Modulation of DNA loop lifetimes by the free energy of loop formation

Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for transcriptional regulation in both prokaryotes and eukaryotes, and the speed of such regulations affects the fitness of individuals. Here, we examine the in vitro looping dynamics of the classic Lac repressor gene-regulatory motif. We show that both loop association and loop dissociation at the DNA-repressor junctions depend on the elastic deformation of the DNA and protein, and that both looping and unlooping rates approximately scale with the looping J factor, which reflects the system's deformation free energy. We explain this observation by transition state theory and model the DNA-protein complex as an effective worm-like chain with twist. We introduce a finite protein-DNA binding interaction length, in competition with the characteristic DNA deformation length scale, as the physical origin of the previously unidentified loop dissociation dynamics observed here, and discuss the robustness of this behavior to perturbations in several polymer parameters

The effect of endothelial cell overexpression of plasminogen activator inhibitor-1 on smooth muscle cell migration

AbstractIntroduction: Plasminogen activator inhibitor-1 (PAI-1), a known inhibitor of plasminogen activators, may regulate smooth muscle cell migration (SMC) through alteration in matrix metalloproteinase (MMP) activity. Methods: To study the effect of endothelial cell (EC) PAI-1 overexpression on SMC migration, RT-PCR was used to clone the full length PAI-1 gene, which was ligated into the pCMV/myc/ER expression vector. With electroporation, bovine aortic ECs were transfected with either the PAI-1 construct or the empty vector as control. EC PAI-1 overexpression was shown with a specific PAI-1 activity assay and enzyme-linked immunosorbent assay. The effect of EC PAI-1 overexpression on SMC migration was measured with a modified Boyden-chamber assay. SMC MMP expression was measured with zymography. Results: Selected clones (EC9, EC21) had a three-fold to five-fold increase in PAI-1 activity compared with untransfected EC and empty vector EC (ECC). Similarly, enzyme-linked immunosorbent assay results showed a 3.5-fold to 5.5-fold increase in PAI-1 levels in EC9 and EC21 versus ECC. Untransfected EC and ECC had similar effects on SMC migratory patterns. Migration of SMC exposed to PAI-1 overexpressing EC was inhibited by 35% to 57% compared with ECC. This inhibitory effect was reversed with addition of exogenous urokinase-type plasminogen activator (uPA). Zymography showed downregulation of MMP-2 and MMP-9 in SMCs exposed to PAI-1 overexpressing EC. Conclusion: PAI-1 overexpression with transfected EC inhibits SMC migration. This effect may be mediated through decreased SMC MMP activity. (J Vasc Surg 2002;36:164-71.

Cytokine and Adhesion Molecule Requirements for Lung Injury Induced by Anti-Glomerular Basement Membrane Antibody

Acute hemorrhagic lung injury occurs in humans with anti-GBM antibody (Goodpasture's syndrome), however, the mechanism of this injury is still largely unknown. To date, treatment has been confined to steroids and plasmaphoresis. Infusion of anti-GBM antibody into rats caused lung injury with intra-alveolar hemorrhage and intrapulmonary accumulation of neutrophils. Lung injury was dependent on the presence of neutrophils and complement and required both TNFα and IL-1. Experiments employing blocking antibodies to adhesion molecules demonstrated requirements for the β 1 integrin VLA-4, β 2 integrins LFA-1 and Mac-1, and L-selectin. The endothelial cell adhesion molecules, E-selectin and ICAM-1, were also required for the full development of lung injury. Inhibition of TNFα or IL-1 or adhesion molecules reduced both lung injury and tissue neutrophil accumulation. Thus, this study underscores cytokine and adhesion molecule requirements for neutrophil mediated injury in lung and kidney caused by anti-GBM, suggesting potential targets for the treatment of Goodpasture's syndrome in humans.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44520/1/10753_2004_Article_416573.pd

Greater accordance with the Dietary Approaches to Stop Hypertension dietary pattern is associated with lower diet-related greenhouse gas production but higher dietary costs in the United Kingdom.

