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1.
Proc Natl Acad Sci U S A ; 121(8): e2312152121, 2024 Feb 20.
Artículo en Inglés | MEDLINE | ID: mdl-38346195

RESUMEN

Subsurface sandstone reservoirs sealed by overlying, low-permeability layers provide capacity for long-term sequestration of anthropogenic waste. Leakage can occur if reservoir pressures rise sufficiently to fracture the seal. Such pressures can be generated within the reservoir by vigorous injection of waste or, over thousands of years, by natural processes. In either case, the precise role of intercalated mudstones in the long-term evolution of reservoir pressure remains unclear; these layers have variously been viewed as seals, as pressure sinks, or as pressure sources. Here, we use the geological record of episodic fluid venting in the Levant Basin to provide striking evidence for the pressure-source hypothesis. We use a Bayesian framework to combine recently published venting data, which record critical subsurface pressures since ∼2 Ma, with a stochastic model of pressure evolution to infer a pressure-recharge rate of ∼30 MPa/Myr. To explain this large rate, we quantify and compare a range of candidate mechanisms. We find that poroelastic pressure diffusion from mudstones provides the most plausible explanation for these observations, amplifying the ∼3 MPa/Myr recharge caused primarily by tectonic compression. Since pressurized mudstones are ubiquitous in sedimentary basins, pressure diffusion from mudstones is likely to promote seal failure globally.

2.
Proc Natl Acad Sci U S A ; 120(8): e2203448120, 2023 Feb 21.
Artículo en Inglés | MEDLINE | ID: mdl-36780525

RESUMEN

In applications critical to the geological, materials, and engineering sciences, deformation occurs at strain rates too small to be accessible experimentally. Instead, extrapolations of empirical relationships are used, leading to epistemic uncertainties in predictions. To address these problems, we construct a theory of the fundamental processes affecting dislocations: storage and recovery. We then validate our theory for olivine deformation. This model explains the empirical relationships among strain rate, applied stress, and dislocation density in disparate laboratory regimes. It predicts the previously unexplained dependence of dislocation density on applied stress in olivine. The predictions of our model for Earth conditions differ from extrapolated empirical relationships. For example, it predicts rapid, transient deformation in the upper mantle, consistent with recent measurements of postseismic creep.

3.
Proc Natl Acad Sci U S A ; 119(28): e2204761119, 2022 Jul 12.
Artículo en Inglés | MEDLINE | ID: mdl-35867751

RESUMEN

It is established that changes in sea level influence melt production at midocean ridges, but whether changes in melt production influence the pattern of bathymetry flanking midocean ridges has been debated on both theoretical and empirical grounds. To explore the dynamics that may give rise to a sea-level influence on bathymetry, we simulate abyssal hills using a faulting model with periodic variations in melt supply. For 100-ky melt-supply cycles, model results show that faults initiate during periods of amagmatic spreading at half-rates >2.3 cm/y and for 41-ky melt-supply cycles at half-rates >3.8 cm/y. Analysis of bathymetry across 17 midocean ridge regions shows characteristic wavelengths that closely align with the predictions from the faulting model. At intermediate-spreading ridges (half-rates >2.3 cm/y and [Formula: see text]3.8 cm/y) abyssal hill spacing increases with spreading rate at 0.99 km/(cm/y) or 99 ky (n [Formula: see text] 12; 95% CI, 87 to 110 ky), and at fast-spreading ridges (half-rates >3.8 cm/y) spacing increases at 38 ky (n [Formula: see text] 5; 95% CI, 29 to 47 ky). Including previously published analyses of abyssal-hill spacing gives a more precise alignment with the primary periods of Pleistocene sea-level variability. Furthermore, analysis of bathymetry from fast-spreading ridges shows a highly statistically significant spectral peak (P < 0.01) at the 1/(41-ky) period of Earth's variations in axial tilt. Faulting models and observations both support a linkage between glacially induced sea-level change and the fabric of the sea floor over the late Pleistocene.

