Search

This paper presents a high-level overview of site characterization, risk analysis and monitoring priorities for underground energy-related product storage or sequestration facilities. The siting of an underground storage or sequestration facility depends on several important factors beginning with the area of review. Collection of all existing and available records and data from within the rock volume, including potential vulnerabilities such as prior containment issues, proximity to infrastructure and/or population centres, must be evaluated. Baselining of natural processes before storage or sequestration operations begin provides the basis for assessing the effects of storage or sequestration on the surroundings. These initial investigations include geological, geophysical and geochemical analyses of the suitability of the geological host rock and environs for storage or sequestration. A risk analysis identifies and evaluates threats and hazards, the potential impact should they develop into unwanted circumstances or events and the consequences to the facility should any of them occur. This forms the basis for framing effective mitigation measures. A comprehensive monitoring programme that may include downhole well surveillance, observation wells, geochemical sampling and well testing ensures that the facility operates as designed and that unforeseen issues, such as product migration or loss of integrity, can be identified and mitigated. In addition to these technical issues, human factors and public perception of a project are a critical part of the site characterization, construction and operational phases of a project. Despite differences between underground storage and sequestration, the characterization, risk analysis and monitoring approaches that were developed for underground natural gas storage or for carbon dioxide sequestration could be used for underground storage or sequestration of any type of energy-related product. Recommendations from this work include: (1) develop an industry-standard evaluation protocol (workflow) for the evaluation of salt beds, saline aquifers, depleted hydrocarbon reservoirs, underground mines and cased wellbores for potential underground storage or sequestration development beyond those in use today; and (2) develop an industry-wide collaborative process whereby incident and near-miss data related to underground storage or sequestration operations can be reported, documented and shared for use in refining risk analysis modelling.

Geological structures in the subsurface have been used for the storage of energy and waste products for over a century. Depleted oil and gas fields, saline aquifers or engineered caverns in salt or crystalline rocks are used worldwide to store energy fluids intended to provide demand buffers and sustained energy supply. The transition of our energy system into a clean, renewable-based system will most likely require an expansion of these subsurface storage activities, to host a wide variety of energy products (e.g. natural gas, hydrogen, heat or waste energy products, like CO 2 ) to balance the inherent intermittence of the renewable energy supply. Ensuring the safety and effectiveness of these subsurface storage operations is therefore crucial to achieve the sought-after renewable energy transition while ensuring energy security.

HighlightsIn-channel sediment and TP storage were quantified along 13.5 km of a stream.TP and sediment masses were 1 and 3 times greater than their respective annual watershed load.Colluvial material at streambank toe represented the dominant storage pool.Sinuous stream reaches exhibited significantly greater storage versus channelized reaches.Abstract. In-channel storage of both fine sediment and sediment-bound phosphorus has been recognized as potentially large contributors to respective watershed loads, yet they are rarely quantified in the field. In this field-based study, we quantified and characterized in-channel fine sediment and total phosphorus (TP) storage within a third-order stream. We hypothesized storage to be significant within the context of watershed-scale sediment and TP loads and that storage trends are influenced by channel characteristics and hydraulics. In May 2015, the volume of stored in-channel sediment was estimated within a 13.5 km stretch of Walnut Creek, an alluvial stream draining an agriculturally dominated watershed in Jasper County, Iowa, USA. Storage volume was estimated in-field through a series of 240 transects which were stratified across reaches of the varying channel and hydraulic conditions (e.g., sinuosity, stream power). Overall storage volume was broken down into feature classes (e.g., point bars) based on in-channel depositional processes. Following in-field quantification, feature class sediment samples were collected and analyzed for physical properties (e.g., bulk density) and TP concentration. Physical and chemical analyses, coupled with in-field volume estimation, allowed for watershed-scale masses of in-channel sediment and TP to be calculated and then placed within the context of respective annual loads. Sediment and TP were estimated to be stored at ~2.7 Mg m-1 and 0.7 kg m-1, respectively. Sinuous reaches exhibited significantly greater sediment storage volume (p < 0.001) and depth (p < 0.001) versus straight reaches. Reach sinuosity exhibited a significant positive correlation (p = 0.03) with storage mass and represented the most effective storage predictor. The majority of storage mass (72%) was represented by colluvial material accumulations at the streambank toe. Loose bed sediment was the second greatest contributor to storage mass (18%), with the remaining feature classes (e.g., bars) representing a combined ~10%. Sediment storage mass was ~3.25 times greater than the watershed suspended sediment load for 2015. The TP mass was found to be nearly equal to the respective watershed load for 2015. In-channel sediment and TP storage masses within Walnut Creek were found to be significant in comparison to respective annual loads, and thus storage is expected to play a significant role in respective watershed routing, loading, and the overall budgets of these parameters. Though challenging, quantification of in-channel fine sediment and TP storage is necessary to relate source contributions (e.g., streambank erosion) to watershed loads and is critical to account for interannual sediment and TP export. Keywords: Channel evolution, Channel morphology, Iowa, Sinuosity, Stream power, Water quality, Watershed export.

