bluuebunny/crossref_metadata_2025 huggingface dataset:
Metabolomics coupled with pathway analysis characterizes metabolic changes in response to BDE-3 induced reproductive toxicity in mice
Authors: Wei Ziheng , Xi Jing , Gao Songyan , You Xinyue , Li Na , Cao Yiyi , Wang Liupeng , Luan Yang , Dong Xin
Published: March 2018

Polybrominated diphenyl ethers (PBDEs) may affect male reproductive function. 4-bromodiphenyl ether (BDE-3), the photodegradation products of higher brominated PBDEs, is the most fundamental mono-BDE in environment but is less studied. The purpose of this study was to investigate the reproductive toxicity induced by BDE-3 and explore the mechanism by metabolomics approach. In this study, mice were treated intragastrically with BDE-3 for consecutive six weeks at the dosages of 0.0015, 1.5, 10 and 30 mg/kg. The reproductive toxicity was evaluated by sperm analysis and histopathology examinations. UPLC-Q-TOF/MS was applied to profile the metabolites of testis tissue, urine and serum samples in the control and BDE-3 treated mice. Results showed the sperm count was dose-dependently decreased and percentage of abnormal sperms increased by the treatment of BDE-3. Histopathology examination also revealed changes in seminiferous tubules and epididymides in BDE-3 treated mice. Metabolomics analysis revealed that different BDE-3 groups showed metabolic disturbances to varying degrees. We identified 76, 38 and 31 differential metabolites in testis tissue, urine and serum respectively. Pathway analysis revealed several pathways including Tyrosine metabolism, Purine metabolism and Riboflavin metabolism, which may give a possible explanation for the toxic mechanism of BDE-3. This study indicates that UHPLC-Q-TOFMS-based metabolomics approach provided a better understanding of PBDEs-induced toxicity dynamically.
Structural and Functional Connectivity Changes Beyond Visual Cortex in a Later Phase of Visual Perceptual Learning
Authors: Kang Dong-Wha , Kim Dongho , Chang Li-Hung , Kim Yong-Hwan , Takahashi Emi , Cain Matthew S. , Watanabe Takeo , Sasaki Yuka
Published: March 2018

The neural mechanisms of visual perceptual learning (VPL) remain unclear. Previously we found that activation in the primary visual cortex (V1) increased in the early encoding phase of training, but returned to baseline levels in the later retention phase. To examine neural changes during the retention phase, we measured structural and functional connectivity changes using MRI. After weeks of training on a texture discrimination task, the fractional anisotropy of the inferior longitudinal fasciculus, a major tract connecting visual and anterior areas, was increased, as well as the functional connectivity between V1 and anterior regions mediated by the ILF. These changes were strongly correlated with behavioral performance improvements. These results suggest a two-phase model of VPL in which localized functional changes in V1 in the encoding phase of training are followed by changes in both structural and functional connectivity in ventral visual processing, perhaps leading to the long-term stabilization of VPL.
Schramm-Loewner evolution and perimeter of percolation clusters of correlated random landscapes
Authors: de Castro C. P. , Luković M. , Pompanin G. , Andrade R. F. S. , Herrmann H. J.
Published: March 2018

Motivated by the fact that many physical landscapes are characterized by long-range height-height correlations that are quantified by the Hurst exponent H, we investigate the statistical properties of the iso-height lines of correlated surfaces in the framework of Schramm-Loewner evolution (SLE). We show numerically that in the continuum limit the external perimeter of a percolating cluster of correlated surfaces with H ∈ [−1, 0] is statistically equivalent to SLE curves. Our results suggest that the external perimeter also retains the Markovian properties, confirmed by the absence of time correlations in the driving function and the fact that the latter is Gaussian distributed for any specific time. We also confirm that for all H the variance of the winding angle grows logarithmically with size.
Identification of potential key protein interaction networks of BK virus nephropathy in patients receiving kidney transplantation
Authors: Jia Linpei , Fu Wenjing , Jia Rufu , Wu Leiyun , Li Xiaoxia , Jia Qiang , Zhang Hongliang
Published: March 2018

We aim to identify the key protein interaction networks and implicated pathways of BK virus nephropathy (BKVN) via bioinformatic methods. The microarray dataGSE75693of 30 patients with stable kidney transplantation and 15 with BKVN were downloaded and analyzed by using thelimmapackage to identify differentially expressed genes (DEGs). Then the gene ontology (GO) functional enrichment analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were done to investigate the molecular function (MF), biological process (BP), cellular components (CC) and pathways of DEGs. Finally, protein-protein interactions (PPIs) were constructed, and the hub proteins were  identified. As a result, 249 up-regulated genes and 253 down-regulated genes of BKVN patients were selected based on criteria ofP > 0.01 and fold change >2.0. GO and KEGG showed that DEGs were mainly located in nucleus and cytosol, and were implicated in the immune responses. In the PPI analysis, 26 up-regulated and 8 down-regulated proteins composed the pivotal interaction network. CXCL10, EGF and STAT1 were identified as hub proteins in BKVN. In conclusion, CXCL10, EGF and STAT1 may induce kidney injuries by promoting inflammation and prohibiting reparation of tissue damage in BKVN.
Using spatial mark-recapture for conservation monitoring of grizzly bear populations in Alberta
Authors: Boulanger John , Nielsen Scott E. , Stenhouse Gordon B.
Published: March 2018

