Development of Improved Spectrophotometric Assays for Biocatalytic Silyl Ether Hydrolysis

Reported herein is the development of assays for the spectrophotometric quantification of biocatalytic silicon-oxygen bond hydrolysis. Central to these assays are a series of chromogenic substrates that release highly absorbing phenoxy anions upon cleavage of the sessile bond. These substrates were tested with silicatein, an enzyme from a marine sponge that is known to catalyse the hydrolysis and condensation of silyl ethers. It was found that, of the substrates tested, tert-butyldimethyl(2-methyl-4-nitrophenoxy)silane provided the best assay performance, as evidenced by the highest ratio of enzyme catalysed reaction rate compared with the background (uncatalysed) reaction. These substrates were also found to be suitable for detailed enzyme kinetics measurements, as demonstrated by their use to determine the Michaelis-Menten kinetic parameters for silicatein.

Improving estimates of waning immunity rates in stochastic SIRS models with a hierarchical framework

As most disease causing pathogens require transmission from an infectious individual to a susceptible individual, continued persistence of the pathogen within the population requires the replenishment of susceptibles through births, immigration, or waning immunity. Consider the introduction of an unknown infectious disease into a fully susceptible population where it is not known how long immunity is conferred once an individual recovers from infection. If, initially, the prevalence of disease increases (that is, the infection takes off), the number of infectives will usually decrease to a low level after the first major outbreak. During this post-outbreak period, the disease dynamics may be influenced by stochastic effects and there is a non-zero probability that the epidemic will die out. Die out in this period following the first major outbreak is known as an epidemic fade-out. If the disease does not die out, the susceptible population may be replenished by the waning of immunity, and a second wave may start. In this study, we investigate if the rate of waning immunity (and other epidemiological parameters) can be reliably estimated from multiple outbreak data, in which some outbreaks display epidemic fade-out and others do not. We generated synthetic outbreak data from independent simulations of stochastic SIRS models in multiple communities. Some outbreaks faded-out and some did not. We conducted Bayesian parameter estimation under two alternative approaches: independently on each outbreak and under a hierarchical framework. When conducting independent estimation, the waning immunity rate was poorly estimated and biased towards zero when an epidemic fade-out was observed. However, under a hierarchical approach, we obtained more accurate and precise posterior estimates for the rate of waning immunity and other epidemiological parameters. The greatest improvement in estimates was obtained for those communities in which epidemic fade-out was observed. Our findings demonstrate the feasibility and value of adopting a Bayesian hierarchical approach for parameter inference for stochastic epidemic models.

Superinfection and the hypnozoite reservoir for Plasmodium vivax: a general framework

A characteristic of malaria in all its forms is the potential for superinfection (that is, multiple concurrent blood-stage infections). An additional characteristic of Plasmodium vivax malaria is a reservoir of latent parasites (hypnozoites) within the host liver, which activate to cause (blood-stage) relapses. Here, we present a model of hypnozoite accrual and superinfection for P. vivax. To couple host and vector dynamics for a homogeneously-mixing population, we construct a density-dependent Markov population process with countably many types, for which disease extinction is shown to occur almost surely. We also establish a functional law of large numbers, taking the form of an infinite-dimensional system of ordinary differential equations that can also be recovered by coupling expected host and vector dynamics (i.e. a hybrid approximation) or through a standard compartment modelling approach. Recognising that the subset of these equations that model the infection status of the human hosts has precisely the same form as the Kolmogorov forward equations for a Markovian network of infinite server queues with an inhomogeneous batch arrival process, we use physical insight into the evolution of the latter process to write down a time-dependent multivariate generating function for the solution. We use this characterisation to collapse the infinite-compartment model into a single integrodifferential equation (IDE) governing the intensity of mosquito-to-human transmission. Through a steady state analysis, we recover a threshold phenomenon for this IDE in terms of a parameter [Formula: see text] expressible in terms of the primitives of the model, with the disease-free equilibrium shown to be uniformly asymptotically stable if [Formula: see text] and an endemic equilibrium solution emerging if [Formula: see text]. Our work provides a theoretical basis to explore the epidemiology of P. vivax, and introduces a strategy for constructing tractable population-level models of malarial superinfection that can be generalised to allow for greater biological realism in a number of directions.

How effective were Australian Quarantine Stations in mitigating transmission aboard ships during the influenza pandemic of 1918-19?

