bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermal stratification drives movement of a coastal apex predator
Authors: Aspillaga Eneko , Bartumeus Frederic , Starr Richard M. , López-Sanz Àngel , Linares Cristina , Díaz David , Garrabou Joaquim , Zabala Mikel , Hereu Bernat 
Published: March 2017

AbstractA characterization of the thermal ecology of fishes is needed to better understand changes in ecosystems and species distributions arising from global warming. The movement of wild animals during changing environmental conditions provides essential information to help predict the future thermal response of large marine predators. We used acoustic telemetry to monitor the vertical movement activity of the common dentex (Dentex dentex), a Mediterranean coastal predator, in relation to the oscillations of the seasonal thermocline during two summer periods in the Medes Islands marine reserve (NW Mediterranean Sea). During the summer stratification period, the common dentex presented a clear preference for the warm suprathermoclinal layer, and adjusted their vertical movements following the depth changes of the thermocline. The same preference was also observed during the night, when fish were less active. Due to this behaviour, we hypothesize that inter-annual thermal oscillations and the predicted lengthening of summer conditions will have a significant positive impact on the metabolic efficiency, activity levels, and population dynamics of this species, particularly in its northern limit of distribution. These changes in the dynamics of an ecosystem’s keystone predator might cascade down to lower trophic levels, potentially re-defining the coastal fish communities of the future.
Hydrocortisone-induced parkin prevents dopaminergic cell death via CREB pathway in Parkinson’s disease model
Authors: Ham Sangwoo , Lee Yun-Il , Jo Minkyung , Kim Hyojung , Kang Hojin , Jo Areum , Lee Gum Hwa , Mo Yun Jeong , Park Sang Chul , Lee Yun Song , Shin Joo-Ho , Lee Yunjong 
Published: March 2017

AbstractDysfunctional parkin due to mutations or post-translational modifications contributes to dopaminergic neurodegeneration in Parkinson’s disease (PD). Overexpression of parkin provides protection against cellular stresses and prevents dopamine cell loss in several PD animal models. Here we performed an unbiased high-throughput luciferase screening to identify chemicals that can increase parkin expression. Among promising parkin inducers, hydrocortisone possessed the most favorable profiles including parkin induction ability, cell protection ability, and physicochemical property of absorption, distribution, metabolism, and excretion (ADME) without inducing endoplasmic reticulum stress. We found that hydrocortisone-induced parkin expression was accountable for cell protection against oxidative stress. Hydrocortisone-activated parkin expression was mediated by CREB pathway since gRNA to CREB abolished hydrocortisone’s ability to induce parkin. Finally, hydrocortisone treatment in mice increased brain parkin levels and prevented 6-hydroxy dopamine induced dopamine cell loss when assessed at 4 days after the toxin’s injection. Our results showed that hydrocortisone could stimulate parkin expression via CREB pathway and the induced parkin expression was accountable for its neuroprotective effect. Since glucocorticoid is a physiological hormone, maintaining optimal levels of glucocorticoid might be a potential therapeutic or preventive strategy for Parkinson’s disease.
Analyzing Single Molecule Localization Microscopy Data Using Cubic Splines
Authors: Babcock Hazen P. , Zhuang Xiaowei 
Published: March 2017

AbstractThe resolution of super-resolution microscopy based on single molecule localization is in part determined by the accuracy of the localization algorithm. In most published approaches to date this localization is done by fitting an analytical function that approximates the point spread function (PSF) of the microscope. However, particularly for localization in 3D, analytical functions such as a Gaussian, which are computationally inexpensive, may not accurately capture the PSF shape leading to reduced fitting accuracy. On the other hand, analytical functions that can accurately capture the PSF shape, such as those based on pupil functions, can be computationally expensive. Here we investigate the use of cubic splines as an alternative fitting approach. We demonstrate that cubic splines can capture the shape of any PSF with high accuracy and that they can be used for fitting the PSF with only a 2–3x increase in computation time as compared to Gaussian fitting. We provide an open-source software package that measures the PSF of any microscope and uses the measured PSF to perform 3D single molecule localization microscopy analysis with reasonable accuracy and speed.
Oral administration of Lactobacillus gasseri SBT2055 is effective in preventing Porphyromonas gingivalis-accelerated periodontal disease
Authors: Kobayashi R. , Kobayashi T. , Sakai F. , Hosoya T. , Yamamoto M. , Kurita-Ochiai T. 
Published: March 2017

