bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meshing complex macro-scale objects into self-assembling bricks
Authors: Hacohen Adar , Hanniel Iddo , Nikulshin Yasha , Wolfus Shuki , Abu-Horowitz Almogit , Bachelet Ido 
Published: July 2015

AbstractSelf-assembly provides an information-economical route to the fabrication of objects at virtually all scales. However, there is no known algorithm to program self-assembly in macro-scale, solid, complex 3D objects. Here such an algorithm is described, which is inspired by the molecular assembly of DNA and based on bricks designed by tetrahedral meshing of arbitrary objects. Assembly rules are encoded by topographic cues imprinted on brick faces while attraction between bricks is provided by embedded magnets. The bricks can then be mixed in a container and agitated, leading to properly assembled objects at high yields and zero errors. The system and its assembly dynamics were characterized by video and audio analysis, enabling the precise time- and space-resolved characterization of its performance and accuracy. Improved designs inspired by our system could lead to successful implementation of self-assembly at the macro-scale, allowing rapid, on-demand fabrication of objects without the need for assembly lines.
Dual roles of endogenous and exogenous galectin-1 in the control of testicular immunopathology
Authors: Pérez Cecilia V. , Gómez Leticia G. , Gualdoni Gisela S. , Lustig Livia , Rabinovich Gabriel A. , Guazzone Vanesa A. 
Published: July 2015

AbstractGalectin-1 (Gal-1), a proto-type member of galectin family, is highly expressed in immune privileged sites, including the testis. However, in spite of considerable progress the relevance of endogenous and exogenous Gal-1 in testis pathophysiology have not yet been explored. Here we evaluated the in vivo roles of Gal-1 in experimental autoimmune orchitis (EAO), a well-established model of autoimmune testicular inflammation associated with subfertility and infertility. A significant reduction in the incidence and severity of EAO was observed in mice genetically deficient in Gal-1 (Lgals1−/−) versus wild-type (WT) mice. Testicular histopathology revealed the presence of multifocal testicular damage in WT mice characterized by an interstitial mononuclear cell infiltrate and different degrees of germ cell sloughing of seminiferous tubules. TUNEL assay and assessment of active caspase-3 expression, revealed the prevalence of apoptotic spermatocytes mainly localized in the adluminal compartment of seminiferous tubules in EAO mice. A significant increased number of TUNEL-positive germ cells was detected in EAO testis from WT compared with Lgals1−/− mice. In contrast, exogenous administration of recombinant Gal-1 to WT mice undergoing EAO attenuated the severity of the disease. Our results unveil a dual role of endogenous versus exogenous Gal-1 in the control of autoimmune testis inflammation.
Ant trophallactic networks: simultaneous measurement of interaction patterns and food dissemination
Authors: Greenwald Efrat , Segre Enrico , Feinerman Ofer 
Published: July 2015

AbstractEusocial societies and ants, in particular, maintain tight nutritional regulation at both individual and collective levels. The mechanisms that underlie this control are far from trivial since, in these distributed systems, information about the global supply and demand is not available to any single individual. Here we present a novel technique for non-intervening frequent measurement of the food load of all individuals in an ant colony, including during trophallactic events in which food is transferred by mouth-to-mouth feeding. Ants are imaged using a dual camera setup that produces both barcode-based identification and fluorescence measurement of labeled food. This system provides detailed measurements that enable one to quantitatively study the adaptive food distribution network. To demonstrate the capabilities of our method, we present sample observations that were unattainable using previous techniques and could provide insight into the mechanisms underlying food exchange.
Evidence for Coexistence of Bulk Superconductivity and Itinerant Antiferromagnetism in the Heavy Fermion System CeCo(In1−xCdx)5
Authors: Howald Ludovic , Stilp Evelyn , de Réotier Pierre Dalmas , Yaouanc Alain , Raymond Stéphane , Piamonteze Cinthia , Lapertot Gérard , Baines Christopher , Keller Hugo 
Published: July 2015

