bluuebunny/crossref_metadata_2025 huggingface dataset:
Repression of transcription factor AP-2 alpha by PPARγ reveals a novel transcriptional circuit in basal-squamous bladder cancer
Authors: Yamashita Hironobu , Kawasawa Yuka I. , Shuman Lauren , Zheng Zongyu , Tran Truc , Walter Vonn , Warrick Joshua I. , Chen Guoli , Al-Ahmadie Hikmat , Kaag Matthew , Wong Pak Kin , Raman Jay D. , DeGraff David J.
Published: November 2019

The discovery of bladder cancer transcriptional subtypes provides an opportunity to identify high risk patients, and tailor disease management. Recent studies suggest tumor heterogeneity contributes to regional differences in molecular subtype within the tumor, as well as during progression and following treatment. Nonetheless, the transcriptional drivers of the aggressive basal-squamous subtype remain unidentified. As PPARɣ has been repeatedly implicated in the luminal subtype of bladder cancer, we hypothesized inactivation of this transcriptional master regulator during progression results in increased expression of basal-squamous specific transcription factors (TFs) which act to drive aggressive behavior. We initiated a pharmacologic and RNA-seq-based screen to identify PPARɣ-repressed, basal-squamous specific TFs. Hierarchical clustering of RNA-seq data following treatment of three human bladder cancer cells with a PPARɣ agonist identified a number of TFs regulated by PPARɣ activation, several of which are implicated in urothelial and squamous differentiation. One PPARɣ-repressed TF implicated in squamous differentiation identified is Transcription Factor Activating Protein 2 alpha (TFAP2A). We show TFAP2A and its paralog TFAP2C are overexpressed in basal-squamous bladder cancer and in squamous areas of cystectomy samples, and that overexpression is associated with increased lymph node metastasis and distant recurrence, respectively. Biochemical analysis confirmed the ability of PPARɣ activation to repress TFAP2A, while PPARɣ antagonist and PPARɣ siRNA knockdown studies indicate the requirement of a functional receptor. In vivo tissue recombination studies show TFAP2A and TFAP2C promote tumor growth in line with the aggressive nature of basal-squamous bladder cancer. Our findings suggest PPARɣ inactivation, as well as TFAP2A and TFAP2C overexpression cooperate with other TFs to promote the basal-squamous transition during tumor progression.
Identification of novel genetic variants predisposing to familial oral squamous cell carcinomas
Authors: Huang Yaping , Zhao Jizhi , Mao Guogen , Lee Grace Sanghee , Zhang Jia , Bi Lijun , Gu Liya , Chang Zhijie , Valentino Joseph , Li Guo-Min
Published: November 2019

Oral squamous cell carcinoma (OSCC) is a common subtype of head and neck squamous cell carcinoma (HNSCC), but the pathogenesis underlying familial OSCCs is unknown. Here, we analyzed whole-genome sequences of a family with autosomal dominant expression of oral tongue cancer and identified proto-oncogenesVAV2andIQGAP1as the primary factors responsible for oral cancer in the family. These two genes are also frequently mutated in sporadic OSCCs and HNSCCs. Functional analysis revealed that the detrimental variants target tumorigenesis-associated pathways, thus confirming that these novel genetic variants help to establish a predisposition to familial OSCC.
Global alteration of T-lymphocyte metabolism by PD-L1 checkpoint involves a block of de novo nucleoside phosphate synthesis
Authors: Palaskas Nicolaos Jay , Garcia Jacob David , Shirazi Roksana , Shin Daniel Sanghoon , Puig-Saus Cristina , Braas Daniel , Ribas Antoni , Graeber Thomas Glen
Published: November 2019

Metabolic obstacles of the tumor microenvironment remain a challenge to T-cell-mediated cancer immunotherapies. To better understand the interplay of immune checkpoint signaling and immune metabolism, this study developed and used an optimized metabolite extraction protocol for non-adherent primary human T-cells, to broadly profile in vitro metabolic changes effected by PD-1 signaling by mass spectrometry-based metabolomics and isotopomer analysis. Inhibitory signaling reduced aerobic glycolysis and glutaminolysis. A general scarcity across the panel of metabolites measured supported widespread metabolic regulation by PD-1. Glucose carbon fate analysis supported tricarboxylic acid cycle reliance on pyruvate carboxylation, catabolic-state fluxes into acetyl-CoA and succinyl-CoA, and a block in de novo nucleoside phosphate synthesis that was accompanied by reduced mTORC1 signaling. Nonetheless, exogenous administration of nucleosides was not sufficient to ameliorate proliferation of T-cells in the context of multiple metabolic insufficiencies due to PD-L1 treatment. Carbon fate analysis did not support the use of primarily glucose-derived carbons to fuel fatty acid beta oxidation, in contrast to reports on T-memory cells. These findings add to our understanding of metabolic dysregulation by PD-1 signaling and inform the effort to rationally develop metabolic interventions coupled with immune-checkpoint blockade for increased treatment efficacy.
Invariant patterns of clonal succession determine specific clinical features of myelodysplastic syndromes
Authors: Nagata Yasunobu , Makishima Hideki , Kerr Cassandra M. , Przychodzen Bartlomiej P. , Aly Mai , Goyal Abhinav , Awada Hassan , Asad Mohammad Fahad , Kuzmanovic Teodora , Suzuki Hiromichi , Yoshizato Tetsuichi , Yoshida Kenichi , Chiba Kenichi , Tanaka Hiroko , Shiraishi Yuichi , Miyano Satoru , Mukherjee Sudipto , LaFramboise Thomas , Nazha Aziz , Sekeres Mikkael A. , Radivoyevitch Tomas , Haferlach Torsten , Ogawa Seishi , Maciejewski Jaroslaw P.
Published: November 2019

