Pherotype polymorphism in Streptococcus pneumoniae has no obvious effects on population structure and recombination

Natural transformation in the Gram-positive pathogen Streptococcus pneumoniae occurs when cells become “competent”, a state that is induced in response to high extracellular concentrations of a secreted peptide signal called CSP (Competence Stimulating Peptide) encoded by the comC locus. Two main CSP signal types (pherotypes) are known to dominate the pherotype diversity across strains. Using 4,089 fully sequenced pneumococcal genomes, we confirm that pneumococcal populations are highly genetically structured and that there is significant variation among diverged populations in pherotype frequencies; most carry only a single pherotype. Moreover, we find that the relative frequencies of the two dominant pherotypes significantly vary within a small range across geographical sites. It has been variously proposed that pherotypes either promote genetic exchange among cells expressing the same pherotype, or conversely that they promote recombination between strains bearing different pherotypes. We attempt to distinguish these hypotheses using a bioinformatics approach by estimating recombination frequencies within and between pherotypes across 4,089 full genomes. Despite underlying population structure, we observe extensive recombination between populations; additionally, we found significantly higher (although marginal) rates of genetic exchange between strains expressing different pherotypes than among isolates carrying the same pherotype. Our results indicate that pherotypes do not restrict, and may even slightly facilitate, recombination between strains; however, these marginal effects suggest the more likely possibility that the cause of CSP polymorphism lies outside of its effects on transformation. Our results suggest that the CSP balanced polymorphism does not causally underlie population differentiation. Therefore, when strains carrying different pherotypes encounter one another during co-colonization, genetic exchange can occur without restriction

Physical geomorphometry for elementary land surface segmentation and digital geomorphological mapping

By interpretations related to energy, elementary land surface segmentation can be treated as a physical problem. Many pieces of such a view found in the literature can be combined into a synthetic comprehensive physical approach. The segmentation has to be preceded by defining the character and size of searched units to result from the segmentation. A high-resolution digital elevation model (DEM) is the key input for this task; it should be generalized to the resolution best expressing information about the searched units. Elementary land surface units can be characterized by various parts of potential gravitational energy associated with a set of basic geomorphometric variables. Elevation above sea level (z) represents Global Geomorphic Energy (GGE). Regional and Local Geomorphic Energy (RGE and LGE) are parts of GGE, represented respectively by relative elevation above the local base level (zrel) and local relief (elevation differential in a moving window Δz). Derivation (change) of elevation defines the slope inclination (S), determining the local Potential Energy of Surface (PES) applicable to mass flow. Normal slope line (profile) curvature (kn)s and normal contour (tangential) curvature (kn)c express change in the PES value (ΔPES(kn )s, ΔPES(kn )c), responsible for acceleration/deceleration and convergence/ divergence of flow. Mean curvature (kmean) determines the Potential Energy of Surface applicable to Diffusion (PESD). Energetic interpretation of basic geomorphometric variables enables their direct comparison and systematic evaluation. Consequently, the homogeneity of basic geomorphometric variables defines a hierarchy of states of local geomorphic equilibria: static equilibrium, steady state, and non-steady state dynamic equilibrium. They are local attractors of landform development reflected in the geomorphometric tendency to symmetry (horizontality, various types of linearity, and curvature isotropy, together expressed by gravity concordance). Nonequilibrium and transitional states can be characterized by the PES excess (PESe) determined by difference curvature (kd), by gravity discordant change of the PES characterized by twisting curvature (τg)c, and by Integral Potential Energy of Surface Curvature (IPESC) expressed by Casorati curvature (kC) (general curvedness). Excluding zrel and Δz, all these energy-related geomorphometric variables are local point-based. Local area-based and regional variables such as Glock’s Available Relief, Melton Ruggedness Number, Stream Power Index, Openness, Topographic Position Index, Topographic Wetness Index, and Index of Connectivity also have energetic interpretations although their definition is more complex. Therefore we suggest exclusive use of the local point-based variables in designs of elementary land surface segmentation. The segmentation should take notice of natural interconnections, the hierarchy of geomorphometric variables, elements of Local Geomorphic Energy, and (dis)equilibria states, so that elementary segments are clearly interpretable geomorphologically. This is exemplified by Geographic Object-Based Image Analysis (GEOBIA) segmentation of Sandberg, a territory on the boundary of the Carpathians and Vienna Basin with a complex geomorphic history and marked morphodynamics. Compared with expert-driven field geomorphological mapping, the automatic physically-based segmentation resulted in a more specific delineation and composition of landforms. Physical-geomorphometric characteristics of the elementary forms enabled the formulation of their system and subsequent improvement of the expert-based qualitative genetic analysis, with interpretation leading to a deeper understanding of the development and recent dynamics of the landscape

Pherotype Polymorphism in Streptococcus pneumoniae Has No Obvious Effects on Population Structure and Recombination.

