Epigenetic implications in maternal diabetes and metabolic syndrome-associated risk of orofacial clefts.

Orofacial clefts (OFCs) are one of the most common types of structural birth defects. The etiologies are complicated, involving with genetic, epigenetic, and environmental factors. Studies have found that maternal diabetes and metabolic syndrome are associated with a higher risk of OFCs in offspring. Metabolic syndrome is a clustering of several disease risk factors, including hyperglycemia, dyslipidemia, obesity, and hypertension. Metabolic disease during pregnancy can increase risk of adverse outcomes and significantly influence fetal development, including orofacial formation and fusion. An altered metabolic state may contribute to developmental disorders or congenital defects including OFCs, potentially through epigenetic modulations, such as histone modification, DNA methylation, and noncoding RNA expression to alter activities of critical morphogenetic signaling or related developmental genes. This review summarizes the currently available evidence and underlying mechanisms of how the maternal metabolic syndrome is associated with OFCs in mostly human and some animal studies. It may provide a better understanding of the interactions between intrauterine metabolic status and fetal orofacial development which might be applied toward prevention and treatments of OFCs.

Placental pathology in an unsuspected case of mucolipidosis type II with secondary hyperparathyroidism in a premature infant.

Mucolipidosis type II (MLII, MIM 252500) is a lysosomal storage disorders caused by defects in GNPTAB gene which encodes alpha and beta subunits of N-acetylglucosamine (GlcNAc)-1-phosphotransferase. Neonatal presentation includes coarse facial features, restricted postnatal growth, generalized hypotonia, gingival hypertrophy and multiple skeletal anomalies. Here we present a case of a 26-week gestational age preterm infant with MLII who did not exhibit the typical facial features at birth; however, the diagnosis was suggested from abnormal placental pathology showing trophoblastic lipidosis and initial skeletal abnormalities from chest radiograph revealing generalized diffuse severe bone demineralizing disease and multiple fractures. Biochemical testing revealed elevation of plasma lysosomal enzymes. Homozygous pathogenic variant, designated c.3505_3504del, was discovered from GNPTAB sequencing. Her course was complicated by respiratory distress, secondary hyperparathyroidism, abdominal distention and feeding difficulties. Urine mucopolysaccharides analysis revealed mild elevation of total and individual glycosaminoglycan species in a non-specific pattern. To our knowledge, our case is the most premature example of mucolipidosis type II that has ever been reported to date. This report highlights the importance of placental pathological studies in the diagnosis of lysosomal storage disorders.

Environmental mechanisms of orofacial clefts.

Orofacial clefts (OFCs) are among the most common birth defects and impart a significant burden on afflicted individuals and their families. It is increasingly understood that many nonsyndromic OFCs are a consequence of extrinsic factors, genetic susceptibilities, and interactions of the two. Therefore, understanding the environmental mechanisms of OFCs is important in the prevention of future cases. This review examines the molecular mechanisms associated with environmental factors that either protect against or increase the risk of OFCs. We focus on essential metabolic pathways, environmental signaling mechanisms, detoxification pathways, behavioral risk factors, and biological hazards that may disrupt orofacial development.

Role of epigenetics and miRNAs in orofacial clefts.

Orofacial clefts (OFCs) have multiple etiologies and likely result from an interplay between genetic and environmental factors. Within the last decade, studies have implicated specific epigenetic modifications and noncoding RNAs as additional facets of OFC etiology. Altered gene expression through DNA methylation and histone modification offer novel insights into how specific genes contribute to distinct OFC subtypes. Epigenetics research has also provided further evidence that cleft lip only (CLO) is a cleft subtype with distinct etiology. Polymorphisms or misexpression of genes encoding microRNAs, as well as their targets, contribute to OFC risk. The ability to experimentally manipulate epigenetic changes and noncoding RNAs in animal models, such as zebrafish, Xenopus, mice, and rats, has offered novel insights into the mechanisms of various OFC subtypes. Although much remains to be understood, recent advancements in our understanding of OFC etiology may advise future strategies of research and preventive care.

Cellular and developmental basis of orofacial clefts.