4.
J Cell Sci ; 133(10)2020 05 27.
Artículo en Inglés | MEDLINE | ID: mdl-32317397

RESUMEN

A large fraction of epigenetically silent heterochromatin is anchored to the nuclear periphery via 'tethering proteins' that function to bridge heterochromatin and the nuclear membrane or nuclear lamina. We previously identified a human tethering protein, PRR14, that binds heterochromatin through an N-terminal domain, but the mechanism and regulation of nuclear lamina association remained to be investigated. Here we identify an evolutionarily conserved PRR14 nuclear lamina binding domain (LBD) that is both necessary and sufficient for positioning of PRR14 at the nuclear lamina. We show that PRR14 associates dynamically with the nuclear lamina, and provide evidence that such dynamics are regulated through phosphorylation and dephosphorylation of the LBD. Furthermore, we identify a PP2A phosphatase recognition motif within the evolutionarily conserved C-terminal Tantalus domain of PRR14. Disruption of this motif affects PRR14 localization to the nuclear lamina. The overall findings demonstrate a heterochromatin anchoring mechanism whereby the PRR14 tether simultaneously binds heterochromatin and the nuclear lamina through two separable modular domains. Our findings also describe an optimal PRR14 LBD fragment that could be used for efficient targeting of fusion proteins to the nuclear lamina.


Asunto(s)
Heterocromatina , Lámina Nuclear , Núcleo Celular/metabolismo , Proteínas Cromosómicas no Histona/metabolismo , Heterocromatina/genética , Heterocromatina/metabolismo , Humanos , Membrana Nuclear/genética , Membrana Nuclear/metabolismo , Lámina Nuclear/genética , Lámina Nuclear/metabolismo , Fosforilación
6.
Paediatr Respir Rev ; 32: 23-27, 2019 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-31005455

RESUMEN

BACKGROUND: Aspiration can cause acute symptoms and chronic lung disease in the developing lung. However, the source of aspiration in infants is often unclear, making the choice of intervention difficult. OBJECTIVE: To quantify the source, amount and duration of lung aspiration in infants using gamma scintigraphy. METHODS: Two infants with clinical evidence of gastroesophageal reflux and oropharyngeal dysphagia swallowed formula radiolabeled with 99mtechnetium on Visit 1. Radiolabeled-formula was instilled by nasogastric tube on Visit 2. Lung aspiration was quantified over four hours and expressed as percent of total radioactivity administered. RESULTS: Aspiration was greatest with swallowing, compared to instillation, peaking between 2.0% and 2.4% within 30 min and between 0.40% and 0.65% within 20 min, respectively. Radioactivity remained above zero four hours after either administration. CONCLUSIONS: Quantification of the source, amount and duration of lung aspiration in infants is feasible using gamma scintigraphy. The impact of aspiration accrual on clinical care deserves further investigation.


Asunto(s)
Trastornos de Deglución/diagnóstico por imagen , Deglución , Reflujo Gastroesofágico/diagnóstico por imagen , Aspiración Respiratoria de Contenidos Gástricos/diagnóstico por imagen , Aspiración Respiratoria/diagnóstico por imagen , Humanos , Lactante , Intubación Gastrointestinal , Masculino , Cintigrafía/métodos , Radiofármacos , Azufre Coloidal Tecnecio Tc 99m
7.
Proc Natl Acad Sci U S A ; 112(41): 12616-20, 2015 Oct 13.
Artículo en Inglés | MEDLINE | ID: mdl-26417107

RESUMEN

Chemical differentiation of rocky planets occurs by melt segregation away from the region of melting. The mechanics of this process, however, are complex and incompletely understood. In partially molten rocks undergoing shear deformation, melt pockets between grains align coherently in the stress field; it has been hypothesized that this anisotropy in microstructure creates an anisotropy in the viscosity of the aggregate. With the inclusion of anisotropic viscosity, continuum, two-phase-flow models reproduce the emergence and angle of melt-enriched bands that form in laboratory experiments. In the same theoretical context, these models also predict sample-scale melt migration due to a gradient in shear stress. Under torsional deformation, melt is expected to segregate radially inward. Here we present torsional deformation experiments on partially molten rocks that test this prediction. Microstructural analyses of the distribution of melt and solid reveal a radial gradient in melt fraction, with more melt toward the center of the cylinder. The extent of this radial melt segregation grows with progressive strain, consistent with theory. The agreement between theoretical prediction and experimental observation provides a validation of this theory.

