bluuebunny/crossref_metadata_2025 huggingface dataset:
Spiniform phase-encoded metagratings entangling arbitrary rational-order orbital angular momentum
Authors: Huang Kun , Liu Hong , Restuccia Sara , Mehmood Muhammad Q , Mei Sheng-Tao , Giovannini Daniel , Danner Aaron , Padgett Miles J , Teng Jing-Hua , Qiu Cheng-Wei
Published: March 2018

Quantum entanglements between integer-order and fractional-order orbital angular momentums (OAMs) have been previously discussed. However, the entangled nature of arbitrary rational-order OAM has long been considered a myth due to the absence of an effective strategy for generating arbitrary rational-order OAM beams. Therefore, we report a single metadevice comprising a bilaterally symmetric grating with an aperture, creating optical beams with dynamically controllable OAM values that are continuously varying over a rational range. Due to its encoded spiniform phase, this novel metagrating enables the production of an average OAM that can be increased without a theoretical limit by embracing distributed singularities, which differs significantly from the classic method of stacking phase singularities using fork gratings. This new method makes it possible to probe the unexplored niche of quantum entanglement between arbitrarily defined OAMs in light, which could lead to the complex manipulation of microparticles, high-dimensional quantum entanglement and optical communication. We show that quantum coincidence based on rational-order OAM-superposition states could give rise to low cross-talks between two different states that have no significant overlap in their spiral spectra. Additionally, future applications in quantum communication and optical micromanipulation may be found.
ELF3 promotes epithelial–mesenchymal transition by protecting ZEB1 from miR-141-3p-mediated silencing in hepatocellular carcinoma
Authors: Zheng Longbo , Xu Ming , Xu Junjie , Wu Ke , Fang Qian , Liang Yuelong , Zhou Senjun , Cen Dong , Ji Lin , Han Weili , Cai Xiujun
Published: March 2018

Hepatocellular carcinoma (HCC) is one of the most common malignant cancers and currently the third leading cause of cancer-related deaths, worldwide. Epithelial–mesenchymal transition (EMT) plays a major role in HCC progression. In this study, we first found that the expression of E74-like ETS transcription factor 3 (ELF3), a member of the E-twenty-six family of transcription factors, was increased in HCC tissues, and that ELF3 overexpression was associated with poor prognoses for HCC patients. Gain-of-function and loss-of-function studies revealed that increased ELF3 expression promoted HCC cell proliferation, migration, and invasion, while these processes were inhibited when ELF3 was silenced. Additionally, ELF3 was found to promote EMT, which we demonstrated through decreased E-cadherin expression and increased N-cadherin and fibronectin expression. ELF3 knockdown reversed EMT via repressing ZEB1 expression through miR-141-3p upregulation. Chromatin immunoprecipitation assays revealed that ELF3 bound to the miR-141-3p promoter, suppressing miR-141-3p expression. Taken together, our data show that ELF3 repressed E-cadherin and promoted EMT in HCC cells by suppressing miR-141-3p, thereby activating ZEB1. Thus, ELF3 may be a potential prognostic biomarker and/or therapeutic target for HCC.
The role of endoplasmic reticulum-mitochondria contact sites in the control of glucose homeostasis: an update
Authors: Rieusset Jennifer
Published: March 2018

The contact sites that the endoplasmic reticulum (ER) forms with mitochondria, called mitochondria-associated membranes (MAMs), are a hot topic in biological research, and both their molecular determinants and their numerous roles in several signaling pathways are is continuously evolving. MAMs allow the exchange between both organelles of lipids, calcium (Ca2+), and likely reactive oxygen species, allowing adaptations of both cellular bioenergetics and cell fate depending of cellular needs or stresses. Therefore, it is not surprising that MAMs affect cellular metabolism. Nevertheless, recent arguments suggest that MAMs could also act as key hub of hormonal and/or nutrient signaling in several insulin-sensitive tissues, pointing a specific role of MAMs in the control of glucose homeostasis. Here, I provide a brief review and update on current key signaling roles of the MAMs in the control of glucose homeostasis in both health and metabolic diseases. Particularly, the relevance of ER-mitochondria miscommunication in the disruption of glucose homeostasis is analyzed in details in the liver, skeletal muscle, adipose tissue, and beta cells of the pancreas.
Differentiation by nerve growth factor (NGF) involves mechanisms of crosstalk between energy homeostasis and mitochondrial remodeling
Authors: Martorana Francesca , Gaglio Daniela , Bianco Maria Rosaria , Aprea Federica , Virtuoso Assunta , Bonanomi Marcella , Alberghina Lilia , Papa Michele , Colangelo Anna Maria
Published: March 2018