AbstractProbiotics have been used to treat gastrointestinal disorders. However, the effect of orally intubated probiotics on oral disease remains unclear. We assessed the potential of oral administration of Lactobacillus gasseri SBT2055 (LG2055) for Porphyromonas gingivalis infection. LG2055 treatment significantly reduced alveolar bone loss, detachment and disorganization of the periodontal ligament, and bacterial colonization by subsequent P. gingivalis challenge. Furthermore, the expression and secretion of TNF-α and IL-6 in gingival tissue was significantly decreased in LG2055-administered mice after bacterial infection. Conversely, mouse β-defensin-14 (mBD-14) mRNA and its peptide products were significantly increased in distant mucosal components as well as the intestinal tract to which LG2055 was introduced. Moreover, IL-1β and TNF-α production from THP-1 monocytes stimulated with P. gingivalis antigen was significantly reduced by the addition of human β-defensin-3. These results suggest that gastrically administered LG2055 can enhance immunoregulation followed by periodontitis prevention in oral mucosa via the gut immune system; i.e., the possibility of homing in innate immunity.
Aseismic transient during the 2010–2014 seismic swarm: evidence for longer recurrence of M ≥ 6.5 earthquakes in the Pollino gap (Southern Italy)?
Authors: Cheloni Daniele , D’Agostino Nicola , Selvaggi Giulio , Avallone Antonio , Fornaro Gianfranco , Giuliani Roberta , Reale Diego , Sansosti Eugenio , Tizzani Pietro 
Published: March 2017

AbstractIn actively deforming regions, crustal deformation is accommodated by earthquakes and through a variety of transient aseismic phenomena. Here, we study the 2010–2014 Pollino (Southern Italy) swarm sequence (main shock M
W
5.1) located within the Pollino seismic gap, by analysing the surface deformation derived from Global Positioning System and Synthetic Aperture Radar data. Inversions of geodetic time series show that a transient slip, with the same mechanism of the main shock, started about 3–4 months before the main shock and lasted almost one year, evolving through time with acceleration phases that correlate with the rate of seismicity. The moment released by the transient slip is equivalent to M
W
5.5, significantly larger than the seismic moment release revealing therefore that a significant fraction of the overall deformation is released aseismically. Our findings suggest that crustal deformation in the Pollino gap is accommodated by infrequent “large” earthquakes (M
W
≥ 6.5) and by aseismic episodes releasing a significant fraction of the accrued strain. Lower strain rates, relative to the adjacent Southern Apennines, and a mixed seismic/aseismic strain release are in favour of a longer recurrence for large magnitude earthquakes in the Pollino gap.
Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration
Authors: Kumaresan Deepak , Cross Adam T , Moreira-Grez Benjamin , Kariman Khalil , Nevill Paul , Stevens Jason , Allcock Richard J N , O’Donnell Anthony G , Dixon Kingsley W , Whiteley Andrew S 
Published: March 2017

AbstractMining of mineral resources produces substantial volumes of crushed rock based wastes that are characterised by poor physical structure and hydrology, unstable geochemistry and potentially toxic chemical conditions. Recycling of these substrates is desirable and can be achieved by blending waste with native soil to form a ‘novel substrate’ which may be used in future landscape restoration. However, these post-mining substrate based ‘soils’ are likely to contain significant abiotic constraints for both plant and microbial growth. Effective use of these novel substrates for ecosystem restoration will depend on the efficacy of stored topsoil as a potential microbial inoculum as well as the subsequent generation of key microbial soil functions originally apparent in local pristine sites. Here, using both marker gene and shotgun metagenome sequencing, we show that topsoil storage and the blending of soil and waste substrates to form planting substrates gives rise to variable bacterial and archaeal phylogenetic composition but a high degree of metabolic conservation at the community metagenome level. Our data indicates that whilst low phylogenetic conservation is apparent across substrate blends we observe high functional redundancy in relation to key soil microbial pathways, allowing the potential for functional recovery of key belowground pathways under targeted management.
Single cell imaging and quantification of TDP-43 and α-synuclein intercellular propagation
Authors: Peled Sivan , Sade Dorin , Bram Yaron , Porat Ziv , Kreiser Topaz , Mimouni Michael , Lichtenstein Alexandra , Segal Daniel , Gazit Ehud 
Published: March 2017

