bluuebunny/crossref_metadata_2025_split huggingface dataset:
Promotion of a cancer-like phenotype, through chronic exposure to inflammatory cytokines and hypoxia in a bronchial epithelial cell line model
Authors: Baird Anne-Marie , Gray Steven G. , Richard Derek J. , O’Byrne Kenneth J. 
Published: January 2016

AbstractGlobally, lung cancer accounts for approximately 20% of all cancer related deaths. Five-year survival is poor and rates have remained unchanged for the past four decades. There is an urgent need to identify markers of lung carcinogenesis and new targets for therapy. Given the recent successes of immune modulators in cancer therapy and the improved understanding of immune evasion by tumours, we sought to determine the carcinogenic impact of chronic TNF-α and IL-1β exposure in a normal bronchial epithelial cell line model. Following three months of culture in a chronic inflammatory environment under conditions of normoxia and hypoxia (0.5% oxygen), normal cells developed a number of key genotypic and phenotypic alterations. Important cellular features such as the proliferative, adhesive and invasive capacity of the normal cells were significantly amplified. In addition, gene expression profiles were altered in pathways associated with apoptosis, angiogenesis and invasion. The data generated in this study provides support that TNF-α, IL-1β and hypoxia promotes a neoplastic phenotype in normal bronchial epithelial cells. In turn these mediators may be of benefit for biomarker and/or immune-therapy target studies. This project provides an important inflammatoryin vitromodel for further immuno-oncology studies in the lung cancer setting.
Selective Audiovisual Semantic Integration Enabled by Feature-Selective Attention
Authors: Li Yuanqing , Long Jinyi , Huang Biao , Yu Tianyou , Wu Wei , Li Peijun , Fang Fang , Sun Pei 
Published: January 2016

AbstractAn audiovisual object may contain multiple semantic features, such as the gender and emotional features of the speaker. Feature-selective attention and audiovisual semantic integration are two brain functions involved in the recognition of audiovisual objects. Humans often selectively attend to one or several features while ignoring the other features of an audiovisual object. Meanwhile, the human brain integrates semantic information from the visual and auditory modalities. However, how these two brain functions correlate with each other remains to be elucidated. In this functional magnetic resonance imaging (fMRI) study, we explored the neural mechanism by which feature-selective attention modulates audiovisual semantic integration. During the fMRI experiment, the subjects were presented with visual-only, auditory-only, or audiovisual dynamical facial stimuli and performed several feature-selective attention tasks. Our results revealed that a distribution of areas, including heteromodal areas and brain areas encoding attended features, may be involved in audiovisual semantic integration. Through feature-selective attention, the human brain may selectively integrate audiovisual semantic information from attended features by enhancing functional connectivity and thus regulating information flows from heteromodal areas to brain areas encoding the attended features.
A Fluctuating State in the Framework Compounds (Ba,Sr)Al2O4
Authors: Ishii Yui , Tsukasaki Hirofumi , Tanaka Eri , Mori Shigeo 
Published: January 2016

AbstractThe structural fluctuation in hexagonal Ba1−xSrxAl2O4 with a corner-sharing AlO4 tetrahedral network was characterized at various temperatures using transmission electron microscopy experiments. For x ≤ 0.05, soft modes of q ~ (1/2, 1/2, 0) and equivalent wave vectors condense at a transition temperature (TC) and form a superstructure with a cell volume of 2a × 2b × c. However, TC is largely suppressed by Sr-substitution and disappears for x ≥ 0.1. Furthermore, the q ~ (1/2, 1/2, 0) soft mode deviates from the commensurate value as temperature decreases and survives in nanoscaled regions below ~200 K. These results strongly suggest the presence of a new quantum criticality induced by the soft mode. Two distinct soft modes were observed as honeycomb-type diffuse scatterings in the high-temperature region up to 800 K. This intrinsic structural instability is a unique characteristic of the framework compound and is responsible for this unusually fluctuating state.
The trade-off between heat tolerance and metabolic cost drives the bimodal life strategy at the air-water interface
Authors: Fusi Marco , Cannicci Stefano , Daffonchio Daniele , Mostert Bruce , Pörtner Hans-Otto , Giomi Folco 
Published: January 2016