During craniofacial development, defective growth and fusion of the upper lip and/or palate can cause orofacial clefts (OFCs), which are among the most common structural birth defects in humans. The developmental basis of OFCs includes morphogenesis of the upper lip, primary palate, secondary palate, and other orofacial structures, each consisting of diverse cell types originating from all three germ layers: the ectoderm, mesoderm, and endoderm. Cranial neural crest cells and orofacial epithelial cells are two major cell types that interact with various cell lineages and play key roles in orofacial development. The cellular basis of OFCs involves defective execution in any one or several of the following processes: neural crest induction, epithelial-mesenchymal transition, migration, proliferation, differentiation, apoptosis, primary cilia formation and its signaling transduction, epithelial seam formation and disappearance, periderm formation and peeling, convergence and extrusion of palatal epithelial seam cells, cell adhesion, cytoskeleton dynamics, and extracellular matrix function. The latest cellular and developmental findings may provide a basis for better understanding of the underlying genetic, epigenetic, environmental, and molecular mechanisms of OFCs.

Genetics and signaling mechanisms of orofacial clefts.

Craniofacial development involves several complex tissue movements including several fusion processes to form the frontonasal and maxillary structures, including the upper lip and palate. Each of these movements are controlled by many different factors that are tightly regulated by several integral morphogenetic signaling pathways. Subject to both genetic and environmental influences, interruption at nearly any stage can disrupt lip, nasal, or palate fusion and result in a cleft. Here, we discuss many of the genetic risk factors that may contribute to the presentation of orofacial clefts in patients, and several of the key signaling pathways and underlying cellular mechanisms that control lip and palate formation, as identified primarily through investigating equivalent processes in animal models, are examined.

Aryl Hydrocarbon Receptor Mediates Larval Zebrafish Fin Duplication Following Exposure to Benzofluoranthenes.

The aryl hydrocarbon receptor (AHR) mediates developmental toxicity of several xenobiotic classes including polycyclic aromatic hydrocarbons. Using embryonic zebrafish, we previously identified 4 polycyclic aromatic hydrocarbons that caused a novel phenotype among AHR ligands-growth of a lateral, duplicate caudal fin fold. The window of sensitivity to the most potent inducer of this phenotype, benzo[k]fluoranthene (BkF), was prior to 36 h postfertilization (hpf), although the phenotype was not manifest until 60 hpf. AHR dependency via Ahr2 was demonstrated using morpholino knockdown. Hepatocyte ablation demonstrated that hepatic metabolism of BkF was not required for the phenotype, nor was it responsible for the window of sensitivity. RNA sequencing performed on caudal trunk tissue from BkF-exposed animals collected at 48, 60, 72, and 96 hpf showed upregulation of genes associated with AHR activation, appendage development, and tissue patterning. Genes encoding fibroblast growth factor and bone morphogenic protein ligands, along with retinaldehyde dehydrogenase, were prominently upregulated. Gene Ontology term analysis revealed that upregulated genes were enriched for mesoderm development and fin regeneration, whereas downregulated genes were enriched for Wnt signaling and neuronal development. MetaCore (Clarivate Analytics) systems analysis of orthologous human genes predicted that R-SMADs, AP-1, and LEF1 regulated the expression of an enriched number of gene targets across all time points. Our results demonstrate a novel aspect of AHR activity with implications for developmental processes conserved across vertebrate species.

Non-neural surface ectodermal rosette formation and F-actin dynamics drive mammalian neural tube closure.

The mechanisms underlying mammalian neural tube closure remain poorly understood. We report a unique cellular process involving multicellular rosette formation, convergent cellular protrusions, and F-actin cable network of the non-neural surface ectodermal cells encircling the closure site of the posterior neuropore, which are demonstrated by scanning electron microscopy and genetic fate mapping analyses during mouse spinal neurulation. These unique cellular structures are severely disrupted in the surface ectodermal transcription factor Grhl3 mutants that exhibit fully penetrant spina bifida. We propose a novel model of mammalian neural tube closure driven by surface ectodermal dynamics, which is computationally visualized.

Glucocorticoid receptor-dependent induction of cripto-1 (one-eyed pinhead) inhibits zebrafish caudal fin regeneration.

