Molecular mapping of genes for race-specific overall resistance to stripe rust in wheat cultivar Express

'Express', a hard red spring wheat cultivar that has been widely grown in the western United States, is used to differentiate races of Puccinia striiformis f. sp. tritici, the causal fungal pathogen of wheat stripe rust. To identify genes conferring race-specific, overall resistance to stripe rust, Express was crossed with 'Avocet S'. The parents and F(1), F(2), F(3) and F(5) populations were tested with races PST-1, PST-21, PST-43, and PST-45 of P. striiformis f. sp. tritici in the seedling stage under controlled greenhouse conditions. Two dominant genes for resistance to stripe rust were identified, one conferring resistance to PST-1 and PST-21, and the other conferring resistance to all four races. Linkage groups were constructed for the resistance genes using 146 F(5) lines to establish resistance gene analog and chromosome-specific simple sequence repeat marker polymorphisms. The gene for resistance to races PST-1 and PST-21 was mapped on the long arm of chromosome 1B, and that conferring resistance to all four races was mapped on the long arm of chromosome 5B. We temporarily designate the gene on 1BL as YrExp1 and the gene on 5BL as YrExp2. Polymorphism of at least one of the two markers flanking YrExp2 was detected in 91% of the 44 tested wheat genotypes, suggesting that they would be useful in marker-assisted selection for combining the gene with other resistance genes into many other wheat cultivars. Knowledge of these genes will be useful to understand recent virulence changes in the pathogen populations.

Silencing Livin gene expression to inhibit proliferation and enhance chemosensitivity in tumor cells

Livin, a novel member of the human inhibitors of apoptosis protein (IAP) family, plays an important role in tumor progression and occurrence by inhibiting cell apoptosis. It is selectively expressed in the most common human neoplasms and appears to be involved in tumor cell resistance to chemotherapeutic agents. To investigate its possibility as a therapeutic target for human malignancies, we established two genetically different stable tumor cell lines (LoVo and SPCA-1) and RNA interference (RNAi) technique was employed to downregulate Livin expression in two human tumor cell lines. The specific downregulation of Livin expression in tumor cell lines significantly inhibited in vitro cell proliferation and in vivo tumorigenicity. Furthermore, Livin knockdown led to cell arrest in the G(1)/G(0) phase of cell cycle, eventual apoptosis and chemosensitivity enhancement in tumor cells. All these results indicate that RNAi-mediated downregulation of Livin expression can lead to potent antitumor activity and chemosensitizing effects in human cancers.

Laparoscopically assisted versus open surgery for endometrial cancer--a meta-analysis of randomized controlled trials

There is no clear consensus on the advantages of laparoscopically assisted surgery (LAS) versus open surgery (OS) for endometrial cancer. The present study compared LAS versus OS for patients with endometrial cancer with regard to operative parameters and outcomes. A search of the PubMed, EMBASE, the China Biological Medicine Datadase (CBMdisc), Ovid, and the Cochrane Library identified four studies that met the inclusion criteria for data extraction. Estimates of effectiveness were performed using fixed- and random effects models. The effect was calculated as an odds ratio (OR) or weighted mean difference (WMD) with 95% confidence intervals (CIs). Level of significance was set at P < 0.05. Outcomes of 331 patients were studied. When randomized controlled trials were analyzed, OR for LAS was 0.34 (95% CI: 0.13, 0.89; P = 0.03) for postoperative complications and 0.14 (95% CI: 0.05, 0.39; P = 0.0002) for incidence of transfusion; and WMD for LAS was 263.58 mL (95% CI: 467.71, 59.45 mL; P = 0.01) for blood loss, 38.09 min (95% CI: 10.50, 65.68 min; P = 0.007) for operation time, and 3.35 days (95% CI: 3.84, 2.86 days; P < 0.00001) for hospital stay. There was no difference in patients in terms of recurrence and survival. The present study has shown that LAS was associated with fewer postoperative complications, lower incidence of transfusion, less blood loss, longer operation time, and shorter hospital stay. What's more, no significant difference was found in terms of recurrence and survival. When performed by suitably specialized surgeons in selected patients, it appears to be a better choice than OS.

