bluuebunny/crossref_metadata_2025 huggingface dataset:
Dual extra-retinal origins of microglia in the model of retinal microglia repopulation
Authors: Huang Yubin , Xu Zhen , Xiong Shanshan , Qin Guangrong , Sun Fangfang , Yang Jian , Yuan Ti-Fei , Zhao Lei , Wang Ke , Liang Yu-Xiang , Fu Lin , Wu Tianzhun , So Kwok-Fai , Rao Yanxia , Peng Bo
Published: February 2018

Elucidating the origin of microglia is crucial for understanding their functions and homeostasis. Previous study has indicated that Nestin-positive progenitor cells differentiate into microglia and replenish the brain after depleting most brain microglia. Microglia have also shown the capacity to repopulate the retina after eliminating all retinal microglia. However, the origin(s) of repopulated retinal microglia is/are unknown. In this study, we aim to investigate the origins of repopulated microglia in the retina. Interestingly, we find that repopulated retinal microglia are not derived from Nestin-positive progenitor cells. Instead, they have two origins: the center-emerging microglia are derived from residual microglia in the optic nerve and the periphery-emerging microglia are derived from macrophages in the ciliary body/iris. Therefore, we have for the first time identified the extra-retinal origins of microglia in the adult mammalian retina by using a model of microglial repopulation, which may shed light on the target exploration of therapeutic interventions for retinal degenerative disorders.
VIRMA mediates preferential m6A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation
Authors: Yue Yanan , Liu Jun , Cui Xiaolong , Cao Jie , Luo Guanzheng , Zhang Zezhou , Cheng Tao , Gao Minsong , Shu Xiao , Ma Honghui , Wang Fengqin , Wang Xinxia , Shen Bin , Wang Yizhen , Feng Xinhua , He Chuan , Liu Jianzhao
Published: February 2018

N6-methyladenosine (m6A) is enriched in 3′untranslated region (3′UTR) and near stop codon of mature polyadenylated mRNAs in mammalian systems and has regulatory roles in eukaryotic mRNA transcriptome switch. Significantly, the mechanism for this modification preference remains unknown, however. Herein we report a characterization of the full m6A methyltransferase complex in HeLa cells identifying METTL3/METTL14/WTAP/VIRMA/HAKAI/ZC3H13 as the key components, and we show that VIRMA mediates preferential mRNA methylation in 3′UTR and near stop codon. Biochemical studies reveal that VIRMA recruits the catalytic core components METTL3/METTL14/WTAP to guide region-selective methylations. Around 60% of VIRMA mRNA immunoprecipitation targets manifest strong m6A enrichment in 3′UTR. Depletions of VIRMA and METTL3 induce 3′UTR lengthening of several hundred mRNAs with over 50% targets in common. VIRMA associates with polyadenylation cleavage factors CPSF5 and CPSF6 in an RNA-dependent manner. Depletion of CPSF5 leads to significant shortening of 3′UTR of over 2800 mRNAs, 84% of which are modified with m6A and have increased m6A peak density in 3′UTR and near stop codon after CPSF5 knockdown. Together, our studies provide insights into m6A deposition specificity in 3′UTR and its correlation with alternative polyadenylation.
Molecular probes reveal deviations from Amontons’ law in multi-asperity frictional contacts
Authors: Weber B. , Suhina T. , Junge T. , Pastewka L. , Brouwer A. M. , Bonn D.
Published: February 2018

Amontons’ law defines the friction coefficient as the ratio between friction force and normal force, and assumes that both these forces depend linearly on the real contact area between the two sliding surfaces. However, experimental testing of frictional contact models has proven difficult, because few in situ experiments are able to resolve this real contact area. Here, we present a contact detection method with molecular-level sensitivity. We find that while the friction force is proportional to the real contact area, the real contact area does not increase linearly with normal force. Contact simulations show that this is due to both elastic interactions between asperities on the surface and contact plasticity of the asperities. We reproduce the contact area and fine details of the measured contact geometry by including plastic hardening into the simulations. These new insights will pave the way for a quantitative microscopic understanding of contact mechanics and tribology.
Early circulating tumor DNA dynamics and clonal selection with palbociclib and fulvestrant for breast cancer
Authors: O’Leary Ben , Hrebien Sarah , Morden James P. , Beaney Matthew , Fribbens Charlotte , Huang Xin , Liu Yuan , Bartlett Cynthia Huang , Koehler Maria , Cristofanilli Massimo , Garcia-Murillas Isaac , Bliss Judith M. , Turner Nicholas C.
Published: February 2018

CDK4/6 inhibition substantially improves progression-free survival (PFS) for women with advanced estrogen receptor-positive breast cancer, although there are no predictive biomarkers. Early changes in circulating tumor DNA (ctDNA) level may provide early response prediction, but the impact of tumor heterogeneity is unknown. Here we use plasma samples from patients in the randomized phase III PALOMA-3 study of CDK4/6 inhibitor palbociclib and fulvestrant for women with advanced breast cancer and show that relative change in PIK3CA ctDNA level after 15 days treatment strongly predicts PFS on palbociclib and fulvestrant (hazard ratio 3.94, log-rank p = 0.0013). ESR1 mutations selected by prior hormone therapy are shown to be frequently sub clonal, with ESR1 ctDNA dynamics offering limited prediction of clinical outcome. These results suggest that early ctDNA dynamics may provide a robust biomarker for CDK4/6 inhibitors, with early ctDNA dynamics demonstrating divergent response of tumor sub clones to treatment.
Elongator and codon bias regulate protein levels in mammalian peripheral neurons
Authors: Goffena Joy , Lefcort Frances , Zhang Yongqing , Lehrmann Elin , Chaverra Marta , Felig Jehremy , Walters Joseph , Buksch Richard , Becker Kevin G. , George Lynn
Published: February 2018

