Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically-Encoded Probes for DNA-PAINT

The nuclear pore complex (NPC) is one of the largest and most complex protein assemblies in the cell and, among other functions, serves as the gatekeeper of nucleocytoplasmic transport. Unraveling its molecular architecture and functioning has been an active research topic for decades with recent cryogenic electron microscopy and super-resolution studies advancing our understanding of the architecture of the NPC complex. However, the specific and direct visualization of single copies of NPC proteins is thus far elusive. Herein, we combine genetically-encoded self-labeling enzymes such as SNAP-tag and HaloTag with DNA-PAINT microscopy. We resolve single copies of nucleoporins in the human Y-complex in three dimensions with a precision of circa 3 nm, enabling studies of multicomponent complexes on the level of single proteins in cells using optical fluorescence microscopy

Evaluating the ecological realism of plant species distribution models with ecological indicator values

Species distribution models (SDMs) are routinely applied to assess current as well as future species distributions, for example to assess impacts of future environmental change on biodiversity or to underpin conservation planning. It has been repeatedly emphasized that SDMs should be evaluated based not only on their goodness of fit to the data, but also on the realism of the modelled ecological responses. However, possibilities for the latter are hampered by limited knowledge on the true responses as well as a lack of quantitative evaluation methods. Here we compared modelled niche optima obtained from European-scale SDMs of 1,476 terrestrial vascular plant species with empirical ecological indicator values indicating the preferences of plant species for key environmental conditions. For each plant species we first fitted an ensemble SDM including three modeling techniques (GLM, GAM and BRT) and extracted niche optima for climate, soil, land use and nitrogen deposition variables with a large explanatory power for the occurrence of that species. We then compared these SDM-derived niche optima with the ecological indicator values by means of bivariate correlation analysis. We found weak to moderate correlations in the expected direction between the SDM-derived niche optima and ecological indicator values. The strongest correlation occurred between the modelled optima for growing degree days and the ecological indicator values for temperature. Correlations were weaker for SDM-derived niche optima with a more distal relationship to ecological indicator values (notably precipitation and soil moisture). Further, correlations were consistently highest for BRT, followed by GLM and GAM. Our method gives insight into the ecological realism of modelled niche optima and projected core habitats and can be used to improve SDMs by making a more informed selection of environmental variables and modeling techniques

Averages of Fourier coefficients of Siegel modular forms and representation of binary quadratic forms by quadratic forms in four variables

Let $-d$ be a a negative discriminant and let $T$ vary over a set of representatives of the integral equivalence classes of integral binary quadratic forms of discriminant $-d$. We prove an asymptotic formula for $d \to \infty$ for the average over $T$ of the number of representations of $T$ by an integral positive definite quaternary quadratic form and obtain results on averages of Fourier coefficients of linear combinations of Siegel theta series. We also find an asymptotic bound from below on the number of binary forms of fixed discriminant $-d$ which are represented by a given quaternary form. In particular, we can show that for growing $d$ a positive proportion of the binary quadratic forms of discriminant $-d$ is represented by the given quaternary quadratic form.Comment: v5: Some typos correcte

Human Impacts on Forest Biodiversity in Protected Walnut-Fruit Forests in Kyrgyzstan

We used a spatially explicit model of forest dynamics, supported by empirical field data and socioeconomic data, to examine the impacts of human disturbances on a protected forest landscape in Kyrgyzstan. Local use of 27 fruit and nut species was recorded and modeled. Results indicated that in the presence of fuelwood cutting with or without grazing, species of high socioeconomic impor- tance such as Juglans regia, Malus spp., and Armeniaca vulgaris were largely eliminated from the landscape after 50–150 yr. In the absence of disturbance or in the presence of grazing only, decline of these species occurred at a much lower rate, owing to competi- tive interactions between tree species. This suggests that the current intensity of fuelwood harvesting is not sustainable. Conversely, cur- rent grazing intensities were found to have relatively little impact on forest structure and composition, and could potentially play a positive role in supporting regeneration of tree species. These results indicate that both positive and negative impacts on biodiversity can arise from human populations living within a protected area. Potentially, these could be reconciled through the development of participatory approaches to conservation management within this reserve, to ensure the maintenance of its high conservation value while meeting human needs

Testing Hardy nonlocality proof with genuine energy-time entanglement

We show two experimental realizations of Hardy ladder test of quantum nonlocality using energy-time correlated photons, following the scheme proposed by A. Cabello \emph{et al.} [Phys. Rev. Lett. \textbf{102}, 040401 (2009)]. Unlike, previous energy-time Bell experiments, these tests require precise tailored nonmaximally entangled states. One of them is equivalent to the two-setting two-outcome Bell test requiring a minimum detection efficiency. The reported experiments are still affected by the locality and detection loopholes, but are free of the post-selection loophole of previous energy-time and time-bin Bell tests.Comment: 5 pages, revtex4, 6 figure

