Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)

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Changes in vertical ice extent along the East Antarctic Ice Sheet margin in western Dronning Maud Land – initial field and modelling results of the MAGIC-DML collaboration

Constraining numerical ice sheet models by comparison with observational data is crucial to address the interactions between cryosphere and climate at a wide range of scales. Such models are tested and refined by comparing model predictions of past ice geometries with field-based reconstructions from geological, geomorphological, and ice core data. However, for the East Antarctic Ice sheet, there is a critical gap in the empirical data necessary to reconstruct changes in ice sheet geometry in the Dronning Maud Land (DML) region. In addition, there is poor control on the regional climate history of the ice sheet margin, because ice-core locations, where detailed reconstructions of climate history exist, are located on high inland domes. This leaves numerical models ofregional glaciation history in this near-coastal area largely unconstrained. MAGIC-DML is an ongoing Swedish-US-Norwegian-German-UK collaboration with a focus on improvingice sheet models of the western DML margin by combining advances in modeling with filling critical data gaps regarding the timing and pattern of ice-surface changes. A combination of geomorphological mapping using remote sensing data, field observations, cosmogenic nuclide surface exposure dating, and numerical ice sheetmodeling are being used in an iterative manner to produce a comprehensive reconstruction of the glacial historyof western DML. Here, we present an overview of the project, field evidence for formerly higher ice surfaces and in-situ cosmogenic nuclide measurements from the 2016/17 expedition. Preliminary field evidence indicate that interior sectors of DML have experienced a general decrease in ice sheet thickness since the late Miocene, with potential episodes of increasing thickness in the late Pleistocene (700-300 ka, 250-75 ka). To aid in interpreting these field data, new high-resolution ice sheet model reconstructions, constraining ice sheet configurations during key episodes, are presented

Mid-Pleistocene ice sheet fluctuations from cosmogenic nuclide field constraints in western Dronning Maud Land, Antarctica

The East Antarctic Ice Sheet (EAIS) is generally assumed to have been relatively insensitive to Quaternary climat echange. However, recent studies have shown potential instabilities in coastal, marine sectors of the EAIS. In addition, long-term climate reconstructions and modelling experiments indicate the potential for significant changes in ice volume and ice sheet configuration since the Pliocene. Hence, more empirical evidence for ice surface and ice volume changes is required to discriminate between contrasting inferences. MAGIC-DML is an ongoing Swedish-US-Norwegian-German-UK collaboration focused on improving ice sheetm odels by filling critical data gaps that exist in our knowledge of the timing and pattern of ice surface changes along the western Dronning Maud Land (DML) margin and combining this with advances in numerical techniques. As part of the project, field studies in the 2016/17 and 2017/18 austral summers targeted selected sites spanning accessible altitudes in the Heimefrontfjella, Vestfjella, Ahlmannryggen, Borgmassivet, and Kirwanveggen nunatakranges for in situcosmogenic nuclide sampling. Comparing concentrations of nuclides with widely differing half-lives in bedrock and erratics from a range of altitudes above modern ice surfaces can provide information on ice sheet fluctuations and complex burial and exposure histories, and thus, past configurations of non-erosive ice. Quartz-bearing rock types were sampled and analyzed for 10Be (t1/21.4 My),14C (t1/25.7 ky),26Al (t1/2705ky), and 21Ne (stable), and mafic lithologies for36Cl (t1/2301 ky). Results thus far for 3210Be and 26Al isotope pairs complemented with seven21Ne measurements have yielded some consistent patterns of paleoglaciation for the western DML margin. Eight out of fourteen bedrock samples from high-elevation (1700-2238 m a.s.l.) ridges and summits return some of the oldest exposure ages in Antarctica and have consistent 10Be,26Al, and 21Ne minimum apparent exposure ages of 1.8-4.1 Ma. Initial results therefore indicate that parts of the ice sheet marginal to the Antarctic plateau, along the Heimefrontfjella range, generally have experienced a decrease in ice thickness since the late Miocene. Another six bedrock samples (1556-1732 ma.s.l.) fall in the 300-700 ka range, and they all show significant burial. At face value, perhaps this indicates aregional ice sheet surface above 1700 m a.s.l. for much of the Plio-early Pleistocene. All other samples analyzedto date are erratics from lower elevation and more coastal sites (10 from nunataks at 553-1400 m a.s.l., and 6 froma surface moraine at 1385 m a.s.l.), exhibiting ages between 59 and 275 ka, save for two (4 and 6 ka). Whereas almost all of the nunatak erratics (including the young ones) show significant burial durations, five of the six surface moraine samples do not. These 2016/17 field samples are not yet leading to conclusive age constraints but already start to paint a picture of the western DML margin being relatively stable although there was possibly one or more episodes of relatively limited ice thickening during the last 700 ka

Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote

The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance

Arabidopsis CaM Binding Protein CBP60g Contributes to MAMP-Induced SA Accumulation and Is Involved in Disease Resistance against Pseudomonas syringae