Familial dysautonomia (FD) results from mutation in IKBKAP/ELP1, a gene encoding the scaffolding protein for the Elongator complex. This highly conserved complex is required for the translation of codon-biased genes in lower organisms. Here we investigate whether Elongator serves a similar function in mammalian peripheral neurons, the population devastated in FD. Using codon-biased eGFP sensors, and multiplexing of codon usage with transcriptome and proteome analyses of over 6,000 genes, we identify two categories of genes, as well as specific gene identities that depend on Elongator for normal expression. Moreover, we show that multiple genes in the DNA damage repair pathway are codon-biased, and that with Elongator loss, their misregulation is correlated with elevated levels of DNA damage. These findings link Elongator’s function in the translation of codon-biased genes with both the developmental and neurodegenerative phenotypes of FD, and also clarify the increased risk of cancer associated with the disease.
Whole-exome sequencing reveals the origin and evolution of hepato-cholangiocarcinoma
Authors: Wang Anqiang , Wu Liangcai , Lin Jianzhen , Han Longzhe , Bian Jin , Wu Yan , Robson Simon C. , Xue Lai , Ge Yunxia , Sang Xinting , Wang Wenze , Zhao Haitao
Published: February 2018

Hepatocellular-cholangiocarcinoma (H-ChC) is a rare subtype of liver cancer with clinicopathological features of both hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA). To date, molecular mechanisms underlying the co-existence of HCC and iCCA components in a single tumor remain elusive. Here, we show that H-ChC samples contain substantial private mutations from WES analyses, ranging from 33.1 to 86.4%, indicative of substantive intratumor heterogeneity (ITH). However, on the other hand, numerous ubiquitous mutations shared by HCC and iCCA suggest the monoclonal origin of H-ChC. Mutated genes identified herein, e.g., VCAN, ACVR2A, and FCGBP, are speculated to contribute to distinct differentiation of HCC and iCCA within H-ChC. Moreover, immunohistochemistry demonstrates that EpCAM is highly expressed in 80% of H-ChC, implying the stemness of such liver cancer. In summary, our data highlight the monoclonal origin and stemness of H-ChC, as well as substantial intratumoral heterogeneity.
TET-mediated epimutagenesis of the Arabidopsis thaliana methylome
Authors: Ji Lexiang , Jordan William T. , Shi Xiuling , Hu Lulu , He Chuan , Schmitz Robert J.
Published: February 2018

DNA methylation in the promoters of plant genes sometimes leads to transcriptional repression, and the loss of DNA methylation in methyltransferase mutants results in altered gene expression and severe developmental defects. However, many cases of naturally occurring DNA methylation variations have been reported, whereby altered expression of differentially methylated genes is responsible for agronomically important traits. The ability to manipulate plant methylomes to generate epigenetically distinct individuals could be invaluable for breeding and research purposes. Here, we describe “epimutagenesis,” a method to rapidly generate DNA methylation variation through random demethylation of the Arabidopsis thaliana genome. This method involves the expression of a human ten–eleven translocation (TET) enzyme, and results in widespread hypomethylation that can be inherited to subsequent generations, mimicking mutants in the maintenance of DNA methyltransferase met1. Application of epimutagenesis to agriculturally significant plants may result in differential expression of alleles normally silenced by DNA methylation, uncovering previously hidden phenotypic variations.
High field charge order across the phase diagram of YBa2Cu3Oy
Authors: Laliberté Francis , Frachet Mehdi , Benhabib Siham , Borgnic Benjamin , Loew Toshinao , Porras Juan , Le Tacon Mathieu , Keimer Bernhard , Wiedmann Steffen , Proust Cyril , LeBoeuf David
Published: February 2018

In hole-doped cuprates there is now compelling evidence that inside the pseudogap phase, charge order breaks translational symmetry. In YBa2Cu3O
y
charge order emerges in two steps: a 2D order found at zero field and at high temperature inside the pseudogap phase, and a 3D order that is superimposed below the superconducting transition Tc when superconductivity is weakened by a magnetic field. Several issues still need to be addressed such as the effect of disorder, the relationship between those charge orders and their respective impact on the Fermi surface. Here, we report high magnetic field sound velocity measurements of the 3D charge order in underdoped YBa2Cu3O
y
in a large doping range. We found that the 3D charge order exists over the same doping range as its 2D counterpart, indicating an intimate connection between the two distinct orders. Moreover, our data suggest that 3D charge order has only a limited impact on low-lying electronic states of YBa2Cu3O
y
.
Exogenous hydrogen sulfide gas does not induce hypothermia in normoxic mice
Authors: Hemelrijk Sebastiaan D. , Dirkes Marcel C. , van Velzen Marit H. N. , Bezemer Rick , van Gulik Thomas M. , Heger Michal
Published: February 2018

Hydrogen sulfide (H2S, 80 ppm) gas in an atmosphere of 17.5% oxygen reportedly induces suspended animation in mice; a state analogous to hibernation that entails hypothermia and hypometabolism. However, exogenous H2S in combination with 17.5% oxygen is able to induce hypoxia, which in itself is a trigger of hypometabolism/hypothermia. Using non-invasive thermographic imaging, we demonstrated that mice exposed to hypoxia (5% oxygen) reduce their body temperature to ambient temperature. In contrast, animals exposed to 80 ppm H2S under normoxic conditions did not exhibit a reduction in body temperature compared to normoxic controls. In conclusion, mice induce hypothermia in response to hypoxia but not H2S gas, which contradicts the reported findings and putative contentions.
Fatty Acid Supplementation Reverses the Small Colony Variant Phenotype in Triclosan-Adapted Staphylococcus aureus: Genetic, Proteomic and Phenotypic Analyses
Authors: Bazaid Abdulrahman S. , Forbes Sarah , Humphreys Gavin J. , Ledder Ruth G. , O’Cualain Ronan , McBain Andrew J.
Published: February 2018

