Photodynamic therapy (PDT) - Initiation of apoptosis via activation of stress-activated p38 MAPK and JNK signal pathway in H460 cell lines

AIMS

The purpose of this study was to investigate the photoefficacies of protoporphyrin IX (PpIX) generated by drug precursor 5-aminolevulinic acid (ALA) and its hexyl ester (H-ALA) on two human non-small lung carcinoma cell lines (H460/Bcl-2 and H460/neo).

MAIN METHODS

Drug uptake and the photoefficacies of PpIX were measured by flow cytometry and MTT assay; while the mode of cell death and alternation of signal transduction pathways were studied with 4',6-diamidino-2-phenylindole (DAPI) staining and Western blot analysis, respectively.

KEY FINDINGS

The flow cytometric analysis of H-ALA (5μM) uptake revealed optimal fluorescent intensity at 8h incubation, while ALA (0.5mM) was still far from saturation. The LD(30) of H-ALA-PDT was 30μM, 2J/cm(2), while the LD(30) of ALA-PDT was 3mM, 2J/cm(2). The dark toxicities mediated by both pro-drug H-ALA and ALA were negligible. By DAPI staining, apoptotic cell death was observed. In addition, by Western blot analysis, H-ALA- and ALA-mediated PDT initiated apoptotic cell death via the up-regulation and activation of p38 mitogen activated protein kinase (MAPK), the stress-activated c-jun N-terminal kinases (JNK) and ERK.

SIGNIFICANCE

These results suggested that H-ALA and ALA mediated PDT displayed similar photocytotoxicities towards the two non-small lung cancer cells. Our present study also demonstrates H-ALA or ALA mediated PDT in H460 cells are closely related to the activation of p38 MAPK and JNK signalling pathway.

Growth of dielectric-embedded silicon nanocrystallites for light-emitting device application

Dielectric films with embedded silicon Si nanocrystallites (Si-Nc) have been recognized as promising light-emitting materials for future integrated photonics based on silicon technology. This work reports a novel method of making this kind of material by high-temperature annealing of Si-rich oxide or nitride films which gives rise to the phase separation reaction and the formation of crystalline silicon nanoclusters in the films. Various characteristics of these materials were studied in detail by using transmission electron microscope, X-ray photoelectron spectroscopy (XPS), Raman, and photoluminescence (PL). Strong transverse optical (TO) mode of Si-Nc at around 516 cm(-1) was found in the Raman spectra of the annealed dielectric films. XPS studies indicate that the Si 2p spectra could be transformed from a random bonding structure (as-deposited) to a random mixing of Si-Nc with stoichiometric oxide or nitride phase after the high-temperature annealing. The energy locations of PL were found to depend on the amount of rich Si and the annealing conditions. Longer and higher temperature annealing can result in the growth of the Si-Nc size and leads to a red-shift of PL. Direct correlation among the crystallite sizes with the PL peaks was found.

DNA damage as a biomarker for assessing the effects of suspended solids on the orange-spotted grouper, Epinephelus coioides

In Hong Kong, suspended solids (SS) introduced by dredging and mud disposal activities are a major cause of mass mortality in cage-cultured marine fish. We have used DNA damage in liver cells, as determined by the comet assay, to assess the impact of SS on the orange-spotted grouper Epinephelus coioides. Seabed sediments were collected from a heavily polluted site in Victoria Harbor and two less polluted sites in Port Shelter and Mirs Bay. Sediments from Victoria Harbor contained higher levels of copper (Cu) and polycyclic aromatic hydrocarbons (PAHs) than those from the other sites. In a 10-day experiment, SS from all three sites induced significant increase in comet tail length, but not in percentage (%) tail DNA. In a 20-day experiment, fish exposed to polluted SS from Victoria Harbor exhibited a significant increase in comet tail length after 5 days and % tail DNA after 10 days. After a 10-day recovery period, however, DNA damage was reduced as tail length and % tail DNA returned to control levels. These results suggest that DNA damage measured by the comet assay is a highly sensitive biomarker for assessing the genotoxic effects of SS to marine fish.

Metabolic syndrome, endothelial injury, and subclinical atherosclerosis in patients with systemic lupus erythematosus

OBJECTIVES

To study the link between metabolic syndrome (MetS), endothelial injury, and atherosclerosis in patients with systemic lupus erythematosus (SLE).

