bluuebunny/crossref_metadata_2025_split huggingface dataset:
Liprin-α1 and ERC1 control cell edge dynamics by promoting focal adhesion turnover
Authors: Astro Veronica , Tonoli Diletta , Chiaretti Sara , Badanai Sabrina , Sala Kristyna , Zerial Marino , de Curtis Ivan 
Published: September 2016

AbstractLiprin-α1 and ERC1 are interacting scaffold proteins regulating the motility of normal and tumor cells. They act as part of plasma membrane-associated platforms at the edge of motile cells to promote protrusion by largely unknown mechanisms. Here we identify an amino-terminal region of the liprin-α1 protein (liprin-N) that is sufficient and necessary for the interaction with other liprin-α1 molecules. Similar to liprin-α1 or ERC1 silencing, expression of the liprin-N negatively affects tumor cell motility and extracellular matrix invasion, acting as a dominant negative by interacting with endogenous liprin-α1 and causing the displacement of the endogenous ERC1 protein from the cell edge. Interfering with the localization of ERC1 at the cell edge inhibits the disassembly of focal adhesions, impairing protrusion. Liprin-α1 and ERC1 proteins colocalize with active integrin β1 clusters distinct from those colocalizing with cytoplasmic focal adhesion proteins and influence the localization of peripheral Rab7-positive endosomes. We propose that liprin-α1 and ERC1 promote protrusion by displacing cytoplasmic adhesion components to favour active integrin internalization into Rab7-positive endosomes.
IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies
Authors: Lagkouvardos Ilias , Joseph Divya , Kapfhammer Martin , Giritli Sabahattin , Horn Matthias , Haller Dirk , Clavel Thomas 
Published: September 2016

AbstractThe SRA (Sequence Read Archive) serves as primary depository for massive amounts of Next Generation Sequencing data and currently host over 100,000 16S rRNA gene amplicon-based microbial profiles from various host habitats and environments. This number is increasing rapidly and there is a dire need for approaches to utilize this pool of knowledge. Here we created IMNGS (Integrated Microbial Next Generation Sequencing), an innovative platform that uniformly and systematically screens for and processes all prokaryotic 16S rRNA gene amplicon datasets available in SRA and uses them to build sample-specific sequence databases and OTU-based profiles. Via a web interface, this integrative sequence resource can easily be queried by users. We show examples of how the approach allows testing the ecological importance of specific microorganisms in different hosts or ecosystems and performing targeted diversity studies for selected taxonomic groups. The platform also offers a complete workflow forde novoanalysis of users’ own raw 16S rRNA gene amplicon datasets for the sake of comparison with existing data. IMNGS can be accessed atwww.imngs.org.
Flyglow: Single-fly observations of simultaneous molecular and behavioural circadian oscillations in controls and an Alzheimer’s model
Authors: Khabirova Eleonora , Chen Ko-Fan , O’Neill John S. , Crowther Damian C. 
Published: September 2016

AbstractCircadian rhythms are essential for health and are frequently disturbed in disease. A full understanding of the causal relationships between behavioural and molecular circadian rhythms requires simultaneous longitudinal observations over time in individual organisms. Current experimental paradigms require the measurement of each rhythm separately across distinct populations of experimental organisms, rendering the comparability of the resulting datasets uncertain. We therefore developed FLYGLOW, an assay using clock gene controlled luciferase expression detected by exquisitely sensitive EM-CCD imaging, to enable simultaneous quantification of parameters including locomotor, sleep consolidation and molecular rhythms in single flies over days/weeks. FLYGLOW combines all the strengths of existing techniques and also allows powerful multiparametric paired statistics. We found the age-related transition from rhythmicity to arrhythmicity for each parameter occurs unpredictably, with some flies showing loss of one or more rhythms during middle-age. Using single-fly correlation analysis of rhythm robustness and period we demonstrated the independence of the peripheral clock from circadian behaviours in wild type flies as well as in an Alzheimer’s model. FLYGLOW is a useful tool for investigating the deterioration of behavioural and molecular rhythms in ageing and neurodegeneration. This approach may be applied more broadly within behavioural neurogenetics research.
Helical unwinding and side-chain unlocking unravel the outward open conformation of the melibiose transporter
Authors: Wang Li-Ying , Ravi Vidhya M. , Leblanc Gérard , Padrós Esteve , Cladera Josep , Perálvarez-Marín Alex 
Published: September 2016