Myelodysplastic syndromes (MDS) arise in older adults through stepwise acquisitions of multiple somatic mutations. Here, analyzing 1809 MDS patients, we infer clonal architecture by using a stringent, the single-cell sequencing validated PyClone bioanalytic pipeline, and assess the position of the mutations within the clonal architecture. All 3,971 mutations are grouped based on their rank in the deduced clonal hierarchy (dominant and secondary). We evaluated how they affect the resultant morphology, progression, survival and response to therapies. Mutations of SF3B1, U2AF1, and TP53 are more likely to be dominant, those of ASXL1, CBL, and KRAS are secondary. Among distinct combinations of dominant/secondary mutations we identified 37 significant relationships, of which 12 affect clinical phenotypes, 5 cooperatively associate with poor prognosis. They also predict response to hypomethylating therapies. The clonal hierarchy has distinct ranking and the resultant invariant combinations of dominant/secondary mutations yield novel insights into the specific clinical phenotype of MDS.
Digit-tracking as a new tactile interface for visual perception analysis
Authors: Lio Guillaume , Fadda Roberta , Doneddu Giuseppe , Duhamel Jean‐René , Sirigu Angela
Published: November 2019

Eye‐tracking is a valuable tool in cognitive science for measuring how visual processing resources are allocated during scene exploration. However, eye-tracking technology is largely confined to laboratory‐based settings, making it difficult to apply to large-scale studies. Here, we introduce a biologically‐inspired solution that involves presenting, on a touch‐sensitive interface, a Gaussian‐blurred image that is locally unblurred by sliding a finger over the display. Thus, the user’s finger movements provide a proxy for their eye movements and attention. We validated the method by showing strong correlations between attention maps obtained using finger-tracking vs. conventional optical eye‐tracking. Using neural networks trained to predict empirically‐derived attention maps, we established that identical high‐level features hierarchically drive explorations with either method. Finally, the diagnostic value of digit‐tracking was tested in autistic and brain‐damaged patients. Rapid yet robust measures afforded by this method open the way to large scale applications in research and clinical settings.
The in vivo ISGylome links ISG15 to metabolic pathways and autophagy upon Listeria monocytogenes infection
Authors: Zhang Yifeng , Thery Fabien , Wu Nicholas C. , Luhmann Emma K. , Dussurget Olivier , Foecke Mariko , Bredow Clara , Jiménez-Fernández Daniel , Leandro Kevin , Beling Antje , Knobeloch Klaus-Peter , Impens Francis , Cossart Pascale , Radoshevich Lilliana
Published: November 2019

ISG15 is an interferon-stimulated, ubiquitin-like protein, with anti-viral and anti-bacterial activity. Here, we map the endogenous in vivo ISGylome in the liver followingListeria monocytogenesinfection by combining murine models of reduced or enhanced ISGylation with quantitative proteomics. Our method identifies 930 ISG15 sites in 434 proteins and also detects changes in the host ubiquitylome. The ISGylated targets are enriched in proteins which alter cellular metabolic processes, including upstream modulators of the catabolic and antibacterial pathway of autophagy. Computational analysis of substrate structures reveals that a number of ISG15 modifications occur at catalytic sites or dimerization interfaces of enzymes. Finally, we demonstrate that animals and cells with enhanced ISGylation have increased basal and infection-induced autophagy through the modification of mTOR, WIPI2, AMBRA1, and RAB7. Taken together, these findings ascribe a role of ISGylation to temporally reprogram organismal metabolism following infection through direct modification of a subset of enzymes in the liver.
Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence
Authors: Iranzo Jaime , Wolf Yuri I. , Koonin Eugene V. , Sela Itamar
Published: November 2019

Bacterial and archaeal evolution involve extensive gene gain and loss. Thus, phylogenetic trees of prokaryotes can be constructed both by traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we show here that terminal branches of gene trees are systematically compressed compared to those of genome trees. Thus, sequence evolution is delayed compared to genome evolution by gene gain and loss. The extent of this delay differs widely among bacteria and archaea. Mathematical modeling shows that the divergence delay can result from sequence homogenization by homologous recombination. The model explains how homologous recombination maintains the cohesiveness of the core genome of a species while allowing extensive gene gain and loss within the accessory genome. Once evolving genomes become isolated by barriers impeding homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation.
Zinc anode-compatible in-situ solid electrolyte interphase via cation solvation modulation
Authors: Qiu Huayu , Du Xiaofan , Zhao Jingwen , Wang Yantao , Ju Jiangwei , Chen Zheng , Hu Zhenglin , Yan Dongpeng , Zhou Xinhong , Cui Guanglei
Published: November 2019

