bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Hydrophobic Effect in Solute Partitioning and Interfacial Tension
Authors: Jackson Meyer B. 
Published: January 2016

AbstractStudies of the partitioning of hydrophobic solutes between water and nonpolar solvents provide estimates for the energy cost of creating hydrophobic-water contacts. This energy is a factor of three lower than the work of adhesion derived from interfacial tension measurements. This discrepancy noted by Tanford in 1979 is widely viewed as a serious challenge to our understanding of hydrophobic interactions. However, the interfacial energy of a water-alkane interface depends on chain length. A simple analysis of published data shows that the loss of rotational freedom of an alkane chain at an interface accounts quantitatively for the length-dependent contribution to interfacial tension, leaving a length-independent contribution very close to the free energy of transfer per unit of solvent accessible surface area. This analysis thus clarifies the discrepancy between the thermodynamic and interfacial tension measurements of hydrophobic interaction energy. Alkanes do not loose rotational freedom when transferred between two different liquid phases but they do at an interface. This reconciles the difference between microscopic and macroscopic measurements. Like the partitioning free energy, the work of adhesion also has a large entropy and small enthalpy at 20 oC.
Historical photographs revisited: A case study for dating and characterizing recent loss of coral cover on the inshore Great Barrier Reef
Authors: Clark Tara R. , Leonard Nicole D. , Zhao Jian-xin , Brodie Jon , McCook Laurence J. , Wachenfeld David R. , Duc Nguyen Ai , Markham Hannah L. , Pandolfi John M. 
Published: January 2016

AbstractLong-term data with high-precision chronology are essential to elucidate past ecological changes on coral reefs beyond the period of modern-day monitoring programs. In 2012 we revisited two inshore reefs within the central Great Barrier Reef, where a series of historical photographs document a loss of hard coral cover between c.1890–1994 AD. Here we use an integrated approach that includes high-precision U-Th dating specifically tailored for determining the age of extremely young corals to provide a robust, objective characterisation of ecological transition. The timing of mortality for most of the dead in situ corals sampled from the historical photograph locations was found to coincide with major flood events in 1990–1991 at Bramston Reef and 1970 and 2008 at Stone Island. Evidence of some recovery was found at Bramston Reef with living coral genera similar to what was described in c.1890 present in 2012. In contrast, very little sign of coral re-establishment was found at Stone Island suggesting delayed recovery. These results provide a valuable reference point for managers to continue monitoring the recovery (or lack thereof) of coral communities at these reefs.
Activating mutations in CTNNB1 in aldosterone producing adenomas
Authors: Åkerström Tobias , Maharjan Rajani , Sven Willenberg Holger , Cupisti Kenko , Ip Julian , Moser Ana , Stålberg Peter , Robinson Bruce , Alexander Iwen K. , Dralle Henning , Walz Martin K. , Lehnert Hendrik , Sidhu Stan , Gomez-Sanchez Celso , Hellman Per , Björklund Peyman 
Published: January 2016

AbstractPrimary aldosteronism (PA) is the most common cause of secondary hypertension with a prevalence of 5–10% in unreferred hypertensive patients. Aldosterone producing adenomas (APAs) constitute a large proportion of PA cases and represent a surgically correctable form of the disease. The WNT signaling pathway is activated in APAs. In other tumors, a frequent cause of aberrant WNT signaling is mutation in theCTNNB1gene coding for β-catenin. Our objective was to screen forCTNNB1mutations in a well-characterized cohort of 198 APAs. SomaticCTNNB1mutations were detected in 5.1% of the tumors, occurring mutually exclusive from mutations inKCNJ5, ATP1A1, ATP2B3andCACNA1D. All of the observed mutations altered serine/threonine residues in the GSK3β binding domain in exon 3. The mutations were associated with stabilized β-catenin and increased AXIN2 expression, suggesting activation of WNT signaling. By CYP11B2 mRNA expression, CYP11B2 protein expression and direct measurement of aldosterone in tumor tissue, we confirmed the ability for aldosterone production. This report provides compelling evidence that aberrant WNT signaling caused by mutations inCTNNB1occur in APAs. This also suggests that other mechanisms that constitutively activate the WNT pathway may be important in APA formation.
Short range smectic order driving long range nematic order: example of cuprates
Authors: Markiewicz R. S. , Lorenzana J. , Seibold G. , Bansil A. 
Published: January 2016

