Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, Thellungiella halophila

<p>Abstract</p> <p>Background</p> <p><it>Thellungiella halophila </it>(also known as <it>T. salsuginea</it>) is a model halophyte with a small size, short life cycle, and small genome. <it>Thellungiella </it>genes exhibit a high degree of sequence identity with Arabidopsis genes (90% at the cDNA level). We previously generated a full-length enriched cDNA library of <it>T. halophila </it>from various tissues and from whole plants treated with salinity, chilling, freezing stress, or ABA. We determined the DNA sequences of 20 000 cDNAs at both the 5'- and 3' ends, and identified 9569 distinct genes.</p> <p>Results</p> <p>Here, we completely sequenced 1047 <it>Thellungiella </it>full-length cDNAs representing abiotic-stress-related genes, transcription factor genes, and protein phosphatase 2C genes. The predicted coding sequences, 5'-UTRs, and 3'-UTRs were compared with those of orthologous genes from Arabidopsis for length, sequence similarity, and structure. The 5'-UTR sequences of <it>Thellungiella </it>and Arabidopsis orthologs shared a significant level of similarity, although the motifs were rearranged. While examining the stress-related <it>Thellungiella </it>coding sequences, we found a short splicing variant of <it>T. halophila </it><it>salt overly sensitive 1 </it>(<it>ThSOS1</it>), designated <it>ThSOS1S</it>. ThSOS1S contains the transmembrane domain of ThSOS1 but lacks the C-terminal hydrophilic region. The expression level of <it>ThSOS1S </it>under normal growth conditions was higher than that of <it>ThSOS1</it>. We also compared the expression levels of Na⁺-transport-system genes between <it>Thellungiella </it>and Arabidopsis by using full-length cDNAs from each species as probes. Several genes that play essential roles in Na⁺excretion, compartmentation, and diffusion (<it>SOS1</it>, <it>SOS2</it>, <it>NHX1</it>, and <it>HKT1</it>) were expressed at higher levels in <it>Thellungiella </it>than in Arabidopsis.</p> <p>Conclusions</p> <p>The full-length cDNA sequences obtained in this study will be essential for the ongoing annotation of the <it>Thellungiella </it>genome, especially for further improvement of gene prediction. Moreover, they will enable us to find splicing variants such as <it>ThSOS1S </it>(AB562331).</p

Chryseobacterium indologenes Peritonitis in a Peritoneal Dialysis Patient: A Case Report and Review of Literature

Peritonitis is one of the most important complications in patients with peritoneal dialysis (PD). Appropriate antibiotic treatment against PD-associated peritonitis is necessary to prevent PD catheter removal and withdrawal from PD. Chryseobacterium indologenes is a Gram-negative rod that occurs in the natural environment. C. indologenes is thought to acquire resistance to β-lactam drugs through the production of metallo-β-lactamase and to become resistant to antibiotic therapy through the formation of biofilms. Only a few cases of PD-associated peritonitis caused by C. indologenes have been reported to date, and appropriate treatment strategies have not been clarified. In the past, 5 cases of PD-associated peritonitis caused by C. indologenes have been reported and 2 patients required catheter removal because of recurrence or refractoriness. In this case, a 51-year-old man with PD-associated peritonitis caused by C. indologenes was treated with 2 susceptible antibiotics, including fluoroquinolones to prevent acquired resistance and biofilm formation. There was no recurrence, and catheter removal was not necessary in this case. Collectively, the present case highlighted that PD-associated peritonitis caused by C. indologenes should be treated with 2 susceptible antibiotics including fluoroquinolones for 3 weeks

DsTau: Study of tau neutrino production with 400 GeV protons from the CERN-SPS

In the DsTau experiment at the CERN SPS, an independent and direct way to measure tau neutrino production following high energy proton interactions was proposed. As the main source of tau neutrinos is a decay of Ds mesons, produced in proton-nucleus interactions, the project aims at measuring a differential cross section of this reaction. The experimental method is based on a use of high resolution emulsion detectors for effective registration of events with short lived particle decays. Here we present the motivation of the study, details of the experimental technique, and the first results of the analysis of the data collected during test runs, which prove feasibility of the full scale study of the process in future

