Review of ”Bioinformatics for vaccinology“ edited by Darren R. Flower

Book review of "Bioinformatics for vaccinology" edited by Darren R. Flower

Systemic EBV+ T-cell lymphoma in elderly patients: comparison with children and young adult patients

Fulminant Epstein–Barr virus (EBV+) T-cell lymphoma in immunocompetent elderly patients is rare and its character has not been well defined. This study analyzed the clinicopathological features of five elderly patients (group A: 50–84 years) and compared them with those of eight children and young adult patients with systemic T-cell lymphomas (group B: 10–34 years). Group A more commonly presented with generalized lymphadenopathy (n = 3) than did group B (n = 1). Chronic active EBV infection (n = 3) and hydroa vacciniforme-like eruptions (n = 1) were seen in group B, while group A showed no evidence of chronic EBV infection, but did show chronic hepatitis B or C virus infections (n = 3). The histological and immunophenotypical findings were similar. All patients died within 1 to 14 months of diagnosis. These findings suggest that EBV+ T-cell lymphoma in elderly patients is a unique disease with an underlying derangement of T-cell immunity and failure to eradicate infected virus. Additional factors related to senility may play a role in the disruption of homeostasis between the virus and the host’s immune system

LINE FUSION GENES: a database of LINE expression in human genes

BACKGROUND: Long Interspersed Nuclear Elements (LINEs) are the most abundant retrotransposons in humans. About 79% of human genes are estimated to contain at least one segment of LINE per transcription unit. Recent studies have shown that LINE elements can affect protein sequences, splicing patterns and expression of human genes. DESCRIPTION: We have developed a database, LINE FUSION GENES, for elucidating LINE expression throughout the human gene database. We searched the 28,171 genes listed in the NCBI database for LINE elements and analyzed their structures and expression patterns. The results show that the mRNA sequences of 1,329 genes were affected by LINE expression. The LINE expression types were classified on the basis of LINEs in the 5' UTR, exon or 3' UTR sequences of the mRNAs. Our database provides further information, such as the tissue distribution and chromosomal location of the genes, and the domain structure that is changed by LINE integration. We have linked all the accession numbers to the NCBI data bank to provide mRNA sequences for subsequent users. CONCLUSION: We believe that our work will interest genome scientists and might help them to gain insight into the implications of LINE expression for human evolution and disease. AVAILABILITY

Hypofractionated three-dimensional conformal radiotherapy for medically inoperable early stage non-small-cell lung cancer

Purpose: The purpose of this study was to assess the clinical outcomes of hypofractionated radiotherapy (HFRT) with three-dimensional conformal technique for medically inoperable patients with early stage non-small-cell lung cancer (NSCLC) and to evaluate prognostic factors. Materials and Methods: We performed a retrospective review of 26 patients who underwent HFRT for early stage NSCLC between September 2005 and August 2011. Only clinical stage T1-3N0 was included. The median RT dose was 70 Gy (range, 60 to 72 Gy) and the median biologically equivalent dose (BED) was 94.5 Gy (range, 78.0 to 100.8 Gy). In 84.6% of patients, 4 Gy per fraction was used. Neoadjuvant chemotherapy with paclitaxel and cisplatin was given to 2 of 26 patients. Results: The median follow-up time for surviving patients was 21 months (range, 13 to 49 months). The overall response rate was 53.9%, and the initial local control rate was 100%. The median survival duration was 27.8 months. Rates of 2-year overall survival, progression-free survival (PFS), local control (LC), and locoregional-free survival (LRFS) were 54.3%, 61.1%, 74.6%, and 61.9%, respectively. Multivariate analysis showed that BED (>90 vs. ≤90 Gy) was an independent prognostic factor influencing PFS, LC, and LRFS. Severe toxicities over grade 3 were not observed. Conclusion: Radical HFRT can yield satisfactory disease control with acceptable rates of toxicities in medically inoperable patients with early stage NSCLC. HFRT is a viable alternative for clinics and patients ineligible for stereotactic ablative radiotherapy. BED over 90 Gy and 4 Gy per fraction might be appropriate for HFRT. © 2013. The Korean Society for Radiation Oncology.

