bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activation of hypoxia-inducible factor 1 attenuates periapical inflammation and bone loss
Authors: Hirai Kimito , Furusho Hisako , Hirota Kiichi , Sasaki Hajime 
Published: April 2018

AbstractHypoxia (low oxygen level) is an important feature during infections and affects the host defence mechanisms. The host has evolved specific responses to address hypoxia, which are strongly dependent on the activation of hypoxia-inducible factor 1 (HIF-1). Hypoxia interferes degradation of HIF-1 alpha subunit (HIF-1α), leading to stabilisation of HIF-1α, heterodimerization with HIF-1 beta subunit (HIF-1β) and subsequent activation of HIF-1 pathway. Apical periodontitis (periapical lesion) is a consequence of endodontic infection and ultimately results in destruction of tooth-supporting tissue, including alveolar bone. Thus far, the role of HIF-1 in periapical lesions has not been systematically examined. In the present study, we determined the role of HIF-1 in a well-characterised mouse periapical lesion model using two HIF-1α-activating strategies, dimethyloxalylglycine (DMOG) and adenovirus-induced constitutively active HIF-1α (CA-HIF1A). Both DMOG and CA-HIF1A attenuated periapical inflammation and tissue destruction. The attenuation in vivo was associated with downregulation of nuclear factor-κappa B (NF-κB) and osteoclastic gene expressions. These two agents also suppressed NF-κB activation and subsequent production of proinflammatory cytokines by macrophages. Furthermore, activation of HIF-1α by DMOG specifically suppressed lipopolysaccharide-stimulated macrophage differentiation into M1 cells, increasing the ratio of M2 macrophages against M1 cells. Taken together, our data indicated that activation of HIF-1 plays a protective role in the development of apical periodontitis via downregulation of NF-κB, proinflammatory cytokines, M1 macrophages and osteoclastogenesis.
Life on the edge: active microbial communities in the Kryos MgCl2-brine basin at very low water activity
Authors: Steinle Lea , Knittel Katrin , Felber Nicole , Casalino Claudia , de Lange Gert , Tessarolo Chiara , Stadnitskaia Alina , Sinninghe Damsté Jaap S , Zopfi Jakob , Lehmann Moritz F , Treude Tina , Niemann Helge 
Published: April 2018

Abstract
The Kryos Basin is a deep-sea hypersaline anoxic basin (DHAB) located in the Eastern Mediterranean Sea (34.98°N 22.04°E). It is filled with brine of re-dissolved Messinian evaporites and is nearly saturated with MgCl2-equivalents, which makes this habitat extremely challenging for life. The strong density difference between the anoxic brine and the overlying oxic Mediterranean seawater impedes mixing, giving rise to a narrow chemocline. Here, we investigate the microbial community structure and activities across the seawater–brine interface using a combined biogeochemical, next-generation sequencing, and lipid biomarker approach. Within the interface, we detected fatty acids that were distinctly 13C-enriched when compared to other fatty acids. These likely originated from sulfide-oxidizing bacteria that fix carbon via the reverse tricarboxylic acid cycle. In the lower part of the interface, we also measured elevated rates of methane oxidation, probably mediated by aerobic methanotrophs under micro-oxic conditions. Sulfate reduction rates increased across the interface and were highest within the brine, providing first evidence that sulfate reducers (likely Desulfovermiculus and Desulfobacula) thrive in the Kryos Basin at a water activity of only ~0.4 Aw. Our results demonstrate that a highly specialized microbial community in the Kryos Basin has adapted to the poly-extreme conditions of a DHAB with nearly saturated MgCl2 brine, extending the known environmental range where microbial life can persist.
A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction
Authors: Cai Chen , Leu Andy O , Xie Guo-Jun , Guo Jianhua , Feng Yuexing , Zhao Jian-Xin , Tyson Gene W , Yuan Zhiguo , Hu Shihu 
Published: April 2018