The surface chemistry of solid electrolyte interphase is one of the critical factors that govern the cycling life of rechargeable batteries. However, this chemistry is less explored for zinc anodes, owing to their relatively high redox potential and limited choices in electrolyte. Here, we report the observation of a zinc fluoride-rich organic/inorganic hybrid solid electrolyte interphase on zinc anode, based on an acetamide-Zn(TFSI)2 eutectic electrolyte. A combination of experimental and modeling investigations reveals that the presence of anion-complexing zinc species with markedly lowered decomposition energies contributes to the in situ formation of an interphase. The as-protected anode enables reversible (~100% Coulombic efficiency) and dendrite-free zinc plating/stripping even at high areal capacities (>2.5 mAh cm‒2), endowed by the fast ion migration coupled with high mechanical strength of the protective interphase. With this interphasial design the assembled zinc batteries exhibit excellent cycling stability with negligible capacity loss at both low and high rates.
Author Correction: Lineage tracing of acute myeloid leukemia reveals the impact of hypomethylating agents on chemoresistance selection
Authors: Caiado Francisco , Maia-Silva Diogo , Jardim Carolina , Schmolka Nina , Carvalho Tânia , Reforço Cláudia , Faria Rita , Kolundzija Branka , Simões André E. , Baubec Tuncay , Vakoc Christopher R. , da Silva Maria Gomes , Manz Markus G. , Schumacher Ton N. , Norell Håkan , Silva-Santos Bruno
Published: November 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Publisher Correction: An engineered human Fc domain that behaves like a pH-toggle switch for ultra-long circulation persistence
Authors: Lee Chang-Han , Kang Tae Hyun , Godon Ophélie , Watanabe Makiko , Delidakis George , Gillis Caitlin M. , Sterlin Delphine , Hardy David , Cogné Michel , Macdonald Lynn E. , Murphy Andrew J. , Tu Naxin , Lee Jiwon , McDaniel Jonathan R. , Makowski Emily , Tessier Peter M. , Meyer Aaron S. , Bruhns Pierre , Georgiou George
Published: November 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: C/EBPβ regulates delta-secretase expression and mediates pathogenesis in mouse models of Alzheimer’s disease
Authors: Wang Zhi-Hao , Gong Ke , Liu Xia , Zhang Zhentao , Sun Xiaoou , Wei Zheng Zachory , Yu Shan Ping , Manfredsson Fredric P. , Sandoval Ivette M. , Johnson Peter F. , Jia Jianping , Wang Jian-Zhi , Ye Keqiang
Published: November 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Multi-dimensional computational pipeline for large-scale deep screening of compound effect assessment: an in silico case study on ageing-related compounds
Authors: Gupta Vipul , Crudu Alina , Matsuoka Yukiko , Ghosh Samik , Rozot Roger , Marat Xavier , Jäger Sibylle , Kitano Hiroaki , Breton Lionel
Published: November 2019

Designing alternative approaches to efficiently screen chemicals on the efficacy landscape is a challenging yet indispensable task in the current compound profiling methods. Particularly, increasing regulatory restrictions underscore the need to develop advanced computational pipelines for efficacy assessment of chemical compounds as alternative means to reduce and/or replace in vivo experiments. Here, we present an innovative computational pipeline for large-scale assessment of chemical compounds by analysing and clustering chemical compounds on the basis of multiple dimensions—structural similarity, binding profiles and their network effects across pathways and molecular interaction maps—to generate testable hypotheses on the pharmacological landscapes as well as identify potential mechanisms of efficacy on phenomenological processes. Further, we elucidate the application of the pipeline on a screen of anti-ageing-related compounds to cluster the candidates based on their structure, docking profile and network effects on fundamental metabolic/molecular pathways associated with the cell vitality, highlighting emergent insights on compounds activities based on the multi-dimensional deep screen pipeline.
Monitored data on occupants’ presence and actions in an office building
Authors: Mahdavi Ardeshir , Berger Christiane , Tahmasebi Farhang , Schuss Matthias
Published: November 2019

Within a study, an open plan area and one closed office in a university building with a floor area of around 200 m2 were monitored. The present data set covers a period of one year (from 2013-01-01 to 2013-12-31). The collected data pertains to indoor environmental conditions (temperature, humidity) as well as plug loads and external factors (temperature, humidity, wind speed, and global irradiance) along with occupants’ presence and operation of windows and lights. The monitored data can be used for multiple purposes, including the development and validation of occupancy-related models.
X-ray Fokker–Planck equation for paraxial imaging
Authors: Paganin David M. , Morgan Kaye S.
Published: November 2019

The Fokker–Planck equation can be used in a partially-coherent imaging context to model the evolution of the intensity of a paraxial x-ray wave field with propagation. This forms a natural generalisation of the transport-of-intensity equation. The x-ray Fokker–Planck equation can simultaneously account for both propagation-based phase contrast, and the diffusive effects of sample-induced small-angle x-ray scattering, when forming an x-ray image of a thin sample. Two derivations are given for the Fokker–Planck equation associated with x-ray imaging, together with a Kramers–Moyal generalisation thereof. Both equations are underpinned by the concept of unresolved speckle due to unresolved sample micro-structure. These equations may be applied to the forward problem of modelling image formation in the presence of both coherent and diffusive energy transport. They may also be used to formulate associated inverse problems of retrieving the phase shifts due to a sample placed in an x-ray beam, together with the diffusive properties of the sample. The domain of applicability for the Fokker–Planck and Kramers–Moyal equations for paraxial imaging is at least as broad as that of the transport-of-intensity equation which they generalise, hence the technique is also expected to be useful for paraxial imaging using visible light, electrons and neutrons.
Effective pollination of Aeschynanthus acuminatus (Gesneriaceae) by generalist passerines, in sunbird-absent East Asia
Authors: Chen Kai-Hsiu , Lu Jing-Yi , Wang Chun-Neng
Published: November 2019

