bluuebunny/crossref_metadata_2025 huggingface dataset:
A geographically-diverse collection of 418 human gut microbiome pathway genome databases
Authors: Hahn Aria S. , Altman Tomer , Konwar Kishori M. , Hanson Niels W. , Kim Dongjae , Relman David A. , Dill David L. , Hallam Steven J.
Published: April 2017

Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GutCyc, a compendium of environmental pathway genome databases (ePGDBs) constructed from 418 assembled human microbiome datasets using MetaPathways, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the Pathway Tools software, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GutCyc provides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn’s disease, and type 2 diabetes. GutCyc data products are searchable online, or may be downloaded and explored locally using MetaPathways and Pathway Tools.
A resource for assessing information processing in the developing brain using EEG and eye tracking
Authors: Langer Nicolas , Ho Erica J. , Alexander Lindsay M. , Xu Helen Y. , Jozanovic Renee K. , Henin Simon , Petroni Agustin , Cohen Samantha , Marcelle Enitan T. , Parra Lucas C. , Milham Michael P. , Kelly Simon P.
Published: April 2017

We present a dataset combining electrophysiology and eye tracking intended as a resource for the investigation of information processing in the developing brain. The dataset includes high-density task-based and task-free EEG, eye tracking, and cognitive and behavioral data collected from 126 individuals (ages: 6–44). The task battery spans both the simple/complex and passive/active dimensions to cover a range of approaches prevalent in modern cognitive neuroscience. The active task paradigms facilitate principled deconstruction of core components of task performance in the developing brain, whereas the passive paradigms permit the examination of intrinsic functional network activity during varying amounts of external stimulation. Alongside these neurophysiological data, we include an abbreviated cognitive test battery and questionnaire-based measures of psychiatric functioning. We hope that this dataset will lead to the development of novel assays of neural processes fundamental to information processing, which can be used to index healthy brain development as well as detect pathologic processes.
A high-throughput molecular data resource for cutaneous neurofibromas
Authors: Gosline Sara J.C. , Weinberg Hubert , Knight Pamela , Yu Thomas , Guo Xindi , Prasad Nripesh , Jones Angela , Shrestha Shristi , Boone Braden , Levy Shawn E. , La Rosa Salvatore , Guinney Justin , Bakker Annette
Published: April 2017

Neurofibromatosis type 1 (NF1) is a genetic disorder with a range of clinical manifestations such as widespread growth of benign tumours called neurofibromas, pain, learning disorders, bone deformities, vascular abnormalities and even malignant tumours. With the establishment of the Children’s Tumour Foundation biobank, neurofibroma samples can now be collected directly from patients to be analysed by the larger scientific community. This work describes a pilot study to characterize one class of neurofibroma, cutaneous neurofibromas, by molecularly profiling of ~40 cutaneous neurofibromas collected from 11 individual patients. Data collected from each tumour includes (1) SNP Arrays, (2) Whole genome sequencing (WGS) and (3) RNA-Sequencing. These data are now freely available for further analysis at http://www.synapse.org/cutaneousNF.
X-ray computed tomography library of shark anatomy and lower jaw surface models
Authors: Kamminga Pepijn , De Bruin Paul W. , Geleijns Jacob , Brazeau Martin D.
Published: April 2017

The cranial diversity of sharks reflects disparate biomechanical adaptations to feeding. In order to be able to investigate and better understand the ecomorphology of extant shark feeding systems, we created a x-ray computed tomography (CT) library of shark cranial anatomy with three-dimensional (3D) lower jaw reconstructions. This is used to examine and quantify lower jaw disparity in extant shark species in a separate study. The library is divided in a dataset comprised of medical CT scans of 122 sharks (Selachimorpha, Chondrichthyes) representing 73 extant species, including digitized morphology of entire shark specimens. This CT dataset and additional data provided by other researchers was used to reconstruct a second dataset containing 3D models of the left lower jaw for 153 individuals representing 94 extant shark species. These datasets form an extensive anatomical record of shark skeletal anatomy, necessary for comparative morphological, biomechanical, ecological and phylogenetic studies.
The contemporary distribution of Trypanosoma cruzi infection in humans, alternative hosts and vectors
Authors: Browne Annie J. , Guerra Carlos A. , Alves Renato Vieira , da Costa Veruska Maia , Wilson Anne L. , Pigott David M. , Hay Simon I. , Lindsay Steve W. , Golding Nick , Moyes Catherine L.
Published: April 2017

Chagas is a potentially fatal chronic disease affecting large numbers of people across the Americas and exported throughout the world through human population movement. It is caused by the Trypanosoma cruzi parasite, which is transmitted by triatomine vectors to humans and a wide range of alternative host species. The database described here was compiled to allow the risk of vectorial transmission to humans to be mapped using geospatial models. The database collates all available records, published since 2003, for prevalence and occurrence of infection in humans, vectors and alternative hosts, and links each record to a defined time and location. A total of 16,802 records of infection have been extracted from the published literature and unpublished sources. The resulting database can be used to improve our understanding of the geographic variation in vector infection prevalence and to estimate the risk of vectorial transmission of T. cruzi to humans.
Correction: Corrigendum: Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice
Authors: Belik Jaques , Shifrin Yulia , Arning Erland , Bottiglieri Teodoro , Pan Jingyi , Daigneault Michelle C. , Allen-Vercoe Emma
Published: April 2017

