Architectural protein subclasses shape 3D organization of genomes during lineage commitment.

Understanding the topological configurations of chromatin may reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here, we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor cells. We observe a hierarchy of 3D interactions that undergo marked reorganization at the submegabase scale during differentiation. Distinct combinations of CCCTC-binding factor (CTCF), Mediator, and cohesin show widespread enrichment in chromatin interactions at different length scales. CTCF/cohesin anchor long-range constitutive interactions that might form the topological basis for invariant subdomains. Conversely, Mediator/cohesin bridge short-range enhancer-promoter interactions within and between larger subdomains. Knockdown of Smc1 or Med12 in embryonic stem cells results in disruption of spatial architecture and downregulation of genes found in cohesin-mediated interactions. We conclude that cell-type-specific chromatin organization occurs at the submegabase scale and that architectural proteins shape the genome in hierarchical length scales.

Revisiting Montreal: New Insights into Symptoms and Their Causes, and Implications for the Future of GERD.

The Montreal definition of gastroesophageal reflux disease (GERD) provided a rationale for acid suppression medication without investigation, thus enhancing the management of the substantial symptom burden in these patients. Increased proton-pump inhibitor use has also highlighted their limitations, with one third of "typical" symptoms known to be refractory. Most refractory symptoms are ascribed to reflux hypersensitivity (RH) and functional heartburn (FH). RH may be caused by impaired esophageal mucosal barrier function and sensitization of peripheral esophageal receptors. Central sensitization may also contribute to the perception of non-pathologic reflux in RH, and the perception of physiological stimuli in FH. Importantly, mechanisms underlying GERD, RH, and FH are (in theory) not mutually exclusive, further complicating patient management. Methods used to distinguish GERD from RH and FH are impractical for use in epidemiological studies and pragmatic care and may have limited diagnostic accuracy. This is impeding accurate prevalence estimates and risk factor determination and the identification of new therapies. Direct assessment of mucosal barrier function by measuring impedance is a promising candidate for improved diagnosis. Ultimately though the concept of GERD as a composite, symptom-based entity needs re-evaluation, so that new understandings of upper GI symptoms can direct more precise management.

Genomic location of the major ribosomal protein gene locus determines Vibrio cholerae global growth and infectivity.

The effects on cell physiology of gene order within the bacterial chromosome are poorly understood. In silico approaches have shown that genes involved in transcription and translation processes, in particular ribosomal protein (RP) genes, localize near the replication origin (oriC) in fast-growing bacteria suggesting that such a positional bias is an evolutionarily conserved growth-optimization strategy. Such genomic localization could either provide a higher dosage of these genes during fast growth or facilitate the assembly of ribosomes and transcription foci by keeping physically close the many components of these macromolecular machines. To explore this, we used novel recombineering tools to create a set of Vibrio cholerae strains in which S10-spec-α (S10), a locus bearing half of the ribosomal protein genes, was systematically relocated to alternative genomic positions. We show that the relative distance of S10 to the origin of replication tightly correlated with a reduction of S10 dosage, mRNA abundance and growth rate within these otherwise isogenic strains. Furthermore, this was accompanied by a significant reduction in the host-invasion capacity in Drosophila melanogaster. Both phenotypes were rescued in strains bearing two S10 copies highly distal to oriC, demonstrating that replication-dependent gene dosage reduction is the main mechanism behind these alterations. Hence, S10 positioning connects genome structure to cell physiology in Vibrio cholerae. Our results show experimentally for the first time that genomic positioning of genes involved in the flux of genetic information conditions global growth control and hence bacterial physiology and potentially its evolution.

An att site-based recombination reporter system for genome engineering and synthetic DNA assembly.

