Stochastic models for regulatory networks of the genetic toggle switch

Bistability arises within a wide range of biological systems from the λ phage switch in bacteria to cellular signal transduction pathways in mammalian cells. Changes in regulatory mechanisms may result in genetic switching in a bistable system. Recently, more and more experimental evidence in the form of bimodal population distributions indicates that noise plays a very important role in the switching of bistable systems. Although deterministic models have been used for studying the existence of bistability properties under various system conditions, these models cannot realize cell-to-cell fluctuations in genetic switching. However, there is a lag in the development of stochastic models for studying the impact of noise in bistable systems because of the lack of detailed knowledge of biochemical reactions, kinetic rates, and molecular numbers. In this work, we develop a previously undescribed general technique for developing quantitative stochastic models for large-scale genetic regulatory networks by introducing Poisson random variables into deterministic models described by ordinary differential equations. Two stochastic models have been proposed for the genetic toggle switch interfaced with either the SOS signaling pathway or a quorum-sensing signaling pathway, and we have successfully realized experimental results showing bimodal population distributions. Because the introduced stochastic models are based on widely used ordinary differential equation models, the success of this work suggests that this approach is a very promising one for studying noise in large-scale genetic regulatory networks.

Prandtl number scaling of natural convection of an inclined flat plate due to uniform surface heat flux

A new scaling analysis has been performed for the unsteady natural convection boundary layer under a downward facing inclined plate with uniform heat flux. The development of the thermal or viscous boundary layers may be classified into three distinct stages including a start-up stage, a transitional stage and a steady stage, which can be clearly identified in the analytical as well as numerical results. Earlier scaling shows that the existing scaling laws of the boundary layer thickness, velocity and steady state time scale for the natural convection flow on a heated plate of uniform heat flux provide a very poor prediction of the Prandtl number dependency of the flow. However, those scalings performed very well with Rayleigh number and aspect ratio dependency. In this study, a new Prandtl number scaling has been developed using a triple-layer integral approach for Pr > 1. It is seen that in comparison to the direct numerical simulations, the new scaling performs considerably better than the previous scaling.

Single crystal raman spectroscopy of natural finnemanite and comparison with the synthesised analogue

The single crystal Raman spectra of natural mineral finnemanite Pb5(AsO3)3Cl from the Långban locality, Filipstad district, Värmland province, Sweden are presented for the first time. It is a hexagonal mineral belonging to the ortho arsenite group, where the [AsO3]3- ion is isolated. The spectra of finnemanite are characterized by a strong band at 734 cm-1 overlying a shoulder at 726 cm-1, and broad overlapping bands in the lower wavenumber with the strongest band positioned at 174 cm-1. Band assignments were made based on band symmetry, experimental band positions from literature and DFT calculated Raman spectrum, and spectral comparison with other ortho arsenite minerals reinerite, cafarsite, and nealite and synthetic lead arsenite compounds Pb2(AsO2)3Cl, Pb2As2O5, and PbAs2O4 . The band at 734 cm-1 was assigned to υ1(AsO3), bands at 726 and 640 cm-1 assigned to υ3, 372 and 357 cm-1 to υ2, and 244, 239 and 207 cm-1 to υ4. The single crystal spectra of finnemanite showed good mode separation, allowing bands to be assigned a symmetry species of Ag, E1g, or E2g.

Single crystal raman spectroscopy of natural paulmooreite Pb2As2O5 and in comparison with the synthesised analogue

The single crystal Raman spectra of natural mineral paulmooreite Pb2As2O5 from the Långban locality, Filipstad district, Värmland province, Sweden are presented for the first time. It is a monoclinic mineral containing an isolated [As2O5]4-. Depolarised and single crystal spectra of the natural and synthetic sample compare favorably and are characterized by strong bands around 186 and 140 cm-1 and three medium bands at 800 – 700 cm-1. Band assignments were made based on band symmetry and spectral comparison between experimental band positions and those resulting from Hartree-Fock calculation of an isolated [As2O5]4- ion. Spectral comparison was also made with lead arsenites such as synthetic PbAs2O4 and Pb2(AsO2)3Cl and natural finnemanite in order to determine the contribution of the terminal and bridging O in paulmooreite. Bands at 760 – 733 cm-1 were assigned to terminal As-O vibrations, whereas stretches of the bridging O occur at 562 and 503 cm-1. The single crystal spectra showed good mode separation, allowing bands to be assigned a symmetry species of Ag or Bg.

Scaling analysis of natural convection boundary layers : Application to attic space

The natural convection thermal boundary layer adjacent to an inclined flat plate and inclined walls of an attic space subject to instantaneous and ramp heating and cooling is investigated. A scaling analysis has been performed to describe the flow behaviour and heat transfer. Major scales quantifying the flow velocity, flow development time, heat transfer and the thermal and viscous boundary layer thicknesses at different stages of the flow development are established. Scaling relations of heating-up and cooling-down times and heat transfer rates have also been reported for the case of attic space. The scaling relations have been verified by numerical simulations over a wide range of parameters. Further, a periodic temperature boundary condition is also considered to show the flow features in the attic space over diurnal cycles.

