It is unclear how important CRISPR-Cas systems are for protecting natural populations of bacteria against infections by mobile genetic elements

This is the final version. Available on open access from the National Academy of Sciences via the DOI in this recordData Availability: All study data are included in the article and SI Appendix.Articles on CRISPR commonly open with some variant of the phrase “these short palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements.” There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude, and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical–computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect them.Natural Environment Research Council (NERC)Biotechnology and Biological Sciences Research Council (BBSRC)European Research Council (ERC)US National Institutes of General Medical ScienceEmory Universit

Transcriptomic Profiling in Childhood H1N1/09 Influenza Reveals Reduced Expression of Protein Synthesis Genes

We compared the blood RNA transcriptome of children hospitalized with influenza A H1N1/09, respiratory syncytial virus (RSV) or bacterial infection, and healthy controls. Compared to controls, H1N1/09 patients showed increased expression of inflammatory pathway genes and reduced expression of adaptive immune pathway genes. This was validated on an independent cohort. The most significant function distinguishing H1N1/09 patients from controls was protein synthesis, with reduced gene expression. Reduced expression of protein synthesis genes also characterized the H1N1/09 expression profile compared to children with RSV and bacterial infection, suggesting that this is a key component of the pathophysiological response in children hospitalized with H1N1/09 infection

Nongenomic oestrogen signalling in oestrogen receptor negative breast cancer cells: a role for the angiotensin II receptor AT1

INTRODUCTION: Oestrogens can mediate some of their cell survival properties through a nongenomic mechanism that involves the mitogen-activated protein kinase (MAPK) pathway. The mechanism of this rapid signalling and its dependence on a membrane bound oestrogen receptor (ER), however, remains controversial. The role of G-protein-coupled receptor and epidermal growth factor (EGF) receptor in an ER-independent signalling pathway modulated by oestrogen was investigated. METHODS: ER-positive and ER-negative breast cancer cell lines (MCF-7 and SKBR3) and primary breast cancer cell cultures were used in this study. Cell proliferation was assessed using standard MTT assays. Protein and cAMP levels were detected by Western blotting and ELISA, respectively. Antigen localization was performed by immunocytochemistry, immunohistochemistry and immunofluorescence. Protein knockdown was achieved using small interfering RNA technologies. RESULTS: EGF and oestrogen, alone and in combination, induced cell proliferation and phosphorylation of MAPK proteins Raf and ERK (extracellular signal regulated kinase)1/2 in both ER-negative SKBR3 and ER-positive MCF-7 human breast cancer cell lines. Increased Raf phosphorylation was also observed in primary human breast cultures derived from ER-positive and ER-negative breast tumours. Oestrogen induced an increase in intracellular cAMP in ER-negative SKBR3 human breast cancer cells. Oestrogen-mediated cell growth and phosphorylation of MAPK was modified by the EGF receptor antagonist AG1478, the G-protein antagonist pertussis toxin, and the angiotensin II receptor antagonist saralasin. Knockdown of angiotensin II type 1 receptor (AT1) protein expression with small interfering RNA attenuated oestrogen-induced Raf phosphorylation in ER-negative cells. AT1 receptor was found to be expressed in the cell membrane of breast tumour epithelial cells. CONCLUSION: These findings provide evidence that, in breast cancer cells, oestrogen can signal through AT1 to activate early cell survival mechanisms in an ER-independent manner

Endothelin receptor B antagonists decrease glioma cell viability independently of their cognate receptor

