Structural Analysis ofArabidopsis thaliana Chromosome 5. VI. Sequence Features of the Regions of 1,367,185 bp Covered by 19 Physically Assigned P1 and TAC Clones

Nineteen Pl and TAC clones, which have been mapped on the finephysical map of the Arabidopsis thaliana chromosome 5, weresequenced according to the shotgun-based strategy, and theirstructural features were analysed. The total length of the regionssequenced in this study was 1,367,185 bp. Combining this withthe regions covered by 90 P1 and TAC clones proviously reported,the total length of chromosome 5 sequenced to date becomes 8,058,855bp. On the basis of similarity search against protein and ESTdatabases and gene modeling with computer programs, a totalof 330 potential protein-coding regions were identified, bringingan average density of the genes to approximately one gene per4.1 kb. Introns were identified in 81.0% of the potential proteingenes for which the entire gene structure was predicted, withan average number per gene of 4.2 and an average length of theintrons of 180 bp. The RNA-coding genes identified were 9 tRNAgenes corresponding to 8 amino acid species and 2 genes forU2 nuclear RNA. These sequence features are essentially identicalto those in the previously reported sequences. The sequencedata and gene information are available on the World Wide Webdatabase KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.     

Failure to respond to interferon-α 2a therapy is associated with increased hepatic iron levels in patients with chronic hepatitis C

Recent reports suggest the hepatic iron concentration (HIC) may influence the activity of hepatitis and the response to interferon (IFN) therapy in patients with chronic hepatitis C (CH-C). We have evaluated iron status in 28 patients with CH-C and determined if pretreatment iron status can predict the response to IFN-α therapy in these patients. Increased serum iron, transferrin saturation, and ferritin levels were observed in 3 (11%), 11 (39%), and 5 (18%) patients, respectively. Hepatic iron deposits were histologically detected in 17 (61%) patients, and 14 of them had stainable hepatocytic iron. However, all HIC values were within the normal range (203–1279 μg/g). Seven of 17 patients treated with IFN-α for 6 mo had normalization of serum transaminases and disappearance of serum HCV-RNA (responders). Nonresponders had a significantly higher median HIC compared with responders (710 vs 343 μg/g, respectively;p < 0.05). There was no significant difference in other pretreatment iron parameters, serum HCV-RNA level, or HCV-genotype between responders and nonresponders. In conclusion, mild hepatic iron accumulation occurs in patients with CH-C. Increased hepatic iron stores are associated with poor response to IFN therapy. Pretreatment HIC may be an additional host-specific parameter with a predictive value for responsiveness to IFN therapy, in addition to well-known predictive viral factors.     

Characterization of β-D-xyloside-initiated glycosaminoglycan synthesized by human skin fibroblasts in the presence of tunicamycin

Human skin fibroblasts were incubated with a fluorogenic xyloside, 4-methylumbelliferyl--D-xyloside (Xyl-MU), in the presence or absence of tunicamycin. The xyloside-initiated glycosaminoglycans (GAG-MUs) were isolated from the culture medium, and their structures characterized. When the cells were incubated with Xyl-MU in the presence of 0.2 g ml–1 tunicamycin, the synthesis of GAG-MU was increased about three fold, compared with the control value in the absence of tunicamycin (cells exposed to Xyl-MU alone). The structures of GAG-MUs synthesized in the presence or absence of tunicamycin were compared by HPLC analysis using gel-filtration and ion-exchange columns, enzymatic digestion, and unsaturated disaccharide composition analysis. The data indicated that cells incubated with tunicamycin produced more undersulfated and shorter GAG-MUs than cells without tynicamycin. These results suggest that tunicamycin inhibits the elongation and sulfation of glycosaminoglycan (GAG) chains and that, as a result, GAG-MUs with shorter chains and undersulfated residues, but possessing a large number of GAG chains, are synthesized in the presence of tunicamycin.     

Temporal rules in vocal exchanges of phees and trills in common marmosets (Callithrix jacchus)

Marmosets exchange two types of calls: phees and trills. We played back phees and trills to investigate the temporal rules of vocal exchanges using ten captive common marmosets (Callithrix jacchus). The marmosets usually emitted the same type of vocalizations just after the stimulus playbacks, and similar regularities were observed in the temporal intervals of phees and in trills. They vocalized with shorter intervals when they responded with trills rather than phees, and, after the first call, they repeatedly vocalized trills with shorter intervals than phees. These results suggest that the temporal rules between phees and trills are qualitatively similar but quantitatively different. These results might be owing to the different distances over which these contact calls are used. Am. J. Primatol. 71:617–622, 2009. © 2009 Wiley‐Liss, Inc.     

Floral anatomy of Neotropical species of Mayacaceae

The Mayacaceae are a monogeneric monocot family of herbs that grow on swampy areas in the Americas and in Africa. Both the number of species constituting the family and its inter-familial relationships are unclear. By describing and comparing the floral anatomy of Mayaca fluviatilis, M. fluviatilis f. kunthii, M. longipes and M. sellowiana we have identified some features that delimit the species. These include: arrangement of flowers on the stem, shape of stamens, size of apical pores, disposition of microsporangia, number of ovules and shape of the stylar canal. We concluded that M. fluviatilis f. kunthii should be considered as a species (M. kunthii) rather than a forma. Other characters such as number of stamens and microsporangia, placentation, ovule type and cell numbers in the pollen grain support the placement of the Mayacaceae within Poales.     

