bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions
Authors: Bletz Molly C. , Goedbloed Daniel J. , Sanchez Eugenia , Reinhardt Timm , Tebbe Christoph C. , Bhuju Sabin , Geffers Robert , Jarek Michael , Vences Miguel , Steinfartz Sebastian 
Published: December 2016

AbstractComplex microbial communities inhabit vertebrate digestive systems but thorough understanding of the ecological dynamics and functions of host-associated microbiota within natural habitats is limited. We investigate the role of environmental conditions in shaping gut and skin microbiota under natural conditions by performing a field survey and reciprocal transfer experiments with salamander larvae inhabiting two distinct habitats (ponds and streams). We show that gut and skin microbiota are habitat-specific, demonstrating environmental factors mediate community structure. Reciprocal transfer reveals that gut microbiota, but not skin microbiota, responds differentially to environmental change. Stream-to-pond larvae shift their gut microbiota to that of pond-to-pond larvae, whereas pond-to-stream larvae change to a community structure distinct from both habitat controls. Predicted functions, however, match that of larvae from the destination habitats in both cases. Thus, microbial function can be matched without taxonomic coherence and gut microbiota appears to exhibit metagenomic plasticity.
Dendritic excitation–inhibition balance shapes cerebellar output during motor behaviour
Authors: Jelitai Marta , Puggioni Paolo , Ishikawa Taro , Rinaldi Arianna , Duguid Ian 
Published: December 2016

AbstractFeedforward excitatory and inhibitory circuits regulate cerebellar output, but how these circuits interact to shape the somatodendritic excitability of Purkinje cells during motor behaviour remains unresolved. Here we perform dendritic and somatic patch-clamp recordings in vivo combined with optogenetic silencing of interneurons to investigate how dendritic excitation and inhibition generates bidirectional (that is, increased or decreased) Purkinje cell output during self-paced locomotion. We find that granule cells generate a sustained depolarization of Purkinje cell dendrites during movement, which is counterbalanced by variable levels of feedforward inhibition from local interneurons. Subtle differences in the dendritic excitation–inhibition balance generate robust, bidirectional changes in simple spike (SSp) output. Disrupting this balance by selectively silencing molecular layer interneurons results in unidirectional firing rate changes, increased SSp regularity and disrupted locomotor behaviour. Our findings provide a mechanistic understanding of how feedforward excitatory and inhibitory circuits shape Purkinje cell output during motor behaviour.
Improvement of system capacitance via weavable superelastic biscrolled yarn supercapacitors
Authors: Choi Changsoon , Kim Kang Min , Kim Keon Jung , Lepró Xavier , Spinks Geoffrey M. , Baughman Ray H. , Kim Seon Jeong 
Published: December 2016

AbstractYarn-based supercapacitors having improved performance are needed for existing and emerging wearable applications. Here, we report weavable carbon nanotube yarn supercapacitors having high performance because of high loadings of rapidly accessible charge storage particles (above 90 wt% MnO2). The yarn electrodes are made by a biscrolling process that traps host MnO2nanoparticles within the galleries of helically scrolled carbon nanotube sheets, which provide strength and electrical conductivity. Despite the high loading of brittle metal oxide particles, the biscrolled solid-state yarn supercapacitors are flexible and can be made elastically stretchable (up to 30% strain) by over-twisting to produce yarn coiling. The maximum areal capacitance of the yarn electrodes were up to 100 times higher than for previously reported fibres or yarn supercapacitors. Similarly, the energy density of complete, solid-state supercapacitors made from biscrolled yarn electrodes with gel electrolyte coating were significantly higher than for previously reported fibre or yarn supercapacitors.
Cyst-Wall-Protein-1 is fundamental for Golgi-like organelle neogenesis and cyst-wall biosynthesis in Giardia lamblia
Authors: Ebneter Jacqueline A. , Heusser Sally D. , Schraner Elisabeth M. , Hehl Adrian B. , Faso Carmen 
Published: December 2016

