bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryo-EM Studies of Drp1 Reveal Cardiolipin Interactions that Activate the Helical Oligomer
Authors: Francy Christopher A. , Clinton Ryan W. , Fröhlich Chris , Murphy Colleen , Mears Jason A. 
Published: August 2017

AbstractDynamins are mechano-chemical GTPases involved in the remodeling of cellular membranes. In this study, we have investigated the mechanism of dynamin-related protein 1 (Drp1), a key mediator of mitochondrial fission. To date, it is unclear how Drp1 assembles on the mitochondrial outer membrane in response to different lipid signals to induce membrane fission. Here, we present cryo-EM structures of Drp1 helices on nanotubes with distinct lipid compositions to mimic membrane interactions with the fission machinery. These Drp1 polymers assemble exclusively through stalk and G-domain dimerizations, which generates an expanded helical symmetry when compared to other dynamins. Interestingly, we found the characteristic gap between Drp1 and the lipid bilayer was lost when the mitochondrial specific lipid cardiolipin was present, as Drp1 directly interacted with the membrane. Moreover, this interaction leads to a change in the helical structure, which alters G-domain interactions to enhance GTPase activity. These results demonstrate how lipid cues at the mitochondrial outer membrane (MOM) can alter Drp1 structure to activate the fission machinery.
Functional association of cellular microtubules with viral capsid assembly supports efficient hepatitis B virus replication
Authors: Iwamoto Masashi , Cai Dawei , Sugiyama Masaya , Suzuki Ryosuke , Aizaki Hideki , Ryo Akihide , Ohtani Naoko , Tanaka Yasuhito , Mizokami Masashi , Wakita Takaji , Guo Haitao , Watashi Koichi 
Published: August 2017

AbstractViruses exploit host factors and environment for their efficient replication. The virus-host interaction mechanisms for achieving an optimal hepatitis B virus (HBV) replication have been largely unknown. Here, a single cell cloning revealed that HepAD38 cells, a widely-used HBV-inducible cell line, contain cell clones with diverse permissiveness to HBV replication. The HBV permissiveness was impaired upon treatment with microtubule inhibitor nocodazole, which was identified as an HBV replication inhibitor from a pharmacological screening. In the microtubule-disrupted cells, the efficiency of HBV capsid assembly was remarkably decreased without significant change in pre-assembly process. We further found that HBV core interacted with tubulin and co-localized with microtubule-like fibriforms, but this association was abrogated upon microtubule-disassembly agents, resulting in attenuation of capsid formation. Our data thus suggest a significant role of microtubules in the efficient capsid formation during HBV replication. In line with this, a highly HBV permissive cell clone of HepAD38 cells showed a prominent association of core-microtubule and thus a high capacity to support the capsid formation. These findings provide a new aspect of virus-cell interaction for rendering efficient HBV replication.
Abnormal Electroretinogram after Kir7.1 Channel Suppression Suggests Role in Retinal Electrophysiology
Authors: Shahi Pawan K. , Liu Xinling , Aul Bryce , Moyer Andrea , Pattnaik Akshita , Denton Jerod , Pillers De-Ann M. , Pattnaik Bikash R. 
Published: August 2017

AbstractThe KCNJ13 gene encodes the inwardly rectifying potassium channel, Kir7.1. Mutations in this gene cause childhood blindness, in which the a- and b-wave responses of electroretinogram (ERG) are abolished. The ERG a-wave is the light-induced hyperpolarization of retinal photoreceptors, and the b-wave is the depolarization of ON-bipolar cells. The Kir7.1 channel is localized to the apical aspects of retinal pigment epithelium (RPE) cells and contributes to a delayed c-wave response. We sought to understand why a defect in an RPE ion-channel result in abnormal electrophysiology at the level of the retinal neurons. We have established the expression of Kir7.1 channels in the mouse RPE. ERGs recorded after mice Kir7.1 suppression by shRNA, or by blocking with VU590, showed reduced a-, b- and c-wave amplitudes. In contrast, the Kir7.1 blocker had no effect on the ex-vivo isolated mouse retina ERG where the RPE is not attached to the isolated retina preparation. Finally, we confirmed the specificity of VU590 action by inhibition of native mouse RPE Kir7.1 current in patch-clamp experiment. We propose that mutant RPE Kir7.1 channels contribute directly to the abnormal ERG associated with blindness via alterations in sub-retinal space K+ homeostasis in the vicinity of the photoreceptor outer segment.
Closing the bandgap for III-V nitrides toward mid-infrared and THz applications
Authors: Lu Pengfei , Liang Dan , Chen Yingjie , Zhang Chunfang , Quhe Ruge , Wang Shumin 
Published: August 2017