Natural transformation in the Gram-positive pathogen Streptococcus pneumoniae occurs when cells become "competent," a state that is induced in response to high extracellular concentrations of a secreted peptide signal called competence stimulating peptide (CSP) encoded by the comC locus. Two main CSP signal types (pherotypes) are known to dominate the pherotype diversity across strains. Using 4,089 fully sequenced pneumococcal genomes, we confirm that pneumococcal populations are highly genetically structured and that there is significant variation among diverged populations in pherotype frequencies; most carry only a single pherotype. Moreover, we find that the relative frequencies of the two dominant pherotypes significantly vary within a small range across geographical sites. It has been variously proposed that pherotypes either promote genetic exchange among cells expressing the same pherotype, or conversely that they promote recombination between strains bearing different pherotypes. We attempt to distinguish these hypotheses using a bioinformatics approach by estimating recombination frequencies within and between pherotypes across 4,089 full genomes. Despite underlying population structure, we observe extensive recombination between populations; additionally, we found significantly higher (although marginal) rates of genetic exchange between strains expressing different pherotypes than among isolates carrying the same pherotype. Our results indicate that pherotypes do not restrict, and may even slightly facilitate, recombination between strains; however, these marginal effects suggest the more likely possibility that the cause of CSP polymorphism lies outside of its effects on transformation. Our results suggest that the CSP balanced polymorphism does not causally underlie population differentiation. Therefore, when strains carrying different pherotypes encounter one another during cocolonization, genetic exchange can occur without restriction

The Polar Bear Management Agreement for the Southern Beaufort Sea : An Evaluation of the First Ten Years of a Unique Conservation Agreement

Polar bears (Ursus maritimus) of the southern Beaufort Sea population, distributed from approximately Icy Cape, west of Point Barrow, Alaska, to Pearce Point, east of Paulatuk in Canada, are harvested by hunters from both countries. In Canada, quotas to control polar bear hunting have been in place, with periodic modifications, since 1968. In Alaska, passage of the United Sates Marine Mammal Protection Act (MMPA) of 1972 banned polar bear hunting unless done by Alaska Natives for subsistence hunt, leaving open the potential for an overharvest with no possible legal management response until the population was declared depleted. Recognizing that as a threat to the conservation of the shared polar bear population, the Inuvialuit Game Council from Canada and the North Slope Borough from Alaska negotiated and signed a user-to-user agreement, the Polar Bear Management Agreement for the Southern Beaufort Sea, in 1988. We reviewed the functioning of the agreement through its first 10 years and concluded that, overall, it has been successful because both the total harvest and the proportion of females in the harvest have been contained within sustainable limits. However, harvest monitoring needs to be improved in Alaska, and awareness of the need to prevent overharvest of females needs to be increased in both countries. This agreement is a useful model for other user-to-user conservation agreements.Les ours polaires (Ursus maritimus) constituant la population de la mer de Beaufort méridionale sont répartis d'environ Icy Cape, à l'ouest de Point Barrow (Alaska), à Pearce Point, à l'est de Paulatuk (Canada). Ils sont prélevés par des chasseurs des deux pays. Au Canada, les quotas visant le contrôle de la chasse à l'ours polaire sont en vigueur - avec des modifications périodiques - depuis 1968. En Alaska, l'adoption en 1972 de la loi américaine (MMPA) visant la protection des mammifères marins a interdit la chasse à l'ours polaire sauf la chasse de subsistance pratiquée par les Autochtones alaskiens. La MMPA n'a toutefois placé aucune restriction sur le nombre ou la composition de la chasse de subsistance, laissant la porte ouverte à une éventuelle surexploitation sans possibilité d'une réaction de gestion sur le plan légal jusqu'à ce que la population soit déclarée décimée. Reconnaissant en cela une menace à la conservation de la population commune d'ours polaires, le Conseil canadien de gestion du gibier et le North Slope Borough de l'Alaska ont négocié et signé en 1988 une entente entre usagers, le Polar Bear Management Agreement pour la mer de Beaufort méridionale. On a examiné le fonctionnement de l'entente durant sa première décennie pour conclure que, dans l'ensemble, elle a porté fruit car le total des prises et la proportion de femelles prélevées ont été maintenus dans des limites viables. Il faut toutefois améliorer le contrôle du prélèvement en Alaska et accroître dans les deux pays la sensibilisation à la nécessité de prévenir une surexploitation des femelles. Cette entente constitue un modèle pour d'autres accords entre usagers en matière de conservation