AbstractWe present a model for describing the combined presence of nematic and ‘smectic’ or stripe-like orders seen in recent scanning tunneling microscopy (STM) experiments on cuprates. The smectic order is treated as an electronic charge density wave with an associated Peierls distortion or a ‘Pomeranchuk wave’. This primary order is restricted to nanoscale domains by disorder effects, while the secondary coupling to strain generates the nematic order with a considerably longer range. A variety of experimental results are shown to be consistent with our theoretical predictions.
Correlating confocal microscopy and atomic force indentation reveals metastatic cancer cells stiffen during invasion into collagen I matrices
Authors: Staunton Jack R. , Doss Bryant L. , Lindsay Stuart , Ros Robert 
Published: January 2016

AbstractMechanical interactions between cells and their microenvironment dictate cell phenotype and behavior, calling for cell mechanics measurements in three-dimensional (3D) extracellular matrices (ECM). Here we describe a novel technique for quantitative mechanical characterization of soft, heterogeneous samples in 3D. The technique is based on the integration of atomic force microscopy (AFM) based deep indentation, confocal fluorescence microscopy, finite element (FE) simulations and analytical modeling. With this method, the force response of a cell embedded in 3D ECM can be decoupled from that of its surroundings, enabling quantitative determination of the elastic properties of both the cell and the matrix. We applied the technique to the quantification of the elastic properties of metastatic breast adenocarcinoma cells invading into collagen hydrogels. We found that actively invading and fully embedded cells are significantly stiffer than cells remaining on top of the collagen, a clear example of phenotypical change in response to the 3D environment. Treatment with Rho-associated protein kinase (ROCK) inhibitor significantly reduces this stiffening, indicating that actomyosin contractility plays a major role in the initial steps of metastatic invasion.
Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite
Authors: Cobbold Simon A. , Santos Joana M. , Ochoa Alejandro , Perlman David H. , Llinás Manuel 
Published: January 2016

AbstractLysine acetylation is a ubiquitous post-translational modification in many organisms including the malaria parasite Plasmodium falciparum, yet the full extent of acetylation across the parasite proteome remains unresolved. Moreover, the functional significance of acetylation or how specific acetyl-lysine sites are regulated is largely unknown. Here we report a seven-fold expansion of the known parasite ‘acetylome’, characterizing 2,876 acetylation sites on 1,146 proteins. We observe that lysine acetylation targets a diverse range of protein complexes and is particularly enriched within the Apicomplexan AP2 (ApiAP2) DNA-binding protein family. Using quantitative proteomics we determined that artificial perturbation of the acetate/acetyl-CoA balance alters the acetyl-lysine occupancy of several ApiAP2 DNA-binding proteins and related transcriptional proteins. This metabolic signaling could mediate significant downstream transcriptional responses, as we show that acetylation of an ApiAP2 DNA-binding domain ablates its DNA-binding propensity. Lastly, we investigated the acetyl-lysine targets of each class of lysine deacetylase in order to begin to explore how each class of enzyme contributes to regulating the P. falciparum acetylome.
A cotton miRNA is involved in regulation of plant response to salt stress
Authors: Gao Shuai , Yang Lu , Zeng Hou Qing , Zhou Zhao Sheng , Yang Zhi Min , Li Hua , Sun Di , Xie Fuliang , Zhang Baohong 
Published: January 2016

AbstractThe present study functionally identified a new microRNA (microRNA ovual line 5, miRNVL5) with its target geneGhCHRfrom cotton (Gossypium hirsutum). The sequence of miRNVL5 precursor is 104 nt long, with a well developed secondary structure. GhCHR contains two DC1 and three PHD Cys/His-rich domains, suggesting thatGhCHRencodes a zinc-finger domain-containing transcription factor. miRNVL5 andGhCHRexpress at various developmental stages of cotton. Under salt stress (50–400 mM NaCl), miRNVL5 expression was repressed, with concomitant high expression ofGhCHRin cotton seedlings. Ectopic expression ofGhCHRinArabidopsisconferred salt stress tolerance by reducing Na+accumulation in plants and improving primary root growth and biomass. Interestingly,Arabidopsisconstitutively expressing miRNVL5 showed hypersensitivity to salt stress. AGhCHRorthorlous gene At2g44380 fromArabidopsisthat can be cleaved by miRNVL5 was identified by degradome sequencing, but no confidential miRNVL5 homologs inArabidopsishave been identified. Microarray analysis of miRNVL5 transgenicArabidopsisshowed six downstream genes (CBF1,CBF2,CBF3,ERF4,AT3G22920andAT3G49200), which were induced by salt stress in wild-type but repressed in miRNVL5-expressingArabidopsis. These results indicate that miRNVL5 is involved in regulation of plant response to salt stress.
Natural motion trajectory enhances the coding of speed in primate extrastriate cortex
Authors: Davies Amanda J. , Chaplin Tristan A. , Rosa Marcello G. P. , Yu Hsin-Hao 
Published: January 2016