Staphylococcus aureus can develop a small colony variant (SCV) phenotype in response to sub-lethal exposure to the biocide triclosan. In the current study, whole genome sequencing was performed and changes in virulence were investigated in five Staphylococcus aureus strains following repeated exposure to triclosan. Following exposure, 4/5 formed SCV and exhibited point mutations in the triclosan target gene fabI with 2/4 SCVs showing mutations in both fabI and fabD. The SCV phenotype was in all cases immediately reversed by nutritional supplementation with fatty acids or by repeated growth in the absence of triclosan, although fabI mutations persisted in 3/4 reverted SCVs. Virulence, determined using keratinocyte invasion and Galleria mellonella pathogenicity assays was significantly (p < 0.05) attenuated in 3/4 SCVs and in the non-SCV triclosan-adapted bacterium. Proteomic analysis revealed elevated FabI in 2/3 SCV and down-regulation in a protein associated with virulence in 1/3 SCV. In summary, attenuated keratinocyte invasion and larval virulence in triclosan-induced SCVs was associated with decreases in growth rate and virulence factor expression. Mutation occurred in fabI, which encodes the main triclosan target in all SCVs and the phenotype was reversed by fatty acid supplementation, demonstrating an association between fatty acid metabolism and triclosan-induced SCV.
Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1
Authors: Milić Dalibor , Dick Markus , Mulnaes Daniel , Pfleger Christopher , Kinnen Anna , Gohlke Holger , Groth Georg
Published: February 2018

Synthetic peptides derived from ethylene-insensitive protein 2 (EIN2), a central regulator of ethylene signalling, were recently shown to delay fruit ripening by interrupting protein–protein interactions in the ethylene signalling pathway. Here, we show that the inhibitory peptide NOP-1 binds to the GAF domain of ETR1 – the prototype of the plant ethylene receptor family. Site-directed mutagenesis and computational studies reveal the peptide interaction site and a plausible molecular mechanism for the ripening inhibition.
Metabolic characterization of directly reprogrammed renal tubular epithelial cells (iRECs)
Authors: Lagies Simon , Pichler Roman , Kaminski Michael M. , Schlimpert Manuel , Walz Gerd , Lienkamp Soeren S. , Kammerer Bernd
Published: February 2018

Fibroblasts can be directly reprogrammed to induced renal tubular epithelial cells (iRECs) using four transcription factors. These engineered cells may be used for disease modeling, cell replacement therapy or drug and toxicity testing. Direct reprogramming induces drastic changes in the transcriptional landscape, protein expression, morphological and functional properties of cells. However, how the metabolome is changed by reprogramming and to what degree it resembles the target cell type remains unknown. Using untargeted gas chromatography-mass spectrometry (GC-MS) and targeted liquid chromatography-MS, we characterized the metabolome of mouse embryonic fibroblasts (MEFs), iRECs, mIMCD-3 cells, and whole kidneys. Metabolic fingerprinting can distinguish each cell type reliably, revealing iRECs are most similar to mIMCD-3 cells and clearly separate from MEFs used for reprogramming. Treatment with the cytotoxic drug cisplatin induced typical changes in the metabolic profile of iRECs commonly occurring in acute renal injury. Interestingly, metabolites in the medium of iRECs, but not of mIMCD-3 cells or fibroblast could distinguish treated and non-treated cells by cluster analysis. In conclusion, direct reprogramming of fibroblasts into renal tubular epithelial cells strongly influences the metabolome of engineered cells, suggesting that metabolic profiling may aid in establishing iRECs as in vitro models for nephrotoxicity testing in the future.
The energy sensor OsSnRK1a confers broad-spectrum disease resistance in rice
Authors: Filipe Osvaldo , De Vleesschauwer David , Haeck Ashley , Demeestere Kristof , Höfte Monica
Published: February 2018

Sucrose non-fermenting-1-related protein kinase-1 (SnRK1) belongs to a family of evolutionary conserved kinases with orthologs in all eukaryotes, ranging from yeasts (SnF1) to mammals (AMP-Activated kinase). These kinases sense energy deficits caused by nutrient limitation or stress and coordinate the required adaptations to maintain energy homeostasis and survival. In plants, SnRK1 is a global regulator of plant metabolism and is also involved in abiotic stress responses. Its role in the response to biotic stress, however, is only starting to be uncovered. Here we studied the effect of altered SnRK1a expression on growth and plant defense in rice. OsSnRK1a overexpression interfered with normal growth and development and increased resistance against both (hemi)biotrophic and necrotrophic pathogens, while OsSnRK1a silencing in RNAi lines increased susceptibility. OsSnRK1a overexpression positively affected the salicylic acid pathway and boosted the jasmonate-mediated defense response after inoculation with the blast fungus Pyricularia oryzae. Together these findings strongly suggest OsSnRK1a to be involved in plant basal immunity and favor a model whereby OsSnRK1a acts as a master switch that regulates growth-immunity trade-offs.
Fat accretion measurements strengthen the relationship between feed conversion efficiency and Nitrogen isotopic discrimination while rumen microbial genes contribute little
Authors: Meale Sarah J. , Auffret Marc D. , Watson Mick , Morgavi Diego P. , Cantalapiedra-Hijar Gonzalo , Duthie Carol-Anne , Roehe Rainer , Dewhurst Richard J.
Published: February 2018

