bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plant organ evolution revealed by phylotranscriptomics in Arabidopsis thaliana
Authors: Lei Li , Steffen Joshua G. , Osborne Edward J. , Toomajian Christopher 
Published: August 2017

AbstractThe evolution of phenotypes occurs through changes both in protein sequence and gene expression levels. Though much of plant morphological evolution can be explained by changes in gene expression, examining its evolution has challenges. To gain a new perspective on organ evolution in plants, we applied a phylotranscriptomics approach. We combined a phylostratigraphic approach with gene expression based on the strand-specific RNA-seq data from seedling, floral bud, and root of 19Arabidopsis thalianaaccessions to examine the age and sequence divergence of transcriptomes from these organs and how they adapted over time. Our results indicate that, among the sense and antisense transcriptomes of these organs, the sense transcriptomes of seedlings are the evolutionarily oldest across all accessions and are the most conserved in amino acid sequence for most accessions. In contrast, among the sense transcriptomes from these same organs, those from floral bud are evolutionarily youngest and least conserved in sequence for most accessions. Different organs have adaptive peaks at different stages in their evolutionary history; however, all three show a common adaptive signal from the Magnoliophyta to Brassicale stage. Our research highlights how phylotranscriptomic analyses can be used to trace organ evolution in the deep history of plant species.
Chloroplast genomes of Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea: Structures and comparative analysis
Authors: Asaf Sajjad , Khan Abdul Latif , Khan Muhammad Aaqil , Waqas Muhammad , Kang Sang-Mo , Yun Byung-Wook , Lee In-Jung 
Published: August 2017

AbstractWe investigated the complete chloroplast (cp) genomes of non-model Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea using Illumina paired-end sequencing to understand their genetic organization and structure. Detailed bioinformatics analysis revealed genome sizes of both subspecies ranging between 154.4~154.5 kbp, with a large single-copy region (84,197~84,158 bp), a small single-copy region (17,738~17,813 bp) and pair of inverted repeats (IRa/IRb; 26,264~26,259 bp). Both cp genomes encode 130 genes, including 85 protein-coding genes, eight ribosomal RNA genes and 37 transfer RNA genes. Whole cp genome comparison of A. halleri ssp. gemmifera and A. lyrata ssp. petraea, along with ten other Arabidopsis species, showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. The location and distribution of repeat sequences were determined, and sequence divergences of shared genes were calculated among related species. Comparative phylogenetic analysis of the entire genomic data set and 70 shared genes between both cp genomes confirmed the previous phylogeny and generated phylogenetic trees with the same topologies. The sister species of A. halleri ssp. gemmifera is A. umezawana, whereas the closest relative of A. lyrata spp. petraea is A. arenicola.
Three-dimensional illusion thermal device for location camouflage
Authors: Wang Jing , Bi Yanqiang , Hou Quanwen 
Published: August 2017

AbstractThermal metamaterials, proposed in recent years, provide a new method to manipulate the energy flux in heat transfer, and result in many novel thermal devices. In this paper, an illusion thermal device for location camouflage in 3-dimensional heat conduction regime is proposed based on the transformation thermodynamics. The heat source covered by the device produces a fake signal outside the device, which makes the source look like appearing at another position away from its real position. The parameters required by the device are deduced and the method is validated by simulations. The possible scheme to obtain the thermal conductivities required in the device by composing natural materials is supplied, and the influence of some problems in practical fabrication process of the device on the effect of the camouflage is also discussed.
AmotL2 integrates polarity and junctional cues to modulate cell shape
Authors: Hultin Sara , Subramani Aravindh , Hildebrand Sebastian , Zheng Yujuan , Majumdar Arindam , Holmgren Lars 
Published: August 2017

AbstractThe assembly of individual epithelial or endothelial cells into a tight cellular sheet requires stringent control of cell packing and organization. These processes are dependent on the establishment and further integration of cellular junctions, the cytoskeleton and the formation of apical-basal polarity. However, little is known how these subcellular events are coordinated. The (Angiomotin) Amot protein family consists of scaffold proteins that interact with junctional cadherins, polarity proteins and the cytoskeleton. In this report, we have studied how these protein complexes integrate to control cellular shapes consistent with organ function. Using gene-inactivating studies in zebrafish and cell culture systems in vitro, we show that Par3 to be essential for localization of AmotL2 to cellular junctions to associate with VE/E-cadherin and subsequently the organization of radial actin filaments. Our data provide mechanistic insight in how critical processes such as aortic lumen expansion as well as epithelial packing into hexagonal shapes are controlled.
Comparative transcriptional profiling of tildipirosin-resistant and sensitive Haemophilus parasuis
Authors: Lei Zhixin , Fu Shulin , Yang Bing , Liu Qianying , Ahmed Saeed , Xu Lei , Xiong Jincheng , Cao Jiyue , Qiu Yinsheng 
Published: August 2017