Neuronal differentiation involves extensive modification of biochemical and morphological properties to meet novel functional requirements. Reorganization of the mitochondrial network to match the higher energy demand plays a pivotal role in this process. Mechanisms of neuronal differentiation in response to nerve growth factor (NGF) have been largely characterized in terms of signaling, however, little is known about its impact on mitochondrial remodeling and metabolic function. In this work, we show that NGF-induced differentiation requires the activation of autophagy mediated by Atg9b and Ambra1, as it is disrupted by their genetic knockdown and by autophagy blockers. NGF differentiation involves the induction of P-AMPK and P-CaMK, and is prevented by their pharmacological inhibition. These molecular events correlate with modifications of energy and redox homeostasis, as determined by ATP and NADPH changes, higher oxygen consumption (OCR) and ROS production. Our data indicate that autophagy aims to clear out exhausted mitochondria, as determined by enhanced localization of p62 and Lysotracker-red to mitochondria. In addition, we newly demonstrate that NGF differentiation is accompanied by increased mitochondrial remodeling involving higher levels of fission (P-Drp1) and fusion proteins (Opa1 and Mfn2), as well as induction of Sirt3 and the transcription factors mtTFA and PPARγ, which regulate mitochondria biogenesis and metabolism to sustain increased mitochondrial mass, potential, and bioenergetics. Overall, our data indicate a new NGF-dependent mechanism involving mitophagy and extensive mitochondrial remodeling, which plays a key role in both neurogenesis and nerve regeneration.
Sensitive and frequent identification of high avidity neo-epitope specific CD8
+
T cells in immunotherapy-naive ovarian cancer
Authors: Bobisse Sara , Genolet Raphael , Roberti Annalisa , Tanyi Janos L. , Racle Julien , Stevenson Brian J. , Iseli Christian , Michel Alexandra , Le Bitoux Marie-Aude , Guillaume Philippe , Schmidt Julien , Bianchi Valentina , Dangaj Denarda , Fenwick Craig , Derré Laurent , Xenarios Ioannis , Michielin Olivier , Romero Pedro , Monos Dimitri S. , Zoete Vincent , Gfeller David , Kandalaft Lana E. , Coukos George , Harari Alexandre
Published: March 2018

Immunotherapy directed against private tumor neo-antigens derived from non-synonymous somatic mutations is a promising strategy of personalized cancer immunotherapy. However, feasibility in low mutational load tumor types remains unknown. Comprehensive and deep analysis of circulating and tumor-infiltrating lymphocytes (TILs) for neo-epitope specific CD8+ T cells has allowed prompt identification of oligoclonal and polyfunctional such cells from most immunotherapy-naive patients with advanced epithelial ovarian cancer studied. Neo-epitope recognition is discordant between circulating T cells and TILs, and is more likely to be found among TILs, which display higher functional avidity and unique TCRs with higher predicted affinity than their blood counterparts. Our results imply that identification of neo-epitope specific CD8+ T cells is achievable even in tumors with relatively low number of somatic mutations, and neo-epitope validation in TILs extends opportunities for mutanome-based personalized immunotherapies to such tumors.
A comprehensive evaluation of module detection methods for gene expression data
Authors: Saelens Wouter , Cannoodt Robrecht , Saeys Yvan
Published: March 2018

A critical step in the analysis of large genome-wide gene expression datasets is the use of module detection methods to group genes into co-expression modules. Because of limitations of classical clustering methods, numerous alternative module detection methods have been proposed, which improve upon clustering by handling co-expression in only a subset of samples, modelling the regulatory network, and/or allowing overlap between modules. In this study we use known regulatory networks to do a comprehensive and robust evaluation of these different methods. Overall, decomposition methods outperform all other strategies, while we do not find a clear advantage of biclustering and network inference-based approaches on large gene expression datasets. Using our evaluation workflow, we also investigate several practical aspects of module detection, such as parameter estimation and the use of alternative similarity measures, and conclude with recommendations for the further development of these methods.
Author Correction: Single shot laser writing with sub-nanosecond and nanosecond bursts of femtosecond pulses
Authors: Okhrimchuk Andrey , Fedotov Sergey , Glebov Ivan , Sigaev Vladimir , Kazansky Peter
Published: March 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Publisher Correction: QTL mapping and molecular characterization of the classical D locus controlling seed and flower color in Linum usitatissimum (flax)
Authors: Sudarshan Gurudatt Pavagada , Kulkarni Manoj , Akhov Leonid , Ashe Paula , Shaterian Hamid , Cloutier Sylvie , Rowland Gordon , Wei Yangdou , Selvaraj Gopalan
Published: March 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.
Enabling Controlling Complex Networks with Local Topological Information
Authors: Li Guoqi , Deng Lei , Xiao Gaoxi , Tang Pei , Wen Changyun , Hu Wuhua , Pei Jing , Shi Luping , Stanley H. Eugene
Published: March 2018

Complex networks characterize the nature of internal/external interactions in real-world systems including social, economic, biological, ecological, and technological networks. Two issues keep as obstacles to fulfilling control of large-scale networks: structural controllability which describes the ability to guide a dynamical system from any initial state to any desired final state in finite time, with a suitable choice of inputs; and optimal control, which is a typical control approach to minimize the cost for driving the network to a predefined state with a given number of control inputs. For large complex networks without global information of network topology, both problems remain essentially open. Here we combine graph theory and control theory for tackling the two problems in one go, using only local network topology information. For the structural controllability problem, a distributed local-game matching method is proposed, where every node plays a simple Bayesian game with local information and local interactions with adjacent nodes, ensuring a suboptimal solution at a linear complexity. Starring from any structural controllability solution, a minimizing longest control path method can efficiently reach a good solution for the optimal control in large networks. Our results provide solutions for distributed complex network control and demonstrate a way to link the structural controllability and optimal control together.
A Mathematical Model for the Sounds Produced by Knuckle Cracking
Authors: Chandran Suja V. , Barakat A. I.
Published: March 2018

