A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks

We derive a convex optimization problem on a steady-state nonequilibrium network of biochemical reactions, with the property that energy conservation and the second law of thermodynamics both hold at the problem solution. This suggests a new variational principle for biochemical networks that can be implemented in a computationally tractable manner. We derive the Lagrange dual of the optimization problem and use strong duality to demonstrate that a biochemical analogue of Tellegen's theorem holds at optimality. Each optimal flux is dependent on a free parameter that we relate to an elementary kinetic parameter when mass action kinetics is assumed.

Single spin asymmetries in charged pion production from semi-inclusive deep inelastic scattering on a transversely polarized 3He Target at Q2 = 1.4-2.7 GeV2

We report the first measurement of target single spin asymmetries in the semi-inclusive (3)He(e,e'π(±))X reaction on a transversely polarized target. The experiment, conducted at Jefferson Lab using a 5.9 GeV electron beam, covers a range of 0.16 < x < 0.35 with 1.4 < Q(2) < 2.7 GeV(2). The Collins and Sivers moments were extracted from the azimuthal angular dependence of the measured asymmetries. The π(±) Collins moments for (3)He are consistent with zero, except for the π(+) moment at x = 0.35, which deviates from zero by 2.3σ. While the π(-) Sivers moments are consistent with zero, the π(+) Sivers moments favor negative values. The neutron results were extracted using the nucleon effective polarization and measured cross section ratios of proton to (3)He, and are largely consistent with the predictions of phenomenological fits and quark model calculations.

Clinical correlates of white matter blood flow perfusion changes in Sturge-Weber syndrome: a dynamic MR perfusion-weighted imaging study

BACKGROUND AND PURPOSE

Low brain tissue perfusion due to abnormal venous drainage is thought to be a central mechanism of brain damage in SWS. Here, HR-PWI was used to quantify WM perfusion abnormalities and to correlate these with brain atrophy and clinical variables.

MATERIALS AND METHODS

Fourteen children (age range, 0.8-10.0 years) with unilateral SWS underwent MR imaging examinations, including HR-PWI. rCBV, rCBF, and MTT in the affected WM and in contralateral homotopic WM were measured. AI for each perfusion parameter was correlated with age, brain atrophy, and motor and seizure variables as well as IQ.

RESULTS

Increased perfusion was seen in the affected hemisphere in 5 children and decreased perfusion in 9 children. Brain atrophy was more severe in the low-perfusion group (P = .01) and was related to both CBF-AI and CBV-AI (r = -0.69, P = .007; r = -0.64, P = .014, respectively). Older children had lower CBV values on the affected side (r = -0.62, P = .02). Longer duration of epilepsy was related to lower CBF (more negative CBF-AI, r = -0.58, P = .03) and low CBV (r = -0.55, P = .04) on the affected side. Lower perfusion was associated with more frequent seizures (rCBF-AI: r = -0.56, P = .04; rCBV-AI: r = -0.63, P = .02).

CONCLUSIONS

Increased perfusion in the affected cerebral WM may indicate an early stage of SWS without severe brain atrophy. Decreased perfusion is associated with frequent seizures, long duration of epilepsy, and brain atrophy.

Assessment of cardiac diastolic dysfunction in HIV-infected people without cardiovascular symptoms in China

This study assessed cardiac diastolic dysfunction (DD) in HIV-infected subjects without cardiovascular symptoms in China. Eighty-four HIV-infected patients without cardiovascular symptoms were recruited and compared with 30 HIV-negative control subjects. Cardiac DD was evaluated using echocardiography including tissue Doppler imaging. DD was detected in 47.6% of AIDS patients and 42.8% of HIV-positive patients, which was significantly higher than in HIV-negative controls. After logistic regression analysis, HIV infection was independently correlated with cardiac DD (P < 0.05). Among HIV-positive subjects, logistic regression analysis showed that zidovudine exposure was associated with higher prevalence of DD (P < 0.05). Asymptomatic cardiac DD was observed frequently in HIV-infected subjects. HIV infection itself and zidovudine exposure were correlated with a higher prevalence of cardiac DD.

