bluuebunny/crossref_metadata_2025_split huggingface dataset:
Salmonella Enteritidis ST183: emerging and endemic biotypes affecting western European hedgehogs (Erinaceus europaeus) and people in Great Britain
Authors: Lawson Becki , Franklinos Lydia H. V. , Rodriguez-Ramos Fernandez Julia , Wend-Hansen Clare , Nair Satheesh , Macgregor Shaheed K. , John Shinto K. , Pizzi Romain , Núñez Alejandro , Ashton Philip M. , Cunningham Andrew A. , M. de Pinna Elizabeth 
Published: January 2018

AbstractThe impacts of hedgehog (Erinaceus europaeus) Salmonella infection on public health and on animal welfare and conservation are unknown. We isolated Salmonella Enteritidis multi-locus sequence-type (ST)183 from 46/170 (27%) hedgehog carcasses (27 S. Enteritidis phage type (PT)11, 18 of a novel PT66 biotype and one with co-infection of these PTs) and from 6/208 (3%) hedgehog faecal samples (4 PT11, 2 PT66) from across Great Britain, 2012–2015. Whole genome phylogenetic analysis of the hedgehog isolates and ST183 from people in England and Wales found that PT11 and PT66 form two divergent clades. Hedgehog and human isolates were interspersed throughout the phylogeny indicating that infections in both species originate from a common population. PT11 was recovered from hedgehogs across England and Scotland, consistent with endemic infection. PT66 was isolated from Scotland only, possibly indicating a recent emergence event. People infected with ST183 were four times more likely to be aged 0–4 years than people infected by the more common ST11 S. Enteritidis. Evidence for human ST183 infection being non-foodborne included stronger correlation between geographic and genetic distance, and significantly increased likelihood of infection in rural areas, than for ST11. These results are consistent with hedgehogs acting as a source of zoonotic infection.
Ecophysiological response of native and exotic salt marsh vegetation to waterlogging and salinity: Implications for the effects of sea-level rise
Authors: Li Shi-Hua , Ge Zhen-Ming , Xie Li-Na , Chen Wei , Yuan Lin , Wang Dong-Qi , Li Xiu-Zhen , Zhang Li-Quan 
Published: January 2018

AbstractThe ecophysiological characteristics of native Phragmites australis and exotic Spartina alterniflora grown under waterlogging and salinity were investigated to explore their adaptation potential to sea level rise. The seasonal course of phenotypic traits, photosynthetic activity and chlorophyll fluorescence parameters of P. australis did not change remarkably under shallow flooding, whereas these variables were sensitive to increasing salinity. Waterlogging exacerbated the negative effects of salinity on shoot growth and photosynthetic activity of P. australis, and the combined stresses led to an absence of tassel and reproductive organs. By contrast, S. alterniflora performed well under both stresses and showed an obvious adaptation of salt secretion with increasing salinity. Light salinity was the optimal condition for S. alterniflora, and the tassel growth, chlorophyll content and fluorescence characters under moderate stresses did not differ notably. The Na+ and Cl− concentrations in leaves of both species increased, and the K+ content decreased in response to salinity. Under moderate and high saline levels, the ion concentrations in S. alterniflora were maintained at relatively consistent levels with increased salt secretion. We expect the degradation of P. australis and further colonization of S. alterniflora under prolonged flooding and saltwater intrusion from sea level rise on the coastline of China.
Development of a yeast internal-subunit eGFP labeling strategy and its application in subunit identification in eukaryotic group II chaperonin TRiC/CCT
Authors: Zang Yunxiang , Wang Huping , Cui Zhicheng , Jin Mingliang , Liu Caixuan , Han Wenyu , Wang Yanxing , Cong Yao 
Published: January 2018

