bluuebunny/crossref_metadata_2025 huggingface dataset:
What the City Has to Offer: Urbanization and Women's Empowerment in Turkey
Authors: Cinar Kursat , Ugur-Cinar Meral
Published: May 2018

This article examines the relationship between urbanization and women's empowerment through the Turkish case. The article first tests statistically the overall impact of urbanization on women's empowerment by tapping into educational, economic, and political indicators at the province level. The results yield a positive relationship between urbanization and women's empowerment. We argue that these empowerment indicators demonstrate the necessary conditions of women's empowerment, yet whether these are sufficient for women to feel empowered needs to be further tested. To do so, the article utilizes an extensive original survey of 334 well-educated urban women in 43 out of 81 provinces of Turkey to examine the extent to which the results found in the quantitative section are paralleled by the actual experiences of women. The survey analysis reveals prospects and obstacles that well-educated women face in old and new urban centers. This nonrandom, purposive sample of seemingly empowered urban women shows that the barriers faced by these women would easily multiply when lower strata of society are reached. The Turkish case demonstrates that societal transformations such as urbanization have an imprint on the fates of women, yet further women's empowerment needs collective action at the political, legal, and societal levels.
Yet more on a stochastic economic model: Part 5: a vector autoregressive (VAR) Model for retail prices and wages
Authors: Wilkie A. D. , Şahin Şule
Published: May 2018

In this paper we develop a vector autoregressive model for retail prices and wages within the Wilkie model. The results turn out to be a slight improvement over the original model, but the simulated results are not very different.
What Makes Us Feel Good or Bad
Authors: Schmidt Barbara , Warns Luise , Hellmer Meike , Ulrich Natalie , Hewig Johannes
Published: May 2018

Abstract. Affective science calls for methods to induce mood in an engaging and ecologically valid way. We present a method employing a naturally occurring scenario that fits these criteria: a job interview. Participants got positive or negative feedback from a fictive expert to induce positive or negative mood. After mood induction, we assessed participants’ decision making behavior in the so-called information sampling task (IST). Results show that our mood induction successfully changed valence, dominance, and state self-esteem ratings, while there were no differences in arousal ratings. Decision making in the IST was not influenced by the induced mood. Effect sizes of mood induction were equally high for positive and negative mood concerning valence ratings (d = .8) with participants scoring high on self-control showing smaller mood induction effects. We conclude that our mood induction technique is an effective and natural way to induce mood in the laboratory, meeting current criteria of affective science.
Influence of Early Family Cohesion on Future Orientation
Authors: Zheng Lei , Gan Yiqun
Published: May 2018

Abstract. Future orientation is defined as a disposition that is characterized by goal-related thoughts, plans, motivations, feelings, and actions. Early experiences are critical for the development of future orientation. The purpose of the present research was to examine whether the FKBP5 (FK506 binding protein 5) rs1360780 polymorphism moderates associations between early family cohesion and adulthood future orientation. In total, 1,007 Chinese Han individuals participated in the present study. The results indicated that early family cohesion is associated with adulthood future orientation, and that FKBP5 polymorphisms play a moderating role between these factors. Specifically, individuals with the TT genotype and a history of poor family cohesion exhibited a lower degree of future orientation whereas those with good family cohesion showed a higher level of this trait. However, individuals with the CC/CT genotype expressed lower levels of environmental susceptibility. In line with the differential susceptibility model, these findings demonstrate that the TT genotype is more malleable to environmental influences. Accordingly, individuals with this genotype suffer a higher risk of exhibiting poor future orientation when exposed to negative experiences, and positive psychological traits under enriching environmental influences.
Direct and Indirect Effects of Agreeableness on Overconfidence
Authors: Sukenik Shraga , Reizer Abira , Koslovsky Meni
Published: May 2018

Abstract. Agreeableness is generally thought to be a personality trait with positive outcomes, especially with regards to the creation and maintenance of harmonious interpersonal relationships. The potential negative consequences of agreeableness are discussed less often. This study explores the potential for overconfidence among agreeable people. In addition, self-esteem and perceived similarity were examined as an explanation for the indirect effects of agreeableness on overconfidence. Specifically, within each pair of 104 student dyads who had worked jointly on a project in an undergraduate course, one acted as a rater and the other as a ratee. The raters were asked to evaluate their partner’s performance, while the ratees were asked how they thought the raters had evaluated their performance. Our measure of overconfidence was the gap between the partner’s evaluation of the participant’s performance and the participant’s belief in how this performance was evaluated. Additional measures filled out by the subjects included agreeableness, friendship, self-esteem, and perceived similarity. Results indicated that self-esteem and perceived similarity provide an approach for understanding the indirect effects of the agreeableness-overconfidence association.
A Sand‐Gravel Gilbert Delta Subject to Base Level Change
Authors: Chavarrías Víctor , Blom Astrid , Orrú Clara , Martín‐Vide Juan Pedro , Viparelli Enrica
Published: May 2018

