bluuebunny/crossref_metadata_2025_split huggingface dataset:
Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers
Authors: Spencer Sarah J , Tamminen Manu V , Preheim Sarah P , Guo Mira T , Briggs Adrian W , Brito Ilana L , A Weitz David , Pitkänen Leena K , Vigneault Francois , Virta Marko P Juhani , Alm Eric J 
Published: September 2015

Abstract
Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.
Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants
Authors: Berni Canani Roberto , Sangwan Naseer , Stefka Andrew T , Nocerino Rita , Paparo Lorella , Aitoro Rosita , Calignano Antonio , Khan Aly A , Gilbert Jack A , Nagler Cathryn R 
Published: September 2015

Abstract
Dietary intervention with extensively hydrolyzed casein formula supplemented with Lactobacillus rhamnosus GG (EHCF+LGG) accelerates tolerance acquisition in infants with cow’s milk allergy (CMA). We examined whether this effect is attributable, at least in part, to an influence on the gut microbiota. Fecal samples from healthy controls (n=20) and from CMA infants (n=19) before and after treatment with EHCF with (n=12) and without (n=7) supplementation with LGG were compared by 16S rRNA-based operational taxonomic unit clustering and oligotyping. Differential feature selection and generalized linear model fitting revealed that the CMA infants have a diverse gut microbial community structure dominated by Lachnospiraceae (20.5±9.7%) and Ruminococcaceae (16.2±9.1%). Blautia, Roseburia and Coprococcus were significantly enriched following treatment with EHCF and LGG, but only one genus, Oscillospira, was significantly different between infants that became tolerant and those that remained allergic. However, most tolerant infants showed a significant increase in fecal butyrate levels, and those taxa that were significantly enriched in these samples, Blautia and Roseburia, exhibited specific strain-level demarcations between tolerant and allergic infants. Our data suggest that EHCF+LGG promotes tolerance in infants with CMA, in part, by influencing the strain-level bacterial community structure of the infant gut.
Growth rates and rRNA content of four marine bacteria in pure cultures and in the Delaware estuary
Authors: Lankiewicz Thomas S , Cottrell Matthew T , Kirchman David L 
Published: September 2015

Abstract
Interpretation of 16S ribosomal RNA (rRNA) to 16S rRNA gene ratios (rRNA:rDNA) is based on a limited number of studies with rapidly growing copiotrophic bacteria. The most abundant bacteria in the ocean are oligotrophs, which probably grow more slowly than those bacteria whose rRNA:rDNA versus growth rate relationships are known. To examine whether rRNA:rDNA varies differently in oligotrophic marine bacteria than in copiotrophic bacteria, we used quantitative PCR and reverse transcriptase quantitative PCR to measure rRNA:rDNA in two marine copiotrophs and in two marine oligotrophs, including Candidatus Pelagibacter ubique HTCC1062, a coastal isolate of SAR11, the most abundant bacterial clade in the ocean. The rRNA:rDNA ratios for the two copiotrophs were similar to those expected on the basis of an analysis of previously studied copiotrophic bacteria, while the ratios for the two oligotrophs were substantially lower than predicted even given their slow growth rates. The rRNA:rDNA ratios determined along a transect in the Delaware estuary suggested that SAR11 bacteria grow at rates close to the growth rate in culture, while rates of the two copiotrophs were far below those observed in laboratory cultures. Our results have implications for interpreting rRNA:rDNA from natural communities, understanding growth strategies and comparing regulatory mechanisms in copiotrophs and oligotrophs.
Metagenomic reconstructions of bacterial CRISPR loci constrain population histories
Authors: Sun Christine L , Thomas Brian C , Barrangou Rodolphe , Banfield Jillian F 
Published: September 2015

