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  • American Association for the Advancement of Science (AAAS)  (33)
  • 1
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 377, No. 6614 ( 2022-09-30)
    Abstract: The Perseverance rover landed in Jezero crater on Mars on 18 February 2021 with three scientific objectives: to explore the geologic setting of the crater, to identify ancient habitable environments and assess the possibility of past martian life, and to collect samples for potential transport to Earth for analysis in laboratories. In the 290 martian days (sols) after landing, Perseverance explored rocks of the Jezero crater floor. RATIONALE Jezero, a 45-km-diameter crater, was selected for investigation by Perseverance because orbital observations had shown that it previously contained an open-system lake, prior to ~3.5 billion years ago. Major climate change then left Mars in its current cold and dry state. On Earth, broadly similar environments of similar age to Jezero contain evidence of microbial life. Jezero crater contains a well-preserved delta, identified as a target for astrobiological investigation by the rover. Perseverance landed ~2 km away from the delta, on rocks of the crater floor. Previously proposed origins for these rocks have ranged from lake (or river) sediments to lava flows. Olivine-rich rocks identified on the crater floor, as well as in the area surrounding Jezero, have previously been attributed to a widely distributed impact melt or volcanic deposit, variably altered to carbonate. We used Perseverance to investigate the origin of the crater floor rocks and to acquire samples of them. RESULTS The Jezero crater floor consists of two geologic units: the informally named Máaz formation covers much of the crater floor and surrounds the other unit, which is informally named the Séítah formation. Máaz rocks display a range of morphologies: structureless boulders, flagstone-like outcrops, and ridges that are several meters high. The ridges expose prominent layers, ranging in thickness from a few centimeters to a few tens of centimeters. Rocks of Séítah are often tabular and strongly layered, with layer thicknesses ranging from centimeters to meters. Máaz and Séítah rocks display no outcrop or grain-scale evidence for transport by wind or water. Perseverance observations show that the Máaz rocks consist of 0.5- to 1-mm interlocking crystals of pyroxene and plagioclase. Combined with bulk chemical composition measurements, this suggests Máaz is an igneous unit that cooled slowly. In contrast, most Séítah rocks are very rich in magnesium and are dominated by densely packed 2- to 3-mm-diameter crystals of olivine, surrounded by pyroxene. These properties indicate settling and accumulation of olivine near the base of a thick magma body, such as an intrusion, lava lake, or thick lava flow. Ground-penetrating radar indicates that Séítah rocks dip beneath the Máaz formation. We hypothesize that Máaz could be the magmatic complement to the Séítah olivine-rich rocks or, alternatively, Máaz could be a series of basaltic lavas that flowed over and around the older Séítah formation. The olivines in the Séítah formation are rimmed with magnesium-iron carbonate, likely produced by interaction with CO 2 -rich water. Máaz formation rocks contain an aqueously deposited iron oxide or iron silicate alteration product. Both units commonly contain patches of bright-white salts, including sodium perchlorate and various sulfate minerals. Although both rock units have been altered by water, preservation of the original igneous minerals and the absence of aluminous clay minerals indicate that the alteration occurred under low water/rock ratio and that there was little loss of soluble species to the surroundings. It remains unclear when these aqueous processes occurred and whether they relate to the lake that once filled Jezero. The exposure of the olivine-rich Séítah rocks at the surface, the absence of lake or river sediment in the exploration area, and several nearby erosional remnant hills of delta sediment indicate that substantial crater floor erosion occurred after formation of these igneous units. Samples of both of these geologic units were collected as drill cores. The drill cores were stored in ultraclean sample tubes, for potential transport to Earth by future missions in the early 2030s. CONCLUSION The floor of Jezero crater explored by Perseverance consists of two distinct igneous units that have both experienced reactions with liquid water. Multiple rock cores were collected from these units for potential transport to Earth and analysis in terrestrial laboratories. Sample collection by Perseverance on Mars. This image mosaic was acquired by the WATSON camera on the rover’s robot arm. Rock cores were drilled from the two holes (arrow) in an igneous rock of the Máaz formation. The 6-cm-long, 1.3-cm-diameter cores were sealed into individual sample tubes and are now stored inside the rover.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2022
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    detail.hit.zdb_id: 2066996-3
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  • 2
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 378, No. 6615 ( 2022-10-07)
    Abstract: Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century. Expanse of SARS-CoV-2 sequencing capacity in Africa. ( A ) African countries (shaded in gray) and institutions (red circles) with on-site sequencing facilities that are capable of producing SARS-CoV-2 whole genomes locally. ( B ) The number of SARS-CoV-2 genomes produced per country and the proportion of those genomes that were produced locally, regionally within Africa, or abroad. ( C ) Decreased turnaround time of sequencing output in Africa to an almost real-time release of genomic data.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2022
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    detail.hit.zdb_id: 2066996-3
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  • 3
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 362, No. 6420 ( 2018-12-14)
