bluuebunny/crossref_metadata_2025 huggingface dataset:
New Constraints on Thermal and Dielectric Properties of Lunar Regolith from LRO Diviner and CE‐2 Microwave Radiometer
Authors: Feng Jianqing , Siegler Matthew A. , Hayne Paul O.
Published: January 2020

We derive a new constraint on the thermal and dielectric properties of the lunar regolith layer by reconciling data from the Lunar Reconnaissance Orbiter (LRO) Diviner infrared radiometer and Chang'E‐2 (CE‐2) microwave radiometer (MRM). The bolometric Bond albedo of the lunar surface, which characterizes the ability of the lunar surface to reflect visible radiation, is a function of incidence angle. We determined the Bond albedo by using the Lunar Orbiter Laser Altimeter 1,064‐nm normal albedo and the surface temperature at noon as a function of latitude. The results suggest a modification to existing regolith thermal conductivity models based on a fit to the diurnal variation of Diviner data. Based on the thermal model, a 1‐D radiative transfer and dielectric properties model is developed to fit MRM data for the global Moon. With a new dielectric loss tangent equation for highland regolith applied, our model matches MRM data well at 19.35 and 37 GHz, which are generally accepted to be well calibrated. A global map of loss tangent of the Moon at these frequencies is also obtained by fitting the diurnal amplitude of microwave brightness temperature (TB) of each location on the Moon. We find that the loss tangent of highlands regolith has a slight frequency dependence and is larger than previous studies. We also identify a large discrepancy between our theoretical model and TB obtained by CE‐2 MRM at low frequencies, which is attributed to issues caused by contamination on calibration horn.
Planktic Foraminiferal Test Size and Weight Response to the Late Pliocene Environment
Authors: Todd C. L. , Schmidt D. N. , Robinson M. M. , De Schepper S.
Published: January 2020

Atmospheric carbon dioxide (pCO2atm) is impacting the ocean and marine organisms directly via changes in carbonate chemistry and indirectly via a range of changes in physical parameters most dominantly temperature. To assess potential impacts of climate change on carbonate production in the open ocean, we measured size and weight of planktic foraminifers during the late Pliocene atpCO2atmconcentrations comparable to today and global temperatures 2 to 3 °C warmer. Size of all foraminifers was measured at Atlantic Ocean Deep Sea Drilling Project (DSDP) Site 610, Ocean Drilling Program (ODP) Site 999, and Integrated Ocean Drilling Program (IODP) Site U1313. Test size was smaller during the Pliocene than in modern assemblages under the same environmental conditions. During the cold marine isotope stage (MIS) M2, size increased at Site 999, potentially linked to intensified stratification of the surface ocean in response to the closure of the Central American Seaway. At Site U1313, test size tracks the warming throughout the late Pliocene. Size‐normalized weight (SNW) ofGlobigerina bulloidesat Site U1313 decreased during warmer temperature intervals. SNW ofGlobigerinoides ruber(white) at Site 999 displays high‐frequency variability not correlated to temperature. Yet during the glacial period within MIS M2, test weight was higher during higher temperatures. Our results support studies in the modern ocean, which challenge the view that carbonate chemistry is the primary driver for calcification. To better understand processes driving changes in SNW, computer tomography was used to quantify calcite to volume ratios. During interglacial periods, lower calcite volume but higher test volume suggests less suitable conditions for calcification. As this signal is not evident in SNW, subtle changes in calcification might not be observed by the weight‐based method.
Cross-disorder genetic analyses implicate dopaminergic signaling as a biological link between Attention-Deficit/Hyperactivity Disorder and obesity measures
Authors: Mota Nina Roth , Poelmans Geert , Klein Marieke , Torrico Bàrbara , Fernàndez-Castillo Noèlia , Cormand Bru , Reif Andreas , Franke Barbara , Arias Vásquez Alejandro
Published: January 2020

Attention-Deficit/Hyperactivity Disorder (ADHD) and obesity are frequently comorbid, genetically correlated, and share brain substrates. The biological mechanisms driving this association are unclear, but candidate systems, like dopaminergic neurotransmission and circadian rhythm, have been suggested. Our aim was to identify the biological mechanisms underpinning the genetic link between ADHD and obesity measures and investigate associations of overlapping genes with brain volumes. We tested the association of dopaminergic and circadian rhythm gene sets with ADHD, body mass index (BMI), and obesity (using GWAS data of N = 53,293, N = 681,275, and N = 98,697, respectively). We then conducted genome-wide ADHD–BMI and ADHD–obesity gene-based meta-analyses, followed by pathway enrichment analyses. Finally, we tested the association of ADHD–BMI overlapping genes with brain volumes (primary GWAS data N = 10,720–10,928; replication data N = 9428). The dopaminergic gene set was associated with both ADHD (P = 5.81 × 10−3) and BMI (P = 1.63 × 10−5); the circadian rhythm was associated with BMI (P = 1.28 × 10−3). The genome-wide approach also implicated the dopaminergic system, as the Dopamine-DARPP32 Feedback in cAMP Signaling pathway was enriched in both ADHD–BMI and ADHD–obesity results. The ADHD–BMI overlapping genes were associated with putamen volume (P = 7.7 × 10−3; replication data P = 3.9 × 10−2)—a brain region with volumetric reductions in ADHD and BMI and linked to inhibitory control. Our findings suggest that dopaminergic neurotransmission, partially through DARPP-32-dependent signaling and involving the putamen, is a key player underlying the genetic overlap between ADHD and obesity measures. Uncovering shared etiological factors underlying the frequently observed ADHD–obesity comorbidity may have important implications in terms of prevention and/or efficient treatment of these conditions.
Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics
Authors: Hao Liping , Michaelsen Thomas Yssing , Singleton Caitlin Margaret , Dottorini Giulia , Kirkegaard Rasmus Hansen , Albertsen Mads , Nielsen Per Halkjær , Dueholm Morten Simonsen
Published: January 2020

