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41.
Trygve Bakken Lindsay Cowell Brian D. Aevermann Mark Novotny Rebecca Hodge Jeremy A. Miller Alexandra Lee Ivan Chang Jamison McCorrison Bali Pulendran Yu Qian Nicholas J. Schork Roger S. Lasken Ed S. Lein Richard H. Scheuermann 《BMC bioinformatics》2017,18(17):559
Background
A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and therapeutic/vaccine responses. In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting from the application of new high-throughput, high-content cytometry and sequencing technologies. The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology.Results
In this paper, we provide examples of state-of-the-art cellular biomarker characterization using high-content cytometry and single cell RNA sequencing, and present strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies, including “context annotations” in the form of standardized experiment metadata about the specimen source analyzed and marker genes that serve as the most useful features in machine learning-based cell type classification models. We also propose a statistical strategy for comparing new experiment data to these standardized cell type representations.Conclusion
The advent of high-throughput/high-content single cell technologies is leading to an explosion in the number of distinct cell types being identified. It will be critical for the bioinformatics community to develop and adopt data standard conventions that will be compatible with these new technologies and support the data representation needs of the research community. The proposals enumerated here will serve as a useful starting point to address these challenges.42.
M. V. Ivanov A. Yu. Lein Yu. M. Miller S. K. Yusupov N. V. Pimenov B. Wehrli I. I. Rusanov A. Zehnder 《Microbiology》2000,69(4):449-459
The isotopic composition of particulate organic carbon (POC) from the Black Sea deep-water zone was studied during a Russian-Swiss
expedition in May 1998. POC from the upper part of the hydrogen sulfide zone (the C-layer) was found to be considerably enriched
with the12C isotope, as compared to the POC of the oxycline and anaerobic zone. In the C-layer waters, the concurrent presence of dissolved
oxygen and hydrogen sulfide and an increased rate of dark CO2 fixation were recorded, suggesting that the change in the POC isotopic composition occurs at the expense of newly formed
isotopically light organic matter of the biomass of autotrophic bacteria involved in the sulfur cycle. In the anaerobic waters
below the C-layer, the organic matter of the biomass of autotrophs is consumed by the community of heterotrophic microorganisms;
this results in weighting of the POC isotopic composition. Analysis of the data obtained and data available in the literature
allows an inference to be made about the considerable seasonable variability of the POC δ13C value, which depends on the ratio of terrigenic and planktonogenic components in the particulate organic matter. 相似文献
43.
M. Rapp V. Lein F. Lacoudre J. Lafferty E. Müller G. Vida V. Bozhanova A. Ibraliu P. Thorwarth H. P. Piepho W. L. Leiser T. Würschum C. F. H. Longin 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2018,131(6):1315-1329
Key message
Simultaneous improvement of protein content and grain yield by index selection is possible but its efficiency largely depends on the weighting of the single traits. The genetic architecture of these indices is similar to that of the primary traits.Abstract
Grain yield and protein content are of major importance in durum wheat breeding, but their negative correlation has hampered their simultaneous improvement. To account for this in wheat breeding, the grain protein deviation (GPD) and the protein yield were proposed as targets for selection. The aim of this work was to investigate the potential of different indices to simultaneously improve grain yield and protein content in durum wheat and to evaluate their genetic architecture towards genomics-assisted breeding. To this end, we investigated two different durum wheat panels comprising 159 and 189 genotypes, which were tested in multiple field locations across Europe and genotyped by a genotyping-by-sequencing approach. The phenotypic analyses revealed significant genetic variances for all traits and heritabilities of the phenotypic indices that were in a similar range as those of grain yield and protein content. The GPD showed a high and positive correlation with protein content, whereas protein yield was highly and positively correlated with grain yield. Thus, selecting for a high GPD would mainly increase the protein content whereas a selection based on protein yield would mainly improve grain yield, but a combination of both indices allows to balance this selection. The genome-wide association mapping revealed a complex genetic architecture for all traits with most QTL having small effects and being detected only in one germplasm set, thus limiting the potential of marker-assisted selection for trait improvement. By contrast, genome-wide prediction appeared promising but its performance strongly depends on the relatedness between training and prediction sets.44.
Laminin and a basement membrane extract have different effects on axonal and dendritic outgrowth from embryonic rat sympathetic neurons in vitro 总被引:2,自引:0,他引:2
We have characterized the effects of laminin and a basement membrane extract (BME) on the morphology of embryonic rat sympathetic neurons maintained in tissue culture in the absence of nonneuronal cells. Neurons were grown on polylysine-coated coverslips in the presence or absence of laminin or BME in serum-free medium. Axons were distinguished from dendrites using intracellular dye injections, immunocytochemistry, and [3H]uridine autoradiography. In short-term (less than or equal to 24 hr) culture, laminin had a potent neurite-promoting effect, causing increases in the number of processes, total neuritic length, and neuritic branching. In long-term (3-35 days) cultures chronically exposed to laminin, most (greater than 75%) neurons maintained supernumerary axons but failed to form dendrites. In contrast, most neurons (greater than 70%) grown in long-term culture on polylysine in the absence of laminin were unipolar, extending a single axon. BME caused sympathetic neurons to extend multiple (range, 1-15) dendrites. Morphometric measurements made after 1 month of exposure to BME indicated that the amount of dendritic growth that occurred in vitro was similar to that normally occurring during a comparable period in situ. BME did not cause changes in the number of axons per neuron or in the uptake of neurotransmitter. Preliminary characterization of the dendrite-promoting activity of BME suggests that it resides in extracellular matrix (ECM) molecules and not in low-molecular weight contaminants. These observations indicate that (1) axonal and dendritic growth may be differentially regulated by various constituents of the ECM, and (2) such process-specific interactions can significantly affect the morphological development of sympathetic neurons. 相似文献
45.
46.
47.
Nehring Paula Hertwig Fabig H. Grimm Rieger H. Fankhänel M. Klinkowski Scholz Alfred Lein W. Schreiner 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1958,28(5):253-256
Ohne Zusammenfassung 相似文献
48.
Rothe R. Kaplan A. Lein Harte H. Nachtscheim Sartorius H. Hirsch H. Marquardt A. Reitberger K. Egle Straub Schwanitz E. Siebs Nolte H. Reich 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1954,24(6):181-184
Ohne Zusammenfassung 相似文献
49.
50.
v. Witsch Freisleben Wulff F. Schwanitz A. Th. Czaja Schmidt Karl Paech Fuchs H. Stubbe Lein R. Schick Hoffmann Schröck Sessous 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1942,14(6):146-152
Ohne Zusammenfassung 相似文献