Abstract
Microbially mediated anaerobic oxidation of methane (AOM) is a key process in the regulation of methane emissions to the atmosphere. Iron can serve as an electron acceptor for AOM, and it has been suggested that Fe(III)-dependent AOM potentially comprises a major global methane sink. Although it has been proposed that anaerobic methanotrophic (ANME) archaea can facilitate this process, their active metabolic pathways have not been confirmed. Here we report the enrichment and characterisation of a novel archaeon in a laboratory-scale bioreactor fed with Fe(III) oxide (ferrihydrite) and methane. Long-term performance data, in conjunction with the 13C- and 57Fe-labelling batch experiments, demonstrated that AOM was coupled to Fe(III) reduction to Fe(II) in this bioreactor. Metagenomic analysis showed that this archaeon belongs to a novel genus within family Candidatus Methanoperedenaceae, and possesses genes encoding the “reverse methanogenesis” pathway, as well as multi-heme c-type cytochromes which are hypothesised to facilitate dissimilatory Fe(III) reduction. Metatranscriptomic analysis revealed upregulation of these genes, supporting that this archaeon can independently mediate AOM using Fe(III) as the terminal electron acceptor. We propose the name Candidatus “Methanoperedens ferrireducens” for this microorganism. The potential role of “M. ferrireducens” in linking the carbon and iron cycles in environments rich in methane and iron should be investigated in future research.
Micro-scale intermixing: a requisite for stable and synergistic co-establishment in a four-species biofilm
Authors: Liu Wenzheng , Russel Jakob , Burmølle Mette , Sørensen Søren J , Madsen Jonas S 
Published: April 2018

Abstract
Microorganisms frequently coexist in complex multispecies communities, where they distribute non-randomly, reflective of the social interactions that occur. It is therefore important to understand how social interactions and local spatial organization influences multispecies biofilm succession. Here the localization of species pairs was analyzed in three dimensions in a reproducible four-species biofilm model, to study the impact of spatial positioning of individual species on the temporal development of the community. We found, that as the biofilms developed, species pairs exhibited distinct intermixing patterns unique to the four-member biofilms. Higher biomass and more intermixing were found in four-species biofilms compared to biofilms with fewer species. Intriguingly, in local regions within the four member biofilms where Microbacterium oxydans was scant, both biomass and intermixing of all species were lowered, compared to regions where M. oxydans was present at typical densities. Our data suggest that Xanthomonas retroflexus and M. oxydans, both low abundant biofilm-members, intermixed continuously during the development of the four-species biofilm, hereby facilitating their own establishment. In turn, this seems to have promoted distinct spatial organization of Stenotrophomonas rhizophila and Paenibacillus amylolyticus enabling enhanced growth of all four species. Here local intermixing of bacteria advanced the temporal development of a multi-species biofilm.
Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote
Authors: Xin Yueyong , Shi Yang , Niu Tongxin , Wang Qingqiang , Niu Wanqiang , Huang Xiaojun , Ding Wei , Yang Lei , Blankenship Robert E. , Xu Xiaoling , Sun Fei 
Published: April 2018

AbstractPhotosynthetic prokaryotes evolved diverse light-harvesting (LH) antennas to absorb sunlight and transfer energy to reaction centers (RC). The filamentous anoxygenic phototrophs (FAPs) are important early branching photosynthetic bacteria in understanding the origin and evolution of photosynthesis. How their photosynthetic machinery assembles for efficient energy transfer is yet to be elucidated. Here, we report the 4.1 Å structure of photosynthetic core complex from Roseiflexus castenholzii by cryo-electron microscopy. The RC–LH complex has a tetra-heme cytochrome c bound RC encompassed by an elliptical LH ring that is assembled from 15 LHαβ subunits. An N-terminal transmembrane helix of cytochrome c inserts into the LH ring, not only yielding a tightly bound cytochrome c for rapid electron transfer, but also opening a slit in the LH ring, which is further flanked by a transmembrane helix from a newly discovered subunit X. These structural features suggest an unusual quinone exchange model of prokaryotic photosynthetic machinery.
Hard magnetic properties in nanoflake van der Waals Fe3GeTe2
Authors: Tan Cheng , Lee Jinhwan , Jung Soon-Gil , Park Tuson , Albarakati Sultan , Partridge James , Field Matthew R. , McCulloch Dougal G. , Wang Lan , Lee Changgu 
Published: April 2018

