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https://www.readbyqxmd.com/read/28936984/what-makes-the-universe-accelerate-a-review-on-what-dark-energy-could-be-and-how-to-test-it
#1
Philippe Brax
Explaining the origin of the acceleration of the expansion of the Universe remains as challenging as ever. In this review, we present different approaches from dark energy to modified gravity. We also emphasize the quantum nature of the problem and the need for an explanation which should violate Weinberg's no go theorem. This might involve a self-tuning mechanism or the acausal sequestering of the vacuum energy. Laboratory tests of the coupling to matter of nearly massless scalar fields, which could be one of the features required to explain the cosmic acceleration, are also reviewed...
September 22, 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28928211/the-crispr-spacer-space-is-dominated-by-sequences-from-species-specific-mobilomes
#2
Sergey A Shmakov, Vassilii Sitnik, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin
Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average)...
September 19, 2017: MBio
https://www.readbyqxmd.com/read/28900024/metabolic-roles-of-uncultivated-bacterioplankton-lineages-in-the-northern-gulf-of-mexico-dead-zone
#3
J Cameron Thrash, Kiley W Seitz, Brett J Baker, Ben Temperton, Lauren E Gillies, Nancy N Rabalais, Bernard Henrissat, Olivia U Mason
Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called "dead zones," are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown...
September 12, 2017: MBio
https://www.readbyqxmd.com/read/28894419/molecular-connectivity-predefines-polypharmacology-aliphatic-rings-chirality-and-sp-3-centers-enhance-target-selectivity
#4
Stefania Monteleone, Julian E Fuchs, Klaus R Liedl
Dark chemical matter compounds are small molecules that have been recently identified as highly potent and selective hits. For this reason, they constitute a promising class of possible candidates in the process of drug discovery and raise the interest of the scientific community. To this purpose, Wassermann et al. (2015) have described the application of 2D descriptors to characterize dark chemical matter. However, their definition was based on the number of reported positive assays rather than the number of known targets...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28894102/recovery-of-nearly-8-000-metagenome-assembled-genomes-substantially-expands-the-tree-of-life
#5
Donovan H Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J Woodcroft, Paul N Evans, Philip Hugenholtz, Gene W Tyson
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination...
September 11, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28883069/probing-the-frontiers-of-particle-physics-with-tabletop-scale-experiments
#6
REVIEW
David DeMille, John M Doyle, Alexander O Sushkov
The field of particle physics is in a peculiar state. The standard model of particle theory successfully describes every fundamental particle and force observed in laboratories, yet fails to explain properties of the universe such as the existence of dark matter, the amount of dark energy, and the preponderance of matter over antimatter. Huge experiments, of increasing scale and cost, continue to search for new particles and forces that might explain these phenomena. However, these frontiers also are explored in certain smaller, laboratory-scale "tabletop" experiments...
September 8, 2017: Science
https://www.readbyqxmd.com/read/28860364/india-s-dark-matter-quest
#7
Pallava Bagla
No abstract text is available yet for this article.
September 1, 2017: Science
https://www.readbyqxmd.com/read/28836317/ccbuilder-2-0-powerful-and-accessible-coiled-coil-modeling
#8
Christopher W Wood, Derek N Woolfson
The increased availability of user-friendly and accessible computational tools for biomolecular modeling would expand the reach and application of biomolecular engineering and design. For protein modeling, one key challenge is to reduce the complexities of 3D protein folds to sets of parametric equations that nonetheless capture the salient features of these structures accurately. At present, this is possible for a subset of proteins, namely repeat proteins. The α-helical coiled coil provides one such example, which represents ≈ 3 - 5% of all known protein-encoding regions of DNA...
August 24, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28829043/novel-use-of-uv-broad-band-excitation-and-stretched-exponential-function-in-the-analysis-of-fluorescent-dissolved-organic-matter-study-of-interaction-between-protein-and-humic-like-components
#9
Suraj Kumar Panigrahi, Ashok Kumar Mishra
A combination of broad-band UV radiation (UV A and UV B; 250-400 nm) and a stretched exponential function (StrEF) has been utilised in efforts towards convenient and sensitive detection of fluorescent dissolved organic matter (FDOM). This approach enables accessing the gross fluorescence spectral signature of both protein-like and humic-like components in a single measurement. Commercial FDOM components are excited with the broad-band UV excitation; the variation of spectral profile as a function of varying component ratio is analysed...