Carbon capture and sequestration (CCS) is widely recognized as an important component of technological approaches to directly address carbon dioxide (CO 2 ) emissions. The geological sequestration aspect of CCS requires careful site selection and assessment of processes when planning a CCS project, including coupled fluid flow–thermal–geochemical–geomechanical phenomena. In this paper, we present a high-level overview of carbon capture utilization and sequestration (CCUS): the geological sequestration aspect, global projects/facilities, regulatory framework and financial incentives for CCUS. We review the current research areas in geomechanics (including pore pressure–stress coupling, fault reactivation and caprock integrity) associated with geological CO 2 sequestration and discuss the role of rock physics in monitoring, verification and accounting activities. Finally, we suggest research needs that are critical to facilitating the deployment of CCS and improving geomechanical assessments of CO 2 sequestration sites.

After fertilization, remodeling of the oocyte and sperm genomes is essential to convert these highly differentiated non-dividing transcriptionally quiescent cells into early cleavage-stage transcriptionally active totipotent blastomeres. This developmental transition is accompanied by cell cycle adaptation such as lengthening or shortening of the gap phases G1 and G2. However, regulation of these cell cycle changes is poorly understood, especially in mammals. Checkpoint kinase 1 (CHK1) is a protein kinase that regulates cell cycle progression in somatic cells. Here, we show that CHK1 regulates cell cycle progression in early mouse embryos by restraining CDK1 kinase activity due to CDC25A phosphatase degradation. CHK1 kinase also ensures the long G2 phase needed for genome activation and reprogramming gene expression in 2-cell stage mouse embryos. Last,Chk1depletion leads to DNA damage and chromosome segregation errors that result in aneuploidy and infertility.

MicroRNAs (miRNAs) are small, noncoding RNAs that regulate gene expression after transcription. miRNAs are present in transcriptionally quiescent full-grown oocytes and preimplantation embryos that display a low level of transcription prior to embryonic genome activation. The role of miRNAs, if any, in preimplantation development is not known. The temporal pattern of expression of miRNAs during bovine preimplantation development was determined by small RNA-sequencing using eggs and preimplantation embryos (1-cell, 2-cell, 4-cell, 8-cell, 16-cell, morula, and blastocyst). Embryos cultured in the presence of α-amanitin, which permitted the distinguishing of maternal miRNAs from embryonic miRNAs, indicated that embryonic miRNA expression was first detected at the two-cell stage but dramatically increased during the morula and blastocyst stages. Targeting DGCR8 by a small-interfering RNA/morpholino approach revealed a role for miRNAs in the morula-to-blastocyst transition. Knockdown of DGCR8 not only inhibited expression of embryonically expressed miRNAs but also inhibited the morula-to-blastocyst transition. In addition, RNA-sequencing identified an increased relative abundance of messenger RNAs potentially targeted by embryonic miRNAs in DGCR8-knockdown embryos when compared with controls. Results from these experiments implicate an essential role for miRNAs in bovine preimplantation embryo development.

10 p.-4 fig., The ovarian reserve defines the female reproductive lifespan, which in humans spans decades due to robust maintenance of meiotic arrest in oocytes residing in primordial follicles. Epigenetic reprogramming, including DNA demethylation, accompanies meiotic entry, but the chromatin changes that underpin the generation and preservation of ovarian reserves are poorly defined. We report that the Polycomb Repressive Complex 1 (PRC1) establishes repressive chromatin states in perinatal mouse oocytes that directly suppress the gene expression program of meiotic prophase-I and thereby enable the transition to dictyate arrest. PRC1 dysfuction causes depletion of the ovarian reserve and leads to premature ovarian failure. Our study demonstrates a fundamental role for PRC1-mediated gene silencing in female reproductive lifespan, and reveals a critical window of epigenetic programming required to establish ovarian reserve., Funding sources: National Institutes of Health grants R01GM122776 and R35GM141085 to S.H.N.

