bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive transcriptome analyses reveal tomato plant responses to tobacco rattle virus-based gene silencing vectors
Authors: Zheng Yi , Ding Biao , Fei Zhangjun , Wang Ying 
Published: August 2017

AbstractIn plants, virus-induced gene silencing (VIGS) is a popular tool for functional genomic studies or rapidly assessing individual gene functions. However, molecular details regarding plant responses to viral vectors remain elusive, which may complicate experimental designs and data interpretation. To this end, we documented whole transcriptome changes of tomato elicited by the application of the most widely used tobacco rattle virus (TRV)-based vectors, using comprehensive genome-wide analyses. Our data illustrated multiple biological processes with functional implications, including (1) the enhanced activity of miR167 in guiding the cleavage of an auxin response factor; (2) reduced accumulation of phased secondary small interfering RNAs from two genomic loci; (3) altered expression of ~500 protein-coding transcripts; and (4) twenty long noncoding RNAs specifically responsive to TRV vectors. Importantly, we unraveled large-scale changes in mRNA alternative splicing patterns. These observations will facilitate future application of VIGS vectors for functional studies benefiting the plant research community and help deepen the understanding of plant-virus interactions.
Maximizing energy coupling to complex plasmonic devices by injecting light into eigenchannels
Authors: Jo Yonghyeon , Choi Wonjun , Seo Eunsung , Ahn Junmo , Park Q-Han , Jhon Young Min , Choi Wonshik 
Published: August 2017

AbstractSurface plasmon polaritons have attracted broad attention in the optoelectronics field due to their ability to merge nanoscale electronics with high-speed optical communication. As the complexity of optoelectronic devices increases to meet various needs, this integration has been hampered by the low coupling efficiency of light to plasmonic modes. Here we present a method to maximize the coupling of far-field optical waves to plasmonic waves for arbitrarily complex devices. The method consists of experimentally identifying the eigenchannels of a given nanostructure and shaping the wavefront of incident light to a particular eigenchannel that maximizes the generation of plasmonic waves. Our proposed approach increases the coupling efficiency almost four-fold with respect to the uncontrolled input. Our study will help to facilitate the integration of electronics and photonics.
Nonsteroidal Anti-inflammatory Drug Interaction with Prostacyclin Synthase Protects from Miscarriage
Authors: Velez Edwards Digna R. , Edwards Todd L. , Bray Michael J. , Torstenson Eric , Jones Sarah , Shrubsole Martha J. , Muff Harvey J. , Hartmann Katherine E. 
Published: August 2017

AbstractThis study evaluates the relationship between single nucleotide polymorphisms (SNPs) in nonsteroidal anti-inflammatory drug (NSAID) metabolism and related pathways and spontaneous abortion (SAB, gestation < 20 weeks) risk. Women were enrolled in Right from the Start (2004–2010) prospective cohort. Periconceptional NSAIDs reported through the sixth week of pregnancy were obtained from study interviews. We evaluated 201 SNPs in 600 European American women. Interaction analyses between NSAID use and SNPs were conducted using logistic regression, adjusted for confounders. We also evaluated prostaglandin E2 urinary metabolite (PGE-M) in an independent population for association with SNPs using linear regression. NSAID use was reported by 63% of cases and 62% controls. The most significant interaction was at prostacyclin synthase (PGIS) rs5602 (OR = 0.34, 95% CI 0.19–0.60, p = 2.45 × 10−4) and was significant after a Bonferroni correction. NSAID users were protected from SAB (OR = 0.78, 95% CI 0.56–1.10), while non-NSAID users were at increased risk (OR = 2.11, 95% CI 1.35–3.29) in rs5602 stratified analyses. rs5602 also associated with increased PGE-M levels (Beta = 0.09, 95% CI −0.002–0.19, p = 0.033). We identified an association between a PGIS variant and SAB risk that is modified by NSAIDs use during pregnancy and directly associated with increased levels of PGE metabolites. This suggests the potential use of genetic information to guide pharmaceutical intervention to prevent adverse pregnancy outcomes.
Farnesoid X receptor activation protects the kidney from ischemia-reperfusion damage
Authors: Gai Zhibo , Chu Lei , Xu Zhenqiang , Song Xiaoming , Sun Dongfeng , Kullak-Ublick Gerd A. 
Published: August 2017