Overcoming depolarizing resonances with dual helical partial Siberian snakes

Acceleration of polarized protons in the energy range of 5 to 25 GeV is challenging. In a medium energy accelerator, the depolarizing spin resonances are strong enough to cause significant polarization loss but full Siberian snakes cause intolerably large orbit excursions and are also not feasible since straight sections usually are too short. Recently, two helical partial Siberian snakes with double pitch design have been installed in the Brookhaven Alternating Gradient Synchrotron (AGS). With a careful setup of optics at injection and along the energy ramp, this combination can eliminate the intrinsic and imperfection depolarizing resonances otherwise encountered during acceleration to maintain a high intensity polarized beam in medium energy synchrotrons. The observation of partial snake resonances of higher than second order will also be described.

Decision Making in Fuzzy Discrete Event Systems1

The primary goal of the study presented in this paper is to develop a novel and comprehensive approach to decision making using fuzzy discrete event systems (FDES) and to apply such an approach to real-world problems. At the theoretical front, we develop a new control architecture of FDES as a way of decision making, which includes a FDES decision model, a fuzzy objective generator for generating optimal control objectives, and a control scheme using both disablement and enforcement. We develop an online approach to dealing with the optimal control problem efficiently. As an application, we apply the approach to HIV/AIDS treatment planning, a technical challenge since AIDS is one of the most complex diseases to treat. We build a FDES decision model for HIV/AIDS treatment based on expert's knowledge, treatment guidelines, clinic trials, patient database statistics, and other available information. Our preliminary retrospective evaluation shows that the approach is capable of generating optimal control objectives for real patients in our AIDS clinic database and is able to apply our online approach to deciding an optimal treatment regimen for each patient. In the process, we have developed methods to resolve the following two new theoretical issues that have not been addressed in the literature: (1) the optimal control problem has state dependent performance index and hence it is not monotonic, (2) the state space of a FDES is infinite.

REW– exit-wave reconstruction and alignments for focus-variation high-resolution transmission electron microscopy images

A Windows-based computer program has been developed for exit-wave reconstruction and experimental high-resolution transmission electron microscopy image alignment. While the exit-wave reconstruction is performed mainly using the maximum-likelihood method, image alignments may be carried out using several algorithms, including the time-consuming but robust genetic algorithm.

Genetics and molecular mapping of genes for race-specific all-stage resistance and non-race-specific high-temperature adult-plant resistance to stripe rust in spring wheat cultivar Alpowa

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most widespread and destructive wheat diseases worldwide. Growing resistant cultivars is the preferred control of the disease. The spring wheat cultivar 'Alpowa' has both race-specific, all-stage resistance and non-race-specific, high-temperature adult-plant (HTAP) resistances to stripe rust. To identify genes for the stripe rust resistances, Alpowa was crossed with 'Avocet Susceptible' (AVS). Seedlings of the parents, and F(1), F(2) and F(3) progeny were tested with races PST-1 and PST-21 of P. striiformis f. sp. tritici under controlled greenhouse conditions. Alpowa has a single partially dominant gene, designated as YrAlp, conferring all-stage resistance. Resistance gene analog polymorphism (RGAP) and simple sequence repeat (SSR) techniques were used to identify molecular markers linked to YrAlp. A linkage group of five RGAP markers and two SSR markers was constructed for YrAlp using 136 F(3) lines. Amplification of a set of nulli-tetrasomic Chinese Spring lines with RGAP markers Xwgp47 and Xwgp48 and the two SSR markers indicated that YrAlp is located on the short arm of chromosome 1B. To map quantitative trait loci (QTLs) for the non-race-specific HTAP resistance, the parents and 136 F(3) lines were tested at two sites near Pullman and one site near Mount Vernon, Washington, under naturally infected conditions. A major HTAP QTL was consistently detected across environments and was located on chromosome 7BL. Because of its chromosomal location and the non-race-specific nature of the HTAP resistance, this gene is different from previously described genes for adult-plant resistance, and is therefore designated Yr39. The gene contributed to 64.2% of the total variation of relative area under disease progress curve (AUDPC) data and 59.1% of the total variation of infection type data recorded at the heading-flowering stages. Two RGAP markers, Xwgp36 and Xwgp45 with the highest R (2) values were closely linked to Yr39, should be useful for incorporation of the non-race-specific resistance gene into new cultivars and for combining Yr39 with other genes for durable and high-level resistance.

