The 3Ns chromosome of Psathyrostachys huashanica carries the gene(s) underlying wheat stripe rust resistance

Stripe rust (Puccinia striiformis tritici (Pst)) is one of the most destructive diseases of wheat in the world. Exploiting and utilizing stripe rust resistance genes of wild species has become an essential strategy for resistance breeding. Psathyrostachyshuashanica Keng ex Kuo is a wild species in Triticeae that has been used for wheat improvement because of its high resistance or immunity to stripe rust. In this study, 9 wheat-P. huashanica addition lines were characterized by Giemsa C-banding, genomic in situ hybridization (GISH), and disease resistance evaluation. Giemsa C-banding and GISH demonstrated that lines 163-5, 165-1, 183-5, 240-3, and 240-4 are P. huashanica 3Ns chromosome monosomic addition lines; lines 183-1 and 183-20 are P. huashanica 3Ns chromosome disomic addition lines; line 165-20 is a P. huashanica 3Ns and 4Ns chromosomes double disomic addition line, and line 219-1 is a P. huashanica 1Ns and 3Ns/5A chromosomes double disomic addition-substitution line. All these addition lines with P. huashanica 3Ns chromosome(s) expressed high resistance or immunity to stripe rust. By comparing the series of wheat-P. huashanica chromosome addition lines, we concluded that the P. huashanica 3Ns chromosome carries the gene(s) for resistance or immunity to stripe rust. These addition lines can be used as a donor source of novel stripe rust resistance to wheat breeding programs.

Mechanical Properties and Porosity of Organo-Silicate Glass (OSG) Low-k Dielectric Films

Low-k material integration issues that plague the microelectronics industry include the compromise in mechanical properties that one incurs in abandoning fully dense silica dieletrics. Typical elastic moduli of OSG low-k dieletric films are 2-10 GPa with corresponding hardnesses of 0.5 to 1.5 GPa. In the present study, the hardness and elastic modulus properties measured by nanoindentation of porous silica based low-k films are correlated with in initial estimates of density using a novel technique of spectroscopic ellispsometry. Transmission electron microscopy and X-ray photoelectron spectroscopy show the structural and chemical similarity of the films. Nanoindentation and spectroscopic ellipsometry results reflect significant deviations in material behavior from that expected from a simple model of silica (SiO2) with included voids or porosity, suggesting that the methyl groups are actively participating in the mechanical and optical properties of the material.

Relationship between serum hepatitis B virus DNA and surface antigen with covalently closed circular DNA in HBeAg-negative patients

Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) is responsible for viral persistence. This study aimed to investigate the serum surrogate markers for cccDNA and to evaluate the intrahepatic viral events associated with disease activity in HBeAg-negative chronic hepatitis B patients. Thirty-three treatment-naïve patients with a negative HBeAg who had a liver biopsy were studied. Active disease was defined as a serum alanine aminotransferase >40 IU/L and a serum HBV DNA >10,000 copies/ml. This study showed significant correlation between serum HBV DNA and both log cccDNA (r = 0.41, P = 0.018) and log total intrahepatic HBV DNA (r = 0.71, P < 0.0001). No significant correlation was observed between serum HBsAg and log cccDNA (P = 0.15) or log total intrahepatic HBV DNA (P = 0.97). Fourteen and 19 patients had inactive and active disease, respectively. The median log cccDNA and log total intrahepatic HBV DNA (copies/10(6) cells) were significantly higher in patients with active disease compared with those with inactive disease (4.11 vs. 3.53, P = 0.03 and 5.46 vs. 4.64, P < 0.001, respectively). The HBV replicative efficiency, defined as the ratio of serum HBV DNA to cccDNA, was approximately 20% higher in patients with active disease. No significant difference was observed in the HBsAg levels and the ratio of serum HBsAg to cccDNA between the two groups. In conclusion, serum HBV DNA, but not HBsAg, reflects the amount of cccDNA and the replication efficiency of HBV in patients with HBeAg-negative chronic hepatitis B.