BACKGROUND: Direct manipulation of the genome is a widespread technique for genetic studies and synthetic biology applications. The tyrosine and serine site-specific recombination systems of bacteriophages HK022 and ΦC31 are widely used for stable directional exchange and relocation of DNA sequences, making them valuable tools in these contexts. We have developed site-specific recombination tools that allow the direct selection of recombination events by embedding the attB site from each system within the ß-lactamase resistance coding sequence (bla). RESULTS: The HK and ΦC31 tools were developed by placing the attB sites from each system into the signal peptide cleavage site coding sequence of bla. All possible open reading frames (ORFs) were inserted and tested for recombination efficiency and bla activity. Efficient recombination was observed for all tested ORFs (3 for HK, 6 for ΦC31) as shown through a cointegrate formation assay. The bla gene with the embedded attB site was functional for eight of the nine constructs tested. CONCLUSIONS: The HK/ΦC31 att-bla system offers a simple way to directly select recombination events, thus enhancing the use of site-specific recombination systems for carrying out precise, large-scale DNA manipulation, and adding useful tools to the genetics toolbox. We further show the power and flexibility of bla to be used as a reporter for recombination.

Genome engineering in Vibrio cholerae: a feasible approach to address biological issues.

Although bacteria with multipartite genomes are prevalent, our knowledge of the mechanisms maintaining their genome is very limited, and much remains to be learned about the structural and functional interrelationships of multiple chromosomes. Owing to its bi-chromosomal genome architecture and its importance in public health, Vibrio cholerae, the causative agent of cholera, has become a preferred model to study bacteria with multipartite genomes. However, most in vivo studies in V. cholerae have been hampered by its genome architecture, as it is difficult to give phenotypes to a specific chromosome. This difficulty was surmounted using a unique and powerful strategy based on massive rearrangement of prokaryotic genomes. We developed a site-specific recombination-based engineering tool, which allows targeted, oriented, and reciprocal DNA exchanges. Using this genetic tool, we obtained a panel of V. cholerae mutants with various genome configurations: one with a single chromosome, one with two chromosomes of equal size, and one with both chromosomes controlled by identical origins. We used these synthetic strains to address several biological questions--the specific case of the essentiality of Dam methylation in V. cholerae and the general question concerning bacteria carrying circular chromosomes--by looking at the effect of chromosome size on topological issues. In this article, we show that Dam, RctB, and ParA2/ParB2 are strictly essential for chrII origin maintenance, and we formally demonstrate that the formation of chromosome dimers increases exponentially with chromosome size.

Geologic Constraints on the Formation and Evolution of Saturn's Mid-Sized Moons.

Saturn's mid-sized icy moons have complex relationships with Saturn's interior, the rings, and with each other, which can be expressed in their shapes, interiors, and geology. Observations of their physical states can, thus, provide important constraints on the ages and formation mechanism(s) of the moons, which in turn informs our understanding of the formation and evolution of Saturn and its rings. Here, we describe the cratering records of the mid-sized moons and the value and limitations of their use for constraining the histories of the moons. We also discuss observational constraints on the interior structures of the moons and geologically-derived inferences on their thermal budgets through time. Overall, the geologic records of the moons (with the exception of Mimas) include evidence of epochs of high heat flows, short- and long-lived subsurface oceans, extensional tectonics, and considerable cratering. Curiously, Mimas presents no clear evidence of an ocean within its surface geology, but its rotation and orbit indicate a present-day ocean. While the moons need not be primordial to produce the observed levels of interior evolution and geologic activity, there is likely a minimum age associated with their development that has yet to be determined. Uncertainties in the populations impacting the moons makes it challenging to further constrain their formation timeframes using craters, whereas the characteristics of their cores and other geologic inferences of their thermal evolutions may help narrow down their potential histories. Disruptive collisions may have also played an important role in the formation and evolution of Saturn's mid-sized moons, and even the rings of Saturn, although more sophisticated modeling is needed to determine the collision conditions that produce rings and moons that fit the observational constraints. Overall, the existence and physical characteristics of Saturn's mid-sized moons provide critical benchmarks for the development of formation theories.

Effect of comorbidity on mortality in patients with peptic ulcer bleeding: systematic review and meta-analysis.