BACKGROUND: The Dietary Approaches to Stop Hypertension (DASH) diet is a proven way to prevent and control hypertension and other chronic disease. Because the DASH diet emphasizes plant-based foods, including vegetables and grains, adhering to this diet might also bring about environmental benefits, including lower associated production of greenhouse gases (GHGs). OBJECTIVE: The objective was to examine the interrelation between dietary accordance with the DASH diet and associated GHGs. A secondary aim was to examine the retail cost of diets by level of DASH accordance. DESIGN: In this cross-sectional study of adults aged 39-79 y from the European Prospective Investigation into Cancer and Nutrition-Norfolk, United Kingdom cohort (n = 24,293), dietary intakes estimated from food-frequency questionnaires were analyzed for their accordance with the 8 DASH food and nutrient-based targets. Associations between DASH accordance, GHGs, and dietary costs were evaluated in regression analyses. Dietary GHGs were estimated with United Kingdom-specific data on carbon dioxide equivalents associated with commodities and foods. Dietary costs were estimated by using national food prices from a United Kingdom-based supermarket comparison website. RESULTS: Greater accordance with the DASH dietary targets was associated with lower GHGs. Diets in the highest quintile of accordance had a GHG impact of 5.60 compared with 6.71 kg carbon dioxide equivalents/d for least-accordant diets (P < 0.0001). Among the DASH food groups, GHGs were most strongly and positively associated with meat consumption and negatively with whole-grain consumption. In addition, higher accordance with the DASH diet was associated with higher dietary costs, with the mean cost of diets in the top quintile of DASH scores 18% higher than that of diets in the lowest quintile (P < 0.0001). CONCLUSIONS: Promoting wider uptake of the DASH diet in the United Kingdom may improve population health and reduce diet-related GHGs. However, to make the DASH diet more accessible, food affordability, particularly for lower income groups, will have to be addressed.Supported by the British Heart Foundation (BHF), Economic and Social Research Council, Medical Research Council, the National Institute for Health Research, and the Wellcome Trust under the auspices of the UK Clinical Research Collaboration. PS was supported by the BHF grant number 021/P&C/Core/2010/HPRG. AM was supported by the Oxford Martin School.This is the final published version. It first appeared at http://dx.doi.org/10.3945/ajcn.114.09063

CT scanning for diagnosing blunt ureteral and ureteropelvic junction injuries

<p>Abstract</p> <p>Background</p> <p>Blunt ureteral and ureteropelvic (UPJ) injuries are extremely rare and very difficult to diagnose. Many of these injuries are missed by the initial trauma evaluation.</p> <p>Methods</p> <p>Trauma registry data was used to identify all blunt trauma patients with ureteral or UPJ injuries, from 1 April 2001 to 30 November 2006. Demographics, injury information and outcomes were determined. Chart review was then performed to record initial clinical and all CT findings.</p> <p>Results</p> <p>Eight patients had ureteral or UPJ injuries. Subtle findings such as perinephric stranding and hematomas, and low density retroperitoneal fluid were evident on all initial scans, and prompted delayed excretory scans in 7/8 cases. As a result, ureteral and UPJ injuries were diagnosed immediately for these seven patients. These findings were initially missed in the eighth patient because significant associated visceral findings mandated emergency laparotomy. All ureteral and UPJ injuries have completely healed except for the case with the delay in diagnosis.</p> <p>Conclusion</p> <p>Most blunt ureteral and UPJ injuries can be identified if delayed excretory CT scans are performed based on initial CT findings of perinephric stranding and hematomas, or the finding of low density retroperitoneal fluid.</p

A network analysis to identify mediators of germline-driven differences in breast cancer prognosis.

