A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments

Background Methane oxidizing prokaryotes in marine sediments are believed to function as a methane filter reducing the oceanic contribution to the global methane emission. In the anoxic parts of the sediments, oxidation of methane is accomplished by anaerobic methanotrophic archaea (ANME) living in syntrophy with sulphate reducing bacteria. This anaerobic oxidation of methane is assumed to be a coupling of reversed methanogenesis and dissimilatory sulphate reduction. Where oxygen is available aerobic methanotrophs take part in methane oxidation. In this study, we used metagenomics to characterize the taxonomic and metabolic potential for methane oxidation at the Tonya seep in the Coal Oil Point area, California. Two metagenomes from different sediment depth horizons (0-4 cm and 10-15 cm below sea floor) were sequenced by 454 technology. The metagenomes were analysed to characterize the distribution of aerobic and anaerobic methanotrophic taxa at the two sediment depths. To gain insight into the metabolic potential the metagenomes were searched for marker genes associated with methane oxidation. Results Blast searches followed by taxonomic binning in MEGAN revealed aerobic methanotrophs of the genus Methylococcus to be overrepresented in the 0-4 cm metagenome compared to the 10-15 cm metagenome. In the 10-15 cm metagenome, ANME of the ANME-1 clade, were identified as the most abundant methanotrophic taxon with 8.6% of the reads. Searches for particulate methane monooxygenase (pmoA) and methyl-coenzyme M reductase (mcrA), marker genes for aerobic and anaerobic oxidation of methane respectively, identified pmoA in the 0-4 cm metagenome as Methylococcaceae related. The mcrA reads from the 10-15 cm horizon were all classified as originating from the ANME-1 clade. Conclusions Most of the taxa detected were present in both metagenomes and differences in community structure and corresponding metabolic potential between the two samples were mainly due to abundance differences. The results suggests that the Tonya Seep sediment is a robust methane filter, where taxa presently dominating this process could be replaced by less abundant methanotrophic taxa in case of changed environmental conditions

Simulating Reionization in Numerical Cosmology

The incorporation of radiative transfer effects into cosmological hydrodynamical simulations is essential for understanding how the intergalactic medium (IGM) makes the transition from a neutral medium to one that is almost fully ionized. Here, we present an approximate numerical method designed to study in a statistical sense how a cosmological density field is ionized by a set of discrete point sources. A diffuse background radiation field is also computed self-consistently in our procedure. The method requires relatively few time steps and can be employed with simulations having high resolution. We describe the details of the algorithm and provide a description of how the method can be applied to the output from a pre-existing cosmological simulation to study the systematic reionization of a particular ionic species. As a first application, we compute the reionization of He II by quasars in the redshift range 3 to 6.Comment: 37 pages, 7 figures, Submitted to New

Quasars near the line of sight towards Q 0302-003 and the transverse proximity effect

We report the discovery of the faint (V=21.7) quasar QSO03027-0010 at z=2.808 in the vicinity of Q0302-003, one of the few quasars observed with STIS to study intergalactic HeII absorption. Together with another newly discovered QSO at z=2.29, there are now 6 QSOs known near the line of sight towards Q0302-003, of which 4 are located within the redshift region 2.76<=z<=3.28 covered by the STIS spectrum. We correlated the opacity variations in the HI and HeII Lyman forest spectra with the locations of known quasars. There is no significant proximity effect in the HI Lyman alpha forest for any of the QSOs, except for the well-known line of sight effect for Q0302-003 itself. By comparing the absorption properties in HI and HeII, we estimated the fluctuating hardness of the extragalactic UV radiation field along this line of sight. We find that close to each foreground quasar, the ionizing background is considerably harder than on average. In particular, our newly discovered QSO03027-0010 shows such a hardness increase despite being associated with an overdensity in the HI Lyman forest. We argue that the spectral hardness is a sensitive physical measure to reveal the influence of QSOs onto the UV background even over scales of several Mpc, and that it breaks the density degeneracy hampering the traditional transverse proximity effect analysis. We infer from our sample that there is no need for significantly anisotropic UV radiation from the QSOs. From the transverse proximity effect detected in the sample we obtain minimum quasar lifetimes in the range ~10-30 Myr.Comment: 15 pages, 9 figures, accepted by A&A, problems with paper size fixe