METHODS

Consecutive SLE patients without a history of arterial thrombosis were screened for atherosclerosis at the carotid and coronary arteries by B-mode ultrasound [intima-media thickness (IMT)] and multidetector computed tomography (MDCT) scan (Agatston calcium scores), respectively. Plasma levels of homocysteine, high-sensitivity C-reactive protein (hsCRP), soluble vascular cell adhesion molecule (sVCAM)-1, P-selectin, and soluble thrombomodulin (sTM) were assayed. Patients were stratified according to the National Cholesterol Education Program (NCEP) Adult Treatment Panel III (ATP III) criteria for MetS, using the Asian criteria for abdominal obesity. Risk factors for atherosclerosis were studied.

RESULTS

Of the 123 SLE patients (93% women; age 47.9+/-11 years; SLE duration 10.9+/-7.0 years) studied, 20 (16.3%) had MetS. The prevalence of MetS in the SLE patients was significantly higher than in 492 age- and sex-matched healthy controls (9.6%; p=0.03). Coronary calcification and abnormal carotid IMT were detected in 38 (31%) and 72 (59%) of SLE patients, respectively. Patients with MetS had a significantly higher Agatston score (69.5+/-95 vs. 16.4+/-57; p=0.03) and a numerically higher carotid IMT (p=0.43) than those without. In a logistic regression model, the MetS [odds ratio (OR) 3.11, 95% confidence interval (CI) 1.01-9.59, p=0.049] was associated with coronary atherosclerosis after adjustment for age and other risk factors. In addition, patients with MetS had significantly higher levels of hsCRP (p=0.002), homocysteine (p=0.03), and sTM (p=0.01).

CONCLUSIONS

The MetS is more prevalent in SLE patients than the general population and is associated with endothelial injury and coronary atherosclerosis. More aggressive control of risk factors is justified in these patients.

Decreased expression of T lymphocyte co-stimulatory molecule CD26 on invariant natural killer T cells in systemic lupus erythematosus

CD26, a T cell co-stimulatory molecule and dipeptidyl peptidase IV for the degradation of interferon-gamma-induced chemokine, participates in multiple immunopathological roles in leukocyte homing and inflammation. Decreased circulating concentration of soluble (s)CD26 in patients with systemic lupus erythematosus (SLE), rheumatoid arthritis and murine model of arthritis and encephalomyelitis have been reported. In the present study, the plasma concentration of sCD26 and chemokines, and cell surface expression of CD26 on monocytes, CD4+T lymphocytes, CD8+T lymphocytes, CD19+B lymphocytes and invariant natural killer T (iNKT) lymphocytes were analyzed using ELISA and flow cytometry, respectively, in 23 SLE patients and 14 sex- and age-matched control subjects. Although there was no significant difference between plasma concentrations of soluble CD26 in SLE patients with controls (p > 0.05), there was significant elevated Th1 chemokines CXCL10 and CXCL9 but not Th2 chemokine CCL2, and down-regulation in iNKT lymphocytes number and cell surface expression of CD26 on CD4+T and iNKT lymphocytes of SLE patients compared with controls (all p < 0.05). Decreased circulating number of iNKT cells and CD26 on iNKT cells can be important for the immunopathogenesis by exacerbating Th1-related inflammation in SLE.

