An enhanced median filter for removing noise from MR images

In this paper, a novel decision based median (DBM) filter for enhancing MR images has been proposed. The method is based on eliminating impulse noise from MR images. A median-based method to remove impulse noise from digital MR images has been developed. Each pixel is leveled from black to white like gray-level. The method is adjusted in order to decide whether the median operation can be applied on a pixel. The main deficiency in conventional median filter approaches is that all pixels are filtered with no concern about healthy pixels. In this research, to suppress this deficiency, noisy pixels are initially detected, and then the filtering operation is applied on them. The proposed decision method (DM) is simple and leads to fast filtering. The results are more accurate than other conventional filters. Moreover, DM adjusts itself based on the conditions of local detections. In other words, DM operation on detecting a pixel as a noise depends on the previous decision. As a considerable advantage, some unnecessary median operations are eliminated and the number of median operations reduces drastically by using DM. Decision method leads to more acceptable results in scenarios with high noise density. Furthermore, the proposed method reduces the probability of detecting noise-free pixels as noisy pixels and vice versa

RD21 structure and knock-out lines.

<p><b>A,</b> Gene structure of <i>RD21A</i> (At1g47128). The <i>RD21A</i> gene consists of 5 exons. Mutants <i>rd21-1</i> (SALK_90550) and <i>rd21-2</i> (SALK_65256) contain T-DNA insertions in the third and first introns, respectively. <b>B,</b> Domains encoded by the <i>RD21A</i> open reading frame. The RD21 protein consists of a signal peptide (sp, left), an autoinhibitory prodomain (pro), a protease domain with catalytic cysteine (white stripe), and a granulin domain (right). RD21 exists in two active isoforms: the granulin-containing intermediate (i) RD21, and the mature (m) RD21 lacking the granulin domain. <b>C,</b> The <i>rd21-1</i> line is a null mutant. The <i>rd21-1</i> mutant lacks iRD21 and mRD21 proteins (left) and the major upper signals in the protease activity profile (right). Leaf extracts of Col-0 and <i>rd21-1</i> mutant plants were labelled with DCG-04 and proteins were detected with RD21 antibody and streptavidin-HRP. A remaining signal at 30 kDa is sometimes visible in the <i>rd21</i> mutant lines (<b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029317#pone.0029317.s006" target="_blank">Figure S6</a></b>), and can contain CTB3, XCP2 and XCP1 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029317#pone.0029317-VanderHoorn1" target="_blank">[20]</a>.</p

Mutant <i>rd21</i> lines are not compromised in interactions with <i>Pst</i>DC3000.

<p><b>A,</b> Compatible <i>Pst</i> interactions. (Mutant) Arabidopsis plants were spray-inoculated with <i>Pst</i>DC3000 (vir) and bacterial populations were measured at 0 and 3 dpi. Error bars represent SD of 5 independent bacterial extractions. This experiment was repeated three times with similar results. <b>B,</b> Incompatible <i>Pst</i> interactions. (Mutant) Arabidopsis plants were spray-inoculated with <i>Pst</i>DC3000 avrRpm1 (avr) and bacterial populations were measured at 0 and 3 dpi. Error bars represent SD of 5 independent bacterial extractions. This experiment was repeated three times with similar results.</p

EPIC-like proteins from <i>Hpa</i>.

<p><b>A,</b> Phylogenetic relationship between EPIC proteins. One of 1,000 most parsimonious trees showing the relationship between <i>Pinf</i> and <i>Hpa</i> EPICs. This tree was obtained by heuristic search with bootstrap support. A cystatin from <i>Albugo laibachii</i> was used as outgroup. <b>B,</b> Protein sequence alignment of <i>Hpa</i>EPIC-B and -C with <i>Pinf</i>EPIC1, -2B and 3. *, functionally important residues; NT, N-terminus; L1, loop-1; L2, loop-2. Triangles indicate amino acids at variant codons. <b>C,</b> Distribution of four variant codons found in <i>HpaEPIC-B</i> and <i>-C</i> sequences of various <i>Hpa</i> isolates. The variant codons are indicated with grey and black lines and the amino acid encoding the codons are indicated on the top and bottom. <b>D, </b><i>HpaEPIC-B</i> and <i>-C</i> are expressed during infection. RNA was isolated from Arabidopsis plants infected with <i>Hpa</i> isolates Noco2, Cala2 or Emoy2 at 5 dpi and used as template for RT-PCR with specific primers for <i>HpaEPIC-B</i> and <i>-C</i>.</p

Mutant <i>rd21</i> lines are unaltered in their interactions with <i>Hpa</i>.

