The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion

Assembly of dsDNA bacteriophage is a precisely programmed process. Potential roles of host cell components in phage assembly haven’t been well understood. It was previously reported that two unidentified proteins were present in bacteriophage Sf6 virion (Casjens et al, 2004, J. Mol. Biol. 339, 379–394, Figure 2A). Using tandem mass spectrometry, we have identified the two proteins as outer membrane proteins (OMPs) OmpA and OmpC from its host Shigella flexneri. The transmission electron cryo-microscopy structure of Sf6 shows significant density at specific sites at the phage capsid inner surface. These density fit well with the characteristic beta-barrel domains of OMPs, thus may be due to the two host proteins. Locations of these density suggest a role in Sf6 morphogenesis reminiscent of phage-encoded cementing proteins. These data indicate a new, OMP-related phage:host linkage, adding to previous knowledge that some lambdoid bacteriophage genomes contain OmpC-like genes that express phage-encoded porins in the lysogenic state

The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion

Assembly of dsDNA bacteriophage is a precisely programmed process. Potential roles of host cell components in phage assembly haven’t been well understood. It was previously reported that two unidentified proteins were present in bacteriophage Sf6 virion (Casjens et al, 2004, J. Mol. Biol. 339, 379–394, Figure 2A). Using tandem mass spectrometry, we have identified the two proteins as outer membrane proteins (OMPs) OmpA and OmpC from its host Shigella flexneri. The transmission electron cryo-microscopy structure of Sf6 shows significant density at specific sites at the phage capsid inner surface. These density fit well with the characteristic beta-barrel domains of OMPs, thus may be due to the two host proteins. Locations of these density suggest a role in Sf6 morphogenesis reminiscent of phage-encoded cementing proteins. These data indicate a new, OMP-related phage:host linkage, adding to previous knowledge that some lambdoid bacteriophage genomes contain OmpC-like genes that express phage-encoded porins in the lysogenic state

Expansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza

Tanshinones are the bioactive nor-diterpenoid constituents of the Chinese medicinal herb Danshen (Salvia miltiorrhiza). These groups of chemicals have the characteristic furan D-ring, which differentiates them from the phenolic abietane-type diterpenoids frequently found in the Lamiaceae family. However, how the 14,16-epoxy is formed has not been elucidated. Here, we report an improved genome assembly of Danshen using a highly homozygous genotype. We identify a cytochrome P450 (CYP71D) tandem gene array through gene expansion analysis. We show that CYP71D373 and CYP71D375 catalyze hydroxylation at carbon-16 (C16) and 14,16-ether (hetero)cyclization to form the D-ring, whereas CYP71D411 catalyzes upstream hydroxylation at C20. In addition, we discover a large biosynthetic gene cluster associated with tanshinone production. Collinearity analysis indicates a more specific origin of tanshinones in Salvia genus. It illustrates the evolutionary origin of abietane-type diterpenoids and those with a furan D-ring in Lamiaceae

Reprogramming Primordial Germ Cells into Pluripotent Stem Cells

Background: Specification of primordial germ cells (PGCs) results in the conversion of pluripotent epiblast cells into monopotent germ cell lineage. Blimp1/Prmt5 complex plays a critical role in the specification and maintenance of the early germ cell lineage. However, PGCs can be induced to dedifferentiate back to a pluripotent state as embryonic germ (EG) cells when exposed to exogenous signaling molecules, FGF-2, LIF and SCF. Methodology and Principal Findings: Here we show that Trichostatin A (TSA), an inhibitor of histone deacetylases, is a highly potent agent that can replace FGF-2 to induce dedifferentiation of PGCs into EG cells. A key early event during dedifferentiation of PGCs in response to FGF-2 or TSA is the down-regulation of Blimp1, which reverses and apparently relieves the cell fate restriction imposed by it. Notably, the targets of Blimp1, which include c-Myc and Klf-4, which represent two of the key factors known to promote reprogramming of somatic cells to pluripotent state, are up-regulated. We also found early activation of the LIF/Stat-3 signaling pathway with the translocation of Stat-3 into the nucleus. By contrast, while Prmt5 is retained in EG cells, it translocates from the nucleus to the cytoplasm where it probably has an independent role in regulating pluripotency. Conclusions/Significance: We propose that dedifferentiation of PGCs into EG cells may provide significant mechanistic insights on early events associated with reprogramming of committed cells to a pluripotent state

Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity

BACKGROUND: Metastasis is the primary cause of cancer mortality accounting for 90% of cancer deaths. Our understanding of the molecular mechanisms driving metastasis is rudimentary. RESULTS: We perform whole exome sequencing (WES), RNA sequencing, methylation microarray, and immunohistochemistry (IHC) on 8 pairs of non-small cell lung cancer (NSCLC) primary tumors and matched distant metastases. Furthermore, we analyze published WES data from 35 primary NSCLC and metastasis pairs, and transcriptomic data from 4 autopsy cases with metastatic NSCLC and one metastatic lung cancer mouse model. The majority of somatic mutations are shared between primary tumors and paired distant metastases although mutational signatures suggest different mutagenesis processes in play before and after metastatic spread. Subclonal analysis reveals evidence of monoclonal seeding in 41 of 42 patients. Pathway analysis of transcriptomic data reveals that downregulated pathways in metastases are mainly immune-related. Further deconvolution analysis reveals significantly lower infiltration of various immune cell types in metastases with the exception of CD4+ T cells and M2 macrophages. These results are in line with lower densities of immune cells and higher CD4/CD8 ratios in metastases shown by IHC. Analysis of transcriptomic data from autopsy cases and animal models confirms that immunosuppression is also present in extracranial metastases. Significantly higher somatic copy number aberration and allelic imbalance burdens are identified in metastases. CONCLUSIONS: Metastasis is a molecularly late event, and immunosuppression driven by different molecular events, including somatic copy number aberration, may be a common characteristic of tumors with metastatic plasticity

A proposed prognostic 7-day survival formula for patients with terminal cancer

<p>Abstract</p> <p>Background</p> <p>The ability to identify patients for hospice care results in better end-of-life care. To develop a validated prognostic scale for 7-day survival prediction, a prospective observational cohort study was made of patients with terminal cancer.</p> <p>Methods</p> <p>Patient data gathered within 24 hours of hospital admission included demographics, clinical signs and symptoms and their severity, laboratory test results, and subsequent survival data. Of 727 patients enrolled, data from 374 (training group) was used to develop a prognostic tool, with the other 353 serving as the validation group.</p> <p>Results</p> <p>Five predictors identified by multivariate logistic regression analysis included patient's cognitive status, edema, ECOG performance status, BUN and respiratory rate. A formula of the predictor model based on those five predictors was constructed. When probability was >0.2, death within 7 days was predicted in the training group and validation group, with sensitivity of 80.9% and 71.0%, specificity of 65.9% and 57.7%, positive predictive value of 42.6% and 26.8%, and negative predictive value (NPV) of 91.7% and 90.1%, respectively.</p> <p>Conclusion</p> <p>This predictor model showed a relatively high sensitivity and NPV for predicting 7-day survival among terminal cancer patients, and could increase patient satisfaction by improving end-of-life care.</p

Association of Serum Albumin with Markers of Nutritional Status among HIV-Infected and Uninfected Rwandan Women