Abstract
Bacterial CRISPR-Cas systems provide insight into recent population history because they rapidly incorporate, in a unidirectional manner, short fragments (spacers) from coexisting infective virus populations into host chromosomes. Immunity is achieved by sequence identity between transcripts of spacers and their targets. Here, we used metagenomics to study the stability and dynamics of the type I-E CRISPR-Cas locus of Leptospirillum group II bacteria in biofilms sampled over 5 years from an acid mine drainage (AMD) system. Despite recovery of 452 686 spacers from CRISPR amplicons and metagenomic data, rarefaction curves of spacers show no saturation. The vast repertoire of spacers is attributed to phage/plasmid population diversity and retention of old spacers, despite rapid evolution of the targeted phage/plasmid genome regions (proto-spacers). The oldest spacers (spacers found at the trailer end) are conserved for at least 5 years, and 12% of these retain perfect or near-perfect matches to proto-spacer targets. The majority of proto-spacer regions contain an AAG proto-spacer adjacent motif (PAM). Spacers throughout the locus target the same phage population (AMDV1), but there are blocks of consecutive spacers without AMDV1 target sequences. Results suggest long-term coexistence of Leptospirillum with AMDV1 and periods when AMDV1 was less dominant. Metagenomics can be applied to millions of cells in a single sample to provide an extremely large spacer inventory, allow identification of phage/plasmids and enable analysis of previous phage/plasmid exposure. Thus, this approach can provide insights into prior bacterial environment and genetic interplay between hosts and their viruses.
Erratum: Riverbed methanotrophy sustained by high carbon conversion efficiency
Authors: Trimmer Mark , Shelley Felicity C , Purdy Kevin J , Maanoja Susanna T , Chronopoulou Panagiota-Myrsini , Grey Jonathan 
Published: September 2015

Abstract
Correction to: The ISME Journal (2015) 9, 2304–2314; doi:10.1038/ismej.2015.98 Since the publication of this paper, the author has discovered the incorrect spelling of an author’s name. ‘Grey Jonathan’ should be ‘Jonathan Grey’. The publisher would like to apologize for any inconvenience this may have caused.
Erratum: Making pathogens sociable: the emergence of high relatedness through limited host invasibility
Authors: van Leeuwen Edwin , O’Neill Sarah , Matthews Andrew , Raymond Ben 
Published: September 2015

Abstract
Correction to: The ISME Journal 2015; doi: 10.1038/ismej.2015.111 After the publication of this paper, the authors noticed an error in the title. The correct title is ‘Making pathogens sociable: the emergence of high relatedness through limited host invasibility’. The publisher would like to apologise for any inconvenience this may have caused.
Sub-microWatt threshold nanoisland lasers
Authors: Jang Hoon , Karnadi Indra , Pramudita Putu , Song Jung-Hwan , Soo Kim Ki , Lee Yong-Hee 
Published: September 2015

AbstractUltralow threshold nanolasers have been sought after as power efficient light sources in photonic integrated circuits. Here a single-cell nanobeam laser with a nanoisland quantum well is proposed and demonstrated. Continuous operation at 1.5 μm is achieved at room temperature with an ultralow lasing threshold of 210 nW in absorbed power. The size of the active medium is reduced to 0.7 × 0.25 × 0.02 μm3 by removing the absorptive quantum well region surrounding the central cavity. Relatively thick (420 nm) InP slabs are employed to improve the thermal and mechanical characteristics. The nanoisland-based structures will provide a new platform to engineer fundamental light–matter interactions by controlling the size and the location of the nanoemitters, allowing the realization of highly efficient nanophotonic devices.
Real-time fluorescence imaging with 20 nm axial resolution
Authors: Stabley Daniel R. , Oh Thomas , Simon Sanford M. , Mattheyses Alexa L. , Salaita Khalid 
Published: September 2015

AbstractMeasuring the nanoscale organization of protein structures near the plasma membrane of live cells is challenging, especially when the structure is dynamic. Here we present the development of a two-wavelength total internal reflection fluorescence method capable of real-time imaging of cellular structure height with nanometre resolution. The method employs a protein of interest tagged with two different fluorophores and imaged to obtain the ratio of emission in the two channels. We use this approach to visualize the nanoscale organization of microtubules and endocytosis of the epidermal growth factor receptor.
Lack of association of the iNOS gene polymorphism with risk of cancer: a systematic review and Meta-Analysis
Authors: Jiao Jinghua , Wu Jingyang , Huang Desheng , Liu Lei 
Published: September 2015

