Characterization of Ag-Ion Releasing Zeolite Filled 3D Printed Resins

There has been profound growth in the use of 3D printed materials in dentistry in general, including orthodontics. The opportunity to impart antimicrobial properties to 3D printed parts from existing resins requires the capability of forming a stable colloid incorporating antimicrobial fillers. The objective of this research was to characterize a colloid consisting of a 3D printable resin mixed with Ag-ion releasing zeolites and fumed silica to create 3D printed parts with antiviral properties. The final composite was tested for antiviral properties against SARS-CoV-2 and HIV-1. Antiviral activity was measured in terms of the half-life of SARS-CoV-2 and HIV-1 on the composite surface. The inclusion of the zeolite did not interfere with the kinetics measured on the surface of the ATR crystal. While the depth of cure, measured following ISO4049 guidelines, was reduced from 3.8 mm to 1.4 mm in 5 s, this greatly exceeded the resolution required for 3D printing. The colloid was stable for at least 6 months and the rheological behavior was dependent upon the fumed silica loading. The inclusion of zeolites and fumed silica significantly increased the flexural strength of the composite as measured by a 3 point bend test. The composite released approximately 2500 μg/L of silver ion per gram of composite as determined by potentiometry. There was a significant reduction of the average half-life of SARS-CoV-2 (1.9 fold) and HIV-1 (2.7 fold) on the surface of the composite. The inclusion of Ag-ion releasing zeolites into 3D-printable resin can result in stable colloids that generate composites with improved mechanical properties and antiviral properties.

Messenger RNA capture sequencing of extracellular RNA from human biofluids using a comprehensive set of spike-in controls

Comprehensive transcriptome analysis of extracellular RNA (exRNA) purified from human biofluids is challenging because of the low RNA concentration and compromised RNA integrity. Here, we describe an optimized workflow to (1) isolate exRNA from different types of biofluids and (2) to prepare messenger RNA (mRNA)-enriched sequencing libraries using complementary hybridization probes. Importantly, the workflow includes 2 sets of synthetic spike-in RNA molecules as processing controls for RNA purification and sequencing library preparation and as an alternative data normalization strategy.

For complete details on the use and execution of this protocol, please refer to Hulstaert et al. (2020).

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Extracellular RNA from biofluids has a low concentration and a compromised integrity

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An optimized workflow for mRNA capture sequencing of human biofluids is provided

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Synthetic spike-in RNA molecules serve as processing controls

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Spike-in RNAs allow for data normalization and calculation of mRNA concentration

2018 Ebola virus disease outbreak in Équateur Province, Democratic Republic of the Congo: a retrospective genomic characterisation

BACKGROUND

The 2018 Ebola virus disease (EVD) outbreak in Équateur Province, Democratic Republic of the Congo, began on May 8, and was declared over on July 24; it resulted in 54 documented cases and 33 deaths. We did a retrospective genomic characterisation of the outbreak and assessed potential therapeutic agents and vaccine (medical countermeasures).

METHODS

We used target-enrichment sequencing to produce Ebola virus genomes from samples obtained in the 2018 Équateur Province outbreak. Combining these genomes with genomes associated with known outbreaks from GenBank, we constructed a maximum-likelihood phylogenetic tree. In-silico analyses were used to assess potential mismatches between the outbreak strain and the probes and primers of diagnostic assays and the antigenic sites of the experimental rVSVΔG-ZEBOV-GP vaccine and therapeutics. An in-vitro flow cytometry assay was used to assess the binding capability of the individual components of the monoclonal antibody cocktail ZMapp.

FINDINGS

A targeted sequencing approach produced 16 near-complete genomes. Phylogenetic analysis of these genomes and 1011 genomes from GenBank revealed a distinct cluster, confirming a new Ebola virus variant, for which we propose the name "Tumba". This new variant appears to have evolved at a slower rate than other Ebola virus variants (0·69 × 10^-3 substitutions per site per year with "Tumba" vs 1·06 × 10^-3 substitutions per site per year without "Tumba"). We found few sequence mismatches in the assessed assay target regions and antigenic sites. We identified nine amino acid changes in the Ebola virus surface glycoprotein, of which one resulted in reduced binding of the 13C6 antibody within the ZMapp cocktail.

INTERPRETATION

Retrospectively, we show the feasibility of using genomics to rapidly characterise a new Ebola virus variant within the timeframe of an outbreak. Phylogenetic analysis provides further indications that these variants are evolving at differing rates. Rapid in-silico analyses can direct in-vitro experiments to quickly assess medical countermeasures.

FUNDING

Defense Biological Product Assurance Office.

Medical countermeasures during the 2018 Ebola virus disease outbreak in the North Kivu and Ituri Provinces of the Democratic Republic of the Congo: a rapid genomic assessment

BACKGROUND

The real-time generation of information about pathogen genomes has become a vital goal for transmission analysis and characterisation in rapid outbreak responses. In response to the recently established genomic capacity in the Democratic Republic of the Congo, we explored the real-time generation of genomic information at the start of the 2018 Ebola virus disease (EVD) outbreak in North Kivu Province.

METHODS

We used targeted-enrichment sequencing to produce two coding-complete Ebola virus genomes 5 days after declaration of the EVD outbreak in North Kivu. Subsequent sequencing efforts yielded an additional 46 genomes. Genomic information was used to assess early transmission, medical countermeasures, and evolution of Ebola virus.

FINDINGS

The genomic information demonstrated that the EVD outbreak in the North Kivu and Ituri Provinces was distinct from the 2018 EVD outbreak in Équateur Province of the Democratic Republic of the Congo. Primer and probe mismatches to Ebola virus were identified in silico for all deployed diagnostic PCR assays, with the exception of the Cepheid GeneXpert GP assay.

