Methylation of histone H3 K79 by Dot1L is a hallmark of actively transcribed genes that depends on monoubiquitination of H2B K120 (H2B-Ub) and is an example of histone modification cross-talk that is ...conserved from yeast to humans. We report here cryo-EM structures of Dot1L bound to ubiquitinated nucleosome that show how H2B-Ub stimulates Dot1L activity and reveal a role for the histone H4 tail in positioning Dot1L. We find that contacts mediated by Dot1L and the H4 tail induce a conformational change in the globular core of histone H3 that reorients K79 from an inaccessible position, thus enabling this side chain to insert into the active site in a position primed for catalysis. Our study provides a comprehensive mechanism of cross-talk between histone ubiquitination and methylation and reveals structural plasticity in histones that makes it possible for histone-modifying enzymes to access residues within the nucleosome core.
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•Cryo-EM structures of Dot1L methyltransferase bound to H2B-ubiquitinated nucleosomes•Dot1L bound in poised and active states contacts the ubiquitin I36 hydrophobic patch•The tail of histone H4 binds in a cleft in Dot1L.•A conformational change is induced in histone H3 that enables Dot1L to access H3K79
Unanticipated conformational plasticity in the globular core of histone H3 underlies cross-talk between histone modifications.
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is now widely used for marker/multibiomarker detection in medical diagnosis. We tested a new protocol for ...bacterial identification from blood culture broths in hospital routine by using collection tubes with separator gels on 503 included samples examined over 3 months, where 1.5 mL was injected by a syringe into BD Vacutainer tubes from BACTEC-positive bottles, before processing for bacterial protein extraction. Samples were loaded in duplicate onto the MALDI MS target, allowing a series of 12 samples to be processed in duplicate within 80 min by using Biflex III and BioTyper 2.0 software (Bruker). Including polymicrobial samples, 193 of 213 of Gram-negative bacteria (91.08%) and 284 of 319 of Gram-positive bacteria (89.02%) were correctly identified at the species level. Enterobacteriaceae constituted 35.15% of all species found, Staphylococaceae 37.96%, Streptococaceae and Enterococaceae 20.85%, Pseudomonadaceae 1.69%, and anaerobes 2.44%. In most of the polymicrobial samples, one of the species present was identified (80.9%). Seven isolates remained misidentified as Streptococcus pneumoniae, all belonging to Streptococcus mitis. Staphylococcus aureus was identified better when grown on anaero-aerobic medium, and MALDI BioTyper identification scores as low as 1.4 were pertinent, provided that four successive proposals of the same species were given. This new protocol correlates with conventional microbiology procedures by up to 90%, and by >95% for only monomicrobial samples, and provides a decreased turn-around time for identification of bacteria isolated from blood cultures, making this technology suitable also for blood cultures, with less delay and cost decreases in bacterial diagnostics, and favouring better care of patients.
Roughly 3% of the Earth's land surface burns annually, representing a critical exchange of energy and matter between the land and atmosphere via combustion. Fires range from slow smouldering peat ...fires, to low-intensity surface fires, to intense crown fires, depending on vegetation structure, fuel moisture, prevailing climate, and weather conditions. While the links between biogeochemistry, climate and fire are widely studied within Earth system science, these relationships are also mediated by fuels-namely plants and their litter-that are the product of evolutionary and ecological processes. Fire is a powerful selective force and, over their evolutionary history, plants have evolved traits that both tolerate and promote fire numerous times and across diverse clades. Here we outline a conceptual framework of how plant traits determine the flammability of ecosystems and interact with climate and weather to influence fire regimes. We explore how these evolutionary and ecological processes scale to impact biogeochemical and Earth system processes. Finally, we outline several research challenges that, when resolved, will improve our understanding of the role of plant evolution in mediating the fire feedbacks driving Earth system processes. Understanding current patterns of fire and vegetation, as well as patterns of fire over geological time, requires research that incorporates evolutionary biology, ecology, biogeography, and the biogeosciences.
Tauopathies are widespread neurodegenerative disorders characterised by the intracellular accumulation of hyperphosphorylated tau. Especially in Alzheimer's disease, pathological alterations in the ...retina are discussed as potential biomarkers to improve early diagnosis of the disease. Using mice expressing human mutant P301S tau, we demonstrate for the first time a straightforward optical approach for the in vivo detection of fibrillar tau in the retina. Longitudinal examinations of individual animals revealed the fate of single cells containing fibrillar tau and the progression of tau pathology over several months. This technique is most suitable to monitor therapeutic interventions aimed at reducing the accumulation of fibrillar tau. In order to evaluate if this approach can be translated to human diagnosis, we tried to detect fibrillar protein aggregates in the post-mortem retinas of patients that had suffered from Alzheimer's disease or Progressive Supranuclear Palsy. Even though we could detect hyperphosphorylated tau, we did not observe any fibrillar tau or Aß aggregates. In contradiction to previous studies, our observations do not support the notion that Aβ or tau in the retina are of diagnostic value in Alzheimer's disease.