AbstractA theoretical study of InNBi alloy by using density functional theory is presented. The results show non-linear dependence of the lattice parameters and bulk modulus on Bi composition. The formation energy and thermodynamic stability analysis indicate that the InNBi alloy possesses a stable phase over a wide range of intermediate compositions at a normal growth temperature. The bandgap of InNBi alloy in Wurtzite (WZ) phase closes for Bi composition higher than 1.5625% while that in zinc-blende (ZB) phase decreases significantly at around 356 meV/%Bi. The Bi centered ZB InNBi alloy presents a change from a direct bandgap to an indirect bandgap up to 1.5625% Bi and then an oscillates between indirect bandgap and semi-metallic for 1.5625% to 25% Bi and finally to metallic for higher Bi compositions. For the same Bi composition, its presence in cluster or uniform distribution has a salient effect on band structures and can convert between direct and indirect bandgap or open the bandgap from the metallic gap. These interesting electronic properties enable III-nitride closing the bandgap and make this material a good candidate for future photonic device applications in the mid-infrared to THz energy regime.
Loss of NR2E3 represses AHR by LSD1 reprogramming, is associated with poor prognosis in liver cancer
Authors: Khanal Tilak , Choi Kwangmin , Leung Yuet-Kin , Wang Jiang , Kim Dasom , Janakiram Vinothini , Cho Sung-Gook , Puga Alvaro , Ho Shuk-Mei , Kim Kyounghyun 
Published: August 2017

AbstractThe aryl hydrocarbon receptor (AHR) plays crucial roles in inflammation, metabolic disorder, and cancer. However, the molecular mechanisms regulating AHR expression remain unknown. Here, we found that an orphan nuclear NR2E3 maintains AHR expression, and forms an active transcriptional complex with transcription factor Sp1 and coactivator GRIP1 in MCF-7 human breast and HepG2 liver cancer cell lines. NR2E3 loss promotes the recruitment of LSD1, a histone demethylase of histone 3 lysine 4 di-methylation (H3K4me2), to the AHR gene promoter region, resulting in repression of AHR expression. AHR expression and responsiveness along with H3K4me2 were significantly reduced in the livers of Nr2e3rd7 (Rd7) mice that express low NR2E3 relative to the livers of wild-type mice. SP2509, an LSD1 inhibitor, fully restored AHR expression and H3K4me2 levels in Rd7 mice. Lastly, we demonstrated that both AHR and NR2E3 are significantly associated with good clinical outcomes in liver cancer. Together, our results reveal a novel link between NR2E3, AHR, and liver cancer via LSD1-mediated H3K4me2 histone modification in liver cancer development.
CLEC14a-HSP70-1A interaction regulates HSP70-1A-induced angiogenesis
Authors: Jang Jihye , Kim Mi Ra , Kim Taek-Keun , Lee Woo Ran , Kim Jong Heon , Heo Kyun , Lee Sukmook 
Published: August 2017

AbstractCLEC14a (C-type lectin domain family 14 member) is a tumor endothelial cell marker protein that is known to play an important role in tumor angiogenesis, but the basic molecular mechanisms underlying this function have not yet been clearly elucidated. In this study, using various proteomic tools, we isolated a 70-kDa protein that interacts with the C-type lectin-like domain of CLEC14a (CLEC14a-CTLD) and identified it as heat shock protein 70-1A (HSP70-1A). Co-immunoprecipitation showed that HSP70-1A and CLEC14a interact on endothelial cells. In vitro binding analyses identified that HSP70-1A specifically associates with the region between amino acids 43 and 69 of CLEC14a-CTLD. Competitive blocking experiments indicated that this interacting region of CLEC14a-CTLD significantly inhibits HSP70-1A-induced extracellular signal-regulated kinase (ERK) phosphorylation and endothelial tube formation by directly inhibiting CLEC14a-CTLD-mediated endothelial cell-cell contacts. Our data suggest that the specific interaction of HSP70-1A with CLEC14a may play a critical role in HSP70-1A-induced angiogenesis and that the HSP70-1A-interacting region of CLEC14a-CTLD may be a useful tool for inhibiting HSP70-1A-induced angiogenesis.
Oxygen Mapping of Melanoma Spheroids using Small Molecule Platinum Probe and Phosphorescence Lifetime Imaging Microscopy
Authors: Raza Ahtasham , Colley Helen E. , Baggaley Elizabeth , Sazanovich Igor V. , Green Nicola H. , Weinstein Julia A. , Botchway Stanley W. , MacNeil Sheila , Haycock John W. 
Published: August 2017