One of the challenges in conservation is determining patterns and responses in population density and distribution as it relates to habitat and changes in anthropogenic activities. We applied spatially explicit capture recapture (SECR) methods, combined with density surface modelling from five grizzly bear (Ursus arctos) management areas (BMAs) in Alberta, Canada, to assess SECR methods and to explore factors influencing bear distribution. Here we used models of grizzly bear habitat and mortality risk to test local density associations using density surface modelling. Results demonstrated BMA-specific factors influenced density, as well as the effects of habitat and topography on detections and movements of bears. Estimates from SECR were similar to those from closed population models and telemetry data, but with similar or higher levels of precision. Habitat was most associated with areas of higher bear density in the north, whereas mortality risk was most associated (negatively) with density of bears in the south. Comparisons of the distribution of mortality risk and habitat revealed differences by BMA that in turn influenced local abundance of bears. Combining SECR methods with density surface modelling increases the resolution of mark-recapture methods by directly inferring the effect of spatial factors on regulating local densities of animals.
Combining targeted panel-based resequencing and copy-number variation analysis for the diagnosis of inherited syndromic retinopathies and associated ciliopathies
Authors: Sanchez-Navarro Iker , R. J. da Silva Luciana , Blanco-Kelly Fiona , Zurita Olga , Sanchez-Bolivar Noelia , Villaverde Cristina , Lopez-Molina Maria Isabel , Garcia-Sandoval Blanca , Tahsin-Swafiri Saoud , Minguez Pablo , Riveiro-Alvarez Rosa , Lorda Isabel , Sanchez-Alcudia Rocío , Perez-Carro Raquel , Valverde Diana , Liu Yichuan , Tian Lifeng , Hakonarson Hakon , Avila-Fernandez Almudena , Corton Marta , Ayuso Carmen
Published: March 2018

Inherited syndromic retinopathies are a highly heterogeneous group of diseases that involve retinal anomalies and systemic manifestations. They include retinal ciliopathies, other well-defined clinical syndromes presenting with retinal alterations and cases of non-specific multisystemic diseases. The heterogeneity of these conditions makes molecular and clinical characterization of patients challenging in daily clinical practice. We explored the capacity of targeted resequencing and copy-number variation analysis to improve diagnosis of a heterogeneous cohort of 47 patients mainly comprising atypical cases that did not clearly fit a specific clinical diagnosis. Thirty-three likely pathogenic variants were identified in 18 genes (ABCC6, ALMS1, BBS1, BBS2, BBS12, CEP41, CEP290, IFT172, IFT27, MKKS, MYO7A, OTX2, PDZD7, PEX1, RPGRIP1, USH2A, VPS13B, and WDPCP). Molecular findings and additional clinical reassessments made it possible to accurately characterize 14 probands (30% of the total). Notably, clinical refinement of complex phenotypes was achieved in 4 cases, including 2 de novo OTX2-related syndromes, a novel phenotypic association for the ciliary CEP41 gene, and the co-existence of biallelic USH2A variants and a Koolen-de-Vries syndrome–related 17q21.31 microdeletion. We demonstrate that combining next-generation sequencing and CNV analysis is a comprehensive and useful approach to unravel the extensive phenotypic and genotypic complexity of inherited syndromic retinopathies.
Spatial-temporal profiling of prodiginines and serratamolides produced by endophytic Serratia marcescens harbored in Maytenus serrata
Authors: Eckelmann Dennis , Spiteller Michael , Kusari Souvik
Published: March 2018

An endophytic bacterium, Serratia marcescens MSRBB2, isolated from inner bark of a Cameroonian Maytenus serrata plant, was subjected to the OSMAC (One Strain Many Compounds) approach and metabolic profiling using HPLC-HRMSn. We identified 7 prodiginines along with 26 serratamolides. Their biosynthetic pathways were elucidated by feeding with labeled precursors in combination with HRMSn. Dual-culture confrontation/restriction assays of the bacterial endophyte were devised with coexisting fungal endophytes (Pestalotiopsis virgatula, Aspergillus caesiellus and Pichia spp.) as well as with unrelated, non-endophytic fungi belonging to the same genera. The assays were combined with scanning electron microscopy (SEM) as well as matrix-assisted laser desorption ionization imaging high-resolution mass spectrometry (MALDI-imaging-HRMS) for visualizing, both in high spatial and temporal resolution, the distribution and interplay of the compounds during microbial interactions. We demonstrated the effect of prodigiosin produced by endophytic S. marcescens MSRBB2 as an allelochemical that specifically inhibits coexisting endophytic fungi. Our results provide new insights into the physiological and ecological relevance of prodiginines and serratamolides within the context of allelopathy and chemical defense interaction occurring between coexisting endophytes harbored in M. serrata.
Persistent random deformation model of cells crawling on a gel surface
Authors: Ebata Hiroyuki , Yamamoto Aki , Tsuji Yukie , Sasaki Saori , Moriyama Kousuke , Kuboki Thasaneeya , Kidoaki Satoru
Published: March 2018