Laudatores Temporis Acti, or Why Cosmology is Alive and Well - A Reply to Disney

A recent criticism of cosmological methodology and achievements by Disney (2000) is assessed. Some historical and epistemological fallacies in the said article have been highlighted. It is shown that---both empirically and epistemologically---modern cosmology lies on sounder foundations than it is portrayed. A brief historical account demonstrates that this form of unsatisfaction with cosmology has had a long tradition, and rather meagre results in the course of the XX century.Comment: 11 pages, no figures; a criticism of astro-ph/0009020; Gen. Rel. Grav., accepted for publicatio

Cosmic Hydrogen Was Significantly Neutral a Billion Years After the Big Bang

The ionization fraction of cosmic hydrogen, left over from the big bang, provides crucial fossil evidence for when the first stars and quasar black holes formed in the infant universe. Spectra of the two most distant quasars known show nearly complete absorption of photons with wavelengths shorter than the Ly-alpha transition of neutral hydrogen, indicating that hydrogen in the intergalactic medium (IGM) had not been completely ionized at a redshift z~6.3, about a billion years after the big bang. Here we show that the radii of influence of ionizing radiation from these quasars imply that the surrounding IGM had a neutral hydrogen fraction of tens of percent prior to the quasar activity, much higher than previous lower limits of ~0.1%. When combined with the recent inference of a large cumulative optical depth to electron scattering after cosmological recombination from the WMAP data, our result suggests the existence of a second peak in the mean ionization history, potentially due to an early formation episode of the first stars.Comment: 14 Pages, 2 Figures. Accepted for publication in Nature. Press embargo until publishe

Morbidly Obese Patients—Who Undergoes Bariatric Surgery?

Treatment seeking patients with severe obesity might choose between specialized medical treatment and surgical treatment. Knowledge of what distinguishes patients that choose either treatment is sparse, with greater understanding also needed on what consequences this choice has for the prevalence, remission and new onset of comorbidities, as well as for the bioavailability of drugs. This has prompted the studies in Gunn Signe Jakobsen and her coauthors work on treatment seeking patients with severe obesity focusing on the prevalence of comorbidities, changes in the use of drugs for hypertension, diabetes and dyslipidaemia, as well as changes in bioavailability of atorvastatin. The methods used in the studies in the thesis; "Bariatric surgery and specialized medical treatment for severe obesity Impact on cardiovascular risk factors and postsurgical pharmacokinetics of atorvastatin "; are a cross-sectional study, a registry based cohort study and a prospective pharmacokinetic study. The results of the studies presented were: - The type and number of comorbidities associated with morbid obesity did not necessarily impact upon choice of treatment, but there was an increased odds for choosing surgery for patients with higher BMI, younger age and earlier onset of obesity. - Patients opting for bariatric surgery as opposed to specialized medical treatment had higher odds of experiencing remission, and significantly lower odds for new-onset of drug treated hypertension, diabetes and dyslipidaemia. Bariatric surgery seemed to not only induce remission but was also effective in preventing disease. - The bioavailability of atorvastatin was increased after bariatric surgery, with a normalization in the long term. This knowledge can give a better understanding of the population of patients seeking treatment for severe obesity and should be included in the shared decision process when helping the patient identify their preferences for treatment of severe obesity in the context of their values

In the Beginning: The First Sources of Light and the Reionization of the Universe

The formation of the first stars and quasars marks the transformation of the universe from its smooth initial state to its clumpy current state. In popular cosmological models, the first sources of light began to form at redshift 30 and reionized most of the hydrogen in the universe by redshift 7. Current observations are at the threshold of probing the hydrogen reionization epoch. The study of high-redshift sources is likely to attract major attention in observational and theoretical cosmology over the next decade.Comment: Final revision: 136 pages, including 42 figures; to be published in Physics Reports 2001. References updated, and a few minor corrections made. In this submission, several figures were compressed, resulting in just a slight reduction in quality; a postscript file with the full figures is available at http://www.cita.utoronto.ca/~barkana/review.htm

