bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global distribution and vertical patterns of a prymnesiophyte–cyanobacteria obligate symbiosis
Authors: Cabello Ana M , Cornejo-Castillo Francisco M , Raho Nicolas , Blasco Dolors , Vidal Montserrat , Audic Stéphane , de Vargas Colomban , Latasa Mikel , Acinas Silvia G , Massana Ramon 
Published: September 2015

Abstract
A marine symbiosis has been recently discovered between prymnesiophyte species and the unicellular diazotrophic cyanobacterium UCYN-A. At least two different UCYN-A phylotypes exist, the clade UCYN-A1 in symbiosis with an uncultured small prymnesiophyte and the clade UCYN-A2 in symbiosis with the larger Braarudosphaera bigelowii. We targeted the prymnesiophyte–UCYN-A1 symbiosis by double CARD-FISH (catalyzed reporter deposition-fluorescence in situ hybridization) and analyzed its abundance in surface samples from the MALASPINA circumnavigation expedition. Our use of a specific probe for the prymnesiophyte partner allowed us to verify that this algal species virtually always carried the UCYN-A symbiont, indicating that the association was also obligate for the host. The prymnesiophyte–UCYN-A1 symbiosis was detected in all ocean basins, displaying a patchy distribution with abundances (up to 500 cells ml−1) that could vary orders of magnitude. Additional vertical profiles taken at the NE Atlantic showed that this symbiosis occupied the upper water column and disappeared towards the Deep Chlorophyll Maximum, where the biomass of the prymnesiophyte assemblage peaked. Moreover, sequences of both prymnesiophyte partners were searched within a large 18S rDNA metabarcoding data set from the Tara-Oceans expedition around the world. This sequence-based analysis supported the patchy distribution of the UCYN-A1 host observed by CARD-FISH and highlighted an unexpected homogeneous distribution (at low relative abundance) of B. bigelowii in the open ocean. Our results demonstrate that partners are always in symbiosis in nature and show contrasted ecological patterns of the two related lineages.
Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival
Authors: Greening Chris , Biswas Ambarish , Carere Carlo R , Jackson Colin J , Taylor Matthew C , Stott Matthew B , Cook Gregory M , Morales Sergio E 
Published: September 2015

Abstract
Recent physiological and ecological studies have challenged the long-held belief that microbial metabolism of molecular hydrogen (H2) is a niche process. To gain a broader insight into the importance of microbial H2 metabolism, we comprehensively surveyed the genomic and metagenomic distribution of hydrogenases, the reversible enzymes that catalyse the oxidation and evolution of H2. The protein sequences of 3286 non-redundant putative hydrogenases were curated from publicly available databases. These metalloenzymes were classified into multiple groups based on (1) amino acid sequence phylogeny, (2) metal-binding motifs, (3) predicted genetic organisation and (4) reported biochemical characteristics. Four groups (22 subgroups) of [NiFe]-hydrogenase, three groups (6 subtypes) of [FeFe]-hydrogenases and a small group of [Fe]-hydrogenases were identified. We predict that this hydrogenase diversity supports H2-based respiration, fermentation and carbon fixation processes in both oxic and anoxic environments, in addition to various H2-sensing, electron-bifurcation and energy-conversion mechanisms. Hydrogenase-encoding genes were identified in 51 bacterial and archaeal phyla, suggesting strong pressure for both vertical and lateral acquisition. Furthermore, hydrogenase genes could be recovered from diverse terrestrial, aquatic and host-associated metagenomes in varying proportions, indicating a broad ecological distribution and utilisation. Oxygen content (pO2) appears to be a central factor driving the phylum- and ecosystem-level distribution of these genes. In addition to compounding evidence that H2 was the first electron donor for life, our analysis suggests that the great diversification of hydrogenases has enabled H2 metabolism to sustain the growth or survival of microorganisms in a wide range of ecosystems to the present day. This work also provides a comprehensive expanded system for classifying hydrogenases and identifies new prospects for investigating H2 metabolism.
Structure and function of natural sulphide-oxidizing microbial mats under dynamic input of light and chemical energy
Authors: Klatt Judith M , Meyer Steffi , Häusler Stefan , Macalady Jennifer L , de Beer Dirk , Polerecky Lubos 
Published: September 2015

