191 research outputs found
Depletion of Mediator Kinase Module Subunits Represses Superenhancer-Associated Genes in Colon Cancer Cells
In cancer, oncogene activation is partly mediated by acquired superenhancers, which therefore represent potential targets for inhibition. Superenhancers are enriched for BRD4 and Mediator, and both BRD4 and the Mediator MED12 subunit are disproportionally required for expression of superenhancer-associated genes in stem cells. Here we show that depletion of Mediator kinase module subunit MED12 or MED13 together with MED13L can be used to reduce expression of cancer-acquired superenhancer genes, such as the MYC gene, in colon cancer cells, with a concomitant decrease in proliferation. Whereas depletion of MED12 or MED13/MED13L caused a disproportional decrease of superenhancer gene expression, this was not seen with depletion of the kinases cyclin-dependent kinase 9 (CDK8) and CDK19. MED12-MED13/MED13L-dependent superenhancer genes were coregulated by beta-catenin, which has previously been shown to associate with MED12. Importantly, beta-catenin depletion caused reduced binding of MED12 at the MYC superenhancer. The effect of MED12 or MED13/MED13L depletion on cancer-acquired superenhancer gene expression was more specific than and partially distinct from that of BRD4 depletion, with the most efficient inhibition seen with combined targeting. These results identify a requirement of MED12 and MED13/MED13L for expression of acquired superenhancer genes in colon cancer, implicating these Mediator subunits as potential therapeutic targets for colon cancer, alone or together with BRD4.Peer reviewe
Investigating the chemical species in submicron particles emitted by city buses
Detailed chemical characterization of exhaust particles from 23 individual city buses was performed in Helsinki, Finland. Investigated buses represented different technologies in terms of engines, exhaust after-treatment systems (e.g., diesel particulate filter, selective catalytic reduction, and three-way catalyst) and fuels (diesel, diesel-electric (hybrid), ethanol, and compressed natural gas). Regarding emission standards, the buses operated at EURO III, EURO IV, and EEV (enhanced environmentally friendly vehicle) emission levels. The chemical composition of exhaust particles was determined by using a soot particle aerosol mass spectrometer (SP-AMS). Based on the SP-AMS results, the bus emission particles were dominated by organics and refractory black carbon (rBC). The mass spectra of organics consisted mostly of hydrocarbon fragments (54-86% of total organics), the pattern of hydrocarbon fragments being rather similar regardless of the bus type. Regarding oxygenated organic fragments, ethanol-fueled buses had unique mass-to-charge ratios (m/z) of 45, 73, 87, and 89 (mass fragments of C2H5OC, C3H5O2+, C4H7O2+, and C4H9O2+, respectively) that were not detected for the other bus types at the same level. For rBC, there was a small difference in the ratio of C-4(+) and C-5(+) to C-3(+) for different bus types but also for the individual buses of the same type. In addition to organics and rBC, the presence of trace metals in the bus emission particles was investigated.Peer reviewe
Can forest management based on natural disturbances maintain ecological resilience?
Given the increasingly global stresses on forests, many ecologists argue that managers must maintain ecological resilience: the capacity of ecosystems to absorb disturbances without undergoing fundamental change. In this review we ask: Can the emerging paradigm of natural-disturbance-based management (NDBM) maintain ecological resilience in managed forests? Applying resilience theory requires careful articulation of the ecosystem state under consideration, the disturbances and stresses that affect the persistence of possible alternative states, and the spatial and temporal scales of management relevance. Implementing NDBM while maintaining resilience means recognizing that (i) biodiversity is important for long-term ecosystem persistence, (ii) natural disturbances play a critical role as a generator of structural and compositional heterogeneity at multiple scales, and (iii) traditional management tends to produce forests more homogeneous than those disturbed naturally and increases the likelihood of unexpected catastrophic change by constraining variation of key environmental processes. NDBM may maintain resilience if silvicultural strategies retain the structures and processes that perpetuate desired states while reducing those that enhance resilience of undesirable states. Such strategies require an understanding of harvesting impacts on slow ecosystem processes, such as seed-bank or nutrient dynamics, which in the long term can lead to ecological surprises by altering the forest's capacity to reorganize after disturbance
Bounce behavior of freshly nucleated biogenic secondary organic aerosol particles
The assessment of the climatic impacts and adverse health effects of atmospheric aerosol particles requires detailed information on particle properties. However, very limited information is available on the morphology and phase state of secondary organic aerosol (SOA) particles. The physical state of particles greatly affects particulate-phase chemical reactions, and thus the growth rates of newly formed atmospheric aerosol. Thus verifying the physical phase state of SOA particles gives new and important insight into their formation, subsequent growth, and consequently potential atmospheric impacts. According to our recent study, biogenic SOA particles produced in laboratory chambers from the oxidation of real plant emissions as well as in ambient boreal forest atmospheres can exist in a solid phase in size range >30 nm. In this paper, we extend previously published results to diameters in the range of 17–30 nm. The physical phase of the particles is studied by investigating particle bounce properties utilizing electrical low pressure impactor (ELPI). We also investigate the effect of estimates of particle density on the interpretation of our bounce observations. According to the results presented in this paper, particle bounce clearly decreases with decreasing particle size in sub 30 nm size range. The comparison measurements by ammonium sulphate and investigation of the particle impaction velocities strongly suggest that the decreasing bounce is caused by the differences in composition and phase of large (diameters greater than 30 nm) and smaller (diameters between 17 and 30 nm) particles