8.
Nature ; 468(7325): E6-7; discussion E7-8, 2010 Dec 09.
Artículo en Inglés | MEDLINE | ID: mdl-21150944

RESUMEN

Global systematics in the location of volcanic arcs above subduction zones are widely considered to be a clue to the melting processes that occur at depth, and the locations of the arcs have often been explained in terms of the release of hydrous fluids near the top of the subducting slab (see, for example, refs 3-6). Grove et al. conclude that arc volcano location is controlled by melting in the mantle at temperatures above the water-saturated upper-mantle solidus and below the upper limit of stability of the mineral chlorite and in particular, that the arc fronts lie directly above the shallowest point of such melt regions in the mantle. Here we show that this conclusion is incorrect because the calculated arc locations of Grove et al. are in error owing to the inadequate spatial resolution of their numerical models, and because the agreement that they find between predicted and observed systematics arises from a spurious correlation between calculated arc location and slab dip. A more informative conclusion to draw from their experiments is that the limits of chlorite stability (figure 1b of ref. 7) cannot explain the global systematics in the depth to the slab beneath the sharply localized arc fronts.

9.
Nature ; 467(7316): 700-3, 2010 Oct 07.
Artículo en Inglés | MEDLINE | ID: mdl-20930842

RESUMEN

Segregation of magma from the mantle in subduction zones is one of the principal mechanisms for chemical differentiation of the Earth. Fundamental aspects of this system, in particular the processes by which melt forms and travels to the Earth's surface, remain obscure. Systematics in the location of volcanic arcs, the surface expression of this melting, are widely considered to be a clue to processes taking place at depth, but many mutually incompatible interpretations of this clue exist (for example, see refs 1-6). We discriminate between those interpretations by the use of a simple scaling argument derived from a realistic mathematical model of heat transfer in subduction zones. The locations of the arcs cannot be explained by the release of fluids in reactions taking place near the top of the slab. Instead, the sharpness of the volcanic fronts, together with the systematics of their locations, requires that arcs must be located above the place where the boundary defined by the anhydrous solidus makes its closest approach to the trench. We show that heat carried by magma rising from this region is sufficient to modify the thermal structure of the wedge and determine the pathway through which both wet and dry melts reach the surface.

10.
Postepy Biochem ; 62(3): 280-285, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-28132482

RESUMEN

Collaborations between the Wlodawer and Skalka laboratories have covered a period of almost 30 years. During that time our groups have co-authored 18 publications, including several much cited journal articles, book chapters, and scholarly reviews. It has therefore been most rewarding for us to share enthusiasm, insights, and expertise with our Frederick colleagues over the years, and also to enjoy lasting friendships.


Asunto(s)
Bioquímica/historia , Cristalografía/historia , Proteínas de los Retroviridae/química , Retroviridae/enzimología , Cristalografía/métodos , Historia del Siglo XX , Historia del Siglo XXI , Conformación Proteica , Proteínas de los Retroviridae/metabolismo , Estados Unidos
11.
J Virol ; 87(4): 2137-50, 2013 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-23221555

RESUMEN

Integrated retroviral DNA is subject to epigenetic transcriptional silencing at different frequencies. This process is mediated by repressive DNA methylation and histone modifications on viral chromatin. However, the detailed mechanisms by which retroviral silencing is initiated and maintained are not well understood. Using a model system in which avian sarcoma virus (ASV) DNA is epigenetically repressed in mammalian cells, we previously found that a cellular scaffolding protein, Daxx, acts as an antiretroviral factor that promotes epigenetic repression through recruitment of histone deacetylases (HDACs). Here we show that human Daxx protein levels are increased in response to retroviral infection and that Daxx acts at the time of infection to initiate epigenetic repression. Consistent with a rapid and active antiviral epigenetic response, we found that repressive histone marks and long terminal repeat (LTR) DNA methylation could be detected within 12 h to 3 days postinfection, respectively. Daxx was also found to be required for long-term ASV silencing maintenance and full viral DNA methylation, and it was physically associated with both viral DNA and DNA methyltransferases (DNMTs). These findings support a model in which incoming retroviral protein-DNA complexes are detected by Daxx, and the integrated provirus is rapidly chromatinized and repressed by DNA methylation and histone modification as part of an antiviral response. These results uncover a possible direct and active antiviral mechanism by which DNMTs can be recruited to retroviral DNA.