Monoclonal antibody treatment to prolong the secondary cardiac allograft survival in alloantigen-primed mice

We have previously shown that costimulation blockade using a combination of monoclonal antibodies (mAbs) - CTLA4Ig, antibodies to CD154, LFA-1, and OX40L - can induce tolerance of cardiac allografts in mice with adoptively transferred CD4(+) memory T cells [1]. However, the effect of costimulatory blockade in secondary allograft rejection has not been studied. B6 mice that rejected BALB/c skin grafts for more than 4 weeks (defined as alloantigen-primed mice) were used as recipients. The recipient mice were treated with the mAbs to CD154, LFA-1, OX40L, and CD122 on days 0, 2, 4, and 6 after the secondary transplantation of BALB/c heart. The mean survival time (MST) of secondary cardiac allografts in rats treated with antibodies to CD154 and LFA-1 (2-antibodies approach) and those treated with antibodies to CD154, LFA-1, OX40L, and CD122 (4-antibodies approach) was greater than that of the controls (MST = 6.7 days, 22.2 days, and 3.2 days, respectively). The 4-antibodies approach prevented lymphocytic infiltration in the grafts, inhibited memory T-cells proliferation in the spleen, increased IL-10 secretion in the serum, and enhanced the expression of CD4(+) Foxp3(+) regulatory T cells (Tregs) in spleen. Expression levels of alloreactive antibodies were high in the recipient mice of experimental and control groups. Inhibiting the memory T cells by costimulation blockade extended allograft survival in secondary transplant models but could not induce tolerance of graft. Alloreactive antibodies may participate in alloresponse and play an important role in secondary cardiac allograft rejection.

Significant histopathology in Chinese chronic hepatitis B patients with persistently high-normal alanine aminotransferase

Current guidelines recommend antiviral therapy for chronic hepatitis B (CHB) patients with elevated alanine aminotransferase (ALT) and high viral load. Scant histological data exist for CHB patients with persistently normal ALT (PNALT) because disease progression is thought to be rare. To identify potential predictors of significant histology in the presence of PNALT, we compared the clinical characteristics and histology of Chinese CHB PNALT patients to those in patients with elevated ALT. Percutaneous liver biopsy was performed in 522 CHB patients with Chinese ethnicity who had not had antiviral treatment. Differences in age, ALT, viral load, hepatitis B e antigen (HBeAg) status and liver histology were compared between eligible PNALT (252) and elevated ALT (270) patients. Of the PNALT patients, 38.5% had normal liver histology, 25.4% had significant necroinflammation and/or fibrosis and 8.4% had established cirrhosis. Furthermore, histopathological differences between patients with high-normal ALT (0.5-1.0 x the upper limit of normal (ULN)) and low-normal ALT (≤ 0.5 x ULN) were evaluated. There was a significantly greater prevalence of histopathology in the high-normal group (40.0%) than in the low-normal group (16.6%) (P < 0.001). Multiple logistic regression identified that significant histopathology findings in PNALT patients correlated with age (P < 0.001) and ALT level (P < 0.001), with age >40 years and ALT >0.5 x ULN predicting significant histopathology. Our data indicate that liver biopsy is recommended in CHB patients >40 years of age, particularly when their ALT is 0.5-1.0 x ULN. The findings above provide evidence for indication of antiviral therapy in patients with PNALT and significant histopathological change.

Activity identification of chimeric anti-caspase-3 mRNA hammerhead ribozyme in vitro and in vivo

To study the expression activity of various vectors containing anti-caspase-3 ribozyme cassettes in vivo, and to further study the role of caspas-3 in the apoptotic pathway, we constructed anti-caspase-3 hammerhead ribozyme embedded into the human snRNA U6, and detected the activity of the ribozyme in vitro and in vivo. Meanwhile we compared it with the self-cleaving hammerhead ribozymes that we previously studied, and with the general ribozyme, cloned into RNA polymerase II expression systems. The results showed that the three ribozymes, p1.5RZ107, pRZ107 and pU6RZ107 had the correct structure, and that they could cleave caspase-3 mRNA exactly to produce two fragments: 143nt/553nt. p1.5RZ107 has the highest cleavage efficiency in vitro, almost 80%. However, the U6 chimeric ribozyme, pU6RZ107, has the highest cleavage activity in vivo, almost to 65%, though it has lower cleavage activity in vitro. The cleavage results demonstrated that the pU6RZ107, the U6 chimeric ribozyme, could more efficiently express and downregulate the level of caspase-3 in vivo, and the ribozyme could provide an alternative approach to the research into the mechanism of apoptosis and human gene therapy also.