We previously used a chemical genetics approach with the larval zebrafish to identify small molecule inhibitors of tissue regeneration. This led to the discovery that glucocorticoids (GC) block early stages of tissue regeneration by the inappropriate activation of the glucocorticoid receptor (GR). We performed a microarray analysis to identify the changes in gene expression associated with beclomethasone dipropionate (BDP) exposure during epimorphic fin regeneration. Oncofetal cripto-1 showed > eight-fold increased expression in BDP-treated regenerates. We hypothesized that the mis-expression of cripto-1 was essential for BDP to block regeneration. Expression of cripto-1 was not elevated in GR morphants in the presence of BDP indicating that cripto-1 induction was GR-dependent. Partial translational suppression of Cripto-1 in the presence of BDP restored tissue regeneration. Retinoic acid exposure prevented increased cripto-1 expression and permitted regeneration in the presence of BDP. We demonstrated that BDP exposure increased cripto-1 expression in mouse embryonic stem cells and that regulation of cripto-1 by GCs is conserved in mammals.

Copper release and transformation following natural weathering of nano-enabled pressure-treated lumber.

Commercially available lumber, pressure-treated with micronized copper azole (MCA), has largely replaced other inorganic biocides for residential wood treatment in the USA, yet little is known about how different outdoor environmental conditions impact the release of ionic, nano-scale, or larger (micron-scale) copper from this product. Therefore, we weathered pressure treated lumber for 18 months in five different climates across the continental United States. Copper release was quantified every month and local weather conditions were recorded continuously to determine the extent to which local climate regulated the release of copper from this nano-enabled product during its use phase. Two distinct release trends were observed: In cooler, wetter climates release occurred primarily during the first few months of weathering, as the result of copper leaching from surface/near-surface areas. In warmer, drier climates, less copper was initially released due to limited precipitation. However, as the wood dried and cracked, the exposed copper-bearing surface area increased, leading to increased copper release later in the product lifetime. Single-particle-ICP-MS results from laboratory prepared MCA-wood leachate solutions indicated that a) the predominant form of released copper passed through a filter smaller than 0.45 micrometers and b) released particles were largely resistant to dissolution over the course of 6 wks. Toxicity Characteristic Leaching Procedure (TCLP) testing was conducted on nonweathered and weathered MCA-wood samples to simulate landfill conditions during their end-of-life (EoL) phase and revealed that MCA wood released <10% of initially embedded copper. Findings from this study provide data necessary to complete a more comprehensive evaluation of the environmental and human health impacts introduced through release of copper from pressure treated lumber utilizing life cycle assessment (LCA).

Establishing structure-property-hazard relationships for multi-walled carbon nanotubes: the role of aggregation, surface charge, and oxidative stress on embryonic zebrafish mortality.

Increasing use of carbon nanotubes (CNTs) in consumer and industrials goods increases their potential release, and subsequent risks to environmental and human health. Therefore, it is becoming ever more important that CNTs are designed to reduce or eliminate hazards and that hazard assessment methodologies are robust. Here, oxygen-functionalized multi-walled CNTs (O-MWCNTs), modified under varying redox conditions, were assessed for toxic potential using the zebrafish (Danio rerio) embryo model. Multiple physicochemical properties (e.g., MWCNT aggregate size, morphology, and rate; surface charge and oxygen concentration; and reactive oxygen species (ROS) generation) were characterized and related to zebrafish embryo mortality through the use of multivariate statistical methods. Of these properties, surface charge and aggregate morphology emerged as the greatest predictors of embryo mortality. Interestingly, ROS generation was not significantly correlated to observed mortality, contrary to prior predictions by nanotoxicology researchers. This suggests that the mechanism of MWCNT-induced mortality of embryonic zebrafish is physical, driven by electrostatic and shape effects, both of which are related to nanomaterial aggregation. This raises the importance of rigorously considering aggregation during aqueous-based nanotoxicology assays as nanomaterial aggregation can affect perceived nanomaterial toxicity. As such, future nanotoxicity studies relying on aqueous media must sufficiently consider nanomaterial aggregation.

Aberrant Promoter Hypomethylation in CLL: Does It Matter for Disease Development?

Over the last 30 years, studies of aberrant DNA methylation in hematologic malignancies have been dominated by the primary focus of understanding promoter hypermethylation. These efforts not only resulted in a better understanding of the basis of epigenetic silencing of tumor suppressor genes but also resulted in approval of hypomethylating agents for the treatment of several malignancies, such as myelodysplastic syndrome and acute myeloid leukemia. Recent advances in global methylation profiling coupled with the use of mouse models suggest that aberrant promoter hypomethylation is also a frequent event in hematologic malignancies, particularly in chronic lymphocytic leukemia (CLL). Promoter hypomethylation affects gene expression and, therefore, may play an important role in disease pathogenesis. Here, we review recent findings and discuss the potential involvement of aberrant promoter hypomethylation in CLL.