Activation profile of Toll-like receptors of peripheral blood lymphocytes in patients with systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease associated with aberrant activation of T and B lymphocytes for the production of inflammatory cytokines and autoreactive antibodies. Animal studies of SLE have indicated that Toll-like receptors (TLR) are important in the pathogenesis of murine lupus. In the present clinical study, differential protein expressions of TLR-1-9 of monocytes and different lymphocyte subsets from patients with SLE and normal control subjects were determined by flow cytometry. Results showed that the expression of intracellular TLRs (TLR-3, -8, -9) and extracellular TLRs (TLR-1, -2, -4, -5, -6) were elevated in monocytes, CD4(+) T lymphocytes, CD8(+) T lymphocytes and B lymphocytes of SLE patients compared to control subjects (all P < 0.001). Moreover, cell surface expression of TLR-4 on CD4(+) T lymphocytes and CD8(+) T lymphocytes, and TLR-6 on B lymphocytes, were correlated positively with SLE disease activity index (SLEDAI) (TLR-4 on CD4(+) T lymphocytes and CD8(+) T lymphocytes: r = 0.536, P = 0.04; r = 0.713, P = 0.003; TLR-6 in B lymphocytes: r = 0.572, P = 0.026). In concordance with the above results, there is an observable increased relative induction (%) of inflammatory cytokine interleukin (IL)-1beta, IL-6, IL-10 and IL-12, chemokines CCL2, CXCL8, CCL5 and CXCL10 from peripheral blood mononuclear cells (PBMC) upon differential stimulation by PolyIC (TLR-3 ligand), lipopolysaccharide (TLR-4 ligand), peptidoglycan (TLR-2 ligand), flagellin (TLR-5 ligand), R837 (TLR-7 ligand) and CpG DNA (TLR-9 ligand) in SLE patients compared to controls. These results suggest that the innate immune response for extracellular pathogens and self-originated DNA plays immunopathological roles via TLR activation in SLE.

Interleukin-17A activation on bronchial epithelium and basophils: a novel inflammatory mechanism

Basophils are the accessory cell type for T-helper (Th)2 induction and initiators in immunoglobulin E-mediated chronic allergic inflammation. Basophils and Th17 cells accumulate at the inflammatory sites, such as the airways of allergic asthmatic patients. We investigated the activation of interleukin (IL)-17A on the primary human basophils/KU812 basophilic cells and primary human bronchial epithelial cells/BEAS-2B bronchial epithelial cells. Cytokines, chemokines, adhesion molecules and intracellular signalling molecules were assayed by ELISA or flow cytometry. Co-culture of bronchial epithelial cells and basophils could significantly induce the release of IL-6, an epithelial inflammatory cytokine, and CCL2, a chemokine for basophils, esosinophils and monocytes. Such induction was synergistically enhanced by IL-17A, and direct interaction between these two cells was necessary for IL-17A-induced IL-6 and CCL2 release. Surface expression of intercellular adhesion molecule-1 on bronchial epithelial cells was also upregulated upon their interaction. The interaction of basophils and bronchial epithelial cells under IL-17A stimulation was differentially regulated by extracellular signal-regulated kinase, c-Jun N-terminal protein kinase, p38 mitogen-activated protein kinase and nuclear factor-kappaB pathways. These findings suggest a novel immunopathological role of Th17 cells and basophils in allergic asthma through the activation of granulocyte-mediated inflammation initiated by the direct interaction between basophils and bronchial epithelial cells.

Elevation of Pro-Inflammatory Cytokines, C-Reactive Protein and Cardiac Troponin T in Chronic Renal Failure Patients on Dialysis

Chronic renal failure (CRF) patients suffer from a chronic inflammation. They are at increased risk of cardiovascular disease. In order to investigate this inflammatory process and cardiovascular risk factors associated with haemodialysis (HD) and peritoneal dialysis (PD), we compared serum/plasma pro-inflammatory cytokines, C-reactive protein (CRP), and cardiac troponin T (cTnT) of 146 CRF patients treated or not treated with PD or HD. Serum cytokines and CRP as well as plasma cTnT were measured by enzyme-linked immunosorbent assay, chemiluminescence immunoassay, and electrochemiluminescence immunoassay, respectively. Results indicated that serum interleukin (IL)-18 concentrations were significantly higher in PD and low creatinine clearance pre-dialysis CRF (LCC) patients than HD patients (both p < 0.05). IL-6 and tumour necrosis factor (TNF)-alpha concentrations were significantly higher in PD patients than LCC patients (both p < 0.01). Serum hsCRP and plasma cTnT in HD were significantly higher than LCC (both p < 0.01). The elevation of pro-inflammatory cytokines should play an important role in the chronic inflammation and increased cardiovascular risk of CRF patients on dialysis. We are evaluating further the diagnostic and prognostic applications of pro-inflammatory cytokines and biochemical inflammatory markers for these patients.

