bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic Bacteroidetes
Authors: Villamor Judith , Ramos-Barbero María Dolores , González-Torres Pedro , Gabaldón Toni , Rosselló-Móra Ramón , Meseguer Inmaculada , Martínez-García Manuel , Santos Fernando , Antón Josefa 
Published: November 2017

Abstract
Hypersaline environments close to saturation harbor the highest density of virus-like particles reported for aquatic systems as well as low microbial diversity. Thus, they offer unique settings for studying virus–host interactions in nature. However, no viruses have been isolated so far infecting the two most abundant inhabitants of these systems (that is, the euryarchaeon Haloquadratum walsbyi and the bacteroidetes Salinibacter ruber). Here, using three different co-occurring strains, we have isolated eight viruses infecting the ubiquitous S. ruber that constitute three new different genera (named as ‘Holosalinivirus’, ‘Kryptosalinivirus’ and ‘Kairosalinivirus’) according to their genomic traits, different host range, virus–host interaction capabilities and abundances in natural systems worldwide. Furthermore, to get a more complete and comprehensive view of S. ruber virus assemblages in nature, a microcosm experiment was set with a mixture of S. ruber strains challenged with a brine virus concentrate, and changes of viral populations were monitored by viral metagenomics. Only viruses closely related to kairosalinivirus (strictly lytic and wide host range) were enriched, despite their low initial abundance in the natural sample. Metagenomic analyses of the mesocosms allowed the complete recovery of kairosalinivirus genomes using an ad hoc assembly strategy as common viral metagenomic assembly tools failed despite their abundance, which underlines the limitations of current approaches. The increase of this type of viruses was accompanied by an increase in the diversity of the group, as shown by contig recruitment. These results are consistent with a scenario in which host range, not only virus and host abundances, is a key factor in determining virus fate in nature.
A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer
Authors: Tully Benjamin J , Wheat C Geoff , Glazer Brain T , Huber Julie A 
Published: November 2017

Abstract
The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb3- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.
Polymorphic regenerated silk fibers assembled through bioinspired spinning
Authors: Ling Shengjie , Qin Zhao , Li Chunmei , Huang Wenwen , Kaplan David L. , Buehler Markus J. 
Published: November 2017

AbstractA variety of artificial spinning methods have been applied to produce regenerated silk fibers; however, how to spin regenerated silk fibers that retain the advantages of natural silks in terms of structural hierarchy and mechanical properties remains challenging. Here, we show a bioinspired approach to spin regenerated silk fibers. First, we develop a nematic silk microfibril solution, highly viscous and stable, by partially dissolving silk fibers into microfibrils. This solution maintains the hierarchical structures in natural silks and serves as spinning dope. It is then spun into regenerated silk fibers by direct extrusion in the air, offering a useful route to generate polymorphic and hierarchical regenerated silk fibers with physical properties beyond natural fiber construction. The materials maintain the structural hierarchy and mechanical properties of natural silks, including a modulus of 11 ± 4 GPa, even higher than natural spider silk. It can further be functionalized with a conductive silk/carbon nanotube coating, responsive to changes in humidity and temperature.
ATR kinase inhibition induces unscheduled origin firing through a Cdc7-dependent association between GINS and And-1
Authors: Moiseeva Tatiana , Hood Brian , Schamus Sandy , O’Connor Mark J. , Conrads Thomas P. , Bakkenist Christopher J. 
Published: November 2017

AbstractATR kinase activity slows replication forks and prevents origin firing in damaged cells. Here we describe proteomic analyses that identified mechanisms through which ATR kinase inhibitors induce unscheduled origin firing in undamaged cells. ATR-Chk1 inhibitor-induced origin firing is mediated by Cdc7 kinase through previously undescribed phosphorylations on GINS that induce an association between GINS and And-1. ATR-Chk1 inhibitor-induced origin firing is blocked by prior exposure to DNA damaging agents showing that the prevention of origin firing does not require ongoing ATR activity. In contrast, ATR-Chk1 inhibitor-induced origins generate additional replication forks that are targeted by subsequent exposure to DNA damaging agents. Thus, the sequence of administration of an ATR kinase inhibitor and a DNA damaging agent impacts the DNA damage induced by the combination. Our experiments identify competing ATR and Cdc7 kinase-dependent mechanisms at replication origins in human cells.
Creating nanoscale emulsions using condensation
Authors: Guha Ingrid F. , Anand Sushant , Varanasi Kripa K. 
Published: November 2017

