The FAM13A Long Isoform Regulates Cilia Movement and Co-ordination in Airway Mucociliary Transport

SNPs in the FAM13A locus are amongst the most commonly reported risk alleles associated with chronic obstructive pulmonary disease (COPD) and other respiratory diseases, however the physiological role of FAM13A is unclear. In humans, two major protein isoforms are expressed at the FAM13A locus: 'long' and 'short', but their functions remain unknown, partly due to a lack of isoform conservation in mice. We performed in-depth characterisation of organotypic primary human airway epithelial cell subsets and show that multiciliated cells predominantly express the FAM13A long isoform containing a putative N-terminal Rho GTPase activating protein (RhoGAP) domain. Using purified proteins, we directly demonstrate RhoGAP activity of this domain. In Xenopus laevis, which conserve the long isoform, Fam13a-deficiency impaired cilia-dependent embryo motility. In human primary epithelial cells, long isoform deficiency did not affect multiciliogenesis but reduced cilia co-ordination in mucociliary transport assays. This is the first demonstration that FAM13A isoforms are differentially expressed within the airway epithelium, with implications for the assessment and interpretation of SNP effects on FAM13A expression levels. We also show that the long FAM13A isoform co-ordinates cilia-driven movement, suggesting that FAM13A risk alleles may affect susceptibility to respiratory diseases through deficiencies in mucociliary clearance. This article is open access and distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).

Patterns of ingestion of rats during chronic oral administration of lithium chloride

Chronic lithium administration to rodents is used to explore the potential neural mechanisms of mood stabilization, as well as to model the side effects of chronic lithium on multiple organ systems. Oral administration of lithium in the maintenance diet or drinking water is convenient, but lithium can acutely affect intake and it can mediate acquisition of conditioned taste aversions (CTA). We compared ad libitum food and fluid intake by male rats with LiCl or NaCl solutions as their sole source of fluid across 20 days, with a commonly used dosage of LiCl (24 mM: 1 g / L LiCl). To quantify the pattern of intake, rats were housed in cages equipped with lickometers to detect licks and infrared photobeams to detect food access with 6-s resolution. To determine if rats formed a CTA to LiCl, they were subsequently tested with access to NaCl. Rats showed an immediate avoidance of the LiCl solution, as seen on the first day of access by an increased latency to initiate drinking and a decreased size of drinking bouts. Rats showed a differential response to LiCl vs. NaCl after as few as 5 licks. Chronic consumption of LiCl solution led to significantly decreased food and fluid intake compared to baseline, with concomitant weight loss. The decreased intake was realized by marked changes in the pattern of drinking and feeding bouts: a decrease in per-lick volume and a decrease in licks per drinking bout, and an increase in feeding bout duration resulting in an overall decrease in eating rate. Conversely, chronic NaCl access led to an increase in drinking bout number and licks/bout. The avoidance of LiCl was likely a combination of toxic effects of ingested LiCl and rapid acquisition of a learned aversion to the taste of LiCl, as shown by an extinguishable generalized aversion to NaCl solution during subsequent NaCl test days. The marked effect of chronic oral LiCl on ingestion may impact the oral dosing of lithium as well as the rat's metabolic status.

Behavioral and neural responses to high-strength magnetic fields are reduced in otolith mutant mice

Static high magnetic fields (MFs) interact with the vestibular system of humans and rodents. In rats and mice, exposure to MFs causes perturbations such as head movements, circular locomotion, suppressed rearing, nystagmus, and conditioned taste aversion acquisition. To test the role of otoconia, two mutant mouse models were examined, head-tilt Nox3het (het) and tilted Otop1 (tlt), with mutations, respectively, in Nox3, encoding the NADPH oxidase 3 enzyme, and Otop1, encoding the otopetrin 1 proton channel, which are normally expressed in the otolith organs, and are critical for otoconia formation. Consequently, both mutants show a near complete loss of otoconia in the utricle and saccule, and are nonresponsive to linear acceleration. Mice were exposed to a 14.1 Tesla MF for 30 min. After exposure, locomotor activity, conditioned taste aversion and c-Fos (in het) were assessed. Wild-type mice exposed to the MF showed suppressed rearing, increased latency to rear, locomotor circling, and c-Fos in brainstem nuclei related to vestibular processing (prepositus, spinal vestibular, and supragenual nuclei). Mutant het mice showed no response to the magnet and were similar to sham animals in all assays. Unlike het, tlt mutants exposed to the MF showed significant locomotor circling and suppressed rearing compared with sham controls, although they failed to acquire a taste aversion. The residual responsiveness of tlt versus het mice might reflect a greater semicircular deficit in het mice. These results demonstrate the necessity of the otoconia for the full effect of exposure to high MFs, but also suggest a semicircular contribution.

Climate Change and Health: Challenges to the Local Government Environmental Health Workforce in South Australia

Climate change is the most urgent and significant public health risk facing the globe. In Australia, it has been identified that Environmental Health Officers/Practitioners (EHOs/EHPs, hereafter EHOs) are a currently underutilized source of knowledge and skills that can contribute to climate change adaptation planning at the local government level. The ability of local government EHOs to utilize their local knowledge and skills in human health risk assessment during a public health emergency was demonstrated through their role in the response to COVID-19. This study used a survey and follow up interviews to examine the roles and responsibilities of EHOs during the COVID-19 pandemic and used the results to examine the potential of the workforce to tackle climate change and health related issues. What worked well, what regulatory tools were helpful, how interagency collaboration worked and what barriers or hindering factors existed were also explored. A workforce review of EHOs in South Australia was also undertaken to identify current and future challenges facing EHOs and their capacity to assist in climate change preparedness. The findings demonstrated that the workforce was used in the response to COVID-19 for varying roles by councils, including in education and communication (both internally and externally) as well as monitoring and reporting compliance with directions. Notably, half the workforce believed they could have been better utilized, and the other half thought they were well utilized. The South Australian Local Government Functional Support Group (LGFSG) was praised by the workforce for a successful approach in coordinating multiagency responses and communicating directions in a timely fashion. These lessons learnt from the COVID-19 pandemic should be incorporated into climate change adaptation planning. To ensure consistent messaging and a consolidated information repository, a centralized group should be used to coordinate local government climate change adaptation plans in relation to environmental health and be included in all future emergency management response plans. The surveyed EHOs identified environmental health issues associated with climate change as the most significant future challenge; however, concerningly, participants believe that a lack of adequate resourcing, leading to workforce shortages, increasing workloads and a lack of support, is negatively impacting the workforce's preparedness to deal with these emerging issues. It was suggested that the misperception of environmental health and a failure to recognize its value has resulted in a unique dilemma where EHOs and their councils find themselves caught between managing current workload demands and issues, and endeavouring to prepare, as a priority, for emerging environmental health issues associated with climate change and insufficient resources.

