bluuebunny/crossref_metadata_2025 huggingface dataset:
Correction: Corrigendum: Snf1-related kinase improves cardiac mitochondrial efficiency and decreases mitochondrial uncoupling
Authors: Rines Amy K. , Chang Hsiang-Chun , Wu Rongxue , Sato Tatsuya , Khechaduri Arineh , Kouzu Hidemichi , Shapiro Jason , Shang Meng , Burke Michael A. , Abdelwahid Eltyeb , Jiang Xinghang , Chen Chunlei , Rawlings Tenley A. , Lopaschuk Gary D. , Schumacker Paul T. , Abel E. Dale , Ardehali Hossein
Published: August 2017

Nature Communications 8: Article number: 14095 (2017); Published: 24 January 2017; Updated: 30 August 2017. The authors inadvertently omitted Eltyeb Abdelwahid, who contributed to the generation of animal models and their initial evaluation, from the author list. This has now been corrected in both the PDF and HTML versions of the Article.
Integrative genomics of microglia implicates DLG4 (PSD95) in the white matter development of preterm infants
Authors: Krishnan Michelle L. , Van Steenwinckel Juliette , Schang Anne-Laure , Yan Jun , Arnadottir Johanna , Le Charpentier Tifenn , Csaba Zsolt , Dournaud Pascal , Cipriani Sara , Auvynet Constance , Titomanlio Luigi , Pansiot Julien , Ball Gareth , Boardman James P. , Walley Andrew J. , Saxena Alka , Mirza Ghazala , Fleiss Bobbi , Edwards A. David , Petretto Enrico , Gressens Pierre
Published: August 2017

Preterm birth places infants in an adverse environment that leads to abnormal brain development and cerebral injury through a poorly understood mechanism known to involve neuroinflammation. In this study, we integrate human and mouse molecular and neuroimaging data to investigate the role of microglia in preterm white matter damage. Using a mouse model where encephalopathy of prematurity is induced by systemic interleukin-1β administration, we undertake gene network analysis of the microglial transcriptomic response to injury, extend this by analysis of protein-protein interactions, transcription factors and human brain gene expression, and translate findings to living infants using imaging genomics. We show that DLG4 (PSD95) protein is synthesised by microglia in immature mouse and human, developmentally regulated, and modulated by inflammation; DLG4 is a hub protein in the microglial inflammatory response; and genetic variation in DLG4 is associated with structural differences in the preterm infant brain. DLG4 is thus apparently involved in brain development and impacts inter-individual susceptibility to injury after preterm birth.
Biosynthesis of the nosiheptide indole side ring centers on a cryptic carrier protein NosJ
Authors: Ding Wei , Ji Wenjuan , Wu Yujie , Wu Runze , Liu Wan-Qiu , Mo Tianlu , Zhao Junfeng , Ma Xiaoyan , Zhang Wei , Xu Ping , Deng Zixin , Tang Boping , Yu Yi , Zhang Qi
Published: August 2017

Nosiheptide is a prototypal thiopeptide antibiotic, containing an indole side ring in addition to its thiopeptide-characteristic macrocylic scaffold. This indole ring is derived from 3-methyl-2-indolic acid (MIA), a product of the radical S-adenosylmethionine enzyme NosL, but how MIA is incorporated into nosiheptide biosynthesis remains to be investigated. Here we report functional dissection of a series of enzymes involved in nosiheptide biosynthesis. We show NosI activates MIA and transfers it to the phosphopantetheinyl arm of a carrier protein NosJ. NosN then acts on the NosJ-bound MIA and installs a methyl group on the indole C4, and the resulting dimethylindolyl moiety is released from NosJ by a hydrolase-like enzyme NosK. Surface plasmon resonance analysis show that the molecular complex of NosJ with NosN is much more stable than those with other enzymes, revealing an elegant biosynthetic strategy in which the reaction flux is controlled by protein–protein interactions with different binding affinities.
Emergence of native peptide sequences in prebiotic replication networks
Authors: Nanda Jayanta , Rubinov Boris , Ivnitski Denis , Mukherjee Rakesh , Shtelman Elina , Motro Yair , Miller Yifat , Wagner Nathaniel , Cohen-Luria Rivka , Ashkenasy Gonen
Published: August 2017

Biopolymer syntheses in living cells are perfected by an elaborate error correction machinery, which was not applicable during polymerization on early Earth. Scientists are consequently striving to identify mechanisms by which functional polymers were selected and further amplified from complex prebiotic mixtures. Here we show the instrumental role of non-enzymatic replication in the enrichment of certain product(s). To this end, we analyzed a complex web of reactions in β-sheet peptide networks, focusing on the formation of specific intermediate compounds and template-assisted replication. Remarkably, we find that the formation of several products in a mixture is not critically harmful, since efficient and selective template-assisted reactions serve as a backbone correction mechanism, namely, for keeping the concentration of the peptide containing the native backbone equal to, or even higher than, the concentrations of the other products. We suggest that these findings may shed light on molecular evolution processes that led to current biology.
RETRACTED ARTICLE: Liver X receptors constrain tumor development and metastasis dissemination in PTEN-deficient prostate cancer
Authors: Alioui Anthony , Dufour Julie , Leoni Valerio , Loregger Anke , Moeton Martina , Iuliano Luigi , Zerbinati Chiara , Septier Amandine , Val Pierre , Fouache Allan , Russo Vincenzo , Volle David H. , Lobaccaro Jean-Marc A. , Zelcer Noam , Baron Silvère
Published: August 2017