OBJECTIVES: By systematic review and meta-analysis, we sought to assess the impact of comorbidity on short-term mortality in patients with peptic ulcer bleeding (PUB). METHODS: We conducted systematic searches in PubMed and Embase (January 1989-January 2010). Relative risks (RRs) were pooled across selected studies and an analysis of diagnostic test accuracy was performed to validate the results further. RESULTS: Of 1,572 identified studies, 16 were eligible for inclusion. Only three had a low risk of bias and the overall quality of evidence was low. The risk of death (30-day or in-hospital mortality) was significantly greater in PUB patients with comorbidity than in those without (RR: 4.44; 95% confidence interval (CI): 2.45-8.04). The pooled sensitivity for comorbidity predicting death in patients with PUB was 0.86 (95% CI: 0.66-0.95) and the pooled specificity was 0.53 (95% CI: 0.40-0.65). PUB patients with three or more comorbidities had a greater risk of dying than those with one or two (RR: 3.46; 95% CI: 1.34-8.89). All individual comorbidities that we assessed significantly increased the risk of death associated with PUB. However, RRs were higher for hepatic, renal, and malignant disease (range: 4.04-6.33; no significant heterogeneity) than for cardiovascular and respiratory disease and diabetes (2.39, 2.45, and 1.63, respectively; no significant heterogeneity). CONCLUSIONS: Underlying comorbidity is consistently associated with increased mortality in patients with PUB. The number and type of comorbidities in patients with PUB should be carefully evaluated and factored into initial management strategies.

Promising Antimicrobial Activity and Synergy of Bacteriocins Against Mycobacterium tuberculosis.

In this study, we assessed the potential of bacteriocins and their in vitro synergistic effects in combination with anti-tuberculosis drugs against Mycobacterium tuberculosis. We evaluated the in vitro activity of chemically synthesized bacteriocins in combination with rifampicin (RIF), ofloxacin, and moxifloxacin against the reference M. tuberculosis H37Rv and a clinical-resistant strain. We first screened the bacteriocin PARAGEN collection and found active bacteriocins. We then determined their minimal inhibitory concentration (MIC), minimal bactericidal concentration, and their fractional inhibitory index by the checkerboard microdilution assay. Remarkably, we identified four bacteriocins with interesting antimycobacterial activity alone and in combinations with RIF, ofloxacin, and moxifloxacin, with significant reduction of the MIC that showed impressive synergistic effects against the susceptible and resistant clinical strains. In conclusion, our preliminary results show promising bacteriocins candidate used in a synergistic combination with anti-tuberculosis drugs and emphasize the need for combined therapy as a new strategy to enhance the activity of existing drugs, which may confer very promising therapeutic benefits against M. tuberculosis.

Exploring the Interior of Europa with the Europa Clipper.

The Galileo mission to Jupiter revealed that Europa is an ocean world. The Galileo magnetometer experiment in particular provided strong evidence for a salty subsurface ocean beneath the ice shell, likely in contact with the rocky core. Within the ice shell and ocean, a number of tectonic and geodynamic processes may operate today or have operated at some point in the past, including solid ice convection, diapirism, subsumption, and interstitial lake formation. The science objectives of the Europa Clipper mission include the characterization of Europa's interior; confirmation of the presence of a subsurface ocean; identification of constraints on the depth to this ocean, and on its salinity and thickness; and determination of processes of material exchange between the surface, ice shell, and ocean. Three broad categories of investigation are planned to interrogate different aspects of the subsurface structure and properties of the ice shell and ocean: magnetic induction, subsurface radar sounding, and tidal deformation. These investigations are supplemented by several auxiliary measurements. Alone, each of these investigations will reveal unique information. Together, the synergy between these investigations will expose the secrets of the Europan interior in unprecedented detail, an essential step in evaluating the habitability of this ocean world.

Systematic review: Patterns of proton pump inhibitor use and adherence in gastroesophageal reflux disease.

