In silico quantitative prediction of peptides binding affinity to human MHC molecule: an intuitive quantitative structure-activity relationship approach

In this paper, we have handpicked 23 kinds of electronic properties, 37 kinds of steric properties, 54 kinds of hydrophobic properties and 5 kinds of hydrogen bond properties from thousands of amino acid structural and property parameters. Principal component analysis (PCA) was applied on these parameters and thus ten score vectors involving significant nonbonding properties of 20 coded amino acids were yielded, called the divided physicochemical property scores (DPPS) of amino acids. The DPPS descriptor was then used to characterize the structures of 152 HLA-A*0201-restricted CTL epitopes, and significant variables being responsible for the binding affinities were selected by genetic algorithm, and a quantitative structure-activity relationship (QSAR) model by partial least square was established to predict the peptide-HLA-A*0201 molecule interactions. Statistical analysis on the resulted DPPS-based QSAR models were consistent well with experimental exhibits and molecular graphics display. Diversified properties of the different residues in binding peptides may contribute remarkable effect to the interactions between the HLA-A*0201 molecule and its peptide ligands. Particularly, hydrophobicity and hydrogen bond of anchor residues of peptides may have a significant contribution to the interactions. The results showed that DPPS can well represent the structural characteristics of the antigenic peptides and is a promising approach to predict the affinities of peptide binding to HLA-A*0201 in a efficient and intuitive way. We expect that this physical-principle based method can be applied to other protein-peptide interactions as well.

107 Gb/s coherent optical OFDM transmission over 1000-km SSMF fiber using orthogonal band multiplexing

Coherent optical OFDM (CO-OFDM) has emerged as an attractive modulation format for the forthcoming 100 Gb/s Ethernet. However, even the spectral-efficient implementation of CO-OFDM requires digital-to-analog converters (DAC) and analog-to-digital converters (ADC) to operate at the bandwidth which may not be available today or may not be cost-effective. In order to resolve the electronic bandwidth bottleneck associated with DAC/ADC devices, we propose and elucidate the principle of orthogonal-band-multiplexed OFDM (OBM-OFDM) to subdivide the entire OFDM spectrum into multiple orthogonal bands. With this scheme, the DAC/ADCs do not need to operate at extremely high sampling rate. The corresponding mapping to the mixed-signal integrated circuit (IC) design is also revealed. Additionally, we show the proof-of-concept transmission experiment through optical realization of OBM-OFDM. To the best of our knowledge, we present the first experimental demonstration of 107 Gb/s QPSK-encoded CO-OFDM signal transmission over 1000 km standard-single- mode-fiber (SSMF) without optical dispersion compensation and without Raman amplification. The demonstrated system employs 2x2 MIMO-OFDM signal processing and achieves high electrical spectral efficiency with direct-conversion at both transmitter and receiver.

Potential use of mangroves as constructed wetland for municipal sewage treatment in Futian, Shenzhen, China

A pilot-scale mangrove wetland was constructed in Futian, Shenzhen for municipal sewage treatment. Three identical belts (length: 33m, width: 3m, depth: 0.5m) were filled with stone (bottom), gravel and mangrove sand (surface). Seedlings of two native mangrove species (Kandelia candel, Aegiceras corniculatum) and one exotic species (Sonneratia caseolaris) were transplanted to the belts with one species for each belt. The hydraulic loading was 5m(3)d(-1) and hydraulic retention time 3d. High levels of removal of COD, BOD(5), TN, TP and NH(3)-N were obtained. The treatment efficiency of S. caseolaris and A. corniculatum was higher than that of K. candel. Faster plant growth was obtained for S. caseolaris. The substrate in the S. caseolaris belt also showed higher enzyme activities including dehydrogenase, cellulase, phosphatase, urease and beta-glucosidase. The removal rates of organic matter and nutrients were positively correlated with plant growth. The results indicated that mangroves could be used in a constructed wetland for municipal sewage treatment, providing post-treatment to remove coliforms was also included.

Thymol and related alkyl phenols activate the hTRPA1 channel

BACKGROUND AND PURPOSE

Thymol, a major component of thyme and oregano, has medical uses in oral care products as an astringent and antibiotic. Its distinctive sharp odour and pungent flavour are considered aversive properties. The molecular basis of these aversive properties is not well understood.