AbstractThe intercellular spreading of protein assemblies is a major factor in the progression of neurodegenerative disorders. The quantitative study and visualization of cell-to-cell propagation using tagged-proteins is challenging due to the steric effect of relatively large fluorescence tags and the risk of ‘false positive’ identification when analyzing these rare transmission events. Here, we established a cell culture model to characterize the cell-to-cell transmission of TAR DNA-binding protein and α-synuclein, involved in amyotrophic lateral sclerosis and Parkinson’s disease, respectively, using the small nine amino acid influenza hemagglutinin tag. The novel use of single cell resolution imaging flow cytometry allowed the visualization and quantification of all individual transmission events. Cell-level analysis of these events indicated that the degree of transfer is lower than previously reported based on conventional flow cytometry. Furthermore, our analysis can exclude ‘false positive’ events of cellular overlap and extracellular debris attachment. The results were corroborated by high-resolution confocal microscopy mapping of protein localization.
Jasmonic acid-related resistance in tomato mediates interactions between whitefly and whitefly-transmitted virus
Authors: Sun Yan-Chun , Pan Li-Long , Ying Feng-Ze , Li Ping , Wang Xiao-Wei , Liu Shu-Sheng 
Published: March 2017

AbstractThe indirect interactions between insect vectors, such as whiteflies, and the viruses they transmit, such as begomoviruses, via host plants may produce a range of outcome depending on the species/strain of each of the three organisms involved, and the mechanisms underlying the variations are not well understood. Here, we observed the performance of whiteflies on three types of tomato, which vary in level of jasmonic acid (JA)-related resistance and were either uninfected or infected by a begomovirus, to investigate the role of JA-related resistance in mediating whitefly-begomovirus interactions. Compared to the performance of whiteflies on plants of the wild type, the performance was elevated on plants deficient in JA-related resistance but reduced on plants with a high level of JA-related resistance. Further, on plants with a high level of JA-related resistance, the whitefly performed better on virus-infected than on uninfected plants; however, on tomato plants deficient in JA-related resistance, whitefly performance was less affected by the virus-infection of plants. Additionally, the expression of the JA-regulated defense gene PI-II in tomato plants was repressed by virus infection. These findings suggest that JA-related resistance plays an important role in the tripartite interactions between whitefly, begomovirus and tomato plant.
Garcinol loaded vitamin E TPGS emulsified PLGA nanoparticles: preparation, physicochemical characterization, in vitro and in vivo studies
Authors: Gaonkar Raghuvir H. , Ganguly Soumya , Dewanjee Saikat , Sinha Samarendu , Gupta Amit , Ganguly Shantanu , Chattopadhyay Dipankar , Chatterjee Debnath Mita 
Published: March 2017

AbstractGarcinol (GAR) is a naturally occurring polyisoprenylated phenolic compound. It has been recently investigated for its biological activities such as antioxidant, anti-inflammatory, anti ulcer, and antiproliferative effect on a wide range of human cancer cell lines. Though the outcomes are very promising, its extreme insolubility in water remains the main obstacle for its clinical application. Herein we report the formulation of GAR entrapped PLGA nanoparticles by nanoprecipitation method using vitamin E TPGS as an emulsifier. The nanoparticles were characterized for size, surface morphology, surface charge, encapsulation efficiency and in vitro drug release kinetics. The MTT assay depicted a high amount of cytotoxicity of GAR-NPs in B16F10, HepG2 and KB cells. A considerable amount of cell apoptosis was observed in B16f10 and KB cell lines. In vivo cellular uptake of fluorescent NPs on B16F10 cells was also investigated. Finally the GAR loaded NPs were radiolabeled with technetium-99m with >95% labeling efficiency and administered to B16F10 melanoma tumor bearing mice to investigate the in vivo deposition at the tumor site by biodistribution and scintigraphic imaging study. In vitro cellular uptake studies and biological evaluation confirm the efficacy of the formulation for cancer treatment.
Toroidal Dipolar Excitation in Metamaterials Consisting of Metal nanodisks and a Dielectrc Spacer on Metal Substrate
Authors: Tang Chaojun , Yan Bo , Wang Qiugu , Chen Jing , Yan Zhendong , Liu Fanxin , Chen Naibo , Sui Chenghua 
Published: March 2017

