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1.  Emerging roles of RNA processing factors in regulating long non-coding RNAs 
RNA Biology  2014;11(7):793-797.
Long non-coding RNAs (lncRNAs) can be important regulators of various biological processes such as RNA-directed DNA methylation (RdDM). In the RdDM pathway, recruitment of the DNA methylation complex is mediated through complementary pairing between scaffold RNAs and Argonaute-associated siRNAs. Scaffold RNAs are chromatin-associated lncRNAs transcribed by RNA polymerase Pol V or Pol II, while siRNAs originate from Pol IV- or Pol II-dependent production of lncRNAs. In contrast to the vast literature on co-transcriptional and post-transcriptional processing of mRNAs, information is limited for lncRNA regulation that enables their production and function. Recently Arabidopsis RRP6L1, a plant paralog of the conserved nuclear RNA surveillance protein Rrp6, was shown to mediate RdDM through retention of lncRNAs in the chromatin, thereby revealing that accumulation of functional lncRNAs requires more than simply RNA polymerases. By focusing on the canonical RdDM pathway, here we summarize recent evidence that indicate co-transcriptional and/or post-transcriptional regulation of lncRNAs, and highlight the emerging theme of lncRNA regulation by RNA processing factors.
PMCID: PMC4179953  PMID: 25144332
Long non-coding RNA; Pol IV; Pol V; RNA retention; RNA-directed DNA methylation; Rrp6; splicing; transcriptional silencing
2.  An Rrp6-like Protein Positively Regulates Non-coding RNA Levels and DNA Methylation in Arabidopsis 
Molecular cell  2014;54(3):418-430.
Rrp6-mediated nuclear RNA surveillance tunes eukaryotic transcriptomes through non-coding RNA degradation and mRNA quality control, including exosomal RNA decay and transcript retention triggered by defective RNA processing. It is unclear whether Rrp6 can positively regulate non-coding RNAs and whether RNA retention occurs in normal cells. Here we report that AtRRP6L1, an Arabidopsis Rrp6-like protein, controls RNA-directed DNA methylation through positive regulation of non-coding RNAs. Discovered in a forward genetic screen, AtRRP6L1 mutations decrease DNA methylation independently of exosomal RNA degradation. Accumulation of Pol V-transcribed scaffold RNAs requires AtRRP6L1 that binds to RNAs in vitro and in vivo. AtRRP6L1 helps retain Pol V-transcribed RNAs in chromatin to enable their scaffold function. In addition, AtRRP6L1 is required for genome-wide Pol IV-dependent siRNA production that may involve retention of Pol IV transcripts. Our results suggest that AtRRP6L1 functions in epigenetic regulation by helping with the retention of non-coding RNAs in normal cells.
PMCID: PMC4023806  PMID: 24726328
3.  Efficacy of edaravone on coronary artery bypass patients with myocardial damage after ischemia and reperfusion: a meta analysis 
Objectives: To assess the efficacy and safety of edaravone for myocardial damage during myocardial ischemia and reperfusion (I/R). Methods: We included randomized controlled trials that compared edaravone with placebo or no intervention in patients with acute myocardial infarction or undergoing coronary artery bypass. Two authors selected eligible trials, assessed trial quality and independently extracted the data. Results: Seven clinical trials were eventually included and analyzed in this study, involving 148 participants. Four trials were defined as waiting assessment. All of the three remaining trials compared edaravone and another treatment combined with other treatment alone, used the same dose of edaravone injections (60 mg per day) and course of treatment (14 days), evaluated the effect of edaravone at different times, applied different methods, reported adverse events, and showed no differences between the treatment group and the control group. When pooling all of the trials in one dataset, edaravone appeared to decrease the proportion of participant with marked myocardial damage during I/R as compared with the control group. The meta-analysis also revealed decreased CK-MB, cTnI and MDA, and increased content of SOD. Conclusions: Due to the moderate risk of bias and small sample, our observation of an effective treatment trend of edaravone for I/R requires future larger, high-quality trials to confirm.