The use of biomarkers for feed conversion efficiency (FCE), such as Nitrogen isotopic discrimination (Δ15N), facilitates easier measurement and may be useful in breeding strategies. However, we need to better understand the relationship between FCE and Δ15N, particularly the effects of differences in the composition of liveweight gain and rumen N metabolism. Alongside measurements of FCE and Δ15N, we estimated changes in body composition and used dietary treatments with and without nitrates, and rumen metagenomics to explore these effects. Nitrate fed steers had reduced FCE and higher Δ15N in plasma compared to steers offered non-nitrate containing diets. The negative relationship between FCE and Δ15N was strengthened with the inclusion of fat depth change at the 3rdlumbar vertebrae, but not with average daily gain. We identified 1,700 microbial genes with a relative abundance >0.01% of which, 26 were associated with Δ15N. These genes explained 69% of variation in Δ15N and showed clustering in two distinct functional networks. However, there was no clear relationship between their relative abundances and Δ15N, suggesting that rumen microbial genes contribute little to Δ15N. Conversely, we show that changes in the composition of gain (fat accretion) provide additional strength to the relationship between FCE and Δ15N.
Vacancy assisted He-interstitial clustering and their elemental interaction at fcc-bcc semicoherent metallic interface
Authors: Saikia Ujjal , Sahariah Munima B. , González César , Pandey Ravindra
Published: February 2018

Cu-Nb layered nanocomposite system can be considered as a prototype system to investigate stability of the fcc-bcc semicoherent metallic interfaces. Theoretical simulations based on density functional theory have been performed in order to investigate the stability of different defects in such interfaces. The calculations find the interfacial misfit dislocation intersections as the preferred site for defects including a vacancy, He-interstitial, and a vacancy-He complex in good agreement with previous works. Our results suggest that the presence of a metallic vacancy may act as a sink for defect and favour the migration of He interstitials leading to their aggregation at the interface. The potential capability of the vacancy to accommodate He atoms was also predicted with a higher affinity towards Nb. This aggregation of He atoms is driven by local density of electron and strain in a region in the neighbourhood of Nb. Finally, we propose a plausible picture of defect energetics in the vicinity of the interface based on the Voronoi volume and Bader’s charge analysis. This analysis may replace the conventional methods used for surface energetics mapping which are extremely tedious for such large systems.
PDE4D regulates Spine Plasticity and Memory in the Retrosplenial Cortex
Authors: Baumgärtel Karsten , Green Andrea , Hornberger Diana , Lapira Jennifer , Rex Christopher , Wheeler Damian G. , Peters Marco
Published: February 2018

The retrosplenial cortex (RSC) plays a critical role in episodic memory, but the molecular mechanisms governing plasticity in this structure are poorly understood. Diverse studies have demonstrated a role for RSC in acquisition, early consolidation and retrieval similar to the hippocampus (HC), as well as in systems consolidation similar to the anterior cingulate cortex. Here, we asked whether established molecular and structural substrates of memory consolidation in the HC also engage in RSC shortly after learning. We show striking parallels in training induced gene-activation in HC and RSC following contextual conditioning, which is blocked by systemic administration of an NMDA receptor antagonist. Long-term memory is enhanced by retrosplenial and hippocampal knockdown (KD) of the cAMP specific phosphodiesterase Pde4d. However, while training per se induces lasting spine changes in HC, this does not occur in RSC. Instead, increases in the number of mature dendritic spines are found in the RSC only if cAMP signaling is augmented by Pde4d KD, and spine changes are at least partially independent of training. This research highlights parallels and differences in spine plasticity mechanisms between HC and RSC, and provides evidence for a functional dissociation of the two.
One-step fabrication of robust superhydrophobic and superoleophilic surfaces with self-cleaning and oil/water separation function
Authors: Zhang Zhi-hui , Wang Hu-jun , Liang Yun-hong , Li Xiu-juan , Ren Lu-quan , Cui Zhen-quan , Luo Cheng
Published: February 2018

Superhydrophobic surfaces have great potential for application in self-cleaning and oil/water separation. However, the large-scale practical applications of superhydrophobic coating surfaces are impeded by many factors, such as complicated fabrication processes, the use of fluorinated reagents and noxious organic solvents and poor mechanical stability. Herein, we describe the successful preparation of a fluorine-free multifunctional coating without noxious organic solvents that was brushed, dipped or sprayed onto glass slides and stainless-steel meshes as substrates. The obtained multifunctional superhydrophobic and superoleophilic surfaces (MSHOs) demonstrated self-cleaning abilities even when contaminated with or immersed in oil. The superhydrophobic surfaces were robust and maintained their water repellency after being scratched with a knife or abraded with sandpaper for 50 cycles. In addition, stainless-steel meshes sprayed with the coating quickly separated various oil/water mixtures with a high separation efficiency (>93%). Furthermore, the coated mesh maintained a high separation efficiency above 95% over 20 cycles of separation. This simple and effective strategy will inspire the large-scale fabrication of multifunctional surfaces for practical applications in self-cleaning and oil/water separation.
Association between homocysteine and conventional predisposing factors on risk of stroke in patients with hypertension
Authors: Pang Hui , Han Bing , Fu Qiang , Hao Lin , Zong Zhenkun
Published: February 2018

Previous studies have focused mostly on independent effects of the stroke risk factors, whereas little attention has been paid to interactions between individual factors which may be important for stroke prevention. We collected data related to the patients’ demographic characteristics, history of chronic diseases and lifestyle factors in 2258 patients with primary hypertension. Logistic regression models based on odds ratio (OR) with their associated 95% confidence interval (CI) were used to estimate an independent effect of homocysteine (Hcy) on the risk of stroke but also include the interactions between Hcy and other risk factors. Hcy was associated with an increased OR of the risk of stroke in both hypertension patients (OR, 1.027; 95% CI, 1.016–1.038; P < 0.001) and H-type hypertension patients (OR, 1.026; 95% CI, 1.014–1.037; P < 0.001), after adjustment for potential confounding factors. Among the hypertension participants, three tests of interactions between Hcy and other risk factors were statistically significant: sex, systolic blood pressure and diastolic blood pressure. In conclusion, complexities of the interactions of Hcy stratified by sex and blood pressure need to be considered in predicting overall risk and selecting certain treatments for stroke prevention.
Towards spontaneous parametric down conversion from monolayer MoS2
Authors: Dinparasti Saleh Hatef , Vezzoli Stefano , Caspani Lucia , Branny Artur , Kumar Santosh , Gerardot Brian D. , Faccio Daniele
Published: February 2018