The articular release of the metacarpophalangeal joint produces a typical cracking sound, resulting in what is commonly referred to as the cracking of knuckles. Despite over sixty years of research, the source of the knuckle cracking sound continues to be debated due to inconclusive experimental evidence as a result of limitations in the temporal resolution of non-invasive physiological imaging techniques. To support the available experimental data and shed light onto the source of the cracking sound, we have developed a mathematical model of the events leading to the generation of the sound. The model resolves the dynamics of a collapsing cavitation bubble in the synovial fluid inside a metacarpophalangeal joint during an articular release. The acoustic signature from the resulting bubble dynamics is shown to be consistent in both magnitude and dominant frequency with experimental measurements in the literature and with our own experiments, thus lending support for cavitation bubble collapse as the source of the cracking sound. Finally, the model also shows that only a partial collapse of the bubble is needed to replicate the experimentally observed acoustic spectra, thus allowing for bubbles to persist following the generation of sound as has been reported in recent experiments.
The mode and dynamics of glioblastoma cell invasion into a decellularized tissue-derived extracellular matrix-based three-dimensional tumor model
Authors: Koh IlKyoo , Cha Junghwa , Park Junseong , Choi Junjeong , Kang Seok-Gu , Kim Pilnam
Published: March 2018

Glioblastoma multiforme (GBM) is the most common brain tumor with very aggressive and infiltrative. Extracellular matrix (ECM) plays pivotal roles in the infiltrative characteristics of GBM. To understand the invasive characteristic of GBM, it is necessary to study cell-ECM interaction in the physiologically relevant biomimetic model that recapitulates the GBM-specific ECM microenvironment. Here, we propose biomimetic GBM-specific ECM microenvironment for studying mode and dynamics of glioblastoma cell invasion. Using tissue decellularization process, we constructed a patient tissue-derived ECM (pdECM)-based three-dimensional in vitro model. In our model, GBM cells exhibited heterogeneous morphology and altered the invasion routes in a microenvironment-adaptive manner. We further elucidate the effects of inhibition of ECM remodeling-related enzymatic activity (Matrix metalloproteinase (MMP) 2/9, hyaluronan synthase (HAS)) on GBM cell invasion. Interestingly, after blocking both enzyme activity, GBM cells underwent morphological transition and switch the invasion mode. Such adaptability could render cell invasion resistant to anti-cancer target therapy. There results provide insight of how organ-specific matrix differentially regulates cancer cell phenotype, and have significant implications for the design of matrix with appropriate physiologically relevant properties for in vitro tumor model.
Seasonal bacterial community succession in four typical wastewater treatment plants: correlations between core microbes and process performance
Authors: Zhang Bo , Yu Quanwei , Yan Guoqi , Zhu Hubo , Xu Xiang yang , Zhu Liang
Published: March 2018

To understand the seasonal variation of the activated sludge (AS) bacterial community and identify core microbes in different wastewater processing systems, seasonal AS samples were taken from every biological treatment unit within 4 full-scale wastewater treatment plants. These plants adopted A2/O, A/O and oxidation ditch processes and were active in the treatment of different types and sources of wastewater, some domestic and others industrial. The bacterial community composition was analyzed using high-throughput sequencing technology. The correlations among microbial community structure, dominant microbes and process performance were investigated. Seasonal variation had a stronger impact on the AS bacterial community than any variation within different wastewater treatment system. Facing seasonal variation, the bacterial community within the oxidation ditch process remained more stable those in either the A2/O or A/O processes. The core genera in domestic wastewater treatment systems were Nitrospira, Caldilineaceae, Pseudomonas and Lactococcus. The core genera in the textile dyeing and fine chemical industrial wastewater treatment systems were Nitrospira, Thauera and Thiobacillus.
Cascaded neural networks improving fish species prediction accuracy: the role of the biotic information
Authors: Franceschini Simone , Gandola Emanuele , Martinoli Marco , Tancioni Lorenzo , Scardi Michele
Published: March 2018

Species distribution is the result of complex interactions that involve environmental parameters as well as biotic factors. However, methodological approaches that consider the use of biotic variables during the prediction process are still largely lacking. Here, a cascaded Artificial Neural Networks (ANN) approach is proposed in order to increase the accuracy of fish species occurrence estimates and a case study forLeucos aulain NE Italy is presented as a demonstration case. Potentially useful biotic information (i.e. occurrence of other species) was selected by means of tetrachoric correlation analysis and on the basis of the improvements it allowed to obtain relative to models based on environmental variables only. The prediction accuracy of theL.aulamodel based on environmental variables only was improved by the addition of occurrence data forA.arborellaandS.erythrophthalmus. While biotic information was needed to train the ANNs, the final cascaded ANN model was able to predictL.aulabetter than a conventional ANN using environmental variables only as inputs. Results highlighted that biotic information provided by occurrence estimates for non-target species whose distribution can be more easily and accurately modeled may play a very useful role, providing additional predictive variables to target species distribution models.
Functional analysis of the Drosophila RhoGAP Cv-c protein and its equivalence to the human DLC3 and DLC1 proteins
Authors: Sotillos Sol , Aguilar-Aragon Mario , Hombría James Castelli-Gair
Published: March 2018