Aeschynanthus (Gesneriaceae), a genus comprising approximately 160 species in subtropical Southeast Asia, has red, tubular flowers, typical of a sunbird pollination syndrome. A. acuminatus, the species that is distributed extending to the northern edge of the genus, where the specialized nectarivorous sunbirds are absent, possesses reddish-green flowers and a wide-open corolla tube, flowering time shifts from summer to winter and the species achieves high fruiting success. This atypical flower led us to investigate the pollination biology of this species. Three species of generalist passerines, Grey-cheeked Fulvetta (Alcippe morrisonia, Sylviidae), White-eared Sibia (Heterophasia auricularis, Leiothrichidae) and Taiwan Yuhina (Yuhina brunneiceps, Zosteropidae), were recorded visiting A. acuminatus flowers. Pollination effectiveness was quantified via conspecific pollen presence on stigmas and natural fruit set. The significantly high natural fruit set (60%) and conspecific pollen transfer rate (94%) indicate high reproductive success facilitated by the accurate pollen placement on the birds. The existence of copious (61 µL) and highly diluted (7%) hexose-dominant nectar, together with a major reflectance peak of corolla lobe in the long-wavelength red color spectrum, is consistent with the pollination syndrome of generalist passerines. The high pollination effectiveness of A. acuminatus due to the recruitment of generalist passerines as pollinators, and the specializations of floral traits to match generalist bird pollination, appear crucial in the successful colonization on islands such as Taiwan that lack specialized bird pollinators.
PIPE-T: a new Galaxy tool for the analysis of RT-qPCR expression data
Authors: Zanardi Nicolò , Morini Martina , Tangaro Marco Antonio , Zambelli Federico , Bosco Maria Carla , Varesio Luigi , Eva Alessandra , Cangelosi Davide
Published: November 2019

Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an accurate and fast method to measure gene expression. Reproducibility of the analyses is the main limitation of RT-qPCR experiments. Galaxy is an open, web-based, genomic workbench for a reproducible, transparent, and accessible science. Our aim was developing a new Galaxy tool for the analysis of RT-qPCR expression data. Our tool was developed using Galaxy workbench version 19.01 and functions implemented in several R packages. We developed PIPE-T, a new Galaxy tool implementing a workflow, which offers several options for parsing, filtering, normalizing, imputing, and analyzing RT-qPCR data. PIPE-T requires two input files and returns seven output files. We tested the ability of PIPE-T to analyze RT-qPCR data on two example datasets available in the gene expression omnibus repository. In both cases, our tool successfully completed execution returning expected results. PIPE-T can be easily installed from the Galaxy main tool shed or from Docker. Source code, step-by-step instructions, and example files are available on GitHub to assist new users to install, execute, and test PIPE-T. PIPE-T is a new tool suitable for the reproducible, transparent, and accessible analysis of RT-qPCR expression data.
Growing a LaAlO3/SrTiO3 heterostructure on Ca2Nb3O10 nanosheets
Authors: Torren Alexander J. H. van der , Yuan Huiyu , Liao Zhaoliang , Elshof Johan E. ten , Koster Gertjan , Huijben Mark , Rijnders Guus J. H. M. , Hesselberth Marcel B. S. , Jobst Johannes , Molen Sense van der , Aarts Jan
Published: November 2019

The two-dimensional electron liquid which forms between the band insulators LaAlO3 (LAO) and SrTiO3 (STO) is a promising component for oxide electronics, but the requirement of using single crystal SrTiO3 substrates for the growth limits its applications in terms of device fabrication. It is therefore important to find ways to deposit these materials on other substrates, preferably Si, or Si-based, in order to facilitate integration with existing technology. Interesting candidates are micron-sized nanosheets of Ca2Nb3O10 which can be used as seed layers for perovskite materials on any substrate. We have used low-energy electron microscopy (LEEM) with in-situ pulsed laser deposition to study the subsequent growth of STO and LAO on such flakes which were deposited on Si. We can follow the morphology and crystallinity of the layers during growth, as well as fingerprint their electronic properties with angle resolved reflected electron spectroscopy. We find that STO layers, deposited on the nanosheets, can be made crystalline and flat; that LAO can be grown in a layer-by-layer fashion; and that the full heterostructure shows the signature of the formation of a conducting interface.
Association of Extracellular Vesicle Protein Cargo with Race and Clinical Markers of Mortality
Authors: Noren Hooten Nicole , McFarland Minna H. , Freeman David W. , Mode Nicolle A. , Ezike Ngozi , Zonderman Alan B. , Evans Michele K.
Published: November 2019