Introduction: The edge of the pre-Noachian Borealis impact basin, thought to be the cause of the planetary dichotomy boundary [1-2], crosses the northern Valles Marineris troughs [1-3]. Intense deformation is exposed in the deepest parts of the Ophir and Hebes Chasmata, the northernmost troughs. Structural geology and mineralogical analyses motivate the tentative identification of brittle and brittle-ductile shear zones and hydrothermal activity in the Valles Marineris basement. Implications for the Borealis basin and the proto-Valles Marineris crust are examined. Structural analysis: Crustal right-lateral shear zones are identified in the pre-Noachian basement of Ophir and Hebes Chasmata (Figure 1). In Ophir Chasma, S-C-C' structures, indicate deformation in the brittle-ductile domain. In Hebes Chasma, megabreccia indicates brittle deformation. From scaling relationships [4-5], the shear zones are inferred to be at least hundreds of kilometers long. They do not extend to the surface nor even up into the interior layered deposits (ILD), and are therefore interpreted to affect the Valles Marineris basement only, which at this depth, is interpreted to be of pre-Noachian age. Mineralogy: A new method of non-linear spectral unmixing derived from the LinMin algorithm [6] is implemented and applied to three pre-Noachian basement exposures in a CRISM cube in Ophir Chasma. After gas absorption removal, two groups of minerals are robustly detected (Figure 2): primary minerals of mafic rocks (olivine, hypersthene, augite, anorthite, albite), and sulfates, most of them likely of hydrothermal origin (copiapite, jarosite, szomolnokite). Anhydrite (ROI3) is not diagnostic of any particular environment. Kieserite is interpreted as transported by wind from the neighboring ILDs. S-C-C' structures constrain the granulometry of the sheared rock which, under the assumption that all the primary minerals are detected, would be olivine-gabbronorite (ROI1) or troctolite (ROI2-3). Combined structural and mineralogical analyses point to hydrothermal alteration of a mafic intrusive basement, or contamination of this basement by hydrothermal activity in the ILDs. Relationships with the Borealis basin: The general trend of the shear zones follows the edge of the Borealis as inferred from gravity and topography [4], also of pre-Noachian age, suggesting that they may have initiated as basin ring faults and were reactivated as crustal shears. North of Valles Marineris, the radial component of the remanent magnetic field at the surface [7] shows elongated anomalies that follow the trend of the shear zones and more generally, the expected curved edge of the Borealis basin. The existence of a magnetic field (or dynamo) was coeval with formation of the planetary dichotomy boundary [8]. Two anomalies also correspond to Noachian or pre-Noachian crustal ridges in Ophir Planum, of igneous [9] or tectonic [10] origin. Mapping reveals that the ridges are fractured parallel to the magnetic anomalies, and that their topography guided a hydrologic system (Figure 3). Moreover, these fractures are parallel to a dyke swarm exposed in eastern Candor Chasma [11]. Therefore, the ridges have a volcanotectonic origin within an active hydrologic context. Figure 1. Ophir shear zone (OSZ) and Hebes shear zone (HSZ): (a) location map showing trace of the Borealis impact basin with ±5° uncertainty (dashed area) [5]; (b) zoom on S-C-C' structures in the OSZ, and illustration of shear orientations; (c) zoom on fault megabreccia in the HSZ. HiRISE images ESP_017754_1755 and ESP_040211_1790. Figure 2. Results of nonlinear spectral unmixing applied to basement exposures in Ophir Chasma: (a) CRISM cube location (frt00018b55_07_if165l_trr3); (b) the cube (bands R: 233, G: 78, B: 13); (c) mineral relative abundances, after aerosol contribution removal; (d) best fit plots and HiRISE images of the basement exposures: ESP_051999_1755, ESP_039525_1755, ESP_039525_1755. Figure 3. Features related to hydrothermal activity possibly resulting from the Borealis impact and suggested to explain magnetic banding north of Coprates Chasma. Dykes are located thanks to HiRISE images. The rose diagram was established from 26 representative dykes observed on the eastern Candor Chasma wall; the indicated strike refers to the mean resultant dyke orientation. Magnetic anomalies are from [7]. Topographic contours (spacing 500 m) are from HRSC (ESA/DLR/Freie Univ. Berlin). Circumferential magnetic anomalies are observed at some terrestrial impact craters (e.g.[12]) as well as the Chicxulub impact basin [13] and are due to crystallization of magnetic minerals in an impact-related hydrothermal system [14]. We suggest, therefore, that the magnetic anomalies measured above the Valles Marineris plateau similarly result from hydrothermal activity in response to the Borealis impact, and follow basin ring structures. This hydrothermal activity might be the surface counterpart of deep hydrothermal activity in the basement detected using spectral unmixing [15]. Conclusions: Analysis of northeastern Valles Marineris supports the interpretation of a pre-Noachian Borealis impact basin that would have underlain the later northern troughs of Valles Marineris in the presence of an active dynamo. Large shear zones in the Valles Marineris basement would be reactivated ring faults. Borealis basin formation may have triggered a huge hydrothermal system, identified along these structures and also producing magnetic minerals that generated the observed magnetic anomalies. Primary deposits of base and rare metals likely formed as well. Other evidence of hydrothermal activity at the edge of the Borealis basin would confirm these interpretations. References: [1] Andrews-Hanna J. et al. (2008) Nature, 453, 1212–1215. [2] Marinova M. M. et al. (2008) Nature, 453, 1216–1219. [3] Andrews-Hanna J. (2012) J. Geophys. Res., 117, E03006. [4] Schultz R. A. and Fossen H. (2002) J. Struct. Geol. 24, 1389–1411. [5] Fossen H. (2010) Structural Geology, Cambridge Univ. Press. [6] Schmidt F. et al. (2014) Icarus, 237, 61–74. [7] Langlais B. et al. (2019) J. Geophys Res., 109, E02008. [8] Mittelholz et al. (2020) Sci. Adv., eaba0513. [9] Tanaka K. L. et al. (2014) USGS Sci. Inv. Map 3292. [10] Viviano-Beck et al. (2017) Icarus, 284, 43–58. [11] Mège D. and Gurgurewicz J. (2017) 48th LPSC, Abstract #1087. [12] Hawke P. J. et al. (2006) Explor. Geophys., 37, 191–196. [13] Abramov O. and Kring D. A. Meteor. Planet. Sci., 42, 93–112. [14] Osinski G. R. et al. (2011) Meteor. Planet. Sci., 36, 731–745. [15] Gurgurewicz J. et al., submitted to Commun. Earth Environ.

Recent events resulting from the Covid-19 pandemic precipitated a triage-like environment wherein experienced faculty were forced to convert courses rapidly to online venues. This unexpected circum...