PMCID: PMC4402799  PMID: 25932152
Myocardial; ischemia; reperfusion; edaraone
4.  Minimally invasive video-assisted versus conventional open thyroidectomy on immune response: a meta analysis 
Objectives: The aim of this study was to compare the immune response between the minimally invasive video-assisted thyroidectomy (MIVAT) and conventional thyroidectomy (CT). Methods: An exhaustive literature search was performed in the Medline, Embase, and Cochrane Library to identify the randomized controlled trials comparing the immune response between MIVAT and CT. Relevant data were extracted and statistical analysis was done using RevMan 5.0. Results: Twelve trials including 389 patients were identified. Immune-competent cells demonstrated no significant differences between MIVAT and CT. The including trails were assessed various perioperative plasma cytokine concentrations with no significant differences in interleukin-6 (IL-6), T lymphocytes (CD4+, CD8+, CD4/CD8) and NK cells between the MIVAT and CT. However, meta-analysis showed lower counts on postoperative days at 72 h was showed lower C-reactive protein (CRP) level compared to the preoperation levels but showed no significant difference within 24 h in MIVAT S group compared with CT group. Tumor necrosis factor alpha (TNF-α) level after surgery within 24 h and 72 h showed lower TNF-α level after MIVAT surgery within 24 h and 72 h. Conclusions: This meta-analysis demonstrates that, MIVAT has less immune response outcomes and that it is a more ideal choice for the patients relative to the conventional surgery.
PMCID: PMC4402853  PMID: 25932206
Minimally invasive video-assisted thyroidectomy; conventional thyroidectomy; immune response
5.  Regulation of Active DNA Demethylation by an α-Crystallin Domain Protein in Arabidopsis 
Molecular cell  2014;55(3):361-371.
DNA methylation patterns are dynamically controlled by DNA methylation and active DNA demethylation, but the mechanisms of regulation of active DNA demethylation are not well understood. Through forward genetic screens for Arabidopsis mutants showing DNA hypermethylation at specific loci and increased silencing of reporter genes, we identified IDM2 (increased DNA methylation 2) as a regulator of DNA demethylation and gene silencing. IDM2 dysfunction causes DNA hypermethylation and silencing of reporter genes and some endogenous genes. These effects of idm2 mutations are similar to those of mutations in IDM1, a regulator of active DNA demethylation. IDM2 encodes an α-crystallin domain protein in the nucleus. IDM2 and IDM1 interact physically and partially colocalize at discrete subnuclear foci. IDM2 is required for the full activity of H3K18 acetylation but not H3K23 acetylation of IDM1 in planta. Our results suggest that IDM2 functions in active DNA demethylation and in antisilencing by regulating IDM1.
PMCID: PMC4302764  PMID: 25002145
6.  An AP Endonuclease Functions in Active DNA Demethylation and Gene Imprinting in Arabidopsis 
PLoS Genetics  2015;11(1):e1004905.
Active DNA demethylation in plants occurs through base excision repair, beginning with removal of methylated cytosine by the ROS1/DME subfamily of 5-methylcytosine DNA glycosylases. Active DNA demethylation in animals requires the DNA glycosylase TDG or MBD4, which functions after oxidation or deamination of 5-methylcytosine, respectively. However, little is known about the steps following DNA glycosylase action in the active DNA demethylation pathways in plants and animals. We show here that the Arabidopsis APE1L protein has apurinic/apyrimidinic endonuclease activities and functions downstream of ROS1 and DME. APE1L and ROS1 interact in vitro and co-localize in vivo. Whole genome bisulfite sequencing of ape1l mutant plants revealed widespread alterations in DNA methylation. We show that the ape1l/zdp double mutant displays embryonic lethality. Notably, the ape1l+/−zdp−/− mutant shows a maternal-effect lethality phenotype. APE1L and the DNA phosphatase ZDP are required for FWA and MEA gene imprinting in the endosperm and are important for seed development. Thus, APE1L is a new component of the active DNA demethylation pathway and, together with ZDP, regulates gene imprinting in Arabidopsis.