AbstractThe principle of oxygen and capacity limitation of thermal tolerance in ectotherms suggests that the long-term upper limits of an organism's thermal niche are equivalent to the upper limits of the organism's functional capacity for oxygen provision to tissues. Air-breathing ectotherms show wider thermal tolerances, since they can take advantage of the higher availability of oxygen in air than in water. Bimodal species move from aquatic to aerial media and switch between habitats in response to environmental variations such as cyclical or anomalous temperature fluctuations. Here we tested the prediction that bimodal species cope better with thermal stress than truly aquatic species using the crabPachygrapsus marmoratusas a model species. When in water, oxygen consumption rates ofP. marmoratusacutely rise during warming. Beyond a temperature threshold of 23 °C the crab's aerobic metabolism in air remains lower than in water. In parallel, the haemolymph oxygen partial pressure of submerged animals progressive decreases during warming, while it remains low but constant during emersion. Our results demonstrate the ability of a bimodal breathing ectotherm to extend its thermal tolerance during air-breathing, suggesting that there are temperature-related physiological benefits during the evolution of the bimodal life style.
Metabolic traits of an uncultured archaeal lineage -MSBL1- from brine pools of the Red Sea
Authors: Mwirichia Romano , Alam Intikhab , Rashid Mamoon , Vinu Manikandan , Ba-Alawi Wail , Anthony Kamau Allan , Kamanda Ngugi David , Göker Markus , Klenk Hans-Peter , Bajic Vladimir , Stingl Ulrich 
Published: January 2016

AbstractThe candidate Division MSBL1 (Mediterranean Sea Brine Lakes 1) comprises a monophyletic group of uncultured archaea found in different hypersaline environments. Previous studies propose methanogenesis as the main metabolism. Here, we describe a metabolic reconstruction of MSBL1 based on 32 single-cell amplified genomes from Brine Pools of the Red Sea (Atlantis II, Discovery, Nereus, Erba and Kebrit). Phylogeny based on rRNA genes as well as conserved single copy genes delineates the group as a putative novel lineage of archaea. Our analysis shows that MSBL1 may ferment glucose via the Embden–Meyerhof–Parnas pathway. However, in the absence of organic carbon, carbon dioxide may be fixed via the ribulose bisphosphate carboxylase, Wood-Ljungdahl pathway or reductive TCA cycle. Therefore, based on the occurrence of genes for glycolysis, absence of the core genes found in genomes of all sequenced methanogens and the phylogenetic position, we hypothesize that the MSBL1 are not methanogens, but probably sugar-fermenting organisms capable of autotrophic growth. Such a mixotrophic lifestyle would confer survival advantage (or possibly provide a unique narrow niche) when glucose and other fermentable sugars are not available.
Bispecific Antibody Affords Complete Post-Exposure Protection of Mice from Both Ebola (Zaire) and Sudan Viruses
Authors: Frei Julia C. , Nyakatura Elisabeth K. , Zak Samantha E. , Bakken Russell R. , Chandran Kartik , Dye John M. , Lai Jonathan R. 
Published: January 2016

AbstractFiloviruses (Ebola and Marburg) cause severe hemorrhagic fever. There are five species of ebolavirus; among these, the Ebola (Zaire) and Sudan viruses (EBOV and SUDV, respectively) are highly pathogenic and have both caused recurring, large outbreaks. However, the EBOV and SUDV glycoprotein (GP) sequences are 45% divergent and thus antigenically distinct. Few antibodies with cross-neutralizing properties have been described to date. We used antibody engineering to develop novel bispecific antibodies (Bis-mAbs) that are cross-reactive toward base epitopes on GP from EBOV and SUDV. These Bis-mAbs exhibit potent neutralization against EBOV and SUDV GP pseudotyped viruses as well as authentic pathogens and confer a high degree (in one case 100%) post-exposure protection of mice from both viruses. Our studies show that a single agent that targets the GP base epitopes is sufficient for protection in mice; such agents could be included in panfilovirus therapeutic antibody cocktails.
Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea
Authors: Garg Rohini , Shankar Rama , Thakkar Bijal , Kudapa Himabindu , Krishnamurthy Lakshmanan , Mantri Nitin , Varshney Rajeev K. , Bhatia Sabhyata , Jain Mukesh 
Published: January 2016