Automated staging of zebrafish embryos using machine learning

The zebrafish ( Danio rerio), is an important biomedical model organism used in many disciplines, including development, disease modeling and toxicology, to better understand vertebrate biology. The phenomenon of developmental delay in zebrafish embryos has been widely reported as part of a mutant or treatment-induced phenotype, and accurate characterization of such delays is imperative. Despite this, the only way at present to identify and quantify these delays is through manual observation, which is both time-consuming and subjective. Machine learning approaches in biology are rapidly becoming part of the toolkit used by researchers to address complex questions. In this work, we introduce a machine learning-based classifier that has been trained to detect temporal developmental differences across groups of zebrafish embryos. Our classifier is capable of rapidly analyzing thousands of images, allowing comparisons of developmental temporal rates to be assessed across and between experimental groups of embryos. Finally, as our classifier uses images obtained from a standard live-imaging widefield microscope and camera set-up, we envisage it will be readily accessible to the zebrafish community, and prove to be a valuable resource.

Automated staging of zebrafish embryos using machine learning

The zebrafish ( Danio rerio), is an important biomedical model organism used in many disciplines, including development, disease modeling and toxicology, to better understand vertebrate biology. The phenomenon of developmental delay in zebrafish embryos has been widely reported as part of a mutant or treatment-induced phenotype, and accurate characterization of such delays is imperative. Despite this, the only way at present to identify and quantify these delays is through manual observation, which is both time-consuming and subjective. Machine learning approaches in biology are rapidly becoming part of the toolkit used by researchers to address complex questions. In this work, we introduce a machine learning-based classifier that has been trained to detect temporal developmental differences across groups of zebrafish embryos. Our classifier is capable of rapidly analyzing thousands of images, allowing comparisons of developmental temporal rates to be assessed across and between experimental groups of embryos. Finally, as our classifier uses images obtained from a standard live-imaging widefield microscope and camera set-up, we envisage it will be readily accessible to the zebrafish community, and prove to be a valuable resource.

Generation of left ventricle-like cardiomyocytes with improved structural, functional, and metabolic maturity from human pluripotent stem cells

Decreased left ventricle (LV) function caused by genetic mutations or injury often leads to debilitating and fatal cardiovascular disease. LV cardiomyocytes are, therefore, a potentially valuable therapeutical target. Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are neither homogeneous nor functionally mature, which reduces their utility. Here, we exploit cardiac development knowledge to instruct differentiation of hPSCs specifically toward LV cardiomyocytes. Correct mesoderm patterning and retinoic acid pathway blocking are essential to generate near-homogenous LV-specific hPSC-CMs (hPSC-LV-CMs). These cells transit via first heart field progenitors and display typical ventricular action potentials. Importantly, hPSC-LV-CMs exhibit increased metabolism, reduced proliferation, and improved cytoarchitecture and functional maturity compared with age-matched cardiomyocytes generated using the standard WNT-ON/WNT-OFF protocol. Similarly, engineered heart tissues made from hPSC-LV-CMs are better organized, produce higher force, and beat more slowly but can be paced to physiological levels. Together, we show that functionally matured hPSC-LV-CMs can be obtained rapidly without exposure to current maturation regimes.

Automated staging of zebrafish embryos using machine learning

The zebrafish (Danio rerio), is an important biomedical model organism used in many disciplines, including development, disease modeling and toxicology, to better understand vertebrate biology. The phenomenon of developmental delay in zebrafish embryos has been widely reported as part of a mutant or treatment-induced phenotype, and accurate characterization of such delays is imperative. Despite this, the only way at present to identify and quantify these delays is through manual observation, which is both time-consuming and subjective. Machine learning approaches in biology are rapidly becoming part of the toolkit used by researchers to address complex questions. In this work, we introduce a machine learning-based classifier that has been trained to detect temporal developmental differences across groups of zebrafish embryos. Our classifier is capable of rapidly analyzing thousands of images, allowing comparisons of developmental temporal rates to be assessed across and between experimental groups of embryos. Finally, as our classifier uses images obtained from a standard live-imaging widefield microscope and camera set-up, we envisage it will be readily accessible to the zebrafish community, and prove to be a valuable resource.

Climate Change and Health: Local Government Capacity for Health Protection in Australia

Climate change is the greatest global health threat of the 21st century, with numerous direct and indirect human health consequences. Local governments play a critical role in communities' response to climate change, both through strategies to reduce emissions and adaption plans to respond to changing climate and extreme weather events. Australian local government environmental health officers (EHOs) have the relevant skills and expertise to inform and develop adaptation plans for health protection in the context of climate change. This study used an online survey followed by phone interviews of local government management to determine the extent to which EHOs are involved in adaptation planning in health protection climate change plans. Questions were also asked to determine whether local councils are aware of EHOs' capability to contribute and to gauge the willingness of management to provide EHOs with the workload capacity to do so. The findings demonstrated that although climate adaptation and mitigation planning is occurring in local government, it is not including or considering the public health impacts on the community. Primarily, it was found that this oversight was due to a lack of awareness of the health impacts of climate change outside of a disaster or emergency scenario. Currently, EHOs are an untapped source of knowledge and skills that can contribute to climate change adaption planning. To support this, a framework of local environmental health practice was developed to assist the reconceptualization of the scope of practice required for the planning and response to climate change.

In vitro cellular reprogramming to model gonad development and its disorders

During embryonic development, mutually antagonistic signaling cascades determine gonadal fate toward a testicular or ovarian identity. Errors in this process result in disorders of sex development (DSDs), characterized by discordance between chromosomal, gonadal, and anatomical sex. The absence of an appropriate, accessible in vitro system is a major obstacle in understanding mechanisms of sex-determination/DSDs. Here, we describe protocols for differentiation of mouse and human pluripotent cells toward gonadal progenitors. Transcriptomic analysis reveals that the in vitro-derived murine gonadal cells are equivalent to embryonic day 11.5 in vivo progenitors. Using similar conditions, Sertoli-like cells derived from 46,XY human induced pluripotent stem cells (hiPSCs) exhibit sustained expression of testis-specific genes, secrete anti-Müllerian hormone, migrate, and form tubular structures. Cells derived from 46,XY DSD female hiPSCs, carrying an NR5A1 variant, show aberrant gene expression and absence of tubule formation. CRISPR-Cas9-mediated variant correction rescued the phenotype. This is a robust tool to understand mechanisms of sex determination and model DSDs.

Rostrocaudal patterning and neural crest differentiation of human pre-neural spinal cord progenitors in vitro

The spinal cord emerges from a niche of neuromesodermal progenitors (NMPs) formed and maintained by WNT/fibroblast growth factor (FGF) signals at the posterior end of the embryo. NMPs can be generated from human pluripotent stem cells and hold promise for spinal cord replacement therapies. However, NMPs are transient, which compromises production of the full range of rostrocaudal spinal cord identities in vitro. Here we report the generation of NMP-derived pre-neural progenitors (PNPs) with stem cell-like self-renewal capacity. PNPs maintain pre-spinal cord identity for 7-10 passages, dividing to self-renew and to make neural crest progenitors, while gradually adopting a more posterior identity by activating colinear HOX gene expression. The HOX clock can be halted through GDF11-mediated signal inhibition to produce a PNP and NC population with a thoracic identity that can be maintained for up to 30 passages.

