94 research outputs found

    Multi-wavelength Stellar Polarimetry of the Filamentary Cloud IC5146: I. Dust Properties

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    We present optical and near-infrared stellar polarization observations toward the dark filamentary clouds associated with IC5146. The data allow us to investigate the dust properties (this paper) and the magnetic field structure (Paper II). A total of 2022 background stars were detected in RcR_{c}-, ii'-, HH-, and/or KK-bands to AV25A_V \lesssim 25 mag. The ratio of the polarization percentage at different wavelengths provides an estimate of λmax\lambda_{max}, the wavelength of peak polarization, which is an indicator of the small-size cutoff of the grain size distribution. The grain size distribution seems to significantly change at AVA_V \sim 3 mag, where both the average and dispersion of PRc/PHP_{R_c}/P_{H} decrease. In addition, we found λmax\lambda_{max} \sim 0.6-0.9 μ\mum for AV>2.5A_V>2.5 mag, which is larger than the \sim 0.55 μ\mum in the general ISM, suggesting that grain growth has already started in low AVA_V regions. Our data also reveal that polarization efficiency (PE Pλ/AV\equiv P_{\lambda}/A_V) decreases with AVA_V as a power-law in RcR_c-, ii'-, and KK-bands with indices of -0.71±\pm0.10, -1.23±\pm0.10 and -0.53±\pm0.09. However, HH-band data show a power index change; the PE varies with AVA_V steeply (index of -0.95±\pm0.30) when AV<2.88±0.67A_V < 2.88\pm0.67 mag but softly (index of -0.25±\pm0.06) for greater AVA_V values. The soft decay of PE in high AVA_V regions is consistent with the Radiative Aligned Torque model, suggesting that our data trace the magnetic field to AV20A_V \sim 20 mag. Furthermore, the breakpoint found in HH-band is similar to the AVA_V where we found the PRc/PHP_{R_c}/P_{H} dispersion significantly decreased. Therefore, the flat PE-AVA_V in high AVA_V regions implies that the power index changes result from additional grain growth.Comment: 31 pages, 17 figures, and 3 tables; accepted for publication in Ap

    The effect of aerobic exercise on oxidative stress in patients with chronic kidney disease: a systematic review and meta-analysis with trial sequential analysis

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    The purpose of this study was to investigate how aerobic exercise affects oxidative stress (OS) in patients with chronic kidney disease (CKD). Retrieval dates range from the date the database was established to 19 July 2023, without languages being restricted. A meta-analysis and sensitivity analysis were conducted using RevMan 5.3 and Stata 16.0. The meta-analysis showed that, compared to usual activity or no exercise, aerobic exercise significantly reduced the oxidative markers malondialdehyde (MDA) (mean differences (MD) − 0.96 (95% CI −1.33, − 0.59); p p p = 0.001). Aerobic exercise also increased the antioxidant marker superoxide dismutase (SOD) in CKD patients (standardized mean differences (SMD) 1.30 (95% CI 0.56, 2.04); p = 0.0005). Subgroup analysis showed a significant increase in glutathione peroxidase (GPX) in patients aged ≥60 years (SMD 2.11 (95% CI 1.69, 2.54); p  The results of this review suggest that aerobic exercise improves OS indicators (MDA, SOD, AOPP, and F2-iso) in CKD patients compared to conventional treatment or no exercise and that the effects on GPX and TAC indicators need further confirmation. For better validation of benefits and exploration of the best aerobic exercise regimen to improve OS status with CKD, further studies with high methodological quality and large sample sizes are needed.</p

    Mutations that affect DNA binding and oligomerization are deleterious to plasmid maintenance activity.

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    <p>(A) Southern blot analysis of p8xTR plasmids at 7 days post-transfection in BJAB cell lines expressing wild-type or mutant LANA, as indicated above. The same number of cells were loaded in each lane. (B) Western blot of LANA protein expression levels in BJAB cells used for plasmid maintenance assays shown in panel A probed for LANA or cellular Actin. (C) Quantification of plasmid maintenance assays normalized to wild-type LANA (lane 1). Error bars represent the standard deviation for three independent replicates.</p

    Molecular Basis for Oligomeric-DNA Binding and Episome Maintenance by KSHV LANA

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    <div><p>LANA is the KSHV-encoded terminal repeat binding protein essential for viral replication and episome maintenance during latency. We have determined the X-ray crystal structure of LANA C-terminal DNA binding domain (LANA<sub>DBD</sub>) to reveal its capacity to form a decameric ring with an exterior DNA binding surface. The dimeric core is structurally similar to EBV EBNA1 with an N-terminal arm that regulates DNA binding and is required for replication function. The oligomeric interface between LANA dimers is dispensable for single site DNA binding, but is required for cooperative DNA binding, replication function, and episome maintenance. We also identify a basic patch opposite of the DNA binding surface that is responsible for the interaction with BRD proteins and contributes to episome maintenance function. The structural features of LANA<sub>DBD</sub> suggest a novel mechanism of episome maintenance through DNA-binding induced oligomeric assembly.</p></div

    The tetramer interface is required for cooperative DNA binding.