AbstractDrought and salinity are the major factors that limit chickpea production worldwide. We performed whole transcriptome analyses of chickpea genotypes to investigate the molecular basis of drought and salinity stress response/adaptation. Phenotypic analyses confirmed the contrasting responses of the chickpea genotypes to drought or salinity stress. RNA-seq of the roots of drought and salinity related genotypes was carried out under control and stress conditions at vegetative and/or reproductive stages. Comparative analysis of the transcriptomes revealed divergent gene expression in the chickpea genotypes at different developmental stages. We identified a total of 4954 and 5545 genes exclusively regulated in drought-tolerant and salinity-tolerant genotypes, respectively. A significant fraction (~47%) of the transcription factor encoding genes showed differential expression under stress. The key enzymes involved in metabolic pathways, such as carbohydrate metabolism, photosynthesis, lipid metabolism, generation of precursor metabolites/energy, protein modification, redox homeostasis and cell wall component biogenesis, were affected by drought and/or salinity stresses. Interestingly, transcript isoforms showed expression specificity across the chickpea genotypes and/or developmental stages as illustrated by the AP2-EREBP family members. Our findings provide insights into the transcriptome dynamics and components of regulatory network associated with drought and salinity stress responses in chickpea.
Levels of maternal care in dogs affect adult offspring temperament
Authors: Foyer Pernilla , Wilsson Erik , Jensen Per 
Published: January 2016

AbstractDog puppies are born in a state of large neural immaturity; therefore, the nervous system is sensitive to environmental influences early in life. In primates and rodents, early experiences, such as maternal care, have been shown to have profound and lasting effects on the later behaviour and physiology of offspring. We hypothesised that this would also be the case for dogs with important implications for the breeding of working dogs. In the present study, variation in the mother-offspring interactions of German Shepherd dogs within the Swedish breeding program for military working dogs was studied by video recording 22 mothers with their litters during the first three weeks postpartum. The aim was to classify mothers with respect to their level of maternal care and to investigate the effect of this care on pup behaviour in a standardised temperament test carried out at approximately 18 months of age. The results show that females differed consistently in their level of maternal care, which significantly affected the adult behaviour of the offspring, mainly with respect to behaviours classified as Physical and Social Engagement, as well as Aggression. Taking maternal quality into account in breeding programs may therefore improve the process of selecting working dogs.
Ectopic expression of R3 MYB transcription factor gene OsTCL1 in Arabidopsis, but not rice, affects trichome and root hair formation
Authors: Zheng Kaijie , Tian Hainan , Hu Qingnan , Guo Hongyan , Yang Li , Cai Ling , Wang Xutong , Liu Bao , Wang Shucai 
Published: January 2016

AbstractIn Arabidopsis, a MYB-bHLH-WD40 (MBW) transcriptional activator complex activates the homeodomain protein gene GLABRA2 (GL2), leading to the promotion of trichome formation and inhibition of root hair formation. The same MBW complex also activates single-repeat R3 MYB genes. R3 MYBs in turn, play a negative feedback role by competing with R2R3 MYB proteins for binding bHLH proteins, thus blocking the formation of the MBW complex. By BLASTing the rice (Oryza sativa) protein database using the entire amino acid sequence of Arabidopsis R3 MYB transcription factor TRICHOMELESS1 (TCL1), we found that there are two genes in rice genome encoding R3 MYB transcription factors, namely Oryza sativa TRICHOMELESS1 (OsTCL1) and OsTCL2. Expressing OsTCL1 in Arabidopsis inhibited trichome formation and promoted root hair formation and OsTCL1 interacted with GL3 when tested in Arabidopsis protoplasts. Consistent with these observations, expression levels of GL2, R2R3 MYB transcription factor gene GLABRA1 (GL1) and several R3 MYB genes were greatly reduced, indicating that OsTCL1 is functional R3 MYB. However, trichome and root hair formation in transgenic rice plants overexpressing OsTCL1 remained largely unchanged and elevated expression of OsGL2 was observed in the transgenic rice plants, indicating that rice may use different mechanisms to regulate trichome formation.
Genomic investigation reveals evolution and lifestyle adaptation of endophytic Staphylococcus epidermidis
Authors: Chaudhry Vasvi , Patil Prabhu B. 
Published: January 2016

