bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota
Authors: Hua Zheng-Shuang , Qu Yan-Ni , Zhu Qiyun , Zhou En-Min , Qi Yan-Ling , Yin Yi-Rui , Rao Yang-Zhi , Tian Ye , Li Yu-Xian , Liu Lan , Castelle Cindy J. , Hedlund Brian P. , Shu Wen-Sheng , Knight Rob , Li Wen-Jun
Published: July 2018

Microbes of the phylum Aigarchaeota are widely distributed in geothermal environments, but their physiological and ecological roles are poorly understood. Here we analyze six Aigarchaeota metagenomic bins from two circumneutral hot springs in Tengchong, China, to reveal that they are either strict or facultative anaerobes, and most are chemolithotrophs that can perform sulfide oxidation. Applying comparative genomics to the Thaumarchaeota and Aigarchaeota, we find that they both originated from thermal habitats, sharing 1154 genes with their common ancestor. Horizontal gene transfer played a crucial role in shaping genetic diversity of Aigarchaeota and led to functional partitioning and ecological divergence among sympatric microbes, as several key functional innovations were endowed by Bacteria, including dissimilatory sulfite reduction and possibly carbon monoxide oxidation. Our study expands our knowledge of the possible ecological roles of the Aigarchaeota and clarifies their evolutionary relationship to their sister lineage Thaumarchaeota.
Host-linked soil viral ecology along a permafrost thaw gradient
Authors: Emerson Joanne B. , Roux Simon , Brum Jennifer R. , Bolduc Benjamin , Woodcroft Ben J. , Jang Ho Bin , Singleton Caitlin M. , Solden Lindsey M. , Naas Adrian E. , Boyd Joel A. , Hodgkins Suzanne B. , Wilson Rachel M. , Trubl Gareth , Li Changsheng , Frolking Steve , Pope Phillip B. , Wrighton Kelly C. , Crill Patrick M. , Chanton Jeffrey P. , Saleska Scott R. , Tyson Gene W. , Rich Virginia I. , Sullivan Matthew B.
Published: July 2018

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1–7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8–10, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.
The lincRNA MIRAT binds to IQGAP1 and modulates the MAPK pathway in NRAS mutant melanoma
Authors: Sanlorenzo Martina , Vujic Igor , Esteve-Puig Rosaura , Lai Kevin , Vujic Marin , Lin Kevin , Posch Christian , Dimon Michelle , Moy Adrian , Zekhtser Mitchell , Johnston Katia , Gho Deborah , Ho Wilson , Gajjala Abhinay , Oses Prieto Juan , Burlingame Alma , Daud Adil , Rappersberger Klemens , Ortiz-Urda Susana
Published: July 2018

Despite major advances in targeted melanoma therapies, drug resistance limits their efficacy. Long noncoding RNAs (lncRNAs) are transcriptome elements that do not encode proteins but are important regulatory molecules. LncRNAs have been implicated in cancer development and response to different therapeutics and are thus potential treatment targets; however, the majority of their functions and molecular interactions remain unexplored. In this study, we identify a novel cytoplasmic intergenic lincRNA (MIRAT), which is upregulated following prolonged MAPK inhibition in NRAS mutant melanoma and modulates MAPK signaling by binding to the MEK scaffold protein IQGAP1. Collectively, our results present MIRAT’s direct modulatory effect on the MAPK pathway and highlight the relevance of cytoplasmic lncRNAs as potential targets in drug resistant cancer.
Retraction Note: New molecular tools in Neospora caninum for studying apicomplexan parasite proteins
Authors: Mota Caroline M. , Chen Allan L. , Wang Kevin , Nadipuram Santhosh , Vashisht Ajay A. , Wohlschlegel James A. , Mineo Tiago W. P. , Bradley Peter J.
Published: July 2018

This paper has been retracted at the request of the authors.
Tuning the structure of the Josephson vortex lattice in Bi2Sr2CaCu2O8+δ single crystals with pancake vortices
Authors: Curran P. J. , Mohammed H. A. , Bending S. J. , Koshelev A. E. , Tsuchiya Y. , Tamegai T.
Published: July 2018

In extremely anisotropic cuprate superconductors a lattice of stacks of pancake vortices nucleates when a magnetic field is applied perpendicular to the copper oxide layers, while an orthogonal lattice of highly elliptical Josephson vortices forms when the applied field is parallel to the layers. Under tilted magnetic fields these sublattices can interact in complex ways to form systems of vortex chains and composite vortex lattices. Here we have used high-resolution scanning Hall microscopy (SHM) to map the rich tilted-field vortex phase diagram in an underdoped Bi2Sr2CaCu2O8+δ single crystal. We find that the Josephson vortex lattice spacing has an unexpected non-monotonic dependence on the pancake vortex density reflecting the delicate balance between attractive and repulsive vortex interactions, and actually undergoes a field-driven structural transformation with increasing out-of-plane fields. We also identify particularly stable composite structures composed of vortex chains separated by an integer number of rows of interstitial pancake vortex stacks and are able to establish the precise evolution of vortex-chain phases as the out-of-plane field is increased at small in-plane fields. Our results are in good semi-quantitative agreement with theoretical models and could enable the development of vortex ratchets and lenses based on the interactions between Josephson and pancake vortices.
Cellular stress induces erythrocyte assembly on intravascular von Willebrand factor strings and promotes microangiopathy
Authors: Nicolay Jan P. , Thorn Verena , Daniel Christoph , Amann Kerstin , Siraskar Balasaheb , Lang Florian , Hillgruber Carina , Goerge Tobias , Hoffmann Stefan , Gorzelanny Christian , Huck Volker , Mess Christian , Obser Tobias , Schneppenheim Reinhard , Fleming Ingrid , Schneider Matthias F. , Schneider Stefan W.
Published: July 2018