The influenza pandemic of 1918-19 was the most devastating pandemic of the 20th century. It killed an estimated 50-100 million people worldwide. In late 1918, when the severity of the disease was apparent, the Australian Quarantine Service was established. Vessels returning from overseas and inter-state were intercepted, and people were examined for signs of illness and quarantined. Some of these vessels carried the infection throughout their voyage and cases were prevalent by the time the ship arrived at a Quarantine Station. We study four outbreaks that took place on board the Medic, Boonah, Devon, and Manuka in late 1918. These ships had returned from overseas and some of them were carrying troops that served in the First World War. By analysing these outbreaks under a stochastic Bayesian hierarchical modeling framework, we estimate the transmission rates among crew and passengers aboard these ships. Furthermore, we ask whether the removal of infectious, convalescent, and healthy individuals after arriving at a Quarantine Station in Australia was an effective public health response.

Emulation of epidemics via Bluetooth-based virtual safe virus spread: Experimental setup, software, and data

We describe an experimental setup and a currently running experiment for evaluating how physical interactions over time and between individuals affect the spread of epidemics. Our experiment involves the voluntary use of the Safe Blues Android app by participants at The University of Auckland (UoA) City Campus in New Zealand. The app spreads multiple virtual safe virus strands via Bluetooth depending on the physical proximity of the subjects. The evolution of the virtual epidemics is recorded as they spread through the population. The data is presented as a real-time (and historical) dashboard. A simulation model is applied to calibrate strand parameters. Participants' locations are not recorded, but participants are rewarded based on the duration of participation within a geofenced area, and aggregate participation numbers serve as part of the data. The 2021 experimental data is available as an open-source anonymized dataset, and once the experiment is complete, the remaining data will be made available. This paper outlines the experimental setup, software, subject-recruitment practices, ethical considerations, and dataset description. The paper also highlights current experimental results in view of the lockdown that started in New Zealand at 23:59 on August 17, 2021. The experiment was initially planned in the New Zealand environment, expected to be free of COVID and lockdowns after 2020. However, a COVID Delta strain lockdown shuffled the cards and the experiment is currently extended into 2022.

A Model for Cell Proliferation in a Developing Organism

In mathematical biology, there is a great deal of interest in producing continuum models by scaling discrete agent-based models governed by local stochastic rules. We discuss a particular example of this approach: a model for the proliferation of neural crest cells that can help us understand the development of Hirschprung's disease, a potentially-fatal condition in which the enteric nervous system of a new-born child does not extend all the way through the intestine and colon. Our starting point is a discrete-state, continuous-time Markov chain model proposed by Hywood et al. (2013a) for the location of the neural crest cells that make up the enteric nervous system. Hywood et al. (2013a) scaled their model to derive an approximate second order partial differential equation describing how the limiting expected number of neural crest cells evolve in space and time. In contrast, we exploit the relationship between the above-mentioned Markov chain model and the well-known Yule-Furry process to derive the exact form of the scaled version of the process. Furthermore, we provide expressions for other features of the domain agent occupancy process, such as the variance of the marginal occupancy at a particular site, the distribution of the number of agents that are yet to reach a given site and a stochastic description of the process itself.

Safe Blues: The case for virtual safe virus spread in the long-term fight against epidemics

Viral spread is a complicated function of biological properties, the environment, preventative measures such as sanitation and masks, and the rate at which individuals come within physical proximity. It is these last two elements that governments can control through social-distancing directives. However, infection measurements are almost always delayed, making real-time estimation nearly impossible. Safe Blues is one way of addressing the problem caused by this time lag via online measurements combined with machine learning methods that exploit the relationship between counts of multiple forms of the Safe Blues strands and the progress of the actual epidemic. The Safe Blues protocols and techniques have been developed together with an experimental minimal viable product, presented as an app on Android devices with a server backend. Following initial exploration via simulation experiments, we are now preparing for a university-wide experiment of Safe Blues.

Synthesis of Organosilicon Ligands for Europium (III) and Gadolinium (III) as Potential Imaging Agents

The relaxivity of MRI contrast agents can be increased by increasing the size of the contrast agent and by increasing concentration of the bound gadolinium. Large multi-site ligands able to coordinate several metal centres show increased relaxivity as a result. In this paper, an “aza-type Michael” reaction is used to prepare cyclen derivatives that can be attached to organosilicon frameworks via hydrosilylation reactions. A range of organosilicon frameworks were tested including silsesquioxane cages and dimethylsilylbenzene derivatives. Michael donors with strong electron withdrawing groups could be used to alkylate cyclen on three amine centres in a single step. Hydrosilylation successfully attached these to mono-, di-, and tri-dimethylsilyl-substituted benzene derivatives. The europium and gadolinium complexes were formed and studied using luminescence spectroscopy and relaxometry. This showed the complexes to contain two bound water moles per lanthanide centre and T₁ relaxation time measurements demonstrated an increase in relaxivity had been achieved, in particular for the trisubstituted scaffold 1,3,5-tris((pentane-sDO3A)dimethylsilyl)benzene-Gd₃. This showed a marked increase in the relaxivity (13.1 r_1p/mM⁻¹s⁻¹).

