bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limited influence of the microbiome on the transcriptional profile of female Aedes aegypti mosquitoes
Authors: Hyde Josephine , Correa Maria A. , Hughes Grant L. , Steven Blaire , Brackney Doug E. 
Published: July 2020

AbstractThe microbiome is an assemblage of microorganisms living in association with a multicellular host. Numerous studies have identified a role for the microbiome in host physiology, development, immunity, and behaviour. The generation of axenic (germ-free) and gnotobiotic model systems has been vital to dissecting the role of the microbiome in host biology. We have previously reported the generation of axenic Aedes aegypti mosquitoes, the primary vector of several human pathogenic viruses, including dengue virus and Zika virus. In order to better understand the influence of the microbiome on mosquitoes, we examined the transcriptomes of axenic and conventionally reared Ae. aegypti before and after a blood meal. Our results suggest that the microbiome has a much lower effect on the mosquito’s gene expression than previously thought with only 170 genes influenced by the axenic state, while in contrast, blood meal status influenced 809 genes. The pattern of expression influenced by the microbiome is consistent with transient changes similar to infection rather than sweeping physiological changes. While the microbiome does seem to affect some pathways such as immune function and metabolism, our data suggest the microbiome is primarily serving a nutritional role in development with only minor effects in the adult.
PCDH7 interacts with GluN1 and regulates dendritic spine morphology and synaptic function
Authors: Wang Yuanyuan , Kerrisk Campbell Meghan , Tom Irene , Foreman Oded , Hanson Jesse E. , Sheng Morgan 
Published: July 2020

AbstractThe N-terminal domain (NTD) of the GluN1 subunit (GluN1-NTD) is important for NMDA receptor structure and function, but the interacting proteins of the GluN1-NTD are not well understood. Starting with an unbiased screen of ~ 1,500 transmembrane proteins using the purified GluN1-NTD protein as a bait, we identify Protocadherin 7 (PCDH7) as a potential interacting protein. PCDH7 is highly expressed in the brain and has been linked to CNS disorders, including epilepsy. Using primary neurons and brain slice cultures, we find that overexpression and knockdown of PCDH7 induce opposing morphological changes of dendritic structures. We also find that PCDH7 overexpression reduces synaptic NMDA receptor currents. These data show that PCDH7 can regulate dendritic spine morphology and synaptic function, possibly via interaction with the GluN1 subunit.
The colonic mucosa-associated microbiome in SIV infection: shift towards Bacteroidetes coincides with mucosal CD4+ T cell depletion and enterocyte damage
Authors: Allers Kristina , Stahl-Hennig Christiane , Fiedler Tomas , Wibberg Daniel , Hofmann Jörg , Kunkel Désirée , Moos Verena , Kreikemeyer Bernd , Kalinowski Jörn , Schneider Thomas 
Published: July 2020

AbstractThe intesinal microbiome is considered important in human immunodeficiency virus (HIV) pathogenesis and therefore represents a potential therapeutic target to improve the patients’ health status. Longitudinal alterations in the colonic mucosa-associated microbiome during simian immunodeficiency virus (SIV) infection were investigated using a 16S rRNA amplicon approach on the Illumina sequencing platform and bioinformatics analyses. Following SIV infection of six animals, no alterations in microbial composition were observed before the viral load peaked in the colon. At the time of acute mucosal SIV replication, the phylum Bacteroidetes including the Bacteroidia class as well as the phylum Firmicutes and its families Ruminococcaceae and Eubacteriaceae became more abundant. Enrichment of Bacteroidetes was maintained until the chronic phase of SIV infection. The shift towards Bacteroidetes in the mucosa-associated microbiome was associated with the extent of SIV infection-induced mucosal CD4+ T cell depletion and correlated with increasing rates of enterocyte damage. These observations suggest that Bacteroidetes strains increase during virus-induced mucosal immune destruction. As Bacteroidetes belong to the lipopolysaccharide- and short chain fatty acids-producing bacteria, their rapid enrichment may contribute to inflammatory tissue damage and metabolic alterations in SIV/HIV infection. These aspects should be considered in future studies on therapeutic interventions.
Build-up of serial dependence in color working memory
Authors: Barbosa Joao , Compte Albert 
Published: July 2020

