bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of pulsed electric fields for the elimination of highly drug-resistant Candida grown under modelled microgravity conditions
Authors: Lastauskienė Eglė , Novickij Vitalij , Zinkevičienė Auksė , Girkontaitė Irutė , Paškevičius Algimantas , Švedienė Jurgita , Markovskaja Svetlana , Novickij Jurij 
Published: September 2018

AbstractCandida lusitaniaeandC. guilliermondiiare perfect model organisms for the study ofCandidagenera behaviour in various conditions. Both of them are rare pathogens capable to cause candidiasis in the patients with weakened immune system and can undergo morphology switches related to the increased antifungal drug resistance.Candidagenera yeasts are able to inhabit diverse range of ecological niches including space ships and space stations. During the long-term expeditions, astronauts are affected by various factors that can change the state immune system. In such conditions, the commensal usually non-pathogenic microorganisms can spread through the body of the host and cause infections. Weakened immune system and limited use of drugs in spaceships promote the search of the alternative methods for the biocontrol of microorganisms. Several studies demonstrate that microorganisms are altering their gene expression, physiology, morphology, pathogenicity and evolving resistance to the antifungals under microgravity conditions. Our research indicated that switch to the pseudohyphae morphology leads up 30-fold increased resistance to amphotericin B inC. lusitaniaeandC. guilliermondii. Cultivation of yeasts in rotary cell culture system (RCCS) is related to the altered cell growth and resistance to the antifungal treatment. Our results showed that growth in the RCCS led to the extreme increase in cell resistance to amphotericin B as compared with the standard growth conditions. In our research, we applied electroporation for the biocontrol of twoCandidaspecies.C. lusitaniaeandC. guilliermondiicells grown in RCCS exhibited significantly increased survivability after pulsed electric field (PEF) treatment in comparison with cells grown under routine conditions. We have shown that PEF bursts of 2.5–25 kV cm−1of 100 µs × 8 duration display a dose-dependent permeabilization of both studiedCandidaspecies. Our research indicated that budding cells and pseudohyphae morphology cells, with increased resistance to amphotericin B, can be effectively inactivated after applying PEF higher than 15 kV cm−1.
Modeling CO, CO2and H2O Ice Abundances in the Envelopes of Young Stellar Objects in the Magellanic Clouds
Authors: Pauly Tyler , Garrod Robin T. 
Published: September 2018

AbstractMassive young stellar objects (MYSOs) in the Magellanic Clouds (MCs) show infrared absorption features corresponding to significant abundances of CO, CO2and H2O ice along the line of sight, with the relative abundances of these ices varying between sources in the Magellanic Clouds and the Milky Way. We use our gas-grain chemical code MAGICKAL, with multiple grain sizes and grain temperatures, and further expand it with a treatment for increased interstellar radiation field intensity to model the elevated dust temperatures observed in the MCs. We also adjust the elemental abundances used in the chemical models, guided by observations of HII regions in these metal-poor satellite galaxies. With a grid of models, we are able to reproduce the relative ice fractions observed in MC MYSOs, indicating that metal depletion and elevated grain temperature are important drivers of the MYSO envelope ice composition. The observed shortfall in CO in the Small Magellanic Cloud can be explained by a combination of reduced carbon abundance and increased grain temperatures. The models indicate that a large variation in radiation field strength is required to match the range of observed LMC abundances.
On the origin of O2 and other volatile species in comets
Authors: Taquet Vianney , Furuya Kenji , Walsh Catherine , van Dishoeck Ewine F. 
Published: September 2018

AbstractMolecular oxygen, O2, was recently detected in comet 67P by the ROSINA instrument on board the Rosetta spacecraft with a surprisingly high abundance of 4% relative to H2O, making O2 the fourth most abundant in comet 67P. Other volatile species with similar volatility, such as molecular nitrogen N2, were also detected by Rosetta, but with much lower abundances and much weaker correlations with water. Here, we investigate the chemical and physical origin of O2 and other volatile species using the new constraints provided by Rosetta. We follow the chemical evolution during star formation with state-of-the-art astrochemical models applied to dynamical physical models by considering three origins: i) in dark clouds, ii) during forming protostellar disks, and iii) during luminosity outbursts in disks. The models presented here favour a dark cloud (or “primordial”) grain surface chemistry origin for volatile species in comets, albeit for dark clouds which are slightly warmer and denser than those usually considered as solar system progenitors.
Determining the effect of a non-uniform AGB outflow on its chemistry
Authors: Van de Sande M. , Sundqvist J. O. , Millar T. J. , Decin L. 
Published: September 2018