AbstractNumerous studies have been conducted to examine the molecular mechanism of Haemophilus parasuis resistance to antibiotic, but rarely to tildipirosin. In the current study, transcriptional profiling was applied to analyse the variation in gene expression of JS0135 and tildipirosin-resistant JS32. The growth curves showed that JS32 had a higher growth rate but fewer bacteria than JS0135. The cell membranes of JS32 and a resistant clinical isolate (HB32) were observed to be smoother than those of JS0135. From the comparative gene expression profile 349 up- and 113 downregulated genes were observed, covering 37 GO and 63 KEGG pathways which are involved in biological processes (11), cellular components (17), molecular function (9), cellular processes (1), environmental information processing (4), genetic information processing (9) and metabolism (49) affected in JS32. In addition, the relative overexpression of genes of the metabolism pathway (HAPS_RS09315, HAPS_RS09320), ribosomes (HAPS_RS07815) and ABC transporters (HAPS_RS10945) was detected, particularly the metabolism pathway, and verified with RT-qPCR. Collectively, the gene expression profile in connection with tildipirosin resistance factors revealed unique and highly resistant determinants of H. parasuis to macrolides that warrant further attention due to the significant threat of bacterial resistance.
Signs of innate immune activation and premature immunosenescence in psoriasis patients
Authors: Šahmatova Liisi , Sügis Elena , Šunina Marina , Hermann Helen , Prans Ele , Pihlap Maire , Abram Kristi , Rebane Ana , Peterson Hedi , Peterson Pärt , Kingo Külli , Kisand Kai 
Published: August 2017

AbstractPsoriasis is a chronic inflammatory disease that affects skin and is associated with systemic inflammation and many serious comorbidities ranging from metabolic syndrome to cancer. Important discoveries about psoriasis pathogenesis have enabled the development of effective biological treatments blocking the T helper 17 pathway. However, it has not been settled whether psoriasis is a T cell-mediated autoimmune disease or an autoinflammatory disorder that is driven by exaggerated innate immune signalling. Our comparative gene expression and hierarchical cluster analysis reveal important gene circuits involving innate receptors. Innate immune activation is indicated by increased absent in melanoma 2 (AIM2) inflammasome gene expression and active caspase 1 staining in psoriatic lesional skin. Increased eomesodermin (EOMES) expression in lesional and non-lesional skin is suggestive of innate-like virtual memory CD8+ T cell infiltration. We found that signs of systemic inflammation were present in most of the patients, correlated with the severity of the disease, and pointed to IL-6 involvement in the pathogenesis of psoriatic arthritis. Among the circulating T cell subpopulations, we identified a higher proportion of terminally differentiated or senescent CD8+ T cells, especially in patients with long disease duration, suggesting premature immunosenescence and its possible implications for psoriasis co-morbidities.
Equilibrium Skyrmion Lattice Ground State in a Polar Easy-plane Magnet
Authors: Bordács S. , Butykai A. , Szigeti B. G. , White J. S. , Cubitt R. , Leonov A. O. , Widmann S. , Ehlers D. , von Nidda H.-A. Krug , Tsurkan V. , Loidl A. , Kézsmárki I. 
Published: August 2017

AbstractThe skyrmion lattice state (SkL), a crystal built of mesoscopic spin vortices, gains its stability via thermal fluctuations in all bulk skyrmion host materials known to date. Therefore, its existence is limited to a narrow temperature region below the paramagnetic state. This stability range can drastically increase in systems with restricted geometries, such as thin films, interfaces and nanowires. Thermal quenching can also promote the SkL as a metastable state over extended temperature ranges. Here, we demonstrate more generally that a proper choice of material parameters alone guarantees the thermodynamic stability of the SkL over the full temperature range below the paramagnetic state down to zero kelvin. We found that GaV4Se8, a polar magnet with easy-plane anisotropy, hosts a robust Néel-type SkL even in its ground state. Our supporting theory confirms that polar magnets with weak uniaxial anisotropy are ideal candidates to realize SkLs with wide stability ranges.
Sensitivity to musical emotion is influenced by tonal structure in congenital amusia
Authors: Jiang Cunmei , Liu Fang , Wong Patrick C. M. 
Published: August 2017

