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RcsB, the transcription-associated response regulator of the Rcs phosphorelay two-component signal transduction system, activates cell stress responses associated with desiccation, cell wall biosynthesis, cell division, virulence, biofilm formation, and antibiotic resistance in enteric bacterial pathogens. RcsB belongs to the FixJ/NarL family of transcriptional regulators, which are characterized by a highly conserved C-terminal DNA-binding domain. The N-terminal domain of RcsB belongs to the family of two-component receiver domains. This receiver domain contains the phosphoacceptor site and participates in RcsB dimer formation; it also contributes to dimer formation with other transcription factor partners. Here, we describe the crystal structure of the Escherichia coli RcsB receiver domain in its nonphosphorylated state. The structure reveals important molecular details of phosphorylation-independent dimerization of RcsB and has implication for the formation of heterodimers.

The frequency of occurrences per facility-year, their probabilities, and their uncertainties are critical inputs to hazard and risk management plans for underground storage facilities. We used Bayesian analysis to investigate and quantify the occurrence frequencies at US underground natural gas storage facilities in porous rock and salt-cavern storage facilities. Occurrences for each of the 31 hosting states were classified by storage type, probable cause, and severity. States having the largest number of occurrences at the lowest, nuisance-group level of severity are California and Pennsylvania (for oil-and-gas storage), Iowa and Illinois (for aquifer storage), and Texas (for salt-cavern storage). Those states having the longest operational experience in natural-gas storage, as inferred by the number of facility-years, are Pennsylvania (for oil-and-gas storage), Illinois (for aquifer storage), and Texas (for salt-cavern storage). Bayesian nuisance-group occurrence frequencies are generally within a two order-of-magnitude range, 10−3 to 10−1 (P5–P95), with greater variability for salt-cavern storage. Serious- and catastrophic-group occurrence frequencies for depleted oil-and-gas storages decrease to 10−4 to 10−2 for all states except for California, Colorado, and, for aquifer storage, in Illinois, that remain consistent with their nuisance-group levels. The data do not support previous correlations of high occurrence frequencies with well age or construction practices. Instead, anomalously high occurrence frequencies for individual states might be associated with increased testing of wells and related infrastructure, or particular subsurface conditions that might promote location-specific hazards such as corrosion of well components.

Linear Elastic Fracture Mechanics (LEFM) is a widely applied theory to numerically simulate hydraulic fracture initiation and propagation in the subsurface. However, LEFM with the typical fracture toughness measured from unconfined laboratory tests does not apply to hydraulic fracturing applications under subsurface conditions because the fracture toughness is affected by the confining stress and fluid lag at the fracture tip. Thus, the apparent fracture toughness was proposed by Rubin (1993) to consider the contributions of fluid lag and confining stress. The main objective of this study is to validate the applicability of LEFM with the apparent fracture toughness in simulating hydraulic fracture under subsurface conditions. We utilized the finite element models to compare the near-tip stress state between the LEFM approach and the cohesive zone model (CZM), which considers the effect of confining stress and fluid lag. In addition, we compared the analytical solutions of fracture energy between LEFM and CZM. This study showed that the near-tip stress state of CZM outside the fluid lag and cohesive zone is comparable to the stress field predicted by LEFM with the apparent fracture toughness. However, LEFM with the fracture toughness measured from standard unconfined laboratory tests underestimates the near-tip stress state of fractures under confining stress. This study also revealed that the fracture energy of fluid-driven fractures calculated by CZM is identical to the fracture energy estimated from the approach of LEFM with the apparent fracture toughness. Thus, this study demonstrated that LEFM with the apparent fracture toughness is an appropriate and accurate method to simulate hydraulic fracture propagation in the subsurface.

Stream bank and gully erosion are major sources of nonpoint source pollutants, especially in landscapes dominated by agriculture. Implementation of upland conservation practices in landscapes dominated by agriculture reduces upland sediment transport more than water runoff, leading to excessive stream bank and gully erosion. This review focus on ten different studies conducted in streams in Iowa that investigated riparian land-use impacts on stream banks, gullies, and other riparian sediment sources (cattle loafing areas and cattle stream access points). The riparian land-uses investigated were riparian forest buffers; grass filters; continuous, rotational, and intensive rotational pastures; pastures with cattle fenced out of the stream; and row-cropped fields. Results of these studies indicate that maintaining perennial deep-rooted vegetation in riparian areas and excluding cattle from the stream channel stabilizes stream banks and gullies. Cattle loafing areas and cattle stream access points appear to also be important sediment sources. Re-establishing perennial riparian vegetation is a sustainable and cost-effective conservation practice because it reduces sediment in streams while maintaining the majority of the watershed in agricultural production. The limited available funds for the implementation of holistic watershed conservation practices suggest using targeted approaches, at the watershed scale, to improve conservation practice effectiveness.

Enhancer of zeste homolog 2 (EZH2), a component of the PRC2 complex, trimethylates H3K27, a transcriptionally repressive histone mark. EZH2 is encoded by a dormant maternal mRNA and inhibiting the maturation-associated increase in EZH2 activity using either a combined siRNA/morpholino approach or a small molecule inhibitor (GSK343) inhibits development of diploidized parthenotes to the blastocyst stage but not inseminated eggs, with longer GSK343 treatments leading to progressively greater inhibition of development. GSK343 treatment also results in a decrease in H3K27me3 and a decrease in global transcription in 2-cell parthenotes but not 2-cell embryos derived from inseminated eggs. RNA-sequencing revealed the relative abundance of ~100 zygotically-expressed transcripts is decreased by GSK treatment in parthenotes, but not in embryos, with many of the affected transcripts encoding proteins involved in transcription. A previous study found that parthenotes deficient in maternal Ezh2 readily develop to the blastocyst stage. To reconcile these differences we propose that the H3K27me3 state present in the zygote needs to be faithfully propagated following DNA replication in at least one pronucleus, otherwise development is compromised.