AbstractSerial dependence, how immediately preceding experiences bias our current estimations, has been described experimentally during delayed-estimation of many different visual features, with subjects tending to make estimates biased towards previous ones. It has been proposed that these attractive biases help perception stabilization in the face of correlated natural scene statistics, although this remains mostly theoretical. Color, which is strongly correlated in natural scenes, has never been studied with regard to its serial dependencies. Here, we found significant serial dependence in 7 out of 8 datasets with behavioral data of humans (total n = 760) performing delayed-estimation of color with uncorrelated sequential stimuli. Moreover, serial dependence strength built up through the experimental session, suggesting metaplastic mechanisms operating at a slower time scale than previously proposed (e.g. short-term synaptic facilitation). Because, in contrast with natural scenes, stimuli were temporally uncorrelated, this build-up casts doubt on serial dependencies being an ongoing adaptation to the stable statistics of the environment.
Genome-wide mapping and allelic fingerprinting provide insights into the genetics of resistance to wheat stripe rust in India, Kenya and Mexico
Authors: Juliana Philomin , Singh Ravi Prakash , Huerta-Espino Julio , Bhavani Sridhar , Randhawa Mandeep S. , Kumar Uttam , Joshi Arun Kumar , Bhati Pradeep Kumar , Mir Hector Eduardo Villasenor , Mishra Chandra Nath , Singh Gyanendra Pratap 
Published: July 2020

AbstractStripe or yellow rust (YR) caused by Puccinia striiformis Westend. f. sp. tritici Erikss. is a persistent biotic-stress threatening global wheat production. To broaden our understanding of the shared genetic basis of YR resistance across multi-site and multi-year evaluations, we performed a large genome-wide association study using 43,706 YR observations on 23,346 wheat lines from the International Maize and Wheat Improvement Center evaluated between 2013 and 2019 at sites in India, Kenya and Mexico, against predominant races prevalent in the countries.
We identified 114 repeatable markers tagging 20 quantitative trait loci (QTL) associated with YR on ten chromosomes including 1D, 2A, 2B, 2D, 3A, 4A, 4D, 5A, 5B and 6B, among which four QTL, QYr.cim-2DL.2, QYr.cim-2AS.1, QYr.cim-2BS.2 and QYr.cim-2BS.3 were significant in more than ten datasets.
Furthermore, we report YR-associated allelic fingerprints for the largest panel of wheat breeding lines (52,067 lines) till date, creating substantial opportunities for YR favorable allele enrichment using molecular markers. Overall, the markers and fingerprints reported in this study provide excellent insights into the genetic architecture of YR resistance in different geographical regions, time-periods and wheat germplasm and are a huge resource to the global wheat breeding community for accelerating YR resistance breeding efforts.
Influenza virus infection affects insulin signaling, fatty acid-metabolizing enzyme expressions, and the tricarboxylic acid cycle in mice
Authors: Ohno Marumi , Sekiya Toshiki , Nomura Naoki , Daito Taku ji , Shingai Masashi , Kida Hiroshi 
Published: July 2020

AbstractAlthough the severity of influenza virus infections has been associated with host energy metabolism, the related mechanisms have not yet been clarified. Here we examined the effects of influenza virus infection on host energy metabolism in mice. After infecting mice with intranasal applications of 500 plaque-forming units of A/Puerto Rico/8/34 (H1N1; PR8) virus, the serum levels of most intermediates in the tricarboxylic acid (TCA) cycle and related metabolic pathways were significantly reduced. These data suggest that substrate supply to the TCA cycle is reduced under these conditions, rather than specific metabolic reactions being inhibited. Then, we focused on glucose and fatty acid metabolism that supply substrates to the TCA cycle. Akt phosphorylation following insulin injections was attenuated in the livers of PR8 virus-infected mice. Furthermore, glucose tolerance tests revealed that the PR8 virus-infected mice showed higher blood glucose levels than the vehicle-inoculated control mice. These results suggest that influenza virus infection impairs insulin signaling, which regulates glucose uptake. However, increases in the hepatic expressions of fatty acid-metabolizing enzymes suggest that fatty acids accumulate in liver cells of infected mice. Collectively, our data indicate that influenza virus infection dysregulates host energy metabolism. This line of investigation provides novel insights into the pathogenesis of influenza.
Effect of echinalkamide identified from Echinacea purpurea (L.) Moench on the inhibition of osteoclastogenesis and bone resorption
Authors: Chang Bo Yoon , Lee Seul Ki , Kim Da Eun , Bae Jin Hye , Ho Thanh Tam , Park So-Young , Lee Mi Kyeong , Kim Sung Yeon 
Published: July 2020