<p><b>A,</b> Compatible <i>Hpa</i> interactions. (Mutant) Arabidopsis seedlings were infected with <i>Hpa</i> isolate Noco2, which is virulent on Col-0 but not on Ws. Spores were counted at 7 dpi in triplicate. Error bars represent standard deviation (SD) of three independent spore isolations. This experiment is repeated once with similar results. <b>B,</b> Incompatible <i>Hpa</i> interactions. (Mutant) Arabidopsis seedlings were infected with <i>Hpa</i> isolate Emwa1, which is virulent on Ws-0 but not on Col-0. Spores were counted at 7 dpi in triplicate. Error bars represent SD of three independent spore isolations.</p

Distinct properties of granulin deletion and destabilization mutants.

<p><b>A</b>, Schematic representation of granulin deletion and destabilization mutants. The ΔPG mutant (residues 1–347) lacks both the proline-rich domain (P) and the granulin domain (G), whereas the ΔG mutant (residues 1–374) lacks the granulin domain only. In the 3C3A mutant, a motif of three consecutive Cys residues is replaced by three Ala residues to disrupt three putative disulphide bridges. <b>B</b>, Accumulation, labeling and activity of the RD21 deletion and destabilization mutants. The (mutant) RD21 and empty vector (EV) controls were transiently expressed by agroinfiltration in <i>N. benthamiana</i> and extracts were labeled with 0.2 µM DCG-04 for 1 hour. RD21 protein levels, labeling, and rubisco (R) degradation were detected using anti-RD21 antibody, streptavidin-HRP and coomassie staining, respectively.</p

Adrenomedullin-RAMP2 System Suppresses ER Stress-Induced Tubule Cell Death and Is Involved in Kidney Protection

<div><p>Various bioactive peptides have been implicated in the homeostasis of organs and tissues. Adrenomedullin (AM) is a peptide with various bioactivities. AM-receptor, calcitonin-receptor-like receptor (CLR) associates with one of the subtypes of the accessory proteins, RAMPs. Among the RAMP subisoforms, only RAMP2 knockout mice (−/−) reproduce the phenotype of embryonic lethality of AM−/−, illustrating the importance of the AM-RAMP2-signaling system. Although AM and RAMP2 are abundantly expressed in kidney, their function there remains largely unknown. We used genetically modified mice to assess the pathophysiological functions of the AM-RAMP2 system. RAMP2+/− mice and their wild-type littermates were used in a streptozotocin (STZ)-induced renal injury model. The effect of STZ on glomeruli did not differ between the 2 types of mice. On the other hand, damage to the proximal urinary tubules was greater in RAMP2+/−. Tubular injury in RAMP2+/− was resistant to correction of blood glucose by insulin administration. We examined the effect of STZ on human renal proximal tubule epithelial cells (RPTECs), which express glucose transporter 2 (GLUT2), the glucose transporter that specifically takes up STZ. STZ activated the endoplasmic reticulum (ER) stress sensor protein kinase RNA-like endoplasmic reticulum kinase (PERK). AM suppressed PERK activation, its downstream signaling, and CCAAT/enhancer-binding homologous protein (CHOP)-induced cell death. We confirmed that the tubular damage was caused by ER stress-induced cell death using tunicamycin (TUN), which directly evokes ER stress. In RAMP2+/− kidneys, TUN caused severe injury with enhanced ER stress. In wild-type mice, TUN-induced tubular damage was reversed by AM administration. On the other hand, in RAMP2+/−, the rescue effect of exogenous AM was lost. These results indicate that the AM-RAMP2 system suppresses ER stress-induced tubule cell death, thereby exerting a protective effect on kidney. The AM-RAMP2 system thus has the potential to serve as a therapeutic target in kidney disease.</p></div

Properties of RD21 catalytic mutants.

