Quantification of three-dimensional folding using fluvial terraces: A case study from the Mushi anticline, northern margin of the Chinese Pamir

Fold deformation in three dimensions involves shortening, uplift, and lateral growth. Fluvial terraces represent strain markers that have been widely applied to constrain a fold's shortening and uplift. For the lateral growth, however, the utility of fluvial terraces has been commonly ignored. Situated along northern margin of Chinese Pamir, the Mushi anticline preserves, along its northern flank, flights of passively deformed fluvial terraces that can be used to constrain three-dimensional folding history, especially lateral growth. The Mushi anticline is a geometrically simple fault-tip fold with a total shortening of 740?±?110?m and rock uplift of ~1300?m. Geologic and geomorphic mapping and dGPS surveys reveal that terrace surfaces perpendicular to the fold's strike display increased rotation with age, implying the fold grows by progressive limb rotation. We use a pure-shear fault-tip fold model to estimate a uniform shortening rate of 1.5?+?1.3/?0.5?mm/a and a rock-uplift rate of 2.3?+?2.1/?0.8?mm/a. Parallel to the fold's strike, longitudinal profiles of terrace surfaces also display age-dependent increases in slopes. We present a new model to distinguish lateral growth mechanisms (lateral lengthening and/or rotation above a fixed tip). This model indicates that eastward lengthening of the Mushi anticline ceased by at least ~134?ka and its lateral growth has been dominated by rotation. Our study confirms that terrace deformation along a fold's strike not only can constrain the lateral lengthening rate but can serve to quantify the magnitude and rate of lateral rotation: attributes that are commonly difficult to define when relying on other geomorphic criteria

An Amelogenin Mutation Leads to Disruption of the Odontogenic Apparatus and Aberrant Expression of Notch I

BACKGROUND Amelogenins are highly conserved proteins secreted by ameloblasts in the dental organ of developing teeth. These proteins regulate dental enamel thickness and structure in humans and mice. Mice that express an amelogenin transgene with a P70T mutation (TgP70T) develop abnormal epithelial proliferation in an amelogenin null (KO) background. Some of these cellular masses have the appearance of proliferating stratum intermedium, which is the layer adjacent to the ameloblasts in unerupted teeth. As Notch proteins are thought to constitute the developmental switch that separates ameloblasts from stratum intermedium, these signaling proteins were evaluated in normal and proliferating tissues. METHODS Mandibles were dissected for histology and immunohistochemistry using Notch I antibodies. Molar teeth were dissected for western blotting and RT-PCR for evaluation of Notch levels through imaging and statistical analyses. RESULTS Notch I was immunolocalized to ameloblasts of TgP70TKO mice, KO ameloblasts stained, but less strongly, and wild-type teeth had minimal staining. Cells within the proliferating epithelial cell masses were positive for Notch I and had an appearance reminiscent of calcifying epithelial odontogenic tumor with amyloid-like deposits. Notch I protein and mRNA were elevated in molar teeth from TgP70TKO mice. CONCLUSION Expression of TgP70T leads to abnormal structures in mandibles and maxillae of mice with the KO genetic background and these mice have elevated levels of Notch I in developing molars. As cells within the masses also express transgenic amelogenins, development of the abnormal proliferations suggests communication between amelogenin producing cells and the proliferating cells, dependent on the presence of the mutated amelogenin protein

Cortical and subcortical coordination of visual spatial attention revealed by simultaneous EEG-fMRI recording

Visual spatial attention has been studied in humans with both electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) individually. However, due to the intrinsic limitations of each of these methods used alone, our understanding of the systems-level mechanisms underlying attentional control remains limited. Here, we examined trial-to-trial covariations of concurrently recorded EEG and fMRI in a cued visual spatial attention task in humans, which allowed delineation of both the generators and modulators of the cue-triggered event-related oscillatory brain activity underlying attentional control function. The fMRI activity in visual cortical regions contralateral to the cued direction of attention covaried positively with occipital gamma-band EEG, consistent with activation of cortical regions representing attended locations in space. In contrast, fMRI activity in ipsilateral visual cortical regions covaried inversely with occipital alpha-band oscillations, consistent with attention-related suppression of the irrelevant hemispace. Moreover, the pulvinar nucleus of the thalamus covaried with both of these spatially specific, attention-related, oscillatory EEG modulations. Because the pulvinar's neuroanatomical geometry makes it unlikely to be a direct generator of the scalp-recorded EEG, these covariational patterns appear to reflect the pulvinar's role as a regulatory control structure, sending spatially specific signals to modulate visual cortex excitability proactively. Together, these combined EEG/fMRI results illuminate the dynamically interacting cortical and subcortical processes underlying spatial attention, providing important insight not realizable using either method alone

A simple, low-blank batch purification method for high-precision boron isotope analysis