AbstractPlant cell cultures have been exploited to provide stable production and new secondary metabolites for better pharmacological activity. Fractionation of adventitious root cultures of Echinacea purpurea resulted in the isolation of eleven constituents, including three new compounds. The structures of the three new compounds were determined to be an alkylamide (1), a polyacetylene (2) and a lignan (3) on the basis of combined spectroscopic analysis. To discover new types of antiresorptive agents, we screened for new compounds that regulate osteoclast differentiation, and survival. Among three new compounds, echinalkamide (compound 1) had considerably inhibitory effects on RANKL-induced osteoclast differentiation, and on proliferation of osteoclasts and efficiently attenuated osteoclastic bone resorption without toxicity. In addition, echinalamide treatment inhibited the osteoclast—specific gene expression level. Echinalkamide achieved this inhibitory effect by disturbing phosphorylation of MAPK and activation of osteoclast transcription factors c-Fos and NFATc1. Conclusionally, our study investigated that echinalkamide remarkably inhibited osteoclast differentiation and osteoclast specific gene expression through repression of the MAPK–c-Fos–NFATC1 cascade.
Effects of effortful swallowing on cardiac autonomic control in individuals with neurogenic dysphagia: a prospective observational analytical study
Authors: Gomes Livia M. S. , da Silva Roberta G. , Pedroni Cristiane R. , Garner David M. , Raimundo Rodrigo D. , Valenti Vitor E. 
Published: July 2020

AbstractConsidering that neurogenic oropharyngeal dysphagia is a prevalent condition with or without cardiac disease we should contemplate issues surrounding cardiovascular difficulties during rehabilitation. This study aims to evaluate the effects of effortful swallowing maneuver (ESM) on heart rate variability (HRV) in subjects with neurogenic oropharyngeal dysphagia. We studied 22 individuals [8 Stroke and 14 Parkinson Disease (PD) subjects aged between 41 and 75 years old] with neurogenic oropharyngeal dysphagia regardless of gender. HRV was assessed under two circumstances: spontaneous swallowing versus ESM. Surface electromyography of the suprahyoid muscles was undertaken to measure the swallowing muscle excitation, which then confirmed higher muscle activity during ESM. We attained no changes in HRV between the two swallowing events [HR: spontaneous swallowing 78.68 ± 13.91 bpm vs. ESM 102.57 ± 107.81 bpm, p = 0.201; RMSSD (root-mean square of differences between adjacent normal RR intervals in a time interval): spontaneous swallowing 16.99 ± 15.65 ms vs. ESM 44.74 ± 138.85 ms, p = 0.312; HF (high frequency): spontaneous swallowing 119.35 ± 273 ms2 vs. ESM 99.83 ± 194.58 ms2, p = 0.301; SD1 (standard deviation of the instantaneous variability of the beat-to-beat heart rate): spontaneous swallowing 12.02 ± 1.07 ms vs. ESM 31.66 ± 98.25 ms, p = 0.301]. The effortful swallowing maneuver did not cause clinically significant changes in autonomic control of HR in this group of subjects with oropharyngeal dysphagia.
Isolation, identification, and whole genome sequence analysis of the alginate-degrading bacterium Cobetia sp. cqz5-12
Authors: Cheng Wenwen , Yan Xuanyu , Xiao Jiali , Chen Yunyun , Chen Minghui , Jin Jiayi , Bai Yu , Wang Qi , Liao Zhiyong , Chen Qiongzhen 
Published: July 2020

AbstractAlginate-degrading bacteria or alginate lyases can be used to oligomerize alginate. In this study, an alginate-degrading bacterium with high alginolytic activity was successfully screened by using Sargassum fusiforme sludge. When the strain was grown on a plate containing sodium alginate, the transparent ring diameter (D) was 2.2 cm and the ratio (D/d) of transparent ring diameter to colony diameter (d) was 8.8. After 36 h in culture at a temperature of 28 °C shaken at 150 r/min, the enzymatic activity of the fermentation supernatant reached 160 U/mL, and the enzymatic activity of the bacterial precipitate harvested was 2,645 U/mL. The strain was named Cobetia sp. cqz5-12. Its genome is circular in shape, 4,209,007 bp in size, with a 62.36% GC content. It contains 3,498 predicted coding genes, 72 tRNA genes, and 21 rRNA genes. The functional annotations for the coding genes demonstrated that there were 181 coding genes in the genome related to carbohydrate transport and metabolism and 699 coding genes with unknown functions. Three putative coding genes, alg2107, alg2108 and alg2112, related to alginate degradation were identified by analyzing the carbohydrate active enzyme (CAZy) database. Moreover, proteins Alg2107 and Alg2112 were successfully expressed and exhibited alginate lyase activity.
Fragmentation of plastic objects in a laboratory seawater microcosm
Authors: Gerritse Jan , Leslie Heather A. , de Tender Caroline A. , Devriese Lisa I. , Vethaak A. Dick 
Published: July 2020