Laboratory experiments were conducted on a sand‐gravel Gilbert delta to gain insight on its dynamics under varying base level. Base level rise results in intensified aggradation over the topset, as well as a decrease in topset slope and topset surface coarsening, the signals of which migrate in an upstream direction. Preferential deposition of coarse sediment in the topset results in a finer load at the topset‐foreset break, which creates a fine signature in the foreset deposit. Base level fall has the opposite effects. Entrainment of the topset mobile armor causes a coarsening of the load at the topset‐foreset break and so a coarse signature in the foreset deposit. The entrainment of the topset substrate and fine top part of the foreset may follow, which causes a fining of the load and a fine signature in the foreset deposit. The fact that the upstream sediment supply requires a certain slope and bed surface texture to be transported downstream under quasi‐equilibrium conditions counteracts the effects of base level change. This information travels in the downstream direction. In nature base level change is likely so slow that the upstream sediment load maintains the topset slope and bed surface texture and so keeps the topset in a quasi‐equilibrium state. Base level change is therefore not expected to leave a clear signal in a mixed‐sediment Gilbert delta other than a change in elevation of the topset‐foreset interface.
Increasing Methane Emissions From Natural Land Ecosystems due to Sea‐Level Rise
Authors: Lu Xiaoliang , Zhou Yuyu , Zhuang Qianlai , Prigent Catherine , Liu Yaling , Teuling Adriaan
Published: May 2018

Atmospheric methane (CH4) is one of the most important greenhouse gases. However, there is still a large uncertainty in simulating CH4 emissions from terrestrial ecosystems. Different from modeling studies focusing on response of CH4 emissions to various environmental changes in land ecosystems, this study analyzed the response of CH4 emissions to sea‐level rise (SLR). To do so, a large‐scale surface water routing module was incorporated into an existing CH4 model. This allowed the model to simulate the effect of SLR on river flows and inland water levels. This study focused on these freshwater systems and did not address saltwater intrusion or coastal wetland impacts. Both the annual maximum inundation extent and CH4 emissions at the global level showed a steadily growing trend, with an increase of 1.21 × 105 km2 in extent and an increase of 3.13 Tg CH4/year in CH4 emissions, in a 22‐year SLR experiment from 1993 to 2014. Most of new inundation and methane source areas were located near rivers' deltas and along downstream reaches of rivers. The increase in the inundation extent is primarily influenced by precipitation, channel geomorphic characteristics, and topography of riverside area. The increase of CH4 emissions due to the SLR is largely determined by the inundation extent, but other factors such as air temperature and carbon storage also play roles. Although the current SLR‐induced increases in the inundation extent and CH4 emissions only accounted for 1.0% and 1.3% of their global totals, these increases contributed 7.0% and 17.3% of the mean annual variability in both, respectively, during the study period. Considering that SLR has a long‐term increasing trend, future SLR under a changing climate could play a more important role in global CH4 emissions.
Hurricanes and the Sea: It Takes Two to Tango
Authors: Karnauskas Kristopher , Zhou Lei
Published: May 2018

A new special issue of JGR: Oceans reveals the rich relationship between the ocean and tropical cyclones.
Role of FGFR2b expression and signaling in keratinocyte differentiation: sequential involvement of PKCδ and PKCα
Authors: Rosato Benedetta , Ranieri Danilo , Nanni Monica , Torrisi Maria Rosaria , Belleudi Francesca
Published: May 2018

The tumor suppressor epithelial isoform of the fibroblast growth factor receptor 2 (FGFR2b) induces human keratinocyte early differentiation. Moreover, protein kinases C (PKCs) are known to regulate the differentiation program in several cellular contexts, including keratinocytes. Therefore, in this paper we propose to clarify if FGFR2b could play a role also in the late steps of keratinocyte differentiation and to assess if this receptor-induced process would sequentially involve PKCδ and PKCα isoforms. Immunofluorescence, biochemical, and molecular approaches, performed on 2D cultures or 3D organotypic rafts of human keratinocytes overexpressing FGFR2b by stable transduction, showed that receptor signaling induced the precocious onset and an accelerated progression of keratinocyte differentiation, indicating that FGFR2b is a crucial regulator of the entire program of keratinocyte differentiation. In addition, the use of specific inhibitors and gene silencing approaches through specific siRNA demonstrated that PKCδ controls the onset of FGFR2b-triggered differentiation, while PKCα plays a role restricted to the terminal stages of the process. Molecular analysis revealed that the two PKC isoforms sequentially act via induction of KLF4 and DLX3, two transcription factors linked by negative loops to p63, suggesting that p63 would represent the hub molecule at the crossroad of an intricate signaling network downstream FGFR2b, involving multiple PKC-induced transcription factors.
PTBP3 contributes to the metastasis of gastric cancer by mediating CAV1 alternative splicing
Authors: Liang Xin , Chen Weixia , Shi Haiyang , Gu Xiangyu , Li Yueqi , Qi Yingxue , Xu Ke , Zhao Aiguang , Liu Jianwen
Published: May 2018