Differential mortality rates remain a significant health disparity in the United States, suggesting the need to investigate novel potential molecular markers associated with mortality. Extracellular vesicles (EVs), including exosomes, microvesicles and apoptotic bodies, are lipid-bound vesicles secreted by cells into the circulation. EVs mediate intercellular communication by shuttling functional signaling molecules as cargo. EV characteristics by race in the context of mortality risk factors have not been described. We isolated plasma EVs from a cross-sectional cohort of African Americans (AA) and whites and found no significant differences in EV size, distribution or concentration between race or by sex. However, EV cargo showed increased levels of phospho-p53, total p53, cleaved caspase 3, ERK1/2 and phospho-AKT in white individuals compared to AAs. phospho-IGF-1R levels were significantly higher in females compared to males. EV concentration was significantly associated with several clinical mortality risk factors: high-sensitivity C-reactive protein (hsCRP), homeostatic model assessment of insulin resistance (HOMA-IR), alkaline phosphatase, body mass index, waist circumference and pulse pressure. The association of EV proteins with mortality markers were dependent on race. These data suggest that EV cargo can differ by race and sex and is associated with mortality risk factors.
Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer
Authors: Orellana Luis H. , Hatt Janet K. , Iyer Ramsunder , Chourey Karuna , Hettich Robert L. , Spain Jim C. , Yang Wendy H. , Chee-Sanford Joanne C. , Sanford Robert A. , Löffler Frank E. , Konstantinidis Konstantinos T.
Published: November 2019

To what extent multi-omic techniques could reflect in situ microbial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO3− g−1 dry soil d−1) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4+ → NH2OH → NO → NO2- → NO3−) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteria Nitrosomonas and Nitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.
Fetuin exhibits a strong affinity for plutonium and may facilitate its accumulation in the skeleton
Authors: Vidaud Claude , Miccoli Laurent , Brulfert Florian , Aupiais Jean
Published: November 2019

After entering the blood, plutonium accumulates mainly in the liver and the bones. The mechanisms leading to its accumulation in bone are, however, completely unknown. We already know that another uptake pathway not involving the transferrin-mediated pathways is suspected to intervene in the case of the liver. Fetuin, a protein playing an important role in bone metabolism, is proposed as a potential transporter of Pu from serum to bone. For the first time, the binding constants of these two proteins (transferrin and fetuin) with tetravalent plutonium at physiological pH (pH 7.0) were determined by using capillary electrophoresis (CE) coupled with inductively coupled plasma mass spectrometry (ICP-MS). Their very close values (log10 KPuTf = 26.44 ± 0.28 and log10 KPuFet = 26.20 ± 0.24, respectively) suggest that transferrin and fetuin could compete to chelate plutonium, either in the blood or directly at bone surfaces in the case of Pu deposits. We performed competition reaction studies demonstrating that the relative distribution of Pu-protein complexes is fully explained by thermodynamics. Furthermore, considering the average concentrations of transferrin and fetuin in the blood, our calculation is consistent with the bio-distribution of Pu observed in humans.
Membrane directed expression in Escherichia coli of BBA57 and other virulence factors from the Lyme disease agent Borrelia burgdorferi
Authors: Robertson Karie E. , Truong Chloe D. , Craciunescu Felicia M. , Yang Jay-How , Chiu Po-Lin , Fromme Petra , Hansen Debra T.
Published: November 2019

Membrane-embedded proteins are critical to the establishment, survival and persistence in the host of the Lyme disease bacterium Borrelia burgdorferi (Bb), but to date, there are no solved structures of transmembrane proteins representing these attractive therapeutic targets. All available structures from the genus Borrelia represent proteins expressed without a membrane-targeting signal peptide, thus avoiding conserved pathways that modify, fold and assemble membrane protein complexes. Towards elucidating structure and function of these critical proteins, we directed translocation of eleven expression-optimized Bb virulence factors, including the signal sequence, to the Escherichia coli membrane, of which five, BBA57, HtrA, BB0238, BB0323, and DipA, were expressed with C-terminal His-tags. P66 was also expressed using the PelB signal sequence fused to maltose binding protein. Membrane-associated BBA57 lipoprotein was solubilized by non-ionic and zwitterionic detergents. We show BBA57 translocation to the outer membrane, purification at a level sufficient for structural studies, and evidence for an α-helical multimer. Previous studies showed multiple critical roles of BBA57 in transmission, joint arthritis, carditis, weakening immune responses, and regulating other Bb outer surface proteins. In describing the first purification of membrane-translocated BBA57, this work will support subsequent studies that reveal the precise mechanisms of this important Lyme disease virulence factor.
A Simulated Microgravity Environment Causes a Sustained Defect in Epithelial Barrier Function
Authors: Alvarez Rocio , Stork Cheryl A. , Sayoc-Becerra Anica , Marchelletta Ronald R. , Prisk G. Kim , McCole Declan F.
Published: November 2019

Intestinal epithelial cell (IEC) junctions constitute a robust barrier to invasion by viruses, bacteria and exposure to ingested agents. Previous studies showed that microgravity compromises the human immune system and increases enteropathogen virulence. However, the effects of microgravity on epithelial barrier function are poorly understood. The aims of this study were to identify if simulated microgravity alters intestinal epithelial barrier function (permeability), and susceptibility to barrier-disrupting agents. IECs (HT-29.cl19a) were cultured on microcarrier beads in simulated microgravity using a rotating wall vessel (RWV) for 18 days prior to seeding on semipermeable supports to measure ion flux (transepithelial electrical resistance (TER)) and FITC-dextran (FD4) permeability over 14 days. RWV cells showed delayed apical junction localization of the tight junction proteins, occludin and ZO-1. The alcohol metabolite, acetaldehyde, significantly decreased TER and reduced junctional ZO-1 localization, while increasing FD4 permeability in RWV cells compared with static, motion and flask control cells. In conclusion, simulated microgravity induced an underlying and sustained susceptibility to epithelial barrier disruption upon removal from the microgravity environment. This has implications for gastrointestinal homeostasis of astronauts in space, as well as their capability to withstand the effects of agents that compromise intestinal epithelial barrier function following return to Earth.
Radiosafe micro-computed tomography for longitudinal evaluation of murine disease models
Authors: Berghen Nathalie , Dekoster Kaat , Marien Eyra , Dabin Jérémie , Hillen Amy , Wouters Jens , Deferme Jasmine , Vosselman Thibault , Tiest Eline , Lox Marleen , Vanoirbeek Jeroen , De Langhe Ellen , Bogaerts Ria , Hoylaerts Marc , Lories Rik , Vande Velde Greetje
Published: November 2019