Short-chain fatty acid (SCFA) degradation is an important process in methanogenic ecosystems, and is usually catalyzed by SCFA-oxidizing bacteria in syntrophy with methanogens. Current knowledge of this functional guild is mainly based on isolates or enrichment cultures, but these may not reflect the true diversity and in situ activities of the syntrophs predominating in full-scale systems. Here we obtained 182 medium to high quality metagenome-assembled genomes (MAGs) from the microbiome of two full-scale anaerobic digesters. The transcriptomic response of individual MAG was studied after stimulation with low concentrations of acetate, propionate, or butyrate, separately. The most pronounced response to butyrate was observed for two MAGs of the recently described genus Candidatus Phosphitivorax (phylum Desulfobacterota), expressing a butyrate beta-oxidation pathway. For propionate, the largest response was observed for an MAG of a novel genus in the family Pelotomaculaceae, transcribing a methylmalonyl-CoA pathway. All three species were common in anaerobic digesters at Danish wastewater treatment plants as shown by amplicon analysis, and this is the first time their syntrophic features involved in SCFA oxidation were revealed with transcriptomic evidence. Further, they also possessed unique genomic features undescribed in well-characterized syntrophs, including the metabolic pathways for phosphite oxidation, nitrite and sulfate reduction.
Mycobacterium bovis uses the ESX-1 Type VII secretion system to escape predation by the soil-dwelling amoeba Dictyostelium discoideum
Authors: Butler Rachel E , Smith Alex A , Mendum Tom A , Chandran Aneesh , Wu Huihai , Lefrançois Louise , Chambers Mark , Soldati Thierry , Stewart Graham R
Published: January 2020

Mycobacterium bovis is the causative agent of bovine tuberculosis and the predominant cause of zoonotic tuberculosis in people. Bovine tuberculosis occurs in farmed cattle but also in a variety of wild animals, which form a reservoir of infection. Although direct transmission of tuberculosis occurs between mammals, the low frequency of contact between different host species and abundant shedding of bacilli by infected animals suggests an infectious route via environmental contamination. Other intracellular pathogens that transmit via the environment deploy strategies to survive or exploit predation by environmental amoebae. To explore if M. bovis has this capability, we investigated its interactions with the soil and dung-dwelling amoeba, Dictyostelium discoideum. We demonstrated that M. bovis evades phagocytosis and destruction by D. discoideum and actively transits through the amoeba using the ESX-1 Type VII Secretion System as part of a programme of mechanisms, many of which have been co-opted as virulence factors in the mammalian host. This capacity of M. bovis to utilise an environmental stage between mammalian hosts may enhance its transmissibility. In addition, our data provide molecular evidence to support an evolutionary role for amoebae as training grounds for the pathogenic M. tuberculosis complex.
Organohalide-respiring Desulfoluna species isolated from marine environments
Authors: Peng Peng , Goris Tobias , Lu Yue , Nijsse Bart , Burrichter Anna , Schleheck David , Koehorst Jasper J , Liu Jie , Sipkema Detmer , Sinninghe Damste Jaap S , Stams Alfons J M , Häggblom Max M , Smidt Hauke , Atashgahi Siavash
Published: January 2020

The genus Desulfoluna comprises two anaerobic sulfate-reducing strains, D. spongiiphila AA1T and D. butyratoxydans MSL71T, of which only the former was shown to perform organohalide respiration (OHR). Here we isolated a third strain, designated D. spongiiphila strain DBB, from marine intertidal sediment using 1,4-dibromobenzene and sulfate as the electron acceptors and lactate as the electron donor. Each strain harbors three reductive dehalogenase gene clusters (rdhABC) and corrinoid biosynthesis genes in their genomes, and dehalogenated brominated but not chlorinated organohalogens. The Desulfoluna strains maintained OHR in the presence of 20 mM sulfate or 20 mM sulfide, which often negatively affect other organohalide-respiring bacteria. Strain DBB sustained OHR with 2% oxygen in the gas phase, in line with its genetic potential for reactive oxygen species detoxification. Reverse transcription-quantitative PCR revealed differential induction of rdhA genes in strain DBB in response to 1,4-dibromobenzene or 2,6-dibromophenol. Proteomic analysis confirmed expression of rdhA1 with 1,4-dibromobenzene, and revealed a partially shared electron transport chain from lactate to 1,4-dibromobenzene and sulfate, which may explain accelerated OHR during concurrent sulfate reduction. Versatility in using electron donors, de novo corrinoid biosynthesis, resistance to sulfate, sulfide and oxygen, and concurrent sulfate reduction and OHR may confer an advantage to marine Desulfoluna strains.
Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments
Authors: Hu Ang , Wang Jianjun , Sun Hang , Niu Bin , Si Guicai , Wang Jian , Yeh Chih-Fu , Zhu Xinxin , Lu Xiancai , Zhou Jizhong , Yang Yongping , Ren Minglei , Hu Yilun , Dong Hailiang , Zhang Gengxin
Published: January 2020