AbstractThe ability to estimate the speed of an object irrespective of size or texture is a crucial function of the visual system. However, previous studies have suggested that the neuronal coding of speed in the middle temporal area (MT, a key cortical area for motion analysis in primates) is ambiguous, with most neurons changing their speed tuning depending on the spatial frequency (SF) of a visual pattern. Here we demonstrate that the ability of MT neurons to encode speed is markedly improved when stimuli follow a trajectory across the visual field, prior to entering their receptive fields. We also show that this effect is much less marked in the primary visual area. These results indicate that MT neurons build up on computations performed at earlier levels of the visual system to provide accurate coding of speed in natural situations and provide additional evidence that nonlinear pooling underlie motion processing.
Selection of suitable reference genes for qRT-PCR normalization during leaf development and hormonal stimuli in tea plant (Camellia sinensis)
Authors: Wu Zhi-Jun , Tian Chang , Jiang Qian , Li Xing-Hui , Zhuang Jing 
Published: January 2016

AbstractTea plant (Camellia sinensis) leaf is an important non-alcoholic beverage resource. The application of quantitative real time polymerase chain reaction (qRT-PCR) has a profound significance for the gene expression studies of tea plant, especially when applied to tea leaf development and metabolism. In this study, nine candidate reference genes (i.e.,CsACT7,CsEF-1α,CseIF-4α, CsGAPDH,CsPP2A,CsSAND,CsTBP,CsTIP41andCsTUB) ofC. sinensiswere cloned. The quantitative expression data of these genes were investigated in five tea leaf developmental stages (i.e., 1st, 2nd, 3rd, 4th and older leaves) and normal growth tea leaves subjected to five hormonal stimuli (i.e., ABA, GA, IAA, MeJA and SA) and gene expression stability was calculated using three common statistical algorithms, namely, geNorm, NormFinder and Bestkeeper. Results indicated thatCsTBPandCsTIP41were the most stable genes in tea leaf development andCsTBPwas the best gene under hormonal stimuli; by contrast,CsGAPDHandCsTUBgenes showed the least stability. The gene expression profile ofCsNAMgene was analyzed to confirm the validity of the reference genes in this study. Our data provide basis for the selection of reference genes for future biological research in the leaf development and hormonal stimuli ofC. sinensis.
Generation of 2,000 breast cancer metabolic landscapes reveals a poor prognosis group with active serotonin production
Authors: Leoncikas Vytautas , Wu Huihai , Ward Lara T. , Kierzek Andrzej M. , Plant Nick J. 
Published: January 2016

AbstractA major roadblock in the effective treatment of cancers is their heterogeneity, whereby multiple molecular landscapes are classified as a single disease. To explore the contribution of cellular metabolism to cancer heterogeneity, we analyse the Metabric dataset, a landmark genomic and transcriptomic study of 2,000 individual breast tumours, in the context of the human genome-scale metabolic network. We create personalized metabolic landscapes for each tumour by exploring sets of active reactions that satisfy constraints derived from human biochemistry and maximize congruency with the Metabric transcriptome data. Classification of the personalized landscapes derived from 997 tumour samples within the Metabric discovery dataset reveals a novel poor prognosis cluster, reproducible in the 995-sample validation dataset. We experimentally follow mechanistic hypotheses resulting from the computational study and establish that active serotonin production is a major metabolic feature of the poor prognosis group. These data support the reconsideration of concomitant serotonin-specific uptake inhibitors treatment during breast cancer chemotherapy.
Skeletal muscle Heat shock protein 60 increases after endurance training and induces peroxisome proliferator-activated receptor gamma coactivator 1 α1 expression
Authors: Barone Rosario , Macaluso Filippo , Sangiorgi Claudia , Campanella Claudia , Marino Gammazza Antonella , Moresi Viviana , Coletti Dario , Conway de Macario Everly , Macario Alberto JL , Cappello Francesco , Adamo Sergio , Farina Felicia , Zummo Giovanni , Di Felice Valentina 
Published: January 2016