AbstractStaphylococcus epidermidis is a major human associated bacterium and also an emerging nosocomial pathogen. There are reports of its association to rodents, sheep and plants. However, comparative and evolutionary studies of ecologically diverse strains of S. epidermidis are lacking. Here, we report the whole genome sequences of four S. epidermidis strains isolated from surface sterilized rice seeds along with genome sequence of type strain. Phylogenomic analysis of rice endophytic S. epidermidis (RESE) with “type strain” unequivocally established their species identity. Whole genome based tree of 93 strains of S. epidermidis revealed RESE as distinct sub-lineage which is more related to rodent sub-lineage than to majority of human lineage strains. Furthermore, comparative genomics revealed 20% variable gene-pool in S. epidermidis, suggesting that genomes of ecologically diverse strains are under flux. Interestingly, we were also able to map several genomic regions that are under flux and gave rise to RESE strains. The largest of these genomic regions encodes a cluster of genes unique to RESE that are known to be required for survival and stress tolerance, apart from those required for adaptation to plant habitat. The genomes and genes of RESE represent distinct ecological resource/sequences and provided first evolutionary insights into adaptation of S. epidermidis to plants.
InGaN/Dilute-As GaNAs Interface Quantum Well for Red Emitters
Authors: Tan Chee-Keong , Borovac Damir , Sun Wei , Tansu Nelson 
Published: January 2016

AbstractThe design of InGaN/dilute-As GaNAs interface quantum well (QW) leads to significant redshift in the transition wavelength with improvement in electron-hole wave function overlap and spontaneous emission rate as compared to that of the conventional In0.2Ga0.8N QW. By using self-consistent six-band k·p band formalism, the nitride active region consisting of 30 Å In0.2Ga0.8N and 10 Å GaN0.95As0.05 interface QW leads to 623.52 nm emission wavelength in the red spectral regime. The utilization of 30 Å In0.2Ga0.8N/10 Å GaN0.95As0.05 interface QW also leads to 8.5 times enhancement of spontaneous emission rate attributed by the improvement in electron-hole wavefunction overlap, as compared to that of conventional 30 Å In0.35Ga0.65N QW for red spectral regime. In addition, the transition wavelength of the interface QW is relatively unaffected by the thickness of the dilute-As GaNAs interface layer (beyond 10 Å). The analysis indicates the potential of using interface QW concept in nitride-based light-emitting diodes for long wavelength emission.
Exposure to Polycyclic Aromatic Hydrocarbons, Plasma Cytokines and Heart Rate Variability
Authors: Yang Binyao , Deng Qifei , Zhang Wangzhen , Feng Yingying , Dai Xiayun , Feng Wei , He Xiaosheng , Huang Suli , Zhang Xiao , Li Xiaohai , Lin Dafeng , He Meian , Guo Huan , Sun Huizhen , Yuan Jing , Lu Jiachun , Hu Frank B. , Zhang Xiaomin , Wu Tangchun 
Published: January 2016

AbstractEpidemiological studies have suggested associations between polycyclic aromatic hydrocarbons (PAHs) and heart rate variability (HRV). However, the roles of plasma cytokines in these associations are limited. In discovery stage of this study, we used Human Cytokine Antibody Arrays to examine differences in the concentrations of 280 plasma cytokines between 8 coke-oven workers and 16 community residents. We identified 19 cytokines with significant different expression (fold change ≥2 or ≤−2 and q-value <5%) between exposed workers and controls. 4 cytokines were selected to validate in 489 coke-oven workers by enzyme-linked immunosorbent assays in validation stage. We found OH-PAHs were inversely associated with brain-derived neurotrophic factor (BDNF) (p < 0.05) and interquartile range (IQR) increases in OH-PAHs were associated with >16% BDNF decreases. Additionally, OH-PAHs were positively associated with activated leukocyte cell adhesion molecule (ALCAM) and C-reactive protein (CRP) (p < 0.05) and IQR increases in OH-PAHs were associated with >20% increases in CRP. We also found significant associations between these cytokines and HRV (p < 0.05) and IQR increases in BDNF and CRP were associated with >8% decreases in HRV. Our results indicated PAH exposure was associated with plasma cytokines and higher cytokines were associated with decreased HRV, but additional human and potential mechanistic studies are needed.
An innovative platform for quick and flexible joining of assorted DNA fragments
Authors: De Paoli Henrique Cestari , Tuskan Gerald A. , Yang Xiaohan 
Published: January 2016

