bluuebunny/crossref_metadata_2025_split huggingface dataset:
Centromere evolution and CpG methylation during vertebrate speciation
Authors: Ichikawa Kazuki , Tomioka Shingo , Suzuki Yuta , Nakamura Ryohei , Doi Koichiro , Yoshimura Jun , Kumagai Masahiko , Inoue Yusuke , Uchida Yui , Irie Naoki , Takeda Hiroyuki , Morishita Shinich 
Published: November 2017

AbstractCentromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20–345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320–350 million years ago. The centromeres do not all evolve at a similar pace; rather, centromeric monomers in non-acrocentric chromosomes evolve significantly faster than those in acrocentric chromosomes. Using methylation sensitive SMRT reads, we uncover centromeres are mostly hypermethylated but have hypomethylated sub-regions that acquire unique sequence compositions independently. These findings reveal the potential of non-acrocentric centromere evolution to contribute to speciation.
Oscillatory brain activity in spontaneous and induced sleep stages in flies
Authors: Yap Melvyn H. W. , Grabowska Martyna J. , Rohrscheib Chelsie , Jeans Rhiannon , Troup Michael , Paulk Angelique C. , van Alphen Bart , Shaw Paul J. , van Swinderen Bruno 
Published: November 2017

AbstractSleep is a dynamic process comprising multiple stages, each associated with distinct electrophysiological properties and potentially serving different functions. While these phenomena are well described in vertebrates, it is unclear if invertebrates have distinct sleep stages. We perform local field potential (LFP) recordings on flies spontaneously sleeping, and compare their brain activity to flies induced to sleep using either genetic activation of sleep-promoting circuitry or the GABAAagonist Gaboxadol. We find a transitional sleep stage associated with a 7–10 Hz oscillation in the central brain during spontaneous sleep. Oscillatory activity is also evident when we acutely activate sleep-promoting neurons in the dorsal fan-shaped body (dFB) ofDrosophila. In contrast, sleep following Gaboxadol exposure is characterized by low-amplitude LFPs, during which dFB-induced effects are suppressed. Sleep in flies thus appears to involve at least two distinct stages: increased oscillatory activity, particularly during sleep induction, followed by desynchronized or decreased brain activity.
The sensitivity of donor – acceptor charge transfer to molecular geometry in DAN – NDI based supramolecular flower-like self-assemblies
Authors: Kobaisi Mohammad Al , Bhosale Rajesh S. , El-Khouly Mohamed E. , La Duong Duc , Padghan Sachin D. , Bhosale Sidhanath V. , Jones Lathe A. , Antolasic Frank , Fukuzumi Shunichi , Bhosale Sheshanath V. 
Published: November 2017

AbstractA charge-transfer (CT) complex self-assembled from an electron acceptor (NDI-EA: naphthalene diimide with appended diamine) and an electron donor (DAN: phosphonic acid-appended dialkoxynapthalene) in aqueous medium. The aromatic core of the NDI and the structure of DAN1 were designed to optimize the dispersive interactions (π-π and van der Waals interactions) in the DAN1–NDI-EA self-assembly, while the amino groups of NDI also interact with the phosphonic acid of DAN1 via electrostatic forces. This arrangement prevented crystallization and favored the directional growth of 3D flower nanostructures. This molecular geometry that is necessary for charge transfer to occur was further evidenced by using a mismatching DAN2 structure. The flower-shaped assembly was visualized by scanning electron and transmission electron microscopy. The formation of the CT complex was determined by UV-vis and cyclic voltammetry and the photoinduced electron transfer to produce the radical ion pair was examined by femtosecond laser transient absorption spectroscopic measurements.
Phloem-limited reoviruses universally induce sieve element hyperplasia and more flexible gateways, providing more channels for their movement in plants
Authors: Lv Ming-Fang , Xie Li , Song Xi-Jiao , Hong Jian , Mao Qian-Zhuo , Wei Tai-Yun , Chen Jian-Ping , Zhang Heng-Mu 
Published: November 2017

