ALBERT

Description: Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana . The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships among and within these lineages remain largely unclear. Here, we present a highly supported phylogeny with six major clades using nuclear markers from newly sequenced transcriptomes of 32 Brassicaceae species and large data sets from additional taxa for a total of 55 species spanning 29 out of 51 tribes. Clade A consisting of Lineage I and Macropodium nivale is sister to combined Clade B (with Lineage II and others) and a new Clade C. The ABC clade is sister to Clade D with species previously weakly associated with Lineage II and Clade E (Lineage III) is sister to the ABCD clade. Clade F (the tribe Aethionemeae) is sister to the remainder of the entire family. Molecular clock estimation reveals an early radiation of major clades near or shortly after the Eocene–Oligocene boundary and subsequent nested divergences of several tribes of the previously polytomous Expanded Lineage II. Reconstruction of ancestral morphological states during the Brassicaceae evolution indicates prevalent parallel (convergent) evolution of several traits over deep times across the entire family. These results form a foundation for future evolutionary analyses of structures and functions across Brassicaceae.

Description: New genes, which provide material for evolutionary innovation, have been extensively studied for many years in animals where it is observed that they commonly show an expression bias for the testis. Thus, the testis is a major source for the generation of new genes in animals. The source tissue for new genes in plants is unclear. Here, we find that new genes in plants show a bias in expression to mature pollen, and are also enriched in a gene coexpression module that correlates with mature pollen in Arabidopsis thaliana . Transposable elements are significantly enriched in the new genes, and the high activity of transposable elements in the vegetative nucleus, compared with the germ cells, suggests that new genes are most easily generated in the vegetative nucleus in the mature pollen. We propose an "out of pollen" hypothesis for the origin of new genes in flowering plants.

Description: Inclusion body myositis (IBM), a degenerative and inflammatory disorder of skeletal muscle, and Alzheimer's disease share protein derangements and attrition of postmitotic cells. Overexpression of cyclins and proliferating cell nuclear antigen (PCNA) and evidence for DNA replication is reported in Alzheimer's disease brain, possibly contributing to neuronal death. It is unknown whether aberrant cell cycle reentry also occurs in IBM. We examined cell cycle markers in IBM compared with normal control, polymyositis (PM) and non-inflammatory dystrophy sample sets. Next, we tested for evidence of reentry and DNA synthesis in C2C12 myotubes induced to express β-amyloid (Aβ42). We observed increased levels of Ki-67, PCNA and cyclins E/D1 in IBM compared with normals and non-inflammatory conditions. Interestingly, PM samples displayed similar increases. Satellite cell markers did not correlate with Ki-67-affected myofiber nuclei. DNA synthesis and cell cycle markers were induced in Aβ-bearing myotubes. Cell cycle marker and cyclin protein expressions were also induced in an experimental allergic myositis-like model of PM in mice. Levels of p21 (Cip1/WAF1), a cyclin-dependent kinase inhibitor, were decreased in affected myotubes. However, overexpression of p21 did not rescue cells from Aβ-induced toxicity. This is the first report of cell cycle reentry in human myositis. The absence of rescue and evidence for reentry in separate models of myodegeneration and inflammation suggest that new DNA synthesis may be a reactive response to either or both stressors.

Description: Recently, cyber-physical systems (CPSs) have emerged as a cutting edge technology for next-generation industrial applications, and are undergoing rapid development and inspiring numerous application domains. In this article, we propose a novel CPS application for energy management framework (EMF) toward autonomous electric vehicle (AEV) in smart grid. We first give a brief overview of related technologies, including open research issues of CPS, enabling wireless communication technologies for CPS, smart grid, AEV and its path planning, energy-efficient design for AEV, etc. Then we design EMF from the following aspects, such as AEV with wireless sensor networks (WSNs) navigation, smart grid communication architecture for EMF and AEV charging station. The proposed EMF is able to collect the real-time power consumption status and demand from AEV and charging stations. We also address EMF to overcome some issues, such as real-time traffic information. Subsequently, the energy-efficient design schemes for AEV are proposed and formulated from the point of view of path planning and event-based control technique. Finally, we outline the issues and challenges for EMF.

Description: The geometry of the entire crust from the northern part of the Tarim Basin to the southwestern Tian Shan east of Kashi is imaged on a N-S–directed explosive-source deep seismic-reflection profile. The profile reflects the sedimentary formations in the northern part of the Tarim Basin and the fold-and-thrust belt of the southern Tian Shan. N-dipping reflectors of the lower crust, as well as fluctuations in Moho depth, below which several mantle reflectors were observed, reveal the fine crustal structure beneath the junction of the southwest Tian Shan and the Tarim Basin. Mesozoic–Cenozoic shortening of the southwestern Tian Shan occurred at a crustal scale involving detachment-related folding in the basin directed northward toward the mountains and reverse faulting in the mountains directed toward the basin. In addition, a crocodile fabric developed within the lower crust beneath the basin area. The lithospheric structure revealed by the seismic-reflection section between the Tarim Basin and the Tian Shan Mountains reflects a process of intracontinental collision.