Implementation of in vivo high-resolution micro-computed tomography (µCT), a powerful tool for longitudinal analysis of murine lung disease models, is hampered by the lack of data on cumulative low-dose radiation effects on the investigated disease models. We aimed to measure radiation doses and effects of repeated µCT scans, to establish cumulative radiation levels and scan protocols without relevant toxicity. Lung metastasis, inflammation and fibrosis models and healthy mice were weekly scanned over one-month with µCT using high-resolution respiratory-gated 4D and expiration-weighted 3D protocols, comparing 5-times weekly scanned animals with controls. Radiation dose was measured by ionization chamber, optical fiberradioluminescence probe and thermoluminescent detectors in a mouse phantom. Dose effects were evaluated by in vivo µCT and bioluminescence imaging read-outs, gold standard endpoint evaluation and blood cell counts. Weekly exposure to 4D µCT, dose of 540–699 mGy/scan, did not alter lung metastatic load nor affected healthy mice. We found a disease-independent decrease in circulating blood platelets and lymphocytes after repeated 4D µCT. This effect was eliminated by optimizing a 3D protocol, reducing dose to 180–233 mGy/scan while maintaining equally high-quality images. We established µCT safety limits and protocols for weekly repeated whole-body acquisitions with proven safety for the overall health status, lung, disease process and host responses under investigation, including the radiosensitive blood cell compartment.
Physiological strength electric fields modulate human T cell activation and polarisation
Authors: Arnold Christina E. , Rajnicek Ann M. , Hoare Joseph I. , Pokharel Swechha Mainali , Mccaig Colin D. , Barker Robert N. , Wilson Heather M.
Published: November 2019

The factors and signals driving T cell activation and polarisation during immune responses have been studied mainly at the level of cells and chemical mediators. Here we describe a physical driver of these processes in the form of physiological-strength electric fields (EFs). EFs are generated at sites where epithelium is disrupted (e.g. wounded skin/bronchial epithelia) and where T cells frequently are present. Using live-cell imaging, we show human primary T cells migrate directionally to the cathode in low strength (50/150 mV/mm) EFs. Strikingly, we show for the first time that EFs significantly downregulate T cell activation following stimulation with antigen-activated APCs or anti-CD3/CD28 antibodies, as demonstrated by decreased IL-2 secretion and proliferation. These EF-induced functional changes were accompanied by a significant dampening of CD4+ T cell polarisation. Expression of critical markers of the Th17 lineage, RORγt and IL-17, and the Th17 polarisation mediator phospho-STAT3 were reduced significantly, while STAT1, ERK and c-Jun phosphorylation were comparatively unaffected suggesting STAT3 modulation by EFs as one mechanism driving effects. Overall, we identify electrical signals as important contributors to the co-ordination and regulation of human T cell functions, paving the way for a new research area into effects of naturally occurring and clinically-applied EFs in conditions where control of T cell activity is paramount.
Regulation of protein kinase Cδ Nuclear Import and Apoptosis by Mechanistic Target of Rapamycin Complex-1
Authors: Layoun Antonio , Goldberg Alexander A. , Baig Ayesha , Eng Mikaela , Attias Ortal , Nelson Kristoff , Carella Alexandra , Amberber Nahomi , Fielhaber Jill A. , Joung Kwang-Bo , Schmeing T. Martin , Han Yingshan , Downey Jeffrey , Divangahi Maziar , Roux Philippe P. , Kristof Arnold S.
Published: November 2019

Inactivation of the protein complex ‘mechanistic target of rapamycin complex 1’ (mTORC1) can increase the nuclear content of transcriptional regulators of metabolism and apoptosis. Previous studies established that nuclear import of signal transducer and activator of transcription-1 (STAT1) requires the mTORC1-associated adaptor karyopherin-α1 (KPNA1) when mTORC1 activity is reduced. However, the role of other mTORC1-interacting proteins in the complex, including ‘protein kinase C delta’ (PKCδ), have not been well characterized. In this study, we demonstrate that PKCδ, a STAT1 kinase, contains a functional ‘target of rapamycin signaling’ (TOS) motif that directs its interaction with mTORC1. Depletion of KPNA1 by RNAi prevented the nuclear import of PKCδ in cells exposed to the mTORC1 inhibitor rapamycin or amino acid restriction. Mutation of the TOS motif in PKCδ led to its loss of regulation by mTORC1 or karyopherin-α1, resulting in increased constitutive nuclear content. In cells expressing wild-type PKCδ, STAT1 activity and apoptosis were increased by rapamycin or interferon-β. Those expressing the PKCδ TOS mutant exhibited increased STAT1 activity and apoptosis; further enhancement by rapamycin or interferon-β, however, was lost. Therefore, the TOS motif in PKCδ is a novel structural mechanism by which mTORC1 prevents PKCδ and STAT1 nuclear import, and apoptosis.
Association between impulsivity traits and body mass index at the observational and genetic epidemiology level
Authors: Meyre David , Mohamed Sebat , Gray Joshua C. , Weafer Jessica , MacKillop James , de Wit Harriet
Published: November 2019