Identifying the underlying genetic drivers of the heritability of breast cancer prognosis remains elusive. We adapt a network-based approach to handle underpowered complex datasets to provide new insights into the potential function of germline variants in breast cancer prognosis. This network-based analysis studies ~7.3 million variants in 84,457 breast cancer patients in relation to breast cancer survival and confirms the results on 12,381 independent patients. Aggregating the prognostic effects of genetic variants across multiple genes, we identify four gene modules associated with survival in estrogen receptor (ER)-negative and one in ER-positive disease. The modules show biological enrichment for cancer-related processes such as G-alpha signaling, circadian clock, angiogenesis, and Rho-GTPases in apoptosis

Nominal Henkin Semantics: simply-typed lambda-calculus models in nominal sets

We investigate a class of nominal algebraic Henkin-style models for the simply typed lambda-calculus in which variables map to names in the denotation and lambda-abstraction maps to a (non-functional) name-abstraction operation. The resulting denotations are smaller and better-behaved, in ways we make precise, than functional valuation-based models. Using these new models, we then develop a generalisation of \lambda-term syntax enriching them with existential meta-variables, thus yielding a theory of incomplete functions. This incompleteness is orthogonal to the usual notion of incompleteness given by function abstraction and application, and corresponds to holes and incomplete objects.Comment: In Proceedings LFMTP 2011, arXiv:1110.668

Association Between Results of a Gene Expression Signature Assay and Recurrence-Free Interval in Patients With Stage II Colon Cancer in Cancer and Leukemia Group B 9581 (Alliance)

PURPOSE: Conventional staging methods are inadequate to identify patients with stage II colon cancer (CC) who are at high risk of recurrence after surgery with curative intent. ColDx is a gene expression, microarray-based assay shown to be independently prognostic for recurrence-free interval (RFI) and overall survival in CC. The objective of this study was to further validate ColDx using formalin-fixed, paraffin-embedded specimens collected as part of the Alliance phase III trial, C9581. PATIENTS AND METHODS: C9581 evaluated edrecolomab versus observation in patients with stage II CC and reported no survival benefit. Under an initial case-cohort sampling design, a randomly selected subcohort (RS) comprised 514 patients from 901 eligible patients with available tissue. Forty-nine additional patients with recurrence events were included in the analysis. Final analysis comprised 393 patients: 360 RS (58 events) and 33 non-RS events. Risk status was determined for each patient by ColDx. The Self-Prentice method was used to test the association between the resulting ColDx risk score and RFI adjusting for standard prognostic variables. RESULTS: Fifty-five percent of patients (216 of 393) were classified as high risk. After adjustment for prognostic variables that included mismatch repair (MMR) deficiency, ColDx high-risk patients exhibited significantly worse RFI (multivariable hazard ratio, 2.13; 95% CI, 1.3 to 3.5; P < .01). Age and MMR status were marginally significant. RFI at 5 years for patients classified as high risk was 82% (95% CI, 79% to 85%), compared with 91% (95% CI, 89% to 93%) for patients classified as low risk. CONCLUSION: ColDx is associated with RFI in the C9581 subsample in the presence of other prognostic factors, including MMR deficiency. ColDx could be incorporated with the traditional clinical markers of risk to refine patient prognosis

The Demise of Islet Allotransplantation in the US: A Call for an Urgent Regulatory Update The ISLETS FOR US Collaborative

Islet allotransplantation in the United States (US) is facing an imminent demise. Despite nearly three decades of progress in the field, an archaic regulatory framework has stymied US clinical practice. Current regulations do not reflect the state-of-the-art in clinical or technical practices. In the US, islets are considered biologic drugs and more than minimally manipulated human cell and tissue products (HCT/Ps). Across the world, human islets are appropriately defined as minimally manipulated tissue which has led to islet transplantation becoming a standard-of-care procedure for patients with type 1 diabetes mellitus and problematic hypoglycemia. As a result of the outdated US regulations, only eleven patients underwent allo-ITx in the US between 2011-2016 and all in the setting of a clinical trial. Herein, we describe the current regulations pertaining to islet transplantation in the United States. We explore the progress which has been made in the field and demonstrate why the regulatory framework must be updated to both, better reflect our current clinical practice and to deal with upcoming challenges. We propose specific updates to current regulations which are required for the renaissance of ethical, safe, effective, and affordable allo-ITx in the United States