The proteomic response of cheliped myofibril tissue in the eurythermal porcelain crab Petrolisthes cinctipes to heat shock following acclimation to daily temperature fluctuations.

The porcelain crab Petrolisthes cinctipes lives under rocks and in mussel beds in the mid-intertidal zone where it experiences immersion during high tide and saturating humid conditions in air during low tide, which can increase habitat temperature by up to 20°C. To identify the biochemical changes affected by increasing temperature fluctuations and subsequent heat shock, we acclimated P. cinctipes for 30 days to one of three temperature regimes: (1) constant 10°C, (2) daily temperature fluctuations between 10 and 20°C (5 h up-ramp to 20°C, 1 h down-ramp to 10°C) and (3) 10-30°C (up-ramp to 30°C). After acclimation, animals were exposed to either 10°C or a 30°C heat shock to analyze the proteomic changes in claw muscle tissue. Following acclimation to 10-30°C (measured at 10°C), enolase and ATP synthase increased in abundance. Following heat shock, isoforms of arginine kinase and glycolytic enzymes such as aldolase, triose phosphate isomerase and glyceraldehyde 3-phosphate dehydrogenase increased across all acclimation regimes. Full-length isoforms of hemocyanin increased abundance following acclimation to 10-30°C, but hemocyanin fragments increased after heat shock following constant 10°C and fluctuating 10-20°C, possibly playing a role as antimicrobial peptides. Following constant 10°C and fluctuating 10-20°C, paramyosin and myosin heavy chain type-B increased in abundance, respectively, whereas myosin light and heavy chain decreased with heat shock. Actin-binding proteins, which stabilize actin filaments (filamin and tropomyosin), increased during heat shock following 10-30°C; however, actin severing and depolymerization proteins (gelsolin and cofilin) increased during heat shock following 10-20°C, possibly promoting muscle fiber restructuring. RAF kinase inhibitor protein and prostaglandin reductase increased during heat shock following constant 10°C and fluctuating 10-20°C, possibly inhibiting an immune response during heat shock. The results suggest that ATP supply, muscle fiber restructuring and immune responses are all affected by temperature fluctuations and subsequent acute heat shock in muscle tissue. Furthermore, although heat shock after acclimation to constant 10°C and fluctuating 10-30°C showed the greatest effects on the proteome, moderately fluctuating temperatures (10-20°C) broadened the temperature range over which claw muscle was able to respond to an acute heat shock with limited changes in the muscle proteome.

Diphosphanes derived from phobane and phosphatrioxa-adamantane: similarities, differences and anomalies.

The homodiphosphanes CgP-PCg (1) and PhobP-PPhob (2) and the heterodiphosphanes CgP-PPhob (3), CgP-PPh(2) (4a), CgP-P(o-Tol)(2) (4b), CgP-PCy(2) (4c), CgP-P(t)Bu(2) (4d), PhobP-PPh(2) (5a), PhobP-P(o-Tol)(2) (5b), PhobP-PCy(2) (5c), PhobP-P(t)Bu(2) (5d) where CgP = 6-phospha-2,4,8-trioxa-1,3,5,7-tetramethyladamant-9-yl and PhobP = 9-phosphabicyclo[3.3.1]nonan-9-yl have been prepared from CgP(BH(3))Li or PhobP(BH(3))Li and the appropriate halophosphine. The formation of 1 is remarkably diastereoselective, with the major isomer (97% of the product) assigned to rac-1. Restricted rotation about the P-P bond of the bulky meso-1 is detected by variable temperature (31)P NMR spectroscopy. Diphosphane 3 reacts with BH(3) to give a mixture of CgP(BH(3))-PPhob and CgP-PPhob(BH(3)) which was unexpected in view of the predicted much greater electron-richness of the PhobP site. Each of the diphosphanes was treated with dimethylacetylene dicarboxylate (DMAD) in order to determine their propensity for diphosphination. The homodiphosphanes 1 and 2 did not react with DMAD. The CgP-containing heterodiphosphanes 4a-d all added to DMAD to generate the corresponding cis alkenes CgPCH(CO(2)Me)=CH(CO(2)Me)PR(2) (6a-d) which have been used in situ to form chelate complexes of the type [MCl(2)(diphos)] (7a-d) where M = Pd or Pt. The PhobP-containing heterodiphosphanes 3 and 5a-d react anomalously with DMAD and do not give the products of diphosphination. The X-ray crystal structures of the diphosphanes 2, 3, 4a, and 5a, the monoxide and dioxide of diphosphane 1, and the platinum chelate complex 7c have been determined and their structures are discussed.