Transport and fate of dissolved nitrous oxide (N2O) in groundwater and its significance to nitrogen dynamics within agro-ecosystems are poorly known in spite of significant potential of N2O to global warming and ozone depletion. Increasing denitrification in riparian buffers may trade a reduction in nitrate (NO3−) transport to surface waters for increased N2O emissions resulting from denitrification-produced N2O dissolved in groundwater being emitted into the air when groundwater flows into a stream or a river. This study quantifies the transport and fate of NO3− and dissolved N2O moving from crop fields through riparian buffers, assesses whether groundwater exported from crop fields and riparian buffers is a significant source of dissolved N2O emissions, and evaluates the Intergovernmental Panel on Climate Change (IPCC) methodology to estimate dissolved N2O emission. We measured concentrations of NO3−; chloride (Cl−); pH; dissolved N2O, dissolved oxygen (DO), and organic carbon (DOC) in groundwater under a multi-species riparian buffer, a cool-season grass filter, and adjacent crop fields located in the Bear Creek watershed in central Iowa, USA. In both the multi-species riparian buffer and the cool-season grass filter, concentrations of dissolved N2O in the groundwater did not change as it passed through the sites, even when the concentrations of groundwater NO3− were decreased by 50% and 59%, respectively, over the same periods. The fraction of N lost to leaching and runoff (0.05) and the modified N2O emission factor, [ratio of dissolved N2O flux to N input (0.00002)] determined for the cropped fields indicate that the current IPCC methodology overestimates dissolved N2O flux in the sites. A low ratio between dissolved N2O flux and soil N2O emission (0.0003) was estimated in the cropped fields. These results suggest that the riparian buffers established adjacent to crop fields for water quality functions (enhanced denitrification) decreased NO3− and were not a source of dissolved N2O. Also, the flux of dissolved N2O from the cropped field was negligible in comparison to soil N2O emission in the crop fields.

In mice, transcription initiates at the mid-one-cell stage and transcriptional activity dramatically increases during the two-cell stage, a process called zygotic gene activation (ZGA). Associated with ZGA is a marked change in the pattern of gene expression that occurs after the second round of DNA replication. To distinguish ZGA before and after the second-round DNA replication, the former and latter are called minor and major ZGA, respectively. Although major ZGA are required for development beyond the two-cell stage, the function of minor ZGA is not well understood. Transiently inhibiting minor ZGA with 5, 6-dichloro-1-β-d-ribofuranosyl-benzimidazole (DRB) resulted in the majority of embryos arresting at the two-cell stage and retention of the H3K4me3 mark that normally decreases. After release from DRB, at which time major ZGA normally occurred, transcription initiated with characteristics of minor ZGA but not major ZGA, although degradation of maternal mRNA normally occurred. Thus, ZGA occurs sequentially starting with minor ZGA that is critical for the maternal-to-zygotic transition.

Mice lacking Cnot6l, a deadenylase component of the CCR4–NOT complex, are viable, but females have ∼40% smaller litters. Cnot6l is a maternal-effect gene acting in maternal mRNA degradation., Removal of poly(A) tail is an important mechanism controlling eukaryotic mRNA turnover. The major eukaryotic deadenylase complex CCR4-NOT contains two deadenylase components, CCR4 and CAF1, for which mammalian CCR4 is encoded by Cnot6 or Cnot6l paralogs. We show that Cnot6l apparently supplies the majority of CCR4 in the maternal CCR4-NOT in mouse, hamster, and bovine oocytes. Deletion of Cnot6l yielded viable mice, but Cnot6l−/− females exhibited ∼40% smaller litter size. The main onset of the phenotype was post-zygotic: fertilized Cnot6l−/− eggs developed slower and arrested more frequently than Cnot6l+/− eggs, suggesting that maternal CNOT6L is necessary for accurate oocyte-to-embryo transition. Transcriptome analysis revealed major transcriptome changes in Cnot6l−/− ovulated eggs and one-cell zygotes. In contrast, minimal transcriptome changes in preovulatory Cnot6l−/− oocytes were consistent with reported Cnot6l mRNA dormancy. A minimal overlap between transcripts sensitive to decapping inhibition and Cnot6l loss suggests that decapping and CNOT6L-mediated deadenylation selectively target distinct subsets of mRNAs during oocyte-to-embryo transition in mouse.

Strategies to reduce nitrate-nitrogen (nitrate) pollution delivered to streams often seek to increase groundwater residence time to achieve measureable results, yet the effects of tile drainage on residence time have not been well documented. In this study, we used a geographic information system groundwater travel time model to quantify the effects of artificial subsurface drainage on groundwater travel times in the 7443-ha Bear Creek watershed in north-central Iowa. Our objectives were to evaluate how mean groundwater travel times changed with increasing drainage intensity and to assess how tile drainage density reduces groundwater contributions to riparian buffers. Results indicate that mean groundwater travel times are reduced with increasing degrees of tile drainage. Mean groundwater travel times decreased from 5.6 to 1.1 yr, with drainage densities ranging from 0.005 m (7.6 mi) to 0.04 m (62 mi), respectively. Model simulations indicate that mean travel times with tile drainage are more than 150 times faster than those that existed before settlement. With intensive drainage, less than 2% of the groundwater in the basin appears to flow through a perennial stream buffer, thereby reducing the effectiveness of this practice to reduce stream nitrate loads. Hence, strategies, such as reconnecting tile drainage to buffers, are promising because they increase groundwater residence times in tile-drained watersheds.

