bluuebunny/crossref_metadata_2025 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

Recent 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

In 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

The 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

Culturing 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

Mycobacterium 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

Thirst 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

Investigating 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

Y14 (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

Identifying 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

Congenital 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

While 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

Inactivation 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

Head 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

Photochemical 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

Copper-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

The 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.
Gyrotropic Zener tunneling and nonlinear IV curves in the zero-energy Landau level of graphene in a strong magnetic field
Authors: Laitinen Antti , Kumar Manohar , Hakonen Pertti , Sonin Edouard
Published: January 2018

We have investigated tunneling current through a suspended graphene Corbino disk in high magnetic fields at the Dirac point, i.e. at filling factor ν = 0. At the onset of the dielectric breakdown the current through the disk grows exponentially before ohmic behaviour, but in a manner distinct from thermal activation. We find that Zener tunneling between Landau sublevels dominates, facilitated by tilting of the source-drain bias potential. According to our analytic modelling, the Zener tunneling is strongly affected by the gyrotropic force (Lorentz force) due to the high magnetic field.
Decoding hind limb kinematics from neuronal activity of the dorsal horn neurons using multiple level learning algorithm
Authors: Yeganegi Hamed , Fathi Yaser , Erfanian Abbas
Published: January 2018

Decoding continuous hind limb joint angles from sensory recordings of neural system provides a feedback for closed-loop control of hind limb movement using functional electrical stimulation. So far, many attempts have been done to extract sensory information from dorsal root ganglia and sensory nerves. In this work, we examine decoding joint angles trajectories from the single-electrode extracellular recording of dorsal horn gray matter of the spinal cord during passive limb movement in anesthetized cats. In this study, a processing framework based on ensemble learning approach is propose to combine firing rate (FR) and interspike interval (ISI) information of the neuronal activity. For this purpose, a stacked generalization approach based on recurrent neural network is proposed to enhance decoding accuracy of the movement kinematics. The results show that the high precision neural decoding of limb movement can be achieved even with a single electrode implanted in the spinal cord gray matter.
Paper-based inkjet bioprinting to detect fluorescence resonance energy transfer for the assessment of anti-inflammatory activity
Authors: Samson Annie Agnes Suganya , Lee Jungmi , Song Joon Myong
Published: January 2018

For the first time, a paper-based fluorescence resonance energy transfer (FRET) determination with cyclic AMP (cAMP)-specific phosphodiesterase 4B (PDE4B) inhibitory assay using an inkjet-printing technique is proposed. Non-fabricated parchment paper is found to constitute a unique substrate to measure fluorescent energy transfer, due to its insignificant self-absorption, and enables efficient sample interaction. Here, we report the responsive FRET signals generated on paper, upon sequentially printing reaction components on parchment paper using a conventional inkjet printer equipped with four cartridges. After printing, the energy emitted by Eu chelate was transferred by FRET to ULight molecule on paper, detected at 665 nm. In the absence of free cAMP, a maximum FRET signal was achieved on paper, while a decrease in FRET signals was recorded when free cAMP produced by PDE4B inhibitors compete with Eu-cAMP, binding with ULight-mAb. The IM50 value was determined as 2.46 × 10−13 mole for roliparm and 1.86 × 10−13 mole for roflumilast, to effectively inhibit PDE4B activity. Inkjet printing-based FRET signal determination utilizes components that are less than the femtomole range, which was four-orders less than the standard assay method. The methodology reported here constitutes an innovative approach towards the determination of FRET signals generated on paper.
Predicting Fibrosis Progression in Renal Transplant Recipients Using Laser-Based Infrared Spectroscopic Imaging
Authors: Varma Vishal K. , Kajdacsy-Balla Andre , Akkina Sanjeev , Setty Suman , Walsh Michael J.
Published: January 2018