Advanced prostate cancer (PCa) is a clinical challenge as no curative therapeutic is available. In this context, a better understanding of metastasis and resistance mechanisms in PCa is an important issue. As phosphatase and tensin homolog (PTEN) loss is the most common genetic lesion in such cancer, we investigate human data sets for mechanisms that can constrain cancer evolution in this setting. Here we report a liver X receptor (LXR) signature, which tightly correlates with PTEN loss, in PCa. Accordingly, the LXR pathway is deregulated in prostate carcinomas in Pten-null mice. Genetic ablation of LXRs in Pten-null mice, exacerbates PCa invasiveness and metastatic dissemination, which involves mesenchymal transition and accumulation of matrix metalloproteinases. Mechanistically, PTEN deletion governed LXR transcriptional activity through deregulation of cholesterol de novo synthesis, resulting in accumulation of endogenous LXR ligands. Our study therefore reveals a functional circuit linking PTEN and LXR, and highlights LXRs as metabolic gatekeepers that are able to constrain PCa progression.
Land-locked mammalian Golgi reveals cargo transport between stable cisternae
Authors: Dunlop Myun Hwa , Ernst Andreas M. , Schroeder Lena K. , Toomre Derek K. , Lavieu Grégory , Rothman James E.
Published: August 2017

The Golgi is composed of a stack of cis, medial, trans cisternae that are biochemically distinct. The stable compartments model postulates that permanent cisternae communicate through bi-directional vesicles, while the cisternal maturation model postulates that transient cisternae biochemically mature to ensure anterograde transport. Testing either model has been constrained by the diffraction limit of light microscopy, as the cisternae are only 10–20 nm thick and closely stacked in mammalian cells. We previously described the unstacking of Golgi by the ectopic adhesion of Golgi cisternae to mitochondria. Here, we show that cargo processing and transport continue—even when individual Golgi cisternae are separated and “land-locked” between mitochondria. With the increased spatial separation of cisternae, we show using three-dimensional live imaging that cis-Golgi and trans-Golgi remain stable in their composition and size. Hence, we provide new evidence in support of the stable compartments model in mammalian cells.
Lineage overwhelms environmental conditions in determining rhizosphere bacterial community structure in a cosmopolitan invasive plant
Authors: Bowen Jennifer L. , Kearns Patrick J. , Byrnes Jarrett E. K. , Wigginton Sara , Allen Warwick J. , Greenwood Michael , Tran Khang , Yu Jennifer , Cronin James T. , Meyerson Laura A.
Published: August 2017

Plant–microbe interactions play crucial roles in species invasions but are rarely investigated at the intraspecific level. Here, we study these interactions in three lineages of a globally distributed plant, Phragmites australis. We use field surveys and a common garden experiment to analyze bacterial communities in the rhizosphere of P. australis stands from native, introduced, and Gulf lineages to determine lineage-specific controls on rhizosphere bacteria. We show that within-lineage bacterial communities are similar, but are distinct among lineages, which is consistent with our results in a complementary common garden experiment. Introduced P. australis rhizosphere bacterial communities have lower abundances of pathways involved in antimicrobial biosynthesis and degradation, suggesting a lower exposure to enemy attack than native and Gulf lineages. However, lineage and not rhizosphere bacterial communities dictate individual plant growth in the common garden experiment. We conclude that lineage is crucial for determination of both rhizosphere bacterial communities and plant fitness.
Parkinson’s disease associated with pure ATXN10 repeat expansion
Authors: Schüle Birgitt , McFarland Karen N. , Lee Kelsey , Tsai Yu-Chih , Nguyen Khanh-Dung , Sun Chao , Liu Mei , Byrne Christie , Gopi Ramesh , Huang Neng , Langston J. William , Clark Tyson , Gil Francisco Javier Jiménez , Ashizawa Tetsudo
Published: August 2017

Large, non-coding pentanucleotide repeat expansions of ATTCT in intron 9 of the ATXN10 gene typically cause progressive spinocerebellar ataxia with or without seizures and present neuropathologically with Purkinje cell loss resulting in symmetrical cerebellar atrophy. These ATXN10 repeat expansions can be interrupted by sequence motifs which have been attributed to seizures and are likely to act as genetic modifiers. We identified a Mexican kindred with multiple affected family members with ATXN10 expansions. Four affected family members showed clinical features of spinocerebellar ataxia type 10 (SCA10). However, one affected individual presented with early-onset levodopa-responsive parkinsonism, and one family member carried a large repeat ATXN10 expansion, but was clinically unaffected. To characterize the ATXN10 repeat, we used a novel technology of single-molecule real-time (SMRT) sequencing and CRISPR/Cas9-based capture. We sequenced the entire span of ~5.3–7.0 kb repeat expansions. The Parkinson’s patient carried an ATXN10 expansion with no repeat interruption motifs as well as an unaffected sister. In the siblings with typical SCA10, we found a repeat pattern of ATTCC repeat motifs that have not been associated with seizures previously. Our data suggest that the absence of repeat interruptions is likely a genetic modifier for the clinical presentation of l-Dopa responsive parkinsonism, whereas repeat interruption motifs contribute clinically to epilepsy. Repeat interruptions are important genetic modifiers of the clinical phenotype in SCA10. Advanced sequencing techniques now allow to better characterize the underlying genetic architecture for determining accurate phenotype–genotype correlations.
Rotigotine transdermal patch and sleep in Parkinson’s disease: where are we now?
Authors: Rosa-Grilo Miguel , Qamar Mubasher A. , Taddei Raquel N. , Pagonabarraga Javier , Kulisevsky Jaime , Sauerbier Anna , Chaudhuri K. Ray
Published: August 2017

