bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carbon nanotubes allow capture of krypton, barium and lead for multichannel biological X-ray fluorescence imaging
Authors: Serpell Christopher J. , Rutte Reida N. , Geraki Kalotina , Pach Elzbieta , Martincic Markus , Kierkowicz Magdalena , De Munari Sonia , Wals Kim , Raj Ritu , Ballesteros Belén , Tobias Gerard , Anthony Daniel C. , Davis Benjamin G. 
Published: October 2016

AbstractThe desire to study biology in situ has been aided by many imaging techniques. Among these, X-ray fluorescence (XRF) mapping permits observation of elemental distributions in a multichannel manner. However, XRF imaging is underused, in part, because of the difficulty in interpreting maps without an underlying cellular ‘blueprint’; this could be supplied using contrast agents. Carbon nanotubes (CNTs) can be filled with a wide range of inorganic materials, and thus can be used as ‘contrast agents’ if biologically absent elements are encapsulated. Here we show that sealed single-walled CNTs filled with lead, barium and even krypton can be produced, and externally decorated with peptides to provide affinity for sub-cellular targets. The agents are able to highlight specific organelles in multiplexed XRF mapping, and are, in principle, a general and versatile tool for this, and other modes of biological imaging.
The uronic acid content of coccolith-associated polysaccharides provides insight into coccolithogenesis and past climate
Authors: Lee Renee B. Y. , Mavridou Despoina A. I. , Papadakos Grigorios , McClelland Harry L. O. , Rickaby Rosalind E. M. 
Published: October 2016

AbstractUnicellular phytoplanktonic algae (coccolithophores) are among the most prolific producers of calcium carbonate on the planet, with a production of ∼1026coccoliths per year. During their lith formation, coccolithophores mainly employ coccolith-associated polysaccharides (CAPs) for the regulation of crystal nucleation and growth. These macromolecules interact with the intracellular calcifying compartment (coccolith vesicle) through the charged carboxyl groups of their uronic acid residues. Here we report the isolation of CAPs from modern day coccolithophores and their prehistoric predecessors and we demonstrate that their uronic acid content (UAC) offers a species-specific signature. We also show that there is a correlation between the UAC of CAPs and the internal saturation state of the coccolith vesicle that, for most geologically abundant species, is inextricably linked to carbon availability. These findings suggest that the UAC of CAPs reports on the adaptation of coccolithogenesis to environmental changes and can be used for the estimation of past CO2concentrations.
Biotic and abiotic controls on co-occurring nitrogen cycling processes in shallow Arctic shelf sediments
Authors: McTigue N. D. , Gardner W. S. , Dunton K. H. , Hardison A. K. 
Published: October 2016

AbstractThe processes that convert bioavailable inorganic nitrogen to inert nitrogen gas are prominent in continental shelf sediments and represent a critical global sink, yet little is known of these pathways in the Arctic where 18% of the world’s continental shelves are located. Moreover, few data from the Arctic exist that separate loss processes like denitrification and anaerobic ammonium oxidation (anammox) from recycling pathways like dissimilatory nitrate reduction to ammonium (DNRA) or source pathways like nitrogen fixation. Here we present measurements of these co-occurring processes using 15N tracers. Denitrification was heterogeneous among stations and an order of magnitude greater than anammox and DNRA, while nitrogen fixation was undetectable. No abiotic factors correlated with interstation variability in biogeochemical rates; however, bioturbation potential explained most of the variation. Fauna-enhanced denitrification is a potentially important but overlooked process on Arctic shelves and highlights the role of the Arctic as a significant global nitrogen sink.
Wnt and Neuregulin1/ErbB signalling extends 3D culture of hormone responsive mammary organoids
Authors: Jardé Thierry , Lloyd-Lewis Bethan , Thomas Mairian , Kendrick Howard , Melchor Lorenzo , Bougaret Lauriane , Watson Peter D. , Ewan Kenneth , Smalley Matthew J. , Dale Trevor C. 
Published: October 2016