INTERPRETATION

The first two coding-complete genomes provided actionable information in real-time for the deployment of the rVSVΔG-ZEBOV-GP Ebola virus envelope glycoprotein vaccine, available therapeutics, and sequence-based diagnostic assays. Based on the mutations identified in the Ebola virus surface glycoprotein (GP₁₂) observed in all 48 genomes, deployed monoclonal antibody therapeutics (mAb114 and ZMapp) should be efficacious against the circulating Ebola virus variant. Rapid Ebola virus genomic characterisation should be included in routine EVD outbreak response procedures to ascertain efficacy of medical countermeasures.

FUNDING

Defense Biological Product Assurance Office.

Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave

Background

Crassulacean acid metabolism (CAM) enhances plant water-use efficiency through an inverse day/night pattern of stomatal closure/opening that facilitates nocturnal CO₂ uptake. CAM has evolved independently in over 35 plant lineages, accounting for ~ 6% of all higher plants. Agave species are highly heat- and drought-tolerant, and have been domesticated as model CAM crops for beverage, fiber, and biofuel production in semi-arid and arid regions. However, the genomic basis of evolutionary innovation of CAM in genus Agave is largely unknown.

Results

Using an approach that integrated genomics, gene co-expression networks, comparative genomics and protein structure analyses, we investigated the molecular evolution of CAM as exemplified in Agave. Comparative genomics analyses among C₃, C₄ and CAM species revealed that core metabolic components required for CAM have ancient genomic origins traceable to non-vascular plants while regulatory proteins required for diel re-programming of metabolism have a more recent origin shared among C₃, C₄ and CAM species. We showed that accelerated evolution of key functional domains in proteins responsible for primary metabolism and signaling, together with a diel re-programming of the transcription of genes involved in carbon fixation, carbohydrate processing, redox homeostasis, and circadian control is required for the evolution of CAM in Agave. Furthermore, we highlighted the potential candidates contributing to the adaptation of CAM functional modules.

Conclusions

This work provides evidence of adaptive evolution of CAM related pathways. We showed that the core metabolic components required for CAM are shared by non-vascular plants, but regulatory proteins involved in re-reprogramming of carbon fixation and metabolite transportation appeared more recently. We propose that the accelerated evolution of key proteins together with a diel re-programming of gene expression were required for CAM evolution from C₃ ancestors in Agave.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4964-7) contains supplementary material, which is available to authorized users.

Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing

Next generation sequencing (NGS) technologies have revolutionized the genomics field and are becoming more commonplace for identification of human infectious diseases. However, due to the low abundance of viral nucleic acids (NAs) in relation to host, viral identification using direct NGS technologies often lacks sufficient sensitivity. Here, we describe an approach based on two complementary enrichment strategies that significantly improves the sensitivity of NGS-based virus identification. To start, we developed two sets of DNA probes to enrich virus NAs associated with respiratory diseases. The first set of probes spans the genomes, allowing for identification of known viruses and full genome sequencing, while the second set targets regions conserved among viral families or genera, providing the ability to detect both known and potentially novel members of those virus groups. Efficiency of enrichment was assessed by NGS testing reference virus and clinical samples with known infection. We show significant improvement in viral identification using enriched NGS compared to unenriched NGS. Without enrichment, we observed an average of 0.3% targeted viral reads per sample. However, after enrichment, 50%–99% of the reads per sample were the targeted viral reads for both the reference isolates and clinical specimens using both probe sets. Importantly, dramatic improvements on genome coverage were also observed following virus-specific probe enrichment. The methods described here provide improved sensitivity for virus identification by NGS, allowing for a more comprehensive analysis of disease etiology.

Ion release and in vitro enamel fluoride uptake associated with pit and fissure sealants containing microencapsulated remineralizing agents

PURPOSE

To determine if pit-and-fissure sealants with microencapsulated remineralizing agents with sustained release of fluoride, calcium and phosphate ions could promote enamel fluoride uptake by demineralized tooth structure.

METHODS

Sealants that contained 5 w/w% microcapsules with aqueous solutions of 5M Ca(NO3)2 or 0.8M NaF or 6.0M K2HPO4 or a mixture of all three were prepared. Ion release profiles were measured as a function of time. Enamel fluoride uptake by demineralized tooth structure was determined.

RESULTS

Sustained release of fluoride, calcium and phosphate ions from a sealant was demonstrated. Fluoride uptake by demineralized enamel was significantly increased compared to a control sealant manufactured without microcapsules (P< 0.01). Bovine enamel that contained 2.2±2.1 µg F/g of enamel prior to exposure to a sealant without microcapsules had 2.3±0.5 after 90 days. Enamel exposed to sealant with 5w/% NaF microcapsules went from 3.5±3.5 µg F/g of enamel prior to exposure to 148±76 after 90 days. Enamel exposed to sealant with 2 w/w% NaF, 2 w/w% Ca(NO3)2 and 1 w/w% K2HPO4 microcapsules went from 1.7±0.7 µg F/g of enamel prior to exposure to 190±137 after 90 days.

CLINICAL SIGNIFICANCE

Sealants with encapsulated remineralizing agents were capable of releasing biologically available fluoride, calcium, and phosphate ions. Incorporation of these microcapsules in pit and fissure sealants is a promising method for remineralization determined by enamel fluoride uptake measurements.

Complete genome sequence of a KI polyomavirus isolated from an otherwise healthy child with severe lower respiratory tract infection

Unbiased, deep sequencing of a nasal specimen from an otherwise healthy 13-month-old boy hospitalized in intensive care revealed high gene expression and the complete genome of a novel isolate of KI polyomavirus (KIPyV). Further investigation detected minimal gene expression of additional viruses, suggesting that KIPyV was potentially the causal agent. Analysis of the complete genome of isolate NMKI001 revealed it is different from all previously reported genomes and contains two amino acid differences as compared to the closest virus isolate, Stockholm 380 (EF127908). J. Med. Virol. 89:926-930, 2017. © 2016 Wiley Periodicals, Inc.