We investigated the association between impulsivity related traits and BMI at the observational and genetic epidemiology level in a cross-sectional population of healthy young American-European adults. We studied 998 students and university staff of European ancestry recruited from Chicago (Illinois) and Athens (Georgia). We measured 14 impulsivity variables using three broad categories: impulsive choice, action and personality. Weight and height of participants were measured by research assistants. The single-nucleotide polymorphism (SNP) rs3751812 in the fat mass and obesity-associated (FTO) gene was genotyped using the Illumina PsychArray BeadChip platform. Within the three broad domains of impulsivity, 4 parameters (delay discounting of rewards area under the curve and average of k indexes, Conner’s continuous performance test, and negative urgency) were associated with BMI. The FTO rs3751812 minor allele T was associated with higher BMI. Of the 14 impulsivity variables, rs3751812 T was associated with more premeditation and perseverance, before and after adjusting for BMI. The association between FTO rs3751812 and BMI adjusted for premeditation remained significant, but disappeared after adjusting for perseverance and for both perseverance and premeditation traits. Our observational and genetic data indicate a complex pattern of association between impulsive behaviors and BMI in healthy young American-European adults.
Permeability of the small intestinal mucus for physiologically relevant studies: Impact of mucus location and ex vivo treatment
Authors: Macierzanka Adam , Mackie Alan R. , Krupa Lukasz
Published: November 2019

The small intestinal mucus is a complex colloidal system that coats the intestinal mucosa. It allows passage on nutrients/pharmaceuticals from the gut lumen towards the epithelium, whilst preventing it from direct contact with luminal microorganisms. Mucus collected from intestinal tissue is often used in studies looking at inter-mucosal transport of food particulates, drug carriers, etc. However, detaching the highly hydrated native mucus from the tissue and storing it frozen prior to use may disrupt its physiological microstructure, and thus selective barrier properties. Multiple-particle tracking experiments showed that microstructural organisation of native, jejunal mucus depends on its spatial location in the intestinal mucosa. The inter-villus mucus was less heterogeneous than the mucus covering villi tips in the pig model used. Collecting mucus from tissue and subjecting it to freezing and thawing did not significantly affect (P > 0.05) its permeability to model, sub-micron sized particles, and the microviscosity profile of the mucus reflected the overall profiles recorded for the native mucus in the tissue. This implies the method of collecting and storing mucus is a reliable ex vivo treatment for the convenient planning and performing of mucus-permeability studies that aim to mimic physiological conditions of the transport of molecules/particles in native mucus.
GaAs epilayers grown on patterned (001) silicon substrates via suspended Ge layers
Authors: Ballabio Andrea , Bietti Sergio , Scaccabarozzi Andrea , Esposito Luca , Vichi Stefano , Fedorov Alexey , Vinattieri Anna , Mannucci Cosimo , Biccari Francesco , Nemcsis Akos , Toth Lajos , Miglio Leo , Gurioli Massimo , Isella Giovanni , Sanguinetti Stefano
Published: November 2019

We demonstrate the growth of low density anti-phase boundaries, crack-free GaAs epilayers, by Molecular Beam Epitaxy on silicon (001) substrates. The method relies on the deposition of thick GaAs on a suspended Ge buffer realized on top of deeply patterned Si substrates by means of a three-temperature procedure for the growth. This approach allows to suppress, at the same time, both threading dislocations and thermal strain in the epilayer and to remove anti-phase boundaries even in absence of substrate tilt. Photoluminescence measurements show the good uniformity and the high optical quality of AlGaAs/GaAs quantum well structures realized on top of such GaAs layer.
Compositional and mechanical properties of growing cortical bone tissue: a study of the human fibula
Authors: Lefèvre Emmanuelle , Farlay Delphine , Bala Yohann , Subtil Fabien , Wolfram Uwe , Rizzo Sébastien , Baron Cécile , Zysset Philippe , Pithioux Martine , Follet Hélène
Published: November 2019

Human cortical bone contains two types of tissue: osteonal and interstitial tissue. Growing bone is not well-known in terms of its intrinsic material properties. To date, distinctions between the mechanical properties of osteonal and interstitial regions have not been investigated in juvenile bone and compared to adult bone in a combined dataset. In this work, cortical bone samples obtained from fibulae of 13 juveniles patients (4 to 18 years old) during corrective surgery and from 17 adult donors (50 to 95 years old) were analyzed. Microindentation was used to assess the mechanical properties of the extracellular matrix, quantitative microradiography was used to measure the degree of bone mineralization (DMB), and Fourier transform infrared microspectroscopy was used to evaluate the physicochemical modifications of bone composition (organic versus mineral matrix). Juvenile and adult osteonal and interstitial regions were analyzed for DMB, crystallinity, mineral to organic matrix ratio, mineral maturity, collagen maturity, carbonation, indentation modulus, indicators of yield strain and tissue ductility using a mixed model. We found that the intrinsic properties of the juvenile bone were not all inferior to those of the adult bone. Mechanical properties were also differently explained in juvenile and adult groups. The study shows that different intrinsic properties should be used in case of juvenile bone investigation.
Stitchless support-free 3D printing of free-form micromechanical structures with feature size on-demand
Authors: Jonušauskas Linas , Baravykas Tomas , Andrijec Dovilė , Gadišauskas Tomas , Purlys Vytautas
Published: November 2019

