The Haemonchus contortus kinome - a resource for fundamental molecular investigations and drug discovery

Background: Protein kinases regulate a plethora of essential signalling and other biological pathways in all eukaryotic organisms, but very little is known about them in most parasitic nematodes. Methods: Here, we defined, for the first time, the entire complement of protein kinases (kinome) encoded in the barber’s pole worm (Haemonchus contortus) through an integrated analysis of transcriptomic and genomic datasets using an advanced bioinformatic workflow. Results: We identified, curated and classified 432 kinases representing ten groups, 103 distinct families and 98 subfamilies. A comparison of the kinomes of H. contortus and Caenorhabditis elegans (a related, free-living nematode) revealed considerable variation in the numbers of casein kinases, tyrosine kinases and Ca^(2+) /calmodulin-dependent protein kinases, which likely relate to differences in biology, habitat and life cycle between these worms. Moreover, a suite of kinase genes was selectively transcribed in particular developmental stages of H. contortus, indicating central roles in developmental and reproductive processes. In addition, using a ranking system, drug targets (n = 13) and associated small-molecule effectors (n = 1517) were inferred. Conclusions: The H. contortus kinome will provide a useful resource for fundamental investigations of kinases and signalling pathways in this nematode, and should assist future anthelmintic discovery efforts; this is particularly important, given current drug resistance problems in parasitic nematodes

Effects of overstory tree density, site preparation, and ground vegetation on natural Scots pine seedling emergence and survival in northern boreal pine forests

Natural regeneration is a commonly used forest regeneration method in northern Finland. It is not known, however, what would be the optimal overstory density and ground vegetation composition for seedling emergence and survival, and if site preparation is needed to accompany overstory density manipulation. We studied the effects of overstory density (unthinned control and thinning to 50,150, and 250 trees.ha(-1)) and ground vegetation removal (mechanical site preparation with disc trenching) on the number of naturally germinated pine seedlings and survival of individual seedlings over a period of 8 to 11 years. Bare mineral soil was a superior seedbed compared to intact vegetation cover, even though the mortality rate was high on mineral soil. Greater cover of lingonberry, crowberry, and slash had a negative effect on seedling number. Seedling mortality was initially high (60% died during the first 2 years) but decreased throughout the first 5 years. The survival rate of seedlings located in the mineral soil of the upper part of the disc trencher track was twice as high as that of seedlings located in the lower part of the track. High coverage of hair mosses (Polytrichum spp.) was associated with poorer seedling survival. An overstory density of 50-150 trees.ha(-1) with site preparation seems to be an efficient treatment to promote regeneration under these circumstances.Peer reviewe

Molecular Mechanisms of Membrane Deformation by I-BAR Domain Proteins

SummaryBackgroundGeneration of membrane curvature is critical for the formation of plasma membrane protrusions and invaginations and for shaping intracellular organelles. Among the central regulators of membrane dynamics are the BAR superfamily domains, which deform membranes into tubular structures. In contrast to the relatively well characterized BAR and F-BAR domains that promote the formation of plasma membrane invaginations, I-BAR domains induce plasma membrane protrusions through a poorly understood mechanism.ResultsWe show that I-BAR domains induce strong PI(4,5)P2 clustering upon membrane binding, bend the membrane through electrostatic interactions, and remain dynamically associated with the inner leaflet of membrane tubules. Thus, I-BAR domains induce the formation of dynamic membrane protrusions to the opposite direction than do BAR and F-BAR domains. Strikingly, comparison of different I-BAR domains revealed that they deform PI(4,5)P2-rich membranes through distinct mechanisms. IRSp53 and IRTKS I-BARs bind membranes mainly through electrostatic interactions, whereas MIM and ABBA I-BARs additionally insert an amphipathic helix into the membrane bilayer, resulting in larger tubule diameter in vitro and more efficient filopodia formation in vivo. Furthermore, FRAP analysis revealed that whereas the mammalian I-BAR domains display dynamic association with filopodia, the C. elegans I-BAR domain forms relatively stable structures inside the plasma membrane protrusions.ConclusionsThese data define I-BAR domain as a functional member of the BAR domain superfamily and unravel the mechanisms by which I-BAR domains deform membranes to induce filopodia in cells. Furthermore, our work reveals unexpected divergence in the mechanisms by which evolutionarily distinct groups of I-BAR domains interact with PI(4,5)P2-rich membranes

Analyses of Compact Trichinella Kinomes Reveal a MOS-like Protein Kinase with a Unique N-terminal Domain