Scientific Reports 7: Article number: 39854; published online: 12 January 2017; updated: 11 April 2017 In the original version of this Article, all instances of “Adlercreutzia equolifaciens” were incorrectly given as “Aldercreutzia equolifaciens”. This error has now been corrected in the PDF and HTML versions of the Article.
Geographic barriers and Pleistocene climate change shaped patterns of genetic variation in the Eastern Afromontane biodiversity hotspot
Authors: Mairal Mario , Sanmartín Isabel , Herrero Alberto , Pokorny Lisa , Vargas Pablo , Aldasoro Juan J. , Alarcón Marisa
Published: April 2017

The Eastern African Afromontane forest is getting increased attention in conservation studies because of its high endemicity levels and shrinking geographic distribution. Phylogeographic studies have found evidence of high levels of genetic variation structured across the Great Rift System. Here, we use the epiphytic plant species Canarina eminii to explore causal explanations for this pattern. Phylogeographic analyses were undertaken using plastid regions and AFLP fragments. Population genetic analyses, Statistical Parsimony, and Bayesian methods were used to infer genetic diversity, genealogical relationships, structure, gene flow barriers, and the spatiotemporal evolution of populations. A strong phylogeographic structure was found, with two reciprocally monophyletic lineages on each side of the Great Rift System, high genetic exclusivity, and restricted gene flow among mountain ranges. We explain this pattern by topographic and ecological changes driven by geological rifting in Eastern Africa. Subsequent genetic structure is attributed to Pleistocene climatic changes, in which sky-islands acted as long-term refuges and cradles of genetic diversity. Our study highlights the importance of climate change and geographic barriers associated with the African Rift System in shaping population genetic patterns, as well as the need to preserve the high levels of exclusive and critically endangered biodiversity harboured by current patches of the Afromontane forest.
An inter-residue network model to identify mutational-constrained regions on the Ebola coat glycoprotein
Authors: Quinlan Devin S. , Raman Rahul , Tharakaraman Kannan , Subramanian Vidya , del Hierro Gabriella , Sasisekharan Ram
Published: April 2017

Recently, progress has been made in the development of vaccines and monoclonal antibody cocktails that target the Ebola coat glycoprotein (GP). Based on the mutation rates for Ebola virus given its natural sequence evolution, these treatment strategies are likely to impose additional selection pressure to drive acquisition of mutations in GP that escape neutralization. Given the high degree of sequence conservation among GP of Ebola viruses, it would be challenging to determine the propensity of acquiring mutations in response to vaccine or treatment with one or a cocktail of monoclonal antibodies. In this study, we analyzed the mutability of each residue using an approach that captures the structural constraints on mutability based on the extent of its inter-residue interaction network within the three-dimensional structure of the trimeric GP. This analysis showed two distinct clusters of highly networked residues along the GP1-GP2 interface, part of which overlapped with epitope surfaces of known neutralizing antibodies. This network approach also permitted us to identify additional residues in the network of the known hotspot residues of different anti-Ebola antibodies that would impact antibody-epitope interactions.
Correlated Mutation in the Evolution of Catalysis in Uracil DNA Glycosylase Superfamily
Authors: Xia Bo , Liu Yinling , Guevara Jose , Li Jing , Jilich Celeste , Yang Ye , Wang Liangjiang , Dominy Brian N. , Cao Weiguo
Published: April 2017

Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG. Conversion of EG doublet in family 4 Thermus thermophilus UDGa to QD doublet increases the catalytic efficiency by over one hundred-fold and seventeen-fold over the E41Q and G42D single mutation, respectively, rectifying the strong correlation in the doublet. Molecular dynamics simulations suggest that the correlated mutations in the doublet in motif 1 position the catalytic H155 in motif 2 to stabilize the leaving uracilate anion. The integrated approach has important implications in studying enzyme evolution and protein structure and function.
Structural and magnetic properties of multi-core nanoparticles analysed using a generalised numerical inversion method
Authors: Bender P. , Bogart L. K. , Posth O. , Szczerba W. , Rogers S. E. , Castro A. , Nilsson L. , Zeng L. J. , Sugunan A. , Sommertune J. , Fornara A. , González-Alonso D. , Barquín L. Fernández , Johansson C.
Published: April 2017

The structural and magnetic properties of magnetic multi-core particles were determined by numerical inversion of small angle scattering and isothermal magnetisation data. The investigated particles consist of iron oxide nanoparticle cores (9 nm) embedded in poly(styrene) spheres (160 nm). A thorough physical characterisation of the particles included transmission electron microscopy, X-ray diffraction and asymmetrical flow field-flow fractionation. Their structure was ultimately disclosed by an indirect Fourier transform of static light scattering, small angle X-ray scattering and small angle neutron scattering data of the colloidal dispersion. The extracted pair distance distribution functions clearly indicated that the cores were mostly accumulated in the outer surface layers of the poly(styrene) spheres. To investigate the magnetic properties, the isothermal magnetisation curves of the multi-core particles (immobilised and dispersed in water) were analysed. The study stands out by applying the same numerical approach to extract the apparent moment distributions of the particles as for the indirect Fourier transform. It could be shown that the main peak of the apparent moment distributions correlated to the expected intrinsic moment distribution of the cores. Additional peaks were observed which signaled deviations of the isothermal magnetisation behavior from the non-interacting case, indicating weak dipolar interactions.
English phonology and an acoustic language universal
Authors: Nakajima Yoshitaka , Ueda Kazuo , Fujimaru Shota , Motomura Hirotoshi , Ohsaka Yuki
Published: April 2017