AbstractVirion distribution and ultrastructural changes induced by the infection of maize or rice with four different reoviruses were examined. Rice black streaked dwarf virus (RBSDV, genus Fijivirus), Rice ragged stunt virus (RRSV, genus Oryzavirus), and Rice gall dwarf virus (RGDV, genus Phytoreovirus) were all phloem-limited and caused cellular hyperplasia in the phloem resulting in tumors or vein swelling and modifying the cellular arrangement of sieve elements (SEs). In contrast, virions of Rice dwarf virus (RDV, genus Phytoreovirus) were observed in both phloem and mesophyll and the virus did not cause hyperplasia of SEs. The three phloem-limited reoviruses (but not RDV) all induced more flexible gateways at the SE-SE interfaces, especially the non-sieve plate interfaces. These flexible gateways were also observed for the first time at the cellular interfaces between SE and phloem parenchyma (PP). In plants infected with any of the reoviruses, virus-like particles could be seen within the flexible gateways, suggesting that these gateways may serve as channels for the movement of plant reoviruses with their large virions between SEs or between SEs and PP. SE hyperplasia and the increase in flexible gateways may be a universal strategy for the movement of phloem-limited reoviruses.
Molecular architecture of potassium chloride co-transporter KCC2
Authors: Agez Morgane , Schultz Patrick , Medina Igor , Baker David J. , Burnham Matthew P. , Cardarelli Ross A. , Conway Leslie C. , Garnier Kelly , Geschwindner Stefan , Gunnarsson Anders , McCall Eileen J. , Frechard Alexandre , Audebert Stéphane , Deeb Tarek Z. , Moss Stephen J. , Brandon Nicholas J. , Wang Qi , Dekker Niek , Jawhari Anass 
Published: November 2017

AbstractKCC2 is a neuron specific K+-Cl− co-transporter that controls neuronal chloride homeostasis, and is critically involved in many neurological diseases including brain trauma, epilepsies, autism and schizophrenia. Despite significant accumulating data on the biology and electrophysiological properties of KCC2, structure-function relationships remain poorly understood. Here we used calixarene detergent to solubilize and purify wild-type non-aggregated and homogenous KCC2. Specific binding of inhibitor compound VU0463271 was demonstrated using surface plasmon resonance (SPR). Mass spectrometry revealed glycosylations and phosphorylations as expected from functional KCC2. We show by electron microscopy (EM) that KCC2 exists as monomers and dimers in solution. Monomers are organized into “head” and “core” domains connected by a flexible “linker”. Dimers are asymmetrical and display a bent “S-shape” architecture made of four distinct domains and a flexible dimerization interface. Chemical crosslinking in reducing conditions shows that disulfide bridges are involved in KCC2 dimerization. Moreover, we show that adding a tag to the C-terminus is detrimental to KCC2 function. We postulate that the conserved KCC2 C-ter may be at the interface of dimerization. Taken together, our findings highlight the flexible multi-domain structure of KCC2 with variable anchoring points at the dimerization interface and an important C-ter extremity providing the first in-depth functional architecture of KCC2.
Adrenomedullin protects Leydig cells against lipopolysaccharide-induced oxidative stress and inflammatory reaction via MAPK/NF-κB signalling pathways
Authors: Hu Wei , Shi Lei , Li Ming-yong , Zhou Pang-hu , Qiu Bo , Yin Ke , Zhang Hui-hui , Gao Yong , Kang Ran , Qin Song-lin , Ning Jin-zhuo , Wang Wei , Zhang Li-jun 
Published: November 2017

AbstractThis study aimed to explore the possible benefits of adrenomedullin (ADM) in preventing oxidative stress and inflammation by using an in vitro primary culture model of rat Leydig cells exposed to lipopolysaccharide (LPS). Cell proliferation was detected through CCK-8 and BrdU incorporation assays. ROS were determined with a DCFDA kit, and cytokine concentrations were measured with ELISA assay kits. Protein production was examined by immunohistochemical staining and Western blot, and gene expression was observed through RT-qPCR. Results revealed that ADM significantly reduced LPS-induced cytotoxicity, and pretreatment with ADM significantly suppressed ROS overproduction and decreased 4-HNE and 8-OHdG expression levels and concentrations. ADM pretreatment also significantly attenuated the overactivation of enzymatic antioxidants, namely, superoxide dismutase, catalase, thioredoxin reductase, glutathione peroxidase, glutathione reductase and glutathione-S-transferase. ADM supplementation reversed the significantly increased gene expression levels and concentrations of TNF-α, IL-1β, TGF-β1, MCP-1 and MIF. ADM pretreatment significantly inhibited the gene expression and protein production of TLR-2 and 4. Furthermore, ADM pretreatment markedly reduced the phosphorylation of JNK, ERK 1/2 and p38, phosphorylation and degradation of IκBα and nuclear translocation of p65. Our findings demonstrated that ADM protects Leydig cells from LPS-induced oxidative stress and inflammation, which might be associated with MAPK/NF-κB signalling pathways.
Rare earth element geochemistry characteristics of seawater and porewater from deep sea in western Pacific
Authors: Deng Yinan , Ren Jiangbo , Guo Qingjun , Cao Jun , Wang Haifeng , Liu Chenhui 
Published: November 2017