Author Summary
DNA cytosine methylation (5-methylcytosine, 5-meC) is an important epigenetic mark, and methylation patterns are coordinately controlled by methylation and demethylation reactions during development and reproduction. In plants, REPRESSOR OF SILENCING (ROS1) is one of the well characterized 5-meC DNA glycosylases that initiate active DNA demethylation by 5-meC excision. Our previous work showed that a 3′-DNA phosphatase, ZDP, functions downstream of ROS1 during active DNA demethylation in Arabidopsis. Here we found that the apurinic/apyrimidinic endonuclease APE1L functions downstream of ROS1 in a ZDP-independent branch of the active DNA demethylation pathway in Arabidopsis. In plants, gene imprinting requires the 5-meC DNA glycosylase Demeter (DME) that has been proposed to initiate a base excision repair pathway for active DNA demethylation in the central cell in female gametophyte. However, besides DME, no other base excision repair enzymes have been found to be important for gene imprinting. Our results show that APE1L and ZDP act jointly downstream of DME to regulate gene imprinting in plants, and suggest that DME-initiated active DNA demethylation in the central cell and endosperm uses both APE- and ZDP-dependent mechanisms.
PMCID: PMC4287435  PMID: 25569774
7.  Augmenting iron accumulation in cassava by the beneficial soil bacterium Bacillus subtilis (GBO3) 
Cassava (Manihot esculenta), a major staple food in the developing world, provides a basic carbohydrate diet for over half a billion people living in the tropics. Despite the iron abundance in most soils, cassava provides insufficient iron for humans as the edible roots contain 3–12 times less iron than other traditional food crops such as wheat, maize, and rice. With the recent identification that the beneficial soil bacterium Bacillus subtilis (strain GB03) activates iron acquisition machinery to increase metal ion assimilation in Arabidopsis, the question arises as to whether this plant-growth promoting rhizobacterium also augments iron assimilation to increase endogenous iron levels in cassava. Biochemical analyses reveal that shoot-propagated cassava with GB03-inoculation exhibit elevated iron accumulation after 140 days of plant growth as determined by X-ray microanalysis and total foliar iron analysis. Growth promotion and increased photosynthetic efficiency were also observed for greenhouse-grown plants with GB03-exposure. These results demonstrate the potential of microbes to increase iron accumulation in an important agricultural crop and is consistent with idea that microbial signaling can regulate plant photosynthesis.
PMCID: PMC4524923  PMID: 26300897
cassava; Bacillus subtilis; iron induction; plant growth promotion; X-ray microanalysis
8.  The effects of bacterial volatile emissions on plant abiotic stress tolerance 
Plant growth-promoting rhizobacteria (PGPR) are beneficial plant symbionts that have been successfully used in agriculture to increase seedling emergence, plant weight, crop yield, and disease resistance. Some PGPR strains release volatile organic compounds (VOCs) that can directly and/or indirectly mediate increases in plant biomass, disease resistance, and abiotic stress tolerance. This mini-review focuses on the enhancement of plant abiotic stress tolerance by bacterial VOCs. The review considers how PGPR VOCs induce tolerance to salinity and drought stress and also how they improve sulfur and iron nutrition in plants. The potential complexities in evaluating the effects of PGPR VOCs are also discussed.
PMCID: PMC4585079  PMID: 26442083
plant growth-promoting rhizobacteria; volatile organic compounds; abiotic stress; salinity; drought; sulfur nutrition; iron deficiency
9.  Local Application of Sodium Salicylate Enhances Auditory Responses in the Rat’s Dorsal Cortex of the Inferior Colliculus 
Sodium salicylate (SS) is a widely used medication with side effects on hearing. In order to understand these side effects, we recorded sound-driven local-field potentials in a neural structure, the dorsal cortex of the inferior colliculus (ICd). Using a microiontophoretic technique, we applied SS at sites of recording and studied how auditory responses were affected by the drug. Furthermore, we studied how the responses were affected by combined local application of SS and an agonists/antagonist of the type-A or type-B γ-aminobutyric acid receptor (GABAA or GABAB receptor). Results revealed that SS applied alone enhanced auditory responses in the ICd, indicating that the drug had local targets in the structure. Simultaneous application of the drug and a GABAergic receptor antagonist synergistically enhanced amplitudes of responses. The synergistic interaction between SS and a GABAA receptor antagonist had a relatively early start in reference to the onset of acoustic stimulation and the duration of this interaction was independent of sound intensity. The interaction between SS and a GABAB receptor antagonist had a relatively late start, and the duration of this interaction was dependent on sound intensity. Simultaneous application of the drug and a GABAergic receptor agonist produced an effect different from the sum of effects produced by the two drugs released individually. These differences between simultaneous and individual drug applications suggest that SS modified GABAergic inhibition in the ICd. Our results indicate that SS can affect sound-driven activity in the ICd by modulating local GABAergic inhibition.
