bluuebunny/crossref_metadata_2025_split huggingface dataset:
A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis
Authors: Savary Romain , Masclaux Frédéric G , Wyss Tania , Droh Germain , Cruz Corella Joaquim , Machado Ana Paula , Morton Joseph B , Sanders Ian R 
Published: October 2017

Abstract
Arbuscular mycorrhizal fungi (AMF; phylum Gomeromycota) associate with plants forming one of the most successful microbe–plant associations. The fungi promote plant diversity and have a potentially important role in global agriculture. Plant growth depends on both inter- and intra-specific variation in AMF. It was recently reported that an unusually large number of AMF taxa have an intercontinental distribution, suggesting long-distance gene flow for many AMF species, facilitated by either long-distance natural dispersal mechanisms or human-assisted dispersal. However, the intercontinental distribution of AMF species has been questioned because the use of very low-resolution markers may be unsuitable to detect genetic differences among geographically separated AMF, as seen with some other fungi. This has been untestable because of the lack of population genomic data, with high resolution, for any AMF taxa. Here we use phylogenetics and population genomics to test for intra-specific variation in Rhizophagus irregularis, an AMF species for which genome sequence information already exists. We used ddRAD sequencing to obtain thousands of markers distributed across the genomes of 81 R. irregularis isolates and related species. Based on 6 888 variable positions, we observed significant genetic divergence into four main genetic groups within R. irregularis, highlighting that previous studies have not captured underlying genetic variation. Despite considerable genetic divergence, surprisingly, the variation could not be explained by geographical origin, thus also supporting the hypothesis for at least one AMF species of widely dispersed AMF genotypes at an intercontinental scale. Such information is crucial for understanding AMF ecology, and how these fungi can be used in an environmentally safe way in distant locations.
Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria
Authors: Neuenschwander Stefan M , Ghai Rohit , Pernthaler Jakob , Salcher Michaela M 
Published: October 2017

Abstract
Actinobacteria of the acI lineage are the most abundant microbes in freshwater systems, but there are so far no pure living cultures of these organisms, possibly because of metabolic dependencies on other microbes. This, in turn, has hampered an in-depth assessment of the genomic basis for their success in the environment. Here we present genomes from 16 axenic cultures of acI Actinobacteria. The isolates were not only of minute cell size, but also among the most streamlined free-living microbes, with extremely small genome sizes (1.2–1.4 Mbp) and low genomic GC content. Genome reduction in these bacteria might have led to auxotrophy for various vitamins, amino acids and reduced sulphur sources, thus creating dependencies to co-occurring organisms (the ‘Black Queen’ hypothesis). Genome analyses, moreover, revealed a surprising degree of inter- and intraspecific diversity in metabolic pathways, especially of carbohydrate transport and metabolism, and mainly encoded in genomic islands. The striking genotype microdiversification of acI Actinobacteria might explain their global success in highly dynamic freshwater environments with complex seasonal patterns of allochthonous and autochthonous carbon sources. We propose a new order within Actinobacteria (‘Candidatus Nanopelagicales’) with two new genera (‘Candidatus Nanopelagicus’ and ‘Candidatus Planktophila’) and nine new species.
Temporal dynamics of uncultured viruses: a new dimension in viral diversity
Authors: Arkhipova Ksenia , Skvortsov Timofey , Quinn John P , McGrath John W , Allen Christopher C R , Dutilh Bas E , McElarney Yvonne , Kulakov Leonid A 
Published: October 2017

Abstract
Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other. Temporal analysis of 732 viral genus-level clusters demonstrated that one-fifth were undetectable at specific periods of the year. Based on host predictions for a subset of reconstructed viral genomes, we for the first time reveal three distinct patterns of host–pathogen dynamics, where the viruses may peak before, during or after the peak in their host’s abundance, providing new possibilities for modelling of their interactions. Time series metagenomics opens up a new dimension in viral profiling, which is essential to understand the full scale of viral diversity and evolution, and the ecological roles of these important factors in the global ecosystem.
Influence of resistance breeding in common bean on rhizosphere microbiome composition and function
Authors: Mendes Lucas William , Raaijmakers Jos M , de Hollander Mattias , Mendes Rodrigo , Tsai Siu Mui 
Published: October 2017