A wide range of sleep dysfunction complicates Parkinson’s disease during its course from prodromal to palliative stage. It is now increasingly acknowledged that sleep disturbances are thus integral to the disease and pose a significant burden impacting on quality of life of patients. Sleep fragmentation, restless legs syndrome, nocturia, and nocturnal pain are regarded as one of the main components of night-time sleep dysfunction with possible secondary impact on cognition and well-being. The role of dopaminergic therapies, particularly using a continuous drug delivery strategy in managing some of these sleep issues, have been reported but the overall concept remains unclear. This review provides an overview of several aspects of night-time sleep dysfunction in Parkinson’s disease and describes all available published open-label and blinded studies that investigated the use of rotigotine transdermal patch targeting sleep. Blinded studies have suggested beneficial effects of rotigotine transdermal patch on maintenance insomnia and restless legs syndrome in Parkinson’s disease patients. Open-label studies support these observations and also suggest beneficial effects on nocturia and nocturnal pain.
Transcriptome analysis of inflammation-related gene expression in endothelial cells activated by complement MASP-1
Authors: Schwaner Endre , Németh Zsuzsanna , Jani Péter K. , Kajdácsi Erika , Debreczeni Márta L. , Doleschall Zoltán , Dobó József , Gál Péter , Rigó János , András Kinga , Hegedűs Tamás , Cervenak László
Published: August 2017

Mannan-binding lectin-associated serine protease 1 (MASP-1), the most abundant enzyme of the complement lectin pathway, is able to stimulate human umbilical vein endothelial cells (HUVECs) to alter the expression of several cytokines and adhesion molecules. This study has assessed to what extent MASP-1 is able to modify the transcriptional pattern of inflammation-related (IR) genes in HUVECs. We utilized Agilent microarray to analyse the effects of recombinant MASP-1 (rMASP-1) in HUVECs, on a set of 884 IR genes. Gene Set Enrichment Analysis showed an overall activation of inflammation-related genes in response to rMASP-1. rMASP-1 treatment up- and down-regulated 19 and 11 IR genes, respectively. Most of them were previously unidentified, such as genes of chemokines (CXCL1, CXCL2, CXCL3), inflammatory receptors (TLR2, BDKRB2) and other inflammatory factors (F3, LBP). Expression of IR genes changed early, during the first 2 hours of activation. Both p38-MAPK inhibitor and NFκB inhibitor efficiently suppressed the effect of rMASP-1. We delineated 12 transcriptional factors as possible regulators of rMASP-1-induced IR genes. Our microarray-based data are in line with the hypothesis that complement lectin pathway activation, generating active MASP-1, directly regulates inflammatory processes by shifting the phenotype of endothelial cells towards a more pro-inflammatory type.
Hemoglobin diffusion and the dynamics of oxygen capture by red blood cells
Authors: Longeville Stéphane , Stingaciu Laura-Roxana
Published: August 2017

Translational diffusion of macromolecules in cell is generally assumed to be anomalous due high macromolecular crowding of the milieu. Red blood cells are a special case of cells filled quasi exclusively (95% of the dry weight of the cell) with an almost spherical protein: hemoglobin. Hemoglobin diffusion has since a long time been recognized as facilitating the rate of oxygen diffusion through a solution. We address in this paper the question on how hemoglobin diffusion in the red blood cells can help the oxygen capture at the cell level and hence to improve oxygen transport. We report a measurement by neutron spin echo spectroscopy of the diffusion of hemoglobin in solutions with increasing protein concentration. We show that hemoglobin diffusion in solution can be described as Brownian motion up to physiological concentration and that hemoglobin diffusion in the red blood cells and in solutions at similar concentration are the same. Finally, using a simple model and the concentration dependence of the diffusion of the protein reported here, we show that hemoglobin concentration observed in human red blood cells ($$\simeq $$
≃
330 g.L−1) corresponds to an optimum for oxygen transport for individuals under strong activity.
Relative contribution of groundwater to plant transpiration estimated with stable isotopes
Authors: Barbeta Adrià , Peñuelas Josep
Published: August 2017

Water stored underground in the saturated and subsurface zones below the soil are important sources of water for plants in water-limited ecosystems. The presence of deep-rooted plants worldwide, however, suggests that the use of groundwater is not restricted to arid and seasonally dry ecosystems. We compiled the available data (71 species) on the relative contribution of groundwater to plant water estimated using stable isotopes and mixing models, which provided information about relative groundwater use, and analyzed their variation across different climates, seasons, plant types, edaphic conditions, and landscape positions. Plant use of groundwater was more likely at sites with a pronounced dry season, and represented on average 49 per cent of transpired water in dry seasons and 28 per cent in wet seasons. The relative contribution of groundwater to plant-water uptake was higher on rocky substrates (saprolite, fractured bedrock), which had reduced groundwater uptake when this source was deep belowground. In addition, we found that the connectivity between groundwater pools and plant water may be quantitatively larger and more widespread than reported by recent global estimations based on isotopic averaged values. Earth System Models should account for the feedbacks between transpiration and groundwater recharge.
Lytic EBV infection investigated by detection of Soluble Epstein-Barr virus ZEBRA in the serum of patients with PTLD
Authors: Habib Mohammed , Buisson Marlyse , Lupo Julien , Agbalika Felix , Socié Gérard , Germi Raphaele , Baccard Monique , Imbert-Marcille Berthe-Marie , Dantal Jacques , Morand Patrice , Drouet Emmanuel
Published: August 2017