In general, cells move on a substrate through extension and contraction of the cell body. Though cell movement should be explained by taking into account the effect of such shape fluctuations, past approaches to formulate cell-crawling have not sufficiently quantified the relationship between cell movement (velocity and trajectory) and shape fluctuations based on experimental data regarding actual shaping dynamics. To clarify this relationship, we experimentally characterized cell-crawling in terms of shape fluctuations, especially extension and contraction, by using an elasticity-tunable gel substrate to modulate cell shape. As a result, an amoeboid swimmer-like relation was found to arise between the cell velocity and cell-shape dynamics. To formulate this experimentally-obtained relationship between cell movement and shaping dynamics, we established a persistent random deformation (PRD) model based on equations of a deformable self-propelled particle adopting an amoeboid swimmer-like velocity-shape relationship. The PRD model successfully explains the statistical properties of velocity, trajectory and shaping dynamics of the cells including back-and-forth motion, because the velocity equation exhibits time-reverse symmetry, which is essentially different from previous models. We discuss the possible application of this model to classify the phenotype of cell migration based on the characteristic relation between movement and shaping dynamics.
Timing of the Saalian- and Elsterian glacial cycles and the implications for Middle – Pleistocene hominin presence in central Europe
Authors: Lauer Tobias , Weiss Marcel
Published: March 2018

By establishing a luminescence-based chronology for fluvial deposits preserved between the Elsterian- and Saalian tills in central Germany, we obtained information on the timing of both the Middle Pleistocene glacial cycles and early human appearance in central Europe. The luminescence ages illustrate different climatic driven fluvial aggradation periods during the Saalian glacial cycle spanning from 400–150 ka. The ages of sediments directly overlying the Elsterian till are approximately 400 ka and prove that the first extensive Fennoscandian ice sheet extension during the Quaternary correlates with MIS 12 and not with MIS 10. Furthermore, the 400 ka old fluvial units contain Lower Paleolithic stone artefacts that document the first human appearance in the region. In addition, we demonstrate that early MIS 8 is a potential date for the onset of the Middle Paleolithic in central Germany, as Middle Paleolithic stone artefacts are correlated with fluvial units deposited between 300 ka and 200 ka. However, the bulk of Middle Paleolithic sites date to MIS 7 in the region. The fluvial units preserved directly under the till of the southernmost Saalian ice yield an age of about 150 ka, and enable a correlation of the Drenthe stage to late MIS 6.
Environmental complexity buffers against stress-induced negative judgement bias in female chickens
Authors: Zidar Josefina , Campderrich Irene , Jansson Emelie , Wichman Anette , Winberg Svante , Keeling Linda , Løvlie Hanne
Published: March 2018

Cognitive processes are often biased by emotions. In humans, affective disorders are accompanied by pessimistic judgement, while optimistic judgement is linked to emotional stability. Similar to humans, animals tend to interpret ambiguous stimuli negatively after experiencing stressful events, although the long-lasting impact on judgement bias has rarely been investigated. We measure judgement bias in female chicks (Gallus gallus domesticus) after exposure to cold stress, and before and after exposure to additional unpredictable stressors. Additionally, we explore if brain monoamines can explain differences in judgement bias. Chicks exposed to cold stress did not differ in judgement bias compared to controls, but showed sensitivity to additional stressors by having higher motivation for social reinstatement. Environmental complexity reduced stress-induced negative judgement bias, by maintaining an optimistic bias in individuals housed in complex conditions even after stress exposure. Moreover, judgement bias was related to dopamine turnover rate in mesencephalon, with higher activity in individuals that had a more optimistic response. These results demonstrate that environmental complexity can buffer against negative effects of additive stress and that dopamine relates to judgement bias in chicks. These results reveal that both internal and external factors can mediate emotionally biased judgement in animals, thus showing similarities to findings in humans.
Identification of an Arg-Leu-Arg tripeptide that contributes to the binding interface between the cytokine MIF and the chemokine receptor CXCR4
Authors: Lacy Michael , Kontos Christos , Brandhofer Markus , Hille Kathleen , Gröning Sabine , Sinitski Dzmitry , Bourilhon Priscila , Rosenberg Eric , Krammer Christine , Thavayogarajah Tharshika , Pantouris Georgios , Bakou Maria , Weber Christian , Lolis Elias , Bernhagen Jürgen , Kapurniotu Aphrodite
Published: March 2018

MIF is a chemokine-like cytokine that plays a role in the pathogenesis of inflammatory and cardiovascular disorders. It binds to the chemokine-receptors CXCR2/CXCR4 to trigger atherogenic leukocyte migration albeit lacking canonical chemokine structures. We recently characterized an N-like-loop and the Pro-2-residue of MIF as critical molecular determinants of the CXCR4/MIF binding-site and identified allosteric agonism as a mechanism that distinguishes CXCR4-binding to MIF from that to the cognate ligand CXCL12. By using peptide spot-array technology, site-directed mutagenesis, structure-activity-relationships, and molecular docking, we identified the Arg-Leu-Arg (RLR) sequence-region 87–89 that – in three-dimensional space – ‘extends’ the N-like-loop to control site-1-binding to CXCR4. Contrary to wildtype MIF, mutant R87A-L88A-R89A-MIF fails to bind to the N-terminal of CXCR4 and the contribution of RLR to the MIF/CXCR4-interaction is underpinned by an ablation of MIF/CXCR4-specific signaling and reduction in CXCR4-dependent chemotactic leukocyte migration of the RLR-mutant of MIF. Alanine-scanning, functional competition by RLR-containing peptides, and molecular docking indicate that the RLR residues directly participate in contacts between MIF and CXCR4 and highlight the importance of charge-interactions at this interface. Identification of the RLR region adds important structural information to the MIF/CXCR4 binding-site that distinguishes this interface from CXCR4/CXCL12 and will help to design MIF-specific drug-targeting approaches.
Surface enhanced Raman spectroscopy of Chlamydia trachomatis and Neisseria gonorrhoeae for diagnostics, and extra-cellular metabolomics and biochemical monitoring
Authors: Chen Y. , Premasiri W. R. , Ziegler L. D.
Published: March 2018