AbstractIn the generic phase diagram of heavy fermion systems, tuning an external parameter such as hydrostatic or chemical pressure modifies the superconducting transition temperature. The superconducting phase forms a dome in the temperature—tuning parameter phase diagram, which is associated with a maximum of the superconducting pairing interaction. Proximity to antiferromagnetism suggests a relation between the disappearance of antiferromagnetic order and superconductivity. We combine muon spin rotation, neutron scattering and x-ray absorption spectroscopy techniques to gain access to the magnetic and electronic structure of CeCo(In1−xCdx)5 at different time scales. Different magnetic structures are obtained that indicate a magnetic order of itinerant character, coexisting with bulk superconductivity. The suppression of the antiferromagnetic order appears to be driven by a modification of the bandwidth/carrier concentration, implying that the electronic structure and consequently the interplay of superconductivity and magnetism is strongly affected by hydrostatic and chemical pressure.
Comparative analysis of essential genes in prokaryotic genomic islands
Authors: Zhang Xi , Peng Chong , Zhang Ge , Gao Feng 
Published: July 2015

AbstractEssential genes are thought to encode proteins that carry out the basic functions to sustain a cellular life and genomic islands (GIs) usually contain clusters of horizontally transferred genes. It has been assumed that essential genes are not likely to be located in GIs, but systematical analysis of essential genes in GIs has not been explored before. Here, we have analyzed the essential genes in 28 prokaryotes by statistical method and reached a conclusion that essential genes in GIs are significantly fewer than those outside GIs. The function of 362 essential genes found in GIs has been explored further by BLAST against the Virulence Factor Database (VFDB) and the phage/prophage sequence database of PHAge Search Tool (PHAST). Consequently, 64 and 60 eligible essential genes are found to share the sequence similarity with the virulence factors and phage/prophages-related genes, respectively. Meanwhile, we find several toxin-related proteins and repressors encoded by these essential genes in GIs. The comparative analysis of essential genes in genomic islands will not only shed new light on the development of the prediction algorithm of essential genes, but also give a clue to detect the functionality of essential genes in genomic islands.
miRNA-133 augments coelomocyte phagocytosis in bacteria-challenged Apostichopus japonicus via targeting the TLR component of IRAK-1 in vitro and in vivo
Authors: Lu Meng , Zhang Peng-Juan , Li Cheng-Hua , Lv Zhi-Meng , Zhang Wei-Wei , Jin Chun-Hua 
Published: July 2015

AbstractIn this study, we explored the potential roles of miRNA-133 in regulating TLR pathways in the sea cucumber Apostichopus japonicus. Target screening of RNA-Seq data successfully identified interleukin-1 receptor-associated kinase (AjIRAK−1) as a putative target of miR-133. This result was further validated by negative expression profiles in Vibrio splendidus-challenged coelomocytes and lipopolysaccharide (LPS)-exposed cell cultures. HEK-293T cells transfected with a dual-luciferase reporter fused to the 3′UTR of wild-type or mutant AjIRAK-1 exhibited a 52.9% reduction in luciferase activity (p < 0.01) compared to controls. Co-infection with a miR-133 mimics or a specific siRNA targeting AjIRAK-1 significantly repressed the mRNA and protein expression levels of AjIRAK-1 and its downstream molecules, such as AjTRAF6 and Ajp105, in primary coelomocytes. In contrast, a miR-133 inhibitor significantly increased the expression of these TLR pathway members. The injection of miR-133 agomir or AjIRAK-1 siRNA into sea cucumbers not only decreased the expression of AjIRAK-1 and its downstream molecules but also significantly increased V. splendidus coelomocyte phagocytosis. All of the present data provide direct evidence that miR-133 is involved in TLR cascade modulation through AjIRAK-1 targeting to promote V. splendidus coelomocyte phagocytosis in these non-model invertebrates.
Decrease of mRNA Editing after Spinal Cord Injury is Caused by Down-regulation of ADAR2 that is Triggered by Inflammatory Response
Authors: Narzo Antonio Fabio Di , Kozlenkov Alexey , Ge Yongchao , Zhang Bin , Sanelli Leo , May Zacnicte , Li Yanqing , Fouad Karim , Cardozo Christopher , Koonin Eugene V , Bennett David J , Dracheva Stella 
Published: July 2015