Asunto(s)
Proteínas Adaptadoras Transductoras de Señales/metabolismo , Virus del Sarcoma Aviar/genética , Metilación de ADN , Represión Epigenética , Regulación Viral de la Expresión Génica , Interacciones Huésped-Patógeno , Proteínas Nucleares/metabolismo , Animales , Virus del Sarcoma Aviar/fisiología , Línea Celular , Proteínas Co-Represoras , Silenciador del Gen , Humanos , Chaperonas Moleculares
12.
Virol J ; 11: 100, 2014 May 28.
Artículo en Inglés | MEDLINE | ID: mdl-24884573

RESUMEN

BACKGROUND: The antiviral protein Daxx acts as a restriction factor of avian sarcoma virus (ASV; Retroviridae) in mammalian cells by promoting epigenetic silencing of integrated proviral DNA. Although Daxx is encoded by a type I (α/ß) interferon-stimulated gene, the requirement for Daxx in the interferon anti-retroviral response has not been elucidated. In this report, we describe the results of experiments designed to investigate the role of Daxx in the type I interferon-induced anti-ASV response. FINDINGS: Using an ASV reporter system, we show that type I interferons are potent inhibitors of ASV replication. We demonstrate that, while Daxx is necessary to silence ASV gene expression in the absence of interferons, type I interferons are fully-capable of inducing an antiviral state in the absence of Daxx. CONCLUSIONS: These results provide evidence that Daxx is not essential for the anti-ASV interferon response in mammalian cells, and that interferons deploy multiple, redundant antiviral mechanisms to protect cells from ASV.


Asunto(s)
Proteínas Adaptadoras Transductoras de Señales/inmunología , Virus del Sarcoma Aviar/inmunología , Virus del Sarcoma Aviar/fisiología , Interferón Tipo I/inmunología , Proteínas Nucleares/inmunología , Replicación Viral , Animales , Aves , Línea Celular , Proteínas Co-Represoras , Humanos , Chaperonas Moleculares
13.
Echocardiography ; 31(4): 442-8, 2014 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-24199601

RESUMEN

BACKGROUND: Pulmonary hypertension (PH) in patients with systemic hypertension and preserved ejection fraction (PEF) has been described. However, the pathophysiology and consequences are not entirely clear. We sought to distinguish the clinical and anatomic features among hypertensive patients with or without coexistent PH. METHODS: Echocardiograms and records of hypertensive patients with left ventricular (LV) hypertrophy and PEF from January 2009 to January 2011 were reviewed. We identified 174 patients, including 36 with PH (calculated pulmonary artery systolic pressure [PASP] ≥ 35 mmHg), and 138 with normal pulmonary pressures. RESULTS: Hypertensive patients with PH were older (76 ± 13 vs. 65 ± 13 years, P < 0.0001), more often female (91, 70%), had lower estimated glomerular filtration rate (eGFR) (63 ± 44 vs. 88 ± 48 mL/min, P = 0.002), and higher pro-BNP levels (3141 ± 4253 vs. 1219 ± 1900 pg/mL, P = 0.003). PH patients also had larger left atrial areas (23.7 ± 3.8 vs. 20.8 ± 4.6 cm(2) , P = 0.002), evidence of diastolic dysfunction (i.e., septal E/e' 17.6 ± 8.6 vs. 12.7 ± 4.4, P = 0.0005), and higher calculated peripheral vascular resistance (PVR) (2.3 ± 1.1 vs. 1.6 ± 0.4, P < 0.0001). Both PVR and septal E/e' showed strong linear correlation with PASP (P < 0.0001 and P < 0.0001, respectively). CONCLUSIONS: Hypertension in elderly patients is frequently complicated by LV diastolic dysfunction and secondary PH. These hypertensive patients tended to have reduced renal function and higher pro-BNP. Because of the known morbidity and mortality associated with PH, these observations have potentially important implications for target medical therapy.