A silviculture-oriented spatio-temporal model for germination in Pinus pinea L. in the Spanish Northern Plateau based on a direct seeding experiment
Natural regeneration in Pinus pinea stands
commonly fails throughout the Spanish Northern Plateau
under current intensive regeneration treatments. As a
result, extensive direct seeding is commonly conducted to
guarantee regeneration occurrence. In a period of rationalization
of the resources devoted to forest management,
this kind of techniques may become unaffordable. Given
that the climatic and stand factors driving germination
remain unknown, tools are required to understand the
process and temper the use of direct seeding. In this study,
the spatio-temporal pattern of germination of P. pinea was
modelled with those purposes. The resulting findings will
allow us to (1) determine the main ecological variables
involved in germination in the species and (2) infer adequate
silvicultural alternatives. The modelling approach
focuses on covariates which are readily available to forest
managers. A two-step nonlinear mixed model was fitted to
predict germination occurrence and abundance in P. pinea
under varying climatic, environmental and stand conditions,
based on a germination data set covering a 5-year
period. The results obtained reveal that the process is primarily
driven by climate variables. Favourable conditions
for germination commonly occur in fall although the
optimum window is often narrow and may not occur at all
in some years. At spatial level, it would appear that germination
is facilitated by high stand densities, suggesting
that current felling intensity should be reduced. In accordance
with other studies on P. pinea dispersal, it seems that
denser stands during the regeneration period will reduce
the present dependence on direct seeding
Habitat effects on the breeding performance of three forest-dwelling hawks
PLoS ONE 10(9): e0137877Habitat loss causes population declines, but the mechanisms are rarely known. In the European Boreal Zone, loss of old forest due to intensive forestry is suspected to cause declines in forest-dwelling raptors by reducing their breeding performance. We studied the boreal breeding habitat and habitat-associated breeding performance of the northern goshawk (Accipiter gentilis), common buzzard (Buteo buteo) and European honey buzzard (Pernis apivorus). We combined long-term Finnish bird-of-prey data with multi-source national forest inventory data at various distances (100–4000 m) around the hawk nests. We found that breeding success of the goshawk was best explained by the habitat within a 2000-m radius around the nests; breeding was more successful with increasing proportions of old spruce forest and water, and decreasing proportions of young thinning forest. None of the habitat variables affected significantly the breeding success of the common buzzard or the honey buzzard, or the brood size of any of the species. The amount of old spruce forest decreased both around goshawk and common buzzard nests and throughout southern Finland in 1992–2010. In contrast, the area of young forest increased in southern Finland but not around hawk nests. We emphasize the importance of studying habitats at several spatial and temporal scales to determine the relevant species-specific scale and to detect environmental changes. Further effort is needed to reconcile the socioeconomic and ecological functions of forests and habitat requirements of old forest specialists.Peer reviewe
The value of plantation forests for plant, invertebrate and bird diversity and the potential for cross-taxon surrogacy
As the area of plantation forest expands worldwide and natural, unmanaged forests decline there is much interest in the potential for planted forests to provide habitat for biodiversity. In regions where little semi-natural woodland remains, the biodiversity supported by forest plantations, typically non-native conifers, may be particularly important. Few studies provide detailed comparisons between the species diversity of native woodlands which are being depleted and non-native plantation forests, which are now expanding, based on data collected from multiple taxa in the same study sites. Here we compare the species diversity and community composition of plants, invertebrates and birds in Sitka spruce- (Picea sitchensis-) dominated and Norway spruce- (Picea abies-) dominated plantations, which have expanded significantly in recent decades in the study area in Ireland, with that of oak- and ash-dominated semi-natural woodlands in the same area. The results show that species richness in spruce plantations can be as high as semi-natural woodlands, but that the two forest types support different assemblages of species. In areas where non-native conifer plantations are the principle forest type, their role in the provision of habitat for biodiversity conservation should not be overlooked. Appropriate management should target the introduction of semi-natural woodland characteristics, and on the extension of existing semi-natural woodlands to maintain and enhance forest species diversity. Our data show that although some relatively easily surveyed groups, such as vascular plants and birds, were congruent with many of the other taxa when looking across all study sites, the similarities in response were not strong enough to warrant use of these taxa as surrogates of the others. In order to capture a wide range of biotic variation, assessments of forest biodiversity should either encompass several taxonomic groups, or rely on the use of indicators of diversity that are not species based
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