AbstractWe recently showed that spinal cord injury (SCI) leads to a decrease in mRNA editing of serotonin receptor 2C (5-HT2CR) contributing to post-SCI spasticity. Here we study post-SCI mRNA editing and global gene expression using massively parallel sequencing. Evidence is presented that the decrease in 5-HT2CR editing is caused by down-regulation of adenosine deaminase ADAR2 and that editing of at least one other ADAR2 target, potassium channel Kv1.1, is decreased after SCI. Bayesian network analysis of genome-wide transcriptome data indicates that down-regulation of ADAR2 (1) is triggered by persistent inflammatory response to SCI that is associated with activation of microglia and (2) results in changes in neuronal gene expression that are likely to contribute both to post-SCI restoration of neuronal excitability and muscle spasms. These findings have broad implications for other diseases of the Central Nervous System and could open new avenues for developing efficacious antispastic treatments.
Volatile organic compounds in truffle (Tuber magnatum Pico): comparison of samples from different regions of Italy and from different seasons
Authors: Vita Federico , Taiti Cosimo , Pompeiano Antonio , Bazihizina Nadia , Lucarotti Valentina , Mancuso Stefano , Alpi Amedeo 
Published: July 2015

AbstractIn this paper volatile organic compounds (VOCs) fromTuber magnatumfruiting bodies were analyzed using a PTR-TOF-MS instrument. The aim was to characterize the VOC's profile of the fruiting bodies and identify if any VOCs were specific to a season and geographical areas. Multiple factorial analysis (MFA) was carried out on the signals obtained by MS. Experiments using ITS region sequencing proved that theT. magnatumlife cycle includes the formation of fruiting bodies at two different times of the year. The VOCs profiles diverge when different seasonal and geographical productions are considered. Using PTR-TOF-MS, compounds present at levels as low pptv were detected. This made it possible to determine both the origin of fruiting bodies (Alba and San Miniato) and the two biological phases of fruiting bodies formation in San Miniato truffles.
Functional diversity and properties of multiple xylanases from Penicillium oxalicum GZ-2
Authors: Liao Hanpeng , Zheng Haiping , Li Shuixian , Wei Zhong , Mei Xinlan , Ma Hongyu , Shen Qirong , Xu Yangchun 
Published: July 2015

AbstractA multiple xylanase system with high levels of xylanase activity produced from Penicillium oxalicum GZ-2 using agricultural waste as a substrate has been previously reported. However, the eco-physiological properties and origin of the multiplicity of xylanases remain unclear. In the present study, eight active bands were detected using zymography and all bands were identified as putative xylanases using MALDI-TOF-MS/MS. These putative xylanases are encoded by six different xylanase genes. To evaluate the functions and eco-physiological properties of xylanase genes, xyn10A, xyn11A, xyn10B and xyn11B were expressed in Pichia pastoris. The recombinant enzymes xyn10A and xyn10B belong to the glycoside hydrolase (GH) family 10 xylanases, while xyn11A and xyn11B belong to GH11 xylanases. Biochemical analysis of the recombinant proteins revealed that all enzymes exhibited xylanase activity against xylans but with different substrate specificities, properties and kinetic parameters. These results demonstrated that the production of multiple xylanases in P. oxalicum GZ-2 was attributed to the genetic redundancy of xylanases and the post-translational modifications, providing insight into a more diverse xylanase system for the efficient degradation of complex hemicelluloses.
Enhanced cuticular penetration as the mechanism for synergy of insecticidal constituents of rosemary essential oil in Trichoplusia ni
Authors: Tak Jun-Hyung , Isman Murray B. 
Published: July 2015

AbstractSynergistic interactions between constituents of essential oils have been reported for several areas of research. In the present study, mechanisms that could explain the synergistic action of the two major insecticidal constituents of rosemary oil, 1,8-cineole and camphor against the cabbage looper, Trichoplusia ni were investigated. 1,8-Cineole was more toxic than camphor when applied topically to larvae and when coadministered in their ratio naturally occurring in rosemary oil, the binary mixture was synergistic. However, when injected directly into larvae, camphor was more toxic than 1,8-cineole. GC-MS analyses showed that penetration of topically-applied camphor was significantly enhanced when it was mixed with 1,8-cineole in the natural ratio. A bioassay combining injection and topical application methods confirmed the increased penetration of both compounds when mixed, showing the same bioactivity as seen for higher amounts applied individually. Lowered surface tension as well as increased solubility of camphor by 1,8-cineole, along with the interaction between 1,8-cineole and the lipid layer of the insect’s cuticle may explain the enhanced penetration of camphor. Because of the similarities in biological function of animal and microbial membranes, our finding has potential for application in other fields of study.
Identification and characterization of a novel ISG15-ubiquitin mixed chain and its role in regulating protein homeostasis
Authors: Fan Jun-Bao , Arimoto Kei-lchiro , Motamedchaboki Khatereh , Yan Ming , Wolf Dieter A. , Zhang Dong-Er 
Published: July 2015