We present a detailed study of the second order nonlinearity of 2D (mono-atomic layer) dichalcogenide MoS2, both in the visible and in the IR regime, and test its potential for spontaneous parametric down-conversion (SPDC), the amplification of vacuum fluctuations mediated by optical nonlinearity. We develop a model of SPDC from a deeply subwavelength nonlinear medium, where phase matching conditions are completely relaxed, and make predictions about the rate of emitted photons, their momentum, polarisation and spectrum. We show that detection in the visible spectral region is hindered by the strong photoluminescence background. Moving to the IR regime we observe indications of SPDC by performing polarization, power dependence and lifetime measurements around 1560 nm. We show that the signal from a single monolayer is qualitatively different from that generated by multi-layer MoS2. Finally, we characterize the latter as a new kind of photo-luminescence emission which is enhanced at the edges of multi-layer MoS2.
Analysis of (CAG)n expansion in ATXN1, ATXN2 and ATXN3 in Chinese patients with multiple system atrophy
Authors: Zhou X. , Wang C. , Ding D. , Chen Z. , Peng Y. , Peng H. , Hou X. , Wang P. , Hou X. , Ye W. , Li T. , Yang H. , Qiu R. , Xia K. , Sequeiros J. , Tang B. , Jiang H.
Published: February 2018

Multiple system atrophy (MSA) is a complex and multifactorial neurodegenerative disease, and its pathogenesis remains uncertain. Patients with MSA or spinocerebellar ataxia (SCA) show overlapping clinical phenotypes. Previous studies have reported that intermediate or long CAG expansions in SCA genes have been associated with other neurodegenerative disease. In this study, we screened for the number of CAG repeats in ATXN1, 2 and 3 in 200 patients with MSA and 314 healthy controls to evaluate possible associations between (CAG)n in these three polyQ-related genes and MSA. Our findings indicated that longer repeat lengths in ATXN2 were associated with increased risk for MSA in Chinese individuals. No relationship was observed between CAG repeat length in the three examined genes and age at onset (AO) of MSA.
Anisogamy evolved with a reduced sex-determining region in volvocine green algae
Authors: Hamaji Takashi , Kawai-Toyooka Hiroko , Uchimura Haruka , Suzuki Masahiro , Noguchi Hideki , Minakuchi Yohei , Toyoda Atsushi , Fujiyama Asao , Miyagishima Shin-ya , Umen James G. , Nozaki Hisayoshi
Published: February 2018

Male and female gametes differing in size—anisogamy—emerged independently from isogamous ancestors in various eukaryotic lineages, although genetic bases of this emergence are still unknown. Volvocine green algae are a model lineage for investigating the transition from isogamy to anisogamy. Here we focus on two closely related volvocine genera that bracket this transition—isogamous Yamagishiella and anisogamous Eudorina. We generated de novo nuclear genome assemblies of both sexes of Yamagishiella and Eudorina to identify the dimorphic sex-determining chromosomal region or mating-type locus (MT) from each. In contrast to the large (>1 Mb) and complex MT of oogamous Volvox, Yamagishiella and Eudorina MT are smaller (7–268 kb) and simpler with only two sex-limited genes—the minus/male-limited MID and the plus/female-limited FUS1. No prominently dimorphic gametologs were identified in either species. Thus, the first step to anisogamy in volvocine algae presumably occurred without an increase in MT size and complexity.
Formal synthesis of chelamidine alkaloids and their derivatives
Authors: Li Rui-Qi , He Yu , Ding Yao , Ang Chee-Kiat , Tian Jie-Sheng , Loh Teck-Peng
Published: February 2018

A concise two-step operation of α-amination of aldehydes and subsequent Friedel–Crafts/Prins-type cyclization towards accessing tetrahydrobenzo[c]phenanthridine and related structures was developed. In addition, the effectiveness of this protocol was also demonstrated in the formal synthesis of homochelidonine and chelamidine.
Improved NOE fitting for flexible molecules based on molecular mechanics data – a case study with S-adenosylmethionine
Authors: Bame Jessica , Hoeck Casper , Carrington Matthew J. , Butts Craig P. , Jäger Christof M. , Croft Anna K.
Published: February 2018

Using the important biomolecule S-adenosyl methionine as an exemplar, we provide a new, enhanced approach for fitting MD data to high-accuracy NOE data, providing improvements in structure determination.
Energy vs. density on paths toward more exact density functionals
Authors: Kepp Kasper P.
Published: February 2018

The density-energy balance of density functionals is quantified using trial densities. Density errors commonly amount to only a few kJ mol−1.
Site specificity of halogen bonding involving aromatic acceptors
Authors: Ang Shi Jun , Mak Adrian M. , Sullivan Michael B. , Wong Ming Wah
Published: February 2018

Based on Cambridge structural database survey and quantum chemical studies, aromatic halogen bond (XB) acceptors are found to have unique pattern of XB binding sites and rim specificity.
Renaissance of graphene-related materials in photovoltaics due to the emergence of metal halide perovskite solar cells
Authors: Petridis Costantinos , Kakavelakis George , Kymakis Emmanuel
Published: February 2018