SERS spectra excited at 785 nm of the bacteria Chlamydia trahomatis (elementary bodies, EB) and Neisseria gonorrheoae, the causative pathogens for the two most common sexually transmitted diseases (STD), chlamydia and gonorrhea, respectively, are reported. Although both are Gram-negative bacteria, the SERS signatures of C. trachomatis and N. gonorrheoae are completely different. N. gonorrheoae SERS spectra are due to the starvation induced nucleotide metabolites adenine and guanine, and the surface associated co-enzyme nicotinamide adenine dinucleotide and are very similar on Au and Ag although the spectrum appears more rapidly on Ag. The C. trachomatis SERS spectrum is dominated by the vibrational features of cell surface proteins. While features attributable to specific residues and the amide backbone characterize the C. trachomatis spectrum on Ag, the corresponding SERS spectrum on Au substrates displays vibrational characteristics of aggregated proteins. The prospects for the development of a SERS based platform for rapid (<one hour), low-cost bacterial STD diagnostics are promising based on these initial studies. Furthermore, this biomedical application demonstrates the potential for SERS to be a sensitive real time probe of the dynamics of biochemical activity in the cell wall and extracellular regions of microorganisms.
CD4+ and CD8+ T Cells Exert Regulatory Properties During Experimental Acute Aristolochic Acid Nephropathy
Authors: Baudoux Thomas , Husson Cécile , De Prez Eric , Jadot Inès , Antoine Marie-Hélène , Nortier Joëlle L. , Hougardy Jean-Michel
Published: March 2018

Experimental aristolochic acid nephropathy is characterized by transient acute proximal tubule necrosis and inflammatory cell infiltrates followed by interstitial fibrosis and tubular atrophy. The respective role of T-cell subpopulations has never been studied in the acute phase of the mouse model, and was heretofore exclusively investigated by the use of several depletion protocols. As compared to mice injected with aristolochic acids alone, more severe acute kidney injury was observed after CD4+ or CD8+ T-cells depletion. TNF-alpha and MCP-1 mRNA renal expressions were also increased. In contrast, regulatory T-cells depletion did not modify the severity of the aristolochic acids induced acute kidney injury, suggesting an independent mechanism. Aristolochic acids nephropathy was also associated with an increased proportion of myeloid CD11bhighF4/80mid and a decreased proportion of their counterpart CD11blowF4/80high population. After CD4+ T-cell depletion the increase in the CD11bhighF4/80mid population was even higher whereas the decrease in the CD11blowF4/80high population was more marked after CD8+ T cells depletion. Our results suggest that CD4+ and CD8+ T-cells provide protection against AA-induced acute tubular necrosis. Interestingly, T-cell depletion was associated with an imbalance of the CD11bhighF4/80mid and CD11blowF4/80high populations.
Exercise Mitigates Alcohol Induced Endoplasmic Reticulum Stress Mediated Cognitive Impairment through ATF6-Herp Signaling
Authors: George Akash K. , Behera Jyotirmaya , Kelly Kimberly E. , Mondal Nandan K. , Richardson Kennedy P. , Tyagi Neetu
Published: March 2018

Chronic ethanol/alcohol (AL) dosing causes an elevation in homocysteine (Hcy) levels, which leads to the condition known as Hyperhomocysteinemia (HHcy). HHcy enhances oxidative stress and blood-brain-barrier (BBB) disruption through modulation of endoplasmic reticulum (ER) stress; in part by epigenetic alternation, leading to cognitive impairment. Clinicians have recommended exercise as a therapy; however, its protective effect on cognitive functions has not been fully explored. The present study was designed to observe the protective effects of exercise (EX) against alcohol-induced epigenetic and molecular alterations leading to cerebrovascular dysfunction. Wild-type mice were subjected to AL administration (1.5 g/kg-bw) and subsequent treadmill EX for 12 weeks (5 day/week@7–11 m/min). AL affected mouse brain through increases in oxidative and ER stress markers, SAHH and DNMTs alternation, while decreases in CBS, CSE, MTHFR, tight-junction proteins and cellular H2S levels. Mechanistic study revealed that AL increased epigenetic DNA hypomethylation of Herp promoter. BBB dysfunction and cognitive impairment were observed in the AL treated mice. AL mediated transcriptional changes were abolished by administration of ER stress inhibitor DTT. In conclusion, exercise restored Hcy and H2S to basal levels while ameliorating AL-induced ER stress, diminishing BBB dysfunction and improving cognitive function via ATF6-Herp-signaling. EX showed its protective efficacy against AL-induced neurotoxicity.
Boson peak, heterogeneity and intermediate-range order in binary SiO2-Al2O3 glasses
Authors: Ando Mariana F. , Benzine Omar , Pan Zhiwen , Garden Jean-Luc , Wondraczek Katrin , Grimm Stephan , Schuster Kay , Wondraczek Lothar
Published: March 2018

