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  • Oxford University Press  (16)
  • American Association for the Advancement of Science (AAAS)  (6)
  • Geological Society of America (GSA)  (3)
  • 1
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    No high Tibetan Plateau until the Neogene (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉The Late Paleogene surface height and paleoenvironment for the core area of the Qinghai-Tibetan Plateau (QTP) remain critically unresolved. Here, we report the discovery of the youngest well-preserved fossil palm leaves from Tibet. They were recovered from the Late Paleogene (Chattian), ca. 25.5 ± 0.5 million years, paleolake sediments within the Lunpola Basin (32.033°N, 89.767°E), central QTP at a present elevation of 4655 m. The anatomy of palms renders them intrinsically susceptible to freezing, imposing upper bounds on their latitudinal and altitudinal distribution. Combined with model-determined paleoterrestrial lapse rates, this shows that a high plateau cannot have existed in the core of Tibet in the Paleogene. Instead, a deep paleovalley, whose floor was 4 km) high mountain systems, formed a topographically highly varied landscape. This finding challenges prevailing views on tectonic processes, monsoon dynamics, and the evolution of Asian biodiversity.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Meroblastic cleavage identifies some Ediacaran Doushantuo (China) embryo-like fossils as metazoans (2016)
    Geological Society of America (GSA)
    In: Geology
    Details
    Publication Date: 2016-08-23
    Description: Ediacaran Doushantuo (Formation) embryo-like fossils (EDEFs, ca. 600 Ma) from South China display cellular and sub-cellular structures and provide a unique window on the early evolution of multicellular eukaryotes. But there have been widely disparate interpretations of these fossils. Here we report new fossil embryo-like forms from the Doushantuo phosphorite that exhibit a meroblastic cleavage pattern. Our results from high-resolution propagation phase contrast–synchrotron radiation X-ray microtomography (PPC-SRµCT) demonstrate that these fossils preserve features directly comparable to those of modern meroblastic animal embryos that utilize discoidal cleavage. Given that discoidal-type meroblastic cleavage occurs only in metazoans, the phylogenetic positions of these fossils probably fall into the animal branch of the holozoan tree. Meroblastic as well as holoblastic cleavage forms were thus present by ca. 600 Ma, substantiating the conclusion derived from molecular clock estimates that a variety of metazoan lineages had evolved by the mid-Ediacaran after the termination of the Marinoan glaciation, if not earlier.
    Print ISSN: 0091-7613
    Electronic ISSN: 1943-2682
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 3
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    RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-03
    Description: 16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately, which always generated incongruent or conflict signals on both taxonomic and functional classifications. Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene flanking region sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. Through extensive testing on clonal bacterial strain, salivary microbiome and bacterial epibionts of marine kelp, we demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. By recognizing almost all 16S rRNA copies, the RiboFR-seq approach can effectively reduce the taxonomic abundance bias resulted from 16S rRNA copy number variation. We believe that RiboFR-Seq, which provides an integrated view of 16S rRNA profiles and metagenomes, will help us better understand diverse microbial communities.
    Keywords: Massively Parallel (Deep) Sequencing, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    The exome sequencing identified the mutation in YARS2 encoding the mitochondrial tyrosyl-tRNA synthetase as a nuclear modifier for the phenotypic manifestation of Leber's hereditary optic neuropathy-associated mitochondrial DNA mutation (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-29
    Description: Leber's hereditary optic neuropathy (LHON) is the most common mitochondrial disorder. Nuclear modifier genes are proposed to modify the phenotypic expression of LHON-associated mitochondrial DNA (mtDNA) mutations. By using an exome sequencing approach, we identified a LHON susceptibility allele (c.572G〉T, p.191Gly〉Val) in YARS2 gene encoding mitochondrial tyrosyl-tRNA synthetase, which interacts with m.11778G〉A mutation to cause visual failure. We performed functional assays by using lymphoblastoid cell lines derived from members of Chinese families (asymptomatic individuals carrying m.11778G〉A mutation, or both m.11778G〉A and heterozygous p.191Gly〉Val mutations and symptomatic subjects harboring m.11778G〉A and homozygous p.191Gly〉Val mutations) and controls lacking these mutations. The 191Gly〉Val mutation reduced the YARS2 protein level in the mutant cells. The aminoacylated efficiency and steady-state level of tRNA Tyr were markedly decreased in the cell lines derived from patients both carrying homozygous YARS2 p.191Gly〉Val and m.11778G〉A mutations. The failure in tRNA Tyr metabolism impaired mitochondrial translation, especially for polypeptides with high content of tyrosine codon such as ND4, ND5, ND6 and COX2 in cells lines carrying homozygous YARS2 p.191Gly〉Val and m.11778G〉A mutations. The YARS2 p.191Gly〉Val mutation worsened the respiratory phenotypes associated with m.11778G〉A mutation, especially reducing activities of complexes I and IV. The respiratory deficiency altered the efficiency of mitochondrial ATP synthesis and increased the production of reactive oxygen species. Thus, mutated YARS2 aggravates mitochondrial dysfunctions associated with the m.11778G〉A mutation, exceeding the threshold for the expression of blindness phenotype. Our findings provided new insights into the pathophysiology of LHON that were manifested by interaction between mtDNA mutation and mutated nuclear-modifier YARS2 .