EXPERIMENTAL APPROACH

The ability of thymol to activate human transient receptor potential channel A1 (hTRPA1) expressed in stably transfected human embryonic kidney 293 (HEK293) cells was measured by membrane potential and calcium-sensitive dyes in a fluorescence-imaging plate reader (FLIPR) assay. Direct activation of hTRPA1 currents was measured by whole-cell voltage clamp recording. Intracellular calcium changes were measured using fura-2 dye. The FLIPR assay was also used to measure membrane potential changes elicited by thymol after pretreatment with camphor, a known TRPA1 inhibitor. The ability of related alkyl phenols to activate hTRPA1 was also determined.

KEY RESULTS

Thymol potently activated a membrane potential response and intracellular calcium increase in hTRPA1-expressing HEK293 cells in a concentration-dependent manner. Activation by thymol desensitized hTRPA1 to further exposure to thymol or the known ligand allyl isothiocyanate (AITC). The related phenols 2-tert-butyl-5-methylphenol, 2,6-diisopropylphenol (propofol) and carvacrol also activated hTRPA1. Phenols with less bulky carbon substitutions and lower logP values were less potent in general. The response to thymol was blocked by camphor.

CONCLUSIONS AND IMPLICATIONS

These results suggest a role for hTRPA1 activation in the reported pungent and aversive properties of some of these pharmaceutically important phenols.

Molecular cloning and expression analysis of a novel CONSTANS-like gene from potato

A full-length cDNA of a StCONSTANS-like (StCOL) gene was cloned from potato (Solanum tuberosum L.) by RT-PCR and RACE. The predicted amino acid sequence of this cDNA has a high degree of identity with other homologous members of the CO or COL family. Analysis of mRNA levels for StCOL shows that it is highly expressed in leaves and becomes weaker during tuberization; moreover, is independent of gibberellin A(3) and sucrose.

Role of SNAREs and H+-ATPase in the targeting of proton pump-coated vesicles to collecting duct cell apical membrane

Recycling of H(+)-ATPase to the apical plasma membrane, mediated by vesicular exocytosis and endocytosis, is an important mechanism for controlling H(+) secretion by the collecting duct. We hypothesized that SNAREs (soluble N-ethylmaleimide-sensitive factor attachment proteins) may be involved in the targeting of H(+)-ATPase-coated vesicles. Using a tissue culture model of collecting duct H(+) secretory cells (inner medullary collecting duct (IMCD) cells), we demonstrated that they express the proteins required for SNARE-mediated exocytosis and form SNARE-fusion complexes upon stimulation of H(+)-ATPase exocytosis. Furthermore, exocytic amplification of apical H(+)-ATPase is sensitive to clostridial toxins that cleave SNAREs and thereby inhibit secretion. Thus, SNAREs are critical for H(+)-ATPase cycling to the plasma membrane. The process in IMCD cells has a feature distinct from that of neuronal cells: the SNARE complex includes and requires the vesicular cargo (H(+)-ATPase) for targeting. Using chimeras and truncations of syntaxin 1, we demonstrated that there is a specific cassette within the syntaxin 1 H3 domain that mediates binding of the SNAREs and a second distinct H3 region that binds H(+)-ATPase. Utilizing point mutations of the B1 subunit of the H(+)-ATPase, we document that this subunit contains specific targeting information for the H(+)-ATPase itself. In addition, we found that Munc-18-2, a regulator of exocytosis, plays a multifunctional role in this system: it regulates SNARE complex formation and the affinity of syntaxin 1 for H(+)-ATPase.

[Survival after laser-induced interstitial thermotherapy of colorectal liver metastases--a comparison of first clinical experiences with current therapy results]

PURPOSE

Laser-induced interstitial thermotherapy (LITT) is a minimally invasive procedure for local tumor ablation. This report discusses the long-term results of this therapy in non-surgical patients with colorectal liver metastases.

MATERIALS AND METHODS

In total, we treated 163 colorectal liver metastases in 85 patients by MR-guided LITT.

