Trends and Developments in Bioinformatics in 2010: Prospects and Perspectives

To survey major developments and trends in the field of Bioinformatics in 2010 and their relationships to those of previous years, with emphasis on long-term trends, on best practices, on quality of the science of informatics, and on quality of science as a function of informatics.

A critical review of articles in the literature of Bioinformatics over the past year.

Our main results suggest that Bioinformatics continues to be a major catalyst for progress in Biology and Translational Medicine, as a consequence of new assaying technologies, most predominantly Next Generation Sequencing, which are changing the landscape of modern biological and medical research. These assays critically depend on bioinformatics and have led to quick growth of corresponding informatics methods development. Clinical-grade molecular signatures are proliferating at a rapid rate. However, a highly publicized incident at a prominent university showed that deficiencies in informatics methods can lead to catastrophic consequences for important scientific projects. Developing evidence-driven protocols and best practices is greatly needed given how serious are the implications for the quality of translational and basic science.

Several exciting new methods have appeared over the past 18 months, that open new roads for progress in bioinformatics methods and their impact in biomedicine. At the same time, the range of open problems of great significance is extensive, ensuring the vitality of the field for many years to come.

Identification of 18 genes encoding necrosis-inducing proteins from the plant pathogen Phytophthora capsici (Pythiaceae: Oomycetes)

Phytophthora capsici is an aggressive plant pathogen that affects solanaceous and cucurbitaceous hosts. Necrosis-inducing Phytophthora proteins (NPPs) are a group of secreted toxins found particularly in oomycetes. Several NPPs from Phytophthora species trigger plant cell death and activate host defense gene expression. We isolated 18 P. capsici NPP genes, of which 12 were active during hypha growth from a Phytophthora stain isolated from pepper (Capsicum annuum) plants in China. The 18 predicted proteins had a sequence homology of 46.26%. The 18 Pcnpp sequences had a conserved GHRHDWE motif and fell into two groups. Eleven sequences in group 1 had two conserved cysteine residues, whereas the other seven sequences in group 2 lacked these two cysteine residues. A phylogenetic tree was constructed on the basis of the alignment of the predicted protein sequences of 52 selected NPP genes from oomycetes, fungi and bacteria from Genbank. The tree did not rigorously follow the taxonomic classification of the species; all the NPPs from oomycetes formed their own clusters, while fungal sequences were grouped into two separate clades, indicating that based on NPPs, we can separate oomycetes from fungi and bacteria, and that expansion of the NPP family was a feature of Phytophthora evolution.

Epigenetic control of expression of the human L- and M- pigment genes

Epigenetics alters gene expression by chromatin modification without changing the sequence of DNA. DNA methylation is an essential signal for epigenetic gene regulation. Methylation of cytosine bases at CpG dinucleotides in DNA results in chromatin condensation resulting in suppression of gene expression. DNA methylation has been shown to play important roles in cell differentiation, genomic imprinting and X-chromosome inactivation. We compared the CpG methylation patterns of the promoters of the L-opsin gene (OPN1LW) and the M-opsin gene (OPN1MW), plus a DNase I hypersensitive (DHS) site located about 8 kb (kilobases) upstream of the OPN1LW gene. Comparisons were made using the human retinoblastoma cell line WERI, which expresses the L and M opsin genes when treated with thyroid hormone (T3), and a lymphoblastoid cell line GM06990 that does not express these genes. The results showed that the great majority of the 14 CpGs located within the proximal 200 bp (base pairs) of each promoter, plus 20 bp of the 5'-untranslated region, were hypo-methylated in WERI-Rb-1 cells, whether or not treated with T3, but almost totally methylated in the lymphoblastoid cell line. Three of the CpGs that are located beyond 200 bp from the transcription start site of OPN1LW were hyper-methylated in both WERI and lymphoblastoid cells. Significant differential methylation was also observed within the DHS region (24 CpGs). This DHS region contains a highly conserved motif that binds CCCTC-binding factor (CTCF), referred to as a 'chromatin insulator or boundary element', that has been shown to regulate gene expression at several genome locations. The results suggest that DNA methylation is likely to contribute to regulation of expression of the L- and M-opsin genes during differentiation, as well as to the retinal L:M cone ratio. In addition, thyroid hormone induction of the opsin genes does not appear to alter DNA methylation.

