Synthetic biology open language visual (SBOL Visual) version 2.3.

People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.3 of SBOL Visual, which builds on the prior SBOL Visual 2.2 in several ways. First, the specification now includes higher-level "interactions with interactions," such as an inducer molecule stimulating a repression interaction. Second, binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes. Finally, a new "unspecified interaction" glyph is added for visualizing interactions whose nature is unknown, the "insulator" glyph is deprecated in favor of a new "inert DNA spacer" glyph, and the polypeptide region glyph is recommended for showing 2A sequences.

Synthetic biology open language visual (SBOL visual) version 2.2.

People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.2 of SBOL Visual, which builds on the prior SBOL Visual 2.1 in several ways. First, the grounding of molecular species glyphs is changed from BioPAX to SBO, aligning with the use of SBO terms for interaction glyphs. Second, new glyphs are added for proteins, introns, and polypeptide regions (e. g., protein domains), the prior recommended macromolecule glyph is deprecated in favor of its alternative, and small polygons are introduced as alternative glyphs for simple chemicals.

A synthetic system for asymmetric cell division in Escherichia coli.

We describe a synthetic genetic circuit for controlling asymmetric cell division in Escherichia coli in which a progenitor cell creates a differentiated daughter cell while retaining its original phenotype. Specifically, we engineered an inducible system that can bind and segregate plasmid DNA to a single position in the cell. Upon cell division, colocalized plasmids are kept by one and only one of the daughter cells. The other daughter cell receives no plasmid DNA and is irreversibly differentiated from its sibling. In this way, we achieved asymmetric cell division through asymmetric plasmid partitioning. We then used this system to achieve physical separation of genetically distinct cells by tying motility to differentiation. Finally, we characterized an orthogonal inducible circuit that enables the simultaneous asymmetric partitioning of two plasmid species, resulting in cells that have four distinct differentiated states. These results point the way toward the engineering of multicellular systems from prokaryotic hosts.

Communicating Structure and Function in Synthetic Biology Diagrams.

Biological engineers often find it useful to communicate using diagrams. These diagrams can include information both about the structure of the nucleic acid sequences they are engineering and about the functional relationships between features of these sequences and/or other molecular species. A number of conventions and practices have begun to emerge within synthetic biology for creating such diagrams, and the Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard to organize, systematize, and extend such conventions in order to produce a coherent visual language. Here, we describe SBOL Visual version 2, which expands previous diagram standards to include new functional interactions, categories of molecular species, support for families of glyph variants, and the ability to indicate modular structure and mappings between elements of a system. SBOL Visual 2 also clarifies a number of requirements and best practices, significantly expands the collection of glyphs available to describe genetic features, and can be readily applied using a wide variety of software tools, both general and bespoke.

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1.

People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species . Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.1 of SBOL Visual, which builds on the prior SBOL Visual 2.0 standard by expanding diagram syntax to include methods for showing modular structure and mappings between elements of a system, interactions arrows that can split or join (with the glyph at the split or join indicating either superposition or a chemical process), and adding new glyphs for indicating genomic context (e.g., integration into a plasmid or genome) and for stop codons.

Comparison of Clopidogrel With Prasugrel and Ticagrelor in Patients With Acute Coronary Syndrome: Clinical Outcomes From the National Cardiovascular Database ACTION Registry.

BACKGROUND: We aimed to compare the clinical outcomes of clopidogrel, prasugrel, and ticagrelor in clinical practice using the National Cardiovascular Database ACTION Registry®. Treatment guidelines for patients with acute coronary syndrome (ACS) undergoing percutaneous coronary intervention recommend dual antiplatelet therapy (DAPT) for 12 months. Few clinical trials have compared the safety and efficacy of clopidogrel with that of newer antiplatelet therapies. METHODS: A retrospective study of patients hospitalized for ACS at Cleveland Clinic Akron General was conducted. Data elements included detailed medical history and clinical outcomes during hospital stay. The primary outcome was a composite of major clinical events (cardiogenic shock, atrial fibrillation, ventricular fibrillation, ventricular tachycardia, heart failure, bleeding, and mechanical ventilation). The independent variable was the type of DAPT. Statistical analyses were performed using Chi-square and Mann-Whitney U tests. A post-hoc analysis was performed to compare between the antiplatelet drugs head-to-head. RESULTS: Subjects (n = 1,388) admitted between January 2011 and March 2016 with ACS and treated with clopidogrel, prasugrel, or ticagrelor were included in the study. Mean age was 65 ± 14 years and 46% had ST-segment elevation myocardial infarction. Prasugrel administration within 24 h was associated with a lower incidence of the composite outcome (P = 0.049), bleeding (P = 0.028), and heart failure (P = 0.002). CONCLUSION: There was a significant difference between the type of antiplatelet drug and clinical outcomes in ACS patients who were treated with DAPT. Observations from current study may provide important information for prescribers in clinical decision-making.