This literature review presents the research progress and future perspectives of graphene-based based mesoscopic and planar perovskite solar cells.
Gold as a modifier of metal nanoparticles: effect on structure and catalysis
Authors: Prati L. , Villa A. , Jouve A. , Beck A. , Evangelisti C. , Savara A.
Published: February 2018

Bimetallic gold based catalysts have been prepared using a sol immobilisation technique. Depending on the second metal different structure have been obtained.
Palladium functionalized phosphinite polyethyleneimine grafted magnetic silica nanoparticles as an efficient catalyst for the synthesis of isoquinolino[1,2-b]quinazolin-8-ones
Authors: Bahadorikhalili Saeed , Mahdavi Mohammad , Ma’mani Leila , Shafiee Abbas , Mahdavi Hossein , Akbarzadeh Tahmineh
Published: February 2018

Novel 5-methyl-8H-isoquinolino[1,2-b]quinazolin-8-one derivatives are synthesized using a reusable immobilized palladium catalyzed intramolecular carbon–carbon bond formation.
Facile synthesis of microporous sulfur-doped carbon spheres as electrodes for ultrasensitive detection of ascorbic acid in food and pharmaceutical products
Authors: Emran Mohammed Y. , Shenashen Mohamed A. , Abdelwahab Adel A. , Abdelmottaleb Mohamed , El-Safty Sherif A.
Published: February 2018

The active interfacial surface of S-doped microporous carbon spheres strongly binds with ascorbic acid in food and pharmaceutical products.
Synthesis of a novel CO2-based alcohol amine compound and its usage in obtaining a water- and solvent-resistant coating
Authors: Li Xiaoyun , Ke Jiexi , Wang Junwei , Kang Maoqing , Wang Feng , Zhao Yuhua , Li Qifeng
Published: February 2018

The novelty of the work: a water- and solvent-resistant coating was produced from a novel CO2-based alcohol amine chain extender.
Synthesis of water-soluble and bio-taggable CdSe@ZnS quantum dots
Authors: Ramalingam G. , Saravanan K. Venkata , Vizhi T. Kayal , Rajkumar M. , Baskar Kathirvelu
Published: February 2018

Mystristic capped CdSe QDs with schematic diagram and formation mechanism of bio-taggable CdSe@ZnS QDs.
A highly efficient and stable organic additive for the positive electrolyte in vanadium redox flow batteries: taurine biomolecules containing –NH2and –SO3H functional groups
Authors: Hwang Jinyeon , Kim Bo-mi , Moon Joonhee , Mehmood Asad , Ha Heung Yong
Published: February 2018

A taurine biomolecule performs as an efficient organic additive for the positive electrolyte of a vanadium redox flow battery (VRFB).
Cells may feel a hard substrate even on a grafted layer of soft hydrogel
Authors: Wang Shuhao , Zan Fei , Ke Yu , Wu Gang
Published: February 2018

Different cells have diverse sensibility to sense the substrate on grafted soft hydrogel layers with variable depth.
Light-emitting diodes of colloidal quantum dots and nanorod heterostructures for future emissive displays
Authors: Jiang Yiran , Cho Seong-Yong , Shim Moonsub
Published: February 2018

Tunable, narrow-linewidth photoluminescence and solution processability make colloidal quantum dots, especially their anisotropic heterostructures, unique emitter materials for a variety of photonic and optoelectronic applications.
Infrared ion spectroscopy: an analytical tool for the study of metabolites
Authors: Cismesia Adam P. , Bell Matthew R. , Tesler Larry F. , Alves Melanie , Polfer Nicolas C.
Published: February 2018

Vibrational ion spectroscopy techniques coupled with mass spectrometry are applied to standard metabolites as a proof-of-principle demonstration for the structural identification of unknown metabolites.
Spinach-based fluorescent light-up biosensors for multiplexed and label-free detection of microRNAs
Authors: Ying Zhan-Ming , Tu Bin , Liu Lan , Tang Hao , Tang Li-Juan , Jiang Jian-Hui
Published: February 2018

A novel Spinach-based fluorescent light-up biosensor utilizing the T7 in vitro transcription process to generate unmodified Spinach sequences for multiplexed microRNA detection has been developed.
An ultrafast one-step assay for the visual detection of RNA virus
Authors: Ma Cuiping , Jing Hao , Zhang Pansong , Han Lingzhi , Zhang Meiling , Wang Fuxin , Niu Shuyan , Shi Chao
Published: February 2018

A one-step, rapid, and visual method was developed for the detection of RNA viruses and a few copies of the Zika RNA virus were directly detected within 25 min by naked-eye observation.
Modulating the rigidity of nanoparticles for tumor penetration
Authors: Deng Hongzhang , Song Kun , Zhang Jianhua , Deng Liandong , Dong Anjie , Qin Zhihai
Published: February 2018

Nanoparticles with cores that varied in mechanical rigidity were prepared to test the relationship between their rigidity and their ability to penetrate tumors.
Role of the (H2O)n (n = 1–3) cluster in the HO2 + HO → 3O2 + H2O reaction: mechanistic and kinetic studies
Authors: Zhang Tianlei , Lan Xinguang , Qiao Zhangyu , Wang Rui , Yu Xiaohu , Xu Qiong , Wang Zhiyin , Jin Linxia , Wang ZhuQing
Published: February 2018

Upon incorporation of the catalyst (H2O)n (n = 1–3) into the reaction HO2 + HO → H2O + 3O2, the catalytic effects of water, water dimer, and water trimer mainly arise from the contribution of a single molecule of water vapor.
The role of unique spatial structure in the volume phase transition behavior of poly(N-isopropylacrylamide)-based interpenetrating polymer network microgels including a thermosensitive poly(ionic liquid)
Authors: Ma Lan , Wu Peiyi
Published: February 2018