Polypyrimidine tract-binding protein 3 (PTBP3) is an essential RNA-binding protein with roles in RNA splicing, 3′ end processing and translation. Although increasing evidence implicates PTBP3 in several cancers, its role in gastric cancer metastasis remains poorly explored. In this study, we found that PTBP3 was upregulated in the gastric cancer tissues of patients with lymph node metastasis. Patients with high PTBP3 expression levels had significantly shorter survival than those with low PTBP3 expression. Overexpression/knockdown of PTBP3 expression had no effect on proliferation, whereas it regulated migration and invasion in vitro. In addition, when a mouse xenotransplant model of MKN45 was established, knockdown of PTBP3 in MKN45 cells caused the formation of tumours that were smaller in size than their counterparts, with suppression of tumour lymphangiogenesis and metastasis to regional lymph nodes. Furthermore, we identified caveolin 1 (CAV1) as a downstream target of PTBP3. RNA immunoprecipitation (RIP) assays and dual-luciferase reporter gene assays indicated that PTBP3 interacted with the CU-rich region of the CAV1 gene to downregulate CAV1α expression. Knockdown of CAV1α abrogated the reduction of FAK and Src induced by PTBP3 knockdown. In summary, our findings provide experimental evidence that PTBP3 may function as a metastatic gene in gastric cancer by regulating CAV1 through alternative splicing.
Pigment epithelium-derived factor hinders photoreceptor cell death by reducing intracellular calcium in the degenerating retina
Authors: Comitato Antonella , Subramanian Preeti , Turchiano Giandomenico , Montanari Monica , Becerra S. Patricia , Marigo Valeria
Published: May 2018

Calcium ions play a critical role in neuronal cell death. Pigment epithelium-derived factor (PEDF) is a promising neuroprotective protein for photoreceptor cells but the mechanisms mediating its effects against retinal degeneration are still not well characterized. We addressed this question in the rd1 degenerating mouse retina that bears a mutation in the Pde6b gene encoding one subunit of the phosphodiesterase enzyme. Loss of phosphodiesterase activity in rod photoreceptor cells increases cyclic guanosine monophosphate (cGMP) levels leading to a rise in intracellular calcium. Short-term treatments with recombinant human PEDF protein decreased intracellular calcium in photoreceptors in vivo. Taking advantage of calcium pump blockers, we defined that PEDF signaling acts on PMCA calcium pumps to lower intracellular calcium. PEDF restrained cell death pathways activated by high calcium levels and engaging calpains, BAX and AIF. The neurotrophic effects were mediated by the PEDF receptor (PEDF-R), encoded by the PNPLA2 gene. Finally, peptides containing the neurotrophic domain of PEDF targeted these same cell death pathways in vivo. The findings reveal rescue from death of degenerating photoreceptor cells by a PEDF-mediated preservation of intracellular calcium homeostasis.
miR-5591-5p regulates the effect of ADSCs in repairing diabetic wound via targeting AGEs/AGER/JNK signaling axis
Authors: Li Qiang , Xia Sizhan , Yin Yating , Guo Yanping , Chen Feifei , Jin Peisheng
Published: May 2018

Advanced glycation end products/advanced glycation end products receptor (AGEs/AGER) interaction triggers reactive oxygen species (ROS) generation and activates downstream signal pathways and induces apoptosis in endothelial progenitor cells. A number of studies have revealed the involvement of microRNAs (miRNAs) in regulating intracellular ROS production and apoptosis. However, few studies explore the role of miRNAs in regulating the effect of adipose tissue-derived stem cells (ADSCs) in repairing diabetic wound and the associated cellular mechanisms remain unclear. In this study, ADSCs were exposed to AGEs, then siRNA for AGER was transfected into ADSCs. We found that AGEs/AGER axis induced ROS generation and apoptosis in ADSCs. AGEs treatment downregulated miR-5591-5p in ADSCs, which directly targeted AGER. miR-5591-5p suppressed AGEs/AGER axis-mediated ROS generation and apoptosis in ADSCs in vitro. In addition, miR-5591-5p promoted cell survival and enhanced the ability of ADSCs for repairing cutaneous wound in vivo. Furthermore, we confirmed that c-jun kinase (JNK) signal was involved in the inhibitory effect of miR-5591-5p on AGEs/AGER axis-induced ROS generation and apoptosis in ADSCs. Thus, these results indicated that miR-5591-5p targeting AGEs/AGER/JNK signaling axis possibly regulates the effect of ADSCs in repairing diabetic wound.
Regulation of proliferation and cell cycle by protein regulator of cytokinesis 1 in oral squamous cell carcinoma
Authors: Wu Fanglong , Shi Xueke , Zhang Rui , Tian Yuan , Wang Xiangjian , Wei Changlei , Li Duo , Li Xiaoyu , Kong Xiangli , Liu Yurong , Guo Weihua , Guo Yiqing , Zhou Hongmei
Published: May 2018

Protein regulator of cytokinesis 1 (PRC1), a microtubule-associated protein, has emerged as a critical regulator of proliferation and apoptosis, acting predominantly in numerous tumors. However, its function in oral squamous cell carcinoma (OSCC) is still unknown. To establish the roles of PRC1 in OSCC, 95 oral clinical samples (54 OSCC, 24 oral leukoplakia [OLK], and 17 normal oral mucosa) and seven oral cell lines (6 OSCC and 1 normal oral cell lines) were analyzed using a series of molecular and genomic assays both in vivo and in vitro were conducted in this study. Herein, we provide evidence demonstrating that expression of PRC1 closely correlates with the degree of epithelial dysplasia in OLK (n = 24) (p < 0.001), and the poor differentiation, large tumor volume, lymph node metastasis, and high-clinical stage in OSCC (n = 54) (p < 0.05), illustrating that PRC1 has a promotive influence on tumor progression in OSCC. Simultaneously, we observed that PRC1 knockdown in OSCC cell lines caused G2/M phase arrest (p < 0.05), inhibited cell proliferation in vitro (p < 0.05) and tumor growth in vivo (p < 0.001). Furthermore, the effects of PRC1 on the regulation of proliferation and cell cycle transition in OSCC samples were mediated by p53. The p53/PRC1/EGFR signaling pathway was found to be implicated in the tumor progression of OSCC. Based on our data, we demonstrate that PRC1 is a key factor in regulating proliferation and the cell cycle, pointing to the potential benefits of PRC1-targeted therapies for OSCC.
High-resolution AFM structure of DNA G-wires in aqueous solution
Authors: Bose Krishnashish , Lech Christopher J. , Heddi Brahim , Phan Anh Tuân
Published: May 2018

