bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Ultra-Stable, Monomeric Green Fluorescent Protein For Direct Volumetric Imaging of Whole Organs Using CLARITY
Authors: Scott Daniel J. , Gunn Natalie J. , Yong Kelvin J. , Wimmer Verena C. , Veldhuis Nicholas A. , Challis Leesa M. , Haidar Mouna , Petrou Steven , Bathgate Ross A. D. , Griffin Michael D. W. 
Published: January 2018

AbstractRecent advances in thick tissue clearing are enabling high resolution, volumetric fluorescence imaging of complex cellular networks. Fluorescent proteins (FPs) such as GFP, however, can be inactivated by the denaturing chemicals used to remove lipids in some tissue clearing methods. Here, we solved the crystal structure of a recently engineered ultra-stable GFP (usGFP) and propose that the two stabilising mutations, Q69L and N164Y, act to improve hydrophobic packing in the core of the protein and facilitate hydrogen bonding networks at the surface, respectively. usGFP was found to dimerise strongly, which is not desirable for some applications. A point mutation at the dimer interface, F223D, generated monomeric usGFP (muGFP). Neurons in whole mouse brains were virally transduced with either EGFP or muGFP and subjected to Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging/Immunostaining/In situhybridization-compatible Tissue-hYdrogel (CLARITY) clearing. muGFP fluorescence was retained after CLARITY whereas EGFP fluorescence was highly attenuated, thus demonstrating muGFP is a novel FP suitable for applications where high fluorescence stability and minimal self-association are required.
Anti-correlated cortical networks arise from spontaneous neuronal dynamics at slow timescales
Authors: Kodama Nathan X. , Feng Tianyi , Ullett James J. , Chiel Hillel J. , Sivakumar Siddharth S. , Galán Roberto F. 
Published: January 2018

AbstractIn the highly interconnected architectures of the cerebral cortex, recurrent intracortical loops disproportionately outnumber thalamo-cortical inputs. These networks are also capable of generating neuronal activity without feedforward sensory drive. It is unknown, however, what spatiotemporal patterns may be solely attributed to intrinsic connections of the local cortical network. Using high-density microelectrode arrays, here we show that in the isolated, primary somatosensory cortex of mice, neuronal firing fluctuates on timescales from milliseconds to tens of seconds. Slower firing fluctuations reveal two spatially distinct neuronal ensembles, which correspond to superficial and deeper layers. These ensembles are anti-correlated: when one fires more, the other fires less and vice versa. This interplay is clearest at timescales of several seconds and is therefore consistent with shifts between active sensing and anticipatory behavioral states in mice.
Dynamic modelling of the mTOR signalling network reveals complex emergent behaviours conferred by DEPTOR
Authors: Varusai Thawfeek M. , Nguyen Lan K. 
Published: January 2018

AbstractThe mechanistic Target of Rapamycin (mTOR) signalling network is an evolutionarily conserved network that controls key cellular processes, including cell growth and metabolism. Consisting of the major kinase complexes mTOR Complex 1 and 2 (mTORC1/2), the mTOR network harbours complex interactions and feedback loops. The DEP domain-containing mTOR-interacting protein (DEPTOR) was recently identified as an endogenous inhibitor of both mTORC1 and 2 through direct interactions, and is in turn degraded by mTORC1/2, adding an extra layer of complexity to the mTOR network. Yet, the dynamic properties of the DEPTOR-mTOR network and the roles of DEPTOR in coordinating mTORC1/2 activation dynamics have not been characterised. Using computational modelling, systems analysis and dynamic simulations we show that DEPTOR confers remarkably rich and complex dynamic behaviours to mTOR signalling, including abrupt, bistable switches, oscillations and co-existing bistable/oscillatory responses. Transitions between these distinct modes of behaviour are enabled by modulating DEPTOR expression alone. We characterise the governing conditions for the observed dynamics by elucidating the network in its vast multi-dimensional parameter space, and develop strategies to identify core network design motifs underlying these dynamics. Our findings provide new systems-level insights into the complexity of mTOR signalling contributed by DEPTOR.
Human Placental-Derived Adherent Stromal Cells Co-Induced with TNF-α and IFN-γ Inhibit Triple-Negative Breast Cancer in Nude Mouse Xenograft Models
Authors: Allen Hoshea , Shraga-Heled Niva , Blumenfeld Michal , Dego-Ashto Tamar , Fuchs-Telem Dana , Gilert Ariel , Aberman Zami , Ofir Racheli 
Published: January 2018