Renal transplants have not seen a significant improvement in their 10-year graft life. Chronic damage accumulation often leads to interstitial fibrosis and tubular atrophy (IF/TA) and thus graft function loss over time. For this reason, IF/TA has been the chief suspect for a potential prognostic marker for long term outcomes. In this study, we have used infrared spectroscopic (IR) imaging to interrogate the biochemistry of regions of fibrosis from renal transplant biopsies to identify a biochemical signature that can predict rapid progression of fibrosis. IR imaging represents an approach that permits label-free biochemical imaging of human tissues towards identifying novel biomarkers for disease diagnosis or prognosis. Two cohorts were identified as progressors (n = 5, > 50% fibrosis increase between time points) and non-progressors (n = 5, < 5% increase between time points). Each patient had an early time point and late time point biopsy. Collagen associated carbohydrate moieties (ν(C–O), 1035 cm−1 and ν(C–O–C),1079 cm−1) spectral ratios demonstrated good separation between the two cohorts (p = 0.001). This was true for late and early time point biopsies suggesting the regions of fibrosis are biochemically altered in cases undergoing progressive fibrosis. Thus, IR imaging can potentially predict rapid progression of fibrosis using histologically normal early time point biopsies.
Towards Electrotuneable Nanoplasmonic Fabry–Perot Interferometer
Authors: Weir Hayley , Edel Joshua B. , Kornyshev Alexei A. , Sikdar Debabrata
Published: January 2018

Directed voltage-controlled assembly and disassembly of plasmonic nanoparticles (NPs) at electrified solid–electrolyte interfaces (SEI) offer novel opportunities for the creation of tuneable optical devices. We apply this concept to propose a fast electrotuneable, NP-based Fabry–Perot (FP) interferometer, comprising two parallel transparent electrodes in aqueous electrolyte, which form the polarizable SEI for directed assembly–disassembly of negatively charged NPs. An FP cavity between two reflective NP-monolayers assembled at such interfaces can be formed or deconstructed under positive or negative polarization of the electrodes, respectively. The inter-NP spacing may be tuned via applied potential. Since the intensity, wavelength, and linewidth of the reflectivity peak depend on the NP packing density, the transmission spectrum of the system can thus be varied. A detailed theoretical model of the system’s optical response is presented, which shows excellent agreement with full-wave simulations. The tuning of the peak transmission wavelength and linewidth is investigated in detail. Design guidelines for such NP-based FP systems are established, where transmission characteristics can be electrotuned in-situ, without mechanically altering the cavity length.
Impact of wave whitecapping on land falling tropical cyclones
Authors: Bruneau Nicolas , Toumi Ralf , Wang Shuai
Published: January 2018

Predicting tropical cyclone structure and evolution remains challenging. Particularly, the surface wave interactions with the continental shelf and their impact on tropical cyclones have received very little attention. Through a series of state-of-the-art high-resolution, fully-coupled ocean-wave and atmosphere-ocean-wave experiments, we show here, for the first time, that in presence of continental shelf waves can cause substantial cooling of the sea surface. Through whitecapping there is a transfer of momentum from the surface which drives deeper vertical mixing. It is the waves and not just the wind which become the major driver of stratified coastal ocean ahead-of-cyclone cooling. In the fully-coupled atmosphere-ocean-wave model a negative feedback is found. The maximum wind speed is weaker and the damaging footprint area of hurricane-force winds is reduced by up to 50% due to the strong wave induced ocean cooling ahead. Including wave-ocean coupling is important to improve land falling tropical cyclone intensity predictions for the highly populated and vulnerable coasts.
Autapses promote synchronization in neuronal networks
Authors: Fan Huawei , Wang Yafeng , Wang Hengtong , Lai Ying-Cheng , Wang Xingang
Published: January 2018