RESULTS

The overall lethality was 1.1%. The mean survival period of all treated patients was 3.3+/-0.3 years (CI: 2.8; 3.8; Kaplan-Meier method) with a calculation start date of the diagnosis of the metastases. The mean survival period after LITT was 2.6+/-0.2 years (CI 2.2; 3.0). There was a substantial learning curve with respect to the indication for LITT and the technical procedure of the intervention itself. In the first period (50 patients; 1998-2001), the mean survival period was 2.2+/-0.2 years (CI: 1.8; 2.7). Thereafter (35 patients 2001-2006), the mean survival period increased to 2.9+/-0.3 years (CI: 2.4; 3.4; log rank Test; p=0.0097). In the latter group, the 1-year survival rate was 93% and the 3-year survival rate was 56%.

CONCLUSION

MR-guided LITT is a treatment suitable for non-surgical patients suffering from colorectal liver metastases. The complication rate of the procedure is comparatively low. The survival periods after the procedure are longer than those reported for similar patient populations after chemotherapy alone.

A heat shock protein gene (hsp22.4) from Chaetomium globosum confers heat and Na2CO3 tolerance to yeast

A small heat shock protein gene (hsp22.4) was cloned from Chaetomium globosum using rapid amplification of cDNA ends (RACE). The 986-bp full-length hsp22.4 cDNA contains a 609-bp open reading frame encoding a 202-amino-acid protein with an estimated molecular mass of 22.4 kDa. The hsp22.4 gene was amplified using specific primers in the 5' and 3' untranslated regions of the hsp22.4 cDNA. The temporal expression of hsp22.4 was measured in C. globosum by real-time reverse transcriptase-polymerase chain reaction after exposure to heat, cold, Na(2)CO(3), and NaCl. The expression of hsp22.4 was induced by heat and Na(2)CO(3) treatment and inhibited by cold and NaCl treatment. The hsp22.4 gene was inserted into pYES2 containing the inducible GAL1 promoter and transferred into yeast (Saccharomyces cerevisiae) for expression. The hsp22.4 transgenic yeast displayed significantly greater resistance to heat and Na(2)CO(3) stresses than control (yeast cells transformed with empty pYES2), suggesting that the expression of hsp22.4 gene confers not only heat tolerance but also significant alkali (Na(2)CO(3)) stress tolerance.

Renal pathological change in patients with type 2 diabetes is not always diabetic nephropathy: a report of 52 cases

AIMS

The present study examined the relationship between clinical features and renal histological changes in the Type 2-diabetic patients and evaluated the usefulness of renal biopsy in the diagnosis of diabetic versus non-diabetic kidney disease.

METHODS

52 patients with Type 2-diabetic mellitus were retrospectively analyzed for differential clinical, laboratory features and pathological characteristics including overt proteinuria (> 0.5 g/day), elevated serum creatinine and/or the development of hematuria.

RESULTS

Of 52 patients, 20 cases (38.5%) showed no detectable diabetic lesions and, thus, were diagnosed as non-diabetic renal disease (NDRD), while 32 patients (61.5%) exhibited diabetic nephropathy. Interestingly, while 29 patients showed diabetic nephropathy (DN) alone, NDRD was also found in 3 patients with DN. Clinically, 24 out of 52 patients (46.16%) had a diagnosis consistent with the pathological findings, while 10 (19.23%) were diagnosed incorrectly. Compared to NDRD patients, patients with DN had prolonged diabetic history with or without retinopathy, while 25% of patients with NDRD exhibited mesangial proliferative glomerulonephritis.

CONCLUSIONS

NDRD was a common feature in Type 2-diabetic patients with renal involvement. The absence of retinopathy and short periods of diabetic history may be useful indicators for diagnosis of NDRD clinically.

Dihydropyrimidine dehydrogenase activity correlates with fluorouracil sensitivity in breast cancer

The fluoropyrimidine drug fluorouracil (FU) is one of the most frequently prescribed chemotherapeutic drugs for the curative and palliative treatment of various cancer patients. The identification of biological factors associated with tumors either responsiveness or resistance to FU chemotherapy, including FU, is increasingly being recognized as an important field of clinical cancer research.