PMCID: PMC4231951  PMID: 25452744
auditory system; GABAA receptor; GABAB receptor; hearing; midbrain; tinnitus; microiontophoresis
10.  Protocol: a beginner’s guide to the analysis of RNA-directed DNA methylation in plants 
Plant Methods  2014;10:18.
DNA methylation is a conserved epigenetic mark that controls genome stability, development and environmental responses in many eukaryotes. DNA methylation can be guided by non-coding RNAs that include small interfering RNAs and scaffold RNAs. Although measurement of DNA methylation and regulatory non-coding RNAs is desirable for many biologists who are interested in exploring epigenetic regulation in their areas, conventional methods have limitations and are technically challenging. For instance, traditional siRNA detection through RNA hybridization requires relatively large amount of small RNAs and involves radioactive isotopes. An alternative approach is RT-qPCR that employs stem loop primers during reverse transcription; however, it requires a prerequisite that the exact sequences of siRNAs should be known.
By using the model organism Arabidopsis thaliana, we developed an easy-to-follow, integrative procedure for time-efficient, quantitative measurement of DNA methylation, small interfering RNAs, and scaffold RNAs. Starting with simplified nucleic acid manipulation, we examined DNA methylation levels by using Chop PCR (methylation-sensitive enzyme digestion followed by PCR), which allowed for fast screening for DNA methylation mutants without the need of transgenic reporters. We deployed a simple bioinformatics method for mining published small RNA databases, in order to obtain the nucleotide (nt) sequences of individual 24nt siRNAs within the regions of interest. The protocol of commercial TaqMan Small RNA Assay was subsequently optimized for reliable quantitative detection of individual siRNAs. We used nested qPCR to quantify scaffold RNAs that are of low abundance and without Poly-A tails. In addition, nuclei fraction enables separation of chromatin-associated scaffold RNAs from their cognate non-scaffold transcripts that have been released from chromatin.
We have developed a procedure for quantitative investigations on nucleic acids that are core components of RNA-directed DNA methylation. Our results not only demonstrated the efficacy of this procedure, but also provide lists of methylation-sensitive restriction enzymes, novel DNA methylation marker loci, and related siRNA sequences, all of which can be valuable for future epigenetic studies. Importantly, step-by-step protocols are provided in details such that the approaches can be easily followed by biologists with little experience in epigenetics.
PMCID: PMC4065543  PMID: 24955108
Epigenetics; RNA-directed DNA methylation; siRNA; Scaffold RNA; Pol IV; Pol V; Nuclei fractionation
11.  Mechanisms of Small RNA Generation from Cis-NATs in Response to Environmental and Developmental Cues 
Molecular Plant  2013;6(3):704-715.
This review summarizes the current findings on the occurrence and characteristics of cis-natural antisense transcripts (NATs) and nat-siRNAs; discusses the biogenesis, regulations and functions of nat-siRNAs; and highlights the advantages and limitations of new technologies on cis-NATs detection.
A large proportion of eukaryotic genomes is transcribed from both positive and negative strands of DNA and thus may generate overlapping sense and antisense transcripts. Some of these so-called natural antisense transcripts (NATs) are possibly co-regulated. When the overlapping sense and antisense transcripts are expressed at the same time in the same cell in response to various developmental and environmental cues; they may form double-stranded RNAs, which could be recognized by the small RNA biogenesis machinery and processed into small interfering RNAs (siRNAs). cis-NAT-derived siRNAs (nat-siRNAs) are present in plants, animals, and fungi. In plants, the presence of nat-siRNAs is supported not only by Northern blot and genetic analyses, but also by the fact that there is an overall sixfold enrichment of siRNAs in the overlapping regions of cis-NATs and 19%–29% of the siRNA-generating cis-NATs in plants give rise to siRNAs only in their overlapping regions. Silencing mediated by nat-siRNAs is one of the mechanisms for regulating the expression of the cis-NATs. This review focuses on challenging issues related to the biogenesis mechanisms as well as regulation and detection of nat-siRNAs. The advantages and limitations of new technologies for detecting cis-NATs, including direct RNA sequencing and strand-specific RNA sequencing, are also discussed.
PMCID: PMC3660955  PMID: 23505223
gene expression; gene regulation; gene silencing.