Neurological disorders such as epileptic seizures are believed to be caused by neuronal synchrony. However, to ascertain the causal role of neuronal synchronization in such diseases through the traditional approach of electrophysiological data analysis remains a controversial, challenging, and outstanding problem. We offer an alternative principle to assess the physiological role of neuronal synchrony based on identifying structural anomalies in the underlying network and studying their impacts on the collective dynamics. In particular, we focus on autapses - time delayed self-feedback links that exist on a small fraction of neurons in the network, and investigate their impacts on network synchronization through a detailed stability analysis. Our main finding is that the proper placement of a small number of autapses in the network can promote synchronization significantly, providing the computational and theoretical bases for hypothesizing a high degree of synchrony in real neuronal networks with autapses. Our result that autapses, the shortest possible links in any network, can effectively modulate the collective dynamics provides also a viable strategy for optimal control of complex network dynamics at minimal cost.
19F-perfluorocarbon-labeled human peripheral blood mononuclear cells can be detected in vivo using clinical MRI parameters in a therapeutic cell setting
Authors: Fink Corby , Gaudet Jeffrey M. , Fox Matthew S. , Bhatt Shashank , Viswanathan Sowmya , Smith Michael , Chin Joseph , Foster Paula J. , Dekaban Gregory A.
Published: January 2018

A 19Fluorine (19F) perfluorocarbon cell labeling agent, when employed with an appropriate cellular MRI protocol, allows for in vivo cell tracking. 19F cellular MRI can be used to non-invasively assess the location and persistence of cell-based cancer vaccines and other cell-based therapies. This study was designed to determine the feasibility of labeling and tracking peripheral blood mononuclear cells (PBMC), a heterogeneous cell population. Under GMP-compliant conditions human PBMC were labeled with a 19F-based MRI cell-labeling agent in a manner safe for autologous re-injection. Greater than 99% of PBMC labeled with the 19F cell-labeling agent without affecting functionality or affecting viability. The 19F-labeled PBMC were detected in vivo in a mouse model at the injection site and in a draining lymph node. A clinical cellular MR protocol was optimized for the detection of PBMC injected both at the surface of a porcine shank and at a depth of 1.2 cm, equivalent to depth of a human lymph node, using a dual 1H/19F dual switchable surface radio frequency coil. This study demonstrates it is feasible to label and track 19F-labeled PBMC using clinical MRI protocols. Thus, 19F cellular MRI represents a non-invasive imaging technique suitable to assess the effectiveness of cell-based cancer vaccines.
Three-Dimensional Physical Model-Assisted Planning and Navigation for Laparoscopic Partial Nephrectomy in Patients with Endophytic Renal Tumors
Authors: Fan Gang , Li Jun , Li Mingfeng , Ye Mingji , Pei Xiaming , Li Feiping , Zhu Shuai , Weiqin Han , Zhou Xiao , Xie Yu
Published: January 2018

Resection of completely endophytic renal tumors is a huge challenge for surgeons due to a lack of definite visual clues, especially in the laparoscopic approach. Three-dimensional (3D) kidney models, which can illustrate the clear relationship between renal masses and surrounding health tissues, were considered as reliable tools for understanding renal tumor characteristics in previous studies. We hypothesized that 3D kidney models can be used not only for planning but also for navigating laparoscopic partial nephrectomy (LPN) in patients with completely endophytic renal tumors. In this study, we successfully constructed five cases of 3D kidney models for assisted planning and navigation for LPN in endophytic renal tumors. The renal masses and surrounding normal parenchyma of the patient-specific 3D models were dyed by different colorants for clear illustration. All patients experienced acceptable perioperative outcomes, and no patient suffered serious relative complications. The 3D kidney models were considered as a reliable tool based on clinical outcome and postoperative questionnaire results. This study is the first report of 3D kidney models for patients with completely endophytic tumors. 3D kidney models can aid surgeons in understanding the characteristics of renal tumors and potentially support assisted planning and performance of LPN in endophytic tumor cases.
Partially oxidized polyvinyl alcohol conduitfor peripheral nerve regeneration
Authors: Stocco Elena , Barbon Silvia , Lora Lucia , Grandi Francesca , Sartore Leonardo , Tiengo Cesare , Petrelli Lucia , Dalzoppo Daniele , Parnigotto Pier Paolo , Macchi Veronica , De Caro Raffaele , Porzionato Andrea , Grandi Claudio
Published: January 2018