Discovering Classes of Strongly Equivalent Logic Programs

In this paper we apply computer-aided theorem discovery technique to discover theorems about strongly equivalent logic programs under the answer set semantics. Our discovered theorems capture new classes of strongly equivalent logic programs that can lead to new program simplification rules that preserve strong equivalence. Specifically, with the help of computers, we discovered exact conditions that capture the strong equivalence between a rule and the empty set, between two rules, between two rules and one of the two rules, between two rules and another rule, and between three rules and two of the three rules.

Ammonium exchange in aqueous solution using Chinese natural clinoptilolite and modified zeolite

In this study, the Chinese natural clinoptilolite (sample 1) was fused with sodium hydroxide prior to hydrothermal reaction, and it was transformed to modified zeolite Na-Y (sample 2). The uptake of ammonium ion from aqueous solutions in the concentration range 50-250 mg NH(4)(+)/l on to the two samples was compared and the equilibrium isotherms have been got. The influence of other cations present in water upon the ammonia uptake was also determined. The cations studied were potassium, calcium and magnesium. In all cases the anionic counterion present was chloride. The results showed that sample 2 exhibited much higher uptake capacity compared with sample 1. At the initial concentration of 250 mg NH(4)(+)/l, the ammonium ion uptake value of sample 2 was 19.29 mg NH(4)(+)g(-1) adsorbent, while sample 1 was only 10.49 mg NH(4)(+)g(-1) adsorbent. For the natural clinoptilolite, the effect of the metal ions suggested an order of preference K(+)>Ca(2+)>Mg(2+). These contrasted with the modified zeolite, where the order appeared to be Mg(2+)>Ca(2+)>K(+).

FEM model for evaluating buttock tissue response under sitting load

Development of a model for evaluating tissue compression during sitting has been hampered by limitation of implementing the anatomical and mechanical parameters of the various layers of tissue. This study proposes a new method to setup and validate a finite element model for buttock tissue to evaluate the tissue response under external sitting load. Multi-layer tissue deformation was measured with ultrasound imaging under simulated sitting load, applied and monitored through an indenter which integrates ultrasound probe and force/pressure sensors. Subject-specific FE model can then be setup and validated. Pilot test of this model revealed that the highest peak stress was found in the vicinity of the ischial tuberosity and the greatest deformation seen in the muscle layer. The authors conclude that this new method allows accurate multi-layer tissue deformation be obtained under close to real sitting load, therefore, provides a better way to evaluate tissue response to external sitting load for seated individuals in a true and subject-specific fashion, which may provide helpful information to improve the sitting comfort and prevent pressure ulcers in wheelchair bound individuals.

Reducing whole-body vibration of vehicle drivers with a new sitting concept

A new car seat design, which allows the back part of the seat (BPS) to lower down while a protruded cushion supports the lumbar spine, was quantitatively tested to determine its effectiveness in reducing whole-body vibration (WBV) in automobile drivers. Results on 12 drivers show that, by reducing contact between the seat and the ischial tuberosities (TTs), the new seating design reduced both contact pressure and amplitude of harmful vibrations transmitted through the body. Significant reduction of WBV, in terms of RMS and VDV, was found as large as 30% by this seating design (P < 0.05), especially at lumbar spine region. This reduction in WBV allows more sustained driving than permitted by conventional seating devices, by around 2 hours daily, before reaching harmful WBV levels. The new seating design also promotes improved posture by restoring normal spinal curvature. Such seating devices, implemented in cars, buses, large trucks, and other high-vibration vehicles, may effectively reduce the risk of musculoskeletal disorders among long term drivers.