AbstractNanoscale emulsions are essential components in numerous products, ranging from processed foods to novel drug delivery systems. Existing emulsification methods rely either on the breakup of larger droplets or solvent exchange/inversion. Here we report a simple, scalable method of creating nanoscale water-in-oil emulsions by condensing water vapor onto a subcooled oil-surfactant solution. Our technique enables a bottom-up approach to forming small-scale emulsions. Nanoscale water droplets nucleate at the oil/air interface and spontaneously disperse within the oil, due to the spreading dynamics of oil on water. Oil-soluble surfactants stabilize the resulting emulsions. We find that the oil-surfactant concentration controls the spreading behavior of oil on water, as well as the peak size, polydispersity, and stability of the resulting emulsions. Using condensation, we form emulsions with peak radii around 100 nm and polydispersities around 10%. This emulsion formation technique may open different routes to creating emulsions, colloidal systems, and emulsion-based materials.
PINK1-mediated phosphorylation of LETM1 regulates mitochondrial calcium transport and protects neurons against mitochondrial stress
Authors: Huang En , Qu Dianbo , Huang Tianwen , Rizzi Nicoletta , Boonying Wassamon , Krolak Dorothy , Ciana Paolo , Woulfe John , Klein Christine , Slack Ruth S. , Figeys Daniel , Park David S. 
Published: November 2017

AbstractMutations in PTEN-induced kinase 1 (PINK1) result in a recessive familial form of Parkinson’s disease (PD). PINK1 loss is associated with mitochondrial Ca2+ mishandling, mitochondrial dysfunction, as well as increased neuronal vulnerability. Here we demonstrate that PINK1 directly interacts with and phosphorylates LETM1 at Thr192 in vitro. Phosphorylated LETM1 or the phospho-mimetic LETM1-T192E increase calcium release in artificial liposomes and facilitates calcium transport in intact mitochondria. Expression of LETM1-T192E but not LETM1-wild type (WT) rescues mitochondrial calcium mishandling in PINK1-deficient neurons. Expression of both LETM1-WT and LETM1-T192E protects neurons against MPP+–MPTP-induced neuronal death in PINK1 WT neurons, whereas only LETM1-T192E protects neurons under conditions of PINK1 loss. Our findings delineate a mechanism by which PINK1 regulates mitochondrial Ca2+ level through LETM1 and suggest a model by which PINK1 loss leads to deficient phosphorylation of LETM1 and impaired mitochondrial Ca2+ transport..
Rapid termination of the African Humid Period triggered by northern high-latitude cooling
Authors: Collins James A. , Prange Matthias , Caley Thibaut , Gimeno Luis , Beckmann Britta , Mulitza Stefan , Skonieczny Charlotte , Roche Didier , Schefuß Enno 
Published: November 2017

AbstractThe rapidity and synchrony of the African Humid Period (AHP) termination at around 5.5 ka are debated, and it is unclear what caused a rapid hydroclimate response. Here we analysed the hydrogen isotopic composition of sedimentary leaf-waxes (δDwax) from the Gulf of Guinea, a proxy for regional precipitation in Cameroon and the central Sahel-Sahara. Our record indicates high precipitation during the AHP followed by a rapid decrease at 5.8–4.8 ka. The similarity with a δDwax record from northern East Africa suggests a large-scale atmospheric mechanism. We show that northern high- and mid-latitude cooling weakened the Tropical Easterly Jet and, through feedbacks, strengthened the African Easterly Jet. The associated decrease in precipitation triggered the AHP termination and combined with biogeophysical feedbacks to result in aridification. Our findings suggest that extratropical temperature changes, albeit smaller than during the glacial and deglacial, were important in triggering rapid African aridification during the Holocene.
Prevalence and detection of low-allele-fraction variants in clinical cancer samples
Authors: Shin Hyun-Tae , Choi Yoon-La , Yun Jae Won , Kim Nayoung K. D. , Kim Sook-Young , Jeon Hyo Jeong , Nam Jae-Yong , Lee Chung , Ryu Daeun , Kim Sang Cheol , Park Kyunghee , Lee Eunjin , Bae Joon Seol , Son Dae Soon , Joung Je-Gun , Lee Jeeyun , Kim Seung Tae , Ahn Myung-Ju , Lee Se-Hoon , Ahn Jin Seok , Lee Woo Yong , Oh Bo Young , Park Yeon Hee , Lee Jeong Eon , Lee Kwang Hyuk , Kim Hee Cheol , Kim Kyoung-Mee , Im Young-Hyuck , Park Keunchil , Park Peter J. , Park Woong-Yang 
Published: November 2017