AbstractMolecular dynamics simulations have been used to study the alternate access mechanism of the melibiose transporter from Escherichia coli. Starting from the outward-facing partially occluded form, 2 out of 12 simulations produced an outward full open form and one partially open, whereas the rest yielded fully or partially occluded forms. The shape of the outward-open form resembles other outward-open conformations of secondary transporters. During the transporter opening, conformational changes in some loops are followed by changes in the periplasm region of transmembrane helix 7. Helical curvature relaxation and unlocking of hydrophobic and ionic locks promote the outward opening of the transporter making accessible the substrate binding site. In particular, FRET studies on mutants of conserved aromatic residues of extracellular loop 4 showed lack of substrate binding, emphasizing the importance of this loop for making crucial interactions that control the opening of the periplasmic side. This study indicates that the alternate access mechanism for the melibiose transporter fits better into a flexible gating mechanism rather than the archetypical helical rigid-body rocker-switch mechanism.
Ultrabroadband Design for Linear Polarization Conversion and Asymmetric Transmission Crossing X- and K- Band
Authors: Zhang Linbo , Zhou Peiheng , Chen Haiyan , Lu Haipeng , Xie Haiyan , Zhang Li , Li En , Xie Jianliang , Deng Longjiang 
Published: September 2016

AbstractIn this work, a high-efficiency and broadband reflective converter using ultrathin planar metamaterial (MM) composed of single-layered SRR is firstly realized. Numerical and experimental results demonstrate that the cross-polarization conversion reflectance above 0.84 is achieved from 8.6 to 18.6 GHz for linearly polarized (LP) incident waves under normal incidence. Subsequently, a multi-layered MM based on SRR enables a dramatic improvement of the recently demonstrated asymmetric transmission (AT) effect. Theoretical and measured results present that strong one-way transmission of two orthogonally polarized waves crossing C- and K- band has been observed. These two separated AT pass-bands have a function of selective polarization filter, which can be switched on/off by changing the polarization state of incident waves. The physical mechanisms are elucidated by taking advantage of electric fields and current distributions. Considering the broad bandwidth and the dual band, we believe that these two structures will be beneficial for designing polarization-controlled and selective transmission converter.
Linking in domain-swapped protein dimers
Authors: Baiesi Marco , Orlandini Enzo , Trovato Antonio , Seno Flavio 
Published: September 2016

AbstractThe presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, makes such dimers suitable candidates to validate the possibility that mutual entanglement between chains may play a similar role for protein complexes. We suggest that such entanglement is captured by the linking number. This represents, for two closed curves, the number of times that each curve winds around the other. We show that closing the curves is not necessary, as a novel parameter G′, termed Gaussian entanglement, is strongly correlated with the linking number. Based on 110 non redundant domain-swapped dimers, our analysis evidences a high fraction of chains with a significant intertwining, that is with |G′| > 1. We report that Nature promotes configurations with negative mutual entanglement and surprisingly, it seems to suppress intertwining in long protein dimers. Supported by numerical simulations of dimer dissociation, our results provide a novel topology-based classification of protein-swapped dimers together with some preliminary evidence of its impact on their physical and biological properties.
Species specific exome probes reveal new insights in positively selected genes in nonhuman primates
Authors: Su Zheng , Zhang Junjie , Kumar Chanchal , Molony Cliona , Lu Hongchao , Chen Ronghua , Stone David J. , Ling Fei , Liu Xiao 
Published: September 2016

AbstractNonhuman primates (NHP) are important biomedical animal models for the study of human disease. Of these, the most widely used models in biomedical research currently are from the genus Macaca. However, evolutionary genetic divergence between human and NHP species makes human-based probes inefficient for the capture of genomic regions of NHP for sequencing and study. Here we introduce a new method to resequence the exome of NHP species by a designed capture approach specifically targeted to the NHP, and demonstrate its superior performance on four NHP species or subspecies. Detailed investigation on biomedically relevant genes demonstrated superior capture by the new approach. We identified 28 genes that appeared to be pseudogenized and inactivated in macaque. Finally, we identified 187 genes showing strong evidence for positive selection across all branches of the primate phylogeny including many novel findings.
The MADS-Box transcription factor Bcmads1 is required for growth, sclerotia production and pathogenicity of Botrytis cinerea
Authors: Zhang Zhanquan , Li Hua , Qin Guozheng , He Chang , Li Boqiang , Tian Shiping 
Published: September 2016