Prandtl number scaling of natural convection of the flow on an inclined at plate due to uniform surface heat flux

A new scaling analysis has been performed for the unsteady natural convection boundary layer under a downward facing inclined plate with uniform heat flux. The development of the thermal or viscous boundary layers may be classified into three distinct stages including an early stage, a transitional stage and a steady stage, which can be clearly identified in the analytical as well as numerical results. Earlier scaling shows that the existing scaling laws of the boundary layer thickness, velocity and steady state time scales for the natural convection flow on a heated plate of uniform heat flux provide a very poor prediction of the Prandtl number dependency. However, those scalings performed very well with Rayleigh number and aspect ratio dependency. In this study, a modifed Prandtl number scaling has been developed using a triple-layer integral approach for Pr > 1. It is seen that in comparison to the direct numerical simulations, the new scaling performs considerably better than the previous scaling.

Persistence of multiple genetic lineages within intra-host populations of Ross River virus

We examined the structure and extent of genetic diversity in intrahost populations of Ross River virus (RRV) in samples from six human patients, focusing on the nonstructural (nsP3) and structural (E2) protein genes. Strikingly, although the samples were collected from contrasting ecological settings 3,000 kilometers apart in Australia, we observed multiple viral lineages in four of the six individuals, which is indicative of widespread mixed infections. In addition, a comparison with previously published RRV sequences revealed that these distinct lineages have been in circulation for at least 5 years, and we were able to document their long-term persistence over extensive geographical distances

Finite volume approach of natural convection in a triangular enclosure with localized heating from below

In this study, natural convection heat transfer and buoyancy driven flows have been investigated in a right angled triangular enclosure. The heater located on the bottom wall while the inclined wall is colder and the remaining walls are maintained as adiabatic. Governing equations of natural convection are solved through the finite volume approach, in which buoyancy is modeled via the Boussinesq approximation. Effects of different parameters such as Rayleigh number, aspect ratio, prantdl number and heater location are considered. Results show that heat transfer increases when the heater is moved toward the right corner of the enclosure. It is also revealed that increasing the Rayleigh number, increases the strength of free convection regime and consequently increases the value of heat transfer rate. Moreover, larger aspect ratio enclosure has larger Nusselt number value. In order to have better insight, streamline and isotherms are shown.

Abundance of Natural Riparian Forests and Tree Plantations in the Amudarya Delta of Uzbekistan and their impact on emissions of soil-borne greenhouse gases

Through a forest inventory in parts of the Amudarya river delta, Central Asia, we assessed the impact of ongoing forest degradation on the emissions of greenhouse gases (GHG) from soils. Interpretation of aerial photographs from 2001, combined with data on forest inventory in 1990 and field survey in 2003 provided comprehensive information about the extent and changes of the natural tugai riparian forests and tree plantations in the delta. The findings show an average annual deforestation rate of almost 1.3% and an even higher rate of land use change from tugai forests to land with only sparse tree cover. These annual rates of deforestation and forest degradation are higher than the global annual forest loss. By 2003, the tugai forest area had drastically decreased to about 60% compared to an inventory in 1990. Significant differences in soil GHG emissions between forest and agricultural land use underscore the impact of the ongoing land use change on the emission of soil-borne GHGs. The conversion of tugai forests into irrigated croplands will release 2.5 t CO2 equivalents per hectare per year due to elevated emissions of N2O and CH4. This demonstrates that the ongoing transformation of tugai forests into agricultural land-use systems did not only lead to a loss of biodiversity and of a unique ecosystem, but substantially impacts the biosphere-atmosphere exchange of GHG and soil C and N turnover processes.

Vibrational spectroscopy of natural cave mineral monetite CaHPO4 and the synthetic analog

Monetite is a phosphate mineral formed by the reaction of the chemicals in bat guano with calcite substrates and is commonly found in caves. The analog of the mineral monetite CaHPO4 has been synthesized and the Raman and infrared spectra of the natural monetite originating from the Murra-el-elevyn Cave, Eucla, Western Australia, compared. Monetite is characterized by a complex set of phosphate bands that arise because of two sets of pairs of phosphate units in the unit cell. Raman and infrared bands are assigned to HPO4(2-), OH stretching and bending vibrations. Infrared bands at 1346 and 1402 cm−1 are assigned to POH deformation modes. Vibrational spectroscopy confirms the presence of monetite in the cave system.