Asunto(s)
Insuficiencia Cardíaca Diastólica/diagnóstico por imagen , Hipertensión Pulmonar/diagnóstico por imagen , Hipertrofia Ventricular Izquierda/diagnóstico por imagen , Volumen Sistólico/fisiología , Resistencia Vascular/fisiología , Factores de Edad , Anciano , Anciano de 80 o más Años , Estudios de Cohortes , Ecocardiografía/métodos , Femenino , Estudios de Seguimiento , Insuficiencia Cardíaca Diastólica/complicaciones , Humanos , Hipertensión/complicaciones , Hipertensión/diagnóstico , Hipertensión/diagnóstico por imagen , Hipertensión Pulmonar/complicaciones , Hipertensión Pulmonar/diagnóstico , Hipertrofia Ventricular Izquierda/fisiopatología , Modelos Lineales , Masculino , Persona de Mediana Edad , Estudios Retrospectivos , Medición de Riesgo , Índice de Severidad de la Enfermedad , Factores Sexuales , Estadísticas no Paramétricas , Factores de Tiempo
14.
Int J Cardiovasc Imaging ; 40(6): 1201-1209, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38630211

RESUMEN

This study assesses the agreement of Artificial Intelligence-Quantitative Computed Tomography (AI-QCT) with qualitative approaches to atherosclerotic disease burden codified in the multisociety 2022 CAD-RADS 2.0 Expert Consensus. 105 patients who underwent cardiac computed tomography angiography (CCTA) for chest pain were evaluated by a blinded core laboratory through FDA-cleared software (Cleerly, Denver, CO) that performs AI-QCT through artificial intelligence, analyzing factors such as % stenosis, plaque volume, and plaque composition. AI-QCT plaque volume was then staged by recently validated prognostic thresholds, and compared with CAD-RADS 2.0 clinical methods of plaque evaluation (segment involvement score (SIS), coronary artery calcium score (CACS), visual assessment, and CAD-RADS percent (%) stenosis) by expert consensus blinded to the AI-QCT core lab reads. Average age of subjects were 59 ± 11 years; 44% women, with 50% of patients at CAD-RADS 1-2 and 21% at CAD-RADS 3 and above by expert consensus. AI-QCT quantitative plaque burden staging had excellent agreement of 93% (k = 0.87 95% CI: 0.79-0.96) with SIS. There was moderate agreement between AI-QCT quantitative plaque volume and categories of visual assessment (64.4%; k = 0.488 [0.38-0.60]), and CACS (66.3%; k = 0.488 [0.36-0.61]). Agreement between AI-QCT plaque volume stage and CAD-RADS % stenosis category was also moderate. There was discordance at small plaque volumes. With ongoing validation, these results demonstrate a potential for AI-QCT as a rapid, reproducible approach to quantify total plaque burden.


Asunto(s)
Inteligencia Artificial , Angiografía por Tomografía Computarizada , Angiografía Coronaria , Enfermedad de la Arteria Coronaria , Estenosis Coronaria , Placa Aterosclerótica , Valor Predictivo de las Pruebas , Índice de Severidad de la Enfermedad , Calcificación Vascular , Humanos , Femenino , Persona de Mediana Edad , Masculino , Anciano , Reproducibilidad de los Resultados , Calcificación Vascular/diagnóstico por imagen , Estenosis Coronaria/diagnóstico por imagen , Enfermedad de la Arteria Coronaria/diagnóstico por imagen , Vasos Coronarios/diagnóstico por imagen , Interpretación de Imagen Radiográfica Asistida por Computador , Tomografía Computarizada Multidetector , Variaciones Dependientes del Observador
15.
Artículo en Inglés | MEDLINE | ID: mdl-38483420