12.  Chemical probes in plant epigenetics studies 
Plant Signaling & Behavior  2013;8(9):e25364.
Transcription potential is determined by the accessibility of DNA sequences within the context of chromatin, which is coordinately controlled by various epigenetic modifications. Chemical inhibition of epigenetic regulators provides a quick and effective approach to investigate the roles of epigenetic modifications in controlling many biological processes, especially for species in which genetic information is limited. This mini-review provides a brief overview of epigenetic regulators in the model organism Arabidopsis thaliana and summarizes compounds that have been applied in plant epigenetics studies, with highlights in the applications of these chemical probes in mechanistic and functional investigations.
PMCID: PMC4002629  PMID: 23838953
plant epigenetics; chemical inhibitors; DNA methylation; histone modification; methyltransferase inhibitors
13.  The Quantitative Imaging Network: NCI's Historical Perspective and Planned Goals 
Translational Oncology  2014;7(1):1-4.
The purpose of this editorial is to provide a brief history of National Institutes of Health National Cancer Institute (NCI) workshops as related to quantitative imaging within the oncology setting. The editorial will then focus on the recently supported NCI initiatives, including the Quantitative Imaging Network (QIN) initiative and its organizational structure, including planned research goals and deliverables. The publications in this issue of Translational Oncology come from many of the current members of this QIN research network.
PMCID: PMC3998696  PMID: 24772201
14.  Dynamic Chemical Communication between Plants and Bacteria through Airborne Signals: Induced Resistance by Bacterial Volatiles 
Journal of Chemical Ecology  2013;39(7):1007-1018.
Certain plant growth-promoting rhizobacteria (PGPR) elicit induced systemic resistance (ISR) and plant growth promotion in the absence of physical contact with plants via volatile organic compound (VOC) emissions. In this article, we review the recent progess made by research into the interactions between PGPR VOCs and plants, focusing on VOC emission by PGPR strains in plants. Particular attention is given to the mechanisms by which these bacterial VOCs elicit ISR. We provide an overview of recent progress in the elucidation of PGPR VOC interactions from studies utilizing transcriptome, metabolome, and proteome analyses. By monitoring defense gene expression patterns, performing 2-dimensional electrophoresis, and studying defense signaling null mutants, salicylic acid and ethylene have been found to be key players in plant signaling pathways involved in the ISR response. Bacterial VOCs also confer induced systemic tolerance to abiotic stresses, such as drought and heavy metals. A review of current analytical approaches for PGPR volatile profiling is also provided with needed future developments emphasized. To assess potential utilization of PGPR VOCs for crop plants, volatile suspensions have been applied to pepper and cucumber roots and found to be effective at protecting plants against plant pathogens and insect pests in the field. Taken together, these studies provide further insight into the biological and ecological potential of PGPR VOCs for enhancing plant self-immunity and/or adaptation to biotic and abiotic stresses in modern agriculture.
PMCID: PMC3738840  PMID: 23881442
PGPR; ISR; IST; Volatile organic compounds; Headspace
15.  Effect of advanced glycation end products on the expression of hypoxia-inducible factor-1α and vascular endothelial growth factor proteins in RF/6A cells 
The aim of this study was to investigate the effect of advanced glycation end products (AGEs) on the expression of hypoxia-inducible factor-1α (HIF-1α) and vascular endothelial growth factor (VEGF) proteins in RF/6A cells cultured in vitro, and to investigate the association between the expression of HIF-1α and VEGF proteins. RF/6A cells were cultured in vitro and treated with AGEs and non-glycated albumin control at various concentrations (0, 50, 100, 200, 400 and 800 mg/l) for 24 h. The expression of the VEGF protein was detected by ELISA, and western blot analysis was used to determine the levels of HIF-1α protein. The expression of HIF-1α and VEGF proteins was significantly higher in the AGE group compared with the non-glycated control group (all P<0.05). With the increase in concentration of AGEs, the expression levels of HIF-1α and VEGF protein increased and reached a maximum at 200 mg/l AGE, then decreased at 400 and 800 mg/l. However this effect was not observed in the non-glycated control groups. There was a positive correlation between the expression of HIF-1α and VEGF (P<0.05). AGEs induced the expression of HIF-1α and VEGF proteins in RF/6A cells in a concentration-dependent manner. AGEs may upregulate the expression of VEGF protein by increasing the levels of HIF-1α protein, demonstrating the potential role of HIF-1α-targeted therapy in neovascularization.