RhoGAP proteins control the precise regulation of the ubiquitous small RhoGTPases. The Drosophila Crossveinless-c (Cv-c) RhoGAP is homologous to the human tumour suppressor proteins Deleted in Liver Cancer 1–3 (DLC1-3) sharing an identical arrangement of SAM, GAP and START protein domains. Here we analyse in Drosophila the requirement of each Cv-c domain to its function and cellular localization. We show that the basolateral membrane association of Cv-c is key for its epithelial function and find that the GAP domain targeted to the membrane can perform its RhoGAP activity independently of the rest of the protein, implying the SAM and START domains perform regulatory roles. We propose the SAM domain has a repressor effect over the GAP domain that is counteracted by the START domain, while the basolateral localization is mediated by a central, non-conserved Cv-c region. We find that DLC3 and Cv-c expression in the Drosophila ectoderm cause identical effects. In contrast, DLC1 is inactive but becomes functional if the central non-conserved DLC1 domain is substituted for that of Cv-c. Thus, these RhoGAP proteins are functionally equivalent, opening up the use of Drosophila as an in vivo model to analyse pharmacologically and genetically the human DLC proteins.
Cardiac Actions of a Small Molecule Inhibitor Targeting GATA4–NKX2-5 Interaction
Authors: Kinnunen Sini M. , Tölli Marja , Välimäki Mika J. , Gao Erhe , Szabo Zoltan , Rysä Jaana , Ferreira Mónica P. A. , Ohukainen Pauli , Serpi Raisa , Correia Alexandra , Mäkilä Ermei , Salonen Jarno , Hirvonen Jouni , Santos Hélder A. , Ruskoaho Heikki
Published: March 2018

Transcription factors are fundamental regulators of gene transcription, and many diseases, such as heart diseases, are associated with deregulation of transcriptional networks. In the adult heart, zinc-finger transcription factor GATA4 is a critical regulator of cardiac repair and remodelling. Previous studies also suggest that NKX2-5 plays function role as a cofactor of GATA4. We have recently reported the identification of small molecules that either inhibit or enhance the GATA4–NKX2-5 transcriptional synergy. Here, we examined the cardiac actions of a potent inhibitor (3i-1000) of GATA4–NKX2-5 interaction in experimental models of myocardial ischemic injury and pressure overload. In mice after myocardial infarction, 3i-1000 significantly improved left ventricular ejection fraction and fractional shortening, and attenuated myocardial structural changes. The compound also improved cardiac function in an experimental model of angiotensin II -mediated hypertension in rats. Furthermore, the up-regulation of cardiac gene expression induced by myocardial infarction and ischemia reduced with treatment of 3i-1000 or when micro- and nanoparticles loaded with 3i-1000 were injected intramyocardially or intravenously, respectively. The compound inhibited stretch- and phenylephrine-induced hypertrophic response in neonatal rat cardiomyocytes. These results indicate significant potential for small molecules targeting GATA4–NKX2-5 interaction to promote myocardial repair after myocardial infarction and other cardiac injuries.
Rare variants in drug target genes contributing to complex diseases, phenome-wide
Authors: Verma Shefali Setia , Josyula Navya , Verma Anurag , Zhang Xinyuan , Veturi Yogasudha , Dewey Frederick E. , Hartzel Dustin N. , Lavage Daniel R. , Leader Joe , Ritchie Marylyn D. , Pendergrass Sarah A.
Published: March 2018

The DrugBank database consists of ~800 genes that are well characterized drug targets. This list of genes is a useful resource for association testing. For example, loss of function (LOF) genetic variation has the potential to mimic the effect of drugs, and high impact variation in these genes can impact downstream traits. Identifying novel associations between genetic variation in these genes and a range of diseases can also uncover new uses for the drugs that target these genes. Phenome Wide Association Studies (PheWAS) have been successful in identifying genetic associations across hundreds of thousands of diseases. We have conducted a novel gene based PheWAS to test the effect of rare variants in DrugBank genes, evaluating associations between these genes and more than 500 quantitative and dichotomous phenotypes. We used whole exome sequencing data from 38,568 samples in Geisinger MyCode Community Health Initiative. We evaluated the results of this study when binning rare variants using various filters based on potential functional impact. We identified multiple novel associations, and the majority of the significant associations were driven by functionally annotated variation. Overall, this study provides a sweeping exploration of rare variant associations within functionally relevant genes across a wide range of diagnoses.
Author Correction: Metabolic pathway and cell adaptation mechanisms revealed through genomic, proteomic and transcription analysis of a Sphingomonas haloaromaticamans strain degrading ortho-phenylphenol
Authors: Perruchon Chiara , Vasileiadis Sotirios , Rousidou Constantina , Papadopoulou Evangelia S. , Tanou Georgia , Samiotaki Martina , Garagounis Constantinos , Molassiotis Athanasios , Papadopoulou Kalliope K. , Karpouzas Dimitrios G.
Published: March 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.
Assessment of intrinsic and extrinsic signaling pathway in excitotoxic retinal ganglion cell death
Authors: Fahrenthold Berkeley K. , Fernandes Kimberly A. , Libby Richard T.
Published: March 2018

