Replication-biased genome organisation in the crenarchaeon Sulfolobus

<p>Abstract</p> <p>Background</p> <p>Species of the crenarchaeon <it>Sulfolobus </it>harbour three replication origins in their single circular chromosome that are synchronously initiated during replication.</p> <p>Results</p> <p>We demonstrate that global gene expression in two <it>Sulfolobus </it>species is highly biased, such that early replicating genome regions are more highly expressed at all three origins. The bias by far exceeds what would be anticipated by gene dosage effects alone. In addition, early replicating regions are denser in archaeal core genes (enriched in essential functions), display lower intergenic distances, and are devoid of mobile genetic elements.</p> <p>Conclusion</p> <p>The strong replication-biased structuring of the <it>Sulfolobus </it>chromosome implies that the multiple replication origins serve purposes other than simply shortening the time required for replication. The higher-level chromosomal organisation could be of importance for minimizing the impact of DNA damage, and may also be linked to transcriptional regulation.</p

Measurements of Non-Wetting Phase Trapping Applied to Carbon Dioxide Storage

We measure the trapped non-wetting phase saturation as a function of the initial saturation in sand packs. The application of the work is for carbon dioxide (CO2) storage in aquifers where capillary trapping is a rapid and effective mechanism to render injected CO2 immobile. We used analogue fluids at ambient conditions. The trapped saturation initially rises linearly with initial saturation to a value of 0.11 for oil/water systems and 0.14 for gas/water systems. There then follows a region where the residual saturation is constant with further increases in initial saturation

Agrarian diet and diseases of affluence – Do evolutionary novel dietary lectins cause leptin resistance?

BACKGROUND: The global pattern of varying prevalence of diseases of affluence, such as obesity, cardiovascular disease and diabetes, suggests that some environmental factor specific to agrarian societies could initiate these diseases. PRESENTATION OF THE HYPOTHESIS: We propose that a cereal-based diet could be such an environmental factor. Through previous studies in archaeology and molecular evolution we conclude that humans and the human leptin system are not specifically adapted to a cereal-based diet, and that leptin resistance associated with diseases of affluence could be a sign of insufficient adaptation to such a diet. We further propose lectins as a cereal constituent with sufficient properties to cause leptin resistance, either through effects on metabolism central to the proper functions of the leptin system, and/or directly through binding to human leptin or human leptin receptor, thereby affecting the function. TESTING THE HYPOTHESIS: Dietary interventions should compare effects of agrarian and non-agrarian diets on incidence of diseases of affluence, related risk factors and leptin resistance. A non-significant (p = 0.10) increase of cardiovascular mortality was noted in patients advised to eat more whole-grain cereals. Our lab conducted a study on 24 domestic pigs in which a cereal-free hunter-gatherer diet promoted significantly higher insulin sensitivity, lower diastolic blood pressure and lower C-reactive protein as compared to a cereal-based swine feed. Testing should also evaluate the effects of grass lectins on the leptin system in vivo by diet interventions, and in vitro in various leptin and leptin receptor models. Our group currently conducts such studies. IMPLICATIONS OF THE HYPOTHESIS: If an agrarian diet initiates diseases of affluence it should be possible to identify the responsible constituents and modify or remove them so as to make an agrarian diet healthier

CO2-wettability of low to high rank coal seams: Implications for carbon sequestration and enhanced methane recovery

Coal seams offer tremendous potential for carbon geo-sequestration with the dual benefit of enhanced methane recovery. In this context, it is essential to characterize the wettability of the coal–CO2–water system as it significantly impacts CO2 storage capacity and methane recovery efficiency. Technically, wettability is influenced by reservoir pressure, coal seam temperature, water salinity and coal rank. Thus a comprehensive investigation of the impact of the aforementioned parameters on CO2-wettability is crucial in terms of storage site selection and predicting the injectivity behaviour and associated fluid dynamics. To accomplish this, we measured advancing and receding water contact angles using the pendent drop tilted plate technique for coals of low, medium and high ranks as a function of pressure, temperature and salinity and systematically investigated the associated trends. We found that high rank coals are strongly CO2-wet, medium rank coals are weakly CO2-wet, and low rank coals are intermediate-wet at typical storage conditions. Further, we found that CO2-wettability of coal increased with pressure and salinity and decreased with temperature irrespective of coal rank. We conclude that at a given reservoir pressure, high rank coal seams existing at low temperature are potentially more efficient with respect to CO2-storage and enhanced methane recovery due to increased CO2-wettability and thus increased adsorption trapping

CO2 wettability of seal and reservoir rocks and the implications for carbon geo-sequestration