By comparing with the linear homopolymer mixture, the influence of spatial structure on the phase behavior of thermosensitive interpenetrating polymer network (IPN) microgels was clarified.
Rhenium(i) based irregular pentagonal-shaped metallacavitands
Authors: Bhol Mamina , Shankar Bhaskaran , Sathiyendiran Malaichamy
Published: February 2018

A new synthetic principle, i.e. the treatment of Re2(CO)10, a rigid bis-chelating donor, and a flexible ditopic nitrogen donor possessing four arene/heteroarene units connected by three methylene bridges, was developed for making irregular pentagonal-shaped metallacavitand.
Investigation of modified nanopore arrays using FIB/SEM tomography
Authors: Holzinger Angelika , Neusser Gregor , Austen Benjamin J. J. , Gamero-Quijano Alonso , Herzog Grégoire , Arrigan Damien W. M. , Ziegler Andreas , Walther Paul , Kranz Christine
Published: February 2018

FIB/SEM tomography and energy dispersive X-ray (EDX) spectroscopy are employed to study the interface between two immiscible electrolyte solutions at nanopore arrays, which were electrochemically modified by silica.
Extended lead(ii) architectures engineered via tetrel bonding interactions
Authors: Mahmoudi Ghodrat , Zangrando Ennio , Mitoraj Mariusz P. , Gurbanov Atash V. , Zubkov Fedor I. , Moosavifar Maryam , Konyaeva Irina A. , Kirillov Alexander M. , Safin Damir A.
Published: February 2018

The cooperative action of multiple non-covalent interactions allowed for the assembly of a new series of PbII coordination compounds.
Correction: Mechanical and thermal properties of grain boundary in a planar heterostructure of graphene and hexagonal boron nitride
Authors: Li Yinfeng , Wei Anran , Ye Han , Yao Haimin
Published: February 2018

Correction for ‘Mechanical and thermal properties of grain boundary in a planar heterostructure of graphene and hexagonal boron nitride’ by Yinfeng Li, et al., Nanoscale, 2018, DOI: 10.1039/c7nr07306b.
Effect of particle size distribution on the electrochemical performance of micro-sized silicon-based negative materials
Authors: Wu Shuaijin , Yu Bing , Wu Zhaohui , Fang Sheng , Shi Bimeng , Yang Juanyu
Published: February 2018

Si has been extensively examined as a potential alternative to carbonaceous negative materials, because it shows exceptional gravimetric capacity and abundance.
Design, synthesis, and time-gated cell imaging of carbon-bridged triangulenium dyes with long fluorescence lifetime and red emission
Authors: Rosenberg M. , Rostgaard K. R. , Liao Z. , Madsen A. Ø. , Martinez K. L. , Vosch T. , Laursen B. W.
Published: February 2018

Introduction of an isopropyl bridge in the triangulenium skeleton leads to a new series of redshifted triangulenium dyes with high fluorescence quantum yields and remarkable long fluorescence lifetime allowing for time-gated cell imaging.
A zeolitic imidazolate framework-derived ZnSe/N-doped carbon cube hybrid electrocatalyst as the counter electrode for dye-sensitized solar cells
Authors: Jian Siou-Ling , Huang Yi-June , Yeh Min-Hsin , Ho Kuo-Chuan
Published: February 2018

A ZIF-ZnSe-NC composite derived from ZIF-7 was synthesized and used as the electrocatalyst for the counter electrode (CE) in dye-sensitized solar cells, which performed better than that using a Pt CE.
Prognostic values of aquaporins mRNA expression in human ovarian cancer
Authors: Chetry Mandika , Li Saisai , Liu Hailing , Hu Xiaoli , Zhu Xueqiong
Published: February 2018

Aquaporins (AQPs), a family of transmembrane channel, are composed of 13 identified members (AQP0–12). Accumulating evidences reported that AQPs were correlated with various biological roles and represented a prognostic predictor in various cancer types. However, the prognostic value of AQPs expression in ovarian cancer remains unclear. Using ‘Kaplan–Meier plotter’ (KM plotter) online database, we explored the predictive prognostic value of individual AQPs members’ mRNA expression to overall survival (OS) in different clinical data, such as histology, pathological grades, clinical stages, TP53 status, and applied chemotherapy in ovarian cancer patients. Our results revealed that higher AQP0, AQP1, and AQP4 mRNA expression were correlated with poor OS, whereas higher AQP3, AQP5, AQP6, AQP8, AQP10, and AQP11 showed better OS in ovarian cancer patients. Moreover, AQP4 and AQP8 showed poor OS in TP53-mutated ovarian cancer patients and AQP1 presented unfavorable OS in both TP53 mutated and wild ovarian cancer patients. Additionally, AQP3, AQP6, and AQP11 mRNA expression were correlated with better OS, whereas AQP0 and AQP1 showed poor OS in all ovarian cancer patients treated with Platin, Taxol, and Taxol + Platin chemotherapy. AQP5, AQP8, and AQP10 were associated with improved OS, however, AQP4 predicted unfavorable OS in all patients treated with Platin chemotherapy. Our results suggest that individual AQPs, except AQP2 and AQP9, are associated with unique prognostic significance and may thus act as new predictive prognostic indicators and potential drug therapeutic target in ovarian cancer.
Cysteine modifiers suggest an allosteric inhibitory site on the CAL PDZ domain
Authors: Zhao Yu , Cushing Patrick R. , Smithson David C. , Pellegrini Maria , Pletnev Alexandre A. , Al-Ayyoubi Sahar , Grassetti Andrew V. , Gerber Scott A. , Guy R. Kiplin , Madden Dean R.
Published: February 2018