Excitotoxicity leads to the activation of a cytotoxic cascade that causes neuronal death. In the retina, retinal ganglion cells (RGCs) die after an excitotoxic insult. Multiple pathways have been proposed to contribute to RGC death after an excitotoxic insult, including TNF signaling, JNK activation, and ER stress. To test the importance of these pathways in RGC death after excitotoxic injury, the excitotoxin N-methyl-D-aspartate (NMDA) was intravitreally injected into mice deficient in components of these pathways. Absence ofTnfor its canonical downstream mediator,Bid, did not confer short- or long-term protection to RGCs. Despite known activation in RGCs and a prominent role in mediating RGC death after other insults, attenuating JNK signaling did not prevent RGC death after excitotoxic insult. Additionally, deficiency of the ER stress protein DDIT3 (CHOP), which has been shown to be involved in RGC death, did not lessen NMDA induced RGC death. Furthermore, absence of bothJun(JNK’s canonical target) andDdit3, which together provide robust, long-term protection to RGC somas after axonal insult, did not lessen RGC death. Collectively, these results indicate that the drivers of excitotoxic injury remain to be identified and/or multiple cell death pathways are activated in response to injury.
Fusion of a highly N-glycosylated polypeptide increases the expression of ER-localized proteins in plants
Authors: Kang Hyangju , Park Youngmin , Lee Yongjik , Yoo Yun-Joo , Hwang Inhwan
Published: March 2018

Plants represent promising systems for producing various recombinant proteins. One key area of focus for improving this technology is developing methods for producing recombinant proteins at high levels. Many methods have been developed to increase the transcript levels of recombinant genes. However, methods for increasing protein production involving steps downstream of transcription, including translation, have not been fully explored. Here, we investigated the effects of N-glycosylation on protein production and provide evidence that N-glycosylation greatly increases the expression levels of ER-targeted recombinant proteins. Fusion of the extracellular domain (M domain) of protein tyrosine phosphatase receptor type C (CD45), which contains four putative N-glycosylation sites to a model protein, leptin at the C-terminus, increased recombinant protein levels by 6.1 fold. This increase was specific to ER-targeted proteins and was dependent on N-glycosylation. Moreover, expression levels of leptin, leukemia inhibitory factor and GFP were also greatly increased by fusion of M domain at either the N or C-terminus. Furthermore, the increase in protein levels resulted from enhanced translation, but not transcription. Based on these results, we propose that fusing a small domain containing N-glycosylation sites to target proteins is a powerful technique for increasing the expression levels of recombinant proteins in plants.
Exploring Ugi-Azide Four-Component Reaction Products for Broad-Spectrum Influenza Antivirals with a High Genetic Barrier to Drug Resistance
Authors: Zhang Jiantao , Hu Yanmei , Foley Christopher , Wang Yuanxiang , Musharrafieh Rami , Xu Shuting , Zhang Yongtao , Ma Chunlong , Hulme Christopher , Wang Jun
Published: March 2018

Influenza viruses are respiratory pathogens that are responsible for seasonal influenza and sporadic influenza pandemic. The therapeutic efficacy of current influenza vaccines and small molecule antiviral drugs is limited due to the emergence of multidrug-resistant influenza viruses. In response to the urgent need for the next generation of influenza antivirals, we utilized a fast-track drug discovery platform by exploring multi-component reaction products for antiviral drug candidates. Specifically, molecular docking was applied to screen a small molecule library derived from the Ugi-azide four-component reaction methodology for inhibitors that target the influenza polymerase PAC-PB1N interactions. One hit compound 5 was confirmed to inhibit PAC-PB1N interactions in an ELISA assay and had potent antiviral activity in an antiviral plaque assay. Subsequent structure-activity relationship studies led to the discovery of compound 12a, which had broad-spectrum antiviral activity and a higher in vitro genetic barrier to drug resistance than oseltamivir. Overall, the discovery of compound 12a as a broad-spectrum influenza antiviral with a high in vitro genetic barrier to drug resistance is significant, as it offers a second line of defense to combat the next influenza epidemics and pandemics if vaccines and oseltamivir fail to confine the disease outbreak.
In situ immobilisation of toxic metals in soil using Maifan stone and illite/smectite clay
Authors: Ou Jieyong , Li Hong , Yan Zengguang , Zhou Youya , Bai Liping , Zhang Chaoyan , Wang Xuedong , Chen Guikui
Published: March 2018

Clay minerals have been proposed as amendments for remediating metal-contaminated soils owing to their abundant reserves, high performance, simplicity of use and low cost. Two novel clay minerals, Maifan stone and illite/smectite clay, were examined in the in situ immobilisation of soil metals. The application of 0.5% Maifan stone or illite/smectite clay to field soils significantly decreased the fractions of diethylenetriaminepentaacetic acid (DTPA)-extractable Cd, Ni, Cr, Zn, Cu and Pb. Furthermore, reductions of 35.4% and 7.0% in the DTPA-extractable fraction of Cd were obtained with the Maifan stone and illite/smectite clay treatments, respectively, which also significantly reduced the uptake of Cd, Ni, Cr, Zn, Cu and Pb in the edible parts of Brassica rapa subspecies pekinensis, Brassica campestris and Spinacia oleracea. Quantitatively, the Maifan stone treatment reduced the metal uptake in B. rapa ssp. Pekinensis, B. campestris and S. oleracea from 11.6% to 62.2%, 4.6% to 41.8% and 11.3% to 58.2%, respectively, whereas illite/smectite clay produced reductions of 8.5% to 62.8% and 4.2% to 37.6% in the metal uptake in B. rapa ssp. Pekinensis and B. campestris, respectively. Therefore, both Maifan stone and illite/smectite clay are promising amendments for contaminated soil remediation.
The evolution of insecticide resistance in the brown planthopper (Nilaparvata lugens Stål) of China in the period 2012–2016
Authors: Wu Shun-Fan , Zeng Bin , Zheng Chen , Mu Xi-Chao , Zhang Yong , Hu Jun , Zhang Shuai , Gao Cong-Fen , Shen Jin-Liang
Published: March 2018