PMCID: PMC3671897  PMID: 23737911
hypoxia-inducible factor-1α; vascular endothelial growth factor; advanced glycation end products; RF/6A cells
16.  Molecular Mimicry Regulates ABA Signaling by SnRK2 Kinases and PP2C Phosphatases 
Science (New York, N.Y.)  2011;335(6064):85-88.
Abscisic acid (ABA) is an essential hormone for plants to survive environmental stresses. At the center of the ABA signaling network is a subfamily of type 2C protein phosphatases (PP2Cs), which form exclusive interactions with ABA receptors and subfamily 2 Snfl-related kinase (SnRK2s). Here, we report a SnRK2-PP2C complex structure, which reveals marked similarity in PP2C recognition by SnRK2 and ABA receptors. In the complex, the kinase activation loop docks into the active site of PP2C, while the conserved ABA-sensing tryptophan of PP2C inserts into the kinase catalytic cleft, thus mimicking receptor-PP2C interactions. These structural results provide a simple mechanism that directly couples ABA binding to SnRK2 kinase activation and highlight a new paradigm of kinase-phosphatase regulation through mutual packing of their catalytic sites.
PMCID: PMC3584687  PMID: 22116026
17.  Positive and Negative Relationship between Anxiety and Depression of Patients in Pain: A Bifactor Model Analysis 
PLoS ONE  2012;7(10):e47577.
The relationship between anxiety and depression in pain patients has not been clarified comprehensively. Previous research has identified a common factor in anxiety and depression, which may explain why depression and anxiety are strongly correlated. However, the specific clinical features of anxiety and depression seem to pull in opposite directions.
The purpose of this study is to develop a statistical model of depression and anxiety, based on data from pain patients using Hospital Anxiety and Depression Scale (HADS). This model should account for the positive correlation between depression and anxiety in terms of a general factor and also demonstrate a latent negative correlation between the specific factors underlying depression and anxiety.
The anxiety and depression symptoms of pain patients were evaluated using the HADS and the severity of their pain was assessed with the visual analogue scale (VAS). We developed a hierarchical model of the data using an IRT method called bifactor analysis. In addition, we tested this hierarchical model with model fit comparisons with unidimensional, bidimensional, and tridimensional models. The correlations among anxiety, depression, and pain severity were compared, based on both the bidimensional model and our hierarchical model.
The bidimensional model analysis found that there was a large positive correlation between anxiety and depression (r = 0.638), and both scores were significantly positively correlated with pain severity. After extracting general factor of distress using bifactor analysis, the specific factors underlying anxiety and depression were weakly but significantly negatively correlated (r = −0.245) and only the general factor was significantly correlated with pain severity. Compared with the three first-order models, the bifactor hierarchical model had the best model fit.
Our results support the hypothesis that apart from distress, anxiety and depression are inversely correlated. This finding has not been convincingly demonstrated in previous research.
PMCID: PMC3475698  PMID: 23094064
18.  RNA-directed DNA Methylation 
Current opinion in plant biology  2011;14(2):142-147.
DNA methylation is an important epigenetic mechanism for silencing transposons and other repetitive elements, and for stable repression of specific transgenes and endogenous genes. Plants can utilize small interfering RNAs (siRNAs) to guide de novo DNA methyltransferases for the establishment of sequence-specific DNA methylation. Genetic and biochemical approaches have identified many components involved in RNA-directed DNA methylation (RdDM). These components function in one or more of the following three aspects: biogenesis of siRNAs, production of scaffold RNAs, and the assembly of an effector complex that involves the complementary pairing between the guide siRNAs and nascent scaffold RNAs and which recruits the DNA methyltransferases. Recent studies not only unveiled new molecular players and novel interactions, but also suggested spatial and temporal segregation of the RdDM process within the nucleus.
PMCID: PMC3096526  PMID: 21420348
19.  Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function 
Genome Biology  2012;13(3):R20.
Many eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, and yeasts. However, many questions remain regarding the features and biogenesis of nat-siRNAs.