Globally, fire maintains many mesic habitats in an open canopy state by killing woody plants while reducing the size of those able to resprout. Where fire is frequent, tree saplings are often ...suppressed by a "fire trap" of repeated topkill (death of aerial biomoass) and resprouting, preventing them from reaching adult size. The ability to tolerate repeated topkill is an essential life-history trait that allows a sapling to persist until it experiences a long fire-free interval, during which it can escape the fire trap. We hypothesized that persistence in the fire trap results from a curvilinear relationship between pre-burn size and resprout size, which causes a plant to approach an equilibrial size in which post-fire biomass recovery is equal to fire-induced biomass loss. We also predicted that the equilibrial stem size is positively related to resource availability. To test these hypotheses, we collected data on pre-burn and resprout size of five woody plant species at wetland ecotones in longleaf pine savanna subjected to frequent burning. As expected, all species exhibited similar curvilinear relationships between pre-burn size and resprout size. The calculated equilibrial sizes were strong predictors of mean plant size across species and growing conditions, supporting the persistence equilibrium model. An alternative approach using matrix models yielded similar results. Resprouting was less vigorous in dry sites than at wet sites, resulting in smaller equilibrial stem sizes in drier sites; extrapolating these results provides an explanation for the absence of these species in xeric uplands. This new framework offers a straightforward approach to guide data collection for experimental, comparative, and modeling studies of plant persistence and community dynamics in frequently burned habitats.
Climate change vulnerability assessment of species Foden, Wendy B.; Young, Bruce E.; Akçakaya, H. Resit ...
Wiley interdisciplinary reviews. Climate change,
January/February 2019, Letnik:
10, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Assessing species' vulnerability to climate change is a prerequisite for developing effective strategies to conserve them. The last three decades have seen exponential growth in the number of studies ...evaluating how, how much, why, when, and where species will be impacted by climate change. We provide an overview of the rapidly developing field of climate change vulnerability assessment (CCVA) and describe key concepts, terms, steps and considerations. We stress the importance of identifying the full range of pressures, impacts and their associated mechanisms that species face and using this as a basis for selecting the appropriate assessment approaches for quantifying vulnerability. We outline four CCVA assessment approaches, namely trait‐based, correlative, mechanistic and combined approaches and discuss their use. Since any assessment can deliver unreliable or even misleading results when incorrect data and parameters are applied, we discuss finding, selecting, and applying input data and provide examples of open‐access resources. Because rare, small‐range, and declining‐range species are often of particular conservation concern while also posing significant challenges for CCVA, we describe alternative ways to assess them. We also describe how CCVAs can be used to inform IUCN Red List assessments of extinction risk. Finally, we suggest future directions in this field and propose areas where research efforts may be particularly valuable.
This article is categorized under:
Climate, Ecology, and Conservation > Extinction Risk
Assessing species' vulnerability to climate change is becoming a prerequisite for conservation planning, but choosing approaches, methods and data can be challenging. Key to informing such choices is consideration of the full range of climate change pressures and their likely mechanisms of impact on individuals, subpopulations and species. Navigate a sound path through do's and don'ts, and explore resources and future perspectives in this exciting field.
Forest encroachment into savannas is a widespread phenomenon, the rate of which may depend on soil conditions, species composition or changes in stand structure. As savanna specialist trees are ...replaced by generalist species, rates of stand development may increase. Because generalists can persist in forests, they are likely to grow more quickly and survive longer in dense stands, compared to savanna specialists. Furthermore, the faster growth rates of generalists may allow them to overtop and outcompete savanna specialists, causing rapid species turnover.
We measured growth and survival of 6,147 individuals of 112 species of savanna and generalist tree species over a period of 10 years in an ecological reserve in Assis, São Paulo State, Brazil. We modelled growth and mortality as a function of soil texture and nutrients, tree size, competitive neighbourhood, and membership in savanna or generalist (species which can persist in forests and savannas) functional groups.
Tree growth and survival was strongly influenced by competition, as estimated by the basal area of trees taller than a focal tree. At the stand level, savanna species are unable to contribute basal area growth in closed stands, while generalist species continue to increase in basal area even at high stand basal area. This phenomenon is driven by differences in growth and mortality. Generalists grew faster than savanna species, both in height and diameter. This difference in growth rates led to savanna species becoming suppressed more rapidly than generalists. When suppressed, savanna species were more than twice as likely to die than were generalists. Soils had inconsistent and mostly weak effects which were difficult to separate from gradients of stand structure.
Synthesis. We demonstrate that the presence of generalist trees accelerates the rates of basal area accumulation due to their greater growth rates and tolerance of shading. Generalists outcompete savanna trees by growing faster in the open and overtopping savanna specialists. Due to the slow growth and high mortality of savanna species in the shade, they are unable to form closed‐canopy stands. Accounting for differences among functional types and development of vegetation structure is critical for modelling forest encroachment.
Resumo
O adensamento das savanas vem ocorrendo em larga escala, em taxas que dependem das condições de solo, composição de espécies ou mudanças estruturais das comunidades. À medida que árvores especialistas em savana são substituídas por espécies generalistas, o adensamento é acelerado. As generalistas podem persistir em florestas, podendo crescer mais rápido e sobreviver por mais tempo que as especialistas em savana. As generalistas podem ainda sombrear e suprimir as especialistas de savana, causando rápida substituição de espécies.