AbstractIn order to investigate the association between the iNOS gene polymorphisms and susceptibility to cancer, a search of English papers was done using Pubmed, the Cochrane Library, Embase, ISI Web of Science, Google (scholar) database and all Chinese reports were conducted using CBMDisc, Chongqing VIP database and CNKI database. A total of eight studies were included in this meta-analysis including 1,920 cases and 2,373 controls. The results indicated that the polymorphisms in iNOS gene (C150T(Ser608 Leu) polymorphism and polymorphic (CCTTT)n repeats) had no association with cancer risk for all genetic models. This meta-analysis suggested that the polymorphisms in the iNOS gene were not associated with cancer risk.
A comprehensive study on different modelling approaches to predict platelet deposition rates in a perfusion chamber
Authors: Pallarès Jordi , Senan Oriol , Guimerà Roger , Vernet Anton , Aguilar-Mogas Antoni , Vilahur Gemma , Badimon Lina , Sales-Pardo Marta , Cito Salvatore 
Published: September 2015

AbstractThrombus formation is a multiscale phenomenon triggered by platelet deposition over a protrombotic surface (eg. a ruptured atherosclerotic plaque). Despite the medical urgency for computational tools that aid in the early diagnosis of thrombotic events, the integration of computational models of thrombus formation at different scales requires a comprehensive understanding of the role and limitation of each modelling approach. We propose three different modelling approaches to predict platelet deposition. Specifically, we consider measurements of platelet deposition under blood flow conditions in a perfusion chamber for different time periods (3, 5, 10, 20 and 30 minutes) at shear rates of 212 s−1, 1390 s−1 and 1690 s−1. Our modelling approaches are: i) a model based on the mass-transfer boundary layer theory; ii) a machine-learning approach; and iii) a phenomenological model. The results indicate that the three approaches on average have median errors of 21%, 20.7% and 14.2%, respectively. Our study demonstrates the feasibility of using an empirical data set as a proxy for a real-patient scenario in which practitioners have accumulated data on a given number of patients and want to obtain a diagnosis for a new patient about whom they only have the current observation of a certain number of variables.
Investigation of the methylation of Numb by the SET8 protein lysine methyltransferase
Authors: Weirich Sara , Kusevic Denis , Kudithipudi Srikanth , Jeltsch Albert 
Published: September 2015

AbstractIt has been reported that the Numb protein is methylated at lysine 158 and 163 and that this methylation is introduced by the SET8 protein lysine methyltransferase [Dhami et al., (2013) Molecular Cell 50, 565–576]. We studied this methylation in vitro using peptide arrays and recombinant Numb protein as substrates. Numb peptides and protein were incubated with recombinant SET8 purified after expression in E. coli or human HEK293 cells. However, no methylation of Numb by SET8 was detectable. SET8 methylation of Histone H4 and p53 peptides and proteins, which were used as positive controls, was readily observed. While SET8 methylation of Numb in cells cannot be ruled out, based on our findings, more evidence is needed to support this claim. It appears likely that another not yet identified PKMT is responsible for the reported methylation of Numb in cells.
Statin-activated nuclear receptor PXR promotes SGK2 dephosphorylation by scaffolding PP2C to induce hepatic gluconeogenesis
Authors: Gotoh Saki , Negishi Masahiko 
Published: September 2015

AbstractStatin therapy is known to increase blood glucose levels in humans. Statins utilize pregnane X receptor (PXR) and serum/glucocorticoid regulated kinase 2 (SGK2) to activate phosphoenolpyruvate carboxykinase 1 (PEPCK1) and glucose-6-phosphatase (G6Pase) genes, thereby increasing glucose production in human liver cells. Here, the novel statin/PXR/SGK2-mediated signaling pathway has now been characterized for hepatic gluconeogenesis. Statin-activated PXR scaffolds the protein phosphatase 2C (PP2C) and SGK2 to stimulate PP2C to dephosphorylate SGK2 at threonine 193. Non-phosphorylated SGK2 co-activates PXR-mediated trans-activation of promoters of gluconeogenic genes in human liver cells, thereby enhancing gluconeogenesis. This gluconeogenic statin-PXR-SGK2 signal is not present in mice, in which statin treatment suppresses hepatic gluconeogenesis. These findings provide the basis for statin-associated side effects such as an increased risk for Type 2 diabetes.
Fabrication of efficient planar perovskite solar cells using a one-step chemical vapor deposition method
Authors: Tavakoli Mohammad Mahdi , Gu Leilei , Gao Yuan , Reckmeier Claas , He Jin , Rogach Andrey L. , Yao Yan , Fan Zhiyong 
Published: September 2015