Surgical reconstruction of peripheral nerves injuries with wide substance-loss is still a challenge. Many studies focused on the development of artificial nerve conduits made of synthetic or biological materials but the ideal device has not yet been identified. Here, we manufactured a conduit for peripheral nerve regeneration using a novel biodegradable hydrogel we patented that is oxidized polyvinyl alcohol (OxPVA). Thus, its characteristics were compared with neat polyvinyl alcohol (PVA) and silk-fibroin (SF) conduits, through in vitro and in vivo analysis. Unlike SF, OxPVA and neat PVA scaffolds did not support SH-SY5Y adhesion and proliferation in vitro. After implantation in rat model of sciatic nerve transection, the three conduits sustained the regeneration of the injured nerve filling a gap of 5 mm in 12 weeks. Implanted animals showed a good gait recovery. Morphometric data related to the central portion of the explanted conduit interestingly highlighted a significantly better outcome for OxPVA scaffolds compared to PVA conduits in terms of axon density, also with respect to the autograft group. This study suggests the potential of our novel biomaterial for the development of conduits for clinical use in case of peripheral nerve lesions with substance loss.
Closed-loop control of zebrafish behaviour in three dimensions using a robotic stimulus
Authors: Kim Changsu , Ruberto Tommaso , Phamduy Paul , Porfiri Maurizio
Published: January 2018

Robotics is continuously being integrated in animal behaviour studies to create customizable, controllable, and repeatable stimuli. However, few systems have capitalized on recent breakthroughs in computer vision and real-time control to enable a two-way interaction between the animal and the robot. Here, we present a “closed-loop control” system to investigate the behaviour of zebrafish, a popular animal model in preclinical studies. The system allows for actuating a biologically-inspired 3D-printed replica in a 3D workspace, in response to the behaviour of a zebrafish. We demonstrate the role of closed-loop control in modulating the response of zebrafish, across a range of behavioural and information-theoretic measures. Our results suggest that closed-loop control could enhance the degree of biomimicry of the replica, by increasing the attraction of live subjects and their interaction with the stimulus. Interactive experiments hold promise to advance our understanding of zebrafish, offering new means for high throughput behavioural phenotyping.
Low density neutrophils (LDN) in postoperative abdominal cavity assist the peritoneal recurrence through the production of neutrophil extracellular traps (NETs)
Authors: Kanamaru Rihito , Ohzawa Hideyuki , Miyato Hideyo , Matsumoto Shiro , Haruta Hidenori , Kurashina Kentaro , Saito Shin , Hosoya Yoshinori , Yamaguchi Hironori , Yamashita Hiroharu , Seto Yasuyuki , Lefor Alan Kawarai , Sata Naohiro , Kitayama Joji
Published: January 2018

Many types of immune cells appear in peritoneal cavity after abdominal surgery. In patients who underwent laparotomy due to gastric cancer, peritoneal lavages were obtained before and after surgical procedure. Cells were recovered from intermediate layer after Ficoll-Hypaque centrifugation and analyzed for phenotypes and functions, especially focused on low density neutrophils (LDN). The number of CD66b (+) LDN with mature phenotype was markedly elevated in postoperative as compared with preoperative lavages. Short term culture of the purified LDN produced many threadlike structures positive for SYTOX, nucleic acid staining, as well as histone and myeloperoxidase, suggesting the NETs formation. Human gastric cancer cells, MKN45, OCUM-1 and NUGC-4, were selectively attached on the NETs, which was totally abolished by the pretreatment of DNAse I. Intraperitoneal (IP) co-transfer of the LDN with MKN45 in nude mice strongly augments the metastasis formation on peritoneum, which was strongly suppressed by the following IP administration of DNAse I. Many NETs-like structures were detected on the surface of human omental tissue resected by gastrectomy. NETs on peritoneal surface can assist the clustering and growth of free tumor cells disseminated in abdomen. Disruption of the NETs by DNAse might be useful to prevent the peritoneal recurrence after abdominal surgery.
Single-cell RNA-sequencing resolves self-antigen expression during mTEC development
Authors: Miragaia Ricardo J. , Zhang Xiuwei , Gomes Tomás , Svensson Valentine , Ilicic Tomislav , Henriksson Johan , Kar Gozde , Lönnberg Tapio
Published: January 2018

