NAD tagSeq reveals that NAD+-capped RNAs are mostly produced from a large number of protein-coding genes in Arabidopsis.

The 5' end of a eukaryotic mRNA transcript generally has a 7-methylguanosine (m7G) cap that protects mRNA from degradation and mediates almost all other aspects of gene expression. Some RNAs in Escherichia coli, yeast, and mammals were recently found to contain an NAD+ cap. Here, we report the development of the method NAD tagSeq for transcriptome-wide identification and quantification of NAD+-capped RNAs (NAD-RNAs). The method uses an enzymatic reaction and then a click chemistry reaction to label NAD-RNAs with a synthetic RNA tag. The tagged RNA molecules can be enriched and directly sequenced using the Oxford Nanopore sequencing technology. NAD tagSeq can allow more accurate identification and quantification of NAD-RNAs, as well as reveal the sequences of whole NAD-RNA transcripts using single-molecule RNA sequencing. Using NAD tagSeq, we found that NAD-RNAs in Arabidopsis were produced by at least several thousand genes, most of which are protein-coding genes, with the majority of these transcripts coming from <200 genes. For some Arabidopsis genes, over 5% of their transcripts were NAD capped. Gene ontology terms overrepresented in the 2,000 genes that produced the highest numbers of NAD-RNAs are related to photosynthesis, protein synthesis, and responses to cytokinin and stresses. The NAD-RNAs in Arabidopsis generally have the same overall sequence structures as the canonical m7G-capped mRNAs, although most of them appear to have a shorter 5' untranslated region (5' UTR). The identification and quantification of NAD-RNAs and revelation of their sequence features can provide essential steps toward understanding the functions of NAD-RNAs

A single amino acid substitution in the R3 domain of GLABRA1 leads to inhibition of trichome formation in Arabidopsis without affecting its interaction with GLABRA3

GLABRA1 (GL1) is an R2R3 MYB transcription factor that regulates trichome formation in Arabidopsis by interacting with the bHLH transcription factor GLABRA3 (GL3) or ENHANCER OF GL3 (EGL3). The conserved [D/E]L×2 [R/K]×3L×6L×3R amino acid signature in the R3 domain of MYB proteins has been shown to be required for the interaction of MYBs with R/B‐like bHLH transcription factors. By using genetic and molecular analyses, we show that the glabrous phenotype in the nph4‐1 mutant is caused by a single nucleotide mutation in the GL1 gene, generating a Ser to Phe substitution (S92F) in the conserved [D/E]L×2[R/K]×3L×6L×3R amino acid signature of GL1. Activation of the integrated GL2p:GUS reporter gene in protoplasts by cotransfection of GL1 and GL3 or EGL3 was abolished by this GL1‐S92F substitution. However, GL1‐S92F interacted successfully with GL3 or EGL3 in protoplast transfection assays. Unlike VPGL1GL3, the fusion protein VPGL1‐S92FGL3 failed to activate the integrated GL2p:GUS reporter gene in transfected protoplasts. These results suggested that the S92 in the conserved [D/E]L×2 [R/K]×3L×6L×3R amino acid signature of GL1 is not essential for the interaction of GL1 and GL3, but may play a role in the binding of GL1 to the promoters of its target genes.The R2R3 MYB transcription factor GL1 is a key regulator of trichome formation in Arabidopsis. The conserved [D/E]L×2[R/K]×3L×6L×3R amino acid signature in the R3 domain is required for the interaction of MYBs with R/B‐like bHLH transcription factors. S92F amino acid substantiation in the conserved [D/E]L×2[R/K]×3L×6L×3R signature in GL1 lead to loss‐of‐function mutation of GL1. However, our results indicate that Ser92 residue is not required for the interaction of GL1 with bHLH transcription factor GL3 or EGL3, but may required for binding of GL1 to its target genes.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/145310/1/pce12695_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/145310/2/pce12695.pd

Apoptotic mechanism of human leukemia K562/A02 cells induced by magnetic iron oxide nanoparticles co-loaded with daunorubicin and 5-bromotetrandrin