Microangiopathy with subsequent organ damage represents a major complication in several diseases. The mechanisms leading to microvascular occlusion include von Willebrand factor (VWF), notably the formation of ultra-large von Willebrand factor fibers (ULVWFs) and platelet aggregation. To date, the contribution of erythrocytes to vascular occlusion is incompletely clarified. We investigated the platelet-independent interaction between stressed erythrocytes and ULVWFs and its consequences for microcirculation and organ function under dynamic conditions. In response to shear stress, erythrocytes interacted strongly with VWF to initiate the formation of ULVWF/erythrocyte aggregates via the binding of Annexin V to the VWF A1 domain. VWF-erythrocyte adhesion was attenuated by heparin and the VWF-specific protease ADAMTS13. In an in vivo model of renal ischemia/reperfusion injury, erythrocytes adhered to capillaries of wild-type but not VWF-deficient mice and later resulted in less renal damage. In vivo imaging in mice confirmed the adhesion of stressed erythrocytes to the vessel wall. Moreover, enhanced eryptosis rates and increased VWF binding were detected in blood samples from patients with chronic renal failure. Our study demonstrates that stressed erythrocytes have a pronounced binding affinity to ULVWFs. The discovered mechanisms suggest that erythrocytes are essential for the pathogenesis of microangiopathies and renal damage by actively binding to ULVWFs.
Soil evaporation and organic matter turnover in the Sub-Taiga and Forest-Steppe of southwest Siberia
Authors: Kayler Zachary E. , Brédoire Félix , McMillan Helene , Barsukov Pavel A. , Rusalimova Olga , Nikitich Polina , Bakker Mark R. , Zeller Bernd , Fontaine Sébastien , Derrien Delphine
Published: July 2018

Southwest Siberia encompasses the forest-steppe and sub-taiga climatic zones and has historically been utilized for agriculture. Coinciding with predicted changes in climate for the region is the pressure of agricultural development; however, a characterization of the soil water and carbon dynamics is lacking. We assessed current soil water properties and soil organic carbon turnover in forests and grasslands for two sites that span the forest steppe and sub-taiga bioclimatic zones. Soil evaporation was 0.62 ± 0.17 mm d−1 (mean ± standard error) in grasslands and 0.45 ± 0.08 mm d−1 in the forests of the forest-steppe site. Evaporation at the sub-taiga site was 1.80 ± 1.70 mm d−1 in grasslands and 0.96 ± 0.05 mm d−1 in forest plots. Evaporation was significantly greater at the sub-taiga site than the forest-steppe site. The density of fine roots explained the soil water isotopic patterns between vegetation types and sites. We found soil organic matter turnover to be three times faster in the sub-taiga site than in the forest-steppe site. Our results show that while climate factors, in particular snow levels, between the two sites are drivers for water and carbon cycles, site level hydrology, soil characteristics, and vegetation directly interact to influence the water and carbon dynamics.
A Poly(ionic liquid) Gel Electrolyte for Efficient all Solid Electrochemical Double-Layer Capacitor
Authors: Taghavikish M. , Subianto S. , Gu Y. , Sun X. , Zhao X. S. , Choudhury N. Roy
Published: July 2018

Polyionic liquid based gels have stimulated significant interest due to their wide applications in flexible electronics, such as wearable electronics, roll-up displays, smart mobile devices and implantable biosensors. Novel supported liquid gel electrolyte using polymerisable ionic liquid and an acrylate monomer, has been developed in this work by entrapping ionic liquid during polymerisation instead of post polymerisation impregnation. The chemically crosslinked polyionic liquid gel electrolyte (PIL) is prepared using 2-hydroxyethylmethacrylate (HEMA) monomer and a polymerisable ionic liquid, 1,4-di(vinylimidazolium)butane bisbromide (DVIMBr) in an ionic liquid (IL- 1-butyl-3 methylimidazolium hexafluorophosphate) as the polymerisation solvent, which resulted in in-situ entrapment of the IL in the gel during polymerisation and crosslinking of the polymer. The supported liquid gel electrolyte (SLG) material was characterised with thermal analysis, infrared spectroscopy, and dynamic mechanical analysis, and was found to be stable with good mechanical properties. The electrochemical analysis showed that these chemically cross-linked PIL gel electrolyte-supported ILs are suitable for solid-state, flexible supercapacitor applications.
Contrasting biogeography and diversity patterns between diatoms and haptophytes in the central Pacific Ocean
Authors: Endo Hisashi , Ogata Hiroyuki , Suzuki Koji
Published: July 2018

Diatoms and haptophytes are two major phytoplankton groups, playing pivotal roles in global biogeochemical cycles and marine ecosystems. In general, diatoms have higher growth rates than haptophytes, whereas haptophytes tend to have higher nutrient uptake affinity. However, precise linkages between their ecological traits and geographical distributions remain poorly understood. Herein, we examined the basin-scale variability of the abundance and taxonomic composition of these two phytoplankton groups across 35 sites in the Pacific Ocean using DNA metabarcoding. The diatom community was generally dominated by a few genera at each sample site, whereas the haptophyte community consisted of a large number of genera in most of the sites. The coexistence of various haptophyte genera might be achieved by diversification of their ecophysiological traits such as mixotrophy. On the other hand, the diatom community might experience greater inter-genus competition due to the rapid uptake of nutrients. Our data further supports the notion that their distinct ecological strategies underlie the emergence of contrasting diversity patterns of these phytoplankton groups in the central Pacific at a basin scale.
Large body size constrains dispersal assembly of communities even across short distances
Authors: Bailey Richard I. , Molleman Freerk , Vasseur Chloe , Woas Steffen , Prinzing Andreas
Published: July 2018