Cardiovascular Effects of Exposure to Cigarette Smoke and Electronic Cigarettes: Clinical Perspectives From the Prevention of Cardiovascular Disease Section Leadership Council and Early Career Councils of the American College of Cardiology.

Cardiovascular morbidity and mortality as a result of inhaled tobacco products continues to be a global healthcare crisis, particularly in low- and middle-income nations lacking the infrastructure to develop and implement effective public health policies limiting tobacco use. Following initiation of public awareness campaigns 50 years ago in the United States, considerable success has been achieved in reducing the prevalence of cigarette smoking and exposure to secondhand smoke. However, there has been a slowing of cessation rates in the United States during recent years, possibly caused by high residual addiction or fatigue from cessation messaging. Furthermore, tobacco products have continued to evolve faster than the scientific understanding of their biological effects. This review considers selected updates on the genetics and epigenetics of smoking behavior and associated cardiovascular risk, mechanisms of atherogenesis and thrombosis, clinical effects of smoking and benefits of cessation, and potential impact of electronic cigarettes on cardiovascular health.

Umbilical cord blood-selected CD133(+) cells exhibit vasculogenic functionality in vitro and in vivo.

BACKGROUND AIMS: Current clinical trials utilize non-selected bone marrow (BM) mononuclear cells (MNC) to augment vasculo genesis within ischemic vascular beds. Recent reports have identified a diminished number and function of hemat-opoietic stem cells (HSC) from aged and diseased patients. Umbilical cord blood (UCB) provides a potential robust allo-geneic source of HSC for therapeutic vasculogenesis. METHODS: MNC and magnetically isolated CD133(+) cells were assessed for viability (trypan blue) and surface phenotype (flow cytometry). To test in vivo functionality of the cells, NOD/SCID mice underwent ligation of the right femoral artery followed immediately by cell injection. Blood flow recovery, necrosis, BM engraftment of human cells and histologic capillary density were determined. Cells were tested for potential mechanisms mediating the in vivo effects, including migration, cytokine secretion and angiogenic augmentation (Matrigel assays). RESULTS: Surface expression analysis showed CD31 (PECAM) expression was greatly increased in UCB CD133(+) cells compared with BM MNC. At 28 days, perfusion ratios were highest in animals receiving UCB CD133(+) cells, while animals receiving BM CD133(+) cells and BM MNC demonstrated perfusion ratios statistically higher than in animals treated with cytokine media alone. Animals receiving CD133(+) cells showed a statistically higher capillary density, reduced severe digit necrosis and increased engraftment in the BM than animals treated with unselected BM MNC. In vitro studies showed equivalent migration to stromal-derived factor-1 (SDF-1), increased production of tumor necrosis factor alpha (TNF-alpha) and increased branch points with the co-incubation of CD133(+) cells with human umbilical vein endothelial cells (HUVEC) in the Matrigel angiogenesis assay. CONCLUSIONS: Taken together, UCB CD133(+) cells exhibit robust vasculogenic functionality compared with BM MNC in response to ischemia.

Myocardial stunning following combined modality combretastatin-based chemotherapy: two case reports and review of the literature.

Myocardial stunning, known as stress cardiomyopathy, broken-heart syndrome, transient left ventricular apical ballooning, and Takotsubo cardiomyopathy, has been reported after many extracardiac stressors, but not following chemotherapy. We report 2 cases with characteristic electrocardiographic and echocardiographic features following combined modality therapy with combretastatin, a vascular-disrupting agent being studied for treatment of anaplastic thyroid cancer. In 1 patient, an ECG performed per protocol 18 hours after drug initiation showed deep, symmetric T-wave inversions in limb leads I and aVL and precordial leads V(2) through V(6). Echocardiography showed mildly reduced overall left ventricular systolic function with akinesis of the entire apex. The patient had mild elevations of troponin I. Coronary angiography revealed no epicardial coronary artery disease. The electrocardiographic and echocardiographic abnormalities resolved after several weeks. The patient remains stable from a cardiovascular standpoint and has not had a recurrence during follow-up. An electrocardiogram performed per protocol in a second patient showed deep, symmetric T-wave inversions throughout the precordial leads and a prolonged QT interval. Echocardiography showed mildly reduced left ventricular function with hypokinesis of the apical-septal wall. Acute coronary syndrome was ruled out, and both the electrocardiographic and echocardiographic changes resolved at follow-up. Although the patient remained pain-free without recurrence of anginal symptoms during long-term follow-up, the patient developed progressive malignancy and died.