AbstractAccurate detection of genomic alterations using high-throughput sequencing is an essential component of precision cancer medicine. We characterize the variant allele fractions (VAFs) of somatic single nucleotide variants and indels across 5095 clinical samples profiled using a custom panel, CancerSCAN. Our results demonstrate that a significant fraction of clinically actionable variants have low VAFs, often due to low tumor purity and treatment-induced mutations. The percentages of mutations under 5% VAF across hotspots in EGFR, KRAS, PIK3CA, and BRAF are 16%, 11%, 12%, and 10%, respectively, with 24% for EGFR T790M and 17% for PIK3CA E545. For clinical relevance, we describe two patients for whom targeted therapy achieved remission despite low VAF mutations. We also characterize the read depths necessary to achieve sensitivity and specificity comparable to current laboratory assays. These results show that capturing low VAF mutations at hotspots by sufficient sequencing coverage and carefully tuned algorithms is imperative for a clinical assay.
Strain-shear coupling in bilayer MoS2
Authors: Lee Jae-Ung , Woo Sungjong , Park Jaesung , Park Hee Chul , Son Young-Woo , Cheong Hyeonsik 
Published: November 2017

AbstractLayered materials such as graphite and transition metal dichalcogenides have extremely anisotropic mechanical properties owing to orders of magnitude difference between in-plane and out-of-plane interatomic interaction strengths. Although effects of mechanical perturbations on either intralayer or interlayer interactions have been extensively investigated, mutual correlations between them have rarely been addressed. Here, we show that layered materials have an inevitable coupling between in-plane uniaxial strain and interlayer shear. Because of this, the uniaxial in-plane strain induces an anomalous splitting of the degenerate interlayer shear phonon modes such that the split shear mode along the tensile strain is not softened but hardened contrary to the case of intralayer phonon modes. We confirm the effect by measuring Raman shifts of shear modes of bilayer MoS2 under strain. Moreover, by analyzing the splitting, we obtain an unexplored off-diagonal elastic constant, demonstrating that Raman spectroscopy can determine almost all mechanical constants of layered materials.
Observation of transverse spin Nernst magnetoresistance induced by thermal spin current in ferromagnet/non-magnet bilayers
Authors: Kim Dong-Jun , Jeon Chul-Yeon , Choi Jong-Guk , Lee Jae Wook , Surabhi Srivathsava , Jeong Jong-Ryul , Lee Kyung-Jin , Park Byong-Guk 
Published: November 2017

AbstractElectric generation of spin current via spin Hall effect is of great interest as it allows an efficient manipulation of magnetization in spintronic devices. Theoretically, pure spin current can be also created by a temperature gradient, which is known as spin Nernst effect. Here, we report spin Nernst effect-induced transverse magnetoresistance in ferromagnet/non-magnetic heavy metal bilayers. We observe that the magnitude of transverse magnetoresistance in the bilayers is significantly modified by heavy metal and its thickness. This strong dependence of transverse magnetoresistance on heavy metal evidences the generation of thermally induced pure spin current in heavy metal. Our analysis shows that spin Nernst angles of W and Pt have the opposite sign to their spin Hall angles. Moreover, our estimate implies that the magnitude of spin Nernst angle would be comparable to that of spin Hall angle, suggesting an efficient generation of spin current by the spin Nernst effect.
Anisotropic attosecond charge carrier dynamics and layer decoupling in quasi-2D layered SnS2
Authors: Eads Calley N. , Bandak Dmytro , Neupane Mahesh R. , Nordlund Dennis , Monti Oliver L. A. 
Published: November 2017