Minimum stable structure of the receptor for advanced glycation end product possesses multi ligand binding ability

The receptor for advanced glycation end products (RAGE) is a multi-ligand receptor involved in the development of diabetic complications. Although the soluble form of the extracellular domain maintains the ability to bind multi-ligands, it is unstable and degrades into several peptide species during storage. Proteolysis with thrombin or factor Xa revealed several protease sensitive sites. Most sensitive site is located between Arg228 and Val229, and peptide bond next to Arg216, Arg116, Arg114 and Trp271 are also cleaved. Seven truncated extracellular domains of RAGE were engineered in order to obtain a stable soluble fragment. RAGE 143 (Ala23-Thr143) is not only protease resistant but also shows the same ligand-binding ability as that of the full-length extracellular domain. The resultant minimum RAGE 143 works as a stable recognition devise to detect advanced glycation end products (AGEs).

A Multi-Threshold Sampling Method for TOF PET Signal Processing

As an approach to realizing all-digital data acquisition for positron emission tomography (PET), we have previously proposed and studied a multi-threshold sampling method to generate samples of a PET event waveform with respect to a few user-defined amplitudes. In this sampling scheme, one can extract both the energy and timing information for an event. In this paper, we report our prototype implementation of this sampling method and the performance results obtained with this prototype. The prototype consists of two multi-threshold discriminator boards and a time-to-digital converter (TDC) board. Each of the multi-threshold discriminator boards takes one input and provides up to 8 threshold levels, which can be defined by users, for sampling the input signal. The TDC board employs the CERN HPTDC chip that determines the digitized times of the leading and falling edges of the discriminator output pulses. We connect our prototype electronics to the outputs of two Hamamatsu R9800 photomultiplier tubes (PMTs) that are individually coupled to a 6.25×6.25×25mm(3) LSO crystal. By analyzing waveform samples generated by using four thresholds, we obtain a coincidence timing resolution of about 340 ps and an ∼18% energy resolution at 511 keV. We are also able to estimate the decay-time constant from the resulting samples and obtain a mean value of 44ns with an ∼9 ns FWHM. In comparison, using digitized waveforms obtained at a 20 GSps sampling rate for the same LSO/PMT modules we obtain ∼300 ps coincidence timing resolution, ∼14% energy resolution at 511 keV, and ∼5 ns FWHM for the estimated decay-time constant. Details of the results on the timing and energy resolutions by using the multi-threshold method indicate that it is a promising approach for implementing digital PET data acquisition.

Anticaries effect of compounds extracted from Galla chinensis in a multispecies biofilm model

INTRODUCTION

Galla Chinensis is a leaf gall known to have some antibacterial effects. Using an in vitro biofilm model of dental plaque, the present study aimed to evaluate the anticaries effects of Galla Chinensis and its chemical fractions.

METHODS

A four-organism bacterial consortium (Streptococcus sanguis, Streptococcus mutans, Actinomyces naeslundii, Lactobacillus rhamnosus) was grown on hydroxyapatite (HA) discs, bovine enamel blocks, and glass surfaces in a continuous culture system and exposed to repeated solution pulses. Galla Chinensis extracts, sucrose solutions, and sodium fluoride solutions were pulsed into different flow cells. The pH value of the planktonic phase in each flow cell was recorded and the bacteria colonizing the biofilm on the HA discs were counted. Enamel blocks were observed using a polarized microscope and lesion depth was evaluated. The biofilm morphology was examined with a fluorescence microscope and the images captured were analyzed on an image analysis system.

RESULTS

When Galla Chinensis extract, its chemical fraction, or fluoride was added to the sucrose solution, the planktonic phase pH remained higher than that in the sucrose alone. A lower level of colonization on the HA surface was also observed in the groups to which Galla Chinensis and fluoride were added compared with the control sucrose group, and this was reflected in both the total viable count and the biofilm imaging, which showed fewer cariogenic bacteria and a less compact biofilm, respectively. Enamel demineralization in both the fluoride group and the Galla Chinensis group was significantly less than that in the sucrose group.

CONCLUSIONS

Galla Chinensis and fluoride may inhibit the cariogenicity of the oral biofilm. Galla Chinensis appears to be a promising source of new agents that may prevent dental caries.