SummaryMaternal genomic imprints are established during oogenesis. Histone deacetylases (HDACs) 1 and 2 are required for oocyte development in mouse, but their role in genomic imprinting is unknown. We find that Hdac1:Hdac2−/− double-mutant growing oocytes exhibit global DNA hypomethylation and fail to establish imprinting marks for Igf2r, Peg3, and Srnpn. Global hypomethylation correlates with increased retrotransposon expression and double-strand DNA breaks. Nuclear-associated DNMT3A2 is reduced in double-mutant oocytes, and injecting these oocytes with Hdac2 partially restores DNMT3A2 nuclear staining. DNMT3A2 co-immunoprecipitates with HDAC2 in mouse embryonic stem cells. Partial loss of nuclear DNMT3A2 and HDAC2 occurs in Sin3a−/− oocytes, which exhibit decreased DNA methylation of imprinting control regions for Igf2r and Srnpn, but not Peg3. These results suggest seminal roles of HDAC1/2 in establishing maternal genomic imprints and maintaining genomic integrity in oocytes mediated in part through a SIN3A complex that interacts with DNMT3A2.

Initiation of zygotic transcription in mammals is poorly understood. In mice, zygotic transcription is first detected shortly after pronucleus formation in 1-cell embryos, but the identity of the transcribed loci and mechanisms regulating their expression are not known. Using total RNA-Seq, we have found that transcription in 1-cell embryos is highly promiscuous, such that intergenic regions are extensively expressed and thousands of genes are transcribed at comparably low levels. Striking is that transcription can occur in the absence of defined core-promoter elements. Furthermore, accumulation of translatable zygotic mRNAs is minimal in 1-cell embryos because of inefficient splicing and 3′ processing of nascent transcripts. These findings provide novel insights into regulation of gene expression in 1-cell mouse embryos that may confer a protective mechanism against precocious gene expression that is the product of a relaxed chromatin structure present in 1-cell embryos. The results also suggest that the first zygotic transcription itself is an active component of chromatin remodeling in 1-cell embryos.

The substantial epigenetic remodeling that occurs during early stages of mammalian embryonic development likely contributes to reprogramming the parental genomes from a differentiated to a totipotent state and activation of the embryonic genome. Trimethylation of lysine 27 of histone 3 (H3K27me3) is a repressive mark that undergoes global dynamic changes during preimplantation development of several species. To ascertain the role of H3K27me3 in bovine preimplantation development we perturbed the activity of KDM6B, which demethylates H3K27me3. Knockdown of maternal KDM6B mRNA inhibited the reduction in global levels of H3K27me3 from 2-cell to 8-cell embryo stages and compromised development to the blastocyst stage; embryos that developed to the blastocyst stage had fewer inner cell mass (ICM) and trophectoderm (TE) cells. In addition, the transcriptome of KDM6B knockdown embryos was altered at the 8-cell stage and characterized by downregulation of transcripts related to transcriptional regulation, chromatin remodeling, and protein catabolism. Inhibiting the catalytic activity of KDM6B with a specific small molecule inhibitor also prevented the global decrease in H3K27me3 and compromised development to the blastocyst stage. These results indicate that histone demethylation activity, mediated by KDM6B, is required for the global decrease in H3K27me3, correct activation of the embryonic genome, and development to the blastocyst stage in bovine embryos.

Streambank erosion may represent a significant source of sediment and phosphorus (P) to overall watershed loads; however, watershed-scale quantification of contributions is rare. In addition, streambanks are often comprised of highly variable stratigraphic source materials (e.g., alluvial deposits), which may differentially impact in-channel P dynamics once eroded. The objective of this study was to quantify sediment and total phosphorus (TP) losses from four materials comprising streambanks within a 5218 ha watershed in Iowa, USA. Streambank-face surveys, erosion pins, and soil analyses were used to quantify surface area representation, recession, and losses of sediment and TP over a two-year period. Cumulative, whole-bank gross mean recession totaled 18.6 cm over two years, and material-specific gross mean recession ranged from 15.5 to 64.1 cm. Cumulative, whole-bank mean gross mass losses totaled 0.28 Mg sediment and 0.7 × 10−5 Mg TP per meter channel length. Annual sediment losses equated to 4–44% of historic suspended sediment loads. Stratigraphy was significant in gross material erosion and losses, with lower materials (i.e., bank toe region) exhibiting the greatest recession rates and cumulative recession. Weathered/colluvial material dominated total bank face surface area (88.3%), and contributed the greatest proportion of sediment and TP mass loss (66, 68%, respectively) versus other streambank materials.

Stream bank erosion and deposition are complex phenomena because of the many factors that influence them. These factors can be spatial such as bank aspect, height and slope or temporal such as seasonal and yearly precipitation and streamflow events. Riparian land-use also has a major influence. This study investigated for two years, spatial and temporal patterns and dominant geomorphologic processes of stream bank erosion and deposition along a 10 km reach of Bear Creek in north-central Iowa, USA. The channel sub-reaches used were adjacent to a riparian forest buffer, a perennial grass filter and a continuously grazed pasture. Two plots were placed in each sub-reach; one on a north-facing outside bank (north-bank) and the other on a south-facing outside bank (south-bank). Each plot had two photo-electronic erosion pins (PEEPs) placed at 1/3 of the bank height (bottom-bank) and the other at 2/3 of the bank height (top-bank). PEEP daily measurements were compared to daily precipitation and streamflow. The continuously grazed pasture banks had the highest erosion rates. The grass area banks had approximately equal rates of erosion and deposition. The riparian forest buffer banks had high erosion rates during the second year. In the continuously grazed pasture, fluvial entrainment was the dominant erosion process, although minor mass failures also caused erosion. In the riparian forest buffer most erosion was recorded after moderate streamflows removed the bank soil loosened by freeze–thaw cycling. This occurred in late winter/early spring, when trees provide primarily mechanical but not hydraulic reinforcement to stream banks and on the lower part of the banks that have less extensive root networks. Overall, stream bank erosion and deposition in each sub-reach occurred during different time periods and under different processes and conditions. This indicates the need for continuous erosion and deposition measurements along with continuous soil moisture, soil temperature and streamflow measurements to fully comprehend these erosion phenomena.