AbstractMADS-box transcription factors are highly conserved in eukaryotic species and involved in a variety of biological processes. Little is known, however, regarding the function of MADS-box genes in Botrytis cinerea, a fungal pathogen with a wide host range. Here, the functional role of the B. cinerea MADS-box gene, Bcmads1, was characterized in relation to the development, pathogenicity and production of sclerotia. The latter are formed upon incubation in darkness and serve as survival structures during winter and as the female parent in sexual reproduction. Bcmads1 is indispensable for sclerotia production. RT-qPCR analysis suggested that Bcmads1 modulated sclerotia formation by regulating the expression of light-responsive genes. Bcmads1 is required for the full virulence potential of B. cinerea on apple fruit. A comparative proteomic analysis identified 63 proteins, representing 55 individual genes that are potential targets of Bcmads1. Among them, Bcsec14 and Bcsec31 are associated with vesicle transport. Deletion of Bcsec14 and Bcsec31 resulted in a reduction in the virulence and protein secretion of B. cinerea. These results suggest that Bcmads1 may influence sclerotia formation by modulating light responsive gene expression and regulate pathogenicity by its effect on the protein secretion process.
Exposure to HT-2 toxin causes oxidative stress induced apoptosis/autophagy in porcine oocytes
Authors: Zhang Yue , Han Jun , Zhu Cheng-Cheng , Tang Feng , Cui Xiang-Shun , Kim Nam-Hyung , Sun Shao-Chen 
Published: September 2016

AbstractT-2 toxin is a main type A trichothecene mycotoxin which is the most toxic trichothecence. T-2 toxin has posed various toxic effects on human and animals in vigorous cell proliferation tissues like lymphoid, hematopoietic and gastrointestinal tissues, while HT-2 toxin is the major metabolite which is deacetylated by T-2 toxin. In this study, we focused on the toxic effects of HT-2 on porcine oocyte maturation. We treated the porcine oocyte with HT-2 toxin in vitro, and we first found that HT-2 treatment inhibited porcine oocyte polar body extrusion and cumulus cell expansion. We observed the disrupted meiotic spindle morphology after treatment, which might be due to the reduced p-MAPK protein level. Actin distribution was also disturbed, indicating that HT-2 affects cytoskeleton of porcine oocytes. We next explored the causes for the failure of oocyte maturation after HT-2 treatment. We found that HT-2 treated oocytes showed the increased ROS level, which indicated that oxidative stress had occurred. We also detected autophagy as well as early apoptosis in the treatment oocytes. Due to the fact that oxidative stress could induced apoptosis, our results indicated that HT-2 toxin caused oxidative stress induced apoptosis and autophagy, which further affected porcine oocyte maturation.
Decreased IL7Rα and TdT expression underlie the skewed immunoglobulin repertoire of human B-cell precursors from fetal origin
Authors: Rother Magdalena B. , Jensen Kristin , van der Burg Mirjam , van de Bovenkamp Fleur S. , Kroek Roel , van IJcken Wilfred F. J. , van der Velden Vincent H. J. , Cupedo Tom , Olstad Ole K. , van Dongen Jacques J. M. , van Zelm Menno C. 
Published: September 2016

AbstractNewborns are unable to mount antibody responses towards certain antigens. This has been related to the restricted repertoire of immunoglobulin (Ig) genes of their B cells. The mechanisms underlying the restricted fetal Ig gene repertoire are currently unresolved. We here addressed this with detailed molecular and cellular analysis of human precursor-B cells from fetal liver, fetal bone marrow (BM), and pediatric BM. In the absence of selection processes, fetal B-cell progenitors more frequently used proximal V, D and J genes in complete IGH gene rearrangements, despite normal Ig locus contraction. Fewer N-nucleotides were added in IGH gene rearrangements in the context of low TdT and XRCC4 expression. Moreover, fetal progenitor-B cells expressed lower levels of IL7Rα than their pediatric counterparts. Analysis of progenitor-B cells from IL7Rα-deficient patients revealed that TdT expression and N-nucleotides additions in Dh-Jh junctions were dependent on functional IL7Rα. Thus, IL7Rα affects TdT expression, and decreased expression of this receptor underlies at least in part the skewed Ig repertoire formation in fetal B-cell precursors. These new insights provide a better understanding of the formation of adaptive immunity in the developing fetus.
Blocking 5-HT2 receptor restores cardiovascular disorders in type 1 experimental diabetes
Authors: García-Pedraza José-Ángel , Ferreira-Santos Pedro , Aparicio Rubén , Montero María-José , Morán Asunción 
Published: September 2016