Abstract LB-329: Enhancing the resolution and accelerating the pace of translational fusion characterization in oncology by RNA sequencing

Chromosomal rearrangements are common markers of cancer progression across a wide range of cancer types, and therefore, identification of fusion transcripts in cancer biopsies may have potential to provide tumor-specific insight toward diagnosis, prognosis and precision treatment. Currently, routine methods for fusion detection using fluorescent in-situ hybridization (FISH) provide a low-resolution view of the aberrant fusion transcript. We describe an RNA-Seq approach designed to survey cancer fusions in a single assay by selectively enriching the cancer transcriptome using probes that target the coding regions of over 1385 cancer-associated genes.

We tested the performance of the 1385 gene, RNA-Seq Pan-Cancer panel on RNA extracted from 47 patient-derived samples from brain, sarcoma and leukemia, including blood, bone marrow, and formalin-fixed paraffin-embedded (FFPE) samples. Each sample harbored at least one orthogonally verified gene fusion transcript, previously confirmed by FISH or Reverse Transcriptase PCR (RT-PCR). RNA-Seq libraries were prepared from 10-100 ng of total RNA from blood or bone marrow and 20-200 ng total RNA from FFPE tissue and subsequently enriched by hybridization to the Pan-Cancer panel. All samples yielded sufficient library and were sequenced with 76 base-pair paired-end reads on an Illumina MiSeq at 8 samples per flow cell (∼3 million reads per sample). Sequencing data was analyzed using RNA-Seq with STAR aligner and Manta fusion caller. Using this capture-based single-assay approach, we successfully detected fusions commonly associated with leukemia (BCR-ABL1, MLL-MLLT3, MLL-AFF1, RUNX1-ETV6, EBF1-PDGFRB, TCF3-PBX1, IKZF1-PAX5), sarcoma (EWSR1-ATF1, EWSR1-FLI1, JAZF1-SUZ12, SS18-SSX, FUS-DDIT3, FUS-KLF17, YWHAE-FAM22B) and brain cancer (KIAA1459-BRAF) consistent with previously confirmed RT-PCR or FISH results. Several examples of previously unknown fusion partners or additional structural information that were not identified from the FISH or RT-PCR testing were also uncovered in this study. These cases are described in detail.

In summary, we show that selective enrichment of RNA-Seq libraries with cancer-specific probes enables detection of known and novel fusions across a broad range of cancer pathologies in a single reaction, creating new opportunities for discovery and translational cancer studies.

Citation Format: Lisa C. Watson, Stephen M. Gross, Felix Schlesinger, Anthony Mai, Mariko Kellogg, Steve Lee, Claire Attwooll, Monica Brenca, David Swanson, Andrew Wong, Angelo P. Dei Tos, Claudia Haferlach, Torsten Haferlach, Wolfgang Kern, Roberta Maestro, Manja Meggendorfer, Niroshan Nadarajah, Maurizio Polano, Sabrina Rossi, Marta Sbaraglia, George S. Charames, Gary P. Schroth, Grace DeSantis. Enhancing the resolution and accelerating the pace of translational fusion characterization in oncology by RNA sequencing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-329.

Molecular Evidence of Sexual Transmission of Ebola Virus

A suspected case of sexual transmission from a male survivor of Ebola virus disease (EVD) to his female partner (the patient in this report) occurred in Liberia in March 2015. Ebola virus (EBOV) genomes assembled from blood samples from the patient and a semen sample from the survivor were consistent with direct transmission. The genomes shared three substitutions that were absent from all other Western African EBOV sequences and that were distinct from the last documented transmission chain in Liberia before this case. Combined with epidemiologic data, the genomic analysis provides evidence of sexual transmission of EBOV and evidence of the persistence of infective EBOV in semen for 179 days or more after the onset of EVD. (Funded by the Defense Threat Reduction Agency and others.).

Abstract 4884: Highly sensitive fusion transcript detection and quantification in cancer

Gene fusion detection in cancer samples can provide tumor-specific information for cancer research, clinical diagnosis and targeted treatment. Common fusion detection methods such as qPCR and FISH are restricted to known fusion junctions and limited in the number of genes that can be detected in parallel. In contrast, RNA sequencing is a powerful approach for simultaneous discovery of all possible fusion junctions in a single reaction. But, the sequencing depth required for sensitive detection of fusions from whole-transcriptome libraries can be cost-prohibitive. Here we describe a cancer-specific capture-based approach for fusion detection by RNA sequencing that requires only a fraction of the sequencing depth of whole-transcriptome methods. We designed oligo probes that densely target coding regions of over 200 clinically relevant gene fusions and cancer-associated genes. This oligo panel was used to capture cancer-specific fusions from total RNA-Seq libraries. We used commonly studied cancer cell lines including MCF-7, K562, PC-3, LnCAP, A431 and Universal Human Reference RNA (UHRR) to compare the sensitivity of fusion detection across three RNA-Seq library prep methods: (1) cancer panel library capture (2) whole-transcriptome library capture and (3) PolyA selection. We show that probes targeting individual exons can robustly capture well-characterized cancer gene fusions such as BCR-ABL and BCAS4-BCAS3, as well as translocations where fusion junctions are unknown. Furthermore, these comparisons demonstrate the enhanced sequencing efficiency of the targeted cancer panel, while maintaining highly accurate quantitation of gene expression. We show that selective enrichment of RNA-Seq libraries with cancer-specific capture probes enables high-resolution mapping of genomic rearrangements in patient cancer samples, even those derived from FFPE, facilitating sequencing studies that were not previously possible.