AbstractHeat shock protein 60 (Hsp60) is a chaperone localizing in skeletal muscle mitochondria, whose role is poorly understood. In the present study, the levels of Hsp60 in fibres of the entire posterior group of hindlimb muscles (gastrocnemius, soleus and plantaris) were evaluated in mice after completing a 6-week endurance training program. The correlation between Hsp60 levels and the expression of four isoforms of peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC1α) were investigated only in soleus. Short-term overexpression of hsp60, achieved by in vitro plasmid transfection, was then performed to determine whether this chaperone could have a role in the activation of the expression levels of PGC1α isoforms. The levels of Hsp60 protein were fibre-type specific in the posterior muscles and endurance training increased its content in type I muscle fibers. Concomitantly with the increased levels of Hsp60 released in the blood stream of trained mice, mitochondrial copy number and the expression of three isoforms of PGC1α increased. Overexpressing hsp60 in cultured myoblasts induced only the expression of PGC1 1α, suggesting a correlation between Hsp60 overexpression and PGC1 1 α activation.
A microbial carbonate response in synchrony with the end-Triassic mass extinction across the SW UK
Authors: Ibarra Yadira , Corsetti Frank A. , Greene Sarah E. , Bottjer David J. 
Published: January 2016

AbstractThe eruption of the Central Atlantic Magmatic Province (CAMP)—the largest igneous province known—has been linked to the end-Triassic mass extinction event, however reconciling the response of the biosphere (at local and nonlocal scales) to potential CAMP-induced geochemical excursions has remained challenging. Here we present a combined sedimentary and biological response to an ecosystem collapse in Triassic-Jurassic strata of the southwest United Kingdom (SW UK) expressed as widely distributed carbonate microbialites and associated biogeochemical facies. The microbialites (1) occur at the same stratigraphic level as the mass extinction extinction, (2) host a negative isotope excursion in δ13Corg found in other successions around the world and (3) co-occur with an acme of prasinophyte algae ‘disaster taxa’ also dominant in Triassic-Jurassic boundary strata of other European sections. Although the duration of microbialite deposition is uncertain, it is likely that they formed rapidly (perhaps fewer than ten thousand years), thus providing a high-resolution glimpse into the initial carbon isotopic perturbation coincident with the end-Triassic mass extinction. These findings indicate microbialites from the SW UK capture a nonlocal biosedimentary response to the cascading effects of massive volcanism and add to the current understanding of paleoecology in the aftermath of the end-Triassic extinction.
Regulation of human cerebro-microvascular endothelial baso-lateral adhesion and barrier function by S1P through dual involvement of S1P1 and S1P2 receptors
Authors: Wiltshire Rachael , Nelson Vicky , Kho Dan Ting , Angel Catherine E. , O’Carroll Simon J. , Graham E. Scott 
Published: January 2016

AbstractHerein we show that S1P rapidly and acutely reduces the focal adhesion strength and barrier tightness of brain endothelial cells. xCELLigence biosensor technology was used to measure focal adhesion, which was reduced by S1P acutely and this response was mediated through both S1P1 and S1P2 receptors. S1P increased secretion of several pro-inflammatory mediators from brain endothelial cells. However, the magnitude of this response was small in comparison to that mediated by TNFα or IL-1β. Furthermore, S1P did not significantly increase cell-surface expression of any key cell adhesion molecules involved in leukocyte recruitment, included ICAM-1 and VCAM-1. Finally, we reveal that S1P acutely and dynamically regulates microvascular endothelial barrier tightness in a manner consistent with regulated rapid opening followed by closing and strengthening of the barrier. We hypothesise that the role of the S1P receptors in this process is not to cause barrier dysfunction, but is related to controlled opening of the endothelial junctions. This was revealed using real-time measurement of barrier integrity using ECIS ZΘ TEER technology and endothelial viability using xCELLigence technology. Finally, we show that these responses do not occur simply though the pharmacology of a single S1P receptor but involves coordinated action of S1P1 and S1P2 receptors.
Tcstv1 and Tcstv3 elongate telomeres of mouse ES cells
Authors: Zhang Qian , Dan Jiameng , Wang Hua , Guo Renpeng , Mao Jian , Fu Haifeng , Wei Xiawei , Liu Lin 
Published: January 2016