On-line multi-slice computed tomography interactive overlay with conventional X-ray: a new and advanced imaging fusion concept.

BACKGROUND: Computed tomography (CT) has revolutionized noninvasive cardiovascular evaluations. Complicated percutaneous procedures require precise imaging guidance that conventional X-ray is often unable to provide. By combining X-ray imaging with real-time, interactive, CT-based landmarks, interventional procedures could be facilitated. We describe two cases using the first CT/Live X-ray overlay in which this technology shows its potential. CASE REPORTS: A 31-year-old male with an anatomically complicated atrial septal defect (ASD) was referred for percutaneous closure. Transesophageal echocardiography (TEE) revealed an inferior location of the ASD complicated by it's proximity to a prominent Eustachian ridge. The CT was used to create a patient-specific physical model in preparation for the procedure and an in-lab real-time CT overlay allowing successful closure. A second case of a 41-year-old male with coronary artery disease status-post coronary artery bypass, aortic valve replacement (AVR), and aortic root replacement with an abnormal coronary computed tomography angiogram (CTA). In a prior procedure years ago the saphenous vein graft (SVG) to the left anterior descending artery (LAD) could not be cannulated during invasive angiography, given the patient's complicated and unusual anatomy. Using CT overlay, the superiorly and anteriorly located SVG was cannulated successfully. DISCUSSION: CT/Live X-ray overlay provided an adequate anatomical intra-procedural ASD evaluation, defect sizing, and guidance in one case and localization of an anatomically challenging graft ostium in the other case. Adding the CT landmarks as an overlay to traditional X-ray techniques provides a revolutionary and advanced imaging fusion concept that should improve procedural success.

Drug insight: vascular disrupting agents and angiogenesis--novel approaches for drug delivery.

Vascular disrupting agents (VDAs), or endothelial disrupting agents, attempt to exploit the vascular endothelium that supplies rapidly dividing neoplasms. Unlike antiangiogenesis agents (e.g. the monoclonal antibody bevacizumab; and tyrosine kinase inhibitors sorafenib and sunitinib) that disrupt endothelial cell survival mechanisms and the development of a new tumor blood supply, VDAs are designed to disrupt the already established abnormal vasculature that supports tumors, by targeting their dysmorphic endothelial cells. Tumor vascular endothelium is characterized by its increased permeability, abnormal morphology, disorganized vascular networks, and variable density. VDAs induce rapid shutdown of tumor blood supply, causing subsequent tumor death from hypoxia and nutrient deprivation. The safety profile of this class of compounds is more indicative of agents that are indeed 'vascularly' active. For example, VDAs can cause: acute coronary and other thrombophlebitic syndromes; alterations in blood pressure, heart rate, and ventricular conduction; transient flush and hot flashes; neuropathy; and tumor pain. Despite these cardiovascular concerns some patients have benefited from VDAs in early clinical trials. Further drug development of VDAs must include the combination of these agents with other novel biological agents, cytotoxic chemotherapy, and radiotherapy. Close monitoring of patients receiving VDAs for any cardiovascular toxicity is imperative.

The safety of autologous intracoronary stem cell injections in a porcine model of chronic myocardial ischemia.