AbstractThe development of in vitro culture systems quantitatively and qualitatively recapitulating normal breast biology is key to the understanding of mammary gland biology. Current three-dimensional mammary culture systems have not demonstrated concurrent proliferation and functional differentiation ex vivo in any system for longer than 2 weeks. Here, we identify conditions including Neuregulin1 and R-spondin 1, allowing maintenance and expansion of mammary organoids for 2.5 months in culture. The organoids comprise distinct basal and luminal compartments complete with functional steroid receptors and stem/progenitor cells able to reconstitute a complete mammary gland in vivo. Alternative conditions are also described that promote enrichment of basal cells organized into multiple layers surrounding a keratinous core, reminiscent of structures observed in MMTV-Wnt1 tumours. These conditions comprise a unique tool that should further understanding of normal mammary gland development, the molecular mechanism of hormone action and signalling events whose deregulation leads to breast tumourigenesis.
A robust gene-stacking method utilizing yeast assembly for plant synthetic biology
Authors: Shih Patrick M. , Vuu Khanh , Mansoori Nasim , Ayad Leïla , Louie Katherine B. , Bowen Benjamin P. , Northen Trent R. , Loqué Dominique 
Published: October 2016

AbstractThe advent and growth of synthetic biology has demonstrated its potential as a promising avenue of research to address many societal needs. However, plant synthetic biology efforts have been hampered by a dearth of DNA part libraries, versatile transformation vectors and efficient assembly strategies. Here, we describe a versatile system (named jStack) utilizing yeast homologous recombination to efficiently assemble DNA into plant transformation vectors. We demonstrate how this method can facilitate pathway engineering of molecules of pharmaceutical interest, production of potential biofuels and shuffling of disease-resistance traits between crop species. Our approach provides a powerful alternative to conventional strategies for stacking genes and traits to address many impending environmental and agricultural challenges.
AtSWEET13 and AtSWEET14 regulate gibberellin-mediated physiological processes
Authors: Kanno Yuri , Oikawa Takaya , Chiba Yasutaka , Ishimaru Yasuhiro , Shimizu Takafumi , Sano Naoto , Koshiba Tomokazu , Kamiya Yuji , Ueda Minoru , Seo Mitsunori 
Published: October 2016

AbstractTransmembrane transport of plant hormones is required for plant growth and development. Despite reports of a number of proteins that can transport the plant hormone gibberellin (GA), the mechanistic basis for GA transport and the identities of the transporters involved remain incomplete. Here, we provide evidence that Arabidopsis SWEET proteins, AtSWEET13 and AtSWEET14, which are members of a family that had previously been linked to sugar transport, are able to mediate cellular GA uptake when expressed in yeast and oocytes. A double sweet13 sweet14 mutant has a defect in anther dehiscence and this phenotype can be reversed by exogenous GA treatment. In addition, sweet13 sweet14 exhibits altered long distant transport of exogenously applied GA and altered responses to GA during germination and seedling stages. These results suggest that AtSWEET13 and AtSWEET14 may be involved in modulating GA response in Arabidopsis.
In vivo correction of anaemia in β-thalassemic mice by γPNA-mediated gene editing with nanoparticle delivery
Authors: Bahal Raman , Ali McNeer Nicole , Quijano Elias , Liu Yanfeng , Sulkowski Parker , Turchick Audrey , Lu Yi-Chien , Bhunia Dinesh C. , Manna Arunava , Greiner Dale L. , Brehm Michael A. , Cheng Christopher J. , López-Giráldez Francesc , Ricciardi Adele , Beloor Jagadish , Krause Diane S. , Kumar Priti , Gallagher Patrick G. , Braddock Demetrios T. , Mark Saltzman W. , Ly Danith H. , Glazer Peter M. 
Published: October 2016

AbstractThe blood disorder, β-thalassaemia, is considered an attractive target for gene correction. Site-specific triplex formation has been shown to induce DNA repair and thereby catalyse genome editing. Here we report that triplex-forming peptide nucleic acids (PNAs) substituted at the γ position plus stimulation of the stem cell factor (SCF)/c-Kit pathway yielded high levels of gene editing in haematopoietic stem cells (HSCs) in a mouse model of human β-thalassaemia. Injection of thalassemic mice with SCF plus nanoparticles containing γPNAs and donor DNAs ameliorated the disease phenotype, with sustained elevation of blood haemoglobin levels into the normal range, reduced reticulocytosis, reversal of splenomegaly and up to 7% β-globin gene correction in HSCs, with extremely low off-target effects. The combination of nanoparticle delivery, next generation γPNAs and SCF treatment may offer a minimally invasive treatment for genetic disorders of the blood that can be achieved safely and simply by intravenous administration.
Efficacy and safety of levodopa–carbidopa intestinal gel from a study in Japanese, Taiwanese, and Korean advanced Parkinson’s disease patients
Authors: Murata Miho , Mihara Masahito , Hasegawa Kazuko , Jeon Beomseok , Tsai Chon-Haw , Nishikawa Noriko , Oeda Tomoko , Yokoyama Masayuki , Robieson Weining Z , Ryman Davis , Eaton Susan , Chatamra Krai , Benesh Janet 
Published: October 2016