Küpffer cells promote acute rejection via induction of Th17 differentiation in rat liver allografts

BACKGROUND

Th17, a newly identified CD4+ T-cell subset, has been implicated in transplant rejection. Differentiation of Th17 cells is associated with transforming growth factor-β (TGF-β) and interleukin-6 (IL-6), which are the main products of Küpffer cells.

OBJECTIVE

To determine whether Küpffer cells promote acute liver allograft rejection by inducing Th17 cell differentiation.

METHODS

A rat model of allogeneic liver transplantation using Dark Agouti (DA) to Brown Norway (BN) rats was established with or without gadolinium chloride (GdCl(3)) pretreatment. Isogeneic liver transplantation (BN to BN) was performed as a control. Concentrations of cytokines secreted by Küpffer cells or Th17-related cytokines detected in the liver and peripheral blood were analyzed using immunohistochemistry assays, flow cytometry, and enzyme-linked immunosorbent assays. Survival differences were compared between treatment groups. In vitro, Küpffer cells from liver grafts were isolated and co-cultured with naïve CD4 T cells.

RESULTS

Both Küpffer cells and Th17 cells infiltrated liver allografts, accompanied by an increase in concentrations of IL-6 and TGF-β. Pretreatment with GdCl(3) attenuated intragraft infiltration of Küpffer cells and Th17 cells, and decreased IL-6 and TGF-β concentrations. Liver function improved after pretreatment, and mean (SD) survival time was prolonged, compared with the control group (16.33 [0.96] days vs 11.50 [0.99] days, respectively; P < .01). In vitro, Küpffer cells from livers with allografts secreted significantly higher concentrations of IL-6 and TGF-β and induced Th17 differentiation more effectively compared with livers with isografts (30.8% vs 8.1%, respectively).

CONCLUSION

Küpffer cells have the potential to induce Th17 cells by secreting IL-6 and TGF-β, and as a result, promote acute liver allograft rejection.

Evaluation of low-cost cathode catalysts for high yield biohydrogen production in microbial electrolysis cell

As an ideal fuel due to the advantages of no pollution, high combustion heat and abundant sources, hydrogen gas can be produced from organic matter through the electrohydrogenesis process in microbial electrolysis cells. But in many MECs, platinum is often used as catalyst, which limits the practical applications of MECs. To reduce the cost of the MECs, Ni-based alloy cathodes were developed by electrodepositing. In this paper hydrogen production using Ni-W-P cathode was studied for the first time in a single-chamber membrane-free MEC. At an applied voltage of 0.9 V, MECs with Ni-W-P cathodes obtained a hydrogen production rate of 1.09 m3/m3/day with an cathodic hydrogen recovery of 74%, a Coulombic efficiency of 56% and an electrical energy efficiency relative to electrical input of 139%, which was the best result of reports in this study. The Ni-W-P cathode demonstrated a better electrocatalytic activity than the Ni-Ce-P cathode and achieved a comparable performance to the Pt cathode in terms of hydrogen production rate, Coulombic efficiency, cathodic hydrogen recovery and electrical energy efficiency at 0.9 V.

Abstract P5-05-04: E-Cadherin and Its Proteolytic Fragments Trump Epithelial-Mesenchymal Transition and Function as Dominant Oncogenes in Inflammatory Breast Cancer

Background: Inflammatory breast cancer (IBC) and its lymphovascular embolic signature seem to challenge the dogma of prerequisite epithelialmesenchymal transition (EMT) in human breast cancer progression by the apparent maintenance of an epithelial state in all stages of IBC. Previous studies with a human xenograft model of inflammatory breast cancer, MARY-X, demonstrated that overexpressed E-cadherin moderated the formation of the lymphovascular embolus in vivo and tumoral spheroids of super-high density in vitro. Although slug, snail and twist are increased in MARY-X spheroids and may decrease E-cadherin transcription to some extent, their effects are neutralized and frankly overridden by the post-transcriptional regulation of E-cadherin which includes its altered degradation and trafficking which, in turn, maintain the epithelial state. Materials and Methods: Because of the uniqueness of the MARY-X model and the observation that E-cadherin was not functioning as a tumor suppressor gene whose loss was triggering EMT but rather whose overexpression was mediating increased survival and resistance to apoptosis, we decided to examine the fate and role of E-cadherin more closely.