AbstractSolid tumours display varied oxygen levels and this characteristic can be exploited to develop new diagnostic tools to determine and exploit these variations. Oxygen is an efficient quencher of emission of many phosphorescent compounds, thus oxygen concentration could in many cases be derived directly from relative emission intensity and lifetime. In this study, we extend our previous work on phosphorescent, low molecular weight platinum(II) complex as an oxygen sensing probe to study the variation in oxygen concentration in a viable multicellular 3D human tumour model. The data shows one of the first examples of non-invasive, real-time oxygen mapping across a melanoma tumour spheroid using one-photon phosphorescence lifetime imaging microscopy (PLIM) and a small molecule oxygen sensitive probe. These measurements were quantitative and enabled real time oxygen mapping with high spatial resolution. This combination presents as a valuable tool for optical detection of both physiological and pathological oxygen levels in a live tissue mass and we suggest has the potential for broader clinical application.
Membrane association of the bacterial riboregulator Hfq and functional perspectives
Authors: Malabirade Antoine , Morgado-Brajones Javier , Trépout Sylvain , Wien Frank , Marquez Ileana , Seguin Jérôme , Marco Sergio , Velez Marisela , Arluison Véronique 
Published: August 2017

AbstractHfq is a bacterial RNA binding protein that carries out several roles in genetic expression regulation, mainly at the post-transcriptional level. Previous studies have shown its importance in growth and virulence of bacteria. Here, we provide the direct observation of its ability to interact with membranes. This was established by co-sedimentation assay, cryo-transmission electron (cryo-TEM) and atomic force (AFM) microscopies. Furthermore, our results suggest a role for its C-terminus amyloidogenic domain in membrane disruption. Precisely, AFM images of lipid bilayers in contact with Hfq C-terminus fibrils show the emergence of holes with a size dependent on the time of interaction. Cryo-TEM observations also show that liposomes are in contact with clusters of fibrils, with occasional deformation of the vesicles and afterward the apparition of a multitude of tiny vesicles in the proximity of the fibrils, suggesting peptide-induced breakage of the liposomes. Finally, circular dichroism spectroscopy demonstrated a change in the secondary structure of Hfq C-terminus upon interaction with liposomes. Altogether, these results show an unexpected property of Hfq and suggest a possible new role for the protein, exporting sRNA outside of the bacterial cell.
Tillage and nitrogen fertilization enhanced belowground carbon allocation and plant nitrogen uptake in a semi-arid canola crop–soil system
Authors: Sarker Jharna Rani , Singh Bhupinder Pal , He Xinhua , Fang Yunying , Li Guangdi D. , Collins Damian , Cowie Annette L. 
Published: August 2017

AbstractCarbon (C) and nitrogen (N) allocation and assimilation are coupled processes, likely influencing C accumulation, N use efficiency and plant productivity in agro-ecosystems. However, dynamics and responses of these processes to management practices in semi-arid agro-ecosystems are poorly understood. A field-based13CO2and urea-15N pulse labelling experiment was conducted to track how C and N allocation and assimilation during canola growth from flowering to maturity were affected by short-term (2-year) tillage (T) and no-till (NT) with or without 100 kg urea-N ha−1(T-0, T-100, NT-0, NT-100) on a Luvisol in an Australian semi-arid region. The T-100 caused greater (P < 0.05) belowground C allocation and higher (P < 0.05) translocation of soil N to shoots and seeds, compared to other treatments. Microbial N uptake was rapid and greatest in the fertilized (cf. non-fertilized) treatments, followed by a rapid release of microbial immobilized N, thus increasing N availability for plant uptake. In contrast, management practices had insignificant impact on soil C and N stocks, aggregate stability, microbial biomass, and13C retention in aggregate-size fractions. In conclusion, tillage and N fertilization increased belowground C allocation and crop N uptake and yield, possiblyviaenhancing root–microbial interactions, with minimal impact on soil properties.
Semi-transparent Perovskite Solar Cells Developed by Considering Human Luminosity Function
Authors: Kim Gyu Min , Tatsuma Tetsu 
Published: August 2017