AbstractSuccessful synthetic biology efforts rely on conceptual and experimental designs in combination with testing of multi-gene constructs. Despite recent progresses, several limitations still hinder the ability to flexibly assemble and collectively share different types of DNA segments. Here, we describe an advanced system for joining DNA fragments from a universal library that automatically maintains open reading frames (ORFs) and does not require linkers, adaptors, sequence homology, amplification or mutation (domestication) of fragments in order to work properly. This system, which is enhanced by a unique buffer formulation, provides unforeseen capabilities for testing and sharing, complex multi-gene circuitry assembled from different DNA fragments.
SALO, a novel classical pathway complement inhibitor from saliva of the sand fly Lutzomyia longipalpis
Authors: Ferreira Viviana P. , Fazito Vale Vladimir , Pangburn Michael K. , Abdeladhim Maha , Ferreira Mendes-Sousa Antonio , Coutinho-Abreu Iliano V. , Rasouli Manoochehr , Brandt Elizabeth A. , Meneses Claudio , Lima Kolyvan Ferreira , Nascimento Araújo Ricardo , Horácio Pereira Marcos , Kotsyfakis Michalis , Oliveira Fabiano , Kamhawi Shaden , Ribeiro Jose M. C. , Gontijo Nelder F. , Collin Nicolas , Valenzuela Jesus G. 
Published: January 2016

AbstractBlood-feeding insects inject potent salivary components including complement inhibitors into their host’s skin to acquire a blood meal. Sand fly saliva was shown to inhibit the classical pathway of complement; however, the molecular identity of the inhibitor remains unknown. Here, we identified SALO as the classical pathway complement inhibitor. SALO, an 11 kDa protein, has no homology to proteins of any other organism apart from New World sand flies. rSALO anti-complement activity has the same chromatographic properties as the Lu. longipalpis salivary gland homogenate (SGH)counterparts and anti-rSALO antibodies blocked the classical pathway complement activity of rSALO and SGH. Both rSALO and SGH inhibited C4b deposition and cleavage of C4. rSALO, however, did not inhibit the protease activity of C1s nor the enzymatic activity of factor Xa, uPA, thrombin, kallikrein, trypsin and plasmin. Importantly, rSALO did not inhibit the alternative or the lectin pathway of complement. In conclusion our data shows that SALO is a specific classical pathway complement inhibitor present in the saliva of Lu. longipalpis. Importantly, due to its small size and specificity, SALO may offer a therapeutic alternative for complement classical pathway-mediated pathogenic effects in human diseases.
Liquid-induced colour change in a beetle: the concept of a photonic cell
Authors: Mouchet Sébastien R. , Van Hooijdonk Eloise , Welch Victoria L. , Louette Pierre , Colomer Jean-François , Su Bao-Lian , Deparis Olivier 
Published: January 2016

AbstractThe structural colour of male Hoplia coerulea beetles is notable for changing from blue to green upon contact with water. In fact, reversible changes in both colour and fluorescence are induced in this beetle by various liquids, although the mechanism has never been fully explained. Changes enacted by water are much faster than those by ethanol, in spite of ethanol’s more rapid spread across the elytral surface. Moreover, the beetle’s photonic structure is enclosed by a thin scale envelope preventing direct contact with the liquid. Here, we note the presence of sodium, potassium and calcium salts in the scale material that mediate the penetration of liquid through putative micropores. The result leads to the novel concept of a “photonic cell”: namely, a biocompatible photonic structure that is encased by a permeable envelope which mediates liquid-induced colour changes in that photonic structure. Engineered photonic cells dispersed in culture media could revolutionize the monitoring of cell-metabolism.
A Signaling Lipid Associated with Alzheimer’s Disease Promotes Mitochondrial Dysfunction
Authors: Kennedy Michael A. , Moffat Tia C. , Gable Kenneth , Ganesan Suriakarthiga , Niewola-Staszkowska Karolina , Johnston Anne , Nislow Corey , Giaever Guri , Harris Linda J. , Loewith Robbie , Zaremberg Vanina , Harper Mary-Ellen , Dunn Teresa , Bennett Steffany A. L. , Baetz Kristin 
Published: January 2016

AbstractFundamental changes in the composition and distribution of lipids within the brain are believed to contribute to the cognitive decline associated with Alzheimer’s disease (AD). The mechanisms by which these changes in lipid composition affect cellular function and ultimately cognition are not well understood. Although “candidate gene” approaches can provide insight into the effects of dysregulated lipid metabolism they require a preexisting understanding of the molecular targets of individual lipid species. In this report we combine unbiased gene expression profiling with a genome-wide chemogenomic screen to identify the mitochondria as an important downstream target of PC(O-16:0/2:0), a neurotoxic lipid species elevated in AD. Further examination revealed that PC(O-16:0/2:0) similarly promotes a global increase in ceramide accumulation in human neurons which was associated with mitochondrial-derived reactive oxygen species (ROS) and toxicity. These findings suggest that PC(O-16:0/2:0)-dependent mitochondrial dysfunction may be an underlying contributing factor to the ROS production associated with AD.