It remains poorly understood how histone modifications regulate changes in gene expression during preimplantation development. Using a bovine model, we profiled changes in two activating (H3K4me3 and H3K27ac) and two repressive (H3K9me3 and H3K27me3) marks in oocytes, 2-, 4- and 8-cell embryos (that developed in the presence or absence of the transcription inhibitor a-amanitin), morula, blastocysts, inner cell mass cells and trophectoderm. In oocytes, we find that broad bivalent domains of H3K4me3 and H3K27me3 mark developmental genes, and that prior to genome activation, H3K9me3 and H3K27me3 co-occupy gene bodies. During genome activation, chromatin accessibility is established before canonical H3K4me3 and H3K27ac, and although embryonic transcription is required for this active remodeling, it is dispensable for maintenance of pre-established histone marks. Finally, blastocyst lineages are defined by differential Polycomb repression and transcription factor activity. Overall, these results further support the use of bovine as a more appropriate model system than the mouse to study genome activation and cell lineage specification during human preimplantation development.

Stream bank erosion in agricultural landscapes is a major pathway for non-point source sediment and phosphorus loading of receiving waters. Previous studies have shown direct and indirect effects of land use on stream bank erosion, and identified high erosion rates within riparian pastures. One potential impact of agricultural land-use on stream bank erosion is the alteration of stream stage characteristics, including an increase in frequency of high-stage events over short periods of time (forming flash hydrographs). The objective of this study was to assess the relationship between the number of high stream stages and corresponding stream bank soil erosion. The study was conducted in six grazed pasture stream reaches within the Rathbun Lake Watershed, a reservoir on the Chariton River located within the Southern Iowa Drift Plain. The erosion pin method was utilized to measure the change in stream bank erosion in response to differences in the number of high stream-stage events, which were monitored by pressure transducers. The measured seasonal bank erosion rates were correlated with the different stream stages data to assess their impact on stream bank erosion. Based on the different model assumptions, there were generally strong linear relationships between high stage and bank erosion. Approximately 75% of the variability in stream bank erosion rates was directly linked to the number of high stages/erosive stream flow depths. Conservation practices that reduce these erosion rates will be those that increase soil-water infiltration, reduce the frequency of high stream flow events and increase bank stability through perennial vegetation cover or reducing disturbance within the riparian zone.

SummaryA core-based fracture prediction method is used to illustrate a value-of-information (VOI) decision-analysis protocol to inform completion decisions in tight gas sandstones. The ratio of late host-rock cement to available pore volume (PV), or degradation index, uses petrographic observations of cement distributions in core (including sidewall cores) to predict whether nearby but unsampled fractures (widths > 0.5 to 1 mm) are sealed (nonconductive) or open (conductive). Measurements from four sandstone plays suggest that the index correctly predicts open vs. sealed fractures with an accuracy in excess of 80%. The value added is calculated using Bayesian inference in which the accuracy of the index serves as the likelihood of the prior distribution of open fractures to assess the posterior probability that data represent a useful predictor of producibility. VOI of the prediction method is more than three times the cost to acquire the data. VOI is most sensitive to play-specific geologic and cost parameters including cost to drill, expected revenue from a successful well, cost of completion, cost of acquiring data for the index, and fracture probability distributions. The approach provides a way to value acquiring fracture data and points to a need for zone-specific production data in tight gas sandstones.

Volunteer cleanup operations collect large datasets on anthropogenic litter that are seldom analyzed. Here we assess the influence of land use in both near-stream and watershed scale source domains on anthropogenic litter concentration (standing stock, kg km−1) in riparian zones of Iowa, USA. We utilized riparian litter concentration data on four classes of anthropogenic litter (metal, recyclable, garbage, and tires) from volunteer cleanup operations. Anthropogenic litter data were tested for correlation with near-stream and watershed scale land uses (developed, road density, agricultural, and open lands). Road density (road length/area) and developed land use (% area) were significantly correlated to anthropogenic litter, but agricultural (% area) and open lands (% area) were not. Metal objects correlated to near-stream road density (r = 0.79, p = 0.02), while garbage and recyclable materials correlated to watershed scale road density (r = 0.69, p = 0.06 and r = 0.71, p = 0.05 respectively). These differences in the important spatial scales of land use may be related to differences in transport characteristics of anthropogenic litter. Larger, denser metal objects may be transported more slowly through the watershed/channelized system and thus, dependent on more proximal sources, whereas smaller, less dense garbage and recyclable material are likely transported more rapidly, resulting in concentrations that depend more on watershed scale supply. We developed a linear regression model that used near-stream road density and the total amount of observed litter to predict an average anthropogenic litter density of 188 kg km−1 and a standing stock of 946 t in all Iowa streams (>4th Strahler order). The techniques employed in this study can be applied to other professional and volunteer litter datasets to develop prevention and cleanup efforts, inform investigations of process, and assess management actions.

