Phylogeny based discovery of regulatory elements

BACKGROUND: Algorithms that locate evolutionarily conserved sequences have become powerful tools for finding functional DNA elements, including transcription factor binding sites; however, most methods do not take advantage of an explicit model for the constrained evolution of functional DNA sequences. RESULTS: We developed a probabilistic framework that combines an HKY85 model, which assigns probabilities to different base substitutions between species, and weight matrix models of transcription factor binding sites, which describe the probabilities of observing particular nucleotides at specific positions in the binding site. The method incorporates the phylogenies of the species under consideration and takes into account the position specific variation of transcription factor binding sites. Using our framework we assessed the suitability of alignments of genomic sequences from commonly used species as substrates for comparative genomic approaches to regulatory motif finding. We then applied this technique to Saccharomyces cerevisiae and related species by examining all possible six base pair DNA sequences (hexamers) and identifying sequences that are conserved in a significant number of promoters. By combining similar conserved hexamers we reconstructed known cis-regulatory motifs and made predictions of previously unidentified motifs. We tested one prediction experimentally, finding it to be a regulatory element involved in the transcriptional response to glucose. CONCLUSION: The experimental validation of a regulatory element prediction missed by other large-scale motif finding studies demonstrates that our approach is a useful addition to the current suite of tools for finding regulatory motifs

Environment-specific combinatorial cis-regulation in synthetic promoters

When a cell's environment changes, a large transcriptional response often takes place. The exquisite sensitivity and specificity of these responses are controlled in large part by the combinations of cis-regulatory elements that reside in gene promoters and adjacent control regions. Here, we present a study aimed at accurately modeling the relationship between combinations of cis-regulatory elements and the expression levels they drive in different environments. We constructed four libraries of synthetic promoters in yeast, consisting of combinations of transcription factor binding sites and assayed their expression in four different environments. Thermodynamic models relating promoter sequences to their corresponding four expression levels explained at least 56% of the variation in expression in each library through the different conditions. Analyses of these models suggested that a large fraction of regulated gene expression is explained by changes in the effective concentration of sequence-specific transcription factors, and we show that in most cases, the corresponding transcription factors are expressed in a pattern that is predicted by the thermodynamic models. Our analysis uncovered two binding sites that switch from activators to repressors in different environmental conditions. In both the cases, the switch was not the result of a single transcription factor changing regulatory modes, but most likely due to competition between multiple factors binding to the same site. Our analysis suggests that this mode of regulation allows for large and steep changes in expression in response to changing transcription factor concentrations. Our results demonstrate that many complex changes in gene expression are accurately explained by simple changes in the effective concentrations of transcription factors

Pulmonary hypertension is a manifestation of congestive heart failure and left ventricular diastolic dysfunction in octogenarians with severe aortic stenosis

Previous studies have suggested that pulmonary hypertension (PH) in severe aortic stenosis (AS) is a risk factor for operative mortality with aortic valve replacement (AVR). Conversely, others have shown that patients with AS and PH extract a large symptomatic and survival benefit from AVR compared with those patients not treated surgically. We sought to evaluate the prevalence, severity, and mechanism of PH in an elderly patient cohort with severe AS. We prospectively evaluated 41 patients aged ≥80 years with severe AS. All patients underwent cardiac catheterization and transthoracic echocardiography within 24 hours. We found that PH was common in this cohort: 32 patients (78%) had PH; however, the predominant mechanism of PH was left heart congestion. Patients with PH had nearly double the pulmonary artery wedge pressure of patients without PH (23 vs. 13 mmHg; P ≤ 0.001). In patients with PH compared with those without, pulmonary vascular resistance was higher yet still under 3 Wood units (WU; 2.9 vs. 1.5 WU; P = 0.001), and the transpulmonary gradient (11 vs. 7 mmHg; P = 0.01) and diastolic pulmonary gradient (DPG; 3.0 vs. 2.7 mmHg; P = 0.74) were in normal range. Left ventricular diastolic abnormalities were more common in patients with severe AS and PH. Right ventricular (RV) dysfunction was common (13/41 patients, 32%), but the PH and non-PH groups had similar tricuspid annular plane systolic excursion (2.0 vs. 2.3 cm; P = 0.15). Only 2 subjects had both RV dysfunction and an elevated DPG. In conclusion, PH is common in elderly patients with severe AS. This occurs largely due to left heart congestion, with a relative absence of pulmonary vascular disease and RV dysfunction, and as such, PH may serve as a heart failure equivalent in these patients

Variables influencing sentencing severity: Intercourt differences in Connecticut

Studies of criminal-court dispositions have traditionally aggregated courts along political and geographic boundaries. This article suggests that courts should be analyzed individually, even within the same jurisdiction, as a means of increasing the explanatory capacity of the variables involved. Further, it is contended that intercourt differences are a result of organizational influences operating within each court.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25848/1/0000411.pd

Create a translational medicine knowledge repository - Research downsizing, mergers and increased outsourcing have reduced the depth of in-house translational medicine expertise and institutional memory at many pharmaceutical and biotech companies: how will they avoid relearning old lessons?