AbstractThe genome of the protozoan parasite Giardia lamblia is organized in two diploid nuclei, which has so far precluded complete analysis of gene function. Here we use a previously developed Cre/loxP-based knock-out and selection marker salvage strategy in the human-derived isolate WB-C6 to eliminate all four copies of the Cyst-Wall-Protein-1 locus (CWP1). Because these loci are silenced in proliferating trophozoites and highly expressed only in encysting cells, CWP1 ablation allows functional characterization of a conditional phenotype in parasites induced to encyst. We show that encysting Δcwp1 cells are unable to establish the stage-regulated trafficking machinery with Golgi-like encystation-specific vesicles required for cyst-wall formation but show morphological hallmarks of cyst development and karyokinesis. This ‘pseudocyst’ phenotype is rescued by transfection of Δcwp1 cells with an episomally maintained CWP1 expression vector. Genome editing in genera Giardia and Trypanosoma are the only reported examples addressing questions on pathogen transmission within the Excavata supergroup.
Simulating and Optimising Quantum Thermometry Using Single Photons
Authors: Tham W. K. , Ferretti H. , Sadashivan A. V. , Steinberg A. M. 
Published: December 2016

AbstractA classical thermometer typically works by exchanging energy with the system being measured until it comes to equilibrium, at which point the readout is related to the final energy state of the thermometer. A recent paper noted that with a quantum thermometer consisting of a single spin/qubit, temperature discrimination is better achieved at finite times rather than once equilibration is essentially complete. Furthermore, preparing a qubit thermometer in a state with quantum coherence instead of an incoherent one improves its sensitivity to temperature differences. Implementing a recent proposal for efficiently emulating an arbitrary quantum channel, we use the quantum polarisation state of individual photons as models of “single-qubit thermometers” which evolve for a certain time in contact with a thermal bath. We investigate the optimal thermometer states for temperature discrimination, and the optimal interaction times, confirming that there is a broad regime where quantum coherence provides a significant improvement. We also discuss the more practical question of thermometers composed of a finite number of spins/qubits (greater than one), and characterize the performance of an adaptive protocol for making optimal use of all the qubits.
Self-assembled and intercalated film of reduced graphene oxide for a novel vacuum pressure sensor
Authors: Ahn Sung Il , Jung Jura , Kim Yongwoo , Lee Yujin , Kim Kukjoo , Lee Seong Eui , Kim Sungyun , Choi Kyeong-Keun 
Published: December 2016

AbstractWe report a new method for measuring vacuum pressures using Van der Waals (VDW) interactions between reduced graphene oxide (RGO) sheets. For this purpose, we utilized a reaction-based self-assembly process to fabricate various intercalated RGO (i-RGO) films, and monitored their electrical behavior with changing pressure and temperature. Pumping to remove gas from a vacuum chamber produced a decrease in the sheet resistance of i-RGO. With further pumping, distinctly different sheet resistance behaivors were observed depending on the measurement temperature. With increasing vacuum pressure, the resistance increased at 100 °C, whereas it decreased at 30 °C. Two types of VDW interactions are proposed to explain these features: a local VDW interaction between RGO sheets that resulted in V-shaped curves of sheet resistance with pressure changes and broad VDW interactions that occur between RGO sheets when the elastic force required to bend carbon clusters on an RGO sheet exceeds their vibrational energy at low temperatures. On the basis of the results, we propose that the resistance behavior of i-RGO as a function of vacuum pressure can be interpreted as the sum of the two different VDW interactions.
Roles of human POLD1 and POLD3 in genome stability
Authors: Tumini Emanuela , Barroso Sonia , -Calero Carmen Pérez , Aguilera Andrés 
Published: December 2016

AbstractDNA replication is essential for cellular proliferation. If improperly controlled it can constitute a major source of genome instability, frequently associated with cancer and aging. POLD1 is the catalytic subunit and POLD3 is an accessory subunit of the replicative Pol δ polymerase, which also functions in DNA repair, as well as the translesion synthesis polymerase Pol ζ, whose catalytic subunit is REV3L. In cells depleted of POLD1 or POLD3 we found a differential but general increase in genome instability as manifested by DNA breaks, S-phase progression impairment and chromosome abnormalities. Importantly, we showed that both proteins are needed to maintain the proper amount of active replication origins and that POLD3-depletion causes anaphase bridges accumulation. In addition, POLD3-associated DNA damage showed to be dependent on RNA-DNA hybrids pointing toward an additional and specific role of this subunit in genome stability. Interestingly, a similar increase in RNA-DNA hybrids-dependent genome instability was observed in REV3L-depleted cells. Our findings demonstrate a key role of POLD1 and POLD3 in genome stability and S-phase progression revealing RNA-DNA hybrids-dependent effects for POLD3 that might be partly due to its Pol ζ interaction.
Evidence for a LOS and a capsular polysaccharide in Capnocytophaga canimorsus
Authors: Renzi Francesco , Ittig Simon J. , Sadovskaya Irina , Hess Estelle , Lauber Frederic , Dol Melanie , Shin Hwain , Mally Manuela , Fiechter Chantal , Sauder Ursula , Chami Mohamed , Cornelis Guy R. 
Published: December 2016