Accumulation of Insensitive Munition Compounds in the Earthworm Eisenia andrei from Amended Soil: Methodological Considerations for Determination of Bioaccumulation Factors

The present study investigates the bioaccumulation of the insensitive munition compounds 2,4-dinitroanisole (DNAN) and 3-nitro-1,2,4-triazol-5-one (NTO), developed for future weapons systems to replace current munitions containing sensitive explosives. The earthworm Eisenia andrei was exposed to sublethal concentrations of DNAN or NTO amended in Sassafras sandy loam. Chemical analysis indicated that 2- and 4-amino-nitroanisole (2-ANAN and 4-ANAN, respectively) were formed in DNAN-amended soils. The SumDNAN (sum of DNAN, 2-ANAN, and 4-ANAN concentrations) in soil decreased by 40% during the 14-d exposure period. The SumDNAN in the earthworm body residue increased until day 3 and decreased thereafter. Between days 3 and 14, there was a 73% decrease in tissue uptake that was greater than the 23% decrease in the soil concentration, suggesting that the bioavailable fraction may have decreased over time. By day 14, the DNAN concentration accounted for only 45% of the SumDNAN soil concentration, indicating substantial DNAN transformation in the presence of earthworms. The highest bioaccumulation factor (BAF; the tissue-to-soil concentration ratio) was 6.2 ± 1.0 kg/kg (dry wt) on day 3 and decreased to 3.8 ± 0.8 kg/kg by day 14. Kinetic studies indicated a BAF of 2.3 kg/kg, based on the earthworm DNAN uptake rate of 2.0 ± 0.24 kg/kg/d, compared with the SumDNAN elimination rate of 0.87 d^-1 (half-life = 0.79 d). The compound DNAN has a similar potential to bioaccumulate from soil compared with trinitrotoluene. The NTO concentration in amended soil decreased by 57% from the initial concentration (837 mg NTO/kg dry soil) during 14 d, likely due to the formation of unknown transformation products. The bioaccumulation of NTO was negligible (BAF ≤ 0.018 kg/kg dry wt). Environ Toxicol Chem 2021;40:1713-1725. © 2021 SETAC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

Ventricular, atrial, and outflow tract heart progenitors arise from spatially and molecularly distinct regions of the primitive streak

The heart develops from 2 sources of mesoderm progenitors, the first and second heart field (FHF and SHF). Using a single-cell transcriptomic assay combined with genetic lineage tracing and live imaging, we find the FHF and SHF are subdivided into distinct pools of progenitors in gastrulating mouse embryos at earlier stages than previously thought. Each subpopulation has a distinct origin in the primitive streak. The first progenitors to leave the primitive streak contribute to the left ventricle, shortly after right ventricle progenitor emigrate, followed by the outflow tract and atrial progenitors. Moreover, a subset of atrial progenitors are gradually incorporated in posterior locations of the FHF. Although cells allocated to the outflow tract and atrium leave the primitive streak at a similar stage, they arise from different regions. Outflow tract cells originate from distal locations in the primitive streak while atrial progenitors are positioned more proximally. Moreover, single-cell RNA sequencing demonstrates that the primitive streak cells contributing to the ventricles have a distinct molecular signature from those forming the outflow tract and atrium. We conclude that cardiac progenitors are prepatterned within the primitive streak and this prefigures their allocation to distinct anatomical structures of the heart. Together, our data provide a new molecular and spatial map of mammalian cardiac progenitors that will support future studies of heart development, function, and disease.

Saracatinib is an efficacious clinical candidate for fibrodysplasia ossificans progressiva

Currently, no effective therapies exist for fibrodysplasia ossificans progressiva (FOP), a rare congenital syndrome in which heterotopic bone is formed in soft tissues owing to dysregulated activity of the bone morphogenetic protein (BMP) receptor kinase ALK2 (also known as ACVR1). From a screen of known biologically active compounds, we identified saracatinib as a potent ALK2 kinase inhibitor. In enzymatic and cell-based assays, saracatinib preferentially inhibited ALK2, compared with other receptors of the BMP/TGF-β signaling pathway, and induced dorsalization in zebrafish embryos consistent with BMP antagonism. We further tested the efficacy of saracatinib using an inducible ACVR1^Q207D-transgenic mouse line, which provides a model of heterotopic ossification (HO), as well as an inducible ACVR1^R206H-knockin mouse, which serves as a genetically and physiologically faithful FOP model. In both models, saracatinib was well tolerated and potently inhibited the development of HO, even when administered transiently following soft tissue injury. Together, these data suggest that saracatinib is an efficacious clinical candidate for repositioning in FOP treatment, offering an accelerated path to clinical proof-of-efficacy studies and potentially significant benefits to individuals with this devastating condition.

The migratory pathways of the cells that form the endocardium, dorsal aortae, and head vasculature in the mouse embryo

Background

Vasculogenesis in amniotes is often viewed as two spatially and temporally distinct processes, occurring in the yolk sac and in the embryo. However, the spatial origins of the cells that form the primary intra-embryonic vasculature remain uncertain. In particular, do they obtain their haemato-endothelial cell fate in situ, or do they migrate from elsewhere? Recently developed imaging techniques, together with new Tal1 and existing Flk1 reporter mouse lines, have allowed us to investigate this question directly, by visualising cell trajectories live and in three dimensions.

Results

We describe the pathways that cells follow to form the primary embryonic circulatory system in the mouse embryo. In particular, we show that Tal1-positive cells migrate from within the yolk sac, at its distal border, to contribute to the endocardium, dorsal aortae and head vasculature. Other Tal1 positive cells, similarly activated within the yolk sac, contribute to the yolk sac vasculature. Using single-cell transcriptomics and our imaging, we identify VEGF and Apela as potential chemo-attractants that may regulate the migration into the embryo. The dorsal aortae and head vasculature are known sites of secondary haematopoiesis; given the common origins that we observe, we investigate whether this is also the case for the endocardium. We discover cells budding from the wall of the endocardium with high Tal1 expression and diminished Flk1 expression, indicative of an endothelial to haematopoietic transition.

Conclusions

In contrast to the view that the yolk sac and embryonic circulatory systems form by two separate processes, our results indicate that Tal1-positive cells from the yolk sac contribute to both vascular systems. It may be that initial Tal1 activation in these cells is through a common mechanism.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12861-021-00239-3.

The New Environmental Health in Australia: Failure to Launch?

BACKGROUND

The New Environmental Health is an approach to environmental health adopted in 1999. The new approach was in response to emerging health risks from the pressures that development placed on the environment, climate change, and increasing vulnerabilities of local communities. The new approach heralded a change in perception and roles within environmental health. Twenty years on, it seems these changes have not been embraced by local government.

METHODS

To determine whether this was the case, we assessed the use of the term "environmental health" in local government annual reports, and where environmental health functions sit within the organisational structure of councils.