Results: We discovered that E-cadherin underwent extensive proteolytic processing which resulted in fragments also mediating increased survival and resistance to apoptosis. In both MARY-X and the MARY-X spheroids, Western blot revealed 5 E-cadherin bands: one full length (120 kDa) and four fragments: E-cad/NFT1 (100 kDa), E-cad/NTF2 (95 kDa), E-cad/NTF3 (85 kDa), E-cad/NTF4 (80kDa). Corresponding E-cad/CTF1-4 fragments were also generated. Compared to MARY-X, NFT1 was dramatically increased in the MARY-X spheroids whereas NFT2-4 were significantly decreased. These E-cadherin fragments were produced by specific proteolytic cleavage based on inhibitor studies: NFT1 was produced by calpain, NFT2 by γ-secretase, NFT3 by a matrix metalloproteinase and NFT4 by an unknown mechanism. Predictably levels of calpain activity were significantly increased in the MARY-X spheroids. NFT1 generatedby increased calpain activity retained the p120ctn binding site but lost both the β-catenin and α-binding sites, facilitating its 360° distribution around the cell. Calpain inhibition decreased NFT1 without any affect on full length E-cadherin yet induced disadherence of intact spheroids and prevented the assembly of de novo spheroids. Identical proteolytic fragments of E-cadherin were observed in 3 other human IBC cell lines as well as in lymphovascular emboli of human IBC cases obtained by laser capture microdissection.

Discussion: The selective proteolytic processing of E-cadherin ultimately then is responsible for the increased survival of the lymphovascular embolus of IBC and its resistance to chemotherapy-induced apoptosis. Select NT proteolytic fragments may function as adhesion molecules whereas select CT proteolytic fragments may function as transcription factors which confer this survival advantage. E-cadherin and its proteolytic fragments then both trump EMT as well as function as dominant oncogenes in IBC.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P5-05-04.

The lymphovascular embolus of inflammatory breast cancer exhibits a Notch 3 addiction

Inflammatory breast carcinoma (IBC) is characterized by exaggerated lymphovascular invasion (LVI), recapitulated in our human xenograft, MARY-X. This model exhibited lymphovascular emboli in vivo and corresponding spheroids in vitro. Owing to the morphological and gene profile resemblance of these spheroids to embryonal blastocysts, we wondered whether they might exhibit embryonic stem cell signaling. Specifically we investigated Notch and observed selective Notch 3 activation by expression profiling, reverse transcriptase- and real-time PCR, western blot and immunofluorescence in vitro, and immunohistochemistry in vivo. Notch 3 intracellular domain (N3icd) and six target genes, HES-5, HEY-1, c-Myc, Deltex-1, NRARP and PBX1, markedly increased in MARY-X. In addition, a significant percentage of MARY-X cells expressed aldehyde dehydrogenase (ALDH), a stem cell marker. Only the ALDH(+) cells were capable of secondary spheroidgenesis, tumorigenicity and self-renewal. Inhibiting Notch 3 activation in vitro with γ-secretase inhibitors (GSIs) or small interfering RNA resulted in a downregulation of Notch target genes, including CD133, and an induction of caspase 3-mediated apoptosis. Transfection of N3icd but not Notch 1 intracellular domain into normal human mammary epithelial cells resulted in increased expression of Notch target genes and induction of spheroidgenesis. GSI in vivo resulted in inhibitory but diffusion-limited effects on Notch 3 signaling, resulting in xenograft growth reduction. The lymphovascular emboli of human IBC exhibited dual N3icd and ALDH1 immunoreactivities independently of molecular subtype. This Notch 3 addiction of lymphovascular emboli might be exploited in future therapeutic strategies.