AbstractDeep-sea sediments contain high concentrations of rare earth element (REE) which have been regarded as a huge potential resource. Understanding the marine REE cycle is important to reveal the mechanism of REE enrichment. In order to determine the geochemistry characteristics and migration processes of REE, seawater, porewater and sediment samples were systematically collected from the western Pacific for REE analysis. The results show a relatively flat REE pattern and the HREE (Heavy REE) enrichment in surface and deep seawater respectively. The HREE enrichment distribution patterns, low concentrations of Mn and Fe and negative Ce anomaly occur in the porewater, and high Mn/Al ratios and low U concentrations were observed in sediment, indicating oxic condition. LREE (Light REE) and MREE (Middle REE) enrichment in upper layer and depletion of MREE in deeper layer were shown in porewater profile. This study suggests that porewater flux in the western Pacific basin is a minor source of REEs to seawater, and abundant REEs are enriched in sediments, which is mainly caused by the extensive oxic condition, low sedimentation rate and strong adsorption capacity of sediments. Hence, the removal of REEs of porewater may result in widespread REE-rich sediments in the western Pacific basin.
A half-site multimeric enzyme achieves its cooperativity without conformational changes
Authors: Vivoli Mirella , Pang Jiayun , Harmer Nicholas J. 
Published: November 2017

AbstractCooperativity is a feature many multimeric proteins use to control activity. Here we show that the bacterial heptose isomerase GmhA displays homotropic positive and negative cooperativity among its four protomers. Most similar proteins achieve this through conformational changes: GmhA instead employs a delicate network of hydrogen bonds, and couples pairs of active sites controlled by a unique water channel. This network apparently raises the Lewis acidity of the catalytic zinc, thus increasing the activity at one active site at the cost of preventing substrate from adopting a reactive conformation at the paired negatively cooperative site – a “half-site” behavior. Our study establishes the principle that multimeric enzymes can exploit this cooperativity without conformational changes to maximize their catalytic power and control. More broadly, this subtlety by which enzymes regulate functions could be used to explore new inhibitor design strategies.
Identification of a histone family gene signature for predicting the prognosis of cervical cancer patients
Authors: Li Xiaofang , Tian Run , Gao Hugh , Yang Yongkang , Williams Bryan R. G. , Gantier Michael P. , McMillan Nigel A. J. , Xu Dakang , Hu Yiqun , Gao Yan’e 
Published: November 2017

AbstractHeterogeneity in terms of tumor characteristics, prognosis, and survival among cancer patients is an unsolved issue. Here, we systematically analyzed the aberrant expression patterns of cervical cancer using RNA-Seq data from The Cancer Genome Atlas (TCGA). We incorporated gene profiling, molecular signatures, functional and pathway information with gene set enrichment and protein-protein interaction (PPI) network analysis, to identify sub-networks of genes. Those identified genes relating to DNA replication and DNA repair-mediated signaling pathways associated with systemic lupus erythematosus (SLE). Next, we combined cross-validated prognostic scores to build an integrated prognostic model for survival prediction. The combined approach revealed that the DNA repair-mediated including the functional interaction module of 18 histone genes (Histone cluster 1 H2A, B and H4), were significantly correlated with the survival rate. Furthermore, five of these histone genes were highly expressed in three cervical cancer cohorts from the Oncomine database. Comparison of high and low histone variant-expressing human cervical cancer cell lines revealed different responses to DNA damage, suggesting protective functions of histone genes against DNA damage. Collectively, we provide evidence that two SLE-associated gene sets (HIST1H2BD and HIST1H2BJ; and HIST1H2BD, HIST1H2BJ, HIST1H2BH, HIST1H2AM and HIST1H4K) can be used as prognostic factors for survival prediction among cervical cancer patients.
Control of the interaction strength of photonic molecules by nanometer precise 3D fabrication
Authors: Rawlings Colin D. , Zientek Michal , Spieser Martin , Urbonas Darius , Stöferle Thilo , Mahrt Rainer F. , Lisunova Yuliya , Brugger Juergen , Duerig Urs , Knoll Armin W. 
Published: November 2017

