Characterisation of <i>Burkholderia cepacia</i> from clinical and environmental origins.

Burkholderia cepacia isolates were obtained from the sputum of cystic fibrosis patients or isolated from the environment. The isolates were characterised phenotypically by determining antibiotic resistance profiles and their ability to macerate onion tissue, and genetically by PCR ribotyping and macro-restriction analysis (genome fingerprinting). The replicon (chromosomal) organisation was determined by pulsed field gel electrophoresis (PFGE) and the presence of plasmids was also investigated. Plasmid transfer by conjugation was also investigated. A high degree of genetic and phenotypic variation was found both within and between clinical and environmental populations of B. cepacia. Environmental isolates were generally less resistant to antibiotics but showed greater ability to macerate onion tissue. Genetic characterisation showed little evidence of acquisition of B. cepacia from the environment by CF patients, but revealed strong evidence supporting person-to-person transmission of B. cepacia in the Cardiff CF centre and other European centres. Two or more chromosomes were found in 93 % of B. cepacia isolates tested, and were also found in other closely related species suggesting such organisation may be common in P-2 proteobacteria. Plasmids, often in excess of 100 kb, were found to be harboured in 52 % of isolates, though were more commonly found in CF isolates (65 % of isolates) than environmental isolates (23 % of isolates). Plasmid transfer by conjugation was demonstrated into, between and from B. cepacia strains. Evidence of plasmids encoding antibiotic resistance was also found

Archaeological Monitoring of South Alamo Street Improvements, Pereida Street to César Chávez Boulevard, San Antonio, Bexar County, Texas

From October 31, 2018, through February 13, 2019, the Center for Archaeological Research (CAR) at The University of Texas at San Antonio conducted archaeological monitoring for the South Alamo Street Improvements Project located in downtown San Antonio, Bexar County, Texas. The excavation of 20 boreholes and more than 772 meters of trench were monitored. The work was performed for the City of San Antonio (COSA) to fulfill the requirements of the COSA’s Unified Development Code and the Antiquities Code of Texas. The project was conducted under Texas Antiquities Permit No. 8563. Dr. Paul Shawn Marceaux, CAR Director, served as the Principal Investigator, and Sarah Wigley served as the Project Archaeologist. The project area is located on COSA property along South Alamo Street between César Chávez Boulevard and Pereida Street in central San Antonio. The monitoring consisted of trenching for the installation of an electrical conduit and the excavation of boreholes for new light poles located on either side of South Alamo Street between Turner Street and Pereida Street. The project area runs directly through the two national Historic Districts, the Lavaca Neighborhood Historic District and the South Alamo Street-South St. Mary’s Street Historic District, and it is included in the two local Historic Districts (the Lavaca Neighborhood and King William Historic District). These Historic Districts are known to contain significant historic sites, including the Acequia Madre de Valero (41BX8) and the Concepción Acequia (41BX1887; COSA Office of Historic Preservation 2019a). During the monitoring, part of an intact wall of the Acequia Madre de Valero (41BX8) was uncovered near the intersection of Beauregard Street on the west side of South Alamo Street, although documentation of the feature was limited to the extent of the utility trench. In addition to the acequia wall section, five other architectural features, some potentially Spanish Colonial in nature, were documented, and four new sites designated 41BX2286, 41BX2287, 41BX2288, and 41BX2289 were recorded. A small number of temporally diagnostic historic artifacts were collected during the course of the project. The CAR recommends that the section of 41BX8 (Acequia Madre de Valero) documented during the course of this project is eligible for inclusion to the National Register of Historical Places (NRHP) and designation as a State Antiquities Landmark (SAL), and all impacts should be avoided. Site 41BX8 has previously been determined to be eligible for inclusion on the NRHP, and it is designated as a Historic American Engineering Record and a Recorded Texas Historic Landmark (THC 2019). The portion of the site that was encountered during monitoring remains intact. It was covered with a protective layer of sand before backfilling. Site 41BX2286, a portion of a historic limestone and mortar wall, should also be avoided until its significance can be more clearly defined. Currently, the CAR cannot determine this site’s potential eligibility for inclusion to the NRHP or listing as a SAL due to the limited nature of the investigation. The portion of the site documented during monitoring remains intact. It was covered with a protective layer of sand before backfilling. The CAR recommends that sites 41BX2287, 41BX2288, and 41BX2289 are not significant. The portions of these sites documented during monitoring remain intact and were covered with a protective layer of sand before backfilling. These three sites are not recommended as eligible for inclusion to the NRHP or for designation as SAL. All artifacts collected during the course of this project are curated at the CAR. All forms, documents, and photographs complied during the project and a copy of this report are archived in Project Accession file 2180 at the CAR