Experimental demonstration of isotropic negative permeability in a three-dimensional dielectric composite

Isotropic negative permeability resulting from Mie resonance is demonstrated in a three-dimensional (3D) dielectric composite consisting of an array of dielectric cubes. A strong subwavelength magnetic resonance, corresponding to the first Mie resonance, was excited in dielectric cubes by electromagnetic wave. Negative permeability is verified in the magnetic resonance area via microwave measurement and the dispersion properties. The resonance relies on the size and permittivity of the cubes. It is promising for construction of novel isotropic 3D left-handed materials with a simple structure.

Leptin plays a role in ruptured human brain arteriovenous malformations

INTRODUCTION

Intracerebral hemorrhage (ICH) is one of the most common clinical manifestations of human brain arteriovenous malformation (BAVM). However, the hemorrhagic mechanism of BAVM is still unclear. Leptin, first discovered in obesity research, has not been systematically studied in BAVM and ICH. We investigated expression and effect of leptin on human BAVM.

METHODS

Specimens were obtained from 6 BAVM patients, who had been divided into either hemorrhagic or non-hemorrhagic groups. Leptin, leptin receptor, and signal transducers and activators of transcription-3 (STAT3) were analyzed by different methods, such as gene chips, reverse transcription-polymerase chain reaction (RT-PCR), immunohistochemistry, and Western blot. Perinidal brain tissue around each BAVM served as control.

RESULTS

Gene chips and RT-PCR found transcriptional leptin raised at least 2 levels in hemorrhagic BAVM. Immunohistochemical slices also showed higher expression of leptin, leptin receptor, and STAT3 on nidus part of hemorrhagic BAVM than non-hemorrhagic ones. On Western blot analysis, hemorrhagic BAVMs had higher levels of leptin (p < 0.01).

CONCLUSIONS

The transcriptional and translational levels of leptin, leptin receptor, and STAT3 were higher in hemorrhagic BAVM, suggesting that leptin may play an important role in the hemorrhagic mechanism of BAVM.

Glycogen phosphorylase inhibitors: a free energy perturbation analysis of glucopyranose spirohydantoin analogues

GP catalyzes the phosphorylation of glycogen to Glc-1-P. Because of its fundamental role in the metabolism of glycogen, GP has been the target for a systematic structure-assisted design of inhibitory compounds, which could be of value in the therapeutic treatment of type 2 diabetes mellitus. The most potent catalytic-site inhibitor of GP identified to date is spirohydantoin of glucopyranose (hydan). In this work, we employ MD free energy simulations to calculate the relative binding affinities for GP of hydan and two spirohydantoin analogues, methyl-hydan and n-hydan, in which a hydrogen atom is replaced by a methyl- or amino group, respectively. The results are compared with the experimental relative affinities of these ligands, estimated by kinetic measurements of the ligand inhibition constants. The calculated binding affinity for methyl-hydan (relative to hydan) is 3.75 +/- 1.4 kcal/mol, in excellent agreement with the experimental value (3.6 +/- 0.2 kcal/mol). For n-hydan, the calculated value is 1.0 +/- 1.1 kcal/mol, somewhat smaller than the experimental result (2.3 +/- 0.1 kcal/mol). A free energy decomposition analysis shows that hydan makes optimum interactions with protein residues and specific water molecules in the catalytic site. In the other two ligands, structural perturbations of the active site by the additional methyl- or amino group reduce the corresponding binding affinities. The computed binding free energies are sensitive to the preference of a specific water molecule for two well-defined positions in the catalytic site. The behavior of this water is analyzed in detail, and the free energy profile for the translocation of the water between the two positions is evaluated. The results provide insights into the role of water molecules in modulating ligand binding affinities. A comparison of the interactions between a set of ligands and their surrounding groups in X-ray structures is often used in the interpretation of binding free energy differences and in guiding the design of new ligands. For the systems in this work, such an approach fails to estimate the order of relative binding strengths, in contrast to the rigorous free energy treatment.