BACKGROUND & AIMS: Variation in how proton pump inhibitors (PPIs) are taken likely influences their clinical effectiveness, and must be considered when estimating PPI failure rates. This review aimed to systematically investigate the literature on patterns of PPI use in patients with gastroesophageal reflux disease (GERD). METHODS: PubMed and Embase were searched (1989-May 2010) to identify observational studies providing information on patterns of PPI use in patients with GERD. RESULTS: Of 902 studies identified, 13 met prespecified selection criteria. Across 2 database studies, 53.8%-67.7% of patients with GERD had a medication possession ratio (MPR) of >0.80. Across 2 more database studies, the mean MPR for the study population was 0.68 to 0.84. Across 3 surveys, 70%-84% of patients reported daily PPI use. In 2 surveys, the presence and severity of reflux symptoms increased PPI adherence, as did Barrett's esophagus in another 2 studies. Across 3 surveys, 11%-22.2% of patients reported twice daily PPI use, and across 6 studies 11.0%-44.8% of patients took GERD medication in addition to a PPI. CONCLUSIONS: The results of this systematic review suggest that the majority of patients with GERD are relatively adherent to their PPI, although substantially different estimates were obtained using MPR data compared with surveys. Severe symptoms and the presence of Barrett's esophagus may increase PPI adherence, and other GERD medication is frequently taken in addition to a PPI. Limitations of studies in this area include inferring adherence from indirect MPR data, and recall bias associated with patient surveys.

In vitro and in vivo production and split-intein mediated ligation (SIML) of circular bacteriocins.

Circular bacteriocins are antimicrobial peptides produced by bacteria that after synthesis undergo a head-to-tail circularization. Compared to their linear counterparts, circular bacteriocins are, in general, very stable to temperature and pH changes and more resistant to proteolytic enzymes, being considered as one of the most promising groups of antimicrobial peptides for their potential biotechnological applications. Up to now, only a reduced number of circular bacteriocins have been identified and fully characterized, although many operons potentially coding for new circular bacteriocins have been recently found in the genomes of different bacterial species. The production of these peptides is very complex and depends on the expression of different genes involved in their synthesis, circularization, and secretion. This complexity has greatly limited the identification and characterization of these bacteriocins, as well as their production in heterologous microbial hosts. In this work, we have evaluated a synthetic biology approach for the in vitro and in vivo production combined with a split-intein mediated ligation (SIML) of the circular bacteriocin garvicin ML (GarML). The expression of one single gene is enough to produce a protein that after intein splicing, circularizes in an active peptide with the exact molecular mass and amino acid sequence as native GarML. In vitro production coupled with SIML has been validated with other, well described and not yet characterized, circular bacteriocins. The results obtained suggest that this synthetic biology tool holds great potential for production, engineering, improving and testing the antimicrobial activity of circular bacteriocins.

Improving the Usability of Galileo and Voyager Images of Jupiter's Moon Europa.

NASA's Voyager 1, Voyager 2, and Galileo spacecraft acquired hundreds of images of Jupiter's moon Europa. These images provide the only moderate- to high-resolution views of the moon's surface and are therefore a critical resource for scientific analysis and future mission planning. Unfortunately, uncertain knowledge of the spacecraft's position and pointing during image acquisition resulted in significant errors in the location of the images on the surface. The result is that adjacent images are poorly aligned, with some images displaced by more than 100 km from their correct location. These errors severely degrade the usability of the Voyager and Galileo imaging data sets. To improve the usability of these data sets, we used the U.S. Geological Survey Integrated Software for Imagers and Spectrometers to build a nearly global image tie-point network with more than 50,000 tie points and 135,000 image measurements on 481 Galileo and 221 Voyager images. A global least-squares bundle adjustment of our final Europa tie-point network calculated latitude, longitude, and radius values for each point by minimizing residuals globally, and resulted in root mean square (RMS) uncertainties of 246.6 m, 307.0 m, and 70.5 m in latitude, longitude, and radius, respectively. The total RMS uncertainty was 0.32 pixels. This work enables direct use of nearly the entire Galileo and Voyager image data sets for Europa. We are providing the community with updated NASA Navigation and Ancillary Information Facility Spacecraft, Planet, Instrument, C-matrix (pointing), and Events kernels, mosaics of Galileo images acquired during each observation sequence, and individual processed and projected level 2 images.