Abstract
We studied the interaction between phototrophic and chemolithoautotrophic sulphide-oxidizing microorganisms in natural microbial mats forming in sulphidic streams. The structure of these mats varied between two end-members: one characterized by a layer dominated by large sulphur-oxidizing bacteria (SOB; mostly Beggiatoa-like) on top of a cyanobacterial layer (B/C mats) and the other with an inverted structure (C/B mats). C/B mats formed where the availability of oxygen from the water column was limited (&lt;5 μm). Aerobic chemolithotrophic activity of the SOB depended entirely on oxygen produced locally by cyanobacteria during high light conditions. In contrast, B/C mats formed at locations where oxygen in the water column was comparatively abundant (&gt;45 μm) and continuously present. Here SOB were independent of the photosynthetic activity of cyanobacteria and outcompeted the cyanobacteria in the uppermost layer of the mat where energy sources for both functional groups were concentrated. Outcompetition of photosynthetic microbes in the presence of light was facilitated by the decoupling of aerobic chemolithotrophy and oxygenic phototrophy. Remarkably, the B/C mats conserved much less energy than the C/B mats, although similar amounts of light and chemical energy were available. Thus ecosystems do not necessarily develop towards optimal energy usage. Our data suggest that, when two independent sources of energy are available, the structure and activity of microbial communities is primarily determined by the continuous rather than the intermittent energy source, even if the time-integrated energy flux of the intermittent energy source is greater.
Antibodies to a conformational epitope on gp41 neutralize HIV-1 by destabilizing the Env spike
Authors: Lee Jeong Hyun , Leaman Daniel P. , Kim Arthur S. , Torrents de la Peña Alba , Sliepen Kwinten , Yasmeen Anila , Derking Ronald , Ramos Alejandra , de Taeye Steven W. , Ozorowski Gabriel , Klein Florian , Burton Dennis R. , Nussenzweig Michel C. , Poignard Pascal , Moore John P. , Klasse Per Johan , Sanders Rogier W. , Zwick Michael B. , Wilson Ian A. , Ward Andrew B. 
Published: September 2015

AbstractThe recent identification of three broadly neutralizing antibodies (bnAbs) against gp120–gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. By using biochemical, biophysical and computational methods, we map the previously unknown trimer epitopes of two related antibodies, 3BC315 and 3BC176. A cryo-EM reconstruction of a soluble Env trimer bound to 3BC315 Fab at 9.3 Å resolution reveals that the antibody binds between two gp41 protomers, and neutralizes the virus by accelerating trimer decay. In contrast, bnAb 35O22 binding to a partially overlapping quaternary epitope at the gp120–gp41 interface does not induce decay. A conserved gp41-proximal glycan at N88 was also shown to play a role in the binding kinetics of 3BC176 and 3BC315. Finally, our data suggest that the dynamic structure of the Env trimer influences exposure of bnAb epitopes.
Sub-10-fs population inversion in N2+ in air lasing through multiple state coupling
Authors: Xu Huailiang , Lötstedt Erik , Iwasaki Atsushi , Yamanouchi Kaoru 
Published: September 2015

AbstractLaser filamentation generated when intense laser pulses propagate in air has been an attractive phenomenon having a variety of potential applications such as detection and spectroscopy of gases at far distant places. It was discovered recently that the filamentation in air induces ‘lasing’, showing that electronically excited N2+ is population-inverted, exhibiting marked contrast to the common understanding that molecular ions generated by intense laser fields are prepared mostly in their electronic ground states. Here, to clarify the mechanism of the population inversion, we adopt few-cycle laser pulses, and experimentally demonstrate that the lasing at 391 nm occurs instantaneously after N2+ is produced. Numerical simulations clarify that the population inversion is realized by the post-ionization couplings among the lowest three electronic states of N2+. Our results shed light on the controversy over the mechanism of the air lasing, and show that this post-ionization coupling can be a general mechanism of the atmospheric lasing.
Femtosecond structural transformation of phase-change materials far from equilibrium monitored by coherent phonons
Authors: Hase Muneaki , Fons Paul , Mitrofanov Kirill , Kolobov Alexander V. , Tominaga Junji 
Published: September 2015