The brown planthopper,Nilaparvata lugens, is an economically important pest on rice in Asia. Chemical control is still the most efficient primary way for rice planthopper control. However, due to the intensive use of insecticides to control this pest over many years, resistance to most of the classes of chemical insecticides has been reported. In this article, we report on the status of eight insecticides resistance inNilaparvata lugens(Stål) collected from China over the period 2012–2016. All of the field populations collected in 2016 had developed extremely high resistance to imidacloprid, thiamethoxam, and buprofezin. Synergism tests showed that piperonyl butoxide (PBO) produced a high synergism of imidacloprid, thiamethoxam, and buprofezin effects in the three field populations, YA2016, HX2016, and YC2016. Functional studies using both double-strand RNA (dsRNA)-mediated knockdown in the expression ofCYP6ER1and transgenic expression ofCYP6ER1inDrosophila melanogastershowed thatCYP6ER1confers imidacloprid, thiamethoxam and buprofezin resistance. These results will be beneficial for effective insecticide resistance management strategies to prevent or delay the development of insecticide resistance in brown planthopper populations.
Analytical prediction of the piezoelectric d33 response of fluoropolymer arrays with tubular air channels
Authors: Zhukov Sergey , Eder-Goy Dagmar , Fedosov Sergey , Xu Bai-Xiang , von Seggern Heinz
Published: March 2018

The present study is focused on tubular multi-channel arrays composed of commercial fluoropolymer (FEP) tubes with different wall thickness. After proper charging in a high electric field, such tubular structures exhibit a large piezoelectric $${{\boldsymbol{d}}}_{{\bf{33}}}$$

d

33

coefficient significantly exceeding the values of classical polymer ferroelectrics and being even comparable to conventional lead-free piezoceramics. The quasistatic piezoelectric $${{\boldsymbol{d}}}_{{\bf{33}}}$$

d

33

coefficient was theoretically derived and its upper limits were evaluated considering charging and mechanical properties of the arrays. In order to optimize the $${{\boldsymbol{d}}}_{{\bf{33}}}$$

d

33

coefficient the remanent polarization and the mechanical properties were taken into account, both being strongly dependent on the air channel geometry as well as on the wall thickness of the FEP tubes. The model predictions are compared with experimental d33 coefficients for two particular arrays with equal air gaps of 250 μm, but with different wall thickness of utilized FEP tubes of 50 μm and 120 μm, respectively. Analytical modeling allows for the prediction that arrays made of FEP tubes with a wall thickness of 10 μm are foreseen to exhibit a superb piezoelectric response of up to 600 pC/N if the height of stadium-like shaped air channels is reduced down to 50 μm, making them potentially interesting for application as highly sensitive sensors and energy harvesting.
Helminth infection protects against high fat diet-induced obesity via induction of alternatively activated macrophages
Authors: Su Chien wen , Chen Chih-Yu , Li Yali , Long Shao Rong , Massey William , Kumar Deepak Vijaya , Walker W. Allan , Shi Hai Ning
Published: March 2018

Epidemiological studies indicate an inverse correlation between the prevalence of the so-called western diseases, such as obesity and metabolic syndrome, and the exposure to helminths. Obesity, a key risk factor for many chronic health problems, is rising globally and is accompanied by low-grade inflammation in adipose tissues. The precise mechanism by which helminths modulate metabolic syndrome and obesity is not fully understood. We infected high fat diet (HFD)-induced obese mice with the intestinal nematode parasite Heligmosomoides polygyrus and observed that helminth infection resulted in significantly attenuated obesity. Attenuated obesity corresponded with marked upregulation of uncoupling protein 1 (UCP1), a key protein involved in energy expenditure, in adipose tissue, suppression of glucose and triglyceride levels, and alteration in the expression of key genes involved in lipid metabolism. Moreover, the attenuated obesity in infected mice was associated with enhanced helminth-induced Th2/Treg responses and M2 macrophage polarization. Adoptive transfer of helminth-stimulated M2 cells to mice that were not infected with H. polygyrus resulted in a significant amelioration of HFD-induced obesity and increased adipose tissue browning. Thus, our results provide evidence that the helminth-dependent protection against obesity involves the induction of M2 macrophages.
In-situ tensile testing of ZrCu-based metallic glass composites
Authors: Sun H. C. , Ning Z. L. , Wang G. , Liang W. Z. , Pauly S. , Huang Y. J. , Guo S. , Xue X. , Sun J. F.
Published: March 2018