AbstractIn a previous multinational, randomized, double-blind, double-dummy study, levodopa–carbidopa intestinal gel (LCIG) was tolerable and significantly improved ‘off’ time in advanced Parkinson’s disease (PD) patients. However, efficacy and safety in the Asian population has not yet been demonstrated. In this open-label study, efficacy and safety of LCIG were assessed in Japanese, Korean, and Taiwanese advanced PD patients with motor complications not adequately controlled by available PD medication. The patients were treated with LCIG monotherapy for 12 weeks. The primary end point was the mean change from baseline to week 12 in ‘off’ time, as reported in the PD Symptom Diary, normalized to a 16 h waking day and analyzed by a mixed-model repeated-measures analysis. Adverse events (AEs) were recorded. Thirty-one patients were enrolled (23 Japanese, 4 Taiwanese, 4 Korean) and 28 (90%) completed the study. For those who completed the study, the mean (s.d.) total daily levodopa dose from LCIG was 1,206.3 (493.6) mg/day at final visit (n=28); last observation carried forward (n=30) was 1,227.6 (482.8) mg/day. There was a significant mean change (s.d.) of −4.6 (3.0) hours of ‘off’ time from baseline (mean (s.d.)=7.4 (2.3)) to week 12 (n=29), P<0.001. All the patients had an AE, with the most frequently reported being incision site pain (42%); 1 (3.2%) discontinued treatment because of an AE and later died because of sepsis, which the investigator considered unrelated to LCIG treatment. These results suggest that LCIG is efficacious and tolerable in Japanese, Taiwanese, and Korean advanced PD patients.
Extracellular HSP60 triggers tissue regeneration and wound healing by regulating inflammation and cell proliferation
Authors: Pei Wuhong , Tanaka Katsuya , Huang Sunny C , Xu Lisha , Liu Baoying , Sinclair Jason , Idol Jennifer , Varshney Gaurav K , Huang Haigen , Lin Shuo , Nussenblatt Robert B , Mori Ryoichi , Burgess Shawn M 
Published: October 2016

AbstractAfter injury, zebrafish can restore many tissues that do not regenerate well in mammals, making it a useful vertebrate model for studying regenerative biology. We performed a systematic screen to identify genes essential for hair cell regeneration in zebrafish, and found that the heat shock protein Hspd1 (Hsp60) has a critical role in the regeneration of hair cells and amputated caudal fins. We showed HSP60-injected extracellularly promoted cell proliferation and regeneration in both hair cells and caudal fins. We showed that hspd1 mutant was deficient in leukocyte infiltration at the site of injury. Topical application of HSP60 in a diabetic mouse skin wound model dramatically accelerated wound healing compared with controls. Stimulation of human peripheral blood mononuclear cells with HSP60 triggered a specific induction of M2 phase CD163-positive monocytes. Our results demonstrate that the normally intracellular chaperonin HSP60 has an extracellular signalling function in injury inflammation and tissue regeneration, likely through promoting the M2 phase for macrophages.
Diverse Colletotrichum species cause anthracnose of tea plants (Camellia sinensis (L.) O. Kuntze) in China
Authors: Wang Yu-Chun , Hao Xin-Yuan , Wang Lu , Bin Xiao  , Wang Xin-Chao , Yang Ya-Jun 
Published: October 2016

AbstractAnthracnose caused by Colletotrichum is one of the most severe diseases that can afflict Camellia sinensis. However, research on the diversity and geographical distribution of Colletotrichum in China remain limited. In this study, 106 Colletotrichum isolates were collected from diseased leaves of Ca. sinensis cultivated in the 15 main tea production provinces in China. Multi-locus phylogenetic analysis coupled with morphological identification showed that the collected isolates belonged to 11 species, including 6 known species (C. camelliae, C. cliviae, C. fioriniae, C. fructicola, C. karstii, and C. siamense), 3 new record species (C. aenigma, C. endophytica, and C. truncatum), 1 novel species (C. wuxiense), and 1 indistinguishable strain, herein described as Colletotrichum sp. Of these species, C. camelliae and C. fructicola were the dominant species causing anthracnose in Ca. sinensis. In addition, our study provided further evidence that phylogenetic analysis using a combination of ApMat and GS sequences can be used to effectively resolve the taxonomic relationships within the C. gloeosporioides species complex. Finally, pathogenicity tests suggested that C. camelliae, C. aenigma, and C. endophytica are more invasive than other species after the inoculation of the leaves of Ca. sinensis.
Problems and Solutions in Click Chemistry Applied to Drug Probes
Authors: Zhong Weilong , Sun Bo , Lu Cheng , Yu Hengheng , Wang Changhua , He Lingfei , Gu Ju , Chen Shuang , Liu Yanrong , Jing Xiangyan , Bi Zhun , Yang Guang , Zhou Honggang , Sun Tao , Yang Cheng 
Published: October 2016

