17 research outputs found
A two weight local Tb theorem for the Hilbert transform
We obtain a two weight local Tb theorem for any elliptic and gradient
elliptic fractional singular integral operator T on the real line, and any pair
of locally finite positive Borel measures on the line. This includes the
Hilbert transform and in a sense improves on the T1 theorem by the authors and
M. Lacey.Comment: 121 pages, 3 figures, 50 pages of appendices. We correct three gaps
in the treatment of the stopping form in v12: the proof of Lemma 9.3 there
requires a larger size functional, a collection of pairs is missing from the
decomposition at the bottom of page 149, and an error was made in the
definition of restricted norm of a stopping form. Main results unchange
Degradable Semiconducting Oligomer Amphiphile for Ratiometric Photoacoustic Imaging of Hypochlorite
Upregulation
of highly reactive oxygen species (ROS) such as hypochlorite
(ClO<sup>–</sup>) is associated with many pathological conditions
including cardiovascular diseases, neuron degeneration, lung injury,
and cancer. However, real-time imaging of ClO<sup>–</sup> is
limited to the probes generally relying on fluorescence with shallow
tissue-penetration depth. We here propose a self-assembly approach
to develop activatable and degradable photoacoustic (PA) nanoprobes
for <i>in vivo</i> imaging of ClO<sup>–</sup>. A
near-infrared absorbing amphiphilic oligomer is synthesized to undergo
degradation in the presence of a specific ROS (ClO<sup>–</sup>), which integrates a π-conjugated but ClO<sup>–</sup> oxidizable backbone with hydrophilic PEG side chains. This molecular
architecture allows the oligomer to serve as a degradable nanocarrier
to encapsulate the ROS-inert dye and self-assemble into structurally
stable nanoparticles through both π–π stacking
and hydrophobic interactions. The self-assembled nanoprobe exhibits
sensitive and specific ratiometric PA signals toward ClO<sup>–</sup>, permitting ratiometric PA imaging of ClO<sup>–</sup> in
the tumor of living mice
Characterization of Natural Antisense Transcript, Sclerotia Development and Secondary Metabolism by Strand-Specific RNA Sequencing of <i>Aspergillus flavus</i>
<div><p><i>Aspergillus flavus</i> has received much attention owing to its severe impact on agriculture and fermented products induced by aflatoxin. Sclerotia morphogenesis is an important process related to <i>A. flavus</i> reproduction and aflatoxin biosynthesis. In order to obtain an extensive transcriptome profile of <i>A. flavus</i> and provide a comprehensive understanding of these physiological processes, the isolated mRNA of <i>A. flavus</i> CA43 cultures was subjected to high-throughput strand-specific RNA sequencing (ssRNA-seq). Our ssRNA-seq data profiled widespread transcription across the <i>A. flavus</i> genome, quantified vast transcripts (73% of total genes) and annotated precise transcript structures, including untranslated regions, upstream open reading frames (ORFs), alternative splicing variants and novel transcripts. We propose natural antisense transcripts in <i>A. flavus</i> might regulate gene expression mainly on the post-transcriptional level. This regulation might be relevant to tune biological processes such as aflatoxin biosynthesis and sclerotia development. Gene Ontology annotation of differentially expressed genes between the mycelia and sclerotia cultures indicated sclerotia development was related closely to <i>A. flavus</i> reproduction. Additionally, we have established the transcriptional profile of aflatoxin biosynthesis and its regulation model. We identified potential genes linking sclerotia development and aflatoxin biosynthesis. These genes could be used as targets for controlled regulation of aflatoxigenic strains of <i>A. flavus</i>.</p></div
Detailed annotation of the <i>A. flavus</i> gene model.
<p>(A) A novel transcript (TU134) identified in contig gi|156128545|gb|AAIH02000077.1| in the forward orientation. Red bar, the novel transcript TU134 identified in the mycelia sample. Red curve, expression level (log<sub>2</sub>-transformed reads count) of the transcripts located in the forward strand. Green curve, the expression level of the transcripts located in the reverse strand. (B) Scatterplot and histograms showing the length distribution of the 5′- and 3′-UTRs of <i>A. flavus</i> CA43 genes. (C) UTR and uORF illustration for an annotated <i>A. flavus</i> gene (AFLG2_08360).</p
Illustration of AS events (RI, SE, A5SS and A3SS) identified in the <i>A. flavus</i> transcriptome.
<p>(A) Green bar, the transcriptional active region (TAR). Orange bar, <i>A. flavus</i> annotated genes. Knuckle lines (black or red), the relation with TARs or exons. The types and amounts of AS events are shown. (B) Amino acid alignment and homologous 3D modeling of AFL2G_07666 (<i>SphK</i>) and its AS variant (<i>SphK</i> _variant). Broken line, the skipped exon of <i>SphK</i>.</p
Genes expressed differentially between <i>A. flavus</i> mycelia and sclerotia states.
