Displaying all 16 publications

  1. Zhang X, Li C, Zhou Y, Huang J, Yu T, Liu X, et al.
    iScience, 2020 Apr 24;23(4):101032.
    PMID: 32304863 DOI: 10.1016/j.isci.2020.101032
    Hanging Coffin is a unique and ancient burial custom that has been practiced in southern China, Southeast Asia, and near Oceania regions for more than 3,000 years. Here, we conducted mitochondrial whole-genome analyses of 41 human remains sampled from 13 Hanging Coffin sites in southern China and northern Thailand, which were dated between ∼2,500 and 660 years before present. We found that there were genetic connections between the Hanging Coffin people living in different geographic regions. Notably, the matrilineal genetic diversity of the Hanging Coffin people from southern China is much higher than those from northern Thailand, consistent with the hypothesized single origin of the Hanging Coffin custom in southern China about 3,600 years ago, followed by its dispersal in southern China through demic diffusion, whereas the major dispersal pattern in Southeast Asia is cultural assimilation in the past 2,000 years.
  2. Chek MF, Kim SY, Mori T, Tan HT, Sudesh K, Hakoshima T
    iScience, 2020 May 22;23(5):101084.
    PMID: 32388399 DOI: 10.1016/j.isci.2020.101084
    Biodegradable polyester polyhydroxyalkanoate (PHA) is a promising bioplastic material for industrial use as a replacement for petroleum-based plastics. PHA synthase PhaC forms an active dimer to polymerize acyl moieties from the substrate acyl-coenzyme A (CoA) into PHA polymers. Here we present the crystal structure of the catalytic domain of PhaC from Chromobacterium sp. USM2, bound to CoA. The structure reveals an asymmetric dimer, in which one protomer adopts an open conformation bound to CoA, whereas the other adopts a closed conformation in a CoA-free form. The open conformation is stabilized by the asymmetric dimerization and enables PhaC to accommodate CoA and also to create the product egress path. The bound CoA molecule has its β-mercaptoethanolamine moiety extended into the active site with the terminal SH group close to active center Cys291, enabling formation of the reaction intermediate by acylation of Cys291.
  3. Niemann J, Gopalakrishnan S, Yamaguchi N, Ramos-Madrigal J, Wales N, Gilbert MTP, et al.
    iScience, 2021 Jan 22;24(1):101904.
    PMID: 33364590 DOI: 10.1016/j.isci.2020.101904
    The Japanese or Honshū wolf was one the most distinct gray wolf subspecies due to its small stature and endemicity to the islands of Honshū, Shikoku, and Kyūshū. Long revered as a guardian of farmers and travellers, it was persecuted from the 17th century following a rabies epidemic, which led to its extinction in the early 20th century. To better understand its evolutionary history, we sequenced the nuclear genome of a 19th century Honshū wolf specimen to an average depth of coverage of 3.7✕. We find Honshū wolves were closely related to a lineage of Siberian wolves that were previously believed to have gone extinct in the Late Pleistocene, thereby extending the survival of this ancient lineage until the early 20th century. We also detected significant gene flow between Japanese dogs and the Honshū wolf, corroborating previous reports on Honshū wolf dog interbreeding.
  4. Westbury MV, Petersen B, Garde E, Heide-Jørgensen MP, Lorenzen ED
    iScience, 2019 Apr 08.
    PMID: 31054839 DOI: 10.1016/j.isci.2019.03.023
    The narwhal (Monodon monoceros) is a highly specialized endemic Arctic cetacean, restricted to the Arctic seas bordering the North Atlantic. Low levels of genetic diversity have been observed across several narwhal populations using mitochondrial DNA and microsatellites. Despite this, the global abundance of narwhals was recently estimated at ∼170,000 individuals. However, the species is still considered vulnerable to changing climates due to its high specialization and restricted Arctic distribution. We assembled and annotated a genome from a narwhal from West Greenland. We find relatively low diversity at the genomic scale and show that this did not arise by recent inbreeding, but rather has been stable over an extended evolutionary timescale. We also find that the current large global abundance most likely reflects a recent rapid expansion from a much smaller founding population.