We investigate the self-assembly of short pieces of the Tetrahymena telomeric DNA sequence d[G4T2G4] in physiologically relevant aqueous solution using atomic force microscopy (AFM). Wire-like structures (G-wires) of 3.0 nm height with well-defined surface periodic features were observed. Analysis of high-resolution AFM images allowed their classification based on the periodicity of these features. A major species is identified with periodic features of 4.3 nm displaying left-handed ridges or zigzag features on the molecular surface. A minor species shows primarily left-handed periodic features of 2.2 nm. In addition to 4.3 and 2.2 nm ridges, background features with periodicity of 0.9 nm are also observed. Using molecular modeling and simulation, we identify a molecular structure that can explain both the periodicity and handedness of the major G-wire species. Our results demonstrate the potential structural diversity of G-wire formation and provide valuable insight into the structure of higher-order intermolecular G-quadruplexes. Our results also demonstrate how AFM can be combined with simulation to gain insight into biomolecular structure.
Stereodivergent synthesis of vicinal quaternary-quaternary stereocenters and bioactive hyperolactones
Authors: Zheng Haifeng , Wang Yan , Xu Chaoran , Xu Xi , Lin Lili , Liu Xiaohua , Feng Xiaoming
Published: May 2018

Although great success has been achieved in asymmetric Claisen rearrangement for the synthesis of chiral γ,δ-unsaturated carbonyl compounds bearing vicinal tertiary-quaternary stereocenters, the development of asymmetric versions for stereodivergent construction of adjacent quaternary-quaternary stereocenters remains a formidable challenge because of the high steric hindrance. Here we report a catalytic enantioselective dearomatization Claisen rearrangement of allyl furyl ethers catalyzed by chiral N,N′-dioxide-NiII complex catalysts. A variety of chiral γ,δ-unsaturated carbonyl compounds bearing vicinal quaternary-quaternary stereocenters were obtained with excellent outcomes under mild conditions. Furthermore, we disclosed that by matching the configuration of the catalysts and the alkene unit of the substrates, four stereoisomers of the products could be prepared in excellent yields and stereoselectivities. Finally, the fascination of this strategy was demonstrated by stereodivergent synthesis of bioactive natural products hyperolactones B, C, and their epimers. A possible catalytic model was proposed to explain the origin of the asymmetric induction.
Ultracold Rydberg molecules
Authors: Shaffer J. P. , Rittenhouse S. T. , Sadeghpour H. R.
Published: May 2018

Ultracold molecules formed from association of a single Rydberg atom with surrounding atoms or molecules and those from double Rydberg excitations are discussed in this review. Ultralong-range Rydberg molecules possess a novel molecular bond resulting from scattering of the Rydberg electron from the perturber atoms or molecules. The strong interactions between Rydberg atoms in ultracold gases may lead to formation of macroscopic Rydberg macrodimers. The exquisite control over the properties of the Rydberg electron means that interesting and unusual few-body and quantum many-body features can be realized in such systems.
Dynamically induced cascading failures in power grids
Authors: Schäfer Benjamin , Witthaut Dirk , Timme Marc , Latora Vito
Published: May 2018

Reliable functioning of infrastructure networks is essential for our modern society. Cascading failures are the cause of most large-scale network outages. Although cascading failures often exhibit dynamical transients, the modeling of cascades has so far mainly focused on the analysis of sequences of steady states. In this article, we focus on electrical transmission networks and introduce a framework that takes into account both the event-based nature of cascades and the essentials of the network dynamics. We find that transients of the order of seconds in the flows of a power grid play a crucial role in the emergence of collective behaviors. We finally propose a forecasting method to identify critical lines and components in advance or during operation. Overall, our work highlights the relevance of dynamically induced failures on the synchronization dynamics of national power grids of different European countries and provides methods to predict and model cascading failures.
Iodine-catalyzed diazo activation to access radical reactivity
Authors: Li Pan , Zhao Jingjing , Shi Lijun , Wang Jin , Shi Xiaodong , Li Fuwei
Published: May 2018

Transition-metal-catalyzed diazo activation is a classical way to generate metal carbene, which are valuable intermediates in synthetic organic chemistry. An alternative iodine-catalyzed diazo activation is disclosed herein under either photo-initiated or thermal-initiated conditions, which represents an approach to enable carbene radical reactivity. This metal-free diazo activation strategy were successfully applied into olefin cyclopropanation and epoxidation, and applying this method to pyrrole synthesis under thermal-initiated conditions further demonstrates the unique reactivity using this method over typical metal-catalyzed conditions.
Coulombic-enhanced hetero radical pairing interactions
Authors: Zheng Xujun , Zhang Yang , Cao Ning , Li Xin , Zhang Shuoqing , Du Renfeng , Wang Haiying , Ye Zhenni , Wang Yan , Cao Fahe , Li Haoran , Hong Xin , Sue Andrew C.-H. , Yang Chuluo , Liu Wei-Guang , Li Hao
Published: May 2018