The phenotypic and genotypic characterization of Enterobacter sakazakii strains from infant formula milk

Enterobacter sakazakii is an emerging foodborne pathogen associated with severe diseases in neonates. Infant formula milk (IFM) has been identified as one of the major contaminated sources and a transmission vehicle. To determine the phenotypic and genotypic characterization of this pathogen, 22 E. sakazakii strains isolated from IFM by an FDA-recommended method and PCR on the alpha-glucosidase gene were subtyped by random amplified polymorphic DNA (RAPD)-PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR, and antibiotic resistance patterns. At a similarity threshold of 80%, 16 ERIC-PCR fingerprint types were identified with a discriminatory power (D) of 0.933, and 18 RAPD-PCR types were identified with D of 0.973. Resistance to 9 antibiotics tested by disk diffusion assay revealed 6 antibiotic resistance patterns with D of 0.749. The comparison of characterization indicated that RAPD-PCR and ERIC-PCR have high discriminatory power showing genetic diversity of E. sakazakii isolates, and ERIC-PCR patterns showed a closer correlation than RAPD-PCR patterns to phenotypic characterization and the brands of IFM. Overall, the ERIC-PCR typing method could be used for tracing sources of E. sakazakii isolates in the food chain.

Hsa-miR-9 methylation status is associated with cancer development and metastatic recurrence in patients with clear cell renal cell carcinoma

The long-term prognosis for clear cell renal cell carcinoma (ccRCC) is dramatically altered by the development of metastatic recurrence. However, there are very few indicators that can predict which patient will develop a recurrence. MicroRNAs regulate many cellular processes and have been shown to be associated with cancer development and recurrence. More recently it has been shown that microRNA genes can be epigenetically modified in cancer, resulting in aberrant silencing of microRNA genes with tumor suppressor functions. In this study, we show that two genes encoding for hsa-miR-9 are significantly hypermethylated in ccRCC tumors compared with adjacent normal tissues (P-value <0.001 for both miR-9-1 and miR-9-3) resulting in decreased expression, and that the methylation of these genes was more significant in DNA obtained from the primary tumor for patients who developed a recurrence (P-value: 0.012 and 0.009 for miR-9-1 and miR-9-3, respectively) than in tumors from nonrecurrent patients. Furthermore, methylation of miR-9-3 was significantly associated with an increased risk of recurrence (hazard ratio: 5.85, 95% confidence intervals: 1.30-26.35) and high methylation levels of either miR-9-1 or miR-9-3 resulted in a significant, nearly 30-month decrease in recurrence-free survival time (P-value: 0.034 and 0.007 for miR-9-1 and miR-9-3, respectively). Our results demonstrate that hsa-miR-9 is involved in the development of ccRCC while also having a role in the development of metastatic recurrence.

Summer fluxes of atmospheric greenhouse gases N2O, CH4 and CO2 from mangrove soil in South China

The atmospheric fluxes of N(2)O, CH(4) and CO(2) from the soil in four mangrove swamps in Shenzhen and Hong Kong, South China were investigated in the summer of 2008. The fluxes ranged from 0.14 to 23.83 micromol m(-2)h(-1), 11.9 to 5168.6 micromol m(-2)h(-1) and 0.69 to 20.56 mmol m(-2)h(-1) for N(2)O, CH(4) and CO(2), respectively. Futian mangrove swamp in Shenzhen had the highest greenhouse gas fluxes, followed by Mai Po mangrove in Hong Kong. Sha Kong Tsuen and Yung Shue O mangroves in Hong Kong had similar, low fluxes. The differences in both N(2)O and CH(4) fluxes among different tidal positions, the landward, seaward and bare mudflat, in each swamp were insignificant. The N(2)O and CO(2) fluxes were positively correlated with the soil organic carbon, total nitrogen, total phosphate, total iron and NH(4)(+)-N contents, as well as the soil porosity. However, only soil NH(4)(+)-N concentration had significant effects on CH(4) fluxes.