AbstractMouse embryonic stem cell (ESC) cultures exhibit a heterogeneous mixture of metastable cells sporadically entering the 2-cell (2C)-embryo-like state, critical for ESC potency. One of 2-cell genes, Zscan4, has been shown to be responsible for telomere maintenance, genomic stability and pluripotency of mouse ESCs. Functions of other 2C-genes in ESCs remain elusive. Here we show that 2C-genes Tcstv1 and Tcstv3 play a role in regulation of telomere lengths. Overexpression or knockdown Tcstv1 and Tcstv3 does not immediately affect proliferation, pluripotency and differentiation in vitro of ESCs. However, ectopic expression of Tcstv1 or Tcstv3 results in telomere elongation, whereas Tcstv1/3 knockdown shortens telomeres of ESCs. Overexpression of Tcstv1 or Tcstv3 does not alter telomere stability. Furthermore, Tcstv1 can increase Zscan4 protein levels and telomere recombination by telomere sister chromatid exchange (T-SCE). Depletion of Tcstv1/3 reduces Zscan4 protein levels. Together, Tcstv1 and Tcstv3 are involved in telomere maintenance that is required for long-term self-renewal of mouse ESCs. Our data also suggests that Tcstv1/3 may co-operate and stabilize Zscan4 protein but the molecular bases remain to be determined.
Schima superba outperforms other tree species by changing foliar chemical composition and shortening construction payback time when facilitated by shrubs
Authors: Liu Nan , Guo Qinfeng , Ren Hai , Sun Zhongyu 
Published: January 2016

AbstractA 3.5-year field experiment was conducted in a subtropical degraded shrubland to assess how a nurse plant, the native shrubRhodomyrtus tomentosa, affects the growth of the target treesPinus elliottii,Schima superba,Castanopsis fissaandMichelia macclureiand to probe the intrinsic mechanisms from leaf chemical composition, construction cost (CC) and payback time aspects. We compared tree seedlings grown nearby shrub canopy (canopy subplots, CS) and in open space (open subplots, OS).S. superbain CS showed greater growth, whileP. elliottiiandM. macclureiwere lower when compared to the plants grown in the OS. The reduced levels of high-cost compounds (proteins) and increased levels of low-cost compounds (organic acids) caused reduced CC values forP. elliottiigrowing in CS. While, the levels of both low-cost minerals and high-cost proteins increased in CS such that CC values ofS. superbawere similar in OS and CS. Based on maximum photosynthetic rates,P. elliottiirequired a longer payback time to construct required carbon in canopy than in OS, but the opposite was true forS. superba. The information from this study can be used to evaluate the potential of different tree species in the reforestation of subtropical degraded shrublands.
Neuron-derived FGF10 ameliorates cerebral ischemia injury via inhibiting NF-κB-dependent neuroinflammation and activating PI3K/Akt survival signaling pathway in mice
Authors: Li Yong-Hua , Fu Hai-Long , Tian Mou-Li , Wang Yong-Qiang , Chen Wei , Cai Lin-Lin , Zhou Xu-Hui , Yuan Hong-Bin 
Published: January 2016

AbstractFGF10 is a member of fibroblast growth factors (FGFs). We previously showed that FGF10 protects neuron against oxygen-glucose deprivation injury in vitro; however, the effect of FGF10 in ischemic stroke in vivo is unknown. In the present study, we showed that FGF10 was mainly expressed in neurons but not astrocytes and detected FGF10 in mouse cerebrospinal fluid. The FGF10 levels in neurons culture medium and cell lysate were much higher than those in astrocytes. FGF10 expression in brain tissue and FGF10 level in CSF were increased in mouse middle cerebral artery occlusion (MCAO) model. Administration of FGF10 into lateral cerebroventricle not only decreased MCAO-induced brain infarct volume and neurological deficit, but also reduced the number of TUNEL-positive cells and activities of Caspases. Moreover, FGF10 treatment depressed the triggered inflammatory factors (TNF-α and IL-6) and NF-κB signaling pathway and increased phosphorylation of PI3K/Akt signaling pathway. Blockade of PI3K/Akt signaling pathway by wortmannin and Akt1/2-kinase inhibitor, partly compromised the neuroprotection of FGF10. However, blockade of PI3K/Akt signaling pathway did not impair the anti-inflammation action of FGF10. Collectively, our results demonstrate that neuron-derived FGF10 ameliorates cerebral ischemia injury via inhibiting NF-κB-dependent neuroinflammation and activating PI3K/Akt survival signaling pathway in mice.