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ~32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene

Renal tubular Sirt1 attenuates diabetic albuminuria by epigenetically suppressing Claudin-1 overexpression in podocytes

Sirtuin 1 (Sirt1), a NAD[superscript +]-regulated deacetylase with numerous known positive effects on cellular and whole-body metabolism, is expressed in the renal cortex and medulla. It is known to have protective effects against age-related disease, including diabetes. Here we investigated the protective role of Sirt1 in diabetic renal damage. We found that Sirt1 in proximal tubules (PTs) was downregulated before albuminuria occurred in streptozotocin-induced or obese (db/db) diabetic mice. PT-specific SIRT1 transgenic and Sirt1 knockout mice showed prevention and aggravation of the glomerular changes that occur in diabetes, respectively, and nondiabetic knockout mice exhibited albuminuria, suggesting that Sirt1 in PTs affects glomerular function. Downregulation of Sirt1 and upregulation of the tight junction protein Claudin-1 by SIRT1-mediated epigenetic regulation in podocytes contributed to albuminuria. We did not observe these phenomena in 5/6 nephrectomized mice. We also demonstrated retrograde interplay from PTs to glomeruli using nicotinamide mononucleotide (NMN) from conditioned medium, measurement of the autofluorescence of photoactivatable NMN and injection of fluorescence-labeled NMN. In human subjects with diabetes, the levels of SIRT1 and Claudin-1 were correlated with proteinuria levels. These results suggest that Sirt1 in PTs protects against albuminuria in diabetes by maintaining NMN concentrations around glomeruli, thus influencing podocyte function.Japan. Ministry of Education, Culture, Sports, Science and Technology (Grant 22790800

アレルギー性気道炎症における性ホルモンおよびリンパ球の役割

Epidemiological data indicate that the prevalence and severity of asthma is higher among females than males after puberty. The influence of sex on asthma incidence suggests that sex hormones could play a role in the pathogenesis of the condition associated with asthma. However, the mechanisms of the affect of sex are not clear. Therefore, in the current study, we investigated the sex differences in allergic inflammation in terms of lymphocyte function, using a murine model of allergic asthma. In either BALB/c or C57BL/6J mice, the airway inflammation in female mice sensitized with OVA followed by OVA inhalation was more severe than that in male mice. The contents of Th2 cytokines, such as IL-4, IL-5 and IL-13, in bronchoalveolar lavage fluid from female mice were significantly increased compared with male mice. The airway inflammation in female mice after adoptive transfer of splenocyte from sensitized female mice was more severe than that in any other combination of donors and recipients. Furthermore, splenocytes from sensitized female mice produced more Th2 cytokines than those from sensitized male mice, upon stimulation with OVA. The degree of airway inflammation induced by lipopolysaccharide inhalation was not significantly different between male and female mice. Our findings suggest that sex differences in allergic airway inflammation are due to those in not only sex hormones but also lymphocytes function

Negative conversion of T-SPOT results after hemodialysis: case series and literature review

Abstract Background Latent tuberculosis infection (LTBI) affects 11.9% of outpatients under maintenance hemodialysis in Japan. In addition, the risk of reactivation of LTBI in hemodialysis patients is up to 10–25 times higher than that in the general population. Therefore, the accurate diagnosis and treatment for LTBI are extremely important. The interferon-γ release assays are widely used for screening LTBI; however, the impact of hemodialysis on the assay results has been uncertain. Case presentation Twenty-seven hemodialysis patients (17 males, 69.9 ± 10.1 year old) were performed T-SPOT®.TB test (T-SPOT) both before and after hemodialysis. In cases where T-SPOT results were different before and after hemodialysis, T-SPOT was re-evaluated in a same manner. As a result, two cases showed consistent T-SPOT diagnostic discrepancy before and after hemodialysis in two measurements. In the first case, T-SPOT was indeterminate/positive before hemodialysis, but changed to negative after hemodialysis. In the second case, T-SPOT was positive before hemodialysis, but changed to indeterminate after hemodialysis. Conclusions We experienced the negative conversion of T-SPOT after hemodialysis in cases of LTBI. T-SPOT may show false-negative when measured after hemodialysis due to immunomodulation caused by hemodialysis