Salicylic acid (SA)-induced defense responses are important factors during effector triggered immunity and microbe-associated molecular pattern (MAMP)-induced immunity in plants. This article presents evidence that a member of the Arabidopsis CBP60 gene family, CBP60g, contributes to MAMP-triggered SA accumulation. CBP60g is inducible by both pathogen and MAMP treatments. Pseudomonas syringae growth is enhanced in cbp60g mutants. Expression profiles of a cbp60g mutant after MAMP treatment are similar to those of sid2 and pad4, suggesting a defect in SA signaling. Accordingly, cbp60g mutants accumulate less SA when treated with the MAMP flg22 or a P. syringae hrcC strain that activates MAMP signaling. MAMP-induced production of reactive oxygen species and callose deposition are unaffected in cbp60g mutants. CBP60g is a calmodulin-binding protein with a calmodulin-binding domain located near the N-terminus. Calmodulin binding is dependent on Ca2+. Mutations in CBP60g that abolish calmodulin binding prevent complementation of the SA production and bacterial growth defects of cbp60g mutants, indicating that calmodulin binding is essential for the function of CBP60g in defense signaling. These studies show that CBP60g constitutes a Ca2+ link between MAMP recognition and SA accumulation that is important for resistance to P. syringae

Aging impacts transcriptomes but not genomes of hormone-dependent breast cancers

Age is one of the most important risk factors for human malignancies, including breast cancer; in addition, age-at-diagnosis has been shown to be an independent indicator of breast cancer prognosis. However, except for inherited forms of breast cancer, there is little genetic or epigenetic understanding of the biological basis linking aging with sporadic breast cancer incidence and its clinical behavior

Human plague: An old scourge that needs new answers

Yersinia pestis, the bacterial causative agent of plague, remains an important threat to human health. Plague is a rodent-borne disease that has historically shown an outstanding ability to colonize and persist across different species, habitats, and environments while provoking sporadic cases, outbreaks, and deadly global epidemics among humans. Between September and November 2017, an outbreak of urban pneumonic plague was declared in Madagascar, which refocused the attention of the scientific community on this ancient human scourge. Given recent trends and plague’s resilience to control in the wild, its high fatality rate in humans without early treatment, and its capacity to disrupt social and healthcare systems, human plague should be considered as a neglected threat. A workshop was held in Paris in July 2018 to review current knowledge about plague and to identify the scientific research priorities to eradicate plague as a human threat. It was concluded that an urgent commitment is needed to develop and fund a strong research agenda aiming to fill the current knowledge gaps structured around 4 main axes: (i) an improved understanding of the ecological interactions among the reservoir, vector, pathogen, and environment; (ii) human and societal responses; (iii) improved diagnostic tools and case management; and (iv) vaccine development. These axes should be cross-cutting, translational, and focused on delivering context-specific strategies. Results of this research should feed a global control and prevention strategy within a “One Health” approach

Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)

DATA AVAILABILITY : Genome data have been deposited in Genbank (short read archive, Supplementary Data Table 3). Coding sequences of Z. japonica and Z. marina for the ASTRAL analysis can be found on figshare (https://doi.org/10.6084/m9.figshare.21626327.v1). VCF files of the 11,705 core SNPs can be accessed at https://doi.org/10.6084/m9.figshare.21629471.v1. Source data for Fig. 1b,c are given, as well as statistics of sequencing coverage, mapping rate and further specifications of each sequenced library (Supplementary Tables 1–3). Source data are provided with this paper.CODE AVAILABILITY : Custom-made scripts are deposited on GitHub for SNP filtering (github.com/leiyu37/populationGenomics_ZM.git), for clone mate detection (github.com/leiyu37/Detecting-clonemates.git), for heterozygote and nucleotide diversity quantification (github.com/leiyu37/populationGenomics_ZM.git) and to prepare SplitsTree input files (https://github.com/leiyu37/populationGenomics_ZM/blob/main/10_SplitsTree/vcf2alignment.py) and SNAPP input files (github.com/mmatschiner/snapp_prep). Scripts for calculating D-statistics are available at github.com/mmatschiner/tutorials/blob/master/analysis_of_introgression_with_snp_data/src/plot_d.rb. Scripts to prepare the gene presence/absence analysis are deposited on https://github.com/leiyu37/populationGenomics_ZM/tree/main/gene_presense_absence_analysis. Further software code for the MSMC analysis are found at http://lh3lh3.users.sourceforge.net/snpable.shtml (generation of mappability mask file for each of six chromosomes using SNPable) and at https://github.com/stschiff/msmc-tools (generation of ramet-specific mask file based on a bam file using bamCaller.py).SUPPLEMENTARY MATERIAL : Supplementary Notes 1–8, Tables 1–6 and Figs. 1–12.SUPPLEMENTARY DATA : Table 1: Sequence coverage. Supplementary Data Table 2: Mapping rate. Supplementary Data Table 3: Accession number of each library.SOURCE DATA : Fig. 1b,c.Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.Open access funding provided by GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel. The China Scholarship Council, the Helmholtz School for Marine Data Science, the US Department of Energy Joint Genome Institute Community Sequencing Program, the Office of Science of the US Department of Energy and the National Science Foundation.http://www.nature.com/nplantshj2024BiochemistryGeneticsMicrobiology and Plant PathologyLife below wate

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children