Direct activation of Transient Receptor Potential Vanilloid 1(TRPV1) by Diacylglycerol (DAG)

The capsaicin receptor, known as transient receptor potential channel vanilloid subtype 1 (TRPV1), is activated by a wide range of noxious stimulants and putative ligands such as capsaicin, heat, pH, anandamide, and phosphorylation by protein kinase C (PKC). However, the identity of endogenous activators for TRPV1 under physiological condition is still debated. Here, we report that diacylglycerol (DAG) directly activates TRPV1 channel in a membrane-delimited manner in rat dorsal root ganglion (DRG) neurons. 1-oleoyl-2-acetyl-sn-glycerol (OAG), a membrane-permeable DAG analog, elicited intracellular Ca2+ transients, cationic currents and cobalt uptake that were blocked by TRPV1-selective antagonists, but not by inhibitors of PKC and DAG lipase in rat DRG neurons or HEK 293 cells heterologously expressing TRPV1. OAG induced responses were about one fifth of capsaicin induced signals, suggesting that OAG displays partial agonism. We also found that endogenously produced DAG can activate rat TRPV1 channels. Mutagenesis of rat TRPV1 revealed that DAG-binding site is at Y511, the same site for capsaicin binding, and PtdIns(4,5)P2binding site may not be critical for the activation of rat TRPV1 by DAG in heterologous system. We propose that DAG serves as an endogenous ligand for rat TRPV1, acting as an integrator of Gq/11-coupled receptors and receptor tyrosine kinases that are linked to phospholipase C

A Prospective, Randomized, 6-Month Comparison of the Coronary Vasomotor Response Associated With a Zotarolimus- Versus a Sirolimus-Eluting Stent Differential Recovery of Coronary Endothelial Dysfunction

ObjectivesWe prospectively compared coronary endothelial dysfunction in patients with zotarolimus-eluting stent (ZES) versus sirolimus-eluting stent (SES) implantation at 6-month follow-up.BackgroundA ZES has been associated with uniform and rapid healing of the endothelium.MethodsFifty patients were randomly treated with intravascular ultrasound-guided stenting with a single stent to the mid-segment of the left anterior descending artery (20 ZES, 20 SES, and 10 bare-metal stents), and endothelial function was estimated before and after intervention at 6-month follow-up by incremental acetylcholine (Ach) (10, 20, 50, and 100 μg/min) and nitrate (200 μg/min) infusions into the left coronary ostium. The vascular response was quantitatively measured in the 5-mm segments proximal and distal to the stent.ResultsIn the drug-eluting stent groups, more intense vasoconstriction to incremental doses of Ach was observed at 6-month follow-up compared with the responses before stenting. Endothelial function associated with the ZES was more preserved at 6-month follow-up compared with the SES. Vasoconstriction to Ach was more prominent in the distal segments than the proximal segments in both the ZES and SES groups. Endothelium-independent vasodilation to nitrate did not differ significantly among the study groups.ConclusionsVasoconstriction in response to Ach in the peri-stent region was less pronounced in the ZES group than the SES group at 6-month follow-up, which suggests that endothelial function associated with ZES can be more preserved than the SES

Classification of rice (oryza sativa l. japonica nipponbare) immunophilins (fkbps, cyps) and expression patterns under water stress

<p>Abstract</p> <p>Background</p> <p>FK506 binding proteins (FKBPs) and cyclophilins (CYPs) are abundant and ubiquitous proteins belonging to the peptidyl-prolyl <it>cis/trans </it>isomerase (PPIase) superfamily, which regulate much of metabolism through a chaperone or an isomerization of proline residues during protein folding. They are collectively referred to as immunophilin (IMM), being present in almost all cellular organs. In particular, a number of IMMs relate to environmental stresses.</p> <p>Results</p> <p>FKBP and CYP proteins in rice (<it>Oryza sativa </it>cv. Japonica) were identified and classified, and given the appropriate name for each IMM, considering the ortholog-relation with <it>Arabidopsis </it>and <it>Chlamydomonas </it>or molecular weight of the proteins. 29 FKBP and 27 CYP genes can putatively be identified in rice; among them, a number of genes can be putatively classified as orthologs of <it>Arabidopsis </it>IMMs. However, some genes were novel, did not match with those of <it>Arabidopsis </it>and <it>Chlamydomonas</it>, and several genes were paralogs by genetic duplication. Among 56 IMMs in rice, a significant number are regulated by salt and/or desiccation stress. In addition, their expression levels responding to the water-stress have been analyzed in different tissues, and some subcellular IMMs located by means of tagging with GFP protein.</p> <p>Conclusion</p> <p>Like other green photosynthetic organisms such as <it>Arabidopsis </it>(23 FKBPs and 29 CYPs) and <it>Chlamydomonas </it>(23 FKBs and 26 CYNs), rice has the highest number of IMM genes among organisms reported so far, suggesting that the numbers relate closely to photosynthesis. Classification of the putative FKBPs and CYPs in rice provides the information about their evolutional/functional significance when comparisons are drawn with the relatively well studied genera, <it>Arabidopsis </it>and <it>Chlamydomonas</it>. In addition, many of the genes upregulated by water stress offer the possibility of manipulating the stress responses in rice.</p