AbstractThis study aimed to determine whether the serotonergic modulation, through selective 5-HT2 receptor blockade, restores cardiovascular disturbances in type 1 diabetic rats. Diabetes was induced by alloxan (150 mg/kg, s.c.) and maintained for 4 weeks. 5-HT2 receptor was blocked by sarpogrelate (30 mg/kg.day; 14 days; p.o.). Systolic blood pressure (SBP), heart rate (HR), glycaemia and body weight (BW) were monitored periodically. Animals were sacrificed at the end of the study and the heart, right kidney and thoracic aorta were removed; plasma samples were also obtained. Left ventricular hypertrophy index (LVH) and renal hypertrophy index (RH) were determined. Vascular function was studied in aorta rings; additionally, superoxide anion (O2•−) production (by lucigenin-enhanced chemiluminescence) and lipid peroxidation (by thiobarbituric acid reactive substances assay) were measured. Neither alloxan nor sarpogrelate treatments altered HR, LVH or endothelium-independent relaxation. SBP, glycaemia, BW, RH, O2•− production and lipid peroxidation were significantly altered in diabetic animals compared with controls. Sarpogrelate treatment considerably decreased SBP, RH, O2•− production and lipid peroxidation. Endothelium-dependent relaxation was severely reduced in diabetic animal aortas compared to controls; sarpogrelate treatment markedly improved it. Our outcomes show that selectively blocking 5-HT2 receptors has beneficial effects on impaired cardiovascular parameters in diabetes.
Zephycandidine A, the First Naturally Occurring Imidazo[1,2-f]phenanthridine Alkaloid from Zephyranthes candida, Exhibits Significant Anti-tumor and Anti-acetylcholinesterase Activities
Authors: Zhan Guanqun , Qu Xiaolan , Liu Junjun , Tong Qingyi , Zhou Junfei , Sun Bin , Yao Guangmin 
Published: September 2016

AbstractZephycandidine A (1), the first naturally occurring imidazo[1,2-f]phenanthridine alkaloid, was isolated from Zephyranthes candida (Amaryllidaceae). The structure of 1 was elucidated by spectroscopic analyses and NMR calculation and a plausible biogenetic pathway for zephycandidine A (1) was proposed. Zephycandidine A (1) exhibited significant cytotoxicity against five cancer cell lines with IC50 values ranging from 1.98 to 7.03 μM with selectivity indices as high as 10 when compared to the normal Beas-2B cell. Further studies suggested that zephycandidine A (1) induces apoptosis in leukemia cells by the activation of caspase-3, upregulation of Bax, downregulation of Bcl-2 and degradation of PARP expression. In addition, zephycandidine A (1) showed acetylcholinesterase (AChE) inhibitory activity and the docking studies of zephycandidine A (1) and galanthamine (2) with AChE revealed that interactions with W286 and Y337 are necessary.
Single-pulse enhanced coherent diffraction imaging of bacteria with an X-ray free-electron laser
Authors: Fan Jiadong , Sun Zhibin , Wang Yaling , Park Jaehyun , Kim Sunam , Gallagher-Jones Marcus , Kim Yoonhee , Song Changyong , Yao Shengkun , Zhang Jian , Zhang Jianhua , Duan Xiulan , Tono Kensuke , Yabashi Makina , Ishikawa Tetsuya , Fan Chunhai , Zhao Yuliang , Chai Zhifang , Gao Xueyun , Earnest Thomas , Jiang Huaidong 
Published: September 2016