Cisternal Organization of the Endoplasmic Reticulum during Mitosis

The endoplasmic reticulum (ER) of animal cells is a single, dynamic, and continuous membrane network of interconnected cisternae and tubules spread out throughout the cytosol in direct contact with the nuclear envelope. During mitosis, the nuclear envelope undergoes a major rearrangement, as it rapidly partitions its membrane-bound contents into the ER. It is therefore of great interest to determine whether any major transformation in the architecture of the ER also occurs during cell division. We present structural evidence, from rapid, live-cell, three-dimensional imaging with confirmation from high-resolution electron microscopy tomography of samples preserved by high-pressure freezing and freeze substitution, unambiguously showing that from prometaphase to telophase of mammalian cells, most of the ER is organized as extended cisternae, with a very small fraction remaining organized as tubules. In contrast, during interphase, the ER displays the familiar reticular network of convolved cisternae linked to tubules

Aquatic community response to volcanic eruptions on the Ecuadorian Andean flank: evidence from the palaeoecological record

Aquatic ecosystems in the tropical Andes are under increasing pressure from human modification of the landscape (deforestation and dams) and climatic change (increase of extreme events and 1.5 °C on average temperatures are projected for AD 2100). However, the resilience of these ecosystems to perturbations is poorly understood. Here we use a multi-proxy palaeoecological approach to assess the response of aquatic ecosystems to a major mechanism for natural disturbance, volcanic ash deposition. Specifically, we present data from two Neotropical lakes located on the eastern Andean flank of Ecuador. Laguna Pindo (1°27.132′S–78°04.847′W) is a tectonically formed closed basin surrounded by a dense mid-elevation forest, whereas Laguna Baños (0°19.328′S–78°09.175′W) is a glacially formed lake with an inflow and outflow in high Andean Páramo grasslands. In each lake we examined the dynamics of chironomids and other aquatic and semi-aquatic organisms to explore the effect of thick (> 5 cm) volcanic deposits on the aquatic communities in these two systems with different catchment features. In both lakes past volcanic ash deposition was evident from four large tephras dated to c.850 cal year BP (Pindo), and 4600, 3600 and 1500 cal year BP (Baños). Examination of the chironomid and aquatic assemblages before and after the ash depositions revealed no shift in composition at Pindo, but a major change at Baños occurred after the last event around 1500 cal year BP. Chironomids at Baños changed from an assemblage dominated by Pseudochironomus and Polypedilum nubifer-type to Cricotopus/Paratrichocladius type-II, and such a dominance lasted for approximately 380 years. We suggest that, despite potential changes in the water chemistry, the major effect on the chironomid community resulted from the thickness of the tephra being deposited, which acted to shallow the water body beyond a depth threshold. Changes in the aquatic flora and fauna at the base of the trophic chain can promote cascade effects that may deteriorate the ecosystem, especially when already influenced by human activities, such as deforestation and dams, which is frequent in the high Andes

Contrasting stomatal sensitivity to temperature and soil drought in mature alpine conifers

Conifers growing at high elevations need to optimize their stomatal conductance (g(s)) for maximizing photosynthetic yield while minimizing water loss under less favourable thermal conditions. Yet the ability of high-elevation conifers to adjust their g(s) sensitivity to environmental drivers remains largely unexplored. We used 4 years of sap flow measurements to elucidate intraspecific and interspecific variability of g(s) in Larix decidua Mill. and Picea abies (L.) Karst along an elevational gradient and contrasting soil moisture conditions. Site- and species-specific g(s) response to main environmental drivers were examined, including vapour pressure deficit, air temperature, solar irradiance, and soil water potential. Our results indicate that maximum g(s) of L. decidua is >2 times higher, shows a more plastic response to temperature, and down-regulates g(s) stronger during atmospheric drought compared to P. abies. These differences allow L. decidua to exert more efficient water use, adjust to site-specific thermal conditions, and reduce water loss during drought episodes. The stronger plasticity of g(s) sensitivity to temperature and higher conductance of L. decidua compared to P. abies provide new insights into species-specific water use strategies, which affect species' performance and should be considered when predicting terrestrial water dynamics under future climatic change

A forest typology for monitoring sustainable forest management: The case of European Forest Types

Sustainable forest management (SFM) is presently widely accepted as the overriding objective for forest policy and practice. Regional processes are in progress all over the world to develop and implement criteria and indicators of SFM. In continental Europe, a set of 35 Pan-European indicators has been endorsed under the Ministerial Conference on the Protection of Forests in Europe (MCPFE) to measure progress towards SFM in the 44 countries of the region. The formulation of seven indicators (forest area, growing stock, age structure/diameter distribution, deadwood, tree species composition, damaging agents, naturalness) requires national data to be reported by forest types. Within the vast European forest area the values taken by these indicators show a considerable range of variation, due to variable natural conditions and anthropogenic influences. Given this variability, it is very difficult to grasp the meaning of these indicators when taken out of their ecological background. The paper discusses the concepts behind, and the requirements of, a classification more soundly ecologically framed and suitable for MCPFE reporting than the three (un-informative) classes adopted so far: broadleaved forest, coniferous forest, mixed broadleaved and coniferous forest. We propose a European Forest Types scheme structured into a reasonably higher number of classes, that would improve the specificity of the indicators reported under the MCPFE process and its understanding.L'articolo è disponibile sul sito dell'editore www.tandf.co.uk/journals

Elliptic Curves over Real Quadratic Fields are Modular

We prove that all elliptic curves defined over real quadratic fields are modular.Comment: 38 pages. Magma scripts available as ancillary files with this arXiv versio