AbstractCulturing 3D-expanded human placental-derived adherent stromal cells (ASCs) in the presence of tumor necrosis factor-alpha (TNF-α) and interferon-gamma (IFN-γ) transiently upregulated the secretion of numerous anti-proliferative, anti-angiogenic and pro-inflammatory cytokines. In a 3D-spheroid screening assay, conditioned medium from these induced-ASCs inhibited proliferation of cancer cell lines, including triple-negative breast cancer (TNBC) lines.In vitroco-culture studies of induced-ASCs with MDA-MB-231 human breast carcinoma cells, a model representing TNBC, supports a mechanism involving immunomodulation and angiogenesis inhibition.In vivostudies in nude mice showed that intramuscular administration of induced-ASCs halted MDA-MB-231 cell proliferation, and inhibited tumor progression and vascularization. Thirty percent of treated mice experienced complete tumor remission. Murine serum concentrations of the tumor-supporting cytokines Interleukin-6 (IL-6), Vascular endothelial growth factor (VEGF) and Granulocyte-colony stimulating factor (G-CSF) were lowered to naïve levels. A somatic mutation analysis identified numerous genes which could be screened in patients to increase a positive therapeutic outcome. Taken together, these results show that targeted changes in the secretion profile of ASCs may improve their therapeutic potential.
Mycobacterium tuberculosis Exploits a Molecular Off Switch of the Immune System for Intracellular Survival
Authors: von Both Ulrich , Berk Maurice , Agapow Paul-Michael , Wright Joseph D. , Git Anna , Hamilton Melissa Shea , Goldgof Greg , Siddiqui Nazneen , Bellos Evangelos , Wright Victoria J. , Coin Lachlan J. , Newton Sandra M. , Levin Michael 
Published: January 2018

AbstractMycobacterium tuberculosis(M. tuberculosis) survives and multiplies inside human macrophages by subversion of immune mechanisms. Although these immune evasion strategies are well characterised functionally, the underlying molecular mechanisms are poorly understood. Here we show that during infection of human whole blood withM. tuberculosis, host gene transcriptional suppression, rather than activation, is the predominant response. Spatial, temporal and functional characterisation of repressed genes revealed their involvement in pathogen sensing and phagocytosis, degradation within the phagolysosome and antigen processing and presentation. To identify mechanisms underlying suppression of multiple immune genes we undertook epigenetic analyses. We identified significantly differentially expressed microRNAs with known targets in suppressed genes. In addition, after searching regions upstream of the start of transcription of suppressed genes for common sequence motifs, we discovered novel enriched composite sequence patterns, which corresponded toAlurepeat elements, transposable elements known to have wide ranging influences on gene expression. Our findings suggest that to survive within infected cells, mycobacteria exploit a complex immune “molecular off switch” controlled by both microRNAs andAluregulatory elements.
Drinking by amphibious fish: convergent evolution of thirst mechanisms during vertebrate terrestrialization
Authors: Katayama Yukitoshi , Sakamoto Tatsuya , Saito Kazuhiro , Tsuchimochi Hirotsugu , Kaiya Hiroyuki , Watanabe Taro , Pearson James T. , Takei Yoshio 
Published: January 2018

AbstractThirst aroused in the forebrain by angiotensin II (AngII) or buccal drying motivates terrestrial vertebrates to search for water, whereas aquatic fish can drink surrounding water only by reflex swallowing generated in the hindbrain. Indeed, AngII induces drinking through the hindbrain even after removal of the whole forebrain in aquatic fish. Here we show that AngII induces thirst also in the amphibious mudskipper goby without direct action on the forebrain, but through buccal drying. Intracerebroventricular injection of AngII motivated mudskippers to move into water and drink as with tetrapods. However, AngII primarily increased immunoreactive c-Fos at the hindbrain swallowing center where AngII receptors were expressed, as in other ray-finned fish, and such direct action on the forebrain was not found. Behavioural analyses showed that loss of buccal water on land by AngII-induced swallowing, by piercing holes in the opercula, or by water-absorptive gel placed in the cavity motivated mudskippers to move to water for refilling. Since sensory detection of water at the bucco-pharyngeal cavity like ‘dry mouth’ has recently been noted to regulate thirst in mammals, similar mechanisms seem to have evolved in distantly related species in order to solve osmoregulatory problems during terrestrialization.
Application of Weighted Gene Co-expression Network Analysis for Data from Paired Design
Authors: Li Jianqiang , Zhou Doudou , Qiu Weiliang , Shi Yuliang , Yang Ji-Jiang , Chen Shi , Wang Qing , Pan Hui 
Published: January 2018