AbstractThe molecular composition of the stellar outflows of AGB stars is determined by the stellar elemental carbon-to-oxygen abundance ratio, together with the physical circumstances in the innermost region of the outflow. Near the stellar surface, thermal equilibrium (TE) can be assumed. This leads to a certain molecular composition with a O- or C-rich signature. However, several molecular species have been detected that are not expected to be present in the inner region under the assumption of TE chemistry. As a solution to explain the presence of these unexpected species, non-equilibrium chemistry in the inner region of the outflow has been proposed. The outflows of AGB stars are generally not spherically symmetric or homogeneous, which influences the penetration of interstellar UV photons throughout the outflow. We investigate the effect of a clumpy, non-homogeneous outflow on the composition of the inner region by introducing a simple porosity formalism in our chemical model.
Processing of astrophysical ices by soft X-rays and swift ions
Authors: Pilling Sergio 
Published: September 2018

AbstractThe employment of soft X-rays and swift ions has been used in laboratory to simulate the physicochemical processing of astrophysical ice analogs by energetic photons and cosmic rays. This processing includes excitation, ionization and molecular dissociation, desorption, as well as triggers the formation of new compounds. Here we present some results from experiments employing infrared spectroscopy in two different laboratories: LNLS/CNPEM in Campinas/Brazil and GANIL/CIRIL/CIMAP in Caen/France. Among the results are the formation of alkenes and aromatic compounds during the irradiation of saturated hydrocarbon-containing ices by cosmic ray analogs, the production of the nucleobase adenine during soft X-ray photolysis of N2:CH4 ice, as well as the formation of peptide bonds during the bombardment of frozen glycine by cosmic ray analogs. The interaction between cosmic ray analogs and ionizing soft X-rays probed in the laboratory allows us to identify reaction routes that lead to chemistry enhancement of astrophysical ices and help us put constrains in prebiotic chemistry.
A role for APP in Wnt signalling links synapse loss with β-amyloid production
Authors: Elliott Christina , Rojo Ana I. , Ribe Elena , Broadstock Martin , Xia Weiming , Morin Peter , Semenov Mikhail , Baillie George , Cuadrado Antonio , Al-Shawi Raya , Ballard Clive G. , Simons Paul , Killick Richard 
Published: September 2018

AbstractIn Alzheimer’s disease (AD), the canonical Wnt inhibitor Dickkopf-1 (Dkk1) is induced by β-amyloid (Aβ) and shifts the balance from canonical towards non-canonical Wnt signalling. Canonical (Wnt-β-catenin) signalling promotes synapse stability, while non-canonical (Wnt-PCP) signalling favours synapse retraction; thus Aβ-driven synapse loss is mediated by Dkk1. Here we show that the Amyloid Precursor Protein (APP) co-activates both arms of Wnt signalling through physical interactions with Wnt co-receptors LRP6 and Vangl2, to bi-directionally modulate synapse stability. Furthermore, activation of non-canonical Wnt signalling enhances Aβ production, while activation of canonical signalling suppresses Aβ production. Together, these findings identify a pathogenic-positive feedback loop in which Aβ induces Dkk1 expression, thereby activating non-canonical Wnt signalling to promote synapse loss and drive further Aβ production. The Swedish familial AD variant of APP (APPSwe) more readily co-activates non-canonical, at the expense of canonical Wnt activity, indicating that its pathogenicity likely involves direct effects on synapses, in addition to increased Aβ production. Finally, we report that pharmacological inhibition of the Aβ-Dkk1-Aβ positive feedback loop with the drug fasudil can restore the balance between Wnt pathways, prevent dendritic spine withdrawal in vitro, and reduce Aβ load in vivo in mice with advanced amyloid pathology. These results clarify a relationship between Aβ accumulation and synapse loss and provide direction for the development of potential disease-modifying treatments.
Hepatic Ago2-mediated RNA silencing controls energy metabolism linked to AMPK activation and obesity-associated pathophysiology
Authors: Zhang Cai , Seo Joonbae , Murakami Kazutoshi , Salem Esam S. B. , Bernhard Elise , Borra Vishnupriya J. , Choi Kwangmin , Yuan Celvie L. , Chan Calvin C. , Chen Xiaoting , Huang Taosheng , Weirauch Matthew T. , Divanovic Senad , Qi Nathan R. , Thomas Hala Einakat , Mercer Carol A. , Siomi Haruhiko , Nakamura Takahisa 
Published: September 2018