Diffusion tensor tractography-based group mapping of the pyramidal tract in relapsing-remitting multiple sclerosis patients

BACKGROUND AND PURPOSE

Many studies have reported abnormal changes in relapsing-remitting multiple sclerosis (RRMS) by histogram and region-of-interest-based methods by using diffusion tenor imaging. However, there are few studies on specific white matter fiber tracts of RRMS. Our study sought to use diffusion tensor tractography-based group mapping to investigate the presence of abnormal diffusion in the normal-appearing pyramidal tract (PYT) of RRMS and its possible mechanism.

METHODS

A PYT probability map was first constructed from data on 20 healthy patients based on the deterministic-based tractography method. The PYT probability map was then applied to 29 RRMS patients to calculate diffusion indices of the PYT. In this study, 4 quantitative indices-fractional anisotropy (FA), directionally averaged diffusion coefficient (D(av)), axial diffusion coefficient (lambda(1)), and radial diffusion coefficient (lambda(23))-were used to characterize the abnormal diffusion.

RESULTS

Compared with healthy controls, RRMS patients had a significantly higher D(av) and lambda(23) but a lower FA and a trend toward a lower lambda(1) in the normal-appearing PYT. In RRMS patients, PYT lesions had a significantly higher lambda(23) and a lower FA, but there were no differences for D(av) and lambda(1) when compared with the normal-appearing PYT. Moreover, the diffusion indices derived from the normal-appearing PYT were significantly correlated with PYT lesion volumes by using the Spearman correlation analysis.

CONCLUSION

Our findings confirm the presence of abnormal diffusion in the normal-appearing PYT of RRMS patients and suggest that wallerian degeneration might be its mechanism.

Modulation of the oxidative stress and nuclear factor kappaB activation by theaflavin 3,3'-gallate in the rats exposed to cerebral ischemia-reperfusion

The major pathobiological mechanisms of IR injury include excitotoxicity, oxidative stress, and inflammation. TF3, a major constituent of black tea, possesses biological functions such as anti-oxidative and anti-inflammatory activities. The purpose of this study was to verify the neuronal protective potential of TF3 and its mechanisms against cerebral IR injury in rats. TF3 administration (10 and 20 mg.kg-1) ameliorated the infarct volume. TF3 also decreased the content of MDA and NO. TF3 significantly increased the activity of SOD and GSH-Px, which were reduced by IR injury. Administration of TF3 decreased mRNA and protein expression of COX-2 and iNOS. DNA binding and Western blotting revealed an increase in NF-kappaB activation and IkappaB depletion in IR brain tissue. Pretreatment with TF3 markedly inhibited IRinduced increase in nuclear localization of NF-kappaB, and preserved IkappaB in the cytoplasm. The results show that TF3 exerts protective effects against cerebral IR injury by reducing oxidative stress and modulating the NF-kappaB activation.

The wrap-around problem and optimal padding in the exit wave reconstruction using HRTEM images

A free fast Fourier transform software FFTW (www.fftw.org) is used in the exit wave reconstruction and shown to be able to handle images of any size effectively. The wrap-around problem commonly encountered in the exit wave reconstruction is investigated, and a new padding scheme is proposed and its performance is investigated. It is shown that while the usual wrap-around problem may be solved via padding the input high-resolution transmission electron microscopy (HRTEM) images with zero or averaged image intensities, the reconstructed exit wave at its boundary is inevitably distorted by the discontinuity of image intensities at the boundary. The proposed new padding scheme is shown to be able to provide a good estimate of the image intensities immediately outside the boundaries of the HRTEM images, reducing the estimated image intensity discontinuity across the boundaries and therefore providing a larger undistorted view of the exit wave.

