Rice protein-binding microarrays: a tool to detect cis-acting elements near promoter regions in rice.

MAIN CONCLUSION: The present study showed that a rice (Oryza sativa)-specific protein-binding microarray (RPBM) can be applied to analyze DNA-binding motifs with a TF where binding is evaluated in extended natural promoter regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements. Transcription factors (TFs) regulate gene expression at the transcriptional level by binding a specific DNA sequence. Thus, predicting the DNA-binding motifs of TFs is one of the most important areas in the functional analysis of TFs in the postgenomic era. Although many methods have been developed to address this challenge, many TFs still have unknown DNA-binding motifs. In this study, we designed RPBM with 40-bp probes and 20-bp of overlap, yielding 49 probes spanning the 1-kb upstream region before the translation start site of each gene in the entire genome. To confirm the efficiency of RPBM technology, we selected two previously studied TFs, OsWOX13 and OsSMF1, and an uncharacterized TF, OsWRKY34. We identified the ATTGATTG and CCACGTCA DNA-binding sequences of OsWOX13 and OsSMF1, respectively. In total, 635 and 932 putative feature genes were identified for OsWOX13 and OsSMF1, respectively. We discovered the CGTTGACTTT DNA-binding sequence and 195 putative feature genes of OsWRKY34. RPBM could be applicable in the analysis of DNA-binding motifs for TFs where binding is evaluated in the promoter and 5' upstream CDS regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements.

Recurrent Drought Conditions Enhance the Induction of Drought Stress Memory Genes in Glycine max L.

Plants remember what they have experienced and are thereby able to confront repeated stresses more promptly and strongly. A subset of the drought responsive genes, called stress memory genes, displayed greatly elevated levels under recurrent drought conditions. To screen for a set of drought stress memory genes in soybean (Glycine max L.), we designed a 180K DNA chip comprising 60-bp probes synthesized in situ to examine 55,589 loci. Through microarray analysis using the DNA chip, we identified 2,162 and 2,385 genes with more than fourfold increases or decreases in transcript levels, respectively, under initial (first) drought stress conditions, when compared with the non-treated control. The transcript levels of the drought-responsive genes returned to basal levels during recovery (watered) states, and 392 and 613 genes displayed more than fourfold elevated or reduced levels, respectively, under subsequent (second) drought conditions, when compared to those observed under the first drought stress conditions. Gene Ontology and MapMan analyses classified the drought-induced memory genes exhibiting elevated levels of transcripts into several functional categories, including those involved in tolerance responses to abiotic stresses, which encode transcription factors, protein phosphatase 2Cs, and late embryogenesis abundant proteins. The drought-repressed memory genes exhibiting reduced levels of transcripts were classified into categories including photosynthesis and primary metabolism. Co-expression network analysis revealed that the soybean drought-induced and -repressed memory genes were equivalent to 172 and 311 Arabidopsis genes, respectively. The soybean drought stress memory genes include genes involved in the dehydration memory responses of Arabidopsis.

Antenatal sonographic features of persistent extrahepatic vitelline vein aneurysm confused with umbilical vein varix.

Background: The persistent vitelline vein is a portal venous system malformation arising during the embryonic period. These abnormal blood vessels frequently thrombose and can lead superior mesenteric vein obstruction or portal hypertension. Case report: We visualized a fetal intra-abdominal cystic mass with turbulent flow on prenatal ultrasound at 28 weeks' gestation. Initially diagnosed as an umbilical vein varix, it was later determined to be an extrahepatic persistent vitelline vein with an internal thrombus by postnatal ultrasound. It was successfully surgically excised. Conclusion: When an abnormal abdominal vascular structure near the umbilicus is found during prenatal ultrasonography, the persistent vitelline vein should be included in the differential diagnosis to allow prompt evaluation and treatment after birth.

Superhydrophobic plasmonic nanoarchitectures based on aluminum hydroxide nanotemplates.