AbstractInvestigating how genes jointly affect complex human diseases is important, yet challenging. The network approach (e.g., weighted gene co-expression network analysis (WGCNA)) is a powerful tool. However, genomic data usually contain substantial batch effects, which could mask true genomic signals. Paired design is a powerful tool that can reduce batch effects. However, it is currently unclear how to appropriately apply WGCNA to genomic data from paired design. In this paper, we modified the current WGCNA pipeline to analyse high-throughput genomic data from paired design. We illustrated the modified WGCNA pipeline by analysing the miRNA dataset provided by Shiahet al. (2014), which contains forty oral squamous cell carcinoma (OSCC) specimens and their matched non-tumourous epithelial counterparts. OSCC is the sixth most common cancer worldwide. The modified WGCNA pipeline identified two sets of novel miRNAs associated with OSCC, in addition to the existing miRNAs reported by Shiahet al. (2014). Thus, this work will be of great interest to readers of various scientific disciplines, in particular, genetic and genomic scientists as well as medical scientists working on cancer.
C-terminal short arginine/serine repeat sequence-dependent regulation of Y14 (RBM8A) localization
Authors: Tatsuno Takanori , Ishigaki Yasuhito 
Published: January 2018

AbstractY14 (RBM8A) is an RNA recognition motif-containing protein that forms heterodimers with MAGOH and serves as a core factor of the RNA surveillance machinery for the exon junction complex (EJC). The role of the Y14 C-terminal serine/arginine (RS) repeat-containing region, which has been reported to undergo modifications such as phosphorylation and methylation, has not been sufficiently investigated. Thus, we aimed to explore the functional significance of the Y14 C-terminal region. Deletion or dephosphorylation mimic mutants of the C-terminal region showed a shift in localization from the nucleoplasmic region; in addition, the C-terminal RS repeat-containing sequence itself exhibited the potential for nucleolar localization. Additionally, the regulation of Y14 localization by the C-terminal region was further found to be exquisitely controlled by MAGOH binding. Cumulatively, our findings, which demonstrated that Y14 localization is regulated not only by the previously reported N-terminal localization signal but also by the C-terminal RS repeat-containing region through phosphorylation and MAGOH binding to Y14, provide new insights for the mechanism of localization of short RS repeat-containing proteins.
Seabirds fighting for land: phenotypic consequences of breeding area constraints at a small remote archipelago
Authors: Nunes Guilherme Tavares , Bertrand Sophie , Bugoni Leandro 
Published: January 2018

AbstractIdentifying associations between phenotypes and environmental parameters is crucial for understanding how natural selection acts at the individual level. In this context, genetically isolated populations can be useful models for identifying the forces selecting fitness-related traits. Here, we use a comprehensive dataset on a genetically and ecologically isolated population of the strictly marine bird, the brown boobySula leucogaster, at the tropical and remote Saint Peter and Saint Paul Archipelago, mid-Atlantic Ocean, in order to detect phenotypic adjustments from interindividual differences in diet, foraging behaviour, and nest quality. For this, we took biometrics of all individuals of the colony breeding in 2014 and 2015 and tested their associations with nest quality, diet parameters, and foraging behaviour. While body size was not related to the foraging parameters, the body size of the females (responsible for nest acquisition and defence) was significantly associated with the nest quality, as larger females occupied high-quality nests. Our findings suggest that the small breeding area, rather than prey availability, is a limiting factor, emphasizing the role of on-land features in shaping phenotypic characteristics and fitness in land-dependent marine vertebrates.
Characterization of human small heat shock protein HSPB1 α-crystallin domain localized mutants associated with hereditary motor neuron diseases
Authors: Weeks Stephen D. , Muranova Lydia K. , Heirbaut Michelle , Beelen Steven , Strelkov Sergei V. , Gusev Nikolai B. 
Published: January 2018