AbstractStrong quantum confinement effects lead to striking new physics in two-dimensional materials such as graphene or transition metal dichalcogenides. While spectroscopic fingerprints of such quantum confinement have been demonstrated widely, the consequences for carrier dynamics are at present less clear, particularly on ultrafast timescales. This is important for tailoring, probing, and understanding spin and electron dynamics in layered and two-dimensional materials even in cases where the desired bandgap engineering has been achieved. Here we show by means of core–hole clock spectroscopy that SnS2 exhibits spin-dependent attosecond charge delocalization times (τdeloc) for carriers confined within a layer, τdeloc < 400 as, whereas interlayer charge delocalization is dynamically quenched in excess of a factor of 10, τdeloc > 2.7 fs. These layer decoupling dynamics are a direct consequence of strongly anisotropic screening established within attoseconds, and demonstrate that important two-dimensional characteristics are also present in bulk crystals of van der Waals-layered materials, at least on ultrafast timescales.
Thermal crumpling of perforated two-dimensional sheets
Authors: Yllanes David , Bhabesh Sourav S. , Nelson David R. , Bowick Mark J. 
Published: November 2017

AbstractThermalized elastic membranes without distant self-avoidance are believed to undergo a crumpling transition when the microscopic bending stiffness is comparable to kT, the scale of thermal fluctuations. Most potential physical realizations of such membranes have a bending stiffness well in excess of experimentally achievable temperatures and are therefore unlikely ever to access the crumpling regime. We propose a mechanism to tune the onset of the crumpling transition by altering the geometry and topology of the sheet itself. We carry out extensive molecular dynamics simulations of perforated sheets with a dense periodic array of holes and observe that the critical temperature is controlled by the total fraction of removed area, independent of the precise arrangement and size of the individual holes. The critical exponents for the perforated membrane are compatible with those of the standard crumpling transition.
Membrane curvature induced by proximity of anionic phospholipids can initiate endocytosis
Authors: Hirama Takashi , Lu Stella M. , Kay Jason G. , Maekawa Masashi , Kozlov Michael M. , Grinstein Sergio , Fairn Gregory D. 
Published: November 2017

AbstractThe plasma membrane is uniquely enriched in phosphatidylserine (PtdSer). This anionic phospholipid is restricted almost exclusively to the inner leaflet of the plasmalemma. Because of their high density, the headgroups of anionic lipids experience electrostatic repulsion that, being exerted asymmetrically, is predicted to favor membrane curvature. We demonstrate that cholesterol limits this repulsion and tendency to curve. Removal of cholesterol or insertion of excess PtdSer increases the charge density of the inner leaflet, generating foci of enhanced charge and curvature where endophilin and synaptojanin are recruited. From these sites emerge tubules that undergo fragmentation, resulting in marked endocytosis of PtdSer. Shielding or reduction of the surface charge or imposition of outward membrane tension minimized invagination and PtdSer endocytosis. We propose that cholesterol associates with PtdSer to form nanodomains where the headgroups of PtdSer are maintained sufficiently separated to limit spontaneous curvature while sheltering the hydrophobic sterol from the aqueous medium.
Influenza virus genome reaches the plasma membrane via a modified endoplasmic reticulum and Rab11-dependent vesicles
Authors: de Castro Martin Isabel Fernández , Fournier Guillaume , Sachse Martin , Pizarro-Cerda Javier , Risco Cristina , Naffakh Nadia 
Published: November 2017

