bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rice Galaxy: an open resource for plant science
Authors: Juanillas Venice , Dereeper Alexis , Beaume Nicolas , Droc Gaetan , Dizon Joshua , Mendoza John Robert , Perdon Jon Peter , Mansueto Locedie , Triplett Lindsay , Lang Jillian , Zhou Gabriel , Ratharanjan Kunalan , Plale Beth , Haga Jason , Leach Jan E. , Ruiz Manuel , Thomson Michael , Alexandrov Nickolai , Larmande Pierre , Kretzschmar Tobias , Mauleon Ramil P. 
Published: June 2018

AbstractBackgroundRice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high density genotyping platforms for genome variation analysis and gene discovery. Germplasm collections representing rice diversity, improved varieties and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high density genotype data available. Combining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci (QTL) discovery and molecular marker development. Comparative sequence analyses across QTL regions facilitate the discovery of novel alleles. Analyses involving DNA sequences and large genotyping matrices for thousands of samples, however, pose a challenge to non-computer savvy rice researchers.FindingsWe adopted the Galaxy framework to build the federated Rice Galaxy resource, with shared datasets, tools, and analysis workflows relevant to rice research. The shared datasets include high density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from nine published rice genomes. Rice Galaxy includes tools for designing single nucleotide polymorphism (SNP) assays, analyzing genome-wide association studies, population diversity, rice-bacterial pathogen diagnostics, and a suite of published genomic prediction methods. A prototype Rice Galaxy compliant to Open Access, Open Data, and Findable, Accessible, Interoperable, and Reproducible principles is also presented.ConclusionsRice Galaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science.
The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates
Authors: Sarver Brice A. J. , Pennell Matthew W. , Brown Joseph W. , Keeble Sara , Hardwick Kayla M. , Sullivan Jack , Harmon Luke J. 
Published: June 2018

AbstractComparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. However, the effect that the selection of these priors has on the inference of comparative parameters has not been thoroughly investigated. Such uncertainty may systematically bias phylogenetic reconstruction and, subsequently, parameter estimation. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we use BEAST to simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation rates and extinction rates) from these trees. When substitution rate heterogeneity is large, parameter estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.
The Vibrio H-ring facilitates the outer membrane penetration of polar-sheathed flagellum
Authors: Zhu Shiwei , Nishikino Tatsuro , Kojima Seiji , Homma Michio , Liu Jun 
Published: June 2018

AbstractThe bacterial flagellum has evolved as one of the most remarkable nanomachines in nature. It provides swimming and swarming motilities that are often essential for the bacterial life cycle and for pathogenesis. Many bacteria such as Salmonella and Vibrio species use flagella as an external propeller to move to favorable environments, while spirochetes utilize internal periplasmic flagella to drive a serpentine movement of the cell bodies through tissues. Here we use cryo-electron tomography to visualize the polar-sheathed flagellum of Vibrio alginolyticus with particular focus on a Vibrio specific feature, the H-ring. We characterized the H-ring by identifying its two components FlgT and FlgO. Surprisingly, we discovered that the majority of flagella are located within the periplasmic space in the absence of the H-ring, which are dramatically different from external flagella in wild-type cells. Our results indicate the H-ring has a novel function in facilitating the penetration of the outer membrane and the assembly of the external sheathed flagella. This unexpected finding is however consistent with the notion that the flagella have evolved to adapt highly diverse needs by receiving or removing accessary genes.Significance StatementFlagellum is the major organelle for motility in many bacterial species. While most bacteria possess external flagella such as the multiple peritrichous flagella found in Escherichia coli and Salmonella enterica or the single polar-sheathed flagellum in Vibrio spp., spirochetes uniquely assemble periplasmic flagella, which are embedded between their inner and outer membranes. Here, we show for the first time that the external flagella in Vibrio alginolyticus can be changed as periplasmic flagella by deleting two flagellar genes. The discovery here may provide a new paradigm to understand the molecular basis underlying flagella assembly, diversity, and evolution.
Insight into relationship between micro-consortia, nitrogen source and petroleum degradation at low temperature anaerobic condition
Authors: Yu Jicheng , Chen Chao , Liu Changjian , Yu Dongning , Chen Shuai , Yuan Fenghao , Fu Yang , Liu Qiu 
Published: June 2018