Real-time analysis of drilling mud loss data is an effective tool to characterize the size, distribution and permeability of natural fractures. The estimated properties of natural fractures can then be used to modify the drilling fluid properties and design remedial mud loss treatment to stop further drilling fluid loss. Moreover, characterization of natural fracture provides crucial information for the design and application of reservoir stimulation operations.In this paper, we present a theoretical model to simulate the invasion of the drilling fluid into natural fractures. Mathematical modelling was performed for two types of rheology constitutive models which are commonly used for drilling fluids, namely Bingham Plastic and Herschel-Bulkley. The fluid leak-off into the formation is modelled using Carter's model. Moreover, a simplified local elasticity equation is used for the fracture width variation due to fluid pressure. A forward finite-difference numerical scheme is used to solve the pressure drop equation. The developed model is then validated against well-known analytical solutions and numerical simulations. Parametric studies were conducted to evaluate the impact of the fracture deformability, formation leak-off properties, drilling fluid rheology, and the pore fluid contribution. Finally, the output of the developed model is compared with the field data of a welldocumented mud loss incident.The obtained results indicate that the incorporating the effect of the fluid leak-off may significantly increase the rate of mud loss volume. Therefore, for highly permeable formations (such as carbonates), considering the impact of the fluid leak-off effect seems necessary for a realistic characterization of the mud loss problem. Fracture deformability affects the mud loss volume, with higher deformability leading to a larger mud loss volume. Also, the numerical results confirmed that the rate and magnitude of mud loss volume is significantly affected by the rheological properties of the drilling fluid, in particular the yield stress. In contrast, the effect of pore fluid seems relatively negligible for typical formation fluid types. Comparing the results of our simulation with mud loss field data shows that the developed model can accurately predict the rate and total volume of mud loss into the fractures. Moreover, it shows that incorporating the impact of the fluid leak-off and the fracture stiffness may significantly affect the fracture width prediction. Therefore, these factors should be considered to obtain an accurate estimate of the natural fracture aperture.

Mendel's First Law of Genetics states that a pair of alleles segregates randomly during meiosis so that one copy of each is represented equally in gametes. Whereas male meiosis produces four equal sperm, in female meiosis only one cell, the egg, survives, and the others degenerate. Meiotic drive is a process in which a selfish DNA element exploits female meiotic asymmetry and segregates preferentially to the egg in violation of Mendel's First Law, thereby increasing its transmission to the offspring and frequency in a population. In principle, the selfish element can consist either of a centromere that increases its transmission via an altered kinetochore connection to the meiotic spindle or a centromere-like element that somehow bypasses the kinetochore altogether in doing so. There are now examples from eukaryotic model systems for both types of meiotic drive. Although meiotic drive has profound evolutionary consequences across many species, relatively little is known about the underlying mechanisms. We discuss examples in various systems and open questions about the underlying cell biology, and propose a mechanism to explain biased segregation in mammalian female meiosis.

Double-stranded RNA (dsRNA) induces sequence-specific mRNA degradation in most eukaryotic organisms via a conserved pathway known as RNA interference (RNAi). Post-transcriptional gene silencing by RNAi is also connected with transcriptional silencing of cognate sequences. In plants, this transcriptional silencing is associated with sequence-specific DNA methylation. To address whether this mechanism operates in mammalian cells, we used bisulfite sequencing to analyze DNA in mouse oocytes constitutively expressing long dsRNA against the Mos gene. Our data show that long dsRNA induces efficient Mos mRNA knockdown but not CpG and non-CpG DNA methylation of the endogenous Mos sequence in oocytes and early embryos. These data demonstrate that dsRNA does not directly induce DNA methylation in the trans form of this sequence in these mammalian cells.

SummaryMammalian karyotypes (number and structure of chromosomes) can vary dramatically over short evolutionary time frames [1–3]. There are examples of massive karyotype conversion, from mostly telocentric (centromere terminal) to mostly metacentric (centromere internal), in 102–105 years [4, 5]. These changes typically reflect rapid fixation of Robertsonian (Rb) fusions, a common chromosomal rearrangement that joins two telocentric chromosomes at their centromeres to create one metacentric [5]. Fixation of Rb fusions can be explained by meiotic drive: biased chromosome segregation during female meiosis in violation of Mendel’s first law [3, 6, 7]. However, there is no mechanistic explanation of why fusions would preferentially segregate to the egg in some populations, leading to fixation and karyotype change, while other populations preferentially eliminate the fusions and maintain a telocentric karyotype. Here we show, using both laboratory models and wild mice, that differences in centromere strength predict the direction of drive. Stronger centromeres, manifested by increased kinetochore protein levels and altered interactions with spindle microtubules, are preferentially retained in the egg. We find that fusions preferentially segregate to the polar body in laboratory mouse strains when the fusion centromeres are weaker than those of telocentrics. Conversely, fusion centromeres are stronger relative to telocentrics in natural house mouse populations that have changed karyotype by accumulating metacentric fusions. Our findings suggest that natural variation in centromere strength explains how the direction of drive can switch between populations. They also provide a cell biological basis of centromere drive and karyotype evolution.

Suban field in southern Sumatra, Indonesia, is a fractured carbonate/crystalline wet-gas reservoir in a tectonically active island-arc setting. Reservoir-scale right-oblique reverse faults and folds that have trapped the hydrocarbons have been related previously to deformation in the back-arc setting of Sumatra associated with oblique subduction of the Indo-Australian Plate at the Sunda trench. Increased well productivity in some parts of the field was inferred to correlate with completing wells in the damage zones of critically stressed faults. Satellite interferometry acquired in 2008 through 2011 involving specially stacked and filtered interferograms, following prior applications to heavy-oil fields and Arctic sea ice, reveals active deformation in Suban field. Several areas of localized subsidence potentially exceeding ∼5 mm/yr have been identified in the field. Horizontal movements of comparable magnitude were resolved above the major right-oblique, critically stressed fault zone in the southwestern part of the field, corroborating wellbore-based inferences from the reservoir. Block-tectonic models constrained by GPS measurements across the entire Sumatra contractional orogen predict comparable magnitudes and directions for horizontal motions observed locally at Suban. The combination of InSAR and GPS-based plate-tectonic models provides a robust tool for monitoring the deformation of oil and gas fields in tectonically active areas.