Although biodiversity and ecosystem functions are strongly shaped by contemporary environments, such as climate and local biotic and abiotic attributes, relatively little is known about how they depend on long-term geological processes. Here, along a 3000-m elevational gradient with tectonic faults on the Tibetan Plateau (that is, Galongla Mountain in Medog County, China), we study the joint effects of geological and contemporary environments on biological communities, such as the diversity and community composition of plants and soil bacteria, and ecosystem functions. We find that these biological communities and ecosystem functions generally show consistent elevational breakpoints at 2000–2800 m, which coincide with Indus-Yalu suture zone fault and are similar to the elevational breakpoints of soil bacteria on another mountain range 1000 km away. Mean annual temperature, soil pH and moisture are the primary contemporary determinants of biodiversity and ecosystem functions, which support previous findings. However, compared with the models excluding geological processes, inclusion of geological effects, such as parent rock and weathering, increases 67.9 and 35.9% of the explained variations in plant and bacterial communities, respectively. Such inclusion increases 27.6% of the explained variations in ecosystem functions. The geological processes thus provide additional links to ecosystem properties, which are prominent but show divergent effects on biodiversity and ecosystem functions: parent rock and weathering exert considerable direct effects on biodiversity, whereas indirectly influence ecosystem functions via interactions with biodiversity and contemporary environments. Thus, the integration of geological processes with environmental gradients could enhance our understanding of biodiversity and, ultimately, ecosystem functioning across different climatic zones.
Compensatory mutations modulate the competitiveness and dynamics of plasmid-mediated colistin resistance in Escherichia coli clones
Authors: Yang Qiu E , MacLean Craig , Papkou Andrei , Pritchard Manon , Powell Lydia , Thomas David , Andrey Diego O , Li Mei , Spiller Brad , Yang Wang , Walsh Timothy R
Published: January 2020

The emergence of mobile colistin resistance (mcr) threatens to undermine the clinical efficacy of the last antibiotic that can be used to treat serious infections caused by Gram-negative pathogens. Here we measure the fitness cost of a newly discovered MCR-3 using in vitro growth and competition assays. mcr-3 expression confers a lower fitness cost than mcr-1, as determined by competitive ability and cell viability. Consistent with these findings, plasmids carrying mcr-3 have higher stability than mcr-1 plasmids across a range of Escherichia coli strains. Crucially, mcr-3 plasmids can stably persist, even in the absence of colistin. Recent compensatory evolution has helped to offset the cost of mcr-3 expression, as demonstrated by the high fitness of mcr-3.5 as opposed to mcr-3.1. Reconstructing all of the possible evolutionary trajectories from mcr-3.1 to mcr-3.5 reveals a complex fitness landscape shaped by negative epistasis between compensatory and neutral mutations. Our findings highlight the importance of fitness costs and compensatory evolution in driving the dynamics and stability of mobile colistin resistance in bacterial populations, and they highlight the need to understand how processes (other than colistin use) impact mcr dynamics.
The roles of RNA in DNA double-strand break repair
Authors: Bader Aldo S. , Hawley Ben R. , Wilczynska Ania , Bushell Martin
Published: January 2020

Effective DNA repair is essential for cell survival: a failure to correctly repair damage leads to the accumulation of mutations and is the driving force for carcinogenesis. Multiple pathways have evolved to protect against both intrinsic and extrinsic genotoxic events, and recent developments have highlighted an unforeseen critical role for RNA in ensuring genome stability. It is currently unclear exactly how RNA molecules participate in the repair pathways, although many models have been proposed and it is possible that RNA acts in diverse ways to facilitate DNA repair. A number of well-documented DNA repair factors have been described to have RNA-binding capacities and, moreover, screens investigating DNA-damage repair mechanisms have identified RNA-binding proteins as a major group of novel factors involved in DNA repair. In this review, we integrate some of these datasets to identify commonalities that might highlight novel and interesting factors for future investigations. This emerging role for RNA opens up a new dimension in the field of DNA repair; we discuss its impact on our current understanding of DNA repair processes and consider how it might influence cancer progression.
B cell-intrinsic epigenetic modulation of antibody responses by dietary fiber-derived short-chain fatty acids
Authors: Sanchez Helia N. , Moroney Justin B. , Gan Huoqun , Shen Tian , Im John L. , Li Tianbao , Taylor Julia R. , Zan Hong , Casali Paolo
Published: January 2020

Short-chain fatty acids (SCFAs) butyrate and propionate are metabolites from dietary fiber's fermentation by gut microbiota that can affect differentiation or functions of T cells, macrophages and dendritic cells. We show here that at low doses these SCFAs directly impact B cell intrinsic functions to moderately enhance class-switch DNA recombination (CSR), while decreasing at higher doses over a broad physiological range, AID and Blimp1 expression, CSR, somatic hypermutation and plasma cell differentiation. In human and mouse B cells, butyrate and propionate decrease B cell Aicda and Prdm1 by upregulating select miRNAs that target Aicda and Prdm1 mRNA-3′UTRs through inhibition of histone deacetylation (HDAC) of those miRNA host genes. By acting as HDAC inhibitors, not as energy substrates or through GPR-engagement signaling in these B cell-intrinsic processes, these SCFAs impair intestinal and systemic T-dependent and T-independent antibody responses. Their epigenetic impact on B cells extends to inhibition of autoantibody production and autoimmunity in mouse lupus models.
Conjunction of triboelectric nanogenerator with induction coils as wireless power sources and self-powered wireless sensors
Authors: Zhang Chi , Chen Jinkai , Xuan Weipeng , Huang Shuyi , You Bin , Li Wenjun , Sun Lingling , Jin Hao , Wang Xiaozhi , Dong Shurong , Luo Jikui , Flewitt A. J. , Wang Zhong Lin
Published: January 2020