AbstractRNA silencing inhibits mRNA translation. While mRNA translation accounts for the majority of cellular energy expenditure, it is unclear if RNA silencing regulates energy homeostasis. Here, we report that hepatic Argonaute 2 (Ago2)-mediated RNA silencing regulates both intrinsic energy production and consumption and disturbs energy metabolism in the pathogenesis of obesity. Ago2 regulates expression of specific miRNAs including miR-802, miR-103/107, and miR-148a/152, causing metabolic disruption, while simultaneously suppressing the expression of genes regulating glucose and lipid metabolism, including Hnf1β, Cav1, and Ampka1. Liver-specific Ago2-deletion enhances mitochondrial oxidation and ATP consumption associated with mRNA translation, which results in AMPK activation, and improves obesity-associated pathophysiology. Notably, hepatic Ago2-deficiency improves glucose metabolism in conditions of insulin receptor antagonist treatment, high-fat diet challenge, and hepatic AMPKα1-deletion. The regulation of energy metabolism by Ago2 provides a novel paradigm in which RNA silencing plays an integral role in determining basal metabolic activity in obesity-associated sequelae.
Deglacial mobilization of pre-aged terrestrial carbon from degrading permafrost
Authors: Winterfeld Maria , Mollenhauer Gesine , Dummann Wolf , Köhler Peter , Lembke-Jene Lester , Meyer Vera D. , Hefter Jens , McIntyre Cameron , Wacker Lukas , Kokfelt Ulla , Tiedemann Ralf 
Published: September 2018

AbstractThe mobilization of glacial permafrost carbon during the last glacial–interglacial transition has been suggested by indirect evidence to be an additional and significant source of greenhouse gases to the atmosphere, especially at times of rapid sea-level rise. Here we present the first direct evidence for the release of ancient carbon from degrading permafrost in East Asia during the last 17 kyrs, using biomarkers and radiocarbon dating of terrigenous material found in two sediment cores from the Okhotsk Sea. Upscaling our results to the whole Arctic shelf area, we show by carbon cycle simulations that deglacial permafrost-carbon release through sea-level rise likely contributed significantly to the changes in atmospheric CO2 around 14.6 and 11.5 kyrs BP.
CXCL12 and MYC control energy metabolism to support adaptive responses after kidney injury
Authors: Yakulov Toma A. , Todkar Abhijeet P. , Slanchev Krasimir , Wiegel Johannes , Bona Alexandra , Groß Martin , Scholz Alexander , Hess Isabell , Wurditsch Anne , Grahammer Florian , Huber Tobias B. , Lecaudey Virginie , Bork Tillmann , Hochrein Jochen , Boerries Melanie , Leenders Justine , de Tullio Pascal , Jouret François , Kramer-Zucker Albrecht , Walz Gerd 
Published: September 2018

AbstractKidney injury is a common complication of severe disease. Here, we report that injuries of the zebrafish embryonal kidney are rapidly repaired by a migratory response in 2-, but not in 1-day-old embryos. Gene expression profiles between these two developmental stages identifycxcl12aandmycaas candidates involved in the repair process. Zebrafish embryos withcxcl12a,cxcr4b, ormycadeficiency display repair abnormalities, confirming their role in response to injury. In mice with a kidney-specific knockout,Cxcl12andMycgene deletions suppress mitochondrial metabolism and glycolysis, and delay the recovery after ischemia/reperfusion injury. Probing these observations in zebrafish reveal that inhibition of glycolysis slows fast migrating cells and delays the repair after injury, but does not affect the slow cell movements during kidney development. Our findings demonstrate thatCxcl12andMycfacilitate glycolysis to promote fast migratory responses during development and repair, and potentially also during tumor invasion and metastasis.
Gut fungal dysbiosis correlates with reduced efficacy of fecal microbiota transplantation in Clostridium difficile infection
Authors: Zuo Tao , Wong Sunny H. , Cheung Chun Pan , Lam Kelvin , Lui Rashid , Cheung Kitty , Zhang Fen , Tang Whitney , Ching Jessica Y. L. , Wu Justin C. Y. , Chan Paul K. S. , Sung Joseph J. Y. , Yu Jun , Chan Francis K. L. , Ng Siew C. 
Published: September 2018