Through deep sequencing, we identified more than 17,000 unique siRNAs corresponding to cis-NATs from biotic and abiotic stress-challenged Arabidopsis thaliana and 56,000 from abiotic stress-treated rice. These siRNAs were enriched in the overlapping regions of NATs and exhibited either site-specific or distributed patterns, often with strand bias. Out of 1,439 and 767 cis-NAT pairs identified in Arabidopsis and rice, respectively, 84 and 119 could generate at least 10 siRNAs per million reads from the overlapping regions. Among them, 16 cis-NAT pairs from Arabidopsis and 34 from rice gave rise to nat-siRNAs exclusively in the overlap regions. Genetic analysis showed that the overlapping double-stranded RNAs could be processed by Dicer-like 1 (DCL1) and/or DCL3. The DCL3-dependent nat-siRNAs were also dependent on RNA-dependent RNA polymerase 2 (RDR2) and plant-specific RNA polymerase IV (PolIV), whereas only a fraction of DCL1-dependent nat-siRNAs was RDR- and PolIV-dependent. Furthermore, the levels of some nat-siRNAs were regulated by specific biotic or abiotic stress conditions in Arabidopsis and rice.
Our results suggest that nat-siRNAs display distinct distribution patterns and are generated by DCL1 and/or DCL3. Our analysis further supported the existence of nat-siRNAs in plants and advanced our understanding of their characteristics.
PMCID: PMC3439971  PMID: 22439910
20.  The level and distribution of the GABABR1 and GABABR2 receptor subunits in the rat's inferior colliculus 
The type B γ-aminobutyric acid receptor (GABAB receptor) is an important neurotransmitter receptor in the midbrain auditory structure, the inferior colliculus (IC). A functional GABAB receptor is a heterodimer consisting of two subunits, GABABR1 and GABABR2. Western blotting and immunohistochemical experiments were conducted to examine the expression of the two subunits over the IC including its central nucleus, dorsal cortex, and external cortex (ICc, ICd, and ICx). Results revealed that the two subunits existed in both cell bodies and the neuropil throughout the IC. The two subunits had similar regional distributions over the IC. The combined level of cell body and neuropil labeling was higher in the ICd than the other two subdivisions. Labeling in the ICc and ICx was stronger in the dorsal than the ventral regions. In spite of regional differences, no defined boundaries were formed between different areas. For both subunits, the regional distribution of immunoreactivity in the neuropil was parallel to that of combined immunoreactivity in the neuropil and cell bodies. The density of labeled cell bodies tended to be higher but sizes of cell bodies tended to be smaller in the ICd than in the other subdivisions. No systematic regional changes were found in the level of cell body immunoreactivity, except that GABABR2-immunoreactive cell bodies in the ICd had slightly higher optic density (OD) than in other regions. Elongated cell bodies existed throughout the IC. Many labeled cell bodies along the outline of the IC were oriented in parallel to the outline. No strong tendency of orientation was found in labeled cell bodies in ICc. Regional distributions of the subunits in ICc correlated well with inputs to this subdivision. Our finding regarding the contrast in the level of neuropil immunoreactivity among different subdivisions is consistent with the fact that the GABAB receptor has different pre- and postsynaptic functions in different IC regions.
PMCID: PMC3506002  PMID: 23189044
hearing; auditory system; auditory midbrain; GABA; GABAB receptor; GABABR1 subunit; GABABR2 subunit; inhibition
21.  Potent in vitro and in vivo anticancer activities of des-methyl, des-amino pateamine A, a synthetic analogue of marine natural product pateamine A 
Molecular cancer therapeutics  2009;8(5):1250-1260.
We report here that des-methyl, des-amino pateamine A (DMDA-PatA), a structurally simplified analogue of the marine natural product pateamine A, has potent antiproliferative activity against a wide variety of human cancer cell lines while showing relatively low cytotoxicity against nonproliferating, quiescent human fibroblasts. DMDA-PatA retains almost full in vitro potency in P-glycoprotein-overexpressing MES-SA/D×5-R×1 human uterine sarcoma cells that are significantly resistant to paclitaxel, suggesting that DMDA-PatA is not a substrate for P-glycoprotein-mediated drug efflux. Treatment of proliferating cells with DMDA-PatA leads to rapid shutdown of DNA synthesis in the S phase of the cell cycle. Cell-free studies show that DMDA-PatA directly inhibits DNA polymerases α and γ in vitro albeit at concentrations considerably higher than those that inhibit cell proliferation. DMDA-PatA shows potent anticancer activity in several human cancer xenograft models in nude mice, including significant regressions observed in the LOX and MDA-MB-435 melanoma models. DMDA-PatA thus represents a promising natural product-based anticancer agent that warrants further investigation.