197 MOLECULAR CLONING AND EXPRESSION OF THE CASHMERE GOAT IZUMO GENE

During the fertilization process, complex events are involved in the fusion between the reacted spermatozoa and the mature oocyte. Fusion implies that many proteins are present on the cell membrane of the gametes. Recently, a new protein, Izumo, has been shown to play a role in the sperm–egg fusion. Izumo was identified through the generation of a monoclonal antibody that inhibits this fusion. This protein belongs to the immunoglobulin superfamily type I transmembrane protein. Izumo can be detected only after acrosome reaction at the spermatozoal surface. The cashmere goat Izumo gene was identified and cloned by 3′ and 5′ rapid amplification of cDNA ends-PCR. The expression of cashmere goat Izumo was examined by RT-PCR and Northern blotting. The full-length cDNA of cashmere goat Izumo contains 1536 bp and an open reading frame of 1035 bp, encoding a polypeptide of 344 amino acids with a calculated molecular mass of 38.76 kDa and a theoretical isoelectric point of 8.18. This predicted amino acid sequence showed 89.82% amino acid identity with the bovine Izumo. The deduced amino acid sequence contained 3 conserved domains of the signal peptide, immunoglobulin-like domain, and transmembrane region. Reverse transcription-PCR and Northern blotting analysis showed that cashmere goat Izumo transcripts were highly expressed in the testis, caput, corpus, cauda epididymis. Cashmere goat Izumo may play a role in the biological process of fertilization. This work was supported by the National Natural Science Foundation (No. 30560103 and No.30740043), China, and the China Postdoctoral Science Foundation.

Trends and developments in bioinformatics in 2010: prospects and perspectives

OBJECTIVES

To survey major developments and trends in the field of Bioinformatics in 2010 and their relationships to those of previous years, with emphasis on long-term trends, on best practices, on quality of the science of informatics, and on quality of science as a function of informatics.

METHODS

A critical review of articles in the literature of Bioinformatics over the past year.

RESULTS

Our main results suggest that Bioinformatics continues to be a major catalyst for progress in Biology and Translational Medicine, as a consequence of new assaying technologies, most pre-dominantly Next Generation Sequencing, which are changing the landscape of modern biological and medical research. These assays critically depend on bioinformatics and have led to quick growth of corresponding informatics methods development. Clinical-grade molecular signatures are proliferating at a rapid rate. However, a highly publicized incident at a prominent university showed that deficiencies in informatics methods can lead to catastrophic consequences for important scientific projects. Developing evidence-driven protocols and best practices is greatly needed given how serious are the implications for the quality of translational and basic science.

CONCLUSIONS

Several exciting new methods have appeared over the past 18 months, that open new roads for progress in bioinformatics methods and their impact in biomedicine. At the same time, the range of open problems of great significance is extensive, ensuring the vitality of the field for many years to come.

Single-Dirac-cone topological surface states in the TlBiSe(2) class of topological semiconductors

We investigate several strong spin-orbit coupling ternary chalcogenides related to the (Pb,Sn)Te series of compounds. Our first-principles calculations predict the low-temperature rhombohedral ordered phase in TlBiTe₂, TlBiSe₂, and TlSbX₂ (X=Te, Se, S) to be topologically nontrivial. We identify the specific surface termination that realizes the single Dirac cone through first-principles surface state computations. This termination minimizes effects of dangling bonds, making it favorable for photoemission experiments. In addition, our analysis predicts that thin films of these materials could harbor novel 2D quantum spin Hall states, and support odd-parity topological superconductivity.

Effect of lithium on smooth muscle contraction and phosphorylation of myosin light chain by MLCK

The aims of our study were to investigate into the effect of lithium on smooth muscle contraction and phosphorylation of myosin light chain (MLC20) by MLCK and to find out the clue of its mechanism. Isolated rabbit duodenum smooth muscle strips were used to study the effects of lithium on their contractile activity under the condition of Krebs' solution by means of HW-400S constant temperature smooth muscle trough. Myosin and MLCK were purified from the chicken gizzard smooth muscle. Myosin phosphorylation was determined by Glycerol-PAGE, myosin Mg2+ -ATPase activity was measured by Pi liberation method. Lithium (10-40 mM) inhibited the contraction in duodenum in a dose-related and time-dependent manner. Lithium could also inhibit the extent of myosin phosphorylation in a dose-related and time-dependent manner, whereas it inhibited Mg2+ -ATPase activity in a dose-related manner. Lithium inhibited smooth muscle contraction by inhibition of myosin phosphorylation and Mg2+ -ATPase activity.