Dispersal limitation has been considered to decrease with body size in animals and to be an important factor limiting community assembly on spatially isolated patches. Here we hypothesize that for flightless bark-dwelling oribatid mites dispersal limitation onto young trees might increase with body size (due to a decrease in aerial dispersal capacities), and it might occur even within a spatially contiguous forest canopy. We suppressed dispersal limitation towards branches from young trees by physically connecting them to branches from old trees and analyzed the impacts on community composition, accounting for branch microhabitat variables. Suppression of dispersal limitation increased community evenness and mean body size of mites on branches from young trees. Across all species, large species body-size corresponds to an abundance increase after suppression of dispersal limitation. Consistently, on no-contact control branches, mite body-sizes were larger on branches from old compared to young trees. Our study suggests that colonization/performance trade-offs might affect community assembly even across seemingly contiguous habitats. Overall, a previously underappreciated factor selecting against large body size in flightless canopy-dwelling invertebrates might be that large bodies makes these invertebrates fall faster and disperse less, not more.
Chronic Electrical Stimulation Promotes the Excitability and Plasticity of ESC-derived Neurons following Glutamate-induced Inhibition In vitro
Authors: Latchoumane Charles-Francois V. , Jackson LaDonya , Sendi Mohammad S. Eslampanah , Tehrani Kayvan F. , Mortensen Luke J. , Stice Steven L. , Ghovanloo Maysam , Karumbaiah Lohitash
Published: July 2018

Functional electrical stimulation (FES) is rapidly gaining traction as a therapeutic tool for mediating the repair and recovery of the injured central nervous system (CNS). However, the underlying mechanisms and impact of these stimulation paradigms at a molecular, cellular and network level remain largely unknown. In this study, we used embryonic stem cell (ESC)-derived neuron and glial co-cultures to investigate network maturation following acute administration of L-glutamate, which is a known mediator of excitotoxicity following CNS injury. We then modulated network maturation using chronic low frequency stimulation (LFS) and direct current stimulation (DCS) protocols. We demonstrated that L-glutamate impaired the rate of maturation of ESC-derived neurons and glia immediately and over a week following acute treatment. The administration of chronic LFS and DCS protocols individually following L-glutamate infusion significantly promoted the excitability of neurons as well as network synchrony, while the combination of LFS/DCS did not. qRT-PCR analysis revealed that LFS and DCS alone significantly up-regulated the expression of excitability and plasticity-related transcripts encoding N-methyl-D-aspartate (NMDA) receptor subunit (NR2A), brain-derived neurotrophic factor (BDNF) and Ras-related protein (RAB3A). In contrast, the simultaneous administration of LFS/DCS down-regulated BDNF and RAB3A expression. Our results demonstrate that LFS and DCS stimulation can modulate network maturation excitability and synchrony following the acute administration of an inhibitory dose of L-glutamate, and upregulate NR2A, BDNF and RAB3A gene expression. Our study also provides a novel framework for investigating the effects of electrical stimulation on neuronal responses and network formation and repair after traumatic brain injury.
Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases
Authors: Wang Kun , Wu Di , Zhang Haoyue , Das Avinash , Basu Mahashweta , Malin Justin , Cao Kan , Hannenhalli Sridhar
Published: July 2018

Alternative splicing contributes to phenotypic diversity at multiple biological scales, and its dysregulation is implicated in both ageing and age-associated diseases in human. Cross-tissue variability in splicing further complicates its links to age-associated phenotypes and elucidating these links requires a comprehensive map of age-associated splicing changes across multiple tissues. Here, we generate such a map by analyzing ~8500 RNA-seq samples across 48 tissues in 544 individuals. Employing a stringent model controlling for multiple confounders, we identify 49,869 tissue-specific age-associated splicing events of 7 distinct types. We find that genome-wide splicing profile is a better predictor of biological age than the gene and transcript expression profiles, and furthermore, age-associated splicing provides additional independent contribution to age-associated complex diseases. We show that the age-associated splicing changes may be explained, in part, by concomitant age-associated changes of the upstream splicing factors. Finally, we show that our splicing-based model of age can successfully predict the relative ages of cells in 8 of the 10 paired longitudinal data as well as in 2 sets of cell passage data. Our study presents the first systematic investigation of age-associated splicing changes across tissues, and further strengthening the links between age-associated splicing and age-associated diseases.
Predictors of Early Onset Multiple Organ Dysfunction in Major Burn Patients with Ventilator Support: Experience from A Mass Casualty Explosion
Authors: Feng Jia-Yih , Chien Jung-Yien , Kao Kuo-Chin , Tsai Cheng-Liang , Hung Fang Ming , Lin Fan-Min , Hu Han-Chung , Huang Kun-Lun , Yu Chong-Jen , Yang Kuang-Yao
Published: July 2018