AbstractWe have investigated numerically toroidal dipolar excitation at optical frequency in metamaterials whose unit cell consists of three identical Ag nanodisks and a SiO2 spacer on Ag substrate. The near-field plasmon hybridization between individual Ag nanodisks and substrate forms three magnetic dipolar resonances, at normal incidence of plane electromagnetic waves. The strong coupling among three magnetic dipolar resonances leads to the toroidal dipolar excitation, when space-inversion symmetry is broke along the polarization direction of incident light. The influences of some geometrical parameters on the resonance frequency and the excitation strength of toroidal dipolar mode are studied in detail. The radiated power from toroidal dipole is also compared with that from conventional electric and magnetic multipoles.
Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer
Authors: Bhalla Sherry , Chaudhary Kumardeep , Kumar Ritesh , Sehgal Manika , Kaur Harpreet , Sharma Suresh , Raghava Gajendra P. S. 
Published: March 2017

AbstractIn this study, an attempt has been made to identify expression-based gene biomarkers that can discriminate early and late stage of clear cell renal cell carcinoma (ccRCC) patients. We have analyzed the gene expression of 523 samples to identify genes that are differentially expressed in the early and late stage of ccRCC. First, a threshold-based method has been developed, which attained a maximum accuracy of 71.12% with ROC 0.67 using single gene NR3C2. To improve the performance of threshold-based method, we combined two or more genes and achieved maximum accuracy of 70.19% with ROC of 0.74 using eight genes on the validation dataset. These eight genes include four underexpressed (NR3C2, ENAM, DNASE1L3, FRMPD2) and four overexpressed (PLEKHA9, MAP6D1, SMPD4, C11orf73) genes in the late stage of ccRCC. Second, models were developed using state-of-art techniques and achieved maximum accuracy of 72.64% and 0.81 ROC using 64 genes on validation dataset. Similar accuracy was obtained on 38 genes selected from subset of genes, involved in cancer hallmark biological processes. Our analysis further implied a need to develop gender-specific models for stage classification. A web server, CancerCSP, has been developed to predict stage of ccRCC using gene expression data derived from RNAseq experiments.
Probiotics may delay the progression of nonalcoholic fatty liver disease by restoring the gut microbiota structure and improving intestinal endotoxemia
Authors: Xue Li , He Juntao , Gao Ning , Lu Xiaolan , Li Ming , Wu Xiaokang , Liu Zeshi , Jin Yaofeng , Liu Jiali , Xu Jiru , Geng Yan 
Published: March 2017

AbstractGut-derived bacterial lipopolysaccharide (LPS) and subsequent hepatic toll-like receptor 4 (TLR4) activation have been recognized to be involved in the onset of diet-induced nonalcoholic fatty liver disease (NAFLD), but little is known about the variation of LPS and TLR4 during the progression of NAFLD. Probiotics were able to inhibit proliferation of harmful bacteria and improve gastrointestinal barrier function. However, it’s unclear whether LPS/TLR4 is involved in the protection effect of probiotics on NAFLD. In this study, we described characteristic of gut microbiota structure in the progression of NAFLD, and we also analyzed the relationship between gut microbiota and LPS/TLR4 in this process. Furthermore, we applied probiotics intervention to investigate the effect of probiotics on gut flora structure, intestinal integrity, serum LPS, liver TLR4 and liver pathology. Our results showed that serum LPS and liver TLR4 were highly increased during progression of NAFLD, with gut flora diversity and gut mircobiological colonization resistance (B/E) declining. Furthermore, probiotics could improve gut microbiota structure and liver pathology. Probiotics could also downregulate serum LPS and liver TLR4. Our results suggested that both gut flora alteration and endotoxemia may be involved in the progression of NAFLD. Probiotics may delay the progression of NAFLD via LPS/TLR4 signaling.
Structural Basis for pH-mediated Regulation of F-actin Severing by Gelsolin Domain 1
Authors: Fan Jing-song , Goh Honzhen , Ding Ke , Xue Bo , Robinson Robert C. , Yang Daiwen 
Published: March 2017

