3,347 research outputs found
Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis
Natronomonas pharaonis is an archaeon adapted to two extreme conditions: high salt concentration and alkaline pH. It has become one of the model organisms for the study of extremophilic life. Here, we present a genome-scale, manually curated metabolic reconstruction for the microorganism. The reconstruction itself represents a knowledge base of the haloalkaliphile's metabolism and, as such, would greatly assist further investigations on archaeal pathways. In addition, we experimentally determined several parameters relevant to growth, including a characterization of the biomass composition and a quantification of carbon and oxygen consumption. Using the metabolic reconstruction and the experimental data, we formulated a constraints-based model which we used to analyze the behavior of the archaeon when grown on a single carbon source. Results of the analysis include the finding that Natronomonas pharaonis, when grown aerobically on acetate, uses a carbon to oxygen consumption ratio that is theoretically near-optimal with respect to growth and energy production. This supports the hypothesis that, under simple conditions, the microorganism optimizes its metabolism with respect to the two objectives. We also found that the archaeon has a very low carbon efficiency of only about 35%. This inefficiency is probably due to a very low P/O ratio as well as to the other difficulties posed by its extreme environment
Machine-learning of atomic-scale properties based on physical principles
We briefly summarize the kernel regression approach, as used recently in
materials modelling, to fitting functions, particularly potential energy
surfaces, and highlight how the linear algebra framework can be used to both
predict and train from linear functionals of the potential energy, such as the
total energy and atomic forces. We then give a detailed account of the Smooth
Overlap of Atomic Positions (SOAP) representation and kernel, showing how it
arises from an abstract representation of smooth atomic densities, and how it
is related to several popular density-based representations of atomic
structure. We also discuss recent generalisations that allow fine control of
correlations between different atomic species, prediction and fitting of
tensorial properties, and also how to construct structural kernels---applicable
to comparing entire molecules or periodic systems---that go beyond an additive
combination of local environments
How Firms Adapt and Interact in Open Source Ecosystems: Analyzing Stakeholder Influence and Collaboration Patterns
[Context and motivation] Ecosystems developed as Open Source Software (OSS) are considered to be highly innovative and reactive to new market trends due to their openness and wide-ranging contributor base. Participation in OSS often implies opening up of the software development process and exposure towards new stakeholders. [Question/Problem] Firms considering to engage in such an environment should carefully consider potential opportunities and challenges upfront. The openness may lead to higher innovation potential but also to frictional losses for engaged firms. Further, as an ecosystem progresses, power structures and influence on feature selection may fluctuate accordingly. [Principal ideas/results] We analyze the Apache Hadoop ecosystem in a quantitative longitudinal case study to investigate changing stakeholder influence and collaboration patterns. Further, we investigate how its innovation and time-to-market evolve at the same time. [Contribution] Findings show collaborations between and influence shifting among rivaling and non-competing firms. Network analysis proves valuable on how an awareness of past, present and emerging stakeholders, in regards to power structure and collaborations may be created. Furthermore, the ecosystemβs innovation and time-to-market show strong variations among the release history. Indications were also found that these characteristics are influenced by the way how stakeholders collaborate with each other
Identification and characterization of a novel non-structural protein of bluetongue virus
Bluetongue virus (BTV) is the causative agent of a major disease of livestock (bluetongue). For over two decades, it has been widely accepted that the 10 segments of the dsRNA genome of BTV encode for 7 structural and 3 non-structural proteins. The non-structural proteins (NS1, NS2, NS3/NS3a) play different key roles during the viral replication cycle. In this study we show that BTV expresses a fourth non-structural protein (that we designated NS4) encoded by an open reading frame in segment 9 overlapping the open reading frame encoding VP6. NS4 is 77β79 amino acid residues in length and highly conserved among several BTV serotypes/strains. NS4 was expressed early post-infection and localized in the nucleoli of BTV infected cells. By reverse genetics, we showed that NS4 is dispensable for BTV replication in vitro, both in mammalian and insect cells, and does not affect viral virulence in murine models of bluetongue infection. Interestingly, NS4 conferred a replication advantage to BTV-8, but not to BTV-1, in cells in an interferon (IFN)-induced antiviral state. However, the BTV-1 NS4 conferred a replication advantage both to a BTV-8 reassortant containing the entire segment 9 of BTV-1 and to a BTV-8 mutant with the NS4 identical to the homologous BTV-1 protein. Collectively, this study suggests that NS4 plays an important role in virus-host interaction and is one of the mechanisms played, at least by BTV-8, to counteract the antiviral response of the host. In addition, the distinct nucleolar localization of NS4, being expressed by a virus that replicates exclusively in the cytoplasm, offers new avenues to investigate the multiple roles played by the nucleolus in the biology of the cell
Of cattle, sand flies and men : a systematic review of risk factor analyses for South Asian visceral leishmaniasis and implications for elimination
Background: Studies performed over the past decade have identified fairly consistent epidemiological patterns of risk
factors for visceral leishmaniasis (VL) in the Indian subcontinent.
Methods and Principal Findings: To inform the current regional VL elimination effort and identify key gaps in knowledge,
we performed a systematic review of the literature, with a special emphasis on data regarding the role of cattle because
primary risk factor studies have yielded apparently contradictory results. Because humans form the sole infection reservoir,
clustering of kala-azar cases is a prominent epidemiological feature, both at the household level and on a larger scale.
Subclinical infection also tends to show clustering around kala-azar cases. Within villages, areas become saturated over a
period of several years; kala-azar incidence then decreases while neighboring areas see increases. More recently, post kalaazar
dermal leishmaniasis (PKDL) cases have followed kala-azar peaks. Mud walls, palpable dampness in houses, and peridomestic
vegetation may increase infection risk through enhanced density and prolonged survival of the sand fly vector.
Bed net use, sleeping on a cot and indoor residual spraying are generally associated with decreased risk. Poor micronutrient
status increases the risk of progression to kala-azar. The presence of cattle is associated with increased risk in some studies
and decreased risk in others, reflecting the complexity of the effect of bovines on sand fly abundance, aggregation, feeding
behavior and leishmanial infection rates. Poverty is an overarching theme, interacting with individual risk factors on multiple
levels.
Conclusions: Carefully designed demonstration projects, taking into account the complex web of interconnected risk
factors, are needed to provide direct proof of principle for elimination and to identify the most effective maintenance
activities to prevent a rapid resurgence when interventions are scaled back. More effective, short-course treatment
regimens for PKDL are urgently needed to enable the elimination initiative to succeed
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