Organ dysfunction is common in patients with major burns and associated with poor outcomes. The risk factors for early onset multiple organ dysfunction syndrome (MODS) in major burn patients with invasive ventilator support has rarely been evaluated before. In this study, major burn patients with invasive ventilator support from 499 victims suffered in a mass casualty color dust explosion were retrospectively enrolled. The development of early MODS that occurred within 5 days after burn injury was determined and the risk factors associated with early MODS were analyzed. A total of 88 patients from five medical centers were included. Their mean total body surface area (TBSA) was 60.9 ± 15.8%, and 45 (51.1%) patients had early MODS. Hematologic failure was the most common organ failure (68.6%), followed by respiratory failure (48.9%). Independent clinical factors associated with early MODS included TBSA ≥55% (OR: 3.83; 95% CI: 1.29–11.37) and serum albumin level <2.1 g/dL upon admission (OR: 3.43; 95% CI: 1.01–11.57). Patients with early MODS had prolonged ventilator dependence and longer ICU admission than those without early MODS. Our results showed that early MODS in major burn patients with invasive ventilator support is very common and can be predicted early on admission.
Phytolith assemblage analysis for the identification of rice paddy
Authors: Huan Xiujia , Lu Houyuan , Zhang Jianping , Wang Can
Published: July 2018

The rice arable system is of importance to both society and the environment. The emergence of rice paddies was a crucial step in the transition from pre-domestic cultivation to systematic land use and management. However, many aspects of the formation of rice farming systems remain unclear. An important reason is the lack of reliable methods for identifying early rice paddies. One possible means of remedying this knowledge deficit is through analysis of phytolith assemblages, which are closely related to their parent plant communities. In this study, phytolith assemblages from 27 surface soil samples from wild rice fields, 91 surface soil samples from modern rice paddies, and 50 soil samples from non-rice fields were analysed to establish a discriminant function. This discriminant function enabled classification of 89.3% of the samples into appropriate groups. Further, the results suggested that phytolith assemblages can be used to identify rice fields and differentiate between wild rice fields and domesticated rice fields. The method was demonstrated to be an effective way of utilising the large amounts of unidentifiable phytoliths discovered at archaeological sites to provide a modern analogue that may be a valuable key to unlocking the past.
Impact of honey on dental erosion and adhesion of early bacterial colonizers
Authors: Habluetzel Alexandra , Schmid Christoph , Carvalho Thiago S. , Lussi Adrian , Eick Sigrun
Published: July 2018

The aim was to investigate if honey causes erosion and if salivary pellicle modified with honey, or its components, or the by-product propolis has a protective effect against dental erosion and adhesion of early bacterial colonizers. The tested substances were: 3 types of honey, methylglyoxal (MGO), hydrogen peroxide, propolis. First in the erosion experiment, 120 human enamel specimens were covered with salivary pellicle and modified with the substances. Then they were eroded with 1% citric acid, pH 3.6 for 2 min, before surface hardness was measured. In the microbiological assay, the enamel specimens (n = 126) covered with modified salivary pellicle were contaminated with bacterial suspensions. The antimicrobial activity of each substance and their effect on early bacterial colonizer adhesion and biofilm formation were determined. Despite a low pH, honey did not cause erosion. On the other hand, pellicle modification with the tested solutions did not protect the enamel from erosion. Microbiologically, the 3 honeys inhibited species-specific growth of oral bacteria. Propolis decreased initial attachment of Streptococcus gordonii, while one honey inhibited demineralization of enamel by biofilm. In conclusion, pellicle modification with honey, or its components, or propolis did neither protect against erosion nor promote it. Propolis presented some bacterial adhesion inhibition.
Study of an AC dielectric barrier single micro-discharge filament over a water film
Authors: Vanraes Patrick , Nikiforov Anton , Bogaerts Annemie , Leys Christophe
Published: July 2018

In the last decades, AC powered atmospheric dielectric barrier discharges (DBDs) in air with a liquid electrode have been proposed as a promising plasma technology with versatile applicability in medicine, agriculture and water treatment. The fundamental features of the micro-discharge filaments that make up this type of plasma have, however, not been studied yet in sufficient detail. In order to address this need, we investigated a single DBD micro-discharge filament over a water film in a sphere-to-sphere electrode configuration, by means of ICCD imaging and optical emission spectroscopy. When the water film temporarily acts as the cathode, the plasma duration is remarkably long and shows a clear similarity with a resistive barrier discharge, which we attribute to the resistive nature of the water film and the formation of a cathode fall. As another striking difference to DBD with solid electrodes, a constant glow-like plasma is observed at the water surface during the entire duration of the applied voltage cycle, indicating continuous plasma treatment of the liquid. We propose several elementary mechanisms that might underlie the observed unique behavior, based on the specific features of a water electrode.
Involvement of Endothelin 1 in Remote Preconditioning-Induced Cardioprotection through connexin 43 and Akt/GSK-3β Signaling Pathway
Authors: Zhang Min , Gu Wei Wei , Hong Xing yu
Published: July 2018

