bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide characterization and expression profiling of immune genes in the diamondback moth, Plutella xylostella (L.)
Authors: Xia Xiaofeng , Yu Liying , Xue Minqian , Yu Xiaoqiang , Vasseur Liette , Gurr Geoff M. , Baxter Simon W. , Lin Hailan , Lin Junhan , You Minsheng 
Published: May 2015

AbstractThe diamondback moth,Plutella xylostella(L.), is a destructive pest that attacks cruciferous crops worldwide. Immune responses are important for interactions between insects and pathogens and information on these underpins the development of strategies for biocontrol-based pest management. Little, however, is known about immune genes and their regulation patterns inP. xylostella. A total of 149 immune-related genes in 20 gene families were identified through comparison ofP. xylostellagenome with the genomes of other insects. Complete and conserved Toll, IMD and JAK-STAT signaling pathways were found inP. xylostella. Genes involved in pathogen recognition were expanded and more diversified than genes associated with intracellular signal transduction. Gene expression profiles showed that the IMD pathway may regulate expression of antimicrobial peptide (AMP) genes in the midgut and be related to an observed down-regulation of AMPs in experimental lines of insecticide-resistantP. xylostella. A bacterial feeding study demonstrated thatP. xylostellacould activate different AMPs in response to bacterial infection. This study has established a framework of comprehensive expression profiles that highlight cues for immune regulation in a major pest. Our work provides a foundation for further studies on the functions ofP. xylostellaimmune genes and mechanisms of innate immunity.
A metabolomic study of the PPARδ agonist GW501516 for enhancing running endurance in Kunming mice
Authors: Chen Wei , Gao Rong , Xie Xinni , Zheng Zhibing , Li Haijing , Li Song , Dong Fangting , Wang Lili 
Published: May 2015

AbstractExercise can increase peroxisome proliferator-activated receptor-δ (PPARδ) expression in skeletal muscle. PPARδ regulates muscle metabolism and reprograms muscle fibre types to enhance running endurance. This study utilized metabolomic profiling to examine the effects of GW501516, a PPARδ agonist, on running endurance in mice. While training alone increased the exhaustive running performance, GW501516 treatment enhanced running endurance and the proportion of succinate dehydrogenase (SDH)-positive muscle fibres in both trained and untrained mice. Furthermore, increased levels of intermediate metabolites and key enzymes in fatty acid oxidation pathways were observed following training and/or treatment. Training alone increased serum inositol, glucogenic amino acids and branch chain amino acids. However, GW501516 increased serum galactose and β-hydroxybutyrate, independent of training. Additionally, GW501516 alone raised serum unsaturated fatty acid levels, especially polyunsaturated fatty acids, but levels increased even more when combined with training. These findings suggest that mechanisms behind enhanced running capacity are not identical for GW501516 and training. Training increases energy availability by promoting catabolism of proteins and gluconeogenesis, whereas GW501516 enhances specific consumption of fatty acids and reducing glucose utilization.
Formation of Poly[d(A-T)2] Specific Z-DNA by a Cationic Porphyrin
Authors: Jang Yoon Jung , Lee Changyun , Kim Seog K. 
Published: May 2015

AbstractTypical CD spectrum of the right-handed poly[d(A-T)2] was reversed when trans-bis(N-methylpyrimidium-4-yl)diphenyl porphyrin (trans-BMPyP) was bound, suggesting that the helicity of the polynucleotide was reversed to the left-handed form. The formation of the left-handed Z-form poly[d(A-T)2] was confirmed by 31P NMR, in which a single 31P peak of B-form poly[d(A-T)2] was split into two peaks, which is similar to the conventional B-Z transition of poly[d(G-C)2] induced by the high ionic strength. The observed B-Z transition is unique for poly[d(A-T)2]. The other polynucleotides, including poly[d(G-C)2], poly(dG)·poly(dC) and poly(dA)·poly(dT) remained as the right-handed form in the presence of the same porphyrin. This observation suggests that the porphyrin array that was formed along the poly[d(A-T)2] provides a template to which left-handed poly[d(A-T)2] is associated with an electrostatic interaction.
Tau co-organizes dynamic microtubule and actin networks
Authors: Elie Auréliane , Prezel Elea , Guérin Christophe , Denarier Eric , Ramirez-Rios Sacnicte , Serre Laurence , Andrieux Annie , Fourest-Lieuvin Anne , Blanchoin Laurent , Arnal Isabelle 
Published: May 2015