AbstractTwo-dimensional van der Waals materials have demonstrated fascinating optical and electrical characteristics. However, reports on magnetic properties and spintronic applications of van der Waals materials are scarce by comparison. Here, we report anomalous Hall effect measurements on single crystalline metallic Fe3GeTe2 nanoflakes with different thicknesses. These nanoflakes exhibit a single hard magnetic phase with a near square-shaped magnetic loop, large coercivity (up to 550 mT at 2 K), a Curie temperature near 200 K and strong perpendicular magnetic anisotropy. Using criticality analysis, the coupling length between van der Waals atomic layers in Fe3GeTe2 is estimated to be ~5 van der Waals layers. Furthermore, the hard magnetic behaviour of Fe3GeTe2 can be well described by a proposed model. The magnetic properties of Fe3GeTe2 highlight its potential for integration into van der Waals magnetic heterostructures, paving the way for spintronic research and applications based on these devices.
Fighting biofilms with lantibiotics and other groups of bacteriocins
Authors: Mathur Harsh , Field Des , Rea Mary C. , Cotter Paul D. , Hill Colin , Ross R. Paul 
Published: April 2018

AbstractBiofilms are sessile communities of bacteria typically embedded in an extracellular polymeric matrix. Bacterial cells embedded in biofilms are inherently recalcitrant to antimicrobials, compared to cells existing in a planktonic state, and are notoriously difficult to eradicate once formed. Avenues to tackle biofilms thus far have largely focussed on attempting to disrupt the initial stages of biofilm formation, including adhesion and maturation of the biofilm. Such an approach is advantageous as the concentrations required to inhibit formation of biofilms are generally much lower than removing a fully established biofilm. The crisis of antibiotic resistance in clinical settings worldwide has been further exacerbated by the ability of certain pathogenic bacteria to form biofilms. Perhaps the most notorious biofilm formers described from a clinical viewpoint have been methicillin-resistant Staphylococcus aureus (MRSA), Staphylococcus epidermidis, Pseudomonas aeruginosa, Gardnerella vaginalis and Streptococcus mutans, the latter of which is found in oral biofilms. Due to the dearth of novel antibiotics in recent decades, compounded by the increasing rate of emergence of resistance amongst pathogens with a propensity for biofilm formation, solutions are urgently required to mitigate these crises. Bacteriocins are a class of antimicrobial peptides, which are ribosomally synthesised and often are more potent than their antibiotic counterparts. Here, we review a selection of studies conducted with bacteriocins with the ultimate objective of inhibiting biofilms. Overall, a deeper understanding of the precise means by which a biofilm forms on a substrate as well as insights into the mechanisms by which bacteriocins inhibit biofilms is warranted.
Detection of endogenous S1292 LRRK2 autophosphorylation in mouse tissue as a readout for kinase activity
Authors: Kluss Jillian H. , Conti Melissa M. , Kaganovich Alice , Beilina Aleksandra , Melrose Heather L. , Cookson Mark R. , Mamais Adamantios 
Published: April 2018

AbstractParkinson’s disease-linked mutations in LRRK2 enhance the kinase activity of the protein, therefore targeting LRRK2 kinase activity is a promising therapeutic approach. Phosphorylation at S935 of LRRK2 and of its Rab GTPase substrates have proven very useful biomarkers to monitor its kinase activity. Complementary to these approaches autophosphorylation of LRRK2 can be used as a direct kinase activity readout but to date detection of autophosphorylation at endogenous levels in vivo has been limited. We developed a fractionation-based enrichment method to successfully detect endogenous S1292 LRRK2 autophosphorylation in mouse tissues and highlight S1292 as a physiological readout candidate for LRRK2 kinase activity in vivo.
The role of whistleblowers in protecting the safety and integrity of the food supply
Authors: Moy Gerald G. 
Published: April 2018