The present study was aimed to explore the role of endothelins in remote preconditioning (RP)-induced myocardial protection in ischemia-reperfusion (IR) injury. RP stimulus was given by subjecting hind limb to four cycles of ischemia and reperfuion (5 minutes each) using blood pressure cuff in male rats. Following RP, hearts were isolated and subjected to 30 minutes of ischemia and 120 minutes of reperfusion on Langendorff apparatus. The extent of myocardial injury was determined by measuring the levels of LDH-1, CK-MB and cardiac troponin T (cTnT) in coronary effluent; caspase-3 activity and Bcl 2 expression in heart (apoptosis); infarct size by triphenyl tetrazolium chloride and contractility parameters including left ventricular developed pressure, dp/dtmax dp/dtmin and heart rate. RP reduced ischemia reperfusion-induced myocardial injury, increased the levels of endothelin 1 (in blood), Akt-P, GSK-3β-P and P-connexin 43 (in hearts). Pretreatment with ETA receptor antagonist, BQ 123 (1 and 2 mg/kg), ETB receptor antagonist, BQ 788 (1 and 3 mg/kg) and dual inhibitor of ETA and ETB receptor, bonsentan (25 and 50 mg/kg) abolished these effects of RP. However, the effects of bonsentan were more pronounced in comparison to BQ 123 and BQ 788. It is concluded that RP stimulus may release endothelin 1 in the blood, which may activate myocardial ETA and ETB receptors to trigger cardioprotection through connexin 43 and Akt/GSK-3β pathway.
Collective resonances near zero energy induced by a point defect in bilayer graphene
Authors: You Jhih-Shih , Tang Jian-Ming , Huang Wen-Min
Published: July 2018

Intrinsic defects give rise to scattering processes governing the transport properties of mesoscopic systems. We investigate analytically and numerically the local density of states in Bernal stacking bilayer graphene with a point defect. With Bernal stacking structure, there are two types of lattice sites. One corresponds to connected sites, where carbon atoms from each layer stack on top of each other, and the other corresponds to disconnected sites. From our theoretical study, a picture emerges in which the pronounced zero-energy peak in the local density of states does not attribute to zero-energy impurity states associated to two different types of defects but to a collective phenomenon of the low-energy resonant states induced by the defect. To corroborate this description, we numerically show that at small system size N, where N is the number of unit cells, the zero-energy peak near the defect scales as 1/lnN for the quasi-localized zero-energy state and as 1/N for the delocalized zero-energy state. As the system size approaches to the thermodynamic limit, the former zero-energy peak becomes a power-law singularity 1/|E| in low energies, while the latter is broadened into a Lorentzian shape. A striking point is that both types of zero-energy peaks decay as 1/r2 away from the defect, manifesting the quasi-localized character. Based on our results, we propose a general formula for the local density of states in low-energy and in real space. Our study sheds light on this fundamental problem of defects.
Substitution of linoleic acid with α-linolenic acid or long chain n-3 polyunsaturated fatty acid prevents Western diet induced nonalcoholic steatohepatitis
Authors: Jeyapal Sugeedha , Kona Suryam Reddy , Mullapudi Surekha Venkata , Putcha Uday Kumar , Gurumurthy Puvaneswari , Ibrahim Ahamed
Published: July 2018

Imbalance in the n-6 polyunsaturated fatty acids (PUFA) and n-3 PUFA in the Western diet may increase the risk of nonalcoholic fatty liver disease (NAFLD). This study investigates the impact of substitution of linoleic acid with α-linolenic acid (ALA) or long chain (LC) n-3 PUFA and hence decreasing n-6:n-3 fatty acid ratio on high fat, high fructose (HFHF) diet induced nonalcoholic steatohepatitis (NASH). Male Sprague-Dawley rats were divided into four groups and fed control diet, HFHF diet (n-6:n-3 ratio of 200), HFHF diet with ALA (n-6:n-3 ratio of 2) or HFHF diet with LC n-3 PUFA (n-6:n-3 ratio of 5) for 24 weeks. Rats fed HFHF diet with n-6:n-3 ratio of 200 resulted in hepatic steatosis, induced glucose intolerance, insulin resistance and oxidative stress accompanied by increase in markers of inflammation, plasma lipids and aminotransferase levels. Histopathological examination of liver further confirmed the establishment of NASH. ALA and LC n-3 PUFA supplementation prevented hepatic steatosis and dyslipidemia by inhibiting lipogenesis and increasing insulin sensitivity. Furthermore, n-3 PUFA supplementation attenuated hepatic oxidative stress by restoring antioxidant status, decreased inflammation and preserved hepatic architecture. These finding suggest that decreasing n-6:n-3 ratio prevented HFHF induced NASH by attenuating oxidative stress and inflammation.
Uncertainty Quantification of Extratropical Forest Biomass in CMIP5 Models over the Northern Hemisphere
Authors: Yang Cheng-En , Mao Jiafu , Hoffman Forrest M. , Ricciuto Daniel M. , Fu Joshua S. , Jones Chris D. , Thurner Martin
Published: July 2018

Simplified representations of processes influencing forest biomass in Earth system models (ESMs) contribute to large uncertainty in projections. We evaluate forest biomass from eight ESMs outputs archived in the Coupled Model Intercomparison Project Phase 5 (CMIP5) using the biomass data synthesized from radar remote sensing and ground-based observations across northern extratropical latitudes. ESMs exhibit large biases in the forest distribution, forest fraction, and mass of carbon pools that contribute to uncertainty in forest total biomass (biases range from −20 Pg C to 135 Pg C). Forest total biomass is primarily positively correlated with precipitation variations, with surface temperature becoming equally important at higher latitudes, in both simulations and observations. Relatively small differences in forest biomass between the pre-industrial period and the contemporary period indicate uncertainties in forest biomass were introduced in the pre-industrial model equilibration (spin-up), suggesting parametric or structural model differences are a larger source of uncertainty than differences in transient responses. Our findings emphasize the importance of improved (1) models of carbon allocation to biomass compartments, (2) distribution of vegetation types in models, and (3) reproduction of pre-industrial vegetation conditions, in order to reduce the uncertainty in forest biomass simulated by ESMs.
Response Surface Methodology-Genetic Algorithm Based Medium Optimization, Purification, and Characterization of Cholesterol Oxidase from Streptomyces rimosus
Authors: Srivastava Akanksha , Singh Vineeta , Haque Shafiul , Pandey Smriti , Mishra Manisha , Jawed Arshad , Shukla P. K. , Singh P. K. , Tripathi C. K. M.
Published: July 2018

