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The Q protein of bacteriophage lambda is a transcription antiterminator that modifies the elongation properties of E. coli RNA polymerase (RNAP). To do this, DNA-bound (lambda)Q must first engage a paused elongation complex. Here we show that this engagement of (lambda)Q with RNAP involves an interaction between (lambda)Q and sigma(70), demonstrating that sigma(70) can be a target of regulation during elongation. Furthermore, we provide evidence that this interaction between (lambda)Q and sigma(70) stabilizes a conformation of RNAP that requires the disengagement of a segment of sigma(70) from the core enzyme. Recent structure-based models posit that the transition from the initiation to the elongation phase of transcription involves the staged displacement of sigma(70) from the RNAP core. Our findings provide support for this proposal.

Background: Preoperative/Neoadjuvant treatment (NT) is increasingly used in unresectable pancreatic cancer (PDAC). However,~40% of patients cannot be resected after NT and reliable preoperative response evaluation is currently lacking. We investigated CA 19-9 levels and their dynamics during NT for prediction of resectability and survival.Methods: We screened our institution's database for patients who underwent exploration or resection after NT with gemcitabine-based therapy (GEM) or FOLFIRINOX (FOL). Pre-and post-NT CA 19-9, resection rate and survival were analyzed.Results: Of 318 patients 165 (51.9%) were resected and 153 (48.1%) received exploration. In the FOL group (n = 103; 32.4%), a post-NT CA 19-9 cutoff at 91.8 U/ml had a sensitivity of 75.0% and a specificity of 76.9% for completing resection with an AUC of 0.783 in the ROC analysis (95% CI: 0.692-0.874; p < 0.001. PPV: 84.2%, NPV: 65.2%). Resected patients above the cutoff did not benefit from resection. Post-NT CA 19-9 <91.8 U/ml (OR 11.63, p < 0.001) and CA 19-9 ratio of <0.4 (OR 5.77, p = 0.001) were independent predictors for resectability in FOL patients.Discussion: CA 19-9 levels after neoadjuvant treatment with FOLFIRINOX predict resectability and survival of PDAC more accurately than dynamic values and should be incorporated into response evaluation and surgical decision-making.

Pluripotent stem cells, including induced pluripotent and embryonic stem cells (ESCs), have less developed mitochondria than somatic cells and, therefore, rely more heavily on glycolysis for energy production. However, how mitochondrial homeostasis matches the demands of nuclear reprogramming and regulates pluripotency in ESCs is largely unknown. Here, we identified ATG3-dependent autophagy as an executor for both mitochondrial remodeling during somatic cell reprogramming and mitochondrial homeostasis regulation in ESCs. Dysfunctional autophagy by Atg3 deletion inhibited mitochondrial removal during pluripotency induction, resulting in decreased reprogramming efficiency and accumulation of abnormal mitochondria in established iPSCs. In Atg3 null mouse ESCs, accumulation of aberrant mitochondria was accompanied by enhanced ROS generation, defective ATP production and attenuated pluripotency gene expression, leading to abnormal self-renewal and differentiation. These defects were rescued by reacquisition of wild-type but not lipidation-deficient Atg3 expression. Taken together, our findings highlight a critical role of ATG3-dependent autophagy for mitochondrial homeostasis regulation in both pluripotency acquirement and maintenance.

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BackgroundAvian pathogenic Escherichia coli (APEC) is a major cause of disease impacting animal health. The bone marrow is the reservoir of immature immune cells; however, it has not been examined to date for gene expression related to developmental changes (cell differentiation, maturation, programming) after APEC infection. Here, we study gene expression in the bone marrow between infected and non-infected animals, and between infected animals with mild (resistant) versus severe (susceptible) pathology, at two times post-infection.ResultsWe sequenced 24 bone marrow RNA libraries generated from the six different treatment groups with four replicates each, and obtained an average of 22 million single-end, 100-bp reads per library. Genes were detected as differentially expressed (DE) between APEC treatments (mild pathology, severe pathology, and mock-challenged) at a given time point, or DE between 1 and 5 days post-infection (dpi) within the same treatment group. Results demonstrate that many immune cells, genes and related pathways are key contributors to the different responses to APEC infection between susceptible and resistant birds and between susceptible and non-challenged birds, at both times post-infection. In susceptible birds, lymphocyte differentiation, proliferation, and maturation were greatly impaired, while the innate and adaptive immune responses, including dendritic cells, monocytes and killer cell activity, TLR- and NOD-like receptor signaling, as well as T helper cells and many cytokine activities, were markedly enhanced. The resistant birds’ immune system, however, was similar to that of non-challenged birds.ConclusionThe DE genes in the immune cells and identified signaling models are representative of activation and resolution of infection in susceptible birds at both post-infection days. These novel results characterizing transcriptomic response to APEC infection reveal that there is combinatorial activity of multiple genes controlling myeloid cells, and B and T cell lymphopoiesis, as well as immune responses occurring in the bone marrow in these early stages of response to infection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1850-4) contains supplementary material, which is available to authorized users.

This study was aimed to reveal the changes in survival rates and prognostic factors to survival of chondroblastic osteosarcoma (COS).Patients from the Surveillance, Epidemiology, and End Results (SEER) database were retrieved. Kaplan–Meier survival analysis and Cox proportional hazard model were used during analysis.There were significant differences on overall survival between subtypes of osteosarcoma (P < .001∗). Overall survival of COS did not change significantly during last forty years (P = .610), and cancer-specific survival increased to a plateau in 1980s and then remained stable (P = .058). Younger onset age, patients of white race, well and moderately differentiated tumors, and surgery independently predicted better overall (Hazard ratio [HR]: 1.034, P < .001∗; HR: 0.538, P = .004∗; HR: 0.240, P = .020∗ and HR: 0.350, P < .001∗, respectively) and cancer-specific (HR: 1.031, P = .002∗; HR: 0.592, P = .036∗; HR: 0.098, P = .027∗ and HR: 0.253, P < .001∗, respectively) survival. Metastasis at diagnosis independently predicted worse overall (HR: 3.108, P < .001∗) and cancer-specific (HR: 4.26, P < .001∗) survival compared to no metastasis.Younger onset age, white race, well and moderately differentiated tumors, no metastasis at diagnosis and surgical resection can independently predict better overall and cancer-specific survival of COS.

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