Current understanding of the human microbiome

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature Medicine 24 (2018): 392–400, doi:10.1038/nm.4517.Our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. Improvements in the throughput and accuracy of DNA sequencing of the genomes of microbial communities associated with human samples, complemented by analysis of transcriptomes, proteomes, metabolomes and immunomes, and mechanistic experiments in model systems, have vastly improved our ability to understand the structure and function of the microbiome in both diseased and healthy states. However, many challenges remain. In this Review, we focus on studies in humans to describe these challenges, and propose strategies that leverage existing knowledge to move rapidly from correlation to causation, and ultimately to translation.Many of the studies described here in our laboratories were supported by the NIH, NSF, DOE, and the Alfred P. Sloan Foundation.2018-10-1

Repaired tetralogy of Fallot: the roles of cardiovascular magnetic resonance in evaluating pathophysiology and for pulmonary valve replacement decision support

Surgical management of tetralogy of Fallot (TOF) results in anatomic and functional abnormalities in the majority of patients. Although right ventricular volume load due to severe pulmonary regurgitation can be tolerated for many years, there is now evidence that the compensatory mechanisms of the right ventricular myocardium ultimately fail and that if the volume load is not eliminated or reduced by pulmonary valve replacement the dysfunction might be irreversible. Cardiovascular magnetic resonance (CMR) has evolved during the last 2 decades as the reference standard imaging modality to assess the anatomic and functional sequelae in patients with repaired TOF. This article reviews the pathophysiology of chronic right ventricular volume load after TOF repair and the risks and benefits of pulmonary valve replacement. The CMR techniques used to comprehensively evaluate the patient with repaired TOF are reviewed and the role of CMR in supporting clinical decisions regarding pulmonary valve replacement is discussed

Modeling the Basal Dynamics of P53 System

The tumor suppressor p53 has become one of most investigated genes. Once activated by stress, p53 leads to cellular responses such as cell cycle arrest and apoptosis.Most previous models have ignored the basal dynamics of p53 under nonstressed conditions. To explore the basal dynamics of p53, we constructed a stochastic delay model by incorporating two negative feedback loops. We found that protein distribution of p53 under nonstressed condition is highly skewed with a fraction of cells showing high p53 levels comparable to those observed under stressed conditions. Under nonstressed conditions, asynchronous and spontaneous p53 pulses are triggered by basal DNA double strand breaks produced during normal cell cycle progression. The first peaking times show a predominant G1 distribution while the second ones are more widely distributed. The spontaneous pulses are triggered by an excitable mechanism. Once initiated, the amplitude and duration of pulses remain unchanged. Furthermore, the spontaneous pulses are filtered by ataxia telangiectasia mutated protein mediated posttranslational modifications and do not result in substantial p21 transcription. If challenged by externally severe DNA damage, cells generate synchronous p53 pulses and induce significantly high levels of p21. The high expression of p21 can also be partially induced by lowering the deacetylation rate.Our results demonstrated that the dynamics of p53 under nonstressed conditions is initiated by an excitable mechanism and cells become fully responsive only when cells are confronted with severe damage. These findings advance our understanding of the mechanism of p53 pulses and unlock many opportunities to p53-based therapy

Impact of right ventricular endocardial trabeculae on volumes and function assessed by CMR in patients with tetralogy of Fallot

<p>The objective of this study was to assess the impact of right ventricular (RV) trabeculae and papillary muscles on measured volumes and function assessed by cardiovascular magnetic resonance imaging in patients with repaired tetralogy of Fallot. Sixty-five patients with repaired tetralogy of Fallot underwent routine cardiovascular magnetic resonance imaging. Endocardial and epicardial contours were drawn manually and included trabeculae and papillary muscles in the blood volume. Semi-automatic threshold-based segmentation software excluded these structures. Both methods were compared in terms of end-diastolic, end-systolic and stroke volume, ejection fraction and mass. Observer agreement was determined for all measures. Exclusion of trabeculae and papillary muscle in the RV blood volume decreased measured RV end-diastolic volume by 15 % (from 140 +/- A 35 to 120 +/- A 32 ml/m(2)) compared to inclusion, end-systolic volume by 21 % (from 74 +/- A 23 to 59 +/- A 20 ml/m(2)), stroke volume by 9 % (from 66 +/- A 16 to 60 +/- A 16 ml/m(2)) and relatively increased ejection fraction by 7 % (from 48 +/- A 7 to 51 +/- A 8 %) and end-diastolic mass by 79 % (from 28 +/- A 7 to 51 +/- A 10 g/m(2)), p <.01. Excluding trabeculae and papillary muscle resulted in an improved interobserver agreement of RV mass compared to including these structures (coefficient of agreement of 87 versus 78 %, p <.01). Trabeculae and papillary muscle significantly affect measured RV volumes, function and mass. Semi-automatic threshold-based segmentation software can reliably exclude trabeculae and papillary muscles from the RV blood volume.</p>