310 research outputs found
Genetic dissection of maize regeneration and wheat disease resistance
No full textDoctor of PhilosophyGenetics Interdepartmental Program - Plant PathologySanzhen LiuThe growing human population worldwide and the changing growth environments require significant crop improvement, which can be accelerated by plant genome engineering. Developing plant cultivars amenable to transformation and improving understanding of the genetic bases of important phenotypic traits can facilitate the use of advanced genome engineering technologies. This dissertation is focused on the genetic analysis of maize transformation and wheat resistance to the disease of leaf rust. The results will provide knowledge to improve crop transformation and wheat disease resistance.
Plant transformation is a powerful tool for crop improvement and gene function validation. However, the transformation efficiency of maize is highly dependent on the tissue types and the genotypes. The maize inbred line A188 is amenable to transformation. A188 also exhibits many contrasting traits to the inbred line B73, which is recalcitrant to transformation. B73 was used to generate the first maize reference genome. The lack of genome sequences of A188 limits the use of A188 as a model for functional studies. Here, a chromosome-level genome assembly of A188 was constructed using long reads and optical physical maps. Genome comparison of A188 with B73 based on both whole genome alignments and sequencing read depths identified approximately 1.1 Gb syntenic sequences as well as extensive structural variation. Further, transcriptome and epigenome analyses with the A188 reference genome revealed enhanced gene expression of defense pathways and altered DNA methylation patterns of embryonic callus. The A188 genome assembly provides a foundational resource for analyses of genome variation and gene function in maize. In maize, morphologic types of calli induced from immature embryos are associated with the regeneration capability, which is a major factor determining the transformation efficiency. Here, two contrasting callus types, slow-growth type I calli and fast-growth type II calli, from the selected B73xA188 F2 population were sequenced using Genotyping-By-Sequencing (GBS) and RNA-Seq. With both approaches, the genomic loci associated with the callus type were mapped to chromosomes 2, 5, 6, 8, and 9. From F2 RNA-Seq, differentially expressed genes were identified from the comparison of type II and I calli. In addition, RNA-Seq analysis was performed using fast- and slow-growth calli identified for the A188 calli. Gene ontology (GO) enrichment analysis showed that the down-regulated genes in type II F2 calli and fast-growth A188 calli, as respectively compared to type I calli and slow-growth A188 calli, are overrepresented in the pathway related to cell wall organization, suggesting the role of cell wall formation in the callus development.
Besides maize genetic and genomic studies, the dissertation includes the cloning of a leaf rust resistance gene in wheat. Wheat leaf rust disease is caused by a fungal pathogen, Puccinia triticina. The Lr42 gene from the wheat wild relative Aegilops tauschii confers resistance to all leaf rust races tested to date. Through bulked segregant RNA-Seq (BSR-Seq) mapping and further fine mapping, we identified an Lr42 candidate gene, which encodes a nucleotide-binding site leucine-rich repeat (NLR) protein. Transformation of the candidate gene to a leaf rust-susceptible wheat cultivar markedly enhanced the disease resistance, confirming the candidate NLR gene is the Lr42 gene. Cloning of Lr42 expands the repertoire of cloned rust resistance genes, as well as provides precise diagnostic gene markers for wheat improvement
Recent advances in the production processes of hydrothermal liquefaction biocrude and aid-in investigation techniques
No full textResearch on convolutional neural network based on improved Relu piecewise activation function
No full textComparative Genomic Read Depth for Studying Genomic Copy Number Variation
No full textCGRD is a pipeline to compare sequencing read depths from two samples along a reference genome. Three major steps include:
define effective genomic bins each of which harbors certain non-repetitive sequences
align reads and count read depths per bin for both samples
combine neighboring bins with similar fold changes in read depth between the two samples (segmentation)
From the result, genomic segments with similar and differential (higher or lower) read depths are obtained. Therefore, genomic copy number variation (CNV) based on read depths can be extracted from the result and visualized on the genome map
Control of the electron dynamics in solid-state high harmonic generation on ultrafast time scales by a polarization-skewed laser pulse
No full textDataset of the publication “Control of the electron dynamics in solid-state high harmonic generation on ultrafast time scales by a polarization-skewed laser pulse”, by X. Song, S. Yang, G. Wang, J. Lin, L. Wang, T. Meier, and W. Yang, published in Optics Express 31, 18862 (2023) , https://doi.org/10.1364/OE.491418 .
