skip to main content

Explore Research Products in the NSF-PAR

  • Home
  • Search Results
  • Page 1 of 1

Search for: All records

Creators/Authors contains: "Chen, Chong"

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. ; ; ; ; ; ; ; ; ; ( , mSystems)
    Wilkins, Laetitia G. (Ed.)
    Beneficial relationships between animals and microbial organisms (symbionts) are ubiquitous in nature. In the ocean, microbial symbionts are typically acquired from the environment and their composition across geographic locations is often shaped by adaptation to local habitat conditions. However, it is currently unknown how generalizable these patterns are across symbiotic systems that have contrasting ecological characteristics. To address this question, we compared symbiont population structure between deep-sea hydrothermal vent mussels and co-occurring but ecologically distinct snail species. Our analyses show that mussel symbiont populations are less partitioned by geography and do not demonstrate evidence for environmental adaptation. We posit that the mussel's mixotrophic feeding mode may lower its need to affiliate with locally adapted symbiont strains, while microhabitat stability and symbiont genomic mixing likely favors persistence of symbiont strains across geographic locations. Altogether, these findings further our understanding of the mechanisms shaping symbiont population structure in marine environmentally transmitted symbioses. 
    more » « less
    Full Text Available 
  2. ; ; ; ; ( , Philosophical Transactions of the Royal Society B: Biological Sciences)
    null (Ed.)
    Choosing the optimum assembly approach is essential to achieving a high-quality genome assembly suitable for comparative and evolutionary genomic investigations. Significant recent progress in long-read sequencing technologies such as PacBio and Oxford Nanopore Technologies (ONT) has also brought about a large variety of assemblers. Although these have been extensively tested on model species such as Homo sapiens and Drosophila melanogaster , such benchmarking has not been done in Mollusca, which lacks widely adopted model species. Molluscan genomes are notoriously rich in repeats and are often highly heterozygous, making their assembly challenging. Here, we benchmarked 10 assemblers based on ONT raw reads from two published molluscan genomes of differing properties, the gastropod Chrysomallon squamiferum (356.6 Mb, 1.59% heterozygosity) and the bivalve Mytilus coruscus (1593 Mb, 1.94% heterozygosity). By optimizing the assembly pipeline, we greatly improved both genomes from previously published versions. Our results suggested that 40–50X of ONT reads are sufficient for high-quality genomes, with Flye being the recommended assembler for compact and less heterozygous genomes exemplified by C. squamiferum , while NextDenovo excelled for more repetitive and heterozygous molluscan genomes exemplified by M. coruscus . A phylogenomic analysis using the two updated genomes with 32 other published high-quality lophotrochozoan genomes resulted in maximum support across all nodes, and we show that improved genome quality also leads to more complete matrices for phylogenomic inferences. Our benchmarking will ensure efficiency in future assemblies for molluscs and perhaps also for other marine phyla with few genomes available. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’. 
    more » « less
    Full Text Available 
  3. ; ; ; ; ; ; ( , WWW '21: Proceedings of the Web Conference 2021)
    null (Ed.)
    Full Text Available 
  4. ; ; ; ; ; ; ; ; ; ; et al ( , Marine Policy)
    Full Text Available 
  5. ; ; ; ; ; ; ; ( , EcoMat)
    Abstract

    Hole transport layer (HTL) is very important for the power conversion efficiency (PCE) and stability of perovskite solar cells (PSCs). As current state‐of‐the‐art HTL, Li‐TFSI doped spiro‐OMeTAD often suffers low conductivity and the hydrolysis of the additive Li‐TFSI, which significantly hinders the further improvement of PCE of PSCs. Besides, conventional spiro‐OMeTAD has no functional of directly passivating the perovskite crystal defects. Herein, multifunctional TiO2nanoparticles (NPs)‐modified CNT (CNT:TiO2) doped spiro‐OMeTAD (spiro‐OMeTAD+CNT:TiO2) HTL is reported for the first time. The incorporated CNT:TiO2not only significantly increases the conductivity of spiro‐OMeTAD+CNT:TiO2, but also effectively passivates the crystal defects of perovskite layer. The optimized PSCs with spiro‐OMeTAD+CNT:TiO2HTL achieved a peak PCE of 21.53%, much higher than that (17.90%) of the conventional spiro‐OMeTAD based PSCs and also show significantly improved stability.image

     
    more » « less
  6. ; ; ; ; ; ( , Physical Review A)
  7. ; ; ; ; ; ; ; ; ; ; et al ( , The Plant Journal)
    Summary