Investigating the medium range order in amorphous Ta₂O₅ coatings

Ion-beam sputtered amorphous heavy metal oxides, such as Ta2O5, are widely used as the high refractive index layer of highly reflective dielectric coatings. Such coatings are used in the ground based Laser Interferometer Gravitational-wave Observatory (LIGO), in which mechanical loss, directly related to Brownian thermal noise, from the coatings forms an important limit to the sensitivity of the LIGO detector. It has previously been shown that heat-treatment and TiO2 doping of amorphous Ta2O5 coatings causes significant changes to the levels of mechanical loss measured and is thought to result from changes in the atomic structure. This work aims to find ways to reduce the levels of mechanical loss in the coatings by understanding the atomic structure properties that are responsible for it, and thus helping to increase the LIGO detector sensitivity. Using a combination of Reduced Density Functions (RDFs) from electron diffraction and Fluctuation Electron Microscopy (FEM), we probe the medium range order (in the 2-3 nm range) of these amorphous coatings

Shell Neurons of the Master Circadian Clock Coordinate the Phase of Tissue Clocks Throughout the Brain and Body

Background: Daily rhythms in mammals are programmed by a master clock in the suprachiasmatic nucleus (SCN). The SCN contains two main compartments (shell and core), but the role of each region in system-level coordination remains ill defined. Herein, we use a functional assay to investigate how downstream tissues interpret region-specific outputs by using in vivo exposure to long day photoperiods to temporally dissociate the SCN. We then analyze resulting changes in the rhythms of clocks located throughout the brain and body to examine whether they maintain phase synchrony with the SCN shell or core. Results: Nearly all of the 17 tissues examined in the brain and body maintain phase synchrony with the SCN shell, but not the SCN core, which indicates that downstream oscillators are set by cues controlled specifically by the SCN shell. Interestingly, we also found that SCN dissociation diminished the amplitude of rhythms in core clock gene and protein expression in brain tissues by 50–75 %, which suggests that light-driven changes in the functional organization of the SCN markedly influence the strength of rhythms in downstream tissues. Conclusions: Overall, our results reveal that body clocks receive time-of-day cues specifically from the SCN shell, which may be an adaptive design principle that serves to maintain system-level phase relationships in a changing environment. Further, we demonstrate that lighting conditions alter the amplitude of the molecular clock in downstream tissues, which uncovers a new form of plasticity that may contribute to seasonal changes in physiology and behavior

The Very Low Albedo of WASP-12b From Spectral Eclipse Observations with Hubble\textit{Hubble}

We present an optical eclipse observation of the hot Jupiter WASP-12b using the Space Telescope Imaging Spectrograph on board the Hubble Space Telescope. These spectra allow us to place an upper limit of $A_g < 0.064$ (97.5% confidence level) on the planet's white light geometric albedo across 290--570 nm. Using six wavelength bins across the same wavelength range also produces stringent limits on the geometric albedo for all bins. However, our uncertainties in eclipse depth are $\sim$40% greater than the Poisson limit and may be limited by the intrinsic variability of the Sun-like host star --- the solar luminosity is known to vary at the $10^{-4}$ level on a timescale of minutes. We use our eclipse depth limits to test two previously suggested atmospheric models for this planet: Mie scattering from an aluminum-oxide haze or cloud-free Rayleigh scattering. Our stringent nondetection rules out both models and is consistent with thermal emission plus weak Rayleigh scattering from atomic hydrogen and helium. Our results are in stark contrast with those for the much cooler HD 189733b, the only other hot Jupiter with spectrally resolved reflected light observations; those data showed an increase in albedo with decreasing wavelength. The fact that the first two exoplanets with optical albedo spectra exhibit significant differences demonstrates the importance of spectrally resolved reflected light observations and highlights the great diversity among hot Jupiters.Comment: 8 pages, 4 figures, 1 table, published in ApJL, in pres

Evaluation of the risk of cardiovascular events with clarithromycin using both propensity score and self-controlled study designs