The importance of streambank erosion to watershed-scale sediment export is being increasingly recognized. However few studies have quantified bank erosion and watershed sediment flux at the basin scale across temporal and spatial scales. In this study we evaluated the spatial distribution, extent, and temporal frequency of bank erosion in the 5218 ha Walnut Creek watershed in Iowa across a seven year period. We inventoried severely eroding streambanks along over 10 km of stream and monitored erosion pins at 20 sites within the watershed. Annual streambank recession rates ranged from 0.6 cm/yr during years of hydrological inactivity to 28.2 cm/yr during seasons with high discharge rates, with an overall average of 18.8 cm/yr. The percentage of total basin export attributed to streambank erosion along the main stem of Walnut Creek ranged from 23 to 53%. Large variations in individual site, annual rates and percentage of annual load suggested that developing direct relationships between streambank erosion rates and total sediment discharge may be confounded by the timing and magnitude of discharge events, storage of sediments within channel system and the remobilization of eroded material.

During mouse oocyte maturation histones are deacetylated, and inhibiting this deacetylation leads to abnormal chromosome segregation and aneuploidy. RBBP7 is a component of several different complexes that contain histone deacetylases, and therefore could be implicated in histone deacetylation. We find that Rbbp7 is a dormant maternal mRNA that is recruited for translation during oocyte maturation to regulate the histone deacetylation. Importantly, we show that the maturation-associated decrease of histone acetylation is required for localization and function of the chromosomal passenger complex (CPC) during oocyte meiotic maturation. This finding can explain the phenotypes of oocytes where Rbbp7 is depleted by an siRNA/morpholino cocktail including severe chromosome misalignment, improper kinetochore–microtubule attachments, impaired SAC function, cytokinesis defects, and increased incidence of aneuploidy at metaphase II (Met II). These results implicate RBBP7 as a novel regulator of histone deacetylatio...

Compaction of loose, granular materials commonly results in the loss of porosity and, hence, a volumetric decrease of the material by the localization of deformation bands. Different types of deformation bands tend to form at a range of specific angles to maximum compression (σ1), as documented in numerous field and laboratory studies. Usually, localization of bands occurs at low angles to σ1 during deformation involving volumetric increase and at higher angles during compaction of the material. Generally in agreement with field and laboratory orientation measurements, several models have been used to obtain the optimum angle deformation band formation with respect to σ1. However, some field and laboratory studies report deformation bands with substantial compaction across them that have orientations requiring material dilation to be in accord with those models. This discrepancy is explored by modeling the orientations of structures under progressive deformation for all combinations of simultaneous pure and simple shear. Our results allow for shear-enhanced compaction at the onset of dilational shear band formation, thus accounting for both the band orientation as well as the observed compaction within the bands. These findings indicate that compaction localized within a deformation band is not simply related to a total volumetric decrease of the material, since the transition between localization of compaction and dilation is found not to coincide with the transition of volume decrease to increase of the material, and hence to the material′s mechanical response at a given stress state.

Summary Mammalian oocytes are arrested in metaphase of second meiosis (MII) until fertilization. This arrest is enforced by the cytostatic factor (CSF), which maintains the M-phase promoting factor (MPF) in a highly active state. Although the continuous synthesis and degradation of cyclin B to maintain the CSF-mediated MII arrest is well established, it is unknown whether cyclin-dependent kinase 1 (Cdk1) phosphorylations are involved in this arrest in mouse oocytes. Here, we show that a dynamic equilibrium of Cdk1 phosphorylation is required to maintain MII arrest. When the Cdc25A phosphatase is downregulated, mouse oocytes are released from MII arrest and MPF becomes inactivated. This inactivation occurs in the absence of cyclin B degradation and is dependent on Wee1B-mediated phosphorylation of Cdk1. Thus, our data demonstrate that Cdk1 activity is maintained during MII arrest not only by cyclin turnover but also by steady state phosphorylation.

The restoration of riparian zones has been an important issue in many regions for the recovery of ecosystem functions. The objective of this study was to assess soil aggradation in a 7-year established riparian switchgrass buffer (SGB) and in a non-buffered riparian zone with an annual row crop (ARC). We measured the aggregate size distribution and stability of macroaggregates, aggregate-associated soil organic carbon, soil organic matter fractions and the chemical composition of light particulate organic matter to monitor soil aggregation in a riparian soil following the conversion of agricultural row crops to switchgrass filters. Aggregate size fractions were separated by wet sieving using the aggregate size-stability protocol. The proportion of soil and total organic C was quantified for each aggregate size class. Soil organic matter fractions were isolated by size and density into light particulate organic matter and heavy particulate organic matter and mineral fraction organic matter. The categorization of aggregates by size and water stability (slaking resistance) showed a significantly larger (p < 0.001) proportion of water-unstable large macroaggregates (>2000 µm) under SGB (34%) compared to that under ARC (29%), while the proportion of water-unstable small macroaggregates (250–2000 µm) was significantly higher under ARC (14%) than under SGB (10%). Our results showed that the amounts of light and heavy particulate organic matter did not change in the short-term (7 years) after SGB establishment. It appears that the lower soil stabilization and soil organic C storage under SGB is related to (i) the large number of coarse roots; (ii) lower inputs of light and heavy particulate organic matter; (iii) no changes in the alkyl-C/O-alkyl-C ratio over time; and (iv) light particulate organic matter with a high C/N ratio.