Evaluation of POSSUM in predicting post-operative morbidity in patients undergoing pancreaticoduodenectomy

The Physiological and Operative Severity Score for the enUmeration of Mortality and Morbidity (POSSUM) is a predictive scoring system for post-operative morbidity. The present study assessed the value of POSSUM in predicting post-operative morbidity following pancreaticoduodenectomy (PD). POSSUM scores were prospectively calculated for 265 consecutive cases of PD performed between 2005 and 2007. Expected morbidity was estimated based on POSSUM scores and was compared with observed morbidity. Patients were also stratified into one of four groups based on their individual POSSUM scores and subsequent risk of morbidity. Mean expected morbidity was 43.81% (116 cases) and mean observed morbidity was 39.62% (105 cases) (no statistically significant difference). It is concluded that the POSSUM scoring system has high value for predicting the risk of morbidity in PD patients.

Microbial community variation and functions to excess sludge reduction in a novel gravel contact oxidation reactor

Excess biomass produced within the degradation processes of organic pollutants is creating environmental challenges. The gravel contact oxidation reactor (GCOR) filled with crushed stone globular aggregates as carriers, has been demonstrated capable of reducing the excess sludge effectively in some pilot and small-scale engineering studies. In order to evaluate the variation and structure of the microbial community and their functions to excess sludge reduction in GCOR, a conventional activated sludge reactor (ASR) was studied as a comparison. The 16S rDNA library of the universal bacteria was constructed, Shannon's diversity index (H) and Species evenness (E) were calculated with distance-based operational taxonomic unit and richness (DOTUR) for microbial diversity. Real-time quantity PCR and optical microscope were used for absolute bacterial DNA concentration and eukarya identification, respectively. Meanwhile, the suspended solid index in GCOR and ASR was detected for assessing the excess sludge production. The results indicated that the most abundant bacteria in GCOR were those related to the beta-Proteobacteria group, then gamma-Proteobacteria and to Cytophaga-Flexibacter-Bacteriode (CFB). In the ASR samples major bacteria were in the closest match with gamma-Proteobacteria, then beta-Proteobacteria and CFB. Shannon's index (H) was higher (3.41) for diversity of bacteria extracted from the carrier samples in GCOR than that (2.71) from the sludge sample in ASR. Species evenness (E) for the isolates from GCOR and ASR samples was 0.97 and 0.96, respectively. Comparison of the universal bacteria population in GCOR and ASR shows that the total bacterial DNA concentration on the GCOR carriers were 8.98 x 10(5) microg/ microl, twice that in ASR of 4.67 x 10(5) microg/ microl under normal operation of two reactors. But the MLSS in GCOR was only 4.5mg/L, 25 times less than that in ASR of 115.4 mg/L. The most representative eukarya were protozoa both in GCOR (15 no. per 20 ml) and in ASR (15 no. per 20 ml); the next abundant group was attachment plants 10 no. per 20 ml in GCOR and 4 no. per 20 ml in ASR, respectively. Rotifers and copepoda belonging to metazoan were only present in GCOR (8 no. per 20 ml for both rotifers and copepoda). The microbial diversity and population difference both in the GCOR carriers and ASR sludge indicated that the diverse microbes, a large amount of biomass forming longer microbial food chains attached on the carriers may be the main functions for the excess sludge reduction in GCOR.

From surgeon-apothecary to statesman: Sun Yat-sen at the Hong Kong College of Medicine

Despite being of peasant stock from a small village on the southern coast of China, Sun Yat-sen (1866-1925), the founder and first provisional president of the Republic of China, was exposed to Western education early in life. Educated first in Hawaii and then in the British Crown Colony of Hong Kong, he was influenced by Christianity, democracy and liberalism. It was the years of his tertiary education at the Hong Kong College of Medicine that moulded his ultimate destiny as the healer of a nation. This article examines the importance of this medical college and its two stalwarts, Sir Patrick Manson and Sir James Cantlie, in the transformation that shaped China's modern history.