Resolvin E1 protects the rat heart against reperfusion injury

The purpose of the present study was to assess whether resolvin E1 (RvE1), an anti-inflammatory mediator derived from eicosapentaenoic acid, would limit myocardial infarct size in the rat. The H9c2 cell line was used to assess whether RvE1 has direct protective effects on cardiomyocytes. In in vivo experiments, Male Sprague-Dawley rats underwent 30 min of ischemia/4 h of reperfusion. Before reperfusion, rats received intravenous RvE1 (0, 0.03, 0.1, or 0.3mg/kg). In in vitro experiments, H9c2 cells were incubated with RvE1 (0, 1, 10, 100, or 1000 nM). Cells were subjected to 18 h of incubation under normoxic conditions, 16 h of hypoxia, or 16 h of hypoxia and 2 h of reoxygenation. In vivo, RvE1 dose dependently reduced infarct size (30.7 +/- 1.7% of the area at risk in the control group and 29.1 +/- 1.6%, 14.7 +/- 1.3%, and 9.0 +/- 0.6% in the 0.03, 0.1, and 0.3 mg/kg groups, respectively, P < 0.001). In vitro, RvE1 increased viability and decreased apoptosis in a dose-dependent fashion in cells exposed to hypoxia or hypoxia/reoxygenation. A maximal effect was achieved at a concentration of 100 nM. RvE1 augmented phosphoinositide 3-kinase activity, attenuated caspase-3 activity, and augmented calcium-dependent nitric oxide synthase activity in cells exposed to hypoxia or hypoxia/reoxygenation. RvE1 increased Akt, ERK1/2, and endothelial nitric oxide synthase phosphorylation and attenuated the levels of activated caspase-3 and phosphorylated p38 levels. AG-1478, an EGF receptor tyrosine kinase inhibitor, blocked the protective effect of RvE1 both in vivo and in vitro and attenuated the RvE1-induced increase in Akt and ERK1/2 phosphorylation. In conclusion, RvE1, an anti-inflammatory mediator derived from eicosapentaenoic acid, has a direct protective effect on cardiomyocytes against ischemia-reperfusion injury and limits infarct size when administered intravenously before reperfusion.

TRE17/USP6 oncogene translocated in aneurysmal bone cyst induces matrix metalloproteinase production via activation of NF-kappaB

Aneurysmal bone cyst (ABC) is an aggressive, pediatric bone tumor characterized by extensive destruction of the surrounding bone. Though first described over 60 years ago, its molecular etiology remains poorly understood. Recent work revealed that ABCs harbor translocation of TRE17/USP6, leading to its transcriptional upregulation. TRE17 encodes a ubiquitin-specific protease (USP), and a TBC domain that mediates binding to the Arf6 GTPase. However, the mechanisms by which TRE17 overexpression contributes to tumor pathogenesis, and the role of its USP and TBC domains are unknown. ABCs are characterized by osteolysis, inflammatory recruitment, and extensive vascularization, processes in which matrix proteases play a prominent role. This led us to explore whether TRE17 regulates the production of matrix metalloproteinases (MMPs). In the current study, we demonstrate that TRE17 is sufficient to induce expression of MMP-9 and MMP-10, in a manner requiring its USP activity, but not its ability to bind Arf6. TRE17 induces transcription of MMP-9 through activation of NFκB, mediated in part by the GTPase RhoA and its effector kinase, ROCK. Furthermore, xenograft studies demonstrate that TRE17 induces formation of tumors that reproduce multiple features of ABC, including a high degree of vascularization, with an essential role for the USP domain. In sum, these studies reveal that TRE17 is sufficient to initiate tumorigenesis, identify MMPs as novel TRE17 effectors that likely contribute to ABC pathogenesis, and define the underlying signaling mechanism of their induction.