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  • 1
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecotoxicology 26 (2017): 820-830, doi:10.1007/s10646-017-1813-4.
    Description: Mathematical models are essential for combining data from multiple sources to quantify population endpoints. This is especially true for species, such as marine mammals, for which data on vital rates are difficult to obtain. Since the effects of an environmental disaster are not fixed, we develop time-varying (nonautonomous) matrix population models that account for the eventual recovery of the environment to the pre-disaster state. We use these models to investigate how lethal and sublethal impacts (in the form of reductions in the survival and fecundity, respectively) affect the population’s recovery process. We explore two scenarios of the environmental recovery process and include the effect of demographic stochasticity. Our results provide insights into the relationship between the magnitude of the disaster, the duration of the disaster, and the probability that the population recovers to pre-disaster levels or a biologically relevant threshold level. To illustrate this modeling methodology, we provide an application to a sperm whale population. This application was motivated by the 2010 Deepwater Horizon oil rig explosion in the Gulf of Mexico that has impacted a wide variety of species populations including oysters, fish, corals, and whales.
    Description: This research is part of the Littoral Acoustic Demonstration Center-Gulf Ecological Monitoring and Modeling (LADC-GEMM) consortium project supported by Gulf of Mexico Research Initiative Year 5–7 Consortia Grants (RFP-IV). Hal Caswell also acknowledges support from ERC Advanced Grant 322989.
    Keywords: Population recovery ; Environmental disasters ; Stochastic modeling ; Lethal impact ; Sublethal impact ; Sperm whales
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Li, K., Sidorovskaia, N. A., Guilment, T., Tang, T., & Tiemann, C. O. Decadal assessment of sperm whale site-specific abundance trends in the northern Gulf of Mexico using passive acoustic data. Journal of Marine Science and Engineering, 9(5), (2021): 454, https://doi.org/10.3390/jmse9050454.
    Description: Passive acoustic monitoring has been successfully used to study deep-diving marine mammal populations. To assess regional population trends of sperm whales in the northern Gulf of Mexico (GoM), including impacts of the Deepwater Horizon platform oil spill in 2010, the Littoral Acoustic Demonstration Center-Gulf Ecological Monitoring and Modeling (LADC-GEMM) consortium collected broadband acoustic data in the Mississippi Valley/Canyon area between 2007 and 2017 using bottom-anchored moorings. These data allow the inference of short-term and long-term variations in site-specific abundances of sperm whales derived from their acoustic activity. A comparison is made between the abundances of sperm whales at specific sites in different years before and after the oil spill by estimating the regional abundance density. The results show that sperm whales were present in the region throughout the entire monitoring period. A habitat preference shift was observed for sperm whales after the 2010 oil spill with higher activities at sites farther away from the spill site. A comparison of the 2007 and 2015 results shows that the overall regional abundance of sperm whales did not recover to pre-spill levels. The results indicate that long-term spatially distributed acoustic monitoring is critical in characterizing sperm whale population changes and in understanding how environmental stressors impact regional abundances and the habitat use of sperm whales.
    Description: This research was made possible by the 2015–2019 consortium grant from The Gulf of Mexico Research Initiative.
    Keywords: Passive acoustic monitoring ; Sperm whale ; Population density ; Gulf of Mexico ; Oil spill
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
    Publication Date: 2012-08-29
    Description: Background: Gene fusion is ubiquitous over the course of evolution. It is expected to increase the diversity and complexity of transcriptomes and proteomes through chimeric sequence segments or altered regulation. However, chimeric mRNAs in pigs remain unclear. Here we identified some chimeric mRNAs in pigs and analyzed the expression of them across individuals and breeds using RNA-sequencing data. Results: The present study identified 669 putative chimeric mRNAs in pigs, of which 251 chimeric candidates were detected in a set of RNA-sequencing data. The 618 candidates had clear trans-splicing sites, 537 of which obeyed the canonical GU-AU splice rule. Only two putative pig chimera variants whose fusion junction was overlapped with that of a known human chimeric mRNA were found. A set of unique chimeric events were considered middle variances in the expression across individuals and breeds, and revealed non-significant variance between sexes. Furthermore, the genomic region of the 5[PRIME] partner gene shares a similar DNA sequence with that of the 3[PRIME] partner gene for 458 putative chimeric mRNAs. The 81 of those shared DNA sequences significantly matched the known DNA-binding motifs in the JASPAR CORE database. Four DNA motifs shared in parental genomic regions had significant similarity with known human CTCF binding sites. Conclusions: The present study provided detailed information on some pig chimeric mRNAs. We proposed a model that trans-acting factors, such as CTCF, induced the spatial organisation of parental genes to the same transcriptional factory so that parental genes were coordinatively transcribed to give birth to chimeric mRNAs.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 4
    Publication Date: 2015-12-28
    Description: Objectives. The complimentary value of computed tomographic enterography (CTE) and double-balloon enteroscopy (DBE) combined with capsule endoscopy (CE) was evaluated in the diagnosis of obscure gastrointestinal bleeding (OGIB). Methods. Patients who received CE examinations at Ruijin Hospital between July 2007 and July 2014 with the indication of OGIB were identified, and those who also underwent DBE and/or CTE were included. Their clinical information was retrieved, and results from each test were compared with findings from the other two examinations. Results. The overall diagnostic yield of CE was comparable with DBE (73.9% versus 60.9%) but was significantly higher than the yield of CTE (87% versus 25%, ). The diagnostic yield of angiodysplasia at CE was significantly higher than CTE (73% versus 8%, ) and DBE (39.1% versus 17.4%, ), while no significant difference was found between the three approaches for small bowel tumors. DBE and CTE identified small bowel diseases undetected or undetermined by CE. Conversely, CE improved diagnosis in the cases with negative CTE and DBE, and findings at initial CE directed further diagnosis made by DBE. Conclusions. Combination of the three diagnostic platforms provides complementary value in the diagnosis of OGIB.