Description: Streptococcus mutans is widely recognized as one of the key etiological agents of human dental caries. Despite its role in this important disease, our present knowledge of gene content variability across the species and its relationship to adaptation is minimal. Estimates of its demographic history are not available. In this study, we generated genome sequences of 57 S. mutans isolates, as well as representative strains of the most closely related species to S. mutans (S. ratti, S. macaccae, and S. criceti) , to identify the overall structure and potential adaptive features of the dispensable and core components of the genome. We also performed population genetic analyses on the core genome of the species aimed at understanding the demographic history, and impact of selection shaping its genetic variation. The maximum gene content divergence among strains was approximately 23%, with the majority of strains diverging by 5–15%. The core genome consisted of 1,490 genes and the pan-genome approximately 3,296. Maximum likelihood analysis of the synonymous site frequency spectrum (SFS) suggested that the S. mutans population started expanding exponentially approximately 10,000 years ago (95% confidence interval [CI]: 3,268–14,344 years ago), coincidental with the onset of human agriculture. Analysis of the replacement SFS indicated that a majority of these substitutions are under strong negative selection, and the remainder evolved neutrally. A set of 14 genes was identified as being under positive selection, most of which were involved in either sugar metabolism or acid tolerance. Analysis of the core genome suggested that among 73 genes present in all isolates of S. mutans but absent in other species of the mutans taxonomic group, the majority can be associated with metabolic processes that could have contributed to the successful adaptation of S. mutans to its new niche, the human mouth, and with the dietary changes that accompanied the origin of agriculture.

Description: Field, structural, kinematic, and deformation temperature analyses were conducted on rocks from the Lhagoi Kangri gneiss dome (southern Tibet) in order to establish the geologic history of the dome, identify major phases of deformation within the dome, and to relate these phases of deformation to the tectonic evolution of the Himalayan middle crust. The Lhagoi Kangri dome, one of a series of gneiss-cored domes in southern Tibet, records stratigraphy and structural features similar to previously studied north Himalayan gneiss domes. Field mapping reveals a sequence of rocks that comprise a cover of unmetamorphosed to amphibolite-grade siliciclastic and minor carbonate rocks overlying a core predominantly composed of foliated and lineated orthogneiss intruded by relatively undeformed granite, which also intrudes the cover rocks both concordantly and discordantly. Field observations and microstructural analyses suggest that the contact between the core and cover rocks was originally a nonconformity, but we do not rule out the possibility of subsequent slip along the surface, as has been reported for correlative structures in other domes. Lhagoi Kangri rocks were pervasively deformed during at least two major tectonic phases. The earliest deformation event (D1) resulted in shortening and thickening of crust, the record of which is largely eliminated, particularly in lower structural levels, by transposition and recrystallization during the second phase of deformation (D2). Ductile deformation during D2 is characterized at higher structural levels by crenulation cleavage that tightens with depth, while at lower structural levels D2 manifests as a distributed shear zone that records some evidence of both plane strain and coaxial flattening, possibly indicating overall heterogeneous general shear. The shear zone is ~3 km thick and contains rocks with mostly symmetrical top-to-north and top-to-south shear sense indicators with a dominant top-to-north component at lower structural levels. Microstructural analyses and quartz c-axis fabrics indicate a range of D2 shear zone temperatures from 200 to 300 °C at the upper boundary to ≥630 °C at the lowest structural levels sampled with minimal evidence of lower temperature overprinting. The interpreted temperatures define a wide range in thermal field gradients (18–90 °C/km) that suggest that temperature indicators were locked in at relatively late stages of D2. The structural framework and kinematic history of the Lhagoi Kangri dome are similar to previously studied north Himalayan gneiss domes as well as to transects through the South Tibetan detachment system, which supports previous interpretations of structural continuity between the north Himalayan gneiss domes and other middle crustal exposures in the Himalaya. The Lhagoi Kangri distributed shear zone, in particular, may represent a deeper ductile manifestation of the South Tibetan detachment system.