AbstractUnambiguous subunit assignment in a multicomponent complex is critical for thorough understanding of the machinery and its functionality. The eukaryotic group II chaperonin TRiC/CCT folds approximately 10% of cytosolic proteins and is important for the maintenance of cellular homeostasis. TRiC consists of two rings and each ring has eight homologous but distinct subunits. Unambiguous subunit identification of a macromolecular machine such as TRiC through intermediate or low-resolution cryo-EM map remains challenging. Here we present a yeast internal-subunit eGFP labeling strategy termed YISEL, which can quickly introduce an eGFP tag in the internal position of a target subunit by homologous recombination, and the tag labeled protein can be expressed in endogenous level. Through this method, the labeling efficiency and tag-occupancy is ensured, and the inserted tag is usually less mobile compared to that fused to the terminus. It can also be used to bio-engineer other tag in the internal position of a protein in yeast. By applying our YISEL strategy and combined with cryo-EM 3D reconstruction, we unambiguously identified all the subunits in the cryo-EM map of TRiC, demonstrating the potential for broad application of this strategy in accurate and efficient subunit identification in other challenging complexes.
Transcriptome sequence analysis and mining of SSRs in Jhar Ber (Ziziphus nummularia (Burm.f.) Wight & Arn) under drought stress
Authors: Yadav Radha , Lone Showkat Ahmad , Gaikwad Kishor , Singh Nagendra Kumar , Padaria Jasdeep Chatrath 
Published: January 2018

AbstractZiziphus nummularia (Burm.f.) Wight & Arn., a perennial shrub that thrives in the arid regions, is naturally tolerant to drought. However, there are limited studies on the genomics of drought tolerance in Ziziphus sp. In this study, RNA-sequencing of one month old seedlings treated with PEG 6000 was performed using Roche GS-FLX454 Titanium pyrosequencing. A total of 367,176 raw sequence reads were generated, and upon adapter trimming and quality filtration 351,872 reads were assembled de novo into 32,739 unigenes. Further characterization of the unigenes indicated that 73.25% had significant hits in the protein database. Kyoto encyclopedia of genes and genomes database (KEGG) identified 113 metabolic pathways from the obtained unigenes. A large number of drought-responsive genes were obtained and among them differential gene expression of 16 highly induced genes was validated by qRT-PCR analysis. To develop genic-markers, 3,425 simple sequence repeats (SSRs) were identified in 2,813 unigene sequences. The data generated shall serve as an important reservoir for the identification and characterization of drought stress responsive genes for development of drought tolerant crops.
Insulin-degrading enzyme is not secreted from cultured cells
Authors: Song Eun Suk , Rodgers David W. , Hersh Louis B. 
Published: January 2018

AbstractInsulin-degrading enzyme (IDE) functions in the catabolism of bioactive peptides. Established roles include degrading insulin and the amyloid beta peptide (Aβ), linking it to diabetes and Alzheimer’s disease. IDE is primarily located in the cytosol, and a longstanding question is how it gains access to its peptide substrates. Reports suggest that IDE secreted by an unconventional pathway participates in extracellular hydrolysis of insulin and Aβ. We find that IDE release from cultured HEK-293 or BV-2 cells represents only ~1% of total cellular IDE, far less than has been reported previously. Importantly, lactate dehydrogenase (LDH) and other cytosolic enzymes are released at the same relative level, indicating that extracellular IDE results from a loss of cell integrity, not secretion. Lovastatin increases IDE release from BV-2 cells as reported, but this release is mirrored by LDH release. Cell viability assays indicate lovastatin causes a loss of cell integrity, explaining its effect on IDE release. IDE is present in an exosome-enriched fraction from BV-2 cell conditioned media, however it represents only ~0.01% of the total cellular enzyme and is unlikely to be a significant source of IDE. These results call into question the secretion of IDE and its importance in extracellular peptide degradation.
Silver nanoparticles have lethal and sublethal adverse effects on development and longevity by inducing ROS-mediated stress responses
Authors: Mao Bin-Hsu , Chen Zi-Yu , Wang Ying-Jang , Yan Shian-Jang 
Published: January 2018