Self-assembly of fluoride-encapsulated polyhedral oligomeric silsesquioxane (POSS) nanocrystals

The self-assembly and crystal packing of a unique series of nanocrystalline fluoride ion-encapsulated polyhedral oligomeric silsesquioxane (F-POSS) compounds, with substituted electron-withdrawing group (EWG) perfluorinated alkyl chain arms of varying lengths, were investigated.

Influence of the initial chemical conditions on the rational design of silica particles

The influence of the water content in the initial composition on the size of silica particles produced using the Stöber process is well known. We have shown that there are three morphological regimes defined by compositional boundaries. At low water levels (below stoichiometric ratio of water:tetraethoxysilane), very high surface area and aggregated structures are formed; at high water content (>40 wt%) similar structures are also seen. Between these two boundary conditions, discrete particles are formed whose size are dictated by the water content. Within the compositional regime that enables the classical Stöber silica, the structural evolution shows a more rapid attainment of final particle size than the rate of formation of silica supporting the monomer addition hypothesis. The clearer understanding of the role of the initial composition on the output of this synthesis method will be of considerable use for the establishment of reliable reproducible silica production for future industrial adoption.

Facile synthesis of novel hybrid POSS biomolecules via “Click” reactions

A novel alkyne-terminated cubic-octameric POSS was synthesised in high yield and click chemistry has been used to attach bio-oligomers.

Synthesis of Novel Podocarpa-8,11,13-Triene-7- and 13-Nitriles and Evaluation of their Anti-Inflammatory and Cytotoxic Activity

A series of novel podocarpa-8,11,13-triene-7- and 13-nitriles were prepared from the naturally occurring labdane diterpenoid (+)-manool, using podocarp-8(14)-en-13-one and 13-methoxypodocarpa-8,11,13-trien-7-one as key intermediates and TMSCN and acetonitrile as source of the nitrile. The synthesised compounds were screened for cytotoxicity against mouse macrophage cell line (RAW 264.7), human colon adenocarcinoma cell lines (HT-29) and human prostate adenocarcinoma cell lines (PC3) and for anti-inflammatory, as measured by the inhibition of nitric oxide (NO) production by RAW cells. 7-Oxopodocarpa-8,11,13-triene-13-nitrile exhibited significant inhibition of NO production (IC50 = 6 μM) and was not cytotoxic.

Proof of the Hamiltonicity-Trace Conjecture for Singularly Perturbed Markov Chains

We prove the conjecture formulated in Litvak and Ejov (2009), namely, that the trace of the fundamental matrix of a singularly perturbed Markov chain that corresponds to a stochastic policy feasible for a given graph is minimised at policies corresponding to Hamiltonian cycles.

A Geometric Product-Form Distribution for a Queueing Network by Non-Standard Batch Arrivals and Batch Transfers

We introduce a batch service discipline, called assemble-transfer batch service, for continuous-time open queueing networks with batch movements. Under this service discipline a requested number of customers is simultaneously served at a node, and transferred to another node as, possibly, a batch of different size, if there are sufficient customers there; the node is emptied otherwise. We assume a Markovian setting for the arrival process, service times and routing, where batch sizes are generally distributed.

Under the assumption that extra batches arrive while nodes are empty, and under a stability condition, it is shown that the stationary distribution of the queue length has a geometric product form over the nodes if and only if certain conditions are satisfied for the extra arrivals. This gives a new class of queueing networks which have tractable stationary distributions, and simultaneously shows that the product form provides a stochastic upper bound for the stationary distribution of the corresponding queueing network without the extra arrivals.

Decay rates for quasi-birth-and-death processes with countably many phases and tridiagonal block generators

We consider the class of level-independent quasi-birth-and-death (QBD) processes that have countably many phases and generator matrices with tridiagonal blocks that are themselves tridiagonal and phase independent. We derive simple conditions for possible decay rates of the stationary distribution of the ‘level’ process. It may be possible to obtain decay rates satisfying these conditions by varying only the transition structure at level 0. Our results generalize those of Kroese, Scheinhardt, and Taylor, who studied in detail a particular example, the tandem Jackson network, from the class of QBD processes studied here. The conditions derived here are applied to three practical examples.

N,N-Bis-(dimethylfluorosilylmethyl)amides of N-organosulfonylproline and sarcosine: synthesis, structure, stereodynamic behaviour and in silico studies

(O→Si)-Chelate difluorides R₃R₂NCH(R₁)C(O)N(CH₂SiMe₂F)₂, were synthesized by silylmethylation of amides R₃R₂NCH(R₁)C(O)NH₂, subsequent hydrolysis of unstable dichlorides into 2,6-disilamorpholines and the reaction of the latter compounds with BF₃·Et₂O.

