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PacBio assembly of a Plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family.
Plasmodium knowlesi has risen in importance as a zoonotic parasite that has been causing regular episodes of malaria throughout South East Asia. The P. knowlesi genome sequence generated in 2008 highlighted and confirmed many similarities and differences in Plasmodium species, including a global view of several multigene families, such as the large SICAvar multigene family encoding the variant antigens known as the schizont-infected cell agglutination proteins. However, repetitive DNA sequences are the bane of any genome project, and this and other Plasmodium genome projects have not been immune to the gaps, rearrangements and other pitfalls created by these genomic features. Today, long-read PacBio and chromatin conformation technologies are overcoming such obstacles. Here, based on the use of these technologies, we present a highly refined de novo P. knowlesi genome sequence of the Pk1(A+) clone. This sequence and annotation, referred to as the 'MaHPIC Pk genome sequence', includes manual annotation of the SICAvar gene family with 136 full-length members categorized as type I or II. This sequence provides a framework that will permit a better understanding of the SICAvar repertoire, selective pressures acting on this gene family and mechanisms of antigenic variation in this species and other pathogens
Flooding Regime Impacts on Radiation, Evapotranspiration, and Latent Energy Fluxes over Groundwater-Dependent Riparian Cottonwood and Saltcedar Forests
© 2015 James Cleverly et al. Radiation and energy balances are key drivers of ecosystem water and carbon cycling. This study reports on ten years of eddy covariance measurements over groundwater-dependent ecosystems (GDEs) in New Mexico, USA, to compare the role of drought and flooding on radiation, water, and energy budgets of forests differing in species composition (native cottonwood versus nonnative saltcedar) and flooding regime. After net radiation (700-800 W m-2), latent heat flux was the largest energy flux, with annual values of evapotranspiration exceeding annual precipitation by 250-600%. Evaporative cooling dominated the energy fluxes of both forest types, although cottonwood generated much lower daily values of sensible heat flux (<-5 MJ m-2 d-1). Drought caused a reduction in evaporative cooling, especially in the saltcedar sites where evapotranspiration was also reduced, but without a substantial decline in depth-to-groundwater. Our findings have broad implications on water security and the management of native and nonnative vegetation within semiarid southwestern North America. Specifically, consideration of the energy budgets of GDEs as they respond to fluctuations in climatic conditions can inform the management options for reducing evapotranspiration and maintaining in-stream flow, which is legally mandated as part of interstate and international water resources agreements
Mercury chemostratigraphy across the Cambrian Series 2 – Series 3 boundary: evidence for increased volcanic activity coincident with extinction?
Flood basalt volcanism represented by the Kalkarindji Province (Australia) is temporally associated with a trilobite mass extinction at the Cambrian Series 2 – Series 3 boundary, providing one of the oldest potential links between volcanism and biotic crisis in the Phanerozoic. However, the relative timing of flood basalt volcanism (Kalkarindji Province, Australia) and the trilobite extinctions, first recorded in North America, is not known. Mercury (Hg) enrichment in the sedimentary record provides a potential proxy for volcanism which may facilitate improved chronologies of eruption and extinction. Here we report mercury records for three sections from mid-shelf strata of the Great Basin (western USA) that straddle the Series 2 – Series 3 boundary. One section (Oak Springs Summit, NV) features a Hg enrichment at the start of the extinction interval, but mercury anomalies are also present at lower levels. These older anomalies may record either earlier phases of Kalkarindji volcanism, eruptions in other locations, or may be the result of sedimentary and/or diagenetic processes affecting the Hg record. In the Carrara Formation at Emigrant Pass, CA, the precise extinction horizon is not well defined, but a carbon isotope anomaly (the Redlichiid-Olenellid Extinction Carbon isotope Event; ROECE) provides a stratigraphic tie point to the Oak Springs Summit section. At Emigrant Pass, Hg enrichments precede the ROECE interval and are absent in the inferred extinction zone. The Pioche Formation at Ruin Wash, NV, lacks Hg enrichment at the extinction horizon but contains older enrichments. The inconsistent Hg records between the three sections demonstrate that factors controlling Hg accumulation and preservation in marine sedimentary environments are not yet fully understood. The effects of redox fluctuations may complicate one-to-one association of sedimentary Hg enrichments and massive volcanism at the Cambrian Series 2 – Series 3 boundary and elsewhere in the geologic record
Bioconversion of cellulose into bisabolene using Ruminococcus flavefaciens and Rhodosporidium toruloides
In this study, organic acids were demonstrated as a promising carbon source for bisabolene production by the non-conventional yeast, Rhodosporidium toruloides, at microscale with a maximum titre of 1055 ± 7 mg/L. A 125-fold scale-up of the optimal process, enhanced bisabolene titres 2.5-fold to 2606 mg/L. Implementation of a pH controlled organic acid feeding strategy at this scale lead to a further threefold improvement in bisabolene titre to 7758 mg/L, the highest reported microbial titre. Finally, a proof-of-concept sequential bioreactor approach was investigated. Firstly, the cellulolytic bacterium Ruminococcus flavefaciens was employed to ferment cellulose, yielding 4.2 g/L of organic acids. R. toruloides was subsequently cultivated in the resulting supernatant, producing 318 ± 22 mg/L of bisabolene. This highlights the feasibility of a sequential bioprocess for the bioconversion of cellulose, into biojet fuel candidates. Future work will focus on enhancing organic acid yields and the use of real lignocellulosic feedstocks to further enhance bisabolene production
A constitutive law for dense granular flows
A continuum description of granular flows would be of considerable help in
predicting natural geophysical hazards or in designing industrial processes.