Acoustic analyses of eight different languages/dialects had revealed a language universal: Three spectral factors consistently appeared in analyses of power fluctuations of spoken sentences divided by critical-band filters into narrow frequency bands. Examining linguistic implications of these factors seems important to understand how speech sounds carry linguistic information. Here we show the three general categories of the English phonemes, i.e., vowels, sonorant consonants, and obstruents, to be discriminable in the Cartesian space constructed by these factors: A factor related to frequency components above 3,300 Hz was associated only with obstruents (e.g., /k/ or /z/), and another factor related to frequency components around 1,100 Hz only with vowels (e.g., /a/ or /i/) and sonorant consonants (e.g., /w/, /r/, or /m/). The latter factor highly correlated with the hypothetical concept of sonority or aperture in phonology. These factors turned out to connect the linguistic and acoustic aspects of speech sounds systematically.
Studies on the growth performance of different broiler strains at high altitude and evaluation of probiotic effect on their survivability
Authors: Kalia Sahil , K. Bharti Vijay , Gogoi Deepak , Giri Arup , Kumar Bhuvnesh
Published: April 2017

Identification of appropriate breeds of broilers and development of new feed additives is required for the development of poultry industry at high altitude. Therefore, this experiment was conducted first to identify the suitable broiler strain for this region. One week old chicks (150) from three broiler strains, i.e. Vencobb, RIR cross-bred, and Hubbard were randomly selected and divided equally into three groups. All the chicks were provided the same basal diet. The body weight gain and feed: gain responses were significantly (P < 0.05) improved in RIR cross-bred. Mortality was also observed lower in RIR cross-bred. Thereafter, the second trial was conducted in RIR cross-bred to evaluate the effect of probiotic supplementation (T1@ 9 gm/kg feed, T2@ 18 gm/kg feed) on their performance and mortality. No significant differences (P > 0.05) were observed in weight gain, feed intake, feed: gain, and water intake among the three groups, however, mortality from ascites and coccidiosis was reduced in probiotic treated groups. Hence, our results suggest that RIR cross-bred is suitable for rearing in high altitude regions and probiotic supplementation has no beneficial effects on production performance of broilers at high altitude. However, probiotic supplementation indicated lesser loss due to mortality of birds.
Intestinal microbiome in children with severe and complicated acute viral gastroenteritis
Authors: Chen Shih-Yen , Tsai Chi-Neu , Lee Yun-Shien , Lin Chun-Yuan , Huang Kuan-Yeh , Chao Hsun-Ching , Lai Ming-Wei , Chiu Cheng-Hsun
Published: April 2017

The aim of the present study was to evaluate the microbiota of children with severe or complicated acute viral gastroenteritis (AGE). To that end, next-generation sequencing (NGS) technology was used to sequence the 16S ribosomal RNA (16S rRNA) gene in 20 hospitalized pediatric patients with severe or complicated AGE and a further 20 otherwise healthy children; the fecal microbiome was then assessed. Comparative metagenomics data were analyzed by a Wilcoxon rank–sum test and hierarchical clustering analysis of bacterial reads. The statistical analyses showed a significantly decreased Shannon diversity index (entropy score) of the intestinal microbiota in patients with severe AGE compared with normal controls (P = 0.017) and patients with mild-to-moderate AGE (P = 0.011). The intestinal microbiota score of the 5 patients with rotavirus AGE was significantly lower than that of those with norovirus infection (P = 0.048). Greater richness in Campylobacteraceae (P = 0.0003), Neisseriaceae (P = 0.0115), Methylobacteriaceae (P = 0.0004), Sphingomonadaceae (P = 0.0221), and Enterobacteriaceae (P = 0.0451) was found in patients with complicated AGE compared with normal controls. The data suggest a significant reduction in intestinal microbial diversity in patients with severe AGE, particularly those with rotavirus infection.
Reproductive stage physiological and transcriptional responses to salinity stress in reciprocal populations derived from tolerant (Horkuch) and susceptible (IR29) rice
Authors: Razzaque Samsad , Haque Taslima , Elias Sabrina M. , Rahman Md. Sazzadur , Biswas Sudip , Schwartz Scott , Ismail Abdelbagi M. , Walia Harkamal , Juenger Thomas E. , Seraj Zeba I.
Published: April 2017

Global increase in salinity levels has made it imperative to identify novel sources of genetic variation for tolerance traits, especially in rice. The rice landrace Horkuch, endemic to the saline coastal area of Bangladesh, was used in this study as the source of tolerance in reciprocal crosses with the sensitive but high-yielding IR29 variety for discovering transcriptional variation associated with salt tolerance in the resulting populations. The cytoplasmic effect of the Horkuch background in leaves under stress showed functional enrichment for signal transduction, DNA-dependent regulation and transport activities. In roots the enrichment was for cell wall organization and macromolecule biosynthesis. In contrast, the cytoplasmic effect of IR29 showed upregulation of apoptosis and downregulation of phosphorylation across tissues relative to Horkuch. Differential gene expression in leaves of the sensitive population showed downregulation of GO processes like photosynthesis, ATP biosynthesis and ion transport. Roots of the tolerant plants conversely showed upregulation of GO terms like G-protein coupled receptor pathway, membrane potential and cation transport. Furthermore, genes involved in regulating membrane potentials were constitutively expressed only in the roots of tolerant individuals. Overall our work has developed genetic resources and elucidated the likely mechanisms associated with the tolerance response of the Horkuch genotype.
Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes
Authors: Wong Hon Lun , Visscher Pieter T. , White III Richard Allen , Smith Daniela-Lee , Patterson Molly M. , Burns Brendan P.
Published: April 2017

