Developing the transcription & translation machinery of plasmodium falciparum as a target for next generation interventions against malaria

Malaria remains a serious global threat but exploiting the essential processes of transcription and translation within the malaria parasite may enable the development of next generation interventions. Until recently these two processes have not been extensively pursued for the purposes of drug development, parasite growth inhibition and malaria antigen production. Whilst antimalarial compounds have helped millions of individuals exposed to malaria, they lack the ability to truly eradicate malaria. Vaccines offer real potential for disease eradication however, there is currently no licensed malaria vaccine. As such the following strategies were pursued that exploit the transcription and translation machinery of the most virulent malaria parasite, P. falciparum. Firstly, to facilitate the discovery of translation inhibitors with novel modes of action (MoA), a dual in vitro translation (Dual-IVT) assay was developed. Translationally active lysates from human and P. falciparum were used to screen a library of 400 bioactive compounds revealing four with parasite specific activity. The human element of the Dual-IVT assay, during the initial stages of the COVID-19 was then shifted towards COVID-19 antigen production. Next, with a view to develop transcription as a target for next-generation antimalarials selection-linked integration was used to facilitate the characterisation of the three nuclear DNA directed RNA polymerase (RNAP) complexes from P. falciparum. Introducing affinity tags enabled their purification from parasite lysate. Exploits are underway to take advantage of recent advances in cryo-EM technology. Purifying each of the three complexes and solving 5 their structures to atomic resolution will increase our understanding of them. Finally, although most malaria vaccine candidates have focused on the circumsporozoite protein (CSP). This strategy has resulted in short-lasting, low efficacy protection based on small sections of CSP that are used due to difficulty in its expression. To advance CSP beyond its current limitations, attempts were made to construct a P. falciparum derived cell-free protein synthesis system. This allowed the production of the ectodomain of CSP which, may have resulted in its translocation into endogenous microsomes. Through exploitation of the parasite translation machinery and the use of genetic tools, this work aims to establish technologies that will contribute to the discovery of new parasite specific translation inhibitors, further our understanding of transcription and enable the production of difficult to express Plasmodium proteins.Open Acces

Further study of the Over-Barrier Model to compute charge exchange processes

In this paper we study theoretically the process of electron capture between one-optical-electron atoms (e.g. hydrogenlike or alkali atoms) and ions at low-to-medium impact velocities ($v/v_e \approx 1$) working on a modification of an already developed classical In this work we present an improvement over the Over Barrier Model (OBM) described in a recent paper [F. Sattin, Phys. Rev. A {\bf 62}, 042711 (2000)]. We show that: i) one of the two free parameters there introduced actually comes out consistently from the starting assumptions underlying the model; ii) the modified model thus obtained is as much accurate as the former one. Furthermore, we show that OBMs are able to accurately predict some recent results of state selective electron capture, at odds with what previously supposed.Comment: RevTeX, 7 pages, 4 eps figures. To appear in Physical Review A (2001-september issue

High-Throughput Screening Platform To Identify Inhibitors of Protein Synthesis with Potential for the Treatment of Malaria

Artemisinin-based combination therapies have been crucial in driving down the global burden of malaria, the world’s largest parasitic killer. However, their efficacy is now threatened by the emergence of resistance in Southeast Asia and sub-Saharan Africa. Thus, there is a pressing need to develop new antimalarials with diverse mechanisms of action. One area of Plasmodium metabolism that has recently proven rich in exploitable antimalarial targets is protein synthesis, with a compound targeting elongation factor 2 now in clinical development and inhibitors of several aminoacyl-tRNA synthetases in lead optimization. Given the promise of these components of translation as viable drug targets, we rationalized that an assay containing all functional components of translation would be a valuable tool for antimalarial screening and drug discovery. Here, we report the development and validation of an assay platform that enables specific inhibitors of Plasmodium falciparum translation (PfIVT) to be identified. The primary assay in this platform monitors the translation of a luciferase reporter in a P. falciparum lysate-based expression system. Hits identified in this primary assay are assessed in a counterscreen assay that enables false positives that directly interfere with the luciferase to be triaged. The remaining hit compounds are then assessed in an equivalent human IVT assay. This platform of assays was used to screen MMV’s Pandemic and Pathogen Box libraries, identifying several selective inhibitors of protein synthesis. We believe this new high-throughput screening platform has the potential to greatly expedite the discovery of antimalarials that act via this highly desirable mechanism of action