Description: Most of the Himalayan Cenozoic leucogranites are products of partial melting of metapelite sources. In the Malashan-Gyirong area (southern Tibet), the geochemical compositions of leucogranites define two groups with distinct whole-rock major elements, large ion lithophile elements, rare earth elements, high field strength elements, and Sr and Hf isotope ratios. Based on published experimental results that define generalized melting reactions of metapelitic sources, we infer that these leucogranites are the products of two different types of crustal anatexis: fluid-fluxed melting and fluid-absent melting of muscovite in metasedimentary sources. As compared to the leucogranites derived from fluid-absent melting, those from fluid-fluxed melting have relatively higher Ca, Sr, Ba, Zr, Hf, Th, and light rare earth element concentrations, and Zr/Hf, Eu/Eu*, and Nd/Nd*, but lower Rb, Nb, Ta, and U concentrations, Rb/Sr and 87 Sr/ 86 Sr ratios, and Hf (t). The geochemical differences can be explained by melting behaviors of major (muscovite, feldspar) and accessory minerals (zircon and monazite) during different modes of crustal anatexis. The systematic elemental and isotopic signatures of different types of crustal anatexis and, in particular, the coupling of major and trace elements that results from common influences on rock-forming and accessory mineral behaviors provide tools with which to refine our understanding of the nature of crustal anatexis.

Description: Autosomal-dominant polycystic kidney disease (ADPKD) and von Hippel-Lindau (VHL) disease lead to large kidney cysts that share pathogenetic features. The polycystin-1 (PC1) and pVHL proteins may therefore participate in the same key signaling pathways. Jade-1 is a pro-apoptotic and growth suppressive ubiquitin ligase for beta-catenin and transcriptional coactivator associated with histone acetyltransferase activity that is stabilized by pVHL in a manner that correlates with risk of VHL renal disease. Thus, a relationship between Jade-1 and PC1 was sought. Full-length PC1 bound, stabilized and colocalized with Jade-1 and inhibited Jade-1 ubiquitination. In contrast, the cytoplasmic tail or the naturally occurring C-terminal fragment of PC1 (PC1-CTF) promoted Jade-1 ubiquitination and degradation, suggesting a dominant-negative mechanism. ADPKD-associated PC1 mutants failed to regulate Jade-1, indicating a potential disease link. Jade-1 ubiquitination was mediated by Siah-1, an E3 ligase that binds PC1. By controlling Jade-1 abundance, PC1 and the PC1-CTF differentially regulate Jade-1-mediated transcriptional activity. A key target of PC1, the cyclin-dependent kinase inhibitor p21, is also up-regulated by Jade-1. Through Jade-1, PC1 and PC1 cleaved forms may exert fine control of beta-catenin and canonical Wnt signaling, a critical pathway in cystic renal disease. Thus, Jade-1 is a transcription factor and ubiquitin ligase whose activity is regulated by PC1 in a manner that is physiologic and may correlate with disease. Jade-1 may be an important therapeutic target in renal cystogenesis.

Description: Field, structural, kinematic, and deformation temperature analyses were conducted on rocks from the Lhagoi Kangri gneiss dome (southern Tibet) in order to establish the geologic history of the dome, identify major phases of deformation within the dome, and to relate these phases of deformation to the tectonic evolution of the Himalayan middle crust. The Lhagoi Kangri dome, one of a series of gneiss-cored domes in southern Tibet, records stratigraphy and structural features similar to previously studied north Himalayan gneiss domes. Field mapping reveals a sequence of rocks that comprise a cover of unmetamorphosed to amphibolite-grade siliciclastic and minor carbonate rocks overlying a core predominantly composed of foliated and lineated orthogneiss intruded by relatively undeformed granite, which also intrudes the cover rocks both concordantly and discordantly. Field observations and microstructural analyses suggest that the contact between the core and cover rocks was originally a nonconformity, but we do not rule out the possibility of subsequent slip along the surface, as has been reported for correlative structures in other domes. Lhagoi Kangri rocks were pervasively deformed during at least two major tectonic phases. The earliest deformation event (D1) resulted in shortening and thickening of crust, the record of which is largely eliminated, particularly in lower structural levels, by transposition and recrystallization during the second phase of deformation (D2). Ductile deformation during D2 is characterized at higher structural levels by crenulation cleavage that tightens with depth, while at lower structural levels D2 manifests as a distributed shear zone that records some evidence of both plane strain and coaxial flattening, possibly indicating overall heterogeneous general shear. The shear zone is ~3 km thick and contains rocks with mostly symmetrical top-to-north and top-to-south shear sense indicators with a dominant top-to-north component at lower structural levels. Microstructural analyses and quartz c-axis fabrics indicate a range of D2 shear zone temperatures from 200 to 300 °C at the upper boundary to ≥630 °C at the lowest structural levels sampled with minimal evidence of lower temperature overprinting. The interpreted temperatures define a wide range in thermal field gradients (18–90 °C/km) that suggest that temperature indicators were locked in at relatively late stages of D2. The structural framework and kinematic history of the Lhagoi Kangri dome are similar to previously studied north Himalayan gneiss domes as well as to transects through the South Tibetan detachment system, which supports previous interpretations of structural continuity between the north Himalayan gneiss domes and other middle crustal exposures in the Himalaya. The Lhagoi Kangri distributed shear zone, in particular, may represent a deeper ductile manifestation of the South Tibetan detachment system.