Sodium-glucose cotransporter 2 inhibitor effects on heart failure hospitalization and cardiac function: systematic review.

AIMS: To systematically review randomized controlled trials assessing effects of sodium-glucose cotransporter 2 inhibitors (SGLT2is) on hospitalization for heart failure (HHF) and cardiac structure/function and explore randomized controlled trial (RCT)-derived evidence for SGLT2i efficacy mechanisms in heart failure (HF). METHODS AND RESULTS: Systematic searches of Medline and Embase were performed. In seven trials [3730-17 160 patients; low risk of bias (RoB)], SGLT2is significantly reduced the relative risk of HHF by 27-39% vs. placebo, including in two studies in patients with HF with reduced ejection fraction with or without type-2 diabetes mellitus (T2DM). Improvements in conventional cardiovascular risk factors, including glycaemic levels, cannot account for these effects. Five trials (56-105 patients; low RoB) assessed the effects of 6-12 months of SGLT2i treatment on left ventricular structure/function; four reported significant improvements vs. placebo, and one did not. Five trials (low RoB) assessed SGLT2i treatment effects on serum N-terminal pro B-type natriuretic peptide levels; significant reductions vs. placebo were reported after 8-12 months (two studies; 3730-4744 patients) but not ≤12 weeks (three studies; 80-263 patients). Limited available RCT-derived evidence suggests various possible cardioprotective SGLT2i mechanisms, including improved haemodynamics (natriuresis and reduced interstitial fluid without blood volume contraction/neurohormonal activation) and vascular function, enhanced erythropoiesis, reduced tissue sodium and epicardial fat/inflammation, decreased sympathetic tone, and beneficial changes in cellular energetics. CONCLUSIONS: Sodium-glucose cotransporter 2 inhibitors reduce HHF regardless of T2DM status, and reversal of adverse left ventricular remodelling likely contributes to this efficacy. Hypothesis-driven mechanistic trials remain sparse, although numerous trials are planned or ongoing.

Undiagnosed microscopic colitis: a hidden cause of chronic diarrhoea and a frequently missed treatment opportunity.

Microscopic colitis (MC) is a treatable cause of chronic, non-bloody, watery diarrhoea, but physicians (particularly in primary care) are less familiar with MC than with other causes of chronic diarrhoea. The colon in patients with MC is usually macroscopically normal. MC can only be diagnosed by histological examination of colonic biopsies (subepithelial collagen band >10 µm (collagenous colitis) or >20 intraepithelial lymphocytes per 100 epithelial cells (lymphocytic colitis), both with lamina propria inflammation). The UK National Health Service exerts downward pressure to minimise colonoscopy referrals. Furthermore, biopsies are often not taken according to guidelines. These factors work against MC diagnosis. In this review, we note the high incidence of MC (comparable to ulcerative colitis and Crohn's disease) and its symptomatic overlap with irritable bowel syndrome. We also highlight problems with the recommendation by National Health Service/National Institute for Health and Care Excellence guidelines for inflammatory bowel diseases that colonoscopy referrals should be based on a faecal calprotectin level of ≥100 µg/g. Faecal calprotectin is <100 µg/g in over half of individuals with active MC, building into the system a propensity to misdiagnose MC as irritable bowel syndrome. This raises important questions-how many patients with MC have already been misdiagnosed, and how do we address this silent burden? Clarity is needed around pathways for MC management; MC is poorly acknowledged by the UK healthcare system and it is unlikely that best practices are being followed adequately. There is an opportunity to identify and treat patients with MC more effectively.

Ceres: Astrobiological Target and Possible Ocean World.