Critical properties and finite--size estimates for the depinning transition of directed random polymers

We consider models of directed random polymers interacting with a defect line, which are known to undergo a pinning/depinning (or localization/delocalization) phase transition. We are interested in critical properties and we prove, in particular, finite--size upper bounds on the order parameter (the {\em contact fraction}) in a window around the critical point, shrinking with the system size. Moreover, we derive a new inequality relating the free energy \tf and an annealed exponent $\mu$ which describes extreme fluctuations of the polymer in the localized region. For the particular case of a $(1+1)$--dimensional interface wetting model, we show that this implies an inequality between the critical exponents which govern the divergence of the disorder--averaged correlation length and of the typical one. Our results are based on on the recently proven smoothness property of the depinning transition in presence of quenched disorder and on concentration of measure ideas.Comment: 15 pages, 1 figure; accepted for publication on J. Stat. Phy

Hierarchical pinning models, quadratic maps and quenched disorder

We consider a hierarchical model of polymer pinning in presence of quenched disorder, introduced by B. Derrida, V. Hakim and J. Vannimenius in 1992, which can be re-interpreted as an infinite dimensional dynamical system with random initial condition (the disorder). It is defined through a recurrence relation for the law of a random variable {R_n}_{n=1,2,...}, which in absence of disorder (i.e., when the initial condition is degenerate) reduces to a particular case of the well-known Logistic Map. The large-n limit of the sequence of random variables 2^{-n} log R_n, a non-random quantity which is naturally interpreted as a free energy, plays a central role in our analysis. The model depends on a parameter alpha>0, related to the geometry of the hierarchical lattice, and has a phase transition in the sense that the free energy is positive if the expectation of R_0 is larger than a certain threshold value, and it is zero otherwise. It was conjectured by Derrida et al. (1992) that disorder is relevant (respectively, irrelevant or marginally relevant) if 1/2<alpha<1 (respectively, alpha<1/2 or alpha=1/2), in the sense that an arbitrarily small amount of randomness in the initial condition modifies the critical point with respect to that of the pure (i.e., non-disordered) model if alpha is larger or equal to 1/2, but not if alpha is smaller than 1/2. Our main result is a proof of these conjectures for the case alpha different from 1/2. We emphasize that for alpha>1/2 we find the correct scaling form (for weak disorder) of the critical point shift.Comment: 26 pages, 2 figures. v3: Theorem 1.6 improved. To appear on Probab. Theory Rel. Field

A classical Over Barrier Model to compute charge exchange between ions and one-optical-electron atoms

In this paper we study theoretically the process of electron capture between one-optical-electron atoms (e.g. hydrogenlike or alkali atoms) and ions at low-to-medium impact velocities (v/v_e <= 1) working on a modification of an already developed classical Over Barrier Model (OBM) [V. Ostrovsky, J. Phys. B: At. Mol. Opt. Phys. {\bf 28} 3901 (1995)], which allows to give a semianalytical formula for the cross sections. The model is discussed and then applied to a number of test cases including experimental data as well as data coming from other sophisticated numerical simulations. It is found that the accuracy of the model, with the suggested corrections and applied to quite different situations, is rather high.Comment: 12 pages REVTEX, 5 EPSF figures, submitted to Phys Rev

