Promoting Microbiology Education Through the iGEM Synthetic Biology Competition

Synthetic biology has developed rapidly in the 21st century. It covers a range of scientific disciplines that incorporate principles from engineering to take advantage of and improve biological systems, often applied to specific problems. Methods important in this subject area include the systematic design and testing of biological systems and, here, we describe how synthetic biology projects frequently develop microbiology skills and education. Synthetic biology research has huge potential in biotechnology and medicine, which brings important ethical and moral issues to address, offering learning opportunities about the wider impact of microbiological research. Synthetic biology projects have developed into wide-ranging training and educational experiences through iGEM, the International Genetically Engineered Machines competition. Elements of the competition are judged against specific criteria and teams can win medals and prizes across several categories. Collaboration is an important element of iGEM and all DNA constructs synthesised by iGEM teams are made available to all researchers through the Registry for Standard Biological Parts. An overview of microbiological developments in the iGEM competition is provided. This review is targeted at educators that focus on microbiology and synthetic biology, but will also be of value to undergraduate and postgraduate students with an interest in this exciting subject area

Microbiology survey shows authors have most to gain from peer review

In the week that an international team of publishers, science communicators and other scholarly organisations launch the second international Peer Review Week, the preliminary findings from our new survey reveal that authors gain more from peer review than the people who do the actual review

Characterization of a temperature-sensitive DNA ligase from Escherichia coli

DNA ligases are essential enzymes in cells due to their ability to join DNA strand breaks formed during DNA replication. Several temperature-sensitive mutant strains of Escherichia coli, including strain GR501, have been described which can be complemented by functional DNA ligases. Here, it is shown that the ligA251 mutation in E. coli GR501 strain is a cytosine to thymine transition at base 43, which results in a substitution of leucine by phenylalanine at residue 15. The protein product of this gene (LigA251) is accumulated to a similar level at permissive and non-permissive temperatures. Compared to wild-type LigA, at 20 °C purified LigA251 has 20-fold lower ligation activity in vitro, and its activity is reduced further at 42 °C, resulting in 60-fold lower ligation activity than wild-type LigA. It is proposed that the mutation in LigA251 affects the structure of the N-terminal region of LigA. The resulting decrease in DNA ligase activity at the non-permissive temperature is likely to occur as the result of a conformational change that reduces the rate of adenylation of the ligase

Advances in understanding large-scale responses of the water cycle to climate change

Globally, thermodynamics explains an increase in atmospheric water vapor with warming of around 7%/°C near to the surface. In contrast, global precipitation and evaporation are constrained by the Earth's energy balance to increase at ∼2–3%/°C. However, this rate of increase is suppressed by rapid atmospheric adjustments in response to greenhouse gases and absorbing aerosols that directly alter the atmospheric energy budget. Rapid adjustments to forcings, cooling effects from scattering aerosol, and observational uncertainty can explain why observed global precipitation responses are currently difficult to detect but are expected to emerge and accelerate as warming increases and aerosol forcing diminishes. Precipitation increases with warming are expected to be smaller over land than ocean due to limitations on moisture convergence, exacerbated by feedbacks and affected by rapid adjustments. Thermodynamic increases in atmospheric moisture fluxes amplify wet and dry events, driving an intensification of precipitation extremes. The rate of intensification can deviate from a simple thermodynamic response due to in‐storm and larger‐scale feedback processes, while changes in large‐scale dynamics and catchment characteristics further modulate the frequency of flooding in response to precipitation increases. Changes in atmospheric circulation in response to radiative forcing and evolving surface temperature patterns are capable of dominating water cycle changes in some regions. Moreover, the direct impact of human activities on the water cycle through water abstraction, irrigation, and land use change is already a significant component of regional water cycle change and is expected to further increase in importance as water demand grows with global population

Fourth-Generation Fan Assessment Numeration System (FANS) Design and Performance Specifications

The Fan Assessment Numeration System (FANS) is a measurement device for generating ventilation fan performance curves. Three different-sized FANS currently exist for assessing ventilation fans commonly used in poultry and livestock housing systems. All FANS consist of an array of anemometers inside an aluminum shroud that traverse the inlet or outlet of a ventilation fan. The FANS design has been updated several times since its inception and is currently in its fourth-generation (G4). The current design iteration (FANS-G4) is reported in this article with an emphasis on the hardware and software control, data acquisition systems, and operational reliability. Six FANS-G4 units were fabricated at the University of Kentucky (UK) Agricultural Machinery Research Laboratory and calibrated at the University of Illinois Urbana-Champaign (UIUC) Bioenvironmental and Structural Systems (BESS) Laboratory. Results demonstrated that the FANS-G4 was capable of measuring volumetric airflow to within 0.6% of full-scale (FS), which ranged from 15,000 to 56,000 m3 h-1

