PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups

<p>Abstract</p> <p>Background</p> <p>The elucidation of transcriptional regulation in plant genes is important area of research for plant scientists, following the mapping of various plant genomes, such as <it>A. thaliana</it>, <it>O. sativa </it>and <it>Z. mays</it>. A variety of bioinformatic servers or databases of plant promoters have been established, although most have been focused only on annotating transcription factor binding sites in a single gene and have neglected some important regulatory elements (tandem repeats and CpG/CpNpG islands) in promoter regions. Additionally, the combinatorial interaction of transcription factors (TFs) is important in regulating the gene group that is associated with the same expression pattern. Therefore, a tool for detecting the co-regulation of transcription factors in a group of gene promoters is required.</p> <p>Results</p> <p>This study develops a database-assisted system, PlantPAN (Plant Promoter Analysis Navigator), for recognizing combinatorial <it>cis</it>-regulatory elements with a distance constraint in sets of plant genes. The system collects the plant transcription factor binding profiles from PLACE, TRANSFAC (public release 7.0), AGRIS, and JASPER databases and allows users to input a group of gene IDs or promoter sequences, enabling the co-occurrence of combinatorial transcription factor binding sites (TFBSs) within a defined distance (20 bp to 200 bp) to be identified. Furthermore, the new resource enables other regulatory features in a plant promoter, such as CpG/CpNpG islands and tandem repeats, to be displayed. The regulatory elements in the conserved regions of the promoters across homologous genes are detected and presented.</p> <p>Conclusion</p> <p>In addition to providing a user-friendly input/output interface, PlantPAN has numerous advantages in the analysis of a plant promoter. Several case studies have established the effectiveness of PlantPAN. This novel analytical resource is now freely available at <url>http://PlantPAN.mbc.nctu.edu.tw</url>.</p

Shorter GT repeat polymorphism in the heme oxygenase-1 gene promoter has protective effect on ischemic stroke in dyslipidemia patients

<p>Abstract</p> <p>Background</p> <p>The microsatellite polymorphism of heme oxygenase (HO)-1 gene promoter has been shown to be associated with the susceptibility to ischemic event, including coronary artery disease (CAD), myocardial infarction, and peripheral vascular disease. We aimed to examine whether the length of (GT)_nrepeats in HO-1 gene promoter is associated with ischemic stroke in people with CAD risk factors, especially low level of HDL.</p> <p>Methods</p> <p>A total of 183 consecutive firstever ischemic stroke inpatients and 164 non-stroke patients were screened for the length of (GT)_nrepeats in HO-1 promoter. The long (L) and short (S) genotype are defined as the averaged repeat number >26 and ≦26, respectively.</p> <p>Results</p> <p>Stroke patients tended to have more proportions of hypertension, diabetics and genotype L, than those of genotype S. Patients with genotype L of HO-1 gene promoter have higher stroke risk in comparison with genotype S especially in dyslipidemia individuals. The significant differences on stroke risk in multivariate odds ratios were found especially in people with low HDL-C levels.</p> <p>Conclusions</p> <p>Subjects carrying longer (GT)_nrepeats in HO-1 gene promoter may have greater susceptibility to develop cerebral ischemic only in the presence of low HDL-C, suggesting the protective effects in HO-1 genotype S in the process of ischemic stroke, particularly in subjects with poor HDL-C status.</p

Insolation-paced sea level and sediment flux during the early Pleistocene in Southeast Asia

Global marine archives from the early Pleistocene indicate that glacial-interglacial cycles, and their corresponding sea-level cycles, have predominantly a periodicity of ~ 41 kyrs driven by Earth’s obliquity. Here, we present a clastic shallow-marine record from the early Pleistocene in Southeast Asia (Cholan Formation, Taiwan). The studied strata comprise stacked cyclic successions deposited in offshore to nearshore environments in the paleo-Taiwan Strait. The stratigraphy was compared to both a δ18O isotope record of benthic foraminifera and orbital parameters driving insolation at the time of deposition. Analyses indicate a strong correlation between depositional cycles and Northern Hemisphere summer insolation, which is precession-dominated with an obliquity component. Our results represent geological evidence of precession-dominated sea-level fluctuations during the early Pleistocene, independent of a global ice-volume proxy. Preservation of this signal is possible due to the high-accommodation creation and high-sedimentation rate in the basin enhancing the completeness of the stratigraphic record