AbstractEmotional communication in music depends on multiple attributes including psychoacoustic features and tonal system information, the latter of which is unique to music. The present study investigated whether congenital amusia, a lifelong disorder of musical processing, impacts sensitivity to musical emotion elicited by timbre and tonal system information. Twenty-six amusics and 26 matched controls made tension judgments on Western (familiar) and Indian (unfamiliar) melodies played on piano and sitar. Like controls, amusics used timbre cues to judge musical tension in Western and Indian melodies. While controls assigned significantly lower tension ratings to Western melodies compared to Indian melodies, thus showing a tonal familiarity effect on tension ratings, amusics provided comparable tension ratings for Western and Indian melodies on both timbres. Furthermore, amusics rated Western melodies as more tense compared to controls, as they relied less on tonality cues than controls in rating tension for Western melodies. The implications of these findings in terms of emotional responses to music are discussed.
Structural basis for Ccd1 auto-inhibition in the Wnt pathway through homomerization of the DIX domain
Authors: Terawaki Shin-ichi , Fujita Shohei , Katsutani Takuya , Shiomi Kensuke , Keino-Masu Kazuko , Masu Masayuki , Wakamatsu Kaori , Shibata Naoki , Higuchi Yoshiki 
Published: August 2017

AbstractWnt signaling plays an important role in governing cell fate decisions. Coiled-coil-DIX1 (Ccd1), Dishevelled (Dvl), and Axin are signaling proteins that regulate the canonical pathway by controlling the stability of a key signal transducer β-catenin. These proteins contain the DIX domain with a ubiquitin-like fold, which mediates their interaction in the β-catenin destruction complex through dynamic head-to-tail polymerization. Despite high sequence similarities, mammalian Ccd1 shows weaker stimulation of β-catenin transcriptional activity compared with zebrafish (z) Ccd1 in cultured cells. Here, we show that the mouse (m) Ccd1 DIX domain displays weaker ability for homopolymerization than that of zCcd1. Furthermore, X-ray crystallographic analysis of mCcd1 and zCcd1 DIX domains revealed that mCcd1 was assembled into a double-helical filament by the insertion of the β1-β2 loop into the head-to-tail interface, whereas zCcd1 formed a typical single-helical polymer similar to Dvl1 and Axin. The mutation in the contact interface of mCcd1 double-helical polymer changed the hydrodynamic properties of mCcd1 so that it acquired the ability to induce Wnt-specific transcriptional activity similar to zCcd1. These findings suggest a novel regulatory mechanism by which mCcd1 modulates Wnt signaling through auto-inhibition of dynamic head-to-tail homopolymerization.
Antioxidant Activity of Quercetin and Its Glucosides from Propolis: A Theoretical Study
Authors: Zheng Yan-Zhen , Deng Geng , Liang Qin , Chen Da-Fu , Guo Rui , Lai Rong-Cai 
Published: August 2017

AbstractAmong the multiple components of propolis, flavonoids contribute greatly to the antioxidant activities of propolis. Flavonoids mainly exist in the form of sugar-conjugated derivatives. Quercetin glycosides represent the predominant flavonoid fraction in propolis. In this work, density functional theory (DFT) calculations were applied to analyze the antioxidative properties of quercetin and its glucosides in the gas and in the liquid phase (ethanol, water). Three main antioxidant mechanisms, hydrogen atom transfer (HAT), single electron transfer followed by proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET) were used to analyze the antioxidative capacity of the investigated compounds. Solvent effects dominantly affect SET-PT and SPLET. Thus, the thermodynamically preferred mechanism can be altered. HAT and SPLET are the thermodynamically dominant mechanisms in gas and solvent phases, respectively. Therefore, in the gas phase, the sequence of the antioxidative capacity is similar with the bond dissociation enthalpy values: quercetin > quercetin-5-O-glucoside > quercetin-7-O-glucoside > quercetin-3-O-glucoside > quercetin-3′-O-glucoside > quercetin-4′-O-glucoside. While, in the solvent phases, the sequence is similar with the proton affinity values: quercetin-4′-O-glucoside > quercetin-5-O-glucoside > quercetin > quercetin-3-O-glucoside > quercetin-7-O-glucoside > quercetin-3′-O-glucoside. OH groups in B-ring and C-ring contribute mainly to the antioxidative activities of quercetin and glucosides compared with A-ring.
Axial multi-image phase retrieval under tilt illumination
Authors: Guo Cheng , Li Qiang , Wei Ce , Tan Jiubin , Liu Shutian , Liu Zhengjun 
Published: August 2017