AbstractSemi-transparent solar cells draw a great deal of attention because their applications include, for instance, photovoltaic windows. General approach to semi-transparent cells is using thin active layers or island-type structures. Here we take human luminosity function into account, and develop solar cells that harvest photons in the wavelength regions in which human eyes are less sensitive to light. We used an organic-inorganic hybrid perovskite, which is sensitive to light particularly in the blue and deep-blue regions, and plasmonic silver nanocubes that enhance light harvesting in the red and deep-red ranges. In order to tune the plasmonic wavelength to that range, we took advantage of electrode-coupled plasmons (ECPs). We prepared non-plasmonic semi-transparent solar cells, and reduced the active layer thickness and introduced ECPs, so that the visual transparency index and power conversion efficiency of the cell were improved by 28% and 6%, respectively, of the initial values.
Broadband angle- and permittivity-insensitive nondispersive optical activity based on planar chiral metamaterials
Authors: Song Kun , Su Zhaoxian , Wang Min , Silva Sinhara , Bhattarai Khagendra , Ding Changlin , Liu Yahong , Luo Chunrong , Zhao Xiaopeng , Zhou Jiangfeng 
Published: August 2017

AbstractBecause of the strong inherent resonances, the giant optical activity obtained via chiral metamaterials generally suffers from high dispersion, which has been a big stumbling block to broadband applications. In this paper, we propose a type of planar chiral metamaterial consisting of interconnected metal helix slat structures with four-fold symmetry, which exhibits nonresonant Drude-like response and can therefore avoid the highly dispersive optical activity resulting from resonances. It shows that the well-designed chiral metamaterial can achieve nondispersive and pure optical activity with high transmittance in a broadband frequency range. And the optical activity of multi-layer chiral metamaterials is proportional to the layer numbers of single-layer chiral metamaterial. Most remarkably, the broadband behaviors of nondispersive optical activity and high transmission are insensitive to the incident angles of electromagnetic waves and permittivity of dielectric substrate, thereby enabling more flexibility in polarization manipulation.
Transglutaminase 2 regulates osteoclast differentiation via a Blimp1-dependent pathway
Authors: Kim Woo-Shin , Kim Haemin , Jeong Eui Man , Kim Hyung Joon , Lee Zang Hee , Kim In-Gyu , Kim Hong-Hee 
Published: August 2017

AbstractTransglutaminase 2 (TG2) performs multiple reactions, including transamidation, and also plays a role in signal transduction as a GTP-binding protein. In this study, we reveal that TG2 controls osteoclast differentiation and bone homeostasis in mice. Osteoclasts specifically expressed the TG2 isoform among eight TG family members. Suppression in TG2 expression with siRNA led to increased osteoclast formation from primary mouse precursor cells in response to receptor activator of nuclear factor kappaB ligand (RANKL). This osteoclastogenic effect of TG2 knockdown was associated with enhanced induction of c-Fos and NFATc1 by RANKL. Moreover, TG2 knockdown up-regulated B lymphocyte-induced maturation protein 1 (Blimp1), which represses anti-osteoclastogenic genes, in a manner dependent on the NF-κB signaling pathway. To the contrary, TG2 overexpression inhibited osteoclast formation and the expression of osteoclastogenic genes. Consistent with these in vitro results, TG2 knockout mice exhibited lower trabecular bone mass and increased number of osteoclasts compared with wild-type mice. Taken together, our results provide strong evidence that TG2 plays an important role in bone metabolism by suppressing excessive osteoclastogenesis via the regulation of the NF-κB-Blimp1 signaling pathway.
Rate-limiting steps in transcription dictate sensitivity to variability in cellular components
Authors: Mäkelä Jarno , Kandavalli Vinodh , Ribeiro Andre S. 
Published: August 2017

AbstractCell-to-cell variability in cellular components generates cell-to-cell diversity in RNA and protein production dynamics. As these components are inherited, this should also cause lineage-to-lineage variability in these dynamics. We conjectured that these effects on transcription are promoter initiation kinetics dependent. To test this, first we used stochastic models to predict that variability in the numbers of molecules involved in upstream processes, such as the intake of inducers from the environment, acts only as a transient source of variability in RNA production numbers, while variability in the numbers of a molecular species controlling transcription of an active promoter acts as a constant source. Next, from single-cell, single-RNA level time-lapse microscopy of independent lineages of Escherichia coli cells, we demonstrate the existence of lineage-to-lineage variability in gene activation times and mean RNA production rates, and that these variabilities differ between promoters and inducers used. Finally, we provide evidence that this can be explained by differences in the kinetics of the rate-limiting steps in transcription between promoters and induction schemes. We conclude that cell-to-cell and consequent lineage-to-lineage variability in RNA and protein numbers are both promoter sequence-dependent and subject to regulation.
Regional genetic diversity for NNV grouper viruses across the Indo-Asian region – implications for selecting virus resistance in farmed groupers
Authors: Knibb Wayne , Luu Giang , Premachandra H. K. A. , Lu Ming-Wei , Nguyen Nguyen Hong 
Published: August 2017