Enhancing in vitro selection techniques to assist the discovery, understanding and use of inorganic binding peptides

Reflecting the increasing interest in combinatorial approaches, peptide phage display has seen an unprecedented expansion in a wide range of research areas. Its application to the discovery and analysis of metal binding peptides has opened up new research directions and largely contributed to the nanotechnology field. The rationale behind the need to identify such peptides varies depending on the final aim of the research and its application. Therefore, the possibility to modify the selection technique according to the different requirements would allow for a more systematic approach to be adopted and would ultimately provide substantial benefits. Although the standard panning method can be virtually applied to any target, its use for the identification of metal binding peptides does not provide the characteristics and the flexibility required for an efficient and tailored selection. Here we report on the development of a new panning method that can contribute to a faster, versatile and more informative analysis. Through the use of rolling-circle amplification, polymerase reaction and wild type phage, we have converted the standard selection technique into a more dynamic process in which adjustments can be evaluated and made consistently with the need of the experiment. The successfulness of the improved method is demonstrated in a number of panning experiments with different inorganic targets. The modifications applied to each selection are described and comparisons between the results obtained are made in order to extensively assess and evaluate the impact of the new process. The importance of tailoring the screening method to the specific objectives of a study is also considered. New binder sequences for the materials included in the investigation are identified; their sequences and distinctive characteristics are reported and their ability to act as templates for the nucleation of inorganic material is demonstrated and discussed.

Spinal pethidine for elective caesarean section

Pethidine (meperidine) is a unique member of the opioid family. In addition to its analgesic activity, it also has significant local anaesthetic activity. This property enables it to be used as the sole agent for spinal anaesthesia. We describe the successful use of intrathecal pethidine 1 mg/kg for an elective lower segment caesarean section in a patient presumed to be allergic to amide local anaesthetics. There were no significant adverse effects in either the mother or the newborn.

Decay rates for some quasi-birth-and-death processes with phase-dependent transition rates

Recently, there has been considerable interest in the calculation of decay rates for models that can be viewed as quasi-birth-and-death (QBD) processes with infinitely many phases. In this paper we make a contribution to this endeavour by considering some classes of models in which the transition function is not homogeneous in the phase direction. We characterize the range of decay rates that are compatible with the dynamics of the process away from the boundary. In many cases, these rates can be attained by changing the transition structure of the QBD process at level 0. Our approach, which relies on the use of orthogonal polynomials, is an extension of that in Motyer and Taylor (2006) for the case where the generator has homogeneous blocks.

Myths of ideal hospital occupancy

Significant problems in health care, such as access block and long waiting lists for elective surgery, have led to calls for keeping hospital occupancy at no more than 85%. It is elementary queueing theory that a finite-capacity system with variable demand cannot sustain both full utilisation and full availability. However, the statement that there is a single level of ideal or safe occupancy suitable for all situations is a simplistic interpretation and application of the underlying science. We argue that specific study and action are necessary to understand and deal with the problems of long waiting lists and access block in any given health care facility.

Anticancer activities of two sesquiterpene lactones, millerenolide and thieleanin isolated from Viguiera sylvatica and Decachaeta thieleana

The present study was carried out in order to examine the anticancer properties of two sesquiterpene lactones, millerenolide and thieleanin, isolated from Viguiera sylvatica and Decachaeta thieleana, against cell lines in vitro, and on the growth B16/BL6 melanoma tumors in C57BL/6 mice. Millerenolide and thieleanin showed a similar pattern of cytotoxicity with the greatest effect on viability being evident with A549 human lung cancer cells (IC(50) - 40 and 32 microM respectively), and with the 3T3/HER2 cell line which are 3T3 mouse fibroblasts transfected with the HER2 oncogene (IC(50) - 16 and 28 microM respectively). The parent 3T3 cells and the B16/BL6 mouse melanoma cells were less sensitive to these compounds, with thieleanin showing an IC(50) with B16/BL6 greater than the highest dose tested (203 microM). Treatment with millerenolide (8 mg/kg, i.p. on days 0, 2 and 4 post-inoculation) significantly inhibited the growth of subcutaneous B16/BL6 tumors in C57BL/6 mice, (50% inhibition at day 25, P=0.015), as well as retarding the appearance of detectable tumor (millerenolide - day 15.2+/-0.4 vs control - day 12.8+/-0.5, mean+/-SEM, P=0.011). In contrast, treatment with thieleanin (8 mg/kg every other day up to the day of kill) neither retarded the appearance of the tumor nor its growth.