AbstractFarnesoid X receptor (FXR) activation has been reported to reduce inflammation and oxidative stress. Because both inflammation and oxidative stress are critical for tissue destruction during kidney ischemia reperfusion (I/R) injury, we investigated the protective role of FXR against kidney damage induced by I/R in mice. Mice undergoing renal I/R developed the typical features of acute kidney injury (AKI): increased creatinine, albuminuria, tubular necrosis and apoptosis. Inflammatory cytokine production and oxidative stress were also markedly increased. In mice pretreated with 6-ethyl-chenodeoxycholic acid (6-ECDCA), a selective FXR agonist, I/R induced changes were prevented and renal function and structure were improved. Moreover, FXR activation also effectively prevented the subsequent progression of AKI to chronic kidney disease (CKD) by ameliorating glomerulosclerosis and interstitial fibrosis and by suppressing fibrogenic gene expression. FXR mRNA levels were inversely correlated with the progression to CKD in mice and with the degree of interstitial fibrosis in human biopsies. In further experiments administering 6-ECDCA to renal proximal tubular cells cultured under hypoxia, the renoprotective effects of FXR activation were associated with inhibition of oxidative and ER stress and with increased antioxidant activity. In conclusion, FXR agonists may have a therapeutic role in conditions associated with ischemic kidney damage.
Fast free-of-acrylamide clearing tissue (FACT)—an optimized new protocol for rapid, high-resolution imaging of three-dimensional brain tissue
Authors: Xu Na , Tamadon Amin , Liu Yaan , Ma Tong , Leak Rehana K. , Chen Jun , Gao Yanqin , Feng Yi 
Published: August 2017

AbstractFast Free-of-Acrylamide Clearing Tissue (FACT) is a new sodium dodecyl sulfate (SDS)-based clearing protocol for the chemical clearing and imaging of brain tissue containing transgenic or immunolabeled fluorescent proteins. In the present study, we have developed this new method and optimized multiple dimensions of the workflow, including reduced clearing time, improved efficiency of fluorescent signals without the need for electrophoretic or complex instrumentations, preservation of cytoarchitectural details, optimized confocal microscopy, and accelerated data collection. We systematically compared seven clearing protocols with the FACT protocol, using transgenic mouse brains with fluorochrome expression in microglia. Only six days were required for detecting transgene-labeled markers in a 1-mm thick brain slice from adult mice, and 14 days were required for detecting antibody-labeled markers in the same-sized tissue. Preservation of fluorescent signal was achieved by decreasing clearing time, adjusting the pH of the SDS solution, and using the appropriate temperature for tissue clearing, all of which contributed to the superiority of our method. We conclude that the FACT protocol can be successfully applied to the fluorescent imaging of mouse brain tissue, and will facilitate structural analyses and connectomics of large assemblies of cells and their networks in the context of three-dimensional organ systems.
Cesarean section without medical indication and risks of childhood allergic disorder, attenuated by breastfeeding
Authors: Chu Shuyuan , Zhang Yunting , Jiang Yanrui , Sun Wanqi , Zhu Qi , Wang Bin , Jiang Fan , Zhang Jun 
Published: August 2017

AbstractCaesarean section (CS) may increase the risk of asthma and allergic diseases in children, but previous studies could not preclude the potential confounding effect of underlying medical indications for CS. We aim to assess the association between CS itself (without indications) and risks of asthma and allergic rhinitis in children. The 2014 Shanghai Children’s Health, Education and Lifestyle Evaluation was a large population-based survey with cluster random probability sampling in 26 primary schools in Shanghai, China, in 2014. The mode of delivery and child history of asthma and allergic rhinitis were reported by parents. We included 12639 children in our analysis. CS without medical indication was associated with an increased risk of childhood asthma. CS without medical indication and CS for fetal complications were associated with increased risks of childhood allergic rhinitis, respectively. In children fed by exclusive breastfeeding or mixed feeding in the first four months after birth, these risks were not significant. In contrast, in children fed by exclusive formula milk, CS was highly significantly associated with childhood asthma and allergic rhinitis. In conclusion, CS without medical indication was associated with increased risks of both childhood asthma and allergic rhinitis. Breastfeeding in early infancy may attenuate these risks.
Sleep problems and injury risk among juveniles: A systematic review and meta-analysis of observational studies
Authors: Wang Yun-Bing , Guo Zhen-Lang , Zhang Fan , Zhang Yong , Wang Shu-Sheng , Zhao Yong 
Published: August 2017