AbstractThe crosstalk between microtubules and actin is essential for cellular functions. However, mechanisms underlying the microtubule-actin organization by cross-linkers remain largely unexplored. Here, we report that tau, a neuronal microtubule-associated protein, binds to microtubules and actin simultaneously, promoting in vitro co-organization and coupled growth of both networks. By developing an original assay to visualize concomitant microtubule and actin assembly, we show that tau can induce guided polymerization of actin filaments along microtubule tracks and growth of single microtubules along actin filament bundles. Importantly, tau mediates microtubule-actin co-alignment without changing polymer growth properties. Mutagenesis studies further reveal that at least two of the four tau repeated motifs, primarily identified as tubulin-binding sites, are required to connect microtubules and actin. Tau thus represents a molecular linker between microtubule and actin networks, enabling a coordination of the two cytoskeletons that might be essential in various neuronal contexts.
Shaping a Subwavelength Needle with Ultra-long Focal Length by Focusing Azimuthally Polarized Light
Authors: Qin Fei , Huang Kun , Wu Jianfeng , Jiao Jiao , Luo Xiangang , Qiu Chengwei , Hong Minghui 
Published: May 2015

AbstractFlat optics, which could planarize and miniaturize the traditional optical elements, possesses the features of extremely low profile and high integration for advanced manipulation of light. Here we proposed and experimentally demonstrated a planar metalens to realize an ultra-long focal length of ~240λ with a large depth of focus (DOF) of ~12λ, under the illumination of azimuthally polarized beam with vortical phase at 633 nm. Equally important is that such a flat lens could stably keep a lateral subwavelength width of 0.42λ to 0.49λ along the needle-like focal region. It exhibits one-order improvement in the focal length compared to the traditional focal lengths of 20~30λ of flat lens, under the criterion of having subwavelength focusing spot. The ultra-long focal length ensures sufficient space for subsequent characterization behind the lens in practical industry setups, while subwavelength cross section and large DOF enable high resolution in transverse imaging and nanolithography and high tolerance in axial positioning in the meantime. Such planar metalens with those simultaneous advantages is prepared by laser pattern generator rather than focused ion beam, which makes the mass production possible.
Rice (Oryza sativa L) plantation affects the stability of biochar in paddy soil
Authors: Wu Mengxiong , Feng Qibo , Sun Xue , Wang Hailong , Gielen Gerty , Wu Weixiang 
Published: May 2015

AbstractConversion of rice straw into biochar for soil amendment appears to be a promising method to increase long-term carbon sequestration and reduce greenhouse gas (GHG) emissions. The stability of biochar in paddy soil, which is the major determining factor of carbon sequestration effect, depends mainly on soil properties and plant functions. However, the influence of plants on biochar stability in paddy soil remains unclear. In this study, bulk and surface characteristics of the biochars incubated without rice plants were compared with those incubated with rice plants using a suite of analytical techniques. Results showed that although rice plants had no significant influence on the bulk characteristics and decomposition rates of the biochar, the surface oxidation of biochar particles was enhanced by rice plants. Using 13C labeling we observed that rice plants could significantly increase carbon incorporation from biochar into soil microbial biomass. About 0.047% of the carbon in biochar was incorporated into the rice plants during the whole rice growing cycle. These results inferred that root exudates and transportation of biochar particles into rice plants might decrease the stability of biochar in paddy soil. Impact of plants should be considered when predicting carbon sequestration potential of biochar in soil systems.
An odor detection system based on automatically trained mice by relative go no-go olfactory operant conditioning
Authors: He Jing , Wei JingKuan , Rizak Joshua D. , Chen YanMei , Wang JianHong , Hu XinTian , Ma YuanYe 
Published: May 2015