Background: Endothelin receptor antagonists inhibit the progression of many cancers, but research into their influence on glioma has been limited. Methods: We treated glioma cell lines, LN-229 and SW1088, and melanoma cell lines, A375 and WM35, with two endothelin receptor type B (ETRB)-specific antagonists, A-192621 and BQ788, and quantified viable cells by the capacity of their intracellular esterases to convert non-fluorescent calcein AM into green-fluorescent calcein. We assessed cell proliferation by labeling cells with carboxyfluorescein diacetate succinimidyl ester and quantifying the fluorescence by FACS analysis. We also examined the cell cycle status using BrdU/propidium iodide double staining and FACS analysis. We evaluated changes in gene expression by microarray analysis following treatment with A-192621 in glioma cells. We examined the role of ETRB by reducing its expression level using small interfering RNA (siRNA). Results: We report that two ETRB-specific antagonists, A-192621 and BQ788, reduce the number of viable cells in two glioma cell lines in a dose- and time-dependent manner. We describe similar results for two melanoma cell lines. The more potent of the two antagonists, A-192621, decreases the mean number of cell divisions at least in part by inducing a G2/M arrest and apoptosis. Microarray analysis of the effects of A-192621 treatment reveals up-regulation of several DNA damage-inducible genes. These results were confirmed by real-time RT-PCR. Importantly, reducing expression of ETRB with siRNAs does not abrogate the effects of either A-192621 or BQ788 in glioma or melanoma cells. Furthermore, BQ123, an endothelin receptor type A (ETRA)-specific antagonist, has no effect on cell viability in any of these cell lines, indicating that the ETRB-independent effects on cell viability exhibited by A-192621 and BQ788 are not a result of ETRA inhibition. Conclusion: While ETRB antagonists reduce the viability of glioma cells in vitro, it appears unlikely that this effect is mediated by ETRB inhibition or cross-reaction with ETRA. Instead, we present evidence that A-192621 affects glioma and melanoma viability by activating stress/DNA damage response pathways, which leads to cell cycle arrest and apoptosis. This is the first evidence linking ETRB antagonist treatment to enhanced expression of DNA damage-inducible genes

High Energy Bounds on Soft N=4 SYM Amplitudes from AdS/CFT

Using the AdS/CFT correspondence, we study the high-energy behavior of colorless dipole elastic scattering amplitudes in N=4 SYM gauge theory through the Wilson loop correlator formalism and Euclidean to Minkowskian analytic continuation. The purely elastic behavior obtained at large impact-parameter L, through duality from disconnected AdS_5 minimal surfaces beyond the Gross-Ooguri transition point, is combined with unitarity and analyticity constraints in the central region. In this way we obtain an absolute bound on the high-energy behavior of the forward scattering amplitude due to the graviton interaction between minimal surfaces in the bulk. The dominant "Pomeron" intercept is bounded by alpha less than or equal to 11/7 using the AdS/CFT constraint of a weak gravitational field in the bulk. Assuming the elastic eikonal approximation in a larger impact-parameter range gives alpha between 4/3 and 11/7. The actual intercept becomes 4/3 if one assumes the elastic eikonal approximation within its maximally allowed range L larger than exp{Y/3}, where Y is the total rapidity. Subleading AdS/CFT contributions at large impact-parameter due to the other d=10 supergravity fields are obtained. A divergence in the real part of the tachyonic KK scalar is cured by analyticity but signals the need for a theoretical completion of the AdS/CFT scheme.Comment: 25 pages, 3 eps figure

Reggeon exchange from gauge/gravity duality

We perform the analysis of quark-antiquark Reggeon exchange in meson-meson scattering, in the framework of the gauge/gravity correspondence in a confining background. On the gauge theory side, Reggeon exchange is described as quark-antiquark exchange in the t channel between fast projectiles. The corresponding amplitude is represented in terms of Wilson loops running along the trajectories of the constituent quarks and antiquarks. The paths of the exchanged fermions are integrated over, while the "spectator" fermions are dealt with in an eikonal approximation. On the gravity side, we follow a previously proposed approach, and we evaluate the Wilson-loop expectation value by making use of gauge/gravity duality for a generic confining gauge theory. The amplitude is obtained in a saddle-point approximation through the determination near the confining horizon of a Euclidean "minimal surface with floating boundaries", i.e., by fixing the trajectories of the exchanged quark and antiquark by means of a minimisation procedure, which involves both area and length terms. After discussing, as a warm-up exercise, a simpler problem on a plane involving a soap film with floating boundaries, we solve the variational problem relevant to Reggeon exchange, in which the basic geometry is that of a helicoid. A compact expression for the Reggeon-exchange amplitude, including the effects of a small fermion mass, is then obtained through analytic continuation from Euclidean to Minkowski space-time. We find in particular a linear Regge trajectory, corresponding to a Regge-pole singularity supplemented by a logarithmic cut induced by the non-zero quark mass. The analytic continuation leads also to companion contributions, corresponding to the convolution of the same Reggeon-exchange amplitude with multiple elastic rescattering interactions between the colliding mesons.Comment: 60+1 pages, 14 figure