Fractional moment bounds and disorder relevance for pinning models

We study the critical point of directed pinning/wetting models with quenched disorder. The distribution K(.) of the location of the first contact of the (free) polymer with the defect line is assumed to be of the form K(n)=n^{-\alpha-1}L(n), with L(.) slowly varying. The model undergoes a (de)-localization phase transition: the free energy (per unit length) is zero in the delocalized phase and positive in the localized phase. For \alpha<1/2 it is known that disorder is irrelevant: quenched and annealed critical points coincide for small disorder, as well as quenched and annealed critical exponents. The same has been proven also for \alpha=1/2, but under the assumption that L(.) diverges sufficiently fast at infinity, an hypothesis that is not satisfied in the (1+1)-dimensional wetting model considered by Forgacs et al. (1986) and Derrida et al. (1992), where L(.) is asymptotically constant. Here we prove that, if 1/21, then quenched and annealed critical points differ whenever disorder is present, and we give the scaling form of their difference for small disorder. In agreement with the so-called Harris criterion, disorder is therefore relevant in this case. In the marginal case \alpha=1/2, under the assumption that L(.) vanishes sufficiently fast at infinity, we prove that the difference between quenched and annealed critical points, which is known to be smaller than any power of the disorder strength, is positive: disorder is marginally relevant. Again, the case considered by Forgacs et al. (1986) and Derrida et al. (1992) is out of our analysis and remains open.Comment: 20 pages, 1 figure; v2: few typos corrected, references revised. To appear on Commun. Math. Phy

Asymptotics of Toeplitz Determinants and the Emptiness Formation Probability for the XY Spin Chain

We study an asymptotic behavior of a special correlator known as the Emptiness Formation Probability (EFP) for the one-dimensional anisotropic XY spin-1/2 chain in a transverse magnetic field. This correlator is essentially the probability of formation of a ferromagnetic string of length $n$ in the antiferromagnetic ground state of the chain and plays an important role in the theory of integrable models. For the XY Spin Chain, the correlator can be expressed as the determinant of a Toeplitz matrix and its asymptotical behaviors for $n \to \infty$ throughout the phase diagram are obtained using known theorems and conjectures on Toeplitz determinants. We find that the decay is exponential everywhere in the phase diagram of the XY model except on the critical lines, i.e. where the spectrum is gapless. In these cases, a power-law prefactor with a universal exponent arises in addition to an exponential or Gaussian decay. The latter Gaussian behavior holds on the critical line corresponding to the isotropic XY model, while at the critical value of the magnetic field the EFP decays exponentially. At small anisotropy one has a crossover from the Gaussian to the exponential behavior. We study this crossover using the bosonization approach.Comment: 40 pages, 9 figures, 1 table. The poor quality of some figures is due to arxiv space limitations. If You would like to see the pdf with good quality figures, please contact Fabio Franchini at "[email protected]

Forest fluxes and mortality response to drought: model description (ORCHIDEE-CAN-NHA r7236) and evaluation at the Caxiuanã drought experiment

Extreme drought events in Amazon forests are expected to become more frequent and more intense with climate change, threatening ecosystem function and carbon balance. Yet large uncertainties exist on the resilience of this ecosystem to drought. A better quantification of tree hydraulics and mortality processes is needed to anticipate future drought effects on Amazon forests. Most state-of-the-art dynamic global vegetation models are relatively poor in their mechanistic description of these complex processes. Here, we implement a mechanistic plant hydraulic module within the ORCHIDEE-CAN-NHA r7236 land surface model to simulate the percentage loss of conductance (PLC) and changes in water storage among organs via a representation of the water potentials and vertical water flows along the continuum from soil to roots, stems and leaves. The model was evaluated against observed seasonal variability in stand-scale sap flow, soil moisture and productivity under both control and drought setups at the Caxiuanã throughfall exclusion field experiment in eastern Amazonia between 2001 and 2008. A relationship between PLC and tree mortality is built in the model from two empirical parameters, the cumulated duration of drought exposure that triggers mortality, and the mortality fraction in each day exceeding the exposure. Our model captures the large biomass drop in the year 2005 observed 4 years after throughfall reduction, and produces comparable annual tree mortality rates with observation over the study period. Our hydraulic architecture module provides promising avenues for future research in assimilating experimental data to parameterize mortality due to drought-induced xylem dysfunction. We also highlight that species-based (isohydric or anisohydric) hydraulic traits should be further tested to generalize the model performance in predicting the drought risks.</p