The ZEBRA protein (encoded by the BZLF1 gene), is the major transcription factor of EBV, expressed upon EBV lytic cycle activation. Several studies highlighted the critical role of EBV lytic infection as a risk factor for lymphoproliferative disorders like post-transplant lymphoproliferative disease (PTLD). Here, we use an antigen-capture ELISA assay specifically designed to detecting the circulating soluble ZEBRA (sZEBRA) in serum samples (threshold value determined at 40ng/mL). We retrospectively investigated a population of 66 transplanted patients comprising 35 PTLD. All the samples from a control population (30 EBV-seronegative subjects and 25 immunocompetent individuals with EBV serological reactivation), classified as sZEBRA < 40ng/mL were assigned as negative. At PTLD diagnosis, EBV genome (quantified by qPCR with EBV DNA>200 copies/mL) and sZEBRA were detectable in 51% and 60% of cases, respectively. In the patients who developed a pathologically-confirmed PTLD, the mean sZEBRA value in cases, was 399 ng/mL +/− 141versus53ng/mL +/− 7 in patients who did not (p  < 0,001). This is the first report relating to the detection of the circulating ZEBRA in serum specimens, as well as the first analysis dealing with the lytic cycle of EBV in PTLD patients with this new biomarker.
Hidden Criticality of Counterion Condensation Near a Charged Cylinder
Authors: Cha Minryeong , Yi Juyeon , Kim Yong Woon
Published: August 2017

Counterion condensation onto a charged cylinder, known as the Manning transition, has received a great deal of attention since it is essential to understand the properties of polyelectrolytes in ionic solutions. However, the current understanding is still far from complete and poses a puzzling question: While the strong-coupling theory valid at large ionic correlations suggests a discontinuous nature of the counterion condensation, the mean-field theory always predicts a continuous transition at the same critical point. This naturally leads to a question how one can reconcile the mean-field theory with the strong-coupling prediction. Here, we study the counterion condensation transition on a charged cylinder via Monte Carlo simulations. Varying the cylinder radius systematically in relation to the system size, we find that in addition to the Manning transition, there exists a novel transition where all counterions are bound to the cylinder and the heat capacity shows a drop at a finite Manning parameter. A finite-size scaling analysis is carried out to confirm the criticality of the complete condensation transition, yielding the same critical exponents with the Manning transition. We show that the existence of the complete condensation is essential to explain how the condensation nature alters from continuous to discontinuous transition.
Mitochondrial cyclophilin D ablation is associated with the activation of Akt/p70S6K pathway in the mouse kidney
Authors: Klawitter Jelena , Pennington Alexander , Klawitter Jost , Thurman Joshua M. , Christians Uwe
Published: August 2017

The mitochondrial matrix protein cyclophilin D (CypD) is an essential component of the mitochondrial permeability transition pore (MPTP). Here we characterized the effects of CypD ablation on bioenergetics in the kidney. CypD loss triggers a metabolic shift in Ppif−/− male and female mouse kidneys towards glycolysis and Krebs cycle activity. The shift is accompanied by increased glucose consumption and a transcriptional upregulation of effectors of glucose metabolism in the kidney. These included activation of Akt, AMPK (only in males) and p70S6K kinases. Gender specific differences between the Ppif−/− male and female mouse kidneys were observed including activation of pro-surviving ERK1/2 kinase and inhibited expression of pro-apoptotic and pro-fibrotic JNK and TGFβ1 proteins in Ppif−/− females. They also showed the highest expression of phosphorylated-ERK1/2 and Akt S473 proteins of all four investigated animal groups. Furthermore, Ppif−/− females showed higher lactate concentrations and ATP/ADP-ratios in the kidney than males. These metabolic and transcriptional modifications could provide an additional level of protection to Ppif−/− females. In summary, loss of mitochondrial CypD results in a shift in bioenergetics and in activation of glucose-metabolism regulating Akt/AMPK/p70S6 kinase pathways that is expected to affect the capability of Ppif−/− mice kidneys to react to stimuli and injury.
Damage-free peripheral nerve stimulation by 12-ns pulsed electric field
Authors: Casciola Maura , Xiao Shu , Pakhomov Andrei G.
Published: August 2017

Modern technologies enable deep tissue focusing of nanosecond pulsed electric field (nsPEF) for non-invasive nerve and muscle stimulation. However, it is not known if PEF orders of magnitude shorter than the activation time of voltage-gated sodium channels (VGSC) would evoke action potentials (APs). One plausible scenario requires the loss of membrane integrity (electroporation) and resulting depolarization as an intermediate step. We report, for the first time, that the excitation of a peripheral nerve can be accomplished by 12-ns PEF without electroporation. 12-ns stimuli at 4.1–11 kV (3.3–8.8 kV/cm) evoked APs similarly to conventional stimuli (100–250 μs, 1–5 V, 103–515 V/m), except for having higher selectivity for the faster nerve fibers. Nerves sustained repeated tetanic stimulations (50 Hz or 100 Hz for 1 min) alternately by 12-ns PEF and by conventional pulses. Such tetani caused a modest AP decrease, to a similar extent for both types of stimuli. Nerve refractory properties were not affected. The lack of cumulative damages even from tens of thousands of 12-ns stimuli and the similarities with the conventional stimulation prove VGSC activation by nsPEF without nerve membrane damage.
Cortical and trabecular morphology is altered in the limb bones of mice artificially selected for faster skeletal growth
Authors: Farooq Saira , Leussink Shannon , Sparrow Leah M. , Marchini Marta , Britz Hayley M. , Manske Sarah L. , Rolian Campbell
Published: August 2017

Bone strength is influenced by mineral density and macro- and microstructure. Research into factors that contribute to bone morphology and strength has focused on genetic, environmental and morphological factors (e.g., body mass index), but little is known regarding the impact of rates of skeletal elongation on adult skeletal morphology and strength. Using micro-CT, we examined the impact of rates of skeletal elongation on bone cortical and trabecular morphology, and on rates of estrogen-dependent bone loss in the tibia in CD-1 mice, and in mice with accelerated skeletal growth (Longshanks). Groups of adult mice (n = 7/group) were subjected to ovariectomy or sham surgeries, scanned for 6 weeks, and indices of bone morphology were collected. Results show that Longshanks mice had significantly less trabecular bone at skeletal maturity, characterized by fewer, thinner trabeculae, and furthermore lost trabecular bone more slowly in response to ovariectomy. Artificial selection for rapid skeletal growth relative to somatic growth thus had a significant impact on trabecular bone morphology in Longshanks. Our data do not unequivocally demonstrate a causal relationship between rapid bone growth and reduced trabecular bone quality, but suggest that rapid linear bone growth may influence the risk of cancellous bone fragility.
A comprehensive characterization of the impact of mycophenolic acid on the metabolism of Jurkat T cells
Authors: Fernández-Ramos Ana A. , Marchetti-Laurent Catherine , Poindessous Virginie , Antonio Samantha , Petitgas Céline , Ceballos-Picot Irène , Laurent-Puig Pierre , Bortoli Sylvie , Loriot Marie-Anne , Pallet Nicolas
Published: August 2017