However, the constitutive equations for dry granular flows, which govern how
the material moves under shear, are still a matter of debate. One difficulty is
that grains can behave like a solid (in a sand pile), a liquid (when poured
from a silo) or a gas (when strongly agitated). For the two extreme regimes,
constitutive equations have been proposed based on kinetic theory for
collisional rapid flows, and soil mechanics for slow plastic flows. However,
the intermediate dense regime, where the granular material flows like a liquid,
still lacks a unified view and has motivated many studies over the past decade.
The main characteristics of granular liquids are: a yield criterion (a critical
shear stress below which flow is not possible) and a complex dependence on
shear rate when flowing. In this sense, granular matter shares similarities
with classical visco-plastic fluids such as Bingham fluids. Here we propose a
new constitutive relation for dense granular flows, inspired by this analogy
and recent numerical and experimental work. We then test our three-dimensional
(3D) model through experiments on granular flows on a pile between rough
sidewalls, in which a complex 3D flow pattern develops. We show that, without
any fitting parameter, the model gives quantitative predictions for the flow
shape and velocity profiles. Our results support the idea that a simple
visco-plastic approach can quantitatively capture granular flow properties, and
could serve as a basic tool for modelling more complex flows in geophysical or
industrial applications.Comment: http://www.nature.com/nature/journal/v441/n7094/abs/nature04801.htm
Fragments of the earliest land plants
The earliest fossil evidence for land plants comes from microscopic dispersed spores. These microfossils are abundant and widely distributed in sediments, and the earliest generally accepted reports are from rocks of mid-Ordovician age (Llanvirn, 475 million years ago). Although distribution, morphology and ultrastructure of the spores indicate that they are derived from terrestrial plants, possibly early relatives of the bryophytes, this interpretation remains controversial as there is little in the way of direct evidence for the parent plants. An additional complicating factor is that there is a significant hiatus between the appearance of the first dispersed spores and fossils of relatively complete land plants (megafossils): spores predate the earliest megafossils (Late Silurian, 425 million year ago) by some 50 million years. Here we report the description of spore-containing plant fragments from Ordovician rocks of Oman. These fossils provide direct evidence for the nature of the spore-producing plants. They confirm that the earliest spores developed in large numbers within sporangia, providing strong evidence that they are the fossilized remains of bona fide land plants. Furthermore, analysis of spore wall ultrastructure supports liverwort affinities
Transplanckian axions !?