Caseinolytic protease: a protein vaccine which could elicit serotype-independent protection against invasive pneumococcal infection

Invasive pneumococcal diseases incur significant mortality, morbidity and economic costs. The most effective strategy currently available to reduce the burden of these diseases is vaccination. In this study, we evaluated the protective efficacy of immunizing mice with caseinolytic protease (ClpP) protein antigen whose gene sequences were shown to be highly conserved in different strains of Streptococcus pneumoniae in an invasive-disease model (intraperitoneal infection model), and protection against invasive challenge with 12 different serotypes of S. pneumoniae was assessed in two murine strains. Our findings demonstrated that active immunization with ClpP and passive immunization with antibodies specific for ClpP could elicit serotype-independent protection effectively against invasive pneumococcal infection. Therefore, to our knowledge, this study is the first report that immunization with single pneumococcal ClpP protein antigen could protect against such broad-range pneumococal strains, which thus supports the development of ClpP as a human penumococcal vaccine.

Usefulness of laboratory mental stress test in patients with stable coronary artery disease

BACKGROUND AND HYPOTHESIS

Many episodes of ischemia in daily life are silent occurring during sedentary activities and may be related to mental stress. In 35 patients with stable angina and positive exercise test awaiting bypass surgery, we investigated whether laboratory mental stress tests would trigger ischemia of a comparable severity to that occurring in daily life and attempted to elucidate some of the underlying mechanisms.

METHODS

All patients underwent exercise testing, personality assessment, 2-day Holter monitoring, and laboratory mental stress tests while on their usual medications.

RESULTS

Only four patients (12%) had positive mental stress test (ST depression > or = 0.1 mV). All episodes were silent and usually associated with fast heart rate (> 90 beats/min). In contrast, ambulatory ischemia was common (average duration of 51 min per 24 h), and at least one episode was recorded in 27 patients (77%) including the 4 with positive test. Patients with positive mental stress test had a higher heart rate during testing (124 +/- 24 vs. 86 +/- 16 beats/min, p < 0.01), and a shorter exercise time and time to 1 mm ST depression on cycle ergometry than those with negative mental stress test. None of the four patients were on beta blockers. There was no difference in personality inventory between the two groups. Comparisons between patients with and without positive mental stress test revealed no difference in the duration and frequency of ambulatory ischemia, or in the occurrence of silent ischemia. However, the heart rate at onset of ambulatory ischemia tended to be higher in the patients with positive mental stress test (96 +/- 9 vs. 62 +/- 43, p = 0.07). Further subgroup analysis in patients without beta blockers (4 mental stress test positive and 18 negative) showed similar results.

CONCLUSIONS

Laboratory mental stress test is a weak inducer of ischemia detected by electrocardiographic monitoring in patients with frequent ambulatory ischemia. Wall motion evaluation during mental stress test may improve sensitivity. While larger scale studies may determine its clinical role, the present study illustrated that patients with heightened heart rate response to mental stress were identified in whom beta blockers could be the drug of choice.

Photoluminescence of silicon nanocrystals embedded in silicon oxide

The bonding structure and the optical properties of silicon-rich silicon oxide films which were prepared using plasma-enhanced chemical vapor deposition (PECVD) with thermal oxidation were studied in detail. The composition and bonding structures were explored using X-ray photoelectron spectroscopy (XPS). The luminescent properties were studied using Raman spectroscopy and photoluminescence (PL) measurements. Results show that high-temperature (approximately 1000 degrees C) annealing of as-deposited Si-rich silicon oxide gives rise to phase separation and formation of crystalline Si phases in the oxide films. Upon high temperature annealing, the PL (550-900 nm) intensity was significantly reduced in stoichiometric oxide or in low Si-content (prepared with [N2O]/[SiH4] gas flow ratio > 2.5) films whereas an opposite trend was found in higher Si-rich samples. Particularly, for the red band (650 nm) and the infrared band (750 nm), the PL intensity was significantly enhanced by annealing slightly Si-rich samples ([N2O] / [SiH4] = 2.5) at 1100 degrees C. This observation was explained by the formation of Si nanocrystallites via phase separation reaction and the removal of defect-related absorption centers during annealing.

