Intracellular dynamics of HIV infection

Early studies of HIV infection dynamics suggested that virus-producing HIV-infected cells had an average half-life of approximately 1 day. However, whether this average behavior is reflective of the dynamics of individual infected cells is unclear. Here, we use HIV-enhanced green fluorescent protein (EGFP) constructs and flow cytometry sorting to explore the dynamics of cell infection, viral protein production, and cell death in vitro. By following the numbers of productively infected cells expressing EGFP over time, we show that infected cell death slows down over time. Although infected cell death in vivo could be very different, our results suggest that the constant decay of cell numbers observed in vivo during antiretroviral treatment could reflect a balance of cell death and delayed viral protein production. We observe no correlation between viral protein production and death rate of productively infected cells, showing that viral protein production is not likely to be the sole determinant of the death of HIV-infected cells. Finally, we show that all observed features can be reproduced by a simple model in which infected cells have broad distributions of productive life spans, times to start viral protein production, and viral protein production rates. This broad spectrum of the level and timing of viral protein production provides new insights into the behavior and characteristics of HIV-infected cells

MINFLUX nanoscopy delivers 3D multicolor nanometer resolution in cells.

The ultimate goal of biological super-resolution fluorescence microscopy is to provide three-dimensional resolution at the size scale of a fluorescent marker. Here we show that by localizing individual switchable fluorophores with a probing donut-shaped excitation beam, MINFLUX nanoscopy can provide resolutions in the range of 1 to 3 nm for structures in fixed and living cells. This progress has been facilitated by approaching each fluorophore iteratively with the probing-donut minimum, making the resolution essentially uniform and isotropic over scalable fields of view. MINFLUX imaging of nuclear pore complexes of a mammalian cell shows that this true nanometer-scale resolution is obtained in three dimensions and in two color channels. Relying on fewer detected photons than standard camera-based localization, MINFLUX nanoscopy is poised to open a new chapter in the imaging of protein complexes and distributions in fixed and living cells

Communication

Visualizing the functional interactions of biomolecules such as proteins and nucleic acids is key to understanding cellular life on the molecular scale. Spatial proximity is often used as a proxy for the direct interaction of biomolecules. However, current techniques to visualize spatial proximity are either limited by spatial resolution, dynamic range, or lack of single-molecule sensitivity. Here, we introduce Proximity-PAINT (pPAINT), a variation of the super-resolution microscopy technique DNA-PAINT. pPAINT uses a split-docking-site configuration to detect spatial proximity with high sensitivity, low false-positive rates, and tunable detection distances. We benchmark and optimize pPAINT using designer DNA nanostructures and demonstrate its cellular applicability by visualizing the spatial proximity of alpha- and beta-tubulin in microtubules using super-resolution detection. © 2020 Wiley-VCH GmbH

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

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

Association Between Efavirenz-Based Compared With Nevirapine-Based Antiretroviral Regimens and Virological Failure in HIV-Infected Children

Importance Worldwide, the nonnucleoside reverse transcriptase inhibitors (NNRTIs) efavirenz and nevirapine are commonly used in first-line antiretroviral regimens in both adults and children with human immunodeficiency virus (HIV) infection. Data on the comparative effectiveness of these medications in children are limited. Objective To investigate whether virological failure is more likely among children who initiated 1 or the other NNRTI-based HIV treatment. Design, Setting, and Participants Retrospective cohort study of children (aged 3–16 years) who initiated efavirenz-based (n=421) or nevirapine-based (n=383) treatment between April 2002 and January 2011 at a large pediatric HIV care setting in Botswana. Main Outcomes and Measures The primary outcome was time from initiation of therapy to virological failure. Virological failure was defined as lack of plasma HIV RNA suppression to less than 400 copies/mL by 6 months or confirmed HIV RNA of 400 copies/mL or greater after suppression. Cox proportional hazards regression analysis compared time to virological failure by regimen. Multivariable Cox regression controlled for age, sex, baseline immunologic category, baseline clinical category, baseline viral load, nutritional status, NRTIs used, receipt of single-dose nevirapine, and treatment for tuberculosis. Results With a median follow-up time of 69 months (range, 6–112 months; interquartile range, 23–87 months), 57 children (13.5%; 95% CI, 10.4%–17.2%) initiating treatment with efavirenz and 101 children (26.4%; 95% CI, 22.0%–31.1%) initiating treatment with nevirapine had virological failure. There were 11 children (2.6%; 95% CI, 1.3%–4.6%) receiving efavirenz and 20 children (5.2%; 95% CI, 3.2%–7.9%) receiving nevirapine who never achieved virological suppression. The Cox proportional hazard ratio for the combined virological failure end point was 2.0 (95% CI, 1.4–2.7; log rank P Conclusions and Relevance Among children aged 3 to 16 years infected with HIV and treated at a clinic in Botswana, the use of efavirenz compared with nevirapine as initial antiretroviral treatment was associated with less virological failure. These findings may warrant additional research evaluating the use of efavirenz and nevirapine for pediatric patients