The crucial capability of T cells for discrimination between self and non-self peptides is based on negative selection of developing thymocytes by medullary thymic epithelial cells (mTECs). The mTECs purge autoreactive T cells by expression of cell-type specific genes referred to as tissue-restricted antigens (TRAs). Although the autoimmune regulator (AIRE) protein is known to promote the expression of a subset of TRAs, its mechanism of action is still not fully understood. The expression of TRAs that are not under the control of AIRE also needs further characterization. Furthermore, expression patterns of TRA genes have been suggested to change over the course of mTEC development. Herein we have used single-cell RNA-sequencing to resolve patterns of TRA expression during mTEC development. Our data indicated that mTEC development consists of three distinct stages, correlating with previously described jTEC, mTEChi and mTEClo phenotypes. For each subpopulation, we have identified marker genes useful in future studies. Aire-induced TRAs were switched on during jTEC-mTEC transition and were expressed in genomic clusters, while otherwise the subsets expressed largely overlapping sets of TRAs. Moreover, population-level analysis of TRA expression frequencies suggested that such differences might not be necessary to achieve efficient thymocyte selection.
A De Novo FOXP1 Truncating Mutation in a Patient Originally Diagnosed as C Syndrome
Authors: Urreizti Roser , Damanti Sarah , Esteve Carla , Franco-Valls Héctor , Castilla-Vallmanya Laura , Tonda Raul , Cormand Bru , Vilageliu Lluïsa , Opitz John M. , Neri Giovanni , Grinberg Daniel , Balcells Susana
Published: January 2018

De novo FOXP1 mutations have been associated with intellectual disability (ID), motor delay, autistic features and a wide spectrum of speech difficulties. C syndrome (Opitz C trigonocephaly syndrome) is a rare and genetically heterogeneous condition, characterized by trigonocephaly, craniofacial anomalies and ID. Several different chromosome deletions and and point mutations in distinct genes have been associated with the disease in patients originally diagnosed as Opitz C. By whole exome sequencing we identified a de novo splicing mutation in FOXP1 in a patient, initially diagnosed as C syndrome, who suffers from syndromic intellectual disability with trigonocephaly. The mutation (c.1428 + 1 G > A) promotes the skipping of exon 16, a frameshift and a premature STOP codon (p.Ala450GLyfs*13), as assessed by a minigene strategy. The patient reported here shares speech difficulties, intellectual disability and autistic features with other FOXP1 syndrome patients, and thus the diagnosis for this patient should be changed. Finally, since trigonocephaly has not been previously reported in FOXP1 syndrome, it remains to be proved whether it may be associated with the FOXP1 mutation.
Visual field loss and vision-related quality of life in the Italian Primary Open Angle Glaucoma Study
Authors: Rulli Eliana , Quaranta Luciano , Riva Ivano , Poli Davide , Hollander Lital , Galli Fabio , Katsanos Andreas , Oddone Francesco , Torri Valter , Weinreb Robert N. ,   Italian Study Group on QoL in Glaucoma, Varano L. , Carchedi T. , Talarico S. , Frezzotti P. , Parravano F. , Motolese I. , Bagaglia S. A. , Rossi G. C. M. , Lateri S. , Bossolesi L. , Carmassi L. , Rolle T. , Piccini R. , Ratiglia R. , Rossi A. , Gandolfi S. , Tagliavini V. , Ungaro N. , Fossarello M. , Cucca A. , Zucca I. , Uva M. , Bonacci E. , Cardarella G. , Tognetto D. , Vattovani O. , Vallon P. , Iannacone F. , Fontana L. , Marchi S. , Manni G. L. , Jannetta D. , Roberti G. , Rossetti L. , Maggiolo E. , Oneta O. , Sborgia C. , Cantatore F. , Mastropasqua L. , Agnifili L. , Campos E. , Gizzi C. , Giannaccare G. , Pucci V. , Cassamali M. , Costagliola C. , Traverso C. , Scotto R. , Musolino M. , Landi L. , Bagnis A.
Published: January 2018