Metabolic reprogramming is critical for T cell fate and polarization and is regulated by metabolic checkpoints, including Myc, HIF-1α, AMPK and mTORC1. Our objective was to determine the impact of mycophenolic acid (MPA) in comparison with rapamycin (Rapa), an inhibitor of mTORC1, on the metabolism of Jurkat T cells. We identified a drug-specific transcriptome signature consisting of the key enzymes and transporters involved in glycolysis, glutaminolysis or nucleotide synthesis. MPA produced an early and transient drop in the intracellular ATP content related to the inhibition of de novo synthesis of purines, leading to the activation of the energy sensor AMPK. MPA decreases glycolytic flux, consistent with a reduction in glucose uptake, but also in the oxidation of glutamine. Additionally, both drugs reduce aerobic glycolysis. The expression of HIF-1α and Myc, promoting the activation of glycolysis and glutaminolysis, was inhibited by MPA and Rapa. In conclusion, we report that MPA profoundly impacts the cellular metabolism of Jurkat T cells by generating an energetic distress, decreasing the glycolytic and glutaminolytic fluxes and by targeting HIF-1α and Myc. These findings open interesting perspectives for novel combinatorial therapeutic strategies targeting metabolic checkpoints to block the proliferation of T cells.
Antibody-dependent fragmentation is a newly identified mechanism of cell killing in vivo
Authors: Liew Pei Xiong , Kim Jung Hwan , Lee Woo-Yong , Kubes Paul
Published: August 2017

The prevailing view is that therapeutic antibodies deplete cells through opsonization and subsequent phagocytosis, complement-dependent lysis or antibody-dependent cellular-cytotoxicity. We used high resolution in vivo imaging to identify a new antibody-dependent cell death pathway where Kupffer cells ripped large fragments off crawling antibody-coated iNKT cells. This antibody-dependent fragmentation process resulted in lethality and depletion of crawling iNKT cells in the liver sinusoids and lung capillaries. iNKT cell depletion was Fcy-receptor dependent and required iNKT cell crawling. Blood, spleen or joint iNKT cells that did not crawl were not depleted. The antibody required high glycosylation for sufficiently strong binding of the iNKT cells to the Fc Receptors on Kupffer cells. Using an acetaminophen overdose model, this approach functionally depleted hepatic iNKT cells and affected the severity of liver injury. This study reveals a new mechanism of antibody-dependent killing in vivo and raises implications for the design of new antibodies for cancer and auto-reactive immune cells.
Deep Phospho- and Phosphotyrosine Proteomics Identified Active Kinases and Phosphorylation Networks in Colorectal Cancer Cell Lines Resistant to Cetuximab
Authors: Abe Yuichi , Nagano Maiko , Kuga Takahisa , Tada Asa , Isoyama Junko , Adachi Jun , Tomonaga Takeshi
Published: August 2017

Abnormality in cellular phosphorylation is closely related to oncogenesis. Thus, kinase inhibitors, especially tyrosine kinase inhibitors (TKIs), have been developed as anti-cancer drugs. Genomic analyses have been used in research on TKI sensitivity, but some types of TKI resistance have been unclassifiable by genomic data. Therefore, global proteomic analysis, especially phosphotyrosine (pY) proteomic analysis, could contribute to predict TKI sensitivity and overcome TKI-resistant cancer. In this study, we conducted deep phosphoproteomic analysis to select active kinase candidates in colorectal cancer intrinsically resistant to Cetuximab. The deep phosphoproteomic data were obtained by performing immobilized metal-ion affinity chromatography-based phosphoproteomic and highly sensitive pY proteomic analyses. Comparison between sensitive (LIM1215 and DLD1) and resistant cell lines (HCT116 and HT29) revealed active kinase candidates in the latter, most of which were identified by pY proteomic analysis. Remarkably, genomic mutations were not assigned in most of these kinases. Phosphorylation-based signaling network analysis of the active kinase candidates indicated that SRC-PRKCD cascade was constitutively activated in HCT116 cells. Treatment with an SRC inhibitor significantly inhibited proliferation of HCT116 cells. In summary, our results based on deep phosphoproteomic data led us to propose novel therapeutic targets against cetuximab resistance and showed the potential for anti-cancer therapy.
Plant-expressed cocaine hydrolase variants of butyrylcholinesterase exhibit altered allosteric effects of cholinesterase activity and increased inhibitor sensitivity
Authors: Larrimore Katherine E. , Kazan I. Can , Kannan Latha , Kendle R. Player , Jamal Tameem , Barcus Matthew , Bolia Ashini , Brimijoin Stephen , Zhan Chang-Guo , Ozkan S. Banu , Mor Tsafrir S.
Published: August 2017