Citation Format: Lisa C. Watson, Stephen M. Gross, Irina Khrevtukova, Smita Pathak, Claire Attwooll, Jason Goode, Anthony Mai, Gary P. Schroth. Highly sensitive fusion transcript detection and quantification in cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4884. doi:10.1158/1538-7445.AM2015-4884

A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing

RNA-sequencing (RNA-seq) enables in-depth exploration of transcriptomes, but typical sequencing depth often limits its comprehensiveness. In this study, we generated nearly 3 billion RNA-Seq reads, totaling 341 Gb of sequence, from a Zea mays seedling sample. At this depth, a near complete snapshot of the transcriptome was observed consisting of over 90% of the annotated transcripts, including lowly expressed transcription factors. A novel hybrid strategy combining de novo and reference-based assemblies yielded a transcriptome consisting of 126,708 transcripts with 88% of expressed known genes assembled to full-length. We improved current annotations by adding 4,842 previously unannotated transcript variants and many new features, including 212 maize transcripts, 201 genes, 10 genes with undocumented potential roles in seedlings as well as maize lineage specific gene fusion events. We demonstrated the power of deep sequencing for large transcriptome studies by generating a high quality transcriptome, which provides a rich resource for the research community.

De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana

BACKGROUND

Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis), and existing technologies for ethanol production, agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits.

RESULTS

Here, we present comprehensive, high quality de novo transcriptome assemblies of two Agave species, A. tequilana and A. deserti, built from short-read RNA-seq data. Our analyses support completeness and accuracy of the de novo transcriptome assemblies, with each species having a minimum of approximately 35,000 protein-coding genes. Comparison of agave proteomes to those of additional plant species identifies biological functions of gene families displaying sequence divergence in agave species. Additionally, a focus on the transcriptomics of the A. deserti juvenile leaf confirms evolutionary conservation of monocotyledonous leaf physiology and development along the proximal-distal axis.

CONCLUSIONS

Our work presents a comprehensive transcriptome resource for two Agave species and provides insight into their biology and physiology. These resources are a foundation for further investigation of agave biology and their improvement for bioenergy development.

The control of phosphate ion release from ion permeable microcapsules formulated into rosin varnish and resin glaze

OBJECTIVES

The occurrence of recurrent caries at the interface of dental materials and the enamel surface is an important performance issue. The objective of this study was to investigate the most effective way to control the release rate of bioavailable phosphate ions contained in aqueous solutions within ion permeable microcapsules formulated into rosin based varnishes and resin based sealants, in order to promote remineralization.

METHODS

Microcapsules that contained aqueous solutions of K2HPO4 with concentrations from 0.8 to 7.4M were prepared. 3-50w/w% of microcapsules were loaded into both rosin and resin based dental formulations.

RESULTS

The effect of initial salt solution concentration inside the microcapsules and weight percent loading of the microcapsules on release rate were contrasted. The effect of microcapsule loading was found to be highly dependent on the continuous phase. In rosin, 3-15w/w% loading resulted in rapid release of ions. Higher weight percent loadings were initially slower but resulted in sustained release of ions. In resin, 3-15w/w% formulations slowly released ions for at least 300 days, while higher loading formulations released an initial burst of ions. Initial salt solution concentration contained inside the microcapsule affected ion release rate. Initial rate of ion release was greatest at a concentration that was less than the maximum concentration studied in both continuous phases.

SIGNIFICANCE

Phosphate ion release can be controlled from resin or rosin based dental material by adjusting initial salt solution concentration in microcapsules or percent loading of microcapsules. The potential for burst release from a varnish or slow, sustained release from a sealant has been demonstrated.

Maize RNA polymerase IV defines trans-generational epigenetic variation

The maize (Zea mays) RNA Polymerase IV (Pol IV) largest subunit, RNA Polymerase D1 (RPD1 or NRPD1), is required for facilitating paramutations, restricting expression patterns of genes required for normal development, and generating small interfering RNA (siRNAs). Despite this expanded role for maize Pol IV relative to Arabidopsis thaliana, neither the general characteristics of Pol IV-regulated haplotypes, nor their prevalence, are known. Here, we show that specific haplotypes of the purple plant1 locus, encoding an anthocyanin pigment regulator, acquire and retain an expanded expression domain following transmission from siRNA biogenesis mutants. This conditioned expression pattern is progressively enhanced over generations in Pol IV mutants and then remains heritable after restoration of Pol IV function. This unusual genetic behavior is associated with promoter-proximal transposon fragments but is independent of sequences required for paramutation. These results indicate that trans-generational Pol IV action defines the expression patterns of haplotypes using co-opted transposon-derived sequences as regulatory elements. Our results provide a molecular framework for the concept that induced changes to the heterochromatic component of the genome are coincident with heritable changes in gene regulation. Alterations of this Pol IV-based regulatory system can generate potentially desirable and adaptive traits for selection to act upon.

Tm1: a mutator/foldback transposable element family in root-knot nematodes

Three closely related parthenogenetic species of root-knot nematodes, collectively termed the Meloidogyne incognita-group, are economically significant pathogens of diverse crop species. Remarkably, these asexual root-knot nematodes are capable of acquiring heritable changes in virulence even though they lack sexual reproduction and meiotic recombination. Characterization of a near isogenic pair of M. javanica strains differing in response to tomato with the nematode resistance gene Mi-1 showed that the virulent strain carried a deletion spanning a gene called Cg-1. Herein, we present evidence that the Cg-1 gene lies within a member of a novel transposable element family (Tm1; Transposon in Meloidogyne-1). This element family is defined by composite terminal inverted repeats of variable lengths similar to those of Foldback (FB) transposable elements and by 9 bp target site duplications. In M. incognita, Tm1 elements can be classified into three general groups: 1) histone-hairpin motif elements; 2) MITE-like elements; 3) elements encoding a putative transposase. The predicted transposase shows highest similarity to gene products encoded by aphids and mosquitoes and resembles those of the Phantom subclass of the Mutator transposon superfamily. Interestingly, the meiotic, sexually-reproducing root-knot nematode species M. hapla has Tm1 elements with similar inverted repeat termini, but lacks elements with histone hairpin motifs and contains no elements encoding an intact transposase. These Tm1 elements may have impacts on root-knot nematode genomes and contribute to genetic diversity of the asexual species.