In binary aluminosilicate liquids and glasses, heterogeneity on intermediate length scale is a crucial factor for optical fiber performance, determining the lower limit of optical attenuation and Rayleigh scattering, but also clustering and precipitation of optically active dopants, for example, in the fabrication of high-power laser gain media. Here, we consider the low-frequency vibrational modes of such materials for assessing structural heterogeneity on molecular scale. We determine the vibrational density of states VDoS g(ω) using low-temperature heat capacity data. From correlation with low-frequency Raman spectroscopy, we obtain the Raman coupling coefficient. Both experiments allow for the extraction of the average dynamic correlation length as a function of alumina content. We find that this value decreases from about 3.9 nm to 3.3 nm when mildly increasing the alumina content from zero (vitreous silica) to 7 mol%. At the same time, the average inter-particle distance increases slightly due to the presence of oxygen tricluster species. In accordance with Loewensteinian dynamics, this proves that mild alumina doping increases structural homogeneity on molecular scale.
A band of bound states in the continuum induced by disorder
Authors: Xiao Yi-Xin , Zhang Zhao-Qing , Chan C. T.
Published: March 2018

Bound states in the continuum usually refer to the phenomenon of a single or a few discrete bound states embedded in a continuous spectrum of extended states. Here we propose a simple mechanism to achieve a band of bound states in the continuum in a class of disordered quasi-1D and quasi-2D systems, where the bound states and extended states overlap completely in a spectral range. The systems are partially disordered in a way that a band of extended states always exists, not affected by the randomness, whereas the states in all other bands become localized and cover the entire spectrum of extended states. We demonstrate such disordered-induced bound states in the continuum in disordered multi-chain and multi-layer systems.
Lumenal exposed regions of the D1 protein of PSII are long enough to be degraded by the chloroplast Deg1 protease
Authors: Knopf Ronit Rimon , Adam Zach
Published: March 2018

Degradation of the D1 protein of photosystem II (PSII) reaction center is a pre-requisite for the repair cycle from photoinhibition. Two types of thylakoid proteases, FtsH and Deg, have been demonstrated to participate in this process. However, the location of the proteolytic sites of the lumenal Deg1 protease within its internal sphere raised the question whether the lumenal-exposed regions of D1 are indeed long enough to reach these sites. Implanting these regions into the stable GFP rendered it sensitive to the presence of Deg1 in vitro, demonstrating that the flexible regions of D1 that protrude into the lumen can penetrate through the three side-openings of Deg1 and reach its internal proteolytic sites. This mode of action, facilitating cooperation between proteases on both sides of the thylakoid membranes, should be applicable to the degradation of other integral thylakoid membrane proteins as well.
Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes
Authors: Klaesson Axel , Grannas Karin , Ebai Tonge , Heldin Johan , Koos Björn , Leino Mattias , Raykova Doroteya , Oelrich Johan , Arngården Linda , Söderberg Ola , Landegren Ulf
Published: March 2018

We have redesigned probes forin situproximity ligation assay (PLA), resulting in more efficient localized detection of target proteins.In situPLA depends on recognition of target proteins by pairs of antibody-oligonucleotide conjugates (PLA probes), which jointly give rise to DNA circles that template localized rolling circle amplification reactions. The requirement for dual recognition of the target proteins improves selectivity by ignoring any cross-reactivity not shared by the antibodies, and it allows detection of protein-protein interactions and post-translational modifications. We herein describe an improved design of the PLA probes –UnFold probes – where all elements required for formation of circular DNA strands are incorporated in the probes. Premature interactions between the UnFold probes are prevented by including an enzymatic “unfolding” step in the detection reactions. This allows DNA circles to form by pairs of reagents only after excess reagents have been removed. We demonstrate the performance of UnFold probes for detection of protein-protein interactions and post-translational modifications in fixed cells and tissues, revealing considerably more efficient signal generation. We also apply the UnFold probes to detect IL-6 in solution phase after capture on solid supports, demonstrating increased sensitivity over both normal sandwich enzyme-linked immunosorbent assays and conventional PLA assays.
Recurrence of task-related electroencephalographic activity during post-training quiet rest and sleep
Authors: Murphy Michael , Stickgold Robert , Parr Mittie Elaine , Callahan Cameron , Wamsley Erin J.
Published: March 2018

Offline reactivation of task-related neural activity has been demonstrated in animals but is difficult to directly observe in humans. We sought to identify potential electroencephalographic (EEG) markers of offline memory processing in human subjects by identifying a set of characteristic EEG topographies (“microstates”) that occurred as subjects learned to navigate a virtual maze. We hypothesized that these task-related microstates would appear during post-task periods of rest and sleep. In agreement with this hypothesis, we found that one task-related microstate was increased in post-training rest and sleep compared to baseline rest, selectively for subjects who actively learned the maze, and not in subjects performing a non-learning control task. Source modeling showed that this microstate was produced by activity in temporal and parietal networks, which are known to be involved in spatial navigation. For subjects who napped after training, the increase in this task-related microstate predicted the magnitude of subsequent change in performance. Our findings demonstrate that task-related EEG patterns re-emerge during post-training rest and sleep.
LentiPro26: novel stable cell lines for constitutive lentiviral vector production
Authors: Tomás H. A. , Rodrigues A. F. , Carrondo M. J. T. , Coroadinha A. S.
Published: March 2018