This work was supported by NERC IAPETUS PhD Studentships NE/RO12253/1 to M.T., J.C.B. and E.L., an IAPETUS2 PhD Studentship NE/S007431/1 to C.X.; S.N. was supported by the MOST 111-2116M-002-032-MY3 Grant; J.W.B.R acknowledges support from NERC (Grant NE/N011716/1) and from the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant agreement 805246).Boron (B) isotopes are widely used in the Earth sciences to trace processes ranging from slab recycling in the mantle to changes in ocean pH and atmospheric CO2. Boron isotope analysis is increasingly achieved by multi-collector inductively coupled plasma mass spectrometry, which requires separation of B from the sample matrix. Traditional column chromatography methods for this separation have a well-established track record but are time consuming and prone to contamination from airborne blank. Here, we present an extensive array of tests that establish a novel method for B purification using a batch method. We discuss the key controls and limitations on sample loading, matrix removal and B elution including sample volume, ionic strength, buffer to acid ratio and elution volume, all of which may also help optimize column-based methods. We find consistent, low procedural blanks of 10 ± 16 pg and excellent reproducibility: 10 ng NIST RM 8301 foram [8301f] yields 14.58 ± 0.11‰ 2SD n = 15; 2.5 ng 8301f yields 14.60 ± 0.19‰ 2SD, n = 31; and overall long term 2SD on n = 218 samples pooling different sample sizes yields 14.62 ± 0.21‰ 2SD. This method also offers significant advantages in throughput, allowing the processing of 24 samples in ∼5 hr. This boron batch method thus provides a fast, reproducible, low-blank method for purification of boron for high precision isotopic analyses.Peer reviewe

Chemomechanics of ionically conductive ceramics for electrical energy conversion and storage

Functional materials for energy conversion and storage exhibit strong coupling between electrochemistry and mechanics. For example, ceramics developed as electrodes for both solid oxide fuel cells and batteries exhibit cyclic volumetric expansion upon reversible ion transport. Such chemomechanical coupling is typically far from thermodynamic equilibrium, and thus is challenging to quantify experimentally and computationally. In situ measurements and atomistic simulations are under rapid development to explore how this coupling can be used to potentially improve both device performance and durability. Here, we review the commonalities of coupling between electrochemical and mechanical states in fuel cell and battery materials, illustrating with specific cases the progress in materials processing, in situ characterization, and computational modeling and simulation. We also highlight outstanding questions and opportunities in these applications – both to better understand the limiting mechanisms within the materials and to significantly advance the durability and predictability of device performance required for renewable energy conversion and storage.United States. Dept. of Energy (Basic Energy Sciences Division of Materials Sciences and Engineering, grant DE-SC0002633)United States. Dept. of Energy (Office of Science, Graduate Fellowship Program (DOE SCGF))United States. American Recovery and Reinvestment Act of 2009 (ORISE-ORAU, contract no. DE-AC05-06OR23100))United States. Dept. of Energy. Division of Materials Sciences and Engineering (MIT/DMSE Salapatas Fellowship)United States. Air Force Office of Scientific Research (Presidential Early Career Award in Science and Engineering (PECASE)

Dual stresses of flooding and agricultural land use reduce earthworm populations more than the individual stressors

Global climate change is leading to a significant increase in flooding events in many countries. Current practices to prevent damage to downstream urban areas include allowing the flooding of upstream agricultural land. Earthworms are ecosystem engineers, but their abundances in arable land are already reduced due to pressure from farming practices. If flooding increases on agricultural land, it is important to understand how earthworms will respond to the dual stresses of flooding and agricultural land use. The earthworm populations under three land uses (pasture, field margin, and crops), across two UK fields, were sampled seasonally over an 18-month period in areas of the fields which flood frequently and areas which flood only rarely. Earthworm abundance in the crop and pasture soils and total earthworm biomass in the crop soils was significantly lower in the frequently flooded areas than in the rarely flooded areas. The relative percentage difference in the populations between the rarely and frequently flooded areas was greater in the crop soils (−59.18% abundance, −63.49% biomass) than the pasture soils (−13.39% abundance, −9.66% biomass). In the margin soils, earthworm abundance was significantly greater in the frequently flooded areas (+140.56%), likely due to higher soil organic matter content and lower bulk density resulting in soil conditions more amenable to earthworms. The findings of this study show that earthworm populations already stressed by the activities associated with arable land use are more susceptible to flooding than populations in pasture fields, suggesting that arable earthworm populations are likely to be increasingly at risk with increased flooding

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

International audienceJASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

International audienceJASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release

A genome-wide CRISPR-Cas9 knockout screen identifies essential and growth-restricting genes in human trophoblast stem cells

The recent derivation of human trophoblast stem cells (hTSCs) provides a scalable in vitro model system of human placental development, but the molecular regulators of hTSC identity have not been systematically explored thus far. Here, we utilize a genome-wide CRISPR-Cas9 knockout screen to comprehensively identify essential and growth-restricting genes in hTSCs. By cross-referencing our data to those from similar genetic screens performed in other cell types, as well as gene expression data from early human embryos, we define hTSC-specific and -enriched regulators. These include both well-established and previously uncharacterized trophoblast regulators, such as ARID3A, GATA2, and TEAD1 (essential), and GCM1, PTPN14, and TET2 (growth-restricting). Integrated analysis of chromatin accessibility, gene expression, and genome-wide location data reveals that the transcription factor TEAD1 regulates the expression of many trophoblast regulators in hTSCs. In the absence of TEAD1, hTSCs fail to complete faithful differentiation into extravillous trophoblast (EVT) cells and instead show a bias towards syncytiotrophoblast (STB) differentiation, thus indicating that this transcription factor safeguards the bipotent lineage potential of hTSCs. Overall, our study provides a valuable resource for dissecting the molecular regulation of human placental development and diseases