August 22, 2017: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28827739/actinobacterial-rare-biospheres-and-dark-matter-revealed-in-habitats-of-the-chilean-atacama-desert
#10
Hamidah Idris, Michael Goodfellow, Roy Sanderson, Juan A Asenjo, Alan T Bull
The Atacama Desert is the most extreme non-polar biome on Earth, the core region of which is considered to represent the dry limit for life and to be an analogue for Martian soils. This study focused on actinobacteria because they are keystone species in terrestrial ecosystems and are acknowledged as an unrivalled source of bioactive compounds. Metagenomic analyses of hyper-arid and extreme hyper-arid soils in this desert revealed a remarkable degree of actinobacterial 'dark matter', evidenced by a detected increase of 34% in families against those that are validly published...
August 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821866/detection-of-magnetized-quark-nuggets-a-candidate-for-dark-matter
#11
J Pace VanDevender, Aaron P VanDevender, T Sloan, Criss Swaim, Peter Wilson, Robert G Schmitt, Rinat Zakirov, Josh Blum, James L Cross, Niall McGinley
Quark nuggets are theoretical objects composed of approximately equal numbers of up, down, and strange quarks and are also called strangelets and nuclearites. They have been proposed as a candidate for dark matter, which constitutes ~85% of the universe's mass and which has been a mystery for decades. Previous efforts to detect quark nuggets assumed that the nuclear-density core interacts directly with the surrounding matter so the stopping power is minimal. Tatsumi found that quark nuggets could well exist as a ferromagnetic liquid with a ~10(12)-T magnetic field...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821852/navigability-of-random-geometric-graphs-in-the-universe-and-other-spacetimes
#12
William Cunningham, Konstantin Zuev, Dmitri Krioukov
Random geometric graphs in hyperbolic spaces explain many common structural and dynamical properties of real networks, yet they fail to predict the correct values of the exponents of power-law degree distributions observed in real networks. In that respect, random geometric graphs in asymptotically de Sitter spacetimes, such as the Lorentzian spacetime of our accelerating universe, are more attractive as their predictions are more consistent with observations in real networks. Yet another important property of hyperbolic graphs is their navigability, and it remains unclear if de Sitter graphs are as navigable as hyperbolic ones...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821807/sulfate-reduction-in-sediments-produces-high-levels-of-chromophoric-dissolved-organic-matter
#13
Jenna L Luek, Kaitlyn E Thompson, Randolph K Larsen, Andrew Heyes, Michael Gonsior
Sulfate reduction plays an important role in altering dissolved organic matter (DOM) in estuarine and coastal sediments, although its role in the production of optically active chromophoric DOM (CDOM) and a subset of fluorescent DOM (FDOM) has not been previously investigated in detail. Freshwater sediment slurries were incubated anaerobically with added sulfate and acetate to promote sulfate-reducing bacteria. Ultraviolet visible (UV-Vis) absorbance and 3-dimensional excitation emission matrix (EEM) fluorescence spectra were measured over a five weeks anaerobic dark incubation period...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28796840/yes-research-matters
#14
Mari L Shinohara
My father was diagnosed with stomach cancer recently. Luckily, it was still at an early stage, and endoscopic surgery successfully took care of it. My father was fortunate; since people with stomach cancer do not show clear symptoms in the early stages, the disease is often not diagnosed until it becomes advanced. In his case, the diagnosis started from a suggestion by his doctor to check whether he had a gastric infection with Helicobacter pylori, a bacterial species found in the digestive tract. In Japan, where he lives, a majority of gastric cancer patients (more than 99%) have been infected with H...