Parasitic worms of the genus Trichinella (phylum Nematoda; class Enoplea) represent a complex of at least twelve taxa that infect a range of different host animals, including humans, around the world. They are foodborne, intracellular nematodes, and their life cycles differ substantially from those of other nematodes. The recent characterization of the genomes and transcriptomes of all twelve recognized taxa of Trichinella now allows, for the first time, detailed studies of their molecular biology. In the present study, we defined, curated, and compared the protein kinase complements (kinomes) of Trichinella spiralis and T. pseudospiralis using an integrated bioinformatic workflow employing transcriptomic and genomic data sets. We examined how variation in the kinome might link to unique aspects of Trichinella morphology, biology, and evolution. Furthermore, we utilized in silico structural modeling to discover and characterize a novel, MOS-like kinase with an unusual, previously undescribed N-terminal domain. Taken together, the present findings provide a basis for comparative investigations of nematode kinomes, and might facilitate the identification of Enoplea-specific intervention and diagnostic targets. Importantly, the in silico modeling approach assessed here provides an exciting prospect of being able to identify and classify currently unknown (orphan) kinases, as a foundation for their subsequent structural and functional investigation

Quantum-mechanical model of the Kerr-Newman black hole

We consider a Hamiltonian quantum theory of stationary spacetimes containing a Kerr-Newman black hole. The physical phase space of such spacetimes is just six-dimensional, and it is spanned by the mass $M$, the electric charge $Q$ and angular momentum $J$ of the hole, together with the corresponding canonical momenta. In this six-dimensional phase space we perform a canonical transformation such that the resulting configuration variables describe the dynamical properties of Kerr-Newman black holes in a natural manner. The classical Hamiltonian written in terms of these variables and their conjugate momenta is replaced by the corresponding self-adjoint Hamiltonian operator and an eigenvalue equation for the Arnowitt-Deser-Misner (ADM) mass of the hole, from the point of view of a distant observer at rest, is obtained. In a certain very restricted sense, this eigenvalue equation may be viewed as a sort of "Schr\"odinger equation of black holes". Our "Schr\"odinger equation" implies that the ADM mass, electric charge and angular momentum spectra of black holes are discrete, and the mass spectrum is bounded from below. Moreover, the spectrum of the quantity $M^2-Q^2-a^2$, where $a$ is the angular momentum per unit mass of the hole, is strictly positive when an appropriate self-adjoint extension is chosen. The WKB analysis yields the result that the large eigenvalues of $M$, $Q$ and $a$ are of the form $\sqrt{2n}$, where $n$ is an integer. It turns out that this result is closely related to Bekenstein's proposal on the discrete horizon area spectrum of black holes.Comment: 30 pages, 3 figures, RevTe

An EMG-Assisted Muscle-Force Driven Finite Element Analysis Pipeline to Investigate Joint- and Tissue-Level Mechanical Responses in Functional Activities : Towards a Rapid Assessment Toolbox

Publisher Copyright: © 1964-2012 IEEE.Joint tissue mechanics (e.g., stress and strain) are believed to have a major involvement in the onset and progression of musculoskeletal disorders, e.g., knee osteoarthritis (KOA). Accordingly, considerable efforts have been made to develop musculoskeletal finite element (MS-FE) models to estimate highly detailed tissue mechanics that predict cartilage degeneration. However, creating such models is time-consuming and requires advanced expertise. This limits these complex, yet promising, MS-FE models to research applications with few participants and makes the models impractical for clinical assessments. Also, these previously developed MS-FE models have not been used to assess activities other than gait. This study introduces and verifies a semi-automated rapid state-of-the-art MS-FE modeling and simulation toolbox incorporating an electromyography- (EMG) assisted MS model and a muscle-force driven FE model of the knee with fibril-reinforced poro(visco)elastic cartilages and menisci. To showcase the usability of the pipeline, we estimated joint- and tissue-level knee mechanics in 15 KOA individuals performing different daily activities. The pipeline was verified by comparing the estimated muscle activations and joint mechanics to existing experimental data. To determine the importance of the EMG-assisted MS analysis approach, results were compared to those from the same FE models but driven by static-optimization-based MS models. The EMG-assisted MS-FE pipeline bore a closer resemblance to experiments compared to the static-optimization-based MS-FE pipeline. Importantly, the developed pipeline showed great potential as a rapid MS-FE analysis toolbox to investigate multiscale knee mechanics during different activities of individuals with KOA.Peer reviewe

