Whole genome sequencing and microsatellite analysis of the Plasmodium falciparum E5 NF54 strain show that the var, rifin and stevor gene families follow Mendelian inheritance

Background: Plasmodium falciparum exhibits a high degree of inter-isolate genetic diversity in its variant surface antigen (VSA) families: P. falciparum erythrocyte membrane protein 1, repetitive interspersed family (RIFIN) and subtelomeric variable open reading frame (STEVOR). The role of recombination for the generation of this diversity is a subject of ongoing research. Here the genome of E5, a sibling of the 3D7 genome strain is presented. Short and long read whole genome sequencing (WGS) techniques (Ilumina, Pacific Bioscience) and a set of 84 microsatellites (MS) were employed to characterize the 3D7 and non-3D7 parts of the E5 genome. This is the first time that VSA genes in sibling parasites were analysed with long read sequencing technology. Results: Of the 5733 E5 genes only 278 genes, mostly var and rifin/stevor genes, had no orthologues in the 3D7 genome. WGS and MS analysis revealed that chromosomal crossovers occurred at a rate of 0–3 per chromosome. var, stevor and rifin genes were inherited within the respective non-3D7 or 3D7 chromosomal context. 54 of the 84 MS PCR fragments correctly identified the respective MS as 3D7- or non-3D7 and this correlated with var and rifin/stevor gene inheritance in the adjacent chromosomal regions. E5 had 61 var and 189 rifin/stevor genes. One large non-chromosomal recombination event resulted in a new var gene on chromosome 14. The remainder of the E5 3D7-type subtelomeric and central regions were identical to 3D7. Conclusions: The data show that the rifin/stevor and var gene families represent the most diverse compartments of the P. falciparum genome but that the majority of var genes are inherited without alterations within their respective parental chromosomal context. Furthermore, MS genotyping with 54 MS can successfully distinguish between two sibling progeny of a natural P. falciparum cross and thus can be used to investigate identity by descent in field isolates

Angular Momentum Decomposition for an Electron

We calculate the orbital angular momentum of the `quark' in the scalar diquark model as well as that of the electron in QED (to order $\alpha$). We compare the orbital angular momentum obtained from the Jaffe-Manohar decomposition to that obtained from the Ji relation and estimate the importance of the vector potential in the definition of orbital angular momentum

Local spin operators for fermion simulations

Digital quantum simulation of fermionic systems is important in the context of chemistry and physics. Simulating fermionic models on general purpose quantum computers requires imposing a fermionic algebra on spins. The previously studied Jordan-Wigner and Bravyi-Kitaev transformations are two techniques for accomplishing this task. Here we re-examine an auxiliary fermion construction which maps fermionic operators to local operators on spins. The local simulation is performed by relaxing the requirement that the number of spins should match the number of fermionic modes. Instead, auxiliary modes are introduced to enable non-consecutive fermionic couplings to be simulated with constant low-rank tensor products on spins. We connect the auxiliary fermion construction to other topological models and give examples of the construction

Quantization of gauge fields, graph polynomials and graph cohomology

We review quantization of gauge fields using algebraic properties of 3-regular graphs. We derive the Feynman integrand at n loops for a non-abelian gauge theory quantized in a covariant gauge from scalar integrands for connected 3-regular graphs, obtained from the two Symanzik polynomials. The transition to the full gauge theory amplitude is obtained by the use of a third, new, graph polynomial, the corolla polynomial. This implies effectively a covariant quantization without ghosts, where all the relevant signs of the ghost sector are incorporated in a double complex furnished by the corolla polynomial -we call it cycle homology- and by graph homology.Comment: 44p, many figures, to appea

Effective interaction between a colloid and a soft interface near criticality

Within mean-field theory we determine the universal scaling function for the effective force acting on a single colloid located near the interface between two coexisting liquid phases of a binary liquid mixture close to its critical consolute point. This is the first study of critical Casimir forces emerging from the confinement of a fluctuating medium by at least one soft interface, instead by rigid walls only as studied previously. For this specific system, our semi-analytical calculation illustrates that knowledge of the colloid-induced, deformed shape of the interface allows one to accurately describe the effective interaction potential between the colloid and the interface. Moreover, our analysis demonstrates that the critical Casimir force involving a deformable interface is accurately described by a universal scaling function, the shape of which differs from that one for rigid walls.Comment: 19 pages, 11 figure

Wh-movement vs. scrambling: The brain makes a difference

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Rate Dependence and Role of Disorder in Linearly Sheared Two-Dimensional Foams

The shear flow of two dimensional foams is probed as a function of shear rate and disorder. Disordered foams exhibit strongly rate dependent velocity profiles, whereas ordered foams show rate independence. Both behaviors are captured quantitatively in a simple model based on the balance of the time-averaged drag forces in the foam, which are found to exhibit power-law scaling with the foam velocity and strain rate. Disorder modifies the scaling of the averaged inter-bubble drag forces, which in turn causes the observed rate dependence in disordered foams.Comment: 4 Figures, 4 page