AbstractCapnocytophaga canimorsus is a dog’s and cat’s oral commensal which can cause fatal human infections upon bites or scratches. Infections mainly start with flu-like symptoms but can rapidly evolve in fatal septicaemia with a mortality as high as 40%. Here we present the discovery of a polysaccharide capsule (CPS) at the surface of C. canimorsus 5 (Cc5), a strain isolated from a fulminant septicaemia. We provide genetic and chemical data showing that this capsule is related to the lipooligosaccharide (LOS) and probably composed of the same polysaccharide units. A CPS was also found in nine out of nine other strains of C. canimorsus. In addition, the genomes of three of these strains, sequenced previously, contain genes similar to those encoding CPS biosynthesis in Cc5. Thus, the presence of a CPS is likely to be a common property of C. canimorsus. The CPS and not the LOS confers protection against the bactericidal effect of human serum and phagocytosis by macrophages. An antiserum raised against the capsule increased the killing of C. canimorsus by human serum thus showing that anti-capsule antibodies have a protective role. These findings provide a new major element in the understanding of the pathogenesis of C. canimorsus.
Tracking the Impact of Excisional Cervical Treatment on the Cervix using Biospectroscopy
Authors: Halliwell Diane E. , Kyrgiou Maria , Mitra Anita , Kalliala Ilkka , Paraskevaidis Evangelos , Theophilou Georgios , Martin-Hirsch Pierre L. , Martin Francis L. 
Published: December 2016

AbstractLocal excisional treatment for cervical intra-epithelial neoplasia (CIN) is linked to significant adverse sequelae including preterm birth, with cone depth and radicality of treatment correlating to the frequency and severity of adverse events. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy can detect underlying cervical disease more accurately than conventional cytology. The chemical profile of cells pre- and post-treatment may differ as a result of altered biochemical processes due to excision, or treatment of the disease. Since pre-treatment cervical length varies amongst women, the percentage of cervix excised may correlate more accurately to risk than absolute dimensions. We show that treatment for CIN significantly alters the biochemistry of the cervix, compared with women who have not had treatment; this is due to the removal of cervical tissue rather than the removal of the disease. However, the spectra do not seem to correlate to the cone depth or proportion of cervical length excised. Future research should aim to explore the impact of treatment in a larger cohort.
Disentangling the influence of earthworms in sugarcane rhizosphere
Authors: Braga Lucas P. P. , Yoshiura Caio A. , Borges Clovis D. , Horn Marcus A. , Brown George G. , Drake Harold L. , Tsai Siu M. 
Published: December 2016

AbstractFor the last 150 years many studies have shown the importance of earthworms for plant growth, but the exact mechanisms involved in the process are still poorly understood. Many important functions required for plant growth can be performed by soil microbes in the rhizosphere. To investigate earthworm influence on the rhizosphere microbial community, we performed a macrocosm experiment with and without Pontoscolex corethrurus (EW+ and EW−, respectively) and followed various soil and rhizosphere processes for 217 days with sugarcane. In EW+ treatments, N2O concentrations belowground (15 cm depth) and relative abundances of nitrous oxide genes (nosZ) were higher in bulk soil and rhizosphere, suggesting that soil microbes were able to consume earthworm-induced N2O. Shotgun sequencing (total DNA) revealed that around 70 microbial functions in bulk soil and rhizosphere differed between EW+ and EW− treatments. Overall, genes indicative of biosynthetic pathways and cell proliferation processes were enriched in EW+ treatments, suggesting a positive influence of worms. In EW+ rhizosphere, functions associated with plant-microbe symbiosis were enriched relative to EW− rhizosphere. Ecological networks inferred from the datasets revealed decreased niche diversification and increased keystone functions as an earthworm-derived effect. Plant biomass was improved in EW+ and worm population proliferated.
Genomic Identification and Comparative Expansion Analysis of the Non-Specific Lipid Transfer Protein Gene Family in Gossypium
Authors: Li Feng , Fan Kai , Ma Fanglu , Yue Erkui , Bibi Noreen , Wang Ming , Shen Hao , Hasan Md Mosfeq-Ul , Wang Xuede 
Published: December 2016