We review the literature data published on the topic of CO2 wettability of storage and seal rocks. We first introduce the concept of wettability and explain why it is important in the context of carbon geo-sequestration (CGS) projects, and review how it is measured. This is done to raise awareness of this parameter in the CGS community, which, as we show later on in this text, may have a dramatic impact on structural and residual trapping of CO2. These two trapping mechanisms would be severely and negatively affected in case of CO2-wet storage and/or seal rock. Overall, at the current state of the art, a substantial amount of work has been completed, and we find that: 1. Sandstone and limestone, plus pure minerals such as quartz, calcite, feldspar, and mica are strongly water wet in a CO2-water system. 2. Oil-wet limestone, oil-wet quartz, or coal is intermediate wet or CO2 wet in a CO2-water system. 3. The contact angle alone is insufficient for predicting capillary pressures in reservoir or seal rocks. 4. The current contact angle data have a large uncertainty. 5. Solid theoretical understanding on a molecular level of rock-CO2-brine interactions is currently limited. 6. In an ideal scenario, all seal and storage rocks in CGS formations are tested for their CO2 wettability. 7. Achieving representative subsurface conditions (especially in terms of the rock surface) in the laboratory is of key importance but also very challenging

The role of 'filth flies' in the spread of antimicrobial resistance

'Filth flies' feed and develop in excrement and decaying matter and can transmit enteric pathogens to humans and animals, leading to colonization and infection. Considering these characteristics, 'filth flies' are potential vectors for the spread of antimicrobial resistance (AMR). This review defines the role of flies in the spread of AMR and identifies knowledge gaps. The literature search (original articles, reviews indexed for PubMed) was restricted to the English language. References of identified studies were screened for additional sources. 'Filth flies' are colonized with antimicrobial-resistant bacteria of clinical relevance. This includes extended spectrum beta-lactamase-, carbapenemase-producing and colistin-resistant (mcr-1 positive) bacteria. Resistant bacteria in flies often share the same genotypes with bacteria from humans and animals when their habitat overlap. The risk of transmission is most likely highest for enteric bacteria as they are shed in high concentration in excrements and are easily picked up by flies. 'Filth flies' can 'bio-enhance' the transmission of AMR as bacteria multiply in the digestive tract, mouthparts and regurgitation spots. To better understand the medical importance of AMR in flies, quantitative risk assessment models should be refined and fed with additional data (e.g. vectorial capacity, colonization dose). This requires targeted ecological, epidemiological and in vivo experimental studie

CO2 storage capacity estimation : methodology and gaps

Implementation of CO2 capture and geological storage (CCGS) technology at the scale needed to achieve a significant and meaningful reduction in CO2 emissions requires knowledge of the available CO2 storage capacity. CO2 storage capacity assessments may be conducted at various scales—in decreasing order of size and increasing order of resolution: country, basin, regional, local and site-specific. Estimation of the CO2 storage capacity in depleted oil and gas reservoirs is straightforward and is based on recoverable reserves, reservoir properties and in situ CO2 characteristics. In the case of CO2-EOR, the CO2 storage capacity can be roughly evaluated on the basis of worldwide field experience or more accurately through numerical simulations. Determination of the theoretical CO2 storage capacity in coal beds is based on coal thickness and CO2 adsorption isotherms, and recovery and completion factors. Evaluation of the CO2 storage capacity in deep saline aquifers is very complex because four trapping mechanisms that act at different rates are involved and, at times, all mechanisms may be operating simultaneously. The level of detail and resolution required in the data make reliable and accurate estimation of CO2 storage capacity in deep saline aquifers practical only at the local and site-specific scales. This paper follows a previous one on issues and development of standards for CO2 storage capacity estimation, and provides a clear set of definitions and methodologies for the assessment of CO2 storage capacity in geological media. Notwithstanding the defined methodologies suggested for estimating CO2 storage capacity, major challenges lie ahead because of lack of data, particularly for coal beds and deep saline aquifers, lack of knowledge about the coefficients that reduce storage capacity from theoretical to effective and to practical, and lack of knowledge about the interplay between various trapping mechanisms at work in deep saline aquifer

Capillary trapping quantification in sandstones using NMR relaxometry

© 2017. American Geophysical Union. All Rights Reserved. Capillary trapping of a non-wetting phase arising from two-phase immiscible flow in sedimentary rocks is critical to many geoscience scenarios, including oil and gas recovery, aquifer recharge and, with increasing interest, carbon sequestration. Here we demonstrate the successful use of low field 1 H Nuclear Magnetic Resonance [NMR] to quantify capillary trapping; specifically we use transverse relaxation time [T 2 ] time measurements to measure both residual water [wetting phase] content and the surface-to-volume ratio distribution (which is proportional to pore size] of the void space occupied by this residual water. Critically we systematically confirm this relationship between T 2 and pore size by quantifying inter-pore magnetic field gradients due to magnetic susceptibility contrast, and demonstrate that our measurements at all water saturations are unaffected. Diffusion in such field gradients can potentially severely distort the T 2 -pore size relationship, rendering it unusable. Measurements are performed for nitrogen injection into a range of water-saturated sandstone plugs at reservoir conditions. Consistent with a water-wet system, water was preferentially displaced from larger pores while relatively little change was observed in the water occupying smaller pore spaces. The impact of cyclic wetting/non-wetting fluid injection was explored and indicated that such a regime increased non-wetting trapping efficiency by the sequential occupation of the most available larger pores by nitrogen. Finally the replacement of nitrogen by CO 2 was considered; this revealed that dissolution of paramagnetic minerals from the sandstone caused by its exposure to carbonic acid reduced the in situ bulk fluid T 2 relaxation time on a timescale comparable to our core flooding experiments. The implications of this for the T 2 -pore size relationship are discussed