AbstractOdor detection applications are needed by human societies in various circumstances. Rodent offers unique advantages in developing biologic odor detection systems. This report outlines a novel apparatus designed to train maximum 5 mice automatically to detect odors using a new olfactory, relative go no-go, operant conditioning paradigm. The new paradigm offers the chance to measure real-time reliability of individual animal’s detection behavior with changing responses. All of 15 water-deprivation mice were able to learn to respond to unpredictable delivering of the target odor with higher touch frequencies via a touch sensor. The mice were continually trained with decreasing concentrations of the target odor (n-butanol), the average correct percent significantly dropped when training at 0.01% solution concentration; the alarm algorithm showed excellent recognition of odor detection behavior of qualified mice group through training. Then, the alarm algorithm was repeatedly tested against simulated scenario for 4 blocks. The mice acted comparable to the training period during the tests and provided total of 58 warnings for the target odor out of 59 random deliveries and 0 false alarm. The results suggest this odor detection method is promising for further development in respect to various types of odor detection applications.
A Tale of Two Hyper-diversities: Diversification dynamics of the two largest families of lichenized fungi
Authors: Kraichak Ekaphan , Divakar Pradeep K. , Crespo Ana , Leavitt Steven D. , Nelsen Matthew P. , Lücking Robert , Lumbsch H. Thorsten 
Published: May 2015

AbstractRenewed interests in macroevolutionary dynamics have led to the proliferation of studies on diversification processes in large taxonomic groups, such as angiosperms, mammals and birds. However, such a study has yet to be conducted in lichenized fungi – an extremely successful and diverse group of fungi. Analysing the most comprehensive time-calibrated phylogenies with a new analytical method, we illustrated drastically different diversification dynamics between two hyper-diverse families of lichenized fungi, Graphidaceae and Parmeliaceae, which represent more than a fourth of the total species diversity of lichenized fungi. Despite adopting a similar nutrition mode and having a similar number of species, Graphidaceae exhibited a lower speciation rate, while Parmeliaceae showed a sharp increase in speciation rate that corresponded with the aridification during the Oligocene-Miocene transition, suggesting their adaptive radiation into a novel arid habitat.
Developmentally dynamic genome: Evidence of genetic influences on increases and decreases in conduct problems from early childhood to adolescence
Authors: Pingault Jean-Baptiste , Rijsdijk Frühling , Zheng Yao , Plomin Robert , Viding Essi 
Published: May 2015

AbstractThe development of conduct problems in childhood and adolescence is associated with adverse long-term outcomes, including psychiatric morbidity. Although genes constitute a proven factor of stability in conduct problems, less is known regarding their role in conduct problems’ developmental course (i.e. systematic age changes, for instance linear increases or decreases).Mothers rated conduct problems from age 4 to 16 years in 10,038 twin pairs from the Twins Early Development Study. Individual differences in the baseline level (.78; 95% CI: .68-.88) and the developmental course of conduct problems (.73; 95% CI: .60-.86) were under high and largely independent additive genetic influences. Shared environment made a small contribution to the baseline level but not to the developmental course of conduct problems. These results show that genetic influences not only contribute to behavioural stability but also explain systematic change in conduct problems. Different sets of genes may be associated with the developmental course versus the baseline level of conduct problems. The structure of genetic and environmental influences on the development of conduct problems suggests that repeated preventive interventions at different developmental stages might be necessary to achieve a long-term impact.
Spying on small wildlife sounds using affordable collar-mounted miniature microphones: an innovative method to record individual daylong vocalisations in chipmunks
Authors: Couchoux Charline , Aubert Maxime , Garant Dany , Réale Denis 
Published: May 2015

AbstractTechnological advances can greatly benefit the scientific community by making new areas of research accessible. The study of animal vocal communication, in particular, can gain new insights and knowledge from technological improvements in recording equipment. Our comprehension of the acoustic signals emitted by animals would be greatly improved if we could continuously track the daily natural emissions of individuals in the wild, especially in the context of integrating individual variation into evolutionary ecology research questions. We show here how this can be accomplished using an operational tiny audio recorder that can easily be fitted as an on-board acoustic data-logger on small free-ranging animals. The high-quality 24 h acoustic recording logged on the spy microphone device allowed us to very efficiently collect daylong chipmunk vocalisations, giving us much more detailed data than the classical use of a directional microphone over an entire field season. The recordings also allowed us to monitor individual activity patterns and record incredibly long resting heart rates and to identify self-scratching events and even whining from pre-emerging pups in their maternal burrow.
LRRK2 dephosphorylation increases its ubiquitination
Authors: Zhao Jing , Molitor Tyler P. , Langston J. William , Nichols R. Jeremy 
Published: May 2015