ZrCu-based bulk metallic glass composites (BMGCs) are well known for their plastic deformability, superior to traditional metallic glasses (MGs), which is attributed to a unique dual-phases structure, namely, the glassy matrix and unstable B2 phase. In the present study, in-situ tensile testing is used to trace the deformation process of a ZrCu-based BMGC. Three deformation stages of the BMGC, i.e., the elastic-elastic stage, the elastic-plastic stage, and the plastic-plastic stage are identified. In the elastic-elastic and elastic-plastic stages, the yield strength and elastic limit are major influenced by the volume fraction of the B2 crystals. In the plastic-plastic stage, the B2 phase stimulates the formation of multiple shear bands and deflects the direction of shear bands by disturbing the stress field in front of the crack tip. The deformation-induced martensitic transformation of the metastable B2 phase contributes to the plasticity and work hardening of the composite. This study highlights the formation and propagation of multiple shear bands and reveals the interactions of shear bands with structural heterogeneities in situ. Especially, the blocking of shear bands by crystals and the martensitic transformation of the B2 phase are critical for the mechanistic deformation process and illustrate the function of the B2 phase in the present BMGCs.
Hemocytes in the extrapallial space of Pinctada fucata are involved in immunity and biomineralization
Authors: Huang Jingliang , Li Shiguo , Liu Yangjia , Liu Chuang , Xie Liping , Zhang Rongqing
Published: March 2018

In bivalves, the mantle tissue secretes organic matrix and inorganic ions into the extrapallial space (EPS) to form the shells. In addition, more and more evidences indicate the participation of hemocytes in shell mineralization, but no direct evidence has been reported that verifies the presence of hemocytes in the EPS, and their exact roles in biomineralization remain uncertain. Here, we identified hemocytes from the EPS of Pinctada fucata. Numerous components involved in cellular and humoral immunity were identified by proteome analysis, together with several proteins involved in calcium metabolism. The hemocytes exerted active phagocytosis and significantly upregulated the expression of immune genes after immune stimulation. A group of granulocytes were found to contain numerous calcium-rich vesicles and crystals, which serve as a calcium pool. During shell regeneration, some genes involved in calcium metabolism are upregulated. Strikingly, most of the shell matrix proteins were absent in the hemocytes, suggesting that they might not be solely responsible for directing the growth of the shell. Taken together, our results provided comprehensive information about the function of hemocytes in immunity and shell formation.
Single- and two-photon imaging of human micrometastases and disseminated tumour cells with conjugates of nanobodies and quantum dots
Authors: Ramos-Gomes Fernanda , Bode Julia , Sukhanova Alyona , Bozrova Svetlana V. , Saccomano Mara , Mitkovski Miso , Krueger Julia Eva , Wege Anja K. , Stuehmer Walter , Samokhvalov Pavel S. , Baty Daniel , Chames Patrick , Nabiev Igor , Alves Frauke
Published: March 2018

Early detection of malignant tumours and, especially, micrometastases and disseminated tumour cells is still a challenge. In order to implement highly sensitive diagnostic tools we demonstrate the use of nanoprobes engineered from nanobodies (single-domain antibodies, sdAbs) and fluorescent quantum dots (QDs) for single- and two-photon detection and imaging of human micrometastases and disseminated tumour cells in ex vivo biological samples of breast and pancreatic metastatic tumour mouse models expressing human epidermal growth factor receptor 2 (HER2) or carcinoembryonic antigen (CEA). By staining thin (5–10 µm) paraffin and thick (50 µm) agarose tissue sections, we detected HER2- and CEA-positive human tumour cells infiltrating the surrounding tissues or metastasizing to different organs, including the brain, testis, lung, liver, and lymph nodes. Compared to conventional fluorescently labelled antibodies the sdAb-HER2-QD and sdAb-CEA-QD nanoprobes are superior in detecting micrometastases in tissue sections by lower photobleaching and higher brightness of fluorescence signals ensuring much better discrimination of positive signals versus background. Very high two-photon absorption cross-sections of QDs and small size of the nanoprobes ensure efficient imaging of thick tissue sections unattainable with conventional fluorescent probes. The nanobody–QD probes will help to improve early cancer diagnosis and prognosis of progression by assessing metastasis.
Simple size-controlled synthesis of Au nanoparticles and their size-dependent catalytic activity
Authors: Suchomel Petr , Kvitek Libor , Prucek Robert , Panacek Ales , Halder Avik , Vajda Stefan , Zboril Radek
Published: March 2018

The controlled preparation of Au nanoparticles (NPs) in the size range of 6 to 22 nm is explored in this study. The Au NPs were prepared by the reduction of tetrachloroauric acid using maltose in the presence of nonionic surfactant Tween 80 at various concentrations to control the size of the resulting Au NPs. With increasing concentration of Tween 80 a decrease in the size of produced Au NPs was observed, along with a significant decrease in their size distribution. The size-dependent catalytic activity of the synthesized Au NPs was tested in the reduction of 4-nitrophenol with sodium borohydride, resulting in increasing catalytic activity with decreasing size of the prepared nanoparticles. Eley-Rideal catalytic mechanism emerges as the more probable, in contrary to the Langmuir-Hinshelwood mechanism reported for other noble metal nanocatalysts.
An acute functional screen identifies an effective antibody targeting amyloid-β oligomers based on calcium imaging
Authors: Wang Xueying , Kastanenka Ksenia V. , Arbel-Ornath Michal , Commins Caitlin , Kuzuya Akira , Lariviere Amanda J. , Krafft Grant A. , Hefti Franz , Jerecic Jasna , Bacskai Brian J.
Published: March 2018