AbstractMulticomponent chalcogenides, such as quasi-binary GeTe–Sb2Te3 alloys, are widely used in optical data storage media in the form of rewritable optical discs. Ge2Sb2Te5 (GST) in particular has proven to be one of the best-performing materials, whose reliability allows more than 106 write–erase cycles. Despite these industrial applications, the fundamental kinetics of rapid phase change in GST remain controversial, and active debate continues over the ultimate speed limit. Here we explore ultrafast structural transformation in a photoexcited GST superlattice, where GeTe and Sb2Te3 are spatially separated, using coherent phonon spectroscopy with pump–pump–probe sequences. By analysing the coherent phonon spectra in different time regions, complex structural dynamics upon excitation are observed in the GST superlattice (but not in GST alloys), which can be described as the mixing of Ge sites from two different coordination environments. Our results suggest the possible applicability of GST superlattices for ultrafast switching devices.
Swarming bacteria migrate by Lévy Walk
Authors: Ariel Gil , Rabani Amit , Benisty Sivan , Partridge Jonathan D. , Harshey Rasika M. , Be'er Avraham 
Published: September 2015

AbstractIndividual swimming bacteria are known to bias their random trajectories in search of food and to optimize survival. The motion of bacteria within a swarm, wherein they migrate as a collective group over a solid surface, is fundamentally different as typical bacterial swarms show large-scale swirling and streaming motions involving millions to billions of cells. Here by tracking trajectories of fluorescently labelled individuals within such dense swarms, we find that the bacteria are performing super-diffusion, consistent with Lévy walks. Lévy walks are characterized by trajectories that have straight stretches for extended lengths whose variance is infinite. The evidence of super-diffusion consistent with Lévy walks in bacteria suggests that this strategy may have evolved considerably earlier than previously thought.
Metal oxide-resistive memory using graphene-edge electrodes
Authors: Lee Seunghyun , Sohn Joon , Jiang Zizhen , Chen Hong-Yu , Philip Wong H.-S. 
Published: September 2015

AbstractThe emerging paradigm of ‘abundant-data’ computing requires real-time analytics on enormous quantities of data collected by a mushrooming network of sensors. Todays computing technology, however, cannot scale to satisfy such big data applications with the required throughput and energy efficiency. The next technology frontier will be monolithically integrated chips with three-dimensionally interleaved memory and logic for unprecedented data bandwidth with reduced energy consumption. In this work, we exploit the atomically thin nature of the graphene edge to assemble a resistive memory (∼3 Å thick) stacked in a vertical three-dimensional structure. We report some of the lowest power and energy consumption among the emerging non-volatile memories due to an extremely thin electrode with unique properties, low programming voltages, and low current. Circuit analysis of the three-dimensional architecture using experimentally measured device properties show higher storage potential for graphene devices compared that of metal based devices.
CTRP6 is an endogenous complement regulator that can effectively treat induced arthritis
Authors: Murayama Masanori A. , Kakuta Shigeru , Inoue Asuka , Umeda Naoto , Yonezawa Tomo , Maruhashi Takumi , Tateishi Koichiro , Ishigame Harumichi , Yabe Rikio , Ikeda Satoshi , Seno Akimasa , Chi Hsi-Hua , Hashiguchi Yuriko , Kurata Riho , Tada Takuya , Kubo Sachiko , Sato Nozomi , Liu Yang , Hattori Masahira , Saijo Shinobu , Matsushita Misao , Fujita Teizo , Sumida Takayuki , Iwakura Yoichiro 
Published: September 2015

AbstractThe complement system is important for the host defence against infection as well as for the development of inflammatory diseases. Here we show that C1q/TNF-related protein 6 (CTRP6; gene symbol C1qtnf6) expression is elevated in mouse rheumatoid arthritis (RA) models. C1qtnf6−/− mice are highly susceptible to induced arthritis due to enhanced complement activation, whereas C1qtnf6-transgenic mice are refractory. The Arthus reaction and the development of experimental autoimmune encephalomyelitis are also enhanced in C1qtnf6−/− mice and C1qtnf6−/− embryos are semi-lethal. We find that CTRP6 specifically suppresses the alternative pathway of the complement system by competing with factor B for C3(H2O) binding. Furthermore, treatment of arthritis-induced mice with intra-articular injection of recombinant human CTRP6 cures the arthritis. CTRP6 is expressed in human synoviocytes, and CTRP6 levels are increased in RA patients. These results indicate that CTRP6 is an endogenous complement regulator and could be used for the treatment of complement-mediated diseases.
EZH2-mediated loss of miR-622 determines CXCR4 activation in hepatocellular carcinoma
Authors: Liu Haiou , Liu Yidong , Liu Weisi , Zhang Weijuan , Xu Jiejie 
Published: September 2015