AbstractBiostimulation by addition nutrients has been proved to be an effective bioremediation strategies. Revealing response law of nitrogen source and structure characteristics of anaerobic petroleum degrading microorganisms microbial population will help us optimize nutrient to promote oil degradation. Anaerobic micro-consortia characteristics in the enrichment marine sediment samples with different nitrogen source, combining with analysis of the oil degradation rates were studied in this paper, as well as functional genes involved in petroleum degradation were also analyzed. On the basis of optimizing the best inorganic nitrogen sources and organic nitrogen sources, an effective medium was designed by response surface methodology that used for enriching petroleum degradation micro-consortia. Amplicon sequencing analysis showed that the population of microorganisms migrated obviously when enriched with different nitrogen sources. With the increase of oil degradation rate, the microbial diversity was significantly decreased, and concentrated on a limited number of genera. The reasonable proportions of GammaProteobacteria, Bacteroidetes and Fusobacteria made the greatest contribution to petroleum degradation. Metagenomic analysis unveiled the mixed nitrogen source promoted the expression of functional genes related to petroleum degradation such as the transfer of succinyl-CoA, synthesis of acetyl CoA and β-oxidation cycle, and was beneficial to degradation of petroleum at low temperature anaerobic condition.Originality Significance StatementAddition of nutrients can promote growth of indigenous petroleum degradation-related bacteria and be helpful to the rapid degradation of petroleum. Previous studies accurately characterized aerobic microorganisms on petroleum degradation. However, we still known little about anaerobic microorganisms in marine environment. Most biostimulation methods use inorganic salt as the main nutritional supplement to improve the efficiency of petroleum degradation, but effects of different nitrogen sources on diversity of microorganisms and distribution of functional genes related to petroleum degradation at anaerobic conditions are still unknown. In this research, the effects of nitrogen on petroleum biodegradation, anaerobic microconsortium structure and distribution of genes related to petroleum degradation were unveiled by using amplicon sequencing and metagenomic analysis.
Development and analytical validation of an enzyme-linked immunosorbent assay based on baculovirus recombinant LipL32 protein antigen for the accurate detection of canine leptospirosis
Authors: Orozco-Cabrera Carolina , López-Valencia Gilberto , Cueto-González Sergio Arturo , Guerrero-Velázquez José Guadalupe , Moreno-Torres Kattya , Espinoza-Blandón Kelvin Orlando , Campo Nohemí Castro-Del , Gaxiola-Camacho Soila Maribel , Gómez-Gómez Sergio Daniel , Trasviña-Muñoz Enrique , Torres-Guzmán Cinthya , Monge-Navarro Francisco Javier 
Published: June 2018

AbstractLeptospirainfects a wide range of companion, domestic and wild animal species, shedding the spirochetes into the environment via urine. Dogs become infected by direct or indirect contact with wild or domestic infected animal reservoirs increasing the risk of zoonotic transmission of the disease. The microscopic agglutination test has been used as the gold standard for the diagnosis of leptospirosis but has low sensitivity and is technically complex. Several ELISA tests have been developed based on recombinant proteins ofLeptospirafor the diagnosis of leptospirosis with similar or higher specificity and sensitivity levels than the microscopic agglutination test. Here, we developed and analytically validated an ELISA test based on recombinant LipL32 protein ofLeptospiraexpressed in baculovirus. The LipL32 protein was successfully adapted in an indirect ELISA using dog plasma samples. Optimization of the ELISA resulted in a P/N ratio of 7.18 using only 5 ng of rLipL32 per well. Inter-assay and intra-assay variation showed a CV of 3.96% and 6.98% respectively, suggesting that the ELISA-LipL32 is highly reproducible. When tested with field samples, concordance of the ELISA-LipL32 with a real-time PCR, positive concordance was 100%. Our results indicate that the ELISA-LipL32 has the potential to be used by veterinarians and public health investigators as a safe, rapid, inexpensive and reliable method for the early diagnosis ofLeptospirainfection in dogs. Additional studies are still required for clinical validation on field samples under different epidemiological scenarios.
NudCL2 is an Hsp90 cochaperone to regulate sister chromatid cohesion by stabilizing cohesin subunits
Authors: Yang Yuehong , Wang Wei , Li Min , Zhang Wen , Huang Yuliang , Gao Ya , Zhuo Wei , Yan Xiaoyi , Liu Wei , Wang Fangwei , Chen Dingwei , Zhou Tianhua 
Published: June 2018

AbstractSister chromatid cohesion plays a key role in ensuring precise chromosome segregation during mitosis, which is mediated by the multisubunit complex cohesin. However, the molecular regulation of cohesin subunits stability remains unclear. Here, we show that NudCL2 (NudC-like protein 2) is essential for the stability of cohesin subunits by regulating Hsp90 ATPase activity in mammalian cells. Depletion of NudCL2 induces mitotic defects and premature sister chromatid separation and destabilizes cohesin subunits that interact with NudCL2. Similar defects are also observed upon inhibition of Hsp90 ATPase activity. Interestingly, ectopic expression of Hsp90 efficiently rescues the protein instability and functional deficiency of cohesin induced by NudCL2 depletion, but not vice versa. Moreover, NudCL2 not only binds to Hsp90, but also significantly modulates Hsp90 ATPase activity and promotes the chaperone function of Hsp90. Taken together, these data suggest that NudCL2 is a previously undescribed Hsp90 cochaperone to modulate sister chromatid cohesion by stabilizing cohesin subunits, providing a hitherto unrecognized mechanism that is crucial for faithful chromosome segregation during mitosis.
Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors
Authors: Salmén Fredrik , Vickovic Sanja , Larsson Ludvig , Stenbeck Linnea , Vallon-Christersson Johan , Ehinger Anna , Häkkinen Jari , Borg Åke , Frisén Jonas , Ståhl Patrik L , Lundeberg Joakim 
Published: June 2018