On the visualization of social and other scale-free networks.

This paper proposes novel methods for visualizing specifically the large power-law graphs that arise in sociology and the sciences. In such cases a large portion of edges can be shown to be less important and removed while preserving component connectedness and other features (e.g. cliques) to more clearly reveal the network's underlying connection pathways. This simplification approach deterministically filters (instead of clustering) the graph to retain important node and edge semantics, and works both automatically and interactively. The improved graph filtering and layout is combined with a novel computer graphics anisotropic shading of the dense crisscrossing array of edges to yield a full social network and scale-free graph visualization system. Both quantitative analysis and visual results demonstrate the effectiveness of this approach.

Immunization of nonautoimmune mice with DNA binding domains of the largest subunit of RNA polymerase I results in production of anti-dsDNA and anti-Sm/RNP antibodies.

Antibodies against the N-terminal (NT) but not the basic domain (BD), DNA binding regions of the largest subunit (S1) of RNA polymerase I (RNAPI) were detected in the sera of MRL-lpr/lpr lupus mice. Antibodies against both RNAPI(S1)-NT and -BD, as well as other systemic lupus erythematosus (SLE) autoantigens (La, ribosomal P proteins and Sm/RNP) were produced by rabbits immunized with anti-DNA antibodies that had been affinity purified from SLE patients. Immunization of nonautoimmune mice (Balb/c) with RNAPI(S1)-NT, RNAPI(S1)-BD, or La in the form of GST fusion proteins, induced production of anti-double-stranded (ds) DNA and anti-Sm/RNP. GST-P1 did not induce an anti-dsDNA response in these mice. These results demonstrate that RNAPI(S1)-NT, RNAPI(S1)-BD and La can participate in an anti-autoantigen/anti-DNA antibody loop during an SLE-like autoimmune response.

Visual exploration of complex time-varying graphs.

Many graph drawing and visualization algorithms, such as force-directed layout and line-dot rendering, work very well on relatively small and sparse graphs. However, they often produce extremely tangled results and exhibit impractical running times for highly non-planar graphs with large edge density. And very few graph layout algorithms support dynamic time-varying graphs; applying them independently to each frame produces distracting temporally incoherent visualizations. We have developed a new visualization technique based on a novel approach to hierarchically structuring dense graphs via stratification. Using this structure, we formulate a hierarchical force-directed layout algorithm that is both efficient and produces quality graph layouts. The stratification of the graph also allows us to present views of the data that abstract away many small details of its structure. Rather than displaying all edges and nodes at once, resulting in a convoluted rendering, we present an interactive tool that filters edges and nodes using the graph hierarchy and allows users to drill down into the graph for details. Our layout algorithm also accommodates time-varying graphs in a natural way, producing a temporally coherent animation that can be used to analyze and extract trends from dynamic graph data. For example, we demonstrate the use of our method to explore financial correlation data for the U.S. stock market in the period from 1990 to 2005. The user can easily analyze the time-varying correlation graph of the market, uncovering information such as market sector trends, representative stocks for portfolio construction, and the interrelationship of stocks over time.

Interactive point-based rendering of higher-order tetrahedral data.

Computational simulations frequently generate solutions defined over very large tetrahedral volume meshes containing many millions of elements. Furthermore, such solutions may often be expressed using non-linear basis functions. Certain solution techniques, such as discontinuous Galerkin methods, may even produce non-conforming meshes. Such data is difficult to visualize interactively, as it is far too large to fit in memory and many common data reduction techniques, such as mesh simplification, cannot be applied to non-conforming meshes. We introduce a point-based visualization system for interactive rendering of large, potentially non-conforming, tetrahedral meshes. We propose methods for adaptively sampling points from non-linear solution data and for decimating points at run time to fit GPU memory limits. Because these are streaming processes, memory consumption is independent of the input size. We also present an order-independent point rendering method that can efficiently render volumes on the order of 20 million tetrahedra at interactive rates.