AbstractThe CXC chemokine receptor 4 (CXCR4) exerts a variety of functions at different steps of hepatocellular carcinoma (HCC) progression. The molecular mechanisms and therapeutic value of CXCR4 in the development of HCC remain undefined. Here we show that aberrant CXCR4 overexpression is associated with poor prognosis and aggressive characteristics of HCC. Suppression of CXCR4 activity via CXCR4 knockdown, AMD3100 or neutralizing antibody administration inhibits hepatoma cell tumorigenesis in vitro and in vivo. CXCR4 overexpression displays the opposite effects. Using Mir library screening we identify miR-622 as a regulator of CXCR4. Further studies show that miR-622 directly target the 3′ untranslated region of CXCR4 and is transcriptionally repressed by EZH2-induced H3K27 trimethylation and promoter methylation. EZH2/miR-622 promotes tumorigenesis through CXCR4. EZH2-mediated loss of miR-622 is found to correlate with CXCR4 overexpression and unfavourable prognosis in HCC patients. This study establishes EZH2/miR-622/CXCR4 as a potential adverse prognostic factor and therapeutic target for HCC patients.
‘Purpose in Life’ as a psychosocial resource in healthy aging: an examination of cortisol baseline levels and response to the Trier Social Stress Test
Authors: Fogelman Nia , Canli Turhan 
Published: September 2015

Abstract‘Purpose in Life’ (Purpose) is associated with healthy aging, but it is unknown whether this association is causal. Conceptualizing Purpose as a form of psychosocial resource, one mechanism promoting health could be the regulation of stress hormones. To test this hypothesis, we recruited 44 older community-dwelling adults to examine the association between Purpose and cortisol at baseline, in response to, and recovery from, an acute social laboratory stressor. Purpose did not predict cortisol baseline or reactivity, but did predict a faster recovery to pre-stress baseline levels. The health benefits of Purpose in aging may therefore reflect the combination of a normal stress response, which serves an adaptive benefit of allostasis, with an accelerated stress recovery, which reduces the burden of allostatic load. This model should be tested in future studies using larger samples, multiple related constructs, and longitudinal designs that include participants’ health records.
High-throughput matrix screening identifies synergistic and antagonistic antimalarial drug combinations
Authors: Mott Bryan T. , Eastman Richard T. , Guha Rajarshi , Sherlach Katy S. , Siriwardana Amila , Shinn Paul , McKnight Crystal , Michael Sam , Lacerda-Queiroz Norinne , Patel Paresma R. , Khine Pwint , Sun Hongmao , Kasbekar Monica , Aghdam Nima , Fontaine Shaun D. , Liu Dongbo , Mierzwa Tim , Mathews-Griner Lesley A. , Ferrer Marc , Renslo Adam R. , Inglese James , Yuan Jing , Roepe Paul D. , Su Xin-zhuan , Thomas Craig J. 
Published: September 2015

AbstractDrug resistance in Plasmodium parasites is a constant threat. Novel therapeutics, especially new drug combinations, must be identified at a faster rate. In response to the urgent need for new antimalarial drug combinations we screened a large collection of approved and investigational drugs, tested 13,910 drug pairs and identified many promising antimalarial drug combinations. The activity of known antimalarial drug regimens was confirmed and a myriad of new classes of positively interacting drug pairings were discovered. Network and clustering analyses reinforced established mechanistic relationships for known drug combinations and identified several novel mechanistic hypotheses. From eleven screens comprising >4,600 combinations per parasite strain (including duplicates) we further investigated interactions between approved antimalarials, calcium homeostasis modulators and inhibitors of phosphatidylinositide 3-kinases (PI3K) and the mammalian target of rapamycin (mTOR). These studies highlight important targets and pathways and provide promising leads for clinically actionable antimalarial therapy.
The peptidylarginine deiminase gene is a conserved feature of Porphyromonas gingivalis
Authors: Gabarrini Giorgio , de Smit Menke , Westra Johanna , Brouwer Elisabeth , Vissink Arjan , Zhou Kai , A. Rossen John W. , Stobernack Tim , van Dijl Jan Maarten , Jan van Winkelhoff Arie 
Published: September 2015