Activation of peripheral Th17 lymphocytes in patients with asthma

A recently identified interleukin (IL)-17-producing T-helper (Th) lymphocyte subset, which comprises Th17 cells producing hallmark cytokines IL-17A, IL-17F and IL-22, is involved in chronic inflammatory diseases. Elevated gene and protein expressions of IL-17 are manifested in allergic asthma. We further characterized the activation of Th17 cells in asthmatic patients. Peripheral blood mononuclear cells (PBMC) were purified from 31 asthmatic patients and 20 sex- and age-matched control subjects. The number of IL-17A secreting cells in peripheral blood was enumerated by enzyme-linked immunosorbent spot assay. Cell surface expression of Th17-related chemokine receptor CCR6, and plasma level of IL-17A, IL-17F and IL-22, and ex vivo production of IL-17A and IL-22 were measured by flow cytometry and enzyme-linked immunosorbent assay, respectively. The number of peripheral Th17 lymphocytes, expression of CCR6 on Th cells, and ex vivo IL-23, anti-CD3 and anti-CD28 induced production of IL-22 by PBMC were significantly elevated in asthmatic patients compared with control subjects (all p < 0.01). This clinical study further confirmed increased number of peripheral Th17 lymphocytes and cell surface expression of CCR6 receptors on Th cells in asthmatic patients. Pro-inflammatory cytokine IL-23 can exacerbate disease severity by activating pathogenic Th17 lymphocytes to release downstream inflammatory cytokine IL-22 in asthma.

Expression and functional analysis of toll-like receptors of peripheral blood cells in asthmatic patients: implication for immunopathological mechanism in asthma

BACKGROUND

We investigated the expression profile of toll-like receptors (TLRs) and TLR ligand-activated production profile of asthma-related inflammatory cytokines in asthmatic patients. The expression of TLR1-8 on monocytes, CD4+ T helper lymphocytes, CD8+ T cytotoxic lymphocytes, CD19+ B lymphocytes, and dendritic cells, and ex vivo production of cytokines from peripheral blood mononuclear cells activated by TLR ligands were measured by flow cytometry.

DISCUSSION

Ex vivo productions of TNF-alpha, IL-10, and IL-1beta by TLR4 and TLR5 ligand LPS and flagellin were significantly lower in asthmatic patients (all P < 0.05). Expression of TLR4 and TLR5 was also found to be significantly lower in asthmatic patients when compared to that of control subjects (all P < 0.05). Therefore, the decreased activation of TLR4 and TLR5 in asthmatic patients might contribute to the immunopathological mechanisms of asthma by reducing the release of Th1 and anti-inflammatory cytokines.

Effects of glycemic index meal and CHO-electrolyte drink on cytokine response and run performance in endurance athletes

OBJECTIVE

To examine the effect of the glycemic index (GI) of a pre-exercise (PRE-ex) meal on plasma cytokine responses and endurance performance when carbohydrate-electrolyte (CHO-E) drink was consumed during exercise.

METHODS

Eight endurance-trained male runners (age: 28.6+/-2.7 years; body mass: 61.9+/-1.71 kg; V O(2max): 58.5+/-1.6 ml kg(-1)min(-1)) completed three trials in a randomized order. The pre-exercise meal consisted of either high-GI (HGI) (GI=83), low-GI (LGI) foods (GI=36) or control (CON) (low energy sugar-free jelly) was given to the participant 2h before a 21-km performance run on a level treadmill. During each trial, 2 ml kg(-1) BM of 6.6% CHO-E solution was consumed immediately before exercise and every 2.5-km afterward. Blood samples were collected before (pre-meal), and 120 min after ingestion the meal (120 min), immediately (POST), and 60 min (POST-60 min) after exercise.

RESULTS

No difference was found in time to complete the 21-km run between LGI and HGI. The interleukin-6 (IL-6) level increased by more than 100 times immediately after exercise in the three trials and returned to the basal level only on LGI at POST-60 min. In contrast, interleukin-2 (IL-2) level showed a transitory decrease at POST on CON (p<0.001). Glucose concentrations did not recover to the pre-meal level by POST-60 min on HGI only. Cortisol concentrations increased throughout the exercise and were lower on LGI when compared with CON (p<0.05) at POST-60 min.

CONCLUSIONS

HGI and LGI demonstrated similar performance when CHO-E solution was consumed during a 21-km run. However, pre-exercise LGI meal attenuated the increases in cortisol and quickened the recovery of the increased IL-6 value.

Study of gene-gene interactions for endophenotypic quantitative traits in Chinese asthmatic children

BACKGROUND

Asthma is a complex disease resulting from interactions between multiple genes and environmental factors. Study of gene-gene interactions could provide insight into the pathophysiology of asthma.