AbstractOrganometallic trihalide perovskites are promising materials for photovoltaic applications, which have demonstrated a rapid rise in photovoltaic performance in a short period of time. We report a facile one-step method to fabricate planar heterojunction perovskite solar cells by chemical vapor deposition (CVD), with a solar power conversion efficiency of up to 11.1%. We performed a systematic optimization of CVD parameters such as temperature and growth time to obtain high quality films of CH3NH3PbI3 and CH3NH3PbI3-xClx perovskite. Scanning electron microscopy and time resolved photoluminescence data showed that the perovskite films have a large grain size of more than 1 micrometer and carrier life-times of 10 ns and 120 ns for CH3NH3PbI3 and CH3NH3PbI3-xClx, respectively. This is the first demonstration of a highly efficient perovskite solar cell using one step CVD and there is likely room for significant improvement of device efficiency.
Role of Viscous Dissipative Processes on the Wetting of Textured Surfaces
Authors: Grewal H. S. , Nam Kim Hong , Cho Il-Joo , Yoon Eui-Sung 
Published: September 2015

AbstractWe investigate the role of viscous forces on the wetting of hydrophobic, semi-hydrophobic and hydrophilic textured surfaces as second-order effects. We show that during the initial contact, the transition from inertia- to viscous-dominant regime occurs regardless of their surface topography and chemistry. Furthermore, we demonstrate the effect of viscosity on the apparent contact angle under quasi-static conditions by modulating the ratio of a water/glycerol mixture and show the effect of viscosity, especially on the semi-hydrophobic and hydrophobic textured substrates. The reason why the viscous force does not affect the apparent contact angle of the hydrophilic surface is explained based on the relationship between the disjoining pressure and surface chemistry. We further propose a wetting model that can predict the apparent contact angle of a liquid drop on a textured substrate by incorporating a viscous force component in the force balance equation. This model can predict apparent contact angles on semi-hydrophobic and hydrophobic textured surfaces exhibiting Wenzel state more accurately than the Wenzel model, indicating the importance of viscous forces in determining the apparent contact angle. The modified model can be applied for estimating the wetting properties of arbitrary engineered surfaces.
Introduction of Methyl Groups at C2 and C6 Positions Enhances the Antiangiogenesis Activity of Curcumin
Authors: Koo Hyun-Jung , Shin Sarah , Choi Joon Young , Lee Kyung-Han , Kim Byung-Tae , Choe Yearn Seong 
Published: September 2015

AbstractCurcumin has diverse biological activities, but is known to undergo rapid metabolism via reduction of vinylic double bonds and phase II conjugation. To prevent reductive metabolism of curcumin, we introduced a methyl group at both C2 and C6 positions (compound1) or at the C2 position (compound2) of curcumin, creating steric hindrance on double bonds against metabolizing enzymes. As predicted, these compounds were resistant to reduction by alcohol dehydrogenase. Compound1was further evaluated for its antiangiogenesis activityin vitroandin vivo. It exhibited significantly greater inhibitory activity than curcumin against endothelial cell migration, invasion and tube formation. Similarly, thein vivoMatrigel plug assay in C57BL/6 mice showed more pronounced reduction of blood vessels in the plugs containing1than those containing curcumin. Moreover,1suppressed tumor growth more effectively than curcumin in a U87MG mouse xenograft model by inhibiting angiogenesis.In vivometabolite analysis by liquid chromatography/mass spectrometry demonstrated that1underwent markedly slower reductive metabolism than curcumin. Taken together, our results indicate that1has enhanced antiangiogenesis activity and suppression of tumor growth compared with curcumin, reflecting diminished reductive metabolism owing to the introduction of methyl groups at the C2 and C6 positions of curcumin.
Edges of human embryonic stem cell colonies display distinct mechanical properties and differentiation potential
Authors: Rosowski Kathryn A. , Mertz Aaron F. , Norcross Samuel , Dufresne Eric R. , Horsley Valerie 
Published: September 2015