RESULTS

We found that the New Environmental Health has not been adopted by councils and environmental health relates solely to the delivery of statutory services and legislative compliance.

CONCLUSIONS

One result of this is local environmental health practitioners, who constitute the major health protection capability of councils, are defined by the narrow legislative obligations imposed on councils. This represents a significant lost opportunity as public health is not protected in the way that was envisaged with the adoption of the New Environmental Health.

FAM83F regulates canonical Wnt signalling through an interaction with CK1α

The function of the FAM83F protein, like the functions of many members of the FAM83 family, is poorly understood. Here, we show that injection of Fam83f mRNA into Xenopus embryos causes axis duplication, a phenotype indicative of enhanced Wnt signalling. Consistent with this, overexpression of FAM83F activates Wnt signalling, whereas ablation of FAM83F from human colorectal cancer (CRC) cells attenuates it. We demonstrate that FAM83F is farnesylated and interacts and co-localises with CK1α at the plasma membrane. This interaction with CK1α is essential for FAM83F to activate Wnt signalling, and FAM83F mutants that do not interact with CK1α fail to induce axis duplication in Xenopus embryos and to activate Wnt signalling in cells. FAM83F acts upstream of GSK-3β because the attenuation of Wnt signalling caused by loss of FAM83F can be rescued by GSK-3 inhibition. Introduction of a farnesyl-deficient mutant of FAM83F in cells through CRISPR/Cas9 genome editing redirects the FAM83F-CK1α complex away from the plasma membrane and significantly attenuates Wnt signalling, indicating that FAM83F exerts its effects on Wnt signalling at the plasma membrane.

Vulnerability of progeroid smooth muscle cells to biomechanical forces is mediated by MMP13

Hutchinson-Gilford Progeria Syndrome (HGPS) is a premature aging disease in children that leads to early death. Smooth muscle cells (SMCs) are the most affected cells in HGPS individuals, although the reason for such vulnerability remains poorly understood. In this work, we develop a microfluidic chip formed by HGPS-SMCs generated from induced pluripotent stem cells (iPSCs), to study their vulnerability to flow shear stress. HGPS-iPSC SMCs cultured under arterial flow conditions detach from the chip after a few days of culture; this process is mediated by the upregulation of metalloprotease 13 (MMP13). Importantly, double-mutant LmnaG609G/G609GMmp13-/- mice or LmnaG609G/G609GMmp13+/+ mice treated with a MMP inhibitor show lower SMC loss in the aortic arch than controls. MMP13 upregulation appears to be mediated, at least in part, by the upregulation of glycocalyx. Our HGPS-SMCs chip represents a platform for developing treatments for HGPS individuals that may complement previous pre-clinical and clinical treatments.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of the proteome of SARS CoV-2. THe MD performed is temperature replica-exchange enhanced sampling, making use of the massively parallel supercomputing on the SUMMIT supercomputer at Oak Ridge National Laboratory, with which more than 1ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to ten configurations of each of the 23 SARS CoV-2 systems using AutoDock Vina. We also demonstrate that using Autodock-GPU on SUMMIT, it is possible to perform exhaustive docking of one billion compounds in under 24 hours. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and AI methods to cluster MD trajectories and rescore docking poses.

Maternal pluripotency factors initiate extensive chromatin remodelling to predefine first response to inductive signals

Embryonic development yields many different cell types in response to just a few families of inductive signals. The property of signal-receiving cells that determines how they respond to inductive signals is known as competence, and it differs in different cell types. Here, we explore the ways in which maternal factors modify chromatin to specify initial competence in the frog Xenopus tropicalis. We identify early-engaged regulatory DNA sequences, and infer from them critical activators of the zygotic genome. Of these, we show that the pioneering activity of the maternal pluripotency factors Pou5f3 and Sox3 determines competence for germ layer formation by extensively remodelling compacted chromatin before the onset of inductive signalling. This remodelling includes the opening and marking of thousands of regulatory elements, extensive chromatin looping, and the co-recruitment of signal-mediating transcription factors. Our work identifies significant developmental principles that inform our understanding of how pluripotent stem cells interpret inductive signals.

Pathogenic FAM83G palmoplantar keratoderma mutations inhibit the PAWS1:CK1α association and attenuate Wnt signalling

Background: Two recessive mutations in the FAM83G gene, causing A34E and R52P amino acid substitutions in the DUF1669 domain of the PAWS1 protein, are associated with palmoplantar keratoderma (PPK) in humans and dogs respectively. We have previously reported that PAWS1 associates with the Ser/Thr protein kinase CK1α through the DUF1669 domain to mediate canonical Wnt signalling. Methods: Co-immunoprecipitation was used to investigate possible changes to PAWS1 interactors caused by the mutations. We also compared the stability of wild-type and mutant PAWS1 in cycloheximide-treated cells. Effects on Wnt signalling were determined using the TOPflash luciferase reporter assay in U2OS cells expressing PAWS1 mutant proteins. The ability of PAWS1 to induce axis duplication in Xenopus embryos was also tested. Finally, we knocked-in the A34E mutation at the native gene locus and measured Wnt-induced AXIN2 gene expression by RT-qPCR. Results: We show that these PAWS1 ^A34E and PAWS1 ^R52P mutants fail to interact with CK1α but, like the wild-type protein, do interact with CD2AP and SMAD1. Like cells carrying a PAWS1 ^F296A mutation, which also abolishes CK1α binding, cells carrying the A34E and R52P mutants respond poorly to Wnt signalling to an extent resembling that observed in FAM83G gene knockout cells. Consistent with this observation, these mutants, in contrast to the wild-type protein, fail to induce axis duplication in Xenopus embryos. We also found that the A34E and R52P mutant proteins are less abundant than the native protein and appear to be less stable, both when overexpressed in FAM83G-knockout cells and when knocked-in at the native FAM83G locus. Ala ³⁴ of PAWS1 is conserved in all FAM83 proteins and mutating the equivalent residue in FAM83H (A31E) also abolishes interaction with CK1 isoforms. Conclusions: We propose that mutations in PAWS1 cause PPK pathogenesis through disruption of the CK1α interaction and attenuation of Wnt signalling.

The Spatiotemporal Control of Zygotic Genome Activation

One of the earliest and most significant events in embryonic development is zygotic genome activation (ZGA). In several species, bulk transcription begins at the midblastula transition (MBT) when, after a certain number of cleavages, the embryo attains a particular nuclear-to-cytoplasmic (N/C) ratio, maternal repressors become sufficiently diluted, and the cell cycle slows down. Here we resolve the frog ZGA in time and space by profiling RNA polymerase II (RNAPII) engagement and its transcriptional readout. We detect a gradual increase in both the quantity and the length of RNAPII elongation before the MBT, revealing that >1,000 zygotic genes disregard the N/C timer for their activation and that the sizes of newly transcribed genes are not necessarily constrained by cell cycle duration. We also find that Wnt, Nodal, and BMP signaling together generate most of the spatiotemporal dynamics of regional ZGA, directing the formation of orthogonal body axes and proportionate germ layers.