The applicability of the statistical tools coupled with artificial intelligence techniques was tested to optimize the critical medium components for the production of extracellular cholesterol oxidase (COD; an enzyme of commercial interest) fromStreptomyces rimosusMTCC 10792. The initial medium component screening was performed using Placket-Burman design with yeast extract, dextrose, starch and ammonium carbonate as significant factors. Response surface methodology (RSM) was attempted to develop a statistical model with a significant coefficient of determination (R2 = 0.89847), followed by model optimization using Genetic Algorithm (GA). RSM-GA based optimization approach predicted that the combination of yeast extract, dextrose, starch and ammonium carbonate at concentrations 0.99, 0.8, 0.1, and 0.05 g/100 ml respectively, has resulted in 3.6 folds increase in COD production (5.41 U/ml) in comparison with the un-optimized medium (1.5 U/ml). COD was purified 10.34 folds having specific activity of 12.37 U/mg with molecular mass of 54 kDa. The enzyme was stable at pH 7.0 and 40 °C temperature. The apparent Michaelis constant (Km) and Vmaxvalues of COD were 0.043 mM and 2.21 μmol/min/mg, respectively. This is the first communication reporting RSM-GA based medium optimization, purification and characterization of COD byS. rimosusisolated from the forest soil of eastern India.
Common and rare variants of WNT16, DKK1 and SOST and their relationship with bone mineral density
Authors: Martínez-Gil Núria , Roca-Ayats Neus , Monistrol-Mula Anna , García-Giralt Natàlia , Díez-Pérez Adolfo , Nogués Xavier , Mellibovsky Leonardo , Grinberg Daniel , Balcells Susana
Published: July 2018

Numerous GWAS and candidate gene studies have highlighted the role of the Wnt pathway in bone biology. Our objective has been to study in detail the allelic architecture of three Wnt pathway genes: WNT16, DKK1 and SOST, in the context of osteoporosis. We have resequenced the coding and some regulatory regions of these three genes in two groups with extreme bone mineral density (BMD) (n = ∼50, each) from the BARCOS cohort. No interesting novel variants were identified. Thirteen predicted functional variants have been genotyped in the full cohort (n = 1490), and for ten of them (with MAF > 0.01), the association with BMD has been studied. We have found six variants nominally associated with BMD, of which 2 WNT16 variants predicted to be eQTLs for FAM3C (rs55710688, in the Kozak sequence and rs142005327, within a putative enhancer) withstood multiple-testing correction. In addition, two rare variants in functional regions (rs190011371 in WNT16b 3′UTR and rs570754792 in the SOST TATA box) were found only present in three women each, all with BMD below the mean of the cohort. Our results reinforce the higher importance of regulatory versus coding variants in these Wnt pathway genes and open new ways for functional studies of the relevant variants.
Increased testicular blood flow maintains oxygen delivery and avoids testicular hypoxia in response to reduced oxygen content in inspired air
Authors: Rizzoto G. , Hall C. , Tyberg J. V. , Thundathil J. C. , Caulkett N. A. , Kastelic J. P.
Published: July 2018

Despite a long-standing assertion that mammalian testes operate near hypoxia and increased testicular temperature causes frank hypoxia, we have preliminary evidence that changes are due to hyperthermia per se. The objective was to determine how variations in inspired oxygen concentration affected testicular blood flow, oxygen delivery and extraction, testicular temperature and lactate production. Eight rams were maintained under general anesthesia, with successive decreases in oxygen concentration in inspired air (100, 21 and 13%, respectively). As oxygen concentration decreased from 100 to 13%, there were increases in testicular blood flow (9.6 ± 1.7 vs 12.9 ± 1.9 ml/min/100 g of testis, P < 0.05; mean ± SEM) and conductance (normalized flow; 0.46 ± 0.07 to 1.28 ± 0.19 ml/min/mm Hg/100 g testis (P < 0.05). Increased testicular blood flow maintained oxygen delivery and increased testicular temperature by ~1 °C; this increase was correlated to increased testicular blood flow (r = 0.35, P < 0.0001). Furthermore, oxygen utilization increased concomitantly and there were no significant differences among oxygen concentrations in blood pH, HCO3− or base excess, and no effects of venous-arterial differences in lactate production. In conclusion, under acute hypoxic conditions, testes maintained oxygen delivery and uptake by increasing blood flow and oxygen extraction, with no evidence of anaerobic metabolism. However, additional studies are needed to determine longer-term responses and potential evidence of anaerobic metabolism at the molecular level.
Difference of Sagittal Alignment between Adolescents with Symptomatic Lumbar Isthmic Spondylolisthesis and the General Population
Authors: Zhao Jian , Xiao Yongqiang , Zhai Xiao , Chen Ziqiang , Li Ming
Published: July 2018

