Engineering Bacillus megaterium for production of functional intracellular materials

Background: Over the last 10-15 years, a technology has been developed to engineer bacterial polyhydroxybutyrate (PHB) inclusions as functionalized beads, for applications such as vaccines, diagnostics and enzyme immobilization. This has been achieved by translational fusion of foreign proteins to the PHB synthase (PhaC). The respective fusion protein mediates self-assembly of PHB inclusions displaying the desired protein function. So far, beads have mainly been produced in recombinant Escherichia coli which is problematic for some applications as the lipopolysaccharides (LPS) co-purified with such inclusions are toxic to humans and animals. Results: In this study, we have engineered the formation of functional PHB inclusions in the Gram-positive bacterium Bacillus megaterium, an LPS-free and established industrial production host. As B. megaterium is a natural PHB producer, the PHB-negative strain PHA05 was used to avoid any background PHB production. Plasmid-mediated T7 promoter-driven expression of the genes encoding β-ketothiolase (phaA), acetoacetyl-CoA-reductase (phaB) and PHB synthase (phaC) enabled/effected PHB production by B. megaterium PHA05. To produce functionalized PHB inclusions, the N- and C-terminus of PhaC was fused to four and two IgG binding Z-domains from Staphylococcus aureus, respectively. The ZZ-domain PhaC fusion protein was strongly overproduced at the surface of the PHB inclusions and the corresponding isolated ZZ-domain displaying PHB beads were found to purify IgG with a binding capacity of 40-50 mg IgG/g beads. As B. megaterium has the ability to sporulate and respective endospores could co-purify with cellular inclusions, a sporulation negative production strain was generated by disrupting the spoIIE gene in PHA05. This strain did not produce spores when tested under sporulation inducing conditions and it was still able to synthesize ZZ-domain displaying PHB beads. Conclusions: This study provides proof of concept for the successful genetic engineering of B. megaterium as a host for the production of functionalized PHB beads. Disruption of the spoIIE gene rendered B. megaterium incapable of sporulation but particularly suitable for production of functionalized PHB beads. This sporulation-negative mutant represents an improved industrial production strain for biotechnological processes otherwise impaired by the possibility of endospore formation.fals

An EPTAS for machine scheduling with bag-constraints

Machine scheduling is a fundamental optimization problem in computer science. The task of scheduling a set of jobs on a given number of machines and minimizing the makespan is well studied and among other results, we know that EPTAS's for machine scheduling on identical machines exist. Das and Wiese initiated the research on a generalization of makespan minimization, that includes so called bag-constraints. In this variation of machine scheduling the given set of jobs is partitioned into subsets, so called bags. Given this partition a schedule is only considered feasible when on any machine there is at most one job from each bag. Das and Wiese showed that this variant of machine scheduling admits a PTAS. We will improve on this result by giving the first EPTAS for the machine scheduling problem with bag-constraints. We achieve this result by using new insights on this problem and restrictions given by the bag-constraints. We show that, to gain an approximate solution, we can relax the bag-constraints and ignore some of the restrictions. Our EPTAS uses a new instance transformation that will allow us to schedule large and small jobs independently of each other for a majority of bags. We also show that it is sufficient to respect the bag-constraint only among a constant number of bags, when scheduling large jobs. With these observations our algorithm will allow for some conflicts when computing a schedule and we show how to repair the schedule in polynomial-time by swapping certain jobs around

Quantum phase transition in the one-dimensional extended Peierls-Hubbard model

We consider the one-dimensional extended Hubbard model in the presence of an explicit dimerization $\delta$. For a sufficiently strong nearest neighbour repulsion we establish the existence of a quantum phase transition between a mixed bond-order wave and charge-density wave phase from a pure bond-order wave phase. This phase transition is in the universality class of the two-dimensional Ising model.Comment: 6 pages, 3 figure

Lakeshore Drive

I am a rising senior studying Earth Science, Geology, and Sustainability at the University of Arkansas

Feasibility of Introduced Species into the Westhampton Lake for Pollution Control

Westhampton Lake, located at the University of Richmond in Virginia is a man made lake that feeds into the James river. The lake itself suffers from pollution and above average nutrient loads from external sources. There have been efforts to try to reduce some pollution from the lake but this research proposes and explores the viability of introducing species into the lake for the same purpose. Two types of animals proposed for introduction into the lake are common carp (Cyprinus carpio) and freshwater mussels (Bivalvia: Unionidae). Sterilized common carp are proposed as a short term solution to removal of invasive plant species (can not reproduce and would need to be replenished) because of their foraging ecology to eat undesirable plant species. Freshwater mussels have the potential to filter through e.coli and nutrients that are in excess in the lake. Freshwater mussels are also suffering from dwindling populations and so reintroducing them into the Westhampton lake would be overall beneficial to their survival in Virginia. Research into the nutrient levels of the lake proved that Westhampton Lake has nutrient levels in the range of what mussels could survive in. Common carp, however, would have too many risks associated with their introduction to be recommended. Common carp forage in a way that breaks up soil and could release nutrients into the water and would also likely favor eating native rooted plants as opposed to the invasive duckweed we would be seeking for them to target. Therefore, it is proposed that there be a trial introduction of mussels in enclosed cages in the lake so their health and growth could be monitored before introducing a larger population. Common carp as a means of invasive plant species management should not be pursued