AbstractSmall-molecule fluorescent probes have been widely used in target identification, but this method has many disadvantages. For example, the identified proteins are usually complex, and additional biochemical studies are needed to distinguish real targets from interference results. To address this problem, we propose a series of strategies for improving the efficiency of target identification. First, pretreatment with a lower concentration of hydrogen peroxide can shield against thiol interference. Second, the use of benzophenone as a photo-affinity group is not appropriate, and diazirines are preferred. Third, if cytoskeleton proteins or stress proteins are captured, the interference must be carefully eliminated. The specificity of target identification can be improved by optimizing these three strategies. In this paper, we discuss the problems associated with the use of the click reaction in living cells and provide important complementary techniques for photo-affinity probes based on the click chemistry reaction.
Specific inhibition of ICAM-1 effectively reduces bladder inflammation in a rat model of severe non-bacterial cystitis
Authors: Zhang Xiang , He Hongchao , Lu Guoliang , Xu Tianyuan , Qin Liang , Wang Xianjin , Jin Xingwei , Liu Boke , Zhao Zhonghua , Shen Zhoujun , Shao Yuan 
Published: October 2016

AbstractThe development and progression of bladder pain syndrome/interstitial cystitis (BPS/IC) is closely related to bladder inflammation. Intercellular adhesion molecule 1 (ICAM-1) is associated with bladder inflammation in BPS/IC. We investigated the effect of specific inhibition of ICAM-1 using an anti-ICAM-1 antibody (AIA) on bladder inflammation in a rat model of severe non-bacterial cystitis (NBC) resembling BPS/IC by evaluating the bladder inflammation grade, mast cell infiltration and related cytokines and receptors. We also compared the effects of AIA with the COX-2 inhibitor celecoxib and the neurokinin-1 receptor (NK1R) inhibitor aprepitant. Our NBC model was established by intraperitoneal injection of cyclophosphamide combined with intravesical protamine/lipopolysaccharide, which resulted in severe bladder inflammation and increased mast cell infiltration, similar to the pathological changes of BPS/IC. Inhibition of ICAM-1 by AIA significantly decreased the bladder inflammation grade and mast cell counts, which was accompanied by a reduction of purinergic receptors (P2X2/P2X3), prostaglandin E2, EP1/EP2 receptors, TNF-α, NK1R, and ICAM-1. Moreover, AIA showed superior effects to those of celecoxib and aprepitant treatment in improving the bladder inflammatory response. Our results suggest that ICAM-1 may play a critical role in bladder inflammation in severe NBC and may be used as a novel therapeutic target in non-bacterial bladder inflammation such as BPS/IC.
Discrimination of transgenic soybean seeds by terahertz spectroscopy
Authors: Liu Wei , Liu Changhong , Chen Feng , Yang Jianbo , Zheng Lei 
Published: October 2016

AbstractDiscrimination of genetically modified organisms is increasingly demanded by legislation and consumers worldwide. The feasibility of a non-destructive discrimination of glyphosate-resistant and conventional soybean seeds and their hybrid descendants was examined by terahertz time-domain spectroscopy system combined with chemometrics. Principal component analysis (PCA), least squares-support vector machines (LS-SVM) and PCA-back propagation neural network (PCA-BPNN) models with the first and second derivative and standard normal variate (SNV) transformation pre-treatments were applied to classify soybean seeds based on genotype. Results demonstrated clear differences among glyphosate-resistant, hybrid descendants and conventional non-transformed soybean seeds could easily be visualized with an excellent classification (accuracy was 88.33% in validation set) using the LS-SVM and the spectra with SNV pre-treatment. The results indicated that THz spectroscopy techniques together with chemometrics would be a promising technique to distinguish transgenic soybean seeds from non-transformed seeds with high efficiency and without any major sample preparation.
The Southampton-York Natural Scenes (SYNS) dataset: Statistics of surface attitude
Authors: Adams Wendy J. , Elder James H. , Graf Erich W. , Leyland Julian , Lugtigheid Arthur J. , Muryy Alexander 
Published: October 2016