  5. Jenkins J, Ishak MI, Eales M, Gholinia A, Kulkarni S, Keller TF, et al.
    iScience, 2021 Jul 23;24(7):102818.
    PMID: 34355148 DOI: 10.1016/j.isci.2021.102818
    To robustly assess the antibacterial mechanisms of nanotopographies, it is critical to analyze the bacteria-nanotopography adhesion interface. Here, we utilize focused ion beam milling combined with scanning electron microscopy to generate three-dimensional reconstructions of Staphylococcus aureus or Escherichia coli interacting with nanotopographies. For the first time, 3D morphometric analysis has been exploited to quantify the intrinsic contact area between each nanostructure and the bacterial envelope, providing an objective framework from which to derive the possible antibacterial mechanisms of synthetic nanotopographies. Surfaces with nanostructure densities between 36 and 58 per μm2 and tip diameters between 27 and 50 nm mediated envelope deformation and penetration, while surfaces with higher nanostructure densities (137 per μm2) induced envelope penetration and mechanical rupture, leading to marked reductions in cell volume due to cytosolic leakage. On nanotopographies with densities of 8 per μm2 and tip diameters greater than 100 nm, bacteria predominantly adhered between nanostructures, resulting in cell impedance.
  6. Sinding MS, Ciucani MM, Ramos-Madrigal J, Carmagnini A, Rasmussen JA, Feng S, et al.
    iScience, 2021 Nov 19;24(11):103226.
    PMID: 34712923 DOI: 10.1016/j.isci.2021.103226
    The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey (Bos sauveli) and analyzed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus. We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so.
  7. Zywitza V, Frahm S, Krüger N, Weise A, Göritz F, Hermes R, et al.
    iScience, 2022 Nov 18;25(11):105414.
    PMID: 36388963 DOI: 10.1016/j.isci.2022.105414
    Less than 80 Sumatran rhinos (SR, Dicerorhinus sumatrensis) are left on earth. Habitat loss and limited breeding possibilities are the greatest threats to the species and lead to a continuous population decline. To stop the erosion of genetic diversity, reintroduction of genetic material is indispensable. However, as the propagation rate of captive breeding is far too low, innovative technologies have to be developed. Induced pluripotent stem cells (iPSCs) are a powerful tool to fight extinction. They give rise to each cell within the body including gametes and provide a unique modality to preserve genetic material across time. Additionally, they enable studying species-specific developmental processes. Here, we generate iPSCs from the last male Malaysian SR Kertam, who died in 2019, and characterize them comprehensively. Differentiation in cells of the three germ layers and cerebral organoids demonstrate their high quality and great potential for supporting the rescue of this critically endangered species.
  8. Li N, Yang Y, Shi Z, Lan Z, Arramel A, Zhang P, et al.
    iScience, 2022 Feb 18;25(2):103753.
    PMID: 35128355 DOI: 10.1016/j.isci.2022.103753
    Unique performance of the hybrid organic-inorganic halide perovskites (HOIPs) has attracted great attention because of their continuous exploration and breakthrough in a multitude of energy-related applications. However, the instability and lead-induced toxicity that arise in bulk perovskites are the two major challenges that impede their future commercialization process. To find a solution, a series of two-dimensional HOIPs (2D HOIPs) are investigated to prolong the device lifetime with highly efficient photoelectric conversion and energy storage. Herein, the recent advances of 2D HOIPs and their structural derivatives for the energy realms are summarized and discussed. The basic understanding of crystal structures, physicochemical properties, and growth mechanisms is presented. In addition, the current challenges and future directions to provide a roadmap for the development of next generation 2D HOIPs are prospected.
  9. Khatibi M, Khaidzir KAM, Syed Mahdzar SS
    iScience, 2023 Feb 17;26(2):105951.