This case-control study aimed to investigate differences in the sagittal spinal parameters between the symptomatic spondylolisthesis patients and the general population. Twenty-nine adolescent patients with symptomatic lumbar isthmic spondylolisthesis were included. For each patient, two age-matched, gender-matched and BMI-matched controls were enrolled. Comparison analyses detected higher values in the case group for the following parameters: CL (−22.06 ± 7.552° versus −20.36 ± 7.016°, P < 0.001), T1 Slope (19.84 ± 8.708° versus 13.99 ± 6.537°, P = 0.001), PT (21.54 ± 9.082° versus 8.87 ± 7.863°, P < 0.001), PI (64.45 ± 13.957° versus 43.60 ± 9.669°, P < 0.001), SS (42.90 ± 9.183° versus 34.73 ± 8.265°, P < 0.001), LL (−50.82 ± 21.596° versus −43.78 ± 10.356°, P = 0.042), SVA (16.99 ± 14.625 mm versus 0.32 ± 31.824 mm, P = 0.009), L5 Slope (33.95 ± 13.567° versus 19.03 ± 6.809°, P < 0.001), and L5I (8.90 ± 6.556° versus 1.29 ± 6.726°, P < 0.001). Conversely, TS-CL (6.56 ± 6.716° versus 11.04 ± 7.085°, P = 0.006), cSVA (11.31 ± 6.867 mm versus 17.92 ± 11.832 mm, P = 0.007), and TLK (−2.66 ± 10.101° versus 2.71 ± 7.708°, P = 0.007) were smaller in the case group. Slippage percentage was most correlated with PI (r = 0.530, P = 0.003), followed by PT (r = 0.465, P = 0.011) and L5I (r = 0.433, P = 0.019). Results of binary logistic regression showed that the main risk factor of isthmic spondylolisthesis was PI (OR = 1.145, 95%CI = 1.083–1.210, P < 0.001). Further subgroup analysis also showed that PI was the main risk factor of isthmic spondylolisthesis in the female adolescents (OR = 1.237, 95%CI = 1.086–1.493, P = 0.003) and in the male adolescents (OR = 1.523, 95%CI = 1.093–2.123, P = 0.013). PI was the main risk factor for adolescent symptomatic isthmic spondylolisthesis in the Chinese Han adolescents. The greater PI indicated the higher the progressive risk of spondylolisthesis. In these isthmic spondylolisthesis adolescents, the body always inclined forward and lumbar and cervical lordosis increased.
Comparison between complete genomes of an isolate of Pseudomonas syringae pv. actinidiae from Japan and a New Zealand isolate of the pandemic lineage
Authors: Poulter Russell T. M. , Ho Joycelyn , Handley Thomas , Taiaroa George , Butler Margi I.
Published: July 2018

The modern pandemic of the bacterial kiwifruit pathogen Pseudomonas syringae pv actinidiae (Psa) is caused by a particular Psa lineage. To better understand the genetic basis of the virulence of this lineage, we compare the completely assembled genome of a pandemic New Zealand strain with that of the Psa type strain first isolated in Japan in 1983. Aligning the two genomes shows numerous translocations, constrained so as to retain the appropriate orientation of the Architecture Imparting Sequences (AIMs). There are several large horizontally acquired regions, some of which include Type I, Type II or Type III restriction systems. The activity of these systems is reflected in the methylation patterns of the two strains. The pandemic strain carries an Integrative Conjugative Element (ICE) located at a tRNA-Lys site. Two other complex elements are also present at tRNA-Lys sites in the genome. These elements are derived from ICE but have now acquired some alternative secretion function. There are numerous types of mobile element in the two genomes. Analysis of these elements reveals no evidence of recombination between the two Psa lineages.
Cytokine Regulation in Human CD4 T Cells by the Aryl Hydrocarbon Receptor and Gq-Coupled Receptors
Authors: McAleer Jeremy P. , Fan Jun , Roar Bryanna , Primerano Donald A. , Denvir James
Published: July 2018

Th17 cells contribute to host defense on mucosal surfaces but also provoke autoimmune diseases when directed against self-antigens. Identifying therapeutic targets that regulate Th17 cell differentiation and/or cytokine production has considerable value. Here, we study the aryl hydrocarbon receptor (AhR)-dependent transcriptome in human CD4 T cells treated with Th17-inducing cytokines. We show that the AhR reciprocally regulates IL-17 and IL-22 production in human CD4 T cells. Global gene expression analysis revealed that AhR ligation decreased IL21 expression, correlating with delayed upregulation of RORC during culture with Th17-inducing cytokines. Several of the AhR-dependent genes have known roles in cellular assembly, organization, development, growth and proliferation. We further show that expression of GPR15, GPR55 and GPR68 positively correlates with IL-22 production in the presence of the AhR agonist FICZ. Activation of GPR68 with the lorazepam derivative ogerin resulted in suppression of IL-22 and IL-10 secretion by T cells, with no effect on IL-17. Under neutral Th0 conditions, ogerin and the Gq/11 receptor inhibitor YM254890 blunted IL-22 induction by FICZ. These data reveal the AhR-dependent transcriptome in human CD4 T cells and suggest the mechanism through which the AhR regulates T cell function may be partially dependent on Gq-coupled receptors including GPR68.
Identification and characterization of known and novel microRNAs in strawberry fruits induced by Botrytis cinerea
Authors: Liang Yaoxin , Guan Yuhan , Wang Shaoxi , Li Yanjun , Zhang Zhihong , Li He
Published: July 2018