Demonstration of ignition radiation temperatures in indirect-drive inertial confinement fusion hohlraums

We demonstrate the hohlraum radiation temperature and symmetry required for ignition-scale inertial confinement fusion capsule implosions. Cryogenic gas-filled hohlraums with 2.2 mm-diameter capsules are heated with unprecedented laser energies of 1.2 MJ delivered by 192 ultraviolet laser beams on the National Ignition Facility. Laser backscatter measurements show that these hohlraums absorb 87% to 91% of the incident laser power resulting in peak radiation temperatures of T(RAD)=300 eV and a symmetric implosion to a 100 μm diameter hot core.

A novel Snf2 protein maintains trans-generational regulatory states established by paramutation in maize

Paramutations represent heritable epigenetic alterations that cause departures from Mendelian inheritance. While the mechanism responsible is largely unknown, recent results in both mouse and maize suggest paramutations are correlated with RNA molecules capable of affecting changes in gene expression patterns. In maize, multiple required to maintain repression (rmr) loci stabilize these paramutant states. Here we show rmr1 encodes a novel Snf2 protein that affects both small RNA accumulation and cytosine methylation of a proximal transposon fragment at the Pl1-Rhoades allele. However, these cytosine methylation differences do not define the various epigenetic states associated with paramutations. Pedigree analyses also show RMR1 does not mediate the allelic interactions that typically establish paramutations. Strikingly, our mutant analyses show that Pl1-Rhoades RNA transcript levels are altered independently of transcription rates, implicating a post-transcriptional level of RMR1 action. These results suggest the RNA component of maize paramutation maintains small heterochromatic-like domains that can affect, via the activity of a Snf2 protein, the stability of nascent transcripts from adjacent genes by way of a cotranscriptional repression process. These findings highlight a mechanism by which alleles of endogenous loci can acquire novel expression patterns that are meiotically transmissible.

Maize sex determination and abaxial leaf fates are canalized by a factor that maintains repressed epigenetic states

In maize (Zea mays ssp. mays), the meiotically heritable maintenance of specific transcriptionally repressed epigenetic states is facilitated by a putative RNA-dependent RNA polymerase encoded by mediator of paramutation1 (mop1) and an unknown factor encoded by the required to maintain repression6 (rmr6) locus. These so-called "paramutant" states occur at certain alleles of loci encoding regulators of anthocyanin pigment biosynthesis. Here we show Rmr6 acts to canalize leaf and inflorescence development by prohibiting the ectopic action of key developmental regulators. Phenotypic and genetic analyses suggest that Rmr6 ensures proper adaxial-abaxial polarity of the leaf sheath by limiting the expression domain of a putative adaxializing factor. Similar tests indicate that Rmr6 maintains maize's monoecious pattern of sex determination by restricting the function of the pistil-protecting factor, silkless1, from the apical inflorescence. Phenotypic similarities with mop1 mutant plants together with current models of heterochromatin maintenance and leaf polarity imply Rmr6 functions to maintain epigenetic repression established by non-coding small RNA molecules.

Multiple trans-sensing interactions affect meiotically heritable epigenetic states at the maize pl1 locus

Interactions between specific maize purple plant1 (pl1) alleles result in heritable changes of gene regulation that are manifested as differences in anthocyanin pigmentation. Transcriptionally repressed states of Pl1-Rhoades alleles (termed Pl') are remarkably stable and invariably facilitate heritable changes of highly expressed states (termed Pl-Rh) in Pl'/Pl-Rh plants. However, Pl' can revert to Pl-Rh when hemizygous, when heterozygous with pl1 alleles other than Pl1-Rhoades, or in the absence of trans-acting factors required to maintain repressed states. Cis-linked features of Pl1-Rhoades responsible for these trans-sensing behaviors remain unknown. Here, genetic tests of a pl1 allelic series identify two potentially separate cis-linked features: one facilitating repression of Pl-Rh and another stabilizing Pl' in trans. Neither function is affected in ethyl-methanesulfonate-induced Pl1-Rhoades derivatives that produce truncated PL1 peptides, indicating that PL1 is unlikely to mediate trans interactions. Both functions, however, are impaired in a spontaneous Pl1-Rhoades derivative that fails to produce detectable pl1 RNA. Pl'-like states can also repress expression of a pl1-W22 allele, but this repression is not meiotically heritable. As the Pl' state is not associated with unique small RNA species representing the pl1-coding region, the available data suggest that interactions between elements required for transcription underlie Pl1-Rhoades epigenetic behaviors.