Summary Oil and gas production from unconventional reservoirs, which are usually stratified with layers having different mechanical properties, generally requires the aid of hydraulic–fracturing technology. Predicting hydraulic–fracture–height growth is one of the critical factors in designing successful hydraulic–fracturing treatments. It has been well–documented that the in–situ–stress contrast between adjacent layers and interface properties are the dominating factors in fracture–height containment, whereas the modulus contrast between adjacent layers is generally considered to be of secondary importance in the direct control of fracture–height containment. However, the arrest of fluid–driven fractures at soft layers is often observed in outcrops and hydraulic–fracture–diagnostic field tests. The objective of this study is to investigate fracture–height containment resulting from the modulus contrast between adjacent layers. To illustrate the effect of modulus contrast on fracture–height containment, this study proposes a new approach that uses the effective modulus of a layered reservoir. We use 2D finite–element models to evaluate the effective modulus of a layered reservoir, considering the effects of modulus values, fracture–tip location, height percentage of each rock layer, layer location, the number of layers, and the mechanical anisotropy. Then, the effect of modulus contrast on fracture–height growth is investigated with an analysis of the stress–intensity factor, taking into account the change of the effective modulus as the fracture tip propagates from the stiff layer to the soft layer. This study shows that the detail of layering does not affect the effective modulus and the only important parameters are fracture–tip locations, modulus values, and the height percentage of each rock layer. In addition, this study empirically derives two approximations of effective moduli depending on fracture–tip locations: the modified height–weighted mean and the modified height–weighted harmonic average. Results from combining linear–elastic fracture mechanics with the effective–modulus approximations show that height growth will be inhibited by the soft layer because of a reduced stress–intensity factor. The effective moduli can be applied to other hydraulic–fracture models to take into account the layering effect. This study also shows that soft layers inhibit hydraulic–fracture–height growth in layered reservoirs. As a result, hydraulic–fracture–height containment within a stratified rock stack can be better evaluated by comparing the modulus contrast between adjacent layers.

The objective of this study was to develop a conceptual framework to study soil aggregate dynamics through the integration of aggregation, disruption, stabilization and destabilization processes of soil constituent units. We used aggregate‐size distribution and water stability of macroaggregates to evaluate changes in soil aggregates in two ecosystems where one is the ‘reference’ state and the other is the ‘new’ state. The framework was validated with data from (a) a non‐buffered annual row crop (ARC) system, (b) a no‐till (NT) system and (c) a bare fallow (BF) system. The dynamics of soil aggregates in the ARC were dominated by the disruption of aggregates (the aggregation–disruption index (ADI) was −0.08), in NT they were dominated by the aggregation process (ADI = 0.03) and in BF dominated by the disruption of aggregates (ADI = −0.20). Three pathways were observed: (a) expression of the aggregation process, which is essential in reestablishing soil structure and functionality, (b) expression of the disruption process, which is critical in the destruction of soil structure and (c) prevalence of mixed behaviour, where the dominant process depended on the relative rate of aggregation and disruption. The proposed framework and study of the carbon associated with aggregates could pave the way for the development of a methodology for the quantitative study of soil organic carbon (SOC) dynamics, carbon inputs (outputs), soil carbon fractions, and edaphic and biotic conditions that regulate SOC dynamics. HIGHLIGHTS: Soil aggregate dynamics were assessed within multiple management systems. A new methodology is proposed for the quantitative study of soil aggregate dynamics. Provided an understanding of aggregation, disruption, stabilization and destabilization in aggregate dynamics. Aggregate dynamic pathways of value in land management can minimize deterioration of the environment.

Although in vitro fertilization (IVF) is associated with adverse perinatal outcomes, there is increasing concern about the long-term and sex-specific health implications. Augmenting our IVF mouse model to longitudinally investigate metabolic outcomes in offspring from optimal neonatal litter sizes, we found sex-specific metabolic outcomes in IVF offspring. IVF-conceived females had higher body weight and cholesterol levels compared to naturally conceived females, whereas IVF-conceived males had higher levels of triglycerides and insulin, and increased body fat composition. Through adult liver transcriptomics and proteomics, we identified sexually dimorphic dysregulation of the sterol regulatory element-binding protein (SREBP) pathways that are associated with the sex-specific phenotypes. We also found that global loss of DNA methylation in placenta was linked to higher cholesterol levels in IVF-conceived females. Our findings indicate that IVF procedures have long-lasting sex-specific effects on metabolic health of offspring and lay the foundation to utilize the placenta as a predictor of long-term outcomes.

Although in vitro fertilization (IVF) is associated with adverse perinatal outcomes, an increasing concern is the long-term health implications. We augmented our IVF mouse model to longitudinally investigate cardiometabolic outcomes in offspring from optimal neonatal litter sizes. We found that IVF-conceived females had higher body weight and cholesterol levels compared to naturally-conceived females, whereas IVF-conceived males had higher levels of triglycerides and insulin, and increased body fat composition. Through transcriptomics and proteomics of adult liver, we identified sexually-dimorphic dysregulation of the sterol regulatory element binding protein (SREBP) pathways that are associated with the sex-specfic phenotypes. We also found that global loss of DNA methylation in placenta was linked to higher cholesterol levels in IVF-conceived females. Our findings indicate that IVF procedures have long-lasting sex-specific effects on metabolic health of offspring and lay the foundation to utilize the placenta as a predictor of long-term outcomes.

The shift from maternal to embryonic control is a critical developmental milestone in preimplantation development. Widespread transcriptomic and epigenetic remodeling facilitate this transition from terminally differentiated gametes to totipotent blastomeres, but the identity of transcription factors (TF) and genomic elements regulating embryonic genome activation (EGA) are poorly defined. The timing of EGA is species-specific, e.g., the timing of murine and human EGA differ significantly. To deepen our understanding of mammalian EGA, here we profile changes in open chromatin during bovine preimplantation development. Before EGA, open chromatin is enriched for maternal TF binding, similar to that observed in humans and mice. During EGA, homeobox factor binding becomes more prevalent and requires embryonic transcription. A cross-species comparison of open chromatin during preimplantation development reveals strong similarity in the regulatory circuitry underlying bovine and human EGA compared to mouse. Moreover, TFs associated with murine EGA are not enriched in cattle or humans, indicating that cattle may be a more informative model for human preimplantation development than mice., Preimplantation embryos undergo extensive transcriptomic and epigenomic remodeling. Here the authors assay open chromatin in bovine oocytes, embryos, and embryonic stem cells, and compare the transcriptomes and epigenomes of cattle, human and mouse embryos, revealing species-specific regulation of genome activation.