AbstractThe comprehensive analysis of tumor tissue heterogeneity is crucial for determining specific disease states and establishing suitable treatment regimes. Here, we analyze tumor tissue sections from ten patients diagnosed with HER2+ breast cancer. We obtain and analyze multidimensional, genome-wide transcriptomics data to resolve spatial immune cell distribution and identity within the tissue sections. Furthermore, we determine the extent of immune cell infiltration in different regions of the tumor tissue, including invasive cancer regions. We combine cross-sectioning and computational alignment to build three-dimensional images of the transcriptional landscape of the tumor and its microenvironment. The three-dimensional data clearly demonstrates the heterogeneous nature of tumor-immune interactions and reveal interpatient differences in immune cell infiltration patterns. Our study shows the potential for an improved stratification and description of the tumor-immune interplay, which is likely to be essential in treatment decisions.
Three-dimensional culture of chicken primordial germ cells in chemically defined media containing the functional polymer FP003
Authors: Chen Yi-Chen , Chang Wei-Che , Lin Shau-Ping , Minami Masataka , Jean Christian , Hayashi Hisato , Rival-Gervier Sylvie , Kanaki Tatsuro , Wu Shinn-Chih , Pain Bertrand 
Published: June 2018

AbstractScalable production of avian suspension cell exhibits a valuable potential on therapeutic application by producing recombinant protein and as the substrate for virus growth. This study sought to establish a system with chemically defined components for three-dimensional (3D) culture of chicken primordial germ cells (cPGCs), a pluripotent avian cell type. cPGCs were cultured in medium supplemented with the functional polymer FP003. Viscoelasticity was low in this medium, and cPGCs did not sediment,and consequently their expansion was improved. The total number of cPGCs increased by 17-fold after 1week of culture in 3D-FAot medium, an aseric chemically defined medium containing FP003, indicating that this medium enhances the expansion of cPGCs. Moreover, cPGC cell lines stably expressed the germline-specific reporter VASA:tdTOMATO, as well as other markers of cPGCs, for more than 1 month upon culture in 3D-FAot medium, indicating that the characteristics of these cells are maintained. cPGCs harboring both PGK:EGFP and VASA:tdTOMATO robustly expressed both fluorescent proteins upon culture in 3D-FAot, suggesting that this approach is perspective for recombinant protein production. In summary,this novel 3D culture system can be used to efficiently expand cPGCs in suspension without mechanical stirring or loss of cellular properties. This system provides a platform for large-scale culture ofcPGCs in industry.
MRI-related anxiety in healthy individuals, intrinsic BOLD oscillations at 0.1 Hz and heart rate variability in low frequency bands
Authors: Pfurtscheller Gert , Schwerdtfeger Andreas , Fink David , Brunner Clemens , Aigner Christoph Stefan , Brito Joana , Andrade Alexandre 
Published: June 2018

AbstractParticipation in a MRI scan is associated with increased anxiety, thus possibly impacting baseline recording for functional MRI studies. We investigated in 23 healthy individuals without any former MRI experience (scanner-naïve) the relations between anxiety, 0.1-Hz BOLD oscillations and heart rate variability (HRV) in two separate resting state sessions (R1, R2). BOLD signals were recorded from precentral gyrus (PCG) and insula in both hemispheres. Phase-locking and time delays were computed in the frequency band 0.07–0.13 Hz. Positive (pTD) and negative time delays (nTD) were found. The pTD characterize descending neural BOLD oscillations spreading from PCG to insula and nTD characterize ascending vascular BOLD oscillations related to blood flow in the middle cerebral artery. HRV power in two low frequency bands 0.06–0.1 Hz and 0.1–0.14 Hz was computed. Based on the drop rate of the anxiety level from R1 to R2, two groups could be identified: one with a strong anxiety decline (large drop group) and one with a moderate decline or even anxiety increase (small drop group). A significant correlation was found only between the left-hemispheric time delay (pTD, nTD) of BOLD oscillations and anxiety drop, with a dominance of nTD in the large drop group. The analysis of within-scanner HRV revealed a pronounced increase of low frequency power between both resting states, dominant in the band 0.06–0.1 Hz in the large drop group and in the band 0.1–0.14 Hz in the small drop group. These results suggest different mechanisms related to anxiety processing in healthy individuals. One mechanism (large drop group) could embrace an increase of blood circulation in the territory of the left middle cerebral artery (vascular BOLD) and another (small drop group) translates to rhythmic central commands (neural BOLD) in the frequency band 0.1–0.14 Hz.
A system for gene expression noise control in yeast
Authors: Mundt Max , Anders Alexander , Murray Seán , Sourjik Victor 
Published: June 2018

