SBOL Visual: A Graphical Language for Genetic Designs.

Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic engineering. It consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw illustrations for communication and instruction, and as image assets for computer-aided design. SBOL Visual is a community standard, freely available for personal, academic, and commercial use (Creative Commons CC0 license). We provide prototypical symbol images that have been used in scientific publications and software tools. We encourage users to use and modify them freely, and to join the SBOL Visual community: http://www.sbolstandard.org/visual.

Case study of a non-destructive treatment method for the remediation of military structures containing polychlorinated biphenyl contaminated paint.

Restricted by federal regulations and limited remediation options, buildings contaminated with paint laden with polychlorinated biphenyls (PCBs) have high costs associated with the disposal of hazardous materials. As opposed to current remediation methods which are often destructive and a risk to the surrounding environment, this study suggests a non-metal treatment system (NMTS) and a bimetallic treatment system (BTS) as versatile remediation options for painted industrial structures including concrete buildings, and metal machine parts. In this field study, four areas of a discontinued Department of Defense site were treated and monitored over 3 weeks. PCB levels in paint and treatment system samples were analyzed through gas chromatography/electron capture detection (GC-ECD). PCB concentrations were reduced by 95 percent on painted concrete and by 60-97 percent on painted metal with the majority of the PCB removal occurring within the first week of application. Post treatment laboratory studies including the utilization of an activated metal treatment system (AMTS) further degraded PCBs in BTS and NMTS by up to 82 percent and 99 percent, respectively, indicating that a two-step remediation option is viable. These findings demonstrate that the NMTS and BTS can be an effective, nondestructive, remediation process for large painted structures, allowing for the reuse or sale of remediated materials that otherwise may have been disposed.

Community-driven development for computational biology at Sprints, Hackathons and Codefests.

BACKGROUND: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. RESULTS: This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities. CONCLUSIONS: Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.

Hypoxemic Cardiac Arrest from Aspiration of a Cracker in the Postanesthesia Care Unit: A Case Report.

A 71-year-old woman with coronary artery disease presented for carotid artery revascularization. After general anesthesia, the patient arrived in stable condition to the postanesthesia care unit. While awaiting transfer to her inpatient room, telemetry alarms alerted her nurse, who found the patient unresponsive, cyanotic, and pulseless. Advanced cardiovascular life support was initiated, with return of spontaneous circulation obtained after 1 round of chest compressions. On oropharyngeal examination, food particles were observed and suctioned. The patient then coughed up additional cracker pieces. This case highlights the risk of aspiration from dry, solid foods in the elderly during the postanesthesia recovery period.

Dexmedetomidine for Preventing Sleep Disturbance after Ambulatory Anesthesia: A Case Report.

Propofol anesthesia may impact a patient's sleep quality in the immediate postprocedure timeframe. We describe a 24-year-old man presenting for gastrostomy-jejunostomy tube replacement who reported debilitating sleep-onset disturbances after 3 previous anesthetic exposures for the same procedure. Review of the patient's records revealed the recurring use of propofol infusion. We proposed using dexmedetomidine infusion to potentially avoid another extended sleep disturbance. Following a dexmedetomidine-centered plan, the patient reported experiencing his usual sleep pattern without side-effects for 5 consecutive days postprocedure. This case highlights the potential for propofol-induced sleep disturbance in the ambulatory setting, which may be avoided with dexmedetomidine administration.

Maintaining access to HIV pre-exposure prophylaxis in a pandemic: A service evaluation of telephone-based pre-exposure prophylaxis provision.

OBJECTIVES: The objective was to perform a survey-based service evaluation of our telephone PrEP clinic (Tele-PrEP), which was instituted during the COVID-19 pandemic, to inform future service delivery. METHODS: We administered parallel, web-based, anonymous surveys to PrEP-users who had a Tele-PrEP appointment between 13.11.2020 and 17.12.2020 and all healthcare professionals (HCPs) conducting Tele-PrEP clinics. We used descriptive statistics to summarise demographic and qualitative data, and thematically categorised free text responses using the Framework for a Systems Approach to Healthcare Delivery. RESULTS: 62/117 (53%) PrEP-users and 8/9 (89%) HCPs completed the surveys. Tele-PrEP was rated 'excellent' or 'good' by 61/62 (98%) PrEP-users. All HCPs felt that Tele-PrEP allowed them to assess patients safely and confidently. 10/62 (16%) PrEP-users and 1 (11%) HCP expressed a preference for face-to-face care. Using the Framework for a Systems Approach to Healthcare Delivery we identified key areas important to respondents who highlighted the rapid changes as a result of COVID-19, which required an increase in dedicated resources. HCPs valued teamwork, support/supervision and convenience in achieving quality care for the patient, who in turn, valued convenient, holistic and individualised management to meet their sexual healthcare needs. CONCLUSION: Tele-PrEP is feasible and acceptable. While most respondents rated the service highly, others identified a need/preference for face-to-face appointments.