AbstractApplications for high resolution 3D profiles, so-called grayscale lithography, exist in diverse fields such as optics, nanofluidics and tribology. All of them require the fabrication of patterns with reliable absolute patterning depth independent of the substrate location and target materials. Here we present a complete patterning and pattern-transfer solution based on thermal scanning probe lithography (t-SPL) and dry etching. We demonstrate the fabrication of 3D profiles in silicon and silicon oxide with nanometer scale accuracy of absolute depth levels. An accuracy of less than 1nm standard deviation in t-SPL is achieved by providing an accurate physical model of the writing process to a model-based implementation of a closed-loop lithography process. For transfering the pattern to a target substrate we optimized the etch process and demonstrate linear amplification of grayscale patterns into silicon and silicon oxide with amplification ratios of ∼6 and ∼1, respectively. The performance of the entire process is demonstrated by manufacturing photonic molecules of desired interaction strength. Excellent agreement of fabricated and simulated structures has been achieved.
Factors affecting pitch discrimination performance in a cohort of extensively phenotyped healthy volunteers
Authors: Smith Lauren M. , Bartholomew Alex J. , Burnham Lauren E. , Tillmann Barbara , Cirulli Elizabeth T. 
Published: November 2017

AbstractDespite efforts to characterize the different aspects of musical abilities in humans, many elements of this complex area remain unknown. Musical abilities are known to be associated with factors like intelligence, training, and sex, but a comprehensive evaluation of the simultaneous impact of multiple factors has not yet been performed. Here, we assessed 918 healthy volunteers for pitch discrimination abilities—their ability to tell two tones close in pitch apart. We identified the minimal threshold that the participants could detect, and we found that better performance was associated with higher intelligence, East Asian ancestry, male sex, younger age, formal music training–especially before age 6–and English as the native language. All these factors remained significant when controlling for the others, with general intelligence, musical training, and male sex having the biggest impacts. We also performed a small GWAS and gene-based collapsing analysis, identifying no significant associations. Future genetic studies of musical abilities should involve large sample sizes and an unbiased genome-wide approach, with the factors highlighted here included as important covariates.
Intrapartum antibiotics for GBS prophylaxis alter colonization patterns in the early infant gut microbiome of low risk infants
Authors: Stearns Jennifer C. , Simioni Julia , Gunn Elizabeth , McDonald Helen , Holloway Alison C. , Thabane Lehana , Mousseau Andrea , Schertzer Jonathan D. , Ratcliffe Elyanne M. , Rossi Laura , Surette Michael G. , Morrison Katherine M. , Hutton Eileen K. 
Published: November 2017

AbstractEarly life microbial colonization and succession is critically important to healthy development with impacts on metabolic and immunologic processes throughout life. A longitudinal prospective cohort was recruited from midwifery practices to include infants born at full term gestation to women with uncomplicated pregnancies. Here we compare bacterial community succession in infants born vaginally, with no exposure to antibiotics (n = 53), with infants who were exposed to intrapartum antibiotic prophylaxis (IAP) for Group B Streptococcus (GBS; n = 14), and infants born by C-section (n = 7). Molecular profiles of the 16 S rRNA genes indicate that there is a delay in the expansion of Bifidobacterium, which was the dominate infant gut colonizer, over the first 12 weeks and a persistence of Escherichia when IAP for GBS exposure is present during vaginal labour. Longer duration of IAP exposure increased the magnitude of the effect on Bifidobacterium populations, suggesting a longer delay in microbial community maturation. As with prior studies, we found altered gut colonisation following C-section that included a notable lack of Bacteroidetes. This study found that exposure of infants to IAP for GBS during vaginal birth affected aspects of gut microbial ecology that, although dramatic at early time points, disappeared by 12 weeks of age in most infants.
Inconsistency in the Crown-to-Root Ratios of Single-Rooted Premolars Measured by 2D and 3D Examinations
Authors: Hong Hsiang-Hsi , Liu Heng-Liang , Hong Adrienne , Chao Pu 
Published: November 2017