Activating mutations in the leucine rich repeat protein kinase 2 (LRRK2) gene are the most common cause of inherited Parkinson's disease (PD). LRRK2 is phosphorylated on a cluster of phosphosites including Ser910, Ser935, Ser955 and Ser973, which are dephosphorylated in several PD-related LRRK2 mutants (N1437H, R1441C/G, Y1699C and I2020T) linking the regulation of these sites to PD. These serine residues are also dephosphorylated after kinase inhibition and lose 14-3-3 binding, which serves as a pharmacodynamic marker for inhibited LRRK2. Loss of 14-3-3 binding is well established, but the consequences of dephosphorylation are only now being uncovered. In the present study, we found that potent and selective inhibition of LRRK2 kinase activity leads to dephosphorylation of Ser935 then ubiquitination and degradation of a significant fraction of LRRK2. GNE1023 treatment decreased the phosphorylation and stability of LRRK2 in expression systems and endogenous LRRK2 in A549 cells and in mouse dosing studies. We next established that LRRK2 is ubiquitinated through at least Lys48 and Lys63 ubiquitin linkages in response to inhibition. To investigate the link between dephosphorylation induced by inhibitor treatment and LRRK2 ubiquitination, we studied LRRK2 in conditions where it is dephosphorylated such as expression of PD mutants [R1441G, Y1699C and I2020T] or by blocking 14-3-3 binding to LRRK2 via difopein expression, and found LRRK2 is hyper-ubiquitinated. Calyculin A treatment prevents inhibitor and PD mutant induced dephosphorylation and reverts LRRK2 to a lesser ubiquitinated species, thus directly implicating phosphatase activity in LRRK2 ubiquitination. This dynamic dephosphorylation–ubiquitination cycle could explain detrimental loss-of-function phenotypes found in peripheral tissues of LRRK2 kinase inactive mutants, LRRK2 KO (knockout) animals and following LRRK2 inhibitor administration.
The motor function of Drosophila melanogaster myosin-5 is activated by calcium and cargo-binding protein dRab11
Authors: Ji Huan-Hong , Zhang Hai-Man , Shen Mei , Yao Lin-Lin , Li Xiang-dong 
Published: May 2015

In the Drosophila melanogaster compound eye, myosin-5 (DmM5) plays two distinct roles in response to light stimulation: transport of pigment granules to the rhabdomere base to decrease light exposure and transport of rhodopsin-bearing vesicles to the rhabdomere base to compensate for the rhodopsin loss during light exposure. However, little is known of how the motor function of DmM5 is regulated at the molecular level. In the present study, we overexpressed DmM5 in Sf9 insect cells and investigated its regulation using purified proteins. We found that the actin-activated ATPase activity of DmM5 is significantly lower than that of the truncated DmM5 having the C-terminal globular tail domain (GTD) deleted, indicating that the GTD is the inhibitory domain. The actin-activated ATPase activity of DmM5 is significantly activated by micromolar levels of calcium. DmM5 associates with pigment granules and rhodopsin-bearing vesicles through cargo-binding proteins Lightoid (Ltd) and dRab11 respectively. We found that GTP-bound dRab11, but not Ltd, significantly activates DmM5 actin-activated ATPase activity. Moreover, we identified Gln1689 in the GTD as the critical residue for the interaction with dRab11 and activation of DmM5 motor function by dRab11. Based on those results, we propose that DmM5-dependent transport of pigment granules is directly activated by light-induced calcium influx and the DmM5-dependent transport of rhodopsin-bearing vesicle is activated by active GTP-bound dRab11, whose formation is stimulated by light-induced calcium influx.
The enzyme activities of Caf1 and Ccr4 are both required for deadenylation by the human Ccr4–Not nuclease module
Authors: Maryati Maryati , Airhihen Blessing , Winkler G. Sebastiaan 
Published: May 2015

In eukaryotic cells, the shortening and removal of the poly(A) tail (deadenylation) of cytoplasmic mRNA is a key event in regulated mRNA degradation. A major enzyme involved in deadenylation is the Ccr4–Not deadenylase complex, which can be recruited to its target mRNA by RNA-binding proteins or the miRNA repression complex. In addition to six non-catalytic components, the complex contains two enzymatic subunits with ribonuclease activity: Ccr4 and Caf1 (Pop2). In vertebrates, each deadenylase subunit is encoded by two paralogues: Caf1, which can interact with the anti-proliferative protein BTG2, is encoded by CNOT7 and CNOT8, whereas Ccr4 is encoded by the highly similar genes CNOT6 and CNOT6L. Currently, it is unclear whether the catalytic subunits work co-operatively or whether the nuclease components have unique roles in deadenylation. We therefore developed a method to express and purify a minimal human BTG2–Caf1–Ccr4 nuclease sub-complex from bacterial cells. By using chemical inhibition and well-characterized inactivating amino acid substitutions, we demonstrate that the enzyme activities of Caf1 and Ccr4 are both required for deadenylation in vitro. These results indicate that Caf1 and Ccr4 cooperate in mRNA deadenylation and suggest that the enzyme activities of Caf1 and Ccr4 are regulated via allosteric interactions within the nuclease module.
Efficient replica bitline technique for variation‐tolerant timing generation scheme of SRAM sense amplifiers
Authors: Lu Wenjuan , Peng Chunyu , Tao Youwu , Li Zhengping 
Published: May 2015