AbstractFecal microbiota transplantation (FMT) is effective in treating recurrent Clostridium difficile infection (CDI). Bacterial colonization in recipients after FMT has been studied, but little is known about the role of the gut fungal community, or mycobiota. Here, we show evidence of gut fungal dysbiosis in CDI, and that donor-derived fungal colonization in recipients is associated with FMT response. CDI is accompanied by over-representation of Candida albicans and decreased fungal diversity, richness, and evenness. Cure after FMT is associated with increased colonization of donor-derived fungal taxa in recipients. Recipients of successful FMT (“responders”) display, after FMT, a high relative abundance of Saccharomyces and Aspergillus, whereas “nonresponders” and individuals treated with antibiotics display a dominant presence of Candida. High abundance of C. albicans in donor stool also correlates with reduced FMT efficacy. Furthermore, C. albicans reduces FMT efficacy in a mouse model of CDI, while antifungal treatment reestablishes its efficacy, supporting a potential causal relationship between gut fungal dysbiosis and FMT outcome.
Contribution of allelic imbalance to colorectal cancer
Authors: Palin Kimmo , Pitkänen Esa , Turunen Mikko , Sahu Biswajyoti , Pihlajamaa Päivi , Kivioja Teemu , Kaasinen Eevi , Välimäki Niko , Hänninen Ulrika A. , Cajuso Tatiana , Aavikko Mervi , Tuupanen Sari , Kilpivaara Outi , van den Berg Linda , Kondelin Johanna , Tanskanen Tomas , Katainen Riku , Grau Marta , Rauanheimo Heli , Plaketti Roosa-Maria , Taira Aurora , Sulo Päivi , Hartonen Tuomo , Dave Kashyap , Schmierer Bernhard , Botla Sandeep , Sokolova Maria , Vähärautio Anna , Gladysz Kornelia , Ongen Halit , Dermitzakis Emmanouil , Bramsen Jesper Bertram , Ørntoft Torben Falck , Andersen Claus Lindbjerg , Ristimäki Ari , Lepistö Anna , Renkonen-Sinisalo Laura , Mecklin Jukka-Pekka , Taipale Jussi , Aaltonen Lauri A. 
Published: September 2018

AbstractPoint mutations in cancer have been extensively studied but chromosomal gains and losses have been more challenging to interpret due to their unspecific nature. Here we examine high-resolution allelic imbalance (AI) landscape in 1699 colorectal cancers, 256 of which have been whole-genome sequenced (WGSed). The imbalances pinpoint 38 genes as plausible AI targets based on previous knowledge. Unbiased CRISPR-Cas9 knockout and activation screens identified in total 79 genes within AI peaks regulating cell growth. Genetic and functional data implicate loss of TP53 as a sufficient driver of AI. The WGS highlights an influence of copy number aberrations on the rate of detected somatic point mutations. Importantly, the data reveal several associations between AI target genes, suggesting a role for a network of lineage-determining transcription factors in colorectal tumorigenesis. Overall, the results unravel the contribution of AI in colorectal cancer and provide a plausible explanation why so few genes are commonly affected by point mutations in cancers.
Conserved collateral antibiotic susceptibility networks in diverse clinical strains of Escherichia coli
Authors: Podnecky Nicole L. , Fredheim Elizabeth G. A. , Kloos Julia , Sørum Vidar , Primicerio Raul , Roberts Adam P. , Rozen Daniel E. , Samuelsen Ørjan , Johnsen Pål J. 
Published: September 2018

AbstractThere is urgent need to develop novel treatment strategies to reduce antimicrobial resistance. Collateral sensitivity (CS), where resistance to one antimicrobial increases susceptibility to other drugs, might enable selection against resistance during treatment. However, the success of this approach would depend on the conservation of CS networks across genetically diverse bacterial strains. Here, we examine CS conservation across diverse Escherichia coli strains isolated from urinary tract infections. We determine collateral susceptibilities of mutants resistant to relevant antimicrobials against 16 antibiotics. Multivariate statistical analyses show that resistance mechanisms, in particular efflux-related mutations, as well as the relative fitness of resistant strains, are principal contributors to collateral responses. Moreover, collateral responses shift the mutant selection window, suggesting that CS-informed therapies may affect evolutionary trajectories of antimicrobial resistance. Our data allow optimism for CS-informed therapy and further suggest that rapid detection of resistance mechanisms is important to accurately predict collateral responses.
A considerable fraction of soil-respired CO2 is not emitted directly to the atmosphere
Authors: Sánchez-Cañete Enrique P. , Barron-Gafford Greg A. , Chorover Jon 
Published: September 2018