AIM

to analyze the relationship between intra-tumoral dihydropyrimidine dehydrogenase (DPD) level and FU chemosensitivity, as DPD is the initial and rate-limiting enzyme in the catabolism of FU.

MATERIALS AND METHODS

The histoculture drug response assay (HDRA) was performed for 54 patients. DPD expression was examined in 81 tumor samples from breast cancer patients received two cycles of FU-based primary chemotherapy before operation.

RESULTS

We found that intra-tumoral DPD enzyme activity was inversely correlated with FU cytotoxicity. We also revealed that low DPD expression was correlated with clinical response to FU-based primary chemotherapy.

CONCLUSIONS

Our study indicated that DPD is a promising molecular maker for identifying tumor cells sensitivity in breast cancer patients receiving FU-based chemotherapy.

Kv1.1/1.2 channels are downstream effectors of nitric oxide on synaptic GABA release to preautonomic neurons in the paraventricular nucleus

The paraventricular nucleus (PVN) of the hypothalamus is important for the neural regulation of cardiovascular function. Nitric oxide (NO) increases synaptic GABA release to presympathetic PVN neurons through the cyclic guanosine monophosphate (cGMP)/protein kinase G signaling pathway. However, the downstream signaling mechanisms underlying the effect of NO on synaptic GABA release remain unclear. In this study, whole-cell voltage-clamp recordings were performed on retrograde-labeled spinally projecting PVN neurons in rat brain slices. Bath application of the NO precursor l-arginine or the NO donor S-nitroso-N-acetylpenicillamine (SNAP) significantly increased the frequency of GABAergic miniature inhibitory postsynaptic currents (mIPSCs) in labeled PVN neurons. A specific antagonist of cyclic ADP ribose, 8-bromo-cyclic ADP ribose (8-Br-cADPR), had no significant effect on l-arginine-induced potentiation of mIPSCs. Surprisingly, blocking of voltage-gated potassium channels (Kv) with 4-aminopyridine or alpha-dendrotoxin eliminated the effect of l-arginine on mIPSCs in all labeled PVN neurons tested. The membrane permeable cGMP analog mimicked the effect of l-arginine on mIPSCs, and this effect was blocked by alpha-dendrotoxin. Furthermore, the specific Kv channel blocker for Kv1.1 (dendrotoxin-K) or Kv1.2 (tityustoxin-Kalpha) abolished the effect of l-arginine on mIPSCs in all neurons tested. SNAP failed to inhibit the firing activity of labeled PVN neurons in the presence of dendrotoxin-K, Kalpha. Additionally, the immunoreactivity of Kv1.1 and Kv1.2 subunits was colocalized extensively with synaptophysin in the PVN. These findings suggest that NO increases GABAergic input to PVN presympathetic neurons through a downstream mechanism involving the Kv1.1 and Kv1.2 channels at the nerve terminals.

Automated ligand fishing using human serum albumin-coated magnetic beads

Human serum albumin, HSA, was immobilized onto the surface of silica-based magnetic beads. The beads were used to isolate known HSA ligands from a mixture containing ligands and nonligands. The separation was accomplished manually and was also automated. The results indicate that an automated "ligand-fishing" technique can be developed using magnetic beads containing an immobilized protein.

Enhancement of Mucosal Immune Responses in Chickens by Oral Administration of Cysteamine

Somatostatin, a tetradecapeptide originally isolated from the hypothalamus, can exert an inhibitory effect on the secretion of growth hormone by the anterior pituitary gland. In addition to endocrine organs, somatostatin is also present in the digestive tract and immune organs. In lymphoid tissues, somatostatin appears to play a role in the modulation of the immune response. Cysteamine (CS) is a sulfhydryl reducing agent that is known as a depletory agent of somatostatin. To evaluate its effects on chicken mucosal immune responses, CS was administrated orally to 1-wk-old broilers (40 mg/kg) that were immunized orally with Newcastle disease attenuated vaccine (NDV). The number of IgA-positive cells and intestinal intraepithelial lymphocytes (iIEL) in duodenum and jejunum were examined at 3-, 5-, and 7-wk posttreatment and immunization. The number of somatostatin-positive cells and relative amounts of somatostatin mRNA were also examined in the duodenum. The number of somatostatin-positive cells in the duodenum was reduced (P < 0.05) after CS treatment. In broilers receiving CS and NDV treatment (CS+NDV) the level of IgA-positive cells and iIEL in the duodenum and jejunum was increased (P < 0.05) at 3 and 5 wk posttreatment. The expression of somatostatin mRNA increased (P < 0.05) compared with that of the control group at 5 wk after immunization in broilers receiving CS+NDV or NDV alone. The results suggest that CS can induce proliferation and differentiation of IgA-positive cells and iIEL in the intestinal mucosa of chickens by reducing the number of somatostatin-positive cells.

