A CRISPR/Cas9 Vector System for Tissue-Specific Gene Disruption in Zebrafish

SummaryCRISPR/Cas9 technology of genome editing has greatly facilitated the targeted inactivation of genes in vitro and in vivo in a wide range of organisms. In zebrafish, it allows the rapid generation of knockout lines by simply injecting a guide RNA (gRNA) and Cas9 mRNA into one-cell stage embryos. Here, we report a simple and scalable CRISPR-based vector system for tissue-specific gene inactivation in zebrafish. As proof of principle, we used our vector with the gata1 promoter driving Cas9 expression to silence the urod gene, implicated in heme biosynthesis, specifically in the erythrocytic lineage. Urod targeting yielded red fluorescent erythrocytes in zebrafish embryos, recapitulating the phenotype observed in the yquem mutant. While F0 embryos displayed mosaic gene disruption, the phenotype appeared very penetrant in stable F1 fish. This vector system constitutes a unique tool to spatially control gene knockout and greatly broadens the scope of loss-of-function studies in zebrafish

Sea level budget over 2003-2008: A reevaluation from GRACE space gravimetry, satellite altimetry and Argo

0921-8181From the IPCC 4th Assessment Report published in 2007, ocean thermal expansion contributed by similar to 50% to the 3.1 mm/yr observed global mean sea level rise during the 1993-2003 decade, the remaining rate of rise being essentially explained by shrinking of land ice. Recently published results suggest that since about 2003, ocean thermal expansion change, based on the newly deployed Argo system, is showing a plateau while sea level is still rising, although at a reduced rate (similar to 2.5 mm/yr). Using space gravimetry observations from GRACE, we show that recent years sea level rise can be mostly explained by an increase of the mass of the oceans. Estimating GRACE-based ice sheet mass balance and using published estimates for glaciers melting, we further show that ocean mass increase since 2003 results by about half from an enhanced contribution of the polar ice sheets - compared to the previous decade - and half from mountain glaciers melting. Taking also into account the small GRACE-based contribution from continental waters (<0.2 mm/yr), we find a total ocean mass contribution of similar to 2 mm/yr over 2003-2008. Such a value represents similar to 80% of the altimetry-based rate of sea level rise over that period. We next estimate the steric sea level (i.e., ocean thermal expansion plus salinity effects) contribution from: (1) the difference between altimetry-based sea level and ocean mass change and (2) Argo data. Inferred steric sea level rate from (1) (similar to 0.3 mm/yr over 2003-2008) agrees well with the Argo-based value also estimated here (0.37 mm/yr over 2004-2008). Furthermore, the sea level budget approach presented in this study allows us to constrain independent estimates of the Glacial Isostatic Adjustment (GIA) correction applied to GRACE-based ocean and ice sheet mass changes, as well as of glaciers melting. Values for the CIA correction and glacier contribution needed to close the sea level budget and explain GRACE-based mass estimates over the recent years agree well with totally independent determinations. (C) 2008 Elsevier B.V. All rights reserved

An Improved and Homogeneous Altimeter Sea Level Record from the ESA Climate Change Initiative

Sea Level is a very sensitive index of climate change since it integrates the impacts of ocean warming and ice mass loss from glaciers and the ice sheets. Sea Level has been listed as an Essential Climate Variable (ECV) by the Global Climate Observing System (GCOS). During the past 25 years, the sea level ECV has been measured from space by different altimetry missions that have provided global and regional observations of sea level variations. As part of the Climate Change Initiative (CCI) program of the European Space Agency (ESA) (established in 2010), the Sea Level project (SL_cci) aimed at providing an accurate and homogeneous long-term satellite-based sea level record. At the end of the first phase of the project (2010-2013), an initial version (v1.1) of the sea level ECV has been made available to users (Ablain et al., 2015). During the second phase (2014-2017), improved altimeter standards have been selected to produce new sea level products (called SL_cci v2.0) based on 9 altimeter missions for the period 1993-2015 (https://doi.org/10.5270/esa-sea_level_cci-1993_2015-v_2.0-201612). Corresponding orbit solutions, geophysical corrections and altimeter standards used in this v2.0 dataset are described in details in Quartly et al. (2017). The present paper focuses on the description of the SL_cci v2.0 ECV and associated uncertainty and discusses how it has been validated. Various approaches have been used for the quality assessment such as internal validation, comparisons with sea level records from other groups and with in-situ measurements, sea level budget closure analyses and comparisons with model outputs. Compared to the previous version of the sea level ECV, we show that use of improved geophysical corrections, careful bias reduction between missions and inclusion of new altimeter missions lead to improved sea level products with reduced uncertainties at different spatial and temporal scales. However, there is still room for improvement since the uncertainties remain larger than the GCOS requirements. Perspectives for subsequent evolutions are also discussed