RESUMEN

BACKGROUND: Noninvasive stress testing is commonly used for detection of coronary ischemia but possesses variable accuracy and may result in excessive health care costs. OBJECTIVES: This study aimed to derive and validate an artificial intelligence-guided quantitative coronary computed tomography angiography (AI-QCT) model for the diagnosis of coronary ischemia that integrates atherosclerosis and vascular morphology measures (AI-QCTISCHEMIA) and to evaluate its prognostic utility for major adverse cardiovascular events (MACE). METHODS: A post hoc analysis of the CREDENCE (Computed Tomographic Evaluation of Atherosclerotic Determinants of Myocardial Ischemia) and PACIFIC-1 (Comparison of Coronary Computed Tomography Angiography, Single Photon Emission Computed Tomography [SPECT], Positron Emission Tomography [PET], and Hybrid Imaging for Diagnosis of Ischemic Heart Disease Determined by Fractional Flow Reserve) studies was performed. In both studies, symptomatic patients with suspected stable coronary artery disease had prospectively undergone coronary computed tomography angiography (CTA), myocardial perfusion imaging (MPI), SPECT, or PET, fractional flow reserve by CT (FFRCT), and invasive coronary angiography in conjunction with invasive FFR measurements. The AI-QCTISCHEMIA model was developed in the derivation cohort of the CREDENCE study, and its diagnostic performance for coronary ischemia (FFR ≤0.80) was evaluated in the CREDENCE validation cohort and PACIFIC-1. Its prognostic value was investigated in PACIFIC-1. RESULTS: In CREDENCE validation (n = 305, age 64.4 ± 9.8 years, 210 [69%] male), the diagnostic performance by area under the receiver-operating characteristics curve (AUC) on per-patient level was 0.80 (95% CI: 0.75-0.85) for AI-QCTISCHEMIA, 0.69 (95% CI: 0.63-0.74; P < 0.001) for FFRCT, and 0.65 (95% CI: 0.59-0.71; P < 0.001) for MPI. In PACIFIC-1 (n = 208, age 58.1 ± 8.7 years, 132 [63%] male), the AUCs were 0.85 (95% CI: 0.79-0.91) for AI-QCTISCHEMIA, 0.78 (95% CI: 0.72-0.84; P = 0.037) for FFRCT, 0.89 (95% CI: 0.84-0.93; P = 0.262) for PET, and 0.72 (95% CI: 0.67-0.78; P < 0.001) for SPECT. Adjusted for clinical risk factors and coronary CTA-determined obstructive stenosis, a positive AI-QCTISCHEMIA test was associated with an HR of 7.6 (95% CI: 1.2-47.0; P = 0.030) for MACE. CONCLUSIONS: This newly developed coronary CTA-based ischemia model using coronary atherosclerosis and vascular morphology characteristics accurately diagnoses coronary ischemia by invasive FFR and provides robust prognostic utility for MACE beyond presence of stenosis.

16.
Nucleus ; 14(1): 2165602, 2023 12.
Artículo en Inglés | MEDLINE | ID: mdl-36633363

RESUMEN

The eukaryotic genome is organized in three dimensions within the nucleus. Transcriptionally active chromatin is spatially separated from silent heterochromatin, a large fraction of which is located at the nuclear periphery. However, the mechanisms by which chromatin is localized at the nuclear periphery remain poorly understood. Here we demonstrate that Proline Rich 14 (PRR14) protein organizes H3K9me3-modified heterochromatin at the nuclear lamina. We show that PRR14 dynamically associates with both the nuclear lamina and heterochromatin, and is able to reorganize heterochromatin in the nucleus of interphase cells independent of mitosis. We characterize two functional HP1-binding sites within PRR14 that contribute to its association with heterochromatin. We also demonstrate that PPR14 forms an anchoring surface for heterochromatin at the nuclear lamina where it interacts dynamically with HP1-associated chromatin. Our study proposes a model of dynamic heterochromatin organization at the nuclear lamina via the PRR14 tethering protein.