<p><b>A</b>, Summary of the mutants in the catalytic triad. Each of the three catalytic residues was substituted by Ala to generate three RD21 mutants: C161A, H297A and N317A. <b>B</b>, The catalytic triad in RD21. RD21 was modelled on 1S4V using PyMol. The catalytic residues are at 2.6 Å distances from each other (dashed lines). <b>C</b>, Accumulation, labeling and activity of the RD21 catalytic mutants. The (mutant) RD21 and empty vector (EV) controls were transiently expressed by agroinfiltration in <i>N. benthamiana</i> and extracts were labeled with 0.2 µM DCG-04 for 1 hour. RD21 protein levels, DCG-04 labeling, and rubisco (R) degradation were detected using anti-RD21 antibody, streptavidin-HRP and coomassie staining, respectively. Pro- (p), intermediate (i) and mature (m) isoforms of RD21 were detected. <b>D</b>, Time course of labeling of WT and N317A RD21. Extracts from leaves overexpressing WT and N317A RD21 were incubated at pH 6 with 0.2 µM DCG-04 for various incubation times. RD21 protein levels and DCG-04 labeling were detected using anti-RD21 antibody and streptavidin-HRP, respectively. Rubisco degradation was detected by coomassie staining.</p

SDS activates endogenous RD21.

<p><b>A</b>, The activity of RD21 overexpressed in <i>N. benthamiana</i> leaves is not affected by SDS. Leaf extracts were labeled with DCG-04 at various SDS concentrations. RD21 protein levels and biotinylation was detected on protein blots using anti-RD21 antibody and streptavidin-HRP, respectively. <b>B</b>, Activation of endogenous PLCPs by SDS treatment of leaf extracts of <i>N. benthamiana</i>. <b>C</b>, SDS activates RD21 and inactivates AALP (a) in Arabidopsis leaf extracts. Leaf extracts were labeled with DCG-04 in the presence of various SDS concentrations. Biotinylated proteins were detected on protein blots using streptavidin-HRP. <b>D</b>, SDS activates latent RD21. Arabidopsis leaf extracts from Col-0 and <i>rd21-1</i> plants were labeled with DCG-04 in the presence or absence of 0.1% SDS and 0.1 mM E-64. Biotinylated proteins were detected from protein blots using streptavidin-HRP. *, endogenously biotinylated proteins. <b>E</b>, <i>Ex vivo</i> degradation of rubisco in Arabidopsis leaf extracts is SDS-dependent and mediated by RD21. Leaf extracts of Arabidopsis <i>Col-0</i> and <i>rd21-1</i> mutant plants were incubated at room temperature for 0, 1, 2 and 4 hours in the presence and absence of 0.04% SDS, 0.02 mM E-64 or 1 mM DTT. Rubisco (R) was detected by staining protein gels with coomassie (CBB).</p

<i>N</i>-glycosylation of RD21 demonstrates a Golgi maturation route.

<p><b>A</b>, Explanation of the generated <i>N</i>-glycosylation mutants. RD21 carries a putative <i>N</i>-glycosylation site (PGS) in the prodomain and the granulin domain (black stripes). The second PGS is removed in the –PGS mutant by introducing an N414A substitution. A PGS was introduced in the protease domain of the +PGS mutant by the substitutions D180N and I182T. This PGS is present at the same site in several RD21 orthologs. <b>B</b>, The size-shift of the +PGS mutant is not reverted by PNGaseF treatment after expression in wild-type <i>N. benthamiana</i> plants. –PGS (pJW03), WT (pRH628) and +PGS (pMS48) were expressed by agroinfiltration and protein extracts were treated with and without PNGaseF. Proteins were separated by SDS-PAGE and analyzed by immunoblotting using RD21 antiserum. <b>C</b>, PNGaseF sensitivity is gained by expression of RD21 in glyco-engineered <i>N. benthamiana</i> plants. Wild-type RD21 (WT) and the +PGS mutant RD21 (+PGS) were expressed by agroinfiltration into wild-type <i>N. benthamiana</i> (WT) and transgenic <i>N. benthamiana</i> plants silenced for β-1,2-xylosyltransferase and α-1,3-fucosyltransferase (ΔXF, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032422#pone.0032422-Strasser1" target="_blank">[27]</a>). Protein extracts were treated with and without EndoH or PNGaseF, separated by SDS-PAGE and analyzed by immunoblotting using RD21 antiserum.</p