The role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of putative niches in these systems. In the present study, high throughput amplicon sequencing was undertaken in conjunction with analysis of key biogeochemical properties of two mats (smooth and pustular) from Shark Bay, Australia. One-way analysis of similarity tests indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1%). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Pustular mats were enriched with Halobacteria and Parvarchaeota. Key metabolisms (bacterial and archaeal) were measured, and the rates of oxygen production/consumption and sulfate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic layers and was up to seven-fold higher in smooth than pustular mats. The finding of an abundance of anaerobic methanogens enriched at the surface where oxygen levels were highest, coupled with peak methane production in the oxic zone, suggests putative surface anoxic niches in these microbial mats.
Bitter Taste Receptor Agonists Mitigate Features of Allergic Asthma in Mice
Authors: Sharma Pawan , Yi Roslyn , Nayak Ajay P. , Wang Nadan , Tang Francesca , Knight Morgan J. , Pan Shi , Oliver Brian , Deshpande Deepak A.
Published: April 2017

Asthma is characterized by airway inflammation, mucus secretion, remodeling and hyperresponsiveness (AHR). Recent research has established the bronchodilatory effect of bitter taste receptor (TAS2R) agonists in various models. Comprehensive pre-clinical studies aimed at establishing effectiveness of TAS2R agonists in disease models are lacking. Here we aimed to determine the effect of TAS2R agonists on features of asthma. Further, we elucidated a mechanism by which TAS2R agonists mitigate features of asthma. Asthma was induced in mice using intranasal house dust mite or aerosol ova-albumin challenge, and chloroquine or quinine were tested in both prophylactic and treatment models. Allergen challenge resulted in airway inflammation as evidenced by increased immune cells infiltration and release of cytokines and chemokines in the lungs, which were significantly attenuated in TAS2R agonists treated mice. TAS2R agonists attenuated features of airway remodeling including smooth muscle mass, extracellular matrix deposition and pro-fibrotic signaling, and also prevented mucus accumulation and development of AHR in mice. Mechanistic studies using human neutrophils demonstrated that inhibition of immune cell chemotaxis is a key mechanism by which TAS2R agonists blocked allergic airway inflammation and exerted anti-asthma effects. Our comprehensive studies establish the effectiveness of TAS2R agonists in mitigating multiple features of allergic asthma.
Hydrodynamics of the VanA-type VanS histidine kinase: an extended solution conformation and first evidence for interactions with vancomycin
Authors: Phillips-Jones Mary K. , Channell Guy , Kelsall Claire J. , Hughes Charlotte S. , Ashcroft Alison E. , Patching Simon G. , Dinu Vlad , Gillis Richard B. , Adams Gary G. , Harding Stephen E.
Published: April 2017

VanA-type resistance to glycopeptide antibiotics in clinical enterococci is regulated by the VanSARAtwo-component signal transduction system. The nature of the molecular ligand that is recognised by the VanSAsensory component has not hitherto been identified. Here we employ purified, intact and active VanSAmembrane protein (henceforth referred to as VanS) in analytical ultracentrifugation experiments to study VanS oligomeric state and conformation in the absence and presence of vancomycin. A combination of sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge (SEDFIT, SEDFIT-MSTAR and MULTISIG analysis) showed that VanS in the absence of the ligand is almost entirely monomeric (molar massM = 45.7 kDa) in dilute aqueous solution with a trace amount of high molar mass material (M ~ 200 kDa). The sedimentation coefficientssuggests the monomer adopts an extended conformation in aqueous solution with an equivalent aspect ratio of ~(12 ± 2). In the presence of vancomycin over a 33% increase in the sedimentation coefficient is observed with the appearance of additional higherscomponents, demonstrating an interaction, an observation consistent with our circular dichroism measurements. The two possible causes of this increase ins– either a ligand induced dimerization and/or compaction of the monomer are considered.
Adaptation and evolution of deep-sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow-water species
Authors: Zhang Yanjie , Sun Jin , Chen Chong , Watanabe Hiromi K. , Feng Dong , Zhang Yu , Chiu Jill M.Y. , Qian Pei-Yuan , Qiu Jian-Wen
Published: April 2017

Polynoid scale worms (Polynoidae, Annelida) invaded deep-sea chemosynthesis-based ecosystems approximately 60 million years ago, but little is known about their genetic adaptation to the extreme deep-sea environment. In this study, we reported the first two transcriptomes of deep-sea polynoids (Branchipolynoe pettiboneae, Lepidonotopodium sp.) and compared them with the transcriptome of a shallow-water polynoid (Harmothoe imbricata). We determined codon and amino acid usage, positive selected genes, highly expressed genes and putative duplicated genes. Transcriptome assembly produced 98,806 to 225,709 contigs in the three species. There were more positively charged amino acids (i.e., histidine and arginine) and less negatively charged amino acids (i.e., aspartic acid and glutamic acid) in the deep-sea species. There were 120 genes showing clear evidence of positive selection. Among the 10% most highly expressed genes, there were more hemoglobin genes with high expression levels in both deep-sea species. The duplicated genes related to DNA recombination and metabolism, and gene expression were only enriched in deep-sea species. Deep-sea scale worms adopted two strategies of adaptation to hypoxia in the chemosynthesis-based habitats (i.e., rapid evolution of tetra-domain hemoglobin in Branchipolynoe or high expression of single-domain hemoglobin in Lepidonotopodium sp.).
An optimized transit peptide for effective targeting of diverse foreign proteins into chloroplasts in rice
Authors: Shen Bo-Ran , Zhu Cheng-Hua , Yao Zhen , Cui Li-Li , Zhang Jian-Jun , Yang Cheng-Wei , He Zheng-Hui , Peng Xin-Xiang
Published: April 2017