AbstractAs a ubiquitin-like modifier, ISG15 is conjugated to many cellular proteins in a process termed protein ISGylation. However, the crosstalk between protein ISGylation and the ubiquitin proteasome system is not fully understood. Here, we report that cellular ubiquitin is a substrate of ISG15 and Lys 29 on ubiquitin is the major ISG15 acceptor site. Using a model substrate, we demonstrate that ISG15 can modify ubiquitin, which is immobilized on its substrate, to form ISG15-ubiquitin mixed chains. Furthermore, our results indicate that ISG15-ubiquitin mixed chains do not serve as degradation signals for a ubiquitin fusion degradation substrate. Accordingly, an ISG15-ubiquitin fusion protein, which mimics an ISG15-ubiquitin mixed chain, negatively regulates cellular turnover of ubiquitylated proteins. In addition, ISG15-ubiquitin mixed chains, which are detectable on endogenously ubiquitylated proteins, dampen cellular turnover of these proteins. Thus, our studies unveil an unanticipated interplay between two protein modification systems and highlight its role in coordinating protein homeostasis.
Histone H4 acetylation required for chromatin decompaction during DNA replication
Authors: Ruan Kun , Yamamoto Takaharu G. , Asakawa Haruhiko , Chikashige Yuji , Kimura Hiroshi , Masukata Hisao , Haraguchi Tokuko , Hiraoka Yasushi 
Published: July 2015

AbstractFaithful DNA replication is a prerequisite for cell proliferation. Several cytological studies have shown that chromosome structures alter in the S-phase of the cell cycle. However, the molecular mechanisms behind the alteration of chromosome structures associated with DNA replication have not been elucidated. Here, we investigated chromatin structures and acetylation of specific histone residues during DNA replication using the meiotic nucleus of the fission yeast Schizosaccharomyces pombe. The S. pombe meiotic nucleus provides a unique opportunity for measuring the levels of compaction of chromatin along the chromosome in a defined orientation. By direct measurement of chromatin compaction in living cells, we demonstrated that decompaction of chromatin occurs during meiotic DNA replication. This chromatin decompaction was suppressed by depletion of histone acetyltransferase Mst1 or by arginine substitution of specific lysine residues (K8 and K12) of histone H4. These results suggest that acetylation of histone H4 residues K8 and K12 plays a critical role in loosening chromatin structures during DNA replication.
Graphene with outstanding anti-irradiation capacity as multialkylated cyclopentanes additive toward space application
Authors: Fan Xiaoqiang , Wang Liping 
Published: July 2015

AbstractMultialkylated cyclopentanes (MACs), a class of synthetic hydrocarbon fluid have attracted intensive interest as possible space lubricants due to a series of unique physical and chemical properties. Here, we used graphene with high mechanical strength and chemical inertness as lubricant additive to explore its potential for space application. The effects of space irradiation on graphene and the tribological properties of graphene as lubricant additive were firstly investigated in detail under simulated space environment composed of high vacuum, high/low temperature and irradiation. Results demonstrate that graphene not only possesses outstanding anti–irradiation capacity but also significantly improves the space performance and tribological properties of MACs, which depends on the excellent physicochemical properties and high load-carrying ability of graphene as well as more effective separation of the sliding surfaces.
Grazer-induced morphological defense in Scenedesmus obliquus is affected by competition against Microcystis aeruginosa
Authors: Zhu Xuexia , Wang Jun , Lu Yichun , Chen Qinwen , Yang Zhou 
Published: July 2015