Spin–spin interactions between two identical aromatic radicals have been studied extensively and utilized to establish supramolecular recognition. Here we report that spin-pairing interactions could also take place between two different π-electron radicals, namely a bipyridinium radical cation (BPY+•) and a naphthalene-1,8:4,5-bis(dicarboximide) radical anion (NDI─•). The occurrence of this type of previously unreported hetero radical-pairing interactions is attributed to enhancement effect of Coulombic attraction between these two radicals bearing opposite charges. The Coulombic-enhanced hetero radical pairing interactions are employed to drive host–guest recognition, as well as the reversible switching of a bistable [2]rotaxane.
Publisher Correction: Laser-accelerated particle beams for stress testing of materials
Authors: Barberio M. , Scisciò M. , Vallières S. , Cardelli F. , Chen S. N. , Famulari G. , Gangolf T. , Revet G. , Schiavi A. , Senzacqua M. , Antici P.
Published: May 2018

The original version of the Supplementary Information associated with this Article contained an error in Supplementary Figure 3 in which all panels, with the exception of the bottom-left ‘Ti’ panel, were blank. The HTML has been updated to include a corrected version of the Supplementary Information.
LRRC8/VRAC anion channels enhance β-cell glucose sensing and insulin secretion
Authors: Stuhlmann Till , Planells-Cases Rosa , Jentsch Thomas J.
Published: May 2018

Glucose homeostasis depends critically on insulin that is secreted by pancreatic β-cells. Serum glucose, which is directly sensed by β-cells, stimulates depolarization- and Ca2+-dependent exocytosis of insulin granules. Here we show that pancreatic islets prominently express LRRC8A and LRRC8D, subunits of volume-regulated VRAC anion channels. Hypotonicity- or glucose-induced β-cell swelling elicits canonical LRRC8A-dependent VRAC currents that depolarize β-cells to an extent that causes electrical excitation. Glucose-induced excitation and Ca2+responses are delayed in onset, but not abolished, in β-cells lacking the essential VRAC subunit LRRC8A. WhereasLrrc8adisruption does not affect tolbutamide- or high-K+-induced insulin secretion from pancreatic islets, it reduces first-phase glucose-induced insulin secretion. Mice lacking VRAC in β-cells have normal resting serum glucose levels but impaired glucose tolerance. We propose that opening of LRRC8/VRAC channels increases glucose sensitivity and insulin secretion of β-cells synergistically with KATPclosure. Neurotransmitter-permeable LRRC8D-containing VRACs might have additional roles in autocrine/paracrine signaling within islets.
Single cell analysis of kynurenine and System L amino acid transport in T cells
Authors: Sinclair Linda V. , Neyens Damien , Ramsay George , Taylor Peter M. , Cantrell Doreen A.
Published: May 2018

The tryptophan metabolite kynurenine has critical immunomodulatory properties and can function as an aryl hydrocarbon receptor (AHR) ligand. Here we show that the ability of T cells to transport kynurenine is restricted to cells activated by the T-cell antigen receptor or proinflammatory cytokines. Kynurenine is transported across the T-cell membrane by the System L transporter SLC7A5. Accordingly, the ability of kynurenine to activate the AHR is restricted to T cells that express SLC7A5. We use the fluorescence spectral properties of kynurenine to develop a flow cytometry-based assay for rapid, sensitive and quantitative measurement of the kynurenine transport capacity in a single cell. Our findings provide a method to assess the susceptibility of T cells to kynurenine, and a sensitive single cell assay to monitor System L amino acid transport.
MxB is an interferon-induced restriction factor of human herpesviruses
Authors: Crameri Michel , Bauer Michael , Caduff Nicole , Walker Raphael , Steiner Fiona , Franzoso Francesca D. , Gujer Cornelia , Boucke Karin , Kucera Talissa , Zbinden Andrea , Münz Christian , Fraefel Cornel , Greber Urs F. , Pavlovic Jovan
Published: May 2018

The type I interferon (IFN) system plays an important role in controlling herpesvirus infections, but it is unclear which IFN-mediated effectors interfere with herpesvirus replication. Here we report that human myxovirus resistance protein B (MxB, also designated Mx2) is a potent human herpesvirus restriction factor in the context of IFN. We demonstrate that ectopic MxB expression restricts a range of herpesviruses from the Alphaherpesvirinae and Gammaherpesvirinae, including herpes simplex virus 1 and 2 (HSV-1 and HSV-2), and Kaposi’s sarcoma-associated herpesvirus (KSHV). MxB restriction of HSV-1 and HSV-2 requires GTPase function, in contrast to restriction of lentiviruses. MxB inhibits the delivery of incoming HSV-1 DNA to the nucleus and the appearance of empty capsids, but not the capsid delivery to the cytoplasm or tegument dissociation from the capsid. Our study identifies MxB as a potent pan-herpesvirus restriction factor which blocks the uncoating of viral DNA from the incoming viral capsid.
Revealing isoelectronic size conversion dynamics of metal nanoclusters by a noncrystallization approach
Authors: Yao Qiaofeng , Fung Victor , Sun Cheng , Huang Sida , Chen Tiankai , Jiang De-en , Lee Jim Yang , Xie Jianping
Published: May 2018