Phospholipase C delta 1 is a novel 3p22.3 tumor suppressor involved in cytoskeleton organization, with its epigenetic silencing correlated with high-stage gastric cancer

Located at the important tumor suppressor locus, 3p22, PLCD1 encodes an enzyme that mediates regulatory signaling of energy metabolism, calcium homeostasis and intracellular movements. We identified PLCD1 as a downregulated gene in aerodigestive carcinomas through expression profiling and epigenetic characterization. We found that PLCD1 was expressed in all normal adult tissues but low or silenced in 84% (16/19) gastric cancer cell lines, well correlated with its CpG island (CGI) methylation status. Methylation was further detected in 62% (61/98) gastric primary tumors, but none of normal gastric mucosa tissues. PLCD1 methylation was significantly correlated with tumor high stage. Detailed methylation analysis of 37 CpG sites at the PLCD1 CGI by bisulfite genomic sequencing confirmed its methylation. PLCD1 silencing could be reversed by pharmacological demethylation with 5-aza-2'-deoxycytidine, indicating a direct epigenetic silencing. Ectopic expression of PLCD1 in silenced gastric tumor cells dramatically inhibited their clonogenicity and migration, possibly through downregulating MMP7 expression and hampering the reorganization of cytoskeleton through cofilin inactivation by phosphorylation. Thus, epigenetic inactivation of PLCD1 is common and tumor-specific in gastric cancer, and PLCD1 acts as a functional tumor suppressor involved in gastric carcinogenesis.

Mismatch repair gene mutations in Chinese HNPCC patients

To explore the characteristics of DNA mismatch repair gene mutations in Chinese patients with hereditary non-polyposis colorectal cancer (HNPCC) or Lynch syndrome, the MLH1 and MSH2 genes from probands of 76 HNPCC families were sequenced. By doing so, two frame-shift mutations, three splice-site mutations and fourteen missense mutations (thirteen missense mutations and one nonsense mutation) were identified in the MLH1 gene. In addition, one splice-site mutation and six missense mutations were detected in the MSH2 gene. None of these mutations were detected in 100 matched healthy controls. The remaining mutation-negative cases were subjected to large fragment deletion analysis using multiplex ligation-dependent probe amplification (MLPA). By doing so, five large fragment deletions were detected in the MSH2 gene. No large fragment deletions were detected in the MLH1 gene. We conclude that the MLH1 and MSH2 genes in Chinese HNPCC families exhibit broad mutation spectra.

Overexpression of TNF-alpha and TNFRII in invasive micropapillary carcinoma of the breast: clinicopathological correlations

AIMS

Angiogenesis is essential for tumour growth and metastasis and tumour necrosis factor (TNF)-alpha is a potent angiogenic factor. Invasive micropapillary carcinoma of the breast (IMPC), a rare subtype of breast cancer, possesses a lymphotropic nature with a high incidence of lymph node metastasis and poor prognosis. The aim was to evaluate the role of TNF-alpha and its receptor TNFRII in the vascular development and metastasis of IMPC.

METHODS AND RESULTS

One hundred cases of IMPC and 97 cases of invasive ductal carcinoma, not otherwise specified (IDC) were studied in parallel by immunohistochemistry for TNF-alpha and TNFRII, and microvessel density (MVD) of the tumours was measured. The results showed that the expression of TNF-alpha and TNFRII and the MVD were higher in IMPC than in IDC (P < 0.05). In IMPC, MVD was significantly increased in those with lymph node metastasis compared with those without nodal metastasis (P = 0.001). TNF-alpha expression showed a significant positive correlation with the rate of proliferation, histological grade, lymph node metastasis and MVD (P < 0.05), whereas expression of TNFRII was correlated with TNF-alpha expression and the proliferation of tumour cells in IMPC (P < 0.05).

CONCLUSIONS

Expression of TNF-alpha and TNFRII might play an important role in the angiogenesis, tumour cell proliferation and metastasis of IMPC. These markers could represent new targets for therapeutic intervention, i.e. blocking of TNF-alpha and its signal transduction could be a promising tool for treatment.

Learning in certainty-factor-based multilayer neural networks for classification

The computational framework of rule-based neural networks inherits from the neural network and the inference engine of an expert system. In one approach, the network activation function is based on the certainty factor (CF) model of MYCIN-like systems. In this paper, it is shown theoretically that the neural network using the CF-based activation function requires relatively small sample sizes for correct generalization. This result is also confirmed by empirical studies in several independent domains.