The objectives of this study are to address if and how albumin can be used as an indication of malnutrition in HIV infected and uninfected Africans.In 2005, 710 HIV-infected and 226 HIV-uninfected women enrolled in a cohort study. Clinical/demographic parameters, CD4 count, albumin, liver transaminases; anthropometric measurements and Bioelectrical Impedance Analysis (BIA) were performed. Malnutrition outcomes were defined as body mass index (BMI), Fat-free mass index (FFMI) and Fat mass index (FMI). Separate linear predictive models including albumin were fit to these outcomes in HIV negative and HIV positive women by CD4 strata (CD4>350,200-350 and <200 cells/µl).In unadjusted models for each outcome in HIV-negative and HIV positive women with CD4>350 cells/µl, serum albumin was not significantly associated with BMI, FFMI or FMI. Albumin was significantly associated with all three outcomes (p<0.05) in HIV+ women with CD4 200-350 cells/µl, and highly significant in HIV+ women with CD4<200 cells/µl (P<0.001). In multivariable linear regression, albumin remained associated with FFMI in women with CD4 count<200 cells/µl (p<0.01) but not in HIV+ women with CD4>200.While serum albumin is widely used to indicate nutritional status it did not consistently predict malnutrition outcomes in HIV- women or HIV+ women with higher CD4. This result suggests that albumin may measure end stage disease as well as malnutrition and should not be used as a proxy for nutritional status without further study of its association with validated measures

HIV-1 Matrix Dependent Membrane Targeting Is Regulated by Gag mRNA Trafficking

Retroviral Gag polyproteins are necessary and sufficient for virus budding. Productive HIV-1 Gag assembly takes place at the plasma membrane. However, little is known about the mechanisms by which thousands of Gag molecules are targeted to the plasma membrane. Using a bimolecular fluorescence complementation (BiFC) assay, we recently reported that the cellular sites and efficiency of HIV-1 Gag assembly depend on the precise pathway of Gag mRNA export from the nucleus, known to be mediated by Rev. Here we describe an assembly deficiency in human cells for HIV Gag whose expression depends on hepatitis B virus (HBV) post-transcriptional regulatory element (PRE) mediated-mRNA nuclear export. PRE-dependent HIV Gag expressed well in human cells, but assembled with slower kinetics, accumulated intracellularly, and failed to associate with a lipid raft compartment where the wild-type Rev-dependent HIV-1 Gag efficiently assembles. Surprisingly, assembly and budding of PRE-dependent HIV Gag in human cells could be rescued in trans by co-expression of Rev-dependent Gag that provides correct membrane targeting signals, or in cis by replacing HIV matrix (MA) with other membrane targeting domains. Taken together, our results demonstrate deficient membrane targeting of PRE-dependent HIV-1 Gag and suggest that HIV MA function is regulated by the trafficking pathway of the encoding mRNA

Large trees drive forest aboveground biomass variation in moist lowland forests accross the tropics

peer reviewedaudience: researcher, professional, studentAim Large trees (d.b.h. 70 cm) store large amounts of biomass. Several studies suggest that large trees may be vulnerable to changing climate, potentially leading to declining forest biomass storage. Here we determine the importance of large trees for tropical forest biomass storage and explore which intrinsic (species trait) and extrinsic (environment) variables are associated with the density of large trees and forest biomass at continental and pan-tropical scales. Location Pan-tropical. Methods Aboveground biomass (AGB) was calculated for 120 intact lowland moist forest locations. Linear regression was used to calculate variation in AGB explained by the density of large trees. Akaike information criterion weights (AICcwi) were used to calculate averaged correlation coefficients for all possible multiple regression models between AGB/density of large trees and environmental and species trait variables correcting for spatial autocorrelation. Results Density of large trees explained c. 70% of the variation in pan-tropical AGB and was also responsible for significantly lower AGB in Neotropical [287.8 (mean) 105.0 (SD) Mg ha-1] versus Palaeotropical forests (Africa 418.3 91.8 Mg ha-1; Asia 393.3 109.3 Mg ha-1). Pan-tropical variation in density of large trees and AGB was associated with soil coarseness (negative), soil fertility (positive), community wood density (positive) and dominance of wind dispersed species (positive), temperature in the coldest month (negative), temperature in the warmest month (negative) and rainfall in the wettest month (positive), but results were not always consistent among continents. Main conclusions Density of large trees and AGB were significantly associated with climatic variables, indicating that climate change will affect tropical forest biomass storage. Species trait composition will interact with these future biomass changes as they are also affected by a warmer climate. Given the importance of large trees for variation in AGB across the tropics, and their sensitivity to climate change, we emphasize the need for in-depth analyses of the community dynamics of large trees