Lessons from media reporting of natural disasters : a case study of the 2011 flash floods in Toowoomba and the Lockyer Valley

Practice-led journalism research techniques were used in this study to produce a ‘first draft of history’ recording the human experience of survivors and rescuers during the January 2011 flash flood disaster in Toowoomba and the Lockyer Valley in Queensland, Australia. The study aimed to discover what can be learnt from engaging in journalistic reporting of natural disasters. This exegesis demonstrates that journalism can be both a creative practice and a research methodology. About 120 survivors, rescuers and family members of victims participated in extended interviews about what happened to them and how they survived. Their stories are the basis for two creative outputs of the study: a radio documentary and a non-fiction book, that document how and why people died, or survived, or were rescued. Listeners and readers are taken "into the flood" where they feel anxious for those in peril, relief when people are saved, and devastated when babies, children and adults are swept away to their deaths. In undertaking reporting about the human experience of the floods, several significant elements about journalistic reportage of disasters were exposed. The first related to the vital role that the online social media played during the disaster for individuals, citizen reporters, journalists and emergency services organisations. Online social media offer reporters powerful new reporting tools for both gathering and disseminating news. The second related to the performance of journalists in covering events involving traumatic experiences. Journalists are often required to cover trauma and are often amongst the first-responders to disasters. This study found that almost all of the disaster survivors who were approached were willing to talk in detail about their traumatic experiences. A finding of this project is that journalists who interview trauma survivors can develop techniques for improving their ability to interview people who have experienced traumatic events. These include being flexible with interview timing and selecting a location; empowering interviewees to understand they don’t have to answer every question they are asked; providing emotional security for interviewees; and by being committed to accuracy. Survivors may exhibit posttraumatic stress symptoms but some exhibit and report posttraumatic growth. The willingness of a high proportion of the flood survivors to participate in the flood research made it possible to document a relatively unstudied question within the literature about journalism and trauma – when and why disaster survivors will want to speak to reporters. The study sheds light on the reasons why a group of traumatised people chose to speak about their experiences. Their reasons fell into six categories: lessons need to be learned from the disaster; a desire for the public to know what had happened; a sense of duty to make sure warning systems and disaster responses to be improved in future; personal recovery; the financial disinterest of reporters in listening to survivors; and the timing of the request for an interview. Feedback to the creative-practice component of this thesis - the book and radio documentary - shows that these issues are not purely matters of ethics. By following appropriate protocols, it is possible to produce stories that engender strong audience responses such as that the program was "amazing and deeply emotional" and "community storytelling at its most important". Participants reported that the experience of the interview process was "healing" and that the creative outcome resulted in "a very precious record of an afternoon of tragedy and triumph and the bitter-sweetness of survival".

Thermal treatment of natural goethite : thermal transformation and physical properties

XRD (X-ray diffraction), XRF (X-ray fluorescence), TG (thermogravimetry), FT-IES (Fourier transform infrared emission spectroscopy), FESEM (field emission scanning electron microscope), TEM (transmission electron microscope) and nitrogen–adsorption–desorption analysis were used to characterize the composition and thermal evolution of the structure of natural goethite. The in situ FT-IES demonstrated the start temperature (250 °C) of the transformation of natural goethite to hematite and the thermodynamic stability of protohematite between 250 and 600 °C. The heated products showed a topotactic relationship to the original mineral based on SEM analysis. Finally, the nitrogen–adsorption–desorption isotherm provided the variation of surface area and pore size distribution as a function of temperature. The surface area displayed a remarkable increase up to 350 °C, and then decreased above this temperature. The significant increase in surface area was attributed to the formation of regularly arranged slit-shaped micropores running parallel to elongated direction of hematite microcrystal. The main pore size varied from 0.99 nm to 3.5 nm when heating temperature increases from 300 to 400 °C. The hematite derived from heating goethite possesses high surface area and favors the possible application of hematite as an adsorbent as well as catalyst carrier.

Investigation of lymphotoxin α genetic variants in migraine

Migraine is a common neurological disease with a genetic basis affecting approximately 12% of the population. Pain during a migraine attack is associated with activation of the trigeminal nerve system, which carries pain signals from the meninges and the blood vessels infusing the meninges to the trigeminal nucleus in the brain stem. The release of inflammatory mediators following cortical spreading depression (CSD) may further promote and sustain the activation and sensitization of meningeal nociceptors, inducing the persistent throbbing headache characterised in migraine. Lymphotoxin α (LTA) is a cytokine secreted by lymphocytes and is a member of the tumour necrosis factor (TNF) family. Genetic variation with the TNF and LTA genes may contribute to threshold brain excitability, propagation of neuronal hyperexcitability and thus initiation and maintenance of a migraine attack. Three LTA variants rs2009658, rs2844482 and rs2229094 were identified in a recent pGWAS study conducted in the Norfolk Island population as being potentially implicated in migraine with nominally significant p values of p = 0.0093, p = 0.0088 and p = 0.033 respectively. To determine whether these SNPs played a role in migraine in a general outbred population these SNPs were gentoyped in a large case control Australian Caucasian population and tested for association with migraine. All three SNPs showed no association in our cohort (p > 0.05). Validation of GWAS data in independent case-controls cohorts is essential to establish risk validity within specific population groups. The importance of cytokines in modulating neural inflammation and pain threshold in addition to other studies showing associations between TNF-α and SNPs in the LTA gene with migraine, suggests that LTA could be an important factor contributing to migraine. Although the present study did not support a role for the tested LTA variants in migraine, investigation of other variants within the LTA gene is still warranted.