Current observed global mean sea level rise and acceleration estimated from satellite altimetry and the associated measurement uncertainty

We present the latest release of the global mean sea level (GMSL) record produced by the French space agency Centre National d’Etudes Spatiales (CNES) and distributed on the AVISO+ website. This dataset is based on reprocessed along-track data, so-called L2P 21, of the reference missions TOPEX/Poseidon (TP) and Jason-1, Jason-2 and Jason-3. The L2P 21 CNES/AVISO+ GMSL record covers the period January 1993 to December 2021 and is now delivered with an estimate of its measurement uncertainties following the method presented in Ablain et al. (2019). Based on the latest calibration (Cal) and validation (Val) knowledge, we updated the uncertainty budget of the reference altimetry mission measurements and demonstrate that the CNES/AVISO+ GMSL record now achieves stability of performances of ± 0.3 mm yr−1 at the 90 % confidence level (C.L.) for its trend and ±0.05 mm yr−2 (90 % C.L.) for its acceleration over the 29 years of the altimetry record. Thanks to an analysis of the relative contribution of each measurement uncertainty budget contributor, i.e. the altimeter, the radiometer, the orbit determination and the geophysical corrections, we identified the current limiting factors to the GMSL monitoring stability and accuracy. We find that the radiometer wet troposphere correction (WTC) and the high-frequency errors with timescales shorter than 1 year are the major contributors to the GMSL measurement uncertainty over periods of 10 years (30 %–70 %), for both the trend and acceleration estimations. For longer periods of 20 years, the TP data quality is still a limitation, but more interestingly, the International Terrestrial Reference Frame (ITRF) realization uncertainties becomes dominant over all the other sources of uncertainty. Such a finding challenges the altimetry observing system as it is designed today and highlights clear topics of research to be explored in the future to help the altimetry community to improve the GMSL measurement accuracy and stability.</p

A new phase in the production of quality-controlled sea level data

Sea level is an essential climate variable (ECV) that has a direct effect on many people through inundations of coastal areas, and it is also a clear indicator of climate changes due to external forcing factors and internal climate variability. Regional patterns of sea level change inform us on ocean circulation variations in response to natural climate modes such as El Niño and the Pacific Decadal Oscillation, and anthropogenic forcing. Comparing numerical climate models to a consistent set of observations enables us to assess the performance of these models and help us to understand and predict these phenomena, and thereby alleviate some of the environmental conditions associated with them. All such studies rely on the existence of long-term consistent high-accuracy datasets of sea level. The Climate Change Initiative (CCI) of the European Space Agency was established in 2010 to provide improved time series of some ECVs, including sea level, with the purpose of providing such data openly to all to enable the widest possible utilisation of such data. Now in its second phase, the Sea Level CCI project (SL_cci) merges data from nine different altimeter missions in a clear, consistent and well-documented manner, selecting the most appropriate satellite orbits and geophysical corrections in order to further reduce the error budget. This paper summarises the corrections required, the provenance of corrections and the evaluation of options that have been adopted for the recently released v2.0 dataset (https://doi.org/10.5270/esa-sea_level_cci-1993_2015-v_2.0-201612). This information enables scientists and other users to clearly understand which corrections have been applied and their effects on the sea level dataset. The overall result of these changes is that the rate of rise of global mean sea level (GMSL) still equates to ∼ 3.2 mm yr−1 during 1992–2015, but there is now greater confidence in this result as the errors associated with several of the corrections have been reduced. Compared with v1.1 of the SL_cci dataset, the new rate of change is 0.2 mm yr−1 less during 1993 to 2001 and 0.2 mm yr−1 higher during 2002 to 2014. Application of new correction models brought a reduction of altimeter crossover variances for most corrections