METHODS

We investigated the interactions among 18 single-nucleotide polymorphisms in eight candidate genes for plasma total immunoglobulin E (IgE) concentration and peripheral blood (PB) eosinophil count in 298 Chinese asthmatic children and 175 controls. Generalized multifactor dimensionality reduction and generalized linear model were used to analyze gene-gene interactions for the quantitative traits.

RESULTS

A significant interaction was found between R130Q in IL13 and I50V in IL4RA for plasma total IgE concentration, with a cross-validation (CV) consistency of nine of 10 and a prediction error of 41.1% (P = 0.013). Plasma total IgE concentration was significantly higher in the high-risk than the low-risk groups (P < 0.0001). For PB eosinophil count, significant interaction was found between C-431T in TARC and RsaI_in2 in FCERIB, with a CV consistency of nine of 10 and a prediction error of 40.2% (P = 0.009). PB eosinophil count was significantly higher in the high-risk group than the low-risk groups (P < 0.0001). Generalized linear model also revealed significant gene-gene interaction for the above two endophenotypes with P = 0.013 for plasma total IgE concentration and P = 0.029 for PB eosinophil count respectively.

CONCLUSIONS

Our data suggest significant interactions between IL13 and IL4RA for plasma total IgE concentration, and this is the first report to show significant interaction between TARC and FCERIB for PB eosinophil count in Chinese asthmatic children.

Genomewide selection in oil palm: increasing selection gain per unit time and cost with small populations

Oil palm (Elaeis guineensis Jacq.) requires 19 years per cycle of phenotypic selection. The use of molecular markers may reduce the generation interval and the cost of oil-palm breeding. Our objectives were to compare, by simulation, the response to phenotypic selection, marker-assisted recurrent selection (MARS), and genomewide selection with small population sizes in oil palm, and assess the efficiency of each method in terms of years and cost per unit gain. Markers significantly associated with the trait were used to calculate the marker scores in MARS, whereas all markers were used (without significance tests) to calculate the marker scores in genomewide selection. Responses to phenotypic selection and genomewide selection were consistently greater than the response to MARS. With population sizes of N = 50 or 70, responses to genomewide selection were 4-25% larger than the corresponding responses to phenotypic selection, depending on the heritability and number of quantitative trait loci. Cost per unit gain was 26-57% lower with genomewide selection than with phenotypic selection when markers cost US $1.50 per data point, and 35-65% lower when markers cost $0.15 per data point. With population sizes of N = 50 or 70, time per unit gain was 11-23 years with genomewide selection and 14-25 years with phenotypic selection. We conclude that for a realistic yet relatively small population size of N = 50 in oil palm, genomewide selection is superior to MARS and phenotypic selection in terms of gain per unit cost and time. Our results should be generally applicable to other tree species that are characterized by long generation intervals, high costs of maintaining breeding plantations, and small population sizes in selection programs.

In vitro and clinical immunomodulatory effects of a novel Pentaherbs concoction for atopic dermatitis

BACKGROUND

Our group recently reported a randomized and placebo-controlled clinical trial on the efficacy of a twice-daily concoction of five herbal ingredients (Pentaherbs formulation, PHF) in treating children with atopic dermatitis (AD).

OBJECTIVES

To investigate the immunomodulatory effects that may be induced by PHF treatment.

METHODS

We investigated the effects of PHF on cytotoxicity and proliferation of phytohaemagglutinin (PHA)- and staphylococcal enterotoxin B (SEB)-stimulated peripheral blood mononuclear cells (PBMC) isolated from buffy coat of blood donors. PHF-induced immunomodulation for five inflammatory mediators in cultured PBMC was measured by reverse transcription-polymerase chain reaction and enzyme-linked immunosorbent assay. The effects of a 3-month, open-label study of PHF on circulating inflammatory mediators in children with AD were also assessed.