410. Gene expression analysis in endometriotic lesions using laser capture microdissection

Previous studies examining gene expression profiles in normal endometrium and endometriotic lesions have used RNA extracted from whole tissue samples. Results from these studies can be difficult to interpret as they reflect expression averaged across several different cell types that may be functionally quite different. The aim of this study was to establish laser capture microdissection (LCM) as a technique to examine gene expression in stromal and epithelial cells from normal and ectopic endometrium. We hypothesised that genes associated with inflammation would be elevated in cells from endometriotic lesions. Full thickness uterine samples were collected during abdominal hysterectomy from normal cycling premenopausal women. Endometriotic lesions were collected during abdominal laparoscopy. Samples were either frozen in OCT or stored in RNAlater for 12 h before freezing. Tissues were immunostained with an antibody against CD10 to identify ectopic endometrial stromal cells before LCM. Endometrial epithelial and stromal cells were collected using the PALM MicroLaser System. RNA quality was accessed using Experion. TGFβ1, MMP1, αSMA, SMAD2 and NFκB mRNA was analysed using real-time RT–PCR. Of the endometriotic samples stored in OCT (n = 58), only 14% (n = 8) had visible endometrial glands. Of these, only 37% (n = 3) had RNA of an acceptable quality for further analysis. However, RNA quality and quantity were dramatically improved in 3 of 5 samples collected in RNAlater. In preliminary studies, expression of TGFβ1 and αSMA mRNA was elevated in endometriotic lesions in comparison to the normal endometrium, whereas NFκB expression did not change. We have shown that RNAlater solution is useful to preserve RNA quality for small clinical endometriotic samples and that immuno-guided LCM-generated homogenous cell populations coupled with real-time RT–PCR can provide valuable insights into cell and disease-specific gene expression in endometriotic lesions.

Multiple Wavelength InGaAs Quantum Dot Lasers Using Ion Implantation Induced Intermixing

We demonstrate multiple wavelength InGaAs quantum dot lasers using ion implantation induced intermixing. Proton implantation, followed by annealing is used to create differential interdiffusion in the active region of the devices. The characteristics (lasing-spectra, threshold currents and slope efficiencies) of the multi-wavelength devices are compared to those of as-grown devices and the differences are explained in terms of altered energy level spacing in the annealed quantum dots.

Fibre-optic nonlinear optical microscopy and endoscopy

Nonlinear optical microscopy has been an indispensable laboratory tool of high-resolution imaging in thick tissue and live animals. Rapid developments of fibre-optic components in terms of growing functionality and decreasing size provide enormous opportunities for innovations in nonlinear optical microscopy. Fibre-based nonlinear optical endoscopy is the sole instrumentation to permit the cellular imaging within hollow tissue tracts or solid organs that are inaccessible to a conventional optical microscope. This article reviews the current development of fibre-optic nonlinear optical microscopy and endoscopy, which includes crucial technologies for miniaturized nonlinear optical microscopy and their embodiments of endoscopic systems. A particular attention is given to several classes of photonic crystal fibres that have been applied to nonlinear optical microscopy due to their unique properties for ultrashort pulse delivery and signal collection. Furthermore, fibre-optic nonlinear optical imaging systems can be classified into portable microscopes suitable for imaging behaving animals, rigid endoscopes that allow for deep tissue imaging with minimally invasive manners, and flexible endoscopes enabling imaging of internal organs. Fibre-optic nonlinear optical endoscopy is coming of age and a paradigm shift leading to optical microscope tools for early cancer detection and minimally invasive surgery.

An ion-implanted InP receiver for polarization resolved terahertz spectroscopy

We report on the construction, optical alignment and performance of a receiver which is capable of recording the full polarization state of coherent terahertz radiation. The photoconductive detector was fabricated on InP which had been implanted with Fe(+) ions. The device operated successfully when it was gated with near infrared femtosecond pulses from either a Ti:sapphire laser oscillator or a 1 kHz regenerative laser amplifier. When illuminated with terahertz radiation from a typical photoconductive source, the optimized device had a signal to noise figure of 100:1 with a usable spectral bandwidth of up to 4 THz. The device was shown to be very sensitive to terahertz polarization, being able to resolve changes in polarization of 0.34 degrees. Additionally, we have demonstrated the usefulness of this device for (i) polarization sensitive terahertz spectroscopy, by measuring the birefringence of quartz and (ii) terahertz emission experiments, by measuring the polarization dependence of radiation generated by optical rectification in (110)-ZnTe.