Lentiviral vectors (LVs) are excellent tools to promote gene transfer and stable gene expression. Their potential has been already demonstrated in gene therapy clinical trials for the treatment of diverse disorders. For large scale LV production, a stable producer system is desirable since it allows scalable and cost-effective viral productions, with increased reproducibility and safety. However, the development of stable systems has been challenging and time-consuming, being the selection of cells presenting high expression levels of Gag-Pro-Pol polyprotein and the cytotoxicity associated with some viral components, the main limitations. Hereby is described the establishment of a new LV producer cell line using a mutated less active viral protease to overcome potential cytotoxic limitations. The stable transfection of bicistronic expression cassettes with re-initiation of the translation mechanism enabled the generation of LentiPro26 packaging populations supporting high titers. Additionally, by skipping intermediate clone screening steps and performing only one final clone screening, it was possible to save time and generate LentiPro26-A59 cell line, that constitutively produces titers above 106 TU.mL−1.day−1, in less than six months. This work constitutes a step forward towards the development of improved LV producer cell lines, aiming to efficiently supply the clinical expanding gene therapy applications.
Structural insights into the RNA methyltransferase domain of METTL16
Authors: Ruszkowska Agnieszka , Ruszkowski Milosz , Dauter Zbigniew , Brown Jessica A.
Published: March 2018

N6-methyladenosine (m6A) is an abundant modification in messenger RNA and noncoding RNAs that affects RNA metabolism. Methyltransferase-like protein 16 (METTL16) is a recently confirmed m6A RNA methyltransferase that methylates U6 spliceosomal RNA and interacts with the 3′-terminal RNA triple helix of MALAT1 (metastasis-associated lung adenocarcinoma transcript 1). Here, we present two X-ray crystal structures of the N-terminal methyltransferase domain (residues 1–291) of human METTL16 (METTL16_291): an apo structure at 1.9 Å resolution and a post-catalyticS-adenosylhomocysteine-bound complex at 2.1 Å resolution. The structures revealed a highly conserved Rossmann fold that is characteristic of Class IS-adenosylmethionine-dependent methyltransferases and a large, positively charged groove. This groove likely represents the RNA-binding site and it includes structural elements unique to METTL16. In-depth analysis of the active site led to a model of the methyl transfer reaction catalyzed by METTL16. In contrast to the major m6A methyltransferase heterodimer METTL3/METTL14, full-length METTL16 forms a homodimer and METTL16_291 exists as a monomer based on size-exclusion chromatography. A native gel-shift assay shows that METTL16 binds to the MALAT1 RNA triple helix, but monomeric METTL16_291 does not. Our results provide insights into the molecular structure of METTL16, which is distinct from METTL3/METTL14.
Computational repositioning and preclinical validation of mifepristone for human vestibular schwannoma
Authors: Sagers Jessica E. , Brown Adam S. , Vasilijic Sasa , Lewis Rebecca M. , Sahin Mehmet I. , Landegger Lukas D. , Perlis Roy H. , Kohane Isaac S. , Welling D. Bradley , Patel Chirag J. , Stankovic Konstantina M.
Published: March 2018

The computational repositioning of existing drugs represents an appealing avenue for identifying effective compounds to treat diseases with no FDA-approved pharmacotherapies. Here we present the largest meta-analysis to date of differential gene expression in human vestibular schwannoma (VS), a debilitating intracranial tumor, and use these data to inform the first application of algorithm-based drug repositioning for this tumor class. We apply an open-source computational drug repositioning platform to gene expression data from 80 patient tumors and identify eight promising FDA-approved drugs with potential for repurposing in VS. Of these eight, mifepristone, a progesterone and glucocorticoid receptor antagonist, consistently and adversely affects the morphology, metabolic activity, and proliferation of primary human VS cells and HEI-193 human schwannoma cells. Mifepristone treatment reduces VS cell viability more significantly than cells derived from patient meningiomas, while healthy human Schwann cells remain unaffected. Our data recommend a Phase II clinical trial of mifepristone in VS.
Dynamic analysis of the interactions between Si/SiO2 quantum dots and biomolecules for improving applications based on nano-bio interfaces
Authors: Stan Miruna Silvia , Cinteza Ludmila Otilia , Petrescu Livia , Mernea Maria Alexandra , Calborean Octavian , Mihailescu Dan Florin , Sima Cornelia , Dinischiotu Anca
Published: March 2018

Due to their outstanding properties, quantum dots (QDs) received a growing interest in the biomedical field, but it is of major importance to investigate and to understand their interaction with the biomolecules. We examined the stability of silicon QDs and the time evolution of QDs – protein corona formation in various biological media (bovine serum albumin, cell culture medium without or supplemented with 10% fetal bovine serum-FBS). Changes in the secondary structure of BSA were also investigated over time. Hydrodynamic size and zeta potential measurements showed an evolution in time indicating the nanoparticle-protein interaction. The protein corona formation was also dependent on time, albumin adsorption reaching the peak level after 1 hour. The silicon QDs adsorbed an important amount of FBS proteins from the first 5 minutes of incubation that was maintained for the next 8 hours, and diminished afterwards. Under protein-free conditions the QDs induced cell membrane damage in a time-dependent manner, however the presence of serum proteins attenuated their hemolytic activity and maintained the integrity of phosphatidylcholine layer. This study provides useful insights regarding the dynamics of BSA adsorption and interaction of silicon QDs with proteins and lipids, in order to understand the role of QDs biocorona.
Morphology of Immunomodulation in Breast Cancer Tumor Draining Lymph Nodes Depends on Stage and Intrinsic Subtype
Authors: Seidl Maximilian , Bader Moritz , Vaihinger Astrid , Wellner Ulrich F. , Todorova Rumyana , Herde Bettina , Schrenk Klaudia , Maurer Jochen , Schilling Oliver , Erbes Thalia , Fisch Paul , Pfeiffer Jens , Hoffmann Linda , Franke Kai , Werner Martin , Bronsert Peter
Published: March 2018