Mammalian oocytes are arrested at meiotic prophase I. The dual-specificity phosphatase CDC25B is essential for cyclin-dependent kinase 1 (CDK1) activation that drives resumption of meiosis. CDC25B reverses the inhibitory effect of the protein kinases WEE1 and MYT1 on CDK1 activation. Cdc25b−/− female mice are infertile because oocytes cannot activate CDK1. To identify a role for CDC25B following resumption of meiosis, we restored CDK1 activation in Cdc25b−/− oocytes by inhibiting WEE1 and MYT1, or expressing EGFP-CDC25A or constitutively active EGFP-CDK1 from microinjected complementary RNAs. Forced CDK1 activation in Cdc25b−/− oocytes allowed resumption of meiosis, but oocytes mostly arrested at metaphase I (MI) with intact spindles. Similarly, approximately a third of Cdc25b+/− oocytes with a reduced amount of CDC25B arrested in MI. MI-arrested Cdc25b−/− oocytes also displayed a transient decrease in CDK1 activity similar to Cdc25b+/+ oocytes during the MI-MII transition, whereas Cdc25b+/− oocytes exhibited only a partial anaphase-promoting complex/cyclosome activation and anaphase I entry. Thus, CDC25B is necessary for the resumption of meiosis and the MI-MII transition.

Riparian buffers are a conservation practice that increases vegetation diversity on the agricultural landscape while providing environmental benefits. This study specifically focused on the ability of riparian buffers to remove nitrate from shallow groundwater. There are many studies that assessed nitrate removal within buffers, but not many have a long-term, continuous data set that can analyze for variation in nitrate removal rates over time. Here we report on 21 years of nitrate well data, from 1996 through 2017, for three buffers in the Bear Creek watershed in central Iowa. These buffers are named using abbreviations to help keep landowners anonymous (e.g. RN, RS, and ST). Studied buffers RS and ST showed greater nitrate reduction (or removal) after 10 and 6 years of its establishment, respectively. Buffer RN did not experience a significant nitrate removal increase with time, but instead had higher nitrate removal rates when compared to buffers RS and ST of 10.3 g NO3−-N m−1 day−1 from the start of this study. From this data, we suggest that past land management played a major role in the responses observed. RN had previously been established in cool-season grasses for grazing before being converted to a buffer, while RS and ST had been managed in a corn and soybean rotation. RN was thought to have higher denitrification immediately with increased labile soil carbon input and enhanced soil aggregation due to the grassland perennials, while buffer vegetation establishment increased soil carbon inputs and soil aggregation over time for RS and ST. These nitrate removal trends would not have been observed without access to long-term, continuous data. This study highlighted the importance of long-term data sets and the need to assess conservation practices over time to determine their longevity and efficiency with time.

Natural gas (methane) has rapidly become a critically important component to the energy economies of the United States and other countries. Because storage capacity in the above-ground pipeline network is insufficient to meet demand, natural gas is stored in large underground (UGS) facilities both in the US and, to an increasing extent, throughout the world. Defining a baseline for the frequency of reported and documented off-normal occurrences, including human error, process safety, mechanical or operational issues, or natural events with or without leakage, at UGS facilities is critical to maintaining safe operation and to the development of appropriate risk management plans and regulatory approaches.We have analyzed the frequency of off-normal occurrences at US UGS facilities hosted by each US state. Some 31 states host UGS facilities in porous rock (depleted oil-and-gas field and aquifer), and/or solution-mined salt cavern storage facilities. Data are based upon extensive searches of information available in the public domain and not all occurrences involve the stored gas or its release but which, in combination with other factors, could lead to significant problems. The number of reported occurrences, normalized by the number of facilities and the years of active operation, define the mean occurrence frequency per facility-year for each state. Bayesian probabilistic analysis then characterizes the historical occurrence frequencies and uncertainties, parsed by storage facility type, above-ground or below-ground causes, and severity of occurrence.Both UGS facility-years and nuisance-level occurrences for depleted field storages are highly variable from state to state, for both above-ground and below-ground causes. Aquifer storage facilities show large numbers of occurrences relative to the number of facility-years, with above-ground occurrences identified for four states and a smaller number of below-ground occurrences found for a larger number of states. Salt-cavern storage has a large number of occurrences over a relatively small number of facility-years: most of which are associated with below-ground causes.Nuisance-level occurrence frequencies for porous-rock storage facilities and for both above-ground and below-ground causes, are generally in the range of 10–1 to 10–3 occurrences per facility-year except for those in California, which exceed 10–1 occurrences per facility-year. Serious or catastrophic occurrence frequencies for depleted field storage facilities decrease to less than about 10–2 occurrences per facility-year for most states. Nuisance-level occurrence frequencies for salt-cavern storage facilities exceed 10–2 occurrences per facility-year for below-ground causes, whilst serious or catastrophic occurrences decrease to about 10–3 to 10–1 occurrences per facility-year.

