Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli

Nucleoid-associated proteins (NAPs) are global regulators of gene expression in Escherichia coli, which affect DNA conformation by bending, wrapping and bridging the DNA. Two of these—H-NS and Fis—bind to specific DNA sequences and structures. Because of their importance to global gene expression, the binding of these NAPs to the DNA was previously investigated on a genome-wide scale using ChIP-chip. However, variation in their binding profiles across the growth phase and the genome-scale nature of their impact on gene expression remain poorly understood. Here, we present a genome-scale investigation of H-NS and Fis binding to the E. coli chromosome using chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-seq). By performing our experiments under multiple time-points during growth in rich media, we show that the binding regions of the two proteins are mutually exclusive under our experimental conditions. H-NS binds to significantly longer tracts of DNA than Fis, consistent with the linear spread of H-NS binding from high- to surrounding lower-affinity sites; the length of binding regions is associated with the degree of transcriptional repression imposed by H-NS. For Fis, a majority of binding events do not lead to differential expression of the proximal gene; however, it has a significant indirect effect on gene expression partly through its effects on the expression of other transcription factors. We propose that direct transcriptional regulation by Fis is associated with the interaction of tandem arrays of Fis molecules to the DNA and possible DNA bending, particularly at operon-upstream regions. Our study serves as a proof-of-principle for the use of ChIP-seq for global DNA-binding proteins in bacteria, which should become significantly more economical and feasible with the development of multiplexing techniques

Vaccination History of Respondents Vaccinated in 2009–2010 (Weighted)^*.

<p>*The poststratification weights were computed using data from the Current Population Survey and adjust for known sampling probabilities; sample stratification; and non-response to panel recruitment and panel attrition.</p><p>**p-value for differences across always/sometimes/rarely.</p><p>Vaccination History of Respondents Vaccinated in 2009–2010 (Weighted)^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114863#nt103" target="_blank">*</a>}.</p

Overview of selected sample characteristics (n = 4,040)^*.

<p>*The poststratification weights were computed using data from the Current Population Survey and adjust for known sampling probabilities; sample stratification; and non-response to panel recruitment and panel attrition.</p><p>**Calculated for only those respondents who reported receiving their first influenza vaccination three or more years prior to the fielding of the survey.</p><p>Overview of selected sample characteristics (n = 4,040)^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114863#nt101" target="_blank">*</a>}.</p

A systematic review on the role of imaging in early recurrent prostate cancer

CONTEXT: In patients treated for prostate cancer, a rising serum prostate-specific antigen (PSA) level is a first sign of relapse, but imaging is needed to determine the localization of the recurrence, which may be local, in lymph nodes, and/or metastatic. With the increasing success rate of earlier salvage therapy, the diagnosis has become pertinent when the recurrent PSA level is still very low. OBJECTIVE: To systematically review the literature on the role of the existing imaging techniques in patients with early recurrent prostate cancer. EVIDENCE ACQUISITION: A systematic literature search across the MEDLINE and EMBASE databases was conducted in February 2018, searching for original studies reporting on imaging in a (sub)group of patients with recurrent PSA levels not higher than 5ng/ml. This systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines. The methodological quality of the studies was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) tool. EVIDENCE SYNTHESIS: A total of 98 studies were included in this systematic review, reporting on the role of transrectal ultrasonography (TRUS), computed tomography (CT), bone scintigraphy (BS), single-photon emission CT, multiparametric magnetic resonance imaging (mpMRI), whole-body MRI (wbMRI), and positron emission tomography (PET)-CT/MRI using 18F fluoro-deoxy-glucose, 11C choline, 18F (fluoro)(methyl)choline, 11C acetate, 18F FACBC (fluciclovine) and prostate-specific membrane antigen (PSMA)-based tracers. CT and BS were not sufficiently sensitive in the early recurrence setting. For the detection of local recurrence, TRUS or mpMRI can be used; however, at the lowest PSA levels, few data were available, only after radical prostatectomy, showing a wide range of positivity. TRUS or mpMRI need to be combined with (PET)-CT to assess distant disease, but new techniques such as wbMRI, PET-MRI, or PET-CT allow for an all-in-one approach. At recurrent PSA levels <0.5ng/ml, detection rates up to 31.3% were reported using (11)C choline PET-CT and up to 65.0% using (68)Ga PSMA-11 PET-CT. At recurrent PSA levels <0.2ng/ml, detection rates of (68)Ga PSMA-11 PET-CT ranged from 11.3% to as high as 58.3%. CONCLUSIONS: Detection rates of different imaging techniques depend on the PSA level at the time of imaging. Recent advanced imaging techniques may detect the localization of the recurrence, even when the PSA levels are still very low. PATIENT SUMMARY: In patients treated for prostate cancer, a rising serum prostate-specific antigen (PSA) level is a sign of recurrence of the disease. Advanced imaging techniques may demonstrate the localization of the recurrence, even when the PSA levels are still very low

In vivo magnetic resonance imaging of acute brain inflammation using microparticles of iron oxide.

Multiple sclerosis is a disease of the central nervous system that is associated with leukocyte recruitment and subsequent inflammation, demyelination and axonal loss. Endothelial vascular cell adhesion molecule-1 (VCAM-1) and its ligand, alpha4beta1 integrin, are key mediators of leukocyte recruitment, and selective inhibitors that bind to the alpha4 subunit of alpha4beta1 substantially reduce clinical relapse in multiple sclerosis. Urgently needed is a molecular imaging technique to accelerate diagnosis, to quantify disease activity and to guide specific therapy. Here we report in vivo detection of VCAM-1 in acute brain inflammation, by magnetic resonance imaging in a mouse model, at a time when pathology is otherwise undetectable. Antibody-conjugated microparticles carrying a large amount of iron oxide provide potent, quantifiable contrast effects that delineate the architecture of activated cerebral blood vessels. Their rapid clearance from blood results in minimal background contrast. This technology is adaptable to monitor the expression of endovascular molecules in vivo in various pathologies