    LIKE HETEROCHROMATIN PROTEIN1 (LHP1) encodes the only plant homologue of the metazoan HETEROCHROMATIN PROTEIN1 (HP1) protein family. The LHP1 protein is necessary for proper epigenetic regulation of a range of developmental processes in plants. LHP1 is a transcriptional repressor of flowering‐related genes, such asFLOWERING LOCUS T(FT),FLOWERING LOCUS C(FLC),AGAMOUS(AG) andAPETALA 3(AP3). We found that LHP1 interacts with importin α‐1 (IMPα‐1), importin α‐2 (IMPα‐2) and importin α‐3 (IMPα‐3) bothin vitroandin vivo. A genetic approach revealed that triple mutation ofimpα‐1,impα‐2andimpα‐3resulted in Arabidopsis plants with a rapid flowering phenotype similar to that of plants with mutations inlhp1due to the upregulation ofFTexpression. Nuclear targeting of LHP1 was severely impaired in theimpαtriple mutant, resulting in the de‐repression of LHP1 target genesAG,AP3andSHATTERPROOF 1as well asFT. Therefore, the importin proteins IMPα‐1, ‐2 and ‐3 are necessary for the nuclear import of LHP1.

     
    more » « less
  8. ; ; ; ; ; ; ; ; ; ; et al ( , Global Ecology and Biogeography)
    Abstract Motivation

    Traits are increasingly being used to quantify global biodiversity patterns, with trait databases growing in size and number, across diverse taxa. Despite growing interest in a trait‐based approach to the biodiversity of the deep sea, where the impacts of human activities (including seabed mining) accelerate, there is no single repository for species traits for deep‐sea chemosynthesis‐based ecosystems, including hydrothermal vents. Using an international, collaborative approach, we have compiled the first global‐scale trait database for deep‐sea hydrothermal‐vent fauna – sFDvent (sDiv‐funded trait database for theFunctionalDiversity ofvents). We formed a funded working group to select traits appropriate to: (a) capture the performance of vent species and their influence on ecosystem processes, and (b) compare trait‐based diversity in different ecosystems. Forty contributors, representing expertise across most known hydrothermal‐vent systems and taxa, scored species traits using online collaborative tools and shared workspaces. Here, we characterise the sFDvent database, describe our approach, and evaluate its scope. Finally, we compare the sFDvent database to similar databases from shallow‐marine and terrestrial ecosystems to highlight how the sFDvent database can inform cross‐ecosystem comparisons. We also make the sFDvent database publicly available online by assigning a persistent, unique DOI.

     Main types of variable contained

    Six hundred and forty‐six vent species names, associated location information (33 regions), and scores for 13 traits (in categories: community structure, generalist/specialist, geographic distribution, habitat use, life history, mobility, species associations, symbiont, and trophic structure). Contributor IDs, certainty scores, and references are also provided.

     Spatial location and grain

    Global coverage (grain size: ocean basin), spanning eight ocean basins, including vents on 12 mid‐ocean ridges and 6 back‐arc spreading centres.

     Time period and grain

    sFDvent includes information on deep‐sea vent species, and associated taxonomic updates, since they were first discovered in 1977. Time is not recorded. The database will be updated every 5 years.

     Major taxa and level of measurement

    Deep‐sea hydrothermal‐vent fauna with species‐level identification present or in progress.

     Software format

    .csv and MS Excel (.xlsx).

     
    more » « less