Aim: Some previous studies suggest a long term association between clarithromycin use and cardiovascular events. This study investigates this association for clarithromycin given as part of Helicobacter pylori treatment (HPT). Methods: Our source population was the Clinical Practice Research Datalink (CPRD), a UK primary care database. We conducted a self-controlled case series (SCCS), a case–time–control study (CTC) and a propensity score adjusted cohort study comparing the rate of cardiovascular events in the 3 years after exposure to HPT containing clarithromycin with exposure to clarithromycin free HPT. Outcomes were first incident diagnosis of myocardial infarction (MI), arrhythmia and stroke. For the cohort analysis we included secondary outcomes all cause and cardiovascular mortality. Results: Twenty-eight thousand five hundred and fifty-two patients were included in the cohort. The incidence rate ratio of first MI within 1 year of exposure to HPT containing clarithromycin was 1.07 (95% CI 0.85, 1.34, P = 0.58) and within 90 days was 1.43 (95% CI 0.99, 2.09 P = 0.057) in the SCCS analysis. CTC and cohort results were consistent with these findings. Conclusions There was some evidence for a short term association for first MI but none for a long term association for any outcome

Incidence of adult Huntington's disease in the UK: a UK-based primary care study and a systematic review.

OBJECTIVES: The prevalence of Huntington's disease (HD) recorded in the UK primary care records has increased twofold between 1990 and 2010. This investigation was undertaken to assess whether this might be due to an increased incidence. We have also undertaken a systematic review of published estimates of the incidence of HD. SETTING: Incident patients with a new diagnosis of HD were identified from the primary care records of the Clinical Practice Research Datalink (CPRD). The systematic review included all published estimates of the incidence of HD in defined populations. PARTICIPANTS: A total of 393 incident cases of HD were identified from the CPRD database between 1990 and 2010 from a total population of 9,282,126 persons. PRIMARY AND SECONDARY OUTCOME MEASURES: The incidence of HD per million person-years was estimated. From the systematic review, the extent of heterogeneity of published estimates of the incidence of HD was examined using the I(2) statistic. RESULTS: The data showed that the incidence of HD has remained constant between 1990 and 2010 with an overall rate of 7.2 (95% CI 6.5 to 7.9) per million person-years. The systematic review identified 14 independent estimates of incidence with substantial heterogeneity and consistently lower rates reported in studies from East Asia compared with those from Australia, North America and some--though not all--those from Europe. Differences in incidence estimates did not appear to be explained solely by differences in case ascertainment or diagnostic methods. CONCLUSIONS: The rise in the prevalence of diagnosed HD in the UK, between 1990 and 2010, cannot be attributed to an increase in incidence. Globally, estimates of the incidence of HD show evidence of substantial heterogeneity with consistently lower rates in East Asia and parts of Europe. Modifiers may play an important role in determining the vulnerability of different populations to expansions of the HD allele

Ice sheet record of recent sea-ice behavior and polynya variability in the Amundsen Sea, West Antarctica

Author Posting. © American Geophysical Union, 2013. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 118 (2013): 118–130, doi:10.1029/2012JC008077.Our understanding of past sea-ice variability is limited by the short length of satellite and instrumental records. Proxy records can extend these observations but require further development and validation. We compare methanesulfonic acid (MSA) and chloride (Cl–) concentrations from a new firn core from coastal West Antarctica with satellite-derived observations of regional sea-ice concentration (SIC) in the Amundsen Sea (AS) to evaluate spatial and temporal correlations from 2002–2010. The high accumulation rate (~39 g∙cm–2∙yr–1) provides monthly resolved records of MSA and Cl–, allowing detailed investigation of how regional SIC is recorded in the ice-sheet stratigraphy. Over the period 2002–2010 we find that the ice-sheet chemistry is significantly correlated with SIC variability within the AS and Pine Island Bay polynyas. Based on this result, we evaluate the use of ice-core chemistry as a proxy for interannual polynya variability in this region, one of the largest and most persistent polynya areas in Antarctica. MSA concentrations correlate strongly with summer SIC within the polynya regions, consistent with MSA at this site being derived from marine biological productivity during the spring and summer. Cl– concentrations correlate strongly with winter SIC within the polynyas as well as some regions outside the polynyas, consistent with Cl– at this site originating primarily from winter sea-ice formation. Spatial correlations were generally insignificant outside of the polynya areas, with some notable exceptions. Ice-core glaciochemical records from this dynamic region thus may provide a proxy for reconstructing AS and Pine Island Bay polynya variability prior to the satellite era.This research was supported by an award from the Department of Energy Office of Science Graduate Fellowship Program (DOE SCGF) to ASC, a James E. and Barbara V. Moltz Research Fellowship to SBD, and by grants from NSF-OPP (#ANT-0632031 & #ANT-0631973); NSF-MRI (#EAR-1126217); NASA Cryosphere Program (#NNX10AP09G); and a WHOI Andrew W. Mellon Foundation Award for Innovative Research.2013-07-2