Mendel’s First Law of Genetics states that a pair of alleles segregates randomly during meiosis so that one copy of each is represented equally in gametes. Whereas male meiosis produces four equal sperm, in female meiosis only one cell, the egg, survives, and the others degenerate. Meiotic drive is a process in which a selfish DNA element exploits female meiotic asymmetry and segregates preferentially to the egg in violation of Mendel’s First Law, thereby increasing its transmission to the offspring and frequency in a population. In principle, the selfish element can consist either of a centromere that increases its transmission via an altered kinetochore connection to the meiotic spindle or a centromere-like element that somehow bypasses the kinetochore altogether in doing so. There are now examples from eukaryotic model systems for both types of meiotic drive. Although meiotic drive has profound evolutionary consequences across many species, relatively little is known about the underlying mechanisms. We discuss examples in various systems and open questions about the underlying cell biology, and propose a mechanism to explain biased segregation in mammalian female meiosis.

RcsB, the transcription‐associated response regulator of the Rcs phosphorelay two‐component signal transduction system, activates cell stress responses associated with desiccation, cell wall biosynthesis, cell division, virulence, biofilm formation, and antibiotic resistance in enteric bacterial pathogens. RcsB belongs to the FixJ/NarL family of transcriptional regulators, which are characterized by a highly conserved C‐terminal DNA‐binding domain. The N‐terminal domain of RcsB belongs to the family of two‐component receiver domains. This receiver domain contains the phosphoacceptor site and participates in RcsB dimer formation; it also contributes to dimer formation with other transcription factor partners. Here, we describe the crystal structure of the Escherichia coli RcsB receiver domain in its nonphosphorylated state. The structure reveals important molecular details of phosphorylation‐independent dimerization of RcsB and has implication for the formation of heterodimers.

Although time-lapse analysis of early embryo cleavage parameters (morphokinetics) predicts blastocyst development, it has not been definitively linked to establishing pregnancy and live birth. For example, a direct comparison of the developmental potential of embryos with optimal kinetic parameters compared to suboptimal kinetics has not been performed with human embryos. To ascertain whether such a linkage exists, we developed a mouse model of morphokinetic analysis of early embryo cleavage using time-lapse microscopy to predict blastocyst formation and tested whether cleavage parameters predict pregnancy outcome by transferring morphokinetically optimal and suboptimal embryos into a single host. Using classification and regression trees, we established that the timing of the second and third mitotic divisions (division from two to three and three to four cells, respectively) predicts blastocyst development in the mouse. Using this prediction model, we found that the incidence of sustained implantation at mid-gestation was significantly higher for the optimal compared to suboptimal embryos. In addition, the incidence of resorption among implanted embryos was significantly higher in the suboptimal compared to the optimal group. Transcript profiling of optimal and suboptimal embryos revealed minimal differences between the two groups, suggesting that time-lapse imaging of early embryo cleavage events provides additional information regarding developmental competence apart from gene expression.

Livestock grazing of riparian areas can have a major impact on stream banks and stream integrity if improperly managed. The goals of this study were to determine the sediment and phosphorus (P) losses from stream bank soils under varying cattle stocking rates and to identify additional factors that impact stream bank erosion in the southern Iowa Drift Plain. The research was conducted on 13 cooperating beef cow-calf farms within the Rathbun Lake Watershed in south central Iowa. Over three years, stream bank erosion rates were estimated by using an erosion pin method. Eroded stream bank lengths and area, soil bulk density, and total P (TP) content in stream bank soil were measured to calculate soil and TP losses via stream bank erosion. The length of severely eroded stream banks and soil compaction of the riparian areas of the pastures were positively related to stocking rates. There was no direct relationship between bank erosion and stocking rate. These results suggest that use of riparian areas as pasture can negatively impact the integrity of the major source areas and that the impact could be reduced through management of livestock stocking densities within these riparian areas.

Tufekcioglu, Mustafa, Richard C. Schultz, George N. Zaimes, Thomas M. Isenhart, and Aydin Tufekcioglu, 2012. Riparian Grazing Impacts on Streambank Erosion and Phosphorus Loss via Surface Runoff. Journal of the American Water Resources Association (JAWRA) 1-11. DOI: 10.1111/j.1752-1688.2012.12004.x Abstract: Surface runoff is one of the major pathways of sediment and phosphorus (P) transport to surface waters. Rainfall simulations were conducted on nine grazed pasture sites with different stocking rates in three different Iowa (United States) regions. The purpose of the simulations was to determine the impacts of cattle grazing on the amounts of sediment and P in surface runoff within a 15-m wide strip on both sides of the stream from different source areas (SAs). These riparian SAs included stream-side loafing areas, cattle streambank access paths to the stream, and the other vegetated areas adjacent to the streambanks. The runoff samples collected during the simulations were analyzed for suspended sediment (SS) and total phosphorus (TP). Soil bulk density and antecedent soil moisture samples were collected around the rainfall simulation plots to identify differences in compaction, infiltration, and surface runoff among the SAs. SS and TP losses from access paths and loafing areas within the 15-m wide strips accounted for up to 72 and 55% of the total losses, respectively, even though they accounted for only 2.7% of the total area within the 15-m wide strips. This suggests that access paths and loafing areas require special attention to mitigate the impacts of cattle on stream water pollution. Significant correlations were found between stocking rates and both SS and TP losses suggesting that low stocking rates can reduce sediment and P export to streams from the SAs.