Regulation of Nur77 nuclear export by c-Jun N-terminal kinase and Akt

Proapoptotic nuclear receptor family member Nur77 translocates from the nucleus to the mitochondria, where it interacts with Bcl-2 to trigger apoptosis. Nur77 translocation is induced by certain apoptotic stimuli, including the synthetic retinoid-related 6-[3-(1-adamantyl)-4-hydroxyphenyl]-2-naphthalenecarboxylic acid (AHPN)/CD437 class. In this study, we investigated the molecular mechanism by which AHPN/CD437 analog (E)-4-[3-(1-adamantyl)-4-hydroxyphenyl]-3-chlorocinnamic acid (3-Cl-AHPC) induces Nur77 nuclear export. Our results demonstrate that 3-Cl-AHPC effectively activated Jun N-terminal kinase (JNK), which phosphorylates Nur77. Inhibition of JNK activation by a JNK inhibitor suppressed 3-Cl-AHPC-induced Nur77 nuclear export and apoptosis. In addition, several JNK upstream activators, including the phorbol ester TPA, anisomycin and MAPK kinase kinase-1 (MEKK1), phosphorylated Nur77 and induced its nuclear export. However, Nur77 phosphorylation by JNK, although essential, was not sufficient for inducing Nur77 nuclear export. Induction of Nur77 nuclear export by MEKK1 required a prolonged MEKK1 activation and was attenuated by Akt activation. Expression of constitutively active Akt prevented MEKK1-induced Nur77 nuclear export. Conversely, transfection of dominant-negative Akt or treatment with a phosphatidylinositol 3-kinase (PI3-K) inhibitor accelerated MEKK1-induced Nur77 nuclear export. Furthermore, mutation of an Akt phosphorylation residue Ser351 in Nur77 abolished the effect of Akt or the PI3-K inhibitor. Together, our results demonstrate that both activation of JNK and inhibition of Akt play a role in translocation of Nur77 from the nucleus to the cytoplasm.

Safety and efficacy of an infectious bronchitis virus used for chicken embryo vaccination

Commercial vaccines for in ovo vaccination have not yet been developed for infectious bronchitis virus (IBV), the major coronavirus in the poultry industry. Recombinant IBVs based on the Beaudette strain expressing the Beaudette spike protein (Beau-R) or that from the virulent M41 strain (BeauR-M41(S)) were assessed for their potential as prototype vaccines for application to 18-day-old embryos. Pathogenicity was assessed by observing the effect on hatchability, and/or the production of nasal discharge and/or the effects on ciliary activity in the trachea at various time points post hatch. In contrast to commercial IBV vaccines given in ovo, the Beau-R and BeauR-M41(S) strains did not reduce hatchability or cause nasal discharge, and caused minimal damage to the ciliated epithelium of the trachea. The presence of the spike protein from a virulent virus did not increase the pathogenicity of the virus according to the criteria used. Assessment of the BeauR-M41(S) strain for efficacy showed that it protected up to 90% of chicks against challenge with virulent IB virus (M41) in a dose dependent manner. Further egg passage of the BeauR-M41(S) strain (BeauR-M41(S) EP10) did not increase its pathogenicity though it did improve its efficacy, based on serology and protection against a virulent challenge. BeauR-M41(S) EP10 was more efficacious than BeauR-M41(S) protecting more birds against virulent challenge and providing a better serological antibody response. BeauR-M41(S) EP10 induced a serological response similar to that of a commercial vaccine given at day-old though the commercial vaccine provided slightly higher efficacy. These results are promising for the development of embryo safe efficacious IBV vaccines for in ovo application.

Circulating levels of beta2-glycoprotein I in thrombotic disorders and in inflammation

Beta2-glycoprotein I (beta2GPI) is a plasma protein suspected to have a role in inhibition of thrombosis. This suspicion is reinforced by the observation that beta2GPI is the major target for autoantibodies in the antiphospholipid syndrome. However, little is known about its circulating levels in common thrombotic diseases or inflammation. We measured beta2GPI levels in 344 healthy controls, 58 normal pregnancies, 102 patients with non-haemorrhagic stroke, 121 patients with acute coronary syndrome and 200 patients with elevated C-reactive protein (CRP). In healthy individuals, we found a strong positive correlation between age and beta2GPI concentration (r = 0.274, P < 0.001) and that beta2GPI levels fall significantly after the eighth week of pregnancy (P = 0.002). We also found significantly reduced levels of beta2GPI in patients with stroke and in elderly patients with myocardial syndrome (P = 0.013 and 0.043). However, in neither group did beta2GPI levels change in the following six months, suggesting that the reduced levels were not a transient post-event phenomenon. In patients with inflammation, beta2GPI levels showed a significant negative correlation with CRP (r = -0.284, P < 0.001) and positively correlated with albumin and transferrin (r = 0.372 and 0.453, respectively with P < 0.001 for both). Furthermore, the largest reduction in beta2GPI levels occurred in patients with the highest CRP values (P < 0.001).