A robot-assisted orthopedic telesurgery system

A robot-assisted orthopedic telesurgery system, named HIT-RAOTS, has been developed according to Chinese conventional operation method. Its main function includes obtaining images with information of position and orientation of fracture, providing fracture information for doctors, assisting the doctors to complete the reposition of fracture and locking operation of intramedullary nail. In this system, a 6-dof force-reflecting master device, with a pantographic parallelogram mechanisms driven by harmonic DC servomotors, is used to control the slave manipulator movement and to translate the force from the operating room to the surgeon console; A slave robot system integrated a 6-dof force sensor, with a parallel manipulator actuated by six AC servomotors, is applied for the accurate repositioning; A virtual simulation system and human-machine interface are also developed. PI controller based on local network is used to realize the teleoperation. Only little irradiation is issued during the reposition. It can assist surgeons to perform bone-setting more safely by reducing irradiation damage to both surgeries and patients, more easily by releasing the surgeons from the heavy operation and more perfect by improving accuracy of reposition.

Silica encapsulation and magnetic properties of FePt nanoparticles

Core-shell nanoparticles have emerged as an important class of functional nanostructures with potential applications in many diverse fields, especially in health sciences. We have used a modified aqueous sol-gel route for the synthesis of size-selective FePt@SiO2 core-shell nanoparticles. In this approach, oleic acid and olyel amine stabilized FePt nanoparticles are first encapsulated through an aminopropoxysilane (APS) monolayer and then subsequent condensation of triethoxysilane (TEOS) on FePt particle surface. These well-defined FePt@SiO2 core-shell nanoparticles with narrow size distribution become colloidal in aqueous media, and can thus be used as carrier fluid for biomolecular complexes. In comparison, the scarce hydrophilic nature of oleic acid monolayers on FePt particle surface yields an edgy partial coating of silica when only TEOS is applied for the surface modification. The synthesized core-shell nanoparticles were characterized by direct techniques of high resolution transmission electron microscopy (HRTEM), EDS and indirectly via UV-vis absorption and FTIR studies. The FePt@SiO2 nanoparticles exhibit essential characteristics of superparamagnetic behavior, as investigated by SQUID magnetometry. The blocking temperatures (T(B)) of FePt and FePt@SiO2 (135 and 80 K) were studied using zero field cooled (ZFC)/field cooled (FC) curves.

Effects of exercise on adiponectin and adiponectin receptor levels in rats

Adiponectin reportedly reduces insulin-resistance. Exercise has also been shown to lessen insulin-resistance, though it is not known whether exercise increases levels of adiponectin and/or its receptors or whether its effects are dependent on exercise intensity and/or frequency. Catecholamine levels have been shown to increase during exercise and to fluctuate based on exercise intensity and duration. In light of this information, we examined the effects of exercise on catecholamine, adiponectin, and adiponectin receptor levels in rats. Our data showed that blood adiponectin levels increased by 150% in animals that exercised at a rate of 30 m/min for 60 min 2 days per week, but not 5 days, per week; no such increase was observed in rats that exercised at a rate of 25 m/min for 30 min. The effects of exercise on adiponectin receptor mRNA were variable, with adiponectin receptor 1 (AdipoR1) levels in muscle increasing up to 4 times while adiponectin receptor 2 (AdipoR2) levels in liver fell to below half in response to exercise at a rate of 25 m/min for 30 min 5 days per week. We also observed that urinary epinephrine levels and plasma lipids were elevated by exercise at a rate of 25 m/min for 30 min 2 days per week. Exercise frequency at a rate of 25 m/min for 30 min correlated with AdipoR1 and AdipoR2 mRNA expression in the muscle and liver, respectively (r=0.640, p<0.05 and r=-0.808, p<0.0005, respectively). Urinary epinephrine levels correlated with AdipoR2 mRNA expression in liver tissues (r=-0.664, p<0.05) in rats that exercised at a rate of 25 m/min for 30 min. Thus, exercise may regulate adiponectin receptor mRNA expression in tissues, which might cause increases in glucose uptake and fatty acid oxidation in the muscle. The effect of exercise on adiponectin levels depends on the specific conditions of the exercise.