AbstractSix-domain gelsolin regulates actin structural dynamics through its abilities to sever, cap and uncap F-actin. These activities are modulated by various cellular parameters like Ca2+ and pH. Until now, only the molecular activation mechanism of gelsolin by Ca2+ has been understood relatively well. The fragment comprising the first domain and six residues from the linker region into the second domain has been shown to be similar to the full-length protein in F-actin severing activity in the absence of Ca2+ at pH 5. To understand how this gelsolin fragment is activated for F-actin severing by lowering pH, we solved its NMR structures at both pH 7.3 and 5 in the absence of Ca2+ and measured the pKa values of acidic amino acid residues and histidine residues. The overall structure and dynamics of the fragment are not affected significantly by pH. Nevertheless, local structural changes caused by protonation of His29 and Asp109 result in the activation on lowering the pH, and protonation of His151 directly effects filament binding since it resides in the gelsolin/actin interface. Mutagenesis studies support that His29, Asp109 and His151 play important roles in the pH-dependent severing activity of the gelsolin fragment.
Coumarin-chalcone hybrid instigates DNA damage by minor groove binding and stabilizes p53 through post translational modifications
Authors: Ashraf Raghib , Hamidullah  , Hasanain Mohammad , Pandey Praveen , Maheshwari Mayank , Singh L. Ravithej , Siddiqui M. Quadir , Konwar Rituraj , Sashidhara Koneni V. , Sarkar Jayanta 
Published: March 2017

AbstractS009-131, a coumarin-chalcone hybrid, had been shown to possess anti-proliferative and anti-tumour effect by triggering apoptosis. In this report, we investigated role of DNA damage signalling pathway in S009-131 induced cancer cell death. Here we show that S009-131 causes DNA damage by potential binding to the minor groove which led to the phosphorylation and activation of ATM and DNA-PK, but not ATR, at earlier time points in order to initiate repair process. S009-131 induced DNA damage response triggered activation of p53 through phosphorylation at its key residues. Pharmacological inhibition of PIKKs abrogated S009-131 induced phosphorylation of p53 at Ser 15. DNA damage induced phosphorylation resulted in reduced proteasomal degradation of p53 by disrupting p53-MDM2 interaction. Additionally, our docking studies revealed that S009-131 might also contribute to increased cellular p53 level by occupying p53 binding pocket of MDM2. Posttranslational modifications of p53 upon S009-131 treatment led to enhanced affinity of p53 towards responsive elements (p53-RE) in the promoter regions of target genes and increased transcriptional efficiency. Together, the results suggest that S009-131 cleaves DNA through minor groove binding and eventually activates PIKKs associated DNA damage response signalling to promote stabilization and enhanced transcriptional activity of p53 through posttranslational modifications at key residues.
Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum
Authors: Singh Pradeep , Singh Gagandeep , Bhandawat Abhishek , Singh Gopal , Parmar Rajni , Seth Romit , Sharma Ram Kumar 
Published: March 2017

AbstractTrillium govanianum, an endangered medicinal herb native to the Himalaya, is less studied at the molecular level due to the non-availability of genomic resources. To facilitate the basic understanding of the key genes and regulatory mechanism of pharmaceutically important biosynthesis pathways, first spatial transcriptome sequencing of T. govanianum was performed. 151,622,376 (~11.5 Gb) high quality reads obtained using paired-end Illumina sequencing were de novo assembled into 69,174 transcripts. Functional annotation with multiple public databases identified array of genes involved in steroidal saponin biosynthesis and other secondary metabolite pathways including brassinosteroid, carotenoid, diterpenoid, flavonoid, phenylpropanoid, steroid and terpenoid backbone biosynthesis, and important TF families (bHLH, MYB related, NAC, FAR1, bZIP, B3 and WRKY). Differentially expressed large number of transcripts, together with CYPs and UGTs suggests involvement of these candidates in tissue specific expression. Combined transcriptome and expression analysis revealed that leaf and fruit tissues are the main site of steroidal saponin biosynthesis. In conclusion, comprehensive genomic dataset created in the current study will serve as a resource for identification of potential candidates for genetic manipulation of targeted bioactive metabolites and also contribute for development of functionally relevant molecular marker resource to expedite molecular breeding and conservation efforts in T. govanianum.