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

Island properties dominate species traits in determining plant colonizations in an archipelago system

The extrinsic determinants hypothesis emphasizes the essential role of environmental heterogeneity in species' colonization. Consequently, high resident species diversity can increase community susceptibility to colonizations because good habitats may support more species that are functionally similar to colonizers. On the other hand, colonization success is also likely to depend on species traits. We tested the relative importance of environmental characteristics and species traits in determining colonization success using census data of 587 vascular plant species collected about 70 yr apart from 471 islands in the archipelago of SW Finland. More specifically, we explored potential new colonization as a function of island properties (e.g. location, area, habitat diversity, number of resident species per unit area), species traits (e.g. plant height, life-form, dispersal vector, Ellenberg indicator values, association with human impact), and species' historical distributions (number of inhabited islands, nearest occurrence). Island properties and species' historical distributions were more effective than plant traits in explaining colonization outcomes. Contrary to the extrinsic determinants hypothesis, colonization success was neither associated with resident species diversity nor habitat diversity per se, although colonization was lowest on sparsely vegetated islands. Our findings lead us to propose that while plant traits related to dispersal and establishment may enhance colonization, predictions of plant colonizations primarily require understanding of habitat properties and species' historical distributions.Peer reviewe

Long-term changes to the frequency of occurrence of British moths are consistent with opposing and synergistic effects of climate and land-use changes

1. Species’ distributions are likely to be affected by a combination of environmental drivers. We used a data set of 11 million species occurrence records over the period 1970–2010 to assess changes in the frequency of occurrence of 673 macro-moth species in Great Britain. Groups of species with different predicted sensitivities showed divergent trends, which we interpret in the context of land-use and climatic changes. 2. A diversity of responses was revealed: 260 moth species declined significantly, whereas 160 increased significantly. Overall, frequencies of occurrence declined, mirroring trends in less species-rich, yet more intensively studied taxa. 3. Geographically widespread species, which were predicted to be more sensitive to land use than to climate change, declined significantly in southern Britain, where the cover of urban and arable land has increased. 4. Moths associated with low nitrogen and open environments (based on their larval host plant characteristics) declined most strongly, which is also consistent with a land-use change explanation. 5. Some moths that reach their northern (leading edge) range limit in southern Britain increased, whereas species restricted to northern Britain (trailing edge) declined significantly, consistent with a climate change explanation. 6. Not all species of a given type behaved similarly, suggesting that complex interactions between species’ attributes and different combinations of environmental drivers determine frequency of occurrence changes. 7. Synthesis and applications. Our findings are consistent with large-scale responses to climatic and land-use changes, with some species increasing and others decreasing. We suggest that land-use change (e.g. habitat loss, nitrogen deposition) and climate change are both major drivers of moth biodiversity change, acting independently and in combination. Importantly, the diverse responses revealed in this species-rich taxon show that multifaceted conservation strategies are needed to minimize negative biodiversity impacts of multiple environmental changes. We suggest that habitat protection, management and ecological restoration can mitigate combined impacts of land-use change and climate change by providing environments that are suitable for existing populations and also enable species to shift their ranges