AbstractRecent studies have reported inconsistent results regarding the association between sleep problems and injury risk among juveniles. Moreover, the extent of this risk remains largely unexplored. Thus, a systematic review and meta-analysis was conducted by our team to determine whether sleep problems increase the incidence of injuries among juveniles. PubMed, PsycINFO, Embase, and Cochrane Library databases were searched for relevant studies that explored the association between sleep problems and injury risk and have been published before July 2016. Multivariate adjusted odds ratio (OR) and associated 95% confidence intervals (CIs) were extracted and pooled using random-effects models. A total of 10 observational studies involving 73,418 participants were identified. Meta-analysis findings suggested that juveniles with sleep problems held a 1.64 times higher risk of injury than that of juveniles without sleep problems (OR: 1.64, 95% CI: 1.44–1.85). This relationship was also supported by subgroup analyses, which were based on different countries and study designs. The current evidence indicates that sleep problems are significantly associated with injury risk among juveniles. Sleep problems are highly important for young people; hence, sleep researchers and occupational physicians should focus on this aspect. Nevertheless, high-quality and adequately powered observational studies are still needed.
Microbial communities in marine sediments modify success of an invasive macrophyte
Authors: Gribben Paul E. , Nielsen Shaun , Seymour Justin R. , Bradley Daniel J. , West Matthew N. , Thomas Torsten 
Published: August 2017

AbstractInvasive plants have extensive impacts on ecosystem function and biodiversity globally. Our inability to manage invasive species stems in part from a lack of understanding of the processes that control their successful establishment and spread. To date, studies have largely considered how above-ground processes control native/invasive plant interactions. Emerging research from terrestrial and wetland ecosystems demonstrates that below-ground processes under microbial control can determine the outcome of interactions between native and invasive plants. Whether sediment microbes modify the success of invasive macrophytes in marine ecosystems is untested, despite marine sediment microbes controlling many ecological processes (e.g. nutrient cycling) comparable to those in terrestrial ecosystems. We first show that sediment bacterial communities differ between the native seagrassZostera capricorniand the invasive algaCaulerpa taxifoliaand that those differences relate to functional changes in sulfur cycling between the macrophytes. Second, by experimentally manipulating the microbial communities we show that intact microbial communities inZ.capricornisediments provide biotic resistance by reducingC.taxifoliafragment growth 119% compared to when they are inactive, and intact microbial communities inC.taxifoliasediments have positive feedbacks by increasing fragment growth 200%. Thus, similar to terrestrial ecosystems, microorganisms appear to indirectly control the success of invasive macrophytes in marine ecosystems.
Enhanced Second Harmonic Generation by Mode Matching in Gain-assisted Double-plasmonic Resonance Nanostructure
Authors: Pan Gui-Ming , Yang Da-Jie , Zhou Li , Hao Zhong-Hua , Wang Qu-Quan 
Published: August 2017

AbstractWe theoretically study the gain-assisted double plasmonic resonances to enhance second harmonic generation (SHG) in a centrosymmetric multilayered silver-dielectric-gold-dielectric (SDGD) nanostructure. Introducing gain media into the dielectric layers can not only compensate the dissipation and lead to giant amplification of surface plasmons (SPs), but also excite local quadrupolar plasmon which can boost SHG by mode matching. Specifically, as the quadrupolar mode dominates SHG in our nanostructure, under the mode matching condition, the intensity of second harmonic near-field can be enhanced by 4.43 × 102 and 1.21 × 105 times when the super-resonance is matched only at the second harmonic (SH) frequency or fundamental frequency, respectively. Moreover, the intensity of SHG near-field is enhanced by as high as 6.55 × 107 times when the nanostructure is tuned to double super-resonances at both fundamental and SH frequencies. The findings in this work have potential applications in the design of nanosensors and nanolasers.
Targeted disruption of supraspinal motor circuitry reveals a distributed network underlying Restless Legs Syndrome (RLS)-like movements in the rat
Authors: Guo Chun-Ni , Yang Wen-Jia , Zhan Shi-Qin , Yang Xi-Fei , Chen Michael C. , Fuller Patrick M. , Lu Jun 
Published: August 2017