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    <p>(A) DNA binding induces oligomerization of LANA<sub>DBD</sub>. In the absence of crosslinker (EGS), wild-type and F1037A/F1041A migrate as monomers (lanes 1 and 2). Addition of increasing concentrations of EGS produces mostly dimers and tetramers of wild-type (lanes 3–5). Addition of LBS1 DNA induces oligomerization (each successive band is the addition of one monomer) in wild-type (lanes 6–9). The oligomer interface mutant F1037A/F1041A has a greatly reduced propensity to form higher molecular weight oligomers (lanes 9–11). (B) Agarose gel EMSA of full-length FLAG-tagged LANA wild-type or mutant proteins (indicated above each lane) binding to DNA probes for LBS1 (lanes 1–9), or LBS1/2 (lanes 10–18). (C) Western blot of affinity purified FLAG-LANA proteins used for EMSA in panel B.</p

    Plasmid replication activity is dependent on DNA binding activity and the oligomerization interface.

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    <p>(A) Quantification of DNA replication assays of wild-type or mutant LANA (as indicated) after transient transfection with p8xTR in 293T cells. Activity is relative to wild-type LANA and error bars represent the standard deviation for three independent replicates. (B–G) Representative Southern blot replication assay showing BglII linearization (B and E) or BglII+DpnI (C and E) digestion of p8xTR. Arrows indicate full-length DpnI resistant replicated plasmid used for quantification in panel A. Smaller DNA fragments represent unreplicated input or incomplete replication products of p8xTR plasmid. (D and G) Western blot for detection of LANA proteins used in replication assays.</p

    Oligomeric interface affects DNA binding and cooperativity.

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    <p>(A) Dissociation constants for mutants of LANA<sub>DBD</sub> as determined by fluorescence polarization using an LBS1 oligomer. (B) Representative isotherms of the FP assays for wild-type (cooperative), F1037A/F1041A (non-cooperative), 1021–1153 (increased cooperativity), and M1117A (negative cooperativity) to illustrate the fit of the data using a Hill coefficient. The error bars represent the standard deviation of three independent replicates. Fits not shown in this panel are available in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003672#ppat.1003672.s003" target="_blank">Figure S3</a>.</p

    The basic patch of LANA<sub>DBD</sub> interacts with the ET domain of BRD2 and BRD4.

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    <p>(A) Wild-type LANA (lane 2) is able to co-immunoprecipitate BRD4 and mutations in the N-terminal arm (lanes 11–15), the tetrameric interface (lanes 3–5 and 7), and the interior portion of the basic patch (lanes 9–10) do not affect this interaction. However, mutation of Lys1138, Lys1140, and Lys1141 results in decreased levels of BRD4 interaction (lanes 6 and 8). IP and input are shown for BRD4 (top panels) and LANA (lower panels). (B–E) LANA<sub>DBD</sub> is able to interact with BRD2 (B) and BRD4 (C) ET domains. Ni-NTA resin was loaded with LANA or His-tagged BRD ET domain (input, I) and the flow-through (F) was collected. Untagged LANA was then added and the unbound (U) fraction was collected. Complex formation is indicated by the presence of BRD (dark arrows) and LANA (open arrows) in the elution fraction (E). EBNA1<sub>DBD</sub> was not able to interact with either BRD2 or BRD4 ET domains (D, E).</p

    Crystal structure of LANA<sub>DBD</sub>.

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    <p>(A) The structure of the LANA<sub>DBD</sub> dimer is shown in orange. (B) This fold is conserved in the functional homolog EBNA1 (PDB 1vhi; <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003672#ppat.1003672-Bochkarev1" target="_blank">[55]</a>. (C) In the crystal structure, five LANA<sub>DBD</sub> dimers interact to form a decameric ring. Each dimer is highlighted in a different color. (D) A zoom-in of the boxed area of (C) highlights the residues involved in the formation of the tetramer interface. It is composed of Phe1037, Phe1041 and Met1117, each shown as sticks.</p
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