The combined characteristics of non-wettabililty and strong plasmonic resonances make superhydrophobic plasmonic nanostructures an appealing tool for ultrasensitive detection in surface-enhanced Raman scattering (SERS). However, inducing superhydrophobic surfaces on originally hydrophilic metals (e.g., gold, silver) while achieving high plasmonic enhancement requires sophisticated surface engineering and often involves complex fabrication processes. In this article, we design and fabricate cost effective and scalable plasmonic nanostructures with both superhydrophobicity (a water contact angle >160°) and high SERS signal (enhancement factor ≈106). Silver-coated aluminum hydroxide nanotemplates are obtained from a simple wet process, followed by thermal evaporation of silver nanoparticles. We find that the largest SERS enhancement is obtained when the contact angle is maximum. This confirms that the control of surface wettability is an effective way to improve detection sensitivity in SERS measurements. The nanotemplates developed in this study could be applied further in various applications, including microfluidic biomolecular optical sensors, photocatalysts, and optoelectronic devices.

A WUSCHEL Homeobox Transcription Factor, OsWOX13, Enhances Drought Tolerance and Triggers Early Flowering in Rice.

Plants have evolved strategies to cope with drought stress by maximizing physiological capacity and adjusting developmental processes such as flowering time. The WOX13 orthologous group is the most conserved among the clade of WOX homeodomain-containing proteins and is found to function in both drought stress and flower development. In this study, we isolated and characterized OsWOX13 from rice. OsWOX13 was regulated spatially in vegetative organs but temporally in flowers and seeds. Overexpression of OsWOX13 (OsWOX13-ov) in rice under the rab21 promoter resulted in drought resistance and early flowering by 7-10 days. Screening of gene expression profiles in mature leaf and panicles of OsWOX13-ov showed a broad spectrum of effects on biological processes, such as abiotic and biotic stresses, exerting a cross-talk between responses. Protein binding microarray and electrophoretic mobility shift assay analyses supported ATTGATTG as the putative cis-element binding of OsWOX13. OsDREB1A and OsDREB1F, drought stress response transcription factors, contain ATTGATTG motif(s) in their promoters and are preferentially expressed in OsWOX13-ov. In addition, Heading date 3a and OsMADS14, regulators in the flowering pathway and development, were enhanced in OsWOX13-ov. These results suggest that OsWOX13 mediates the stress response and early flowering and, thus, may be a regulator of genes involved in drought escape.

Lymphocyte-to-monocyte ratio on day 7 is associated with outcomes in acute ischemic stroke.

The main features of stroke-induced immunosuppression are lymphopenia and deactivation of monocytes in peripheral blood. We hypothesized that lymphocyte-to-monocyte ratio (LMR) in peripheral blood may represent the degree of stroke-induced immunosuppression. To prove this hypothesis, we evaluated whether LMR is associated with risk of post-stroke infection and clinical outcome at 3 months in patients with acute ischemic stroke. We selected patients with stroke in anterior circulation within 24 h from onset. Peripheral blood sampling for differential blood count was performed on days 1 and 7. The LMRs on days 1 and 7 were analyzed to determine associations with excellent outcomes (modified Rankin Scale of score 0-1 at 3 months). One hundred and two patients were included. The initial National Institutes of Health Stroke Scale score (adjusted odd ratio [OR] 0.89; 95% confidence interval [CI], 0.83-0.95; P = 0.001) and LMR on day 7 (adjusted OR 1.49; 95% CI, 1.09-2.02; P = 0.011) were associated with excellent outcomes. LMRs on day 1 were significantly lower in stroke patients with pneumonia (P = 0.007) and pneumonia or urinary tract infection (P = 0.012) than those without infections. LMRs on day 7 were also significantly lower in stroke patients with infection (P = 0.005 in pneumonia, P = 0.003 in urinary tract infection, and P < 0.001 in pneumonia or urinary tract infection) than those without infections. Lower LMRs on day 7 are associated with worse outcomes at 3 months after stroke onset. LMR may be a useful marker for assessing the stroke-induced immunosuppression.

Plasmonic-Photonic Interference Coupling in Submicrometer Amorphous TiO2-Ag Nanoarchitectures.