The aim of this study was to examine the relationship between visual field (VF) loss, vision-related quality of life (QoL) and glaucoma-related symptoms in a large cohort of primary open angle glaucoma (POAG) patients. POAG patients with or without VF defects or “glaucoma suspect” patients were considered eligible. QoL was assessed using the validated versions of the 25-item National Eye Institute Visual Function Questionnaire (NEI-VFQ-25) and glaucoma-related symptoms were assessed using the Glaucoma Symptom Scale (GSS). Patients were classified as having VF damage in one eye (VFD-1), both eyes (VFD-2), or neither eye (VFD-0). 3227 patients were enrolled and 2940 were eligible for the analysis. 13.4% of patients were classified in the VFD-0, 23.7% in the VFD-1, and 62.9% in the VFD-2 group. GSS visual symptoms domain (Func-4) and GSS non-visual symptoms domain (Symp-6) scores were similar for the VFD-0 and VFD-1 groups (p = 0.133 and p = 0.834 for Func-4 and Symp-6, respectively). VFD-0 group had higher scores than VFD-2 both in Func-4 (p < 0.001) and Symp-6 domains (p = 0.035). Regarding the NEI-VFQ-25, our data demonstrated that bilateral VF defects are associated with vision-related QoL deterioration, irrespective of visual acuity.
Dosimetry Prediction for Clinical Translation of 64Cu-Pembrolizumab ImmunoPET Targeting Human PD-1 Expression
Authors: Natarajan Arutselvan , Patel Chirag B. , Habte Frezghi , Gambhir Sanjiv S.
Published: January 2018

The immune checkpoint programmed death 1 receptor (PD-1) expressed on some tumor-infiltrating lymphocytes, and its ligand (PD-L1) expressed on tumor cells, enable cancers to evade the immune system. Blocking PD-1 with the monoclonal antibody pembrolizumab is a promising immunotherapy strategy. Thus, noninvasively quantifying the presence of PD-1 expression in the tumor microenvironment prior to initiation of immune checkpoint blockade may identify the patients likely to respond to therapy. We have developed a 64Cu-pembrolizumab radiotracer and evaluated human dosimetry. The tracer was utilized to image hPD-1 levels in two subcutaneous mouse models: (a) 293 T/hPD-1 cells xenografted into NOD-scid IL-2Rγnull mice (NSG/293 T/hPD-1) and (b) human peripheral blood mononuclear cells engrafted into NSG bearing A375 human melanoma tumors (hNSG/A375). In each mouse model two cohorts were evaluated (hPD-1 blockade with pembrolizumab [blk] and non-blocked [nblk]), for a total of four groups (n = 3–5/group). The xenograft-to-muscle ratio in the NSG/293 T/hPD-1 model at 24 h was significantly increased in the nblk group (7.0 ± 0.5) compared to the blk group (3.4 ± 0.9), p = 0.01. The radiotracer dosimetry evaluation (PET/CT ROI-based and ex vivo) in the hNSG/A375 model revealed the highest radiation burden to the liver. In summary, we validated the 64Cu-pembrolizumab tracer’s specific hPD-1 receptor targeting and predicted human dosimetry.