    Abstract: Despite progress in defining genetic risk for psychiatric disorders, their molecular mechanisms remain elusive. Addressing this, the PsychENCODE Consortium has generated a comprehensive online resource for the adult brain across 1866 individuals. The PsychENCODE resource contains ~79,000 brain-active enhancers, sets of Hi-C linkages, and topologically associating domains; single-cell expression profiles for many cell types; expression quantitative-trait loci (QTLs); and further QTLs associated with chromatin, splicing, and cell-type proportions. Integration shows that varying cell-type proportions largely account for the cross-population variation in expression (with 〉 88% reconstruction accuracy). It also allows building of a gene regulatory network, linking genome-wide association study variants to genes (e.g., 321 for schizophrenia). We embed this network into an interpretable deep-learning model, which improves disease prediction by ~6-fold versus polygenic risk scores and identifies key genes and pathways in psychiatric disorders.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2018
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
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  • 4
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 362, No. 6420 ( 2018-12-14)
    Abstract: To broaden our understanding of human neurodevelopment, we profiled transcriptomic and epigenomic landscapes across brain regions and/or cell types for the entire span of prenatal and postnatal development. Integrative analysis revealed temporal, regional, sex, and cell type–specific dynamics. We observed a global transcriptomic cup-shaped pattern, characterized by a late fetal transition associated with sharply decreased regional differences and changes in cellular composition and maturation, followed by a reversal in childhood-adolescence, and accompanied by epigenomic reorganizations. Analysis of gene coexpression modules revealed relationships with epigenomic regulation and neurodevelopmental processes. Genes with genetic associations to brain-based traits and neuropsychiatric disorders (including MEF2C , SATB2 , SOX5 , TCF4 , and TSHZ3 ) converged in a small number of modules and distinct cell types, revealing insights into neurodevelopment and the genomic basis of neuropsychiatric risks.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2018
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    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
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  • 5
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 375, No. 6586 ( 2022-03-18), p. 1275-1281
    Abstract: A widespread adaptive change in antiherbivore response is seen in a common plant species in urban environments across 160 cities.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2022
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
    SSG: 11
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  • 6
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 361, No. 6398 ( 2018-07-13)
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2018
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
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  • 7
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 362, No. 6420 ( 2018-12-14)
    Abstract: Most genetic risk for psychiatric disease lies in regulatory regions, implicating pathogenic dysregulation of gene expression and splicing. However, comprehensive assessments of transcriptomic organization in diseased brains are limited. In this work, we integrated genotypes and RNA sequencing in brain samples from 1695 individuals with autism spectrum disorder (ASD), schizophrenia, and bipolar disorder, as well as controls. More than 25% of the transcriptome exhibits differential splicing or expression, with isoform-level changes capturing the largest disease effects and genetic enrichments. Coexpression networks isolate disease-specific neuronal alterations, as well as microglial, astrocyte, and interferon-response modules defining previously unidentified neural-immune mechanisms. We integrated genetic and genomic data to perform a transcriptome-wide association study, prioritizing disease loci likely mediated by cis effects on brain expression. This transcriptome-wide characterization of the molecular pathology across three major psychiatric disorders provides a comprehensive resource for mechanistic insight and therapeutic development.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2018
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    detail.hit.zdb_id: 2066996-3
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  • 8
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 374, No. 6567 ( 2021-10-29), p. 544-544
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2021
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
    SSG: 11
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  • 9
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 369, No. 6509 ( 2020-09-11)
    Abstract: Rare genetic variants are abundant across the human genome, and identifying their function and phenotypic impact is a major challenge. Measuring aberrant gene expression has aided in identifying functional, large-effect rare variants (RVs). Here, we expanded detection of genetically driven transcriptome abnormalities by analyzing gene expression, allele-specific expression, and alternative splicing from multitissue RNA-sequencing data, and demonstrate that each signal informs unique classes of RVs. We developed Watershed, a probabilistic model that integrates multiple genomic and transcriptomic signals to predict variant function, validated these predictions in additional cohorts and through experimental assays, and used them to assess RVs in the UK Biobank, the Million Veterans Program, and the Jackson Heart Study. Our results link thousands of RVs to diverse molecular effects and provide evidence to associate RVs affecting the transcriptome with human traits.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2020
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    detail.hit.zdb_id: 2066996-3
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  • 10
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 374, No. 6566 ( 2021-10-22), p. 423-431
    Abstract: The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    RVK:
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2021
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    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
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