AbstractThe rhizosphere microbiome has a key role in plant growth and health, providing a first line of defense against root infections by soil-borne pathogens. Here, we investigated the composition and metabolic potential of the rhizobacterial community of different common bean (Phaseolus vulgaris) cultivars with variable levels of resistance to the fungal root pathogen Fusarium oxysporum (Fox). For the different bean cultivars grown in two soils with contrasting physicochemical properties and microbial diversity, rhizobacterial abundance was positively correlated with Fox resistance. Pseudomonadaceae, bacillaceae, solibacteraceae and cytophagaceae were more abundant in the rhizosphere of the Fox-resistant cultivar. Network analyses showed a modular topology of the rhizosphere microbiome of the Fox-resistant cultivar, suggesting a more complex and highly connected bacterial community than in the rhizosphere of the Fox-susceptible cultivar. Metagenome analyses further revealed that specific functional traits such as protein secretion systems and biosynthesis genes of antifungal phenazines and rhamnolipids were more abundant in the rhizobacterial community of the Fox-resistant cultivar. Our findings suggest that breeding for Fox resistance in common bean may have co-selected for other unknown plant traits that support a higher abundance of specific beneficial bacterial families in the rhizosphere with functional traits that reinforce the first line of defense.
Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline
Authors: Denman Sandra , Doonan James , Ransom-Jones Emma , Broberg Martin , Plummer Sarah , Kirk Susan , Scarlett Kelly , Griffiths Andrew R , Kaczmarek Maciej , Forster Jack , Peace Andrew , Golyshin Peter N , Hassard Francis , Brown Nathan , Kenny John G , McDonald James E 
Published: October 2017

Abstract
Decline-diseases are complex and becoming increasingly problematic to tree health globally. Acute Oak Decline (AOD) is characterized by necrotic stem lesions and galleries of the bark-boring beetle, Agrilus biguttatus, and represents a serious threat to oak. Although multiple novel bacterial species and Agrilus galleries are associated with AOD lesions, the causative agent(s) are unknown. The AOD pathosystem therefore provides an ideal model for a systems-based research approach to address our hypothesis that AOD lesions are caused by a polymicrobial complex. Here we show that three bacterial species, Brenneria goodwinii, Gibbsiella quercinecans and Rahnella victoriana, are consistently abundant in the lesion microbiome and possess virulence genes used by canonical phytopathogens that are expressed in AOD lesions. Individual and polyspecies inoculations on oak logs and trees demonstrated that B. goodwinii and G. quercinecans cause tissue necrosis and, in combination with A. biguttatus, produce the diagnostic symptoms of AOD. We have proved a polybacterial cause of AOD lesions, providing new insights into polymicrobial interactions and tree disease. This work presents a novel conceptual and methodological template for adapting Koch’s postulates to address the role of microbial communities in disease.
Helicity dependent photocurrent in electrically gated (Bi1−x
Sb
x
)2Te3 thin films
Authors: Pan Yu , Wang Qing-Ze , Yeats Andrew L. , Pillsbury Timothy , Flanagan Thomas C. , Richardella Anthony , Zhang Haijun , Awschalom David D. , Liu Chao-Xing , Samarth Nitin 
Published: October 2017

AbstractCircularly polarized photons are known to generate a directional helicity-dependent photocurrent in three-dimensional topological insulators at room temperature. Surprisingly, the phenomenon is readily observed at photon energies that excite electrons to states far above the spin-momentum locked Dirac cone and the underlying mechanism for the helicity-dependent photocurrent is still not understood. Here we show a comprehensive study of the helicity-dependent photocurrent in (Bi1−x
Sb
x
)2Te3 thin films as a function of the incidence angle of the optical excitation, its wavelength and the gate-tuned chemical potential. Our observations allow us to unambiguously identify the circular photo-galvanic effect as the dominant mechanism for the helicity-dependent photocurrent. Additionally, we use an analytical model to relate the directional nature of the photocurrent to asymmetric optical transitions between the topological surface states and bulk bands. The insights we obtain are important for engineering opto-spintronic devices that rely on optical steering of spin and charge currents.
Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates
Authors: Czekster Clarissa M. , Ludewig Hannes , McMahon Stephen A. , Naismith James H. 
Published: October 2017