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    Secure-TWS: Authenticating Node to Multi-user Communication in Shared Sensor Networks (2012)
    Oxford University Press
    Details
    Publication Date: 2012-03-28
    Description: Recent works have shown the usefulness of network and application layer protocols that connect low-power sensor nodes directly to multiple applications and users on the Internet. We propose a security solution for this scenario. While previous works have provided security support for various communication patterns in sensor networks, such as among nodes, from nodes to a base station, and from users to nodes, the security of communication from sensor nodes to multiple users has not been sufficiently addressed. Specifically, we explore this design space and develop a security solution, named Secure Tiny Web Service, for efficient authentication of data sent by a resource-constrained sensor node to multiple users, using digital signatures. We investigate the resource overheads in communication and computation of four suitable signature schemes—the Elliptic Curve Digital Signature Algorithm, the (elliptic curve) Schnorr signature, and the Boneh–Lynn–Shacham and Zhang–Safavi-Naini–Susilo short signature schemes. We implement these schemes on two popular sensor node architectures (based on AVR ATmega128L and MSP430 processors with 802.15.4 radios) and experimentally characterize relevant trade-offs.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 6
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    Elimination of the male reproductive tract in the female embryo is promoted by COUP-TFII in mice (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-08-18
    Description: The sexual differentiation paradigm contends that the female pattern of the reproductive system is established by default because the male reproductive tracts (Wolffian ducts) in the female degenerate owing to a lack of androgen. Here, we discovered that female mouse embryos lacking Coup-tfII (chicken ovalbumin upstream promoter transcription factor II) in the Wolffian duct mesenchyme became intersex—possessing both female and male reproductive tracts. Retention of Wolffian ducts was not caused by ectopic androgen production or action. Instead, enhanced phosphorylated extracellular signal-regulated kinase signaling in Wolffian duct epithelium was responsible for the retention of male structures in an androgen-independent manner. We thus suggest that elimination of Wolffian ducts in female embryos is actively promoted by COUP-TFII, which suppresses a mesenchyme-epithelium cross-talk responsible for Wolffian duct maintenance.
    Keywords: Development
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    A deep root for the Cambrian explosion: Implications of new bio- and chemostratigraphy from the Siberian Platform (2017)
    Geological Society of America (GSA)
    In: Geology
    Details
    Publication Date: 2017-04-12
    Description: Much uncertainty remains as to the temporal relationship between the Ediacaran and Cambrian biotas, yet this is critical to our understanding of the rise of metazoans. Here we present new high-resolution carbon isotope chemostratigraphy and biostratigraphy for a terminal Ediacaran to Cambrian succession on the eastern Siberian Platform, Russia, which shows the presence of a succession of diverse fossil assemblages before the start of the basal Cambrian negative carbon isotope excursion (BACE). Soft-bodied Ediacaran biota ( Beltanelliformis ) occur before the start of the late Ediacaran positive carbon isotope plateau (EPIP), a mixed Ediacaran and Cambrian skeletal biota ( Cloudina , Anabarites , Cambrotubulus ) appears within the EPIP, and diverse Cambrian-type small shelly fossils including Protohertzina and other protocondonts, halkieriids, chancelloriids, hyoliths, hyolithelminthes, and the burrowing trace fossil Diplocraterion appear at the beginning of the BACE. These integrated data show that taxa attributed to so-called Ediacaran and earliest Cambrian skeletal biotas in fact overlap without notable biotic turnover, and thus refute the presence of a large isotope excursion coincident with mass extinction of all Ediacaran biota. We propose a new biozone, the Cloudina - Namacalathus - Sinotubulites Assemblage Zone, to precede the known small shelly fossil (SSF) zones. These observations raise doubts as to whether there is any true separation between the Ediacaran and Cambrian skeletal biotas, and suggest that there is a deep root for the Cambrian explosion of metazoans.