Investigation of a Potential Scintigraphic Tracer for Imaging Apoptosis: Radioiodinated Annexin V-Kunitz Protease Inhibitor Fusion Protein

Radiolabeled annexin V (ANV) has been widely used for imaging cell apoptosis. Recently, a novel ANV-Kunitz-type protease inhibitor fusion protein, ANV-6L15, was found to be a promising probe for improved apoptosis detection based on its higher affinity to phosphatidylserine (PS) compared to native ANV. The present paper investigates the feasibility of apoptosis detection using radioiodinated ANV-6L15. Native ANV and ANV-6L15 were labeled with iodine-123 and iodine-125 using Iodogen method. The binding between the radioiodinated proteins and erythrocyte ghosts or chemical-induced apoptotic cells was examined. ANV-6L15 can be radioiodinated with high yield (40%−60%) and excellent radiochemical purity (>95%). 123I-ANV-6L15 exhibited a higher binding ratio to erythrocyte ghosts and apoptotic cells compared to 123I-ANV. The biodistribution of 123I-ANV-6L15 in mice was also characterized. 123I-ANV-6L15 was rapidly cleared from the blood. High uptake in the liver and the kidneys may limit the evaluation of apoptosis in abdominal regions. Our data suggest that radiolabled ANV-6L15 may be a better scintigraphic tracer than native ANV for apoptosis detection

Extremely rapid up-and-down motions of island arc crust during arc-continent collision

10 pagesMountain building and the rock cycle often involve large vertical crustal motions, but their rates and timescales in unmetamorphosed rocks remain poorly understood. We utilize high-resolution magneto-biostratigraphy and backstripping analysis of marine deposits in an active arc-continent suture zone of eastern Taiwan to document short cycles of vertical crustal oscillations. A basal unconformity formed on Miocene volcanic arc crust in an uplifting forebulge starting ~6 Ma, followed by rapid foredeep subsidence at 2.3–3.2 mm yr−1 (~3.4–0.5 Ma) in response to oceanward-migrating flexural wave. Since ~0.8–0.5 Ma, arc crust has undergone extremely rapid (~9.0–14.4 mm yr−1) uplift to form the modern Coastal Range during transpressional strain. The northern sector may have recently entered another phase of subsidence related to a subduction polarity reversal. These transient vertical crustal motions are under-detected by thermochronologic methods, but are likely characteristic of continental growth by arc accretion over geologic timescales

Functional roles of arginine residues in mung bean vacuolar H+-pyrophosphatase

AbstractPlant vacuolar H+-translocating inorganic pyrophosphatase (V-PPase EC 3.6.1.1) utilizes inorganic pyrophosphate (PPi) as an energy source to generate a H+ gradient potential for the secondary transport of ions and metabolites across the vacuole membrane. In this study, functional roles of arginine residues in mung bean V-PPase were determined by site-directed mutagenesis. Alignment of amino-acid sequence of K+-dependent V-PPases from several organisms showed that 11 of all 15 arginine residues were highly conserved. Arginine residues were individually substituted by alanine residues to produce R→A-substituted V-PPases, which were then heterologously expressed in yeast. The characteristics of mutant variants were subsequently scrutinized. As a result, most R→A-substituted V-PPases exhibited similar enzymatic activities to the wild-type with exception that R242A, R523A, and R609A mutants markedly lost their abilities of PPi hydrolysis and associated H+-translocation. Moreover, mutation on these three arginines altered the optimal pH and significantly reduced K+-stimulation for enzymatic activities, implying a conformational change or a modification in enzymatic reaction upon substitution. In particular, R242A performed striking resistance to specific arginine-modifiers, 2,3-butanedione and phenylglyoxal, revealing that Arg242 is most likely the primary target residue for these two reagents. The mutation at Arg242 also removed F− inhibition that is presumably derived from the interfering in the formation of substrate complex Mg2+–PPi. Our results suggest accordingly that active pocket of V-PPase probably contains the essential Arg242 which is embedded in a more hydrophobic environment

Transcriptomic analyses of regenerating adult feathers in chicken

Transcriptome Expression Data. Table of mapped reads to Galgal4 transcripts for all 15 data sets. FPKM (Fragments per kilobase of exon per million fragments mapped): normalized transcript abundance values for each gene in the indicated tissues. (CSV 1314 kb