AbstractPlant non-specific lipid transfer proteins (nsLTPs) are involved in many biological processes. In this study, 51, 47 and 91nsLTPswere identified inGossypium arboreum, G. raimondiiand their descendant allotetraploidG. hirsutum, respectively. All thensLTPswere phylogenetically divided into 8 distinct subfamilies. Besides, the recent duplication, which is considered cotton-specific whole genome duplication, may have led tonsLTPexpansion inGossypium. Both tandem and segmental duplication contributed tonsLTPexpansion inG. arboreumandG. hirsutum, while tandem duplication was the dominant pattern inG. raimondii. Additionally, the interspecific orthologous gene pairs inGossypiumwere identified. SomeGaLTPsandGrLTPslost their orthologs in the Atand Dtsubgenomes, respectively, ofG. hirsutum. The distribution of theseGrLTPsandGaLTPswithin each subfamily was complementary, suggesting that the loss and retention ofnsLTPsinG. hirsutummight not be random. Moreover, thensLTPsin the Atand Dtsubgenomes might have evolved symmetrically. Furthermore, both intraspecific and interspecific orthologous genes showed considerable expression variation, suggesting that their functions were strongly differentiated. Our results lay an important foundation for expansion and evolutionary analysis of thensLTPfamily inGossypium, and advancensLTPstudies in other plants, especially polyploid plants.
Arabidopsis myrosinases link the glucosinolate-myrosinase system and the cuticle
Authors: Ahuja Ishita , de Vos Ric C. H. , Rohloff Jens , Stoopen Geert M. , Halle Kari K. , Ahmad Samina Jam Nazeer , Hoang Linh , Hall Robert D. , Bones Atle M. 
Published: December 2016

AbstractBoth physical barriers and reactive phytochemicals represent two important components of a plant’s defence system against environmental stress. However, these two defence systems have generally been studied independently. Here, we have taken an exclusive opportunity to investigate the connection between a chemical-based plant defence system, represented by the glucosinolate-myrosinase system, and a physical barrier, represented by the cuticle, using Arabidopsis myrosinase (thioglucosidase; TGG) mutants. The tgg1, single and tgg1 tgg2 double mutants showed morphological changes compared to wild-type plants visible as changes in pavement cells, stomatal cells and the ultrastructure of the cuticle. Extensive metabolite analyses of leaves from tgg mutants and wild-type Arabidopsis plants showed altered levels of cuticular fatty acids, fatty acid phytyl esters, glucosinolates, and indole compounds in tgg single and double mutants as compared to wild-type plants. These results point to a close and novel association between chemical defence systems and physical defence barriers.
Spring maize yield, soil water use and water use efficiency under plastic film and straw mulches in the Loess Plateau
Authors: Lin Wen , Liu Wenzhao , Xue Qingwu 
Published: December 2016

AbstractTo compare the soil water balance, yield and water use efficiency (WUE) of spring maize under different mulching types in the Loess Plateau, a 7-year field experiment was conducted in the Changwu region of the Loess Plateau. Three treatments were used in this experiment: straw mulch (SM), plastic film mulch (PM) and conventional covering without mulch (CK). Results show that the soil water change of dryland spring maize was as deep as 300 cm depth and hence 300 cm is recommended as the minimum depth when measure the soil water in this region. Water use (ET) did not differ significantly among the treatments. However, grain yield was significantly higher in PM compared with CK. WUE was significantly higher in PM than in CK for most years of the experiment. Although ET tended to be higher in PM than in the other treatments (without significance), the evaporation of water in the fallow period also decreased. Thus, PM is sustainable with respect to soil water balance. The 7-year experiment and the supplemental experiment thus confirmed that straw mulching at the seedling stage may lead to yield reduction and this effect can be mitigated by delaying the straw application to three-leaf stage.
Modulation of gut microbiota and delayed immunosenescence as a result of syringaresinol consumption in middle-aged mice
Authors: Cho Si-Young , Kim Juewon , Lee Ji Hae , Sim Ji Hyun , Cho Dong-Hyun , Bae Il-Hong , Lee Hyunbok , Seol Min A. , Shin Hyun Mu , Kim Tae-Joo , Kim Dae-Yong , Lee Su-Hyung , Shin Song Seok , Im Sin-Hyeog , Kim Hang-Rae 
Published: December 2016