The zip file includes a brief description, the data on which the plot of figures 1 – 3 are based, and matlab figure files.This work was supported by the National Natural Science Foundation of China (Grant No. 12074240); Hainan Provincial Natural Science Foundation of China (Grant No.122CXTD504 and 123MS002); Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) project number 231447078 TRR 142 (subproject A10); Sino-German Mobility Programme (Grant No. M-0031)
Emerg Infect Dis
No full textTo determine the cause of a 2008 outbreak of aseptic meningitis in Shandong Province, China, we analyzed samples from outbreak patients and coxsackievirus B3 samples collected during 1990-2010 surveillance. The cause of the outbreak was coxsackievirus B3, genogroup D. Frequent travel might increase importation of other coxsackievirus B3 genogroups
Identification of active and quiescent adipose vascular stromal cells
No full textBackground aims. Recent studies have demonstrated the existence of both active and quiescent stem cells in bone marrow, hair follicle and intestine. We attempted to identify active and quiescent vascular stromal cells (VSC) in adipose tissue. Methods. For identification of active VSC, adult rats were injected intraperitoneally with thymidine analog 5-ethynyl-2-deoxyuridine (EdU) and their subcutaneous tissue harvested 3 days later. For identification of quiescent VSC, newborn rats were injected intraperitoneally with EdU and their subcutaneous tissue harvested 9 weeks later. The harvested adipose tissues were examined for the co-localization of EdU with VSC marker CD34, smooth muscle marker SMA, endothelial marker RECA and pericyte marker CD140b. Results. In adult rat adipose tissues harvested 3 days after EdU injection, there were 28.80 +/- 8.70 (mean +/- SD) EdU<SU++</SU cells/100 x microscopic field, and approximately 6.2% of cell nuclei were labeled with EdU. The percentages of EdU<SU++</SU cells expressing the following markers were approximately: 84 for CD34, 5.6 for RECA (rat endothelial marker), 3.7 for SMA and 14.8 for CD140b. In the adipose tissues of newborn rats that were harvested 9 weeks after EdU injection, the percentages of EdU<SU++</SU cells expressing the following markers were approximately: 76 for CD34, 1.8 for RECA, 0 for SMA and 12.9 for CD140b. In both the short-term (active) and long-term (quiescent) EdU-labeled adipose tissues, the EdU label was consistently co-localized with CD34 and in the proximity of CD140b stain or in the adventitia. Conclusions. Both active and quiescent VSC expressed CD34 and localized to capillaries and the adventitia of larger blood vessels.Cell & Tissue EngineeringBiotechnology & Applied MicrobiologyCell BiologyHematologyMedicine, Research & ExperimentalSCI(E)0ARTICLE2240-2461
Similar spatial patterns of neural coding of category selectivity in FFA and VWFA under different attention conditions
No full textIt has long been debated whether attention alters the categorical selectivity in regions such as the fusiform face area (FFA) and the visual word form area (VWFA). We addressed this issue by examining whether the spatial pattern of neural representations for certain stimulus categories in these regions would change under different attention conditions. Faces. Chinese characters, and textures were presented in a block design fMRI experiment where participants in different runs attended to the stimuli under different conditions of attention. After localizing regions of interest (ROIs) in FFA and VWFA using general linear models, we performed spatial pattern analyses to examine both within- and cross-condition classification in these ROIs. The within-condition results replicated previous findings showing significant classification accuracy reduction when there was less attention compared with more attention. Critically, cross-condition classification in both FFA and VWFA revealed significantly above-chance accuracy for all stimulus categories, suggesting similar spatial neural representations across different attention conditions. Further strengthening this conclusion, when the contrast-to-noise ratio (CNR) of the signals was adjusted to increase signal strength, cross-condition classification accuracy for faces in FFA and for Chinese characters in VWFA improved significantly, even approaching within-condition accuracy. This indicates that attention does not modulate the spatial pattern of neural representations involved in category selectivity, but only changes the signal strength relative to the noise level. (C) 2012 Elsevier Ltd. All rights reserved
Highly efficient grating couplers with mode conversion functions
No full textIn this work, we show the possibility of combining grating couplers and mode converters, both with a high efficiency. The proposed devices are very compact with no extra fabrication efforts required. We have shown that the LP01, LP11a, LP11b and LP21b modes in an optical fiber can be successfully excited directly from the proposed grating couplers, which have the fundamental mode as an input from an integrated waveguide. It is shown the overall efficiency could be as high as 50%
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