Bare-metal stents versus drug-eluting stents in large (≥3.5mm) single coronary artery: Angiographic and clinical outcomes at 6 months

SummaryBackgroundAlthough drug-eluting stents (DES) have been shown to dramatically reduce restenosis and improve the rate of event-free survival in large randomized trials, the benefit of DES appears to be limited to restenosis. In large arteries, it is not clear which type of stent is more superior in angiographic and clinical outcomes between DES and bare-metal stents (BMS). We compared the angiographic and clinical outcomes of DES versus BMS in large arteries (≥3.5mm).MethodTwo hundred and forty patients from March 2002 to March 2007 received stents; 196 patients were treated with DES (44.9% sirolimus-eluting stents; 43.9% paclitaxel-eluting stents; 11.2% zotarolimus-eluting stents) and 44 with cobalt–chromium BMS for single de novo lesions in a large vessel. All subjects received aspirin, clopidogrel, and/or cilostazol as the standard antiplatelet regimen. The angiographic and clinical outcomes were evaluated at 6 months.ResultsFor the baseline characteristics, there were no significant differences between the DES and BMS groups. In addition, for the initially implanted stent there was no difference in the length, stent diameter, and lesion site between the two groups. After 6 months, the follow-up angiogram showed that in-stent diameter restenosis and late loss was more common with BMS than DES (39±21% vs. 19±17%, p=0.007; 1.44±0.83mm vs. 0.62±0.58mm, p=0.009, respectively). However, the target-lesion revascularization/target-vessel revascularization, and total major adverse cardiac events showed no significant differences between the groups (5.3% vs. 3.6%, p=0.62; 5.3% vs. 4.6%, p=0.86, respectively).ConclusionThe DES and cobalt–chromium BMS placed in large coronary arteries showed equally favorable 6-month clinical outcomes, although the 6-month angiographic results appeared more favorable in the DES group than in the BMS group

Six-Month Comparison of Coronary Endothelial Dysfunction Associated With Sirolimus-Eluting Stent Versus Paclitaxel-Eluting Stent

ObjectivesThis study was designed to investigate whether endothelial dysfunction is related to drug-eluting stent (DES) implantation at 6 months after stenting.BackgroundCurrent available DES could delay vessel healing and subsequently impair endothelial function.MethodsEndothelial function was estimated at 6-month follow-up in 75 patients (31 men, mean age 62.1 years) with a DES (39 sirolimus-eluting stents [SES], 36 paclitaxel-eluting stents [PES]), and 10 patients with a bare-metal stent (BMS) to the left anterior descending artery, by incremental acetylcholine (Ach) infusion (20 μg/min, 50 μg/min, 100 μg/min) and nitrate (200 μg/min) into the left coronary ostium. Vascular responses were quantitatively measured in arterial segments 5 mm proximal and distal to DES and compared with corresponding segments in the BMS group and midsegments in the left circumflex artery as a reference nonstented artery. All antianginal agents were withheld for at least 72 h before coronary angiography.ResultsGreater vasoconstriction to Ach was observed in both the SES and PES groups than in the BMS group or control segments of left circumflex artery. Vasoconstriction to Ach was more prominent in arterial segments distal to stents in both SES and PES groups compared with those in the BMS group (p &lt; 0.001). The degree of vasoconstriction to Ach was similar between the SES and PES groups. Endothelium-independent vasodilatation to nitrate did not differ significantly between the study groups.ConclusionsAbnormal vasoconstriction to Ach was found in the SES and PES groups, especially in arterial segments distal to DES at 6 months after stenting, which suggests that DES has a potential long-term adverse effect on local coronary endothelial dysfunction