AbstractPeptide macrocycles are promising therapeutic molecules because they are protease resistant, structurally rigid, membrane permeable, and capable of modulating protein–protein interactions. Here, we report the characterization of the dual function macrocyclase-peptidase enzyme involved in the biosynthesis of the highly toxic amanitin toxin family of macrocycles. The enzyme first removes 10 residues from the N-terminus of a 35-residue substrate. Conformational trapping of the 25 amino-acid peptide forces the enzyme to release this intermediate rather than proceed to macrocyclization. The enzyme rebinds the 25 amino-acid peptide in a different conformation and catalyzes macrocyclization of the N-terminal eight residues. Structures of the enzyme bound to both substrates and biophysical analysis characterize the different binding modes rationalizing the mechanism. Using these insights simpler substrates with only five C-terminal residues were designed, allowing the enzyme to be more effectively exploited in biotechnology.
Genetic accommodation via modified endocrine signalling explains phenotypic divergence among spadefoot toad species
Authors: Kulkarni Saurabh S. , Denver Robert J. , Gomez-Mestre Ivan , Buchholz Daniel R. 
Published: October 2017

AbstractPhenotypic differences among species may evolve through genetic accommodation, but mechanisms accounting for this process are poorly understood. Here we compare hormonal variation underlying differences in the timing of metamorphosis among three spadefoot toads with different larval periods and responsiveness to pond drying. We find that, in response to pond drying, Pelobates cultripes and Spea multiplicata accelerate metamorphosis, increase standard metabolic rate (SMR), and elevate whole-body content of thyroid hormone (the primary morphogen controlling metamorphosis) and corticosterone (a stress hormone acting synergistically with thyroid hormone to accelerate metamorphosis). In contrast, Scaphiopus couchii has the shortest larval period, highest whole-body thyroid hormone and corticosterone content, and highest SMR, and these trait values are least affected by pond drying among the three species. Our findings support that the atypically rapid and canalized development of S. couchii evolved by genetic accommodation of endocrine pathways controlling metamorphosis, showing how phenotypic plasticity within species may evolve into trait variation among species.
A parsimonious neutral model suggests Neanderthal replacement was determined by migration and random species drift
Authors: Kolodny Oren , Feldman Marcus W. 
Published: October 2017

AbstractMost hypotheses in the heated debate about the Neanderthals’ replacement by modern humans highlight the role of environmental pressures or attribute the Neanderthals’ demise to competition with modern humans, who occupied the same ecological niche. The latter assume that modern humans benefited from some selective advantage over Neanderthals, which led to the their extinction. Here we show that a scenario of migration and selectively neutral species drift predicts the Neanderthals’ replacement. Our model offers a parsimonious alternative to those that invoke external factors or selective advantage, and represents a null hypothesis for assessing such alternatives. For a wide range of parameters, this hypothesis cannot be rejected. Moreover, we suggest that although selection and environmental factors may or may not have played a role in the inter-species dynamics of Neanderthals and modern humans, the eventual replacement of the Neanderthals was determined by the repeated migration of modern humans from Africa into Eurasia.
MiR-31 promotes mammary stem cell expansion and breast tumorigenesis by suppressing Wnt signaling antagonists
Authors: Lv Cong , Li Fengyin , Li Xiang , Tian Yuhua , Zhang Yue , Sheng Xiaole , Song Yongli , Meng Qingyong , Yuan Shukai , Luan Liming , Andl Thomas , Feng Xu , Jiao Baowei , Xu Mingang , Plikus Maksim V. , Dai Xing , Lengner Christopher , Cui Wei , Ren Fazheng , Shuai Jianwei , Millar Sarah E. , Yu Zhengquan 
Published: October 2017