The evolution of the Lyman-alpha forest effective optical depth following HeII reionisation

Three independent observational studies have now detected a narrow (\Delta z ~ 0.5) dip centred at z=3.2 in the otherwise smooth redshift evolution of the Lya forest effective optical depth. This feature has previously been interpreted as an indirect signature of rapid photo-heating in the IGM during the epoch of HeII reionisation. We examine this interpretation using a semi-analytic model of inhomogeneous HeII reionisation and high resolution hydrodynamical simulations of the Lya forest. We instead find that a rapid (\Delta z ~ 0.2) boost to the IGM temperature (\Delta T ~ 10^4 K) beginning at z=3.4 produces a well understood and generic evolution in the Lya effective optical depth, where a sudden reduction in the opacity is followed by a gradual, monotonic recovery driven largely by adiabatic cooling in the low density IGM. This behaviour is inconsistent with the narrow feature in the observational data. If photo-heating during HeII reionisation is instead extended over several redshift units, as recent theoretical studies suggest, then the Lya opacity will evolve smoothly with redshift. We conclude that the sharp dip observed in the Lya forest effective optical depth is instead most likely due to a narrow peak in the hydrogen photo-ionisation rate around z=3.2, and suggest that it may arise from the modulation of either reprocessed radiation during HeII reionisation, or the opacity of Lyman limit systems.Comment: 16 pages, 7 figures, accepted to MNRAS with minor revision

A New Astrophysical Constraint on Radiatively Decaying Neutrinos

We calculate constraints on radiatively decaying neutrinos from the recent detection of singly ionized helium in the diffuse intergalactic medium (IGM) at $z \simeq 3.3$. We consider a model in which neutrinos predominantly decay into invisible relativistic particles with a rate $\tau^{-1}$, and with a small branching ratio into the radiative mode. To satisfy the observation of singly ionized helium, which puts a lower bound on the number density of singly ionized helium in the IGM, we show that: for \tau \ga 10^{18} \,{\rm sec}(1 \,{\rm eV}/m_\nu^2), transition moment of neutrinos $\mu_{12}$ is constrained to be \le 4 \hbox{--}8 \times 10^{-17} \,\mu_{\sc B} for 110 \,{\rm eV} \la m_\nu \la 10 \,{\rm keV}. We compare this bound with other astrophysical and cosmological bounds on radiatively decaying neutrinos.Comment: uuencoded file containing TeX file and postscript figure

Burden of disease attributable to risk factors in European countries: a scoping literature review

Objectives: Within the framework of the burden of disease (BoD) approach, disease, and injury burden estimates attributable to risk factors are a useful guide for policy formulation and priority setting in disease prevention. Considering the important differences in methods, and their impact on burden estimates, we conducted a scoping literature review to: (1) map the BoD assessments including risk factors performed across Europe, and (2) identify the methodological choices in comparative risk assessment (CRA) and risk assessment methods. Methods: We searched multiple literature databases, including grey literature websites, and targeted public health agencies' websites. Results: A total of 113 studies were included in the synthesis and further divided into independent BoD assessments (54 studies) and studies linked to the Global Burden of Disease (59 papers). Our results showed that the methods used to perform CRA varied substantially across independent European BoD studies. While there were some methodological choices that were more common than others, we did not observe patterns in terms of country, year, or risk factor. Each methodological choice can affect the comparability of estimates between and within countries and/or risk factors since they might significantly influence the quantification of the attributable burden. From our analysis, we observed that the use of CRA was less common for some types of risk factors and outcomes. These included environmental and occupational risk factors, which are more likely to use bottom-up approaches for health outcomes where disease envelopes may not be available. Conclusions: Our review also highlighted misreporting, the lack of uncertainty analysis, and the under-investigation of causal relationships in BoD studies. Development and use of guidelines for performing and reporting BoD studies will help understand differences, and avoid misinterpretations thus improving comparability among estimates.info:eu-repo/semantics/publishedVersio