PMCID: PMC3026899  PMID: 19417157
22.  Sustained growth promotion in arabidopsis with long-term exposure to the beneficial soil bacterium Bacillus subtilis (GB03) 
Plant Signaling & Behavior  2009;4(10):948-953.
Volatile emissions from the commercial growth promoting soil bacterium Bacillus subtilis (GB03) are effective in augmenting short-term growth, photosynthetic capacity and salt tolerance in Petri-dish grown arabidopsis seedlings. In contrast, the impact sustained GB03 volatile exposure on plant growth and development has yet to be examined. here is provided physical and physiological data establishing that bacterial volatiles induce long-term growth promotion, elevated photosynthetic capacity and iron accumulation, as well as delayed albeit higher seed count compared with water-treated control plants. Plants were grown unrestricted in double Magenta boxes containing solid MS media for up to twelve weeks with GB03 volatiles introduced in separate containers within the chamber so that plant bacterial interactions were only by air-borne transmission. These results establish that GB03 volatiles induce sustained beneficial effects on Arabidopsis growth including robust and extended vegetative growth followed by elevated seed set.
PMCID: PMC2801358  PMID: 19826235
Bacillus subtilis (GB03); photosynthetic efficiency; plant growth promoting rhizobacteria (PGPR); seed set; volatile organic compound (VOCs)
23.  B7 Blockade Alters the Balance between Regulatory T cells and Tumor-reactive T Cells for Immunotherapy of Cancer 
In prostate cancer bearing host, regulatory T cells restrain activity of tumor antigen specific T cells. Since B7:CD28 interactions are needed for both function of CD4+CD25+ Treg cells and the CD8+ effective T cells, targeting this pathway may help to overcome the immunotherapy barriers.
Experimental design
The anti-B7−1/B7−2 mAbs were administrated to a transgenic mouse model of prostate cancer (TRAMP) ectopically expressing SV40 large T antigen (TAg) in different tumor development stages for prevention and therapy of prostate cancer. The treatment was also tested in treating transplanted MC38 colon adenocarcinoma in mice.
Here we showed that short-term administration of anti-B7−1/B7−2 mAbs in TRAMP mice leads to significant inhibited primary tumor growth and the size of metastatic lesions. The treatment is effective to inhibit MC38 colon cancer growth. Correspondingly, this treatment results in a transient reduction of Treg in both thymus and the periphery. In vivo cytotoxicity assay revealed TAg-specific CTL effectors in anti-B7 treated, but not control IgG-treated TRAMP mice.
Transient blockade of B7−1/2 alters the balance between Treg and cancer-reactive T cells to enhance cancer immunotherapy.
PMCID: PMC2693886  PMID: 19188167
regulatory T cells; costimulatory molecule; prostate cancer
25.  Fibroblast growth factor receptor signaling is essential for lens fiber cell differentiation 
Developmental biology  2008;318(2):276-288.
The vertebrate lens provides an excellent model to study the mechanisms that regulate terminal differentiation. Although fibroblast growth factors (FGFs) are thought to be important for lens cell differentiation, it is unclear which FGF receptors mediate these processes during different stages of lens development. Deletion of three FGF receptors (Fgfr1-3) early in lens development demonstrated that expression of only a single allele of Fgfr2 or Fgfr3 was sufficient for grossly normal lens development, while mice possessing only a single Fgfr1 allele developed cataracts and microphthalmia. Profound defects were observed in lenses lacking all three Fgfrs. These included lack of fiber cell elongation, abnormal proliferation in prospective lens fiber cells, reduced expression of the cell cycle inhibitors p27kip1 and p57kip2, increased apoptosis and aberrant or reduced expression of Prox1, Pax6, c-Maf, E-cadherin and α-, β- and γ-crystallins. Therefore, while signaling by FGF receptors is essential for lens fiber differentiation, different FGF receptors function redundantly.
PMCID: PMC2574794  PMID: 18455718
apoptosis; cell cycle; FGF receptor; lens development; lens fiber differentiation; redundancy; conditional knockout

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