AbstractThe green alga Scenedesmus is known for its phenotypic plasticity in response to grazing risk. However, the benefits of colony formation induced by infochemicals from zooplankton should come with costs. That is, a tradeoff in benefit-to-cost ratios is likely under complex environmental conditions. In this study, we hypothesized that the coexistence of Scenedesmus and its competitors decreases the formation of anti-grazer colonies in Scenedesmus. Results demonstrated that the presence of a competitor Microcystis aeruginosa inhibited inducible defensive colony formation of Scenedesmus obliquus and the established defensive colonies negatively affected the competitive ability of S. obliquus. The proportion of induced defensive colonies in cultures was dependent on the relative abundance of competitors. Under low competition intensity, large amount of eight-celled colonies were formed but at the cost of decreased competitive inhibition on M. aeruginosa. By contrast, defensive colony formation of S. obliquus slacked in the presence of high competition intensity to maintain a high displacement rate (competitive ability). In conclusion, S. obliquus exhibited different responses to potential grazing pressure under different intensities of competition, i.e., Scenedesmus morphological response to grazing infochemicals was affected by competition against Microcystis.
Substance P enhances microglial density in the substantia nigra through neurokinin-1 receptor/NADPH oxidase-mediated chemotaxis in mice
Authors: Wang Qingshan , Oyarzabal Esteban , Wilson Belinda , Qian Li , Hong Jau-Shyong 
Published: July 2015

The distribution of microglia varies greatly throughout the brain. The substantia nigra (SN) contains the highest density of microglia among different brain regions. However, the mechanism underlying this uneven distribution remains unclear. Substance P (SP) is a potent proinflammatory neuropeptide with high concentrations in the SN. We recently demonstrated that SP can regulate nigral microglial activity. In the present study, we further investigated the involvement of SP in modulating nigral microglial density in postnatal developing mice. Nigral microglial density was quantified in wild-type (WT) and SP-deficient mice from postnatal day 1 (P1) to P30. SP was detected at high levels in the SN as early as P1 and microglial density did not peak until around P30 in WT mice. SP-deficient mice (TAC1−/−) had a significant reduction in nigral microglial density. No differences in the ability of microglia to proliferate were observed between TAC1−/− and WT mice, suggesting that SP may alter microglial density through chemotaxic recruitment. SP was confirmed to dose-dependently attract microglia using a trans-well culture system. Mechanistic studies revealed that both the SP receptor neurokinin-1 receptor (NK1R) and the superoxide-producing enzyme NADPH oxidase (NOX2) were necessary for SP-mediated chemotaxis in microglia. Furthermore, genetic ablation and pharmacological inhibition of NK1R or NOX2 attenuated SP-induced microglial migration. Finally, protein kinase Cδ (PKCδ) was recognized to couple SP/NK1R-mediated NOX2 activation. Altogether, we found that SP partly accounts for the increased density of microglia in the SN through chemotaxic recruitment via a novel NK1R–NOX2 axis-mediated pathway.
Effects of Different Water Velocities on the Hatchery Rearing Performance and Recovery from Transportation of Rainbow Trout Fed Two Different Rations
Authors: Parker Timothy M. , Barnes Michael E. 
Published: July 2015

AbstractWe examined the effects of exercise on hatchery rearing performance and posttransportation stress recovery, growth, and survival of Rainbow Trout Oncorhynchus mykiss reared for 9 weeks in one of three water velocities (0.5, 1.5, or 3.0 body lengths (BL)/s) and fed either a restricted ration or to satiation. The influence of previous exercise regimes on survival, growth, and stress recovery for 8 weeks after transportation of the fish fed a restricted ration was also evaluated. During hatchery rearing, reduced growth and poorer food conversion ratios at higher velocities (1.5 and 3.0 BL/s) were only observed in restricted ration‐fed fish, with satiation‐fed fish exhibiting no differences in hatchery rearing performance among the water velocities. Condition factor changed with exercise regime and was significantly greater in restricted ration‐fed fish at 3.0 BL/s and satiation‐fed fish at 1.5 and 3.0 BL/s. Hepatosomatic index was unaffected by exercise but was significantly greater in the fish fed to satiation, whereas the viscerosomatic index was not significantly affected by either exercise or ration. Hematocrit was also unaffected by exercise but was significantly lower in fish fed to satiation. Cortisol levels after 9 weeks of hatchery rearing were the same for all exercise regimes regardless of feed ration. Cortisol levels after transportation were also the same for all exercise regimes and cortisol levels returned to pretransportation levels within 24 h. Growth and survival after transportation were the same for all fish regardless of their previous exercise regime. These results indicate that that fish can be reared using adequate velocity to maintain the self‐cleaning properties of hatchery tanks without fear of negatively affecting fish condition or posttransportation performance, although exercise should be paired with adequate food intake to avoid decreased hatchery growth and elevated food conversion ratios.