Oral infection with the Salmonella enterica serovar Gallinarum 9R attenuated live vaccine as a model to characterise immunity to fowl typhoid in the chicken

BACKGROUND: Salmonella enterica serovar Gallinarum (S. Gallinarum) is the causative agent of fowl typhoid, a severe systemic disease of chickens that results in high mortality amongst infected flocks. Due to its virulence, the immune response to S. Gallinarum is poorly characterised. In this study we have utilised infection by the live attenuated S. Gallinarum 9R vaccine strain in inbred chickens to characterise humoral, cellular and cytokine responses to systemic salmonellosis. RESULTS: Infection with 9R results in a mild systemic infection. Bacterial clearance at three weeks post infection coincides with increases in circulating anti-Salmonella antibodies, increased T cell proliferation to Salmonella challenge and increased expression of interferon gamma. These responses peak at four weeks post infection, then decline. Only modest increases of expression of the pro-inflammatory cytokine interleukin-1β were detected early in the infection. CONCLUSION: Infection of chickens with the 9R vaccine strain induces a mild form of systemic salmonellosis. This induces both cellular and humoral immune responses, which peak soon after bacterial clearance. Unlike enteric-associated Salmonella infections the immune response is not prolonged, reflecting the absence of persistence of Salmonella in the gastrointestinal tract. The findings here indicate that the use of the S. Gallinarum 9R vaccine strain is an effective model to study immunity to systemic salmonellosis in the chicken and may be employed in further studies to determine which components of the immune response are needed for protection

Generating and observing soliton dynamics in Bose Einstein Condensates

Bose-Einstein condensates (BECs), a quantum state of matter formed when bosonic atoms are cooled close to absolute zero, have become the premier platform for investigating fundamental physics with atomic vapours. Experiments on Bose-Einstein condensates now achieve exquisite control over many aspects of the system, including interactions, trapping potential, and dynamics. This has precipitated a new wave of research into many-body quantum phenomena and, in particular, solitons. These structures are fundamental excitations of an interacting non-linear medium, of interest to a multitude of scientific disciplines from non-linear optics to financial markets. The highly controllable environment of BECs form an attractive playground for the study of solitons allowing the non-linearity to be dynamically tuned, facilitating deeper investigations into these structures. Consistently generating and analysing solitons in BEC experiments continues to be problematic. In particular, the non-linear dynamics of BECs, though required for the generation of solitons, produce particularly challenging control and optimization problems. These control problems must be solved before further investigations into the fundamental physics of soliton dynamics can be answered. This thesis makes three important advances in the control and measurement of BECs that will lead to better generation and observation of solitons. (1) a theoretical model for a control scheme capable of highly precise wavefunction engineering, (2) the experimental implementation of a machine learning algorithm for online optimisation, and (3) a continuous non-destructive imaging system capable of directly observing soliton dynamics in real-time. Together, these advances provide a suite of tools for manipulating and exploiting solitons in Bose-Einstein condensates. A novel technique was developed theoretically, offering control of the macroscopic wavefunction of a Bose-Einstein condensate with unprecedented spatial resolution and speed. The ability to control the atomic wavefunction at the fundamental length scale is key to the advancement of many quantum technologies such as quantum simulators. The magnetic resonance control scheme is demonstrated through simulation of a 87Rb condensate with the exemplar model generating a single dark soliton with corresponding π phase kink. The soliton represents a structure at the fundamental length scale of the system, and demonstrates the potential of the scheme for precision state engineering. The scheme is extended to generate higher-order soliton modes which are yet to be experimentally realised. A machine learning algorithm based on Gaussian processes was developed and implemented on the evaporative cooling stage of the production of a 87Rb Bose-Einstein condensate, successfully demonstrating fast optimisation to condensation. The Gaussian process develops a statistical model based on the data that enables the characterisation of the relationship between the experimental controls and resultant quality of the BEC. This relationship is often obfuscated through technical details of the apparatus, frustrating the use of theoretical models to design optimal evaporation ramps. These models often only consider ergodic dynamics with two-body s-wave interactions and no other loss rates with better ramps likely exploiting more complex interactions. The internal model generated from the Gaussian process utilised uncertainty in measured data, making the optimisation more robust to experimental noise than alternate methods. The algorithm is shown to produce high quality Bose-Einstein condensates in 10 times fewer experimental iterations than previously used online optimisation techniques. By exploiting information on the sensitivity of each control, the model can be used to aid experimental design. The convergence of the optimisation is further improved by eliminating a superfluous parameter identified by the model. The general usefulness of machine learning compared with bespoke optimisation algorithms has seen machine learning approach ubiquity. Finally, an experimentally straightforward technique for continuous non-destructive imaging of matter-wave solitons was developed and implemented, facilitating measurements of stochastic phenomena. The technique is readily practicable on any ultracold atom experiment with an existing absorption imaging system, simply requiring the probe laser be far-detuned from resonance. With a signal-to-noise of ∼ 33 at 1.25 GHz detuning, the technique is capable of producing 100 images with no observable heating or atom loss. Coupled with a fast optical phase locked loop, the technique can be used in conjunction with absorption imaging to generate a series of non-destructive images followed by a final high signal-to-noise absorption image solely through moving the laser on resonance for the final image. The high performance and utility of this imaging setup make it a powerful tool for ultra-cold atom experiments