Various chloroplast transit peptides (CTP) have been used to successfully target some foreign proteins into chloroplasts, but for other proteins these same CTPs have reduced localization efficiencies or fail completely. The underlying cause of the failures remains an open question, and more effective CTPs are needed. In this study, we initially observed that two E.coli enzymes, EcTSR and EcGCL, failed to be targeted into rice chloroplasts by the commonly-used rice rbcS transit peptide (rCTP) and were subsequently degraded. Further analyses revealed that the N-terminal unfolded region of cargo proteins is critical for their localization capability, and that a length of about 20 amino acids is required to attain the maximum localization efficiency. We considered that the unfolded region may alleviate the steric hindrance produced by the cargo protein, by functioning as a spacer to which cytosolic translocators can bind. Based on this inference, an optimized CTP, named RC2, was constructed. Analyses showed that RC2 can more effectively target diverse proteins, including EcTSR and EcGCL, into rice chloroplasts. Collectively, our results provide further insight into the mechanism of CTP-mediated chloroplastic localization, and more importantly, RC2 can be widely applied in future chloroplastic metabolic engineering, particularly for crop plants.
Over-expression of microRNA-1 causes arrhythmia by disturbing intracellular trafficking system
Authors: Su Xiaomin , Liang Haihai , Wang He , Chen Guizhi , Jiang Hua , Wu Qiuxia , Liu Tianyi , Liu Qiushuang , Yu Tong , Gu Yunyan , Yang Baofeng , Shan Hongli
Published: April 2017

Dysregulation of intracellular trafficking system plays a fundamental role in the progression of cardiovascular disease. Up-regulation of miR-1 contributes to arrhythmia, we sought to elucidate whether intracellular trafficking contributes to miR-1-driven arrhythmia. By performing microarray analyses of the transcriptome in the cardiomyocytes-specific over-expression of microRNA-1 (miR-1 Tg) mice and the WT mice, we found that these differentially expressed genes in miR-1 Tg mice were significantly enrichment with the trafficking-related biological processes, such as regulation of calcium ion transport. Also, the qRT-PCR and western blot results validated that Stx6, Braf, Ube3a, Mapk8ip3, Ap1s1, Ccz1 and Gja1, which are the trafficking-related genes, were significantly down-regulated in the miR-1 Tg mice. Moreover, we found that Stx6 was decreased in the heart of mice after myocardial infarction and in the hypoxic cardiomyocytes, and further confirmed that Stx6 is a target of miR-1. Meanwhile, knockdown of Stx6 in cardiomyocytes resulted in the impairments of PLM and L-type calcium channel, which leads to the increased resting ([Ca2+]i). On the contrary, overexpression of Stx6 attenuated the impairments of miR-1 or hypoxia on PLM and L-type calcium channel. Thus, our studies reveals that trafficking-related gene Stx6 may regulate intracellular calcium and is involved in the occurrence of cardiac arrhythmia, which provides new insights in that miR-1 participates in arrhythmia by regulating the trafficking-related genes and pathway.
Computational analysis of calculated physicochemical and ADMET properties of protein-protein interaction inhibitors
Authors: Lagorce David , Douguet Dominique , Miteva Maria A. , Villoutreix Bruno O.
Published: April 2017

The modulation of PPIs by low molecular weight chemical compounds, particularly by orally bioavailable molecules, would be very valuable in numerous disease indications. However, it is known that PPI inhibitors (iPPIs) tend to have properties that are linked to poor Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) and in some cases to poor clinical outcomes. Previously reported in silico analyses of iPPIs have essentially focused on physicochemical properties but several other ADMET parameters would be important to assess. In order to gain new insights into the ADMET properties of iPPIs, computations were carried out on eight datasets collected from several databases. These datasets involve compounds targeting enzymes, GPCRs, ion channels, nuclear receptors, allosteric modulators, oral marketed drugs, oral natural product-derived marketed drugs and iPPIs. Several trends are reported that should assist the design and optimization of future PPI inhibitors, either for drug discovery endeavors or for chemical biology projects.
SnoN Stabilizes the SMAD3/SMAD4 Protein Complex
Authors: Walldén Karin , Nyman Tomas , Hällberg B. Martin
Published: April 2017

TGF-β signaling regulates cellular processes such as proliferation, differentiation and apoptosis through activation of SMAD transcription factors that are in turn modulated by members of the Ski-SnoN family. In this process, Ski has been shown to negatively modulate TGF-β signaling by disrupting active R-SMAD/Co-SMAD heteromers. Here, we show that the related regulator SnoN forms a stable complex with the R-SMAD (SMAD3) and the Co-SMAD (SMAD4). To rationalize this stabilization at the molecular level, we determined the crystal structure of a complex between the SAND domain of SnoN and the MH2-domain of SMAD4. This structure shows a binding mode that is compatible with simultaneous coordination of R-SMADs. Our results show that SnoN, and SMAD heteromers can form a joint structural core for the binding of other transcription modulators. The results are of fundamental importance for our understanding of the molecular mechanisms behind the modulation of TGF-β signaling.
Correction: Corrigendum: An analysis of disease-gene relationship from Medline abstracts by DigSee
Authors: Kim Jeongkyun , Kim Jung-jae , Lee Hyunju
Published: April 2017