AbstractMicroRNA-mediated post-transcriptional regulation plays key roles in stem cell self-renewal and tumorigenesis. However, the in vivo functions of specific microRNAs in controlling mammary stem cell (MaSC) activity and breast cancer formation remain poorly understood. Here we show that miR-31 is highly expressed in MaSC-enriched mammary basal cell population and in mammary tumors, and is regulated by NF-κB signaling. We demonstrate that miR-31 promotes mammary epithelial proliferation and MaSC expansion at the expense of differentiation in vivo. Loss of miR-31 compromises mammary tumor growth, reduces the number of cancer stem cells, as well as decreases tumor-initiating ability and metastasis to the lung, supporting its pro-oncogenic function. MiR-31 modulates multiple signaling pathways, including Prlr/Stat5, TGFβ and Wnt/β-catenin. Particularly, it activates Wnt/β-catenin signaling by directly targeting Wnt antagonists, including Dkk1. Importantly, Dkk1 overexpression partially rescues miR31-induced mammary defects. Together, these findings identify miR-31 as the key regulator of MaSC activity and breast tumorigenesis.
Preclinical imaging methods for assessing the safety and efficacy of regenerative medicine therapies
Authors: Scarfe Lauren , Brillant Nathalie , Kumar J. Dinesh , Ali Noura , Alrumayh Ahmed , Amali Mohammed , Barbellion Stephane , Jones Vendula , Niemeijer Marije , Potdevin Sophie , Roussignol Gautier , Vaganov Anatoly , Barbaric Ivana , Barrow Michael , Burton Neal C. , Connell John , Dazzi Francesco , Edsbagge Josefina , French Neil S. , Holder Julie , Hutchinson Claire , Jones David R. , Kalber Tammy , Lovatt Cerys , Lythgoe Mark F. , Patel Sara , Patrick P. Stephen , Piner Jacqueline , Reinhardt Jens , Ricci Emanuelle , Sidaway James , Stacey Glyn N. , Starkey Lewis Philip J. , Sullivan Gareth , Taylor Arthur , Wilm Bettina , Poptani Harish , Murray Patricia , Goldring Chris E. P. , Park B. Kevin 
Published: October 2017

AbstractRegenerative medicine therapies hold enormous potential for a variety of currently incurable conditions with high unmet clinical need. Most progress in this field to date has been achieved with cell-based regenerative medicine therapies, with over a thousand clinical trials performed up to 2015. However, lack of adequate safety and efficacy data is currently limiting wider uptake of these therapies. To facilitate clinical translation, non-invasive in vivo imaging technologies that enable careful evaluation and characterisation of the administered cells and their effects on host tissues are critically required to evaluate their safety and efficacy in relevant preclinical models. This article reviews the most common imaging technologies available and how they can be applied to regenerative medicine research. We cover details of how each technology works, which cell labels are most appropriate for different applications, and the value of multi-modal imaging approaches to gain a comprehensive understanding of the responses to cell therapy in vivo.
MAGT1-mediated disturbance of Mg2+ homeostasis lead to exhausted of HBV-infected NK and CD8+ T cells
Authors: Diao Bo , Huang Xiaoyong , Guo Shen , Yang Chengying , Liu Guosong , Chen Yongwen , Wu Yuzhang 
Published: October 2017

AbstractThe magnesium transporter 1 (MAGT1) is a critical regulator of basal intracellular free magnesium ([Mg2+]i) levels. It has been shown that MAGT1 was involved in the disorder in Mg2+ homeostasis after Epstein-Barr virus (EBV) infection. Here, we identified the effects of MAGT1-mediated disturbance of Mg2+ homeostasis on chronic hepatitis B virus (HBV)-infected natural killer (NK) and CD8+ T cells. The expression of MAGT1 was gradually decreased with the increase of infected time in CD8+ T cells, but not with that in NK cells, of the patients. Decreased level of intracellular free Mg2+ ([Mg2+]i) leads to defective expression of programmed cell death 1 (PD-1) and the NK activating receptor (NKG2D) in NK and CD8+ T cells. Our data illustrate that [Mg2+]i plays a key role in control of HBV infection.
Carbon nanowalls as a platform for biological SERS studies
Authors: Dyakonov Pavel , Mironovich Kirill , Svyakhovskiy Sergey , Voloshina Olga , Dagesyan Sarkis , Panchishin Andrey , Suetin Nikolay , Bagratashvili Victor , Timashev Petr , Shirshin Evgeny , Evlashin Stanislav 
Published: October 2017

