiretroviral therapy regimen among patients receiving a non-suppressive regimen, and how this effect differs depending on CD4 T cell count

    Sorting switch of mitochondrial presequence translocase involves coupling of motor module to respiratory chain

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    The mitochondrial presequence translocase transports preproteins to either matrix or inner membrane. Two different translocase forms have been identified: the matrix transport form, which binds the heat-shock protein 70 (Hsp70) motor, and the inner membrane–sorting form, which lacks the motor but contains translocase of inner mitochondrial membrane 21 (Tim21). The sorting form interacts with the respiratory chain in a Tim21-dependent manner. It is unknown whether the respiratory chain–bound translocase transports preproteins and how the switch between sorting form and motor form occurs. We report that the respiratory chain–bound translocase contains preproteins in transit and, surprisingly, not only sorted but also matrix-targeted preproteins. Presequence translocase-associated motor (Pam) 16 and 18, two regulatory components of the six-subunit motor, interact with the respiratory chain independently of Tim21. Thus, the respiratory chain–bound presequence translocase is not only active in preprotein sorting to the inner membrane but also in an early stage of matrix translocation. The motor does not assemble en bloc with the translocase but apparently in a step-wise manner with the Pam16/18 module before the Hsp70 core

    Nutrient dynamics in fen peat in relation to water level management: a mesocosm experiment

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    Peatlands are valuable ecosystems that hold a high biodiversity and provide many ecosystem services such as carbon sequestration, water storage and water purification. However, a large part of the peatlands are drained, often for agricultural purposes, resulting in CO2 emissions, soil subsidence and biodiversity loss. To combat these negative effects, various rewetting measures are being installed which can be combined with varying land-uses such as intensive dairy farming, extensive agriculture, semi-natural grasslands, paludiculture (farming on moist/wet soils) and nature restoration. This broad applicability implies that the extent by which the groundwater level is raised can be fine-tuned to the intended land use. In our study, we conducted a mesocosm experiment in which we exposed intact fen peat cores (80cm, 20cm Ø) to five different water levels (0, 20, 40, 60 cm and variable - surface), two nutrient application levels and two water qualities. For an eight-month period, monthly samples from each peat core were taken at two depths and chemically analyzed. Further, the vegetation in the cores was cut five times throughout the growing season. Above-ground biomass was measured as well as nutrient concentrations in the vegetation. Our results show increased phosphate and ammonium availability upon fully rewetting (0 cm – surface), in contrast to partially rewetted circumstances (20cm – surface) where nutrient availability was lowest. Above-ground biomass was strongly affected by nutrient application and, except for early spring growth, less by water levels. Nitrogen concentrations in the vegetation decreased with increasing water levels indicating stronger nitrogen limitation. This is likely the result of increased denitrification rates under wet circumstances. We conclude that in order to achieve nature restoration under fully rewetted conditions, additional steps must be taken to remove nutrients, particularly phosphorus, from the system. Further, we conclude that partial rewetting can be a solution to slow down the adverse effects of drainage, although agricultural production will decrease

    Dual role of Mic10 in mitochondrial cristae organization and ATP synthase-linked metabolic adaptation and respiratory growth

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    Invaginations of the mitochondrial inner membrane, termed cristae, are hubs for oxidative phosphorylation. The mitochondrial contact site and cristae organizing system (MICOS) and the dimeric F(1)F(o)-ATP synthase play important roles in controlling cristae architecture. A fraction of the MICOS core subunit Mic10 is found in association with the ATP synthase, yet it is unknown whether this interaction is of relevance for mitochondrial or cellular functions. Here, we established conditions to selectively study the role of Mic10 at the ATP synthase. Mic10 variants impaired in MICOS functions stimulate ATP synthase oligomerization like wild-type Mic10 and promote efficient inner membrane energization, adaptation to non-fermentable carbon sources, and respiratory growth. Mic10's functions in respiratory growth largely depend on Mic10(ATPsynthase), not on Mic10(MICOS). We conclude that Mic10 plays a dual role as core subunit of MICOS and as partner of the F(1)F(o)-ATP synthase, serving distinct functions in cristae shaping and respiratory adaptation and growth

    Cellular metabolism regulates contact sites between vacuoles and mitochondria

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    Emerging evidence suggests that contact sites between different organelles form central hubs in the coordination of cellular physiology. Although recent work has emphasized the crucial role of the endoplasmic reticulum in interorganellar crosstalk, the cooperative behavior of other organelles is largely unexplored. Here, we identify a contact site named vCLAMP (vacuole and mitochondria patch) that integrates mitochondria with the lysosome-like vacuole and thus the endocytic pathway. vCLAMPs depend on the vacuolar HOPS tethering complex subunit Vps39/Vam6 and the Rab GTPase Ypt7, which also participate in membrane fusion at the vacuole. Intriguingly, vCLAMPs are located proximal to the ER-mitochondria encounter structure (ERMES) complexes, and an increase in vCLAMPs can rescue the growth defect of ERMES mutants. Importantly, the persistence of vCLAMPs is regulated by phosphorylation of Vps39 and is strongly reduced during respiratory growth. The identification of this organelle contact site reveals a physical and metabolic interconnection between the endocytic pathway and mitochondria
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