BCCIP: A novel marker for radiotherapy benefit in patients with laryngeal cancer

6006

Background: It has been well established that the functionality of the p53 pathway is related to radiosensitivity in various human cancers. The status of proteins regulating p53 activity may also be valuable markers for radiosensitivity. Recent studies have shown that BCCIP (BRCA2 & CDKN1A interacting protein) is essential for maintaining the transactivation activity of wild type p53. We hypothesize that functional BCCIP may contribute to effective radiotherapy in the clinical setting. To test this hypothesis, we analyzed the expression of BCCIP and p53 in a cohort of laryngeal cancer treated with radiotherapy and assessed whether BCCIP and p53, alone or in combination, would correlate with local control and overall survival. Methods: One hundred thirty-five patients treated between 1975 and 2000 for early stage (stage I & II) squamous cell carcinoma of the larynx were included in the study. Treatment consisted of definitive radiation therapy (RT) with standard fields and fractionation to a median dose of 6,590 cGY. Tissue was collected from pre-RT biopsies and constructed in a tissue microarray, with duplicate cores created for each case. BCCIP and p53 expression was analyzed by immunohistochemistry and qualitatively scored with greater than 10% nuclear reactivity the cutoff for positive staining. Results: Expression of BCCIP and wild type p53 in combination was associated with significant improvements in 5-year local control (68.75% vs. 46.27%, p = .04) and 5-year overall survival (67.68% vs. 34.62%, p = .006) compared to patients who did not express BCCIP. Expression of BCCIP or p53 alone was not found to be independently associated with benefits in local control or overall survival. Conclusions: This study provides clinical evidence that BCCIP contributes to effective local control and overall survival in patients with laryngeal cancer treated with radiation. This benefit may be a result of increased radiosensitivity in patients who have functional BCCIP and p53. Using immunohistochemical methods, BCCIP and p53 co-expression can act as markers to identify sub-groups of laryngeal cancer patients who are more likely to be cured with radiotherapy.

No significant financial relationships to disclose.

Automated ligand fishing using human serum albumin-coated magnetic beads

Human serum albumin, HSA, was immobilized onto the surface of silica-based magnetic beads. The beads were used to isolate known HSA ligands from a mixture containing ligands and nonligands. The separation was accomplished manually and was also automated. The results indicate that an automated "ligand-fishing" technique can be developed using magnetic beads containing an immobilized protein.

Pregnancy-induced hypertension and infant mortality in triplets

OBJECTIVE

To assess the effects of pregnancy-induced hypertension on infant mortality in triplets stratified by gestational age at birth.

METHODS

A retrospective cohort study was conducted using the linked 1995-2000 US birth/infant death database. Generalized estimating equations were used to evaluate the observed association.

RESULTS

Pregnancy-induced hypertension was associated with lesser neonatal mortality (odds ration [OR]: 0.34, 95% CI: 0.21, 0.54), postneonatal mortality (OR: 0.54, 95% CI: 0.30, 0.99) and infant mortality (OR, 0.37, 95% CI: 0.25, 0.55) in triplets. It was also associated with a decreased risk of neonatal death (OR, 0.38; 95% CI, 0.21-0.67), postneonatal death (OR, 0.45; 95% CI, 0.21-0.97), and infant death (OR, 0.39; 95% CI, 0.24-0.64) in early preterm triplets, whereas the association was not significant in late preterm or in full-term triplets.

CONCLUSION

Pregnancy-induced hypertension is associated with a decreased risk of infant mortality in triplets. This effect varies with gestational age at birth.