Cancer research of immune-modulating mechanisms mainly addresses the role of tumor-infiltrating immune cells. Mechanisms modulating the adaptive immune system at the primary activation site – the draining lymph node (LN) – are less investigated. Here we present tumor-caused histomorphological changes in tumor draining LNs of breast cancer patients, dependent on the localization (sentinel LN vs. non-sentinel LN), the tumor size, the intrinsic subtype and nodal metastatic status. The quantitative morphological study was conducted in breast cancer patients with at least one sentinel LN and no neoadjuvant therapy. All LNs were annotated considering to their topographical location, stained for IgD/H&E, digitized and quantitatively analyzed. In 206 patients, 394 sentinels and 940 non-sentinel LNs were categorized, comprising 40758 follicles and 7074 germinal centers. Subtype specific immunomorphological patterns were detectable: Follicular density was higher in LNs of Her2 enriched hormone receptor positive and triple-negative breast cancers whereas hormone receptor positive breast cancers showed more macrophage infiltrations in the LN cortex. Follicles are rounder in metastatic LNs and non-sentinel LNs. The identified immunomorphological changes reflect different underlying immunomodulations taking place in the tumor-draining LNs and should therefore be considered as possible prognostic and predictive markers for LN metastasis and therapy associated immunomodulation.
The sudden death and sudden birth of quantum discord
Authors: Xia Wei , Hou Jin-Xing , Wang Xiao-Hui , Liu Si-Yuan
Published: March 2018

The interaction of quantum system and its environment brings out abundant quantum phenomenons. The sudden death of quantum resources, including entanglement, quantum discord and coherence, have been studied from the perspective of quantum breaking channels (QBC). QBC of quantum resources reveal the common features of quantum resources. The definition of QBC implies the relationship between quantum resources. However, sudden death of quantum resources can also appear under some other quantum channels. We consider the dynamics of Bell-diagonal states under a stochastic dephasing noise along the z-direction, and the sudden death and sudden birth of quantum discord are investigated. Next we explain this phenomenon from the geometric structure of quantum discord. According to the above results, the states with sudden death and sudden birth can be filtered in three-parameter space. Then we provide two necessary conditions to judge which kind of noise channels can make Bell-diagonal states sudden death and sudden birth. Moreover, the relation between quantum discord and coherence indicates that the sudden death and sudden birth of quantum discord implies the sudden death and sudden birth of coherence in an optimal basis.
Altered DNA repair; an early pathogenic pathway in Alzheimer’s disease and obesity
Authors: Yu Hao , Harrison Fiona Edith , Xia Fen
Published: March 2018

Unrepaired DNA double-strand breaks (DSBs) are lethal. The present study compared the extent of DSBs, neuronal apoptosis, and status of two major DSB repair pathways - homologous combinational repair (HR) and nonhomologous end-joining (NHEJ) - in hippocampus of 5–6 month and 16–18 month-old wild-type and APP/PSEN1 mice fed control diet or high fat diet (60% fat from lard). We performed immunohistochemical staining and quantification for nuclear foci formation of γ-H2AX for DSBs, RAD51, and 53BP1, which represent the functional status of HR and NHEJ, respectively. Increased γ-H2AX and caspase-3 staining indicated greater DSBs and associated neuronal apoptosis in APP/PSEN1 mice at both ages studied. RAD51-positive foci were fewer in APP/PSEN1 indicating that HR processes may be diminished in these mice, although NHEJ (53BP1 staining) appeared unchanged. High fat diet in young wild-type mice led to similar changes to those observed in APP/PSEN1 mice (γ-H2AX and caspase-3 staining, and fewer RAD51-positive foci). Overall, these data suggest that APP/PSEN1- and high fat diet-associated early accumulation of DSBs and neuronal cell death, resulted at least in part, from inhibition of HR, one of the major DSB repair pathways.
Dynamic interaction of local and transhemispheric networks is necessary for progressive intensification of hippocampal seizures
Authors: Berglind Fredrik , Andersson My , Kokaia Merab
Published: March 2018

The detailed mechanisms of progressive intensification of seizures often occurring in epilepsy are not well understood. Animal models of kindling, with progressive intensification of stimulation-induced seizures, have been previously used to investigate alterations in neuronal networks, but has been obscured by limited recording capabilities during electrical stimulations. Remote networks in kindling have been studied by physical deletions of the connected structures or pathways, inevitably leading to structural reorganisations and related adverse effects. We used optogenetics to circumvent the above-mentioned problems inherent to electrical kindling, and chemogenetics to temporarily inhibit rather than ablate the remote interconnected networks. Progressively intensifying afterdischarges (ADs) were induced by repetitive photoactivation of principal neurons in the hippocampus of anaesthetized transgenic mice expressing ChR2. This allowed, during the stimulation, to reveal dynamic increases in local field potentials (LFPs), which coincided with the start of AD intensification. Furthermore, chemogenetic functional inhibition of contralateral hippocampal neurons via hM4D(Gi) receptors abrogated AD progression. These findings demonstrate that, during repeated activation, local circuits undergo acute plastic changes with appearance of additional network discharges (LFPs), leading to transhemispheric recruitment of contralateral dentate gyrus, which seems to be necessary for progressive intensification of ADs.
Bilateral geochemical asymmetry in the Karoo large igneous province
Authors: Luttinen Arto V.
Published: March 2018