AbstractIn order to understand the mechanisms that guide cell fate decisions during early human development, we closely examined the differentiation process in adherent colonies of human embryonic stem cells (hESCs). Live imaging of the differentiation process reveals that cells on the outer edge of the undifferentiated colony begin to differentiate first and remain on the perimeter of the colony to eventually form a band of differentiation. Strikingly, this band is of constant width in all colonies, independent of their size. Cells at the edge of undifferentiated colonies show distinct actin organization, greater myosin activity and stronger traction forces compared to cells in the interior of the colony. Increasing the number of cells at the edge of colonies by plating small colonies can increase differentiation efficiency. Our results suggest that human developmental decisions are influenced by cellular environments and can be dictated by colony geometry of hESCs.
RBM45 homo-oligomerization mediates association with ALS-linked proteins and stress granules
Authors: Li Yang , Collins Mahlon , Geiser Rachel , Bakkar Nadine , Riascos David , Bowser Robert 
Published: September 2015

AbstractThe aggregation of RNA-binding proteins is a pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). RBM45 is an RNA-binding protein that forms cytoplasmic inclusions in neurons and glia in ALS and FTLD. To explore the role of RBM45 in ALS and FTLD, we examined the contribution of the protein’s domains to its function, subcellular localization and interaction with itself and ALS-linked proteins. We find that RBM45 forms homo-oligomers and physically associates with the ALS-linked proteins TDP-43 and FUS in the nucleus. Nuclear localization of RBM45 is mediated by a bipartite nuclear-localization sequence (NLS) located at the C-terminus. RBM45 mutants that lack a functional NLS accumulate in the cytoplasm and form TDP-43 positive stress granules. Moreover, we identify a novel structural element, termed the homo-oligomer assembly (HOA) domain, that is highly conserved across species and promote homo-oligomerization of RBM45. RBM45 mutants that fail to form homo-oligomers exhibit significantly reduced association with ALS-linked proteins and inclusion into stress granules. These results show that RMB45 may function as a homo-oligomer and that its oligomerization contributes to ALS/FTLD RNA-binding protein aggregation.
Fast Episodes of West-Mediterranean-Tyrrhenian Oceanic Opening and Revisited Relations with Tectonic Setting
Authors: Savelli Carlo 
Published: September 2015

AbstractExtension and calc-alkaline volcanism of the submerged orogen of alpine age (OAA) initiated in Early Oligocene (~33/32 Ma) and reached the stage of oceanic opening in Early-Miocene (Burdigalian), Late-Miocene and Late-Pliocene. In the Burdigalian (~20–16 Ma) period of widespread volcanism of calcalkaline type on the margins of oceanic domain, seafloor spreading originated the deep basins of north Algeria (western part of OAA) and Sardinia/Provence (European margin). Conversely, when conjugate margins’ volcanism has been absent or scarce seafloor spreading formed the plains Vavilov (7.5–6.3 Ma) and Marsili (1.87–1.67 Ma) within OAA eastern part (Tyrrhenian Sea). The contrast between occurrence and lack of margin’s igneous activity probably implies the diversity of the geotectonic setting at the times of oceanization. It appears that the Burdigalian calcalkaline volcanism on the continental margins developed in the absence of subduction. The WNW-directed subduction of African plate probably commenced at ~16/15 Ma (waning Burdigalian seafloor spreading) after ~18/16 Ma of rifting. Space-time features indicate that calcalkaline volcanism is not linked only to subduction. From this view, temporal gap would exist between the steep subduction beneath the Apennines and the previous, flat-type plunge of European plate with opposite direction producing the OAA accretion and double vergence.
Absence of the Electric Aharonov-Bohm Effect due to Induced Charges
Authors: Wang Rui-Feng 
Published: September 2015

AbstractThis paper states that the induced charge should not be neglected in the electric Aharonov-Bohm (A-B) effect. If the induced charge is taken into account, the interference pattern of the moving charge will not change with the potential difference between the two metal tubes. It means that the scalar potential itself can not affect the phase of the moving charge and the true factor affecting the phase of the moving charge is the energy of the system including the moving charge and the induced charge.