AbstractSilver nanoparticles (AgNPs) are widely used in the household, medical and industrial sectors due to their effective bactericidal activities and unique plasmonic properties. Despite the promising advantages, safety concerns have been raised over the usage of AgNPs because they pose potential hazards. However, the mechanistic basis behind AgNPs toxicity, particularly the sublethal effects at the organismal level, has remained unclear. In this study, we used a powerful in vivo platform Drosophila melanogaster to explore a wide spectrum of adverse effects exerted by dietary AgNPs at the organismal, cellular and molecular levels. Lethal doses of dietary AgNPs caused developmental delays and profound lethality in developing animals and young adults. In contrast, exposure to sublethal doses, while not deadly to developing animals, shortened the adult lifespan and compromised their tolerance to oxidative stress. Importantly, AgNPs mechanistically resulted in tissue-wide accumulation of reactive oxygen species (ROS) and activated the Nrf2-dependent antioxidant pathway, as demonstrated by an Nrf2 activity reporter in vivo. Finally, dietary AgNPs caused a variety of ROS-mediated stress responses, including apoptosis, DNA damage, and autophagy. Altogether, our study suggests that lethal and sublethal doses of AgNPs, have acute and chronic effects, respectively, on development and longevity by inducing ROS-mediated stress responses.
Intracellular calcium signal at the leading edge regulates mesodermal sheet migration during Xenopus gastrulation
Authors: Hayashi Kentaro , Yamamoto Takamasa S. , Ueno Naoto 
Published: January 2018

AbstractDuring the gastrulation stage in animal embryogenesis, the cells leading the axial mesoderm migrate toward the anterior side of the embryo, vigorously extending cell protrusions such as lamellipodia. It is thought that the leading cells sense gradients of chemoattractants emanating from the ectodermal cells and translate them to initiate and maintain the cell movements necessary for gastrulation. However, it is unclear how the extracellular information is converted to the intracellular chemical reactions that lead to motion. Here we demonstrated that intracellular Ca2+ levels in the protrusion-forming leading cells are markedly higher than those of the following cells and the axial mesoderm cells. We also showed that inhibiting the intracellular Ca2+ significantly retarded the gastrulation cell movements, while increasing the intracellular Ca2+ with an ionophore enhanced the migration. We further found that the ionophore treatment increased the active form of the small GTPase Rac1 in these cells. Our results suggest that transient intracellular Ca2+ signals play an essential role in the active cell migration during gastrulation.
The dramatic enhancement of ferromagnetism and band gap in Fe-doped In2O3 nanodot arrays
Authors: Jiang Feng-Xian , Chen Dan , Zhou Guo-Wei , Wang Ya-Nan , Xu Xiao-Hong 
Published: January 2018

AbstractOrdered Fe-doped In2O3 nanodot arrays with diameters between 35 nm and 80 nm are fabricated using pulsed laser deposition with the aid of ultrathin porous anodized aluminumoxide templates. The 5 at.% Fe doped In2O3 nanodot arrays are shown to consist of the cubic bixbyite structure of In2O3. The nanodot arrays are demonstrated to be doped by Fe ions with mixed valences of +2 and +3, ruling out the presence of cluster and secondary phase related to Fe. The nanodot arrays exhibit the ferromagnetism at room temperature, where the magnetic moment increases as the dot size is reduced, rising to a maximum of about 230 emu/cm3 (equivalent to an average moment on the Fe ions of 15.30 µB/Fe). This indicates an effect due to the surface of the nanodot arrays. The optical band width is also increased to 4.55 eV for the smallest dot array, thus indicating that the surface states are responsible for the magnetism and also enhance the band gap due to Burstein-Moss effect. Our results will be benefit for understanding the physical properties of oxide semiconductor nanostructures in the application of nano-spintronics devices.
Unidirectional molecular assembly alignment on graphene enabled by nanomechanical symmetry breaking
Authors: Hong Liu , Nishihara Taishi , Hijikata Yuh , Miyauchi Yuhei , Itami Kenichiro 
Published: January 2018

AbstractPrecise fabrication of molecular assemblies on a solid surface has long been of central interest in surface science. Their perfectly oriented growth only along a desired in-plane direction, however, remains a challenge, because of the thermodynamical equivalence of multiple axis directions on a solid-surface lattice. Here we demonstrate the successful fabrication of an in-plane, unidirectional molecular assembly on graphene. Our methodology relies on nanomechanical symmetry breaking effects under atomic force microscopy tip scanning, which has never been used in molecular alignment. Individual one-dimensional (1D) molecular assemblies were aligned along a selected symmetry axis of the graphene lattice under finely-tuned scanning conditions after removing initially-adsorbed molecules. Experimental statistics and computational simulations suggest that the anisotropic tip scanning locally breaks the directional equivalence of the graphene surface, which enables nucleation of the unidirectional 1D assemblies. Our findings will open new opportunities in the molecular alignment control on various atomically flat surfaces.
River self-organisation inhibits discharge control on waterfall migration
Authors: Baynes Edwin R. C. , Lague Dimitri , Attal Mikaël , Gangloff Aurélien , Kirstein Linda A. , Dugmore Andrew J. 
Published: January 2018