BACKGROUND: Intracoronary mononuclear cell therapy may produce angiogenesis in chronic myocardial ischemia. Potential complications include periprocedural infarction secondary to: reduced coronary blood flow; hyperviscosity from the cell preparation; or microvascular dysfunction. To date, no studies to evaluate these potential complications have been reported. The objective of this report was to study the safety and feasibility of intracoronary injections of autologous bone marrow mononuclear cells in a porcine chronic myocardial ischemia model. METHODS: Domestic pigs (n = 5) underwent ameroid cuff placement of the left circumflex artery. Bone marrow-derived mononuclear cells [15 x 10(6) cells] labeled with CM dioctadecyl tetramethylindocarbocyanine were given by intracoronary injection. Animals were sacrificed, and hearts and vital organs were inspected grossly and by histopathology, and bone marrow underwent immunofluorescence microscopy. RESULTS: Troponin I levels, gross inspection and histopathology did not reveal evidence of myocardial infarction. Labeled cells were observed in perivascular structures in myocardium at the injection site in all animals and in the spleen from one animal. Bone marrow aspirates indicated labeled cells. CONCLUSIONS: Intracoronary injection of autologous mononuclear cells in a porcine chronic myocardial ischemia model appears safe. Intracoronary injection resulted in cell localization in the perivascular areas of myocardium supplied by the injected vessel. Cell localization was observed only in the spleen in just one animal. Labeled cells were identified in bone marrow aspirates from three animals following injection, suggesting a role for bone marrow engraftment and repopulation as a possible mechanism for progenitor cell localization in myocardium.

The surface adhesion molecule CXCR4 stimulates mesenchymal stem cell migration to stromal cell-derived factor-1 in vitro but does not decrease apoptosis under serum deprivation.

BACKGROUND: Bone marrow mesenchymal stem cells (MSCs) can be used for myocardial repair following myocardial infarction. Increased expression of stromal cell-derived factor-1 (SDF-1) by an ischemic myocardium attracts CXCR4+ stem cells toward it. CXCR4, the receptor for SDF-1, is important in the migration, homing, and survival of hematopoietic stem cells. Although low levels of CXCR4 expression were found in minor subpopulations of cultured MSCs, most MSCs do not express CXCR4. To optimize the migration and survival of human MSCs, we expressed the CXCR4 gene in these cells using retroviral transduction. MATERIALS AND METHODS: We isolated and cultured MSCs from healthy volunteers and transduced them with a retroviral vector containing either CXCR4 and green fluorescent protein (GFP; CXCR4/GFP vector) or GFP alone (control vector). Flow cytometry confirmed successful transduction and GFP and CXCR4 expression. We used a transwell migration system to study MSC migration to SDF-1. We used Annexin V and propidium iodide stains to assess cell survival before and after the survival challenge. RESULTS: Flow cytometry showed that, on average, 83.4+/-17.7% of transduced MSCs expressed CXCR4. Compared with control MSCs, MSCs transduced with CXCR4 showed significantly more migration toward SDF-1, threefold greater at 3 h and more than fivefold greater at 6 h. Mesenchymal stem cells transduced with CXCR4 showed no significant difference in survival under normal to serum-deprived growth conditions. CONCLUSION: Mesenchymal stem cells can be efficiently transduced to express CXCR4, and transduced MSCs migrate rapidly toward SDF-1. CXCR4 expression does not render survival advantage to MSCs under serum-deprived conditions.

Treatment of heart failure with a normal ejection fraction.

Treatment of diastolic heart failure is divided into acute and chronic management. During acute management, the focus should be treatment of the presenting syndrome, including correction of volume overload, treating hypertension, alleviating ischemia, and controlling tachyarrhythmias. Therefore, acute treatment should include several components: treating volume overload with sodium restriction and diuretics; treating ischemic heart disease with antiplatelet therapy, anticoagulants, and beta blockers; treating hypertension aggressively, using multiple agents if necessary; and treating atrial tachyarrhythmias such as atrial fibrillation with rate-controlling agents, such as beta blockers and possibly nondihydropyridine calcium channel blockers such as diltiazem and verapamil. Antiarrhythmic agents with or without electrical cardioversion may be necessary. Thoroughly evaluate and manage extracardiac precipitants such as anemia and renal failure. Chronic management should also focus on precipitating factors, for which adequate control of hypertension is paramount. Patient education regarding dietary and medication compliance and lifestyle changes is also important. If ischemic heart disease is present, aggressive anti-ischemic therapy is necessary, including revascularization when indicated.

Angiotensin-receptor blockers in heart failure: evidence from the CHARM trial.

The large Candesartan in Heart Failure Assessment of Reduction in Mortality and Morbidity (CHARM) trial recently found that in patients with heart failure who were similar to those whom clinicians see in everyday practice, the angiotensin-receptor blocker candesartan was not only an acceptable alternative to angiotensin-converting enzyme (ACE) inhibitors, but also was beneficial when added to regimens that already included ACE inhibitors and beta-blockers. Candesartan was beneficial in heart failure patients with or without left ventricular systolic dysfunction.