AbstractHerein we report about developing new type of Surface Enhanced Raman Scattering (SERS) substrates based on Au-decorated carbon nanowalls. The designed substrates possess high specific surface area and high sensitivity. Chemical stability of Au perfectly blends with electrical properties and high value of specific surface area of carbon nanowalls. Created structures were applied to detect signals of a typical molecule used for SERS substrates testing, rhodamine 6G, which exhibits electronic absorption in the visible area of spectrum, and biomacromolecules such as tryptophan, guanine, bovine serum albumin and keratin hydrolysates, whose electronic absorption is in the ultraviolet region of spectrum and lies far from the Au plasmonic resonance. The obtained signals for these compounds suggest that the developed substrate is a prominent platform for the detection of biological macromolecules. The properties of the substrate, including its morphology and Au film thickness, as well as the analyte deposition method, were optimized to achieve the optimum Raman signal enhancement. Electric field distribution in the designed structures was calculated to describe the observed dependence of SERS activity on the substrate morphology.
Biochemistry and adaptive colouration of an exceptionally preserved juvenile fossil sea turtle
Authors: Lindgren Johan , Kuriyama Takeo , Madsen Henrik , Sjövall Peter , Zheng Wenxia , Uvdal Per , Engdahl Anders , Moyer Alison E. , Gren Johan A. , Kamezaki Naoki , Ueno Shintaro , Schweitzer Mary H. 
Published: October 2017

AbstractThe holotype (MHM-K2) of the Eocene cheloniineTasbacka danicais arguably one of the best preserved juvenile fossil sea turtles on record. Notwithstanding compactional flattening, the specimen is virtually intact, comprising a fully articulated skeleton exposed in dorsal view. MHM-K2 also preserves, with great fidelity, soft tissue traces visible as a sharply delineated carbon film around the bones and marginal scutes along the edge of the carapace. Here we show that the extraordinary preservation of the type ofT.danicagoes beyond gross morphology to include ultrastructural details and labile molecular components of the once-living animal. Haemoglobin-derived compounds, eumelanic pigments and proteinaceous materials retaining the immunological characteristics of sauropsid-specific β-keratin and tropomyosin were detected in tissues containing remnant melanosomes and decayed keratin plates. The preserved organics represent condensed remains of the cornified epidermis and, likely also, deeper anatomical features, and provide direct chemical evidence that adaptive melanism – a biological means used by extant sea turtle hatchlings to elevate metabolic and growth rates – had evolved 54 million years ago.
The years of life lost on cardiovascular disease attributable to ambient temperature in China
Authors: Luan Guijie , Yin Peng , Li Tiantian , Wang Lijun , Zhou Maigeng 
Published: October 2017

AbstractFew studies have examined the association between ambient temperature and years of life lost (YLL). We aim to explore the burden of cardiovascular disease attributed to non-optimum temperature in China. YLL provides a complementary measure for examining the burden of disease due to ambient temperature. Non-optimal temperature leads to the increase of YLL. The mortality of fourteen cities in China during 2008–2013 was included in this study. We used the Distributed Lag Non-linear Model (DLNM) to estimate the association between daily mean temperature and YLL, controlling for long term trends, day of the week, seasonality and relative humidity. The daily YLL varied from 807 in Changchun to 2751 in Chengdu, with males higher than females. Extreme high and low temperatures were associated with higher YLL. The attributable fraction (AF) to cold effect is from 2.67 (95%CI: −1.63, 6.70) to 8.55 (95%CI: 5.05, 11.90), while the AF to heat effect is from 0.16 (95%CI: 0.06, 0.26) to 2.29 (95%CI: 1.29, 3.19). Cold effect was significantly higher than heat effect on cardiovascular disease in both men and women and for different age groups.