AbstractIn this study we uncovered, through targeted ablation, a potential role for corticospinal, cerebello-rubro-spinal, and hypothalamic A11 dopaminergic systems in the development of restless legs syndrome (RLS)-like movements during sleep. Targeted lesions in select basal ganglia (BG) structures also revealed a major role for nigrostriatal dopamine, the striatum, and the external globus pallidus (GPe) in regulating RLS-like movements, in particular pallidocortical projections from the GPe to the motor cortex. We further showed that pramipexiole, a dopamine agonist used to treat human RLS, reduced RLS-like movements. Taken together, our data show that BG-cortico-spinal, cerebello-rubro-spinal and A11 descending projections all contribute to the suppression of motor activity during sleep and sleep-wake transitions, and that disruption of these circuit nodes produces RLS-like movements. Taken together with findings from recent genomic studies in humans, our findings provide additional support for the concept that the anatomic and genetic etiological bases of RLS are diverse.
Quantitative proteome and phosphoproteome analyses highlight the adherent population during Trypanosoma cruzi metacyclogenesis
Authors: Amorim Juliana C. , Batista Michel , da Cunha Elizabeth S. , Lucena Aline C. R. , Lima Carla V. de Paula , Sousa Karla , Krieger Marco A. , Marchini Fabricio K. 
Published: August 2017

AbstractTrypanosoma cruzi metacyclogenesis is a natural process that occurs inside the triatomine vector and corresponds to the differentiation of non-infective epimastigotes into infective metacyclic trypomastigotes. The biochemical alterations necessary for the differentiation process have been widely studied with a focus on adhesion and nutritional stress. Here, using a mass spectrometry approach, a large-scale phospho(proteome) study was performed with the aim of understanding the metacyclogenesis processes in a quantitative manner. The results indicate that major modulations in the phospho(proteome) occur under nutritional stress and after 12 and 24 h of adhesion. Significant changes involve key cellular processes, such as translation, oxidative stress, and the metabolism of macromolecules, including proteins, lipids, and carbohydrates. Analysis of the signalling triggered by kinases and phosphatases from 7,336 identified phosphorylation sites demonstrates that 260 of these sites are modulated throughout the differentiation process, and some of these modulated proteins have previously been identified as drug targets in trypanosomiasis treatment. To the best of our knowledge, this study provides the first quantitative results highlighting the modulation of phosphorylation sites during metacyclogenesis and the greater coverage of the proteome to the parasite during this process. The data are available via ProteomeXchange with identifier number PXD006171.
Lipidomic Signatures of Nonhuman Primates with Radiation-Induced Hematopoietic Syndrome
Authors: Pannkuk Evan L. , Laiakis Evagelia C. , Singh Vijay K. , Fornace Albert J. 
Published: August 2017

AbstractConcern over potential exposures of ionizing radiation (IR) to large populations has emphasized the need for rapid and reliable methods of biodosimetry to determine absorbed dose and required triage. Lipidomics has emerged as a powerful technique for large-scale lipid identification and quantification. Indirect effects from IR exposure generate reactive oxygen species (ROS) through water hydrolysis and may subsequently damage cellular lipids. Thus, rapid identification of specific affected lipid molecules represents possible targets for biodosimetry. The current study addresses temporal changes in the serum lipidome from 4 h to 28 d in nonhuman primates (NHPs) with radiation-induced hematopoietic syndrome (6.5 Gy exposure, LD50/60). Statistical analyses revealed a highly dynamic temporal response in the serum lipidome after IR exposure. Marked lipidomic perturbations occurred within 24 h post-irradiation along with increases in cytokine levels and C-reactive protein. Decreases were observed in di- and triacylglycerides, sphingomyelins (SMs), lysophosphatidylcholines (LysoPCs), and esterified sterols. Conversely, free fatty acids and monoacylglycerides significantly increased. Decreased levels of SMs and increased levels of LysoPCs may be important markers for biodosimetry ~2 d–3 d post-irradiation. The biphasic and dynamic response to the serum lipidome post-irradiation emphasize the importance of determining the temporal long-term response of possible radiation markers.
A multi-trap microfluidic chip enabling longitudinal studies of nerve regeneration in Caenorhabditis elegans
Authors: Gokce Sertan Kutal , Hegarty Evan Marley , Mondal Sudip , Zhao Peisen , Ghorashian Navid , Hilliard Massimo A. , Ben-Yakar Adela 
Published: August 2017