Here we demonstrate a magnetic resonance coupling based wireless triboelectric nanogenerator (TENG) and fully self-powered wireless sensors. By integrating a microswitch and an inductor with the TENG, the pulsed voltage output is converted into a sinusoidal voltage signal with a fixed frequency. This can be transmitted wirelessly from the transmit coil to the resonant-coupled receiver coil with an efficiency of 73% for a 5 cm distance between the two coils (10 cm diameter). Analytic models of the oscillating and coupled voltage signals for the wireless energy transfer are developed, showing excellent agreement with the experimental results. A TENG of 40 × 50 mm2 can wirelessly light up 70 LEDs or charge up a 15 μF capacitor to 12.5 V in ~90 s. The system is further utilized for two types of fully self-powered wireless chipless sensors with no microelectronic components. The technologies demonstrate an innovative strategy for a wireless ‘green’ power source and sensing.
In vivo functional analysis of non-conserved human lncRNAs associated with cardiometabolic traits
Authors: Ruan Xiangbo , Li Ping , Chen Yi , Shi Yu , Pirooznia Mehdi , Seifuddin Fayaz , Suemizu Hiroshi , Ohnishi Yasuyuki , Yoneda Nao , Nishiwaki Megumi , Shepherdson James , Suresh Abhilash , Singh Komudi , Ma Yonghe , Jiang Cheng-fei , Cao Haiming
Published: January 2020

Unlike protein-coding genes, the majority of human long non-coding RNAs (lncRNAs) are considered non-conserved. Although lncRNAs have been shown to function in diverse pathophysiological processes in mice, it remains largely unknown whether human lncRNAs have such in vivo functions. Here, we describe an integrated pipeline to define the in vivo function of non-conserved human lncRNAs. We first identify lncRNAs with high function potential using multiple indicators derived from human genetic data related to cardiometabolic traits, then define lncRNA’s function and specific target genes by integrating its correlated biological pathways in humans and co-regulated genes in a humanized mouse model. Finally, we demonstrate that the in vivo function of human-specific lncRNAs can be successfully examined in the humanized mouse model, and experimentally validate the predicted function of an obesity-associated lncRNA, LINC01018, in regulating the expression of genes in fatty acid oxidation in humanized livers through its interaction with RNA-binding protein HuR.
Retinoic acid degradation shapes zonal development of vestibular organs and sensitivity to transient linear accelerations
Authors: Ono Kazuya , Keller James , López Ramírez Omar , González Garrido Antonia , Zobeiri Omid A. , Chang Hui Ho Vanessa , Vijayakumar Sarath , Ayiotis Andrianna , Duester Gregg , Della Santina Charles C. , Jones Sherri M. , Cullen Kathleen E. , Eatock Ruth Anne , Wu Doris K.
Published: January 2020

Each vestibular sensory epithelium in the inner ear is divided morphologically and physiologically into two zones, called the striola and extrastriola in otolith organ maculae, and the central and peripheral zones in semicircular canal cristae. We found that formation of striolar/central zones during embryogenesis requires Cytochrome P450 26b1 (Cyp26b1)-mediated degradation of retinoic acid (RA). In Cyp26b1 conditional knockout mice, formation of striolar/central zones is compromised, such that they resemble extrastriolar/peripheral zones in multiple features. Mutants have deficient vestibular evoked potential (VsEP) responses to jerk stimuli, head tremor and deficits in balance beam tests that are consistent with abnormal vestibular input, but normal vestibulo-ocular reflexes and apparently normal motor performance during swimming. Thus, degradation of RA during embryogenesis is required for formation of highly specialized regions of the vestibular sensory epithelia with specific functions in detecting head motions.
Measuring local-directional resolution and local anisotropy in cryo-EM maps
Authors: Vilas Jose Luis , Tagare Hemant D. , Vargas Javier , Carazo Jose Maria , Sorzano Carlos Oscar S.
Published: January 2020

The introduction of local resolution has enormously helped the understanding of cryo-EM maps. Still, for any given pixel it is a global, aggregated value, that makes impossible the individual analysis of the contribution of the different projection directions. We introduce MonoDir, a fully automatic, parameter-free method that, starting only from the final cryo-EM map, decomposes local resolution into the different projection directions, providing a detailed level of analysis of the final map. Many applications of directional local resolution are possible, and we concentrate here on map quality and validation.
Identification of recurrent FHL2-GLI2 oncogenic fusion in sclerosing stromal tumors of the ovary
Authors: Kim Sarah H. , Da Cruz Paula Arnaud , Basili Thais , Dopeso Higinio , Bi Rui , Pareja Fresia , da Silva Edaise M. , Gularte-Mérida Rodrigo , Sun Zhen , Fujisawa Sho , Smith Caitlin G. , Ferrando Lorenzo , Martins Sebastião Ana Paula , Bykov Yonina , Li Anqi , Silveira Catarina , Ashley Charles W. , Stylianou Anthe , Selenica Pier , Samore Wesley R. , Jungbluth Achim A. , Zamarin Dmitriy , Abu-Rustum Nadeem R. , Helin Kristian , Soslow Robert A. , Reis-Filho Jorge S. , Oliva Esther , Weigelt Britta
Published: January 2020

Sclerosing stromal tumor (SST) of the ovary is a rare type of sex cord-stromal tumor (SCST), whose genetic underpinning is currently unknown. Here, using whole-exome, targeted capture and RNA-sequencing, we report recurrent FHL2-GLI2 fusion genes in 65% (17/26) of SSTs and other GLI2 rearrangements in additional 15% (4/26) SSTs, none of which are detected in other types of SCSTs (n = 48) or common cancer types (n = 9,950). The FHL2-GLI2 fusions result in transcriptomic activation of the Sonic Hedgehog (SHH) pathway in SSTs. Expression of the FHL2-GLI2 fusion in vitro leads to the acquisition of phenotypic characteristics of SSTs, increased proliferation, migration and colony formation, and SHH pathway activation. Targeted inhibition of the SHH pathway results in reversal of these oncogenic properties, indicating its role in the pathogenesis of SSTs. Our results demonstrate that the FHL2-GLI2 fusion is likely the oncogenic driver of SSTs, defining a genotypic–phenotypic correlation in ovarian neoplasms.
An artificial spiking afferent nerve based on Mott memristors for neurorobotics
Authors: Zhang Xumeng , Zhuo Ye , Luo Qing , Wu Zuheng , Midya Rivu , Wang Zhongrui , Song Wenhao , Wang Rui , Upadhyay Navnidhi K. , Fang Yilin , Kiani Fatemeh , Rao Mingyi , Yang Yang , Xia Qiangfei , Liu Qi , Liu Ming , Yang J. Joshua
Published: January 2020