AbstractHigh-resolution imaging offers one of the most promising approaches for exploring and understanding the structure and function of biomaterials and biological systems. X-ray free-electron lasers (XFELs) combined with coherent diffraction imaging can theoretically provide high-resolution spatial information regarding biological materials using a single XFEL pulse. Currently, the application of this method suffers from the low scattering cross-section of biomaterials and X-ray damage to the sample. However, XFELs can provide pulses of such short duration that the data can be collected using the “diffract and destroy” approach before the effects of radiation damage on the data become significant. These experiments combine the use of enhanced coherent diffraction imaging with single-shot XFEL radiation to investigate the cellular architecture of Staphylococcus aureus with and without labeling by gold (Au) nanoclusters. The resolution of the images reconstructed from these diffraction patterns were twice as high or more for gold-labeled samples, demonstrating that this enhancement method provides a promising approach for the high-resolution imaging of biomaterials and biological systems.
High Fructose Diet inducing diabetes rapidly impacts olfactory epithelium and behavior in mice
Authors: Rivière Sébastien , Soubeyre Vanessa , Jarriault David , Molinas Adrien , Léger-Charnay Elise , Desmoulins Lucie , Grebert Denise , Meunier Nicolas , Grosmaitre Xavier 
Published: September 2016

AbstractType 2 Diabetes (T2D), a major public health issue reaching worldwide epidemic, has been correlated with lower olfactory abilities in humans. As olfaction represents a major component of feeding behavior, its alteration may have drastic consequences on feeding behaviors that may in turn aggravates T2D. In order to decipher the impact of T2D on the olfactory epithelium, we fed mice with a high fructose diet (HFruD) inducing early diabetic state in 4 to 8 weeks. After only 4 weeks of this diet, mice exhibited a dramatic decrease in olfactory behavioral capacities. Consistently, this decline in olfactory behavior was correlated to decreased electrophysiological responses of olfactory neurons recorded as a population and individually. Our results demonstrate that, in rodents, olfaction is modified by HFruD-induced diabetes. Functional, anatomical and behavioral changes occurred in the olfactory system at a very early stage of the disease.
Dual-Wavelength Terahertz Metasurfaces with Independent Phase and Amplitude Control at Each Wavelength
Authors: Ding Jun , Xu Ningning , Ren Han , Lin Yuankun , Zhang Weili , Zhang Hualiang 
Published: September 2016

AbstractWe have designed, fabricated and characterized dual-wavelength metasurfaces that function at two assigned terahertz wavelengths with independent phase and amplitude control at each wavelength. Specifically, we have designed a dual-wavelength achromatic metasurface-based deflector deflecting the incident wave to the same direction at two selected wavelengths, which has circumvented the critical limitation of strong wavelength dependence in the planar metasurface-based devices caused by the resonant nature of the plasmonic structures. As a proof of concept demonstration, the designed dual-wavelength achromatic deflector has been fabricated and characterized experimentally. The numerical simulations, theoretical predictions and experimental results agree very well with each other, demonstrating the property of independently manipulating the phase profiles at two wavelengths. Furthermore, another unique feature of the designed metasurface is that it can independently tailor both the phase and amplitude profiles at two wavelengths. This property has been numerically validated by engineering a metasurface-based device to simultaneously generate two diffraction orders at two desired wavelengths.
Transcranial focused ultrasound stimulation of human primary visual cortex
Authors: Lee Wonhye , Kim Hyun-Chul , Jung Yujin , Chung Yong An , Song In-Uk , Lee Jong-Hwan , Yoo Seung-Schik 
Published: September 2016

AbstractTranscranial focused ultrasound (FUS) is making progress as a new non-invasive mode of regional brain stimulation. Current evidence of FUS-mediated neurostimulation for humans has been limited to the observation of subjective sensory manifestations and electrophysiological responses, thus warranting the identification of stimulated brain regions. Here, we report FUS sonication of the primary visual cortex (V1) in humans, resulting in elicited activation not only from the sonicated brain area, but also from the network of regions involved in visual and higher-order cognitive processes (as revealed by simultaneous acquisition of blood-oxygenation-level-dependent functional magnetic resonance imaging). Accompanying phosphene perception was also reported. The electroencephalo graphic (EEG) responses showed distinct peaks associated with the stimulation. None of the participants showed any adverse effects from the sonication based on neuroimaging and neurological examinations. Retrospective numerical simulation of the acoustic profile showed the presence of individual variability in terms of the location and intensity of the acoustic focus. With exquisite spatial selectivity and capability for depth penetration, FUS may confer a unique utility in providing non-invasive stimulation of region-specific brain circuits for neuroscientific and therapeutic applications.