AbstractRecovering 3D scenes from 2D images is an under-constrained task; optimal estimation depends upon knowledge of the underlying scene statistics. Here we introduce the Southampton-York Natural Scenes dataset (SYNS: https://syns.soton.ac.uk), which provides comprehensive scene statistics useful for understanding biological vision and for improving machine vision systems. In order to capture the diversity of environments that humans encounter, scenes were surveyed at random locations within 25 indoor and outdoor categories. Each survey includes (i) spherical LiDAR range data (ii) high-dynamic range spherical imagery and (iii) a panorama of stereo image pairs. We envisage many uses for the dataset and present one example: an analysis of surface attitude statistics, conditioned on scene category and viewing elevation. Surface normals were estimated using a novel adaptive scale selection algorithm. Across categories, surface attitude below the horizon is dominated by the ground plane (0° tilt). Near the horizon, probability density is elevated at 90°/270° tilt due to vertical surfaces (trees, walls). Above the horizon, probability density is elevated near 0° slant due to overhead structure such as ceilings and leaf canopies. These structural regularities represent potentially useful prior assumptions for human and machine observers, and may predict human biases in perceived surface attitude.
Fluorescent protein tagging of endogenous protein in brain neurons using CRISPR/Cas9-mediated knock-in and in utero electroporation techniques
Authors: Uemura Takeshi , Mori Takuma , Kurihara Taiga , Kawase Shiori , Koike Rie , Satoga Michiru , Cao Xueshan , Li Xue , Yanagawa Toru , Sakurai Takayuki , Shindo Takayuki , Tabuchi Katsuhiko 
Published: October 2016

AbstractGenome editing is a powerful technique for studying gene functions. CRISPR/Cas9-mediated gene knock-in has recently been applied to various cells and organisms. Here, we successfully knocked in an EGFP coding sequence at the site immediately after the first ATG codon of the β-actin gene in neurons in the brain by the combined use of the CRISPR/Cas9 system and in utero electroporation technique, resulting in the expression of the EGFP-tagged β-actin protein in cortical layer 2/3 pyramidal neurons. We detected EGFP fluorescence signals in the soma and neurites of EGFP knock-in neurons. These signals were particularly abundant in the head of dendritic spines, corresponding to the localization of the endogenous β-actin protein. EGFP knock-in neurons showed no detectable changes in spine density and basic electrophysiological properties. In contrast, exogenously overexpressed EGFP-β-actin showed increased spine density and EPSC frequency, and changed resting membrane potential. Thus, our technique provides a potential tool to elucidate the localization of various endogenous proteins in neurons by epitope tagging without altering neuronal and synaptic functions. This technique can be also useful for introducing a specific mutation into genes to study the function of proteins and genomic elements in brain neurons.
von Willebrand factor contributes to poor outcome in a mouse model of intracerebral haemorrhage
Authors: Zhu Ximin , Cao Yongliang , Wei Lixiang , Cai Ping , Xu Haochen , Luo Haiyu , Bai Xiaofei , Lu Lu , Liu Jian-Ren , Fan Wenying , Zhao Bing-Qiao 
Published: October 2016

AbstractSpontaneous intracerebral haemorrhage (ICH) is the most devastating stroke subtype and has no proven treatment. von Willebrand factor (VWF) has recently been demonstrated to promote inflammation processes. The present study investigated the pathophysiological role of VWF after experimental ICH. Functional outcomes, brain edema, blood-brain barrier (BBB) permeability, cerebral inflammation and levels of intercellular adhesion molecule-1 (ICAM-1) and matrix metalloproteinase-9 (MMP-9) were measured in a mouse model of ICH induced by autologous blood injection. We show that VWF were increased in the plasma and was accumulated in the perihematomal regions of mice subjected to ICH. Injection of VWF resulted in incerased expression of proinflammatory mediators and activation of ICAM-1 and MMP-9, associated with elevated myeloperoxidase, recruitment of neutrophils and microglia. Moreover, mice treated with VWF showed dramatically decreased pericyte coverage, more severe BBB damage and edema formation, and neuronal injury was increased compared with controls. In contrast, blocking antibodies against VWF reduced BBB damage and edema formation and improved neurological function. Together, these data identify a critical role for VWF in cerebral inflammation and BBB damage after ICH. The therapeutic interventions targeting VWF may be a novel strategy to reduce ICH-related injury.