AbstractPeriodontitis is an infective process that ultimately leads to destruction of the soft and hard tissues that support the teeth (the periodontium). Periodontitis has been proposed as a candidate risk factor for development of the autoimmune disease rheumatoid arthritis (RA). Porphyromonas gingivalis, a major periodontal pathogen, is the only known prokaryote expressing a peptidyl arginine deiminase (PAD) enzyme necessary for protein citrullination. Antibodies to citrullinated proteins (anti-citrullinated protein antibodies, ACPA) are highly specific for RA and precede disease onset. Objective of this study was to assess P. gingivalis PAD (PPAD) gene expression and citrullination patterns in representative samples of P. gingivalis clinical isolates derived from periodontitis patients with and without RA and in related microbes of the Porphyromonas genus. Our findings indicate that PPAD is omnipresent in P. gingivalis, but absent in related species. No significant differences were found in the composition and expression of the PPAD gene of P. gingivalis regardless of the presence of RA or periodontal disease phenotypes. From this study it can be concluded that if P. gingivalis plays a role in RA, it is unlikely to originate from a variation in PPAD gene expression.
In situ biomarker discovery and label-free molecular histopathological diagnosis of lung cancer by ambient mass spectrometry imaging
Authors: Li Tiegang , He Jiuming , Mao Xinxin , Bi Ying , Luo Zhigang , Guo Chengan , Tang Fei , Xu Xin , Wang Xiaohao , Wang Mingrong , Chen Jie , Abliz Zeper 
Published: September 2015

AbstractSensitive and spatial exploration of the metabolism of tumors at the metabolome level is highly challenging. In this study, we developed an in situ metabolomics method based on ambient mass spectrometry imaging using air flow-assisted desorption electrospray ionization (AFADESI), which can spatially explore the alteration of global metabolites in tissues with high sensitivity. Using this method, we discovered potential histopathological diagnosis biomarkers (including lipids, amino acids, choline, peptides and carnitine) from 52 postoperative lung cancer tissue samples and then subsequently used these biomarkers to generate images for rapid and label-free histopathological diagnosis. These biomarkers were validated with a sensitivity and a specificity of 93.5% and 100%, respectively. Moreover, a single imaging analysis of a cryosection that visualized all these biomarkers, taking tens of minutes, revealed the type and subtype of the cancer. This method could potentially be used as a molecular pathological tool for rapid clinical lung cancer diagnosis and immediate image-guided surgery.
Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas
Authors: Qu Yanhua , Tian Shilin , Han Naijian , Zhao Hongwei , Gao Bin , Fu Jun , Cheng Yalin , Song Gang , Ericson Per G. P. , Zhang Yong E. , Wang Dawei , Quan Qing , Jiang Zhi , Li Ruiqiang , Lei Fumin 
Published: September 2015

AbstractSpecies that undertake altitudinal migrations are exposed to a considerable seasonal variation in oxygen levels and temperature. How they cope with this was studied in a population of great tit (Parus major) that breeds at high elevations and winters at lower elevations in the eastern Himalayas. Comparison of population genomics of high altitudinal great tits and those living in lowlands revealed an accelerated genetic selection for carbohydrate energy metabolism (amino sugar, nucleotide sugar metabolism and insulin signaling pathways) and hypoxia response (PI3K-akt, mTOR and MAPK signaling pathways) in the high altitudinal population. The PI3K-akt, mTOR and MAPK pathways modulate the hypoxia-inducible factors,HIF-1αandVEGFprotein expression thus indirectly regulate hypoxia induced angiogenesis, erythropoiesis and vasodilatation. The strategies observed in high altitudinal great tits differ from those described in a closely related species on the Tibetan Plateau, the sedentary ground tit (Parus humilis). This species has enhanced selection in lipid-specific metabolic pathways and hypoxia-inducible factor pathway (HIF-1). Comparative population genomics also revealed selection for larger body size in high altitudinal great tits.
Enhanced Reduction of Graphene Oxide on Recyclable Cu Foils to Fabricate Graphene Films with Superior Thermal Conductivity
Authors: Huang Sheng-Yun , Zhao Bo , Zhang Kai , Yuen Matthew M. F. , Xu Jian-Bin , Fu Xian-Zhu , Sun Rong , Wong Ching-Ping 
Published: September 2015

AbstractLarge-area freestanding graphene films are facilely fabricated by reducing graphene oxide films on recyclable Cu foils in H2-containing atmosphere at high temperature. Cu might act as efficient catalysts for considerably improved reduction of graphene oxide according to the SEM, EDS, XRD, XPS, Raman and TGA results. Comparing to the graphene films with ~30 μm thickness reduced without Cu substrate at 900 °C, the thermal conductivity and electrical conductivity of graphene films reduced on Cu foils are enhanced about 140% to 902 Wm−1K−1 and 3.6 × 104 S/m, respectively. Moreover, the graphene films demonstrate superior thermal conductivity of ~1219 Wm−1K−1 as decreasing the thickness of films to ~10 μm. The graphene films also exhibit excellent mechanical properties and flexibility.