Common and distinct transcriptional signatures of mammalian embryonic lethality

The Deciphering the Mechanisms of Developmental Disorders programme has analysed the morphological and molecular phenotypes of embryonic and perinatal lethal mouse mutant lines in order to investigate the causes of embryonic lethality. Here we show that individual whole-embryo RNA-seq of 73 mouse mutant lines (>1000 transcriptomes) identifies transcriptional events underlying embryonic lethality and associates previously uncharacterised genes with specific pathways and tissues. For example, our data suggest that Hmgxb3 is involved in DNA-damage repair and cell-cycle regulation. Further, we separate embryonic delay signatures from mutant line-specific transcriptional changes by developing a baseline mRNA expression catalogue of wild-type mice during early embryogenesis (4-36 somites). Analysis of transcription outside coding sequence identifies deregulation of repetitive elements in Morc2a mutants and a gene involved in gene-specific splicing. Collectively, this work provides a large scale resource to further our understanding of early embryonic developmental disorders.

Mapping Chromatin Features of Xenopus Embryos

Chromatin immunoprecipitation (ChIP) combined with genomic analysis provides a global snapshot of protein-DNA interactions in the context of chromatin, yielding insights into which genome loci might be regulated by the DNA-associated protein under investigation. This protocol is an update of a previous version and describes how to perform ChIP on intact or dissected Xenopus embryos. The ChIP-isolated DNA fragments are suitable for both deep sequencing (ChIP-Seq) and quantitative polymerase chain reaction (ChIP-qPCR). General advice for qPCR and for making ChIP-Seq libraries is offered, and approaches for analyzing ChIP-Seq data are outlined.

Pathogenic FAM83G palmoplantar keratoderma mutations inhibit the PAWS1:CK1α association and attenuate Wnt signalling

Background: Two recessive mutations in the FAM83G gene, causing A34E and R52P amino acid substitutions in the DUF1669 domain of the PAWS1 protein, are associated with palmoplantar keratoderma (PPK) in humans and dogs respectively. We have previously reported that PAWS1 associates with the Ser/Thr protein kinase CK1α through the DUF1669 domain to mediate canonical Wnt signalling. Methods: Co-immunoprecipitation was used to investigate possible changes to PAWS1 interactors caused by the mutations. We also compared the stability of wild-type and mutant PAWS1 in cycloheximide-treated cells. Effects on Wnt signalling were determined using the TOPflash luciferase reporter assay in U2OS cells expressing PAWS1 mutant proteins. The ability of PAWS1 to induce axis duplication in Xenopus embryos was also tested. Finally, we knocked-in the A34E mutation at the native gene locus and measured Wnt-induced AXIN2 gene expression by RT-qPCR. Results: We show that these PAWS1 ^A34E and PAWS1 ^R52P mutants fail to interact with CK1α but, like the wild-type protein, do interact with CD2AP and SMAD1. Like cells carrying a PAWS1 ^F296A mutation, which also abolishes CK1α binding, cells carrying the A34E and R52P mutants respond poorly to Wnt signalling to an extent resembling that observed in FAM83G gene knockout cells. Consistent with this observation, these mutants, in contrast to the wild-type protein, fail to induce axis duplication in Xenopus embryos. We also found that the A34E and R52P mutant proteins are less abundant than the native protein and appear to be less stable, both when overexpressed in FAM83G-knockout cells and when knocked-in at the native FAM83G locus. Ala ³⁴ of PAWS1 is conserved in all FAM83 proteins and mutating the equivalent residue in FAM83H (A31E) also abolishes interaction with CK1 isoforms. Conclusions: We propose that mutations in PAWS1 cause PPK pathogenesis through disruption of the CK1α interaction and attenuation of Wnt signalling.

Dissecting and Culturing Animal Cap Explants

The animal cap explant is a simple but adaptable tool available to developmental biologists. The use of animal cap explants in demonstrating the presence of mesoderm-inducting activity in the Xenopus embryo vegetal pole is one of many elegant examples of their worth. Animal caps respond to a range of growth factors (e.g., Wnts, FGF, TGF-β), making them especially useful for studying signal transduction pathways and gene regulatory networks. Explants are also suitable for examining cell behavior and have provided key insights into the molecular mechanisms controlling vertebrate morphogenesis. In this protocol, we outline two methods to isolate animal cap explants from Xenopus laevis, both of which can be applied easily to Xenopus tropicalis The first method is a standard manual method that can be used in any laboratory equipped with a standard dissecting microscope. For labs planning on dissecting large numbers of explants on a regular basis, a second, high throughput method is described that uses a specialized microcautery surgical instrument.

Mammalian embryo comparison identifies novel pluripotency genes associated with the naïve or primed state

During early mammalian development, transient pools of pluripotent cells emerge that can be immortalised upon stem cell derivation. The pluripotent state, ‘naïve’ or ‘primed’, depends on the embryonic stage and derivation conditions used. Here we analyse the temporal gene expression patterns of mouse, cattle and porcine embryos at stages that harbour different types of pluripotent cells. We document conserved and divergent traits in gene expression, and identify predictor genes shared across the species that are associated with pluripotent states in vivo and in vitro. Amongst these are the pluripotency-linked genes Klf4 and Lin28b. The novel genes discovered include naïve- (Spic, Scpep1 and Gjb5) and primed-associated (Sema6a and Jakmip2) genes as well as naïve to primed transition genes (Dusp6 and Trip6). Both Gjb5 and Dusp6 play a role in pluripotency since their knockdown results in differentiation and downregulation of key pluripotency genes. Our interspecies comparison revealed new insights of pluripotency, pluripotent stem cell identity and a new molecular criterion for distinguishing between pluripotent states in various species, including human.

Summary: Interspecies comparison of mouse, bovine and pig embryos revealed conserved genes which distinguish between naïve and primed pluripotency states, including in human. Some of these genes interfere with the pluripotency network and lead to differentiation.

Transcriptomics of dorso-ventral axis determination in Xenopus tropicalis

Amphibian embryos provide a powerful system to study early cell fate determination because their eggs are externally fertilised, large, and easy to manipulate. Ultraviolet (UV) or lithium chloride (LiCl) treatment are classic embryonic manipulations frequently used to perturb specification of the dorso-ventral (DV) axis by affecting the stability of the maternal Wnt mediator β-catenin. Such treatments result in the formation of so-called ventralised or dorsalised embryos. Although these phenotypes have been well described with respect to their morphology and some aspects of gene expression, their whole transcriptomes have never been systematically characterised and compared. Here we show that at the early gastrula stage UV-treated embryos are transcriptionally more closely related to untreated embryos than to LiCl-treated embryos. Transcriptional comparisons with dissected ventral and dorsal regions of unperturbed gastrula embryos indicate that UV and LiCl treatments indeed enrich for ventral and dorsal cells, respectively. However, these treatments also affect the balance of neural induction in the ectodermal germ layer, with LiCl stimulating pro-neural BMP inhibition and UV preferentially generating epidermis because of elevated BMP levels. Thus the transcriptomes of UV- and LiCl-treated embryos can best be described as ventro-epidermalised and dorso-neuralised. These descriptions notwithstanding, our profiling reveals several hitherto uncharacterized genes with differential expression along the DV axis. At least one of these genes, a RNF220-like ubiquitin ligase, is activated dorsally by β-catenin. Our analysis of UV/LiCl-mediated axis perturbation will enhance the mechanistic understanding of DV axis determination in vertebrates.