AbstractThe action of rivers within valleys is fundamentally important in controlling landscape morphology, and how it responds to tectonic or climate change. The response of landscapes to external forcing usually results in sequential changes to river long profiles and the upstream migration of waterfalls. Currently, models of this response assume a relationship between waterfall retreat rate and drainage area at the location of the waterfall. Using an experimental study, we show that this assumption has limited application. Due to a self-regulatory response of channel geometry to higher discharge through increasing channel width, the bed shear stress at the lip of the experimental waterfall remains almost constant, so there was no observed change in the upstream retreat rate despite an order of magnitude increase in discharge. Crucially, however, the strength of the bedrock material exhibits a clear control on the magnitude of the mean retreat rate, highlighting the importance of lithology in setting the rate at which landscapes respond to external forcing. As a result existing numerical models of landscape evolution that simulate the retreat of waterfalls as a function of drainage area with a fixed erodibility constant should be re-evaluated to consider spatial heterogeneity in erodibility and channel self-organisation.
Microparticles produced by human papillomavirus type 16 E7-expressing cells impair antigen presenting cell function and the cytotoxic T cell response
Authors: Zhang J. , Burn C. , Young K. , Wilson M. , Ly K. , Budhwani M. , Tschirley A. , Braithwaite A. , Baird M. , Hibma M. 
Published: January 2018

AbstractHigh-risk, cancer-causing human papillomaviruses (HPV) cause infections of the epidermis that may progress to cancer, including cervical cancer. Viral persistence, contributed to by viral evasion of the host immune response, is associated with the likelihood of cancer developing. Langerhans cells (LCs) are the only professional antigen presenting cells located in the epidermis, therefore may influence the antiviral immune response. Microparticles, or microvesicles, are small membrane particles shed by cells that can exert effects on other cells at both a local and systemic level. We found increased numbers of microparticles were shed from human or mouse keratinocytes expressing the HPV16 E7 oncoprotein, compared with control keratinocytes. Co-culture of LCs with microparticles from E7-expressing cells suppressed the cytotoxic T cell response. We attributed this, at least in part, to the reduction in surface of CD40 and intracellular pro-inflammatory cytokine IL-12 p40 subunit that we measured in the LCs. The evidence provided here shows that co-culture of E7-microparticles with LCs inhibits antigen-specific cytotoxicity. This is an important finding, suggesting that microparticles from HPV-infected cells could suppress the T cell response by regulating LCs, potentially contributing to persistence of HPV infection and cancer.
A novel small deletion in the NHS gene associated with Nance-Horan syndrome
Authors: Li Huajin , Yang Lizhu , Sun Zixi , Yuan Zhisheng , Wu Shijing , Sui Ruifang 
Published: January 2018

AbstractNance-Horan syndrome is a rare X-linked recessive inherited disease with clinical features including severe bilateral congenital cataracts, characteristic facial and dental abnormalities. Data from Chinese Nance-Horan syndrome patients are limited. We assessed the clinical manifestations of a Chinese Nance-Horan syndrome pedigree and identified the genetic defect. Genetic analysis showed that 3 affected males carried a novel small deletion in NHS gene, c.263_266delCGTC (p.Ala89TrpfsTer106), and 2 female carriers were heterozygous for the same variant. All 3 affected males presented with typical Nance-Horan syndrome features. One female carrier displayed lens opacities centered on the posterior Y-suture in both eyes, as well as mild dental abnormalities. We recorded the clinical features of a Chinese Nance-Horan syndrome family and broadened the spectrum of mutations in the NHS gene.
The spin structures of interlayer coupled magnetic films with opposite chirality
Authors: Kang S. P. , Kim N. J. , Kwon H. Y. , Choi J. W. , Min B. C. , Won C. 
Published: January 2018