The purpose of this study was to assess the induced apoptosis of self-assembled iron oxide magnetic nanoparticles (MNPs) co-loaded with daunorubicin (DNR) and 5-bromotetrandrin (Br Tet) (DNR/Br Tet-MNPs), acting as a drug depot system for the sustained release of the loaded DNR and BrTet, in the drug resistant human leukemia K562/A02 cells and further to explore potential mechanisms. After being incubated for 48 hours, K562/A02 cells were treated with DNR/Br Tet-MNPs or DNR and Br Tet in solution (DNR/Br Tet-Sol). Morphologic characteristics of K562/A02 cells were observed under a fluorescence microscope; cell apoptosis and intracellular accumulation of DNR were analyzed by FACS Calibur flow cytometry. Furthermore, reverse transcriptase polymerase chain reaction (RT-PCR) and Western blotting analyses were performed to study the apoptosis associated gene transcription and protein expression, respectively. Typical apoptotic characteristics, including chromatin condensation and fragmentation of nuclei, were observed and a high rate of apoptosis was detected in K562/A02 cells treated with DNR/Br Tet-MNPs and DNR/Br Tet-Sol. Detection of relative fluorescence intensity of intracellular DNR demonstrated that intracellular DNR was higher in K562/A02 cells treated with DNR/Br Tet-MNPs than that of DNR/Br Tet-Sol. Further study demonstrated that both DNR/Br Tet-MNPs and DNR/Br Tet-Sol reduced the gene transcriptions and protein expressions of bcl-2 and survivin and enhanced that of bax and caspase 3. It is concluded that self-assembled DNR/Br Tet-MNPs, as one of the potential antitumor agents for hematologic malignancies, may effectively induce apoptosis of K562/A02 cells through elevating the ratio of bax/bcl-2, activating caspase 3, and inactivating survivin

Whole Genome Association Analysis of Idiopathic Eosinophilic Enteritis in Brown Egg Layers

Idiopathic Eosinophilic Enteritis (IEE) is an intestine disease that affects absorption of nutrients and performance. Hens of a commercial breeding layer line and its two reciprocal crosses with another line were recorded for IEE related traits and genotyped for over 40,000 genetic markers across the genome. Whole genome association analysis was performed on 288 daughters from high and low incidence sire families. Single marker association analyses of IEE incidence in separate lines showed consistent significant regions on chromosomes 4 and 5 (p\u3c0.001). Simultaneous analyses of all SNPs in all 3 lines using Bayesian whole genome selection methods indicated evidence of associations on chromosomes 1, 2 and 4 for additive effects and on chromosome 5 for dominance effects. Line specific regions also appeared on chromosome Z. With further investigation, these results can be used to develop genetic markers to select against this disease and to understand its genetic basis

Synthesis and antitumor efficacy of daunorubicin-loaded magnetic nanoparticles

Jun Wang1, Baoan Chen1, Jian Chen1, Xiaohui Cai1, Guohua Xia2, Ran Liu1, Pingsheng Chen2, Yu Zhang3, Xuemei Wang31Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China 210009; 2Medical School, Southeast University, Nanjing; 3State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China 210009Background: A promising approach to optimize the disposition of daunorubicin-loaded magnetic nanoparticles (DNR-MNPs) was developed to minimize serious side effects of systematic chemotherapy for cancer.Methods: The physical properties of DNR-MNPs were investigated and their effect on leukemia cells in vitro was evaluated by a standard WST-1 cell proliferation assay. Furthermore, cell apoptosis and intracellular accumulation of DNR were determined by FACSCalibur flow cytometry.Results: Our results showed that the majority of MNPs were spherical and their sizes were from 10 to 20 nm. The average hydrodynamic diameter of DNR-MNPs in water was 94 nm. The in vitro release data showed that the DNR-MNPs have excellent sustained release property. Proliferation of K562 cells was inhibited in a dose-dependent manner by DNR in solution (DNR-Sol) or by DNR-MNPs. The IC50 for DNR-MNPs was slightly higher than that for DNR-Sol. DNR-MNPs also induced less apoptosis in K562 cells than did DNR-Sol. Detection of fluorescence intensity of intracellular DNR demonstrated that DNR-MNPs could be taken up by K562 cells and persistently released DNR in cells.Conclusion: Our study suggests that optimized DNR-MNPs formulation possesses sustained drug-release and favorable antitumor properties, which may be used as a conventional dosage form for antitumor therapy.Keywords: daunorubicin, magnetic iron oxide nanoparticles, drug delivery system, target selection, K562 cell

Transcriptomic diversification of granulosa cells during follicular development between White Leghorn and Silky Fowl hens