The DUF1669 domain of FAM83 family proteins anchor casein kinase 1 isoforms

Members of the casein kinase 1 (CK1) family of serine-threonine protein kinases are implicated in the regulation of many cellular processes, including the cell cycle, circadian rhythms, and Wnt and Hedgehog signaling. Because these kinases exhibit constitutive activity in biochemical assays, it is likely that their activity in cells is controlled by subcellular localization, interactions with inhibitory proteins, targeted degradation, or combinations of these mechanisms. We identified members of the FAM83 family of proteins as partners of CK1 in cells. All eight members of the FAM83 family (FAM83A to FAM83H) interacted with the α and α-like isoforms of CK1; FAM83A, FAM83B, FAM83E, and FAM83H also interacted with the δ and ε isoforms of CK1. We detected no interaction between any FAM83 member and the related CK1γ1, CK1γ2, and CK1γ3 isoforms. Each FAM83 protein exhibited a distinct pattern of subcellular distribution and colocalized with the CK1 isoform(s) to which it bound. The interaction of FAM83 proteins with CK1 isoforms was mediated by the conserved domain of unknown function 1669 (DUF1669) that characterizes the FAM83 family. Mutations in FAM83 proteins that prevented them from binding to CK1 interfered with the proper subcellular localization and cellular functions of both the FAM83 proteins and their CK1 binding partners. On the basis of its function, we propose that DUF1669 be renamed the polypeptide anchor of CK1 domain.

PAWS1 controls Wnt signalling through association with casein kinase 1α

The BMP and Wnt signalling pathways determine axis specification during embryonic development. Our previous work has shown that PAWS1 (also known as FAM83G) interacts with SMAD1 and modulates BMP signalling. Here, surprisingly, we show that overexpression of PAWS1 in Xenopus embryos activates Wnt signalling and causes complete axis duplication. Consistent with these observations in Xenopus, Wnt signalling is diminished in U2OS osteosarcoma cells lacking PAWS1, while BMP signalling is unaffected. We show that PAWS1 interacts and co-localises with the α isoform of casein kinase 1 (CK1), and that PAWS1 mutations incapable of binding CK1 fail both to activate Wnt signalling and to elicit axis duplication in Xenopus embryos.

Innate Immune Response and Off-Target Mis-splicing Are Common Morpholino-Induced Side Effects in Xenopus

Antisense morpholino oligomers (MOs) have been indispensable tools for developmental biologists to transiently knock down (KD) genes rather than to knock them out (KO). Here we report on the implications of genetic KO versus MO-mediated KD of the mesoderm-specifying Brachyury paralogs in the frog Xenopus tropicalis. While both KO and KD embryos fail to activate the same core gene regulatory network, resulting in virtually identical morphological defects, embryos injected with control or target MOs also show a systemic GC content-dependent immune response and many off-target splicing defects. Optimization of MO dosage and increasing incubation temperatures can mitigate, but not eliminate, these MO side effects, which are consistent with the high affinity measured between MO and off-target sequence in vitro. We conclude that while MOs can be useful to profile loss-of-function phenotypes at a molecular level, careful attention must be paid to their immunogenic and off-target side effects.

A NuRD Complex from Xenopus laevis Eggs Is Essential for DNA Replication during Early Embryogenesis

DNA replication in the embryo of Xenopus laevis changes dramatically at the mid-blastula transition (MBT), with Y RNA-independent random initiation switching to Y RNA-dependent initiation at specific origins. Here, we identify xNuRD, an MTA2-containing assemblage of the nucleosome remodeling and histone deacetylation complex NuRD, as an essential factor in pre-MBT Xenopus embryos that overcomes a functional requirement for Y RNAs during DNA replication. Human NuRD complexes have a different subunit composition than xNuRD and do not support Y RNA-independent initiation of DNA replication. Blocking or immunodepletion of xNuRD inhibits DNA replication initiation in isolated nuclei in vitro and causes inhibition of DNA synthesis, developmental delay, and embryonic lethality in early embryos. xNuRD activity declines after the MBT, coinciding with dissociation of the complex and emergence of Y RNA-dependent initiation. Our data thus reveal an essential role for a NuRD complex as a DNA replication factor during early Xenopus development.

Double J Stents in the Treatment of Gynaecological Injury to the Ureter

Ureteric injury is a recognized complication of hysterectomy and may present with obstruction or fistula.

Between 1987 and 1989 in Oxford nine patients with 10 injured ureters underwent attempted retrograde placement of double J stents. Three patients had successful outcomes and one patient with bilateral ureteric obstruction required reimplantation of the right ureter after successful stenting of the left ureter. One patient required removal of a stent due to irritation but her fistula eventually closed. In three patients placement was unsuccessful and in one patient injury to the bladder base prevented the ureteric orifices from being seen and hence stenting was not possible. Thus five of these 10 injured ureters were managed successfully with double J stents.

We advocate the initial use of double J stents in gynaecological ureteric injury. This approach is simple and may cure the fistula. If it is unsuccessful, subsequent reimplantation is not hindered.

PAWS1 controls cytoskeletal dynamics and cell migration through association with the SH3 adaptor CD2AP

Our previous studies of PAWS1 (protein associated with SMAD1; also known as FAM83G) have suggested that this molecule has roles beyond BMP signalling. To investigate these roles, we have used CRISPR/Cas9 to generate PAWS1-knockout U2OS osteosarcoma cells. Here, we show that PAWS1 plays a role in the regulation of the cytoskeletal machinery, including actin and focal adhesion dynamics, and cell migration. Confocal microscopy and live cell imaging of actin in U2OS cells indicate that PAWS1 is also involved in cytoskeletal dynamics and organization. Loss of PAWS1 causes severe defects in F-actin organization and distribution as well as in lamellipodial organization, resulting in impaired cell migration. PAWS1 interacts in a dynamic fashion with the actin/cytoskeletal regulator CD2AP at lamellae, suggesting that its association with CD2AP controls actin organization and cellular migration. Genetic ablation of CD2AP from U2OS cells instigates actin and cell migration defects reminiscent of those seen in PAWS1-knockout cells.

This article has an associated First Person interview with the first authors of the paper.

Summary: PAWS1 (also known as FAM83G) controls cell migration by influencing the organization of F-actin and focal adhesions and the distribution of the actin stress fibre network through its association with CD2AP.