Neuromorphic computing based on spikes offers great potential in highly efficient computing paradigms. Recently, several hardware implementations of spiking neural networks based on traditional complementary metal-oxide semiconductor technology or memristors have been developed. However, an interface (called an afferent nerve in biology) with the environment, which converts the analog signal from sensors into spikes in spiking neural networks, is yet to be demonstrated. Here we propose and experimentally demonstrate an artificial spiking afferent nerve based on highly reliable NbOx Mott memristors for the first time. The spiking frequency of the afferent nerve is proportional to the stimuli intensity before encountering noxiously high stimuli, and then starts to reduce the spiking frequency at an inflection point. Using this afferent nerve, we further build a power-free spiking mechanoreceptor system with a passive piezoelectric device as the tactile sensor. The experimental results indicate that our afferent nerve is promising for constructing self-aware neurorobotics in the future.
Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion
Authors: Gutierrez Jahir M. , Feizi Amir , Li Shangzhong , Kallehauge Thomas B. , Hefzi Hooman , Grav Lise M. , Ley Daniel , Baycin Hizal Deniz , Betenbaugh Michael J. , Voldborg Bjorn , Faustrup Kildegaard Helene , Min Lee Gyun , Palsson Bernhard O. , Nielsen Jens , Lewis Nathan E.
Published: January 2020

In mammalian cells, >25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on the secretion of different proteins. Unraveling its impact on diverse proteins is particularly important for biopharmaceutical production. Here we delineate the core secretory pathway functions and integrate them with genome-scale metabolic reconstructions of human, mouse, and Chinese hamster ovary cells. The resulting reconstructions enable the computation of energetic costs and machinery demands of each secreted protein. By integrating additional omics data, we find that highly secretory cells have adapted to reduce expression and secretion of other expensive host cell proteins. Furthermore, we predict metabolic costs and maximum productivities of biotherapeutic proteins and identify protein features that most significantly impact protein secretion. Finally, the model successfully predicts the increase in secretion of a monoclonal antibody after silencing a highly expressed selection marker. This work represents a knowledgebase of the mammalian secretory pathway that serves as a novel tool for systems biotechnology.
Forces during cellular uptake of viruses and nanoparticles at the ventral side
Authors: Wiegand Tina , Fratini Marta , Frey Felix , Yserentant Klaus , Liu Yang , Weber Eva , Galior Kornelia , Ohmes Julia , Braun Felix , Herten Dirk-Peter , Boulant Steeve , Schwarz Ulrich S. , Salaita Khalid , Cavalcanti-Adam E. Ada , Spatz Joachim P.
Published: January 2020

Many intracellular pathogens, such as mammalian reovirus, mimic extracellular matrix motifs to specifically interact with the host membrane. Whether and how cell-matrix interactions influence virus particle uptake is unknown, as it is usually studied from the dorsal side. Here we show that the forces exerted at the ventral side of adherent cells during reovirus uptake exceed the binding strength of biotin-neutravidin anchoring viruses to a biofunctionalized substrate. Analysis of virus dissociation kinetics using the Bell model revealed mean forces higher than 30 pN per virus, preferentially applied in the cell periphery where close matrix contacts form. Utilizing 100 nm-sized nanoparticles decorated with integrin adhesion motifs, we demonstrate that the uptake forces scale with the adhesion energy, while actin/myosin inhibitions strongly reduce the uptake frequency, but not uptake kinetics. We hypothesize that particle adhesion and the push by the substrate provide the main driving forces for uptake.
Sertoli cell ablation and replacement of the spermatogonial niche in mouse
Authors: Yokonishi Tetsuhiro , McKey Jennifer , Ide Shintaro , Capel Blanche
Published: January 2020

Spermatogonia, which produce sperm throughout the male lifetime, are regulated inside a niche composed of Sertoli cells, and other testis cell types. Defects in Sertoli cells often lead to infertility, but replacement of defective cells has been limited by the inability to deplete the existing population. Here, we use an FDA-approved non-toxic drug, benzalkonium chloride (BC), to deplete testis cell types in vivo. Four days after BC administration, Sertoli cells are preferentially depleted, and can be replaced to promote spermatogenesis from surviving (host) spermatogonia. Seven days after BC treatment, multiple cell types can be engrafted from fresh or cryopreserved testicular cells, leading to complete spermatogenesis from donor cells. These methods will be valuable for investigation of niche-supporting cell interactions, have the potential to lead to a therapy for idiopathic male infertility in the clinic, and could open the door to production of sperm from other species in the mouse.
Tissue-infiltrating macrophages mediate an exosome-based metabolic reprogramming upon DNA damage
Authors: Goulielmaki Evi , Ioannidou Anna , Tsekrekou Maria , Stratigi Kalliopi , Poutakidou Ioanna K. , Gkirtzimanaki Katerina , Aivaliotis Michalis , Evangelou Konstantinos , Topalis Pantelis , Altmüller Janine , Gorgoulis Vassilis G. , Chatzinikolaou Georgia , Garinis George A.
Published: January 2020