AbstractWe studied the fragmentation of conventional thermoplastic and compostable plastic items in a laboratory seawater microcosm. In the microcosm, polyurethane foams, cellulose acetate cigarette filters, and compostable polyester and polylactic acid items readily sank, whereas polyethylene air pouches, latex balloons, polystyrene foams and polypropylene cups remained afloat. Microbial biofilms dominated by Cyanobacteria, Proteobacteria, Planctomycetes and Bacteriodetes grew on the plastics, and caused some of the polyethylene items to sink to the bottom. Electrical resistances (ER) of plastic items decreased as function of time, an indication that seawater had penetrated into microscopic crevices in the plastic that had developed over time. Rate constants for ER decrease in polyethylene items in the microcosm were similar to tensile elongation decrease of polyethylene sheets floating in sea, measured previously by others. Weight loss of plastic items was ≤ 1% per year for polyethylene, polystyrene and polypropylene, 3–5% for latex, polyethylene terephthalate and polyurethane, 15% for cellulose acetate, and 7–27% for polyester and polylactic acid compostable bags. The formation of microplastics observed in the microcosm was responsible for at least part of the weight loss. This study emphasizes the need to obtain experimental data on plastic litter degradation under conditions that are realistic for marine environments.
Tofacitinib treatment aggravates Staphylococcus aureus septic arthritis, but attenuates sepsis and enterotoxin induced shock in mice
Authors: Jarneborn Anders , Mohammad Majd , Engdahl Cecilia , Hu Zhicheng , Na Manli , Ali Abukar , Jin Tao 
Published: July 2020

AbstractTofacitinib, a janus kinase inhibitor, is a novel immunosuppressive drug for treatment of rheumatoid arthritis (RA). Septic arthritis (SA) and sepsis caused byStaphylococcus aureus(S. aureus), for which RA patients are at risk, are infections with high mortality. The aim of this study was to investigate the effect of tofacitinib onS. aureusinfections using mouse models. In vitro tofacitinib treated mouse splenocytes were stimulated withS. aureusderived stimuli. Mice pre-treated with tofacitinib were inoculated intravenously with either arthritogenic- or septic doses ofS. aureus. Arthritis severity and mortality were compared between groups. Additionally, pre-treated mice were challenged with staphylococcal toxin TSST-1 to induce shock. Tofacitinib inhibited splenocyte proliferation and IFN-γ production in response to TSST-1 and deadS. aureus. In SA, tofacitinib treatment aggravated arthritis with more severe bone erosions. However, in sepsis, treated mice displayed significantly prolonged survival compared to controls. Similarly, in staphylococcal enterotoxin-induced shock tofacitinib pre-treatment, but not late treatment dramatically reduced mortality, which was accompanied by decreased levels of TNF-α and IFN-γ. Our findings show that tofacitinib treatment increase susceptibility of SA in mice, but has a positive effect on survival inS. aureus-induced sepsis and a strong protective effect in toxin-induced shock.
Rearing enhancement of Ovalipes trimaculatus (Crustacea: Portunidae) zoea I by feeding on Artemia persimilis nauplii enriched with alternative microalgal diets
Authors: Martelli Antonela , Barbieri Elena S. , Dima Jimena B. , Barón Pedro J. 
Published: July 2020

AbstractThe southern surf crab Ovalipes trimaculatus (de Haan, 1833) presents a high potential for aquaculture. In this study, we analyze the benefits of different dietary treatments on its molt success and fitness of larval stages. Artemia persimilis nauplii were enriched with monospecific (Nannochloropsis oculata, Tetraselmis suecica, Dunaliella salina, Isochrysis galbana and Chaetoceros gracilis) and multispecific (Mix) microalgal diets twice a day over a 48-h period. Mean total length (TL), growth instar number (I) and gut fullness rate (GFR) of nauplii showed significant differences between dietary treatments at several sampling times, optimal results being observed in those providing Mix. Artemia nauplii grown under most experimental dietary treatments reached the capture size limit for Ovalipes trimaculatus zoea I (700 µm) within 24 h. After that time interval, Mix-enriched nauplii were amongst those with higher protein contents. Ovalipes trimaculatus zoea I fed on Artemia nauplii enriched during 24 h under different dietary treatments showed significant differences in survival, inter-molt duration, molting success to zoea II and motility. Optimal results were observed in zoea I fed on Mix-enriched Artemia nauplii. This work not only represents a first step towards the dietary optimization for O. trimaculatus zoeae rearing but also provides the first results on the use of enriched A. persimilis.
Inter-laboratory reproducibility of an untargeted metabolomics GC–MS assay for analysis of human plasma
Authors: Lin Yanping , Caldwell Gary W. , Li Ying , Lang Wensheng , Masucci John 
Published: July 2020