Nós quantificamos o crescimento e a sobrevivência de 6147 indivíduos, de 112 espécies arbóreas típicas de Cerrado ou generalistas, durante 10 anos, na Estação Ecológica de Assis, SP, Brasil. Modelamos o crescimento e a mortalidade em função da textura e nutrientes do solo, tamanho do indivíduo, competição com os vizinhos e grupo funcional categorizado em especialista de savana ou generalista (ocorre também em florestas).
Crescimento e sobrevivência foram fortemente influenciados pela competição, representada pela área basal de árvores maiores que a árvore focal. Nas parcelas mais densas, especialistas em savana não contribuíram para incremento em área basal, enquanto a área basal das generalistas continuou aumentando. As generalistas cresceram mais rápido em diâmetro e altura, rapidamente suprimindo as especialistas em savana, cuja probabilidade de morrer foi duas vezes maior do que entre as generalistas. Os efeitos das propriedades do solo foram fracos e inconsistentes, difíceis de separar do gradiente estrutural da vegetação.
Síntese. Nós demonstramos que a entrada de árvores generalistas acelera a acumulação de área basal no Cerrado, devido às maiores taxas de crescimento e tolerância à sombra. As generalistas crescem mais rápido e ultrapassam as especialistas de savana, suprimindo‐as. O crescimento lento e a alta mortalidade das espécies típicas de Cerrado nos ambientes sombreados impede que se aglomerem em povoamentos densos. As diferenças entre os dois tipos funcionais e grau de desenvolvimento estrutural da vegetação precisam ser contabilizados na modelagem do processo de adensamento.
We demonstrate that the presence of generalist trees accelerates the rates of basal area accumulation due to their greater growth rates and tolerance of shading. Generalists outcompete savanna trees by growing faster in the open and overtopping savanna specialists. Due to the slow growth and high mortality of savanna species in the shade, they are unable to form closed‐canopy stands. Accounting for differences among functional types and development of vegetation structure is critical for modelling forest encroachment.
Editor's Choice
Over the past few decades, research on Alzheimer’s disease (AD) has focused on pathomechanisms linked to two of the major pathological hallmarks of extracellular deposition of beta-amyloid peptides ...and intra-neuronal formation of neurofibrils. Recently, a third disease component, the neuroinflammatory reaction mediated by cerebral innate immune cells, has entered the spotlight, prompted by findings from genetic, pre-clinical, and clinical studies. Various proteins that arise during neurodegeneration, including beta-amyloid, tau, heat shock proteins, and chromogranin, among others, act as danger-associated molecular patterns, that—upon engagement of pattern recognition receptors—induce inflammatory signaling pathways and ultimately lead to the production and release of immune mediators. These may have beneficial effects but ultimately compromise neuronal function and cause cell death. The current review, assembled by participants of the Chiclana Summer School on Neuroinflammation 2016, provides an overview of our current understanding of AD-related immune processes. We describe the principal cellular and molecular players in inflammation as they pertain to AD, examine modifying factors, and discuss potential future therapeutic targets.
Spin Hall effects intermix spin and charge currents even in nonmagnetic materials and, therefore, ultimately may allow the use of spin transport without the need for ferromagnets. We show how spin ...Hall effects can be quantified by integrating Ni{80}Fe{20}|normal metal (N) bilayers into a coplanar waveguide. A dc spin current in N can be generated by spin pumping in a controllable way by ferromagnetic resonance. The transverse dc voltage detected along the Ni{80}Fe{20}|N has contributions from both the anisotropic magnetoresistance and the spin Hall effect, which can be distinguished by their symmetries. We developed a theory that accounts for both. In this way, we determine the spin Hall angle quantitatively for Pt, Au, and Mo. This approach can readily be adapted to any conducting material with even very small spin Hall angles.
An absence of genetic variance in traits under selection is perhaps the oldest explanation for a limit to evolutionary change, but has also been the most easily dismissed. We review a range of ...theoretical and empirical results covering single traits to more complex multivariate systems, and show that an absence of genetic variance may be more common than is currently appreciated. From a single-trait perspective, we highlight that it is becoming clear that some trait types do not display significant levels of genetic variation, and we raise the possibility that species with restricted ranges may differ qualitatively from more widespread species in levels of genetic variance in ecologically important traits. A common misconception in many life-history studies is that a lack of genetic variance in single traits, and genetic constraints as a consequence of bivariate genetic correlations, are different causes of selection limits. We detail how interpretations of bivariate patterns are unlikely to demonstrate genetic limits to selection in many cases. We advocate a multivariate definition of genetic constraints that emphasizes the presence (or otherwise) of genetic variance in the multivariate direction of selection. For multitrait systems, recent results using longer term studies of organisms, in which more is understood concerning what traits may be under selection, have indicated that selection may exhaust genetic variance, resulting in a limit to the selection response.
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