Ceres, the most water-rich body in the inner solar system after Earth, has recently been recognized to have astrobiological importance. Chemical and physical measurements obtained by the Dawn mission enabled the quantification of key parameters, which helped to constrain the habitability of the inner solar system's only dwarf planet. The surface chemistry and internal structure of Ceres testify to a protracted history of reactions between liquid water, rock, and likely organic compounds. We review the clues on chemical composition, temperature, and prospects for long-term occurrence of liquid and chemical gradients. Comparisons with giant planet satellites indicate similarities both from a chemical evolution standpoint and in the physical mechanisms driving Ceres' internal evolution.

HR-pQCT Measures of Bone Microarchitecture Predict Fracture: Systematic Review and Meta-Analysis.

High-resolution peripheral quantitative computed tomography (HR-pQCT) is a noninvasive imaging modality for assessing volumetric bone mineral density (vBMD) and microarchitecture of cancellous and cortical bone. The objective was to (1) assess fracture-associated differences in HR-pQCT bone parameters; and (2) to determine if HR-pQCT is sufficiently precise to reliably detect these differences in individuals. We systematically identified 40 studies that used HR-pQCT (39/40 used XtremeCT scanners) to assess 1291 to 3253 and 3389 to 10,687 individuals with and without fractures, respectively, ranging in age from 10.9 to 84.7 years with no comorbid conditions. Parameters describing radial and tibial bone density, microarchitecture, and strength were extracted and percentage differences between fracture and control subjects were estimated using a random effects meta-analysis. An additional meta-analysis of short-term in vivo reproducibility of bone parameters assessed by XtremeCT was conducted to determine whether fracture-associated differences exceeded the least significant change (LSC) required to discern measured differences from precision error. Radial and tibial HR-pQCT parameters, including failure load, were significantly altered in fracture subjects, with differences ranging from -2.6% (95% confidence interval [CI] -3.4 to -1.9) in radial cortical vBMD to -12.6% (95% CI -15.0 to -10.3) in radial trabecular vBMD. Fracture-associated differences reported by prospective studies were consistent with those from retrospective studies, indicating that HR-pQCT can predict incident fracture. Assessment of study quality, heterogeneity, and publication biases verified the validity of these findings. Finally, we demonstrated that fracture-associated deficits in total and trabecular vBMD and certain tibial cortical parameters can be reliably discerned from HR-pQCT-related precision error and can be used to detect fracture-associated differences in individual patients. Although differences in other HR-pQCT measures, including failure load, were significantly associated with fracture, improved reproducibility is needed to ensure reliable individual cross-sectional screening and longitudinal monitoring. In conclusion, our study supports the use of HR-pQCT in clinical fracture prediction. © 2019 American Society for Bone and Mineral Research.

The NASA Roadmap to Ocean Worlds.

In this article, we summarize the work of the NASA Outer Planets Assessment Group (OPAG) Roadmaps to Ocean Worlds (ROW) group. The aim of this group is to assemble the scientific framework that will guide the exploration of ocean worlds, and to identify and prioritize science objectives for ocean worlds over the next several decades. The overarching goal of an Ocean Worlds exploration program as defined by ROW is to "identify ocean worlds, characterize their oceans, evaluate their habitability, search for life, and ultimately understand any life we find." The ROW team supports the creation of an exploration program that studies the full spectrum of ocean worlds, that is, not just the exploration of known ocean worlds such as Europa but candidate ocean worlds such as Triton as well. The ROW team finds that the confirmed ocean worlds Enceladus, Titan, and Europa are the highest priority bodies to target in the near term to address ROW goals. Triton is the highest priority candidate ocean world to target in the near term. A major finding of this study is that, to map out a coherent Ocean Worlds Program, significant input is required from studies here on Earth; rigorous Research and Analysis studies are called for to enable some future ocean worlds missions to be thoughtfully planned and undertaken. A second finding is that progress needs to be made in the area of collaborations between Earth ocean scientists and extraterrestrial ocean scientists.