AbstractGrouper aquaculture around Asia is impacted by the nervous necrosis virus (NNV) and, in response, host resistance to this infection is being considered as a trait for selection. However efficient selection may be confounded if there are different genetic strains of NNV within and between regions and over years. This study uses statistical approaches and assessment of “characteristic attributes” (i.e. nucleotide positions that discriminate among strains) to assess whether published and new NNV RNA2 cds sequences show genetic differentiation over geography, host species and years. Rather clear evidence was found for regional strains of NNV. Interestingly, most of the geographic defining “characteristic attributes” were in codon position three, and not translated into differences for the protein capsid (i.e. they were synonymous variations), suggesting that while NNV strains were geographically isolated and had diverged in different regions for RNA sequences, selection had largely conserved the protein sequences among regions. The apparent selection constraint on the capsid protein may mitigate the risk that despite geographic subdivision, NNV strain variability will confound genetic selection for host resistance. The existence of regional Asian NNV strains may suggest that hatcheries are at risk from NNV not only from imported material but also from endemic reservoirs.
Iron-dependent reconfiguration of the proteome underlies the intracellular lifestyle of Brucella abortus
Authors: Roset M. S. , Alefantis T. G. , DelVecchio V. G. , Briones G. 
Published: August 2017

AbstractBrucella ssp. is a facultative intracellular pathogen that causes brucellosis, a worldwide zoonosis that affects a wide range of mammals including humans. A critical step for the establishment of a successful Brucella infection is its ability to survive within macrophages. To further understand the mechanisms that Brucella utilizes to adapt to an intracellular lifestyle, a differential proteomic study was performed for the identification of intracellular modulated proteins. Our results demonstrated that at 48 hours post-infection Brucella adjusts its metabolism in order to survive intracellularly by modulating central carbon metabolism. Remarkably, low iron concentration is likely the dominant trigger for reprogramming the protein expression profile. Up-regulation of proteins dedicated to reduce the concentration of reactive oxygen species, protein chaperones that prevent misfolding of proteins, and proteases that degrade toxic protein aggregates, suggest that Brucella protects itself from damage likely due to oxidative burst. This proteomic analysis of B. abortus provides novel insights into the mechanisms utilized by Brucella to establish an intracellular persistent infection and will aid in the development of new control strategies and novel targets for antimicrobial therapy.
A natural chalcone induces apoptosis in lung cancer cells: 3D-QSAR, docking and an in vivo/vitro assay
Authors: Chen Gang , Zhou Di , Li Xue-Zheng , Jiang Zhe , Tan Chengyu , Wei Xiu-Yan , Ling Junhong , Jing Jing , Liu Fen , Li Ning 
Published: August 2017

AbstractThis study was to study the antitumor effect of lonchocarpin (34) from traditional herbal medicine Pongamia pinnata (L.) Pierre and to reveal the underlying mechanism. The cytotoxic activities of lonchocarpin were evaluated in 10 lung cancer cell lines and it exhibited 97.5% activity at a dose of 100 μM in the H292 cell line. A field-based quantitative structure-activity relationship (3D-QSAR) study of 37 flavonoids from P. pinnata was also performed, and the results obtained showed that the hydrophobic interaction could be the crucial factor for the antitumor activity of lonchocarpin. Molecular docking studies revealed that lonchocarpin bound stably to the BH3-binding groove of the Bcl-2 protein with hydrophobic interactions with ALA146. Also, lonchocarpin significantly reduced cell proliferation via modulating Bax/Caspase-9/Caspase-3 pathway. An apoptotic test using flow cytometry showed that lonchocarpin produced about 41.1% and 47.9% apoptosis after treatment for 24 h and 48 h, respectively. Moreover, lonchocarpin inhibited tumor growth in S180-bearing mice with an inhibition rate of 57.94, 63.40 and 72.51%, respectively at a dose of 25, 50 and 100 mg/kg. These results suggest that lonchocarpin is a potentially useful natural agent for cancer treatment.