The synthetic biology open language.

The design and construction of engineered organisms is an emerging new discipline called synthetic biology and holds considerable promise as a new technological platform. The design of biologically engineered systems is however nontrivial, requiring contributions from a wide array of disciplines. One particular issue that confronts synthetic biologists is the ability to unambiguously describe novel designs such that they can be reengineered by a third-party. For this reason, the synthetic biology open language (SBOL) was developed as a community wide standard for formally representing biological designs. A design created by one engineering team can be transmitted electronically to another who can then use this design to reproduce the experimental results. The development and the community of the SBOL standard started in 2008 and has since grown in use with now over 80 participants, including international, academic, and industrial interests. SBOL has stimulated the development of repositories and software tools to help synthetic biologists in their design efforts. This chapter summarizes the latest developments and future of the SBOL standard and its supporting infrastructure.

Laboratory evaluation of a prospective remediation method for PCB-contaminated paint.

BACKGROUND: Paint laden with polychlorinated biphenyls (PCBs) often acts as a point source for environmental contamination. It is advantageous to address contaminated paint before the PCBs transport to surrounding media; however, current disposal methods of painted material introduce a variety of complications. Previous work demonstrates that PCBs can be broken down at ambient temperatures and pressures through a degradation process involving magnesium metal and acidified ethanol. This report is an extension of that work by describing the development of a delivery system for said reaction in preparation for a field test. Two treatment options including the Activated Metal Treatment System (AMTS) and the Non-Metal Treatment System (NMTS) remove and degrade PCBs from painted surfaces. FINDINGS: AMTS decreased the Aroclor® concentration of a solution by more than 97% within 120 minutes and the Aroclor® concentration of industrial paint chips by up to 98% over three weeks. After removing up to 76% of PCBs on a painted surface after seven days, NMTS also removed trace amounts of PCBs in the paint's concrete substrate. The evaporation rate of the solvent (ethanol) from the treatment system was reduced when the application area was increased. The solvent system's ability to remove more than 90% of PCBs was maintained after losing 36% of its mass to solvent evaporation. CONCLUSIONS: The delivery systems, AMTS and NMTS, are able to support the hydrodechlorination reaction necessary for PCB degradation and are therefore attractive options for further studies regarding the remediation of contaminated painted surfaces.

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

Travel distance and transformation of injected emulsified zerovalent iron nanoparticles in the subsurface during two and half years.

Nanoscale zerovalent iron (NZVI) such as Toda Kogyo RNIP-10DS has been used for site remediation, yet information is lacking regarding how far injected NZVI can travel, how long it lasts, and how it transforms to other minerals in a groundwater system. Previously we reported effective mass destruction of chlorinated ethenes dominated by tetrachloroethene (PCE) using emulsified zerovalent iron (EZVI) nanoparticles of RNIP-10DS in a shallow aquifer (1-6 m below ground surface, BGS) at Site 45, Marine Corps Recruit Depot, Parris Island, South Carolina, USA. Here we report test results on transport and transformation of injected EZVI in the subsurface. We employed two EZVI delivery methods: pneumatic injection and direct injection. Effective delivery of EZVI to the targeted zone was achieved with pneumatic injection showing a travel distance from injection points of up to 2.1 m and direct injection showing a travel distance up to 0.89 m. X-ray diffraction and scanning electron microscopy studies on particles harvested from well purge waters indicated that injected black colored NZVI (α-Fe(0)) was transformed largely to black colored cube-like and plate-like magnetites (Fe3O4, 0.1-1 µm, 0-9 months), then to orange colored irregularly shaped lepidocrocite (γ-FeOOH, 0.1-1 µm, 9 months to 2.5 years), then to yellowish lath-like goethite (α-FeOOH, 2-5 µm, 2.5 years) and ferrihydrite-like spherical particles (0.05-0.1 µm) in the top portion of the aquifer (1-2 m BGS). No α-Fe(0) was found in most monitoring wells three months after injection. The formed iron oxides appeared to have a wider range of particle size (submicron to 5 µm) than the pristine NZVI (35-140 nm). Injected NZVI was largely transformed to magnetite (0.1-1 µm) during two and half years in the lower portion of the aquifer (3-6 m).