AbstractThere is a long-standing concern for the lack of reproducibility of the untargeted metabolomic approaches used in pharmaceutical research. Two types of human plasma samples were split into two batches and analyzed in two individual labs for untargeted GC–MS metabolomic profiling. The two labs used the same silylation sample preparation protocols but different instrumentation, data processing software, and database. There were 55 metabolites annotated reproducibly, independent of the labs. The median coefficient variations (CV%) of absolute spectra ion intensities in both labs were less than 30%. However, the comparison of normalized ion intensity among biological groups, were inconsistent across labs. Predicted power based on annotated metabolites was evaluated post various normalization, data transformation and scaling. For the first time our study reveals the numerical details about the variations in metabolomic annotation and relative quantification using plain inter-laboratory GC–MS untargeted metabolomic approaches. Especially we compare several commonly used post-acquisition strategies and found normalization could not strengthen the annotation accuracy or relative quantification precision of untargeted approach, instead it will impact future experimental design. Standardization of untargeted metabolomics protocols, including sample preparation, instrumentation, data processing, etc., is critical for comparison of untargeted data across labs.
Abrogation of Marek’s disease virus replication using CRISPR/Cas9
Authors: Hagag Ibrahim T. , Wight Darren J. , Bartsch Denise , Sid Hicham , Jordan Ingo , Bertzbach Luca D. , Schusser Benjamin , Kaufer Benedikt B. 
Published: July 2020

AbstractMarek’s disease virus (MDV) is a highly cell-associated alphaherpesvirus that causes deadly lymphomas in chickens. While vaccination protects against clinical symptoms, MDV field strains can still circulate in vaccinated flocks and continuously evolve towards greater virulence. MDV vaccines do not provide sterilizing immunity, allowing the virus to overcome vaccine protection, and has increased the need for more potent vaccines or alternative interventions. In this study, we addressed if the CRISPR/Cas9 system can protect cells from MDV replication. We first screened a number of guide RNAs (gRNAs) targeting essential MDV genes for their ability to prevent virus replication. Single gRNAs significantly inhibited virus replication, but could result in the emergence of escape mutants. Strikingly, combining two or more gRNAs completely abrogated virus replication and no escape mutants were observed upon serial passaging. Our study provides the first proof-of-concept, demonstrating that the CRISPR/Cas9 system can be efficiently used to block MDV replication. The presented findings lay the foundation for future research to completely protect chickens from this deadly pathogen.
Photoluminescence of InAs/GaAs quantum dots under direct two-photon excitation
Authors: Hu Xian , Zhang Yang , Guzun Dorel , Ware Morgan E. , Mazur Yuriy I. , Lienau Christoph , Salamo Gregory J. 
Published: July 2020

AbstractSelf-assembled quantum dots grown by molecular beam epitaxy have been a hotbed for various fundamental research and device applications over the past decades. Among them, InAs/GaAs quantum dots have shown great potential for applications in quantum information, quantum computing, infrared photodetection, etc. Though intensively studied, some of the optical nonlinear properties of InAs/GaAs quantum dots, specifically the associated two-photon absorption of the wetting and barrier layers, have not been investigated yet. Here we report a study of the photoluminescence of these dots by using direct two-photon excitation. The quadratic power law dependence of the photoluminescence intensity, together with the ground-state resonant peak of quantum dots appearing in the photoluminescence excitation spectrum, unambiguously confirms the occurrence of the direct two-photon absorption in the dots. A three-level rate equation model is proposed to describe the photogenerated carrier dynamics in the quantum dot-wetting layer-GaAs system. Moreover, higher-order power law dependence of photoluminescence intensity is observed on both the GaAs substrate and the wetting layer by two-photon excitation, which is accounted for by a model involving the third-harmonic generation at the sample interface. Our results open a door for understanding the optical nonlinear effects associated with this fundamentally and technologically important platform.