bluuebunny/crossref_metadata_2025_split huggingface dataset:
An antifungal polyketide associated with horizontally acquired genes supports symbiont-mediated defense in Lagria villosa beetles
Authors: Flórez Laura V. , Scherlach Kirstin , Miller Ian J. , Rodrigues Andre , Kwan Jason C. , Hertweck Christian , Kaltenpoth Martin 
Published: June 2018

AbstractMicrobial symbionts are often a source of chemical novelty and can contribute to host defense against antagonists. However, the ecological relevance of chemical mediators remains unclear for most systems.Lagriabeetles live in symbiosis with multiple strains ofBurkholderiabacteria that protect their offspring against pathogens. Here, we describe the antifungal polyketide lagriamide, and provide evidence supporting that it is produced by an uncultured symbiont,Burkholderia gladioliLv-StB, which is dominant in field-collectedLagria villosa. Interestingly, lagriamide is structurally similar to bistramides, defensive compounds found in marine tunicates. We identify a gene cluster that is probably involved in lagriamide biosynthesis, provide evidence for horizontal acquisition of these genes, and show that the naturally occurring symbiont strains on the egg are protective in the soil environment. Our findings highlight the potential of microbial symbionts and horizontal gene transfer as influential sources of ecological innovation.
TP53 protein levels, RNA-based pathway assessment, and race among invasive breast cancer cases
Authors: Williams Lindsay A. , Butler Ebonee N. , Sun Xuezheng , Allott Emma H. , Cohen Stephanie M. , Fuller Ashley M. , Hoadley Katherine A. , Perou Charles M. , Geradts Joseph , Olshan Andrew F. , Troester Melissa A. 
Published: June 2018

AbstractMutations in tumor suppressor TP53 have been inconsistently linked to breast cancer risk factors and survival. Immunohistochemistry (IHC) staining, a primary clinical means of TP53 mutation determination, only detects mutations that facilitate protein accumulation (e.g., missense mutations). RNA-based pathway methods capture functional status and may aid in understanding the role of TP53 function in racial disparities of breast cancer. TP53 status was assessed among invasive breast cancer cases from the Carolina Breast Cancer Study (CBCS) (2008–2013) using IHC and an established RNA-based TP53 signature (CBCS and The Cancer Genome Atlas (TCGA)). Frequency of TP53 status (IHC, RNA-based) was estimated in association with tumor characteristics, PAM50 intrinsic subtype, age, and race using relative frequency differences (RFDs) and 95% confidence intervals (95% CI) as the measure of association. Approximately 60% of basal-like tumors were TP53 protein positive (IHC), while nearly 100% were TP53 mutant-like (RNA). Luminal A tumors had low frequency of TP53 positivity (IHC: 7.9%) and mutant-like status (RNA: 1.7%). Mutant-like TP53 (RNA) was strongly associated with age ≤50 years, high tumor grade, advanced stage of disease, large tumor size, and basal-like and HER2 intrinsic subtypes. Black race was strongly associated with TP53 mutant-like status (RNA) (RFD: 24.8%, 95% CI: 20.5, 29.0) even after adjusting for age, grade, stage (RFD: 11.3%; 95% CI: 7.6, 15.0). Associations were attenuated and non-significant when measured by IHC. IHC-based TP53 status is an insensitive measurement of TP53 functional status. RNA-based methods suggest a role for TP53 in tumor prognostic features and racial disparities.
Transcriptional analysis of adipose tissue during development reveals depot-specific responsiveness to maternal dietary supplementation
Authors: Fainberg Hernan P. , Birtwistle Mark , Alagal Reham , Alhaddad Ahmad , Pope Mark , Davies Graeme , Woods Rachel , Castellanos Marcos , May Sean T. , Ortori Catharine A. , Barrett David A. , Perry Viv , Wiens Frank , Stahl Bernd , van der Beek Eline , Sacks Harold , Budge Helen , Symonds Michael E. 
Published: June 2018