A two and half-year-performance evaluation of a field test on treatment of source zone tetrachloroethene and its chlorinated daughter products using emulsified zero valent iron nanoparticles.

A field test of emulsified zero valent iron (EZVI) nanoparticles was conducted at Parris Island, SC, USA and was monitored for two and half years to assess the treatment of subsurface-source zone chlorinated volatile organic compounds (CVOCs) dominated by tetrachloroethene (PCE) and its chlorinated daughter products. Two EZVI delivery methods were used: pneumatic injection and direct injection. In the pneumatic injection plot, 2180 L of EZVI containing 225 kg of iron (Toda RNIP-10DS), 856 kg of corn oil, and 22.5 kg of surfactant were injected to remedy an estimated 38 kg of CVOCs. In the direct injection plot, 572 L of EZVI were injected to treat an estimated 0.155 kg of CVOCs. After injection of the EZVI, significant reductions in PCE and trichloroethene (TCE) concentrations were observed in downgradient wells with corresponding increases in degradation products including significant increases in ethene. In the pneumatic injection plot, there were significant reductions in the downgradient groundwater mass flux values for PCE (>85%) and TCE (>85%) and a significant increase in the mass flux of ethene. There were significant reductions in total CVOC mass (86%); an estimated reduction of 63% in the sorbed and dissolved phases and 93% reduction in the PCE DNAPL mass. There are uncertainties in these estimates because DNAPL may have been mobilized during and after injection. Following injection, significant increases in dissolved sulfide, volatile fatty acids (VFA), and total organic carbon (TOC) were observed. In contrast, dissolved sulfate and pH decreased in many wells. The apparent effective remediation seems to have been accomplished by direct abiotic dechlorination by nanoiron followed by biological reductive dechlorination stimulated by the corn oil in the emulsion.

A BioBrick compatible strategy for genetic modification of plants.

BACKGROUND: Plant biotechnology can be leveraged to produce food, fuel, medicine, and materials. Standardized methods advocated by the synthetic biology community can accelerate the plant design cycle, ultimately making plant engineering more widely accessible to bioengineers who can contribute diverse creative input to the design process. RESULTS: This paper presents work done largely by undergraduate students participating in the 2010 International Genetically Engineered Machines (iGEM) competition. Described here is a framework for engineering the model plant Arabidopsis thaliana with standardized, BioBrick compatible vectors and parts available through the Registry of Standard Biological Parts (http://www.partsregistry.org). This system was used to engineer a proof-of-concept plant that exogenously expresses the taste-inverting protein miraculin. CONCLUSIONS: Our work is intended to encourage future iGEM teams and other synthetic biologists to use plants as a genetic chassis. Our workflow simplifies the use of standardized parts in plant systems, allowing the construction and expression of heterologous genes in plants within the timeframe allotted for typical iGEM projects.

Dechlorination of polychlorinated biphenyls using magnesium and acidified alcohols.

Polychlorinated biphenyls (PCBs) were widely used in industry until their regulation in the 1970s. However, due to their inherent stability, they are still a widespread environmental contaminant. A novel method of degradation of PCBs (via hydrodehalogenation) has been observed using magnesium powder, a carboxylic acid, and alcohol solvents and is described in this paper. The rates of degradation were determined while varying the type of acid (formic, acetic, propionic, butyric, valeric, benzoic, ascorbic, and phosphoric), the amount of magnesium from 0.05 to 0.25 g, the amount of acetic acid from 0.5 to 50 µL and the concentration of PCB-151 from 0.1 to 50 µg/mL, as well as the alcohol solvent (methanol, ethanol, propanol, butanol, octanol, and decanol). The results of these studies indicate that the most rapid PCB dechlorination is achieved using a matrix consisting of at least 0.02 g Mg/mL ethanol, and 10 µL acetic acid/mL ethanol in which case 50 ng/µL of PCB-151 is dechlorinated in approximately 40 min.

The use of mechanical alloying for the preparation of palladized magnesium bimetallic particles for the remediation of PCBs.