DNA damage and metabolic disorders are intimately linked with premature disease onset but the underlying mechanisms remain poorly understood. Here, we show that persistent DNA damage accumulation in tissue-infiltrating macrophages carrying an ERCC1-XPF DNA repair defect (Er1F/−) triggers Golgi dispersal, dilation of endoplasmic reticulum, autophagy and exosome biogenesis leading to the secretion of extracellular vesicles (EVs) in vivo and ex vivo. Macrophage-derived EVs accumulate in Er1F/− animal sera and are secreted in macrophage media after DNA damage. The Er1F/− EV cargo is taken up by recipient cells leading to an increase in insulin-independent glucose transporter levels, enhanced cellular glucose uptake, higher cellular oxygen consumption rate and greater tolerance to glucose challenge in mice. We find that high glucose in EV-targeted cells triggers pro-inflammatory stimuli via mTOR activation. This, in turn, establishes chronic inflammation and tissue pathology in mice with important ramifications for DNA repair-deficient, progeroid syndromes and aging.
Ultrafast photomechanical transduction through thermophoretic implosion
Authors: Kavokine Nikita , Zou Shuangyang , Liu Ruibin , Niguès Antoine , Zou Bingsuo , Bocquet Lydéric
Published: January 2020

Since the historical experiments of Crookes, the direct manipulation of matter by light has been both a challenge and a source of scientific debate. Here we show that laser illumination allows to displace a vial of nanoparticle solution over centimetre-scale distances. Cantilever-based force measurements show that the movement is due to millisecond-long force spikes, which are synchronised with a sound emission. We observe that the nanoparticles undergo negative thermophoresis, and ultrafast imaging reveals that the force spikes are followed by the explosive growth of a bubble in the solution. We propose a mechanism accounting for the propulsion based on a thermophoretic instability of the nanoparticle cloud, analogous to the Jeans’s instability that occurs in gravitational systems. Our experiments demonstrate a new type of laser propulsion and a remarkably violent actuation of soft matter, reminiscent of the strategy used by certain plants to propel their spores.
The accumulation profiles of terpene metabolites in three Muscat table grape cultivars through HS-SPME-GCMS
Authors: Sun Lei , Zhu Baoqing , Zhang Xuanyin , Wang Huiling , Yan Ailing , Zhang Guojun , Wang Xiaoyue , Xu Haiying
Published: January 2020

Aroma is an important parameter for table grapes and wines; terpenes are typical compounds in Muscat-type grape cultivars and can be easily perceived by humans because of their low olfactory threshold. Volatile terpenes contribute directly to the aroma character, while glycoside-bound terpenes are potential aromatic compounds and can be changed to their volatile forms via hydrolysis. With gas chromatography-mass spectrometry and a solid-phase microextraction method, an automatic data analysis platform was constructed; terpene compounds were identified and quantified from three table grape cultivars at three stages during berry development, and the raw data were deposited in MetaboLights. Terpene metabolite accumulation profiles are presented in this article for integrative analysis with the transcriptome data and phenotypic data to elucidate the important candidate genes and mechanism for terpene biosynthesis. Our method has applications in the identification and quantification of terpene compounds with very low or trace concentrations.
Application of an electrochemical LAMP-based assay for screening of HPV16/HPV18 infection in cervical samples
Authors: Anton Milan , Moranova Ludmila , Hrstka Roman , Bartosik Martin
Published: January 2020

Clinical evaluation of rapid, simple and inexpensive electrochemical assay using LAMP amplification for detection of two most oncogenic human papillomavirus types, HPV16 and HPV18.
A pilot study on the effects of DHA/EPA-enriched phospholipids on aerobic and anaerobic exercises in mice
Authors: Wang Cheng-Cheng , Ding Lin , Zhang Ling-Yu , Shi Hao-Hao , Xue Chang-Hu , Chi Nai-Qiu , Yanagita Teruyoshi , Zhang Tian-Tian , Wang Yu-Ming
Published: January 2020

DHA/EPA-PL andl-carnitine had significant effects on aerobic exercise, while astaxanthin improved anaerobic exercise. The possible mechanism involved carbohydrate and lipid metabolism, mitochondrial respiratory chain and tricarboxylic acid cycle.
Cuscuta chinensis flavonoids down-regulate the DNA methylation of the H19/Igf2 imprinted control region and estrogen receptor alpha promoter of the testis in bisphenol A exposed mouse offspring
Authors: Wei Yuanyuan , Han Chao , Li Shuying , Cui Yuqing , Bao Yongzhan , Shi Wanyu
Published: January 2020

Exposure to the emerging contaminant bisphenol A (BPA) is ubiquitous and associated with reproductive disorders.
Correction: Protective effects of hydroalcoholic extracts from an ancient apple variety ‘Mela Rosa dei Monti Sibillini’ against renal ischemia/reperfusion injury in rats
Authors: Yousefi-Manesh Hasan , Hemmati Sara , Shirooie Samira , Nabavi Seyed Mohammad , Bonakdar Azita Talebzadeh , Fayaznia Reza , Asgardoon Mohammad Hossein , Dehnavi Ali Zare , Ghafouri Mohammad , Nkuimi Wandjou Joice G. , Caprioli Giovanni , Sut Stefania , Maggi Filippo , Dall'Acqua Stefano
Published: January 2020

Correction for ‘Protective effects of hydroalcoholic extracts from an ancient apple variety ‘Mela Rosa dei Monti Sibillini’ against renal ischemia/reperfusion injury in rats’ by Hasan Yousefi-Manesh et al., Food Funct., 2019, 10, 7544–7552.
In vivodeep-tissue microscopy with UCNP/Janus-dendrimers as imaging probes: resolution at depth and feasibility of ratiometric sensing
Authors: Plunkett Shane , El Khatib Mirna , Şencan İkbal , Porter Jason E. , Kumar Anand T. N. , Collins Joshua E. , Sakadžić Sava , Vinogradov Sergei A.
Published: January 2020

UCNP/Janus-dendrimers enable high-resolution two-photon imaging in the brain up to 1 mm-deep under low-power CW excitation. However, ratiometric sensing using UCNPs and excitation energy transfer is strongly obstructed by tissue absorption.
A multi-dimensional and level-by-level assembly strategy for constructing flexible and sandwich-type nanoheterostructures for high-performance electromagnetic interference shielding
Authors: Wan Caichao , Jiao Yue , Li Xianjun , Tian Wenyan , Li Jian , Wu Yiqiang
Published: January 2020

