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

Multispectral autofluorescence characteristics of reproductive aging in old and young mouse oocytes

Increasing age has a major detrimental impact on female fertility, which, with an ageing population, has major sociological implications. This impact is primarily mediated through deteriorating quality of the oocyte. Deteriorating oocyte quality with biological age is the greatest rate-limiting factor to female fertility. Here we have used label-free, non-invasive multi-spectral imaging to identify unique autofluorescence profiles of oocytes from young and aged animals. Discriminant analysis demonstrated that young oocytes have a distinct autofluorescent profile which accurately distinguishes them from aged oocytes. We recently showed that treatment with the nicotinamide adenine dinucleotide (NAD+) precursor nicotinamide mononucleotide (NMN) restored oocyte quality and fertility in aged animals, and when our analysis was applied to oocytes from aged animals treated with NMN, 85% of these oocytes were classified as having the autofluorescent signature of young animals. Spectral unmixing using the Robust Dependent Component Analysis (RoDECA) algorithm demonstrated that NMN treatment altered the metabolic profile of oocytes, increasing free NAD(P)H, protein bound NAD(P)H, redox ratio and the ratio of bound to free NAD(P)H. The frequency of oocytes with simultaneously high NAD(P)H and flavin content was also significantly increased in mice treated with NMN. Young and Aged + NMN oocytes had a smoother spectral distribution, with the distribution of NAD(P)H in young oocytes specifically differing from that of aged oocytes. Identifying the multispectral profile of oocyte autofluorescence during aging could have utility as a non-invasive and sensitive measure of oocyte quality

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 $N$ axions can still achieve a moderately superplanckian periodicity (by a $\sqrt{N}$ 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 $\mathbf{Z}_N$ 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 $h^0$ and $H^0$ 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 $r=0.08-0.12$, 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