AbstractAge-associated immunological dysfunction (immunosenescence) is closely linked to perturbation of the gut microbiota. Here, we investigated whether syringaresinol (SYR), a polyphenolic lignan, modulates immune aging and the gut microbiota associated with this effect in middle-aged mice. Compared with age-matched control mice, SYR treatment delayed immunosenescence by enhancing the numbers of total CD3+ T cells and naïve T cells. SYR treatment induced the expression of Bim as well as activation of FOXO3 in Foxp3+ regulatory T cells (Tregs). Furthermore, SYR treatment significantly enhanced the Firmicutes/Bacteroidetes ratio compared with that in age-matched controls by increasing beneficial bacteria, Lactobacillus and Bifidobacterium, while reducing the opportunistic pathogenic genus, Akkermansia. In addition, SYR treatment reduced the serum level of lipopolysaccharide-binding protein, an inflammatory marker, and enhanced humoral immunity against influenza vaccination to the level of young control mice. Taken together, these findings suggest that SYR may rejuvenate the immune system through modulation of gut integrity and microbiota diversity as well as composition in middle-aged mice, which may delay the immunosenescence associated with aging.
Differential IL-1β secretion by monocyte subsets is regulated by Hsp27 through modulating mRNA stability
Authors: Hadadi Eva , Zhang Biyan , Baidžajevas Kajus , Yusof Nurhashikin , Puan Kia Joo , Ong Siew Min , Yeap Wei Hseun , Rotzschke Olaf , Kiss-Toth Endre , Wilson Heather , Wong Siew Cheng 
Published: December 2016

AbstractMonocytes play a central role in regulating inflammation in response to infection or injury, and during auto-inflammatory diseases. Human blood contains classical, intermediate and non-classical monocyte subsets that each express characteristic patterns of cell surface CD16 and CD14; each subset also has specific functional properties, but the mechanisms underlying many of their distinctive features are undefined. Of particular interest is how monocyte subsets regulate secretion of the apical pro-inflammatory cytokine IL-1β, which is central to the initiation of immune responses but is also implicated in the pathology of various auto-immune/auto-inflammatory conditions. Here we show that primary human non-classical monocytes, exposed to LPS or LPS + BzATP (3’-O-(4-benzoyl)benzyl-ATP, a P2X7R agonist), produce approx. 80% less IL-1β than intermediate or classical monocytes. Despite their low CD14 expression, LPS-sensing, caspase-1 activation and P2X7R activity were comparable in non-classical monocytes to other subsets: their diminished ability to produce IL-1β instead arose from 50% increased IL-1β mRNA decay rates, mediated by Hsp27. These findings identify the Hsp27 pathway as a novel therapeutic target for the management of conditions featuring dysregulated IL-1β production, and represent an advancement in understanding of both physiological inflammatory responses and the pathogenesis of inflammatory diseases involving monocyte-derived IL-1β.
The proteomic profile of whole and glandular saliva in healthy pain-free subjects
Authors: Jasim Hajer , Olausson Patrik , Hedenberg-Magnusson Britt , Ernberg Malin , Ghafouri Bijar 
Published: December 2016

AbstractDetermination of the variability in the salivary proteome is a prerequisite for the development of saliva as a diagnostic and prognostic tool in particular physiological states. In this context, it is important that technical variability induced by sample collection and processing is kept at minimum to be able to reproducibly assess variability in states of health and disease. In the current study, the proteome profile in unstimulated and stimulated whole, parotid and sublingual saliva was investigated using two-dimensional gel electrophoresis. Saliva samples were structurally collected from ten examined and characterized healthy individuals during the exactly same conditions. The results demonstrated that different collection methods provide clear differences in the snapshot of the salivary proteome and also in the relative amount of specific proteins. The variable nature of the salivary proteome suggests that different approaches may have to be adopted when studying its composition or its possible role as an indicator for particular physiological states. The results emphasize the importance of consistency when collecting saliva samples for proteomic analysis.