    Print ISSN: 1687-6121
    Electronic ISSN: 1687-630X
    Topics: Medicine
    Published by Hindawi
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  • 5
    Publication Date: 2017-03-28
    Description: Niacin, as an antidyslipidemic drug, elicits a strong flushing response by release of prostaglandin (PG) D 2 . However, whether niacin is beneficial for inflammatory bowel disease (IBD) remains unclear. Here, we observed niacin administration-enhanced PGD 2 production in colon tissues in dextran sulfate sodium (DSS)-challenged mice, and protected mice against DSS or 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis in D prostanoid receptor 1 (DP1)-dependent manner. Specific ablation of DP1 receptor in vascular endothelial cells, colonic epithelium, and myeloid cells augmented DSS/TNBS-induced colitis in mice through increasing vascular permeability, promoting apoptosis of epithelial cells, and stimulating pro-inflammatory cytokine secretion of macrophages, respectively. Niacin treatment improved vascular permeability, reduced apoptotic epithelial cells, promoted epithelial cell update, and suppressed pro-inflammatory gene expression of macrophages. Moreover, treatment with niacin-containing retention enema effectively promoted UC clinical remission and mucosal healing in patients with moderately active disease. Therefore, niacin displayed multiple beneficial effects on DSS/TNBS-induced colitis in mice by activation of PGD 2 /DP1 axis. The potential efficacy of niacin in management of IBD warrants further investigation. Niacin, an ancient lipid-lowering drug that elicits a strong flushing response through release of prostaglandin (PG) D 2 . Niacin improves experimentally induced ulcerative colitis in mice and humans through the activation of PGD 2 /DP1 axis.
    Print ISSN: 1757-4676
    Electronic ISSN: 1757-4684
    Topics: Medicine
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  • 6
    Publication Date: 2016-04-21
    Description: Single-nucleotide polymorphisms (SNPs) have become the genetic markers of choice in various genetic, ecological, and evolutionary studies. Genotyping-by-sequencing (GBS) is a next-generation-sequencing based m...
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
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  • 7
    Publication Date: 2017-10-28
    Description: HGF/R-spondin1 rescues liver dysfunction through the induction of Lgr5 + liver stem cells Nature Communications, Published online: 27 October 2017; doi:10.1038/s41467-017-01341-6 Organ regeneration by transplantation of ESC/iPSC-derived tissues is a promising but still challenging approach. Here Lin et al. show that liver damage caused by a chemical insult induces not only fibrosis but also Lgr5 + cell expansion that can be further promoted by treatment with HGF/R-spondin1.
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2015-06-05
    Description: The Journal of Physical Chemistry B DOI: 10.1021/acs.jpcb.5b01613
    Electronic ISSN: 1520-5207
    Topics: Chemistry and Pharmacology , Physics
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  • 9
    Publication Date: 2016-06-09
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
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  • 10
    Publication Date: 2016-06-23
    Description: Structural basis of N6-adenosine methylation by the METTL3–METTL14 complex Nature 534, 7608 (2016). doi:10.1038/nature18298 Authors: Xiang Wang, Jing Feng, Yuan Xue, Zeyuan Guan, Delin Zhang, Zhu Liu, Zhou Gong, Qiang Wang, Jinbo Huang, Chun Tang, Tingting Zou & Ping Yin Chemical modifications of RNA have essential roles in a vast range of cellular processes. N6-methyladenosine (m6A) is an abundant internal modification in messenger RNA and long non-coding RNA that can be dynamically added and removed by RNA methyltransferases (MTases) and demethylases, respectively. An MTase complex comprising methyltransferase-like 3 (METTL3) and methyltransferase-like 14 (METTL14) efficiently catalyses methyl group transfer. In contrast to the well-studied DNA MTase, the exact roles of these two RNA MTases in the complex remain to be elucidated. Here we report the crystal structures of the METTL3–METTL14 heterodimer with MTase domains in the ligand-free, S-adenosyl methionine (AdoMet)-bound and S-adenosyl homocysteine (AdoHcy)-bound states, with resolutions of 1.9, 1.71 and 1.61 Å, respectively. Both METTL3 and METTL14 adopt a class I MTase fold and they interact with each other via an extensive hydrogen bonding network, generating a positively charged groove. Notably, AdoMet was observed in only the METTL3 pocket and not in METTL14. Combined with biochemical analysis, these results suggest that in the m6A MTase complex, METTL3 primarily functions as the catalytic core, while METTL14 serves as an RNA-binding platform, reminiscent of the target recognition domain of DNA N6-adenine MTase. This structural information provides an important framework for the functional investigation of m6A.
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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