An in silico ensemble method for lead discovery: decision forest

Recent progress in combinatorial chemistry and parallel synthesis has radically changed the approach to drug discovery in the pharmaceutical industry. At present, thousands of compounds can be made in a short period, creating a need for fast and effective in silico methods to select the most promising lead candidates. Decision forest is a novel pattern recognition method, which combines the results of multiple distinct but comparable decision tree models to reach a consensus prediction. In this article, a decision forest model was developed using a structurally diverse training data set containing 232 compounds whose estrogen receptor binding activity was tested at the U.S. Food and Drug Administration (FDA)'s National Center for Toxicological Research (NCTR). The model was subsequently validated using a test data set of 463 compounds selected from the literature, and then applied to a large data set with 57,145 compounds as a screening example. The results show that the decision forest method is a fast, reliable and effective in silico approach, which could be useful in drug discovery.

Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling

Background

The completion of the sequencing of human, mouse and rat genomes and knowledge of cross-species gene homologies enables studies of differential gene expression in animal models. These types of studies have the potential to greatly enhance our understanding of diseases such as liver cancer in humans. Genes co-expressed across multiple species are most likely to have conserved functions. We have used various bioinformatics approaches to examine microarray expression profiles from liver neoplasms that arise in albumin-SV40 transgenic rats to elucidate genes, chromosome aberrations and pathways that might be associated with human liver cancer.

Results

In this study, we first identified 2223 differentially expressed genes by comparing gene expression profiles for two control, two adenoma and two carcinoma samples using an F-test. These genes were subsequently mapped to the rat chromosomes using a novel visualization tool, the Chromosome Plot. Using the same plot, we further mapped the significant genes to orthologous chromosomal locations in human and mouse. Many genes expressed in rat 1q that are amplified in rat liver cancer map to the human chromosomes 10, 11 and 19 and to the mouse chromosomes 7, 17 and 19, which have been implicated in studies of human and mouse liver cancer. Using Comparative Genomics Microarray Analysis (CGMA), we identified regions of potential aberrations in human. Lastly, a pathway analysis was conducted to predict altered human pathways based on statistical analysis and extrapolation from the rat data. All of the identified pathways have been known to be important in the etiology of human liver cancer, including cell cycle control, cell growth and differentiation, apoptosis, transcriptional regulation, and protein metabolism.

Conclusion

The study demonstrates that the hepatic gene expression profiles from the albumin-SV40 transgenic rat model revealed genes, pathways and chromosome alterations consistent with experimental and clinical research in human liver cancer. The bioinformatics tools presented in this paper are essential for cross species extrapolation and mapping of microarray data, its analysis and interpretation.

Bladder transitional cell carcinoma: correlation of contrast enhancement on computed tomography with histological grade and tumour angiogenesis

AIM

To investigate the correlation between the degree of contrast enhancement of bladder cancer in the early enhanced phase of helical computed tomography (CT) and microvessel density (MVD), vascular endothelial growth factor (VEGF) and histological grade.

MATERIALS AND METHODS

Sixty-five patients with transitional cell carcinoma of the bladder were examined by incremental unenhanced CT and helical CT at 40-45 s after initiation of intravenous administration of contrast medium before surgery. The CT density in Hounsfield units of bladder carcinomas were measured in the middle of the maximum diameter section of the cancer lesions on unenhanced and enhanced CT. The degree of contrast enhancement of the tumour was determined as the absolute increase in Hounsfield units. Histological grade, VEGF and MVD were analysed for each cancer. The Pearson and Spearman correlation tests were used to determine the strength of the relationships between CT enhancement and histological grade, VEGF expression and MVD.

RESULTS

Different degrees of enhancement were observed in 91 cancers during the early enhanced phase of helical CT. Mean MVDs and mean CT enhancing values of different histological grade groups were statistically different (p < 0.001). A positive correlation was found in the CT-enhancing value of bladder cancer and MVD (Pearson correlation test; r = 0.938, p < 0.001) and histological grade (Spearman rank correlation; r = 0.734, p < 0.001). VEGF of bladder cancer did not correlate with the change in CT attenuation (Spearman rank correlation; r = 0.087, p = 0.410) and MVD (Spearman rank correlation, r = 0.103, p = 0.330).

CONCLUSION

In bladder cancer, the degree of contrast enhancement during the early enhanced helical CT is correlated with the MVD and histological grade of tumour. It is possible that MVD is the histopathological basis of early contrast enhancement of bladder cancer.