AbstractBrown adipose tissue (BAT) undergoes pronounced changes after birth coincident with the loss of the BAT-specific uncoupling protein (UCP)1 and rapid fat growth. The extent to which this adaptation may vary between anatomical locations remains unknown, or whether the process is sensitive to maternal dietary supplementation. We, therefore, conducted a data mining based study on the major fat depots (i.e. epicardial, perirenal, sternal (which possess UCP1 at 7 days), subcutaneous and omental) (that do not possess UCP1) of young sheep during the first month of life. Initially we determined what effect adding 3% canola oil to the maternal diet has on mitochondrial protein abundance in those depots which possessed UCP1. This demonstrated that maternal dietary supplementation delayed the loss of mitochondrial proteins, with the amount of cytochrome C actually being increased. Using machine learning algorithms followed by weighted gene co-expression network analysis, we demonstrated that each depot could be segregated into a unique and concise set of modules containing co-expressed genes involved in adipose function. Finally using lipidomic analysis following the maternal dietary intervention, we confirmed the perirenal depot to be most responsive. These insights point at new research avenues for examining interventions to modulate fat development in early life.
Host-plant induced changes in microbial community structure and midgut gene expression in an invasive polyphage (Anoplophora glabripennis)
Authors: Scully Erin D. , Geib Scott M. , Mason Charles J. , Carlson John E. , Tien Ming , Chen Han-Yi , Harding Scott , Tsai Chung-Jui , Hoover Kelli 
Published: June 2018

AbstractPolyphagous insect herbivores possess diverse mechanisms to overcome challenges of feeding in multiple plant species including, but not limited to, transcriptional plasticity and associations with obligate or facultative symbionts. The Asian longhorned beetle (Anoplophora glabripennis) is a polyphagous wood-feeder capable of developing on over 100 tree species and, like other polyphages, its genome contains amplifications of digestive and detoxification genes. This insect also possesses a diverse gut microbial community, which has the metabolic potential to augment digestive physiology. While the genomic repertoires of A. glabripennis and its microbial community have been studied previously, comparatively less is known about how the gut transcriptome and community change in response to feeding in different hosts. In this study, we show that feeding in two suitable hosts (Acer spp. and Populus nigra) altered the expression levels of multicopy genes linked to digestion and detoxification. However, feeding in a host with documented resistance (Populus tomentosa) induced changes in the transcriptome and community beyond what was observed in insects reared in P. nigra, including the downregulation of numerous β-glucosidases, odorant binding proteins, and juvenile hormone binding proteins, the upregulation of several cuticular genes, and the loss of one major bacterial family from the gut community.
Ultrathin amorphous carbon films synthesized by filtered cathodic vacuum arc used as protective overcoats of heat-assisted magnetic recording heads
Authors: Matlak J. , Komvopoulos K. 
Published: June 2018

AbstractDespite numerous investigations of amorphous carbon (a-C) films, a comprehensive study of the feasibility and optimization of sub-5-nm-thick a-C films deposited onto the write pole of heat-assisted magnetic recording (HAMR) heads is lacking. The main objective of this study was to identify the role of pulse substrate bias voltage and C+ ion incidence angle on the structure and thickness of 1–4-nm-thick a-C films deposited by a rather new thin-film deposition method, known as filtered cathodic vacuum arc (FCVA). The cross-sectional structure of a-C films synthesized under various FCVA conditions was examined by high-resolution transmission electron microscopy (HRTEM), scanning transmission electron microscopy (STEM), and electron energy loss spectroscopy (EELS). It was found that film growth under process conditions of low-to-intermediate substrate bias voltage (in the range of −25 to −100  V), low ion incidence angle (10°), very short deposition time (6 s), and fixed other deposition parameters (65% duty cycle of substrate pulse biasing and 1.48 × 1019 ions/m2·s ion flux) yields a-C films of thickness ≤4 nm characterized by a significant content (~50–60 at%) of tetrahedral (sp3) carbon atom hybridization. A threshold where sp3 hybridization is greatly reduced due to limited film growth was determined from the HRTEM/STEM and EELS measurements. The results of this study demonstrate the viability of FCVA to produce extremely thin and uniform protective a-C films with relatively high sp3 contents for HAMR heads.
Omics approaches revealed how arbuscular mycorrhizal symbiosis enhances yield and resistance to leaf pathogen in wheat
Authors: Fiorilli Valentina , Vannini Candida , Ortolani Francesca , Garcia-Seco Daniel , Chiapello Marco , Novero Mara , Domingo Guido , Terzi Valeria , Morcia Caterina , Bagnaresi Paolo , Moulin Lionel , Bracale Marcella , Bonfante Paola 
Published: June 2018