Scientific Reports 7: Article number: 40154; published online: 05 January 2017; updated: 11 April 2017 In this Article, Jung-jae Kim is incorrectly listed as being affiliated with ‘1 Fusionopolis Way, #21–01 Connexis (South Tower), 138632, Singapore’. The correct affiliation is listed below: Institute for Infocomm Research, Data Analytics Department, 138632, Singapore.
The CACNA1C risk allele rs1006737 is associated with age-related prefrontal cortical thinning in bipolar I disorder
Authors: Soeiro-de-Souza M G , Lafer B , Moreno R A , Nery F G , Chile T , Chaim K , da Costa Leite C , Machado-Vieira R , Otaduy M C G , Vallada H
Published: April 2017

Calcium channels control the inflow of calcium ions into cells and are involved in diverse cellular functions. The CACNA1C gene polymorphism rs1006737 A allele has been strongly associated with increased risk for bipolar disorder (BD) and with modulation of brain morphology. The medial prefrontal cortex (mPFC) has been widely associated with mood regulation in BD, but the role of this CACNA1C polymorphism in mPFC morphology and brain aging has yet to be elucidated. One hundred seventeen euthymic BD type I subjects were genotyped for CACNA1C rs1006737 and underwent 3 T three-dimensional structural magnetic resonance imaging scans to determine cortical thickness of mPFC components (superior frontal cortex (sFC), medial orbitofrontal cortex (mOFC), caudal anterior cingulate cortex (cACC) and rostral anterior cingulate cortex (rACC)). Carriers of the CACNA1C allele A exhibited greater left mOFC thickness compared to non-carriers. Moreover, CACNA1C A carriers showed age-related cortical thinning of the left cACC, whereas among A non-carriers there was not an effect of age on left cACC cortical thinning. In the sFC, mOFC and rACC (left or right), a negative correlation was observed between age and cortical thickness, regardless of CACNA1C rs1006737 A status. Further studies investigating the direct link between cortical thickness, calcium channel function, apoptosis mechanism and their underlying relationship with aging-associated cognitive decline in BD are warranted.
The effect of doping temperature on the nitrogen-bonding configuration of nitrogen-doped graphene by hydrothermal treatment
Authors: Song Jun-ho , Kim Chang-Min , Yang Euntae , Ham Moon-Ho , Kim In S.
Published: April 2017

As doping temperature increase, each type of nitrogen-bonding show the different tendencies. The pyrrolic-N has a high proportion, but a low relative with temperature. Despite smaller contents, the pyridinic-N play a prominent part.
Circulating levels of miR-122 increase post-mortem, particularly following lethal dosing with pentobarbital sodium: implications for pre-clinical liver injury studies
Authors: Clarke Joanna I. , Forootan Shiva Seyed , Lea Jonathan D. , Howell Lawrence S. , Rodriguez Josep Monne , Kipar Anja , Goldring Christopher E. , Park B. Kevin , Copple Ian M. , Antoine Daniel J.
Published: April 2017

microRNA-122 (miR-122) is increasingly being measured in pre-clinical and clinical settings due to greater sensitivity and hepatic specificity compared to the gold standard liver injury biomarker alanine aminotransferase (ALT). In pre-clinical studies, various culling methods can be employed prior to collection of blood samples, including lethal injection with pentobarbital sodium (Pentoject). However, little is known about whether such an approach could alter the circulating levels of miR-122 and compromise the interpretation of data. We therefore exposed C57BL/6J mice to saline or the model hepatotoxin paracetamol and collected blood samples pre-cull (via tail bleed) and post-cull (via cardiac puncture following exposure to a rising concentration of CO2 or intraperitoneal injection of Pentoject). Compared to pre-cull levels there was a significant increase in serum miR-122 level in mice culled with CO2 and, to a much greater extent, in mice culled with Pentoject. As a result, whilst the serum level of miR-122 increased in Pentoject-culled animals exposed to paracetamol, the higher level in saline-treated mice rendered this difference statistically non-significant, in contrast to findings in animals culled with CO2. ALT levels were unaffected by sacrifice method. Consistent with the in vivo findings, exposure of primary mouse hepatocytes to Pentoject provoked a rapid and concentration-dependent release of miR-122 into the culture media. Thus, for optimal design and interpretation of data from pre-clinical liver injury studies in which miR-122 is to be used as a biomarker, we recommend that blood samples are collected pre-cull whenever possible, and that lethal injection with Pentoject is avoided.
Simultaneous determination of sixteen industrial pollutants in infant formula milk powder by dispersive solid phase extraction coupled with ultra-high performance liquid chromatography-tandem mass spectrometry
Authors: He Dong
Published: April 2017

A high-throughput method based on dSPE and UHPLC-MS/MS was developed for sixteen industrial pollutants analysis in infant formula milk powder.
Effect of incorporating flat aromatic molecules on spherical polymeric nanoparticles
Authors: Khomein Piyachai , Thayumanavan S.
Published: April 2017

Charge transport is maintained when anisotropic 2D structures are converted to isotropic 3D nanoparticles.
Hierarchical host–guest assemblies formed on dodecaborate-coated gold nanoparticles
Authors: Assaf Khaleel I. , Hennig Andreas , Peng Shu , Guo Dong-Sheng , Gabel Detlef , Nau Werner M.
Published: April 2017

Undecahydro-mercapto-closo-dodecaborate (BSH), a purely inorganic cluster anion, serves as an unconventional stabilizing ligand for the preparation of gold nanoparticles (AuNPs).
Diversification reactions of γ-silyl allenyl esters: selective conversion to all-carbon quaternary centers and γ-allene dicarbinols
Authors: Jana Susovan , Roy Animesh , Lepore Salvatore D.
Published: April 2017