Knockdown of Laminin gamma-3 (Lamc3) impairs motoneuron guidance in the zebrafish embryo

Background: Previous work in the zebrafish embryo has shown that laminin γ-3 ( lamc3) is enriched in endothelial cells marked by expression of fli1a, but the role of Lamc3 has been unknown. Methods: We use antisense morpholino oligonucleotides, and CRISPR/Cas9 mutagenesis of F0 embryos, to create zebrafish embryos in which lamc3 expression is compromised. Transgenic imaging, immunofluorescence, and in situ hybridisation reveal that Lamc3 loss-of-function affects the development of muscle pioneers, endothelial cells, and motoneurons. Results:  Lamc3 is enriched in endothelial cells during zebrafish development, but it is also expressed by other tissues. Depletion of Lamc3 by use of antisense morpholino oligonucleotides perturbs formation of the parachordal chain and subsequently the thoracic duct, but Lamc3 is not required for sprouting of the cardinal vein. F0 embryos in which lamc3 expression is perturbed by a CRISPR/Cas9 approach also fail to form a parachordal chain, but we were unable to establish a stable lamc3 null line. Lamc3 is dispensable for muscle pioneer specification and for the expression of netrin-1a in these cells. Lamc3 knockdown causes netrin-1a up-regulation in the neural tube and there is increased Netrin-1 protein throughout the trunk of the embryo. Axonal guidance of rostral primary motoneurons is defective in Lamc3 knockdown embryos. Conclusions: We suggest that knockdown of Lamc3 perturbs migration of rostral primary motoneurons at the level of the horizontal myoseptum, indicating that laminin γ3 plays a role in motoneuron guidance.

Correction: Zebrafish atoh8 mutants do not recapitulate morpholino phenotypes

[This corrects the article DOI: 10.1371/journal.pone.0171143.].

Highly variable penetrance of abnormal phenotypes in embryonic lethal knockout mice

Background: Identifying genes that are essential for mouse embryonic development and survival through term is a powerful and unbiased way to discover possible genetic determinants of human developmental disorders. Characterising the changes in mouse embryos that result from ablation of lethal genes is a necessary first step towards uncovering their role in normal embryonic development and establishing any correlates amongst human congenital abnormalities. Methods: Here we present results gathered to date in the Deciphering the Mechanisms of Developmental Disorders (DMDD) programme, cataloguing the morphological defects identified from comprehensive imaging of 220 homozygous mutant and 114 wild type embryos from 42 lethal and subviable lines, analysed at E14.5. Results: Virtually all mutant embryos show multiple abnormal phenotypes and amongst the 42 lines these affect most organ systems. Within each mutant line, the phenotypes of individual embryos form distinct but overlapping sets. Subcutaneous edema, malformations of the heart or great vessels, abnormalities in forebrain morphology and the musculature of the eyes are all prevalent phenotypes, as is loss or abnormal size of the hypoglossal nerve.Conclusions: Overall, the most striking finding is that no matter how profound the malformation, each phenotype shows highly variable penetrance within a mutant line. These findings have challenging implications for efforts to identify human disease correlates.

Highly variable penetrance of abnormal phenotypes in embryonic lethal knockout mice

Background: Identifying genes that are essential for mouse embryonic development and survival through term is a powerful and unbiased way to discover possible genetic determinants of human developmental disorders. Characterising the changes in mouse embryos that result from ablation of lethal genes is a necessary first step towards uncovering their role in normal embryonic development and establishing any correlates amongst human congenital abnormalities.

Methods: Here we present results gathered to date in the Deciphering the Mechanisms of Developmental Disorders (DMDD) programme, cataloguing the morphological defects identified from comprehensive imaging of 220 homozygous mutant and 114 wild type embryos from 42 lethal and subviable lines, analysed at E14.5.

Results: Virtually all mutant embryos show multiple abnormal phenotypes and amongst the 42 lines these affect most organ systems. Within each mutant line, the phenotypes of individual embryos form distinct but overlapping sets. Subcutaneous edema, malformations of the heart or great vessels, abnormalities in forebrain morphology and the musculature of the eyes are all prevalent phenotypes, as is loss or abnormal size of the hypoglossal nerve.

Conclusions: Overall, the most striking finding is that no matter how profound the malformation, each phenotype shows highly variable penetrance within a mutant line. These findings have challenging implications for efforts to identify human disease correlates.

Abstract P4-22-11: Combined targeted therapies for advanced triple negative breast cancer: A phase II trial of nab-paclitaxel and bevacizumab followed by maintenance targeted therapy with bevacizumab and erlotinib

Background: Chemotherapy remains the mainstay of therapy for patients with metastatic triple negative breast cancer (TNBC). We hypothesized that the addition of biologic agents targeting key pathways (bevacizumab targeting angiogenesis and erlotinib directed against EGFR) may prolong progression free survival (PFS) and offer a novel treatment strategy free from chemotherapy for patients with metastatic TNBC.

Methods: Patients with TNBC receiving initial therapy for metastatic disease were eligible for this multicenter phase II trial (NCT00733408) conducted at an academic center and affiliated, community practice sites. Induction therapy included nab-paclitaxel 100 mg/m2 IV Qweek (wk) and Bevacizumab 10 mg/kg IV Q2wks x 24 weeks. Patients free of progression at 24 wks began maintenance therapy with bevacizumab 10 mg/kg IV Q2wks and erlotinib 150 mg po daily until progression with radiographic assessment every 8 wks. Primary objective was PFS with secondary objectives of response rate, overall survival (OS) and safety. All eligible patients were included in the analysis of PFS and OS. Response was evaluated among patients with measurable disease by RECIST 1.1 with central review. Patients with inadequate disease assessments were coded as non-responders. Kaplan-Meier method was used to estimate PFS and OS with patients censored at date of last tumor assessment (PFS) or date of last follow up (OS).

Results: From April 2009 – December 2015, 58 patients (median age 54, range 33-83) were enrolled; 56 (97%) had measurable disease, and all had metastatic TNBC by local assessment. 33 (57%) patients completed induction; 22 (38%) came off study during induction; 3 (5%) continue on maintenance therapy. 4 patients discontinued therapy prior to first assessment. As of June 8, 2016, 53 patients (91%) have progressed. Median follow up for surviving patients is 14.5 months (range 4.1-65.4). Median PFS is 7.7 months (95% CI 5.7, 9.5). Of 56 patients with measurable disease, 38 (66%) had partial response (PR); 10 (17%) with stable disease for clinical benefit rate (CBR) of 86%. Median OS is 18.2 months (95% CI 16.3, 24.5). Most common grade 3-4 toxicities during induction were neutropenia [17 (29%), 1 grade 4], fatigue [13 (22%), all grade 3], leukopenia [7 (12%), all grade 3], and neuropathy [7 (12%), all grade 3]. Rash was most common ≥ grade 3 toxicity during maintenance [4 (7%), grade 3]. One patient experienced clinical CHF during maintenance month 16 requiring bevacizumab discontinuation. Conclusions: Nab-paclitaxel and bevacizumab followed by maintenance targeted therapy with bevacizumab and erlotinib was well tolerated. While the observed PFS did not meet pre-specified criteria of interest, the majority of patients experienced clinical benefit (86%) with 30 (57%) receiving maintenance targeted therapy. Correlative studies are ongoing. Supported by Genentech (OSI4266s), Celegene (AX-CL-BRST-PI-003828) and Janssen.