AbstractAs a coherent diffractive imaging technique, axial multi-image phase retrieval utilizes a series of diffraction patterns on the basis of axial movement diversity to reconstruct full object wave field. Theoretically, fast convergence and high-accuracy of axial multi-image phase retrieval are demonstrated. In experiment, its retrieval suffers from the tilt illumination, in which diffraction patterns will shift in the lateral direction as the receiver traverses along the axis. In this case, the reconstructed result will be blurry or even mistaken. To solve this problem, we introduce cross-correlation calibration to derive the oblique angle and employ tilt diffraction into axial phase retrieval to recover a target, which is successfully demonstrated in simulation and experiment. Also, our method could provide a useful guidance for measuring how obliquely the incident light illuminates in an optical system.
Periphyton effects on bacterial assemblages and harmful cyanobacterial blooms in a eutrophic freshwater lake: a mesocosm study
Authors: Cui Yingshun , Jin Long , Ko So-Ra , Chun Seong-Jun , Oh Hyung-Seok , Lee Chang Soo , Srivastava Ankita , Oh Hee-Mock , Ahn Chi-Yong 
Published: August 2017

AbstractPeriphyton comprises a broad range of autotrophic and heterotrophic organisms that grow on submerged surfaces in aquatic environments. To investigate the ecological roles of periphyton and their symbiotic bacterial assemblages related to the control of cyanobacterial blooms, mesocosm experiments were performed in a eutrophic lake that is usually infested with harmful cyanobacterial blooms. Our results showed that periphyton, together with their symbionts, reduced Chl-aconcentrations (up to 94%), improved water clarity and effectively controlled cyanobacterial blooms in the treatment mesocosm. Planktonic bacterial compositions varied greatly in the pre-bloom/bloom/post-bloom periods in both mesocosms and were mainly influenced by total dissolved nitrogen (TDN) concentrations. The phylumCyanobacteriawas the major component in the water samples until bloom peak, but it was replaced byActinobacteriain the post-bloom period. However, periphyton niches were dominated byAlphaproteobacteriathroughout the experiments,Cyanobacteriaproportion being lower. Overall, the results indicated that periphyton and their unique bacterial partners could effectively compete with cyanobacteria and improve water quality. Their underlying interaction mechanism was also suggested to explain how periphyton and their symbionts can reduce cyanobacterial blooms in eutrophic water.
Thermoelectric transport in temperature-driven two-dimensional topological insulators
Authors: Dong H. M. , Li L. L. , Xu W. , Liu J. L. 
Published: August 2017

AbstractWe theoretically investigate on the thermoelectric (TE) transport properties of edge and bulk states in a temperature-driven two-dimensional (2D) topological insulator (TI) realized from CdTe/HgTe/CdTe quantum wells (QWs). It is found that the temperature can effectively drive a TI phase in CdTe/HgTe/CdTe QWs. We find that the TE transport properties of 2D TI can be governed by edge states, bulk states, or their interplay, depending on driving temperature and chemical potential of the system. Moreover, we find that the TE figure of merit ZT shows a peak at relatively low temperatures due to the competition between bulk and edge transports. This peak vanishes at relatively high temperatures due to the dominance of bulk states in the TE transport. With decreasing the ribbon width of the temperature-driven 2D TI, the low-temperature ZT exhibits two peaks, among which one occurs due to the bulk-edge competition and the other occurs due to the edge-edge hybridization; while the high-temperature ZT first exhibits the bulk-state behavior and then the edge-state one, which is indicative of a bulk-to-edge transition in the TE transport.
GSK3β and ERK regulate the expression of 78 kDa SG2NA and ectopic modulation of its level affects phases of cell cycle
Authors: Pandey Shweta , Talukdar Indrani , Jain Buddhi P. , Tanti Goutam K. , Goswami Shyamal K. 
Published: August 2017