Diclofenac induced in vivo nephrotoxicity may involve oxidative stress-mediated massive genomic DNA fragmentation and apoptotic cell death

Diclofenac (DCLF) is a nonsteroidal anti-inflammatory drug that is widely used for the treatment of osteoarthritis, rheumatoid arthritis, ankylosing spondylitis, and acute muscle pain conditions. Toxic doses of DCLF can cause nephrotoxicity in humans and experimental animals. However, whether this DCLF-induced nephrotoxicity involves apoptotic cell death in addition to necrosis is unknown. The goals of this investigation were to determine whether DCLF-induced nephrotoxicity involves oxidative stress and apoptotic type genomic DNA fragmentation, and if so, whether DCLF-induced oxidative stress and DNA fragmentation cause apoptotic cell death in mouse kidneys. Male ICR mice (CD-1; 25-45 g), fed ad libitum, were administered nephrotoxic doses of DCLF (100, 200, 300 mg/Kg, po) and sacrificed 24 h later. Blood was collected to evaluate renal injury (BUN), lipid peroxidation (MDA: malondialdehyde levels), and superoxide dismutase (SOD) activity (a marker of oxidative stress). Kidney tissues were analyzed both quantitatively and qualitatively to determine the degree and type of DNA damage, and evaluated histopathologically for the presence of apoptotic characteristics in the nucleus of diverse types of kidney cells. Results show that diclofenac is a powerful nephrotoxicant (at 100, 200, and 300 mg/kg: 4.7-, 4.9-, and 5.0-fold increases in BUN compared to the control, respectively) and a strong inducer of oxidative stress (significant increase in MDA levels). Oxidative stress induced by DCLF was also coupled with massive kidney DNA fragmentation (100, 200, and 300 mg/kg: 3-, 8-, and 10-fold increases compared to control, respectively). A dose-dependent increase in MDA levels and SOD activity was also observed, which indicated a link between oxidative stress and nephrotoxicity. Qualitative analysis of DNA fragmentation by gel electrophoresis showed a DNA ladder indicative of Ca2+-Mg2+-endonuclease activation. Histopathological examination of kidney sections revealed numerous apoptotic nuclei across proximal and distal tubular cell linings. Collectively, these data for the first time suggest that DCLF-induced nephrotoxicity may involve production of reactive oxygen species leading to oxidative stress and massive genomic DNA fragmentation, and these two free radical mediated events may ultimately translate into apoptotic cell death of kidney cells in vivo, and reveal a DNA-active role for DCLF.

Acute and long-term safety evaluation of a novel IH636 grape seed proanthocyanidin extract

Grape seed proanthocyanidins are known to possess a broad spectrum of pharmacological, medicinal and therapeutic properties. Previous studies in our laboratories have demonstrated the various protective abilities of a novel IH636 grape seed proanthocyanidin extract (GSPE) against various pathologic conditions. However no extensive safety studies have been conducted on grape seed proanthocyanidins to date. This study demonstrates the acute and chronic safety studies on GSPE. Acute oral toxicity, dermal toxicity, dermal irritation and eye irritation studies have been conducted. The LD50 of GSPE was found to be greater than 5000 mg/kg when administered once orally via gastric intubation to fasted male and female albino rats. The LD50 of GSPE was found to be greater than 2000 mg/kg when administered once for 24 hr to the clipped, intact skin of male and female albino rats. In addition, 2000 mg/kg was found to be the no-observed-effect level (NOEL) for systemic toxicity under the conditions of the study. In a dermal irritation study, GSPE received a descriptive rating classification of moderately irritating. Extensive chronic studies were also conducted. We have assessed the effects of chronic administration of 100 mg GSPE/kg/day for twelve months and its effect on seven vital target organs, namely, brain, heart, intestine, kidney, liver, lung and spleen, and on serum chemistry changes in male B6C3F1 mice. Furthermore, the dose-dependent chronic effects of GSPE in female B6C3F1 mice were evaluated. Mice were fed 0, 100, 250 or 500 mg GSPE/kg/day for six months and the effects of GSPE exposure were examined on brain, duodenum, heart, kidney, liver, lung, pancreas and spleen, and on serum chemistry changes in female mice. These acute studies demonstrated that GSPE is safe and did not cause any detrimental effects in vivo under the conditions investigated in this study.

Young women with physical disabilities: risk factors for symptoms of eating disorders

Women with disabilities are at risk for poor psychological adjustment and unhealthy weight-control practices. This study was conducted to determine the prevalence of symptoms of eating disorders in a clinic-based sample of women who had two disabling conditions and to identify condition-related risk factors that were linked to these symptoms. A cross-sectional survey of 71 women (mean age = 23 yr) with spina bifida or rheumatologically related illnesses was conducted to assess the symptoms of eating disorders, condition-related characteristics, and weight-control practices. Symptoms of eating disorders were measured by the Eating Disorders Inventory (EDI). Eight percent of the respondents reported a sufficient number of symptoms of eating disorders to indicate a possible clinical disorder. More than 20% of the respondents scored at or above the clinical cut-point on at least one of the eight EDI subscales. Selected condition-related characteristics (multiple conditions, condition-affected driving, and uncertainty of illness course) were associated with EDI scores after adjusting for demographic variables, family factors, and weight-control practices.

Early introduction of solid foods among urban African-American participants in WIC

OBJECTIVE

To compare infant feeding practices among low-income, urban, African-American women enrolled in the Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) with current recommendations for infant feeding.

DESIGN

Longitudinal follow-up of women and their infants who participated in a WIC-based breast-feeding promotion project. Women enrolled prenatally at or before 24 weeks of gestation were followed up until 16 weeks postpartum.

SUBJECTS/SETTING

Two hundred seventeen African-American WIC participants in an urban area.

METHODS

Data related to infant feeding practices were collected by interviewers who used a structured questionnaire to determine when nonmilk liquids or solids were introduced to the infant. Reported practices were compared with current recommendations.

STATISTICAL ANALYSIS PERFORMED

Contingency table analysis, including chi 2 tests, and multivariate analysis using logistic regression.

RESULTS

By 7 to 10 days postpartum, approximately a third of infants were receiving some nonmilk liquids or solids; this escalated to 77% by 8 weeks and 93% by 16 weeks postpartum. Women breast-feeding exclusively (i.e., not adding nonmilk liquids or solids) were least likely, and women providing mixed feeding (breast milk and formula) were more likely, than women feeding formula exclusively to introduce nonmilk liquids and solids at each data collection time period.