In this study, we report the crystallinity effects of submicrometer titanium dioxide (TiO2) nanotube (TNT) incorporated with silver (Ag) nanoparticles (NPs) on surface-enhanced Raman scattering (SERS) sensitivity. Furthermore, we demonstrate the SERS behaviors dependent on the plasmonic-photonic interference coupling (P-PIC) in the TNT-AgNP nanoarchitectures. Amorphous TNTs (A-TNTs) are synthesized through a two-step anodization on titanium (Ti) substrate, and crystalline TNTs (C-TNTs) are then prepared by using thermal annealing process at 500 °C in air. After thermally evaporating 20 nm thick Ag on TNTs, we investigate SERS signals according to the crystallinity and P-PIC on our TNT-AgNP nanostructures. (A-TNTs)-AgNP substrates show dramatically enhanced SERS performance as compared to (C-TNTs)-AgNP substrates. We attribute the high enhancement on (A-TNTs)-AgNP substrates with electron confinement at the interface between A-TNTs and AgNPs as due to the high interfacial barrier resistance caused by band edge positions. Moreover, the TNT length variation in (A-TNTs)-AgNP nanostructures results in different constructive or destructive interference patterns, which in turn affects the P-PIC. Finally, we could understand the significant dependency of SERS intensity on P-PIC in (A-TNTs)-AgNP nanostructures. Our results thus might provide a suitable design for a myriad of applications of enhanced EM on plasmonic-integrated devices.

Analysis of Genes with Alternatively Spliced Transcripts in the Leaf, Root, Panicle and Seed of Rice Using a Long Oligomer Microarray and RNA-Seq.

Pre-mRNA splicing further increases protein diversity acquired through evolution. The underlying driving forces for this phenomenon are unknown, especially in terms of gene expression. A rice alternatively spliced transcript detection microarray (ASDM) and RNA sequencing (RNA-Seq) were applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi: leaves, roots, 1-cm-stage panicles and young seeds at 21 days after pollination. Comparison of data obtained by microarray and RNA-Seq showed a bell-shaped distribution and a co-lineation for highly expressed genes. Transcripts were classified according to the degree of organ enrichment using a coefficient value (CV, the ratio of the standard deviation to the mean values): highly variable (CVI), variable (CVII), and constitutive (CVIII) groups. A higher index of the portion of loci with alternatively spliced transcripts in a group (IAST) value was observed for the constitutive group. Genes of the highly variable group showed the characteristics of the examined organs, and alternatively spliced transcripts tended to exhibit the same organ specificity or less organ preferences, with avoidance of 'organ distinctness'. In addition, within a locus, a tendency of higher expression was found for transcripts with a longer coding sequence (CDS), and a spliced intron was the most commonly found type of alternative splicing for an extended CDS. Thus, pre-mRNA splicing might have evolved to retain maximum functionality in terms of organ preference and multiplicity.

RapaNet: A Web Tool for the Co-Expression Analysis of Brassica rapa Genes.

Accumulated microarray data are used for assessing gene function by providing statistical values for co-expressed genes; however, only a limited number of Web tools are available for analyzing the co-expression of genes of Brassica rapa. We have developed a Web tool called RapaNet (http://bioinfo.mju.ac.kr/arraynet/brassica300k/query/), which is based on a data set of 143 B rapa microarrays compiled from various organs and at different developmental stages during exposure to biotic or abiotic stress. RapaNet visualizes correlated gene expression information via correlational networks and phylogenetic trees using Pearson correlation coefficient (r). In addition, RapaNet provides hierarchical clustering diagrams, scatterplots of log ratio intensities, related pathway maps, and cis-element lists of promoter regions. To ascertain the functionality of RapaNet, the correlated genes encoding ribosomal protein (L7Ae), photosystem II protein D1 (psbA), and cytochrome P450 monooxygenase in glucosinolate biosynthesis (CYP79F1) were retrieved from RapaNet and compared with their Arabidopsis homologues. An analysis of the co-expressed genes revealed their shared and unique features.

Delayed postpartum hemoperitoneum due to uterine artery pseudoaneurysm rupture.

A 30-year-old woman experienced severe abdominal pain 8 days after vaginal delivery. The patient was diagnosed with hemoperitoneum due to rupture of the left uterine artery pseudoaneurysm, which was confirmed via ultrasound with color Doppler and computed tomography scans. This patient was treated with bilateral uterine artery embolization to maintain fertility. A uterine artery pseudoaneurysm that causes delayed postpartum hemorrhage can occur after cesarean section or vaginal delivery. A uterine artery pseudoaneurysm can be fatal, so its detection and diagnosis are critical. Herein, we report a case of delayed postpartum hemoperitoneum due to uterine artery pseudoaneurysm rupture.

Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice.

BACKGROUND: Spatial- and temporal-specific expression patterns are primarily regulated at the transcriptional level by gene promoters. Therefore, it is important to identify the binding motifs of transcription factors to better understand the networks associated with embryogenesis. RESULTS: Here, we used a protein-binding microarray (PBM) to identify the binding motifs of OsSMF1, which is a basic leucine zipper transcription factor involved in the regulation of rice seed maturation. OsSMF1 (previously called RISBZ1 or OsbZIP58) is known to interact with GCN4 motifs (TGA(G/C)TCA) to regulate seed storage protein synthesis, and it functions as a key regulator of starch synthesis. Quadruple 9-mer-based PBM analysis and electrophoretic mobility shift assay revealed that OsSMF1 bound to the GCN4 (TGA(G/C)TCA), ACGT (CCACGT(C/G)), and ATGA (GGATGAC) motifs with three different affinities. We predicted 44 putative OsSMF1 target genes using data obtained from both the PBM and RiceArrayNet. Among these putative target genes, 18, 21, and 13 genes contained GCN4, ACGT, and ATGA motifs within their 1-kb promoter regions, respectively. Among them, six genes encoding major grain filling proteins and transcription factors were chosen to confirm the activation of their expression in vivo. OsSMF1 was shown to bind directly to the promoters of Os03g0168500 (GCN4 motif), patatin-like gene (GCN4 motif), α-globulin (ACGT motif), rice prolamin box-binding factor (RPBF) (ATGA motif), and ONAC024 (GCN4 and ACGT motifs) and to regulate their expression. CONCLUSIONS: The results of this study suggest that OsSMF1 is one of the key transcription factors that functions in a wide range of seed developmental processes with different specific binding affinities for the three DNA-binding motifs.

A pepper MSRB2 gene confers drought tolerance in rice through the protection of chloroplast-targeted genes.

BACKGROUND: The perturbation of the steady state of reactive oxygen species (ROS) due to biotic and abiotic stresses in a plant could lead to protein denaturation through the modification of amino acid residues, including the oxidation of methionine residues. Methionine sulfoxide reductases (MSRs) catalyze the reduction of methionine sulfoxide back to the methionine residue. To assess the role of this enzyme, we generated transgenic rice using a pepper CaMSRB2 gene under the control of the rice Rab21 (responsive to ABA protein 21) promoter with/without a selection marker, the bar gene. RESULTS: A drought resistance test on transgenic plants showed that CaMSRB2 confers drought tolerance to rice, as evidenced by less oxidative stress symptoms and a strengthened PSII quantum yield under stress conditions, and increased survival rate and chlorophyll index after the re-watering. The results from immunoblotting using a methionine sulfoxide antibody and nano-LC-MS/MS spectrometry suggest that porphobilinogen deaminase (PBGD), which is involved in chlorophyll synthesis, is a putative target of CaMSRB2. The oxidized methionine content of PBGD expressed in E. coli increased in the presence of H2O2, and the Met-95 and Met-227 residues of PBGD were reduced by CaMSRB2 in the presence of dithiothreitol (DTT). An expression profiling analysis of the overexpression lines also suggested that photosystems are less severely affected by drought stress. CONCLUSIONS: Our results indicate that CaMSRB2 might play an important functional role in chloroplasts for conferring drought stress tolerance in rice.

Fumigant toxicity of summer savory and lemon balm oil constituents and efficacy of spray formulations containing the oils to B- and neonicotinoid-resistant Q-biotypes of Bemisia tabaci (Homoptera: Aleyrodidae).