Optical counterpart of HLX-1 during the 2010 outburst

We studied the optical counterpart of the intermediate-mass black hole candidate HLX-1 in ESO 243-49. We used a set of Very Large Telescope imaging observations from 2010 November, integrated by Swift X-ray data from the same epoch. We measured standard Vega brightnesses U = 23.89 +/- 0.18 mag, B = 25.19 +/- 0.30 mag, V = 24.79 +/- 0.34 mag and R = 24.71 +/- 0.40 mag. Therefore, the source was ~1 mag fainter in each band than in a set of Hubble Space Telescope images taken a couple of months earlier, when the X-ray flux was a factor of 2 higher. We conclude that during the 2010 September observations, the optical counterpart was dominated by emission from an irradiated disk (which responds to the varying X-ray luminosity), rather than by a star cluster around the black hole (which would not change). We modelled the Comptonized, irradiated X-ray spectrum of the disk, and found that the optical luminosity and colours in the 2010 November data are still consistent with emission from the irradiated disk, with a characteristic outer radius r_{out} ~ 2800 r_{in} ~ 10^{13} cm and a reprocessing fraction ~ 2 x 10^{-3}. The optical colours are also consistent with a stellar population with age <~ 6 Myr (at solar metallicity) and mass ~ 10^4 M_{sun}; this is only an upper limit to the mass, if there is also a significant contribution from an irradiated disk. We strongly rule out the presence of a young super-star-cluster, which would be too bright. An old globular cluster might be associated with HLX-1, as long as its mass <~ 2 x 10^6 M_{sun} for an age of 10 Gyr, but it cannot significantly contribute to the observed very blue and variable optical/UV emission.Comment: Accepted by MNRAS on Nov 28; 11 pages, 1.3 MB. v2: same paper, same price, now 20% more authors

A Quantum Mechanical Model of the Reissner-Nordstrom Black Hole

We consider a Hamiltonian quantum theory of spherically symmetric, asymptotically flat electrovacuum spacetimes. The physical phase space of such spacetimes is spanned by the mass and the charge parameters $M$ and $Q$ of the Reissner-Nordstr\"{o}m black hole, together with the corresponding canonical momenta. In this four-dimensional phase space, we perform a canonical transformation such that the resulting configuration variables describe the dynamical properties of Reissner-Nordstr\"{o}m black holes in a natural manner. The classical Hamiltonian written in terms of these variables and their conjugate momenta is replaced by the corresponding self-adjoint Hamiltonian operator, and an eigenvalue equation for the ADM mass of the hole, from the point of view of a distant observer at rest, is obtained. Our eigenvalue equation implies that the ADM mass and the electric charge spectra of the hole are discrete, and the mass spectrum is bounded below. Moreover, the spectrum of the quantity $M^2-Q^2$ is strictly positive when an appropriate self-adjoint extension is chosen. The WKB analysis yields the result that the large eigenvalues of the quantity $\sqrt{M^2-Q^2}$ are of the form $\sqrt{2n}$, where $n$ is an integer. It turns out that this result is closely related to Bekenstein's proposal on the discrete horizon area spectrum of black holes.Comment: 37 pages, Plain TeX, no figure

Integrating farm and air pollution studies in search for immunoregulatory mechanisms operating in protective and high-risk environments

Background Studies conducted in farm environments suggest that diverse microbial exposure promotes children's lung health. The underlying mechanisms are unclear, and the development of asthma-preventive strategies has been delayed. More comprehensive investigation of the environment-induced immunoregulation is required for better understanding of asthma pathogenesis and prevention. Exposure to air pollution, including particulate matter (PM), is a risk factor for asthma, thus providing an excellent counterpoint for the farm-effect research. Lack of comparable data, however, complicates interpretation of the existing information. We aimed to explore the immunoregulatory effects of cattle farm dust (protective, Finland) and urban air PM (high-risk, China) for the first time using identical research methods. Methods We stimulated PBMCs of 4-year-old children (N = 18) with farm dust and size-segregated PM and assessed the expression of immune receptors CD80 and ILT4 on dendritic cells and monocytes as well as cytokine production of PBMCs. Environmental samples were analysed for their composition. Results Farm dust increased the percentage of cells expressing CD80 and the cytokine production of children's immune cells, whereas PM inhibited the expression of important receptors and the production of soluble mediators. Although PM samples induced parallel immune reactions, the size-fraction determined the strength of the effects. Conclusions Our study demonstrates the significance of using the same research framework when disentangling shared and distinctive immune pathways operating in different environments. Observed stimulatory effects of farm dust and inhibitory effects of PM could shape responses towards respiratory pathogens and allergens, and partly explain differences in asthma prevalence between studied environments.Peer reviewe

Particlization in hybrid models

In hybrid models, which combine hydrodynamical and transport approaches to describe different stages of heavy-ion collisions, conversion of fluid to individual particles, particlization, is a non-trivial technical problem. We describe in detail how to find the particlization hypersurface in a 3+1 dimensional model, and how to sample the particle distributions evaluated using the Cooper-Frye procedure to create an ensemble of particles as an initial state for the transport stage. We also discuss the role and magnitude of the negative contributions in the Cooper-Frye procedure.Comment: 18 pages, 28 figures, EPJA: Topical issue on "Relativistic Hydro- and Thermodynamics"; version accepted for publication, typos and error in Eq.(1) corrected, the purpose of sampling and change from UrQMD to fluid clarified, added discussion why attempts to cancel negative contributions of Cooper-Frye are not applicable her