APPLICATIONS/CONCLUSIONS

WIC participants who receive instruction about infant feeding nutrition are no more likely than mothers who do not participate in WIC to follow infant feeding guidelines recommended by the American Academy of Pediatrics in regard to the time when solids should be introduced to infants' diet. Our findings suggest the need for WIC to implement more powerful and innovative educational and motivational strategies to help mothers delay the introduction of nonmilk liquids and solid foods until their infants are 4 to 6 months old, as recommended.

Sources of influence on intention to breastfeed among African-American women at entry to WIC

To examine how individuals within a woman's life influence her infant feeding intention, we interviewed 441 African-American women on the breastfeeding attitudes and experiences of their friends, relatives, mother, and the baby's father. Women were interviewed at entry into prenatal care at clinics associated with one of four Baltimore WIC clinics chosen for a breastfeeding promotion project. Qualitative data were also collected among 80 women. Friends and "other" relatives were not influential. Grandmothers' opinions and experiences were important, but their influence was reduced after considering the opinion of the baby's father. The opinion of the woman's doctor was an independent predictor of infant feeding intention. Breastfeeding promotion programs should recognize the separate influence of fathers, health providers, and grandmothers in women's infant feeding decisions.

WIC-based interventions to promote breastfeeding among African-American Women in Baltimore: effects on breastfeeding initiation and continuation

We evaluated the single and combined effects of introducing a motivational video and peer counseling into four matched WIC clinics on breastfeeding initiation and continuation at 7-10 days among African-American WIC participants. Of the 242 women with complete data, 48% initiated breastfeeding, but only 31% were still breastfeeding at 7-10 days. Initiation was associated with cesarean delivery, infant feeding instruction, no artificial milk discharge pack, attending the peer counselor only-intervention site, and intention to breastfeed. Continuation was influenced by infant feeding instruction, no artificial milk discharge pack, and intention to breastfeed. Overall, trends toward a positive impact of the breastfeeding promotion activities were evident but weak, and largely gone by 7-10 days postpartum.

Counseling and motivational videotapes increase duration of breast-feeding in African-American WIC participants who initiate breast-feeding

OBJECTIVE

To evaluate the relative effects introducing motivational videotapes and/or peer counseling in Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) clinics serving African-American women have on breast-feeding duration.

DESIGN

Experimental intervention study. Pregnant women were enrolled at or before 24 weeks gestation and were followed up until postpartum week 16. Women were interviewed at enrollment, 7 to 10 days, 8 weeks, and 16 weeks postpartum. SUNJECTS/SETTING: One hundred fifteen African-American WIC participants who initiated breast-feeding and who had been enrolled in 1 of 4 clinics.

INTERVENTION

Two-by-two factorial design, in which 4 clinics were randomly assigned to receive either no intervention, a motivational video package intervention, a peer-counseling intervention, or both interventions.

MAIN OUTCOME MEASURES

Breast-feeding duration in weeks and relative risk ratios for breast-feeding cessation before 16 weeks postpartum.

STATISTICAL ANALYSIS PERFORMED

Contingency table analysis, including chi2 tests and log-rank tests; multivariate analysis using Cox proportional hazards regression analysis.

RESULTS

A higher proportion of women were breast-feeding at 8 and 16 weeks postpartum in the intervention clinics than in the control clinic. The proportion of women reporting breast-feeding declined at 8 and 16 weeks postpartum, but the rate of decline was slower in the 3 intervention clinics than in the control clinic. Being younger than 19 years of age or older than 25 years of age, having a male infant, and returning to work or school all negatively affected breastfeeding duration, whereas previous breast-feeding experience positively influenced breast-feeding duration.

APPLICATIONS/CONCLUSIONS

WIC-based peer counselor support and motivational videos can positively affect the duration of breast-feeding among African-American women. WIC nutritionists and other health professionals in contact with this population should expand their efforts toward promoting increased duration of breast-feeding.

Developmental effects of fumonisin B1-containing Fusarium moniliforme culture extract in CD1 mice

Pregnant Charles River CD1 mice were treated with a semipurified extract of Fusarium moniliforme culture containing 0, 12.5, 25, 50 or 100 mg FB1/kg each day orally (diluted in distilled water) between gestational days (GD) 7 and 15 to evaluate the developmental toxicity of FB1. Following sacrifice of dams on GD 18, litters were examined for gross abnormalities and divided equally for skeletal or visceral examination by routine techniques. Significant maternal mortality was observed at doses of 50 and 100 mg FB1/kg. Dose-dependent decreases in maternal body weight gains, number of live offsprings per litter, and mean body weight of the offspring were produced at FB1 doses of 25 mg/kg or higher. The percentage of implants resorbed increased at all doses in a dose-dependant manner. A dose-dependant increase, except at the lowest dose tested, in the incidence of ossification deficits involving digits and sternum, short and wavy ribs, and hydrocephalus of lateral and third ventricles was also evident. Cleft palate was seen only at the highest FB1 dose. Maternal intoxication manifested as a dose-dependant increase in the severity of ascites associated mainly with increased histopathologic scores reflecting hepatocellular damage at day 18. Concommittant increases in serum alanine amino transferase (ALT) on GD 12, reflecting parenchymal liver cell damage, was also observed at all doses above 12.5 mg of FB1/kg. These results suggest that FB1-containing F. moniliforme culture extract is developmentally toxic in mice, and that this toxicity may be mediated by maternal hepatotoxicity.