An assessment was made of the fumigant toxicity of 36 constituents from lemon balm oil (LBO) and summer savory oil (SSO) and another additional nine previously identified compounds of the oils, as well as of the control efficacy of four experimental spray formulations containing individual oils (0.5 and 0.1% sprays) and spinosad 10% suspension concentrate (SC) to females from B- and neonicotinoid-resistant Q-biotypes of Bemisia tabaci (Gennadius) (Homoptera: Aleyrodidae). Based on 24-h LC50 values, Q-biotype females (0.20 microg/cm3) were 40 times less susceptible to dichlorvos than B-biotype females (0.005 microg/cm3). Thymol (LC50, 0.35 microg/cm3) and carvacrol (0.56 microg/cm3) were the most toxic compounds toward Q-biotype females, followed by (1S)-(-)-borneol, alpha-terpineol, nerol, linalool, and carvone (1.06-1.38 microg/cm3). The toxicity of these compounds was virtually identical toward both biotype females, indicating that the terpenoids and the insecticides (neonicotinoids and dichlorvos) do not share a common mode of action or elicit cross-resistance. The 0.5% spray of LBO, SSO, and spinosad 10% SC resulted in >90% mortality toward both biotype females. Global efforts to reduce the level of toxic synthetic insecticides in the agricultural environment justify further studies on LBO- and SSO-derived materials as potential contact-action fumigants for the control of B. tabaci populations.

Adulticidal activity of phthalides identified in Cnidium officinale rhizome to B- and Q-biotypes of Bemisia tabaci.

The residual contact toxicity of three benzofuranoids (Z)-butylidenephthalide (1), (3S)-butylphthalide (2), and (Z)-ligustilide (3) identified in the rhizome of Cnidium officinale (Apiaceae) to B- and Q-biotype females of Bemisia tabaci was evaluated using a leaf-dip bioassay. Results were compared with those of eight conventional insecticides. Based on 24 h LC(50) values, (Z)-butylidenephthalide (254 ppm) and (Z)-ligustilide (268 ppm) were more toxic than (3S)-butylphthalide (339 ppm) against B-biotype females, whereas (Z)-ligustilide (254 ppm) and (3S)-butylphthalide (338 ppm) were more toxic than (Z)-butylidenephthalide (586 ppm) against Q-biotype females. Thiamethoxam, imidacloprid, and acetamiprid differ significantly in toxicity between the B- and Q-biotype females (LC(50), 1.7 to 11.6 vs 364.5 to >3000 ppm). This original finding indicates that the phthalides and the neonicotinoids do not share a common mode of action or elicit cross-resistance. Structure-activity relationship indicates that the presence of conjugation rather than aromaticity appeared to play an important role for phthalide toxicities to the B-biotype females. Global efforts to reduce the level of highly toxic synthetic insecticides in the agricultural environment justify further studies on C. officinale rhizome-derived materials as potential insecticides for the control of B. tabaci populations.

Contact and fumigant toxicity of plant essential oils and efficacy of spray formulations containing the oils against B- and Q-biotypes of Bemisia tabaci.

BACKGROUND: The contact + fumigant toxicity of 92 plant essential oils and control efficacy of 18 experimental spray formulations containing nine selected essential oils (0.5 and 0.1% sprays) and six commercial insecticides to females from B- and Q-biotypes of Bemisia tabaci were evaluated using vapour-phase mortality and spray bioassays. RESULTS: Garlic and oregano (LC50 , 0.15 mL cm(-3) ) were the most toxic oils against B- and Q-biotype females. Strong fumigant toxicity to both biotype females was also obtained from catnip, cinnamon bark, clove bud, clove leaf, davana, savory and vetiver Haiti oils (LC50 , 0.17-0.48 mL cm(-3) ). The 0.5% sprays of these oils (except for thyme red oil) resulted in 90-100% mortality against both biotype females. Only garlic applied as 0.1% spray provided 100% mortality. Spinosad 100 g L(-1) suspension concentrate (SC) treatment resulted in 92 and 95% mortality against both biotype females, whereas acetamiprid 80 g L(-1) wettable powder (WP), imidacloprid 80 g L(-1) SC, thiamethoxam 100 g L(-1) water-dispersible granule (WDG) and pyridaben 200 g L(-1) WP treatments resulted in 89-100% mortality against B-biotype females only. CONCLUSION: In the light of global efforts to reduce the level of highly toxic synthetic insecticides in the agricultural environment, the essential oils described, particularly garlic, cinnamon bark and vetiver Haiti, merit further study as potential insecticides for the control of B. tabaci populations as fumigants with contact action.