Citation Format: Specht JM, Gadi VK, Gralow JR, Korde LA, Linden HM, Salazar LG, Rodler ET, Cundy A, Buening BJ, Baker KK, Redman MW, Kurland BF, Garrison MA, Smith JC, vanHaelst C, Anderson JE. Combined targeted therapies for advanced triple negative breast cancer: A phase II trial of nab-paclitaxel and bevacizumab followed by maintenance targeted therapy with bevacizumab and erlotinib [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-22-11.

Zebrafish atoh8 mutants do not recapitulate morpholino phenotypes

Atoh8 is a bHLH transcription factor expressed in pancreas, skeletal muscle, the nervous system, and cardiovascular tissues during embryological development. Although it has been implicated in the regulation of pancreatic and endothelial cell differentiation, the phenotypic consequences of Atoh8 loss are uncertain. Conclusions from knockout studies in the mouse differ widely depending on the targeting strategy used, while atoh8 knockdown by interfering morpholino oligonucleotides (morpholinos) in zebrafish has led to a range of developmental defects. This study characterised zebrafish embryos homozygous for atoh8^sa1465, a loss-of-function allele of atoh8, in order to provide genetic evidence for the developmental role of Atoh8 in this species. Embryos homozygous for atoh8^sa1465 present normal body morphology, swimbladder inflation, and heart looping, and survive to adulthood. These embryos do not develop pericardial oedema by 72 hpf and are not sensitised to the loss of Fog1 protein, suggesting that this previously described abnormality is not a specific phenotype. Vascular patterning and primitive haematopoiesis are unaffected in atoh8^{sa1465/sa1465} mutant embryos. Together, the data suggest that Atoh8 is dispensible for zebrafish development under standard laboratory conditions.

Efficient Preparation of High-Complexity ChIP-Seq Profiles from Early Xenopus Embryos

Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) has become a powerful tool to acquire a precise and genome-wide snapshot of many chromatin features in vivo. These chromatin profiles are obtained by immunoprecipitation of cross-linked chromatin fragments to enrich the feature of interest. Sequencing and aligning the underlying DNA sequences to the genome make it possible to virtually reconstruct the global distribution of most chromatin features. We present here recent improvements to the ChIP-seq protocol by means of Xenopus embryos to prepare high-complexity DNA libraries from small amounts of biological material. This approach allows researchers to explore the landscape of chromatin regulators and states in early vertebrate embryos or in any biological entity with small numbers of cells.

Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq)

Next-generation sequencing has enabled the genome-wide identification of human DNA replication origins. However, different approaches to mapping replication origins, namely (i) sequencing isolated small nascent DNA strands (SNS-seq); (ii) sequencing replication bubbles (bubble-seq) and (iii) sequencing Okazaki fragments (OK-seq), show only limited concordance. To address this controversy, we describe here an independent high-resolution origin mapping technique that we call initiation site sequencing (ini-seq). In this approach, newly replicated DNA is directly labelled with digoxigenin-dUTP near the sites of its initiation in a cell-free system. The labelled DNA is then immunoprecipitated and genomic locations are determined by DNA sequencing. Using this technique we identify >25,000 discrete origin sites at sub-kilobase resolution on the human genome, with high concordance between biological replicates. Most activated origins identified by ini-seq are found at transcriptional start sites and contain G-quadruplex (G4) motifs. They tend to cluster in early-replicating domains, providing a correlation between early replication timing and local density of activated origins. Origins identified by ini-seq show highest concordance with sites identified by SNS-seq, followed by OK-seq and bubble-seq. Furthermore, germline origins identified by positive nucleotide distribution skew jumps overlap with origins identified by ini-seq and OK-seq more frequently and more specifically than do sites identified by either SNS-seq or bubble-seq.

The unconscious, myth, and the rule of law: Reflections on the persistence of gender inequality

Social order, to remain stable, needs the voluntary compliance of the majority of the population. Such consent requires normative justification. The rational foundation of the rule of law and the democratic state rests on the presumption of the equality of every citizen. Male domination of females nevertheless remains universal even in the most advanced democratic nation states because it is legitimized by the shared assumption that patriarchy reflects the will of God or is dictated by nature. Freud's diagnosis of patriarchy as a collective neurosis of the group mind negates every possible normative justification that can be made for gender hierarchy. Freud made extensive references to myth in developing his analysis of the neurotic foundations of social order. An analysis of the structure of myth suggests that ideological seduction rather than God, nature or biology determines male dominance.

Stress Symptoms One Year after 9/11/01: A Follow-up

This study investigated whether stress symptoms related to attention deficit previously found for a sample ( n = 149) of Chicago-area college students 1 to 5 weeks after the September 11th attacks were present in a comparable sample ( n = 129) 12 to 14 months later. As hypothesized, the later participants had a significantly lower mean score on the scale, Attention Deficit of the Smith Stress Symptoms Inventory, than a different group of participants tested immediately after the attacks. Mean Attention Deficit scores for groups after one year and immediately before September 11th ( n = 320) did not differ statistically. Findings are consistent with the interpretation that elevations in scores on Attention Deficit immediately after September 11th were indeed associated with the catastrophic attacks and not artifacts of time of examination. Consistent with previous research with this inventory, disaster-related traumatic stress scores are lower over time, although here no control group was included.

The Hubbard dimer: a density functional case study of a many-body problem

This review explains the relationship between density functional theory and strongly correlated models using the simplest possible example, the two-site Hubbard model. The relationship to traditional quantum chemistry is included. Even in this elementary example, where the exact ground-state energy and site occupations can be found analytically, there is much to be explained in terms of the underlying logic and aims of density functional theory. Although the usual solution is analytic, the density functional is given only implicitly. We overcome this difficulty using the Levy-Lieb construction to create a parametrization of the exact function with negligible errors. The symmetric case is most commonly studied, but we find a rich variation in behavior by including asymmetry, as strong correlation physics vies with charge-transfer effects. We explore the behavior of the gap and the many-body Green's function, demonstrating the 'failure' of the Kohn-Sham (KS) method to reproduce the fundamental gap. We perform benchmark calculations of the occupation and components of the KS potentials, the correlation kinetic energies, and the adiabatic connection. We test several approximate functionals (restricted and unrestricted Hartree-Fock and Bethe ansatz local density approximation) to show their successes and limitations. We also discuss and illustrate the concept of the derivative discontinuity. Useful appendices include analytic expressions for density functional energy components, several limits of the exact functional (weak- and strong-coupling, symmetric and asymmetric), various adiabatic connection results, proofs of exact conditions for this model, and the origin of the Hubbard model from a minimal basis model for stretched H2.