AbstractSoil CO2 efflux (Fsoil) is commonly considered equal to soil CO2 production (Rsoil), and both terms are used interchangeably. However, a non-negligible fraction of Rsoil can be consumed in the subsurface due to a host of disparate, yet simultaneous processes. The ratio between CO2 efflux/O2 influx, known as the apparent respiratory quotient (ARQ), enables new insights into CO2 losses from Rsoil not previously captured by Fsoil. We present the first study using continuous ARQ estimates to evaluate annual CO2 losses of carbon produced from Rsoil. We found that up to 1/3 of Rsoil was emitted directly to the atmosphere, whereas 2/3 of Rsoil was removed by subsurface processes. These subsurface losses are attributable to dissolution in water, biological activities and chemical reactions. Having better estimates of Rsoil is key to understanding the true influence of ecosystem production on Rsoil, as well as the role of soil CO2 production in other connected processes within the critical zone.
De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome
Authors: Huerlimann Roger , Wade Nicholas M. , Gordon Lavinia , Montenegro Juan D. , Goodall Jake , McWilliam Sean , Tinning Matthew , Siemering Kirby , Giardina Erika , Donovan Dallas , Sellars Melony J. , Cowley Jeff A. , Condon Kelly , Coman Greg J. , Khatkar Mehar S. , Raadsma Herman W. , Maes Gregory E. , Zenger Kyall R. , Jerry Dean R. 
Published: September 2018

AbstractThe black tiger shrimp (Penaeus monodon) remains the second most widely cultured shrimp species globally; however, issues with disease and domestication have seen production levels stagnate over the past two decades. To help identify innovative solutions needed to resolve bottlenecks hampering the culture of this species, it is important to generate genetic and genomic resources. Towards this aim, we have produced the most complete publicly available P. monodon transcriptome database to date based on nine adult tissues and eight early life-history stages (BUSCO - Complete: 98.2% [Duplicated: 51.3%], Fragmented: 0.8%, Missing: 1.0%). The assembly resulted in 236,388 contigs, which were then further segregated into 99,203 adult tissue specific and 58,678 early life-history stage specific clusters. While annotation rates were low (approximately 30%), as is typical for a non-model organisms, annotated transcript clusters were successfully mapped to several hundred functional KEGG pathways. Transcripts were clustered into groups within tissues and early life-history stages, providing initial evidence for their roles in specific tissue functions, or developmental transitions. We expect the transcriptome to provide an essential resource to investigate the molecular basis of commercially relevant-significant traits in P. monodon and other shrimp species.
Transcriptome Analysis of Gossypium hirsutum L. Reveals Different Mechanisms among NaCl, NaOH and Na2CO3 Stress Tolerance
Authors: Zhang Binglei , Chen Xiugui , Lu Xuke , Shu Na , Wang Xiaoge , Yang Xiaomin , Wang Shuai , Wang Junjuan , Guo Lixue , Wang Delong , Ye Wuwei 
Published: September 2018

AbstractAs an important source of fiber and edible oil, cotton has great economic value. In comparison to their individual studies, association and differentiation between salt and alkaline tolerance has not been focused yet by scientists. We have used next-generation RNA-Seq technique to analyze transcriptional changes under salt and alkaline stresses in cotton. Overall, 25,929 and 6,564 differentially expressed genes (DEGs) were identified in roots and leaves, respectively. Gene functional annotation showed that genes involving ionic homeostasis were significantly up-regulated under NaCl stress and Na2CO3 stress, and genes enriched in starch and sucrose metabolism were up-regulated under NaOH stress and Na2CO3 stress. Furthermore, a synergistic enhancing effect between NaCl and NaOH stress was also observed in this study. Likewise, our studies indicate further that genes related with starch and sucrose metabolism were regulated to respond to the high pH under Na2CO3 stress, inducing plant hormone signal transduction and key enzyme reactive oxygen species (ROS) activity to respond to ionic toxicity and intracellular ionic homeostasis. By analyzing the expression profiles of diverse tissues under different salt and alkaline stresses, this study provides valuable ideas for genetic improvements of cotton tolerance to salt-alkaline stress.