An efficient replica bitline (RBL) technique for reducing the variation of sense amplifier enable (SAE) timing is proposed. Both RBLs and four‐fold replica cells compared with the conventional RBL technique are utilised to favour the desired operations. Simulation results show that the standard deviation of SAE can be suppressed by 44.25% and the cycle time is also reduced by ∼30% at a 0.8 V supply voltage in TSMC 65 nm technology. Additionally, the area of the proposed scheme is nearly the same as that of the conventional RBL scheme.
Development of LNA oligonucleotide–PCR clamping technique in investigating the community structures of plant-associated bacteria
Authors: Ikenaga Makoto , Tabuchi Masakazu , Oyama Takuya , Akagi Isao , Sakai Masao 
Published: May 2015

Abstract
Simultaneous extraction of plant organelle (mitochondria and plastid) genes during the DNA extraction step is major limitation in investigating the community structures of plant-associated bacteria. Although locked nucleic acid (LNA) oligonucleotides was designed to selectively amplify the bacterial small subunit rRNA genes by applying the PCR clamping technique, those for plastids were applicable only for particular plants, while those for mitochondria were available throughout most plants. To widen the applicable range, new LNA oligonucleotides specific for plastids were designed, and the efficacy was investigated. PCR without LNA oligonucleotides predominantly amplified the organelle genes, while bacterial genes were predominantly observed in having applied the LNA oligonucleotides. Denaturing gradient gel electrophoresis (DGGE) analysis displayed additional bacterial DGGE bands, the amplicons of which were prepared using the LNA oligonucleotides. Thus, new designed LNA oligonucleotides specific for plastids were effective and have widened the scope in investigating the community structures of plant-associated bacteria.
Aortic Pulse Wave Velocity in Healthy Children and Adolescents: Reference Values for the Vicorder Device and Modifying Factors
Authors: Thurn Daniela , Doyon Anke , Sözeri Betul , Bayazit Aysun K. , Canpolat Nur , Duzova Ali , Querfeld Uwe , Schmidt Bernhard M.W. , Schaefer Franz , Wühl Elke , Melk Anette ,   for the 4C Study Consortium
Published: May 2015

BACKGROUND
Aortic pulse wave velocity (PWV), an indicator of arterial stiffness, independently predicts cardiovascular mortality risk in adults. Arterial stiffening advances with age and seems accelerated in children with certain disease conditions such as chronic kidney disease or diabetes. The Vicorder, an oscillometric device to measure PWV, has been validated in children, but reference values in a large pediatric cohort, association to carotid stiffness and influence of individual and family risk factors have not been determined.

METHODS
Pulse waves were captured in 1,003 healthy children (aged 6–18 years) in 6 centers and gender-specific reference data normalized to age/height were constructed. In 589 children carotid distensibility and intima media thickness were measured. Gestational and family history was reported.

RESULTS
PWV correlated with age (r = 0.57, P &lt; 0.0001) with significant gender-related differences starting at age 9. Further significant correlations were seen for height, weight, body mass index, blood pressure, pulse pressure, and heart rate. Independent predictors for PWV in a multivariate regression analysis were gender, age, height, weight, mean arterial pressure, and heart rate. Risk factors for higher PWV included small for gestational age at birth, secondhand smoking, parental hypertension, and obesity. PWV showed weak correlations with 2 of the carotid distensibility measures, but not with intima media thickness.

CONCLUSION
This study defines reference values for PWV captured by the Vicorder device in children and adolescents and reveals associations with potential cardiovascular risk factors in a healthy population. Gender-specific percentiles for age/height will allow for the assessment of pediatric cohorts using this oscillometric method.