784 research outputs found
Time-Accurate Unsteady Flow Simulations Supporting the SRM T+68-Second Pressure Spike Anomaly Investigation (STS-54B)
Time-accurate unsteady flow simulations are being performed supporting the SRM T+68sec pressure 'spike' anomaly investigation. The anomaly occurred in the RH SRM during the STS-54 flight (STS-54B) but not in the LH SRM (STS-54A) causing a momentary thrust mismatch approaching the allowable limit at that time into the flight. Full-motor internal flow simulations using the USA-2D axisymmetric code are in progress for the nominal propellant burn-back geometry and flow conditions at T+68-sec--Pc = 630 psi, gamma = 1.1381, T(sub c) = 6200 R, perfect gas without aluminum particulate. In a cooperative effort with other investigation team members, CFD-derived pressure loading on the NBR and castable inhibitors was used iteratively to obtain nominal deformed geometry of each inhibitor, and the deformed (bent back) inhibitor geometry was entered into this model. Deformed geometry was computed using structural finite-element models. A solution for the unsteady flow has been obtained for the nominal flow conditions (existing prior to the occurrence of the anomaly) showing sustained standing pressure oscillations at nominally 14.5 Hz in the motor IL acoustic mode that flight and static test data confirm to be normally present at this time. Average mass flow discharged from the nozzle was confirmed to be the nominal expected (9550 lbm/sec). The local inlet boundary condition is being perturbed at the location of the presumed reconstructed anomaly as identified by interior ballistics performance specialist team members. A time variation in local mass flow is used to simulate sudden increase in burning area due to localized propellant grain cracks. The solution will proceed to develop a pressure rise (proportional to total mass flow rate change squared). The volume-filling time constant (equivalent to 0.5 Hz) comes into play in shaping the rise rate of the developing pressure 'spike' as it propagates at the speed of sound in both directions to the motor head end and nozzle. The objectives of the present analysis are to: (1) capture the dynamic responses of the motor combustion gas flow to correlate with available low-frequency (less than 12.5 sample/sec) data and (2) observe the high-frequency (up to 50 Hz) characteristics of the response to determine any potentials for dynamic coupling
Unsteady Flow Simulations in Support of the SSME HEX Turning Vane Cracking Investigation with the ATD HPOTP
Unsteady flow computations are being performed with the P&W (ATD) and the Rocketdyne baseline configurations of the SSME LO2 turbine turnaround duct (TAD) and heat exchanger (HEX). The work is in support of the HEX inner turning vane cracking investigation. Fatigue cracking has occurred during hot firings with the P&W configuration on the HEX inner vane, and it appears the fix will involve changes to the TAD splitter vane position and to the TAD inner wall curvature to reduce the dynamic loading on the inner vane. Unsteady flow computations on the P&W baseline and fix and on the Rocketdyne baseline reference follow steady-flow screening computations done by MSFC/ED32 on several trial configurations arriving at the fix. The P&W TAD inlet velocity profile has a strong radial velocity component that directs the flow toward the inner wall and raises the local velocity a factor of two and the dynamic pressure a factor, of four. The fix is intended to redistribute the flow more evenly across the HEX inner and outer vanes like the Rocketdyne baseline reference. Vane buffeting at frequencies around 4,000 Hz is the leading suspected cause of the problem. Our simulations (work in progress) are being done with the USA 2D axisymmetric code approximating the flow as axisymmetric u+v 2D (axial, u, and radial, v, components only). The HEX coils are included in the model to make sure the fix does not adversely affect the HEX environment. Turbulent kinetic energy, k, levels where k = 1/2 v' rms2 are locally as high as 10,000 ft2/sec2 for the P&W baseline at the engine interface (between the TAD and HEX) at the HEX inner vane location. However, k is less than 8,000 on the HEX outer vane and only about 4,500 on the HEX inner vane for the Rocketdyne baseline. Unsteady turbulence intensity, v'rms/v, and pressure, p', are being computed in the present computations to compare with steady-flow Reynolds-averaged computations where p'rms = const (pk) for overall rms random turbulence from 0.1 to 12,000 Hz frequency. Random overall static, p'rms fluctuations as large as 1.7 psi are estimated from k on the HEX inner vane for the P&W baseline configuration but only about 0.7 psi for the Rocketdyne configuration
Import of cytochrome c into mitochondria
The import of cytochrome c into mitochondria can be resolved into a number of discrete steps. Here we report on the covalent attachment of heme to apocytochrome c by the enzyme cytochrome c heme lyase in mitochondria from Neurospora crassa.
