Simplifying microfluidic separation devices towards field-detection of blood parasites

With our sights set on a simple and inexpensive diagnostics device based on extraction and enrichment of parasites from human blood, we present a device design that relies on a combination of multiple different deterministic lateral displacement arrays. Our end goal is a microfluidic device that will be easy to use in the rural, resource-deprived areas where simple-to-use medical tools are crucially needed for rapid and accurate diagnosis. Here, we exemplify this in the application of blood parasite enrichment from a sample of blood. With trypanosomes as a model system we show a combination of functionalities designed into a single device based on several deterministic lateral displacement arrays of different depths arranged in series. With only one inlet and no expensive or complicated pumping mechanisms to run separations we ensure the level of simplicity necessary for field use

Pathos: a web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry

This work describes a freely available web-based facility which can be used to analyse raw or processed mass spectrometric data from metabolomics experiments and display the metabolites identified – and changes in their experimental abundance – in the context of the metabolic pathways in which they occur. The facility, Pathos (http://motif.gla.ac.uk/Pathos/), employs Java servlets and is underpinned by a relational database populated from the Kyoto Encyclopaedia of Genes and Genomes (KEGG). Input files can contain either raw m/z values from experiments conducted in different modes, or KEGG or MetaCyc IDs assigned by the user on the basis of the m/z values and other criteria. The textual output lists the KEGG pathways on an XHTML page according to the number of metabolites or potential metabolites that they contain. Filtering by organism is also available. For metabolic pathways of interest, the user is able to retrieve a pathway map with identified metabolites highlighted. A particular feature of Pathos is its ability to process relative quantification data for metabolites identified under different experimental conditions, and to present this in an easily comprehensible manner. Results are colour-coded according to the degree of experimental change, and bar charts of the results can be generated interactively from either the text listings or the pathway maps. The visual presentation of the output from Pathos is designed to allow the rapid identification of metabolic areas of potential interest, after which particular results may be examined in detail

Genotypic status of the TbAT1/P2 adenosine transporter of Trypanosoma brucei gambiense isolates from northwestern Uganda following melarsoprol withdrawal

Human African trypanosomiasis (HAT) manifests as a chronic infection caused by <i>Trypanosoma brucei gambiense</i>, or as a more acute form due to <i>T. b. rhodesiense</i>. Both manifestations occur in Uganda and melarsoprol use against the former was jeopardised in the 1990s as reports of reduced efficacy increased to the point where it was dismissed as first-line treatment at some treatment centers. Previous work to elucidate possible mechanisms leading to melarsoprol resistance pointed to a P2 type adenosine transporter known to mediate melarsoprol uptake and previously shown to be mutated in significant numbers of patients not responding to the drug. Our present findings indicate that there is a low prevalence of mutants in foci where melarsoprol relapses are infrequent. In addition we observe that at the Omugo focus where the drug was withdrawn as first line over 6 years ago, the mutant alleles have disappeared, suggesting that drug pressure is responsible for fuelling their spread. Thus constant monitoring for mutants could play a key role in cost-effective HAT management by identifying which foci can still use the less logistically demanding melarsoprol as opposed to the alternative drug eflornithine. What is required now is a simple method for identifying such mutants at the point of care, enabling practitioners to make informed prescriptions at first diagnosis

Monogamy of Correlations vs. Monogamy of Entanglement

A fruitful way of studying physical theories is via the question whether the possible physical states and different kinds of correlations in each theory can be shared to different parties. Over the past few years it has become clear that both quantum entanglement and non-locality (i.e., correlations that violate Bell-type inequalities) have limited shareability properties and can sometimes even be monogamous. We give a self-contained review of these results as well as present new results on the shareability of different kinds of correlations, including local, quantum and no-signalling correlations. This includes an alternative simpler proof of the Toner-Verstraete monogamy inequality for quantum correlations, as well as a strengthening thereof. Further, the relationship between sharing non-local quantum correlations and sharing mixed entangled states is investigated, and already for the simplest case of bi-partite correlations and qubits this is shown to be non-trivial. Also, a recently proposed new interpretation of Bell's theorem by Schumacher in terms of shareability of correlations is critically assessed. Finally, the relevance of monogamy of non-local correlations for secure quantum key distribution is pointed out, although, and importantly, it is stressed that not all non-local correlations are monogamous.Comment: 12 pages, 2 figures. Invited submission to a special issue of Quantum Information Processing. v2: Published version. Open acces

Coupling of spacetime atoms and spin foam renormalisation from group field theory

We study the issue of coupling among 4-simplices in the context of spin foam models obtained from a group field theory formalism. We construct a generalisation of the Barrett-Crane model in which an additional coupling between the normals to tetrahedra, as defined in different 4-simplices that share them, is present. This is realised through an extension of the usual field over the group manifold to a five argument one. We define a specific model in which this coupling is parametrised by an additional real parameter that allows to tune the degree of locality of the resulting model, interpolating between the usual Barrett-Crane model and a flat BF-type one. Moreover, we define a further extension of the group field theory formalism in which the coupling parameter enters as a new variable of the field, and the action presents derivative terms that lead to modified classical equations of motion. Finally, we discuss the issue of renormalisation of spin foam models, and how the new coupled model can be of help regarding this.Comment: RevTeX, 18 pages, no figure