RESULTS

PHF at up to 1 mg mL(-1) dose-dependently suppressed PBMC proliferation. The addition of PHF to cultured PBMC reduced supernatant concentrations of brain-derived neurotrophic factor (BDNF), interferon (IFN)-gamma and tumour necrosis factor (TNF)-alpha in response to PHA, and BDNF and thymus and activation-regulated chemokine (TARC) following SEB stimulation. PHF increased epithelial cell-derived neutrophil activating peptide-78 levels in culture supernatants. At the RNA level, PHF suppressed the transcription of BDNF, TARC, IFN-gamma and TNF-alpha. Twenty-eight children with AD were treated with PHF for 3 months, and their mean plasma concentrations of BDNF and TARC decreased significantly from 1798 pg mL(-1) and 824 pg mL(-1) at baseline to 1378 pg mL(-1) and 492 pg mL(-1) (P = 0.002 and 0.013, respectively) upon study completion.

CONCLUSIONS

PHF possesses in vitro and in vivo immunomodulatory properties that may mediate the clinical efficacy observed in AD treatment.

Compressed indexing and local alignment of DNA

MOTIVATION

Recent experimental studies on compressed indexes (BWT, CSA, FM-index) have confirmed their practicality for indexing very long strings such as the human genome in the main memory. For example, a BWT index for the human genome (with about 3 billion characters) occupies just around 1 G bytes. However, these indexes are designed for exact pattern matching, which is too stringent for biological applications. The demand is often on finding local alignments (pairs of similar substrings with gaps allowed). Without indexing, one can use dynamic programming to find all the local alignments between a text T and a pattern P in O(|T||P|) time, but this would be too slow when the text is of genome scale (e.g. aligning a gene with the human genome would take tens to hundreds of hours). In practice, biologists use heuristic-based software such as BLAST, which is very efficient but does not guarantee to find all local alignments.

RESULTS

In this article, we show how to build a software called BWT-SW that exploits a BWT index of a text T to speed up the dynamic programming for finding all local alignments. Experiments reveal that BWT-SW is very efficient (e.g. aligning a pattern of length 3 000 with the human genome takes less than a minute). We have also analyzed BWT-SW mathematically for a simpler similarity model (with gaps disallowed), and we show that the expected running time is O(/T/(0.628)/P/) for random strings. As far as we know, BWT-SW is the first practical tool that can find all local alignments. Yet BWT-SW is not meant to be a replacement of BLAST, as BLAST is still several times faster than BWT-SW for long patterns and BLAST is indeed accurate enough in most cases (we have used BWT-SW to check against the accuracy of BLAST and found that only rarely BLAST would miss some significant alignments).

AVAILABILITY

www.cs.hku.hk/~ckwong3/bwtsw

CONTACT

twlam@cs.hku.hk.

Hypercytokinemia and hyperactivation of phospho-p38 mitogen-activated protein kinase in severe human influenza A virus infection

BACKGROUND

We postulate that hypercytokinemia plays a role in immunopathogenesis of severe human influenza.

METHODS

We prospectively studied 39 consecutive patients who were hospitalized with severe influenza A virus infection. On laboratory confirmation of the diagnosis, paired acute-phase (obtained at hospital admission) and convalescent-phase (obtained >10 days after hospital admission) plasma samples were collected for assay of 11 cytokines and chemokines (interleukin [IL] 1 beta; IL-6; IL-10; IL-12p70; tumor necrosis factor alpha; IL-8; monokine induced by interferon [IFN]-gamma; IFN-inducible protein 10; monocyte chemoattractant protein 1; regulated upon activation, normal T cell-expressed and secreted; and IFN-gamma) using cytometric bead-array analysis and enzyme-linked immunosorbent assay. Simultaneously, virus concentration in the acute-phase nasopharyngeal aspirate was determined using real-time quantitative reverse-transcriptase polymerase chain reaction. Intracellular signaling molecules regulating lymphocyte activation, phospho-p38 mitogen-activated protein kinase and phospho-extracellular signal-regulated protein kinase in CD4+ and CD8+ T lymphocytes were studied in the acute-phase samples using flow cytometric analysis and were compared with results for samples from healthy control subjects.