The kinetic rate of dechlorination of a polychlorinated biphenyl (PCB-151) by mechanically alloyed Mg/Pd was studied for optimization of the bimetallic system. Bimetal production was first carried out in a small-scale environment using a SPEX 8000M high-energy ball mill with 4-µm-magnesium and palladium impregnated on graphite, with optimized parameters including milling time and Pd-loading. A 5.57-g sample of bimetal containing 0.1257% Pd and ball milled for 3 min resulted in a degradation rate of 0.00176 min(-1)g(-1) catalyst as the most reactive bimetal. The process was then scaled-up, using a Red Devil 5400 Twin-Arm Paint Shaker, fitted with custom plates to hold milling canisters. Optimization parameters tested included milling time, number of ball bearings used, Pd-loading, and total bimetal mass milled. An 85-g sample of bimetal containing 0.1059% Pd and ball-milled for 23 min with 16 ball bearings yielded the most reactive bimetal with a degradation rate of 0.00122 min(-1)g(-1) catalyst. Further testing showed adsorption did not hinder extraction efficiency and that dechlorination products were only seen when using the bimetallic system, as opposed to any of its single components. The bimetallic system was also tested for its ability to degrade a second PCB congener, PCB-45, and a PCB mixture (Arochlor 1254); both contaminants were seen to degrade successfully.

Field demonstration of DNAPL dehalogenation using emulsified zero-valent iron.

This paper describes the results of the first field-scale demonstration conducted to evaluate the performance of nanoscale emulsified zero-valent iron (EZVI) injected into the saturated zone to enhance in situ dehalogenation of dense, nonaqueous phase liquids (DNAPLs) containing trichloroethene (TCE). EZVI is an innovative and emerging remediation technology. EZVI is a surfactant-stabilized, biodegradable emulsion that forms emulsion droplets consisting of an oil-liquid membrane surrounding zero-valent iron (ZVI) particles in water. EZVI was injected over a five day period into eight wells in a demonstration test area within a larger DNAPL source area at NASA's Launch Complex 34 (LC34) using a pressure pulse injection method. Soil and groundwater samples were collected before and after treatment and analyzed for volatile organic compounds (VOCs) to evaluate the changes in VOC mass, concentration and mass flux. Significant reductions in TCE soil concentrations (>80%) were observed at four of the six soil sampling locations within 90 days of EZVI injection. Somewhat lower reductions were observed at the other two soil sampling locations where visual observations suggest that most of the EZVI migrated up above the target treatment depth. Significant reductions in TCE groundwater concentrations (57 to 100%) were observed at all depths targeted with EZVI. Groundwater samples from the treatment area also showed significant increases in the concentrations of cis-1,2-dichloroethene (cDCE), vinyl chloride (VC) and ethene. The decrease in concentrations of TCE in soil and groundwater samples following treatment with EZVI is believed to be due to abiotic degradation associated with the ZVI as well as biodegradation enhanced by the presence of the oil and surfactant in the EZVI emulsion.

Outcome of an optional HCV screening program for blood transfusion recipients in Ireland.

BACKGROUND: An optional (general) HCV testing program for blood and blood component recipients before the introduction of routine donor anti-HCV screening (October 1991) was launched in Ireland in 1995 to complement the targeted lookback program in progress at that time and to identify transfusion-transmitted hepatitis C. STUDY DESIGN AND METHODS: The public were informed of the opportunity to avail of screening by widespread media coverage. Screening was by an initial ELISA (Abbott 3.0, Abbott Laboratories) at the transfusion center laboratories. Reactive samples were referred to a virus reference laboratory where two additional ELISAs (Ortho 3.0, Ortho Clinical Diagnostics; and Murex 3.0, Murex) were performed. Confirmation of ELISA-positive samples was by a RIBA (RIBA 3.0, Chiron Corp.). All patients found to be anti-HCV- seropositive were tested for HCV RNA by PCR and were referred to a hepatologist. RESULTS: A total of 14,917 persons have been tested for hepatitis C in this program to date (85% women). Sixty-one people were confirmed positive for HCV by RIBA 3.0 (0.4%). Excluding persons with other risk factors (n = 15), the HCV positivity rate for blood component transfusion recipients (n = 46) was 0.3 percent. Of the 46 confirmed hepatitis C-positive blood component transfusion recipients, 32 were women (70%), 24 of whom received transfusion for obstetric or gynecologic indications (75%). Thirty-eight of 46 (83%) anti-HCV seropositive transfusion recipients tested had detectable HCV RNA by PCR. CONCLUSION: This program identified 46 transfusion recipients and 10 coagulation factor concentrate recipients, all of whom were previously unaware of their infection. The majority of HCV-positive transfusion recipients identified were women. This may reflect that women are longer living survivors of transfusion therapy or alternatively, in our experience, that Irish women perceive themselves at greater risk of hepatitis C because of the well-publicized association of this virus with recipients (women) of Irish RhIG.