AbstractUsing Monte-Carlo simulations and micromagnetic simulations, we reveal how the spin structural correlation and the skyrmion dynamics are affected by the interlayer coupling in a chiral magnetic bilayer system, in which the two layers have opposite chirality. The interaction through interlayer coupling between chiral magnetic structures influences the static and dynamics properties profoundly. The competition between the Dzyaloshinskii-Moriya interaction and the interlayer interaction allows multiple magnetic structures to be energetically stable, which includes sole skyrmion states (skyrmion appears in only one of the layers) and skyrmion pair states (coupled skyrmions in top and bottom layers). When current driven spin transfer torques are applied to each state, the sole skyrmion state is mainly propelled by a spin transfer torque causing the skyrmion hall effect, but the skyrmion pair state is propelled by a torque from skyrmion-skyrmion interaction and not influenced by the skyrmion hall effect. Also upon application of an external magnetic field, we found the skyrmions in a skyrmion pair state extinguish in an exclusive way, as the annihilation of a skyrmion in one of the layers stabilizes the once paired skyrmion in the other layer, i.e. the skyrmion lattice sites have only one skyrmion in either layer.
Microscale Gene Expression Analysis of Tumor-Associated Macrophages
Authors: Attri Kuldeep S. , Mehla Kamiya , Shukla Surendra K. , Singh Pankaj K. 
Published: January 2018

AbstractMacrophages, apart from being the key effector cells of the innate immune system, also play critical roles during the development and progression of various complex diseases, including cancer. Tumor-associated macrophages, infiltrate tumors during different stages of cancer progression to regulate motility, invasion, and intravasation to metastatic sites. Macrophages can exist in different polarization states associated with unique function in tumors. Since tumor-associated macrophages constitute a very small proportion of tumor cells, analysis of gene expression pattern using normal extraction buffer-based methods remains a challenging task. Therefore, it is imperative to develop low-throughput strategies to investigate transcriptional regulations from a small number of immune cells. Here, we describe an efficient, sensitive, and cost-effective approach for gene expression analysis of a small number of fluorescence-activated sorted tumor-associated macrophages. Our analyses from the different number of stable, primary, and sorted macrophages suggest 5,000 cells is an optimal number for performing quantitative, real-time PCR analysis of multiple genes. Our studies could detect expression of macrophage-specific genes from cultured primary macrophages, and FACS-sorted macrophages from different biological tissues without introducing biases in comparative gene expression ratios. In conclusion, our kit-based method for quantitative gene expression analysis from a small number of cells found in biological tissues will provide an opportunity to study cell-specific, transcriptional changes.
CPAP3 proteins in the mineralized cuticle of a decapod crustacean
Authors: Abehsera Shai , Zaccai Shir , Mittelman Binyamin , Glazer Lilah , Weil Simy , Khalaila Isam , Davidov Geula , Bitton Ronit , Zarivach Raz , Li Shihao , Li Fuhua , Xiang Jianhai , Manor Rivka , Aflalo Eliahu D. , Sagi Amir 
Published: January 2018

AbstractThe pancrustacean theory groups crustaceans and hexapods (once thought to comprise separate clades within the Arthropoda) into a single clade. A key feature common to all pancrustaceans is their chitinous exoskeleton, with a major contribution by cuticular proteins. Among these, are the CPAP3’s, a family of cuticular proteins, first identified in the hexapod Drosophila melanogaster and characterized by an N-terminal signaling peptide and three chitin-binding domains. In this study, CPAP3 proteins were mined from a transcriptomic library of a decapod crustacean, the crayfish Cherax quadricarinatus. Phylogenetic analysis of other CPAP3 proteins from hexapods and other crustaceans showed a high degree of conservation. Characterization of the crayfish proteins, designated CqCPAP3’s, suggested a major role for CPAP3’sin cuticle formation. Loss-of-function experiments using RNAi supported such a notion by demonstrating crucial roles for several CqCPAP3 proteins during molting. A putative mode of action for the CqCPAP3 proteins –theoretically binding three chitin strands– was suggested by the structural data obtained from a representative recombinant CqCPAP3. The similarities between the CqCPAP3 proteins and their hexapod homologues further demonstrated common genetic and proteinaceous features of cuticle formation in pancrustaceans, thereby reinforcing the linkage between these two highly important phylogenetic groups.