RESULTS

Statistically significant increases in plasma IL-6 (3.7-fold increase), IL-8 (2.6-fold increase), IFN-induced protein 10 (4.9-fold increase), and monokine induced by IFN-gamma (2.3-fold increase) concentrations were detected during acute illness (P < .01 for all, by Wilcoxon signed-rank test); the highest concentrations were observed on symptom days 3 and 4. Corresponding plasma cytokine and chemokine concentrations and nasopharyngeal viral loads showed statistically significant correlations (rho = 0.41, 0.49, 0.54, and 0.46, respectively; P < or = .01). Phospho-p38 mitogen-activated protein kinase expression in CD4+ lymphocytes was increased, correlating with cytokine concentrations (e.g., for IFN-induced protein 10, rho = 0.78; P < .01); phospho-extracellular signal-regulated protein kinase was suppressed. Advanced age and comorbidity were associated with aberrant IL-6, IL-8, and monokine induced by IFN-gamma responses (P < .05, by Mann-Whitney U test). An elevated IL-6 concentration was independently associated with prolonged hospitalization (hospitalization for >5 days; P = .02), adjusted for age, comorbidity, and virus load.

CONCLUSIONS

Hypercytokinemia (of proinflammatory and T helper 1 cytokines) is detected in severe influenza, correlating with clinical illness and virus concentration. Hyperactivation of phospho-p38 mitogen-activated protein kinase (in T helper cells) is possibly involved. Early viral suppression may attenuate these potentially deleterious cytokine responses.

Association of prostaglandin-endoperoxide synthase 2 gene polymorphisms with asthma and atopy in Chinese children

BACKGROUND

Cyclooxygenase-2 (COX-2) plays essential roles in inflammation. Previous studies have suggested associations between prostaglandin-endoperoxide synthase 2 (PTGS2) polymorphisms and prostaglandins production in asthma.

OBJECTIVE

We have investigated the effects of Chinese tagging single nucleotide polymorphisms (SNPs) of PTGS2 on asthma traits in 299 Chinese asthmatic children and 175 controls.

METHODS

Plasma total and allergen-specific IgE were measured by enzyme immunoassay. PTGS2.8473T-->C in the 3'-untranslated region of exon 10 and three tag SNPs covering most of the variations in PTGS2 haplotypes in Chinese were genotyped by restriction fragment length polymorphism.

RESULTS

Among the four SNPs, only PTGS2.8473 showed significant association with asthma (P = 0.034) and atopy (P = 0.005 when compared with non-atopic controls; P = 0.023 with all controls). Carriers of the C allele had a 1.5-fold (95% confidence interval: 1.01-2.30) risk of developing asthma than those homozygous for the T allele. Multivariate regression revealed significant correlations between PTGS2.8473 and forced expiratory volume in 1 s (FEV(1); P = 0.002) and peak expiratory flow rate (PEFR; P = 0.001) with age and gender adjusted. Patients with the C allele of PTGS2.8473 had significantly lower FEV(1) (median: 90.0%vs 98.0%; P = 0.0047) and PEFR (70.0%vs 73.5%; P = 0.0065) than those homozygous for the T allele. No significant association between plasma total and allergen-specific IgE and these SNPs or with their haplotypes was found.

CONCLUSIONS

PTGS2.8473 polymorphism is associated with asthma, atopy and lung function but not plasma IgE in Chinese children. This may help to explore the pharmacogenetics of COX-2 inhibitors.

Increased expression of plasma and CD4+ T lymphocyte costimulatory molecule CD26 in adult patients with allergic asthma

CD26, which is a costimulatory molecule and peptidase, is responsible for the degradation of interferon (IFN)-gamma-induced chemokines. To elucidate the immunopathological role of CD26 in allergic asthma, we investigated plasma soluble CD26 (sCD26) concentration and its cell surface expression on lymphocytes, monocytes, CD4+ T helper, CD8+ T suppressor plus cytotoxic T, invariant natural killer T (iNKT), and CD19+ B lymphocytes in allergic asthmatic patients. Plasma sCD26 was significantly elevated in asthmatic patients regardless of inhaled corticosteroid treatment (all P < 0.05). Cell surface expression of CD26 was significantly up-regulated on lymphocytes, especially on CD4+ and iNKT lymphocytes (all P < 0.05), but not on other cell types. Significant positive correlations were found between sCD26 and the percentage of eosinophils, Th2-related chemokines CCL5 and CCL22, and costimulatory molecule sCTLA-4 (all P < 0.05). In conclusion, the aberrant expression of CD26 may contribute to the inflammatory process and Th2 predominance in the immunopathogenesis of allergic asthma.