AbstractBesides improved mineral nutrition, plants colonised by arbuscular mycorrhizal (AM) fungi often display increased biomass and higher tolerance to biotic and abiotic stresses. Notwithstanding the global importance of wheat as an agricultural crop, its response to AM symbiosis has been poorly investigated. We focused on the role of an AM fungus on mineral nutrition of wheat, and on its potential protective effect against Xanthomonas translucens. To address these issues, phenotypical, molecular and metabolomic approaches were combined. Morphological observations highlighted that AM wheat plants displayed an increased biomass and grain yield, as well as a reduction in lesion area following pathogen infection. To elucidate the molecular mechanisms underlying the mycorrhizal phenotype, we investigated changes of transcripts and proteins in roots and leaves during the double (wheat-AM fungus) and tripartite (wheat-AM fungus-pathogen) interaction. Transcriptomic and proteomic profiling identified the main pathways involved in enhancing plant biomass, mineral nutrition and in promoting the bio-protective effect against the leaf pathogen. Mineral and amino acid contents in roots, leaves and seeds, and protein oxidation profiles in leaves, supported the omics data, providing new insight into the mechanisms exerted by AM symbiosis to confer stronger productivity and enhanced resistance to X. translucens in wheat.
Elucidating the hypoxic stress response in barley (Hordeum vulgare L.) during waterlogging: A proteomics approach
Authors: Luan Haiye , Shen Huiquan , Pan Yuhan , Guo Baojian , Lv Chao , Xu Rugen 
Published: June 2018

AbstractWaterlogging is one of the major abiotic stresses that affects barley production and yield quality. Proteomics techniques have been widely utilized to explore the mechanisms involved in the responses to abiotic stress. In this study, two barley genotypes with contrasting responses to waterlogging stress were analyzed with proteomic technology. The waterlogging treatment caused a greater reduction in biomass and photosynthetic performance in the waterlogging-sensitive genotype TF57 than that in the waterlogging-tolerant genotype TF58. Under waterlogging stress, 30, 30, 20 and 20 differentially expressed proteins were identified through tandem mass spectrometry analysis in the leaves, adventitious roots, nodal roots and seminal roots, respectively. Among these proteins, photosynthesis-, metabolism- and energy-related proteins were differentially expressed in the leaves, with oxygen-evolving enhancer protein 1, ATP synthase subunit and heat shock protein 70 being up-regulated in TF58. Pyruvate decarboxylase (PDC), 1-amino cyclopropane 1-carboxylic acid oxidase (ACO), glutamine synthetase (GS), glutathione S-transferases (GST) and beta-1, 3-glucanase in adventitious, nodal and seminal roots were more abundant in TF58 than those in TF57 under waterlogging stress. Ten representative genes were selected for validation by qRT-PCR in different genotypes with known waterlogging tolerance, and the expression levels of three candidate genes (PDC, ACO and GST) increased in the roots of all genotypes in response to the waterlogging stress. These three genes might play a significant role in the adaptation process of barley under waterlogging stress. The current results partially determined the mechanisms of waterlogging tolerance and provided valuable information for the breeding of barley with enhanced tolerance to waterlogging.
Coherent control theory and experiment of optical phonons in diamond
Authors: Sasaki Hiroya , Tanaka Riho , Okano Yasuaki , Minami Fujio , Kayanuma Yosuke , Shikano Yutaka , Nakamura Kazutaka G. 
Published: June 2018

AbstractThe coherent control of optical phonons has been experimentally demonstrated in various physical systems. While the transient dynamics for optical phonons can be explained by phenomenological models, the coherent control experiment cannot be explained due to the quantum interference. Here, we theoretically propose the generation and detection processes of the optical phonons and experimentally confirm our theoretical model using the diamond optical phonon by the doublepump-probe type experiment.
Accumulation of poly(A) RNA in nuclear granules enriched in Sam68 in motor neurons from the SMNΔ7 mouse model of SMA
Authors: Narcís J. Oriol , Tapia Olga , Tarabal Olga , Piedrafita Lídia , Calderó Jordi , Berciano Maria T. , Lafarga Miguel 
Published: June 2018