Correlation of four vascular specific growth factors with carcinogenesis and portal vein tumor thrombus formation in human hepatocellular carcinoma

The aim of the present study was to detect the correlation between the expression of vascular endothelial growth factor (VEGF), angiopoietin 2 (Ang2), ephrinB2 and endocrine gland-derived vascular endothelial growth factor (EG-VEGF) and carcinogenesis or portal vein tumor thrombus (PVTT) formation in human hepatocellular carcinoma (HCC). The expression of VEGF, Ang2, ephrinB2 and EG-VEGF was detected by RT-PCR in 54 cases HCC without PVTT (group A), 9 cases HCC with PVTT (group B), 10 normal liver tissues (group D) and 10 cirrhosis tissues (group C). The samples were also stained with CD34 by immunohistochemistry. Quantitation of microvessel density (MVD) and semi-quantitation of VEGF, Ang2, ephrinB2 and EG-VEGF expression were analyzed to find the relations. The MVD was 146.69 +/- 77.79, 214.07 +/- 54.41, 32.85 +/- 8.49 and 34.83 +/- 8.29 in group A-D respectively with significant difference (F = 19.77, P = 0.000). The MVD in group A was higher than that in group C P = 0.006, but lower than that in group B P < or = 0.05 or 0.01. The expression levels of VEGF165, VEGF189, Ang2 and EG-VEGF mRNA were significantly different among the groups. The expression levels of VEGF165, Ang2 and EG-VEGF mRNA in group A were all higher than those in group C, but lower than those in group B P < 0.05 or 0.01. The MVD was significantly correlated with VEGF165, VEGF189, Ang2 and EG-VEGF mRNA with Spearman's related coefficient being 0.764, 0.510, 0.640 and 0.366 in HCC (P = 0.000, 0.000 0.000 and 0.003). In conclusion VEGF, Ang2 and EG-VEGF mRNA may play a role in angiogenesis and carcinogenesis of HCC. They can promote PVTT formation in HCC by modulating angiogenesis.

Efficacy of prostate stabilizing techniques during brachytherapy procedure

During the prostate brachytherapy procedure, multiple needles are inserted into the prostate and radioactive seeds are deposited. Stabilizing needles are first inserted to provide some rigidity and support to the prostate, ideally this will provide better seed placement and an overall improved treatment. However, there is much speculation regarding the effectiveness of using regular brachytherapy needles as stabilizers. In this study, we explored the efficacy of (1) two types of needles--18 gauge brachytherapy needle vs. 18 gauge hooked needle; and (2) parallel vs. angulated needle configurations to stabilize the prostate. Prostate phantom movement and needle insertion progression were imaged using ultrasound (US). The recorded images were analyzed and prostate displacement was computed from images using implanted artifacts. Experimentation allowed us to further understand the mechanics behind prostate stabilization. We observed superior stabilization by the hooked needles compared to the regular brachytherapy needles (more than 40% for parallel stabilization). Prostate movement was also reduced significantly when regular brachytherapy needles were in an angulated configuration as compared to the parallel configuration (approximately 40%). When the hooked needles were angled for stabilization, further improvement in decreased displacement was observed. In general, for convenience of dosimetric planning, all needles are desired to be in parallel and in this case, hooked needles are better suited to improve stabilization of the prostate. On the other hand, both regular and hooked needles appear to be equally effective in reducing prostate movement when they are in angulated configurations, which will be useful in robotic permanent seed implantation (PSI).