Atom-by-atom engineering of nanomaterials requires atomic-level knowledge of the size evolution mechanism of nanoparticles, which remains one of the greatest mysteries in nanochemistry. Here we reveal atomic-level dynamics of size evolution reaction of molecular-like nanoparticles, i.e., nanoclusters (NCs) by delicate mass spectrometry (MS) analyses. The model size-conversion reaction is [Au23(SR)16]− → [Au25(SR)18]− (SR = thiolate ligand). We demonstrate that such isoelectronic (valence electron count is 8 in both NCs) size-conversion occurs by a surface-motif-exchange-induced symmetry-breaking core structure transformation mechanism, surfacing as a definitive reaction of [Au23(SR)16]− + 2 [Au2(SR)3]− → [Au25(SR)18]− + 2 [Au(SR)2]−. The detailed tandem MS analyses further suggest the bond susceptibility hierarchies in feed and final Au NCs, shedding mechanistic light on cluster reaction dynamics at atomic level. The MS-based mechanistic approach developed in this study also opens a complementary avenue to X-ray crystallography to reveal size evolution kinetics and dynamics.
CRISPR/Cas9-mediated gene targeting in Arabidopsis using sequential transformation
Authors: Miki Daisuke , Zhang Wenxin , Zeng Wenjie , Feng Zhengyan , Zhu Jian-Kang
Published: May 2018

Homologous recombination-based gene targeting is a powerful tool for precise genome modification and has been widely used in organisms ranging from yeast to higher organisms such as Drosophila and mouse. However, gene targeting in higher plants, including the most widely used model plant Arabidopsis thaliana, remains challenging. Here we report a sequential transformation method for gene targeting in Arabidopsis. We find that parental lines expressing the bacterial endonuclease Cas9 from the egg cell- and early embryo-specific DD45 gene promoter can improve the frequency of single-guide RNA-targeted gene knock-ins and sequence replacements via homologous recombination at several endogenous sites in the Arabidopsis genome. These heritable gene targeting can be identified by regular PCR. Our approach enables routine and fine manipulation of the Arabidopsis genome.
Light-induced formation of partially reduced oxygen species limits the lifetime of photosystem 1-based biocathodes
Authors: Zhao Fangyuan , Hardt Steffen , Hartmann Volker , Zhang Huijie , Nowaczyk Marc M. , Rögner Matthias , Plumeré Nicolas , Schuhmann Wolfgang , Conzuelo Felipe
Published: May 2018

Interfacing photosynthetic proteins specifically photosystem 1 (PS1) with electrodes enables light-induced charge separation processes for powering semiartificial photobiodevices with, however, limited long-term stability. Here, we present the in-depth evaluation of a PS1/Os-complex-modified redox polymer-based biocathode by means of scanning photoelectrochemical microscopy. Focalized local illumination of the bioelectrode and concomitant collection of H2O2 at the closely positioned microelectrode provide evidence for the formation of partially reduced oxygen species under light conditions. Long-term evaluation of the photocathode at different O2 concentrations as well as after incorporating catalase and superoxide dismutase reveals the particularly challenging issue of avoiding the generation of reactive species. Moreover, the evaluation of films prepared with inactivated PS1 and free chlorophyll points out additional possible pathways for the generation of oxygen radicals. To avoid degradation of PS1 during illumination and hence to enhance the long-term stability, the operation of biophotocathodes under anaerobic conditions is indispensable.
X-ray structure of a carpet-like antimicrobial defensin–phospholipid membrane disruption complex
Authors: Järvå Michael , Lay Fung T. , Phan Thanh Kha , Humble Cassandra , Poon Ivan K. H. , Bleackley Mark R. , Anderson Marilyn A. , Hulett Mark D. , Kvansakul Marc
Published: May 2018

Defensins are cationic antimicrobial peptides expressed throughout the plant and animal kingdoms as a first line of defense against pathogens. Membrane targeting and disruption is a crucial function of many defensins, however the precise mechanism remains unclear. Certain plant defensins form dimers that specifically bind the membrane phospholipids phosphatidic acid (PA) and phosphatidylinositol 4,5-bisphosphate, thereby triggering the assembly of defensin–lipid oligomers that permeabilize cell membranes. To understand this permeabilization mechanism, here we determine the crystal structure of the plant defensin NaD1 bound to PA. The structure reveals a 20-mer that adopts a concave sheet- or carpet-like topology where NaD1 dimers form one face and PA acyl chains form the other face of the sheet. Furthermore, we show that Arg39 is critical for PA binding, oligomerization and fungal cell killing. These findings identify a putative defensin–phospholipid membrane attack configuration that supports a longstanding proposed carpet mode of membrane disruption.
Super-resolution imaging reveals the sub-diffraction phenotype of Zellweger Syndrome ghosts and wild-type peroxisomes
Authors: Soliman Kareem , Göttfert Fabian , Rosewich Hendrik , Thoms Sven , Gärtner Jutta
Published: May 2018