Daughter\u27s Window

I am a rising senior studying Earth Science, Geology, and Sustainability at the University of Arkansas

Marine Environmental Impact Assessment: Considering cumulative and synergistic impacts within the Australian legal framework

This thesis examines the shortcomings and challenges for Australian marine environmental impact assessment (EIA) legal frameworks to consider and assess cumulative and synergistic impacts, as distinct impact types, from large-scale marine use and development. The thesis aims to identify how the legal frameworks and requirements can be improved to enable better consideration and assessment of these impact types. Emphasis is given to the legal frameworks for marine environmental assessment: EIA and strategic environmental assessment (SEA). In particular, the thesis examines the different characteristics of cumulative and synergistic impacts, and how they are typically defined to be the same type of impact when considered or assessed as part of environmental assessment. Concentrating on this, if environmental assessment frameworks use definitions that do not distinguish the characteristics of these impact types, then there is a risk that detrimental synergistic impacts may be neglected. Thus, it is argued in this thesis that these impact types should be assessed and considered separately. The thesis emphasises that consideration and assessment of cumulative and synergistic impacts should be required in EIA and SEA to enable iterative planning and decisionmaking frameworks. Improving EIA legal requirements for cumulative and synergistic impact consideration and assessment to better inform decision-making is a main focus. Theoretical and practical mechanisms to improve planning and decision-making are also identified to examine how the improvement of knowledge about cumulative and synergistic impacts can assist with achieving goals of marine environmental protection, and reduce uncertainty in environmental assessment and decision-making processes. The precautionary principle and the use of post-approval monitoring (PAM) are two key mechanisms that can assist with the iterative feedback of knowledge about cumulative and synergistic impacts, and the integration of EIA with SEA. Analysis of Australian marine EIA legal frameworks to consider and assess cumulative and synergistic impacts is provided through two case studies. The first case study analyses legislation applicable to the Otways Marine Area and seeks to ascertain the extent of, and approach to, legal requirements to assess these impact types within four Australian jurisdictions (Commonwealth, Victoria, South Australia and Tasmania). The second case study analyses the consistency of approach to cumulative and synergistic impact consideration and assessment within the EIA, decision-making processes and PAM associated with Victoria’s Port Phillip Bay Channel Deepening Project. These two case studies demonstrate that increased attention needs to be given to the consideration and assessment of cumulative and synergistic impacts in EIA. A third case study was undertaken to give insight into the shortcomings and benefits of approaches to cumulative and synergistic assessment when there are legal requirements to consider these impact types in marine environmental assessment legislation. To achieve this, the final case study examined the EIA, PAM programmes, and legal frameworks for existing and approved offshore wind farms in Denmark. The thesis concludes with recommendations for the reform of Australian marine EIA legal frameworks. The recommendations focus on improving legislative requirements for the consideration and assessment of cumulative and synergistic impacts as distinct impact types. This includes through the use of express provisions, distinct definitions and other aiding mechanisms, such as the precautionary principle, and PAM

Perturbation theory for optical excitations in the one-dimensional extended Peierls--Hubbard model

For the one-dimensional, extended Peierls--Hubbard model we calculate analytically the ground-state energy and the single-particle gap to second order in the Coulomb interaction for a given lattice dimerization. The comparison with numerically exact data from the Density-Matrix Renormalization Group shows that the ground-state energy is quantitatively reliable for Coulomb parameters as large as the band width. The single-particle gap can almost triple from its bare Peierls value before substantial deviations appear. For the calculation of the dominant optical excitations, we follow two approaches. In Wannier theory, we perturb the Wannier exciton states to second order. In two-step perturbation theory, similar in spirit to the GW-BSE approach, we form excitons from dressed electron-hole excitations. We find the Wannier approach to be superior to the two-step perturbation theory. For singlet excitons, Wannier theory is applicable up to Coulomb parameters as large as half band width. For triplet excitons, second-order perturbation theory quickly fails completely.Comment: 32 pages, 12 figures, submtted to JSTA

What are the factors that influence outcomes for unaccompanied humanitarian refugee minors leaving out-of-home care in Australia

Unaccompanied humanitarian refugee minors (UHRMs) are recognized globally as a vulnerable group due to their traumatic experiences in their country of origin, and distinct challenges resettling in a new country with limited if any family supports and ambiguous legal status. To date, there has been little research on their experiences within the out-of-home care (OOHC) system in Australia. This paper presents the findings of a small exploratory study, based on semi-structured interviews with young people and support workers, examining the factors that influence their outcomes when transitioning from OOHC at no later than 18 years.  The findings suggest that the availability of social support networks plays a key role in enabling them to access their core housing, education, employment and health care needs