We discuss quantum gravitational effects in Einstein theory coupled to
periodic axion scalars to analyze the viability of several proposals to achieve
superplanckian axion periods (aka decay constants) and their possible
application to large field inflation models. The effects we study correspond to
the nucleation of euclidean gravitational instantons charged under the axion,
and our results are essentially compatible with (but independent of) the Weak
Gravity Conjecture, as follows: Single axion theories with superplanckian
periods contain gravitational instantons inducing sizable higher harmonics in
the axion potential, which spoil superplanckian inflaton field range. A similar
result holds for multi-axion models with lattice alignment (like the
Kim-Nilles-Peloso model). Finally, theories with axions can still achieve a
moderately superplanckian periodicity (by a factor) with no higher
harmonics in the axion potential. The Weak Gravity Conjecture fails to hold in
this case due to the absence of some instantons, which are forbidden by a
discrete gauge symmetry. Finally we discuss the realization of
these instantons as euclidean D-branes in string compactifications.Comment: 46 pages, 6 figures. Added references, clarifications, and missing
factor of 1/2 to instanton action. Conclusions unchange
Multifield Dynamics in Higgs-otic Inflation
In Higgs-otic inflation a complex neutral scalar combination of the and
MSSM Higgs fields plays the role of inflaton in a chaotic fashion. The
potential is protected from large trans-Planckian corrections at large inflaton
if the system is embedded in string theory so that the Higgs fields parametrize
a D-brane position. The inflaton potential is then given by a DBI+CS D-brane
action yielding an approximate linear behaviour at large field. The inflaton
scalar potential is a 2-field model with specific non-canonical kinetic terms.
Previous computations of the cosmological parameters (i.e. scalar and tensor
perturbations) did not take into account the full 2-field character of the
model, ignoring in particular the presence of isocurvature perturbations and
their coupling to the adiabatic modes. It is well known that for generic
2-field potentials such effects may significantly alter the observational
signatures of a given model. We perform a full analysis of adiabatic and
isocurvature perturbations in the Higgs-otic 2-field model. We show that the
predictivity of the model is increased compared to the adiabatic approximation.
Isocurvature perturbations moderately feed back into adiabatic fluctuations.
However, the isocurvature component is exponentially damped by the end of
inflation. The tensor to scalar ratio varies in a region ,
consistent with combined Planck/BICEP results.Comment: 35 pages, 11 figure
Acute effects of nicotine on visual search tasks in young adult smokers
Rationale Nicotine is known to improve performance on tests involving sustained attention and recent research suggests that nicotine may also improve performance on tests involving the strategic allocation of attention and working memory. Objectives We used measures of accuracy and response latency combined with eye-tracking techniques to examine the effects of nicotine on visual search tasks. Methods In experiment 1 smokers and non-smokers performed pop-out and serial search tasks. In experiment 2, we used a within-subject design and a more demanding search task for multiple targets. In both studies, 2-h abstinent smokers were asked to smoke one of their own cigarettes between baseline and tests. Results In experiment 1, pop-out search times were faster after nicotine, without a loss in accuracy. Similar effects were observed for serial searches, but these were significant only at a trend level. In experiment 2, nicotine facilitated a strategic change in eye movements resulting in a higher proportion of fixations on target letters. If the cigarette was smoked on the first trial (when the task was novel), nicotine additionally reduced the total number of fixations and refixations on all letters in the display. Conclusions Nicotine improves visual search performance by speeding up search time and enabling a better focus of attention on task relevant items. This appears to reflect more efficient inhibition of eye movements towards task irrelevant stimuli, and better active maintenance of task goals. When the task is novel, and therefore more difficult, nicotine lessens the need to refixate previously seen letters, suggesting an improvement in working memory
Light propagation and Anderson localization in disordered superlattices containing dispersive metamaterials: Effects of correlated disorder
Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)We have investigated the effects of disorder correlations on light propagation and Anderson localization in one-dimensional dispersive metamaterials. We consider and compare the cases where disorder is uncorrelated to situations where it is totally correlated and anticorrelated. The photonic gaps of the corresponding periodic structure are not completely destroyed by the presence of disorder, which leads to minima in the localization length. In the vicinities of a gap, the behavior of the localization length depends crucially on the physical origin of the gap (Bragg or non-Bragg gaps). Within a Bragg gap, the localization length increases as the degree of disorder increases, an anomalous behavior that only occurs for the uncorrelated and completely correlated cases. In these cases, minima of the localization length at the positions of Bragg gaps are shifted by increasing disorder, which does not occur for the anticorrelated case, where the positions of the minima remain unaltered. Minima in the localization length corresponding to non-Bragg gaps are not shifted by increasing disorder, albeit the widths of these minima are changed. We have found that the asymptotic behavior for the localization length xi proportional to lambda(6) for disordered metamaterials is not affected by correlations. Finally, we have investigated the role of absorption on the delocalized Brewster modes and argue that it could be mitigated in light of the state-of-the-art of metamaterials research.849Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Brazilian Agency FUJBConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP
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