Abstract
We describe an update of MirGeneDB, the manually curated microRNA gene database. Adhering to uniform and consistent criteria for microRNA annotation and nomenclature, we substantially ...expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning over ∼800 million years of animal evolution, and contains a total number of 16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new phylogenetically important species, especially those relevant for the study of whole genome duplication events, and through updating evolutionary nodes of origin for many families and genes, we were able to substantially refine our nomenclature system. All changes are traceable in the specifically developed MirGeneDB version tracker. The performance of read-pages is improved and microRNA expression matrices for all tissues and species are now also downloadable. Altogether, this update represents a significant step toward a complete sampling of all major metazoan phyla, and a widely needed foundation for comparative microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.
Biogenic sources contribute to cloud condensation nuclei (CCN) in the clean marine atmosphere, but few measurements exist to constrain climate model simulations of their importance. The chemical ...composition of individual atmospheric aerosol particles showed two types of sulfate-containing particles in clean marine air masses in addition to mass-based Estimated Salt particles. Both types of sulfate particles lack combustion tracers and correlate, for some conditions, to atmospheric or seawater dimethyl sulfide (DMS) concentrations, which means their source was largely biogenic. The first type is identified as New Sulfate because their large sulfate mass fraction (63% sulfate) and association with entrainment conditions means they could have formed by nucleation in the free troposphere. The second type is Added Sulfate particles (38% sulfate), because they are preexisting particles onto which additional sulfate condensed. New Sulfate particles accounted for 31% (7 cm
) and 33% (36 cm
) CCN at 0.1% supersaturation in late-autumn and late-spring, respectively, whereas sea spray provided 55% (13 cm
) in late-autumn but only 4% (4 cm
) in late-spring. Our results show a clear seasonal difference in the marine CCN budget, which illustrates how important phytoplankton-produced DMS emissions are for CCN in the North Atlantic.
The nighttime is undergoing unprecedented change across much of the world, with natural light cycles altered by the introduction of artificial light emissions. Here we review the extent and dynamics ...of artificial light at night (ALAN), the benefits that ALAN provides, the environmental costs ALAN creates, approaches to mitigating these negative effects, and how costs are likely to change in the future. We particularly highlight the consequences of the increasingly widespread use of light-emitting diode (LED) technology for new lighting installations and to retrofit pre-existing ones. Although this has been characterized as a technological lighting revolution, it also constitutes a revolution in the environmental costs and impacts of ALAN, particularly because the LEDs commonly used for outdoor lighting have significant emissions at the blue wavelengths to which many biological responses are particularly sensitive. It is clear that a very different approach to the use of artificial lighting is required.
A central aim of the "lighting revolution" (the transition to solid-state lighting technology) is decreased energy consumption. This could be undermined by a rebound effect of increased use in ...response to lowered cost of light. We use the first-ever calibrated satellite radiometer designed for night lights to show that from 2012 to 2016, Earth's artificially lit outdoor area grew by 2.2% per year, with a total radiance growth of 1.8% per year. Continuously lit areas brightened at a rate of 2.2% per year. Large differences in national growth rates were observed, with lighting remaining stable or decreasing in only a few countries. These data are not consistent with global scale energy reductions but rather indicate increased light pollution, with corresponding negative consequences for flora, fauna, and human well-being.
The global spread of artificial light is eroding the natural night-time environment. The estimation of the pattern and rate of growth of light pollution on multi-decadal scales has nonetheless proven ...challenging. Here we show that the power of global satellite observable light emissions increased from 1992 to 2017 by at least 49%. We estimate the hidden impact of the transition to solid-state light-emitting diode (LED) technology, which increases emissions at visible wavelengths undetectable to existing satellite sensors, suggesting that the true increase in radiance in the visible spectrum may be as high as globally 270% and 400% on specific regions. These dynamics vary by region, but there is limited evidence that advances in lighting technology have led to decreased emissions.
Recent success in identifying gene-regulatory elements in the context of recombinant adeno-associated virus vectors has enabled cell-type-restricted gene expression. However, within the cerebral ...cortex these tools are largely limited to broad classes of neurons. To overcome this limitation, we developed a strategy that led to the identification of multiple new enhancers to target functionally distinct neuronal subtypes. By investigating the regulatory landscape of the disease gene Scn1a, we discovered enhancers selective for parvalbumin (PV) and vasoactive intestinal peptide-expressing interneurons. Demonstrating the functional utility of these elements, we show that the PV-specific enhancer allowed for the selective targeting and manipulation of these neurons across vertebrate species, including humans. Finally, we demonstrate that our selection method is generalizable and characterizes additional PV-specific enhancers with exquisite specificity within distinct brain regions. Altogether, these viral tools can be used for cell-type-specific circuit manipulation and hold considerable promise for use in therapeutic interventions.
Diffuse glow has been observed around brightly lit cities in nighttime satellite imagery since at least the first publication of large scale maps in the late 1990s. In the literature, this has often ...been assumed to be an error related to the sensor, and referred to as "blooming", presumably in relation to the effect that can occur when using a CCD to photograph a bright light source. Here we show that the effect seen on the DMSP/OLS, SNPP/VIIRS-DNB and ISS is not only instrumental, but in fact represents a real detection of light scattered by the atmosphere. Data from the Universidad Complutense Madrid sky brightness survey are compared to nighttime imagery from multiple sensors with differing spatial resolutions, and found to be strongly correlated. These results suggest that it should be possible for a future space-based imaging radiometer to monitor changes in the diffuse artificial skyglow of cities.
Natural and synthetic steroid hormones, excreted by humans and farmed animals, have been considered as important sources of environmental endocrine disruptors. A suite of estrogens, androgens and ...progestogens was measured in the wastewater treatment plant outfall (WWTPO) of Chascomús city (Buenos Aires province, Argentina), and receiving waters located downstream and upstream from the WWTPO, using solid phase extraction and high-performance liquid chromatography mass spectrometry. The following natural hormones were measured: 17β-estradiol (E2), estrone (E1), estriol (E3), testosterone (T), 5α-dihydrotestosterone (DHT), progesterone (P), 17-hydroxyprogesterone (17OHP) and the synthetic estrogen 17α-ethinylestradiol (EE2). Also, in order to complement the analytical method, the estrogenic activity in these surface water samples was evaluated using the in vitro transactivation bioassay that measures the estrogen receptor (ER) activity using mammalian cells. All-natural steroid hormones measured, except 17OHP, were detected in all analyzed water samples. E3, E1, EE2 and DHT were the most abundant and frequently detected. Downstream of the WWTPO, the concentration levels of all compounds decreased reaching low levels at 4500 m from the WWTPO. Upstream, 1500 m from the WWTPO, six out of eight steroid hormones analyzed were detected: DHT, T, P, 17OHP, E3 and E2. Moreover, water samples from the WWTPO and 200 m downstream from it showed estrogenic activity exceeding that of the EC50 of the E2 standard curve.
In sum, this work demonstrates the presence of sex steroid hormones and estrogenic activity, as measured by an in vitro assay, in superficial waters of the Pampas region. It also suggests the possibility of an unidentified source upstream of the wastewater outfall.
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•Surface waters of the Chascomús Lagoon, Argentina, show high levels of steroids.•E3, E1, EE2 and DHT were the most abundant and frequent steroids found.•EE2 was the only steroid exclusively detected downstream from the WWTP outfall.•Wastewater effluent is not the only source of sex steroid hormones in this area.•These waters show high estrogenic activity compared to other parts of the world.
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