Butyrylcholinesterase (BChE) is an enzyme with broad substrate and ligand specificities and may function as a generalized bioscavenger by binding and/or hydrolyzing various xenobiotic agents and toxicants, many of which target the central and peripheral nervous systems. Variants of BChE were rationally designed to increase the enzyme’s ability to hydrolyze the psychoactive enantiomer of cocaine. These variants were cloned, and then expressed using the magnICON transient expression system in plants and their enzymatic properties were investigated. In particular, we explored the effects that these site-directed mutations have over the enzyme kinetics with various substrates of BChE. We further compared the affinity of various anticholinesterases including organophosphorous nerve agents and pesticides toward these BChE variants relative to the wild type enzyme. In addition to serving as a therapy for cocaine addiction-related diseases, enhanced bioscavenging against other harmful agents could add to the practicality and versatility of the plant-derived recombinant enzyme as a multivalent therapeutic.
Pregnancy-Associated Plasma Protein-A2 and Anthropometry, Lifestyle, and Biochemical Factors in a Human Adult Population
Authors: Steinbrecher Astrid , Janke Jürgen , Poy Matthew N. , Oxvig Claus , Pischon Tobias
Published: August 2017

Pregnancy-associated plasma protein-A2 (PAPP-A2), a metalloproteinase purportedly related to pregnancy, foetal growth and development, has recently been described essential for pre-adult growth. Thus, we measured PAPP-A2 in plasma of a non-pregnant population and determined its associations with lifestyle, anthropometric or biochemical factors. In this cross-sectional study of 387 participants (20–70 years) randomly drawn from registration offices near Berlin, Germany, socio-economic and lifestyle factors were assessed by questionnaires, and anthropometric measures and blood samples were taken by trained personnel. Blood was analysed for standard clinical parameters. PAPP-A2 concentration was measured by ELISA. Generalized linear models were used to estimate associations with anthropometric and biochemical factors adjusted for age, sex, and weight. Adjusted mean PAPP-A2 concentration was slightly higher in women (283 pg/mL) than in men (261 pg/mL, p = 0.05) and positively correlated with age (r = 0.17, p = 0.001). PAPP-A2 concentration was inversely associated with body mass index (−2.7 pg/mL per kg/m2, p = 0.03) and weight (−1.0 pg/mL per kg, p = 0.01) and positively associated with γ-glutamyl transferase (13.6 pg/mL per SD, p = 0.02), aspartate transaminase (18.5 pg/mL per SD, p = 0.002) and lactate dehydrogenase (14.9 pg/mL per SD, p = 0.02). Our results support that PAPP-A2, beyond its established role in early growth and development is relevant in adult metabolisms.
Tumor cells and their crosstalk with endothelial cells in 3D spheroids
Authors: Shoval Hila , Karsch-Bluman Adi , Brill-Karniely Yifat , Stern Tal , Zamir Gideon , Hubert Ayala , Benny Ofra
Published: August 2017

Recapitulating the tumor microenvironment is a central challenge in the development of experimental model for cancer. To provide a reliable tool for drug development and for personalized cancer therapy, it is critical to maintain key features that  exist in the original tumor. Along with this effort, 3-dimentional (3D) cellular models are being extensively studied. Spheroids are self-assembled cell aggregates that possess many important components of the physiological spatial growth and cell-cell interactions. In this study we aimed to investigate the interconnection between tumor and endothelial cells (EC) in hybrid spheroids containing either tumor cell (TC) lines or patient derived cancer cells. Preparation protocols of hybrid spheroids were optimized and their morphology and tissue-like features were analyzed. Our finding show that capillary-like structures are formed upon assembly and growth of TC:EC spheroids and that spheroids’ shape and surface texture may be an indication of spatial invasiveness of cells in the extra-cellular matrix (ECM). Establishing a model of hybrid tumor/stroma spheroids has a crucial importance in the experimental approach for personalized medicine, and may offer a reliable and low-cost method for the goal of predicting drug effects.
Disease mutations reveal residues critical to the interaction of P4-ATPases with lipid substrates
Authors: Gantzel Rasmus H. , Mogensen Louise S. , Mikkelsen Stine A. , Vilsen Bente , Molday Robert S. , Vestergaard Anna L. , Andersen Jens P.
Published: August 2017

Phospholipid flippases (P4-ATPases) translocate specific phospholipids from the exoplasmic to the cytoplasmic leaflet of membranes. While there is good evidence that the overall molecular structure of flippases is similar to that of P-type ATPase ion-pumps, the transport pathway for the “giant” lipid substrate has not been determined. ATP8A2 is a flippase with selectivity toward phosphatidylserine (PS), possessing a net negatively charged head group, whereas ATP8B1 exhibits selectivity toward the electrically neutral phosphatidylcholine (PC). Setting out to elucidate the functional consequences of flippase disease mutations, we have identified residues of ATP8A2 that are critical to the interaction with the lipid substrate during the translocation process. Among the residues pinpointed are I91 and L308, which are positioned near proposed translocation routes through the protein. In addition we pinpoint two juxtaposed oppositely charged residues, E897 and R898, in the exoplasmic loop between transmembrane helices 5 and 6. The glutamate is conserved between PS and PC flippases, whereas the arginine is replaced by a negatively charged aspartate in ATP8B1. Our mutational analysis suggests that the glutamate repels the PS head group, whereas the arginine minimizes this repulsion in ATP8A2, thereby contributing to control the entry of the phospholipid substrate into the translocation pathway.
The role of histone modification and a regulatory single-nucleotide polymorphism (rs2071166) in the Cx43 promoter in patients with TOF
Authors: Gu Ruoyi , Xu Jun , Lin Yixiang , Sheng Wei , Ma Duan , Ma Xiaojing , Huang Guoying
Published: August 2017