Soluble amyloid β oligomers (AβOs) are widely recognized neurotoxins that trigger aberrant signaling in specific subsets of neurons, leading to accumulated neuronal damage and memory disorders in Alzheimer’s disease (AD). One of the profound downstream consequences of AβO-triggered events is dysregulation of cytosolic calcium concentration ([Ca2+]i), which has been implicated in synaptic failure, cytoskeletal abnormalities, and eventually neuronal death. We have developed an in vitro/in vivo drug screening assay to evaluate putative AβO-blocking candidates by measuring AβO-induced real-time changes in [Ca2+]i. Our screening assay demonstrated that the anti-AβO monoclonal antibody ACU3B3 exhibits potent blocking capability against a broad size range of AβOs. We showed that picomolar concentrations of AβOs were capable of increasing [Ca2+]i in primary neuronal cultures, an effect prevented by ACU3B3. Topical application of 5 nM AβOs onto exposed cortical surfaces also elicited significant calcium elevations in vivo, which was completely abolished by pre-treatment of the brain with 1 ng/mL (6.67 pM) ACU3B3. Our results provide strong support for the utility of this functional screening assay in identifying and confirming the efficacy of AβO-blocking drug candidates such as the human homolog of ACU3B3, which may emerge as the first experimental AD therapeutic to validate the amyloid oligomer hypothesis.
Electroencephalographic derived network differences in Lewy body dementia compared to Alzheimer’s disease patients
Authors: Peraza Luis R. , Cromarty Ruth , Kobeleva Xenia , Firbank Michael J. , Killen Alison , Graziadio Sara , Thomas Alan J. , O’Brien John T. , Taylor John-Paul
Published: March 2018

Dementia with Lewy bodies (DLB) and Alzheimer’s disease (AD) require differential management despite presenting with symptomatic overlap. Currently, there is a need of inexpensive DLB biomarkers which can be fulfilled by electroencephalography (EEG). In this regard, an established electrophysiological difference in DLB is a decrease of dominant frequency (DF)—the frequency with the highest signal power between 4 and 15 Hz. Here, we investigated network connectivity in EEG signals acquired from DLB patients, and whether these networks were able to differentiate DLB from healthy controls (HCs) and associated dementias. We analysed EEG recordings from old adults: HCs, AD, DLB and Parkinson’s disease dementia (PDD) patients. Brain networks were assessed with the minimum spanning tree (MST) within six EEG bands: delta, theta, high-theta, alpha, beta and DF. Patients showed lower alpha band connectivity and lower DF than HCs. DLB and PDD showed a randomised MST compared with HCs and AD in high-theta and alpha but not in DF. The MST randomisation in DLB and PDD reflects decreased brain efficiency as well as impaired neural synchronisation. However, the lack of network topology differences at the DF between all dementia groups and HCs may indicate a compensatory response of the brain to the neuropathology.
Non-invasive detection of adeno-associated viral gene transfer using a genetically encoded CEST-MRI reporter gene in the murine heart
Authors: Meier Shelby , Gilad Assaf A. , Brandon J. Anthony , Qian Chenghao , Gao Erhe , Abisambra Jose F. , Vandsburger Moriel
Published: March 2018

Research into gene therapy for heart failure has gained renewed interest as a result of improved safety and availability of adeno-associated viral vectors (AAV). While magnetic resonance imaging (MRI) is standard for functional assessment of gene therapy outcomes, quantitation of gene transfer/expression relies upon tissue biopsy, fluorescence or nuclear imaging. Imaging of gene expression through the use of genetically encoded chemical exchange saturation transfer (CEST)-MRI reporter genes could be combined with clinical cardiac MRI methods to comprehensively probe therapeutic gene expression and subsequent outcomes. The CEST-MRI reporter gene Lysine Rich Protein (LRP) was cloned into an AAV9 vector and either administered systemically via tail vein injection or directly injected into the left ventricular free wall of mice. Longitudinal in vivo CEST-MRI performed at days 15 and 45 after direct injection or at 1, 60 and 90 days after systemic injection revealed robust CEST contrast in myocardium that was later confirmed to express LRP by immunostaining. Ventricular structure and function were not impacted by expression of LRP in either study arm. The ability to quantify and link therapeutic gene expression to functional outcomes can provide rich data for further development of gene therapy for heart failure.
Microbial dynamics and metabolite changes in Chinese Rice Wine fermentation from sorghum with different tannin content
Authors: Xu Jialiang , Wu Huijun , Wang Zhiwei , Zheng Fuping , Lu Xin , Li Zhenpeng , Ren Qing
Published: March 2018

Chinese rice wine (CRW) is the oldest kind of wine in China and is mainly fermented by wheat Qu and yeast with rice, millet, etc. This gives CRW a unique quality, but the flavor components are complex. Its formation is related to microorganisms, but the link between CRW and microorganisms is poorly understood. Here, we used two kinds of sorghum (JZ22 and JB3, of which JZ22 has a higher tannin content) as the raw materials to brew and determined the structural and functional dynamics of the microbiota by metagenomics and flavor analyses. We detected 106 (JZ22) and 109 (JB3) volatile flavor compounds and 8 organic acids. By correlation analysis, we established 687 (JZ22) and 496 (JB3) correlations between the major flavor compounds and microbes. In JZ22, Blautia, Collinsella, Bifidobacterium, Faecalibacterium and Prevotella had the most correlations with flavor production. In JB3, the top 5 genera were Stenotrophomonas, Bdellovibrio, Solibacillus, Sulfuritalea and Achromobacter. In addition, more esters were detected, and more microorganisms correlated with ester generation in JZ22. This study provides a new idea for the micro ecological diversity of CRW fermented with sorghum. This is of significance for improving the quality and broadening the CRW varieties.