Investigation of self-phase modulation based optical regeneration in single mode As2Se3 chalcogenide glass fiber

We investigate the feasibility of all-optical regeneration based on self-phase modulation in single mode As2Se3 chalcogenide fiber. By combining the chalcogenide fiber with a bandpass filter, we achieve a near step-like power transfer function with no pulse distortion. The device is shown to operate with 5.8 ps duration pulses, thus demonstrating the feasibility of this device operating with high bit-rate data signals. These results are achieved with pulse peak powers <10 W in a fully passive device, including only 2.8 m of chalcogenide fiber. We obtain an excellent agreement between theory and experiment and show that both the high nonlinearity of the chalcogenide glass along with its high normal dispersion near 1550 nm enables a significant device length reduction in comparison with silica-based devices, without compromise on the performance. We find that even for only a few meters of fiber, the large normal dispersion of the chalcogenide glass inhibits spectral oscillations that would appear with self-phase modulation alone. We measure the two photon absorption attenuation coefficient and find that it advantageously affects the device transfer function.

siRNA targeting the leader sequence of SARS-CoV inhibits virus replication

SARS-CoV (the SARS-Associated Coronavirus) was reported as a novel virus member in the coronavirus family, which was the cause of severe acute respiratory syndrome. Coronavirus replication occurs through a unique mechanism employing Leader sequence in the transcripts when initiating transcription from the genome. Therefore, we cloned the Leader sequence from SARS-CoV(BJ01), which is identical to that identified from SARS-CoV(HKU-39849), and constructed specific siRNA targeting the Leader sequence. Using EGFP and RFP reporter genes fused with the cloned SARS-CoV Leader sequence, we demonstrated that the siRNA targeting the Leader sequence decreased the mRNA abundance and protein expression levels of the reporter genes in 293T cells. By stably expressing the siRNA in Vero E6 cells, we provided data that the siRNA could effectively and specifically decrease the mRNA abundance of SARS-CoV genes as analyzed by RT-PCR and Northern blot. Our data indicated that the siRNA targeting the Leader sequence inhibited the replication of SARS-CoV in Vero E6 cells by silencing gene expression. We further demonstrated, via transient transfection experiments, that the siRNA targeting the Leader sequence had a much stronger inhibitory effect on SARS-CoV replication than the siRNAs targeting the Spike gene or the antisense oligodeoxynucleotides did. This report provides evidence that targeting Leader sequence using siRNA could be a powerful tool in inhibiting SARS-CoV replication.

Comparison between partial agonist (ME3412) and antagonist (alosetron) of 5-hydroxytryptamine 3 receptor on gastrointestinal function

Therapeutic use of 5-hydroxytryptamine 3 (5-HT(3)) receptor antagonists for diarrhoea-predominant irritable bowel syndrome may be accompanied by constipation. We hypothesized that ME3412, 5-chloro-2-(1,4-diazacycloheptan-1-yl)-7-methylbenzoxazole, a novel partial agonist of the 5-HT(3) receptor, would minimize constipation without reducing antidiarrhoeal activity. Receptor binding studies showed that ME3412 is highly selective for the human 5-HT(3) receptor (K(i) = 1.51 nmol L(-1)). A 5-HT(3) receptor agonist, 2-methyl-5-HT, caused contractile response in the isolated guinea-pig ileum and accelerated secretion in the guinea-pig colonic mucosal preparation. ME3412 and 5-HT(3) receptor antagonist, alosetron, antagonized the 2-methyl-5-HT-induced responses with similar potency in insurmountable and surmountable manner, respectively. ME3412 caused weak agonism in isolated ileum strips and also in the colonic mucosa with intrinsic activity of 0.09 and 0.59, respectively. In conscious dogs, alosetron (3 microg kg(-1) i.v.) suppressed the migrating motor complex (MMC), whereas a relatively high dose (300 microg kg(-1)) of ME3412 was required for inhibition of MMC. ME3412 and alosetron suppressed 5-HT induced-diarrhoea in mice. In contrast, ME3412 did not significantly affect colonic propulsion compared with alosetron. These results imply that the partial agonist may relieve diarrhoea with low risk of inducing constipation.

Direct Evidence of Oxidized Gold on Supported Gold Catalysts

Supported gold catalysts have drawn worldwide interest due to the novel properties and potential applications in industries. However, the origin of the catalytic activity in gold nanoparticles is still not well understood. In this study, time-of-flight secondary ion mass spectroscopy (TOF-SIMS) has been applied to investigate the nature of gold in Au (1.3 wt %)/gamma-Al2O3 and Au (2.8 wt %)/TiO2 catalysts prepared by the deposition-precipitation method. The SIMS spectrum of the supported gold catalysts presented AuO-, AuO2-, and AuOH- ion clusters. These measurements show direct evidence for oxidized gold on supported gold catalysts and may be helpful to gaining better understanding of the origin of the catalytic activity.