Abnormal level of Cx43 expression could result in CHD. Epigenetic modification and disease-associated, non-coding SNPs might influence gene transcription and expression. Our study aimed to determine the role of histone modification and an rSNP (rs2071166) in the Cx43 promoter in patients with TOF. Our results indicate that H3K18ac bind to Cx43 promoter and that their levels are reduced in TOF patients relative to controls. The relationship between the non-coding SNP in the Cx43 gene and TOF patients was evaluated in 158 patients and 300 controls. The C allele of rs2071166 was confirmed to result in an increased risk of TOF (OR = 1.586, 95%CI 1.149–2.189). Individuals with the CC genotype at rs2071166 also showed a significant susceptibility to TOF (OR = 2.961, 95%CI 1.452–6.038). The mRNA level in TOF who were CC genotype was lower than that in patients with the AA/AC genotype. Functional analysis in cells and transgenic zebrafish models showed that rs2071166 decreased the activity of the promoter and could block the interaction between RXRα and RARE. This is the first study to illustrate that epigenetic modification and an rSNP in the Cx43 promoter region play a critical role in TOF by impacting the transcriptional activity and expression level of Cx43.
Responses of CH4 and N2O fluxes to land-use conversion and fertilization in a typical red soil region of southern China
Authors: Wu Xing , Liu Huifeng , Zheng Xunhua , Lu Fei , Wang Shuai , Li Zongshan , Liu Guohua , Fu Bojie
Published: August 2017

Land-use conversion and fertilization have been widely reported as important management practices affecting CH4 and N2O fluxes; however, few long-term in situ measurements are available after land-use conversion from rice paddies to upland cultivation, especially those including the initial stages after conversion. A 3-year field experiment was conducted in rice paddies and a newly converted citrus orchard to measure CH4 and N2O fluxes in response to land-use conversion and fertilization in a red soil region of southern China. Annual CH4 and N2O emissions averaged 303.9 kg C ha−1 and 3.8 kg N ha−1, respectively, for the rice paddies over three cultivation years. Although annual N2O emissions increased two- to threefold after the conversion of rice paddies to citrus orchard, the substantial reduction in CH4 emissions and even shift into a sink for atmospheric CH4 led to significantly lower CO2-eq emissions of CH4 and N2O in the citrus orchard compared to the rice paddies. Moreover, distinct CH4 emissions were observed during the initial stages and sustained for several weeks after conversion. Our results indicated that the conversion of rice paddies to citrus orchards in this region for higher economic benefits may also lead to lower aggregate CH4 and N2O emissions.
Hyaluronic Acid Coated Chitosan Nanoparticles Reduced the Immunogenicity of the Formed Protein Corona
Authors: Almalik Abdulaziz , Benabdelkamel Hicham , Masood Afshan , Alanazi Ibrahim O. , Alradwan Ibrahim , Majrashi Majed A. , Alfadda Assim A. , Alghamdi Waleed M. , Alrabiah Haitham , Tirelli Nicola , Alhasan Ali H.
Published: August 2017

Studying the interactions of nanoparticles (NPs) with serum proteins is necessary for the rational development of nanocarriers. Optimum surface chemistry is a key consideration to modulate the formation of the serum protein corona (PC) and the resultant immune response. We investigated the constituent of the PC formed by hyaluronic acid-coated chitosan NPs (HA-CS NPs). Non-decorated chitosan NPs (CS NPs) and alginate-coated chitosan NPs (Alg-CS NPs) were utilized as controls. Results show that HA surface modifications significantly reduced protein adsorption relative to controls. Gene Ontology analysis demonstrates that HA-CS NPs were the least immunogenic nanocarriers. Indeed, less inflammatory proteins were adsorbed onto HA-CS NPs as opposed to CS and Alg-CS NPs. Interestingly, HA-CS NPs differentially adsorbed two unique anti-inflammatory proteins (ITIH4 and AGP), which were absent from the PC of both controls. On the other hand, CS and Alg-CS NPs selectively adsorbed a proinflammatory protein (Clusterin) that was not found on the surfaces of HA-CS NPs. While further studies are needed to investigate abilities of the PCs of only ITIH4 and AGP to modulate the interaction of NPs with the host immune system, our results suggest that this proof-of-concept could potentially be utilized to reduce the immunogenicity of a wide range of nanomaterials.
Ultrathin Nafion-filled porous membrane for zinc/bromine redox flow batteries
Authors: Kim Riyul , Kim Hyun Gyu , Doo Gisu , Choi Chanyong , Kim Soohyun , Lee Ju-Hyuk , Heo Jiyun , Jung Ho-Young , Kim Hee-Tak
Published: August 2017

In this work, we present a 16 μm-thick Nafion-filled porous membrane for Zn/Br redox flow batteries (ZBBs). By using molecular dynamics simulation and dynamic light scattering analysis, we rationally design Nafion solution for Nafion impregnation into a porous polypropylene (PP) separator. A void-free Nafion/PP membrane is successfully fabricated by using NMP as a solvent for the Nafion solution. The resulting membrane shows a smaller area specific resistance in comparison with 600 μm-thick, commercial SF-600 porous membrane. Due to its dense morphology, Br2 diffusivity of the Nafion/PP membrane is two orders of magnitude lower than that of SF-600, resulting in a comparable Br2 crossover in spite of 37.5 times smaller membrane thickness. As a result, the ZBB based on the Nafion/PP membrane exhibits a higher energy efficiency, demonstrating that ion exchange membrane can outperform the conventional porous membrane by reducing the membrane thickness with inexpensive porous substrate.
Investigation of Mitochondrial Metabolic Response to Doxorubicin in Prostate Cancer Cells: An NADH, FAD and Tryptophan FLIM Assay
Authors: Alam Shagufta Rehman , Wallrabe Horst , Svindrych Zdenek , Chaudhary Ajay K. , Christopher Kathryn G. , Chandra Dhyan , Periasamy Ammasi
Published: August 2017