AbstractTransport of neo-synthesized influenza A virus (IAV) viral ribonucleoproteins (vRNPs) from the nucleus to the plasma membrane involves Rab 11 but the precise mechanism remains poorly understood. We used metal-tagging and immunolabeling to visualize viral proteins and cellular endomembrane markers by electron microscopy of IAV-infected cells. Unexpectedly, we provide evidence that the vRNP components and the Rab11 protein are present at the membrane of a modified, tubulated endoplasmic reticulum (ER) that extends all throughout the cell, and on irregularly coated vesicles (ICVs). Some ICVs are found very close to the ER and to the plasma membrane. ICV formation is observed only in infected cells and requires an active Rab11 GTPase. Against the currently accepted model in which vRNPs are carried onto Rab11-positive recycling endosomes across the cytoplasm, our findings reveal that the endomembrane organelle that is primarily involved in the transport of vRNPs is the ER.
Structural basis for Ragulator functioning as a scaffold in membrane-anchoring of Rag GTPases and mTORC1
Authors: Zhang Tianlong , Wang Rong , Wang Zhijing , Wang Xiangxiang , Wang Fang , Ding Jianping 
Published: November 2017

AbstractAmino acid-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) is mediated by Rag GTPases, which are recruited to the lysosome by the Ragulator complex consisting of p18, MP1, p14, HBXIP and C7orf59; however, the molecular mechanism is elusive. Here, we report the crystal structure of Ragulator, in which p18 wraps around the MP1-p14 and C7orf59-HBXIP heterodimers and the interactions of p18 with MP1, C7orf59, and HBXIP are essential for the assembly of Ragulator. There are two binding sites for the Roadblock domains of Rag GTPases: helix α1 of p18 and the two helices side of MP1-p14. The interaction of Ragulator with Rag GTPases is required for their cellular co-localization and can be competitively inhibited by C17orf59. Collectively, our data indicate that Ragulator functions as a scaffold to recruit Rag GTPases to lysosomal membrane in mTORC1 signaling.
Room temperature magnetization switching in topological insulator-ferromagnet heterostructures by spin-orbit torques
Authors: Wang Yi , Zhu Dapeng , Wu Yang , Yang Yumeng , Yu Jiawei , Ramaswamy Rajagopalan , Mishra Rahul , Shi Shuyuan , Elyasi Mehrdad , Teo Kie-Leong , Wu Yihong , Yang Hyunsoo 
Published: November 2017

AbstractTopological insulators with spin-momentum-locked topological surface states are expected to exhibit a giant spin-orbit torque in the topological insulator/ferromagnet systems. To date, the topological insulator spin-orbit torque-driven magnetization switching is solely reported in a Cr-doped topological insulator at 1.9 K. Here we directly show giant spin-orbit torque-driven magnetization switching in a Bi2Se3/NiFe heterostructure at room temperature captured using a magneto-optic Kerr effect microscope. We identify a large charge-to-spin conversion efficiency of ~1–1.75 in the thin Bi2Se3 films, where the topological surface states are dominant. In addition, we find the current density required for the magnetization switching is extremely low, ~6 × 105 A cm–2, which is one to two orders of magnitude smaller than that with heavy metals. Our demonstration of room temperature magnetization switching of a conventional 3d ferromagnet using Bi2Se3 may lead to potential innovations in topological insulator-based spintronic applications.
A mechanism for FtsZ-independent proliferation in Streptomyces
Authors: Santos-Beneit Fernando , Roberts David M. , Cantlay Stuart , McCormick Joseph R. , Errington Jeff 
Published: November 2017

AbstractThe central player in bacterial cell division, FtsZ, is essential in almost all organisms in which it has been tested, with the most notable exception being Streptomyces. Streptomycetes differ from many bacteria in growing from the cell tip and undergoing branching, similar to filamentous fungi. Here we show that limited cell damage, either mechanical or enzymatic, leads to near complete destruction of mycelial microcolonies of a Streptomyces venezuelae ftsZ mutant. This result is consistent with a lack of ftsZ-dependent cross-walls and may be inconsistent with a recently proposed role for membrane structures in the proliferation of ftsZ mutants in other Streptomyces species. Rare surviving fragments of mycelium, usually around branches, appear to be the preferred sites of resealing. Restoration of growth in hyphal fragments of both wild-type and ftsZ mutant hyphae can occur at multiple sites, via branch-like outgrowths containing DivIVA protein at their tips. Thus, our results highlight branching as a means of FtsZ-independent cell proliferation.