A new phase in the production of quality-controlled sea level data

Sea level is an essential climate variable (ECV) that has a direct effect on many people through inundations of coastal areas, and it is also a clear indicator of climate changes due to external forcing factors and internal climate variability. Regional patterns of sea level change inform us on ocean circulation variations in response to natural climate modes such as El Niño and the Pacific Decadal Oscillation, and anthropogenic forcing. Comparing numerical climate models to a consistent set of observations enables us to assess the performance of these models and help us to understand and predict these phenomena, and thereby alleviate some of the environmental conditions associated with them. All such studies rely on the existence of long-term consistent high-accuracy datasets of sea level. The Climate Change Initiative (CCI) of the European Space Agency was established in 2010 to provide improved time series of some ECVs, including sea level, with the purpose of providing such data openly to all to enable the widest possible utilisation of such data. Now in its second phase, the Sea Level CCI project (SL_cci) merges data from nine different altimeter missions in a clear, consistent and well-documented manner, selecting the most appropriate satellite orbits and geophysical corrections in order to further reduce the error budget. This paper summarises the corrections required, the provenance of corrections and the evaluation of options that have been adopted for the recently released v2.0 dataset (https://doi.org/10.5270/esa-sea_level_cci-1993_2015-v_2.0-201612). This information enables scientists and other users to clearly understand which corrections have been applied and their effects on the sea level dataset. The overall result of these changes is that the rate of rise of global mean sea level (GMSL) still equates to ∼ 3.2 mm yr−1 during 1992–2015, but there is now greater confidence in this result as the errors associated with several of the corrections have been reduced. Compared with v1.1 of the SL_cci dataset, the new rate of change is 0.2 mm yr−1 less during 1993 to 2001 and 0.2 mm yr−1 higher during 2002 to 2014. Application of new correction models brought a reduction of altimeter crossover variances for most corrections

Uncertainty information in climate data records from Earth observation

Climate data records (CDRs) derived from Earth observation (EO) should include rigorous uncertainty information, to support application of the data in policy, climate modelling and numerical weather prediction reanalysis. Uncertainty, error and quality are distinct concepts, and CDR products should follow international norms for presenting quantified uncertainty. Ideally, uncertainty should be quantified per datum in a CDR, and the uncertainty estimates should be able to discriminate more and less certain data with confidence. In this case, flags for data quality should not duplicate uncertainty information, but instead describe complementary information (such as the confidence held in the uncertainty estimate provided, or indicators of conditions violating retrieval assumptions). Errors have many sources and some are correlated across a wide range of time and space scales. Error effects that contribute negligibly to the total uncertainty in a single satellite measurement can be the dominant sources of uncertainty in a CDR on large space and long time scales that are highly relevant for some climate applications. For this reason, identifying and characterizing the relevant sources of uncertainty for CDRs is particularly challenging. Characterisation of uncertainty caused by a given error effect involves assessing the magnitude of the effect, the shape of the error distribution, and the propagation of the uncertainty to the geophysical variable in the CDR accounting for its error correlation properties. Uncertainty estimates can and should be validated as part of CDR validation, where possible. These principles are quite general, but the form of uncertainty information appropriate to different essential climate variables (ECVs) is highly variable, as confirmed by a quick review of the different approaches to uncertainty taken across different ECVs in the European Space Agency’s Climate Change Initiative. User requirements for uncertainty information can conflict with each other, and again a variety of solutions and compromises are possible. The concept of an ensemble CDR as a simple means of communicating rigorous uncertainty information to users is discussed. Our review concludes by providing eight recommendations for good practice in providing and communicating uncertainty in EO-based climate data records

Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma

Genome-wide association studies (GWAS) have identified ~20 melanoma susceptibility loci, most of which are not functionally characterized. Here we report an approach integrating massively-parallel reporter assays (MPRA) with cell-type-specific epigenome and expression quantitative trait loci (eQTL) to identify susceptibility genes/variants from multiple GWAS loci. From 832 high-LD variants, we identify 39 candidate functional variants from 14 loci displaying allelic transcriptional activity, a subset of which corroborates four colocalizing melanocyte cis-eQTL genes. Among these, we further characterize the locus encompassing the HIV-1 restriction gene, MX2 (Chr21q22.3), and validate a functional intronic variant, rs398206. rs398206 mediates the binding of the transcription factor, YY1, to increase MX2 levels, consistent with the cis-eQTL of MX2 in primary human melanocytes. Melanocyte-specific expression of human MX2 in a zebrafish model demonstrates accelerated melanoma formation in a BRAFV600E background. Our integrative approach streamlines GWAS follow-up studies and highlights a pleiotropic function of MX2 in melanoma susceptibility

Heat stored in the Earth system 1960–2020: where does the energy go?

The Earth climate system is out of energy balance, and heat has accumulated continuously over the past decades, warming the ocean, the land, the cryosphere, and the atmosphere. According to the Sixth Assessment Report by Working Group I of the Intergovernmental Panel on Climate Change, this planetary warming over multiple decades is human-driven and results in unprecedented and committed changes to the Earth system, with adverse impacts for ecosystems and human systems. The Earth heat inventory provides a measure of the Earth energy imbalance (EEI) and allows for quantifying how much heat has accumulated in the Earth system, as well as where the heat is stored. Here we show that the Earth system has continued to accumulate heat, with 381±61 ZJ accumulated from 1971 to 2020. This is equivalent to a heating rate (i.e., the EEI) of 0.48±0.1 W m−2. The majority, about 89 %, of this heat is stored in the ocean, followed by about 6 % on land, 1 % in the atmosphere, and about 4 % available for melting the cryosphere. Over the most recent period (2006–2020), the EEI amounts to 0.76±0.2 W m−2. The Earth energy imbalance is the most fundamental global climate indicator that the scientific community and the public can use as the measure of how well the world is doing in the task of bringing anthropogenic climate change under control. Moreover, this indicator is highly complementary to other established ones like global mean surface temperature as it represents a robust measure of the rate of climate change and its future commitment. We call for an implementation of the Earth energy imbalance into the Paris Agreement's Global Stocktake based on best available science. The Earth heat inventory in this study, updated from von Schuckmann et al. (2020), is underpinned by worldwide multidisciplinary collaboration and demonstrates the critical importance of concerted international efforts for climate change monitoring and community-based recommendations and we also call for urgently needed actions for enabling continuity, archiving, rescuing, and calibrating efforts to assure improved and long-term monitoring capacity of the global climate observing system. The data for the Earth heat inventory are publicly available, and more details are provided in Table 4

Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma

Studying cancer metabolism gives insight into tumorigenic survival mechanisms and susceptibilities. In melanoma, we identify HEXIM1, a transcription elongation regulator, as a melanoma tumor suppressor that responds to nucleotide stress. HEXIM1 expression is low in melanoma. Its overexpression in a zebrafish melanoma model suppresses cancer formation, while its inactivation accelerates tumor onset in vivo. Knockdown of HEXIM1 rescues zebrafish neural crest defects and human melanoma proliferation defects that arise from nucleotide depletion. Under nucleotide stress, HEXIM1 is induced to form an inhibitory complex with P-TEFb, the kinase that initiates transcription elongation, to inhibit elongation at tumorigenic genes. The resulting alteration in gene expression also causes anti-tumorigenic RNAs to bind to and be stabilized by HEXIM1. HEXIM1 plays an important role in inhibiting cancer cell-specific gene transcription while also facilitating anti-cancer gene expression. Our study reveals an important role for HEXIM1 in coupling nucleotide metabolism with transcriptional regulation in melanoma