Core genome components and lineage specific expansions in malaria parasites Plasmodium

<p>Abstract</p> <p>Background</p> <p>The increasing resistance of <it>Plasmodium,</it> the malaria parasites, to multiple commonly used drugs has underscored the urgent need to develop effective antimalarial drugs and vaccines. The new direction of genomics-driven target discovery has become possible with the completion of parasite genome sequencing, which can lead us to a better understanding of how the parasites develop the genetic variability that is associated with their response to environmental challenges and other adaptive phenotypes.</p> <p>Results</p> <p>We present the results of a comprehensive analysis of the genomes of six <it>Plasmodium</it> species, including two species that infect humans, one that infects monkeys, and three that infect rodents. The core genome shared by all six species is composed of 3,351 genes, which make up about 22%-65% of the genome repertoire. These components play important roles in fundamental functions as well as in parasite-specific activities. We further investigated the distribution and features of genes that have been expanded in specific Plasmodium lineage(s). Abundant duplicate genes are present in the six species, with 5%-9% of the whole genomes composed lineage specific radiations. The majority of these gene families are hypothetical proteins with unknown functions; a few may have predicted roles such as antigenic variation.</p> <p>Conclusions</p> <p>The core genome components in the malaria parasites have functions ranging from fundamental biological processes to roles in the complex networks that sustain the parasite-specific lifestyles appropriate to different hosts. They represent the minimum requirement to maintain a successful life cycle that spans vertebrate hosts and mosquito vectors. Lineage specific expansions (LSEs) have given rise to abundant gene families in <it>Plasmodium.</it> Although the functions of most families remain unknown, these LSEs could reveal components in parasite networks that, by their enhanced genetic variability, can contribute to pathogenesis, virulence, responses to environmental challenges, or interesting phenotypes.</p

Charmless Two-body B(Bs)→VPB(B_s)\to VP decays In Soft-Collinear-Effective-Theory

We provide the analysis of charmless two-body $B\to VP$ decays under the framework of the soft-collinear-effective-theory (SCET), where $V(P)$ denotes a light vector (pseudoscalar) meson. Besides the leading power contributions, some power corrections (chiraly enhanced penguins) are also taken into account. Using the current available $B\to PP$ and $B\to VP$ experimental data on branching fractions and CP asymmetry variables, we find two kinds of solutions in $\chi^2$ fit for the 16 non-perturbative inputs which are essential in the 87 $B\to PP$ and $B\to VP$ decay channels. Chiraly enhanced penguins can change several charming penguins sizably, since they share the same topology. However, most of the other non-perturbative inputs and predictions on branching ratios and CP asymmetries are not changed too much. With the two sets of inputs, we predict the branching fractions and CP asymmetries of other modes especially $B_s\to VP$ decays. The agreements and differences with results in QCD factorization and perturbative QCD approach are analyzed. We also study the time-dependent CP asymmetries in channels with CP eigenstates in the final states and some other channels such as $\bar B^0/B^0\to\pi^\pm\rho^\mp$ and $\bar B_s^0/B_s^0\to K^\pm K^{*\mp}$. In the perturbative QCD approach, the $(S-P)(S+P)$ penguins in annihilation diagrams play an important role. Although they have the same topology with charming penguins in SCET, there are many differences between the two objects in weak phases, magnitudes, strong phases and factorization properties.Comment: 34 pages, revtex, 2 figures, published at PR

Diquarks and the Semi-Leptonic Decay of Λb\Lambda_{b} in the Hybrid Scheme

In this work we use the heavy-quark-light-diquark picture to study the semileptonic decay $\Lambda_b \to \Lambda_c+l+\bar{\nu}_l$ in the so-called hybrid scheme. Namely, we apply the heavy quark effective theory (HQET) for larger $q^2$ (corresponding to small recoil), which is the invariant mass square of $l+\bar\nu$, whereas the perturbative QCD approach for smaller $q^2$ to calculate the form factors. The turning point where we require the form factors derived in the two approaches to be connected, is chosen near $\rho_{cut}=1.1$. It is noted that the kinematic parameter $\rho$ which is usually adopted in the perturbative QCD approach, is in fact exactly the same as the recoil factor $\omega=v\cdot v'$ used in HQET where $v$, $v'$ are the four velocities of $\Lambda_b$ and $\Lambda_c$ respectively. We find that the final result is not much sensitive to the choice, so that it is relatively reliable. Moreover, we apply a proper numerical program within a small range around $\rho_{cut}$ to make the connection sufficiently smooth and we parameterize the form factor by fitting the curve gained in the hybrid scheme. The expression and involved parameters can be compared with the ones gained by fitting the experimental data. In this scheme the end-point singularities do not appear at all. The calculated value is satisfactorily consistent with the data which is recently measured by the DELPHI collaboration within two standard deviations.Comment: 16 pages, including 4 figures, revtex