Peroxisomes are ubiquitous cell organelles involved in many metabolic and signaling functions. Their assembly requires peroxins, encoded by PEX genes. Mutations in PEX genes are the cause of Zellweger Syndrome spectrum (ZSS), a heterogeneous group of peroxisomal biogenesis disorders (PBD). The size and morphological features of peroxisomes are below the diffraction limit of light, which makes them attractive for super-resolution imaging. We applied Stimulated Emission Depletion (STED) microscopy to study the morphology of human peroxisomes and peroxisomal protein localization in human controls and ZSS patients. We defined the peroxisome morphology in healthy skin fibroblasts and the sub-diffraction phenotype of residual peroxisomal structures (‘ghosts’) in ZSS patients that revealed a relation between mutation severity and clinical phenotype. Further, we investigated the 70 kDa peroxisomal membrane protein (PMP70) abundance in relationship to the ZSS sub-diffraction phenotype. This work improves the morphological definition of peroxisomes. It expands current knowledge about peroxisome biogenesis and ZSS pathoethiology to the sub-diffraction phenotype including key peroxins and the characteristics of ghost peroxisomes.
Uncoupling human and climate drivers of late Holocene vegetation change in southern Brazil
Authors: Robinson Mark , De Souza Jonas Gregorio , Maezumi S. Yoshi , Cárdenas Macarena , Pessenda Luiz , Prufer Keith , Corteletti Rafael , Scunderlick Deisi , Mayle Francis Edward , De Blasis Paulo , Iriarte José
Published: May 2018

In the highlands of southern Brazil an anthropogenitcally driven expansion of forest occurred at the expense of grasslands between 1410 and 900 cal BP, coincident with a period of demographic and cultural change in the region. Previous studies have debated the relative contributions of increasing wetter and warmer climate conditions and human landscape modifications to forest expansion, but generally lacked high resoltiuon proxies to measure these effects, or have relied on single proxies to reconstruct both climate and vegetation. Here, we develop and test a model of natural ecosystem distribution against vegetation histories, paleoclimate proxies, and the archaeological record to distinguish human from temperature and precipitation impacts on the distribution and expansion of Araucaria forests during the late Holocene. Carbon isotopes from soil profiles confirm that in spite of climatic fluctuations, vegetation was stable and forests were spatially limited to south-facing slopes in the absence of human inputs. In contrast, forest management strategies for the past 1400 years expanded this economically important forest beyond its natural geographic boundaries in areas of dense pre-Columbian occupation, suggesting that landscape modifications were linked to demographic changes, the effects of which are still visible today.
Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi
Authors: Fisher Matthew C. , Ghosh Pria , Shelton Jennifer M. G. , Bates Kieran , Brookes Lola , Wierzbicki Claudia , Rosa Gonçalo M. , Farrer Rhys A. , Aanensen David M. , Alvarado-Rybak Mario , Bataille Arnaud , Berger Lee , Böll Susanne , Bosch Jaime , Clare Frances C. , A. Courtois Elodie , Crottini Angelica , Cunningham Andrew A. , Doherty-Bone Thomas M. , Gebresenbet Fikirte , Gower David J. , Höglund Jacob , James Timothy Y. , Jenkinson Thomas S. , Kosch Tiffany A. , Lambertini Carolina , Laurila Anssi , Lin Chun-Fu , Loyau Adeline , Martel An , Meurling Sara , Miaud Claude , Minting Pete , Ndriantsoa Serge , O’Hanlon Simon J. , Pasmans Frank , Rakotonanahary Tsanta , Rabemananjara Falitiana C. E. , Ribeiro Luisa P. , Schmeller Dirk S. , Schmidt Benedikt R. , Skerratt Lee , Smith Freya , Soto-Azat Claudio , Tessa Giulia , Toledo Luís Felipe , Valenzuela-Sánchez Andrés , Verster Ruhan , Vörös Judit , Waldman Bruce , Webb Rebecca J. , Weldon Che , Wombwell Emma , Zamudio Kelly R. , Longcore Joyce E. , Garner Trenton W. J.
Published: May 2018

Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to researchers as part of the BiodivERsA project RACE; here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been applied across 5 continents, 23 countries and in 62 amphibian species. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this group of emerging pathogens.
Smooth muscle-like Ca2+-regulation of actin–myosin interaction in adult jellyfish striated muscle
Authors: Tanaka Hiroyuki , Ishimaru Shiori , Nagatsuka Yasuhiro , Ohashi Keisuke
Published: May 2018

Cnidaria is an animal phylum, whose members probably have the most ancestral musculature. We prepared and characterized, for the first time to our knowledge, native actomyosin from the striated myoepithelium of the adult moon jelly Aurelia sp. The actomyosin contained myosin, paramyosin-like protein, Ser/Thr-kinase, actin, and two isoforms of tropomyosin, but not troponin, which is known to activate contraction dependent on intracellular Ca2+ signaling in almost all striated muscles of bilaterians. Notably, the myosin comprised striated muscle-type heavy chain and smooth muscle-type regulatory light chains. In the presence of Ca2+, the Mg-ATPase activity of actomyosin was stimulated and Ser21 of the regulatory light chain was concomitantly phosphorylated by the addition of calmodulin and myosin light chain kinase prepared from chicken smooth muscle. Collectively, these results suggest that, similar to smooth muscle, the contraction of jellyfish striated muscle is regulated by Ca2+-dependent phosphorylation of the myosin light chain.
Quantitative SUMO proteomics reveals the modulation of several PML nuclear body associated proteins and an anti-senescence function of UBC9
Authors: McManus Francis P. , Bourdeau Véronique , Acevedo Mariana , Lopes-Paciencia Stéphane , Mignacca Lian , Lamoliatte Frédéric , Rojas Pino John W. , Ferbeyre Gerardo , Thibault Pierre
Published: May 2018