AbstractSpinal muscular atrophy (SMA) is a severe motor neuron (MN) disease caused by the deletion or mutation of the survival motor neuron 1 (SMN1) gene, which results in reduced levels of the SMN protein and the selective degeneration of lower MNs. The best-known function of SMN is the biogenesis of spliceosomal snRNPs, the major components of the pre-mRNA splicing machinery. Therefore, SMN deficiency in SMA leads to widespread splicing abnormalities. We used the SMN∆7 mouse model of SMA to investigate the cellular reorganization of polyadenylated mRNAs associated with the splicing dysfunction in MNs. We demonstrate that SMN deficiency induced the abnormal nuclear accumulation in euchromatin domains of poly(A) RNA granules (PARGs) enriched in the splicing regulator Sam68. However, these granules lacked other RNA-binding proteins, such as TDP43, PABPN1, hnRNPA12B, REF and Y14, which are essential for mRNA processing and nuclear export. These effects were accompanied by changes in the alternative splicing of the Sam68-dependent Bcl-x and Nrnx1 genes, as well as changes in the relative accumulation of the intron-containing Chat, Chodl, Myh9 and Myh14 mRNAs, which are all important for MN functions. PARG-containing MNs were observed at presymptomatic SMA stage, increasing their number during the symptomatic stage. Moreover, the massive accumulations of poly(A) RNA granules in MNs was accompanied by the cytoplasmic depletion of polyadenylated mRNAs for their translation. We suggest that the SMN-dependent abnormal accumulation of polyadenylated mRNAs and Sam68 in PARGs reflects a severe dysfunction of both mRNA processing and translation, which could contribute to SMA pathogenesis.
Development of an optimal imaging strategy for selection of patients for affibody-based PNA-mediated radionuclide therapy
Authors: Vorobyeva Anzhelika , Westerlund Kristina , Mitran Bogdan , Altai Mohamed , Rinne Sara , Sörensen Jens , Orlova Anna , Tolmachev Vladimir , Karlström Amelie Eriksson 
Published: June 2018

AbstractAffibody molecules are engineered scaffold proteins, which demonstrated excellent binding to selected tumor-associated molecular abnormalities in vivo and highly sensitive and specific radionuclide imaging of Her2-expressing tumors in clinics. Recently, we have shown that peptide nucleic acid (PNA)-mediated affibody-based pretargeted radionuclide therapy using beta-emitting radionuclide 177Lu extended significantly survival of mice bearing human Her2-expressing tumor xenografts. In this study, we evaluated two approaches to use positron emission tomography (PET) for stratification of patients for affibody-based pretargeting therapy. The primary targeting probe ZHER2:342-SR-HP1 and the secondary probe HP2 (both conjugated with DOTA chelator) were labeled with the positron-emitting radionuclide 68Ga. Biodistribution of both probes was measured in BALB/C nu/nu mice bearing either SKOV-3 xenografts with high Her2 expression or DU-145 xenografts with low Her2 expression. 68Ga-HP2 was evaluated in the pretargeting setting. Tumor uptake of both probes was compared with the uptake of pretargeted 177Lu-HP2. The uptake of both 68Ga-ZHER2:342-SR-HP1 and 68Ga-HP2 depended on Her2-expression level providing clear discrimination of between tumors with high and low Her2 expression. Tumor uptake of 68Ga-HP2 correlated better with the uptake of 177Lu-HP2 than the uptake of 68Ga-ZHER2:342-SR-HP1. The use of 68Ga-HP2 as a theranostics counterpart would be preferable approach for clinical translation.
Silk protein nanofibers for highly efficient, eco-friendly, optically translucent, and multifunctional air filters
Authors: Min Kyungtaek , Kim Sookyoung , Kim Sunghwan 
Published: June 2018

AbstractNew types of air filter technologies are being called because air pollution by particulate matters (PMs) and volatile organic compounds has raised serious concerns for public health. Conventional air filters have limited application and poor degradability and they become non-disposable wastes after use. Here, we report a highly efficient, eco-friendly, translucent, and multifunctional air purification filter that is highly effective for reducing air pollution, protecting the environment, and detecting hazardous chemical vapors encountered in everyday life. Uniform silk protein nanofibers were directly generated on a window screen by an electrospinning process. Optical properties (translucence and scattering) of the silk nanofibrous air filters (SNAFs) are advantageous for achieving viewability and controlling the room temperature. Air filtration efficiencies of the fabricated SNAFs could reach up to 90% and 97% for PMs with sizes under 2.5 and 10 μm, respectively, exceeding the performances of commercial semi-high-efficiency particulate air (semi-HEPA) filters. After use, the SNAFs could be naturally degraded. Furthermore, we demonstrate the ability of SNAFs impregnated with organic dyes to sense hazardous and volatile vapors encountered in everyday life.
Descending neurons from the lateral accessory lobe and posterior slope in the brain of the silkmoth Bombyx mori
Authors: Namiki Shigehiro , Wada Satoshi , Kanzaki Ryohei 
Published: June 2018