AbstractCongenital mutations in human small heat shock protein HSPB1 (HSP27) have been linked to Charcot-Marie-Tooth disease, a commonly occurring peripheral neuropathy. Understanding the molecular mechanism of such mutations is indispensable towards developing future therapies for this currently incurable disorder. Here we describe the physico-chemical properties of the autosomal dominant HSPB1 mutants R127W, S135F and R136W. Despite having a nominal effect on thermal stability, the three mutations induce dramatic changes to quaternary structure. At high concentrations or under crowding conditions, the mutants form assemblies that are approximately two times larger than those formed by the wild-type protein. At low concentrations, the mutants have a higher propensity to dissociate into small oligomers, while the dissociation of R127W and R135F mutants is enhanced by MAPKAP kinase-2 mediated phosphorylation. Specific differences are observed in the ability to form hetero-oligomers with the homologue HSPB6 (HSP20). For wild-type HSPB1 this only occurs at or above physiological temperature, whereas the R127W and S135F mutants form hetero-oligomers with HSPB6 at 4 °C, and the R136W mutant fails to form hetero-oligomers. Combined, the results suggest that the disease-related mutations of HSPB1 modify its self-assembly and interaction with partner proteins thus affecting normal functioning of HSPB1 in the cell.
Intra-Specific Latitudinal Clines in Leaf Carbon, Nitrogen, and Phosphorus and their Underlying Abiotic Correlates in Ruellia Nudiflora
Authors: Abdala-Roberts Luis , Covelo Felisa , Parra-Tabla Víctor , Terán Jorge C. Berny Mier y , Mooney Kailen A. , Moreira Xoaquín 
Published: January 2018

AbstractWhile plant intra-specific variation in the stoichiometry of nutrients and carbon is well documented, clines for such traits have been less studied, despite their potential to reveal the mechanisms underlying such variation. Here we analyze latitudinal variation in the concentration of leaf nitrogen (N), phosphorus (P), carbon (C) and their ratios across 30 populations of the perennial herb Ruellia nudiflora. In addition, we further determined whether climatic and soil variables underlie any such latitudinal clines in leaf traits. The sampled transect spanned 5° latitude (ca. 900 km) and exhibited a four-fold precipitation gradient and 2 °C variation in mean annual temperature. We found that leaf P concentration increased with precipitation towards lower latitudes, whereas N and C did not exhibit latitudinal clines. In addition, N:P and C:P decreased towards lower latitudes and latitudinal variation in the former was weakly associated with soil conditions (clay content and cation exchange capacity); C:N did not exhibit a latitudinal gradient. Overall, these results emphasize the importance of addressing and disentangling the simultaneous effects of abiotic factors associated with intra-specific clines in plant stoichiometric traits, and highlight the previously underappreciated influence of abiotic factors on plant nutrients operating under sharp abiotic gradients over smaller spatial scales.
Distinct modulation of inactivation by a residue in the pore domain of voltage-gated Na+ channels: mechanistic insights from recent crystal structures
Authors: Cervenka Rene , Lukacs Peter , Gawali Vaibhavkumar S. , Ke Song , Koenig Xaver , Rubi Lena , Zarrabi Touran , Hilber Karlheinz , Sandtner Walter , Stary-Weinzinger Anna , Todt Hannes 
Published: January 2018

AbstractInactivation of voltage-gated Na+ channels (VGSC) is essential for the regulation of cellular excitability. The molecular rearrangement underlying inactivation is thought to involve the intracellular linker between domains III and IV serving as inactivation lid, the receptor for the lid (domain III S4-S5 linker) and the pore-lining S6 segements. To better understand the role of the domain IV S6 segment in inactivation we performed a cysteine scanning mutagenesis of this region in rNav 1.4 channels and screened the constructs for perturbations in the voltage-dependence of steady state inactivation. This screen was performed in the background of wild-type channels and in channels carrying the mutation K1237E, which profoundly alters both permeation and gating-properties. Of all tested constructs the mutation I1581C was unique in that the mutation-induced gating changes were strongly influenced by the mutational background. This suggests that I1581 is involved in specific short-range interactions during inactivation. In recently published crystal structures VGSCs the respective amino acids homologous to I1581 appear to control a bend of the S6 segment which is critical to the gating process. Furthermore, I1581 may be involved in the transmission of the movement of the DIII voltage-sensor to the domain IV S6 segment.
Tissue and serum microRNA profile of oral squamous cell carcinoma patients
Authors: Schneider Augusto , Victoria Berta , Lopez Yury Nunez , Suchorska Wiktoria , Barczak Wojciech , Sobecka Agnieszka , Golusinski Wojciech , Masternak Michal M. , Golusinski Pawel 
Published: January 2018