AbstractThe unsafe, illegal, and unethical practices, especially food fraud, by various actors along the food supply chain are old problems that have been made even more challenging by today’s international agri-food network. To combat these practices, the internal reporting to upper management or the external disclosure to regulators or media by persons who become aware of such practices is essential. These persons are colloquially known as whistleblowers. However, a number of impediments to whistleblowing, especially retribution by employers, have limited their contribution to ensuring the safety and integrity of the food supply. This paper presents recent examples of whistleblowing and legislation adopted by countries around the world to encourage and protect whistleblowers, especially from retaliation. Several impediments to whistleblowing are described and suggestions for overcoming them are proposed.
Comparative High-Resolution Transcriptome Sequencing of Lymphoma Cell Lines and de novo Lymphomas Reveals Cell-Line-Specific Pathway Dysregulation
Authors: Taher Leila , Beck Julia , Liu Wen , Roolf Catrin , Soller Jan T. , Rütgen Barbara C. , Hammer Sabine E. , Chodisetti Murali , Sender Sina , Sterenczak Katharina A. , Fuellen Georg , Junghanss Christian , Brenig Bertram , Nolte Ingo , Schütz Ekkehard , Murua Escobar Hugo 
Published: April 2018

AbstractIn dogs as well as humans, lymphoma is one of the most common hematopoietic malignancies. Furthermore, due to its characteristics, canine lymphoma is recognized as a clinically relevant in vivo model to study the corresponding human disease. Immortalized cell lines are widely used as in vitro models to evaluate novel therapeutic agents and characterize their molecular mechanisms. However, it is known that long-term cultivation leads to clonal selection, genetic instability, and loss of the initial heterogenic character, limiting the usefulness of cell lines as preclinical models. Herein, we present a systematic characterization and comparison of the transcriptomic landscape of canine primary B- and T-cell lymphomas, five lymphoid cell lines (CLBL-1, CLBL-1M, GL-1, CL-1, and OSW) and four non-neoplastic control samples. We found that lymphomas and cell lines exhibit a common “differentiation and proliferation signature”. However, our analysis also showed that, independently of the cell of origin, the transcriptional signatures of lymphomas are more similar to each other than they are to those of cell lines. In particular, we observed that not all common therapeutic targets are similarly expressed between lymphomas and lymphoid cell lines, and provide evidence that different lymphoid cell-lines should be used to model distinct aspects of lymphoma dysregulation.
Oxygen-doped carbon nanotubes for near-infrared fluorescent labels and imaging probes
Authors: Iizumi Yoko , Yudasaka Masako , Kim Jaeho , Sakakita Hajime , Takeuchi Tsukasa , Okazaki Toshiya 
Published: April 2018

AbstractChemical modification of carbon nanotube surface can controllably modulate their optical properties. Here we report a simple and effective synthesis method of oxygen-doped single-walled carbon nanotubes (o-SWCNTs), in which a thin film of SWCNTs is just irradiated under the UV light for a few minutes in air. By using this method, the epoxide-type oxygen-adducts (ep-SWCNTs) were produced in addition to the ether-type oxygen-adducts (eth-SWCNTs). The Treated (6, 5) ep-SWCNTs show a red-shifted luminescence at ~1280 nm, which corresponds to the most transparent regions for bio-materials. Immunoassay, fluorescence vascular angiography and observation of the intestinal contractile activity of mice were demonstrated by using the produced o-SWCNTs as infrared fluorescent labels and imaging agents.
Pair bond endurance promotes cooperative food defense and inhibits conflict in coral reef butterflyfish
Authors: Nowicki Jessica P. , Walker Stefan P. W. , Coker Darren J. , Hoey Andrew S. , Nicolet Katia J. , Pratchett Morgan S. 
Published: April 2018

AbstractPair bonding is generally linked to monogamous mating systems, where the reproductive benefits of extended mate guarding and/or of bi-parental care are considered key adaptive functions. However, in some species, including coral reef butterflyfishes (f. Chaetodonitidae), pair bonding occurs in sexually immature and homosexual partners, and in the absence of parental care, suggesting there must be non-reproductive adaptive benefits of pair bonding. Here, we examined whether pair bonding butterflyfishes cooperate in defense of food, conferring direct benefits to one or both partners. We found that pairs ofChaetodon lunulatusandC.baronessause contrasting cooperative strategies. InC.lunulatus, both partners mutually defend their territory, while inC.baronessa, males prioritize territory defence; conferring improvements in feeding and energy reserves in both sexes relative to solitary counterparts. We further demonstrate that partner fidelity contributes to this function by showing that re-pairing invokes intra-pair conflict and inhibits cooperatively-derived feeding benefits, and that partner endurance is required for these costs to abate. Overall, our results suggest that in butterflyfishes, pair bonding enhances cooperative defense of prey resources, ultimately benefiting both partners by improving food resource acquisition and energy reserves.
Short-term visual deprivation boosts the flexibility of body representation
Authors: Radziun Dominika , Ehrsson H. Henrik 
Published: April 2018