Most reproductive biologists who study female gametes will agree with the 16th century anatomist William Harvey’s doctrine: ‘Ex Ovo Omnia’. This phrase, which literally translates to ‘everything from the egg’, recognizes the centrality of the egg in animal development. Eggs are most impressive cells, capable of supporting development of an entirely new organism following fertilization or parthenogenetic activation. Not so uniformly embraced in the field of reproductive biology is the nomenclature used to refer to the female germ cell. What is an oocyte? What is an egg? Are these terms the same, different, interchangeable? Here we provide functional definitions of the oocyte and egg, and how they can be used in the context of mammalian gamete biology and beyond.

Microseismic events suggest that a complicated fracture network develops during hydraulic fracturing treatment in many naturally fractured unconventional reservoirs. One reason for the complexity is the deformation along weak planes such as faults and cemented natural fractures. The interaction of cemented natural fractures with hydraulic fractures generated as part of reservoir stimulation may impede or terminate hydraulic fracture propagation, which depends on several factors such as interfacial bond strength between the cemented natural fractures and the reservoir rock. Most previous studies treat natural fractures as interfaces without considering their thickness. In this study, the semi−circular bend (SCB) tests for specimens with heterogeneity are used to study the fracture−fracture interactions, because the tensile fracture in the SCB test is analogous to the induced hydraulic fracture. With simple experimental setup and good repeatability, the SCB test results provide insights into real hydraulic fracture propagation behavior in naturally fractured reservoirs. We analyze the effects of natural fracture thickness and rock−cement interfacial bond strength, which are not commonly considered. Results show that hydraulic fracture crossing/diverting behavior depends on the approach angle, the rock−cement interfacial bond strength, and the thickness of natural fracture. Results also imply that as hydraulic fractures approach cemented natural fractures, the hydraulic fracture near‒tip stress state is influenced by the tensile and shear strength of the rock−cement interface. In the SCB test, the sample geometry induces shearing along the cemented natural fracture−rock interface, analogous to a frictionally slipping interface in the subsurface. Depending on the frictional strength and the approach angle, the interface may crack apart, and attract a propagating fracture.

Cemented natural fractures (veins) in shale formations generate mechanical heterogeneities which contribute to complex hydraulic fracture network development. Lee et al. (JGR, 2015) experimentally investigated the interaction of propagating tensile fractures with calcite-filled veins in Marcellus shale using Semi-Circular Bend (SCB) tests. In this study, we investigate those experimental results with three-dimensional Discrete Element Method (DEM) modeling to gain further insight in the fracture interaction processes that generate hydraulic fracture complexity. In addition, we quantified the length of fracture diversion distance to show the effect of vein properties, including approach angle, thickness, strength, stiffness, penetration length, on fracture diversion results. The numerical results compared well with the laboratory fracture diversion results. There is a tendency towards fracture diversion as the approach angle becomes smaller and more oblique to the propagating fracture plane. As the stiffness of the vein increased, the microcrack-related damage increased and the bond breakages extended longer to either side of the main fracture path. Samples with thicker veins and increasing penetration length showed a weaker vein response; the induced fracture propagated for a longer distance in veins before kinking back into the rock matrix. In addition, the numerical model confirmed that the opening mode fracture initiated from the notch tip and the intergranular bond failure created microcracks within the vein before the approaching fracture intersected the vein. The failure mode of the bonds between discrete elements in the vein was predominantly tensile mode rather than shear.

The oocyte-to-embryo transition (OET) arguably initiates with formation of a primordial follicle and culminates with reprogramming of gene expression during the course of zygotic genome activation. This transition results in converting a highly differentiated cell, i.e. oocyte, to undifferentiated cells, i.e. initial blastomeres of a preimplantation embryo. A plethora of changes occur during the OET and include, but are not limited to, changes in transcription, chromatin structure, and protein synthesis; accumulation of macromolecules and organelles that will comprise the oocyte's maternal contribution to the early embryo; sequential acquisition of meiotic and developmental competence to name but a few. This review will focus on transcriptional and post-transcriptional changes that occur during OET in mouse because such changes are likely the major driving force for OET. We often take a historical and personal perspective, and highlight how advances in experimental methods often catalyzed conceptual advances in understanding the molecular bases for OET. We also point out questions that remain open and therefore represent topics of interest for future investigation.

Although the targeting and efficacy of erosion management practices have improved, sediment and nutrients continue to degrade surface waters of North America. This study investigated the influence of land use, stream order, and season on streambank erosion and phosphorus (P) transport in the Central Claypan Region of northeast Missouri. The erosion pin method was used to measure bank erosion at 37 sites in Crooked Creek and Otter Creek watersheds from 2008 to 2011. At 18 of the sites, bank vegetation data were collected and watershed characteristics acquired. Bank erosion was highly variable with a mean linear erosion rate of 99 kg m−1 y−1 (66 lb ft−1 yr−1) and a range of −31 to 490 kg m−1 y−1 (−20 to 330 lb ft−1 yr−1); mean bank recession rate was 7.1 cm y−1 (2.8 in yr−1) and ranged from −2.5 to 33 cm y−1 (−1 to 13 in yr−1). Erosion rates were significantly greater in winter (December to March) than other seasons and were highly correlated to winter and annual stream discharge (r ≥ 0.95, p

Assembling egg cells involves cytoplasmic and nuclear processes that together enable embryonic development. A study now defines a set of transcription factors required for cytoplasmic, but not key nuclear, processes.