Asunto(s)
Heterocromatina , Lámina Nuclear , Heterocromatina/metabolismo , Lámina Nuclear/metabolismo , Núcleo Celular/metabolismo , Cromatina/metabolismo , Proteínas Cromosómicas no Histona/metabolismo
17.
Artículo en Inglés | MEDLINE | ID: mdl-37303712

RESUMEN

Background: Cardiovascular disease had a global prevalence of 523 million cases and 18.6 million deaths in 2019. The current standard for diagnosing coronary artery disease (CAD) is coronary angiography either by invasive catheterization (ICA) or computed tomography (CTA). Prior studies employed single-molecule, amplification-independent RNA sequencing of whole blood to identify an RNA signature in patients with angiographically confirmed CAD. The present studies employed Illumina RNAseq and network co-expression analysis to identify systematic changes underlying CAD. Methods: Whole blood RNA was depleted of ribosomal RNA (rRNA) and analyzed by Illumina total RNA sequencing (RNAseq) to identify transcripts associated with CAD in 177 patients presenting for elective invasive coronary catheterization. The resulting transcript counts were compared between groups to identify differentially expressed genes (DEGs) and to identify patterns of changes through whole genome co-expression network analysis (WGCNA). Results: The correlation between Illumina amplified RNAseq and the prior SeqLL unamplified RNAseq was quite strong (r = 0.87), but there was only 9 % overlap in the DEGs identified. Consistent with the prior RNAseq, the majority (93 %) of DEGs were down-regulated ~1.7-fold in patients with moderate to severe CAD (>20 % stenosis). DEGs were predominantly related to T cells, consistent with known reductions in Tregs in CAD. Network analysis did not identify pre-existing modules with a strong association with CAD, but patterns of T cell dysregulation were evident. DEGs were enriched for transcripts associated with ciliary and synaptic transcripts, consistent with changes in the immune synapse of developing T cells. Conclusions: These studies confirm and extend a novel mRNA signature of a Treg-like defect in CAD. The pattern of changes is consistent with stress-related changes in the maturation of T and Treg cells, possibly due to changes in the immune synapse.

18.
Diabetes Care ; 46(2): 416-424, 2023 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-36577120

RESUMEN

OBJECTIVE: This study evaluates the relationship between atherosclerotic plaque characteristics (APCs) and angiographic stenosis severity in patients with and without diabetes. Whether APCs differ based on lesion severity and diabetes status is unknown. RESEARCH DESIGN AND METHODS: We retrospectively evaluated 303 subjects from the Computed TomogRaphic Evaluation of Atherosclerotic Determinants of Myocardial IsChEmia (CREDENCE) trial referred for invasive coronary angiography with coronary computed tomographic angiography (CCTA) and classified lesions as obstructive (≥50% stenosed) or nonobstructive using blinded core laboratory analysis of quantitative coronary angiography. CCTA quantified APCs, including plaque volume (PV), calcified plaque (CP), noncalcified plaque (NCP), low-density NCP (LD-NCP), lesion length, positive remodeling (PR), high-risk plaque (HRP), and percentage of atheroma volume (PAV; PV normalized for vessel volume). The relationship between APCs, stenosis severity, and diabetes status was assessed. RESULTS: Among the 303 patients, 95 (31.4%) had diabetes. There were 117 lesions in the cohort with diabetes, 58.1% of which were obstructive. Patients with diabetes had greater plaque burden (P = 0.004). Patients with diabetes and nonobstructive disease had greater PV (P = 0.02), PAV (P = 0.02), NCP (P = 0.03), PAV NCP (P = 0.02), diseased vessels (P = 0.03), and maximum stenosis (P = 0.02) than patients without diabetes with nonobstructive disease. APCs were similar between patients with diabetes with nonobstructive disease and patients without diabetes with obstructive disease. Diabetes status did not affect HRP or PR. Patients with diabetes had similar APCs in obstructive and nonobstructive lesions. CONCLUSIONS: Patients with diabetes and nonobstructive stenosis had an association to similar APCs as patients without diabetes who had obstructive stenosis. Among patients with nonobstructive disease, patients with diabetes had more total PV and NCP.