AbstractHead and neck cancer is characterized by malignant tumors arising from the epithelium covering the upper aerodigestive tract, and the majority of these epithelial malignancies are squamous cell carcinomas (SCCs) of the oral cavity (OSCCs). The aim of the current work was to identify miRNAs regulated in OSCC cancerous tissue when compared to a healthy adjacent tissue and to verify the presence of the same miRNAs in the circulation of these patients. For that serum samples and biopsies of healthy and tumor tissues were collected from five patients diagnosed with OSCC of the oral cavity, RNA was extracted from these samples and microRNAs libraries were prepared and sequenced. A total 255 miRNAs were identified in tissue and 381 different miRNAs were identified in serum samples. When comparing the miRNA expression between tumor and healthy tissue we identified 48 miRNAs (25 down- and 23 up-regulated) that were differentially expressed (FDR < 0.05). From these 48 differentially expressed miRNAs in tissue, 30 miRNAs were also found in the serum of the same patients. hsa-miR-32-5p was up-regulated in tumor compared to healthy tissue in our study, and was previously shown to be up-regulated in the serum of OSCC patients. Therefore, this suggests that miRNAs can be used as potential non-invasive biomarkers of OSCC.
Effective photo-enhancement of cellular activity of fluorophore-octaarginine antisense PNA conjugates correlates with singlet oxygen formation, endosomal escape and chromophore lipophilicity
Authors: Yarani Reza , Shiraishi Takehiko , Nielsen Peter E. 
Published: January 2018

AbstractPhotochemical internalization (PCI) is a cellular drug delivery method based on the generation of light-induced reactive oxygen species (ROS) causing damage to the endosomal membrane and thereby resulting in drug release to the cytoplasm. In our study a series of antisense fluorophore octaarginine peptide nucleic acid (PNA) conjugates were investigated in terms of PCI assisted cellular activity. It is found that tetramethylrhodamine and Alexa Fluor 555 conjugated octaarginine PNA upon irradiation exhibit more than ten-fold increase in antisense activity in the HeLa pLuc705 luciferase splice correction assay. An analogous fluorescein conjugate did not show any significant enhancement due to photobleaching, and neither did an Alexa Fluor 488 conjugate. Using fluorescence microscopy a correlation between endosomal escape and antisense activity was demonstrated, and in parallel a correlation to localized formation of ROS assigned primarily to singlet oxygen was also observed. The results show that tetramethylrhodamine (and to lesser extent Alexa Fluor 555) conjugated octaarginine PNAs are as effectively delivered to the cytosol compartment by PCI as by chloroquine assisted delivery and also indicate that efficient photodynamic endosomal escape is strongly dependent on the quantum yield for photochemical singlet oxygen formation, photostability as well as the lipophilicity of the chromophore.
The Structure of Metal Binding Domain 1 of the Copper Transporter ATP7B Reveals Mechanism of a Singular Wilson Disease Mutation
Authors: Yu Corey H. , Lee Woonghee , Nokhrin Sergiy , Dmitriev Oleg Y. 
Published: January 2018

AbstractCopper-transporter ATP7B maintains copper homeostasis in the human cells and delivers copper to the biosynthetic pathways for incorporation into the newly synthesized copper-containing proteins. ATP7B is a target of several hundred mutations that lead to Wilson disease, a chronic copper toxicosis. ATP7B contains a chain of six cytosolic metal-binding domains (MBDs), the first four of which (MBD1-4) are believed to be regulatory, and the last two (MBD5-6) are required for enzyme activity. We report the NMR structure of MBD1, the last unsolved metal-binding domain of ATP7B. The structure reveals the disruptive mechanism of G85V mutation, one of the very few disease causing missense mutations in the MBD1-4 region of ATP7B.
X-ray-induced Scintillation Governed by Energy Transfer Process in Glasses
Authors: Masai Hirokazu , Okada Go , Torimoto Aya , Usui Takaaki , Kawaguchi Noriaki , Yanagida Takayuki 
Published: January 2018

AbstractThe efficiency of X-ray-induced scintillation in glasses roughly depends on both the effective atomic number Zeff and the photoluminescence quantum efficiency Qeff of glass, which are useful tools for searching high-performance phosphors. Here, we demonstrate that the energy transfer from host to activators is also an important factor for attaining high scintillation efficiency in Ce-doped oxide glasses. The scintillation intensity of glasses with coexisting fractions of Ce3+ and Ce4+ species is found to be higher than that of a pure-Ce3+-containing glass with a lower Zeff value. Values of total attenuation of each sample indicate that there is a non-linear correlation between the scintillation intensity and the product of total attenuation and Qeff. The obtained results illustrate the difficulty in understanding the luminescence induced by ionizing radiation, including the energy absorption and subsequent energy transfer. Our findings may provide a new approach for synthesizing novel scintillators by tailoring the local structure.