The Next Generation Virgo Cluster Survey. XII. Stellar Populations and Kinematics of Compact, Low-Mass Early-Type Galaxies from Gemini GMOS-IFU Spectroscopy

We present Gemini GMOS-IFU data of eight compact low-mass early-type galaxies (ETGs) in the Virgo cluster. We analyse their stellar kinematics, stellar population, and present two-dimensional maps of these properties covering the central 5"x 7" region. We find a large variety of kinematics: from non- to highly-rotating objects, often associated with underlying disky isophotes revealed by deep images from the Next Generation Virgo Cluster Survey. In half of our objects, we find a centrally-concentrated younger and more metal-rich stellar population. We analyze the specific stellar angular momentum through the lambdaR parameter and find six fast-rotators and two slow-rotators, one having a thin counter-rotating disk. We compare the local galaxy density and stellar populations of our objects with those of 39 more extended low-mass Virgo ETGs from the SMAKCED survey and 260 massive ($M>10^{10}$\Msun) ETGs from the A3D sample. The compact low-mass ETGs in our sample are located in high density regions, often close to a massive galaxy and have, on average, older and more metal-rich stellar populations than less compact low-mass galaxies. We find that the stellar population parameters follow lines of constant velocity dispersion in the mass-size plane, smoothly extending the comparable trends found for massive ETGs. Our study supports a scenario where low-mass compact ETGs have experienced long-lived interactions with their environment, including ram-pressure stripping and gravitational tidal forces, that may be responsible for their compact nature.Comment: Accepted in ApJ, 19 pages, 10 figure

The Design and Validation of the Quantum Mechanics Conceptual Survey

The Quantum Mechanics Conceptual Survey (QMCS) is a 12-question survey of students' conceptual understanding of quantum mechanics. It is intended to be used to measure the relative effectiveness of different instructional methods in modern physics courses. In this paper we describe the design and validation of the survey, a process that included observations of students, a review of previous literature and textbooks and syllabi, faculty and student interviews, and statistical analysis. We also discuss issues in the development of specific questions, which may be useful both for instructors who wish to use the QMCS in their classes and for researchers who wish to conduct further research of student understanding of quantum mechanics. The QMCS has been most thoroughly tested in, and is most appropriate for assessment of (as a posttest only), sophomore-level modern physics courses. We also describe testing with students in junior quantum courses and graduate quantum courses, from which we conclude that the QMCS may be appropriate for assessing junior quantum courses, but is not appropriate for assessing graduate courses. One surprising result of our faculty interviews is a lack of faculty consensus on what topics should be taught in modern physics, which has made designing a test that is valued by a majority of physics faculty more difficult than expected.Comment: Submitted to Physical Review Special Topics: Physics Education Researc

An X-Ray View of the Jet-Cycle in the Radio Loud AGN 3C120

We present a study of the central engine in the broad-line radio galaxy 3C120 using a multi-epoch analysis of a deep XMM-Newton observation and two deep Suzaku pointings (in 2012). In order to place our spectral data into the context of the disk-disruption/jet-ejection cycles displayed by this object, we monitor the source in the UV/X-ray bands, and in the radio band. We find three statistically acceptable spectral models, a disk-reflection model, a jet-model and a jet+disk model. Despite being good descriptions of the data, the disk-reflection model violates the radio constraints on the inclination, and the jet-model has a fine-tuning problem, requiring a jet contribution exceeding that expected. Thus, we argue for a composite jet+disk model. Within the context of this model, we verify the basic predictions of the jet-cycle paradigm, finding a truncated/refilling disk during the Suzaku observations and a complete disk extending down to the innermost stable circular orbit (ISCO) during the XMM-Newton observation. The idea of a refilling disk is further supported by the detection of the ejection of a new jet knot approximately one month after the Suzaku pointings. We also discover a step-like event in one of the Suzaku pointings in which the soft band lags the hard band. We suggest that we are witnessing the propagation of a disturbance from the disk into the jet on a timescale set by the magnetic field.Comment: 14 pages, 10 figures, accepted for publication in Ap