Alteration in the tissue retention of [14C]-caffeine in pregnant mice by dimethylsulfoxide

This study was undertaken to investigate if dimethylsulfoxide (DMSO)-induced potentiation of maternal toxicity and teratogenicity of caffeine (CA) is mediated by DMSO-induced alteration of CA levels in maternal and fetal tissues. Pregnant CD 1 mice were given single dose of [14C]-caffeine intraperitoneally (i.p.) on gestational day 12, in distilled water (DW) or 20% (v/v) solution of DMSO in DW. At 6, 12, and 24 hr following dosing, radioactivity in various maternal and fetal tissues was compared. Significantly (P < or = 0.05) higher CA-derived radioactivity was seen in maternal brain, carcass and heart as well as placenta and fetal heads and bodies 6 hr after dosing with CA in DMSO compared to CA in DW. A concomitant reduction in urinary excretion of CA-derived radioactivity in DMSO group or compared to CA in DW was observed at this time. At 12 hr following dosing, significantly (P < or = 0.05) higher CA-derived radioactivity was noted in maternal heart, brain, and carcass; placenta; and fetal bodies in mice receiving CA in DMSO compared to those receiving CA in DW. These results suggest that increased accumulation of CA in certain maternal and fetal tissues could contribute to the observed increase in maternal and fetal toxicity of CA by DMSO.

Role of albumin's copper binding site in copper uptake by mouse hepatocytes

It is possible, in vitro, to label albumin with copper either exclusively on the specific binding site or partly on the specific site and also on other sites by altering the pH at which the two ligands are mixed. Copper attached exclusively to the specific site is taken up more rapidly than copper attached to that site and others on albumin. The effect is proportional to the amount of copper on the specific site. Additional histidine stimulates uptake irrespective of the copper binding site on albumin. The effect is related to the histidine on position 3 of the albumin, since it is not seen when dog albumin is labeled under the same conditions. The data suggest that the cell recognizes and presumably binds the copper-albumin (CuAlb) complex but may preferentially recognize the ternary complex formed by CuAlb and histidine. We suggest that, in vivo, copper is bound mainly as the ternary complex and that the structure formed, presumably similar to that formed by a copper-histidine complex, is what is actually recognized by the cell. After binding, the albumin and histidine are released, possibly by a reduction step, and the copper is transported across the membrane. If the copper cannot be transported (as occurs when the cells are incubated at 4 degrees C), it blocks further binding of the ternary complex.

The effect of tetrathiomolybdate on the metabolism of copper by hepatocytes and fibroblasts

Tetrathiomolybdate (TTM) has been examined for its effect on copper metabolism in mouse hepatocytes in primary culture and human fibroblasts. It decreased the amount of copper inside hepatocytes, decreased the rate of copper uptake by hepatocytes in a concentration dependent manner, and increased the copper efflux from the cells. TTM appeared to remove copper preferentially from the labile pool, but with a lower affinity than cage chelators. In fibroblasts, TTM only had a marginal effect on copper levels below a concentration of 100 microM and had no clear effect on the rate of copper uptake. TTM was not toxic to human fibroblasts, but in some preparations, a concentration of more than 50 microM was toxic to hepatocytes.

Effect of chelators on copper metabolism and copper pools in mouse hepatocytes

Disorders of copper storage are usually treated by chelation therapy. It is generally thought that the chelators act by mobilizing copper from the liver, hence allowing excretion in the urine. This paper has examined the effect of chelators on copper uptake and storage in mouse hepatocytes. Penicillamine, a clinically important chelator, does not block the uptake of copper or remove copper from hepatocytes. Two other copper chelators, sar and diamsar, which form very stable and kinetically inert Cu2+ complexes by encapsulating the metal ion in an organic cage, were shown to block copper accumulation by the cells and to remove up to 80% of cell-associated copper. They also removed most (approximately 80%) of the 64Cu accumulated by the cells in 30 min, but released only a small percentage (less than 20%) of that accumulated over 18 h. The results show that copper in the hepatocyte can be divided into at least two pools, an easily accessible one, and another, not removable even after long-term incubation with any of the chelators. Most of the copper normally found in the cell appeared to be associated with the former pool.

Uptake of copper by mouse hepatocytes

This study has investigated the uptake of copper by mouse hepatocytes. The cells gave similar results whether they were used right after isolation or maintained overnight on collagen-coated dishes. Uptake from cells in suspension followed two phases: an initial rapid binding followed by a linear uptake phase. The two phases were not so easily distinguishable in cells grown in culture where uptake was linear over the first hour. The uptake showed saturation but may not have followed simple kinetics. Histidine stimulated uptake in a concentration-dependent manner, as did some other amino acids, but copper had very little effect on histidine uptake. The process was not dependent on intracellular adenosine triphosphate (ATP), since inhibitors that substantially reduced ATP levels inside the cell did not alter copper uptake. The inhibitors, however, blocked histidine uptake to varying degrees, suggesting that copper and histidine are taken up by different pathways. The uptake was reduced markedly by N-ethyl maleimide, and preincubation of the cells with "Pronase" resulted in a decrease of uptake. A model for the uptake of copper by hepatocytes that incorporates the data presented in this paper with that produced by earlier workers is suggested.

Atypical antipsychotic agents: patterns of activity in a series of 3-substituted 2-pyridinyl-1-piperazine derivatives

A series of 3-substituted 2-pyridinyl-1-piperazine derivatives have been appended to cyclic imide groups and evaluated for their potential antipsychotic activity. The dopamine receptor affinities of these target molecules, as well as their ability to block apomorphine-induced stereotypy or reverse neuroleptic-induced catalepsy, was dependent on the lipophilic and electronic characteristics of the substituent situated on the pyridine ring. Groups with + omega and - phi values were most consistent with the desired biological profile of the target molecules, the cyano moiety being the optimum choice. Evaluation of compound 12 in a monkey model of amphetamine psychosis, and the regional selectivity it expresses for the A10 dopaminergic cell bodies in electrophysiological experiments, suggest this compound would be an atypical antipsychotic agent with few side effects.