    Print ISSN: 0091-7613
    Electronic ISSN: 1943-2682
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 8
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    An Orthogonal Genetic Algorithm for QoS-Aware Service Composition (2016)
    Oxford University Press
    Details
    Publication Date: 2016-12-10
    Description: Service composition has been proven to be a convincing computing paradigm for rapidly constructing large-scale distributed applications within and across organizational boundaries. Quality of service (QoS)-aware service composition, i.e. selection of the optimal execution plan that maximizes the composition's end-to-end QoS properties, is an active area of research and development endeavors in service composition. In this article, we propose an orthogonal genetic algorithm (OGA) for QoS-aware service composition problem. Its significant feature is to incorporate an orthogonal design method into the initial population generation process and crossover operation. As a result, our algorithm is more robust and can search the solution space in a statistically sound manner. We have executed the OGA to solve 81 randomly generated service composition problems with different sizes and structures based on QWS data set including 2507 real Web services. The results indicate that our OGA can find near-optimal solutions within moderate numbers of generation and has the performance superiority in comparison with many existing optimization algorithms.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 9
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    Demise of Ediacaran dolomitic seas marks widespread biomineralization on the Siberian Platform (2016)
    Geological Society of America (GSA)
    In: Geology
    Details
    Publication Date: 2016-12-21
    Description: The trigger for biomineralization of metazoans in the terminal Ediacaran, ca. 550 Ma, has been suggested to be the rise of oxygenation or an increase in seawater Ca concentration, but geochemical and fossil data have not been fully integrated to demonstrate cause and effect. Here we combine the record of macrofossils with early marine carbonate cement distribution within a relative depth framework for terminal Ediacaran to Cambrian successions on the eastern Siberian Platform, Russia, to interrogate the evolution of seawater chemistry and biotic response. Prior to ca. 545 Ma, the presence of early marine ferroan dolomite cement suggests dominantly ferruginous anoxic "aragonite-dolomite seas", with a very shallow oxic chemocline that supported mainly soft-bodied macrobiota. After ca. 545 Ma, marine cements changed to aragonite and/or high-Mg calcite, and this coincides with the appearance of widespread aragonite and high-Mg calcite skeletal metazoans, suggesting a profound change in seawater chemistry to "aragonite seas" with a deeper chemocline. By early Cambrian Stage 3, the first marine low-Mg calcite cements appear, coincident with the first low-Mg calcite metazoan skeletons, suggesting a further shift to "calcite seas". We suggest that this evolution of seawater chemistry was caused by enhanced continental denudation that increased the input of Ca into oceans so progressively lowering Mg/Ca, which, combined with more widespread oxic conditions, facilitated the rise of skeletal animals and in turn influenced the evolution of skeletal mineralogy.
    Print ISSN: 0091-7613
    Electronic ISSN: 1943-2682
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 10
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    Ancestry of the Australian Termitivorous Numbat (2013)
    Oxford University Press
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    Publication Date: 2013-04-16
    Description: The Australian numbat, Myrmecobius fasciatus , is the only marsupial that feeds almost exclusively on termites and that has a life following the diurnally restricted and dynamic geographical distribution of termites. The millions of years of this adaptation led to unique morphological and anatomical features, especially basicranial and dental characteristics, that make it difficult to identify a clear phylogenetic affiliation to other marsupials. From DNA sequence analyses, the family Myrmecobiidae is placed within the dasyuromorph marsupials, but the exact position varies from study to study, and support values are mostly rather modest. Here, we report the recovery and analysis of approximately 110,000 quasifossilized traces of mobile element insertions into the genome of a dasyurid marsupial (Tasmanian devil), 25 of which are phylogenetically informative for early dasyuromorphial evolution. Fourteen of these ancient retroposon insertions are shared by the 16 Dasyuromorphia species analyzed, including the numbat, but are absent in the outgroups. An additional 11 other insertions are present in all Dasyuridae but are absent in the numbat. These findings place numbats as the sister group to all living Dasyuridae and show that the investigated Dasyuromorphia, including the Myrmecobiidae, constitutes a monophyletic group that is separated from Peramelemorphia, Notoryctemorphia, and other marsupials.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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