AbstractA population of descending neurons connect the brain and thoracic motor center, playing a critical role in controlling behavior. We examined the anatomical organization of descending neurons (DNs) in the brain of the silkmoth Bombyx mori. Moth pheromone orientation is a good model to investigate neuronal mechanisms of behavior. Based on mass staining and single-cell staining, we evaluated the anatomical organization of neurite distribution by DNs in the brain. Dense innervation was observed in the posterior–ventral part of the brain called the posterior slope (PS). We analyzed the morphology of DNs innervating the lateral accessory lobe (LAL), which is considered important for moth olfactory behavior. We observed that all LAL DNs also innervate the PS, suggesting the integration of signals from the LAL and PS. We also identified a set of DNs innervating the PS but not the LAL. These DNs were sensitive to the sex pheromone, suggesting a role of the PS in motor control for pheromone processing. Here we discuss the organization of descending pathways for pheromone orientation.
Bryozoans are Major Modern Builders of South Atlantic Oddly Shaped Reefs
Authors: Bastos Alex C. , Moura Rodrigo L. , Moraes Fernando C. , Vieira Laura S. , Braga Juan Carlos , Ramalho Laís V. , Amado-Filho Gilberto M. , Magdalena Ulises R. , Webster Jody M. 
Published: June 2018

AbstractIn major modern reef regions, either in the Indo-Pacific or the Caribbean, scleractinian corals are described as the main reef framework builders, often associated with crustose coralline algae. We used underwater cores to investigate Late Holocene reef growth and characterise the main framework builders in the Abrolhos Shelf, the largest and richest modern tropical reef complex in the South Western Atlantic, a scientifically underexplored reef province. Rather than a typical coralgal reef, our results show a complex framework building system dominated by bryozoans. Bryozoans were major components in all cores and age intervals (2,000 yrs BP), accounting for up to 44% of the reef framework, while crustose coralline algae and coral accounted for less than 28 and 23%, respectively. Reef accretion rates varied from 2.7 to 0.9 mm yr−1, which are similar to typical coralgal reefs. Bryozoan functional groups encompassed 20 taxa and Celleporaria atlantica (Busk, 1884) dominated the framework at all cores. While the prevalent mesotrophic conditions may have driven suspension-feeders’ dominance over photoautotrophs and mixotrophs, we propose that a combination of historical factors with the low storm-disturbance regime of the tropical South Atlantic also contributed to the region’s low diversity, and underlies the unique mushroom shape of the Abrolhos pinnacles.
Gut microbiota components are associated with fixed airway obstruction in asthmatic patients living in the tropics
Authors: Buendía Emiro , Zakzuk Josefina , San-Juan-Vergara Homero , Zurek Eduardo , Ajami Nadim J. , Caraballo Luis 
Published: June 2018

AbstractMicrobiome composition has been associated to several inflammatory diseases, including asthma. There are few studies exploring the relationships of gut microbiota with airway obstruction pheonotypes in adult asthma, especially those living in the tropics. We sought to evaluate the relationships of gut microbiota with the airway obstruction and other variables of interest in asthmatic patients living in the tropics according to three phenotypes: No Airway Obstruction (NAO), Reversible Airway Obstruction (RAO) or Fixed Airway Obstruction (FAO). We found that Streptococcaceae:Streptococcus and Enterobacteriaceae:Escherichia-Shigella consistently discriminated asthmatic individuals suffering FAO from NAO or RAO, plus Veillonellaceae:Megasphaera when comparing FAO and RAO (p < 0.05; FDR < 0.05). In the FAO, the network showing the genus relations was less complex and interconnected. Several Rumminococcaceae, Lachnospiraceae and Clostridiales were enriched in patients with low specific IgE levels to mites and Ascaris. All patients shared a common exposure framework; control medication usage and smoking habit were uncommon and equally distributed between them. In conclusion, in this tropical asthmatic population, components of human gut microbiota are associated with the presence of a FAO phenotype and lower specific IgE response to mites and Ascaris.