AbstractMicro-computed tomography (micro-CT) was applied to elucidate the relationship between the three-dimensional (3D) root surface area (RSA) and two-dimensional (2D) crown-to-root ratio (CRR) of extracted teeth to classify the periodontitis and assign a periodontal/prosthetic prognosis. A total of 31 maxillary and 35 mandibular single-rooted human premolars were examined. The amount of periodontal support on the basis of 3D RSA and 2D root length (RL) at CRRs of 1:1, 5:4, 3:2, and 2:1 were analyzed. Both maxillary and mandibular premolars demonstrated a nonsignificant RSA percentage at the evaluated CRRs. The coronal 21%–22% 2D RL and the 26%–28% 3D RSA bone loss apical to the cemento-enamel junction corresponded to a CRR of 1:1, relating to mild-moderate periodontitis. The coronal 30%–31% 2D RL and the 41%–42% 3D RSA bone loss corresponded to a CRR of 5:4, correlating to severe periodontitis. More severe clinical attachment loss (CAL) was observed in the 3D RSA measurement than in the 2D RL measurement at the evaluated CRRs. The amount of CAL at the CRR of 1:1 was inadequate to assess the severity of periodontitis on the basis of the 2D RL and 3D RSA measurements.
Burkholderia cepacia lipase immobilized on heterofunctional magnetic nanoparticles and its application in biodiesel synthesis
Authors: Li Kai , Fan Yanli , He Yaojia , Zeng Leping , Han Xiaotao , Yan Yunjun 
Published: November 2017

AbstractBiodiesel production using immobilized lipase as a biocatalyst is a promising process. The performance of immobilized lipase is mainly determined by supporting materials and immobilization method. To avoid the shortcomings of adsorption and covalent bonding methods, in this study, we developed a novel heterofunctional carrier of being strengthened anion exchange and weakened covalent binding to avoid activity loss and improve operational stability of the immobilized lipase. 2,3-epoxypropyltrimethylammonium chloride with epoxy and quaternary ammonium group and glutaraldehyde were grafted onto aminated magnetic nanoparticles (AMNPs) to generate a new matrix, named GEAMNP. Then Burkholderia cepacia lipase (BCL) was immobilized on GEAMNP via anion exchange and covalent bonding. The transesterification between soybean oil and methanol was used to test the activities. Activity recovery of the immobilized BCL was up to 147.4% and the corresponding transesterification activity was 1.5-fold than that of BCL powder. The immobilized lipase was further used for biodiesel production to confirm its feasibility. The fatty acid methyl esters conversion yield could reach 96.8% in the first 12 h. Furthermore, the immobilized lipase, BCL-GEAMNP showed markedly improved operational stability, better reusability and higher esters than BCL-GAMNP, where MNPs were only modified with (3-aminopropyl) triethoxysilane and glutaraldehyde.
Potential ash impact from Antarctic volcanoes: Insights from Deception Island’s most recent eruption
Authors: Geyer A. , Marti A. , Giralt S. , Folch A. 
Published: November 2017

AbstractAsh emitted during explosive volcanic eruptions may disperse over vast areas of the globe posing a threat to human health and infrastructures and causing significant disruption to air traffic. In Antarctica, at least five volcanoes have reported historic activity. However, no attention has been paid to the potential socio-economic and environmental consequences of an ash-forming eruption occurring at high southern latitudes. This work shows how ash from Antarctic volcanoes may pose a higher threat than previously believed. As a case study, we evaluate the potential impacts of ash for a given eruption scenario from Deception Island, one of the most active volcanoes in Antarctica. Numerical simulations using the novel MMB-MONARCH-ASH model demonstrate that volcanic ash emitted from Antarctic volcanoes could potentially encircle the globe, leading to significant consequences for global aviation safety. Results obtained recall the need for performing proper hazard assessment on Antarctic volcanoes, and are crucial for understanding the patterns of ash distribution at high southern latitudes with strong implications for tephrostratigraphy, which is pivotal to synchronize palaeoclimatic records.