<p>(A) WEGO illustration of the up-regulated genes in the <i>A. flavus</i> mycelia and sclerotia states. In total, 3237 of the 4492 up-regulated genes in the mycelia state and 724 of 1149 up-regulated genes in the sclerotia state are assigned to GO categories. (B) The model of regulation of <i>A. flavus</i> reproduction-related genes in the mycelia and sclerotia states. Boxes, DEGs (<i>p</i><0.001 and change >2-fold) between the mycelia and sclerotia states, denoted by the names of their homologs in <i>A. nidulans</i>, <i>S. cerevisiae</i> (Sc) and <i>Neurospora crassa</i> (Nc). Red and green boxes, the up-regulated and the down-regulated genes in the sclerotia state, respectively. White boxes, genes with no significant difference between the mycelia and the sclerotia states. (C) Occurrence of NAT in the <i>veA</i> gene (AFL2G_07468). Yellow curve, NAT in the <i>veA</i> gene. (D) Transcriptional status of the conidial transcriptional factor <i>brlA</i> (AFL2G_00999).</p
Summary of RNA sequencing of <i>A. flavus</i> CA43.
<p>(A) Matching summary of ssRNA-seq reads to the <i>A. flavus</i> genome. (B) Box and whisker plots of log<sub>2</sub>-transformed RPKM for exons, novel transcripts, introns and intergenic regions. Horizontal lines in boxes, the first, median and third quartile. Other horizontal lines, the inner boundaries. Diamonds, data outside the inner boundaries. (C) Mapping coverage of the transcribed <i>A. flavus</i> genes.</p
Construction of pSPI12-cured <i>Salmonella enterica</i> serovar Pullorum and identification of IpaJ as an immune response modulator
<p>In <i>Salmonella</i>, plasmids participate in many pathways involved in virulence, metabolism, and antibiotic resistance. To investigate the function of the <i>ipaJ</i> gene in a multi-copy plasmid pSPI12 prevalent in <i>Salmonella enterica</i> serovar Pullorum (<i>S</i>. Pullorum), we established a method to eliminate the plasmid and constructed the plasmid-cured bacteria C79-13-ΔpSPI12 by using the suicide vector pDM4. Briefly, a 500 bp fragment <i>ipaJU</i> from pSPI12 was cloned into pDM4 and transformed into <i>S.</i> Pullorum C79-13 by conjugative transfer. After homologous recombination, the suicide vector was inserted into pSPI12 to produce pSPI12-pDM4-<i>ipaJU</i>. Induction of the expression of the <i>sacB</i> gene in the suicide vector killed the bacteria harbouring plasmid, while the progeny losing the plasmid survived in the plate with sucrose. The plasmid-cured strain showed extremely decreased ability to infect chicken macrophage HD11 cells and LMH hepatic epithelial cells compared to wild type strain and complementary strain carrying <i>ipaJ</i>. Additionally, IFN-<i>γ</i> mRNA levels were up-regulated in HD11 cells or chicken spleens infected by plasmid-cured strain, but no difference was detected in IL-4 among the three strains. Transforming <i>ipaJ</i> into <i>S.</i> Enteritidis also decreased expression of proinflammatory cytokines in infected macrophages or chicken spleens compared to wild type strain. These results suggest that the <i>ipaJ</i> gene in pSPI12 is involved in <i>S.</i> Pullorum infection and that IpaJ protein modulates immune response.</p
Differential transcription of <i>A. flavus</i> aflatoxin biosynthetic pathway.
<p>(A) The expression status of AF biosynthesis in the mycelia and sclerotia states. (B) The regulation model of AF biosynthesis-related genes in the mycelia and sclerotia states. The orthologs of the AF biosynthetic pathway genes are in the same order as in (A). Boxes, DEGs (<i>p</i><0.001 and change >2-fold) between mycelia and sclerotia states, denoted by the names of their homologs in <i>A. nidulans</i>. Red and green boxes, up-regulated and down-regulated genes in the sclerotia state, respectively. White boxes, genes with no significant change between the mycelia and sclerotia states.</p
NAT analysis in <i>A. flavus</i> CA43.
<p>(A) The relationship between the location of NAT and its corresponding genes. Downstream, Upstream and Inside, NATs located in the downstream, upstream or inside of their corresponding genes, respectively. Intersected, NAT located across one gene and its 5′- or 3′- flanking region. (B) Box and whisker plots of log<sub>2</sub>-transformed RPKM for <i>A. flavus</i> annotated genes with or without NATs. (C) Occurrence of NAT in the <i>SdeA</i> gene (AFL2G_00446). Orange curves, the NAT in the <i>SdeA</i> gene.</p