Protein–protein interactions have become attractive targets for both experimental and therapeutic interventions. The PSD-95/Dlg1/ZO-1 (PDZ) domain is found in a large family of eukaryotic scaffold proteins that plays important roles in intracellular trafficking and localization of many target proteins. Here, we seek inhibitors of the PDZ protein that facilitates post-endocytic degradation of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR): the CFTR-associated ligand (CAL). We develop and validate biochemical screens and identify methyl-3,4-dephostatin (MD) and its analog ethyl-3,4-dephostatin (ED) as CAL PDZ inhibitors. Depending on conditions, MD can bind either covalently or non-covalently. Crystallographic and NMR data confirm that MD attacks a pocket at a site distinct from the canonical peptide-binding groove, and suggests an allosteric connection between target residue Cys319 and the conserved Leu291 in the GLGI motif. MD and ED thus appear to represent the first examples of small-molecule allosteric regulation of PDZ:peptide affinity. Their mechanism of action may exploit the known conformational plasticity of the PDZ domains and suggests that allosteric modulation may represent a strategy for targeting of this family of protein–protein binding modules.
Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia
Authors: Carlson Ross P. , Beck Ashley E. , Phalak Poonam , Fields Matthew W. , Gedeon Tomas , Hanley Luke , Harcombe William R. , Henson Michael A. , Heys Jeffrey J.
Published: February 2018

Resource scarcity is a common stress in nature and has a major impact on microbial physiology. This review highlights microbial acclimations to resource scarcity, focusing on resource investment strategies for chemoheterotrophs from the molecular level to the pathway level. Competitive resource allocation strategies often lead to a phenotype known as overflow metabolism; the resulting overflow byproducts can stabilize cooperative interactions in microbial communities and can lead to cross-feeding consortia. These consortia can exhibit emergent properties such as enhanced resource usage and biomass productivity. The literature distilled here draws parallels between in silico and laboratory studies and ties them together with ecological theories to better understand microbial stress responses and mutualistic consortia functioning.
Cross-talk between blood vessels and neural progenitors in the developing brain
Authors: Tata Mathew , Ruhrberg Christiana
Published: February 2018

The formation of the central nervous system (CNS) involves multiple cellular and molecular interactions between neural progenitor cells (NPCs) and blood vessels to establish extensive and complex neural networks and attract a vascular supply that support their function. In this review, we discuss studies that have performed genetic manipulations of chick, fish and mouse embryos to define the spatiotemporal roles of molecules that mediate the reciprocal regulation of NPCs and blood vessels. These experiments have highlighted core functions of NPC-expressed ligands in initiating vascular growth into and within the neural tube as well as establishing the blood–brain barrier. More recent findings have also revealed indispensable roles of blood vessels in regulating NPC expansion and eventual differentiation, and specific regional differences in the effect of angiocrine signals. Accordingly, NPCs initially stimulate blood vessel growth and maturation to nourish the brain, but blood vessels subsequently also regulate NPC behaviour to promote the formation of a sufficient number and diversity of neural cells. A greater understanding of the molecular cross-talk between NPCs and blood vessels will improve our knowledge of how the vertebrate nervous system forms and likely help in the design of novel therapies aimed at regenerating neurons and neural vasculature following CNS disease or injury.
Two reversible data hiding schemes for VQ‐compressed images based on index coding
Authors: Rahmani Peyman , Dastghaibyfard Gholamhossein
Published: February 2018

This study proposes two reversible data hiding (RDH) schemes for vector quantisation (VQ)‐compressed images based on switching‐tree coding (STC) and dynamic tree‐coding scheme (DTCS). Most developed VQ‐based RDH schemes produce non‐legitimate codes as output. In order to preserve the legitimacy of the embedded VQ code, some schemes embed data into VQ indices by employing an index replacement mechanism and some other schemes perform embedding by adopting one of the possible ways during encoding each index when multiple ways are possible to encode the index. In the current research, two schemes are proposed based on the second mechanism. Outputted code of the proposed schemes is a legitimate STC/DTCS code and the conventional STC/DTCS decoder can decode it to the original VQ index table. The experimental results show that the proposed schemes are feasible and in comparison with some previous RDH schemes, the first one provides higher embedding capacity and the second one embeds a substantial amount of data while provides lower bit rate than most the previous schemes. In addition, the embedding‐efficiency of both proposed schemes is higher than that of the previous schemes.
C/O vs. Mg/Si ratios in solar type stars: The HARPS sample
Authors: Suárez-Andrés L. , Israelian G. , González Hernández J. I. , Adibekyan V. Zh. , Delgado Mena E. , Santos N. C. , Sousa S. G.
Published: February 2018

Context. Aims. We aim to present a detailed study of the magnesium-to-silicon and carbon-to-oxygen ratios (Mg/Si and C/O) and their importance in determining the mineralogy of planetary companions.

Methods. Using 499 solar-like stars from the HARPS sample, we determined C/O and Mg/Si elemental abundance ratios to study the nature of the possible planets formed. We separated the planetary population in low-mass planets (<30 M⊙) and high-mass planets (>30 M⊙) to test for a possible relation with the mass.

Results. We find a diversity of mineralogical ratios that reveal the different kinds of planetary systems that can be formed, most of them dissimilar to our solar system. The different values of the Mg/Si and C/O can determine different composition of planets formed. We found that 100% of our planetary sample present C/O < 0.8. 86% of stars with high-mass companions present 0.8 > C/O > 0.4, while 14% present C/O values lower than 0.4. Regarding Mg/Si, all stars with low-mass planetary companion showed values between one and two, while 85% of the high-mass companion sample does. The other 15% showed Mg/Si values below one. No stars with planets were found with Mg/Si > 2. Planet hosts with low-mass companions present C/O and Mg/Si similar to those found in the Sun, whereas stars with high-mass companions have lower C/O.