    PMID: 36866036 DOI: 10.1016/j.isci.2023.105951
    Neighborhoods have received worldwide interest in sustainability assessment due to their suitable scale for representing the relationship between the individual and the city. Consequently, this has led to a focus on developing neighborhood sustainability assessment (NSA) systems and, thereby, studying the prominent NSA tools. Alternatively, this study aims to uncover formative concepts shaping the assessment of sustainable neighborhoods based on a systematic review of the empirical work by researchers. The study included a Scopus database search for papers measuring neighborhood sustainability and a literature review of 64 journal articles published between 2019 and 2021. Our results suggest that criteria related to sustainable form and morphology are the most widely measured criteria in the reviewed papers, interconnected with multiple aspects of neighborhood sustainability. The paper contributes to expanding the existing knowledge on neighborhood sustainability evaluation, further adding to the literature on designing sustainable cities and communities and achieving Sustainable Development Goal 11.
  10. Liu J, Chai Z, Wang H, Ivanov A, Kubelka V, Freckleton R, et al.
    iScience, 2023 Jun 16;26(6):106928.
    PMID: 37305692 DOI: 10.1016/j.isci.2023.106928
    Arctic environments are changing rapidly and if we are to understand the resilience of species to future changes, we need to investigate alterations in their life histories. Egg size and egg shape are key life-history traits, reflecting parental investment as well as influencing future reproductive success. Here we focus on egg characteristics in two Arctic shorebirds, the Dunlin (Calidris alpina) and the Temminck's stint (Calidris temminckii). Using egg photos that encompass their full breeding ranges, we show that egg characteristics exhibit significant longitudinal variations, and the variation in the monogamous species (Dunlin) is significantly greater than the polygamous species (Temminck's stint). Our finding is consistent with the recent "disperse-to-mate" hypothesis which asserts that polygamous species disperse further to find mates than monogamous species, and by doing so they create panmictic populations. Taken together, Arctic shorebirds offer excellent opportunities to understand evolutionary patterns in life history traits.
  11. Zhivulin VE, Trofimov EA, Zaitseva OV, Sherstyuk DP, Cherkasova NA, Taskaev SV, et al.
    iScience, 2023 Jul 21;26(7):107077.
    PMID: 37485374 DOI: 10.1016/j.isci.2023.107077
    The polycrystalline SrFe12O19 samples deeply substituted up to at.67% by Al3+, Ga3+, In3+, Co3+, and Cr3+ cations with a high configurational mixing entropy were prepared by solid-phase synthesis. Phase purity and unit cell parameters were obtained from XRD and analyzed versus the average ionic radius of the iron sublattice. The crystallite size varied around ∼4.5 μm. A comprehensive study of the magnetization was realized in various fields and temperatures. The saturation magnetization was calculated using the Law of Approach to Saturation. The accompanying magnetic parameters were determined. The magnetic crystallographic anisotropy coefficient and the anisotropy field were calculated. All investigated magnetization curves turned out to be nonmonotonic. The magnetic ordering and freezing temperatures were extracted from the ZFC and FC curves. The average size of magnetic clusters varied around ∼350 nm. The high values of the configurational mixing entropy and the phenomenon of magnetic dilution were taken into account.
  12. Bursell MG, Dikow RB, Figueiró HV, Dudchenko O, Flanagan JP, Aiden EL, et al.
    iScience, 2022 Dec 22;25(12):105647.
    PMID: 36590460 DOI: 10.1016/j.isci.2022.105647
    Similar to other apex predator species, populations of mainland (Neofelis nebulosa) and Sunda (Neofelis diardi) clouded leopards are declining. Understanding their patterns of genetic variation can provide critical insights on past genetic erosion and a baseline for understanding their long-term conservation needs. As a step toward this goal, we present draft genome assemblies for the two clouded leopard species to quantify their phylogenetic divergence, genome-wide diversity, and historical population trends. We estimate that the two species diverged 5.1 Mya, much earlier than previous estimates of 1.41 Mya and 2.86 Mya, suggesting they separated when Sundaland was becoming increasingly isolated from mainland Southeast Asia. The Sunda clouded leopard displays a distinct and reduced effective population size trajectory, consistent with a lower genome-wide heterozygosity and SNP density, relative to the mainland clouded leopard. Our results provide new insights into the evolutionary history and genetic health of this unique lineage of felids.