Femtosecond laser based 3D nanolithography is a powerful tool for fabricating various functional micro- and nano-objects. In this work we present several advances needed to push it from the laboratory level use to the industrial production lines. First, linear stage and galvo-scanners synchronization is employed to produce stitch-free mm-sized structures. Furthermore, it is shown that by varying objective numerical apertures (NA) from 1.4 NA to 0.45 NA, voxel size can be tuned in the range from sub μm to tens of mm, resulting in structuring rates between 1809 μm3/s and 313312 μm3/s at 1 cm/s translation velocity achieved via simultaneous movement of linear stages and scanners. Discovered voxel/throughput scaling peculiarities show good agreement to ones acquired with numerical modeling. Furthermore, support-free 3D printing of complex structures is demonstrated. It is achieved by choosing pre-polymer that is in hard gel form during laser writing and acts as a dissolvable support during manufacturing. All of this is combined to fabricate micromechanical structures. First, 1:40 aspect ratio cantilever and 1.5 mm diameter single-helix spring capable of sustaining extreme deformations for prolonged movement times (up to 10000 deformation cycles) are shown. Then, free-movable highly articulated intertwined micromechanical spider and squids (overall size up to 10 mm) are printed and their movement is tested. The presented results are discussed in the broader sense, touching on the stitching/throughput dilemma and comparing it to the standard microstereolithography. It is shown where multiphoton polymerization can outpace standard stereolithography in terms of throughput while still maintaining superior resolution and higher degree of freedom in terms of printable geometries.
Widespread Sexual Dimorphism in the Transcriptome of Human Airway Epithelium in Response to Smoking
Authors: Yang Chen Xi , Shi Henry , Ding Irving , Milne Stephen , Hernandez Cordero Ana I. , Yang Cheng Wei Tony , Kim Edward Kyoo-Hoon , Hackett Tillie-Louise , Leung Janice , Sin Don D. , Obeidat Ma’en
Published: November 2019

Epidemiological studies have shown that female smokers are at higher risk of chronic obstructive pulmonary disease (COPD). Female patients have worse symptoms and health status and increased risk of exacerbations. We determined the differences in the transcriptome of the airway epithelium between males and females, as well the sex-by-smoking interaction. We processed public gene expression data of human airway epithelium into a discovery cohort of 211 subjects (never smokers n = 68; current smokers n = 143) and two replication cohorts of 104 subjects (21 never, 52 current, and 31 former smokers) and 238 subjects (99 current and 139 former smokers. We analyzed gene differential expression with smoking status, sex, and smoking-by-sex interaction and used network approaches for modules’ level analyses. We identified and replicated two differentially expressed modules between the sexes in response to smoking with genes located throughout the autosomes and not restricted to sex chromosomes. The two modules were enriched in autophagy (up-regulated in female smokers) and response to virus and type 1 interferon signaling pathways which were down-regulated in female smokers compared to males. The results offer insights into the molecular mechanisms of the sexually dimorphic effect of smoking, potentially enabling a precision medicine approach to smoking related lung diseases.
Marine fog inputs appear to increase methylmercury bioaccumulation in a coastal terrestrial food web
Authors: Weiss-Penzias Peter S. , Bank Michael S. , Clifford Deana L. , Torregrosa Alicia , Zheng Belle , Lin Wendy , Wilmers Christopher C.
Published: November 2019

Coastal marine atmospheric fog has recently been implicated as a potential source of ocean-derived monomethylmercury (MMHg) to coastal terrestrial ecosystems through the process of sea-to-land advection of foggy air masses followed by wet deposition. This study examined whether pumas (Puma concolor) in coastal central California, USA, and their associated food web, have elevated concentrations of MMHg, which could be indicative of their habitat being in a region that is regularly inundated with marine fog. We found that adult puma fur and fur-normalized whiskers in our marine fog-influenced study region had a mean (±SE) total Hg (THg) (a convenient surrogate for MMHg) concentration of 1544 ± 151 ng g−1(N = 94), which was three times higher (P < 0.01) than mean THg in comparable samples from inland areas of California (492 ± 119 ng g−1, N = 18). Pumas in California eat primarily black-tailed and/or mule deer (Odocoileus hemionus), and THg in deer fur from the two regions was also significantly different (coastal 28.1 ± 2.9, N = 55, vs. inland 15.5 ± 1.5 ng g−1, N = 40). We suggest that atmospheric deposition of MMHg through fog may be contributing to this pattern, as we also observed significantly higher MMHg concentrations in lace lichen (Ramalina menziesii), a deer food and a bioindicator of atmospheric deposition, at sites with the highest fog frequencies. At these ocean-facing sites, deer samples had significantly higher THg concentrations compared to those from more inland bay-facing sites. Our results suggest that fog-borne MMHg, while likely a small fraction of Hg in all atmospheric deposition, may contribute, disproportionately, to the bioaccumulation of Hg to levels that approach toxicological thresholds in at least one apex predator. As global mercury levels increase, coastal food webs may be at risk to the toxicological effects of increased methylmercury burdens.