Asunto(s)
Aterosclerosis , Enfermedad de la Arteria Coronaria , Estenosis Coronaria , Diabetes Mellitus , Placa Aterosclerótica , Humanos , Constricción Patológica/complicaciones , Estudios Retrospectivos , Enfermedad de la Arteria Coronaria/complicaciones , Placa Aterosclerótica/diagnóstico por imagen , Angiografía Coronaria/métodos , Aterosclerosis/complicaciones , Angiografía por Tomografía Computarizada/métodos , Diabetes Mellitus/epidemiología , Inteligencia Artificial , Estenosis Coronaria/complicaciones , Valor Predictivo de las Pruebas
19.
J Biol Chem ; 286(29): 25710-8, 2011 Jul 22.
Artículo en Inglés | MEDLINE | ID: mdl-21622554

RESUMEN

In the initial step of integration, retroviral integrase (IN) introduces precise nicks in the degenerate, short inverted repeats at the ends of linear viral DNA. The scissile phosphodiester bond is located immediately 3' of a highly conserved CA/GT dinucleotide, usually 2 bp from the ends. These nicks create new recessed 3'-OH viral DNA ends that are required for joining to host cell DNA. Previous studies have indicated that unpairing, "fraying," of the viral DNA ends by IN contributes to end recognition or catalysis. Here, we report that end fraying can be detected independently of catalysis with both avian sarcoma virus (ASV) and human immunodeficiency virus type 1 (HIV-1) IN proteins by use of fluorescence resonance energy transfer (FRET). The results were indicative of an IN-induced intramolecular conformational change in the viral DNA ends (cis FRET). Fraying activity is tightly coupled to the DNA binding capabilities of these enzymes, as follows: an inhibitor effective against both IN proteins was shown to block ASV IN DNA binding and end fraying, with similar dose responses; ASV IN substitutions that reduced DNA binding also reduced end fraying activity; and HIV-1 IN DNA binding and end fraying were both undetectable in the absence of a metal cofactor. Consistent with our previous results, end fraying is sequence-independent, suggesting that the DNA terminus per se is a major structural determinant for recognition. We conclude that frayed ends represent a functional intermediate in which DNA termini can be sampled for suitability for endonucleolytic processing.


Asunto(s)
Virus del Sarcoma Aviar/enzimología , Emparejamiento Base , ADN Viral/química , Integrasa de VIH/metabolismo , VIH-1/enzimología , Virus del Sarcoma Aviar/genética , Virus del Sarcoma Aviar/metabolismo , Secuencia de Bases , Dominio Catalítico , Coenzimas/metabolismo , ADN Viral/genética , ADN Viral/metabolismo , Transferencia Resonante de Energía de Fluorescencia , Integrasa de VIH/química , VIH-1/genética , VIH-1/metabolismo , Metales/metabolismo , Reproducibilidad de los Resultados
20.
Nature ; 442(7103): 676-9, 2006 Aug 10.
Artículo en Inglés | MEDLINE | ID: mdl-16900197

RESUMEN

The volcanoes that lie along the Earth's tectonic boundaries are fed by melt generated in the mantle. How this melt is extracted and focused to the volcanoes, however, remains an unresolved question. Here we present new theoretical results with implications for melt focusing beneath mid-ocean ridges. By modelling laboratory experiments, we test a formulation for magma dynamics and provide an explanation for localized bands of high-porosity and concentrated shear deformation observed in experiments. These bands emerge and persist at 15 degrees-25 degrees to the plane of shear. Past theoretical work on this system predicted the emergence of melt bands but at an angle inconsistent with experiments. Our results suggest that the observed band angle results from a balance of porosity-weakening and strain-rate-weakening deformation mechanisms. Lower band angles are predicted for greater strain-rate weakening. From these lower band angles, we estimate the orientation of melt bands beneath mid-ocean ridges and show that they may enhance magma focusing toward the ridge axis.

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