Prostate cancer (PCa) is one of the leading cancers in men in the USA. Lack of experimental tools that predict therapy response is one of the limitations of current therapeutic regimens. Mitochondrial dysfunctions including defective oxidative phosphorylation (OXPHOS) in cancer inhibit apoptosis by modulating ROS production and cellular signaling. Thus, correction of mitochondrial dysfunction and induction of apoptosis are promising strategies in cancer treatment. We have used Fluorescence Lifetime Imaging Microscopy (FLIM) to quantify mitochondrial metabolic response in PCa cells by tracking auto-fluorescent NAD(P)H, FAD and tryptophan (Trp) lifetimes and their enzyme-bound fractions as markers, before and after treatment with anti-cancer drug doxorubicin. A 3-channel FLIM assay and quantitative analysis of these markers for cellular metabolism show in response to doxorubicin, NAD(P)H mean fluorescence lifetime (τm) and enzyme-bound (a2%) fraction increased, FAD enzyme-bound (a1%) fraction was decreased, NAD(P)H-a2%/FAD-a1% FLIM-based redox ratio and ROS increased, followed by induction of apoptosis. For the first time, a FRET assay in PCa cells shows Trp-quenching due to Trp-NAD(P)H interactions, correlating energy transfer efficiencies (E%) vs NAD(P)H-a2%/FAD-a1% as sensitive parameters in predicting drug response. Applying this FLIM assay as early predictor of drug response would meet one of the important goals in cancer treatment.
Alcohol amplifies ketamine-induced apoptosis in primary cultured cortical neurons and PC12 cells through down-regulating CREB-related signaling pathways
Authors: Zuo Daiying , Sun Feng , Cui Jiahui , Liu Yumiao , Liu Zi , Zhou Xuejiao , Li Zengqiang , Wu Yingliang
Published: August 2017

Recreational use of ketamine (KET) has been increasing worldwide. Previous studies have demonstrated that KET induced neurotoxicity; however, few studies have examined how alcohol (ALC) affects KET-induced neurotoxicity. In light of the fact that some KET abusers combine KET with ALC, the present study was aimed to investigate the effects of ALC on KET-induced neurotoxicity and the underlying mechanismin vitro. Our data revealed that co-treatment with ALC and KET was more detrimental to cell viability than KET single treatment in both PC12 cells and primary cultured rat cortical neurons. Furthermore, ALC exacerbated KET-induced apoptosis characterized by morphological changes and the sub-G1 phase increase, which were mitigated by the pretreatment of CNQX, a known alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA)/kainite (KA) receptor antagonist. In addition, ALC and KET co-treatment led to intracellular Ca2+overload, down-regulation of p-Akt, p-CREB, PKA, CaMK-IV, Bcl-2 and BDNF expression and up-regulation of cleaved caspase-3 and Bax expression, which can be attenuated by CNQX pretreatment. These results indicate that the potentiation of ALC on KET-induced neurotoxicity was related to the down-regulation of CREB-related pathways. Our present study also indicates that ALC and KET co-abuse might cause serious neurotoxicity which should be conveyed to the public and drew enough attention.
Molecular spectrum of laterally coupled quantum rings under intense terahertz radiation
Authors: Baghramyan Henrikh M. , Barseghyan Manuk G. , Laroze David
Published: August 2017

We study the influence of intense THz laser radiation and electric field on molecular states of laterally coupled quantum rings. Laser radiation shows the capability to dissociate quantum ring molecule and add 2-fold degeneracy to the molecular states at the fixed value of the overlapping size between rings. It is shown that coupled to decoupled molecular states phase transition points form almost a straight line with a slope equal to two. In addition, the electric field direction dependent energy spectrum shows unexpected oscillations, demonstrating strong coupling between molecular states. Besides, intraband absorption is considered, showing both blue and redshifts in its spectrum. The obtained results can be useful for the controlling of degeneracy of the discrete energy spectrum of nanoscale structures and in the tunneling effects therein.
Protein tyrosine phosphatase non-receptor 22 and C-Src tyrosine kinase genes are down-regulated in patients with rheumatoid arthritis
Authors: Remuzgo-Martínez Sara , Genre Fernanda , Castañeda Santos , Corrales Alfonso , Moreno-Fresneda Pablo , Ubilla Begoña , Mijares Verónica , Portilla Virginia , González-Vela Jesús , Pina Trinitario , Ocejo-Vinyals Gonzalo , Irure-Ventura Juan , Blanco Ricardo , Martín Javier , Llorca Javier , López-Mejías Raquel , González-Gay Miguel A.
Published: August 2017

Several protein tyrosine phosphatase non-receptor 22 (PTPN22) single-nucleotide polymorphisms (SNPs) have been significantly related with rheumatoid arthritis (RA) susceptibility. Nevertheless, its potential influence on PTPN22 expression in RA has not been completely elucidated. Furthermore, PTPN22 binds to C-Src tyrosine kinase (CSK) forming a key complex in autoimmunity. However, the information of CSK gene in RA is scarce. In this study, we analyzed the relative PTPN22 and CSK expression in peripheral blood from 89 RA patients and 43 controls to determine if the most relevant PTPN22 (rs2488457, rs2476601 and rs33996649) and CSK (rs34933034 and rs1378942) polymorphisms may influence on PTPN22 and CSK expression in RA. The association between PTPN22 and CSK expression in RA patients and their clinical characteristics was also evaluated. Our study shows for the first time a marked down-regulation of PTPN22 expression in RA patients carrying the risk alleles of PTPN22 rs2488457 and rs2476601 compared to controls (p = 0.004 and p = 0.007, respectively). Furthermore, CSK expression was significantly lower in RA patients than in controls (p < 0.0001). Interestingly, a reduced PTPN22 expression was disclosed in RA patients with ischemic heart disease (p = 0.009). The transcriptional suppression of this PTPN22/CSK complex may have a noteworthy clinical relevance in RA patients.