Egg production rate in chicken is related to the continuity of follicle development. In this study, we found that the numbers of white prehierarchical, dominant, and yellow preovulatory follicles in the high-yielding layer breed, White Leghorn (WL), were significantly higher than those in the low egg-yielding variety, Silky Fowl (SF). The proliferation and differentiation of granulosa cells (GCs) play an important role in follicle maturation. Histological observation revealed a large number of melanocytes in the outer granulosa layer of follicles in SF but not in WL. Finally, RNA-sequencing was used to analyze the gene expression profiles and pathways of the GC layer in the follicles in both WL and SF hens. Transcriptome analysis of prehierarchical GCs (phGCs) and preovulatory GCs (poGCs) between WL and SF showed that steroid hormone-, oxytocin synthesis-, tight junction-, and endocytosis-related genes were expressed at higher levels in WL phGCs than in SF phGCs, whereas the insulin signaling pathway- and vascular smooth muscle contraction-related genes were upregulated in SF phGCs. Fatty acid synthesis, calcium signaling, and Wnt signaling pathway-related genes were expressed at higher levels in WL poGCs than in SF poGCs; however, adrenergic signaling, cGMP-PKG, and melanogenesis-related genes were upregulated in SF poGCs. These results indicate that genes that promote GC proliferation and secretion of various sex hormones are more active in WL than in SF hens. The upregulated signaling pathways in SF help in providing energy to GCs and for angiogenesis and melanogenesis. In vitro experiments confirmed that both the proliferation of poGCs and synthesis of reproductive hormones were higher in WL than in SF hens

The changes of T lymphocytes and cytokines in ICR mice fed with Fe3O4 magnetic nanoparticles

The aim of this article is to study the changes inhibited T lymphocytes and cytokines related to the cellular immunity in ICR (imprinting control region) mice fed with Fe3O4 magnetic nanoparticles (Fe3O4-MNPs). The Fe3O4-MNPs were synthesized, and their characteristics such as particle size, zeta potential, and X-ray diffraction patterns were measured and determined. All ICR mice were sacrificed after being exposed to 0, 300, 600, and 1200 mg/kg of Fe3O4-MNPs by single gastric administration for 14 days. Splenocytes proliferation was indicated with stimulate index by MTT assay; release of cytokines in the serum of ICR mice was detected by enzyme-linked immunosorbent assay, and the phenotypic analyses of T-lymphocyte subsets were performed using flow cytometry. Our results indicated that there were no significant differences in splenocyte proliferation and release of cytokines between exposed and control groups. Furthermore, there was no significant difference in the proportions of T-lymphocyte subsets in the low-dose Fe3O4-MNPs group when compared to the control group, but the proportions of CD3+CD4+ and CD3+CD8+ T-lymphocyte subsets both in the medium- and high-dose Fe3O4-MNPs groups were higher than those in the control group. It is concluded that a high dose of Fe3O4-MNPs, to some extent, could influence in vivo immune function of normal ICR mice

Immunohistochemical localization of mu opioid receptor in the marginal division with comparison to patches in the neostriatum of the rat brain

<p>Abstract</p> <p>Background</p> <p>Mu opioid receptor (MOR), which plays key roles in analgesia and also has effects on learning and memory, was reported to distribute abundantly in the patches of the neostriatum. The marginal division (MrD) of the neostriatum, which located at the caudomedial border of the neostriatum, was found to stain for enkephalin and substance P immunoreactivities and this region was found to be involved in learning and memory in our previous study. However, whether MOR also exists in the MrD has not yet been determined.</p> <p>Methods</p> <p>In this study, we used western blot analysis and immunoperoxidase histochemical methods with glucose oxidase-DAB-nickel staining to investigate the expression of MOR in the MrD by comparison to the patches in the neostriatum.</p> <p>Results</p> <p>The results from western blot analyses revealed that the antibody to MOR detected a 53 kDa protein band, which corresponded directly to the molecular weight of MOR. Immunohistochemical results showed that punctate MOR-immunoreacted fibers were observed in the "patch" areas in the rostrodorsal part of the neostriatum but these previous studies showed neither labelled neuronal cell bodies, nor were they shown in the caudal part of the neostriatum. Dorsoventrally oriented dark MOR-immunoreactive nerve fibers with individual labelled fusiform cell bodies were firstly observed in the band at the caudomedial border, the MrD, of the neostriatum. The location of the MOR-immunoreactivity was in the caudomedial border of the neostriatum. The morphology of the labelled fusiform neuronal somatas and the dorsoventrally oriented MOR-immunoreacted fibers in the MrD was distinct from the punctate MOR-immunoreactive diffuse mosaic-patterned patches in the neostriatum.</p> <p>Conclusions</p> <p>The results indicated that MOR was expressed in the MrD as well as in patches in the neostriatum of the rat brain, but with different morphological characteristics. The punctate MOR-immunoreactive and diffuse mosaic-patterned patches were located in the rostrodorsal part of the neostriatum. By contrast, in the MrD, the dorsoventrally parallel oriented MOR-immunoreactive fibers with individual labelled fusiform neuronal somatas were densely packed in the caudomedial border of the neostriatum. The morphological difference in MOR immunoreactivity between the MrD and the patches indicated potential functional differences between them. The MOR most likely plays a role in learning and memory associated functions of the MrD.</p