Several regulators of SUMOylation have been previously linked to senescence but most targets of this modification in senescent cells remain unidentified. Using a two-step purification of a modified SUMO3, we profiled the SUMO proteome of senescent cells in a site-specific manner. We identified 25 SUMO sites on 23 proteins that were significantly regulated during senescence. Of note, most of these proteins were PML nuclear body (PML-NB) associated, which correlates with the increased number and size of PML-NBs observed in senescent cells. Interestingly, the sole SUMO E2 enzyme, UBC9, was more SUMOylated during senescence on its Lys-49. Functional studies of a UBC9 mutant at Lys-49 showed a decreased association to PML-NBs and the loss of UBC9’s ability to delay senescence. We thus propose both pro- and anti-senescence functions of protein SUMOylation.
Publisher Correction: Non-tuberculous Mycobacteria isolated from Pulmonary samples in sub-Saharan Africa - A Systematic Review and Meta Analyses
Authors: Okoi Catherine , Anderson Suzanne T. B. , Antonio Martin , Mulwa Sarah N. , Gehre Florian , Adetifa Ifedayo M. O.
Published: May 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
The trimeric solution structure and fucose-binding mechanism of the core fucosylation-specific lectin PhoSL
Authors: Yamasaki Kazuhiko , Yamasaki Tomoko , Tateno Hiroaki
Published: May 2018

The core α1–6 fucosylation-specific lectin from a mushroom Pholiota squarrosa (PhoSL) is a potential tool for precise diagnosis of cancers. This lectin consists of only 40 amino acids and can be chemically synthesized. We showed here that a synthesized PhoSL peptide formed a trimer by gel filtration and chemical cross-linking assays, and determined a structure of the PhoSL trimer by NMR. The structure possesses a β-prism motif with a three-fold rotational symmetry, where three antiparallel β-sheets are tightly connected by swapping of β-strands. A triad of Trp residues comprises the structural core, forming NH–π electrostatic interactions among the indole rings. NMR analysis with an excess amount of fucose revealed the structural basis for the molecular recognition. Namely, fucose deeply enters a pocket formed at a junction of β-sheet edges, with the methyl group placed at the bottom. It forms a number of hydrophobic and hydrogen-bonding interactions with PhoSL residues. In spite of partial similarities to the structures of other functionally related lectins, the arrangement of the antiparallel β-sheets in the PhoSL trimer is novel as a structural scaffold, and thus defines a novel type of lectin structure.
Perlecan, a heparan sulfate proteoglycan, regulates systemic metabolism with dynamic changes in adipose tissue and skeletal muscle
Authors: Yamashita Yuri , Nakada Satoshi , Yoshihara Toshinori , Nara Takeshi , Furuya Norihiko , Miida Takashi , Hattori Nobutaka , Arikawa-Hirasawa Eri
Published: May 2018

Perlecan (HSPG2), a heparan sulfate proteoglycan, is a component of basement membranes and participates in a variety of biological activities. Here, we show physiological roles of perlecan in both obesity and the onset of metabolic syndrome. The perinatal lethality-rescued perlecan knockout (Hspg2−/−-Tg) mice showed a smaller mass and cell size of white adipose tissues than control (WT-Tg) mice. Abnormal lipid deposition, such as fatty liver, was not detected in the Hspg2−/−-Tg mice, and those mice also consumed more fat as an energy source, likely due to their activated fatty acid oxidation. In addition, the Hspg2−/−-Tg mice demonstrated increased insulin sensitivity. Molecular analysis revealed the significantly relatively increased amount of the muscle fiber type IIA (X) isoform and a larger quantity of mitochondria in the skeletal muscle of Hspg2−/−-Tg mice. Furthermore, the perlecan-deficient skeletal muscle also had elevated levels of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α) protein. PGC1α expression is activated by exercise, and induces mitochondrial biosynthesis. Thus, perlecan may act as a mechano-regulator of catabolism of both lipids and glucose by shifting the muscle fiber composition to oxidative fibers. Our data suggest that downregulation of perlecan is a promising strategy to control metabolic syndrome.
Strain induced electronic structure variation in methyl-ammonium lead iodide perovskite
Authors: Zhang Le , Geng Wei , Tong Chuan-jia , Chen Xueguang , Cao Tengfei , Chen Mingyang
Published: May 2018

Methyl-ammonium lead iodide perovskite (CH3NH3PbI3) has drawn great attention due to its excellent photovoltaic properties. Because of its loosely compacted structure, the structural, electronic and optical properties of CH3NH3PbI3 are sensitive to external modulations. Strain effects on CH3NH3PbI3 are fully investigated by the first principles calculations. The results indicate that the inorganic framework deforms under compression or stretch and the embedded organic CH3NH3+ molecules rotate correspondingly. A band gap oscillation and a new structural phase in response to the external strain were observed for the first time. These phenomena are explained with the nonlinear structural deformation and phase transition under the external strains. The semi-quantitative relationship between the band gap variation and geometry change under the external strain is obtained. We found that the shift of valence band maximum under the external strain is mostly determined by the most stretched or compressed Pb-I bond of CH3NH3PbI3, and the shift of the conduction band minimum under the external strain is likely to be determined by the largest Pb-I-Pb bond angle in the system. These results are important for understanding of strain effects on semiconductors and guiding the experiments to improve the performance of the perovskite solar cells.