Minimal sample requirement for highly multiplexed protein quantification in cell lines and tissues by PCT‐SWATH mass spectrometry

The amount of sample available for clinical and biological proteomic research is often limited and thus significantly restricts clinical and translational research. Recently, we have integrated pressure cycling technology (PCT) assisted sample preparation and SWATH‐MS to perform reproducible proteomic quantification of biopsy‐level tissue samples. Here, we further evaluated the minimal sample requirement of the PCT‐SWATH method using various types of samples, including cultured cells (HeLa, K562, and U251, 500 000 to 50 000 cells) and tissue samples (mouse liver, heart, brain, and human kidney, 3–0.2 mg). The data show that as few as 50 000 human cells and 0.2–0.5 mg of wet mouse and human tissues produced peptide samples sufficient for multiple SWATH‐MS analyses at optimal sample load applied to the system. Generally, the reproducibility of the method increased with decreasing tissue sample amounts. The SWATH maps acquired from peptides derived from samples of varying sizes were essentially identical based on the number, type, and quantity of identified peptides. In conclusion, we determined the minimal sample required for optimal PCT‐SWATH analyses, and found smaller sample size achieved higher quantitative accuracy.     

‘Only Fathers Smoking’ Contributes the Most to Socioeconomic Inequalities: Changes in Socioeconomic Inequalities in Infants’ Exposure to Second Hand Smoke over Time in Japan

BackgroundExposure to second hand smoke (SHS) is one of the major causes of premature death and disease among children. While socioeconomic inequalities exist for adult smoking, such evidence is limited for SHS exposure in children. Thus, this study examined changes over time in socioeconomic inequalities in infants’ SHS exposure in Japan.MethodsThis is a repeated cross-sectional study of 41,833 infants born in 2001 and 32,120 infants born in 2010 in Japan from nationally representative surveys using questionnaires. The prevalence of infants’ SHS exposure was determined and related to household income and parental education level. The magnitudes of income and educational inequalities in infants’ SHS exposure were estimated in 2001 and 2010 using both absolute and relative inequality indices.ResultsThe prevalence of SHS exposure in infants declined from 2001 to 2010. The relative index of inequality increased from 0.85 (95% confidence interval [CI], 0.80 to 0.89) to 1.47 (95% CI, 1.37 to 1.56) based on income and from 1.22 (95% CI, 1.17 to 1.26) to 2.09 (95% CI, 2.00 to 2.17) based on education. In contrast, the slope index of inequality decreased from 30.9 (95% CI, 29.3 to 32.6) to 20.1 (95% CI, 18.7 to 21.5) based on income and from 44.6 (95% CI, 43.1 to 46.2) to 28.7 (95% CI, 27.3 to 30.0) based on education. Having only a father who smoked indoors was a major contributor to absolute income inequality in infants’ SHS exposure in 2010, which increased in importance from 45.1% in 2001 to 67.0% in 2010.ConclusionsThe socioeconomic inequalities in infants’ second hand smoke exposure increased in relative terms but decreased in absolute terms from 2001 to 2010. Further efforts are needed to encourage parents to quit smoking and protect infants from second hand smoke exposure, especially in low socioeconomic households that include non-smoking mothers.     

QuantiFERON-TB Gold In-Tube Assay for Screening Arthritis Patients for Latent Tuberculosis Infection before Starting Anti-Tumor Necrosis Factor Treatment

Background

Patients undergoing anti-tumor necrosis factor (TNF) treatment are at an increased risk of reactivating a latent tuberculosis infection (LTBI). This study evaluated the effectiveness of the QuantiFERON-TB Gold In-Tube (QFT) assay for diagnosing LTBI in arthritis patients undergoing anti-TNF treatment.

Methods

We enrolled 342 consecutive patients from August 2007 to October 2013: 176 (51.5%) patients with ankylosing spondylitis and 166 (48.5%) with rheumatoid arthritis. Screening tests included tuberculin skin test (TST) and QFT assay. Positive QFT results, regardless of TST results, were considered an indicator for LTBI treatment.

Results

Bacillus Calmette-Guérin scars were found in 236 (69.0%) patients. Of 342 patients, TST and QFT were positive in 122 (35.7%) and 103 (30.1%) patients, respectively, and discordant in 101 (29.5%) patients. During a median follow-up duration of 41.7 months, five patients (1.5%) developed TB in a median of 20.8 months after initiation of anti-TNF treatment (428/100,000 person-years). TB did not occur in 62 TST+/QFT+ patients who received LTBI treatment. Of 41 TST−/QFT+ patients who received LTBI treatment, one (2.4%) developed TB 20.5 months after starting anti-TNF treatment (705/100,000 person-years). Of 60 TST+/QFT− patients who did not receive LTBI treatment, two (3.3%) developed TB 20.8 and 22.0 months after starting anti-TNF treatment (871/100,000 person-years). Of 179 TST−/QFT− patients, two (1.1%) developed TB 7.2 and 22.7 months, respectively, after initiating anti-TNF treatment (341/100,000 person-years). TB incidence rate during the follow-up period did not differ among TST−/QFT+, TST+/QFT−, and TST−/QFT− patients (P = 0.661).

Conclusion

QFT might be used instead of TST for diagnosing LTBI in patients before starting anti-TNF therapy in countries, such as Korea, where the TB prevalence is intermediate and the BCG vaccination is mandatory at birth. In the absence of a true gold standard test for LTBI, however, there is still a risk of TB development during anti-TNF treatment.