Taking advantage of an organosilicon auxiliary, allenes are selectively converted under mild conditions to either all-carbon quaternary centers (including via SNAr) or allene dicarbinols depending on the electrophile.
A macrocyclic ‘Co0’ complex: the relevance of ligand non-innocence to reactivity
Authors: Kaspar Manuel , Altmann Philipp J. , Pöthig Alexander , Sproules Stephen , Hess Corinna R.
Published: April 2017

A formally ‘Co0’ compound, containing the redox-active macrocyclic Mabiq ligand, was isolated and characterized. Ligand redox non-innocence in this system has important ramifications for reactivity.
Single-photon Coulomb explosion of methanol using broad bandwidth ultrafast EUV pulses
Authors: Luzon Itamar , Jagtap Krishna , Livshits Ester , Lioubashevski Oleg , Baer Roi , Strasser Daniel
Published: April 2017

Single-photon Coulomb explosion of methanol using broad bandwidth ultrafast EUV pulses towards achieving time resolved imaging of ultrafast dynamics.
Determination of the diffusion coefficient of hydrogen ion in hydrogels
Authors: Schuszter Gábor , Gehér-Herczegh Tünde , Szűcs Árpád , Tóth Ágota , Horváth Dezső
Published: April 2017

Combined conductometric and PFGSE-NMR measurements allow the determination of the diffusion coefficient of hydrogen ions in hydrogels.
Hydrogen purification performance of a nanoporous hexagonal boron nitride membrane: molecular dynamics and first-principle simulations
Authors: Darvish Ganji Masoud , Dodangeh Razieh
Published: April 2017

Double-layer models of porous h-BN monolayers, with pores differing in size and chemistry, were employed for efficient gas separation and purification. Performance was evaluated by DFT calculations and MD simulations.
Charles J. Pedersen's legacy to chemistry
Authors: Izatt Reed M.
Published: April 2017

A remarkable person, Charles J. Pedersen's legacy to chemistry was the serendipitous discovery of crown ethers that netted him the 1987 Nobel Prize.
Catalytic oxidation of aromatic hydrocarbons by a molecular iron–NHC complex
Authors: Lindhorst Anja C. , Schütz Jan , Netscher Thomas , Bonrath Werner , Kühn Fritz E.
Published: April 2017

An iron–NHC complex bearing a tetradentate bis(N-heterocyclic carbene) ligand is applied as catalyst for the oxidation of methyl substituted arene substrates.
Correction: Ionic-liquid-assisted synthesis of the phosphorus interhalides [PBr4][IBr2] and [PBr4][I5Br7]
Authors: Hausmann David , Köppe Ralf , Wolf Silke , Roesky Peter W. , Feldmann Claus
Published: April 2017

Correction for ‘Ionic-liquid-assisted synthesis of the phosphorus interhalides [PBr4][IBr2] and [PBr4][I5Br7]’ by David Hausmann et al., Dalton Trans., 2016, 45, 16526–16532.
In vivoactivation of an [FeFe] hydrogenase using synthetic cofactors
Authors: Khanna N. , Esmieu C. , Mészáros L. S. , Lindblad P. , Berggren G.
Published: April 2017

The [FeFe]-hydrogenase can incorporate synthetic cofactors inside living cells, allowing for artificial enzyme activation underin vivoconditions.
The influence of electromagnetic fields from two commercially available water-treatment devices on calcium carbonate precipitation
Authors: Piyadasa C. , Yeager T. R. , Gray S. R. , Stewart M. B. , Ridgway H. F. , Pelekani C. , Orbell J. D.
Published: April 2017

CaCO3precipitation profiles, tracked by absorbance at 350 nm, showing accelerated precipitation upon exposure of the parent solutions to a pulsed electromagnetic field (PEMF) from a commercially available device.
Insight into the mechanism of gold-catalyzed reduction of nitroarenes based on the substituent effect and in situ IR
Authors: Wang Cui , Zou Wei , Wang Jiasheng , Ge Yuzhen , Lu Rongwen , Zhang Shufen
Published: April 2017

A new insight into the Au–SiO2-catalyzed reduction of nitroarenes based on the substituent effect and in situ IR.
Synthesis and catalytic performance of hierarchically structured beta zeolites by a dual-functional templating approach
Authors: Zhang Kai , Liu Zewei , Wang Min , Yan Xin , Li Chao , Xi Hongxia
Published: April 2017

A beta zeolite possessing a hierarchical structure with excellent catalytic activity and long lifetime was obtained in the presence of a dual-functional amphiphilic surfactant.
Improving target amino acid selectivity in a permissive aminoacyl tRNA synthetase through counter-selection
Authors: Sungwienwong Itthipol , Hostetler Zachary M. , Blizzard Robert J. , Porter Joseph J. , Driggers Camden M. , Mbengi Lea Z. , Villegas José A. , Speight Lee C. , Saven Jeffery G. , Perona John J. , Kohli Rahul M. , Mehl Ryan A. , Petersson E. James
Published: April 2017

We report the selection and characterization of an improved acridon-2-ylalanine aminoacyl tRNA synthetase.
Regiocontrolled functionalization of 2,3-dihalogenoimidazo[1,2-a]pyridines by Suzuki–Miyaura and Sonogashira cross-coupling reactions
Authors: Delaye P.-O. , Pénichon M. , Allouchi H. , Enguehard-Gueiffier C. , Gueiffier A.
Published: April 2017

An efficient method for regiocontrolled functionalization of 2,3-dihalogenoimidazo[1,2-a]pyridine was developed.
Preparation of conductive microfiltration membrane and its performance in a coupled configuration of membrane bioreactor with microbial fuel cell
Authors: Huang Lihua , Li Xiufen , Ren Yueping , Wang Xinhua
Published: April 2017