Retrotransposons are “copy-and-paste” insertional mutagens that substantially contribute to mammalian genome content. Retrotransposons often carry long terminal repeats (LTRs) for retrovirus-like reverse transcription and integration into the genome. We report an extraordinary impact of a group of LTRs from the mammalian endogenous retrovirus-related ERVL retrotransposon class on gene expression in the germline and beyond. In mouse, we identified more than 800 LTRs from ORR1, MT, MT2, and MLT families, which resemble mobile gene-remodeling platforms that supply promoters and first exons. The LTR-mediated gene remodeling also extends to hamster, human, and bovine oocytes. The LTRs function in a stage-specific manner during the oocyte-to-embryo transition by activating transcription, altering protein-coding sequences, producing noncoding RNAs, and even supporting evolution of new protein-coding genes. These functions result, for example, in recycling processed pseudogenes into mRNAs or lncRNAs with regulatory roles. The functional potential of the studied LTRs is even higher, because we show that dormant LTR promoter activity can rescue loss of an essential upstream promoter. We also report a novel protein-coding gene evolution—D6Ertd527e—in which an MT LTR provided a promoter and the 5′ exon with a functional start codon while the bulk of the protein-coding sequence evolved through a CAG repeat expansion. Altogether, ERVL LTRs provide molecular mechanisms for stochastically scanning, rewiring, and recycling genetic information on an extraordinary scale. ERVL LTRs thus offer means for a comprehensive survey of the genome's expression potential, tightly intertwining with gene expression and evolution in the germline.

International audience; Deformation bands are common subseismic structures in porous sandstones that varywith respect to deformation mechanisms, geometries and distribution. The amount of cataclasisinvolved largely determines how they impact fluid flow, and cataclasis is generally promoted bycoarse grain size, good sorting, high porosity and overburden (usually.500–1000 m). Mostbands involve a combination of shear and compaction, and a distinction can be made betweenthose where shear displacement greatly exceeds compaction (compactional shear bands orCSB), where the two are of similar magnitude (shear-enhanced compaction bands or SECB),and pure compaction bands (PCB). The latter two only occur in the contractional regime, are char-acterized by high (70–1008) dihedral angles (SECB) or perpendicularity (PCB) tos1(the maxi-mum principal stress) and are restricted to layers with very high porosity. Contraction generallytends to produce populations of well-distributed deformation bands, whereas in the extensionalregime the majority of bands are clustered around faults. Deformation bands also favour highlyporous parts of a reservoir, which may result in a homogenization of the overall reservoir perme-ability and enhance sweep during hydrocarbon production. A number of intrinsic and external var-iables must therefore be considered when assessing the influence of deformation bands on reservoirperformance.

Summary Agriculture in the temperate zone of the Midwestern USA has removed most riparian buffer zones from the landscape, which impairs the soil functioning of the soil in these ecosystems. The objective of this study was to assess soil degradation in a non-buffered riparian zone with an annual row crop (ARC) and in a longer established (more than 85 years) riparian cool season grass (CSG) buffer in central Iowa, USA. To achieve our objective, we compared the functioning of the target system, ARC, with a system that has been undisturbed since 1990, CSG. We measured the aggregate size distribution and stability of macroaggregrates, aggregate-associated soil organic carbon and particulate organic matter (POM). The categorization of aggregates by size and water stability (slaking resistance) showed a significantly larger (P 250 µm) under CSG (53%) than under ARC (26.3%). On the other hand, soil under ARC had the larger proportion of large and small water-unstable macroaggregates. The results indicate that the concentration of organic C associated with the total water-stable aggregates is 1.9 times greater under CSG (23.9 mg C g−1) than for the ARC (12.4 mg C g−1). The concentration of carbon in light particulate organic matter (LPOM-C) under CSG accounted for 12% of total soil organic carbon (TSOC), but only 6% under ARC management. The chemical composition of LPOM in the ARC soil had a large alkyl-C/O-alkyl C ratio, which suggests more organic matter decomposition than with the CSG. Electronic micrographs showed evidence that under CSG roots and fungal hyphae form an extensive network around the large macroaggregates (> 2000 µm), and thus maintain the stability of the macroaggregates. Preserving the CSG buffer reduces soil erosion and the processes associated with nonpoint source pollutants, which improves water quality in an intensively managed agricultural system. Highlights How do soil aggregation and POM change after conversion of CSG buffer to continuous cultivation? Improved understanding of soil degradation through water-stable and -unstable aggregates and SOC. Lack of disturbance of CSG buffer favours formation of macroaggregates and SOC stabilization. Preserving CSG buffer improves water quality in an intensively managed agricultural system.

Full-grown oocytes are transcriptionally quiescent. Following maturation and fertilization, the early stages of embryonic development occur in the absence (or low levels) of transcription that results in a period of development relying on maternally derived products (e.g., mRNAs and proteins). Two critical steps occur during the transition from maternal to embryo control of development: maternal mRNA clearance and embryonic genome activation with an associated dramatic reprogramming of gene expression required for further development. By combining an RNA polymerase II inhibitor with RNA sequencing, we were able not only to distinguish maternally derived from embryonic transcripts in bovine preimplantation embryos but also to establish that embryonic gene activation is required for clearance of maternal mRNAs as well as to identify putative transcription factors that are likely critical for early bovine development.