AbstractGene expression noise arises from stochastic variation in the synthesis and degradation of mRNA and protein molecules and creates differences in protein numbers across populations of genetically identical cells. Such variability can lead to imprecision and reduced performance of both native and synthetic networks. In principle, gene expression noise can be controlled through the rates of transcription, translation and degradation, such that different combinations of those rates lead to the same protein concentrations but at different noise levels. Here, we present a “noise tuner” which allows orthogonal control over the transcription and the mRNA degradation rates by two different inducer molecules. Combining experiments with theoretical analysis, we show that in this system the noise is largely determined by the transcription rate whereas mean expression can be independently adjusted by mRNA stability. This noise tuner enables twofold changes in gene expression noise over a fivefold range of mean protein levels. We demonstrated the efficacy of the noise tuner in a complex regulatory network by varying gene expression noise in the mating pathway of Saccharomyces cerevisiae, which allowed us to control the output noise and the mutual information transduced through the pathway. The noise tuner thus represents an effective tool of gene expression noise control, both to interrogate noise sensitivity of natural networks and enhance performance of synthetic circuits.
Within-host infectious disease models accommodating cellular coinfection, with an application to influenza
Authors: Koelle Katia , Farrell Alex , Brooke Christopher , Ke Ruian 
Published: June 2018

AbstractWithin-host models are useful tools for understanding the processes regulating viral load dynamics. While existing models have considered a wide range of within-host processes, at their core these models have shown remarkable structural similarity. Specifically, the structure of these models generally consider target cells to be either uninfected or infected, with the possibility of accommodating further resolution (for example, cells that are refractory to infection and cells that are in an eclipse phase). Recent findings, however, indicate that cellular coinfection is the norm rather than the exception for many viral infectious diseases, and that cells with high multiplicity of infection are present over at least some duration of an infection. The reality of these cellular coinfection dynamics is not accommodated in current within-host models although it may be critical for understanding within-host dynamics. This is particularly the case if multiplicity of infection impacts infected cell phenotypes such as their death rate and their viral production rates. Here, we present a new class of within-host disease models that allow for cellular coinfection in a scalable manner by retaining the low-dimensionality that is a desirable feature of many current within-host models. The models we propose adopt the general structure of epidemiological ‘macroparasite’ models that allow hosts to be variably infected by parasites such as nematodes and host phenotypes to flexibly depend on parasite burden. Specifically, our within-host models consider target cells as ‘hosts’ and viral particles as ‘macroparasites’, and allow viral output and infected cell lifespans, among other phenotypes, to depend on a cell’s multiplicity of infection. We show with an application to influenza that these models can be statistically fit to viral load and other within-host data, that they can reproduce notable features of within-host viral dynamics, and that importantin vivoquantities such as the mean multiplicity of cellular infection can be easily quantified with these models once parameterized. The within-host model structure we develop here provides an alternative approach for modeling within-host viral load dynamics and allows for a new class of questions to be addressed that consider the effects of cellular coinfection, collective viral interactions, and viral complementation in within-host viral dynamics and evolution.
Capturing auxin response factors syntax using DNA binding models
Authors: Stigliani Arnaud , Martin-Arevalillo Raquel , Lucas Jérémy , Bessy Adrien , Vinos-Poyo Thomas , Mironova Victoria , Vernoux Teva , Dumas Renaud , Parcy François 
Published: June 2018

ABSTRACTAuxin is a key hormone performing a wealth of functions throughout the plant life cycle. It acts largely by regulating genes at the transcriptional level through a family of transcription factors (TF) called auxin response factors (ARF). Even if all ARF monomers analysed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here we use position weight matrices (PWM) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data. We find that the genome binding of two ARFs (ARF2 and ARF5/Monopteros/MP) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing). We illustrate why PWMs are more versatile to reliably identify ARFbs than the widely used consensus sequences and demonstrate their power with biochemical experiments on the regulatory regions of the IAA19 model gene. Finally, we combined gene regulation by auxin with ARF-bound regions and identified specific ARFbs configurations that are over-represented in auxin up-regulated genes, thus deciphering the ARFbs syntax functional for regulation. This provides a general method to exploit the potential of genome-wide DNA binding assays and decode gene regulation.