August 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28782358/iron-redox-transformations-in-the-presence-of-natural-organic-matter-effect-of-calcium
#15
Chao Jiang, Shikha Garg, T David Waite
The effects of calcium on iron redox transformations in acidic non-irradiated and irradiated Suwannee River Fulvic Acid (SRFA) solutions are investigated in this study. Our results reveal that, even though calcium is redox-inert, it affects the redox transformations of iron with increased Fe(III) reduction rates under irradiated conditions and decreased Fe(II) oxidation rates in the dark in the presence compared to the absence of calcium. While the exact mechanism via which the Fe(III) reduction rate under irradiated conditions is impacted by calcium addition is not clear, the formation of more photo-labile weakly complexed Fe(III)SRFA is most consistent with our experimental results...
August 7, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28777598/primordial-black-holes-from-supersymmetry-in-the-early-universe
#16
Eric Cotner, Alexander Kusenko
Supersymmetric extensions of the standard model generically predict that in the early Universe a scalar condensate can form and fragment into Q balls before decaying. If the Q balls dominate the energy density for some period of time, the relatively large fluctuations in their number density can lead to formation of primordial black holes (PBH). Other scalar fields, unrelated to supersymmetry, can play a similar role. For a general charged scalar field, this robust mechanism can generate black holes over the entire mass range allowed by observational constraints, with a sufficient abundance to account for all dark matter in some parameter ranges...
July 21, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28777592/first-constraints-on-fuzzy-dark-matter-from-lyman-%C3%AE-forest-data-and-hydrodynamical-simulations
#17
Vid Iršič, Matteo Viel, Martin G Haehnelt, James S Bolton, George D Becker
We present constraints on the masses of extremely light bosons dubbed fuzzy dark matter (FDM) from Lyman-α forest data. Extremely light bosons with a de Broglie wavelength of ∼1  kpc have been suggested as dark matter candidates that may resolve some of the current small scale problems of the cold dark matter model. For the first time, we use hydrodynamical simulations to model the Lyman-α flux power spectrum in these models and compare it to the observed flux power spectrum from two different data sets: the XQ-100 and HIRES/MIKE quasar spectra samples...
July 21, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28753376/searching-for-the-qcd-axion-with-gravitational-microlensing
#18
Malcolm Fairbairn, David J E Marsh, Jérémie Quevillon
The phase transition responsible for axion dark matter (DM) production can create large amplitude isocurvature perturbations, which collapse into dense objects known as axion miniclusters. We use microlensing data from the EROS survey and from recent observations with the Subaru Hyper Suprime Cam to place constraints on the minicluster scenario. We compute the microlensing event rate for miniclusters, treating them as spatially extended objects. Using the published bounds on the number of microlensing events, we bound the fraction of DM collapsed into miniclusters f_{MC}...
July 14, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28753364/novel-cosmic-ray-electron-and-positron-constraints-on-mev-dark-matter-particles
#19
Mathieu Boudaud, Julien Lavalle, Pierre Salati
MeV dark matter (DM) particles annihilating or decaying to electron-positron pairs cannot, in principle, be observed via local cosmic-ray (CR) measurements because of the shielding solar magnetic field. In this Letter, we take advantage of spacecraft Voyager 1's capacity for detecting interstellar CRs since it crossed the heliopause in 2012. This opens up a new avenue to probe DM in the sub-GeV energy/mass range that we exploit here for the first time. From a complete description of the transport of electrons and positrons at low energy, we derive predictions for both the secondary astrophysical background and the pair production mechanisms relevant to DM annihilation or decay down to the MeV mass range...
July 14, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28753350/%C3%AE-ray-constraints-on-decaying-dark-matter-and-implications-for-icecube
#20
Timothy Cohen, Kohta Murase, Nicholas L Rodd, Benjamin R Safdi, Yotam Soreq
Utilizing the Fermi measurement of the γ-ray spectrum toward the Inner Galaxy, we derive some of the strongest constraints to date on the dark matter (DM) lifetime in the mass range from hundreds of MeV to above an EeV. Our profile-likelihood-based analysis relies on 413 weeks of Fermi Pass 8 data from 200 MeV to 2 TeV, along with up-to-date models for diffuse γ-ray emission within the Milky Way. We model Galactic and extragalactic DM decay and include contributions to the DM-induced γ-ray flux resulting from both primary emission and inverse-Compton scattering of primary electrons and positrons...
July 14, 2017: Physical Review Letters
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