AbstractSeveral sophisticated microfluidic devices have recently been proposed for femtosecond laser axotomy in the nematode C. elegans for immobilization of the animals for surgery to overcome time-consuming and labor-intensive manual processes. However, nerve regeneration studies require long-term recovery of the animals and multiple imaging sessions to observe the regeneration capabilities of their axons post-injury. Here we present a simple, multi-trap device, consisting of a single PDMS (polydimethylsiloxane) layer, which can immobilize up to 20 animals at the favorable orientation for optical access needed for precise laser surgery and high-resolution imaging. The new device, named “worm hospital” allows us to perform the entire nerve regeneration studies, including on-chip axotomy, post-surgery housing for recovery, and post-recovery imaging all on one microfluidic chip. Utilizing the worm hospital and analysis of mutants, we observed that most but not all neurodevelopmental genes in the Wnt/Frizzled pathway are important for regeneration of the two touch receptor neurons ALM and PLM. Using our new chip, we observed that the cwn-2 and cfz-2 mutations significantly reduced the reconnection possibilities of both neurons without any significant reduction in the regrowth lengths of the severed axons. We observed a similar regeneration phenotype with cwn-1 mutation in ALM neurons only.
Identification of butenolide regulatory system controlling secondary metabolism in Streptomyces albus J1074
Authors: Ahmed Yousra , Rebets Yuriy , Tokovenko Bogdan , Brötz Elke , Luzhetskyy Andriy 
Published: August 2017

AbstractA large majority of genome-encrypted chemical diversity in actinobacteria remains to be discovered, which is related to the low level of secondary metabolism genes expression. Here, we report the application of a reporter-guided screening strategy to activate cryptic polycyclic tetramate macrolactam gene clusters in Streptomyces albus J1074. The analysis of the S. albus transcriptome revealed an overall low level of secondary metabolism genes transcription. Combined with transposon mutagenesis, reporter-guided screening resulted in the selection of two S. albus strains with altered secondary metabolites production. Transposon insertion in the most prominent strain, S. albus ATGSal2P2::TN14, was mapped to the XNR_3174 gene encoding an unclassified transcriptional regulator. The mutant strain was found to produce the avenolide-like compound butenolide 4. The deletion of the gene encoding a putative acyl-CoA oxidase, an orthologue of the Streptomyces avermitilis avenolide biosynthesis enzyme, in the S. albus XNR_3174 mutant caused silencing of secondary metabolism. The homologues of XNR_3174 and the butenolide biosynthesis genes were found in the genomes of multiple Streptomyces species. This result leads us to believe that the discovered regulatory elements comprise a new condition-dependent system that controls secondary metabolism in actinobacteria and can be manipulated to activate cryptic biosynthetic pathways.
A kinetic model of multiple phenotypic states for breast cancer cells
Authors: Qiu Kang , Gao Kai-fu , Yang Li-jian , Zhang Zhao-kang , Wang Ran , Ma Hui-shu , Jia Ya 
Published: August 2017

AbstractQuantitative modeling of microscopic genes regulatory mechanisms in an individual cell is a crucial step towards understanding various macroscopic physiological phenomena of cell populations. Based on the regulatory mechanisms of genes zeb1 and cdh1 in the growth and development of breast cancer cells, we propose a kinetic model at the level of single cell. By constructing the effective landscape of underlying stationary probability for the genes expressions, it is found that (i) each breast cancer cell has three phenotypic states (i.e., the stem-like, basal, and luminal states) which correspond to three attractions of the probability landscape. (ii) The interconversions between phenotypic states can be induced by the noise intensity and the property of phenotypic switching is quantified by the mean first-passage time. (iii) Under certain conditions, the probabilities of each cancer cell appearing in the three states are consistent with the macroscopic phenotypic equilibrium proportions in the breast cancer SUM159 cell line. (iv) Our kinetic model involving the TGF-β signal can also qualitatively explain several macroscopic physiological phenomena of breast cancer cells, such as the “TGF-β paradox” in tumor therapy, the five clinical subtypes of breast cancer cells, and the effects of transient TGF-β on breast cancer metastasis.