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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.

Factors influencing streambank erosion at the field/reach scale include both watershed and riparian land-uses, stream hydrology and channel morphology at the catchment scale. This study assesses the relationship of riparian land-uses, stream morphologic characteristics and catchment scale variables to streambank erosion within grazed riparian pastures in the Southern Iowa Drift Plain. Thirteen cooperating beef cow&ndash, calf farms and their catchments ranging from 2.5 to 12.9 km2 in the Rathbun Lake watershed in South Central Iowa (USA) were chosen to conduct this study. Results suggest that the integration of stream morphologic characteristics and riparian land-uses at both the reach and catchment scale are necessary to explain the current level of streambank erosion measured at the reach scale. Larger catchment size or catchments with more total channel length were found to experience more bank erosion at the reach scale. A significant positive relationship between percent sand-and-silt in the bank soil and bank erosion rates implies that bank soils with less cohesiveness are more erodible. Catchment-scale assessments of the thirteen watersheds showed that within the 50 m corridor on both sides of the stream, 46 to 61% of riparian area was devoted to agricultural use and only 6 to 11% was in ungrazed perennial vegetation, much of it enrolled in the USDA Conservation Reserve Program. Overall, this and previous Rathbun watershed studies have shown that intensive agricultural use of riparian areas over such extents of time and scale could be directly (in field scale) and/or indirectly (watershed scale) related to excessive amounts of streambank erosion (ranging from 8.6 to 38.3 cm/yr) to receiving streams and lakes leading to their impairment and reduction in ecological services. Exclusion of cattle grazing in the riparian areas along buffered stream lengths (2.1% of the total watershed area) of the Rathbun watershed would reduce this impact. This approach could also be applicable to other similar watersheds with extensive land-use under grazed management.

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

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.

Agricultural activities such as row-cropping and grazing, have accelerated stream bank erosion. Accelerated stream bank erosion increases nonpoint source pollutants in aquatic ecosystems, significantly degrading them. Mitigating stream bank erosion is a priority worldwide, especially in agricultural watersheds. The objective of this study was to analyze the impacts of riparian land-use management on stream bank erosion and deposition, along with analyzing its temporal and spatial patterns. The study was conducted in three regions of Iowa (central, northeast and southeast) along 30 stream reaches adjacent to seven different riparian land-uses. The riparian land-uses were riparian forest buffers, grass filters, pastures with the cattle excluded from the stream, intensive rotational grazing, rotational grazing, continuous grazing and row crop fields. Seasonal erosion and deposition data (Spring, Summer and Autumn) were collected along these reaches for 5 years and yearly for the following two years. To analyze the data, conventional statistical methods (ANOVA and Tukey's test) along with innovative techniques (percentile plots, cumulative erosion curves and bubble charts) were utilized. Based on the analysis, of this extensive in time (seven years) and large in size (1500 pins measured 17 times in three regions) field dataset, major results were obtained in regard to stream bank erosion in Iowa, USA. Stream banks exhibited high year-to-year variation in erosion and deposition showcasing the need for long-term datasets to better understand stream bank erosion and deposition. Seasonal erosion, also had high variability with Spring recording the most erosion followed by Summer and Autumn. Certain seasons exhibited high stream bank erosion indicating that managers need to focus on these seasons, to reduce erosion effectively. In addition, seasonal measurements can highlight depositional events that might be masked with annual measurements. Riparian land-uses significantly impacted stream bank erosion. Riparian forest buffers and grass filters significantly mitigated stream bank erosion while traditional agricultural practices like continuous grazing and row-crop agriculture had accelerated stream bank erosion. Finally, the percentile plots, cumulative erosion curves and bubble charts captured some stream bank responses that would have been unnoticed using conventional statistical methods, allowing decision makers, stakeholders and the general public, to support and approve measures to mitigate this environmental problem. Nature-based solutions utilizing riparian perennial vegetation can sustainably mitigate stream bank erosion.

Identification and mitigation of leaks of subsurface fluids such as hydrocarbons at many heavy-oil fields is a first-order concern to operating companies, their regulators and the public. A variety of leaks have been documented at heavy-oil fields in Alberta (Canada) and California (USA). Although the petroleum geology and tectonic framework of fields in these areas differ significantly, production-related uplift of overburden and dilation of pre-existing fractures due to cyclic steam injection are likely to have facilitated the leakage events. As a result, integration of overburden characterization and monitoring with management of steam pressures may provide an effective means of risk mitigation of major leakage events.