A conductive flat microfiltration membrane with graphene (G-FM) was prepared with polyvinylidene fluoride (PVDF) and reduced graphene oxide (RGO) on stainless steel mesh base by the method of immersion-precipitation phase transformation.
Synthesis of polyaniline-wrapped carbon nanotube-supported PtCo catalysts for proton exchange membrane fuel cells: activity and stability tests
Authors: Kaewsai Duanghathai , Piumsomboon Pornpote , Pruksathorn Kejvalee , Hunsom Mali
Published: April 2017

A series of the polyaniline (PAN)-wrapped carbon nanotube (CNT)-supported PtCo (PtCo/xPAN–CNT) catalysts was prepared for the oxygen reduction reaction (ORR) in a proton exchange membrane (PEM) fuel cell.
Bioactive titaminates from molecular layer deposition
Authors: Momtazi L. , Sønsteby H. H. , Dartt D. A. , Eidet J. R. , Nilsen O.
Published: April 2017

Gas phase deposited films with amino acids by molecular layer deposition prove suitable as surfaces for cell growth.
Cytotoxic isovaleryl sucrose esters from Ainsliaea yunnanensis: reduction of mitochondrial membrane potential and increase of reactive oxygen species levels in A549 cells
Authors: Fang Xin , Zhuo Zhi-Guo , Xu Xi-Ke , Ye Ji , Li Hui-Liang , Shen Yun-Heng , Zhang Wei-Dong
Published: April 2017

Eight isovaleryl sucrose esters, named ainslosides A–H (1–8), were isolated fromAinsliaea yunnanensisFranch.
Europium complexes: choice of efficient synthetic routes from RM1 thermodynamic quantities as figures of merit
Authors: Lima Nathalia B. D. , Silva Anderson I. S. , Santos Vanessa F. C. , Gonçalves Simone M. C. , Simas Alfredo M.
Published: April 2017

Faced with many different plausible synthetic pathways for the preparation of europium complexes, the synthetic chemist can now easily compute RM1 thermodynamic quantities for all of them and likely arrive at the most effective synthetic strategies.
Template-directed synthesis of a cubic cyclodextrin polymer with aligned channels and enhanced drug payload
Authors: Singh Vikramjeet , Guo Tao , Wu Li , Xu Jianghui , Liu Botao , Gref Ruxandra , Zhang Jiwen
Published: April 2017

Despite its 3D porous structure, the pharmaceutical applications of cyclodextrin based cross-linked polymers are limited due to their structural irregularities.
Graphene oxide reinforced hydrogels for osteogenic differentiation of human adipose-derived stem cells
Authors: Noh Myungkyung , Kim Su-Hwan , Kim Jiyong , Lee Ju-Ro , Jeong Gun-Jae , Yoon Jeong-Kee , Kang Seokyung , Bhang Suk Ho , Yoon Hee Hun , Lee Jong-Chan , Hwang Nathaniel S. , Kim Byung-Soo
Published: April 2017

In this study, we designed graphene oxide-functionalized polyethylene glycol diacrylate hydrogels to assign cell adhesion-dependent biofunctionality, which resulted in cell adhesion dependent osteogenic differentiation of encapsulated stem cells.
An amino-coordination metal–organic framework for highly selective C2H2/CH4 and C2H2/C2H4 separations through the appropriate control of window sizes
Authors: Zhang Ling , Cui Xili , Xing Huabin , Yang Yu , Cui Yuanjing , Chen Banglin , Qian Guodong
Published: April 2017

An amino-coordination microporous metal-organic framework ZJU-198a was demonstrated as a valuable adsorbent for highly selective C2H2/CH4 and C2H2/C2H4 separations under ambient conditions.
The improved ion clustering and conductivity of a di-quaternized poly(arylene ether ketone sulfone)-based alkaline fuel cell membrane
Authors: Shukla Geetanjali , Shahi Vinod K.
Published: April 2017

Herein, we designed a hydrophobic–hydrophilic phase-separated poly(arylene ether ketone sulfone) (PAEKS) random copolymer-based di-quaternized stable and highly conductive alkaline membrane (AM).
Phosphorus and oxygen dual-doped graphene as superior anode material for room-temperature potassium-ion batteries
Authors: Ma Guangyao , Huang Kangsheng , Ma Jia-Sai , Ju Zhicheng , Xing Zheng , Zhuang Quan-chao
Published: April 2017

The intercalation of potassium ions into graphitic carbon materials has been demonstrated to be feasible while the electrochemical performance of the potassium-ion battery (PIB) is still unsatisfactory.
Printing assembly and structural regulation of graphene towards three-dimensional flexible micro-supercapacitors
Authors: Li Wenbo , Li Yonghe , Su Meng , An Boxing , Liu Jing , Su Dan , Li Lihong , Li Fengyu , Song Yanlin
Published: April 2017

Precise patterning and controllable assembly of graphene into 3D architectures for flexible micro-supercapacitors was achieved by a printing assembly approach.
Electrochemical deposition of dopamine–hyaluronic acid conjugates for anti-biofouling bioelectrodes
Authors: Kim Semin , Jang Yohan , Jang Lindy K. , Sunwoo Sung Hyuk , Kim Tae-il , Cho Seung-Woo , Lee Jae Young
Published: April 2017

Electrochemical deposition of dopamine-hyaluronic acid conjugates onto electrode surfaces can lead to preserved electrochemical activities and anti-biofouling properties of the electrodes.