A new method was developed to measure directly the linkage of heme to apocytochrome c. This method is independent of conformational changes in the protein accompanying heme attachment. Tryptic peptides of [35S]cysteine-labelled apocytochrome c, and of enzymatically formed holocytochrome c, were resolved by reverse-phase HPLC. The cysteine-containing peptide to which heme was attached eluted later than the corresponding peptide from apocytochrome c and could be quantified by counting 35S radioactivity as a measure of holocytochrome c formation. Using this procedure, the covalent attachment of heme to apocytochrome c, which is dependent on the enzyme cytochrome c heme lyase, could be measured. Activity required heme (as hemin) and could be reversibly inhibited by the analogue deuterohemin. Holocytochrome c formation was stimulated 5–10-fold by NADH > NADPH > glutathione and was independent of a potential across the inner mitochondrial membrane. NADH was not required for the binding of apocytochrome c to mitochondria and was not involved in the reduction of the cysteine thiols prior to heme attachment. Holocytochrome c formation was also dependent on a cytosolic factor that was necessary for the heme attaching step of cytochrome c import. The factor was a heat-stable, protease-insensitive, low-molecular-mass component of unknown function.
Cytochrome c heme lyase appeared to be a soluble protein located in the mitochondrial intermembrane space and was distinct from the previously identified apocytochrome c binding protein having a similar location. A model is presented in which the covalent attachment of heme by cytochrome c heme lyase also plays an essential role in the import pathway of cytochrome c
Effects of deletion of the Streptococcus pneumoniae lipoprotein diacylglyceryl transferase gene lgt on ABC transporter function and on growth in vivo
Lipoproteins are an important class of surface associated proteins that have diverse roles and frequently are involved in the virulence of bacterial pathogens. As prolipoproteins are attached to the cell membrane by a single enzyme, prolipoprotein diacylglyceryl transferase (Lgt), deletion of the corresponding gene potentially allows the characterisation of the overall importance of lipoproteins for specific bacterial functions. We have used a Δlgt mutant strain of Streptococcus pneumoniae to investigate the effects of loss of lipoprotein attachment on cation acquisition, growth in media containing specific carbon sources, and virulence in different infection models. Immunoblots of triton X-114 extracts, flow cytometry and immuno-fluorescence microscopy confirmed the Δlgt mutant had markedly reduced lipoprotein expression on the cell surface. The Δlgt mutant had reduced growth in cation depleted medium, increased sensitivity to oxidative stress, reduced zinc uptake, and reduced intracellular levels of several cations. Doubling time of the Δlgt mutant was also increased slightly when grown in medium with glucose, raffinose and maltotriose as sole carbon sources. These multiple defects in cation and sugar ABC transporter function for the Δlgt mutant were associated with only slightly delayed growth in complete medium. However the Δlgt mutant had significantly reduced growth in blood or bronchoalveolar lavage fluid and a marked impairment in virulence in mouse models of nasopharyngeal colonisation, sepsis and pneumonia. These data suggest that for S. pneumoniae loss of surface localisation of lipoproteins has widespread effects on ABC transporter functions that collectively prevent the Δlgt mutant from establishing invasive infection
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types
Therapeutic effects of STAT3 decoy oligodeoxynucleotide on human lung cancer in xenograft mice
<p>Abstract</p> <p>Background</p> <p>Signal transducer and activator of transcription 3 (STAT3) is usually constitutively activated in a variety of malignancies. Therefore, STAT3 may be a promising target for treatment of tumor cells. To explore the possibility of a double-stranded decoy oligodeoxynucleotide (ODN) targeted blocking STAT3 over-activated tumor cells, we, here, evaluate the efficacy of STAT3 decoy ODN on human lung cancer cells <it>in vitro </it>and <it>in vivo</it>.</p> <p>Methods</p> <p>A STAT3 decoy ODN was transfected into A549 lung cancer cell line <it>in vitro </it>by using lipofectamine. The flow cytometry and fluorescent microscopy were used to detect the transfection efficiency and the sub-cellular localization of STAT3 decoy ODN in A549 cells. Cell proliferation was determined by counting cell numbers and [<sup>3</sup>H]-thymidine uptake. Cell apoptosis was examined with Annexin V and propidum iodide by flow cytometry. The expression levels of STAT3 target genes were identified by RT-PCR and immunoblot. For <it>in vivo </it>experiment, A549 lung carcinoma-nude mice xenograft was used as a model to examine the effect of the STAT3 decoy by intratumoral injection. At the end of treatment, TUNEL and immunohistochemistry were used to examine the apoptosis and the expression levels of bcl-xl and cyclin D1 in tumor tissues.</p> <p>Results</p> <p>STAT3 decoy ODN was effectively transfected into A549 lung cancer cells and mainly located in nucleus. STAT3-decoy ODN significantly induced apoptosis and reduced [<sup>3</sup>H]-thymidine incorporation of A549 cells as well as down-regulated STAT3-target genes <it>in vitro</it>. STAT3 decoy ODN also dramatically inhibited the lung tumor growth in xenografted nude mice and decreased gene expression of bcl-xl and cyclin D1.</p> <p>Conclusion</p> <p>STAT3 decoy ODN significantly suppressed lung cancer cells <it>in vitro </it>and <it>in vivo</it>, indicating that STAT3 decoy ODN may be a potential therapeutic approach for treatment of lung cancer.</p
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing
molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas
Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts
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