Virtual reality for physics education

Virtual reality (VR) has reached a point of development where its accessibility and immersion is sufficient to give realistic and memorable experiences. One of the most exciting possibilities is the ability to visualise invisible or impossible worlds. For example, electricity and magnetism are frequently challenging concepts to teach, in particular because students need to build a mental model of what a ‘field’ is. VR gives us the ability to give people a realistic representation of vector fields, of far higher complexity than that possible on a traditional computer screen. Furthermore, it can allow dynamic manipulation, simulation, and testing – effectively offering students a sandbox in which to experiment with these systems. Another exciting application is the use of VR to allow students to experience worlds that manifest their misconceptions. Led by misconceptions well studied and measured using the Force Concept Inventory (Hestenes, Wells, & Swackhamer, 1992), students can be asked to predict what forces exist in a given situation. They are then given a world in which those forces are present, and thus if incorrect, experience a situation that behaves counter-intuitively, thereby triggering cognitive dissonance. They can then be guided via narration, or an instructor to reassess their views and ideally correct their misconception. At ANU, we have been developing both of these apps over the last two years. We will share some positive preliminary results with small groups of student, both qualitative and quantitative

Guide to chicken health and management in Ethiopia: For farmers and development agents

Biotechnology and Biological Sciences Research Council, United KingdomDepartment for International Development, United Kingdo

A quantum sensor: simultaneous precision gravimetry and magnetic gradiometry with a Bose-Einstein condensate

A Bose-Einstein condensate is used as an atomic source for a high precision sensor. A $5\times 10^6$ atom F=1 spinor condensate of $^{87}$Rb is released into free fall for up to $750$ms and probed with a Mach-Zehnder atom interferometer based on Bragg transitions. The Bragg interferometer simultaneously addresses the three magnetic states, $\left| m_f=1,0,-1 \right\rangle$, facilitating a simultaneous measurement of the acceleration due to gravity with an asymptotic precision of $2.1\times 10^{-9}$$\Delta$g/g and the magnetic field gradient to a precision $8$pT/m

Non-destructive shadowgraph imaging of ultracold atoms

An imaging system is presented that is capable of far-detuned non-destructive imaging of a Bose-Einstein condensate with the signal proportional to the second spatial derivative of the density. Whilst demonstrated with application to $^{85}\text{Rb}$, the technique generalizes to other atomic species and is shown to be capable of a signal to noise of ${\sim}25$ at $1$GHz detuning with $100$ in-trap images showing no observable heating or atom loss. The technique is also applied to the observation of individual trajectories of stochastic dynamics inaccessible to single shot imaging. Coupled with a fast optical phase lock loop, the system is capable of dynamically switching to resonant absorption imaging during the experiment.Comment: 4 pages, 5 figure