In the Karoo large igneous province, the geochemical assessment of mantle source variability and structure is hampered by probable crustal contamination overprinting of compositionally diverse flood basalts. Mantle source characteristics have been defined only for exceptional, primitive rock types. Here I use a compiled dataset for over 800 samples to demonstrate that the abundance of Nb relative to Zr, Ti, and Y provides a useful geochemical tracer of mantle sources for variably contaminated rock types of the Karoo province. Variations in the relative abundance of Nb reveal emplacement of distinctive, Nb-undepleted and Nb-depleted magmas in the North Karoo and South Karoo sub-provinces, respectively, and clarify correlation between flood basalts and previously proposed mantle source components. Judging from plate tectonic reconstructions and the compositions of plausible mantle source components, the geochemical bilateral asymmetry in Karoo may reflect tapping of contrasting plume and upper mantle reservoirs in the two sub-provinces.
Cementoin–SLPI fusion protein binds to human monocytes and epithelial cells and shows higher biological activity than SLPI
Authors: Maffía Paulo C. , Guerrieri Diego , Villalonga Ximena , Caro Fiorella , Gómez Sonia , Tateosian Nancy , Bogado Betiana P. , Sánchez Mercedes L. , Ambrosi Nella , Chuluyan Eduardo
Published: March 2018

Secretory Leukocyte Proteinase Inhibitor (SLPI) is an antiinflammatory peptide that blocks the activity of serine proteases, primarily the neutrophil elastase. In an attempt to direct the activity of SLPI on inflamed sites, a chimera consisting of the transglutaminase II substrate domain of trappin 2 (cementoin), and the mature SLPI protein was constructed. Cell attachment and biological activity were compared between SLPI and this chimera. By using whole cell ELISA, fluorescence microscopy and flow cytometry assays we observed that the cementoin-SLPI fusion protein (FP) but not SLPI attached to a human lung epithelial cell line and monocytes. A maximum attachment was achieved 15 min after FP was added to the cell cultures. In an elastase activity assay, we observed that FP retained its antiprotease activity and that at equimolar amount of proteins, FP was more efficient than SLPI in the inhibition. Both, FP and SLPI inhibits IL-2-induced lymphocyte proliferation, however, lower amounts of FP were required to achieve this inhibition. Furthermore, FP binds to mycobacteria and maintained the bactericidal activity observed for SLPI. Overall, these results show that this new chimera is able to attach to the cell surfaces retaining and improving some biological activities described for SLPI.
Morphometric analysis of spread platelets identifies integrin αIIbβ3-specific contractile phenotype
Authors: Lickert Sebastian , Sorrentino Simona , Studt Jan-Dirk , Medalia Ohad , Vogel Viola , Schoen Ingmar
Published: March 2018

Haemostatic platelet function is intimately linked to cellular mechanics and cytoskeletal morphology. How cytoskeletal reorganizations give rise to a highly contractile phenotype that is necessary for clot contraction remains poorly understood. To elucidate this process in vitro, we developed a morphometric screen to quantify the spatial organization of actin fibres and vinculin adhesion sites in single spread platelets. Platelets from healthy donors predominantly adopted a bipolar morphology on fibrinogen and fibronectin, whereas distinguishable, more isotropic phenotypes on collagen type I or laminin. Specific integrin αIIbβ3 inhibitors induced an isotropic cytoskeletal organization in a dose-dependent manner. The same trend was observed with decreasing matrix stiffness. Circular F-actin arrangements in platelets from a patient with type II Glanzmann thrombasthenia (GT) were consistent with the residual activity of a small number of αIIbβ3 integrins. Cytoskeletal morphologies in vitro thus inform about platelet adhesion receptor identity and functionality, and integrin αIIbβ3 mechanotransduction fundamentally determines the adoption of a bipolar phenotype associated with contraction. Super-resolution microscopy and electron microscopies further confirmed the stress fibre-like contractile actin architecture. For the first time, our assay allows the unbiased and quantitative assessment of platelet morphologies and could help to identify defective platelet behaviour contributing to elusive bleeding phenotypes.
Neurons in the Pigeon Nidopallium Caudolaterale Display Value-Related Activity
Authors: Dykes Madeline , Klarer Aylin , Porter Blake , Rose Jonas , Colombo Michael
Published: March 2018

We recorded from neurons in the nidopallium caudolaterale, the avian equivalent of the mammalian prefrontal cortex, in four birds. The birds were required to peck a stimulus that indicated the amount of reward they would receive (small or large) after a certain delay (short or long). We found that the activity of neurons in the nidopallium caudolaterale was modulated by the value of the reward that would be received based on the reward amount and the delay to reward. We found that value coding was most prominent during the presentation of the sample period, and less so during the delay period and during the presentation of the reward itself. Our findings support the view that activity in nidopallium caudolaterale reflects the encoding of the value of reward based on a combination of reward amount and delay to a reward.