Pharmacogenomic analysis of needle biopsies obtained before preoperative docetaxel/capecitabine/FEC (TX/FEC) chemotherapy for breast cancer

10595

Background: Our goal was to evaluate the feasibility of obtaining fine needle biopsies, for pharmacogenomic analysis, in community based oncology practices and develop gene expression-based predictors of pathologic complete response (pCR) to preoperative sequential docetaxel/capecitabine and 5-fluorouracil, epirubicin, cyclophosphamide chemotherapy. Methods: One hundred seventy-five patients were accrued at 29 sites in the US Oncology Research network. FNA specimens were mailed to a central laboratory (MDACC) and gene expression profiling was performed on Affymetrix U133A chips. Results: RNA extraction was started on 140 specimens, 112 of these (80%) yielded ≥1 μg total RNA, 69 were hybridized and 65 (94%) gene expression profiles have passed quality control as of abstract submission date. The analysis plan is to develop a multigene predictor of pCR from the first 80 cases and test its performance independently in the remaining cases. Conclusions: Collection of mandatory research FNA biopsies for pharmacogenomic research is feasible in community practice. Approximately 80% of biopsies yield sufficient RNA for gene expression profiling. In 20% of patients, either technical factors, which can be addressed, or tumor biology (necrotic, rapidly growing tumors) were limiting. Supported by Roche Laboratories, Inc., Nutley, NJ; Pfizer, New York, NY; and Precision Therapeutics, Pittsburgh, PA.

[Table: see text]

Pharmacogenomic analysis of HER2 amplified breast cancer treated with preoperative trastuzumab and paclitaxel, 5-fluorouracil, epirubicin, cyclophosphamide (T/FEC) chemotherapy

545

Background: We performed gene expression analysis to identify molecular predictors of resistance to preoperative concomitant trastuzumab and T/FEC chemotherapy. Methods: Pretreatment fine needle aspirations from 21 patients with HER2 amplified, stages II-III breast cancer were available for transcriptional profiling with Affymetrix U133 A chips. Results: Overall pathologic complete response (pCR) rate was 71%. Age, nuclear grade, tumor size, nodal status or quantitative estrogen and HER2 receptor mRNA expression showed no association with response in univariate and multivariate logistic regression. We tested the accuracy of a 30-gene pCR predictor that was previously developed from patients who received T/FEC only preoperative chemotherapy. This predictor was accurate in validation in T/FEC treated patients (n=51) but showed low sensitivity in patients who also received trastuzumab (sensitivity 53% versus 92%). We could not identify any differentially expressed genes between pCR (n=15) and residual disease (RD, n=6) at a false discovery rate (FDR) <90% in the HER2 amplified trastuzumab-treated cases. Hierarchical clustering using the “Perou intrinsic gene set” also failed to separate pCR from RD. Gene Set Enrichment Analysis with 22 genes from trastuzumab-resistant cell lines showed a modest association with RD (FDR=9%). Conclusions: Clinical variables and pharmacogenomic predictors that predict pCR in the absence of trastuzumab are no longer accurate when trastuzumab is included in the treatment. Trastuzumab-resistance associated genes identified in vitro are also associated with resistance in vivo. Support: Ellence Foundation.

No significant financial relationships to disclose.

Role of lateral alkyl chains in modulation of molecular structures on metal surfaces

We use low energy electron diffraction, scanning tunneling microscopy, first-principles density-functional theory, and molecular mechanics calculations to analyze the adsorption and growth of quinacridone derivatives (QA) with alkyl chains of 4 and 16 carbon atoms on a Ag(110) substrate. Surprisingly, we find that the alkyl chains determine the orientation of the molecular overlayers. While the interaction of QA and the Ag substrate is primarily due to chemical bonding of oxygen to the silver substrate, determining the molecular orientation and preferred adsorption site, the intermolecular arrangement can be adjusted via the length of alkyl chains. We are thus able to fabricate uniform QA films with very well controlled physical properties.