International audience; Propagation energies for five examples of deformation bands in porous sandstones from four field sites in Nevada, Utah, and France were calculated by using the J-integral approach. Pure compaction bands that accommodate primarily closing displacements from the Valley of Fire (Nevada) site have a closing-mode band propagation energy of J I = 5.5 ± 1.6 kJ/m2. Shear-enhanced compaction bands having subequal amounts of normal (closing) and shear strains across them from the same site have propagation energies of J I = 6.11 ± 1.8 kJ/m2 and J II = 1.52 ± 0.5 kJ/m2 for closing and shearing modes respectively. Closing- and shearing-mode band propagation energies for shear-enhanced compaction bands from the Buckskin Gulch (Utah) site, 5.63 ± 1.7 and 1.91 ± 0.57 kJ/m2 and the Uchaux (France) site, 11.0 ± 3.3 and 2.35 ± 0.7 kJ/m2 respectively are comparable to the values for similar structures from the Valley of Fire site. Cataclastic deformation bands at the Orange (France) site accommodate significantly larger values of shear offset than do shear-enhanced compaction bands, with a ratio of shear to closing offset that exceeds 7. The calculated closing- and shearing-mode propagation energies for these shear bands, 17.8 ± 5.4 and 3.3 ± 1.0 kJ/m2 respectively are comparable to those for pure or shear-enhanced compaction bands deformed at approximately the same depth of burial. Strain softening of cataclastic compactional shear bands implies unstable shearing, whereas stable and perhaps strain-hardening shearing may be inferred for shear-enhanced compaction bands. Displacement-length scaling relations for shear-enhanced compaction bands of the form D∝L are consistent with the results and with suggestions of band thickening during growth obtained from bifurcation analyses and with field observations of shear zones in porous host rock.

This study was undertaken to assess the importance of streambank erosion to the total in-stream sediment of two agricultural watersheds within the Central Claypan Areas. The objective of this research was to determine the effect of stream order, adjacent land use, and season on streambank erosion rates. Thirty-four study sites were established in 2007 and 2008 within Crooked and Otter Creek watersheds, two claypan watersheds located in northeastern Missouri. At each site, field assessments of severely to very severely eroding bank length were determined along 300 to 400 m (984 to 1,312 ft) stream reaches. A factorial experimental design was implemented with four land uses (crop, forest, pasture, and riparian forest), three seasons, and three stream orders (1st, 2nd, and 3rd). Each treatment was replicated three times for each stream order, except for the cropped 3rd order treatment as only one suitable treatment site could be found. Streambank erosion was measured using erosion pins, which were installed in randomly assigned plots that included at least 20% of the eroded bank length within each site. The effect of different seasons was assessed by measuring the length of the exposed pins three times per year (March, July, and November). The bulk density and car- bon and nitrogen content of bank material were also determined. Sediment loss rates showed that season and the three-way interaction between season, land use, and stream order were highly significant. Erosion rates were consistently higher in the winter months than spring/ summer and fall seasons; however, the significant three-way interaction precluded a simple interpretation of the seasonal effect. Soil nutrient concentration data showed that forest sites had significantly lower C and N concentrations than other land uses. At the watershed scale, bank sediment accounted for 79% to 96% of the total in-stream sediment and 21% to 24% of the total N exported from the study area. These results indicate that streambanks are the dom- inant source of sediment and a significant source of N in these streams. Therefore, improved management of riparian areas to decrease streambank erosion would result in significant water quality improvement in streams of the Central Claypan Areas in northeastern Missouri.

Recognition of fractures as porosity-reducing deformation bands pervading all sandstone segments of the Teufelsmauer, Subhercynian Creatceous Basin, Germany, motivates a study relating the observed macroscopic and microscopic deformation to the damage zone of the nearby Harz border fault. Deformation bands, confirmed and documented by several porosity-reducing micro-mechanisms, such as cataclasis, particulate flow, pressure solution and a heavy quartz cementation, were mapped and analyzed in terms of the kinematics and deformation intensities expressed by them. Deformation band kinematics are uniform throughout the entire basin and consistent with the large-scale tectonic structures of the area. A strain intensity study highlights two narrow but long zones of deformation bands, sub-parallel to the Harz border fault. Deformation band kinematics, strain intensity, as well as micro-mechanisms are all consistent with a continuous but internally diverse deformation band damage zone of the entire Teufelsmauer structure along the Harz border fault, bringing new insights into the tectonic evolution and the origin of the heavy quartz cementation of the sandstones in the Subhercynian Cretaceous Basin.

Upwind advective energy occurring in edge environments may increase tree water use. In humid agricultural landscapes, advection-enhanced transpiration in riparian buffers may provide hydrologic regulation. The objectives of this study were to determine how water use by trees growing in a riparian buffer in central Iowa is influenced by 1) advective energy, 2) tree position, and 3) thinning (40% LAI reduction). We measured meteorological variables and sap flux density from July to September in 13 trees (2009) and 12 trees (2010) in one thinned plot (TP, treated in Aug 2010) and one untreated (control) plot (UP). The difference in Qs between edge and interior trees (39% higher in 2009) was attributed to the advective energy at the buffer edge. After thinning, maximum Qs increased was greater in TP compared to UP, explained primarily by solar radiation (R=0.7, p

Well-established perennial vegetation in riparian areas of agricultural lands can stabilize the end points of gullies and reduce their overall erosion. The objective of this study was to investigate the impacts of riparian land management on gully erosion. A field survey documented the number of gullies and cattle access points in riparian forest buffers, grass filters, annual row-cropped fields, pastures in which the cattle were fenced out of the stream, and continuously, rotationally and intensive rotationally grazed pastures in three regions of Iowa. Gully lengths, depths and severely eroding bank areas were measured. Gullies exhibited few significant differences among riparian management practices. The most significant differences were exhibited between conservation and agricultural management practices, an indication that conservation practices could reduce gully erosion. Changes in pasture management from continuous to rotational or intensive rotational grazing showed no reductions in gully erosion. It is important to recognize that more significant differences among riparian management practices were not exhibited because the conservation and alternative grazing practices had recently been established. As gully formation is more impacted by upland than riparian management, gully stabilization might require additional upland conservation practices. The existence of numerous cattle access points in pastures where cattle have full access to the stream also indicates that these could be substantial sources of sediment for streams. Finally, the gully banks were less important sediment contributors to streams than the streambanks. The severely eroding bank areas in streams were six times greater than those in the gullies in the monitored reaches.