AbstractShort-term visual deprivation by blindfolding influences tactile acuity and orientation in space and, on a neural level, leads to enhanced excitability of visual and motor cortices. However, to the best of our knowledge, the possible effects of short-term visual deprivation on body representation have not been examined. In the present study, we tested two groups of 30 healthy participants with the somatic rubber hand illusion, a well-established paradigm to probe the dynamic plasticity of body representation. Before the start of the procedure, the experimental group was blindfolded for 120 minutes, while the control group wore transparent goggles for the same amount of time. We found that although there was no difference in the subjective feeling of ownership of the rubber hand during the illusion, the blindfolded group showed a significantly larger recalibration of hand position sense towards the location of the rubber hand than the control group. This finding suggests that short-term visual deprivation boosts plasticity of body representation in terms of multisensory spatial recalibration of hand position sense.
Complete genome analysis of Gluconacetobacter xylinus CGMCC 2955 for elucidating bacterial cellulose biosynthesis and metabolic regulation
Authors: Liu Miao , Liu Lingpu , Jia Shiru , Li Siqi , Zou Yang , Zhong Cheng 
Published: April 2018

AbstractComplete genome sequence of Gluconacetobacter xylinus CGMCC 2955 for fine control of bacterial cellulose (BC) synthesis is presented here. The genome, at 3,563,314 bp, was found to contain 3,193 predicted genes without gaps. There are four BC synthase operons (bcs), among which only bcsI is structurally complete, comprising bcsA, bcsB, bcsC, and bcsD. Genes encoding key enzymes in glycolytic, pentose phosphate, and BC biosynthetic pathways and in the tricarboxylic acid cycle were identified. G. xylinus CGMCC 2955 has a complete glycolytic pathway because sequence data analysis revealed that this strain possesses a phosphofructokinase (pfk)-encoding gene, which is absent in most BC-producing strains. Furthermore, combined with our previous results, the data on metabolism of various carbon sources (monosaccharide, ethanol, and acetate) and their regulatory mechanism of action on BC production were explained. Regulation of BC synthase (Bcs) is another effective method for precise control of BC biosynthesis, and cyclic diguanylate (c-di-GMP) is the key activator of BcsA–BcsB subunit of Bcs. The quorum sensing (QS) system was found to positively regulate phosphodiesterase, which decomposed c-di-GMP. Thus, in this study, we demonstrated the presence of QS in G. xylinus CGMCC 2955 and proposed a possible regulatory mechanism of QS action on BC production.
The impact of storage buffer, DNA extraction method, and polymerase on microbial analysis
Authors: Hallmaier-Wacker Luisa K. , Lueert Simone , Roos Christian , Knauf Sascha 
Published: April 2018

AbstractNext-generation sequencing approaches used to characterize microbial communities are subject to technical caveats that can lead to major distortion of acquired data. Determining the optimal sample handling protocol is essential to minimize the bias for different sample types. Using a mock community composed of 22 bacterial strains of even concentration, we studied a combination of handling conditions to determine the optimal conditions for swab material. Examining a combination of effects simulates the reality of handling environmental samples and may thus provide a better foundation for the standardization of protocols. We found that the choice of storage buffer and extraction kit affects the detected bacterial composition, while different 16S rRNA amplification methods only had a minor effect. All bacterial genera present in the mock community were identified with minimal levels of contamination independent of the choice of sample processing. Despite this, the observed bacterial profile for all tested conditions were significantly different from the expected abundance. This highlights the need for proper validation and standardization for each sample type using a mock community and blank control samples, to assess the bias in the protocol and reduce variation across the datasets.