Genome deletions to overcome the directed loss of gene function in Leishmania

With the global reach of the Neglected Tropical Disease leishmanaisis increasing, coupled with a tiny armoury of therapeutics which all have problems with resistance, cost, toxicity and/or administration, the validation of new drug targets in the causative insect vector borne protozoa Leishmania spp is more important than ever. Before the introduction of CRISPR Cas9 technology in 2015 genetic validation of new targets was carried out largely by targeted gene knockout through homologous recombination, with the majority of genes targeted (~70%) deemed non-essential. In this study we exploit the ready availability of whole genome sequencing technology to reanalyse one of these historic cell lines, a L. major knockout in the catalytic subunit of serine palmitoyltransferase (LCB2), which causes a complete loss of sphingolipid biosynthesis but remains viable and infective. This revealed a number of Single Nucleotide Polymorphisms, but also the complete loss of several coding regions including a gene encoding a putative ABC3A orthologue, a putative sterol transporter. Hypothesising that the loss of such a transporter may have facilitated the directed knockout of the catalytic subunit of LCB2 and the complete loss of de novo sphingolipid biosynthesis, we re-examined LCB2 in a L. mexicana line engineered for straightforward CRISPR Cas9 directed manipulation. Strikingly, LCB2 could not be knocked out indicating essentiality. However, simultaneous deletion of LCB2 and the putative ABC3A was possible. This indicated that the loss of the putative ABC3A facilitated the loss of sphingolipid biosynthesis in Leishmania, and suggested that we should re-examine the many other Leishmania knockout lines where genes were deemed non-essential

Fictitious Magnetic Resonance by Quasi-Electrostatic Field

We propose a new kind of spin manipulation method using a {\it fictitious} magnetic field generated by a quasi-electrostatic field. The method can be applicable to every atom with electron spins and has distinct advantages of small photon scattering rate and local addressability. By using a $\rm{CO_2}$ laser as a quasi-electrostatic field, we have experimentally demonstrated the proposed method by observing the Rabi-oscillation of the ground state hyperfine spin F=1 of the cold $\rm{^{87}Rb}$ atoms and the Bose-Einstein condensate.Comment: 5 pages, 5 figure

Fermions in three-dimensional spinfoam quantum gravity

We study the coupling of massive fermions to the quantum mechanical dynamics of spacetime emerging from the spinfoam approach in three dimensions. We first recall the classical theory before constructing a spinfoam model of quantum gravity coupled to spinors. The technique used is based on a finite expansion in inverse fermion masses leading to the computation of the vacuum to vacuum transition amplitude of the theory. The path integral is derived as a sum over closed fermionic loops wrapping around the spinfoam. The effects of quantum torsion are realised as a modification of the intertwining operators assigned to the edges of the two-complex, in accordance with loop quantum gravity. The creation of non-trivial curvature is modelled by a modification of the pure gravity vertex amplitudes. The appendix contains a review of the geometrical and algebraic structures underlying the classical coupling of fermions to three dimensional gravity.Comment: 40 pages, 3 figures, version accepted for publication in GER

An essential thioredoxin-type protein of Trypanosoma brucei acts as redox-regulated mitochondrial chaperone

Most known thioredoxin-type proteins (Trx) participate in redox pathways, using two highly conserved cysteine residues to catalyze thiol-disulfide exchange reactions. Here we demonstrate that the so far unexplored Trx2 from African trypanosomes (Trypanosoma brucei) lacks protein disulfide reductase activity but functions as an effective temperature-activated and redox-regulated chaperone. Immunofluorescence microscopy and fractionated cell lysis revealed that Trx2 is located in the mitochondrion of the parasite. RNA-interference and gene knock-out approaches showed that depletion of Trx2 impairs growth of both mammalian bloodstream and insect stage procyclic parasites. Procyclic cells lacking Trx2 stop proliferation under standard culture conditions at 27°C and are unable to survive prolonged exposure to 37°C, indicating that Trx2 plays a vital role that becomes augmented under heat stress. Moreover, we found that Trx2 contributes to the in vivo infectivity of T. brucei. Remarkably, a Trx2 version, in which all five cysteines were replaced by serine residues, complements for the wildtype protein in conditional knock-out cells and confers parasite infectivity in the mouse model. Characterization of the recombinant protein revealed that Trx2 can coordinate an iron sulfur cluster and is highly sensitive towards spontaneous oxidation. Moreover, we discovered that both wildtype and mutant Trx2 protect other proteins against thermal aggregation and preserve their ability to refold upon return to non-stress conditions. Activation of the chaperone function of Trx2 appears to be triggered by temperature-mediated structural changes and inhibited by oxidative disulfide bond formation. Our studies indicate that Trx2 acts as a novel chaperone in the unique single mitochondrion of T. brucei and reveal a new perspective regarding the physiological function of thioredoxin-type proteins in trypanosomes