Atrial natriuretic peptide and three-dimensional echocardiography after transcatheter closure of atrial septal defect

<p>Abstract</p> <p>Background</p> <p>Atrial septal defect (ASD) accounts for 10% of all congenital heart lesions and represent the third most congenital cardiac defect seen in adults. Atrial natriuretic peptide (ANP) is an important regulator of the sodium and volume homeostasis. This study was designed to investigate the changes in plasma ANP concentrations and three-dimensional echocardiography (3DE) measurements of cardiac volume in patients with ASD during transcatheter closure of defect.</p> <p>Methods</p> <p>Plasma ANP concentrations and transthoracic 3DE measurements of right ventricular volume were performed in 46 patients with ASD before closure, and at 3 days after closure. 22 healthy subjects matched for age, sex served as control subjects.</p> <p>Results</p> <p>The 46 patients (20 men, 26 women; mean age 26.32 ± 13.28, range 6 to 63 years) were diagnosed to secundum ASD (the stretched diameters of ASD were from 9~36(25.34 ± 7.80 mm), and had been successfully placed Amplatzer septal occluder (the sizes of occluder were from 11 to 40 mm). The results showed that compared with control subjects, plasma ANP concentrations were elevated in patients with ASD. Plasma ANP concentrations positively correlated significantly with pulmonary artery pressure (PAP) (r = 0.74, <it>p </it>< 0.05) and 3DE measurements of cardiac volumes (right ventricular end-diastolic (r = 0.50, <it>p </it>< 0.05) and end-systolic volume (r = 0.50, <it>p </it>< 0.05) and negatively correlated with RVEF (r = -0.38, <it>p </it>< 0.05). Transthoracic 3DE measurements of right ventricular volume and plasma ANP concentrations decreased significantly at 3 days after closure (<it>p </it>< 0.05) compared with it before closure.</p> <p>Conclusion</p> <p>Plasma ANP concentrations were markedly elevated in patients with pulmonary arterial hypertension and right ventricular volume overload and decreased significantly after closure of ASD. This study suggested that ANP may help to identify patients with ASD complicated by pulmonary arterial hypertension and right ventricular volume overload that demanded early intervention and may become effective marker for evaluating changes in cardiac load after transcatheter ASD closure.</p

Detection of Heteroplasmic Mitochondrial DNA in Single Mitochondria

BACKGROUND: Mitochondrial DNA (mtDNA) genome mutations can lead to energy and respiratory-related disorders like myoclonic epilepsy with ragged red fiber disease (MERRF), mitochondrial myopathy, encephalopathy, lactic acidosis and stroke (MELAS) syndrome, and Leber's hereditary optic neuropathy (LHON). It is not well understood what effect the distribution of mutated mtDNA throughout the mitochondrial matrix has on the development of mitochondrial-based disorders. Insight into this complex sub-cellular heterogeneity may further our understanding of the development of mitochondria-related diseases. METHODOLOGY: This work describes a method for isolating individual mitochondria from single cells and performing molecular analysis on that single mitochondrion's DNA. An optical tweezer extracts a single mitochondrion from a lysed human HL-60 cell. Then a micron-sized femtopipette tip captures the mitochondrion for subsequent analysis. Multiple rounds of conventional DNA amplification and standard sequencing methods enable the detection of a heteroplasmic mixture in the mtDNA from a single mitochondrion. SIGNIFICANCE: Molecular analysis of mtDNA from the individually extracted mitochondrion demonstrates that a heteroplasmy is present in single mitochondria at various ratios consistent with the 50/50 heteroplasmy ratio found in single cells that contain multiple mitochondria