MicroRNAs are endogenous small non-coding RNAs that negatively regulate mRNAs, mainly at the post-transcriptional level, and play an important role in resistance response of plants. To date, there are few reports on resistance response of strawberry miRNAs to pathogens. In this study, using high-throughput sequencing, 134 conserved and 35 novel miRNAs were identified in six libraries within the treatment ofBotrytis cinerea. A total 497 potential target genes were predicted usingFragaria vescagenome. Most of the differential expressed miRNAs in strawberry fruits were up-regulated in early libraries and down-regulated in late libraries.PIRL, the target gene of miR5290a, showed the opposite expressed trend compared with miR5290 from T1 to T3 libraries, and functional analysis of thePIRLgene shows that it has obvious resistance toB.cinereain the strawberry fruits with overexpressedPIRLgene. We speculate that miR5290a negatively regulates its target genePIRLto increase resistance to pathogen infection, and further analysis ofPIRLfunction is meaningful for studying the plant-pathogen relationship and improving strawberry fruit quality and yield.
Enhanced Corrosion Protection Performance by Organic-Inorganic Materials Containing Thiocarbonyl Compounds
Authors: Al Zoubi Wail , Ko Young Gun
Published: July 2018

In the present study, the synergistic effect on the corrosion protection properties of Mg alloys subjected to plasma electrolytic oxidation and chemically treated with thiourea as an inhibitor is investigated by surface microstructure analysis, evaluation of the electrochemical performance, and chemical quantum calculations. Physical adsorption of thiourea on the inorganic material surface might be due to physical interaction between thiourea with a low ionization potential serving as an electron donor and the inorganic components with high electron affinities acting as acceptors. The results from potentiodynamic polarization and electrochemical impedance spectroscopy for organic-inorganic coating reveal a clear decrease in the corrosion rate owing to the introduced thiourea.
Runx1-Stat3 signaling regulates the epithelial stem cells in continuously growing incisors
Authors: Sarper Safiye E. , Inubushi Toshihiro , Kurosaka Hiroshi , Ono Minagi Hitomi , Kuremoto Koh-ichi , Sakai Takayoshi , Taniuchi Ichiro , Yamashiro Takashi
Published: July 2018

Rodent incisors grow permanently and the homeostasis of enamel production is maintained by a continuous supply of epithelial progenitors from putative stem cells in the cervical loop. We herein report that Runx1 regulates the Lgr5-expressing epithelial stem cells and their subsequent continuous differentiation into ameloblasts. Mice deficient in epithelial Runx1 demonstrate remarkable shortening of the incisors with underdevelopment of the cervical loop and enamel defects. In this mutant cervical loop, the proliferation of the dental epithelium was significantly disturbed and the expression of Lgr5 and enamel matrix proteins was remarkably downregulated. Interestingly, the expression of Socs3, an inhibitor of Stat3 signaling, was upregulated and Stat3 phosphorylation was suppressed specifically in the mutant cervical loop. The expression of Lgr5 and the enamel matrix protein in the wild-type incisor germs is disturbed by pharmaceutical Stat3 inhibition in vitro., of. Conversely, pharmaceutical activation of Stat3 rescues the defective phenotypes of the Runx1 mutant with upregulated Lgr5 and enamel matrix protein genes. The present results provide the first evidence of the role of Runx1 regulates the Lgr5-expressing epithelial stem cells and differentiation of ameloblast progenitors in the developing incisors. Our study also demonstrates that Stat3 modulates the Runx1-Lgr5 axis in the cervical loop.
Telomere length and survival in primary cutaneous melanoma patients
Authors: Rachakonda Sivaramakrishna , Srinivas Nalini , Mahmoudpour Seyed Hamidreza , Garcia-Casado Zaida , Requena Celia , Traves Victor , Soriano Virtudes , Cardelli Maurizio , Pjanova Dace , Molven Anders , Gruis Nelleke , Nagore Eduardo , Kumar Rajiv
Published: July 2018

Telomere repeats at chromosomal ends, critical to genomic integrity, undergo age-dependent attrition. Telomere length, a polygenic trait, has been associated with risk of several disorders including cancers. In contrast to association of long telomeres with increased risk of several cancers, including melanoma, emerging reports suggest that short telomeres predict poor survival in patients with different cancers. In this study based on 1019 stage I and II cutaneous melanoma patients, we show an association between the patients with short telomeres and poor melanoma-specific survival (HR 2.05, 95% CI 1.33–3.16) compared to patients with long telomeres. Due to inverse correlation between age and telomere length (r -0.19, P < 0.0001), we stratified the patients into quantiles based on age at diagnosis and also carried out age-matched analysis. The effect of short telomeres on survival was determined by using multivariate Cox regression that included composite genetic risk score computed from genotyping of the patients for telomere-length associated polymorphisms. The effect of decreased telomere length on poor melanoma-specific survival was particularly strong in patients within the age quantile below 30 years (HR 3.82, 95% CI 1.10–13.30) and between 30–40 years (HR 2.69, 95% CI 1.03–7.03). Our study shows that in contrast to increased melanoma risk associated with increased telomere length, decreased telomere length predicts poor survival in melanoma subgroups.
Long-range non-diffusive spin transfer in a Hall insulator
Authors: Kulik L. V. , Kuznetsov V. A. , Zhuravlev A. S. , Gorbunov A. V. , Solovyev V. V. , Timofeev V. B. , Kukushkin I. V. , Schmult S.
Published: July 2018

We report on optical visualization of spin propagation more than 100 µm. We present an electronic system in a new state of aggregation, the magnetofermionic condensate, in which the lowest-energy spin excitations − photoexcited spin-triplet magnetoexcitons – freely propagate over long distances, in the order of a millimeter, which implies non-diffusion spin transport. Our results open up a completely new system suitable for spintronic devices.