  13. Huang LL, Li SF, Huang WY, Jin JH, Oskolski AA
    iScience, 2023 Aug 18;26(8):107313.
    PMID: 37554461 DOI: 10.1016/j.isci.2023.107313
    Anatomical structure of mummified wood of Cryptocarya (Lauraceae) from the Upper Pleistocene of Maoming, South China and the woods of 15 extant species of Cryptocarya from China and Malaysia were examined. The fossil wood has been convincingly attributed to extant species Cryptocarya chinensis (Hance) Hemsl. This is the first reliable fossil record of Cryptocarya in Asia. The finding combined with the results of Biomod2 species distribution modeling suggest that the range of C. chinensis in the Late Pleistocene in South China and North Vietnam was very restricted due to increased continental aridity and enhanced temperature seasonality in this region. Thus, modern populations of C. chinensis in Maoming can be considered as glacial relicts. The mines (larval tunnels) produced by the larvae of flies from the genus Phytobia Lioy (Agromyzidae, Diptera) were observed in fossil wood under study. These cambial miners have never been reported in Cryptocarya.
  14. Ryon KA, Tierney BT, Frolova A, Kahles A, Desnues C, Ouzounis C, et al.
    iScience, 2022 Nov 18;25(11):104993.
    PMID: 36299999 DOI: 10.1016/j.isci.2022.104993
    The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic. The consortium has optimized their workflow for the collection, isolation, and sequencing of DNA and RNA collected from these various sites and processing them for metagenomics analysis, including the identification of SARS-CoV-2 and its variants. Here, the Consortium describes its foundations, and its ongoing work to expand on this network and to focus its scope on the mapping, annotation, and prediction of emerging pathogens, mapping microbial evolution and antibiotic resistance, and the discovery of novel organisms and biosynthetic gene clusters.
  15. Yu H, Zahidi I, Chow MF
    iScience, 2023 Sep 15;26(9):107667.
    PMID: 37680487 DOI: 10.1016/j.isci.2023.107667
    As global demand for natural resources escalates, the environmental impact stemming from resource extraction has risen to the forefront of contemporary discussions. This paper probed the potential of using vegetation cover as an ecological barometer to gauge the level of environmental damage and restoration in mining areas: a decline in vegetation cover may signify detrimental impacts from intense mining activities, while an increase may indicate effective local environmental stewardship. Therefore, this paper undertook an assessment and discussion of mining damage and environmental management at China's Ta'ershan Mining Area since 2007, calculating and visualizing FVC (Fractional Vegetation Cover) of the Ta'ershan Mining Area to track changes in vegetation cover between 2007 and 2021. Changes in vegetation cover in the Ta'ershan Mining Area could act as a reflection of both mining-induced damage and subsequent successful environmental management by local authorities, providing a practical way to evaluate ecological effects in resource development.
  16. Gu C, Liang Y, Li J, Shao H, Jiang Y, Zhou X, et al.
    iScience, 2021 Dec 17;24(12):103439.
    PMID: 34988389 DOI: 10.1016/j.isci.2021.103439
    The highest plateau on Earth, Qinghai-Tibet Plateau, contains thousands of lakes with broad salinity and diverse and unique microbial communities. However, little is known about their co-occurring viruses. Herein, we identify 4,560 viral Operational Taxonomic Units (vOTUs) from six viromes of three saline lakes on Qinghai-Tibet Plateau, with less than 1% that could be classified. Most of the predicted vOTUs were associated with the dominant bacterial and archaeal phyla. Virus-encoded auxiliary metabolic genes suggest that viruses influence microbial metabolisms of carbon, nitrogen, sulfur, and lipid; the antibiotic resistance mediation; and their salinity adaption. The six viromes clustered together with the ice core viromes and bathypelagic ocean viromes and might represent a new viral habitat. This study has revealed the unique characteristics and potential ecological roles of DNA viromes in the lakes of the highest plateau and established a foundation for the recognition of the viral roles in plateau lake ecosystems.
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