The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution

BACKGROUND:Giardia lamblia trophozoites colonize the intestines of susceptible mammals and cause diarrhea, which can be prolonged despite an intestinal immune response. The variable expression of the variant-specific surface protein (VSP) genes may contribute to this prolonged infection. Only one is expressed at a time, and switching expression from one gene to another occurs by an epigenetic mechanism.RESULTS:The WB Giardia isolate has been sequenced at 10x coverage and assembled into 306 contigs as large as 870 kb in size. We have used this assembly to evaluate the genomic organization and evolution of the vsp repertoire. We have identified 228 complete and 75 partial vsp gene sequences for an estimated repertoire of 270 to 303, making up about 4% of the genome. The vsp gene diversity includes 30 genes containing tandem repeats, and 14 vsp pairs of identical genes present in either head to head or tail to tail configurations (designated as inverted pairs), where the two genes are separated by 2 to 4 kb of non-coding DNA. Interestingly, over half the total vsp repertoire is present in the form of linear gene arrays that can contain up to 10 vsp gene members. Lastly, evidence for recombination within and across minor clades of vsp genes is provided.CONCLUSIONS:The data we present here is the first comprehensive analysis of the vsp gene family from the Genotype A1 WB isolate with an emphasis on vsp characterization, function, evolution and contributions to pathogenesis of this important pathogen.This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at [email protected]

Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons.

Thaumarchaeota are responsible for a significant fraction of ammonia oxidation in the oceans and in soils that range from alkaline to acidic. However, the adaptive mechanisms underpinning their habitat expansion remain poorly understood. Here we show that expansion into acidic soils and the high pressures of the hadopelagic zone of the oceans is tightly linked to the acquisition of a variant of the energy-yielding ATPases via horizontal transfer. Whereas the ATPase genealogy of neutrophilic Thaumarchaeota is congruent with their organismal genealogy inferred from concatenated conserved proteins, a common clade of V-type ATPases unites phylogenetically distinct clades of acidophilic/acid-tolerant and piezophilic/piezotolerant species. A presumptive function of pumping cytoplasmic protons at low pH is consistent with the experimentally observed increased expression of the V-ATPase in an acid-tolerant thaumarchaeote at low pH. Consistently, heterologous expression of the thaumarchaeotal V-ATPase significantly increased the growth rate of E. coli at low pH. Its adaptive significance to growth in ocean trenches may relate to pressure-related changes in membrane structure in which this complex molecular machine must function. Together, our findings reveal that the habitat expansion of Thaumarchaeota is tightly correlated with extensive horizontal transfer of atp operons

Surface Hopping without Momentum Jumps: A Quantum-Trajectory-Based Approach to Nonadiabatic Dynamics.

We describe a new method for simulating nonadiabatic dynamics using stochastic trajectories. The method, which we call quantum trajectory surface hopping (QTSH), is a variant of the popular fewest-switches surface-hopping (FSSH) approach, but with important differences. We briefly review and significantly extend our recently described consensus surface-hopping (CSH) formalism, which captures quantum effects such as coherence and decoherence via a collective representation of the quantum dynamics at the ensemble level. Using well-controlled further approximations, we derive an independent trajectory limit of CSH that recovers the FSSH stochastic algorithm but rejects the ad hoc momentum rescaling of FSSH in favor of quantum forces that couple classical and quantum degrees of freedom and lead to nonclassical trajectory dynamics. The approach is well-defined in both the diabatic and adiabatic representations. In the adiabatic representation, the classical dynamics are modified by a quantum-state-dependent vector potential, introducing geometric phase effects into the dynamics of multidimensional systems. Unlike FSSH, our method obeys energy conservation without any artificial momentum rescaling, eliminating undesirable features of the former such as forbidden hops and breakdown of the internal consistency of quantum and ensemble-based state probabilities. Corrections emerge naturally in the formalism that allow approximate incorporation of decoherence without the computational expense of the full CSH approach. The method is tested on several model systems. QTSH provides a surface-hopping methodology that has a rigorous foundation and broader applicability than FSSH while retaining the low computational cost of an independent trajectory framework

Particle interactions with single or multiple 3D solar reconnecting current sheets

The acceleration of charged particles (electrons and protons) in flaring solar active regions is analyzed by numerical experiments. The acceleration is modelled as a stochastic process taking place by the interaction of the particles with local magnetic reconnection sites via multiple steps. Two types of local reconnecting topologies are studied: the Harris-type and the X-point. A formula for the maximum kinetic energy gain in a Harris-type current sheet, found in a previous work of ours, fits well the numerical data for a single step of the process. A generalization is then given approximating the kinetic energy gain through an X-point. In the case of the multiple step process, in both topologies the particles' kinetic energy distribution is found to acquire a practically invariant form after a small number of steps. This tendency is interpreted theoretically. Other characteristics of the acceleration process are given, such as the mean acceleration time and the pitch angle distributions of the particles.Comment: 18 pages, 9 figures, Solar Physics, in pres

PRIDE: new developments and new datasets

The PRIDE (http://www.ebi.ac.uk/pride) database of protein and peptide identifications was previously described in the NAR Database Special Edition in 2006. Since this publication, the volume of public data in the PRIDE relational database has increased by more than an order of magnitude. Several significant public datasets have been added, including identifications and processed mass spectra generated by the HUPO Brain Proteome Project and the HUPO Liver Proteome Project. The PRIDE software development team has made several significant changes and additions to the user interface and tool set associated with PRIDE. The focus of these changes has been to facilitate the submission process and to improve the mechanisms by which PRIDE can be queried. The PRIDE team has developed a Microsoft Excel workbook that allows the required data to be collated in a series of relatively simple spreadsheets, with automatic generation of PRIDE XML at the end of the process. The ability to query PRIDE has been augmented by the addition of a BioMart interface allowing complex queries to be constructed. Collaboration with groups outside the EBI has been fruitful in extending PRIDE, including an approach to encode iTRAQ quantitative data in PRIDE XML

Specializing Interpreters using Offline Partial Deduction

We present the latest version of the Logen partial evaluation system for logic programs. In particular we present new binding-types, and show how they can be used to effectively specialise a wide variety of interpreters.We show how to achieve Jones-optimality in a systematic way for several interpreters. Finally, we present and specialise a non-trivial interpreter for a small functional programming language. Experimental results are also presented, highlighting that the Logen system can be a good basis for generating compilers for high-level languages

Upgrades to the Fermilab Numi Beamline

The NuMI beamline at Fermilab has been delivering high-intensity muon neutrino beams to the MINOS experiment since the spring of 2005. A total of 3.4 x 10{sup 20} protons has been delivered to the NuMI target and a maximum beam power of 320 kW has been achieved. An upgrade of the NuMI facility increasing the beam power capability to 700 kW is planned as part of the NOvA experiment. The plans for this upgrade are presented and the possibility of upgrading the NuMI beamline to handle 1.2 MW is considered

Global warming and malaria: knowing the horse before hitching the cart

Speculations on the potential impact of climate change on human health frequently focus on malaria. Predictions are common that in the coming decades, tens – even hundreds – of millions more cases will occur in regions where the disease is already present, and that transmission will extend to higher latitudes and altitudes. Such predictions, sometimes supported by simple models, are persuasive because they are intuitive, but they sidestep factors that are key to the transmission and epidemiology of the disease: the ecology and behaviour of both humans and vectors, and the immunity of the human population. A holistic view of the natural history of the disease, in the context of these factors and in the precise setting where it is transmitted, is the only valid starting point for assessing the likely significance of future changes in climate