A multi-dimensional and level-by-level assembly strategy is developed to construct free-standing and sandwich-type nanoheterostructures achieving an outstanding EMI shielding effectiveness of ∼50.6 dB in the X-band.
GexSi1−x virtual-layer enhanced ferromagnetism in self-assembled Mn0.06Ge0.94 quantum dots grown on Si wafers by molecular beam epitaxy
Authors: Wang Liming , Zhang Yichi , Liu Tao , Zhang Zhi , Hu Huiyong , Zou Jin , Jia Quanjie , Jiang Zuimin
Published: January 2020

The ferromagnetism of MnGe QDs grown on GeSi VS will markedly increase by increasing the Ge composition of GeSi VS.
Zn doped MAPbBr3 single crystal with advanced structural and optical stability achieved by strain compensation
Authors: Li Ruxue , Chen Shaoqing , Li Xia , Yin Guoxin , Gong Youpin , Yu Jiahao , Pang Guotao , Liu Jianxun , Liu Yanjun , Ni Zhenhua , Zhang Liyuan , Chen Rui , Wang Hsing-Lin
Published: January 2020

Strain compensation in a Zn doped MAPbBr3 single crystal under light illumination gives rise to improved photostability in terms of temperature and time to the benefit of photodetector.
Advances in amphiphilic hyperbranched copolymers with an aliphatic hyperbranched 2,2-bis(methylol)propionic acid-based polyester core
Authors: Zhang Xiaojin , Dai Yu , Dai Guofei
Published: January 2020

Amphiphilic hyperbranched copolymers with an aliphatic hyperbranched 2,2-bis(methylol)propionic acid-based polyester core were highlighted.
Epoxidized 1,4-polymyrcene
Authors: Matic Aleksandar , Hess Andreas , Schanzenbach Dirk , Schlaad Helmut
Published: January 2020

Epoxidized 1,4-polymyrcenes with different degrees of epoxidation (25–98%) were prepared and examined according to their chemical and thermal properties.
A dual-mode orthogonally tunable fluorescent system covering the whole white light region
Authors: Jin Wei-Hang , Lu Huan-Huan , Zhang Qi , Qu Da-Hui
Published: January 2020

This research revealed a distinct manipulation manner of a molecular emissive system, that is an orthogonally tunable dual-pathway mode, enabling a multi-color fluorescent system covering the whole white-light region.
Phenanthroline-strapped calix[4]pyrroles: anion receptors displaying affinity reversal as a function of solvent polarity
Authors: Heo Nam Jung , Oh Ju Hyun , Lee Jeong Tae , He Qing , Sessler Jonathan L. , Kim Sung Kuk
Published: January 2020

Calix[4]pyrroles1and2, diametrically strapped with a phenanthrolineviaester and amide linkages, respectively, have been synthesized as anion receptors.
Manometric real-time studies of the mechanochemical synthesis of zeolitic imidazolate frameworks
Authors: Brekalo Ivana , Yuan Wenbing , Mottillo Cristina , Lu Yuneng , Zhang Yuancheng , Casaban Jose , Holman K. Travis , James Stuart L. , Duarte Frédéric , Williams P. Andrew , Harris Kenneth D. M. , Friščić Tomislav
Published: January 2020

We demonstrate a simple method for real-time monitoring of mechanochemical synthesis of metal–organic frameworks, by measuring changes in pressure of gas produced in the reaction.
Surface chemistry dictates stability and oxidation state of supported single metal catalyst atoms
Authors: Alexopoulos Konstantinos , Vlachos Dionisios G.
Published: January 2020

Multi-response maps show that atomically dispersed iron on alumina provides relatively high activity and good stability in low temperature CO oxidation.
Interfacial engineering of a zinc blende/wurtzite homojunction photocatalyst through hybridization with a cobalt phosphide co-catalyst for enhanced visible-light-driven photocatalytic H2 evolution
Authors: Chew Yi-Hao , Ng Boon-Junn , Kong Xin Ying , Putri Lutfi Kurnianditia , Tang Jie-Yinn , Tan Lling-Lling , Chai Siang-Piao
Published: January 2020

The synergy of integrating homojunction and heterojunction structures in one composite was demonstrated by combining CoP and ZB/WZ homojunction-containing Zn0.5Cd0.5S which showed a 20-times enhancement in photocatalytic H2 evolution activity.
Hollow structure engineering of FeCo alloy nanoparticles electrospun in nitrogen-doped carbon enables high performance flexible all-solid-state zinc–air batteries
Authors: Ma Yuanyuan , Zang Wenjie , Sumboja Afriyanti , Mao Lu , Liu Ximeng , Tan Mingyan , Pennycook Stephen J. , Kou Zongkui , Liu Zhaolin , Li Xu , Wang John
Published: January 2020

Hollow structuring of active components is an effective strategy to improve the kinetics of oxygen electrode catalysts, arising from the increased the active surface area, the defects on the exposed surface, and the accessible active sites.
Catalytic depolymerization of Kraft lignin to produce liquid fuels via Ni–Sn metal oxide catalysts
Authors: Zhang Baikai , Li Wenzhi , Dou Xiaomeng , Wang Jindong , Jin Lele , Ogunbiyi Ajibola T. , Li Xiaosen
Published: January 2020

A novel non-noble metal catalyst was used to convert Kraft lignin to liquid fuels.
Conditional deletion of E11/Podoplanin in bone protects against ovariectomy-induced increases in osteoclast formation and activity
Authors: Staines Katherine A. , Hopkinson Mark , Dillon Scott , Stephen Louise A. , Fleming Robert , Sophocleous Antonia , Buttle David J. , Pitsillides Andrew A. , Farquharson Colin
Published: January 2020