Pharmaceutical industry consolidation and overall research downsizing threatens the ability of companies to benefit from their previous investments in translational research as key leaders with the most knowledge of the successful use of biomarkers and translational pharmacology models are laid off or accept their severance packages. Two recently published books may help to preserve this type of knowledge but much of this type of information is not in the public domain. Here we propose the creation of a translational medicine knowledge repository where companies can submit their translational research data and access similar data from other companies in a precompetitive environment. This searchable repository would become an invaluable resource for translational scientists and drug developers that could speed and reduce the cost of new drug development

Monoallelic deletion of the microRNA biogenesis gene Dgcr8 produces deficits in the development of excitatory synaptic transmission in the prefrontal cortex

Abstract Background Neuronal phenotypes associated with hemizygosity of individual genes within the 22q11.2 deletion syndrome locus hold potential towards understanding the pathogenesis of schizophrenia and autism. Included among these genes is Dgcr8, which encodes an RNA-binding protein required for microRNA biogenesis. Dgcr8 haploinsufficient mice (Dgcr8+/-) have reduced expression of microRNAs in brain and display cognitive deficits, but how microRNA deficiency affects the development and function of neurons in the cerebral cortex is not fully understood. Results In this study, we show that Dgcr8+/- mice display reduced expression of a subset of microRNAs in the prefrontal cortex, a deficit that emerges over postnatal development. Layer V pyramidal neurons in the medial prefrontal cortex of Dgcr8+/- mice have altered electrical properties, decreased complexity of basal dendrites, and reduced excitatory synaptic transmission. Conclusions These findings demonstrate that precise microRNA expression is critical for the postnatal development of prefrontal cortical circuitry. Similar defects in neuronal maturation resulting from microRNA deficiency could represent endophenotypes of certain neuropsychiatric diseases of developmental onset

Why growth equals power - and why it shouldn't : constructing visions of China

When discussing the success of China's transition from socialism, there is a tendency to focus on growth figures as an indication of performance. Whilst these figures are indeed impressive, we should not confuse growth with development and assume that the former necessarily automatically generates the latter. Much has been done to reduce poverty in China, but the task is not as complete as some observers would suggest; particularly in terms of access to health, education and welfare, and also in dealing with relative (rather than absolute) depravation and poverty. Visions of China have been constructed that exaggerate Chinese development and power in the global system partly to serve political interests, but partly due to the failure to consider the relationship between growth and development, partly due to the failure to disaggregate who gets what in China, and partly due to the persistence of inter-national conceptions of globalised production, trade, and financial flows

Detection of Multiple Variants of Grapevine Fanleaf Virus in Single Xiphinema index Nematodes

Grapevine fanleaf virus (GFLV) is responsible for a widespread disease in vineyards worldwide. Its genome is composed of two single-stranded positive-sense RNAs, which both show a high genetic diversity. The virus is transmitted from grapevine to grapevine by the ectoparasitic nematode Xiphinema index. Grapevines in diseased vineyards are often infected by multiple genetic variants of GFLV but no information is available on the molecular composition of virus variants retained in X. index following nematodes feeding on roots. In this work, aviruliferous X. index were fed on three naturally GFLV-infected grapevines for which the virome was characterized by RNAseq. Six RNA-1 and four RNA-2 molecules were assembled segregating into four and three distinct phylogenetic clades of RNA-1 and RNA-2, respectively. After 19 months of rearing, single and pools of 30 X. index tested positive for GFLV. Additionally, either pooled or single X. index carried multiple variants of the two GFLV genomic RNAs. However, the full viral genetic diversity found in the leaves of infected grapevines was not detected in viruliferous nematodes, indicating a genetic bottleneck. Our results provide new insights into the complexity of GFLV populations and the putative role of X. index as reservoirs of virus diversity

Pre-existing chronic thromboembolic pulmonary hypertension in acute pulmonary embolism

BACKGROUND Chronic thromboembolic pulmonary hypertension (CTEPH) is considered a complication of pulmonary embolism (PE). However, signs of CTEPH may exist in patients with a first symptomatic PE. RESEARCH QUESTION Which radiologic findings on computed tomography pulmonary angiography (CTPA) at the time of acute PE could indicate the presence of a pre-existing CTEPH? RESULTS We included unselected patients with acute PE who were prospectively followed for 2 years with a structured visit schedule. Two expert radiologists independently assessed patients' baseline CTPAs for pre-existing CTEPH; in case of disagreement, a decision was reached by 2:1 majority with a third expert. In addition, the radiologists checked for predefined individual parameters suggesting chronic PE and pulmonary hypertension. Signs of chronic PE or CTEPH at baseline were identified in 46 (15%) of 303 included patients. Intravascular webs, arterial narrowing or retraction, dilated bronchial arteries and right ventricular hypertrophy were the main drivers of the assessment. Five (1.7%) patients were diagnosed with CTEPH during follow-up. All four patients diagnosed with CTEPH early (83-108 days after acute PE) could be found in enriched subgroups based on the experts' overall assessment or fulfilling a minimum number of the predefined radiologic criteria at baseline. The specificity of pre-existing CTEPH diagnosis and the level of radiologists' agreement improved as the number of required criteria increased. INTERPRETATION Searching for predefined radiologic parameters suggesting pre-existing CTEPH at the time of acute PE diagnosis may allow for targeted follow-up strategies and risk-adapted CTEPH screening, thus facilitating earlier CTEPH diagnosis

Low-Level Radioactive Waste (LLW) Management at the Nevada Test Site (NTS)

In 1978, the Department of Energy, Nevada Operations Office (DOE/NV), established a managed LLW disposal project at the Nevada Test Site (NTS). Two, sites which were already accepting limited amounts of on-site generated waste for disposal and off-site generated Transuranic Waste for interim storage, were selected to house the disposal facilities. In those early days, these sites, located about 15 miles apart, afforded the DOE/NV the opportunity to use at least two technologies to manage its waste cost effectively. The Area 5 Radioactive Waste Management Site (RWMS) uses engineered shallow-land burial cells to dispose packaged waste while the Area 3 RWMS uses subsidence craters formed from underground testing of nuclear weapons for the disposal of packaged and unpackaged bulk waste. The paper describes the technical attributes of both Area 5 and Area 3 facilities, the acceptance process, the disposal processes, and present and future capacities of both sites