With the resurgence of nuclear power and increased interest in advanced nuclear reactors as an option to supply abundant energy without the associated greenhouse gas emissions of the more conventional fossil fuel energy sources, there is a need to establish internationally recognized standards for the verification and validation (V&V) of software used to calculate the thermal–hydraulic behavior of advanced reactor designs for both normal operation and hypothetical accident conditions. To address this need, ASME (American Society of Mechanical Engineers) Standards and Certification has established the V&V 30 Committee, under the jurisdiction of the V&V Standards Committee, to develop a consensus standard for verification and validation of software used for design and analysis of advanced reactor systems. The initial focus of this committee will be on the V&V of system analysis and computational fluid dynamics (CFD) software for nuclear applications. To limit the scope of the effort, the committee will further limit its focus to software to be used in the licensing of High-Temperature Gas-Cooled Reactors. Although software verification will be an important and necessary part of the standard, much of the initial effort of the committee will be focused on the validation of existing software and new models that could be used in the licensing process. In this framework, the Standard should conform to Nuclear Regulatory Commission (NRC) and other regulatory practices, procedures and methods for licensing of nuclear power plants as embodied in the United States (U.S.) Code of Federal Regulations and other pertinent documents such as Regulatory Guide 1.203, “Transient and Accident Analysis Methods” and NUREG-0800, “NRC Standard Review Plan”. In addition, the Standard should be consistent with applicable sections of ASME NQA-1-2008 “Quality Assurance Requirements for Nuclear Facility Applications (QA)”. This paper describes the general requirements for the proposed V&V 30 Standard, which includes: (a) applicable NRC and other regulatory requirements for defining the operational and accident domain of a nuclear system that must be considered if the system is to be licensed, (b) the corresponding calculation domain of the software that should encompass the nuclear operational and accident domain to be used to study the system behavior for licensing purposes, (c) the definition of the scaled experimental data set required to provide the basis for validating the software, (d) the ensemble of experimental data sets required to populate the validation matrix for the software in question, and (e) the practices and procedures to be used when applying a validation standard. Although this initial effort will focus on software for licensing of High-Temperature Gas-Cooled Reactors, it is anticipated that the practices and procedures developed for this Standard can eventually be extended to other nuclear and non-nuclear applications.

A hypothesis to explain the maternal age-dependent increase in formation of aneuploid eggs is deterioration of chromosome cohesion. Although several lines of evidence are consistent with this hypothesis, whether cohesion is actually reduced in naturally aged oocytes has not been directly tested by any experimental perturbation. To directly target cohesion, we increased the activity of separase, the protease that cleaves the meiotic cohesin REC8, in oocytes. We show that cohesion is more susceptible to premature separase activation in old oocytes than in young oocytes, demonstrating that cohesion is significantly reduced. Furthermore, cohesion is protected by two independent mechanisms that inhibit separase, securin and an inhibitory phosphorylation of separase by CDK1; both mechanisms must be disrupted to prematurely activate separase. With the continual loss of cohesins from chromosomes that occurs throughout the natural reproductive lifespan, tight regulation of separase in oocytes may be particularly important to maintain cohesion and prevent aneuploidy.

Extensive land-use changes in Iowa have increased erosional processes and the amount of fines deposited on stream beds. Large amounts of fines cover the other bed substrate that are essential habitat for invertebrates and fish. In Iowa and other agricultural Midwestern states, riparian conservation land-uses are being established to minimize sediment inputs to streams. This study compared stream bed substrate composition in reaches adjacent to: riparian forest buffers, grass filters, row-cropped fields, pastures with cattle fenced out of the stream and continuous, rotational and intensively grazed rotational pastures, in three regions of Iowa. The objective was to examine the impacts of the adjacent riparian land-uses on stream bed substrate composition. The percentages of fines in this study ranged from: 36 to 63% in the central region; 10 to 31% in the northeast region; and 22 to 85% in the southeast region. The high percentage of fines in most stream bed reaches indicates high embeddedness. The high embeddedness resulted in the few significant differences in substrate percentages among riparian land-uses. Decades of agricultural land-uses have heavily impacted stream beds and only significant reductions in surface and bank erosion at the watershed scale can begin to reverse this trend. There were indications that riparian forest buffers and to a lesser degree, pastures with cattle fenced out of the stream, could decrease fines resulting in a more diverse substrate composition. Overall, more targeted approaches for the establishment of conservation land-uses in combination with other restoration practices (e.g. in-stream enhancements) are required to successfully decrease fines on stream beds.

Observations from quartz-rich eolian Navajo Sandstone in the Buckskin Gulch site in southernmost Utah show that pure compaction bands only occur in sandstones where current porosity>0.29 � 3, permeability>10 � 7 darcy, and grain size>0.4 mm e properties restricted to the lower and most coarsegrained and well-sorted parts of grain flow units within the dune units. Hence a direct correlation between stratigraphy and band occurrence has been established that can be used to predict deformation band occurrences in similar sandstone reservoirs. We show that the pure compaction bands formed perpendicular to a subhorizontal s1, bisecting conjugate sets of shear-enhanced compaction bands. The latter bands locally developed into sheardominated bands that transect entire dune units, suggesting that an increase in the amount of simple shear promotes band propagation into less porous and permeable lithologies. Stress considerations indicate that, as a continuous and overlapping sequence of events, pure compaction bands in quartz-rich Navajo Sandstone initiated at 10e20 MPa (w1 km depth), followed by shear-enhanced compaction bands that locally developed into more stratigraphically extensive sheardominated bands. The rare combination of special lithologic and stress conditions may explain why pure compaction bands are rarely observed in naturally deformed sandstones.