E11/Podoplanin (Pdpn) is implicated in early osteocytogenesis and the formation of osteocyte dendrites. This dendritic network is critical for bone modelling/remodelling, through the production of receptor activator of nuclear factor κ B (RANK)-ligand (RANKL). Despite this, the role of Pdpn in the control of bone remodelling is yet to be established in vivo. Here we utilised bone-specific Pdpn conditional knockout mice (cKO) to examine the role of Pdpn in the bone loss associated with ovariectomy (OVX). MicroCT revealed that Pdpn deletion had no significant effect on OVX-induced changes in trabecular microarchitecture. Significant differences between genotypes were observed in the trabecular pattern factor (P<0.01) and structure model index (P<0.01). Phalloidin staining of F-actin revealed OVX to induce alterations in osteocyte morphology in both wild-type (WT) and cKO mice. Histological analysis revealed an expected significant increase in osteoclast number in WT mice (P<0.01, compared with sham). However, cKO mice were protected against such increases in osteoclast number. Consistent with this, serum levels of the bone resorption marker Ctx were significantly increased in WT mice following OVX (P<0.05), but were unmodified by OVX in cKO mice. Gene expression of the bone remodelling markers Rank, Rankl, Opg and Sost were unaffected by Pdpn deletion. Together, our data suggest that an intact osteocyte dendritic network is required for sustaining osteoclast formation and activity in the oestrogen-depleted state, through mechanisms potentially independent of RANKL expression. This work will enable a greater understanding of the role of osteocytes in bone loss induced by oestrogen deprivation.
Survival and prognostic factors of patients with esophageal fistula in advanced esophageal squamous cell carcinoma
Authors: Guan Xin , Liu Chao , Zhou Tianshuo , Ma Zhigang , Zhang Chunhui , Wang Bojun , Yao Yang , Fan Xiaona , Li Zhiwei , Zhang Yanqiao
Published: January 2020

The aim of the present study was to investigate the survival and prognostic factors of patients who were with advanced esophageal squamous cell carcinoma (ESCC) and developed an esophageal fistula. The data from 221 patients with advanced ESCC developed esophageal fistula from January 2008 to December 2017 at the Harbin Medical University Cancer Hospital was retrospectively analyzed. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated by the Cox proportional hazard models. The median survival time after a diagnosis of the esophageal fistula was calculated using the Kaplan–Meier method. We found that the pathogens infected by patients are common bacteria in nosocomial infection. Besides, the incidence rate of esophagomediastinal fistula was the highest (54.2%) in the lower third of the esophagus. Kaplan–Meier analysis revealed a median survival time of 11.00 months and a median post-fistula survival time of 3.63 months in patients who developed esophageal fistula in advanced esophageal cancer. In the univariate analysis, gender, therapies for ESCC before the development of fistula, type of esophageal fistula, treatment of esophageal fistula and hemoglobin (Hb) level were the factors with significant prognostic value. Gender, type of esophageal fistula and Hb level were identified as independent prognostic factors in further multivariate analysis. In summary, our study demonstrated that several factors are significantly related to patients with esophageal fistula and should be concerned about in clinical practice.
T-junction of ferroelectric wires
Authors: Carbone Luciano , Gaudiello Antonio , Hernández-Llanos Pedro
Published: January 2020

In this paper, starting from a non-convex and nonlocal 3D variational mathematical model for the electric polarization in a ferroelectric material, and using an asymptotic process based on dimensional reduction, we analyze junction phenomena for two orthogonal joined ferroelectric wires. Depending on the initial boundary conditions, we get several different limit problems, sometimes uncoupled. We point out that all the limit problems remain non-convex, but the nonlocality disappears.
Insulin-Dependence Predicts Surgical Complications and Hospital Admission following Knee Arthroscopy
Authors: Traven Sophia A. , Reeves Russell A. , Walton Zeke J. , Woolf Shane K. , Slone Harris S.
Published: January 2020

While prior studies have demonstrated that insulin-dependence is an independent risk factor for postoperative complications, morbidity, and mortality following spine and shoulder, hip, and knee arthroplasty, it has not been evaluated in the setting of knee arthroscopy. Therefore, the purpose of this study is to compare the risk of postoperative complications among patients with insulin-dependent diabetes mellitus and noninsulin-dependent diabetes mellitus (IDDM and NIDDM respectively) with the general population following knee arthroscopy. A retrospective analysis of the National Surgical Quality Improvement Program's database for the years 2005 to 2016 was conducted. Logistic regression analyses were used to assess the relationship between diabetic status and outcomes. Multivariate models were established to adjust for age, sex, body mass index, hypertension, congestive heart failure, chronic obstructive pulmonary disease, smoking status, American Society of Anesthesiology classification, and functional status. A total of 86,023 patients were identified. Patients with IDDM were at a much higher risk of surgical complications (odds ratio [OR]: 2.186, 95% confidence interval [CI]: 1.226–1.157), including deep infections (OR: 3.082, 95% CI: 1.753–5.419) and return to operating room [OR] (OR: 1.933, 95% CI: 1.280–2.919), as well as unplanned hospital admission (OR: 1.770, 95% CI: 1.289–2.431). However, NIDDM was not an independent risk factor for subsequent medical or surgical complications, unplanned hospital admission, or 30-day mortality. Patients with IDDM were much more likely to have surgical complications, including deep infection and return to OR, as well as unplanned hospital admission following knee arthroscopy. These risks diminished among those with NIDDM, with their adjusted risk profiles comparable to those without diabetes. Since diabetes occurs in a heterogenous state, more weight should be given to those with insulin-dependence when risk-stratifying patients for surgery. This is a Level III, retrospective comparison study.