AbstractStriatin and SG2NA are essential constituents of the multi-protein STRIPAK assembly harbouring protein phosphatase PP2A and several kinases. SG2NA has several isoforms generated by mRNA splicing and editing. While the expression of striatin is largely restricted to the striatum in brain, that of SG2NAs is ubiquitous. In NIH3T3 cells, only the 78 kDa isoform is expressed. When cells enter into the S phase, the level of SG2NA increases; reaches maximum at the G2/M phase and declines thereafter. Downregulation of SG2NA extends G1 phase and its overexpression extends G2. Ectopic expression of the 35 kDa has no effects on the cell cycle. Relative abundance of phospho-SG2NA is high in the microsome and cytosol and the nucleus but low in the mitochondria. Okadoic acid, an inhibitor of PP2A, increases the level of SG2NA which is further enhanced upon inhibition of proteasomal activity. Phospho-SG2NA is thus more stable than the dephosphorylated form. Inhibition of GSK3β by LiCl reduces its level, but the inhibition of ERK by PD98059 increases it. Thus, ERK decreases the level of phospho-SG2NA by inhibiting GSK3β. In cells depleted from SG2NA by shRNA, the levels of pGSK3β and pERK are reduced, suggesting that these kinases and SG2NA regulate each other’s expression.
Calcium imaging revealed no modulatory effect on odor-evoked responses of the Drosophila antennal lobe by two populations of inhibitory local interneurons
Authors: Strube-Bloss Martin F. , Grabe Veit , Hansson Bill S. , Sachse Silke 
Published: August 2017

AbstractAlthough we have considerable knowledge about how odors are represented in the antennal lobe (AL), the insects’ analogue to the olfactory bulb, we still do not fully understand how the different neurons in the AL network contribute to the olfactory code. In Drosophila melanogaster we can selectively manipulate specific neuronal populations to elucidate their function in odor processing. Here we silenced the synaptic transmission of two distinct subpopulations of multiglomerular GABAergic local interneurons (LN1 and LN2) using shibire (shi
ts
) and analyzed their impact on odor-induced glomerular activity at the AL input and output level. We verified that the employed shi
ts
construct effectively blocked synaptic transmission to the AL when expressed in olfactory sensory neurons. Notably, selective silencing of both LN populations did not significantly affect the odor-evoked activity patterns in the AL. Neither the glomerular input nor the glomerular output activity was modulated in comparison to the parental controls. We therefore conclude that these LN subpopulations, which cover one third of the total LN number, are not predominantly involved in odor identity coding per se. As suggested by their broad innervation patterns and contribution to long-term adaptation, they might contribute to AL–computation on a global and longer time scale.
Differentiation impairs Bach1 dependent HO-1 activation and increases sensitivity to oxidative stress in SH-SY5Y neuroblastoma cells
Authors: Piras Sabrina , Furfaro Anna Lisa , Brondolo Lorenzo , Passalacqua Mario , Marinari Umberto Maria , Pronzato Maria Adelaide , Nitti Mariapaola 
Published: August 2017

AbstractNeuronal adaptation to oxidative stress is crucially important in order to prevent degenerative diseases. The role played by the Nrf2/HO-1 system in favoring cell survival of neuroblastoma (NB) cells exposed to hydrogen peroxide (H2O2) has been investigated using undifferentiated or all-trans retinoic acid (ATRA) differentiated SH-SY5Y cells. While undifferentiated cells were basically resistant to the oxidative stimulus, ATRA treatment progressively decreased cell viability in response to H2O2. HO-1 silencing decreased undifferentiated cell viability when exposed to H2O2, proving the role of HO-1 in cell survival. Conversely, ATRA differentiated cells exposed to H2O2 showed a significantly lower induction of HO-1, and only the supplementation with low doses of bilirubin (0,5–1 μM) restored viability. Moreover, the nuclear level of Bach1, repressor of HO-1 transcription, strongly decreased in undifferentiated cells exposed to oxidative stress, while did not change in ATRA differentiated cells. Furthermore, Bach1 was displaced from HO-1 promoter in undifferentiated cells exposed to H2O2, enabling the binding of Nrf2. On the contrary, in ATRA differentiated cells treated with H2O2, Bach1 displacement was impaired, preventing Nrf2 binding and limiting HO-1 transcription. In conclusion, our findings highlight the central role of Bach1 in HO-1-dependent neuronal response to oxidative stress.